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Talk:Genetic information

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Archive 1 (6 July 2011)
Archive 2 (26 September 2011)

Contents

Dog Fur example

Do the populations actually lose genetic information or merely have them become reccessive. ? Hamster 17:40, 25 September 2011 (UTC)

In that example, they have lost genetic information. Of course, that is a simplified example of how information can be lost; it doesn't say that all variation occurs exactly that way. Also, I'm not aware that genetic information can become recessive. Some genetic information is recessive, some isn't. Philip J. Raymentdiscuss 02:34, 26 September 2011 (UTC)

For those who think they know what genetic information is ...

If there is an allele A which produces an enzyme with a high binding to substrate X and a low binding to substrate Y, and another allele B which produces an enzyme with a moderate binding to both substrates, in which population is the genetic information highest?

  1. A population with only allele A
  2. A population with only allele B
  3. A population with a mix of A and B

--Unsigned comment by Awc (talk)

For those who think that they know what ordinary information is...
Question 2:
If there is a recipe A which produces a cake with a moist, soft, texture and is rather tasteless, and another recipe B which produces a cake with a rock-hard, dry texture and a nice taste, in which recipe book is the recipe information highest?
  1. A recipe book with only recipe A
  2. A recipe book with only recipe B
  3. A recipe book with both recipes A and B
Question 3:
Is question 2...
  1. Helpful to answer the question about genetic information because they are analogous?
  2. Unhelpful because the analogy is flawed? (And if so, how?)
  3. Irrelevant because neither living things nor recipe books have anything that can be called "information" because it's not quantifiable?
Philip J. Raymentdiscuss 02:52, 26 September 2011 (UTC)
I'll take a crack at that, even though I don't understand what "ordinary information" is in more than a colloquial sense. (Now Shannon information is another story.)
You can certainly make a case that the answer to question two is (3). If you go that route, then adding any recipe to your book adds information to it, as long as it is distinct from the other recipes in the book. I'm not sure what I think about question three, but apparently Spetner, Batten, Wieland, and other creationists would pick (2). They go to great lengths to argue that not every new and adaptive variation in a gene introduces new information into the gene pool. I think their point of view should be represented in the article.
I'm not sure what you're getting at with your question about the existence vs. the quantifiability of information. The only argument that requires a quantifiable measure of genetic information is the mathematical argument of some creationists that every mutation produces a quantitative loss in information, therefore the sum of all mutations can only be a quantitative loss in information.
--Awc 07:12, 26 September 2011 (UTC)
...I don't understand what "ordinary information" is in more than a colloquial sense. I've just consulted several on-line dictionaries, and not one gives a colloquial sense for "information". I suspect that what you mean is a non-technical sense. But that's the point: "ordinary" information is "information" used in a non-technical sense, the way people normally use the word in everyday writing and speech.
You can certainly make a case that the answer to question two is (3). If you go that route, then adding any recipe to your book adds information to it, as long as it is distinct from the other recipes in the book. Good answer.
...apparently Spetner, Batten, Wieland, and other creationists would pick (2). Why? On the contrary, they would agree with your reasoning for giving No. 3 as the answer, and therefore pick No. 1.
They go to great lengths to argue that not every new and adaptive variation in a gene introduces new information into the gene pool. Yes, but that doesn't mean that they would go for No. 2. The difference between the recipe book example and genetic information is that no-one would ever claim that the additional recipe originates in anything other than an intelligent mind, yet evolutionists insist that genetic information originates from other than an intelligent mind. Creationists don't claim that new genetic information cannot be generated. They claim that the postulated natural processes can't generate it, and that it would take an intelligence to do so (just like the recipe would). That intelligence could, in principle, be a human being (doing genetic engineering), but that wouldn't account for the origin of living things, given that a human is a living thing, so must exist before he could produce any genetic information. So that leaves only a non-human intelligence as the source. In principle, that non-human intelligence could be an intelligent alien, but that wouldn't explain where his genetic information came from (unless you invoked another alien, and so forth ad infinitum). Which leaves the only possible ultimate source as being a supernatural being, which we call God. (And, once you have God as an ultimate source, Occam's Razor would eliminate the aliens as unnecessary.)
Yes, we all know what creationists claim. What we are trying to figure out is if the arguments they bring to support that belief are valid, or even consistent. If every modified recipe increases the information content of a recipe book, why, according to creationists, doesn't every new and adaptive variation in a gene increase the information content of the gene pool? --Awc 14:10, 26 September 2011 (UTC)
(BTW, what's wrong with ad infinitum? What is more logical about the assumption of a supreme being than the assumption of an eternal universe with eternal life? --Awc 14:34, 26 September 2011 (UTC))
the analogy is flawed because according to Spetner allele A has more information than allele B (and that is important), whereas the tacit assumption is that recipe A and recipe B have the same information content (or it isn't important). --Awc 15:57, 26 September 2011 (UTC)
I'm not sure what you're getting at with your question about the existence vs. the quantifiability of information. It is an objection that is often raised (hello Sterile), so I included it here in case you—or anyone else—felt that options 1 and 2 were insufficient.
The only argument that requires a quantifiable measure of genetic information is the mathematical argument of some creationists that every mutation produces a quantitative loss in information... That's not a mathematical argument. That's a comparative argument. An analogy I've used before is that of two objects (I think I used ladders, but rods or almost any other object that varies in one dimension will do). You don't need to measure (quantify) the two objects in order to determine which is the longer—a simple visual comparison is sufficient. Similar with genetic information: there is at present no way to measure (quantify) genetic information (in the ordinary sense of the word, not the statistical/Shannon/etc. sense), so to say that creationists use a "mathematical" (quantifiable) argument is incorrect (or at the very least, incomplete).
Philip J. Raymentdiscuss 12:08, 26 September 2011 (UTC)
Not all mathematics deals with quantification. Topology, for example, doesn't. Your argument needs three conditions to be valid:
  1. A definition of genetic information in the form of a rule that, given two gene pools, determines which of them has more information.
  2. A demonstration that the state after a mutation always has less information in the sense of (1) that the state before the mutation.
  3. A proof of transitivity: If A has more information than B, and B has more information than C, then A has more information than C.
I'm not sure if the last point will be a problem or not, but I haven't yet even seen the definition required in the first point. --Awc 12:45, 26 September 2011 (UTC)
Yes, we all know what creationists claim. That often doesn't appear to be the case, actually. In fact your next point bears that out:
If every modified recipe increases the information content of a recipe book, why, according to creationists, doesn't every new and adaptive variation in a gene increase the information content of the gene pool? Who says that every modified recipe increases the information content of a recipe book?
Philip J. Rayment, for one: However, it is still clear that A+B comprises more information that just A or just B. --Awc 07:57, 27 September 2011 (UTC)
(BTW, what's wrong with ad infinitum? What is more logical about the assumption of a supreme being than the assumption of an eternal universe with eternal life? The problem with an eternal universe and eternal life is that the laws of physics and biology rule them out. In both cases, things are running down. The 2nd Law of Thermodynamics is recognition of this, and we observe it in so many ways. If you want to stick with scientific observation, then you have to conclude that things have not been around forever. The only way I know of to get out of this quandary is to go outside of scientific observation, outside of naturalism. This gives you at least two possibilities: either you invoke God, or you invoke some other, unobserved, unscientific mechanism, such as cyclic universes. But note that: if you go for such explanations, you are going outside of science and outside of naturalism. So which makes more sense: to invoke a supernatural being with power to create a universe, or invoke natural processes that go against our observations of natural processes?
It's true you would have to inject entropy somehow. Fred Hoyle tried to do it by spontaneously creating one hydrogen atom per cubic meter per billion years. If you want to call that supernatural, that's OK with me. But other very strong evidence points toward a finite age for the universe anyway. If the universe just popped into existence (say, 6,000 years ago, to pick a number), then it could have popped into existence containing life already. But since it really started in a Big Bang 13 billion years ago, we need a process to create life from non-life, whether it be natural or supernatural. (I'd like to close this line of discussion because it is really just a distraction here.) --Awc 07:57, 27 September 2011 (UTC)
Not all mathematics deals with quantification. Topology, for example, doesn't. Okay, you've got me there.
A definition of genetic information in the form of a rule that, given two gene pools, determines which of them has more information. The point of the ladder analogy is that you don't need this. At least not insofar as you can determine this for any two gene pools. To expand that, I don't believe that anyone is claiming that it is (currently) possible to compare any two gene pools and decide which has more information. More on this below.
A demonstration that the state after a mutation always has less information in the sense of (1) that the state before the mutation. This has been shown, but I should clarify. First, it has been shown from observation that this is normally the case. Second, it has been shown from mathematics (I guess maths does come into it here) that this is what is generally going to be the case.
A proof of transitivity: If A has more information than B, and B has more information than C, then A has more information than C. I don't see how this could be disputed.
A reasonable definition of information will have this property. Once your definition is on the table, it is something we can check. Logically, there is no necessity for a comparator to be transitive. I already gave the example of an acoustic illusion. You can also think of Escher's staircases. There are also situations where a vote will elect A running against B, and B running against C, but if A runs against C directly, the vote will go to C. --Awc 07:57, 27 September 2011 (UTC)
...I haven't yet even seen the definition required in the first point. Let's suppose that A, B, C, etc. are all bits of information, and all are different information. Further let's suppose that we have no way of comparing A with B, B with C, A with C, etc., to determine which has more information. However, it is still clear that A+B comprises more information that just A or just B. So comparing any two gene pools to see which has the most information is—like comparing A with B—not possible. However, if we can determine that gene pool X has all the information of gene pool Y plus some further information, then we can conclude that X has more information than Y. Because any two arbitrary gene pools would not be expected to comprise information such that one is a subset of the other, then in most cases the comparison cannot be made. However, there are cases where one is known to be a subset of the other, and that is where one is a copy of the other with a mutation (or other such change). In those cases you only need to look at the change itself, and determine if the change is a gain or a loss (or neutral). To go back to the A, B, C bits of information, you may not be able to tell if A+C is more information than A+B, but A+B+C is certainly more than A+B.
Philip J. Raymentdiscuss 03:15, 27 September 2011 (UTC)
Is it too late to change my mind? (I warned you I don't understand information.) I am no longer so sure that a recipe book with A+B has the most information. No time to explain now, though. --Awc 07:57, 27 September 2011 (UTC)
Philip J. Rayment, for one: Is he important enough to count?  :-)
However, it is still clear that A+B comprises more information that just A or just B. That is not the same as saying every modified recipe increases the information content of a recipe book. Going back to the example with A, B, C, etc. being defined as different bits of information, the recipe book can be described as having the set of information A+B+C+D+E+F+G. If you add H (e.g. another recipe), then you have increased the information content. But if you instead remove F, then this is still a modification, but not an increase, as you have decreased the information. Just because one modification is an increase doesn't mean that all modifications are increases. To put it another way, if a recipe book with recipes A+B has more information than another recipe book with just recipe A, then adding recipe B to the second book is a modification (an increase), but removing recipe B from the first recipe book is also a modification, but a decrease. So not all modifications are increases. (I note that I have been talking about modifying recipe books, whereas you referred to modifying recipes, but this doesn't affect the principle.)
If you want to call that supernatural, that's OK with me. I wouldn't call that supernatural; I'd put that in the other category, of an "other, unobserved, unscientific mechanism".
If the universe just popped into existence (say, 6,000 years ago, to pick a number), then it could have popped into existence containing life already. There's probably more than a magnitude of difference in complexity, but ignoring that, yes, if it popped into existence naturalistically, then each is about equally as unlikely. Which just goes to illustrate how absurd the Big Bang is.
but big bang nucleosynthesis can be shown mathematically to be limited to Hydrogen , small helium and trace Li, Be, B with argument about would any boron be produced. Inless you consider the chances of H or He life then life from the Big Bang theory isnt predicted. Hamster 03:50, 28 September 2011 (UTC)
But since it really started in a Big Bang 13 billion years ago... It did? I thought that was just the atheist origins myth.
Once your definition is on the table... It's already on the table. See information and Genetic information. As far as genetic information is concerned, it's essentially a set of instructions on creating a particular living thing, just as the information in a computer construction manual has a set of instructions on how to build a computer.
Do you have an operational definition, so I can answer questions like the ones I pose above and below? --Awc 13:31, 27 September 2011 (UTC)
Philip J. Raymentdiscuss 09:44, 27 September 2011 (UTC)
(I note that I have been talking about modifying recipe books, whereas you referred to modifying recipes, but this doesn't affect the principle.) I was referring to adding a single new recipe and leaving the others unchanged, just like a mutation adds a new allele to the gene pool without affecting the other alleles. What has me worried is this. If the additional recipe is Aunt Tilly's salt water taffy, then there is an increase in information, because Aunt Tilly knows her way around the kitchen. But suppose there's this funny process where somebody makes ten copies of each recipe in edition N, changing some instruction a little each time, and then somebody else tries them out and keeps only the best 10% of them for edition N+1. Then I'd be willing to say there is more information in each successive edition, but what about in the draft edition in between? I'd say that has less information, even though it contains more recipes. It is certainly less useful as a cookbook. I've often thought about this in relation to evolution. When is the information added to the gene pool in Darwinian evolution? When the mutations occur? Or when they are weeded out through natural selection?
So I'm still looking for an answer to my original question. Here it is again, in a more concrete form:
A->A+B) If there is a strain of bacteria with a chemical pumping mechanism, and an individual in that strain suffers a mutation interfering with the efficiency of that mechanism and thereby bestowing resistance to penicillin, has the information content of the gene pool of that bacteria increased, decreased, or remained unchanged?
A+B->A) How does the information content of the gene pool change if natural selection removes that mutation?
A+B->B) What if the original allele is removed by natural selection?
--Awc 13:18, 27 September 2011 (UTC)
I've said multiple times that I would deal with criteria for more or less, especially given that information appears to be a multi-variable problem. Given that the hypothesis/postulate is that everyday processes don't increase information, or at a rate in which it could effect evolution (whatever you mean by that), it's hard not to see the need for such criteria. (PS: Awc: one of the first conversations I had with Philip about information was about the need for an operational definition; Philip didn't pursue it. See User_talk:Sterile/archive_1. All the best!) Sterile 23:21, 28 September 2011 (UTC)
but big bang nucleosynthesis can be shown mathematically to be limited to Hydrogen , small helium and trace Li, Be, B... The nucleosynthesis perhaps, but the Big Bang is also supposed to have produced stars, planets, galaxies, clusters of galaxies, and super-clusters of galaxies. That's an awful lot of organisation for an undesigned event.
An excellent example of science by uninformed intuition! I can't help making the inference that your "detection" of design in living systems is about as solid as your "detection" of design in cosmological systems. Fortunately, cosmological systems are incomparably simpler and thus we can demonstrate how much design is needed, namely none at all. All you have to do is put matter that interacts only by gravity with a flat spectrum of initial fluctuations into a computer simulation. Viola! Out pop "galaxies, clusters of galaxies, and super-clusters of galaxies". (To get stars and planets you have to add atomic physics, which is a lot more complex, but still do-able.) --Awc 11:08, 29 September 2011 (UTC)
I was referring to adding a single new recipe and leaving the others unchanged... That seems at odds with your references to "modified recipe", but it only serves to underline that it doesn't affect the principle.
But suppose there's this funny process where... Your analogy has a few assumptions and/or omissions that need to be highlighted.
  1. Are the changes to the instructions done randomly, or by those "somebodies" trying to improve the recipes (ignoring for now whether they really are improvements)? The latter is not a good analogy for evolution.
  2. What is the nature of each change? Is it just ingredients or quantities? If the changes are limited to just ingredients or quantities, then again, this is not analogous to evolution, where changes should be able to occur anywhere. Changing one of the ingredients of a fruit cake from raisins to cherries could be called a horizontal change; i.e. no increase or decrease in information. It's like changing the colour of a house: it's different, but neither better nor worse.
  3. What is the granularity of the change? Are individual letters being changed, whole words, or what? If individual letters (or even words) are changed randomly (the nearest analogy to evolution), then you need (in principle) to calculate the proportion of changes that have meaning compared to those that produce gibberish. To be a bit more concrete, if you have the word "evolution" and make a single letter substitution, what's the odds that the change will result in a valid word? There are 25 ways that the first letter can be changed, 25 ways the second letter can be changed, and so on. So there are 25*9 (nine letters) different possible changes that can be made. Off the top of my head I can't think of any single-letter substitutions that produce a valid word, but even if there is one, it's a very small fraction of all possible changes. And even if you do get a valid word, will it still make sense in the context of its sentence? And the sentence in the context of its paragraph? And so on. So the percentage of invalid changes might be in the order of 99.999999%. With genetic information, the actual figures change (3 ways to change the each letter, etc.), but the principle remains the same.
Your analogy seems to assume that there will be sufficient valid changes that some will be selectable, which, based on my comments above, suggests that the analogy is not a good analogy to evolution.
...what about in the draft edition in between? I'd say that has less information, even though it contains more recipes. That depends on my questions above: were any of the changes actually improvements? But this raises another issue for evolution (for which there's a name I can't quite think of at the moment). Suppose you wanted to get to high ground to get a better view. So you climb the hill you are standing next to. Once on top of the hill you can see that there's another hill nearby which is higher and will give a better view. So you go down into the valley in between and climb the higher hill. You've gone down in order to go up. You, as a human, can do this because you can see forward. Evolution can't. Evolution is not aiming for a particular target (the higher hill). So when it goes into the valley, natural selection stops it there because it's got less fit. It won't let it survive on the basis that you have to go down (get less fit) before you can go up (get more fit).
I'd rather not beat every analogy to a pulp, so I'll only answer briefly. In my "funny process" I was thinking of random changes (using "random" in the common sense of "rolling the dice" to determine the change, as well as in the unique creationist sense of being spread uniformly through the recipe) at the quantity and ingredient level, not single letters. Those kinds of changes, like single point mutations in evolution, will usually not make much difference, will often make the product worse, and will sometimes but rarely make it better. --Awc 11:26, 29 September 2011 (UTC)
So I'm still looking for an answer to my original question. Here it is again, in a more concrete form: A->A+B) The chemical pumping mechanism had a purpose: to pump in nutrients. So while it has gained resistance to penicillin, it has lost ability to obtain nutrients. The bacteria is better adapted to a particular environment (one with penicillin), but that doesn't mean that it's gained information. It has become less efficient at taking in nutrients, and has lost information. Put that bacteria back in a normal environment, and it will be less able to survive than bacteria without the mutation. See Superbugs not super after all.
How does the information content of the gene pool change if natural selection removes that mutation? It doesn't change, given that the missing information existed elsewhere in the gene pool.
What if the original allele is removed by natural selection? Then the information content has decreased.
I've said multiple times that I would deal with criteria for more or less, especially given that information appears to be a multi-variable problem. I may be misunderstanding you, but let me repeat that I don't believe that there is any way to determine which of two quite-different sets of information has the most information. However, you (usually?) can look at a single change and work out if it's more or less information. And given that evolution proposes single changes at a time, that is sufficient.
Philip didn't pursue it. Rather, I didn't satisfy your demands so you decided to not discuss it further.
Philip J. Raymentdiscuss 04:16, 29 September 2011 (UTC)
The chemical pumping mechanism had a purpose: to pump in nutrients. That statement assumes design. The designer may have a purpose for the mechanism, but the mechanism itself has no inherent purpose. Let's just say, before it did one thing, and afterwards it did something else. Before the organism was adapted better to one environment, afterwards it was better adapted to a different environment. If you were to discover this bug in a high-penicillin environment, and then found a mutation that made its chemical pump more efficient at the cost of being more susceptible to penicillin, you would probably say the organism has lost information because it is no longer able to protect itself against penicillin. Along the same lines, environments do not have "norms". Some may be more common that others at a particular time and place, but there is no tag on an environment calling it "normal" or "abnormal". If you can't formulate your ideas without referring to "purpose" and "normality", then they don't have anything to say about the theory of evolution one way or the other. --Awc 12:01, 29 September 2011 (UTC)
However, you (usually?) can look at a single change and work out if it's more or less information. To your own satisfaction, I suppose. And if I feel that penicillin immunity, is a new and useful feature for a bug and therefore constitutes new information? Or that the ability to metabolize xylitol at the cost of the ability to metabolize ribitol can be a useful adaptation to a new environment and therefore constitutes new information, regardless of whether the ability to metabolize arabitol goes up or down at the same time? As long as we are both using our intuitive concept of information, there is no basis for a scientific discourse. Even if our intuitive concepts happened to coincide, unless the basis can be formulated and placed on the table we cannot examine whether our reasoning and generalizations are valid. The information argument "sort of feels good", but in the form it has been presented it is not scientific. --Awc 12:01, 29 September 2011 (UTC)
An excellent example of science by uninformed intuition! [rest snipped] Not uninformed intuition at all. Just because materialists manage to tweak computer models with very specific (designed) parameters to recreate their view of the Big Bang doesn't mean that it could have happened that way. In any case, the only real rebuttal to the claims of a finely-tuned universe is the unscientific claims of a multiverse. Design explains the finely-tuned universe. The Big Bang doesn't.
To get stars and planets you have to add atomic physics, which is a lot more complex, but still do-able. Not doable at all. Solar systems have defied real explanation.
Start with these. http://astronomyonline.org/SolarSystem/SolarSystemFormation.asp, http://www.windows2universe.org/our_solar_system/formation.html, http://www.ifa.hawaii.edu/~barnes/ast110_06/foss.html. Hamster 14:14, 30 September 2011 (UTC)
I was thinking of random changes (using "random" in the common sense of "rolling the dice" to determine the change, as well as in the unique creationist sense of being spread uniformly through the recipe)... If you "roll the dice", then you will get changes occurring everywhere, not in particular locations. If you roll the dice enough times, you will get results spread (pretty) evenly over all six numbers. It is nonsense to call this a unique creationist sense.
...at the quantity and ingredient level, not single letters. But that makes it unlike evolution, which doesn't happen at (say) the organ level, but at the DNA nucleotide level. To put it another way, if you are only changing quantities and ingredients, where did the instructions to mix, heat, beat, etc. come from?
Those kinds of changes, like single point mutations in evolution... But they are not like single-point mutations.
That statement assumes design. Granted, the wording does imply that. But part of the reason for that is that it's hard to avoid.
The designer may have a purpose for the mechanism, but the mechanism itself has no inherent purpose. That statement assumes no design. Is it appropriate to say that a keyboard on a computer "has no inherent purpose", although the designer of the computer may have had a purpose?
Along the same lines, environments do not have "norms". No? So a highly-sterile environment with plenty of penicillin, such as in a hospital (i.e. designed by a human), cannot be said to be non-normal?
If you can't formulate your ideas without referring to "purpose" and "normality", then they don't have anything to say about the theory of evolution one way or the other. Then I suppose that evolutionists from Darwin on don't have anything to say about the theory of evolution one way or the other either. For example:

The human body has something akin to its own junk drawer. You can think of organs like the brain and the heart as belonging to your silverware drawer or the cupboard where you keep your plates -- they're useful items you need every day. But the body's junk drawer is full of vestigial organs, or souvenirs of our evolutionary past. We don't use these items for their original purpose anymore, and these parts are stunted mementos of that original function.
How do we know what each organ's original purpose was supposed to be? For that, we turn to Charles Darwin. While he wasn't the first person to identify bodily structures that seemed to serve no purpose, he did propose why we have them. His concept of common descent, a tenet of evolutionary theory, holds that all organisms started with a common ancestor but diverged and changed as certain traits proved more favorable and necessary for survival. In Darwin's 1871 book "The Descent of Man," he identified about a dozen of man's anatomical features he believed to be useless because we don't use them in the same way that other creatures do. This, to Darwin, was proof that we had evolved from our primitive ancestors.[1]

Purpose—or lack of it—is a big part of evolution.
To your own satisfaction, I suppose. No, to the satisfaction of scientists who have studied these.
As long as we are both using our intuitive concept of information, there is no basis for a scientific discourse. The issue I have here is the typical evolutionist one of different standards they apply when discussing (dismissing) creation. For example, people use figurative language commonly enough, and seem to have no problem distinguishing between figurative and literal language (e.g. the woman solved the problem in six minutes vs. she's got her head in the clouds), yet when creationists claim that some parts of the Bible are figurative but others, including the creation account, are literal, suddenly they demand to know how we are supposed to tell the difference, and suggest if not claim that we (the creationists) are distinguishing solely on what we want to believe. Similarly here. Everybody understands the concept of information, whether that be in an encyclopædia, in a recipe book, in an instruction manual, or wherever. And they understand both that a recipe book with more recipes has more information than one with fewer, and that printing the same page twice in a book doesn't mean that it has any more information. But suddenly, when creationists talk about information in living things, they demand to know how to tell when there is more information or less and how to measure it before they'll even accept that it exists. Or they'll claim that any change is an increase in information. That is, suddenly the standards change. And even if you are right that there is no basis for a scientific discourse, that doesn't change the obvious fact that living things have huge amounts of information and that evolution has to explain this and has failed to do so. If there is [truly] no basis for a scientific discourse, then this is an admission that evolution has no basis for scientific discourse on where all the information in living things has come from.
Philip J. Raymentdiscuss 03:43, 30 September 2011 (UTC)

Purpose is not part of evolution. Function is a part of evolution. Purpose is a sneaky way of introducing a designer into the conversation. There is, indeed, a difference. I'd also like to see the figurative language in the peer reviewed scientific literature. And it's very clear how information theory is used in scientific literature, and how it's used in a technical sense, and it's different than the creationists use it. Or are you now saying Shannon information is what creationists mean? Sterile 11:17, 30 September 2011 (UTC)

evolution has in fact answered the question. a myriad of small changes over long time periods, with a boost near the start with horizontal gene transfers. Hamster 03:48, 1 October 2011 (UTC)
Start with these. I'm not saying that they don't have stories. I'm saying that the stories are inadequate as explanations. Those are good examples. One says "At the edge of a spiral galaxy called The Milky Way, a cloud of gas began to collapse. Pulled together by the force of its own gravity...", yet gases expand, they don't contract, unless something forces them to. And this is tacitly acknowledged in your other references, where they say things like

Surrounding supernova can generate shockwaves that will affect the debris in a nearby cloud - if the cloud is shocked enough and debris is forced inward, contraction can begin

and

Scientists believe that the solar system was formed when a cloud of gas and dust in space was disturbed, maybe by the explosion of a nearby star (called a supernova).

In order to create a star, you need an exploding star. So how did the first star get started? That's not explained.
If planetary systems formed from a rotating disk of material around a star, why do some planets have rotations that are not in line with that solar system rotation? That's not explained.
Where do long-term comets come from? That one is explained—with an explanation which has no evidence whatsoever supporting it, the fictional Oort cloud. One of your reference says

The residual debris of our Solar System is locked in two regions:

  • The Kuiper Belt - are area containing rock/ice bodies beyond the orbit of Pluto
  • The Oort cloud - a cloud containing "dirty ice" well beyond the orbit of the Kuiper Belt (comets are from the Oort Cloud)

Notice how matter-of-fact the Oort clould is? There's no hint there that there is no evidence for it; that it has not been observed (like the Kuiper Belt has).
Then consider this. The first reference says

Because the terrestrial planets form close to the proto-sun (the Sun at this point has not initiated fusion) the warmth melts away any ices so rocky planets form. The Gas Giants are at a greater distance and much of the ice and gas remains.

So, smaller, rocky, planets closer in, gas giants further out. However...

Most of the planets discovered orbiting other stars, are found to be gas giants orbiting close to their star.[2]

Astronomers have also discovered gas giants around stars in other solar systems. In fact, these are the only extra-solar planets that scientists have been able to discover as of yet.[3]

But your third reference says

Roughly half of all known extrasolar planets orbit closer than 1 AU to their primary star -- and many of these planets are more massive than Jupiter!

So we have a contradiction. The "explanation" of solar systems says that you get smaller, rock, planets closer in, and gas giants further out. However, in other systems, you get gas giants close in. So what's the explanation?
I'm not doubting that there are explanations. Well, attempted explanations at least. But how good are they?
One of my references above, talking about a particular extra-solar planet says (my emphases)

Astronomers today explain the closeness of the planet by suggesting that the planet formed further away and gradually migrated towards the star. The migration was caused by dust in its orbit, gradually slowed down the orbit and hence forced the planet closer. During this process it probably bulldozed smaller planetesimals orbiting within the orbit of Bellerophon. There is also a possibility that the planet may have thrown them away from the solar system.[4]

Notice how tentative that language is? Especially compared with the apparent certainty of the unobserved Oort Cloud? That sort of tentativeness indicates that they really have no idea, as your third reference was honest enough to admit:

At present we have no idea how giant planets could form so close to their parent stars.


Purpose is not part of evolution. Someone's in denial. I provide a quote showing how purpose (or the lack thereof) is (and always has been) part of evolution, and your response is to simply reassert that it's not.
I'd also like to see the figurative language in the peer reviewed scientific literature. Who said anything about it being in the scientific literature? I don't think you were properly reading what I wrote.
And it's very clear how information theory is used in scientific literature, and how it's used in a technical sense, and it's different than the creationists use it. Or are you now saying Shannon information is what creationists mean? As I'm quite sure I've explained to you before, Shannon information is a statistical measure of data, it has nothing to do with the meaning of the information. And I'm not so sure that you do know how it's used in the scientific literature, in the sense that you have an adequate idea.
evolution has in fact answered the question. a myriad of small changes over long time periods, with a boost near the start with horizontal gene transfers. A "myriad of small changes" is not the same thing as generating new information, and horizontal gene transfer is the transfer of existing information, so doesn't explain the origin of that information.
Philip J. Raymentdiscuss 13:20, 1 October 2011 (UTC)
At present we have no idea how giant planets could form so close to their parent stars and the latest ideas are that they dont form near the star but migrate. There are also suggestions that the star has changed from its original type, as is expected of our own star in about 5 billion years.
If planetary systems formed from a rotating disk of material around a star, why do some planets have rotations that are not in line with that solar system rotation? That's not explained. er, gravitation interactions and collisions within the early system.
yet gases expand, they don't contract, unless something forces them to. perhaps gravity ?
Hamster 14:20, 1 October 2011 (UTC)
Yeah, because "how stuff works" is a reliable source of scientific information. Even using Google scholar with "function in evolution" and "purpose in evolution" is revealing.
The quote that typifies what is meant by information is as follows:
In biology the term information is used with two very different meanings. The first is in reference to the fact that the sequence of bases in DNA codes for the sequence of amino acids in proteins. In this restricted sense, DNA contains information, namely about the primary structure of proteins. The second use of the term information is an extrapolation: it signifies the belief or expectation that the genome somehow also codes for the higher or more complex properties of living things. It is clear that the second type of information, if it exists, must be very different from the simple one-to-one cryptography of the genetic code. This extrapolation is based, loosely, on information theory. But to apply information theory in a proper and useful way it is necessary to identify the manner in which information is to be measured (the units in which it is to be expressed in both sender and receiver, and the total amount of information in the system and in a message), and it is necessary to identify the sender, the receiver and the information channel (or means by which information is transmitted). As it is, there exists no generally accepted method for measuring the amount of information in a biological system, nor even agreement of what the units of information are (atoms, molecules, cells?) and how to encode information about their number, their diversity, and their arrangement in space and time. [Nijhout, H. F. Bioessays, September 1990, vol. 12, no. 9; p.443]

So you may assert that "everybody knows"weasel words detected about "meaningful information," but apparently not everyone does. And, yes, as a result of our conversations, I have read several papers and popular press works about how information is used in science. They usually comment on how gene expression or enzymatic acitivity changes (and may have an increase or decrease of those over many generations) and usually have information about how members of the population can survice better or not. In fact, I've even cited them to you before. Hence, you are just wrong. (Oh, and how good is an explanation that says a diety poofed stuff into existence? There's certainly no physical evidence for it.) Sterile 18:48, 1 October 2011 (UTC)

and the latest ideas are that they dont form near the star but migrate. Yes, there are lots of ad hoc ideas, but no good theories.
er, gravitation interactions and collisions within the early system. More ad hoc ideas.
perhaps gravity ? Gravity requires a (concentrated) mass, which gas doesn't have.
Yeah, because "how stuff works" is a reliable source of scientific information. Are you disputing that Darwin used those arguments? Or that such argument are still used today, such as for junk DNA?
The quote that typifies what is meant by information is as follows: Interesting, in several respects. First, information theory (in a broad sense) has come a long way in the past two decades since the source of your quote. Second, he doesn't say that it's used with only two meanings. Without having access to the context, it could be that he is referring to two different meanings of a given concept of the term. I agree that this seems unlikely, but his definitions do suggest that to me, because the distinction between his first and second meanings seems somewhat arbitrary or unclear. He seems to be saying that DNA has information at the level of proteins, but not necessarily at the level of, say, organs. I would have thought that it was well accepted even then that the DNA codes for more than just individual proteins. Third, I wonder what sort of information you think he is talking about, if not the same information that I'm talking about. Specifically, he says that there is no generally accepted method for measuring information, which would seem to be a completely false statement if he's talking about information in the Shannon sense or similar. Rather, his comments on that seem to fit better with meaningful information.
So you may assert that "everybody knows"weasel words detected about "meaningful information," but apparently not everyone does. My comment (which is not on this page and which you don't reference) was probably about information in it's normal sense, not in a specifically-biological sense, yet you are trying to refute it in a biological context.
I have read several papers and popular press works about how information is used in science. ... Hence, you are just wrong. Sigh, you still miss the point. My argument is that the genetic code contains "information" in the normal sense of that word; my argument is not that everyone understands this point (that the genetic code contains such information). So citing people who don't seem to understand it is hardly relevant.
Oh, and how good is an explanation that says a diety poofed stuff into existence? An explanation that says that a being capable of poofing stuff into existence did so is far better than one that says that stuff poofed into existence from nothing for no reason according to laws of physics that say that this can't happen.
There's certainly no physical evidence for it. There is: the evidence that the universe was designed by an intelligence.
Philip J. Raymentdiscuss 02:40, 10 October 2011 (UTC)
no reason according to laws of physics that say that this can't happen. Please explain. What about the laws of physics prevents evolution from occurring? Sterile 16:18, 10 October 2011 (UTC)
Please explain. What about the laws of physics prevents evolution from occurring? I was not talking about (biological) evolution. Philip J. Raymentdiscuss 01:28, 15 October 2011 (UTC)

And more: If Nijhout's second definition is what you mean by meaningful information (and I wouldn't necessarily disagree with that), then are you agreeing with him that it can't be measured? I guess I'm confused. Actually, I would contend that most biologists would say that if they could measure what Nijhout is writing about, they would say that notions of "more" and "less" don't necessarily correlate with adaption through selection or what I would call evolution. That is, evolution has a direction, but it's determined by the environment that an organism lives in. It's not clear that when a population is placed in a different environment (or slow changes in the same environment) that more information is needed.

It is certainly clear than information theory has progressed, in part to a better understanding of Shannon information and AIC, of which only Shannon has an unambiguous sense for more or less, but the creationists reject. Complexity theory is related to information theory, but those who study it don't agree on a definition of complexity, let alone a clear sense of how it relates to information theory and notions of more or less. So, yes, information theory has progress, but not to a clearer understanding of what you would call meaningful information.

It's also been clearly established by developmental biologists that the series of switches of gene expression and timing for which they fire is clearly not the same as an encyclopedia or recipe book, nor is it clear what more information is for the recipe book at that.

So I guess I think we're no better off than before. Sterile 01:57, 15 October 2011 (UTC)

Reverting recent edits

I'm going to revert recent edits for the following reasons:

  • This one changed references to "genetic information" to "variations of genes". The two are not synonymous (variation need not change the amount of genetic information), and it is the information content that is relevant here.
  • This one, with the edit comment "God and Adam is cute, but not encyclopedic." seems to presume too much. Why are they not encyclopædic? As reworded, it has creationists disputing that creation of genetic information has "ever" been observed, but if God and Adam observed it, then the claim cannot be so all-encompassing. And particularly so given that creationists do recognise that exception. And, in case this is raised as an objection, the supporting quote which doesn't mention those exceptions is not by a biblical creationist, and even if it was would be ignoring those exceptions by the context.
Why can't AsK ignore those exceptions "by the context"? Do you really think anyone would read "the creation of meaningful biological information has [not] ever been observed" and think it is refering to something other than observations by (modern) human beings? If so, then I propose that the article on Neptune also be changed: "This makes it the first planet whose existence was predicted before it was directly observed." -> "This makes it the first planet whose existence was predicted before it was directly observed, except by God."
--Awc 10:38, 26 September 2011 (UTC)
What is the argument that Adam may have witnessed the creation of genetic information? --Awc 11:32, 26 September 2011 (UTC)
What would you think of changing the wording to "No person (except possibly Adam) has observed ..."? --Awc 11:32, 26 September 2011 (UTC)
  • I don't have a strong objection to separating out the examples in the third of these edits, but I don't particularly like that this has resulted in the second example retaining the wording "A similar example..." which is now referring to a different (sub)section, rather than to the previous sentence. But more than that, the accompanying rewording has made it more favourable to evolutionary views, with unnecessary qualifications such as "can be considered" and "Batten argues". I believe that the last example at least is now less accurate. Previously it said that "this appears to not be a random mutation" (my emphasis), which I believe to be an accurate summary of the source reference, but it has now been changed to "Batten argues that the underlying mutation was not random" (my emphasis again), as though claiming that Batten is certain that it was not random, which I don't believe he is being dogmatic about.
Have I got this right? God in his omniscience foresaw that the humans he created would someday produce nylon, and it would useful to Flavobacterium and Pseudomonas if they could eat it, so he pre-programmed into their genes the ability to quickly change their metabolism to digest nylon? Is that what Batten means by "not random"? --Awc 07:26, 26 September 2011 (UTC)
Since you don't have a strong objection, I decided to try again, taking your comments into account. I admit that it is at best a marginal improvement, but I hope we can expand these example a little, and this is the first step. (The first and the fourth of my edits are related to the definition of biological information, which we are discussing in the previous section of this page, so let us take the discussion of those edits there.) --Awc 11:58, 26 September 2011 (UTC)
  • The last of these four edits claims that, according to creationists, "information can be measured by the total number of variants of a gene in a population", and on this basis also implies that creationists can't make up their minds. However, the basis for that comment is an illustration which does have both fewer variants and less information, but does not claim that information can necessarily be measured from the number of variants (see my comment above to the first of these four edits).

Philip J. Raymentdiscuss 03:27, 26 September 2011 (UTC)

Why can't AsK ignore those exceptions "by the context"? Do you really think anyone would read "the creation of meaningful biological information has [not] ever been observed" and think it is refering to something other than observations by (modern) human beings? I was worried that you might use that argument. You might be right, although I'm not convinced. I would suggest that Spetner's context was clearly that of modern scientific investigation. This encyclopædia is not a scientific encyclopædia or textbook; it's an encyclopædia for laymen. That's a different context. Further, this is in the context that we often make a distinction between what is observed (e.g. biological processes) and what isn't (e.g. goo-to-you evolution). Perhaps you're right that context would indicate it, but I'm yet to be convinced.
If so, then I propose that the article on Neptune also be changed... "Observed" there is in the context of being "predicted" mathematically as a result of noticing gravitational interference, which implies human scientific endeavour. I don't think that's (sufficiently) analogous.
What is the argument that Adam may have witnessed the creation of genetic information? Adam existed before Eve was created, and Eve was (obviously) genetically distinct. Of course, Adam was asleep at the time, so didn't actually see it happen, which makes it a weak argument.
A better example would be the creation and naming of the beasts. Adam was certainly awake for that. Its a bit of a question if he recognised it as genetic information or just Oh, wow, thats ugly, but its an example. Hamster 14:28, 26 September 2011 (UTC)
What would you think of changing the wording to "No person (except possibly Adam) has observed ..."? If you assumption is that the word "person" excludes God, I would disagree. The Trinity is sometimes described as three persons in one. "Person" does not exclude God. I might point out that you haven't explained why it's not encyclopædic.
Have I got this right? God in his omniscience foresaw that the humans he created would someday produce nylon, and it would useful to Flavobacterium and Pseudomonas if they could eat it, so he pre-programmed into their genes the ability to quickly change their metabolism to digest nylon? Is that what Batten means by "not random"? No. Rather, God in his wisdom realised that living things would need to adapt to their environment, so programmed into their genes the ability to adapt, and that one way He did that is by allowing selected parts of their genetic information to change. Think of an instruction manual for camouflaged equipment that you find has a number of different versions (i.e. there are a number of different versions of the manual). Did the author write different versions? No, because the variations in the versions only appeared after he died. Did the printers make an error, simply typing (or type-setting the wrong letters)? This might explain it if the places where the variations appeared was random. But what if you notice that the variations are all the same except where it describes what colours to paint the equipment (and the changes relate to what environments, such as jungle or desert, the equipment is to be used in). You would have to realise that the changes were non-random. This analogy falls down because even in this case, the change in colours would be the result of intelligence (by the publisher, for example), but suppose that there was some way that the original author had written the manual as a computer program that randomly selected the colour from a list of possible colours. The actual selection of a particular colour may be random, but the ability to change the colour would have been designed. The application is that a truly-random mutation could occur anywhere, but if you find that "mutations" are occurring in particular places only, or particular changes keep recurring, then you should favour the idea that it is a design feature, not a completely random change, which evolution requires (because it excludes design).
Philip J. Raymentdiscuss 12:38, 26 September 2011 (UTC)
for a camo application you would have either presets to cover the range of environments expected or a visual scanner to read the color and patterns of the environment. In a biological system though you would need a number of changes in what chemicals you need to make to produce the skin color wanted. Toss a chameleon onto a red and white checkered tablecloth and see how well hidden it is. Is there any evidence that an organism has a system to analyse the chemical structure of its surrondings and then synthese the chemicals to break it down into something it can metabolise ? Hamster 15:10, 29 September 2011 (UTC)
I don't think you understand.  ;-) When bacteria are observed to have mutations that allow them to metabolize new food sources (or viruses to produce new proteins to hide from the immune system of their hosts, or flowers to produce new pigments that give them a different color), then they are not producing new information because they are just tweeking some details of one kind of information. On the other hand, when dogs lose the ability to produce short hair, that is a real loss of genetic information because they no longer know how to do something they could do before. As I'm sure you realize, producing long hair is a totally different process from producing short hair. --Awc 15:26, 29 September 2011 (UTC)
A better example would be the creation and naming of the beasts. Adam was certainly awake for that. Yes and no. First, naming them is not a case of seeing the creation of genetic information. The creation of them, however, is. But did Adam see this? Genesis 1:24-26 indicates that God made Adam after He made "livestock, creatures that move along the ground, and wild animals". Genesis 2 looks at part of creation in a different way, and part of that difference is that it is not chronological, unlike Genesis 1. It talks about God creating "the beasts of the field", and it talks about this after it talks about Adam being created. Although some Bible translations, correctly in my view, have this verse saying "Now the Lord God had formed out of the ground all the beasts of the field" (my emphasis), others can be read as God creating after Adam: "The Lord God formed out of the ground every living animal of the field...". Some people explain this as God creating two lots of land animals, the "livestock, creatures that move along the ground, and wild animals" before Adam, and the "beasts of the field" after Adam. If that latter explanation is correct, then yes, Adam would have (effectively) witnessed the creation of genetic information. I'm not convinced of this explanation, and I didn't previously think it worth mentioning, but as you've brought it up, I now have. Philip J. Raymentdiscuss 06:44, 27 September 2011 (UTC)
Eve was (obviously) genetically distinct. Couldn't Eve have identical genes, just Adam's X chromosome doubled and his Y chromosome left out? --Awc 16:14, 27 September 2011 (UTC)
yes, thats probably the easy way, but what happens during sexual reproduction of two identical genomes ? wouldnt all the children be virtually identical ? if God wanted variation he could have suffled a new genome into each of Eves egg cells when she was created. Hamster 20:35, 27 September 2011 (UTC)
We all have two versions of each gene. If Adam had A and B variants of one gene, and Eve had the same, then their children might have AA, or BB, or AB combinations for that gene. Since each gene plays the same game, you probably wouldn't have much trouble telling Cain and Abel apart. --Awc 20:56, 27 September 2011 (UTC)
The application is that a truly-random mutation could occur anywhere, but if you find that "mutations" are occurring in particular places only, or particular changes keep recurring, then you should favour the idea that it is a design feature, not a completely random change, which evolution requires (because it excludes design). I see. I was using the word "random" to mean "not directed". Like, it could have been that giraffes that stretch their necks tend to have mutations for longer necks, or that peppered moths exposed to pollution tend to have mutations making them darker. If creationists don't believe anything in that direction, then I guess I don't need to use a qualifier at all. It looks like we agree on this statement:
Given the genetic mechanisms that exist in living organisms, mutations can result in an increase in genetic information. Such increases in information have been observed to occur in a number of cases, such as the seasonal variations in flu viruses, and bacteria that become immune to penicillin or develop the ability to metabolize new substances.
Now that that is established, you may want to argue that only certain kinds of mutations can increase the genetic information, or that the existing genetic mechanisms themselves could not have developed from mutations. Go wild. --Awc 19:49, 27 September 2011 (UTC)
Couldn't Eve have identical genes, just Adam's X chromosome doubled and his Y chromosome left out? Yes, she probably could have, but that would still make my statement true. In fact that was the point behind my use of "obviously"; at the very least she was genetically female, even if nothing else was different. However, I'm inclined to think that Eve probably had more genetic difference from Adam than just that.
I was using the word "random" to mean "not directed". I'm not sure that I'm getting your point, but perhaps we are talking past each other, because I'm talking about where the mutations occur, and you seem to be talking about which ones are retained.
No big deal. I've grasped the point that when creationists say "not random", they mean "not by the same mechanism that is active on most of the genome". It seems like there should be a less ambiguous way to say that, but we can work with it. --Awc 07:21, 29 September 2011 (UTC)
It looks like we agree on this statement: Errr, no. Where is the evidence that seasonal variation in flu viruses is an increase in information? And creationists have already argued that resistance to penicillin is a decrease in information. So given this lack of observation, where is the evidence that mutations can result in an increase in genetic information?
...you may want to argue that only certain kinds of mutations can increase the genetic information, or that the existing genetic mechanisms themselves could not have developed from mutations. Whether or not there has been an increase in genetic information depends on in what way the information is changed rather than how it was changed. For example, it does not matter how a letter in a word is changed; what matters is what the new word is (or whether it produces gibberish).
Philip J. Raymentdiscuss 04:29, 29 September 2011 (UTC)
Where is the evidence that seasonal variation in flu viruses is an increase in information? At the end of the flu season, a virus looks around and finds it hard to replicate because the immune systems of its hosts have figured out how to identify and attack it. Suddenly, it invents a new protein that the hosts don't recognize because it has never existed before. The virus coats himself with the new protein and finds he can get past the hosts' defenses and start replicating again. Novel, non-obvious, useful—hey, this is patentable! That meets all my criteria for new information. Where does it fail yours? --Awc 12:10, 29 September 2011 (UTC)
if virus always lost information, how many generations until the virus was not viable ? Hamster 14:48, 29 September 2011 (UTC)
When bacteria are observed to have mutations that allow them to metabolize new food sources (or viruses to produce new proteins to hide from the immune system of their hosts, or flowers to produce new pigments that give them a different color), then they are not producing new information because they are just tweeking some details of one kind of information. Not an accurate summary of creationist views, which are that such changes are not necessarily just tweaking, but (almost) always turn out to be just tweaking.
On the other hand, when dogs lose the ability to produce short hair, that is a real loss of genetic information because they no longer know how to do something they could do before. As I'm sure you realize, producing long hair is a totally different process from producing short hair. Another misrepresentation. The dog hair example was an example of how (real) loss of genetic information can occur. Further, it is due to a loss of the gene for long hair, not simply a change in a value for the length of hair. Compare two different hypothetical examples of how hair length could alter:
  1. Hair length is dependant on an instruction that says "produce hair that is x millimetres long".
  2. Hair length is dependant on a combination of two instructions interacting. Those two instructions, which are quite different genetically, say respectively "produce short hair" and "produce long hair".
The point of the "quite different genetically" bit is that one instruction cannot change into the other instruction with a simple point mutation.
In the first example, a random change to the twelfth character might have the instruction say "produce hail that is x millimetres long". In the context of instructions for the construction of a dog, that sentence is now nonsense. But if the random change happened to be to the "x" so that it now had a different value, the instruction would still make sense. But this change would be a horizontal change—neither an increase nor a decrease in information content. Further changes to this value might just as easily restore the original value.
In the second example, if the second instruction is lost so that only one instruction remains, this is not a horizontal change. The instruction is gone, and, because it's not simply a point mutation difference, a mutation won't bring it back (in the example it disappears by sexual reproduction, not by being damaged by point mutation).
...when creationists say "not random", they mean "not by the same mechanism that is active on most of the genome". No, they mean not equally likely to occur anywhere.
Suddenly, it invents a new protein that the hosts don't recognize because it has never existed before. ... That meets all my criteria for new information. Where does it fail yours? That's like a lock that loses one of its pins, or perhaps an accretion on a pin changes its length. There is no new function, no new complexity, no new information, just a lock that the key doesn't fit any more.
if virus always lost information, how many generations until the virus was not viable ? That depends on how critical the losses of information were, on how much redundancy there was, and on what you mean by "viable"? That is, they may no longer have the ability to do what they were supposed to do, but still be able to survive.
Philip J. Raymentdiscuss 04:25, 1 October 2011 (UTC)

Back to the issue of Reverting recent edits, I think we have poked into the subject enough that it would be a better use of time to get back to improving the article now. (As time permits, I may yet respond to some of the comments in this and the preceding section.) I think at least on some points Philip has not been able to make his case. I will start editing again, moving slowly (due to practical constraints on my time, but also from the principle of giving everyone time to discuss and improve the edits), referencing all I can, being careful not to misrepresent any arguments, but also being careful to not to reproduce any assertions uncritically. --Awc 08:03, 4 October 2011 (UTC)

"genetic information" vs. "variations of genes"

This one changed references to "genetic information" to "variations of genes". The two are not synonymous (variation need not change the amount of genetic information), and it is the information content that is relevant here.

Of course they're not synonymous. That's why I changed it. The simple fact is that "no new variations of genes has been introduced". An equivalent statement about "genetic information" is at best a more subtle point. At this point in the article there has not been the least attempt to define the relative quantity of genetic information from anyone's point of view. We need to wait until that has been done, farther below in the article, before making use of the concept of "amount of information". If an additional argument is needed against talking about genetic information content at this point, Philip provides it here. --Awc 12:08, 4 October 2011 (UTC)
The simple fact is that "no new variations of genes has been introduced". It might be a simple fact, but it's not the fact that's relevant at that point. The relevant point is the lack of new genetic information.
Better to have an irrelevant fact than a statement that is susceptible to misinterpretation, potentially misleading, or perhaps even just plain wrong because we haven't defined our terms yet. If you think our readers don't have the patience to wait for the next section, where I am planning to come back to this example, we could move it down into or after the section on Quantification of Information. --Awc 12:44, 10 October 2011 (UTC)
At this point in the article there has not been the least attempt to define the relative quantity of genetic information from anyone's point of view. This point in the article is explaining the relative quantity of genetic information, by pointing out that it hasn't changed. Changing it to something else (variations of genes) is missing the point that is trying to be explained.
If an additional argument is needed against talking about genetic information content at this point, Philip provides it here. I don't see how that supports your case.
Compare two different hypothetical examples of how hair length could alter: 1. Hair length is dependant on an instruction that says "produce hair that is x millimetres long". ... But if the random change happened to be to the "x" so that it now had a different value, the instruction would still make sense. But this change would be a horizontal change—neither an increase nor a decrease in information content. There is nothing in Genetic information#Differentiation and speciation that would make it clear that your model 1 is not being considered. In that case it is invalid to conclude that "Each population has less genetic information than the parent population." --Awc 12:44, 10 October 2011 (UTC)
Philip J. Raymentdiscuss 05:48, 10 October 2011 (UTC)
Better to have an irrelevant fact than a statement that is susceptible to misinterpretation, potentially misleading, or perhaps even just plain wrong because we haven't defined our terms yet. Why? I'd say it's better to clarify than to confuse by including irrelevant material.
Are you asking why an encyclopedia should avoid statements that are susceptible to misinterpretation, potentially misleading, or perhaps even just plain wrong? --Awc 08:12, 17 October 2011 (UTC)
If you think our readers don't have the patience to wait for the next section, where I am planning to come back to this example, we could move it down into or after the section on Quantification of Information. I don't see the problem with the way it was.
Genetic information does not have a consensus definition, so a blanket statement may be true or false depending on whose definition you use. If you were trying to engage in a discussion to improve this article, you would not just say whether you see a problem with your own version, you would also consider and comment on alternative suggestions. --Awc 08:12, 17 October 2011 (UTC)
There is nothing in Genetic information#Differentiation and speciation that would make it clear that your model 1 is not being considered. First, there is something there to indicate that. Second, I also believe that this is sufficiently clear, although perhaps this doesn't apply to people who come to this article with different mindsets. The example talks about two distinct genes, not a gene with a variable value in it.
When you expanded your interpretation of the fur example, you found it necessary to introduce the phrase "quite different genetically". Such language appears nowhere in the article. Why don't you expend some energy making the article clearer, rather than simply reverting to your own version? Especially if you recognize that the perceived clarity may depend on pre-conceptions. --Awc 08:12, 17 October 2011 (UTC)
Philip J. Raymentdiscuss 12:03, 15 October 2011 (UTC)
I am trying to find a version that is accurate, clear, and fair. It would be great if you would either help or get out of the way. My proposed change didn't eliminate reference to information, it only defined what was meant by specifying "in that sense". Since you think that's not enough, I will expand the caveats. Like I said above, there is no consensus definition of genetic information, so an encyclopedic article cannot make a statement of fact about genetic information without first defining the term. --Awc 08:12, 17 October 2011 (UTC)
Are you asking why an encyclopedia should avoid statements that are susceptible to misinterpretation, potentially misleading, or perhaps even just plain wrong? No, I'm asking why it's better to put in something irrelevant what would confuse.
If you were trying to engage in a discussion to improve this article, you would not just say whether you see a problem with your own version, you would also consider and comment on alternative suggestions. If you mean your alternative wording that I reverted, I have commented on it. If you are talking about what you are planning to come back to, I can hardly comment on what you have yet to put forward.
When you expanded your interpretation of the fur example, you found it necessary to introduce the phrase "quite different genetically". Yes, unfortunately I did. I don't really think it's necessary, but it seems to be necessary when talking to some people.
Why don't you expend some energy making the article clearer... It's a matter of time; I've not had the time even to respond to various comments by you and others.
Especially if you recognize that the perceived clarity may depend on pre-conceptions. I'm not sure how much the article should cater for those who are irredeemably opposed to it.
My proposed change didn't eliminate reference to information, it only defined what was meant by specifying "in that sense" Hmmm. I see I missed reverting part of your change. Back to that in a tick.
Like I said above, there is no consensus definition of genetic information, so an encyclopedic article cannot make a statement of fact about genetic information without first defining the term. If there is no consensus definition, how do you provide a definition? You don't need to answer that, because I don't agree anyway. If I wrote something about wealth—say that much wealth brings unhappiness—I don't need to define "wealth" as, say, dollars in the bank. The wealth could be represented in other ways. Similarly (although not identically), just as you don't need to define what form the wealth takes, there is no need (in this context) to define what form the information takes, such as "gene variations". Most people (some anti-creationists seem to be an exception) understand what "information" is. The illustration of the genes gives an example of information in living things, in a manner that is, in my opinion, quite sufficiently clear. I have seen this type of illustration used many times, and I have used it many times myself, and it's only anti-creationists who seem to have a problem with it, and demand precise definitions before they'll concede to understanding what it means.
Philip J. Raymentdiscuss 11:18, 17 October 2011 (UTC)
it's only anti-creationists who seem to have a problem with it, and demand precise definitions Read: Creationists don't look for the problems inherent in their theories or utilize precise definitions. --Awc 12:08, 17 October 2011 (UTC)
That's rich coming from an evolutionist, given that evolutionists are unwilling to question evolution and define evolution as imprecisely as a "change in allele frequencies", a phenomenon that creationists have no trouble with. Philip J. Raymentdiscuss 12:26, 17 October 2011 (UTC)
evolutionists are unwilling to question evolution and define evolution as imprecisely as a "change in allele frequencies" Let's be clear on this. Are you saying that I am (1) unwilling to question evolution, and (2) define evolution generally as a change in allele frequencies? --Awc 12:42, 17 October 2011 (UTC)
How dare they require a definition! Next they'll want a definition for momentum, energy, mass, planet, mole, isotope, enantiomer, and isomer! The outrage! Sterile 12:47, 17 October 2011 (UTC)
Awc, I was avoiding referring to you specifically, but you take the side that generally holds those views. You criticise creationists for look[ing] for the problems inherent in their theories or [not] utili[sing] precise definitions, but do you criticise evolutionists who are guilty of that? Do you disagree with the modern definition of evolution that it relates to changes in allele frequency?
Sterile, instead of mockery, what I would like to see is a clear, unambiguous, usable, definition for species, or an admission that science can be done without such definitions at times.
Philip J. Raymentdiscuss 02:23, 22 October 2011 (UTC)
(outdent)
Species: (1)the lowest taxonomic rank, generally a two part name consisting of gneric and specific name. (2)the members of a group with common characteristics and (generally) capable of breeding. Note: speciation may not be complete in which case members of one species may breed with the parent group. Refer ring species.
you cant do much science if people are talking about different things therefore definitions are essential, essential to any technical endevor really Hamster 03:45, 22 October 2011 (UTC)
How can you (Philip) claim not to be referring to me specifically? That's rich coming from [Awc (who posted the comment referred to),] an evolutionist, given that [all (since not otherwise qualified)] evolutionists are ... I don't think you have any basis for this specific allegation.
My post was not intended as an expression of my personal opinion so much as an objection to your insinuation that, since creationists don't recognize a problem, then no problem exists. If you want to defend the position that there is no problem, then do that with good arguments, not by appealing to what other creationists believe.
Yes, I object to lack of critical distance to one's hypotheses and sloppy thinking no matter who is guilty of it. I don't voice my objection in every case, and I don't find these faults evenly distributed over all groups.
I recognize that the term "evolution", like most words, is used in a variety of ways, several of them by you yourself. When I use the term, I try to make it clear which definition I am using, either explicitly or through context.
--Awc 10:22, 22 October 2011 (UTC)
the members of a group with common characteristics and (generally) capable of breeding "Generally"?? That's an unambiguous definition? And your definition is not the only one. A common definition of species is that they are capable of interbreeding in their natural environment, which leads to creatures on opposite sides of the Grand Canyon being classified as different species, despite being able to interbreed, because they are geographically isolated and therefore cannot interbreed in their natural environment! So if there is more than one definition, how does this constitute a clear, unambiguous, usable, definition? And although you tried to excuse ring species by offering an explanation of why they exist, the point is that this means that the definition is ambiguous. And how do you determine interfertility of extinct creatures known only from the fossil record?
you cant do much science if people are talking about different things therefore definitions are essential, essential to any technical endevor really Why is it that creationists are criticised for not having clear definitions, but evolutionists can get away with such rubbery definitions as that for species? Why the double standards?
How can you (Philip) claim not to be referring to me specifically? I was referring to you specifically, not as holding those views, but as criticising creationists whilst not criticising evolutionists for the same sort of thing.
...[all (since not otherwise qualified)]... Lack of qualification does not imply all; it implies a generalisation.
...your insinuation that, since creationists don't recognize a problem, then no problem exists. I didn't insinuate that. I insinuated that most people, not just creationists, don't recognise a problem, and that only anti-creationists (not even all evolutionists) do.
Yes, I object to lack of critical distance to one's hypotheses and sloppy thinking no matter who is guilty of it. But you are selective in who you criticise.
I don't voice my objection in every case, and I don't find these faults evenly distributed over all groups. But when both the majority (evolutionists) and the minority (creationists) are guilty of it, you criticise the minority. However, this is missing the point. Although I'm sure that everyone agrees that clear definitions are desirable, my real point is that they are not always possible, but that is not reason for criticism. My example from evolutionists is not to say "they are guilty too", but to say "scientists on your side of the fence manage to work with imprecise definitions, so why is it grounds to criticise creationists when they do also?".
When I use the term, I try to make it clear which definition I am using, either explicitly or through context. As do I.
Philip J. Raymentdiscuss 05:30, 23 October 2011 (UTC)
I'm getting lost here. If your accusations are only referring to the polemical statement that started this particular exchange, it's an unimportant misunderstanding, Let's drop it. If this is supposed to be a more general criticism based on my interactions on this site over the last year, then I'd like to know what exactly you are talking about. When was the argumentation of both creationists and evolutionists on the table, with both of them making the same fallacies in roughly the same degree, but I criticized the creationists and not the evolutionists? If you mean when you threw the definition of "species" into the discussion, that won't cut it. Every definition has some fuzzy edges, but the operational definition of "species" is a thousand times more precise than the creationists' definition of "genetic information". (In my recent versions of this article, I have tried to get around the insufferable fuzziness of the concept of information by formulating the argument for creation without using the term information, that is, I essentially tried "to work with the imprecise definition". The argument still fails.) --Awc 10:35, 23 October 2011 (UTC)

Definition of "species" vs. definition of "genetic information"

...the operational definition of "species" is a thousand times more precise than the creationists' definition of "genetic information". I don't agree. I'm not saying that they are exactly equivalent, but both are good enough to work with. Philip J. Raymentdiscuss 11:54, 23 October 2011 (UTC)

All right. Let's look both of them in the mouth. I'll put a definition of species on the table and you do the same for genetic information. --Awc 12:19, 23 October 2011 (UTC)
Species
A group of organisms having common characteristics and capable of mating with one another.
Genetic information
...
I'm not sure what your point is. Yes, you've provided a definition of "species". But it's your definition (as opposed to some other definitions used by scientists), and it has not been established how useful it is, and it is clearly not useful for extinct organisms.
But for the sake of playing along, Genetic information is the set of instructions that describe the construction and operation of living organisms.
Philip J. Raymentdiscuss 14:21, 23 October 2011 (UTC)
does genetic information and I assume you mean DNA have any affect on the operation of an organism ? it certainly is used in reproduction of the cell, but otherwise ?
what other deinition of species is there ? Steriles definition and mine are essentially equivalent and we would have no problems in partially speciated organisms.
yess extinct organisms dont breed (standard biology joke) so its not possible to tell but that does not matter in many cases because the morpholgy of the organism would show a grouping. So these organisms A and B are Aren a and Aren B respectively and both of the Aren group. organism c shows similarities to both a and b but has some differences in form and is 50 million years later so we can label it as Balen a and draw a chart that says from the Aren group we have a descendant Balen. ( I think thats basically correct - feel free to correct it) Hamster 15:43, 23 October 2011 (UTC)


The point is that some of us are having a hard time understanding what you or creationists in general mean by genetic information, so having you state and defend a simple definition might help in that direction. In addition, I want to substantiate my statement that the operational definition of "species" is a thousand times more precise than the creationists' definition of "genetic information".
My definition of species is not perfect (It doesn't cover non-sexual reproduction, and the point of the "common characteristics" part is not clear.), but it's a good start. In principle, we just need to throw some animals in a cage and wait to see if any babies pop out.
Now how about your definition? Let's start with an instruction.
  • How can these instructions be represented? Are we only talking about sequences of base pairs, or is there more to it?
  • If a sequence expresses a protein that does not enhance the ability of the organism to survive, does that still count as genetic information?
  • Given this definition the natural quantification of genetic information would be the number of instructions (assuming they can in principle be counted). Is that reasonable? If two sets of instructions produce the same phenotype, does the one using more instructions have more information?
That should do for a start. Maybe the definition just needs to be adjusted a little to make these things clearer.
--Awc 19:24, 23 October 2011 (UTC)
  • Why is the definition restricted to "instructions"? There are other types of information that are not instructions. Would all the arguments still work if we talked about "genetic instructions" instead of "genetic information"? --Awc 07:22, 24 October 2011 (UTC)
does genetic information and I assume you mean DNA have any affect on the operation of an organism ? it certainly is used in reproduction of the cell, but otherwise ? It is my understanding that it is used for more than just cell reproduction. This says that DNA "contains information or codes necessary for cellular activity, like in the formation of proteins and RNA or ribonucleic acid.", and this, after talking about cell division, says "In addition, when proteins are being made, the double helix unwinds to allow a single strand of DNA to serve as a template. This template strand is then transcribed into mRNA, which is a molecule that conveys vital instructions to the cell's protein-making machinery."
what other deinition of species is there ? As I said, that the organisms reproduce in their natural environment. This definition specifically rules out Awc's suggestion to "throw some animals in a cage and wait to see if any babies pop out.", as a cage is not their natural environment. See also the first two references in the species article, the second of which starts with "Ernst Mayr ... is the author of one of the most popular of the numerous alternative definitions of the species category." (my emphasis)
...that does not matter in many cases because the morpholgy of the organism would show a grouping. So an unusable (in some cases) definition "does not matter", but creationists being unable to provide a definition of "information" that caters for all cases does matter. That's the double standard I've mentioned so often.
look at the definition again. Since the organism is dead the ability to breed is not available. It is possible to study the form. That is one part of the definition so its still reasonable to do that comparison. If it is determined that two fossils are identical in form , allowing for minor variations that occur in any living creatire, it is reasonable to conclude that they appear to be the same species, close relatives, or not related. Hamster 14:37, 25 October 2011 (UTC)
So these organisms A and B are Aren a and Aren B respectively and both of the Aren group. organism c shows similarities to both a and b but has some differences in form and is 50 million years later so we can label it as Balen a and draw a chart that says from the Aren group we have a descendant Balen. I'll have to remember this comment. When creationists point out the lack of evolution in some creatures, evolutionists are quick to claim that evolution does not require that creatures change. But here you are assuming that a difference in time means that it must have evolved enough for it to be a different species.
no thats not my conclusion. I am providing an illustration of a process. I could have said that c appears identical to a and therefore a chart showing Aren A lived from time 1 to time 2 is a reasonable conclusion. As I said the differences between a,b,c are axiomatic to my illustration. Hamster 14:37, 25 October 2011 (UTC)
My definition of species is not perfect (It doesn't cover non-sexual reproduction, and the point of the "common characteristics" part is not clear.), but it's a good start. In principle, we just need to throw some animals in a cage and wait to see if any babies pop out. As I mentioned above, your definition is not the only definition, and it is inconsistent with the most popular definition, that specifically excludes your suggestion of putting some animals in a cage to see if they have babies.
most popular ? i havent seen a dictionery that says other than similar characteristics and fertility. whats your source for most popular ? Hamster 14:37, 25 October 2011 (UTC)
How can these instructions be represented? Are we only talking about sequences of base pairs, or is there more to it? I'm not sure that I follow. The information is carried on the DNA, specifically by the sequence of genetic "letters", which are, of course in the form of base pairs. Information is always carried in the particular arrangement of whatever is carrying it (printed letters, Morse code dots and dashes, sound waves, etc.), so if that's what you mean by "sequences of base pairs", then yes.
If a sequence expresses a protein that does not enhance the ability of the organism to survive, does that still count as genetic information? I think you are trying to jump straight to hard cases rather than get an overall understanding. It's like me asking how you determine the species of an extinct organism before understanding the basic definition of species. In both cases, the question is legitimate, but should come after a basic understanding. (And despite my comments about the rubbery nature of "species", I'm not rejecting it outright; I accept it as a useful definition, albeit not without its problems.) I would point out, however, that enhancing the ability of an organism to survive is not the criterion of "information". The genome could, logically, contain information on, say, colouration that adds beauty, but does nothing to add survival value.
...the natural quantification of genetic information would be the number of instructions ... Is that reasonable? As a starting point, yes, that's reasonable. But...
...(assuming they can in principle be counted)...If two sets of instructions produce the same phenotype, does the one using more instructions have more information? This gets down to the problem with simply counting instructions, so I would answer "no". See more in my list of examples below.
Why is the definition restricted to "instructions"? There are other types of information that are not instructions. Would all the arguments still work if we talked about "genetic instructions" instead of "genetic information"? There are other types of information, but I doubt that there are other kinds of genetic information. See my next section, which gives some examples.
I think that Andrew Lamb's example[5] can't be beaten for a non-technical illustration:
  • She has a yellow vehicle.
  • She has a yellow car.
Lamb's example was to illustrate that the amount of information was not necessarily related to length of data, as the second, shorter, sentence has more information. But ignore the length—the second sentence conveys something that the first sentence doesn't: that the person's vehicle is, specifically, a car. For all we know from the first sentence, the person might have a truck, a hovercraft, a motorbike, a car, or some other sort of vehicle. The second sentence is more specific, and so it tells us something that the first sentence doesn't: the type of vehicle.
So the second sentence has more information than the first. I've pointed to or quoted this example numerous times, and, from memory, nobody has yet acknowledged that they understand this point. Instead they try and ignore it, such as claiming that it's only an analogy for genetic information.
Another point to make is that the sentences are not instructions, yet they are still information. An encyclopædia or a textbook has non-instruction information. A recipe book and a TV repair manual have information in the form of instructions. (Of course, these are generalisations; a textbook might have some instructions for classroom experiments, and a recipe book might have some information about the author's vegetable garden.) Genetic information is instructions. I'm not aware of any non-instruction information in the genetic code.
The instructions themselves could be divided in the instructional part and the values part. A recipe, for example, might say to cook at 100 degrees for ten minutes. The instructional part is to cook at a given temperature for a given time, and the temperature and the time are the value parts. A TV repair manual might say to to remove the cover with a No. 5 screwdriver. The instructional part is to remove the cover with a given screwdriver, and the value part is the number 5. Genetic information might say to produce 400 units of a particular protein. The instruction part is to produce a given amount of the particular protein and the value part is the 400 units.
Compare these three sets of instructions to produce Awc's user name:
  • Method 1
    • Quickly tap the letter A on the keyboard
    • Quickly tap the letter w on the keyboard
    • Quick tap the letter c on the keyboard
  • Method 2
    • To type a letter, quickly tap the letter on the keyboard
    • Type A
    • Type w
    • Type c
  • Method 3
    • To type a letter, quickly tap the letter on the keyboard
    • Type A, w, and c.
These methods appear to have 3, 4, and 2 instructions respectively. But do any contain any information that the other two don't have? Does the second instruction in method 3 count as three instructions or one? This illustrates your (Awc's) quandary about how you count instructions. The second and third methods illustrate what in computer terminology is calling a subroutine. I would think that all three methods have the same information, because they produce the same result; it's simply stated in a different way.
your last instruction actually has 4 instruction
to type a leetter etc (1) type a(2) type w(3) type c (4)
Hamster 14:37, 25 October 2011 (UTC)
Here's three (overly simplified) sets of instructions on building a kite:
  • Method 1
    • Fix two sticks at right angles
    • Attach a sheet of plastic in a diamond shape so that each corner corresponds to an end of a stick
    • Attach a string to the point where the stick cross
  • Method 2
    • Fix two sticks at right angles
    • Attach a sheet of plastic in a diamond shape so that each corner corresponds to an end of a stick
    • Attach a string to the point where the stick cross
    • Attach a tail
  • Method 3
    • Fix two sticks at right angles
    • Attach a sheet of plastic in a diamond shape so that each corner corresponds to an end of a stick
    • Attach a string to the point where the stick cross
    • Paint an aggressive image on the plastic.
Methods 2 and 3 have more information than method 1. Not because they have an extra instruction, but because the instructions contain something that the first method doesn't (instructions for a tail and an image respectively).
There may be no way of determining which of methods 2 and 3 contain more information, because we don't know how to compare the fourth instruction in each case. However, this limitation to our analysis does not stop us from concluding that each of methods 2 and 3 contain more information than method 1.
Philip J. Raymentdiscuss 14:11, 25 October 2011 (UTC)
That's a good start. (I'll try not to bring up the hard cases too soon.) I would like to ask whether genetic information is a property of an organism, a gene pool, or something else. I'll assume the answer is gene pool to keep things simple, but let me know if that's not good enough. What we've got so far is pretty much that genetic information consists of the amino acid sequences of the gene pool. If that was all, we wouldn't really need an extra term for it. Where it gets interesting is when you quantify genetic information, or at least order the relative quantities. You might want to say this DNA is a gene regulating a core function of the cell, but that is just junk, so this contains more genetic information than that. And of course the argument for creation relies on quantification, and not too fuzzy, either. If you could only say mutations might produce some information, but at most just a little bit, then you couldn't rule out that the little bits add up to something humongous, given enough time. So how about the next step?
The relative quantity of genetic information in two different gene pools can be determined by ...
--Awc 21:11, 25 October 2011 (UTC)
No, not quite so fast yet, Awc. I'm still trying to digest "the set of instructions that describe the construction and operation of living organisms". We seem to have simply replaced one unknown, information, with another, instructions. Philip has yet again provided some lovely analogies to computer programs and English language sentences, but I still don't know how this definition applies to biological systems. For example, are 'the set of instructions', which are carried by the arrangement of bases in the DNA, the number of genes in the organism? The total number of proteins that are produced by transcribing those genes (probably a larger number)? Does the protein-coding portion of a gene and its various regulatory sequences (promoters, inhibitors, etc.) count as a single instruction, or multiple instructions, to wit: under condition A, transcribe x copies of gene 1; under condition A', transcribe y copies of gene 1, under condition B transcribe z copies....? What is the principle by which one can distinguish between one instruction that is 'merely' a variation of another, and one that is 'different' than that other? How do we know whether a given portion of the genome contains instructions and therefore information, and which portions, if any, are merely data?--Martin Arrowsmith 00:42, 26 October 2011 (UTC)
Maybe I'm being too generous, but I thought we had replaced the unknown information with the already familiar genome/gene pool. Most of your other questions, number of genes ... total number of proteins ... count as a single instruction, or multiple instructions, and to some extent the last two questions as well, aim at quantification, which is, I think, Where it gets interesting. Either way, let's hear what Philip has to say. (It would be nice if he could draw his examples from genetics instead of linguistics, typing, and kite making.) --Awc 06:44, 26 October 2011 (UTC)
I do await the answer to Awc's question, but I view the "instruction" view of information potentially contradictory to the "linguistic specificity" version. One could put an instruction in an algorithm to remove details about an object, thus reducing a "car" to a "vehicle" with more instructions (which could be viewed as a Kolmogorov complexity concept). It's also not clear to me that more specific linguistically is more information, and despite what Philip claims, I've pointed this out before (here and here).
Even if the claim is "some cases are clear," in reality the vast majority are not clear, and hence making the proposed hypothesis/argument that information doesn't increase useless. Sterile 15:41, 26 October 2011 (UTC)
Which instruction has more information? Which one is more likely to save your life?
  • If you are stranded in the desert, get in a car and drive out of there.
  • If you are stranded in the desert, get in a car or any other kind of vehicle you happen to find because it really doesn't matter, and drive out of there.
--Awc 16:45, 26 October 2011 (UTC)
Sterile and Awc, while I love you like the brothers/sisters (?) I never had, can we PLEASE FOXTROT YHWH not fall into the error of allowing this discussion to be fought on the playing fields of Eton? That is to say, that figuring out what English sentences have more information in them than other English sentences does not actually tell us whether a gene and its promoter are one instruction or two instructions or some other number of instructions. Or whether a novel allele is a new instruction or just a variant instruction, etc. etc. Linguists have all sorts of formulations and theories related to information content in written and spoken language, which they have argued about for many years. I just can't see the value of addressing the issue of biological information via computer program analogies or encryption analogies or whatever when, in the end, if we are going to make use of the definition it has to apply to actual DNA-Protein-cell-organ-organism-population systems. I appreciate the impulse, but I think that we have to present a united front to drag PJR kicking and screaming into the actual biological world. Of course, YMMV, and I won't be offended if you disagree. But why waste effort getting PJR to explain how his theory applies to English only to have to do it all over again to see how it applies to proteins?--Martin Arrowsmith 00:52, 27 October 2011 (UTC)
I can sign off on that. I think my deeper purpose (as if I had one) was to show that even in Philip's analogous universe, his concept of quantifiable information is at best problematical. I'm not sure we will be able to drag Philip anywhere, but I'm relaxed because I think the worst of the nonsense has been eliminated from the article. An open reader who stumbles across the article will go away with the knowledge that the genetic information argument for creation is flimsy. --Awc 06:47, 27 October 2011 (UTC)
Absolutely, Martin, although somewhat ironic given what follows. Sterile 14:12, 27 October 2011 (UTC)
look at the definition again. Since the organism is dead the ability to breed is not available. Precisely. The definition is inadequate.
no thats not my conclusion. I didn't say that it was your conclusion. I said that it was an assumption you made, and your response has done nothing to refute that.
most popular ? ... whats your source for most popular ? Sigh. Try reading my post that you were replying to. I provide the source.
your last instruction actually has 4 instruction: to type a leetter etc (1) type a(2) type w(3) type c (4) Yes, you could count them that way, as I indicated. That was my point, that it's not clear how many instructions an instruction set has. You could say the same of the first instruction. "To type a letter, quickly tap the letter on the keyboard" There are at least three key points here: that you tap, that you do so quickly, and that you do it on the keyboard. So should that be counted as one instruction or three? (Or some other number?) That's my point: simply counting instructions is not very helpful. What you need to do is compare two instruction sets (or even two instructions) and see if one contains something that that the other doesn't. Compare these two:
  • To type a letter, tap the letter on the keyboard
  • To type a letter, quickly tap the letter on the keyboard
So the second of these instructions contains more information than the first, as the second also says that it is to be done quickly, a detail that is not in the first version. So to repeat the point, counting instructions may be a useful first step to understanding this, but it's not actually the way to quantify the amount of information.
I would like to ask whether genetic information is a property of an organism, a gene pool, or something else. ... let me know if that's not good enough. Information is carried in the genes; it's not a property of the genes. Just like information in a book is not a property of the book, the paper, or the ink; it's carried by those things.
You might want to say this DNA is a gene regulating a core function of the cell, but that is just junk, so this contains more genetic information than that. Correct. If the DNA is just junk (we don't know of any; all we know of is DNA that we haven't been able to determine if it has a purpose), then it carries no information.
If you could only say mutations might produce some information, but at most just a little bit, then you couldn't rule out that the little bits add up to something humongous, given enough time. So how about the next step? There are two points to make here.
  • In theory, mutations might produce some information. Just like an explosion in a printing works might produce one of Shakespeare's plays. Is that reasonable? The point is that there is not a physical law preventing it, but the odds are so small that they aren't worth considering, unless you're talking about a very trivial amount (the explosion might produce the first word of one of Shakespeare's plays).
  • I can rule out that those little bits add up to something humungous. If that explosion produces the first word of a play, then perhaps another explosion would produce the second word? But that second explosion would destroy the first word! Unless, somehow, that first word was protected from the second explosion. This is where natural selection is supposed to play a part, keeping the gains whilst destroying the losses. Unfortunately, it doesn't help. Natural selection works on the organism level, not the individual mutation level. So even in a lineage of selected individuals, the rare gain would be swamped by the losses.
The relative quantity of genetic information in two different gene pools can be determined by ... As I've already said, you can really only determine relative quantities for nearly-identical sets of information. Having said that, though, one can also make an estimate for two very different gene pools. To pick an extreme example, I think we'd be pretty safe to say that humans have much more genetic information than bacteria.
We seem to have simply replaced one unknown, information, with another, instructions. Do you want me to define every word of a definition? Perhaps also every word used to define a definition? And so on, ad infinitum?
Philip has yet again provided some lovely analogies to computer programs and English language sentences, but I still don't know how this definition applies to biological systems. Sigh. As I said, I've pointed to or quoted this example numerous times, and, from memory, nobody has yet acknowledged that they understand this point. Instead they try and ignore it, such as claiming that it's only an analogy for genetic information. Thanks for demonstrating that I was right.
However, I did think that I should have provided a biological example, because some people seem to refuse to understand, but I was running out of time. Okay, just for you, here's an example from biological systems. Just like the kite, these are very simplified instructions, for building a bird.
  • Build a body with a light structure and flow-through lungs.
  • Add a head.
  • Add two legs.
  • Add two wings.
  • Add feathers.
Satisfied? I'm sure you're not, yet that is analogous to the kite instructions which you seemed to have no trouble with except that it wasn't biological. In both cases, the simplification is in assuming that the reader of the instructions knows how to do each of those things, whereas in practice the instructions would be a lot more detailed (okay, in the case of living organisms, a lot more detailed).
For example, are 'the set of instructions', which are carried by the arrangement of bases in the DNA, the number of genes in the organism? Are 'the set of instructions' for the kite the number of English letters used? The answer is the same, because the analogy works.
...I view the "instruction" view of information potentially contradictory to the "linguistic specificity" version. It's not.
One could put an instruction in an algorithm to remove details about an object, thus reducing a "car" to a "vehicle" with more instructions Please provide an example that demonstrates this. Awc's example doesn't; it does make one bit less specific, but also adds another bit.
It's also not clear to me that more specific linguistically is more information, and despite what Philip claims, I've pointed this out before... I've never claimed that it is clear to you.
Which one is more likely to save your life? This question is irrelevant to the question of the amount of information.
Which instruction has more information? Which one tells you things that the other doesn't? Also, you are introducing the concept of correct information. Go back to the kite example. You didn't mention that you had any problem with that. But what if the instruction for adding a tail was actually to add a brick? That's still an extra instruction, but one that hinders, not helps. Whether or not the instruction is correct/helpful/useful/less likely to save your life is a separate issue to the number of instructions/amount of information.
...figuring out what English sentences have more information in them than other English sentences does not actually tell us whether a gene and its promoter are one instruction or two instructions or some other number of instructions. They are not meant to. What they are meant to do is help you grasp the concept, which you seem to be fighting against doing. If and when you understand the concept (which is a concept about information, not about English sentences), perhaps then you will be closer to understanding how to apply that concept to genetics.
...I think that we have to present a united front to drag PJR kicking and screaming into the actual biological world. Perhaps you should be entering the world of information rather than the biological world. Werner Gitt—"One of the intrinsic characteristics of life is information.".[6] Braitenberg—"information is an intrinsic part of the essential nature of life."[7] Paul Davies—"We now know that the secret of life lies not with the chemical ingredients as such, but with the logical structure and organisational arrangement of the molecules. … Like a supercomputer, life is an information processing system. … It is the software of the living cell that is the real mystery, not the hardware."[8] Bill Gates—"Biological information is the most important information we can discover, because over the next several decades it will revolutionize medicine. Human DNA is like a computer program but far, far more advanced than any software ever created."[9]
...his concept of quantifiable information is at best problematical. What about the concepts of increases and decreases of information, which is, after all, the point that creationists are making, rather than quantifying it?
Philip J. Raymentdiscuss 13:15, 27 October 2011 (UTC)
That, too. If statements do not have to be correct to constitute information, that's a problematical definition. Your exploding factory doesn't have to reproduce a work of Shakespear, it only has to occasionally produce strings that can be parsed as language in order to be creating information. Does one of us have to convince the other on that before we can move on? Let's just hear how you think you can determine increase or decrease in the amount of genetic information. --Awc 14:27, 27 October 2011 (UTC)

Since the developmental genetic toolkit is highly conserved among phyla (ie., nearly-identical sets of information, differing only by the timing by which genes are expressed and the like, the information content by creationist standards must be similar among organisms in the phyla. Therefore, unless the timing of gene expression constitutes a "dramatic loss" of information, speciation, even among vastly different forms, ought to be nearly information neutral. Hence, you contradict yourself with your own logic. Sterile 15:46, 27 October 2011 (UTC) (PS: Bill Gates?) Sterile 15:50, 27 October 2011 (UTC)

Don Batten says you are incorrect that you can really only determine relative quantities for nearly-identical sets of information:

Does a high degree of similarity mean that two DNA sequences have the same meaning or function? No, not necessarily. Compare the following sentences:
There are many scientists today who question the evolutionary paradigm and its atheistic philosophical implications.
There are not many scientists today who question the evolutionary paradigm and its atheistic philosophical implications.

These sentences have 97% homology and yet have almost opposite meanings! There is a strong analogy here to the way in which large DNA sequences can be turned on or off by relatively small control sequences. The DNA similarity data don’t quite mean what the evolutionary popularizers claim! [emphasisis in original: [10]]

Actually, I would say that even your bacteria and human example is inherently worthless, because mutations are small changes. Given that I and others have asked which sequences contain more information, and you have been unable to tell the difference, it's inherently obvious that there's nothing "in the string" that helps us to differentiate the quantities. Sterile 13:31, 30 October 2011 (UTC)

Don Batten doesn't say what you claim he says. He is talking about a high degree of statistical similarity in the genome as a whole, as claimed by evolutionists for chimps and humans, and pointing out that the statistical similarity does not mean a high degree of similarity of meaning. He's not saying that you can't compare the meaning—the opposite, in fact, as he compares the meaning of two sentences to show that a high statistical similarity is not necessarily correlated with meaning. I have made a similar point further down this page with comparing two sentences about teacher and students.
I would say that even your bacteria and human example is inherently worthless, because mutations are small changes. How does that make it worthless? That appears to be a non-sequitur.
Given that I and others have asked which sequences contain more information, and you have been unable to tell the difference, it's inherently obvious that there's nothing "in the string" that helps us to differentiate the quantities. The difference is in the meaning, or in the function, which you haven't given me.
Philip J. Raymentdiscuss 00:22, 1 November 2011 (UTC)
If statements do not have to be correct to constitute information, that's a problematical definition. Why? Have you never heard anyone say something like "the information in the book is incorrect"? Does it being incorrect mean that it's not information? I'm not denying that it may be a problem in some respects, but not enough to undermine the whole concept.
Your exploding factory doesn't have to reproduce a work of Shakespear, it only has to occasionally produce strings that can be parsed as language in order to be creating information. No, it doesn't have to be a work of Shakespeare, but it has to be large enough to carry meaning. "Had", by itself, carries no meaning. If you opened a book, and the only word there was "had", you'd think "what the..?!". Words only carry meaning in context, so there has to be a context, not a single word. Okay, you didn't say only a single word, but an explosion in a printing works is not going to produce more than a single word, and even that would be extraordinarily unlikely, other than some very short words like "it". The point is that, even if you could show that there is a (very small but) significant chance of having two words together, like "it is", you are not going to get enough that can be parsed as language in order to be creating information".
Let's just hear how you think you can determine increase or decrease in the amount of genetic information. Reread my examples above. Can you not see that an extra instruction is an increase in information?
Since the developmental genetic toolkit is highly conserved among phyla... the information content by creationist standards must be similar among organisms in the phyla. A similar toolkit does not mean that the information content is similar. A handyman will have a set of tools that he can use to fix a leaking tap or build a swinging garden seat. The point is not whether there are common tools, but what is done with those tools.
Therefore, unless the timing of gene expression constitutes a "dramatic loss" of information, speciation, even among vastly different forms, ought to be nearly information neutral. The timing might indeed make a difference. Consider Morse code sent by telegraph: the information in the message is entirely dependent on the timing of the signals.
Hence, you contradict yourself with your own logic. No, it was not my logic that contradicted me. It was your misunderstanding that contradicted me.
(PS: Bill Gates?) Yes.
Philip J. Raymentdiscuss 00:39, 1 November 2011 (UTC)
The difference is in the meaning, or in the function, which you haven't given me. so you are saying that a complete DNA code in itself contains no information because the meaning of that dna is not known, Just as no english sentance written by another person contains no information because its meaning is also unknown ?
you are sort of right with morse code but its the relative rather than absolute timing thats important.
so in an explosion in a type factory four characters are blown into the door. These characters spell RUN! , now that in context of the explosion that has meaning, and in fact is great advice. Hamster 00:58, 1 November 2011 (UTC)
The "toolkit" is the DNA. Even in your sense of the word, it is instructions. (Did you take that literally?) I also have no doubt that the timing makes a difference; that's what the research shows us, which I explained below. Sterile 01:28, 1 November 2011 (UTC)
so you are saying that a complete DNA code in itself contains no information because the meaning of that dna is not known No. I'm saying that I can't tell you which has more information without knowing the meaning; I'm not saying that it doesn't have any.
you are sort of right with morse code but its the relative rather than absolute timing thats important. In that case, yes.
so in an explosion in a type factory four characters are blown into the door. These characters spell RUN! , now that in context of the explosion that has meaning, and in fact is great advice. And what's the chances of that happening? Hmmm.
The "toolkit" is the DNA. I don't know which way you mean this. The toolkit and the DNA are synonymous, which means that the toolkit is all the DNA? Not according to your reference. Or, the toolkit is composed of DNA? I would agree with this, but that doesn't contradict anything I've said.
I also have no doubt that the timing makes a difference... I know, but your point was that it didn't amount to information, while my example of Morse code shows that it can.
Philip J. Raymentdiscuss 04:45, 1 November 2011 (UTC)
There's a short explanation of the toolkit at Wikipedia [11]; the Hox genes are part of the toolkit which I suspect you're familar with from CMI. They are a series of genes (genetic information) conserved among organisms that are expressed during development. The important sentence from the Wikipedia blurb is "This means that a big part of the morphological evolution undergone by organisms is a product of variation in the genetic toolkit, either by the genes changing their expression pattern or acquiring new functions." That is, in developmental terms, there isn't a lot of difference between critters in the phylum. In the commonsense meaning of the word information, I guess what you would call statistical, they are very similar. But it's unclear that you would call them equivalent in meaningful information. (The Hox genes are interesting because the spatial arrangement on the DNA strand corresponds to that of the developing organism.)
The Morse code analogy is far to simplistic to be useful, I would say (multiple genes are being expressed at once/in sequence and depend on each other), and still doesn't give any sense of more or less, as it still assumes that the original encoding had information in the first place, and hence begs the question in the argument that meaningful information must come from an intelligent source. Sterile 03:11, 2 November 2011 (UTC)
...the Hox genes are part of the toolkit which I suspect you're familar with from CMI. That still doesn't change anything I've said.
This means that a big part of the morphological evolution undergone by organisms is a product of variation in the genetic toolkit... To the extent that you seem to be applying that, and likely that Wikipedia is applying that, this conclusion doesn't follow from the evidence. However, I do note that Wikipedia's two examples are of a variation in beak sizes and loss of limbs.
That is, in developmental terms, there isn't a lot of difference between critters in the phylum. That's a completely unwarranted conclusion. Wikipedia mentions the Pax6/eyeless gene which produces eyes in a wide range of creatures. But note that it's producing a range of different eyes, including the mouse version of the gene producing fly eyes in flies. So it's a switch that turns on the development of eyes, but the instructions for the eyes themselves is different in each case. The fact that they have the same (or similar) switch does not mean that there isn't a lot of difference between critters. I could use the same switch to turn on a room light or start a power saw. It's not the switch that makes the difference, but the thing that the switch switches on.
In the commonsense meaning of the word information, I guess what you would call statistical... No, the common sense meaning of the word is not statistical. If a person says that a book has a lot of good information, they are not talking about statistics on how many pages, words, or letters it has.
The Morse code analogy is far to simplistic to be useful... It was merely to make the point that timing can make a difference, that's all.
...it [the Morse code analogy?] still assumes that the original encoding had information in the first place, and hence begs the question in the argument that meaningful information must come from an intelligent source. I don't follow, but you seem to be saying that because switches are similar, no information exists. Apart from anything else, this ignores the information in the instructions that the switches switch on.
Philip J. Raymentdiscuss 05:44, 4 December 2011 (UTC)

Bibliography

I think it would be better to put the bibliographical information directly in the the references, rather than in a separate section. It would make one step less getting to the links, and you wouldn't have to manually look through the alphabetical list. Any objections or thoughts on the matter? --Awc 21:17, 4 October 2011 (UTC)

I agree that your suggestion is one less step in getting to the links. But it one more step in creating the links. When you have multiple references to the one source document, but to different pages in that document, there are (at least) three ways of doing them:
  1. The way this article has, with the references being to sources in the bibliography, and with page numbers in the references. This has the disadvantage you mention.
  2. The way you propose, with the source document being mentioned in the reference. This has the disadvantage of having to repeat the complete source reference (author, document, link, etc.) for each different reference. (References can be combined into one if they are identical, but if they have different page numbers they are not identical.)
  3. A mixture of the two, where a reference is to a page number in a source which is not in the bibliography section, but which is in another reference. For example, reference 1 might be to Fred Smith, 'The problem with pigs', The Pig Journal, December 2004, p.4, and reference 2 might be Fred Smith, 2004, p. 6. This is easier to create than option 2, easier to look up than option 1, but runs the risk that if reference 1 is removed (as it might be if the section of text containing it is removed), then reference 2 is left hanging.
I personally think that none of these are entirely ideal, and I have tried different approaches on different articles. What I would like is a proper discussion and agreement on what approach we should take, on the Style manual talk page.
Philip J. Raymentdiscuss 05:58, 10 October 2011 (UTC)
That just about sums it up. I made my proposal partly because only 4 of the references in this article list page numbers, and none of the references refer to different page numbers of the same article. I agree it would be best if we could agree on a general policy for the Style manual. (It looks like Wikipedia doesn't have a general recommendation, either.) --Awc 11:49, 10 October 2011 (UTC)

point mutations in DNA

this may be a stupid question but anyway ... I have normally discussed mutations in analogy with the dna being considerdd as 4 letters of code read in groups of three characters representing an actual molocule. I realize that DNA is actually a string of these molocules so exactly what changes in a point mutation ? Hamster 18:59, 8 October 2011 (UTC)

Sometimes nothing, since each amino acid is coded for by about two different base pair sequences on average. If the amino acid does change, it is often similar to the previous one. Of course, sometimes a completely different amino acid becomes coded for. You can study it a bit with this picture. I think this tendency to "soft" changes is one of the reasons mutations work so well (at least better than you might expect) at improving the existing function. --Awc 19:53, 8 October 2011 (UTC)
A point mutation is the substitution of one DNA 'letter', or molecule, for another. So changing ATC to ATG would be a point mutation. Depending on the exact change, there may be no change to the amino acid produced, as Awc mentioned, although this may only be true for a particular reading frame and direction.
However, as adenine and guanine are very similar, and thymine and cytosine are also very similar, the change may be to a few atoms rather than substituting an entire molecule. This, I presume, is why A/G and T/C substitutions are far more common than A/T and G/C substitutions.
Philip J. Raymentdiscuss 08:17, 10 October 2011 (UTC)

off topic discussion points

er, gravitation interactions and collisions within the early system. More ad hoc ideas. ad hoc as in well thought out and carefully modelled ? then yes. perhaps gravity ? Gravity requires a (concentrated) mass, which gas doesn't have. well, just no. It would depend on the total masses involved and the topology of the cloud. But any mass exhibits gravity Hamster 04:15, 10 October 2011 (UTC)

Gravity requires a (concentrated) mass, which gas doesn't have. Jupiter? You can disagree with many of Philip's statements, but this one is beyond disagreement. --Awc 07:56, 10 October 2011 (UTC)

ad hoc as in well thought out and carefully modelled ? Ad hoc as in a different explanation is needed for every case. Also, if the ideas are well thought out and carefully modelled, why does one of your references say that "At present we have no idea how giant planets could form so close to their parent stars."?
WE also have no evidence that a gas giant formed in the present position. There are som excellent models of the process of migration towards the star, and suggestions that the planet formed some distance from the star, which then expanded. The refs I used were basically first grade sources for introduction to astronomy, not state of art science. Hamster 15:05, 10 October 2011 (UTC)
well, just no. It would depend on the total masses involved and the topology of the cloud. But any mass exhibits gravity Any mass exhibits gravity, but gas, by it's nature, doesn't have enough concentrated gravity to overcome the nature of a gas to move apart.
Philip J. Raymentdiscuss 08:30, 10 October 2011 (UTC)
Any mass exhibits gravity, but gas, by it's nature, doesn't have enough concentrated gravity to overcome the nature of a gas to move apart. Where the heck do you get such nonsense? It's a quantitative question. The equation relating mass, radius, and temperature to determine whether a spherical ball of gas is gravitationally bound or not is very simple classical physics. (If you need an additional hint, don't forget to include the universal gravitational constant, the Boltzmann constant, and the mass of the hydrogen molecule.) If you can't write this down, then you should recuse yourself from discussing this topic. --Awc 10:02, 10 October 2011 (UTC)
How is it nonsense? And one doesn't need to cite all the figures in order to understand the principle.

To form the sun, or any star, a cloud must be dense enough to collapse and compress the interior so that it becomes hot enough for nuclear fusion to start. But most gas clouds have a tendency to expand rather than contract.
The British mathematician and astrophysicist James Jeans (1877–1946) calculated how massive a cloud must be so that gravity can overcome the tendency for gas to expand. The main points are: high density favours collapse, and high temperature favours expansion. The minimum mass he calculated relates to both of these, and is now called the Jeans Mass (MJ ).
But according to the big bang theory, at the time the first stars were formed, the temperature was so high that the required Jeans Mass would be about 100,000 suns. This is about the same mass as a globular cluster, i.e. no cloud less massive than this could have collapsed into a star, thus no star could have formed this way. Abraham Loeb, of Harvard’s Center for Astrophysics, says, “The truth is that we don’t understand star formation at a fundamental level.”[12]

Philip J. Raymentdiscuss 13:11, 10 October 2011 (UTC)
Oh Philip, why do you just quote these things without expending any effort to understand them more deeply? For one thing, the Jeans mass assumes a perfectly uniform region of gas (contrary to evidence) and, more interestingly, the gas within the Jeans Mass, as it collapses, forms subregions of greater density that collapse faster, which in turn form smaller regions of greater density which collapse faster still, etc. So even if the collapse needs 100K solar masses to initiate, the collapse leads to the formation of lots of smaller stars, not one ultramassive one. So even if the initial gas mixture was completely uniform (and we know from the CMBR that it was not) then the collapse into smaller, denser regions is inevitable over large enough scales.--Martin Arrowsmith 15:49, 10 October 2011 (UTC)
And one doesn't need to cite all the figures in order to understand the principle. I might let you slide through without being able to reproduce the math—although it's really quite simple—if only you did understand the principle. Failing that, you should at least be able to properly quote your sources. Sarfati wrote The main points are: high density favours collapse, and high temperature favours expansion. The minimum mass he calculated relates to both of these, and is now called the Jeans Mass (MJ )., which is correct. You turn that into gas, by it's nature, doesn't have enough concentrated gravity to overcome the nature of a gas to move apart, which is not at all the same thing and is nonsense.
Putting your nonsense aside and turning to Sarfati, he justifies his statement that at the time the first stars were formed, the temperature was so high that the required Jeans Mass would be about 100,000 suns with the calculation (in note 3), According to big bang theory, the temperature was about 3,000 and density about 6,000, therefore MJ ≈ 105 M. The temperature of the universe was 3000 K at the age of recombination, when it was 380,000 years old. No stars formed until the universe was at least 100 Myr old, starting the age of re-ionization. Sarfati may have gotten the Jeans mass right, but his numbers for the Big Bang theory are totally off, making his statements nonsense as well.
--Awc 20:32, 10 October 2011 (UTC)
I find it ironic that there are no criteria for more or less meaningful information and the statement, "Ad hoc as in a different explanation is needed for every case." Because that is what creationists seem to do with information. And without criteria, necessarily they do. Sterile 16:54, 11 October 2011 (UTC)
Yep. I'm still trying to figure out enough of what creationists are claiming to write that section of the article coherently. At the moment I am leaning toward presenting the creationist claims for each observation, one at a time. Whether there is a common thread or chaos underlying it all should hopefully then become more apparent. --Awc 19:43, 11 October 2011 (UTC)
This is a great example of what happens when one even bothers talking to Philip. F*S guys. He has a high school science education. Who do you really think you're talking to here? I can't wait to see what Philip digs up on the CMI site or Sarfati coaches him to say. You could cut the tension with a knife! What wonderous quotmine will be next? More AiG/CMI twaddle that's been handily debunked elsewhere? Or will Philip think for himself and admit he has absolutely no idea what he's talking about? --Unsigned comment by Teh Terrible Asp (talk)
It would be refreshing if he would just admit that structures from stars to super-clusters of galaxies can be produced by undesigned gravitational collapse. The question of genetic information, in constrast, is less tractable and therefore of more interest. --Awc 14:04, 12 October 2011 (UTC)
WE also have no evidence that a gas giant formed in the present position. So are you trying to argue from ignorance?
There are som excellent models of the process of migration towards the star,... If they were so excellent, then you wouldn't have your sources admitting so much difficulty.
...and suggestions that the planet formed some distance from the star, which then expanded. "Suggestions"?? Yes, as I said, all ad hoc.
The refs I used were basically first grade sources for introduction to astronomy, not state of art science. So? They still reflect that the state of the art is that the models are all ad hoc because they can't come up with a good working model that actually fits all the evidence.
Oh Philip, why do you just quote these things without expending any effort to understand them more deeply? How do you know I don't spend the effort?
For one thing, the Jeans mass assumes a perfectly uniform region of gas (contrary to evidence) ... (and we know from the CMBR that it was not...) Actually, the main claim to fame that the CMBR has is that someone was finally able to show some non-uniformity. Extremely little, but just enough to cast some doubt on perfect uniformity. The real lesson of the CMBR is how amazingly uniform the background radiation is. True, not perfectly uniform, but extremely so. Your answer falls into the category of grasping at straws.
So even if the collapse needs 100K solar masses to initiate, the collapse leads to the formation of lots of smaller stars, not one ultramassive one. I never made any claim about an ultramassive one.
I might let you slide through without being able to reproduce the math—although it's really quite simple—if only you did understand the principle. I do understand the principle. It's common knowledge that—even in the gravitational field of Earth—gas expands.
Failing that, you should at least be able to properly quote your sources. Sarfati wrote... If you want to talk about properly quoting sources, Sarfati was describing Jeans' work; it wasn't Sarfati's own comments, although it was Sarfati's summary of Jeans' work.
You turn that into gas, by it's nature, doesn't have enough concentrated gravity to overcome the nature of a gas to move apart, which is not at all the same thing and is nonsense. It's nonsense because...? Yes, Jeans calculated that gas would collapse if it had a high enough density, but that doesn't explain how it came to have a high enough density. What could cause a gas to have such a high density?
Sarfati may have gotten the Jeans mass right, but his numbers for the Big Bang theory are totally off... I've written to Sarfati to get a response.
I find it ironic that there are no criteria for more or less meaningful information... Just because you claim to not understand it doesn't mean that it doesn't exist.
...that is what creationists seem to do with information. Evidence please?
And without criteria, necessarily they do. That does not follow.
This is a great example of what happens when one even bothers talking to Philip. F*S guys. He has a high school science education. Who do you really think you're talking to here? I can't wait to see what Philip digs up on the CMI site or Sarfati coaches him to say. You could cut the tension with a knife! What wonderous quotmine will be next? How about documenting a "quotemine" in the first place (and clearly defining what it is) before you start suggesting that I'll do more.
More AiG/CMI twaddle that's been handily debunked elsewhere? As opposed to this twaddle that accuses creationists of "twaddle" and of their arguments being "debunked" when in fact neither are true?
Or will Philip think for himself and admit he has absolutely no idea what he's talking about? Maybe you could go first instead of simply referring to unspecified others.
It would be refreshing if he would just admit that structures from stars to super-clusters of galaxies can be produced by undesigned gravitational collapse. More refreshing than evolutionists admitting that they have no idea how these things could form?
Philip J. Raymentdiscuss 03:29, 15 October 2011 (UTC)
It's common knowledge that—even in the gravitational field of Earth—gas expands. gas expands within earths gravity field depending on its make up and temperature. The entire earths atmosphere is held by gravity so it does not escape. (and yes I know there is minor loss to space) If earths gravity did not retain the atmosphere what does ? or are we breathing vacuum ? Hamster 04:07, 15 October 2011 (UTC)
it is common practice to model only what you are interested in. So a model of uranus and its close interactions would be of value. Older models were concerned with specific patterns of the debris disk around the sun so did not include all the gravity interactions such as torque, only the primary orbits were done. Now with better computers its possible to add other influences and get a better idea of system formation. We dont yet know exactly what extra solar bodies may have been around but its only been a short time of study. Hamster 04:07, 15 October 2011 (UTC)
WE also have no evidence that a gas giant formed in the present position. So are you trying to argue from ignorance? if you like , I am not bothered by saying there are things I dont know, or things that science doesnt know. If we knew everything then no one would need to do science and everyone could stay home and party. I do know that there are models that show that systems laking solid inner planets show migration 0of outer gas giants toward the sun. Its something about the lack of interactions that boost things to higher orbits. Hamster 04:14, 15 October 2011 (UTC)
What could cause a gas to have such a high density? how about the fact that the matter produced by the big bang has cooled to the point that its not a plasma any more and subatomic particles are now free to combine as atoms of hydrogen ? a gas cloud could also be on a path where it collides with another gas cloud , or a gas cloud might be truck by a pressure wave from something (like a supernova) and get compressed into itself. Hamster 04:21, 15 October 2011 (UTC)
The entire earths atmosphere is held by gravity so it does not escape. Yes. So? What if there was no Earth? Would the gas then spontaneously collapse/compress? That's what is being proposed for star formation.
it is common practice to model only what you are interested in. But if the model doesn't explain other cases, then the model is ad hoc.
We dont yet know exactly what extra solar bodies may have been around but its only been a short time of study. I'm not criticising anyone for not yet having a decent explanation. I'm pointing out that no-one yet has a decent explanation, contrary to the claims of some here that it has all been explained adequately. To put it another way, you can't simultaneously claim that (a) we know how it happened and (b) we don't yet know because its only been a short time of study.
if you like , I am not bothered by saying there are things I dont know, or things that science doesnt know. Yet if I claim that, you object and claim that we do know.
I do know that there are models that show that systems laking solid inner planets show migration 0of outer gas giants toward the sun. Its something about the lack of interactions that boost things to higher orbits. Yes, there are models, but how realistic are they? Models that show a planet migrating towards a star have to account for how the planet (in some cases) ended up with a nearly-circular orbit. A planet moving towards a star will do one of three things: (1) crash into it, (2) have too much momentum, and slingshot away from it, or (3) end up in an elliptical orbit. But the kinetic energy of the planet approaching the star that then goes into orbit around it means that it will normally end up in a highly elliptical orbit. To make that orbit less elliptical, it has to lose energy somehow. To make it almost circular it has to lose a lot of energy, and this has to be done in a very precise way. This is tantamount to invoking a miracle.
how about the fact that the matter produced by the big bang has cooled to the point that its not a plasma any more and subatomic particles are now free to combine as atoms of hydrogen ? That has nothing to do with the density of a cloud.
a gas cloud could also be on a path where it collides with another gas cloud... How do gas clouds "collide"? You just end up with a bigger gas cloud, where there is more expansion pressure.
...a gas cloud might be truck by a pressure wave from something (like a supernova) and get compressed into itself. This demonstrates the circular argument: your mechanism for getting stars need stars (going nova) to already exist!
Philip J. Raymentdiscuss 05:55, 15 October 2011 (UTC)
really phillip, one mechanism for a plasma condensing to a very hot set of atoms about a 100 million years after t=0, a couple mechanisms for new star creation much later when the original plasma is now cooled to a point where atoms can exist in solid/liquid or gas states with colder gas clouds and debris from supernovas. Why is that a problem ? Have you done the maths for two gravitationally bound clouds colliding ? hint the mass doubles at the impact boundary and continues to increase. Realize that a gas cloud has mass and therefore inertia. Hamster 08:04, 15 October 2011 (UTC)
so you accept that a planet has a gravitation binding of its atmosphere ? then whats your problem with massive gas clouds having sufficient gravity to bind them ? look at your own source of Jeans law. Hamster 08:11, 15 October 2011 (UTC)
But if the model doesn't explain other cases, then the model is ad hoc. ok, and thats how people solve problems, one step at a time and from specific solutions to more general cases leading to a general solution.
I'm not criticising anyone for not yet having a decent explanation. of course you are
To put it another way, you can't simultaneously claim that (a) we know how it happened and (b) we don't yet know because its only been a short time of study. yes we can , we can state in fairly detailed terms how it occured and still have some things that are not adequately explained. We can say with a reasonable degree of certainty that the earth was struck by a large object of a specified mass and that collision created the moon. We cant say where the mass came from or where it went at this time. As more probes are sent further out and more of the kuiper belt objects are located and orbits mapped there may be an answer. Hamster 08:26, 15 October 2011 (UTC)
Why is that a problem ? I don't understand the question.
...the mass doubles at the impact boundary and continues to increase. Why does it continue to increase, given that gas spreads out?
so you accept that a planet has a gravitation binding of its atmosphere ? then whats your problem with massive gas clouds having sufficient gravity to bind them ? The massive gas cloud has no concentrated centre of mass like a planet has.
ok, and thats how people solve problems, one step at a time and from specific solutions to more general cases leading to a general solution. It may lead to a solution, but it's not a solution.
of course you are No I'm not.
yes we can , we can state in fairly detailed terms how it occured and still have some things that are not adequately explained. I didn't suggest that you couldn't. But for an evolutionist, a major problem is simply a minor unsolved detail, whereas for a creationist, an unsolved detail is enough to jettison creationism as legitimate. My point wasn't that you can't claim to have solved something unless you have explained every last detail, but that you can't claim to have solved something and simultaneously claim that you don't yet know the cause because it's still early.
Philip J. Raymentdiscuss 11:55, 15 October 2011 (UTC)
Just because you claim to not understand it doesn't mean that it doesn't exist. For the eighty gazillionieth time, what are they? It really is a simple question. And the fact you can answer it is the evidence that it all is ad hoc. It's really that simple. Sterile 18:12, 15 October 2011 (UTC)
"massive gas cloud has no concentrated center of mass like a planet has" The gas cloud has a center of mass, toward which all the atoms are drawn by gravity. A center of mass is not a physical object. For masses of gas greater than the Jeans limit, the tendency of the gas at the center to rebound and expand is exceeded by the pressure of infalling gas from above. Why do you think Jupiter, Saturn, Uranus, and Neptune do not 'spread out'? And your bit earlier dismissing the nonuniformity of the CMBR left me surprised, since to keep the gas from collapsing you need it to be perfectly uniform forever and any divergence from perfect uniformity is sufficient to start the process of gravitational collapse.--Martin Arrowsmith 04:46, 16 October 2011 (UTC)
Philip is being unusually bone-headed on this topic. There's no profit in it. I withdraw from the discussion. --Awc 12:24, 16 October 2011 (UTC)
For the eighty gazillionieth time, what are they? It really is a simple question. For the umpteenth time, see information and genetic information.
And the fact you can answer it is the evidence that it all is ad hoc. Huh?
It's really that simple. Then why are you trying to complicate it?
"massive gas cloud has no concentrated center of mass like a planet has" The gas cloud has a center of mass, toward which all the atoms are drawn by gravity. Only if the gravity is strong enough to overcome the expansive pressure.
A center of mass is not a physical object. It may not be a single physical object, but you won't have one without one or more physical objects.
Why do you think Jupiter, Saturn, Uranus, and Neptune do not 'spread out'? Because there is a concentrated centre of mass, which a cloud does not have. They also have solid/liquid cores. Your argument seems to assume what it sets out to prove: that gas giants can come about only from the collapse of gas clouds, so because these gas giants exist, this shows that the collapse of gas clouds can cause them.
And your bit earlier dismissing the nonuniformity of the CMBR left me surprised, since to keep the gas from collapsing you need it to be perfectly uniform forever and any divergence from perfect uniformity is sufficient to start the process of gravitational collapse. Why? If you inject a gas into a vacuum flask the gas expands to fill the flask; it does not collapse, despite there being a greater concentration in some places (such as around the injecting nozzle) than others. You need more than simply non-uniformity to start a process of gravitational collapse.
Philip J. Raymentdiscuss 11:36, 17 October 2011 (UTC)
you need a really big flask.
center of mass is a mathematical construct, take the mass of small parts, like each gas molocule and map its position. Calculate a bounding box for an approximation and then do a whole lot of calculations to find the point where the mass is equally distributed in any direction, no physical object is required. If the mass is large enough you will get gravity acting toward the center of mass and if its strong enough to overcome the gas pressure you will get a collapse (Jeans mass from your source) During the collapse you might get a gas compressed to a liquid or even a solid Hamster 17:13, 17 October 2011 (UTC)
Like Hamster said, if your flask holds a Jeans mass of gas, it will collapse. Gas on the outer edge of a cloud doesn't need a 'concentrated centre of mass' to fall towards - it will fall toward the center of mass, no matter how diffuse things are at that point. The only way that I know of to keep a universe full of gas from collapsing into stars is to have the gas be perfectly uniform in all directions at all scales, such that there is no net gravitational field in any direction; each gas molecule is pulled equally in all directions forever and ever, amen. But this equilibrium is unstable; if it is disturbed by even the slightest degree (and the CMBR shows that it was) then some volumes will contain a Jeans mass of gas and other overlapping equal volumes will not. Now some of the universe's gas atoms will feel a net gravitational pull in a particular direction, and the process of collapse begins. --Martin Arrowsmith 03:55, 18 October 2011 (UTC)
...if its strong enough to overcome the gas pressure you will get a collapse... The crucial word there being "if".
Gas on the outer edge of a cloud doesn't need a 'concentrated centre of mass' to fall towards - it will fall toward the center of mass, no matter how diffuse things are at that point. On the contrary, on the outer edge, the expansive pressure will be greater than the gravity at that point, so it won't fall towards the centre of mass.
The only way that I know of to keep a universe full of gas from collapsing into stars is to have the gas be perfectly uniform in all directions at all scales... The other way is to have the expansive pressure greater than the gravitational pull.
Now some of the universe's gas atoms will feel a net gravitational pull in a particular direction, and the process of collapse begins. Only if—and that's a big IF—the gravitational pull overcomes the expansive pressure.
Philip J. Raymentdiscuss 13:40, 22 October 2011 (UTC)
you did not read the whole thing about the jeans mass did you ?
jeans mass shows the maths of a large gas volume and the effects of gravity vs pressure
if you have a jeans mass then collapse is certain, lower masses may collapse depending on localised densities or the addition of an external force.
you also seem to be unaware of or ignoring the effects of external forces on gas clouds such as radiation, solar winds or collision of two masses
the sun doesnt exist because it dissipated rather than collapsed  ?
3NkT = 3/5 * GM2/R where if the left side of the equation is larger you get expansion and if the left side is lower you get collapse. read it Here also look up virial theorum.
Hamster 15:23, 22 October 2011 (UTC)
you did not read the whole thing about the jeans mass did you ? I've read quite a bit on it. Which bits are you referring to?
jeans mass shows the maths of a large gas volume and the effects of gravity vs pressure Yes.
if you have a jeans mass then collapse is certain, lower masses may collapse depending on localised densities or the addition of an external force. A bit lower mass.
you also seem to be unaware of or ignoring the effects of external forces on gas clouds such as radiation, solar winds or collision of two masses Where do solar winds come from before the first stars? What radiation are you talking about before the first stars? I've already responded regarding "collision" of two masses, but haven't asked what caused them to collide. Perhaps you could explain that?
the sun doesnt exist because it dissipated rather than collapsed  ? Circular (evolutionary) thinking. (1) The sun could only form from collapse of a gas cloud. (2) The sun exists. (3) Therefore, this shows that the sun was formed from the collapse of a gas cloud. The premise (1) ignores the alternative explanation that the sun was created.
3NkT = 3/5 * GM2/R where if the left side of the equation is larger you get expansion and if the left side is lower you get collapse. So how much mass does that equate to before the existence of heavier elements produced in stars?
Philip J. Raymentdiscuss 05:39, 23 October 2011 (UTC)
Which bits are you referring to? all about jeans mass. Thats what I and martin have been referring to. If you have a jeans mass of gas , it does have the gravity to collapse and it will collapse. All your points around The other way is to have the expansive pressure greater than the gravitational pull. does not apply to a jeans mass. Are you saying that the jeans mass is incorrect ?
are you suggesting that God created the Sun to defy physics by continuing to exist ? does the sun contain the correct masses that would have resulted from the gravitational collapse of a body of gas ?
a Mass of 1/2 a jeans mass may be unstable and collapse. Even smaller masses depending on other conditions may collapse.
there are of course two cases, that of the initial star formation, and then the formation later of further stars. solar winds and radiation obviously come in the second case which is also likely to involve lower mass gas clouds than the initial collapse after the big bang.
of course we ignore creation, because it doesnt work with what is observed. There is a star forming planets being watched now. Unless you poit continuous creation ?
gravity may cause two gas bodies to collide. During a collision inertia will play a part with gravity to result in an increase in density, therefore greater gravity, and so forth.
I gave a link to the website that shows how that formula is derived and how to use it. Its not a complex formula , just needs a few substitution which I leave you to work out.
Hamster 06:05, 23 October 2011 (UTC)
all about jeans mass. Too vague.
All your points around "The other way is to have the expansive pressure greater than the gravitational pull." does not apply to a jeans mass. No, but that comment didn't referring to a Jeans Mass. It said that The only way that I know of to keep a universe full of gas from collapsing into stars... The other way is to have less than a Jeans Mass of gas filling the universe, to put it in those terms.
are you suggesting that God created the Sun to defy physics by continuing to exist ? Of course not. We are talking about what is required for a star to form from a gas cloud, not to exist once formed.
does the sun contain the correct masses that would have resulted from the gravitational collapse of a body of gas ? No.
a Mass of 1/2 a jeans mass may be unstable and collapse. Even smaller masses depending on other conditions may collapse. What conditions? Typical ones, or extremely unlikely ones?
there are of course two cases, that of the initial star formation, and then the formation later of further stars. Yes, and the explanations offered (including the ones you have offered) usually include factors that did not exist for the initial stars.
of course we ignore creation, because it doesnt work with what is observed. Pardon? How do you know it doesn't work? Have you tested it?
There is a star forming planets being watched now. Correction: There is a star which is believed to be forming planets being watched now. How long is planet formation supposed to take? For how much of that time have we been watching? How big is the resulting extrapolation?
gravity may cause two gas bodies to collide. The gravity of the respective clouds? Surely there would not be enough gravitational pull between the two clouds to overcome the expansive pressure, unless the clouds were already so massive that they could collapse on their own.
Its not a complex formula , just needs a few substitution which I leave you to work out. Not prepared to do it yourself? In any case, I'm having difficulty finding the temperature when stars were supposed to have first formed.
Philip J. Raymentdiscuss 13:01, 23 October 2011 (UTC)
if we look into space and see a gas cloud then we know it hasnt dissipated and if we look 100 years later and its still there then it may be gravitationally bound. two objects with mass will have a gravitational attraction, distance time and momentum will determine what happens. If the two clouds are below jeans mass then the are not certain to collapse, colliding may put them over the limit, or it may not , you need to know the masses involved.
http://news.yahoo.com/hawaii-astronomer-captures-image-forming-planet-230958310.html
try 3000 K Awc quoted it somewhere , that may be too hot though Hamster 16:11, 23 October 2011 (UTC)
If a cloud is still there 100 years later, then perhaps all it means is that it hasn't fully dissipated yet.
two objects with mass will have a gravitational attraction, distance time and momentum will determine what happens. And if they are gas, they will also have a repulsive force, which will also help determine what will happen. Why do you so often ignore that factor?
http://news.yahoo.com/hawaii-astronomer-captures-image-forming-planet-230958310.html It's a pity they didn't show the image. Perhaps because it's not obvious from the image what is supposed to be happening. If you see a still image of train on a railway line, how do you tell what it's doing? You might caption the picture "train travelling from A to B", but you can't tell that from the image; you tell that from knowing what trains there are normally doing. That is, your interpretation of what you see is dependent on what else you know or believe. Scientists believe that planets form in a particular way, so when they capture a still image of something, they interpret that within that belief. (And on the timescales that would be involved in naturalistic planet formation, then even images taken over a period of 100 years essentially amount to a "still image".)
try 3000 K Awc quoted it somewhere , that may be too hot though 3000K is not the correct value; I've seen that value in several places, but not for the time concerned. So if that's your best answer, then your implication that it was easy to work out was not correct.
Philip J. Raymentdiscuss 01:01, 1 November 2011 (UTC)
if you use 3000 you get an answer that would show the mass needed for gravitational collapse at that temperature. Look at where temperature is in the equation nd work out for yourself is a lower temperature increases the mass or lowers it. The only question for gravitational collapse is what temperature and mass is required for it to happen.
that equation is the same no matter what values you put into it, using 3000 , 10000, or 212 wont affect how hard the calculation is.
I do not ignore the law controlling the expansion of gases. Its a mathematical law of physics. Why do you insist tat gravity does not exist ?
photos of a planet forming , you are wrong on speeds of gravitational collapse. Perhps study Jeans mass and the equations a bit more.
a gas mass will not disipate to fill a large volume, the "internal pressure" as you call it will become so low that what is left is the brownian motion of the molocules. Any other gas in the same location , such as air, will act to restrict the gases movement.
all of this discussion on gases, expansion and gravity is high school physics Hamster 03:27, 1 November 2011 (UTC)
if you use 3000 you get an answer that would show the mass needed for gravitational collapse at that temperature. But if it's not the right temperature, then it's not much use.
Look at where temperature is in the equation nd work out for yourself is a lower temperature increases the mass or lowers it I already know that a lower temperature decreases the required mass.
that equation is the same no matter what values you put into it, using 3000 , 10000, or 212 wont affect how hard the calculation is. So accuracy doesn't matter to you?
I do not ignore the law controlling the expansion of gases. Yet in "two objects with mass will have a gravitational attraction, distance time and momentum will determine what happens." and various other comments, you've not mentioned it, giving the impression that it's not relevant.
Why do you insist tat gravity does not exist ? Huh? I've never said that it doesn't.
photos of a planet forming , you are wrong on speeds of gravitational collapse. Perhps study Jeans mass and the equations a bit more. Perhaps justify your claim instead of making an assertion then telling me to justify it.
a gas mass will not disipate to fill a large volume, the "internal pressure" as you call it will become so low that what is left is the brownian motion of the molocules. Assuming that the "large volume" is large enough, then that's a fair comment, and would be another reason why the cloud you mention hasn't dissipated after 100 years. But my point is if it's that diffuse that there is virtually no internal pressure left, then there is also very little gravitational attraction.
all of this discussion on gases, expansion and gravity is high school physics I don't recall this sort of discussion when I was in high school. But perhaps that was just my circumstances.
Philip J. Raymentdiscuss 04:56, 1 November 2011 (UTC)

nylon

can any comparisions be drawn between the ability to digest nylon and the ability to use citrate ? The citrate experiment was well documented and the situation seem comperable. Hamster 19:27, 14 October 2011 (UTC)

It's a bit premature to say, since the mechanism behind the cit+ trait has not yet been elucidated. It's possible that a new citrate transport protein was produced de novo (like the nylonase case), but it's more likely that an existing transport protein or metabolic pathway was tweaked in some way.
In regard to Awc's confusion about Batten's position: [disparagement trolling removed] He feigns no hypothesis as to the nature of the designed mechanism - pre-encoded sequences, specific hypermutable regions, supernatural intervention, or whatnot.--Martin Arrowsmith 22:28, 14 October 2011 (UTC)
yes , I got that :) I was trying to work in from the conclusion and show it doesnt work well. That is a bacteria with access to a food source took a long number of generations to develop the trait. If adaption was 'built into' the bacteria it should surely have adapted faster. Hamster 22:53, 14 October 2011 (UTC)
If adaption was 'built into' the bacteria it should surely have adapted faster. That depends on the adaptation mechanism. Philip J. Raymentdiscuss 05:38, 15 October 2011 (UTC)
yes if you want lots of dead bacteria before an adaption occurs Hamster 07:50, 15 October 2011 (UTC)
Your comment doesn't seem to make sense (typical of many of your comments, it is so brief as to be unclear just what it is getting at), but in case it's relevant, I'll point out that not every adaptation is a survival necessity. That is, an adaptation may be an advantage, but the creature may still survive without it. Philip J. Raymentdiscuss 11:58, 15 October 2011 (UTC)
you seemed to offer a hypothesis that adaptive features were built into an organism. I suggested that experimentaly this adaptive feature does not seem to happen in a timely fashion. Would you care to state under what conditions this adaptation would become active ? In the citrate experiment large numbers of bacteria starved to death without the citrate eating ability becoming active. Hamster 16:19, 15 October 2011 (UTC)
I suggested that experimentaly this adaptive feature does not seem to happen in a timely fashion. Perhaps so (according to who's opinion of "timely"?), but that doesn't mean that it's not there. That would be like suggesting that because a stock broker doesn't not pick the best time to buy and sell shares, he's not a stock broker.
Would you care to state under what conditions this adaptation would become active ? The question is vague (and assumes too much). If a bacteria developed an ability to digest nylon, it would be active immediately that it encountered nylon, I would presume. Is that what you meant?
In the citrate experiment large numbers of bacteria starved to death without the citrate eating ability becoming active. Are you sure? That assumes that they had no other source of nourishment. If so, how did the remaining ones survive before they developed the ability?
Philip J. Raymentdiscuss 11:42, 17 October 2011 (UTC)
since Lenskis experiment has been discussed before I will simply remind you that the normal food source was limited to a measured amount as each flask was prepared. This limited the growth of the bacteria and set up a situation where finding another food source was a selective pressure.
if a population all dies because of a lack of food then it doesnt matter if they could have adapted in time. So what criteria would you set for a predefined adaption to be triggered ? (this is a very precise question ) remembering that the adaptation would not appear in the living bacteria but only in a subsequent generation.
according to who's opinion of "timely"? before the death of the entire population would work for me. This presumes you are arguing a preset adaptation and not an ad hoc act of god. Hamster 16:09, 17 October 2011 (UTC)
So what criteria would you set for a predefined adaption to be triggered ? I suspect—and this question tends to confirm it—that you are assuming that the non-random adaptation was programmed to do precisely what happened. I'm not suggesting that. Rather, I believe that the argument is that there is a programmed mechanism to try different things. So the program does not say "Where the normal food source is limited but nylon is available, switch to digesting nylon". Rather, it's saying something like "Where the normal food source is limited, try various other digestive mechanisms until you find one that gets you by". That may work quickly or slowly; it may work in time or it may not. Philip J. Raymentdiscuss 13:48, 22 October 2011 (UTC)
That does seem to be the way it works. (It is amazing, isn't it, how the mechanisms of evolution themselves evolve?) At the end of the process, the species has something it didn't have before, namely the information needed to digest a new type of food. --Awc 14:34, 22 October 2011 (UTC)
Yes, it's amazing. One might even say magical, or (alternatively) miraculous, that the mutation occurred in the specific spot where it could help. But doesn't either mean that it's not science, according to mainstream scientists? Philip J. Raymentdiscuss 05:42, 23 October 2011 (UTC)
so you are saying, I think, that God put in place an adaptive mechanism , that works by a trial and error process to enable a new food source. God doesnt really care if the organism dies before finding the new source. This process seems hardly distinguishable from evolution and would fail any human design review. Hamster 06:12, 23 October 2011 (UTC)
so you are saying, I think, that God put in place an adaptive mechanism I'm not saying that He did; I'm saying that He might have, and that would explain the observations.
God doesnt really care if the organism dies before finding the new source. If He didn't care, why did He provide the mechanism? In any case, you are now invoking theology (what God cares about), but ignoring that, biblically, bacteria are not alive.
This process seems hardly distinguishable from evolution ... On the contrary, how and why would evolution provide such a mechanism?
...and would fail any human design review. That really depends on the goals.
Philip J. Raymentdiscuss 13:05, 23 October 2011 (UTC)
this point is on the change of food source in bacteria. You seem to reject an evolutionery cause in favor of a design feature. Yet your design feature seems to work in a way indistinguishable from random mutations. You dont seem to be suggesting a direct link to whats available in the environment, or a list of food sources being tested in sequence or even randomly. A design feature would be to promote the survival of the population. In a population of say 10,000 bacteria a random choice from a list of say 200 alternatives would by random choice test every alternative in 1 generation this ensuring the populations survival. You state thats not neccessarily going to happen. If a designed feature does not solve the problem for which it was designed then its really a failure. I mentioned God because he is your designer of choice, or do you concede other secular or supernatural designers ?
are you saying God cares nothing for his creations , or only the living by biblical definitions ? Hamster 18:39, 23 October 2011 (UTC)
Yet your design feature seems to work in a way indistinguishable from random mutations. No, not indistinguishable, which is the point. See here.
In a population of say 10,000 bacteria a random choice from a list of say 200 alternatives would by random choice test every alternative in 1 generation this ensuring the populations survival. No, you are still thinking as though failure to find an alternative means that the population is wiped out, which is not the case.
I mentioned God because he is your designer of choice, or do you concede other secular or supernatural designers ? I'm not sure which mention of God you are referring to. No, I'm not conceding other designers (in this case). My point was that you were talking about what you believe would have been God's intentions, whilst ignoring what the Bible says. I didn't suggest that you'd identified the wrong designer.
are you saying God cares nothing for his creations , or only the living by biblical definitions ? I'm saying that you seem to be assuming that He does care about non-living things. I'm not going to say dogmatically that he doesn't, but the Bible does teach that His creation was for man's benefit, and therefore that the rest of creation (other than man) is not as important, and it also doesn't treat bacteria as having the importance of living things. To give an example, God had Noah take representatives of living things on the Ark to survive the flood, but there were quite a few things that weren't taken on board. One, of course, was marine creatures, because (in principle) they can survive a flood. Another was plants. Another was rocks. In some cases (such as the fish), they didn't need to be taken on board because they could survive outside. In other cases, it was because they weren't important enough. Even with the animals, it wasn't important enough that every single one survived, only that representatives survived. The same applies to marine creatures—even though they could survive outside the ark in principle, in practice many would have been (and were) killed. I guess my point regarding bacteria is that there is no reason to believe that God is sufficiently concerned about bacteria to ensure that every species of it survives.
Philip J. Raymentdiscuss 01:19, 1 November 2011 (UTC)

removal of "Effect of selection" section

I removed the entire "Effect of selection" section, as it was built on a faulty argument.

  • "Darwinian evolution works through random mutations alternating with natural selection."
I could have saved that bit, but it would have been almost the only bit left in the section, so out it came. If it had been kept, it would be more accurate to say
"Darwinian evolution is said to work through random mutations being discarded or retained by natural selection."
I considered writing "is said to" or "if it works at all". I didn't because I thought the reader would be smart enough to realize that condition, and the excess verbiage makes it sound clunky. --Awc 16:28, 17 October 2011 (UTC)
  • ...the removal of genes can also be considered a source of information in some cases. A recipe book becomes more useful if the bad recipes are thrown out,...
Removal of bad recipes might make the book easier to use (and, therefore, arguably "more useful"), but that doesn't mean that throwing out those recipes is synonymous with increasing information. You could say that the ratio of information to junk has increased, but the amount of information has not.
They're not synonymous because there are other ways to change the information content than removing recipes. It's pretty unambiguous that a recipe book containing fewer junk recipes is not just arguably easier to use, it is easier to use. It arguably has more information, and, by my intuitive understanding of information (since we do not yet have a way to quantify "recipe information"), information correlates with usefulness. I only want to mention that to stimulate the reader to consider the problem from different angles. --Awc 16:28, 17 October 2011 (UTC)
  • "... and Michelangelo's David contains more information than the block of marble it was carved from."
Yes, but because information (from an intelligent mind) has been added, not because it has been removed. Marble has been removed; information has not.
Information has been added by means of removing extraneous marble. In the same way, information can be added to a gene pool by removing extraneous alleles. Says me. Creationists can use any definition they want to make their case. It doesn't matter whether we agree on what information really is. My point in all this is simply that intuitive notions of information are insufficient to make a scientific argument because they are ambiguous. --Awc 16:28, 17 October 2011 (UTC)
  • "In the case of a gene pool, the elimination of genes that are less fit for the current environment transfers information about that environment into the gene pool."
I think this argument is unsound, but at best it seems to be a transfer of existing information.
It's an argument made in some of the references, and therefore it deserves a place in the article, whether or not you agree with it. It's pretty bold to say a shift to long-fur genes is no increase in information because the information existed previously in the environment. At what point did it stop being just plain cold outside, and the coldness started to be information in and of itself? --Awc 16:28, 17 October 2011 (UTC)
  • "In a similar way, at first thought in the example above, the elimination of the genes for short-hair from the gene pool of the dogs appears to be an unambiguous loss of information."
It is an unambiguous loss of information, if for no other reason than that is the scenario being illustrated.
Some of the references disagree, so it is not unambiguous. --Awc 16:28, 17 October 2011 (UTC)
  • "If, however, the hair length is coded by minor variations in a hair-growing gene, or perhaps even simply by the number of copies of a single hair gene, then the shift to long-haired dogs might be considered neutral in terms of the change in genetic information."
This is fair enough, except that it is dependent on all the previous incorrect claims, so it's out too.
Philip J. Raymentdiscuss 12:54, 15 October 2011 (UTC)
"Darwinian evolution is said to work through random mutations being discarded or retained by natural selection." Natural selection works at the level of the organism, not genes. If the organism is more fit because of a genetic change then it will reproduce more and so those genes may be distributed in the population. I believe the original statement is clearer in terms of whats actually happening.
on the long hair /short hair thing its really moot unless omeone knows the actual mechanism that controls hair length. In humans the hair growth reaches a limit and that hair is shed. That implies a mechanism that is saying "add to this hair 50,000 times and then stop and discard that hair, start again" which would make hair length neutral in terms of information content. (depending on how information is defined)
since some ID proponents are pushing dna as information, a language in fact, one tends to wonder why they have not published the dictionary and grammer rules. it might exhibit some characteristics of a language but without the rules of grammer you cant really tell for sure.
"In the case of a gene pool, the elimination of genes that are less fit for the current environment transfers information about that environment into the gene pool." I am unclear on this one, if a gene is present but inactive it shows a history of the organism. One might find the same gene in another organism that for example allows the synthesis of vitamin D. Since our subject organism had it and it became inactive then it tells us something about the need for Vit D. Hamster 16:40, 15 October 2011 (UTC) Hamster 16:32, 15 October 2011 (UTC)
I have to agree with the removal of these examples, because without a working definition of information it is impossible to demonstrate that any of them represent a loss or gain of information; both cases can be argued. Example: Michelangelo's David -- if the statue's information is the position and identity of all of the atoms that make it up, then the statue has less information than the block because it has fewer atoms. If the information is the string needed to encode the 3-d surface of the block, then the statue may have less or more information than the block, depending on which has more surface area to a certain degree of resolution. If the information of the statue is the physical processes that have occurred since the beginning of the universe to result in the block at any given time, then the statue has more information since more processes have occurred to it than to the block from which it came. Example: recipe book with flawed recipes -- if the information in the book is the number of characters in the book, then the edited book has less information. If it is the odds of a randomly-chosen recipe being 'good', then the edited book has more information. If the broken recipes demonstrate in some way the mechanism by which the book was assembled, they include 'meta-information' so the unedited book has more information. Etc., etc. When all the short-haired dogs are lost from a population, is that a loss of information? Damned if I know - all the dogs may have a new gene coding for a new protein that inhibits the effects of the older genes/proteins which are still present: the longhaired dogs, with more information, are the survivors. The point is that until you can define/measure/quantify information, it's like asking whether chocolate or vanilla is angrier, or whether going from Dallas to Fort Worth represents a loss of purple. --Martin Arrowsmith 04:15, 16 October 2011 (UTC)
I believe the original statement is clearer in terms of whats actually happening. The original statement said that evolution does happen, rather than it being a claim (so that's not accurate), and that it works through "random mutations alternating with natural selection". Rather, it supposedly works with natural selection following mutations (without disagreeing that this cycle is repeated).
on the long hair /short hair thing its really moot unless someone knows the actual mechanism that controls hair length. It's an illustration; it doesn't even need to be true (in this particular case) for it to be a useful illustration. As long as the principle is true in some cases, that is sufficient. So no, the actual mechanism does not need to be known.
since some ID proponents are pushing dna as information, a language in fact, one tends to wonder why they have not published the dictionary and grammer rules. Perhaps they are still working on it? After all, the human genome has only been transcribed into written form for a few years. But what is a list of what DNA letters represent what amino acids, and what sequence of amino acids form what proteins, if not a dictionary, or at least the start of one?
it might exhibit some characteristics of a language but without the rules of grammer you cant really tell for sure. I believe that you can actually, just as you can determine the existence of a cipher without deciphering it.
I am unclear on this one, if a gene is present but inactive it shows a history of the organism. According to evolution, at least.
Since our subject organism had it and it became inactive then it tells us something about the need for Vit D. Again, according to evolution. That it had it and it became inactive is an interpretation, not a fact. The fact is that it has some genetic code that is (a) similar to genetic code in another creature, and (b) apparently inactive. From this an evolutionist interprets the evidence to claim that it was once active and became inactive. That's plausible, but not a known fact. Many claims of inactive genes have turned out to be wrong, for example.
...without a working definition of information it is impossible to demonstrate that any of them represent a loss or gain of information... Yet we have a good idea of what constitutes information. Dictionaries are able to define it, for example.
I think you forgot a winking smiley at the end of that last sentence. Dictionaries define "Christian" too. Does the dictionary get the final say on the matter? They define "beauty" too. Can you tell me whether a Vermeer painting or a Bach contata is more beautiful? We have a good idea of what constitutes beauty, don't we? --Martin Arrowsmith 03:32, 18 October 2011 (UTC)
if the statue's information is the position and identity of all of the atoms that make it up, then the statue has less information than the block because it has fewer atoms. The problem with this is that there is nothing significant about the position and identity of all the atoms. Whereas there is something significant about the 3-D surface of the statue. Think of the 100,000 letters that make up a 20,000-word recipe book; if they are arranged randomly, the recipe book contains no recipes (information), despite it requiring a lot of data to document the position and identity of every letter.
You've lost me, because it seems that you are claiming that a perfect description of a statue to atomic scales contains no information; the information lies where, then? In the impression made on a human mind? Similarly, a string of data contains no information unless is has 'meaning' for a particular reader? I don't follow. But perhaps if you can tell me where the information content of a statue lies, or how to transmit it, or how to increase or decrease it, we can work from there.--Martin Arrowsmith 03:32, 18 October 2011 (UTC)
When all the short-haired dogs are lost from a population, is that a loss of information? Assuming the process in the illustration, yes, as the illustration illustrates.
You have repeatedly said that information was lost in the dog example. FSM help me, I just reviewed those archived discussions. But I still can't tell from that discussion what you think you need to know to measure information. You gave examples that seem to refer to the number of different alleles at a locus, or the number of phenotypes, or the number of 'structures' or 'instructions'. There may be some other examples you used as well. When pressed, you fell back on recipe and linguistic analogies and such. When I tried to restrict things to actual biological mechanisms, you never could say which of two examples (color changing vs. noncolorchanging foxes, remember?) represented more information, even though I made them different at every level - DNA, proteome, phenotype, and fitness. Then we got off on all number of tangents that trailed off. But I digress. --Martin Arrowsmith 03:32, 18 October 2011 (UTC)
all the dogs may have a new gene coding for a new protein that inhibits the effects of the older genes/proteins which are still present: Now you are proposing a different process.
OK, so address it. Can you say whether that's a loss of information? Whatever questions you need to ask to make the determination, I can provide answers for.--Martin Arrowsmith 03:32, 18 October 2011 (UTC)
The point is that until you can define/measure/quantify information, it's like asking whether chocolate or vanilla is angrier, or whether going from Dallas to Fort Worth represents a loss of purple. And yet, despite your claims, I have been able to show which have more and which have less information. So your claims are wrong.
Philip J. Raymentdiscuss 12:06, 17 October 2011 (UTC)
I think you mean that you have 'declared' which have more or less information, and you keep using undefined but evocative terms like 'more or less' and 'instructions' and 'meaning' to back up your declarations. I think in part that this is the effect of a fundamental ignorance of actual biological processes. I don't mean that as an insult - I am fundamentally ignorant of many aspects of Christian theology, just to name one subsection of my large areas of ignorance. If this was a discussion about aspects of the Trinity, and it appeared to you that further discussion was pointless because I lacked the theological underpinnings necessary for my claims to make sense, what would you do? You make statements that clearly imply to me that you are making unwarranted extrapolations from your understanding of metaphors for biological processes back to the processes themselves. I will admit that I don't have the patience to provide you with a full undergraduate level biochemistry education so that you can understand the process rather than the facile analogy. So what would you have me do? I tried to lead you by the hand through the fox example, and I couldn't make any sense of your answers, and at times they weren't even internally consistent. I guess that I'm at a loss as to how to proceed.--Martin Arrowsmith 03:32, 18 October 2011 (UTC)
you havent shown any meaningful gain or loss of "information" except in analogy. You claimed the real mechanism isnt needed because you are arguing an illustration. So you win in a non-real world of your own invention. sorry thats just garbage in garbage out.
it might exhibit some characteristics of a language but without the rules of grammer you cant really tell for sure. I believe that you can actually, just as you can determine the existence of a cipher without deciphering it}} * Xpqtqx zigumvb vmmla uwzm uibpa * let me know if this is a real cipher or garbage.
dna has been known for 50 years. The first complete genome map of a bacteria was 1995. Thats 15 years and there were segments before that. If dna is a language as fact rather than hypothesis then the nouns , verbs, qualifiers etc should be known and a primer on the language available for testing. Where are these creation science documents ?
perhaps you can explain why if dna is a language that the codes produce different results depending on what organism its in ?
an animal is born (thats the mutation part) then it lives and selection processes can operate, then it breeds and a child animal is born (mutation again) Thats clearly mutation alternating with selection in any bloodline You do know that mutations dont happen to living animals ? Hamster 15:07, 17 October 2011 (UTC)
I have to agree with the removal of these examples, because without a working definition of information it is impossible to demonstrate that any of them represent a loss or gain of information; both cases can be argued. I think Martin and I agree on this. The very point I was trying to make with these examples is that gain or loss of information, even in simple cases, is not unambiguous. Apparently my text did not make that entirely clear. I will work on a better formulation and then put it back in, taking as many comments as possible into account. --Awc 16:28, 17 October 2011 (UTC)
Actually I'm brooding over a different organization for this part of the article. That may make this particular question moot. The new organization would probably align more with the creationist way of thinking about the problem, so it might actually make everyone happier. --Awc 16:41, 17 October 2011 (UTC)
I considered writing "is said to" or "if it works at all". I didn't because I thought the reader would be smart enough to realize that condition, and the excess verbiage makes it sound clunky. There is a place for that, but only where it is clear from the context that the evolutionary view is being discussed. I don't believe that applied in this case.
It's pretty unambiguous that a recipe book containing fewer junk recipes is not just arguably easier to use, it is easier to use. Yes, it's easier to use. But that's not the same as saying that it's "more useful", which was what I used "arguably" with.
It arguably has more information... Not if all you've done is discard poor information.
...information correlates with usefulness. They are related, but not synonymous. But the main point is that "usefulness" is not the same as ease of use. If we define "usefulness" as the number of uses that can be made of something (e.g. the number of useful recipes), then discarding useless recipes might make it easier to locate the useful recipes, but the number of useful recipes—and therefore the usefulness—hasn't changed.
Who said they were "synonymous? I said they are "correlated". You said they are "related". We agree. Why do you say "but"?
If we define "usefulness" as ... Sure. That's a possible definition, and it would have the consequence you say. Another possible definition, which is more in line with the "common sense" definiton most people have, is "useful" is what I want to have on my kitchen shelf to get the job done. If we apply your definition to evolution, then we could leave out the natural selection step. A cell containing all the mutations that ever occurred would have the same information as a cell that only retained the ones that work together to sustain life. In my book, that's a problematical definition of information.
--Awc 10:56, 23 October 2011 (UTC)
Information has been added by means of removing extraneous marble. In the same way, information can be added to a gene pool by removing extraneous alleles. "Extraneous" implies that the marble/alleles concerned are somehow distinguishable from the non-extraneous marble/alleles. But this is not the case until it is removed. That is, prior to removal, there is no way of distinguishing the marble to be removed from the rest of the marble, other than by making use of the information. This is not analogous to the removal of genes, which, by being genes, already have information.
My point in all this is simply that intuitive notions of information are insufficient to make a scientific argument because they are ambiguous. Like the definition of "species" is ambiguous (more on this in a subsequent reply)?
It's pretty bold to say a shift to long-fur genes is no increase in information because the information existed previously in the environment. It is you (apparently citing others), not me, who is saying that the information previously existed in the environment.
Some of the references disagree, so it is not unambiguous. What references (to that illustration)?
Dictionaries define "Christian" too. Does the dictionary get the final say on the matter? I never indicated that dictionaries always get the final say. My point was that if dictionaries can define it, you can't argue that it's not defined.
To satisfy your objection, I will no longer refer to any word as 'undefined'. I will instead use the term Not Defined With Sufficient Rigor For Our Purposes, or NDWSRFOP, or NDSR for short. You can suggest a different formation if you like.--Martin Arrowsmith 18:34, 22 October 2011 (UTC)
They define "beauty" too. Can you tell me whether a Vermeer painting or a Bach contata is more beautiful? We have a good idea of what constitutes beauty, don't we? Science also defines species. So can you tell me if two similar fossils are interfertile?
Certainly. Being dead, no two fossils are interfertile. So, which is more beautiful, Bach or Vermeer? 'Beauty' is defined. If you can compare 'information' without being able to measure it, surely you can compare 'beauty' in those cases.--Martin Arrowsmith 18:34, 22 October 2011 (UTC)
...it seems that you are claiming that a perfect description of a statue to atomic scales contains no information; the information lies where, then? I'm not claiming that. I'm claiming that the real information is in the shape; the design; not the precise positions of specific atoms.
Perhaps you are misunderstanding me. A table is made that shows the identity and position of every atom in the statue. From that large amount of data can be extracted the position and identity of all of the atoms that lie on the outer surface of the statue (or, if you prefer, within approx. one optical depth of the surface, or some such other set). Those points, in the aggregate, give you all you would need to know to recreate the shape of the statue. Is there no information in that set of points?--Martin Arrowsmith 18:34, 22 October 2011 (UTC)
Similarly, a string of data contains no information unless is has 'meaning' for a particular reader? No, a string of data has no information unless it has been arranged to carry meaning according to some (language) convention by its author. That's assuming you were asking about whether or not something has meaning, as opposed to how we can determine whether it has meaning.
That is a bombshell claim, which contradicts all of mathematical information theory. Are you making a distinction between data (no author) and information (has an author)? --Martin Arrowsmith 18:34, 22 October 2011 (UTC)
But perhaps if you can tell me where the information content of a statue lies... In its design.
I find that an evasive answer. 'Design'- does that mean the shape, the shape plus the materials, the shape and the materials and the process, the cognitive/emotional state that the designer intended to induce in the viewer, or all of these, or some of them, or none of them? Can the 'design' be conveyed to a person who is not in the presence of the original statue? How?--Martin Arrowsmith 18:34, 22 October 2011 (UTC)
But I still can't tell from that discussion what you think you need to know to measure information. I have said repeatedly that I believe that we have no way of measuring it (which is not the same as not being able to compare it).
How do you compare it without being able to measure it? Can you give me an example of some other quality that you can compare without being able to measure?--Martin Arrowsmith 18:34, 22 October 2011 (UTC)
...you never could say which of two examples (color changing vs. noncolorchanging foxes, remember?) represented more information, even though I made them different at every level - DNA, proteome, phenotype, and fitness. Without reviewing those discussions, perhaps you didn't give me enough "information" about the information?
False. I provided answers to every question you asked. Go back and read that section if you don't believe me. --Martin Arrowsmith 18:34, 22 October 2011 (UTC)
OK, so address it. Can you say whether that's a loss of information? Whatever questions you need to ask to make the determination, I can provide answers for. Okay, I'll try.
all the dogs may have a new gene coding for a new protein that inhibits the effects of the older genes/proteins which are still present In the illustration, the original dogs have both short-hair and long-hair genes. Do these new genes inhibit both? Equally? What is the effect (in terms of hair length)? That is, if they inhibit both short-hair and long-hair genes, does that mean that the dogs don't grow hair at all, or what? Do the new genes do anything apart from inhibit the older genes?
OK. There exist two populations of dogs with a mix of LL, Ll, and ll individuals. LL is long, Ll is med length, and ll is short hair. In one population, a mutation arises that produces a new allele y, which gives rise to a protein which alters the action of the protein produced by the L allele. It does not interact with the l protein product, and it has no other effects. Suppose further if you like that this mutation has gone to fixation in the population purely through drift; the two Lly- founders of the population were sibling offspring of the very first animal with the y allele, and by chance all member of the population are now yy homozygotes. LLyy, Llyy, and llyy are all short haired. What more would you like to know?--Martin Arrowsmith 18:34, 22 October 2011 (UTC)
I think you mean that you have 'declared' which have more or less information... No, I have illustrated it.
...you keep using undefined but evocative terms like 'more or less' and 'instructions' and 'meaning' to back up your declarations. None of those terms are undefined. See a dictionary.
NDWSRFOP. See 'beauty', 'smelly', 'Christian', 'faith'. See a textbook.--Martin Arrowsmith 18:34, 22 October 2011 (UTC)
I think in part that this is the effect of a fundamental ignorance of actual biological processes. I don't mean that as an insult... Well, it is in insult (even if not of me), given that this illustration did not originate with me, but was obtained from a biologist. And, for what it's worth, I've heard (second-hand) that even trained geneticists have remarked on how accurate the illustration is.
I'm not referring here to just the hair example. I'm referring to my impression of the totality of your posts about biological processes. I don't even argue with you that the dog example represents a loss of information for some definition of information - my objection is that you can't or won't give that definition. If you define information as the number of unique alleles at a given locus, then the population has lost information by losing an allele. If you define information as the number of phenotypes (much harder to do) then the population has lost information by losing phenotypes. But you don't use those definitions; you've been asked and you've denied that those are what you are using. You continue to try to talk about biological information only through analogy. That's maybe acceptable if you're trying to introduce a newcomer to a topic, but at some point the analogies have to be put away and you have to actually deal with things directly. At this point I don't think that you are able to do that; you think that your grasp of analogies represents a grasp of the material, and it doesn't.--Martin Arrowsmith 18:34, 22 October 2011 (UTC)
I tried to lead you by the hand through the fox example, and I couldn't make any sense of your answers, and at times they weren't even internally consistent. I reject that they weren't consistent.
I guess that I'm at a loss as to how to proceed. Try thinking about how things (living and otherwise) are designed, instead of assuming that they evolved.
Try to learn how genes and proteins actually work, instead of assuming that linguistic analogies explain it all.--Martin Arrowsmith 18:34, 22 October 2011 (UTC)
you havent shown any meaningful gain or loss of "information" except in analogy. But, by analogy, I have shown it.
Oh, well if you've shown it by analogy, then there can be no doubt that it is correct. Jesus is the Word, a word can be written down and erased but the word doesn't cease to exist after the erasing, therefore Jesus never died and the Resurrection is nonsensical. Or: if Jesus is the Word, and I write the Word Jesus then I have power over Jesus because I can erase or change the word I have written. Analogy triumphs again.--Martin Arrowsmith 18:34, 22 October 2011 (UTC)
You claimed the real mechanism isnt needed because you are arguing an illustration. I claimed that the real mechanism isn't needed for the illustration.
* Xpqtqx zigumvb vmmla uwzm uibpa * let me know if this is a real cipher or garbage. When I said that you can determine the existence of a cipher without deciphering it, I was referring to people who are expert in deciphering. I don't claim that ability. Sometimes it's only possible with a sufficiently-long text. One way is to see if the frequency of letters matches those of, for example, English. For example, the most common letter might have the same frequency as the most common letter in English, and so on. By contrast, if all the letters have the same frequency, then it's probably not a cipher.
Thats 15 years... If dna is a language as fact rather than hypothesis then the nouns , verbs, qualifiers etc should be known and a primer on the language available for testing. It took over 22 years to decipher the hieroglyphics of the Rosetta Stone, probably a much simpler task.
perhaps you can explain why if dna is a language that the codes produce different results depending on what organism its in ? Perhaps for the same reason that the same word in English can have different meanings depending on what sentence (context) it is in. Or perhaps according to what variation of English it is, such as marquee, a big tent in Australian English, and a sign in American English.
Thats clearly mutation alternating with selection in any bloodline That's the repeated cycle that I referred to. But natural selection selects mutations (effectively; I agree that it selects individuals), not the other way around.
You do know that mutations dont happen to living animals ? They do happen in living animals. But if they occur in somatic cells, they are not passed on to offspring.
Philip J. Raymentdiscuss 15:14, 22 October 2011 (UTC)
By contrast, if all the letters have the same frequency, then it's probably not a cipher. With that we can add cryptography to the list of topics on Philip doesn't have the foggiest notion, but feels called to expound upon anyway. It is practically part of the definition of a good cipher that all letters have the same frequency. --Awc 17:18, 22 October 2011 (UTC)
To satisfy your objection, I will no longer refer to any word as 'undefined'. I will instead use the term Not Defined With Sufficient Rigor For Our Purposes, or NDWSRFOP, or NDSR for short. Who gets to decide how much is "sufficient"?
The people that you are trying to convince, that's who. --Martin Arrowsmith 11:13, 23 October 2011 (UTC)
Certainly. Being dead, no two fossils are interfertile. Yet scientists decide whether two fossils are of the same species or not. Is "species" therefore Defined With Sufficient Rigor For Their Purposes, despite the definition being unable to help in the case of fossils? If so, why is the definition of "information" treated differently?
Yes, it is DWSR for their purposes. The interfertility of the fossils is data that is not available, and the species distinctions are always provisional. Several previously described species have been collapsed into single species as further data has been acquired. If there were a means of testing interfertility of fossils, it would be incorporated into the methods used to determine fossil species. It's not that they deny that interfertility is an important aspect of determining species when the organsims under study are alive. If 'information' is a quality or quantity that is as unavailable to us as interfertility data is to paleontologists, then in what way is it useful?--Martin Arrowsmith 11:13, 23 October 2011 (UTC)
Perhaps you are misunderstanding me. ... Those points, in the aggregate, give you all you would need to know to recreate the shape of the statue. Is there no information in that set of points? What is the purpose of the table? To recreate the shape of the statue, or to recreate the statue atom-by-atom? Information is, for example, a set of instructions (for making cakes, machines, living things, statues, etc.). Do you need to know the position of every atom for each of them? For living things, this might be close to true. Not so for cakes, machines, or statues. Yes, your table contains information, but really only for the shape of the statue, not for the position of every atom. I'm deliberately being cautious in my response, because your table could be said to be full of information in particular scenario where the position of every atom was important, although I can't think of one, beyond something like a Star Trek transporter that disassembles and reassembles on an atom-by-atom basis, although even in that case, the position of each atom doesn't really matter.
I still don't follow you. As I see your statement, there is data in the table but only some of that constitutes information. Only the surface contour of the statue contains information. But under other circumstances, there is more information in the table. So the information content within the larger data lump is variable and context-dependent? Then how do two observers agree on the amount of information in the table?--Martin Arrowsmith 11:13, 23 October 2011 (UTC)
That is a bombshell claim, which contradicts all of mathematical information theory. However, we are not talking about mathematical information theory, such as Shannon, etc.
If you are proposing an entirely new formulation of information theory, it is more vital than ever to be able to do so with rigor, rather than relying on qualia like 'meaning'. --Martin Arrowsmith 11:13, 23 October 2011 (UTC)
Are you making a distinction between data (no author) and information (has an author)? In a sense, yes. Do you know of any information (apart from things like DNA, which are begging the question) that does not have an author? How many of books do you know of which did not have authors?
Seismograph recordings. EKG tracings. Light spectra from distant stars. Barometric pressure readings. The photons striking my eye as I look at this computer screen. Pressure waves as registered on my eardrums.--Martin Arrowsmith 11:13, 23 October 2011 (UTC)
I find that an evasive answer. 'Design'- does that mean the shape, the shape plus the materials, the shape and the materials and the process, the cognitive/emotional state that the designer intended to induce in the viewer, or all of these, or some of them, or none of them? The design could be all of those, or at least the first three. If you design something, do you specify just the outcome, or also the materials to use and the process to achieve the outcome?
Can the 'design' be conveyed to a person who is not in the presence of the original statue? How? Plans. Blueprints. Etc. Now I'm quite sure that you know about plans and blueprints, so why the question? Does this indicate that you are still thinking in a completely different mode to what I'm talking about, like a person who can't see the forest for the trees?
Apparently yes, we are in completely different modes. I am blind, and you are trying to explain 'blueness' to me. But rather than telling me about electromagnetic radiation and wavelength, and defining a particular band of wavelengths as 'blue' and explaining the principle and operation of a spectrophotometer so that I can determine for my blind self whether one thing is more blue than another, you go on about how blueness is like sadness and cold, and blueness has meaning and syntax, and blueness cannot be created by naturalistic processes, and all changes of color represent a loss of blueness.
I ask about whether the 'design' can be conveyed to another person because I want to know whether the 'design' can be reduced to a string of digits, or whether it is some property or experience that is in some sense ineffable, like an emotional state.--Martin Arrowsmith 11:13, 23 October 2011 (UTC)
How do you compare it without being able to measure it? Can you give me an example of some other quality that you can compare without being able to measure? I have before (perhaps not to you, but certainly on this site). Length. Which ladder is longer? Do you need to find a measuring tape and measure the length before you can tell which is longer, or just compare the two and visually tell which is longer?
Yes, you've used that with me before. But as I said at the time, that example relies on the fact that we all agree on what 'length' is, and how to measure it, such that we can both determine which ladder has more of 'length'. You and I are not yet to that stage when it comes to 'infomation', just as we are not when it comes to 'beauty' or 'tastiness'. Both 'beauty' and 'tastiness' have perfectly valid dictionary definitions, of course.--Martin Arrowsmith 11:13, 23 October 2011 (UTC)
False. I provided answers to every question you asked. Go back and read that section if you don't believe me. Ah yes, from a quick glance you did. But your claim that I never could say which of two examples (color changing vs. noncolorchanging foxes, remember?) represented more information, even though I made them different at every level - DNA, proteome, phenotype, and fitness is the one that is misleading, because I did answer your question then, by saying that "Going on the information that you have provided, they both appear to have the same amount of information. The only difference is a value difference, not an instruction difference." You then asked how that could be so, and I explained how it could be, and that, it seems from my quick scan, is as far as the conversation went.
"A value difference, not an instruction difference". I still don't know where the bright line is that lets you differentiate the two. To me, the instructions are different between the two fox populations, because they have different alleles at the same locus. Perhaps you mean that the two populations have substituted one quantum of information for an equal amount of different information at some level, so the two subpopulations of foxes have the same overall information as each other. If that is the case, does the larger population of all foxes together still have the same amount of information as before the split, when the new allele and protein and phenotype emerged? If one subpopulation of foxes died out, would it represent a loss of information like the dog example? If not, why are the scenarios different? If so, it would appear that information can be lost perpetually from a population via the loss of novel mutations that do not themselves generate new information, which appears nonsensical.--Martin Arrowsmith 15:03, 23 October 2011 (UTC)
OK. There exist two populations of dogs with a mix of LL, Ll, and ll individuals. [rest snipped]. Okay. Your original question was When all the short-haired dogs are lost from a population, is that a loss of information? I would say that this is probably not a loss of information, as the genes for long and short hair are still present, merely suppressed (in the case of the long-hair genes).
That does not address the existence of a new allele, y, and a new y protein. Surely that represents a new 'instruction', which, since you have said the information in the old genes is still there, must represent a gain in information. If not, why does the existence of y not factor into the determination?--Martin Arrowsmith 15:03, 23 October 2011 (UTC)
NDWSRFOP. See 'beauty', 'smelly', 'Christian', 'faith'. See a textbook. I fail to see how "more" and "less", at the very least, are NDWSRFOP. If you ask if someone has more faith than someone else, you may not know how to tell; you may not know how to measure faith, but you do understand what is meant by "more".
Because at one point you stated (from memory now, feel free to correct me) that information could be related to whether or not something did something 'more or less' without saying what that something was. I'll stipulate that 'more' and 'less' are generally well understood concepts that are DWSR for our purposes unless otherwise specified.--Martin Arrowsmith 15:03, 23 October 2011 (UTC)
...my objection is that you can't or won't give that definition. And yet I have. So my objection is that you (and Sterile) keep falsely accusing me of this. Why do you keep doing that? An answer please.
Because what you describe as a definition makes no sense to me. Seriously. I believe that you are describing qualia but claiming that they have an independent, quantitative existence. You want us to treat 'information' like 'length' when all of the ways you describe or try to define 'information' make it sound more like 'beauty' or 'puissance'; inherently subjective experiences. It reminds me of Schlafly's objections to the Blount/Lenski paper; specifically his complaints about the statistical methods used. He repeated assertions of error without any justification, or even a willingness to engage in other than generalities. He claimed that the weighting of the analysis was incorrect but would not say what the weighting should have been, or even how to find out what it should have been. Did you agree with his approach at the time?--Martin Arrowsmith 11:13, 23 October 2011 (UTC)
You continue to try to talk about biological information only through analogy. Not true.
That's maybe acceptable if you're trying to introduce a newcomer to a topic,... Which seems appropriate in the case of some people here, who have only ever thought of "information" in a mathematical/statistical sense.
Oh, I've thought about it in quite a few other senses, thankyouverymuch. I just don't see how your sense, as I fail to understand it, can be applied to biological systems in a meaningful way (pun intended). I'm in an evolutionary reading book club with my next door neighbor who is a PhD linguist, for crying out loud. I'm quite comfortable with theories of information in human language where "the red car" has more information than "the car" when information content is defined as the inverse of the number of possible worlds in which the statement is true. I'm comfortable with statistical theories of information in which "the red car" has more information than "the car" because the string is four characters longer or some other metric. The fact that I'm not satisfied with your theory of information is that it's a protean unmeasurable mess that is NDSR.--Martin Arrowsmith 15:03, 23 October 2011 (UTC)
...but at some point the analogies have to be put away and you have to actually deal with things directly. At this point I don't think that you are able to do that;... I don't think that you are ready for that, given that you can't even deal with the analogies. But apart from that, I agree, which is why I have gone beyond analogies, in talking about function, etc.
Try to learn how genes and proteins actually work, instead of assuming that linguistic analogies explain it all I thought is was you who was at a loss as to how to proceed. As for genes and proteins, I think it's a case again of not being able to see the forest for the trees. Understanding the mechanics of translation from DNA to RNA to amino acids to proteins is one thing, but understanding the "big picture" of how the DNA is a set of instructions to arrange various molecules in a particular way in order to build a living thing is another thing entirely.
Oh, well if you've shown it by analogy, then there can be no doubt that it is correct. I did not say that, and that does not follow.
With that we can add cryptography to the list of topics on Philip doesn't have the foggiest notion, but feels called to expound upon anyway. It is practically part of the definition of a good cipher that all letters have the same frequency. Then we can add this as an example where my critics overreach and make grand claims on little evidence. You're right that a good cipher has the same frequency of letters, but I was, after all, simply illustrating that there are ways of telling if something is a cipher or not. That my example used the case of a very simple cipher does not mean that I don't know anything about the subject.
Philip J. Raymentdiscuss 06:40, 23 October 2011 (UTC)
So now I was "overreaching and making grand claims on little evidence"? It was you who made the "grand" claim that people who are expert in deciphering ... can determine the existence of a cipher without deciphering it. Specifically you said if all the letters have the same frequency, then it's probably not a cipher. Even if you meant this statement to refer only to simple substitution codes (the sort of thing I learned to decipher in the third grade, so that the reference to experts doesn't make any sense), it is trivial to create a string of random characters with any desired distribution. So how is it possible to determine the existence of a cipher without deciphering it? You may have a good idea whether a string is a cipher or not if you know where it came from, but for that you don't need to be an expert cryptologist and you don't even need to look at the string in question. Of course, you might also be able to rule out certain classes of ciphers, like simple substitution. I'm on pins and needles to hear how you think this trick can be done in general, or to see the statement by an expert that led you to believe it. Otherwise, just admit you got this one wrong and we can all drop the subject (except that Hamster's comment would still be open). --Awc 10:14, 23 October 2011 (UTC)
Who said they were "synonymous? I said they are "correlated". You said they are "related". We agree. Why do you say "but"? I mean "related" as a motor is related to a wheel, but they are not correlated.
Ah. they are not correlated So you do not think, as a general rule, that a system with more information is more useful than a system with less? --Awc 17:14, 23 October 2011 (UTC)
A cell containing all the mutations that ever occurred would have the same information as a cell that only retained the ones that work together to sustain life. In my book, that's a problematical definition of information. I agree that it's problematic. The difference is that "all the mutations that ever occurred" would mean a mass of nonsense, not information. I have already agreed that removing material can increase information (per the statue), but this was not removal of information. The original statement in the article was regarding the removal of genes, which implies that information, not non-information material, was being removed. If the statement had been that "the removal of nucleotides can also be considered a source of information in some cases", the statement would be better, although I would still disagree that the removal was the source of the information. Rather, the removal would constitute an increase in information.
The difference is that "all the mutations that ever occurred" would mean a mass of nonsense, not information. ... The original statement in the article was regarding the removal of genes, which implies that information, not non-information material, was being removed. Which is it? Do all genes contain information, as the second statement implies, or only genes that do something useful, as the first statement implies? --Awc 17:14, 23 October 2011 (UTC)
The people that you are trying to convince, that's who. Ah, okay. So a creationist is wrong simply because an evolutionist sets an unrealistic standard for a definition, while an evolutionist is right because the evolutionist sets a lower standard for evolutionists. I'm glad you cleared that up.
False, and perjorative. In a discussion like this the onus is on each discussant to present an argument that is clear enough to the opponent that the opponent can come to accept or reject the argument on its merits. Do you feel that the concept of 'species' has been so poorly defined that it interferes with your ability to comprehend the entirety of the argument for evolution? I would be happy to try to clear up any lingering confusion you have, if you'll ask. --Martin Arrowsmith 17:03, 23 October 2011 (UTC)
Yes, it is DWSR for their purposes. As I just said, evolutionists set the standard lower for evolutionists.
Hardly. To determine species relationships among living organisms, interfertility is an important data point. To determine species relationships among extinct organisms, interfertility is an unavailable data point, and species determinations are made with other data. Do baramainologists remain permanently agnostic as to the baramins of extinct species because interbreeding experiments can't be done?--Martin Arrowsmith 17:03, 23 October 2011 (UTC)
So the information content withing the larger data lump is variable and context-dependent? It's dependent on the purpose, and all information is context-dependent, so that should not be a surprise.
So to determine the information content of the data, we need more information than just the data? We need further information about the context of the data?--Martin Arrowsmith 17:03, 23 October 2011 (UTC)
If you are proposing an entirely new formulation of information theory, it is more vital than even to be able to do so with rigor, rather than relying on qualia like 'meaning'. I guess that's why there are also definitions like "specified complexity".
I'm going to leave that one alone, since I'd like to get 'information' hammered out first.--Martin Arrowsmith 17:03, 23 October 2011 (UTC)
Seismograph recordings. EKG tracings. Light spectra from distant stars. Barometric pressure readings. The photons striking my eye as I look at this computer screen. Pressure waves as registered on my eardrums. None of them are books, although the one or two which come closest (the last two), to the extent that they are similar do have authors. The others are simply data, not information carrying meaning. I will concede that you have (finally?) come to the point of raising a reasonable argument, but only one that requires a bit more fine-tuning. Although I have previously said that "information" is stuff with "meaning", and you examples come close to fitting that, I've also said that it's things like instructions, which they are not examples of.
Apparently yes, we are in completely different modes. I am blind... I see. So when I say that blue is the colour of the sky, rather than point out that you are blind and don't know the colour of the sky, you let me think that you can see but criticise me for not describing it in a particular way. So what you are telling me is that, like a blind person doesn't know what "blue" looks like, you simply do not know what "information" is. I don't think I've come across that sort of blindness before, at least in sane educated adults.
Har har har. --Martin Arrowsmith 17:03, 23 October 2011 (UTC)
Yes, you've used that with me before. But as I said at the time, that example relies on the fact that we all agree on what 'length' is, and how to measure it... It doesn't require us to know how to measure it.
If we don't know how to measure length, how do we decide that one ladder is longer than the other? By smell? By the emotional state they induce in us?--Martin Arrowsmith 17:03, 23 October 2011 (UTC)
Because what you describe as a definition makes no sense to me. Seriously. You not understanding is not the same thing as me not providing. So I repeat my question: Why do you keep falsely accusing me of not providing a definition?
If you ask me for a definition of a species, am I allowed to respond with whatever I like, and you will be satisfied that I have provided a definition?--Martin Arrowsmith 17:03, 23 October 2011 (UTC)
So how is it possible to determine the existence of a cipher without deciphering it? ... Otherwise, just admit you got this one wrong and we can all drop the subject... Okay, I didn't handle that example as well as I could have. And perhaps a cipher is not the best example, for the reason you mention: that it is designed to not look like a message. However, my reference to experts was to determining the existence of ciphers in general, and I applied that to Hamster's test, while my reference to frequency of letters was merely to illustrate that there are ways of determining the existence of ciphers. I still believe that my basic point is correct, that there are certain patterns one would look for to determine the existence of a cipher. For some support, see here.
... (except that Hamster's comment would still be open). The question, however, did not relate to things that were designed to not look like messages. Perhaps a better example than a cipher would have been an alien language, where (in principle) the existence of intelligence can be determined by the non-random, not-patterned nature of the data, and where there has not been an attempt to disguise the fact that it is a language.
Philip J. Raymentdiscuss 14:04, 23 October 2011 (UTC)
Many ciphers can be cracked because and only because we know the rules of the language it was originally written in. So a simple substitution cipher you can count the occurance rate of each letter and match it to a table and start a reverse substitution. If you get close a reader might recognise a word that is misspelled such as Londim especially if in context. None of that applies to a foreign language where the vocabulary, spelling and grammer are unknown. I offer a message which contains a number. 42. what can we know of this number ? Hamster
None of that applies to a foreign language where the vocabulary, spelling and grammer are unknown. None of that applies, but other things do, which allow us to determine the existence of a language.
I offer a message which contains a number. 42. what can we know of this number ? Very little, without context. In the context of decimal numbering systems, it's the product of 6 x 7. In the context of hexadecimal numbering systems, it's the product of 6 x B. In the context of a particular novel by Douglas Adams, it's supposed to be the answer to life, the universe, and everything. Without knowing the message that contains that number, I can't tell you what it means.
Philip J. Raymentdiscuss 01:27, 1 November 2011 (UTC)

Removal of part of "Horizontal gene transfer" section

I removed the second half of this section, as it amounted to invoking (or at least suggesting) a naturalistic miracle. That is, it involved a highly-implausible scenario that, if a creationist suggested similar, would be greeted with ridicule.

What's the odds that a recipe book (to re-use that example) by accident gains an extra page which is nonsense in that context as it talks about the care of horses, but which makes good sense in a book about equines? Not only is it being proposed that the recipe book gets that page, but that this gets past the proof reader and publisher and therefore survives long enough to somehow end up in the equine book. To bring this back to evolution, if the additional gene is not useful in the original creature, then it is not neutral, but a burden on the creature that has to expend energy maintaining it, and therefore natural selection is supposed to remove it.

Philip J. Raymentdiscuss 13:07, 15 October 2011 (UTC)

lets use the recipe book analogy. In the section on breads you get a small paragraph on making a nice orange glaze. Since orange glaze on bread might be a bit overdone the recipe does not often get used, an occasional orange loaf doesnt make an impact. The paragraph though gets copied and glued into the section on pastries. Suddenly you have the possibility of a fruit danish with an orange glaze ! yummy. Copy that same section into cakes and again yum. Hamster 16:07, 15 October 2011 (UTC)
That's not what was being suggested, as it was suggesting something with no information, not something with a little information. Philip J. Raymentdiscuss 12:08, 17 October 2011 (UTC)
if the additional gene is not useful in the original creature, then it is not neutral ... that would depend on wethere it is active and being expressed wouldn't it ?
please reread your own paragraph above , the page mentioned contains information, just on a different subject. In my analogy consider the bread, pastry, cake sections as different organisms. Horizontal gene transfer is moving between organisms. Hamster 15:16, 17 October 2011 (UTC)
that would depend on wethere it is active and being expressed wouldn't it ? No. An unexpressed gene still requires energy to maintain it.
please reread your own paragraph above , the page mentioned contains information, just on a different subject. Not in the section I removed from the article, which is what I was referring to when I said That's not what was being suggested...
Philip J. Raymentdiscuss 15:22, 22 October 2011 (UTC)
This What's the odds that a recipe book (to re-use that example) by accident gains an extra page which is nonsense in that context as it talks about the care of horses, but which makes good sense in a book about equines? is what I was referring to. Are you saying a page on horses contains no information unless it is in a book on horses ?
No. An unexpressed gene still requires energy to maintain it. do you have any support for that statement ? Hamster 15:50, 22 October 2011 (UTC)
Are you saying a page on horses contains no information unless it is in a book on horses ? That would depend, I guess, on whether there is enough text there to convey information completely out of context. It is the arrangement of letters, words, sentences, etc. which convey information. A single letter by itself almost certainly does not. A single word would not hanging either. If, for example, I said that "Australia used to execute criminals by hanging", the word "hanging" conveys information: it tells you how criminals were executed. But in the sentence before that, the word "hanging" contained no information at all. In fact, it probably had the effect of turning that sentence to gobbledegook, or destroying the information in that sentence. So an out-of-place word does not generally convey information. What about an out of place sentence? Paragraph? Page? I guess at some point there might be enough text that some information is conveyed, but how much more so in the correct place? For example, the page might contain information on how to treat a particular disease in horses, but if you don't know which disease because the particular disease itself is not mentioned on that page, then the page really contains no useful information.
do you have any support for that statement ? Do I really need to? Whenever DNA is copied, it has to be read. This takes energy. Unexpressed DNA is copied too. But if you really want references, see here, here (which refers to some replication taking more energy than other replication), and here, if you accept that source.
Philip J. Raymentdiscuss 10:40, 23 October 2011 (UTC)
so you are now saying useful information rather than just information ? Hamster 15:16, 23 October 2011 (UTC)
I guess I should have said "meaningful" information. Philip J. Raymentdiscuss 02:11, 1 November 2011 (UTC)

new structure

Normally I would be bold and just go ahead and make these changes, but I'm afraid I might not have time to do it in one go, and I'd prefer not to upset any delicate dispositions. I'd like to change "Quantification of information" to "The creationist view". Later I would add another section on "Alternative views", where much of this business would land, like the possibility that removing alleles could be seen as an increase in the information in a gene pool. For a number of reasons, the emphasis here should be on the creationist view, and whether their argument can stand up to scrutiny. Whether the thing they are talking about is best named "genetic information" or "chocolate syrup" doesn't affect the strength of the argument.

I would start with some initial comments on the creationist view, pointing out, among other things, that there is nothing approaching a quantitative definition, that creationists feel that the common intuitive understanding of information is sufficient to make their argument, and that they tend to argue on a case by case basis. (That's all OK. I'm not being dismissive.)

We would probably need some discussion at this point of what "the right kind" of mutations would be for bacteria to Bach or whatever. The starting point would be "the first cell", with working genetic replication mechanisms. Changes in morphology probably don't make a very good argument, even though almost all the differences between a mouse and a man are morphological. I think the creationists would want to - and do - emphasize changes in metabolism, mediated by new enzymes.

Then I would start a series of subsections on the arguments why this and that does not represent an increase in information, with examples. Like ...

  • Shifts in frequencies of alleles - Perhaps the shift in the proportions of light and dark peppered moths between the peak of industrial pollution and the present. The rise of the dark form is not such a good example here since it probably arose recently as a mutation, but it could still be used.
  • Horizontal gene transfer - Often a factor in acquired resistance to antibiotics, but it also occurs (much less often) in vertebrates.
  • Degenerative changes - Clear loss of function, like sightless fish living in caves. Some types of acquired resistance to antibiotics would probably fall in this category.
  • Loss of specificity - Citrate metabolism.
  • Change of detail but not of fundamental function - New strains of flu virus every year, and recognition of new proteins by the immune system. (The argumentation is starting to get trickier.)
  • Non-random mutations - Metabolism of nylon. I'll do my best, but I still think this argument is incoherent.

Any comments before I rev up the wrecking ball? --Awc 20:46, 17 October 2011 (UTC)

swing away ! You might touch on horizontal gene transfer as a current or historical process. Hamster 22:40, 19 October 2011 (UTC)
Oh, be bold! I'm sure it will go well. Sterile 00:58, 20 October 2011 (UTC)
I'd like to change "Quantification of information" to "The creationist view". Later I would add another section on "Alternative views"... I don't see supposedly-neutral encyclopædias like Wikipedia having headings like "The evolutionist view" and "Alternative views" (rather, they have—effectively—"The correct view" and "Alternative views"), so why should we here, when we don't aim to be neutral? However, having said that, it will depend on the exact circumstances.
In the end I chose "The argument for creation". I don't know if this argument is generally used by creationists or only by a few, so "The creationist view" may be presuming too much. Whether it is valid or not, it is still an argument for creation. The ground rules of the site do not require that every argument used by any creationists be accepted uncritically. --Awc 17:12, 22 October 2011 (UTC)
...almost all the differences between a mouse and a man are morphological. That's like saying that almost all the differences between a trashy news-sheet and an encyclopædia are the words, ignoring that there's also a difference in genre, quality, and target audience, to pick three points. (Or do they not count because they are not quantifiable?)
Like Hamster below, I don't see what point you are trying to make. --Awc 17:12, 22 October 2011 (UTC)
Philip J. Raymentdiscuss 15:34, 22 October 2011 (UTC)
lets put the first bit of that sentance in place Changes in morphology probably don't make a very good argument,... So Awc is saying morphology is not a good arguement and you seem to agree with that. Are you claiming in a biological sense, which is what this section (genetic information) is about , that there are very substantial differences which are not morphological ?
in your analogy are you comparing mice to a trashy news sheet? Mice are wonderfully adapted creatures more like a good referance book than "BatBoy returns !" Hamster 16:48, 22 October 2011 (UTC)
The ground rules of the site do not require that every argument used by any creationists be accepted uncritically. Agreed, but the qualified comments should only be used where really appropriate.
No, I'm not likening mice to a trashy news sheet. Mice are wonderfully designed creatures made by God. I'm pointing out that there are greater differences than just the shape or even the arrangement of proteins and other molecules. Even in a biological sense, although I don't see why we should limit the discussion to biology.
I don't know what you don't understand. Do you accept my point about there being more differences between a trashy news-sheet and an encyclopædia than just the words it contains but can't relate that to living things, or don't you even see my point about the printed matter?
Philip J. Raymentdiscuss 11:02, 23 October 2011 (UTC)
since this section is biology the discussions here of other than biology are not relevant to the article.
no I do not agree that biologically there is any significant difference between a man and a mouse, a man and a cat would be closer because a cat is a mammal and a mouse would be rodent but thats fairly minor.
there are technical issues on paper quality, layout, typefaces, binding which are different (morphology) and that is because of the different function each has. If you are trying to say that an encyclopedia is superior then thats strictly a matter of opinion not supported by sales figures, although someone who wants information on say trees would be better served by an encyclopedia. Hamster 15:13, 23 October 2011 (UTC)
no I do not agree that biologically there is any significant difference between a man and a mouse So the fact that a man can talk is not significant?
If you are trying to say that an encyclopedia is superior then thats strictly a matter of opinion not supported by sales figures... What do sales figures have to do with superior quality?
Philip J. Raymentdiscuss 02:15, 1 November 2011 (UTC)
mice make noises as do all animals within the limits of their vocal apparatus. Not a significant difference at all.
sales figures show the user demand. By that criteria the encyclopedoa is of lower value than the trashy news sheet. quality is a matter of opinion. Hamster 03:56, 1 November 2011 (UTC)
mice make noises as do all animals within the limits of their vocal apparatus. Not a significant difference at all. The ability to talk is not significant? Try not talking for a while and see how significant it is. There is a big difference in the limits of their respective vocal apparati (apparatuses?).
sales figures show the user demand. But not quality, which was my point.
quality is a matter of opinion. To some extent, yes, but that doesn't mean that it's not there. Why do you think that higher-quality things generally fetch higher prices? Because the quality is real, not imaginary.
Philip J. Raymentdiscuss 05:00, 1 November 2011 (UTC)
no the quality is not "real" the quality is perceived by those buying to have a value. Why then do things vary in value as fads change ? Hamster 05:10, 1 November 2011 (UTC)
Why then do things vary in value as fads change ? Fads affect demand, not quality. Philip J. Raymentdiscuss 05:19, 1 November 2011 (UTC)

The Argument for Creation

Awc's recent edit refers to Lenski's E. coli having a useful mutation that involves a decrease in specificity. Actually, the mechanism by which the Cit+ bacteria in Lenski's experiment take up and/or utilize citrate has not been determined, at least to my knowledge. Batten's commentary proposes two different mechanisms, so that he can shoot down both proposed mechanisms as mere loss of information. I predict that whenever the actual mechanism is elucidated, Batten and his cohort will describe it as either a loss of information or as a designed adaptive mechanism à la nylonase. --Martin Arrowsmith 21:28, 19 October 2011 (UTC)

there is a lot of info on Lenskis website, including dna sequencing and details of what mutations occured. There was also an interesting article in Nature but I didnt understand the abstract and the article itself is behind a paywall. Most of the stuff seems written for biologists which makes perfect sense. Sadly I need to wait for the Popular Science article to be written ;-) Hamster 21:45, 22 October 2011 (UTC)
There are a number of articles from Lenski's lab that describe quite a few of the mutations that have occurred in his E. coli strains over the years, including changes in cell shape and size and overall mutability; however, the mechanism of the Cit+ trait has not yet been elucidated. It is, of course, an area of ongoing research.--Martin Arrowsmith 22:56, 22 October 2011 (UTC)
Sorry, I got confused on this one. I was thinking of the section "The Dangers of Conclusion Jumping" in Spetner's A Scientific Critique Of Evolution, but that concerns the metabolism of xylitol, not citrate. This will have to be fixed. --Awc 07:20, 20 October 2011 (UTC)
After a quick look you seem to be correct that the mechanism of Cit+ is unknown. That makes it unusable as an example of decreased specificity. It likewise doesn't meet the gold standard of verifiable high specificity. So it's not very useful to this article. I'll put in xylitol metabolism as an example of novel, useful, but less specificity. The real fun will be with nylonase, anyway. --Awc 07:45, 20 October 2011 (UTC)
Batten and his cohort will describe it as either a loss of information or as a designed adaptive mechanism à la nylonase. I predict that it will be described as one or the other because it will be one or the other, a reasonable prediction given that all cases so far have been one or the other. Philip J. Raymentdiscuss 15:39, 22 October 2011 (UTC)
I will counter that if, like Batten, your axiom is that no naturalistic process produces any new information, then ANY and ALL mutations will necessarily either represent a loss of information or be a designed mechanism - i.e. the information was already there at some meta-level (be it pre-existing sequences already buried in the genome, or regions 'designed' to be able to produce novel sequences where the information lies not in the novel sequence but one or more levels up) and was merely 'uncovered' or 'manifested'. There is no third option. No example can be produced that will not fit into one of those two categories. --Martin Arrowsmith 16:49, 22 October 2011 (UTC)
It does not follow that if the axiom is that, then no contra-examples can be produced. Not accepting that a third option can occur does not mean that there is no potential third option which, if it occurred, would show the axiom to be wrong. Philip J. Raymentdiscuss 11:28, 23 October 2011 (UTC)
Axioms can't be wrong; that's deductive logic, not inductive. And how can it be wrong if there's not criteria for what constitutes more information? Indeed, it's hard to say if the lack of falsifiability or the lack of criteria are the bigger problem. It certainly reinforces the ad hoc nature of it all. Sterile 17:15, 24 October 2011 (UTC)
And how can it be wrong if there's not criteria for what constitutes more information? Why do you keep claiming that there's no criteria? Philip J. Raymentdiscuss 02:34, 1 November 2011 (UTC)
And I ask, "Where have you done so?" And you say, "I've given you criteria." Answer the question, Philip, because you have not done so clearly when asked since the inception of this wiki. Sterile 12:48, 1 November 2011 (UTC)
Bradley linked you to a definition here, I briefly explained here (post dated 02:49, 6 April 2009), and here in answer to someone else I linked to the information and genetic information articles which both explain it. And that's just the ones that I could find now, and doesn't include examples, analogies, etc. which help explain it. Philip J. Raymentdiscuss 06:22, 4 December 2011 (UTC)
I followed the links. It is an eloquent admission that you have no criteria. —Awc 20:45, 5 December 2011 (UTC)
Yep. Nothing to indicate what's more or less. Sterile 03:33, 9 December 2011 (UTC)
Perhaps instead of simply asserting that there is no criteria when I have linked to such, you need to explain why the purported criteria is not. Philip J. Raymentdiscuss 03:52, 21 April 2012 (UTC)

common sense says of course there was an increase in information

Philip has recently provided many targets and it would be entertaining to shoot them all down, but he skipped over (perhaps not intentionally) a point which, in contrast to many of the other threads, is central to this topic. I wrote, At the end of the process [the mutation resulting in nylonase], the species has something it didn't have before, namely the information needed to digest a new type of food. Philip has been insisting that we use our intuitive definition of information to decide when an increase in information has occurred or not. With all my reservations on the reliability of that procedure, when I apply it here, my intuition says, of course there was an increase in information. If Philip in his personal intuition still thinks there was no increase in information, then we will have to move beyond intuition if we want to continue communicating.

I could ask (almost) the same question in a different way. If a mutation resulting in a novel protein with a new and useful function is not the right "kind" of mutation to account for first-cell-to-present-species evolution, then what is? Clearly evolution would need very many such mutations, and they would all have to work together, so you might raise the question of irreducible complexity, but why is the appearance of nylonase not a change in "the right direction" for evolution?

--Awc 11:17, 23 October 2011 (UTC)

Philip has been insisting that we use our intuitive definition of information to decide when an increase in information has occurred or not. I dont' believe that I have. Rather, I've been encouraging people to go back to a normal, everyday, definition of information as their starting point (as opposed to thinking of statistical information such as Shannon information, or denying the existence of non-statistical information). I guess I haven't made clear that it's just a starting point because it's been so difficult to get people to do even that.
With all my reservations on the reliability of that procedure, when I apply it here, my intuition says, of course there was an increase in information. If Philip in his personal intuition still thinks there was no increase in information... I hope I have not said that there was no increase in information. I fully accept that increases in information can occur. My point is that they occur only as the result of a mind, not from naturalistic processes, and in the case of the nylonase, that this was the result of an intelligently-designed process, not a naturalistic one.
...why is the appearance of nylonase not a change in "the right direction" for evolution? Assuming that it is an increase in information, then it is a change in the right direction (which is what makes this example almost unique; most are in the wrong direction). But the direction in this case is not the issue. The issue is the source of that information: a naturalistic process (which is the only one that evolution admits), or a designed mechanism.
Philip J. Raymentdiscuss 14:15, 23 October 2011 (UTC)
Does the plasmid, whether or not it was designed, operate according to naturalistic processes? The information on nylonase was not present before the plasmid did its thing, but it was present afterword. Why do you refer to the hypothetical designer of the plasmid as the source of the information, rather than the naturalistic processes taking place in the plasmid? To determine what the source of the nylonase information is, is it necessary to know how the plasmid came to be? --Awc 17:35, 23 October 2011 (UTC)
I hope I have not said that there was no increase in information. As a matter of fact, back around here you said something very close to that. Interpreting some comments of yours, I had written,
It looks like we agree on this statement:
Given the genetic mechanisms that exist in living organisms, mutations can result in an increase in genetic information. Such increases in information have been observed to occur in a number of cases, such as the seasonal variations in flu viruses, and bacteria that become immune to penicillin or develop the ability to metabolize new substances.
You answered,
Errr, no. Where is the evidence that seasonal variation in flu viruses is an increase in information? And creationists have already argued that resistance to penicillin is a decrease in information. So given this lack of observation, where is the evidence that mutations can result in an increase in genetic information? ... Whether or not there has been an increase in genetic information depends on in what way the information is changed rather than how it was changed. For example, it does not matter how a letter in a word is changed; what matters is what the new word is (or whether it produces gibberish).
I would also interpret your last sentence to mean that it does not matter whether plasmids are designed or have involved. If they find a new sequence that produces nylonase, then they have created information.
--Awc 07:02, 24 October 2011 (UTC)
Does the plasmid, whether or not it was designed, operate according to naturalistic processes? It operates according to designed processes.
Why do you refer to the hypothetical designer of the plasmid as the source of the information, rather than the naturalistic processes taking place in the plasmid? Because the (non-hypothetical) designer designed the processes.
To determine what the source of the nylonase information is, is it necessary to know how the plasmid came to be? If the source is related to the origin, then yes.
As a matter of fact, back around here you said something very close to that. Yes, it was close to that. But it wasn't that. The rule is that mutations are unable to produce new information, and that is what I was getting at in my earlier reply that you quote. However, this rule probably does have very rare an trivial exceptions (which of course don't invalidate the rule), and the nylon bug may be one of those rare exceptions, although even that is not certain. Note that in my reply you quote, I reply to two of the three examples you provided: flu variations and bacterial immunity to penicillin. I did not actually disagree with your example of metabolising new substances, as the nylon bug may be one such exception.
I would also interpret your last sentence to mean that it does not matter whether plasmids are designed or have involved. If they find a new sequence that produces nylonase, then they have created information. That is correct in principle (without further commenting on the specific example). If mutations produce a new ability, function, etc., then they have created information. The problem is that random copying mistakes don't create information, just as an explosion in a printing works won't create a book (or even a paragraph) (again, that's the rule, there may be very minor trivial exceptions).
Philip J. Raymentdiscuss 02:50, 1 November 2011 (UTC)
I didn't know you use the word "naturalistic" to refer to the origin of a process. Do we agree that the plasmid, once it is assembled, operates according to the laws of nature, without supernatural interference? Do we agree that the increase of genetic information (assuming there is some) occurs during the time that the plasmid is operating without supernatural interference?
Why are you so hesitant to say that nylonase is an increase in genetic information? Except for the fact that we can be wrong about anything, is there anything pointing to that not being the case? Why do you refer to the acquisition of the ability to digest an entirely new substrate as "trivial"?
—Awc 10:23, 1 November 2011 (UTC)
Why shouldn't the word "naturalistic" be used to refer to origins? (It's not limited to origins, though.)
You weren't just saying "naturalistic origins". You were saying whether a process should be called "naturalistic" or not depends not just on the process itself, but on the origin of that process. If everything in the natural world originated from God, then, with your usage of the term, there are no naturalistic processes at all, making the term completely superfluous. Martin made the same point in the previous section. You replied to him, Not accepting that a third option can occur does not mean that there is no potential third option which, if it occurred, would show the axiom to be wrong. Since we are having trouble understanding how you are using the King's English, this might be a good time for you to give us an example of how it could in principle be shown that a process is naturalistic, not only in its mode of action, but also in its origin. —Awc 16:43, 4 December 2011 (UTC)
Yes, a plasmid, once assembled, normally operates according to the laws of nature. (That is, I'm not saying that God would never interfere, but that would be the rare exception.)
Do we agree that the increase of genetic information (assuming there is some) occurs during the time that the plasmid is operating without supernatural interference? This question is loaded, so of course I agree. It (correctly) assumes my answer to the previous question, so is asking if I agree that increases that occur after the plasmid is assembled occur during the time that there is no supernatural interference, which is the time after the plasmid is assembled.
I wasn't trying to ask a loaded question, I was trying to understand exactly what you are saying, because you seem to be using some terms in a different way than I would expect them to be used. This is important because the argument for creation only talks about whether increases in information can be observed in mutations (possibly coupled with natural selection) occurring in organisms today, not what the ultimate source of life is. Do we need to add another stipulation to the argument? —Awc 17:01, 4 December 2011 (UTC)
I'm hesitant to say that the ability to digest nylon is an increase in genetic information because it's not clear that it is. The ability may be entirely new, and the material that is digested may be entirely new, but was the information that allowed that entirely new? And if it was, was it any more than a trivial change (in information)? To make use of an analogy, a machine for pulping timber might also be used to crush aluminium by the addition of some differently-shaped "teeth". So the material (aluminium) is quite different, the "ability" (to "digest" aluminium) is new, but is the change to the machine—which didn't require any new mechanism, motor, power supply, feed chute, etc.—more than a trivial one? I'm not trying to say that bacterial ability to digest nylon is analogous to this machine; I'm just pointing out that a "new" ability may be due to a trivial change.
Here you are also introducing new language to the argument that totally negates its effectiveness. was the information that allowed that entirely new? Of course any step in an evolutionary proces will build on what's already there so the information introduced will not be entirely new. The argument for creation requires no new information being introduced, not just no entirely new information being introduced. was it any more than a trivial change (in information)? The argument for creation depends on all changes being in the wrong direction. If you admit "trivial" changes in the right direction, then you have to also show that "trivial" times "billions of years" is still not enough. That job is a lot harder and hasn't been attempted, as far as I know. —Awc 17:12, 4 December 2011 (UTC)
Philip J. Raymentdiscuss 06:39, 4 December 2011 (UTC)
You weren't just saying "naturalistic origins". You were saying whether a process should be called "naturalistic" or not depends not just on the process itself, but on the origin of that process. The question is equivalent to asking, was the process designed? If it was designed, then that explains how the process came into being (originated).
If everything in the natural world originated from God, then, with your usage of the term, there are no naturalistic processes at all, making the term completely superfluous. It is superfluous in a non-naturalistic worldview, but of course not everyone holds such a worldview, which is why the term is used—to distinguish naturalistic from non-naturalistic worldviews.
If you only used the term to modify "worldview", that would be a consistent uasage and I could use that key to try to decipher your arguments. Unfortunately, near the beginning of this section you used the term "naturalistic process" several times, for example,
  • My point is that they occur only as the result of a mind, not from naturalistic processes, and in the case of the nylonase, that this was the result of an intelligently-designed process, not a naturalistic one.
  • The issue is the source of that information: a naturalistic process (which is the only one that evolution admits), or a designed mechanism.
I can't figure out how to interpret these statements in light of your new "worldview" usage. In another edit you made today below in #Richard Dawkins, you wrote
  • If evolutionists could provide examples of genetic information being formed naturalistically, then they would be quick to cite them.
This is equally inconsistent with your new statement. It would make sense if you used "naturalistic" like everybody else does to mean "following the laws of nature, without supernatural intervention". If you can't use a term in the common way, can you at least use it consistently? Or else don't use it at all. —Awc 08:19, 5 December 2011 (UTC)
Since we are having trouble understanding how you are using the King's English... It's been the Queen's English for about the last 60 years!
The last British monarch we yanks had any dealing with was George III. —Awc 08:30, 5 December 2011 (UTC)
...give us an example of how it could in principle be shown that a process is naturalistic, not only in its mode of action, but also in its origin. This is the same question as that of determining if something is designed: does it have the characteristics of design, such as specified complexity. Is it the sort of process that a designer would produce, or the sort of process that can be explained without reference to a designer? For example, the genetic code has automated error correction, storage of data within folders and sub-folders, and other such design features used in software.
Where's the example of a process, which, if it occurred, would show creationism to be wrong? —Awc 12:34, 5 December 2011 (UTC)
I wasn't trying to ask a loaded question... No, I didn't think that was the intention.
...the argument for creation only talks about whether increases in information can be observed in mutations (possibly coupled with natural selection) occurring in organisms today, not what the ultimate source of life is. I don't know what you are talking about. Creationists often talk about the origin of life as being something that God did.
What I'm talking about is not arguments for creationism in general, only the one in the context of this article. To make that abundantly clear I even linked the phrase to Genetic_information#The_argument_for_creation. —Awc 13:33, 5 December 2011 (UTC)
Of course any step in an evolutionary proces will build on what's already there so the information introduced will not be entirely new. That's the story, but it doesn't work that way. Yes, the information as a whole will not be entirely new. And even if evolution could produce a wing where only a limb existed before, then it will make use of some existing code; the wings are still composed of bones, flesh, skin, muscles, and tendons, for example. And even the code for feathers (a new feature) will likely use some existing code, such as for binding cells together. But to extrapolate from that to claim that a creature can go from having no wings to having wings entirely through steps so small that each constitutes either no new information or an amount so small as to be negligible is a claim of evolution that simply doesn't stand scrutiny. It's like claiming that a fridge can be turned into an aeroplane by changing one component at a time, without (a) having the final goal in mind, and (b) with each stage being not only viable but "fitter" than the previous stage. That's an extraordinarily ambitious claim, one that has not been demonstrated to be true, and one that is extremely unlikely. Rather, we know from experience that aeroplanes are designed by intelligent beings as aeroplanes.
To go from a limb to a wing requires a whole host of interrelated changes (the creation of feathers, the changes in the brain to control flight, rearrangements of muscles to operate the feathers for flight, changing the structure of bones to make them lighter, and so on). These are not trivial changes, either in the information required or the result. Rather, "entirely" new information is required, i.e. information that didn't exist before. Now my example of changing a limb to a wing may be an unusually large change, and you could probably cite much smaller changes. But the other side of the coin is that the interrelated changes I've mentioned are just broad overviews of the related changes; what detailed changes are actually required for each of them? The point is that any significant change is going to require a whole host of new information, not just a trivial amount. I know, evolution claims that it can get there with trivial changes. And of course trivial changes, such as the ability to digest nylon have been observed. But large changes (i.e. those requiring changes to a whole host of interrelated systems) have not been observed, and these are qualitatively different to those trivial changes.
The argument for creation requires no new information being introduced, not just no entirely new information being introduced. Not entirely true. The argument for evolution requires huge amounts of new information being created. The creation model doesn't require that no new information is introduced, but does predict that virtually no new information will be introduced. And, what you may be getting at, no information being produced does make a very good argument for creation. But a trivial amount does not falsify the creation model. However, the lack of more than a trivial amount does falsify the evolutionary story. (And, as anti-creationists so love to point out, evidence of lots of new information arising through evolutionary processes would not disprove God, although it would make Him appear to be superfluous.)
The argument for creation depends on all changes being in the wrong direction. Not entirely true, for the reason just explained. Further, as also just explained, a trivial amount does not falsify the creation argument.
If you admit "trivial" changes in the right direction, then you have to also show that "trivial" times "billions of years" is still not enough. That job is a lot harder and hasn't been attempted, as far as I know. On the contrary, I have mentioned it before. "Trivial" times "billions of years" is not enough when the trivial amount is swamped by the information-losing changes. Just like a child losing money on every sale from his roadside stand except a few where he made a small profit, you can't say that at the end of the day those few exceptions means that overall he made a profit—the losses swamped the gains. Where this analogy could fall down is if the losses could somehow be isolated and eliminated, such as by the parent bearing the losses but letting his child keep the profits. With evolution, the claim is that natural selection will eliminate the losses and keep the gains, but natural selection is not up to the task of locating and isolating the rare trivial gains and eliminating (all but) every last loss. For one thing, natural selection selects individuals, not genes, and that means selecting all the losses along with the odd gain that might be in that individual.
Philip J. Raymentdiscuss 01:47, 5 December 2011 (UTC)
That's not the song you were singing over at Talk:Irreducible complexity. I wrote The creationist has to argue that all of the astronomical number of paths from one system to the next are implausible, to which you replied (with a nod to Wieland's trains), In order to go from A to B there may be multiple (an almost infinite number of) paths, but if I show that A is actually moving away from B, then that eliminates all the paths that are going towards B, in one fell swoop. There are many arguments for creationism. There is the argument that life exhibits irreducible complexity. There is the argument that harmful mutations must swamp beneficial ones. And there is the argument that all observed mutations are of the "wrong kind". It is only the last argument that is relevant to this article. And the observation of the production of even very small amounts of information negates that argument.
But large changes (i.e. those requiring changes to a whole host of interrelated systems) have not been observed, and these are qualitatively different to those trivial changes. If such large changes had been observed, it would be very uncomfortable for evolutionists. Evolution predicts that "changes to a whole host of interrelated systems" will not occur simultaneously, so their absence is evidence for evolution (except that it could also be considered a prediction of creationism).
—Awc 13:33, 5 December 2011 (UTC)
This is equally inconsistent with your new statement. It would make sense if you used "naturalistic" like everybody else does to mean "following the laws of nature, without supernatural intervention". I don't believe that I'm using it inconsistently. I don't completely agree with your definition, though, so let's clarify that.
The Merriam-Webster dictionary describes "naturalistic" as "of, characterized by, or according with naturalism", and "naturalism" as "a theory denying that an event or object has a supernatural significance; specifically : the doctrine that scientific laws are adequate to account for all phenomena". Wikipedia says that "Naturalism commonly refers to the viewpoint that laws of nature (as opposed to supernatural ones) operate in the universe, and that nothing exists beyond the natural universe or, if it does, it does not affect the natural universe. Followers of naturalism (naturalists) assert that natural laws are the rules that govern the structure and behavior of the natural universe, that the universe is a product of these laws."
So it's a bit bigger than your definition, which could apply to individual cases whilst leaving untouched claims that the supernatural could be an explanation elsewhere. Having said that, though, I'm not sure that it really changes anything. A naturalistic worldview is one which denies the involvement of the supernatural. A naturalistic process is one that denies the involvement of the supernatural. That's using it in exactly the same way.
Where's the example of a process, which, if it occurred, would show creationism to be wrong? I don't think any one example would show creationism as a whole to be wrong, but a common process that generated reasonable amounts of new genetic information would show that a major claim of creationism is wrong.
What I'm talking about is not arguments for creationism in general, only the one in the context of this article. To make that abundantly clear I even linked the phrase to Genetic_information#The_argument_for_creation. And I wasn't talking about arguments for creation in general either. I mentioned the origin of life because the origin of life requires the origin of genetic information.
That's not the song you were singing over at Talk:Irreducible complexity. It's consistent with it. Continue with those trains. If they are going in the wrong direction, then you will never get there. But even a train might roll backwards a tiny bit before accelerating forwards. That small roll backwards makes no real difference.
And there is the argument that all observed mutations are of the "wrong kind". It is only the last argument that is relevant to this article. And the observation of the production of even very small amounts of information negates that argument. No, it doesn't negate it. All it does is qualify it. Trivial exceptions to a rule do not negate the rule.
If such large changes had been observed, it would be very uncomfortable for evolutionists. Evolution predicts that "changes to a whole host of interrelated systems" will not occur simultaneously, so their absence is evidence for evolution (except that it could also be considered a prediction of creationism). I don't agree. I agree that if large changes were observed, it would be uncomfortable for scientists, because it would call, say, much of genetics into question. But evolutionists per se should not have a problem. Further, such changes are, in effect claimed by evolution. If you have a number of parts that work together in a co-ordinated way, how do you change any one without (a) simultaneously changing others, or (b) having an interim stage in which the co-ordinated system is less fit? Evolution won't allow for the latter, leaving only the former as a possibility.
And I'll put it another way. If scientists found evidence that you can get those "large" changes, would that mean that evolution is dead? Or would it simply be one more thing to incorporate into evolution and to use as an argument against creation? I don't believe that it would be "very uncomfortable for evolutionists" at all.
Philip J. Raymentdiscuss 04:39, 21 April 2012 (UTC)

lock and pin analogy

I don't want to distract from some other threads that might be more important, but I happened to notice an old post that I didn't understand. In response to me, Philip wrote

Suddenly, it [a flu virus] invents a new protein that the hosts don't recognize because it has never existed before. ... That meets all my criteria for new information. Where does it fail yours? That's like a lock that loses one of its pins, or perhaps an accretion on a pin changes its length. There is no new function, no new complexity, no new information, just a lock that the key doesn't fit any more.

What I'd like to know is this. If I tell you, "The new code to open the door is 1729", does that message contain information? (Incidently, we had to change the combination because somebody happened to guess the right number and was breaking in all the time.)
--Awc 07:19, 24 October 2011 (UTC)

Now that I've gotten started, I have another question. If I create a string of a million bits with a random process, then presumably that would be complex but not specified. If I then set the password on my computer to that string, every bit becomes important for me to get into my account. Has the string acquired specified complexity? --Awc 09:09, 24 October 2011 (UTC)

If I tell you, "The new code to open the door is 1729", does that message contain information? Yes, it tells you something—what the code is to open the lock.
And the information is new. It didn't exist anywhere until I changed the lock. Just like the virus changing its coat. —Awc 10:27, 1 November 2011 (UTC)
Has the string acquired specified complexity? I would say yes, as you now have to specify a particular string instead of it being random. (I don't think you'd find too many computers that would accept passwords that long, though!).
Philip J. Raymentdiscuss 02:56, 1 November 2011 (UTC)
And the information is new. It didn't exist anywhere until I changed the lock. Just like the virus changing its coat. The information is new, but it came from an intelligence (you). Your new information provided an ability (to open the lock), unlike the virus which I've already explained is like a lock that can no longer be opened.
From the point of view of my security guards, the ability provided by the new combination is keeping the burglars out.
I could choose a new combination by rolling dice and set it up so no one knows what the new number is. Then my system, operating without intelligent intervention, has produced new information. If you want to consider the question of how a third party could figure out that that system was designed and not the result of natural processes, that is a different question.
Look, this is fun and everything, but it isn't getting us anywhere. Didn't we agree to try to keep away from the analogies and discuss real biological systems instead?
—Awc 14:00, 5 December 2011 (UTC)
There was an assumption in your question about the code for the door: that 1729 is the only number which will open the lock. So it's one out of 10,000 possible numbers (assuming that only 4-digit numbers are accepted). The odds of getting the right number by chance are one in 10,000. The odds of getting the wrong number by chance are 9,999 in 10,000. So chance can easily produce a wrong number, but not the right number, for which intelligence is needed. If the lock will accept two or three different numbers, it changes the figures slightly but not the principle. To change the principle, the lock would have to accept, say, 5,000 different numbers, which means that it would be rather useless as a lock.
The virus inventing a new protein that the host doesn't recognise is like getting the wrong number for a lock; many different outcomes produce the same result. A virus inventing a specific new protein, i.e. one that gives an ability that (almost) no other protein would provide, would be a better analogy to the correct combination of a lock.
Philip J. Raymentdiscuss 06:51, 4 December 2011 (UTC)
I could choose a new combination by rolling dice and set it up so no one knows what the new number is. Then my system, operating without intelligent intervention, has produced new information. Incorrect. Your description includes intelligent intervention. I'll illustrate with another analogy.
I hope you agree that language conveys information (I'm using language now to convey information to you, as you use language to convey information to me). But what is language? It's a set of symbols that have agreed-upon meanings. Why does the word "dirt" refer to that combination of minerals in small grains that lie all over the ground? Simply because humans have agreed that the word "dirt" shall mean that. In some cases, words are imitations of reality, such as "quack". (The name for such words is "onomatopoeia".) In other cases, the words are derived from other words. For example, the modern word "computer" means an electronic machine for doing calculations, running programs, etc. It is derived from the idea of computing, which word long predated the modern electronic computer. Some words are created by combining other words, such as "brunch" from "breakfast" and "lunch". What makes a word is not how it was created, but that it has an agreed-upon meaning. That is, if you use the word, someone else will understand it.
Okay, so back to the lock. You generated the password through a random process, but then you, an intelligent being using your intelligence, programmed that password into the lock, in effect creating an agreed-upon "meaning" for the randomly-generated numbers (in this case, agreed between you and the lock). Until you did that, no new information could be said to exist. Rolling the dice generated the numbers. You deciding to use those numbers as your password and programming it into the lock was what turned those numbers into information.
Didn't we agree to try to keep away from the analogies and discuss real biological systems instead? I don't believe so.
Philip J. Raymentdiscuss 05:00, 21 April 2012 (UTC)

DNA like a computer program

lets examine this further.

a computer program can be compiled or interpreted
  • a compiled program does not referance any external codes to perform its function, thats not descriptive of dna
  • an interpreted program requires an interpreter to take the high level instruction and turn it into low level code the machine executing it understands, thats not much like dna either.
  • a program may contain data tables or it can open and read an external data table. DNA seems to be an external data table in that it is opened and read by mechanisms outside itself.
  • some descriptions I have read say dna is more like a template in that mechanisms of the cell build on a dna strand by an almost trial and error method of fitting the required amino-acids(?)
can we kill the concept that dna is a computer program of much greater complexity than windows and accept that dna in itself is a storage block of data that is used by other cellular mechanisms ?
corrections welcome Hamster 15:58, 27 October 2011 (UTC)
I would consider DNA to be more like a compiled program. All analogies are imperfect, and certainly there are differences between computer programs and DNA. But as you point out, there is no one type of computer program anyway, but this doesn't change the fact that the genetic code and computer software are similar in quite a few ways.
a compiled program does not referance any external codes to perform its function, thats not descriptive of dna How is it not?
a program may contain data tables or it can open and read an external data table. DNA seems to be an external data table in that it is opened and read by mechanisms outside itself. I disagree. A computer program usually exists in the form of a file that the operating system opens and reads, and the processor performs actions based on what it reads. DNA is opened and read, and actions are performed based on what it reads.
can we kill the concept that dna is a computer program of much greater complexity than windows and accept that dna in itself is a storage block of data that is used by other cellular mechanisms ? No, we can't. For one thing, various other authorities (such as ones I've quoted above) describe the genetic code as being like software. For another, DNA doesn't appear to be a storage block of data any more than an executable computer file is also a storage block of data used by the operating system and processor.
Philip J. Raymentdiscuss 23:07, 29 October 2011 (UTC)
yes there are 3 types of computer program , compiled to machine code, compiled to an microcode. a machine code program does not require an operating system.
but the actions performed are not dictated entirely by the dna codes. What of the other cellular processes that do that decision making ?
For one thing, various other authorities so arguement from authority.
what part of dna is executable code in itself and what is data that tells the interpreter what to do ? do you understand the difference ?
illustration time: a factory has a machine that takes parts from a number of bins and places them onto the workpiece. The machine reads a paper tape containing codes for each part and a code that says start here and end here, There may be codes that say repeat the last instruction x times. Lets say .......|start|act|ggc|tat|repeat 5|cta|stop|.........................
explain why this code is executable program code and not a data table .
Hamster 23:31, 29 October 2011 (UTC)
yes there are 3 types of computer program , compiled to machine code, compiled to an microcode. That's two! :-) Sure, you can classify them in that way (with the third presumably being interpreted), but you can all classify them in other ways, and break those categories down further. Programs for Android mobile telephones (I got one recently!) for example compile to a bytecode (what you refer to as microcode; see below). But you also have some that are fully interpreted, and ones that sort of semi-compile to a sort of half-way bytecode (VBA is an example, I believe). So there are not necessarily three forms; it depends on how you want to group them. Not that any of this is relevant to the discussion, though.
There is one other point to make, though, although it's a matter of terminology and perhaps there's no definite right and wrong here, but what I believe you are referring to is bytecode, intermediate code, or P-code, not microcode, which I'll come back to below.
microcode is what IBM call it and thats what I learned it as. Other companies call it something else and there are differences in implementations that do not affect this discussion. Hamster 05:06, 30 October 2011 (UTC)
a machine code program does not require an operating system. Then you could break compiled programs down further: those that require an operating system, and those that don't. The vast majority of compiled programs are designed to make use of an operating system. And apart from embedded control systems, virtually all the rest would still use external code, in the BIOS.
no fully compiled program requires an operating system. They may use the library of operating system functions but that is not required Hamster 05:06, 30 October 2011 (UTC)
but the actions performed are not dictated entirely by the dna codes. What of the other cellular processes that do that decision making ? I'm not sure what you are getting at here. With a compiled computer program, you could also argue that the actions are not dictated entirely by the software. Most computer programs respond to external input, whether that be from a human, monitoring equipment, or whatever. Also, I have never claimed that the DNA is the sole source of information in living things.
you say DNA is program code, that is executable instructions. I am pointing out that other cellular processes read the dna and perform actions. What executable code does dna perform Hamster 05:06, 30 October 2011 (UTC)
so arguement from authority. Do you know what an argument from authority is? A fallacious argument from authority, which I assume you are referring to, is an argument based on the authority of someone who is not an authority in that area. Such as an argument about the origins of the planet from a scientist who is an authority on what happens in the present, not an authority on history, of what happened in the past.
and ?
what part of dna is executable code in itself and what is data that tells the interpreter what to do ? do you understand the difference ? I have to wonder if you know the difference. No computer program is executable code in itself. It is executed by the microprocessor, which reads the values in memory and acts on them accordingly. So if an Intel processor encounters the byte value 50 in hexadecimal, it might treat it as the letter "P" if it's considered to be in a string, as the decimal value 80, or as the instruction to push the content of the AX register onto the stack (among other possibilities). You could go so far as to say that the value is interpreted by the processor (although, of course, using "interpreted" in a different sense to how you and I used it above). In fact, modern processors don't have the instructions (such as PUSH AX) hard-wired into the processor, but instead the microprocessor is itself running a microcode (that's what that word means) program that interprets hexadecimal 50 as PUSH AX.
yes you can embed data into a program, but that data is not executable code. If you pass "Philip" to the processor buffer, what do you think will happen ? the program executes commands to set a pointer to the data , and its length and tells the processor what to do with it. The data "philip" is never passed to the processor for execution. Hamster 05:06, 30 October 2011 (UTC)
explain why this code is executable program code and not a data table . It depends on how you look at it. In one sense it is a data table, but in another it's executable code. How, in principle, is the machine reading the paper tape and performing actions based on what it reads, any different to a processor reading an executable file (e.g. an .exe file in DOS or Windows) and performing actions based on what it reads?
Philip J. Raymentdiscuss 04:31, 30 October 2011 (UTC)
It depends on how you look at it no it does not, there is a very clear difference between executable program code and data.
How, in principle, is the machine reading the paper tape and performing actions based on what it reads, any different to a processor reading an executable file (e.g. an .exe file in DOS or Windows) and performing actions based on what it reads? I believe that was my question to you. Since you ask, the paper tape in my example is a data file, not an executable program. I will call the paper tape DNA1. When the assembly robot detects the tape inserted it reads the tape until it finds a start code, that reading is by a program resident in the robot, not in the dna1 file. The robot then reads data from the tape until it hits a stop code where it stops. The assembly is complete and the tape is ejected. One machine in the factory has used its own program to read the dna1 data file and assemble the parts according to the data received.
I am sorry if the word microcode caused confusion. Wether its microcode, p-code- or something else the concept is compiled code that does not run directly on the processor. So there are still 3 broad type of program code, compiled, complied but needing a code later before machine code and interpreted. Those 3 types are fairly important to get a reasonable illustration that has some actual relevance to what happens in the cell. Hamster 05:06, 30 October 2011 (UTC)
microcode is what IBM call it and thats what I learned it as. Okay. I did hint that different people may use the word differently.
no fully compiled program requires an operating system. They may use the library of operating system functions but that is not required Nonsense. 99.99% of compiled programs require an operating system because they are designed on that basis. What you mean is that it's possible to create a fully-compiled program that doesn't need an operating system. I do agree with that, but that's very rarely done.
you say DNA is program code, that is executable instructions. I am pointing out that other cellular processes read the dna and perform actions. And I pointed out that that is what happens with computer programs.
and ? And this means that I was not using a fallacious argument from authority.
yes you can embed data into a program, but that data is not executable code. That depends on your definition. If a program has the code LOAD AX, 54, is the value loaded into the AX register data? I would say that it is, and I guess you would too. Does that mean that it's not part of the executable code? It's not in a separate data segment; it's part of the instruction. I'm not arguing one way or the other; I'm merely pointing out that it depends on how you look at it. As the instruction pointer advances, both the instruction (LOAD AX) and the value (54) are read. The instruction part tells the processor to treat the next part as a value, but there's nothing else there saying "this part is code" and "this part is data". Indeed, a "frameshift" could have the processor reading and trying to execute the "54". The memory values themselves don't do anything; they are simply read by the processor which acts on them. You seem to be trying to make a distinction that doesn't exist: that the instruction parts themselves are self-activating rather than simply being read and acted on by the processor.
no it does not, there is a very clear difference between executable program code and data. Not there is not. Both look largely identical, and in principle the processor could try and execute data. Of course the results would be nonsense, but in theory it's possible. Think of it this way: what if the program wrote code for another program? Is the resulting executable file data or executable code? While the first program writes it, it's data. When the second program is running, it's executable code. Of course, I'm ignoring modern processors which do define data and code segments and don't allow the data in the data segments to be "run". But that just reinforces my point: the difference is not inherent, but one of declaration: this bit is declared to be data, and another is declared to be code. (Of course, data that is not designed to be code won't work.)
I believe that was my question to you. Yes, it was, but you were asking why something you were calling data was not data, but executable code. I'm not recognising that distinction which you were making, so I asked you to justify your distinction.
Since you ask, the paper tape in my example is a data file, not an executable program. Apart from your subsequent description of how it works, this is your only explanation: you simply assert it to be so. You haven't actually explained how they are different.
When the assembly robot detects the tape inserted it reads the tape until it finds a start code, that reading is by a program resident in the robot, not in the dna1 file. The robot then reads data from the tape until it hits a stop code where it stops. The assembly is complete and the tape is ejected. One machine in the factory has used its own program to read the dna1 data file and assemble the parts according to the data received. So here's your description only slightly reworded to show that the same is true of computer code. The onus is on you to point out a relevant difference.
When the computer detects the tape inserted it reads the tape until it finds a start code, that reading is by a processor resident in the computer, not in the dna1 file. The computer then reads data from the tape until it hits a stop code where it stops. The assembly is complete and the tape is ejected. One computer in the factory has used its own processor to read the dna1 data file and assemble the parts according to the data received.
Here's another way of looking at it. Does DNA produce anything by itself, rather than requiring the biological machinery of the cell to read the program? No, it doesn't. But does the computer program do anything by itself, rather than requiring the electronic machinery of the microprocessor? No, it doesn't either.
Also, although I said that I think the genetic code is most like a compiled program, I don't think that point is important. So what if a program requires another program to read it and execute it? It's still a computer program, and the instructions, whether directly controlling the actions of a microprocessor or indirectly controlling the actions of a microprocessor through the intermediary of an interpreter, are still instructions.
I am sorry if the word microcode caused confusion. It didn't. I understood from the context what you meant, and it was only after having written most of my reply that I realised that you had used the "wrong" word, and I had to go back and amend what I had already written.
So there are still 3 broad type of program code... And it still depends on how you want to categorise them. You could say that there are two types: the ones that run directly on the processor and the ones that don't. But such distinctions are somewhat arbitrary and not relevant here.
Those 3 types are fairly important to get a reasonable illustration that has some actual relevance to what happens in the cell. I agree that it's helpful to get the closest analogy. But the fact that there are compiled programs, programs compiled to intermediate code, semi-compiled programs, and interpreted programs just goes to show that there are different approaches to doing the same thing, there may not be an exact equivalent to the genetic code. For example, how many computer programs do you know of that make use of a frame shift to re-use the same code in two different ways? It's essentially not possible with compiled or interpreted code, but it is possible (albeit difficult) with assembled code (there's one you didn't mention!) My first computer's BASIC interpreter had a bit of code like this, but with memory being cheap these days, I doubt that's it's done very much at all. But it's common in DNA, some of which is read with different frame shifts and in both directions. So if you are looking for differences, there's one. But differences like that don't change the similarities.
Philip J. Raymentdiscuss 10:27, 30 October 2011 (UTC)
the point that I am trying to get you to understand is that arguing in analogies is a complete waste of time if we are using different definitions, and that you assert that dna is a computer program without showing what parts are executable code and which parts are data.
I propose that no part of dna is executable code. That it is the other cell mechanisms that initiate reading of dna , and assemble the parts specified.
I didnt mention assembler because it isnt relevant. Any compiled code is machine code or microcode or both. Thats what a compiler does.
I know of many computer programs in commercial use that have multiple definitions for a DATA file.
I also dont know that dna is ever read backwatds. I know in one process the dna strand is unzipped into two strands, one is read diretly forward , and the other is chopped into pieces, read and then reassembled.
The part I object to is the claim that dna is a program of binary code of such complexity that its a billion times more complex than windows. I have seen no published papers that prove this assertion. I have seen several very bad attempts.
the difference between compiled code , microcode and interpreted code and a data file is what mechanisms you would expect to see involved when executing the program. compiled code runs directly on the processor and you need a minor loader to move it there, microcode requires a translation layer, interpreted code requires an interpreter and data needs a program to read it. Any claim should be able to map those functions to cellular processes. As soon as you say "like" as in dna is like a program you are into fairly meaningless analogies as "a raven is like a writing desk", worthless for a meaningful discussion of dna and cell processes in biology
Hamster 15:43, 30 October 2011 (UTC)
I'm not qualified to speak to the computer program issues, but please remember that the genome in isolation does not allow you to model the organism de novo; it only allows you to model the organism if you already have a model of the parent organism and it's environment. Of course, you can't model the parent without having a model of it's parent, and so on ad infinitum. --Martin Arrowsmith 21:27, 30 October 2011 (UTC)
...you assert that dna is a computer program without showing what parts are executable code and which parts are data. It's not just me who asserts it; I've cited others (including non-creationists) making the same claim.
I propose that no part of dna is executable code. That it is the other cell mechanisms that initiate reading of dna , and assemble the parts specified. Yes, you've said that before. But you haven't explained how that is different to a computer which initiates reading of computer code, and performs actions accordingly.
I didnt mention assembler because it isnt relevant. And I wasn't trying to make a serious point about that.
I know of many computer programs in commercial use that have multiple definitions for a DATA file. I don't know what you are getting at here.
I also dont know that dna is ever read backwatds. It is. See Genetic information#Complexity.
The only source cited there is a quote from Sanford, a geneticist who is also an advocate of intelligent design. He apparently cites peer-reviewed articles, but the bibliographic information is incomplete. I would like to know if his evaluation is a consensus among geneticists, or if Sanford is expressing a minority opinion. —Awc 08:47, 1 November 2011 (UTC)
The part I object to is the claim that dna is a program of binary code of such complexity that its a billion times more complex than windows. Who made such a claim that put a specific figure on it? I certainly didn't.
As soon as you say "like" as in dna is like a program you are into fairly meaningless analogies as "a raven is like a writing desk", worthless for a meaningful discussion of dna and cell processes in biology That's a straw-man argument, because the claim was never simply "DNA is like a computer program"; there were always more details of how it was like a computer program.
...the genome in isolation does not allow you to model the organism de novo... And a computer program requires the right computer, so there is similarity here.
Philip J. Raymentdiscuss 03:22, 1 November 2011 (UTC)
since you (philip) dont seem to be able to comprehend the difference between executable code and data tables I am out of this section. The fact is that the dna code fits on an 800 mb cd disk using a miminal compression rate. None of the "how its like a computer program" makes no sense whatever since they never state what bitss of dna are data , which is program code, what cellular component is the cpu analog etc. Hamster 03:42, 1 November 2011 (UTC)
since you (philip) dont seem to be able to comprehend the difference between executable code and data tables I am out of this section. Given that I've already given an example of the difference, it seems instead that you simply have no answer to my argument.
The fact is that the dna code fits on an 800 mb cd disk using a miminal compression rate. The fact is that this fact is completely irrelevant to this discussion.
None of the "how its like a computer program" makes no sense whatever since they never state what bitss of dna are data... On the contrary, it is you who hasn't explained how that invalidates the analogy.
Philip J. Raymentdiscuss 05:09, 1 November 2011 (UTC)
The only source cited there is a quote from Sanford, a geneticist who is also an advocate of intelligent design. Actually the cited source is Sanford, an evolutionist geneticist who became a creationist (not just an ID proponent) because of the genetic evidence.
...the bibliographic information is incomplete. In the quote, Sanford cites "Trifonov (1989)". In his book, the reference section gives this as "Trifonov, E.N. 1989. Multiple codes of nucleotide sequences. Bull. of Mathematical Biology 51: 417-432."
Philip J. Raymentdiscuss 07:06, 4 December 2011 (UTC)
Trifonov is available online here. I don't have time to read it right now. I'm still hoping for an answer to the question of whether his evaluation is a consensus among geneticists, or if Sanford is expressing a minority opinion. —Awc 13:46, 5 December 2011 (UTC)
The existence of multiple codes appears uncontroversial:
  • "In an earlier posting, I promised to provide an overview of alternative codes in DNA. Such examples include alternative splicing and alternative reading frames (ARFs) which I will discuss here" —Panda's Thumb
  • "Trifonov unveiled multiple novel codes in the biological sequences as well as modular structure of proteins. … The codes can overlap each other so that up to 4 different codes can be identified in one DNA sequence (specifically a sequence involved in a nucleosome). According to Trifonov, other codes are yet to be discovered." Wikipedia
Philip J. Raymentdiscuss 05:22, 21 April 2012 (UTC)

Bird construction analogy

trying to reduce size of more specific discussions

again Philip this is an english analogy that does not represent the way dna work in biology therefore it is useless except a an example of english.
my understanding is that dna specifies an overall body plan (say 4 limbs, head tail, insegmented body) and then applies modifiers to specify if a body part is to be a leg, arm, quadruped or biped, then modifiers to say skin, scales or feathers and so forth.
could someone confirm or reject this understanding ? Hamster 16:09, 27 October 2011 (UTC)
...this is an english analogy that does not represent the way dna work in biology therefore it is useless except a an example of english. Because...? Your only justification for this claim starts with my understanding is and ends with could someone confirm or reject this understanding ? In other words, you reject the analogy with speculation.
my understanding is that dna specifies an overall body plan (say 4 limbs, head tail, insegmented body) and then applies modifiers to specify if a body part is to be a leg, arm, quadruped or biped, then modifiers to say skin, scales or feathers and so forth. How is that contradictory to my example? My example was stated to be (very) simplified, and all you've done is add a bit of detail.
Philip J. Raymentdiscuss 23:21, 29 October 2011 (UTC)
these are very simplified instructions, for building a bird.,Build a body with a light structure and flow-through lungs., Add a head., Add two legs., Add two wings., Add feathers.
my point was rhat my understanding of biology is that that is NOT the way an animal is specified. Do you not see that my outline is very different to yours ? I was hoping sterile or awc or martin would comment first. Hamster 23:38, 29 October 2011 (UTC)
No, I don't see that it's very different at all. The main point of my example was that it is a series of instructions. For example, I was never intending to convey the idea that the instructions were in that order, such as the head coming after the body, the legs after the head and before the wings, etc. It was merely that the DNA is a set of instructions. Your instructions have more detail, and are a bit different in form, but are still a series of instructions, which was my point. Philip J. Raymentdiscuss 03:36, 30 October 2011 (UTC)
It is very different (although Martin might be able to explain it better), because of how the toolkit genes work. (See here for example.) The differences between organisms are more when genes are expressed and how long during development. That's when all members of a genetic groupings are a variation of each other; all tetrapods have five fingers, for example. That whole "nested hierarchy" of evolution works really well. Again, it's unclear how someone can assert that they are different in information (because, you know animals are different) and claim that similarity in DNA requires the information to be the same (the genetic toolkit is very similar); at least it's unclear how it's productive as verifying the information-as-loss hypothesis.
The irony is that saying that DNA is instructions still doesn't get us anywhere for evaluating whether mutations are a gain or loss of information. It's unclear if more instructions equate to more information, if instructions with more pieces equate to more information, if more "complexity" or "function" (if those can even be defined) equate with more information, if more cells equate with more information. And if they can, it's unclear why one would reframe everything in terms of information; why not just use the direct measurement? Unless, of course, everything was ad hoc and hand-wavy such that don't need to be pinned down. It's hard to make a correlation when you can't measure a variable, and makes determining cause and effect impossible, as you can't look at a temporal relationship. It's as if the definition of loss is any mutation, an inherently circular and question begging one. Sterile 13:24, 30 October 2011 (UTC)
You rang? Yeah, you're not alone in wondering where Philip's instructions to 'make a head' actually lie in the DNA. In a developing zebrafish with say 20k genes, maybe 15k will be expressed in the head, a different 15k in the midbody, and another 15k in the tail. There might be, say, 5k genes expressed only in the head, but those are not sufficient to build a head by themselves. Even the 15k expressed in the head are insufficient, since their expression may depend on the expression of genes not in the developing head, such as those that establish the 'nonhead' end of the developing embryo. In turn, those depend on the proper expression of genes in the ovary of the mother, which create a chemical nonuniformity of the egg that sets up the whole polarity in the first place. So, the instruction to 'make a head' is present where? Spread diffusely across maybe 18k of the 20k genes of the organsim? The same could be said for the instruction to 'make a fin' and 'make a liver' and 'make an ovary', where each instruction requires a massive overlap with each other instruction. Of course, you could also say that the DNA itself has no instructions, since having a genome worth of DNA in isolation is not enough to allow you to build an organism even if you can transcribe any portion and translate it into protein, as I think I've tried to point out before.
But yes, even if you restrict 'instructions' to 'coding portions of genes' or 'proteins'; ie every protein represents an instruction, including post-translational modified forms, then we still don't have a way to determine when a change in instructions by whatever means represents a loss, gain, or simple change in information.
Or maybe PJR doesn't actually think that there is some specific subset of the genome that you can separate out and say 'here is the instruction to build the head' as opposed to all the other instructions. Maybe that 'head' instruction is some sort of emergent property or essence of the genome. We talk about 'intelligence', after all, but you can't pinpoint where it lies in the brain or identify the specific genes that create it. We claim to measure intelligence, of course, but what we are measuring is the result of a particular test, the results of which are correlated to particular differential socioeconomic outcomes. We don't go into the brain and count neurons or synapses or neurtransmitter levels or something. If PJRs definition of 'information/instruction' is some kind of emergent property like that, then we'll have to wait for the equivalent of an IQ test rather than expecting him to pinpoint where intelligence lies in the genome. Otherwise we're back to arguing about how much beauty there is in something. --Martin Arrowsmith 20:33, 30 October 2011 (UTC)
Of course, it probably doesn't matter how Philip defines information. His flavor of the week, expressed above in #common sense says of course there was an increase in information is to admit that the mutation that produced nylonase is an increase in information. He hasn't yet explained how the information argument can be upheld in that case, but I don't see why on Earth he would still think it is important to determine when information increases or decreases. --Awc 21:31, 30 October 2011 (UTC)
Oh, Martin. I don't think Philip's going to accept emergent properties as an excuse. Of course, that would require explaining it to him. Sterile 01:02, 31 October 2011 (UTC)
all tetrapods have five fingers, for example. Snakes and other legless reptiles don't. Yes, according to evolution, they have evolved from legged creatures, and I'm not even going to assert that that's wrong, but this really does look like a case of an ad hoc rationalisation to make contradictory evidence fit.
That whole "nested hierarchy" of evolution works really well. No, it doesn't. For one, "convergent evolution" is the exception nested hierachy, and convergent evolution is very common. In other words, the exceptions to the rule are so common that the rule cannot be said to work well. For another, although most tetrapods have five fingers/toes, some of them do this by different means. See The pentadactyl limb. So although the morphology is the same, the development—and the genetics—is different, contrary to the expectations of the "nested hierarchy" claim of evolution.
...it's unclear how someone can assert that they are different in information ... and claim that similarity in DNA requires the information to be the same ... Information is carried in the arrangement of letters, nucleotides, etc., so broad similarities do not have to mean that the information is the same, if the arrangement is different. For example, "The teacher said the student was an idiot" and "The student said the teacher was an idiot" are so similar that they both have the same words, but the meaning is different. In the case of living things, much of the information probably is the same, as all living things have a reasonable amount in common, such as motors to generate ATP. But as the sentences about the student and the teacher illustrate, small differences can make a significant difference.
The irony is that saying that DNA is instructions still doesn't get us anywhere for evaluating whether mutations are a gain or loss of information. ON the contrary, I've already illustrated how it does, with the bird example. If the mutation produces a new instruction, for example, there is more information. And if the mutation destroys an instruction, there is less information. That might assume a few things, such as the instruction actually being relevant in context, but the principle remains.
...it's unclear why one would reframe everything in terms of information; why not just use the direct measurement? You mean, say, number of functions? Because that is not the whole picture. If the instruction was changed to be more specific, for example, then the number of functions would not have changed, but the information content might have.
It's hard to make a correlation when you can't measure a variable, and makes determining cause and effect impossible, as you can't look at a temporal relationship. By definition, mutations involve a temporal relationship between forebear and offspring.
It's as if the definition of loss is any mutation, an inherently circular and question begging one. Of course. Because you dismiss everything I say and put your own straw-man interpretation on so that you can claim that it doesn't makes sense.
Yeah, you're not alone in wondering where Philip's instructions to 'make a head' actually lie in the DNA. I'm not suggesting that I know where they lie; I'm suggesting that they exist. Do you dispute that there is something in the DNA that causes a bird to have a head? Or do you think that heads just magically appear on birds without there being anything in the DNA causing it?
So, the instruction to 'make a head' is present where? Spread diffusely across maybe 18k of the 20k genes of the organsim? The same could be said for the instruction to 'make a fin' and 'make a liver' and 'make an ovary', where each instruction requires a massive overlap with each other instruction. They could indeed. The point is not where they lie but the fact that they are there. And yes, just as a section of a computer program will call other sections that will also be called from other parts doesn't mean that the computer program is not a series of instruction, neither does the instructions being spread out and overlapping and used for more than one thing mean that they are not also instructions.
Of course, you could also say that the DNA itself has no instructions, since having a genome worth of DNA in isolation is not enough to allow you to build an organism even if you can transcribe any portion and translate it into protein, as I think I've tried to point out before. That it therefore has no instructions is a non-sequitur. A computer program in isolation can also do nothing; it requires a computer to read it and act on it, as I've pointed out before. But that doesn't mean that a computer program is not a series of instructions.
...we still don't have a way to determine when a change in instructions by whatever means represents a loss, gain, or simple change in information. If you think that, then please stay out of the conversation, because I've explained it over and over and over.
Maybe that 'head' instruction is some sort of emergent property or essence of the genome. I'm not sure that I'm happy with describing it this way, but yes, perhaps that is close to what I'm saying. I did say that the description was very simplified. What I had in mind was that each instruction could be broken down into a series of other instructions. So "Add a head" could be broken down into "add a skull, add a beak, add eyes, add a tongue", and so on. But the same applies to each of those: for the eyes, for example, "add a pupil, add a retina, add the nerves", and so on. So does that mean that there are only the "low-level" instructions and no "high-level" instructions? Well, as far as my point is concerned, it doesn't matter. My point is that the genetic code is a series of instructions. That could be a vast number of low-level instructions that add up to an entire body, or it could be a series of high-level instructions that each call lower-level instructions, each of which call even-lower-level instructions, and so on. Either case fits with my point. However, there is evidence that the higher-level instructions exist, in the form of deformities that some living things sometimes suffer, such as people born with six fingers. Rather than an entire sequence of lower-level instructions being repeated an extra time, it makes much more sense that a single higher-level instruction (that calls lower-level instructions) has been called an extra time. And if I'm not getting confused, something like this is what those Hox genes are thought to be.
His flavor of the week, expressed above in #common sense says of course there was an increase in information is to admit that the mutation that produced nylonase is an increase in information. I did not admit that. I agreed that it could be, not that it was.
He hasn't yet explained how the information argument can be upheld in that case, but I don't see why on Earth he would still think it is important to determine when information increases or decreases. I didn't? Then why did I say I fully accept that increases in information can occur. My point is that they occur only as the result of a mind, not from naturalistic processes...
Oh, Martin. I don't think Philip's going to accept emergent properties as an excuse. Of course, that would require explaining it to him. Gratuitous insults are not welcome here.
Philip J. Raymentdiscuss 11:34, 31 October 2011 (UTC)
...we still don't have a way to determine when a change in instructions by whatever means represents a loss, gain, or simple change in information. If you think that, then please stay out of the conversation, because I've explained it over and over and over.
AND
His flavor of the week, expressed above in #common sense says of course there was an increase in information is to admit that the mutation that produced nylonase is an increase in information. I did not admit that. I agreed that it could be, not that it was.
--Awc 12:18, 31 October 2011 (UTC)
@awc, I dont follow this last post of yours, could you explain briefly on my talk page ?
Oops. If it's that hard to follow, I should explain it here. In the first post, Philip says he knows how to tell whether a change represents a loss or a gain in information. In the second post, he goes out of his way to say the nylonase mutation "could be" either an increase or a decrease. If he knows how to tell in general, why doesn't he just say which it is in this case? — Awc 15:21, 31 October 2011 (UTC)
"The teacher said the student was an idiot" and "The student said the teacher was an idiot" although these sentances have the same words the information content is quite different. Executing a checksum routine on them gives a different checksum and "teacher was an idiot" , "student was an idiot" have a differnt subject for the qualifier. Hamster 14:50, 31 October 2011 (UTC)

If the mutation produces a new instruction, for example, there is more information. And if the mutation destroys an instruction, there is less information. That doesn't reflect biology. The instruction is usually "express leucine" that gets changed to "express alanine" (for example). At best a stop or start codon is introduced. We know what the insruction is. Certainly gene duplication is more instructions, which you've denied as new meaningful information before. Certainly the "newness" of the information is entirely inconsistent with what you said before; it's the new meaningful information (I guess) that's important. It may change the conformation of the protein and consequent activity, for better or for worse. Admittedly, the emergence properties may change the end morphology, but no one really understands how that works, so it's hard to say clearly what happens, and really difficult to say it's "more instructions" with that perspective.

The biology can really be simple, as the NY Times article I linked above demonstrates. A long quote from that article is,

But how could such bills evolve from a simple finch beak? Scientists had assumed that the dramatic alterations in beak shape, height, width and strength would require the accumulation of many chance mutations in many different genes. But evo-devo has revealed that getting a fancy new beak can be simpler than anyone had imagined.

Genes are stretches of DNA that can be switched on so that they will produce molecules known as proteins. Proteins can then do a number of jobs in the cell or outside it, working to make parts of organisms, switching other genes on and so on. When genes are switched on to produce proteins, they can do so at a low level in a limited area or they can crank out lots of protein in many cells.

What Dr. Tabin and colleagues found, when looking at the range of beak shapes and sizes across different finch species, was that the thicker and taller and more robust a beak, the more strongly it expressed a gene known as BMP4 early in development. The BMP4 gene (its abbreviation stands for bone morphogenetic protein, No. 4) produces the BMP4 protein, which can signal cells to begin producing bone. But BMP4 is multitalented and can also act to direct early development, laying out a variety of architectural plans including signaling which part of the embryo is to be the backside and which the belly side. To verify that the BMP4 gene itself could indeed trigger the growth of grander, bigger, nut-crushing beaks, researchers artificially cranked up the production of BMP4 in the developing beaks of chicken embryos. The chicks began growing wider, taller, more robust beaks similar to those of a nut-cracking finch.

In the finches with long, probing beaks, researchers found at work a different gene, known as calmodulin. As with BMP4, the more that calmodulin was expressed, the longer the beak became. When scientists artificially increased calmodulin in chicken embryos, the chicks began growing extended beaks, just like a cactus driller.

So, with just these two genes, not tens or hundreds, the scientists found the potential to recreate beaks, massive or stubby or elongated.

“So now one wants to go in a number of directions,” Dr. Tabin said. “What happens in a stork? What happens in a hummingbird? A parrot?” For the evolution of beaks, the main tool with which a bird handles its food and makes its living, is central not only to Darwin’s finches, but to birds as a whole.

BMP4’s reach does not stop at the birds, however.

In lakes in Africa, the fish known as cichlids have evolved so rapidly into such a huge diversity of species that they have become one of the best known evolutionary radiations. The cichlids have evolved in different shapes and sizes, and with a variety of jaw types specialized for eating certain kinds of food. Robust, thick jaws are excellent at crushing snails, while longer jaws work well for sucking up algae. As with the beaks of finches, a range of styles developed.

Now in a new study, Dr. R. Craig Albertson, an evolutionary biologist at Syracuse University, and Dr. Thomas D. Kocher, a geneticist at the University of New Hampshire, have shown that more robust-jawed cichlids express more BMP4 during development than those with more delicate jaws. To test whether BMP4 was indeed responsible for the difference, these scientists artificially increased the expression of BMP4 in the zebrafish, the lab rat of the fish world. And, reprising the beak experiments, researchers found that increased production of BMP4 in the jaws of embryonic zebrafish led to the development of more robust chewing and chomping parts.

Is that new information? Sterile 20:33, 31 October 2011 (UTC)

In the first post, Philip says he knows how to tell whether a change represents a loss or a gain in information. In the second post, he goes out of his way to say the nylonase mutation "could be" either an increase or a decrease. If he knows how to tell in general, why doesn't he just say which it is in this case? In the first post I deny that we still don't have a way to tell. In the second post, I essentially admit that we cannot tell in every case. There is a big middle ground there.
What else would we need to know about nylonase in order to determine whether it represents an increase in genetic information? In cases that you have identified an not representing an increase in information, how do you know that you know enough about the system? —Awc 14:24, 1 November 2011 (UTC)
Executing a checksum routine on them gives a different checksum and "teacher was an idiot" , "student was an idiot" have a differnt subject for the qualifier. Yes, you've just (a) pointed out a different way of determining that there is a different arrangement of the words (one that could be—but isn't—used for distinguishing between human and chimp DNA, because it would highlight a difference rather than similarity), and (b) explained how the different arrangement of the words conveys a different meaning. None of that changes anything I said.
That doesn't reflect biology. The instruction is usually "express leucine" that gets changed to "express alanine" (for example). At best a stop or start codon is introduced. We know what the insruction is. You are only looking at this at the level of the codon. What is the effect of changing the instruction from "express leucine" to "express alanine"? Does it make sense? To again return to the language analogies that you hate, you might have a sentence that says "the cat sat on the mat", and a change might change "cat" to "pat". To paraphrase you, we know what that word is. (In DNA, every three-letter codon has a meaning, unlike in English where not every combination of letters makes a word.) But does that mean that the resulting sentence still makes sense? No, it doesn't. Just as in language where letters combine to make words which combine to make sentences which combine to make paragraphs which combine to make chapters which combine to make books, the same applies to biology: nucleotides combine to make codons, which correspond to amino acids, which combine to make proteins, which combine to make cells which combine to make organs which combine to make bodies (or something like that). So looking just at the level of codons and noting that all combinations of letters makes a known valid codon says nothing about how those amino acids combine, and how the resulting proteins combine, and so on.
...it's the new meaningful information (I guess) that's important. But as I've also said before, individual words don't mean anything without their context. Similarly, individual amino acids don't mean anything without their context.
It may change the conformation of the protein and consequent activity, for better or for worse. That's getting there. How many examples can you produce of it making it "better" (more information, actually)? Very very few.
The biology can really be simple, as the NY Times article I linked above demonstrates. I think the article is not very objective in places.
But how could such bills evolve from a simple finch beak? This appears to be grossly overstating the change. What happened is that finch beaks changed by getting (according to the article) "taller, broader, more powerful" and "longer". In other words, only a change by degree, not a change in complexity, as implied by their misleading reference to a "simple" finch beak.
I won't give any more examples from the paper, but instead return to your question.
The biology can really be simple, as the NY Times article I linked above demonstrates. It doesn't demonstrate that at all. What it says is that small changes can have a profound affect. But consider the following example.
At work, I have created a MS Word macro that formats a table containing a timetable. Among other things, it sets the font size to 11 point Arial, sets the width of the columns, sets various styles to different parts of the text, etc. It actually sets the sizes, etc. according to the font size of the text in the top left cell, so with a very small change (to the size of that font in the top left cell), it instead sets the font size of all the cells of the table to 6 point Helvetica, the columns to be narrower, and the styles to be a different set of styles. So here is an example where one small change has profound effects. Does that mean that the macro is simple? Not at all. If anything, it hints at its complexity. A designed system can easily be made to select between different results from a simple switch. Perhaps that's why "these discoveries blow people’s minds" as the article says: because they are not recognising that these systems are actually designed.
Philip J. Raymentdiscuss 04:08, 1 November 2011 (UTC)
how about the quantity of BMP4 protein in the embryonic stage determines beak length and some aspects of jaw bone and muscle development.
an ms word macro =/= genetic processes Hamster 05:21, 1 November 2011 (UTC)
how about the quantity of BMP4 protein in the embryonic stage determines beak length and some aspects of jaw bone and muscle development. How about it?
an ms word macro =/= genetic processes Really? And here I was thinking that my macro was able to construct a bird! How silly of me!
Did you miss the point that I was illustrating how a "simple" change does not mean that the entire thing is simple?
Philip J. Raymentdiscuss 05:28, 1 November 2011 (UTC)
anyone who can press an on button knows that changing the state of a button (on/off) can cascade a set ot proccesses that result in a complex result. You use a human designed item to illustrate something in nature must be designed so what I get out of your statements is "an embryo is like an ms word macro" Hamster 05:39, 1 November 2011 (UTC)
There have been quite a few times when a critic ask "how could this be?", and I explain how it could be, only to have a reply saying "everyone knows that". If it is well known, why the original question?
You use a human designed item to illustrate something in nature must be designed so what I get out of your statements is "an embryo is like an ms word macro" Then you are still not understanding. What I'm saying is that a living thing(/embryo) is like my MS Word macro in the particular respect that I explained. I've already pointed out that you ignore such details, and here you are doing it again.
Philip J. Raymentdiscuss 07:35, 1 November 2011 (UTC)

How many examples can you produce of it making it "better" (more information, actually)? Very very few. Irrelevant. (Actually, most of them are benefit neutral, although I had thought you said that was an argument creationist weren't supposed to use any more.) Natural selection takes care of this, if I understand what you are saying (which is hard since you are being vaguye). Hence why, for example, synthetic chemists have evolved bacteria to do their non natural reactions for them. Again, you can't switch off natural selection in some cases and switch off mutations in other cases. You have to consider both. And PS: I refuse to respond to analogies any more because they are not the same thing as genetics. No more MS Word and banana cream pie recipes. Sterile 13:09, 1 November 2011 (UTC)

What else would we need to know about nylonase in order to determine whether it represents an increase in genetic information? I can't say for sure; we would probably need a better understanding of how it all works.
...how do you know that you know enough about the system? It's much easier to come to conclusion on the basis of what we know than on what we don't know. For example, if I know the name of one person in the room (Fred), then I can say with certainty that there is a Fred in the room. But I can't say with certainty that there is not a Tom, Dick, or Harry.
  • What is preventing us from concluding that nylonase represents an increase in genetic information on the basis of what we already know?
  • How do we know that we have a sufficient understanding of how, for example, penicillin resistance all works in order to conclude that it represents a decrease in information?
—Awc 16:17, 5 December 2011 (UTC)
Irrelevant. The proportion of information-gaining mutations vs. information-losing mutations is "irrelevant" to whether or not there are information-gaining mutations???
Actually, most of them are benefit neutral, although I had thought you said that was an argument creationist weren't supposed to use any more. I think you are getting confused with something else.
Natural selection takes care of this, if I understand what you are saying (which is hard since you are being vaguye). Takes care of what? (It's hard to know since you are being vague).
Hence why, for example, synthetic chemists have evolved bacteria to do their non natural reactions for them. Are you invoking intelligent design?
And PS: I refuse to respond to analogies any more because they are not the same thing as genetics. No more MS Word and banana cream pie recipes. An analogy is not the same as the real thing? Duh! That's not reason to ignore them. Of course not having an answer to them might be a reason to ignore them!
Philip J. Raymentdiscuss 07:22, 4 December 2011 (UTC)
Analogies are useful at explaning a concept, but have limits when the analogies break down and are not a susbtitute for a real concept. We have no way of assessing if your "meaningful information gaining or losing mutations" are acquired by a population or the degree to which they are beneficial. Evolution (and, I might add, your more limited version, what you call adaptation) requires that mutations are acquired by a population. One mutation in one individual is not particularly useful in even the creationist model. And again, what's the difference betweeen "better" or "more" information, and a "beneficial" mutation, because to me at least, the former is a proxy for the latter, and you are not supposed to use that argument any more. Can you have a mutation that is more information that is not beneficial, or one that is less information that is beneficial? Again, it's just you playing around in the vagaries of your "information." Unless two people can come to the same conclusion from the same observations, it's not useful as a concept, and certainly not able to discude evolution as a possibility or falsify it.
No, I'm not talking about intelligent design; I'm talking about artificial selection. The chemists do not control which mutations occur. Unless you are saying that God or the designer only controls selection and not mutations. Sterile 16:49, 6 December 2011 (UTC)
What is preventing us from concluding that nylonase represents an increase in genetic information on the basis of what we already know? Probably nothing is preventing us from concluding that it could be an increase in genetic information. But there is sufficient doubt about it to definitely conclude that.
How do we know that we have a sufficient understanding of how, for example, penicillin resistance all works in order to conclude that it represents a decrease in information? Is that a fair question? Or perhaps a badly-expressed (or poorly-understood by me) one? I think that's a judgement call, technically. If you ask someone how to build, say, a letter box, and they say to get some metal and join it together in the right shape, you'd hardly think that gave you a "sufficient understanding". But if they went into a lot more detail, so that you were confident that you knew how to build the letter box, then you would now judge that you had "sufficient understanding".
Analogies are useful at explaning a concept, but have limits when the analogies break down and are not a susbtitute for a real concept. Analogies are also useful for conveying a concept. That analogies break down doesn't affect that the concept—which is independent of the analogy—can be conveyed by an imperfect analogy.
We have no way of assessing if your "meaningful information gaining or losing mutations" are acquired by a population or the degree to which they are beneficial. That's a little garbled. It's easy, in principle, to determine if mutations are acquired by a population. Being beneficial is not the point, as both information-gaining and information-losing mutations may be beneficial in the right circumastances.
Evolution (and, I might add, your more limited version, what you call adaptation)... You mean "'adaptation', which you include in 'evolution'".
And again, what's the difference betweeen "better" or "more" information, and a "beneficial" mutation, because to me at least, the former is a proxy for the latter, and you are not supposed to use that argument any more. The former is not a proxy for the latter. The loss of wings on beetles on a windy island might be beneficial for the beetles, but is a loss of information.
Can you have a mutation that is more information that is not beneficial, or one that is less information that is beneficial? Benefit depends on circumstances. A mutation that adds information for lungs is not a benefit for fish.
Again, it's just you playing around in the vagaries of your "information." No, you are not understanding it, as your questions about benefits show.
No, I'm not talking about intelligent design; I'm talking about artificial selection. Artificial selection involves intelligence, albeit less intelligent design than simply selecting from random changes. See my post above about the random numbers of a password.
Philip J. Raymentdiscuss 05:58, 21 April 2012 (UTC)

Fallacy of arguement in language

Argueing information content in English analogies becomes absurd if you do not account for the fact that each word may be representational of a specific deinition. Comparing car and vehicle as words is meaningless. for example

  • car - a powered vehicle for use on the ground, preffering a hard smooth surface and having generally four wheels at least two of which are driven, a steering system to allow limited directional control, a passanger area containg seating for two to eight passangers and a control area for the driver containing a steering wheel, accelerator and brake pedal and controls for turn signals, lights and ancillary equipment.
  • vehicle - a pasanger or freight carrying device being a car, truck, boat or airplane.
you then have to expand every word used to its definition until every word has been proccesed, and only then can you determine what has more information content.

Hamster 16:22, 27 October 2011 (UTC)

Comparing car and vehicle as words is meaningless. Huh? No it's not. In fact you sort of do that, by providing respective definitions.
you then have to expand every word used to its definition until every word has been proccesed, and only then can you determine what has more information content. To some extent this is true, but it's true of all meaning-carrying information, including DNA. You could compare it to debugging a subroutine. You encounter the word "car" in a sentence. Do you (a) step into the "car" subroutine to find out all it encompasses, or do you (b) step over that subroutine call because you know what it entails? DNA is analogous. It will have a bit of code that effectively says "build a leg", but that instruction requires calling other instructions (subroutines) to perform that action.
But there's another aspect to this. If you were comparing, say, a car and a fridge, then your point might be valid. But given that a car is a subset of all vehicles, then it is more specific, and therefore carries more information content. For that, you don't need to compare all that they encompass; you merely need to know that one is a subset of the other.
Philip J. Raymentdiscuss 04:42, 30 October 2011 (UTC)
yes but only after you have expanded the definitions ad accounted for all the information. If you compare "car" and "vehicle" the vehicle has more information because its a longer string. Thats why a definition of information is critical to any meaningful discussion and only one definition
car is a subset of vehicle , but generally a subset is less information than is contined in the full set so car has less information then the full set of vehicle. A specific car may have more information in a full detailed description. Hamster 05:16, 30 October 2011 (UTC)
...vehicle has more information because its a longer string. String length is not the criterion.
car is a subset of vehicle , but generally a subset is less information than is contined in the full set so car has less information then the full set of vehicle. A specific car may have more information in a full detailed description. A subset of information has less information than the containing set of information, but a more-specific concept has more information than a more general concept, because it tells the listener more than a more general concept. To put it another way, although "car" is a subset of all possible "vehicles", the information is the other way around—because "car" contains all the meaning of "vehicle", plus more information. To make use of your definitions, but removing the examples, a "vehicle" is "a device for carrying things", while a "car" is "a device for carrying things on the ground, generally having four wheels...". So the meaning of "vehicle" is contained within the meaning of "car", but "car" has more meaning that is not included in "vehicle". So as far as information content is concerned, "vehicle" is a subset of "car", even though from a grouping point of view "car" is a subset of "vehicle".
Philip J. Raymentdiscuss 10:41, 30 October 2011 (UTC)
We're still waiting to hear criteria to determine relative amounts of information that we can apply by ourselves, without waiting for you tell tell us on a case by case basis where there is more or less information. We are especially interested in criteria that can be applied to genetic information.
When talking about cars, A subset of information has less information than the containing set of information, but when talking about statues, the subset of the positions of atoms on the surface does not contain less information that the full position of every atom. You hedge your bet on the statue example by talking about significance and importance: there is nothing significant about the position and identity of all the atoms. Whereas there is something significant about the 3-D surface of the statue. and your table could be said to be full of information in particular scenario where the position of every atom was important. In the case of the car, why do you not have to know how the information is going to be used before you declare that "car" has more information than "vehicle"?
I don't really care so much about cars and statues. We are supposed to be talking about genetic information here. There you will have the additional difficulty that you can talk about the significance of information on cars or statues to a particular person, but how do you determine the "significance" of genetic information, which just exists independent of anyone's ideas about it? You could invoke God at that point, but then your argument becomes circular.
--Awc 11:50, 30 October 2011 (UTC)
Hear, hear.--Martin Arrowsmith 21:29, 30 October 2011 (UTC)
Me, too. To be honest, it seems you've assumed all genetic information is meaningful and any change from that is less meaningful. I'd also like a response to the genetic developmental tool kit part above. Sterile 12:47, 30 October 2011 (UTC)
if you do not account for the fact that each word may be representational of a specific deinition. which is what I said in the end of that sentance Hamster 05:16, 30 October 2011 (UTC)
We're still waiting to hear criteria to determine relative amounts of information that we can apply by ourselves, without waiting for you tell tell us on a case by case basis where there is more or less information. I have explained that already. I'm waiting for acknowledgement of what I've already explained.
...but when talking about statues, the subset of the positions of atoms on the surface does not contain less information that the full position of every atom. Yes. So? The bit of me you quoted was about subsets of information, but here you are talking about subsets of positions.
In the case of the car, why do you not have to know how the information is going to be used before you declare that "car" has more information than "vehicle"? Because "car" and "vehicle" have normal uses that carry information. If you are going to use them in non-standard ways (e.g. in languages other than English), then you would have a point.
I don't really care so much about cars and statues. We are supposed to be talking about genetic information here. Perhaps if you did care about understanding "information" in a non-genetic context, you would better understand it in a genetic context.
...how do you determine the "significance" of genetic information, which just exists independent of anyone's ideas about it? You determine its significance to the role of creating and maintaining a living being.
To be honest, it seems you've assumed all genetic information is meaningful and any change from that is less meaningful. I do operate within that paradigm, but I also find that the evidence supports that.
I'd also like a response to the genetic developmental tool kit part above. I've got quite a bit of responding to do yet; I'll get to it when I can.
Philip J. Raymentdiscuss 01:45, 31 October 2011 (UTC)
I have explained that already. I'm waiting for acknowledgement of what I've already explained. ot doesnt seem that anyone agrees with whatever you said.
Yes. So? The bit of me you quoted was about subsets of information, but here you are talking about subsets of positions. he used the word information, so the positions of atoms must contain information.
if you are saying every bit of dna is meaningful then I am gonna say you are wrong.
def: car, a 4 wheel machine , powered by a motor , for conveying passangers over land, using predefined smoothed parhs.
def: vehicle a mchine for transporting humans, animals and freight by land , sea or air, either individually or in combination. A vehicle may be a car, boat, airplane or other machine or object. It may be motorized or operate by wind, wave or muscle.
obviously by this example car has less info than vehicle unless you use a different definition. Definitions are a key to understanding.
Hamster 02:02, 31 October 2011 (UTC)
ot doesnt seem that anyone agrees with whatever you said. So, what's new? That doesn't mean that I haven't said it, does it?
he used the word information, so the positions of atoms must contain information. Non-sequitur.
if you are saying every bit of dna is meaningful then I am gonna say you are wrong. What's your evidence that I'm wrong? I'm not saying that, though, as I recognise that mutations have destroyed some of the information.
obviously by this example car has less info than vehicle unless you use a different definition. Definitions are a key to understanding. I agree that definitions are a key to undestanding, but your example doesn't support your case. You don't explain why your example makes your point, so I'll assume that it's either the number of words or the number of "things" (e.g. car, boat, airplane or other machine or object) that you mention.
The number of words is not a measure of information.
As for the number of "things", although this might have the appearance of more information, it actually provides less information, as you know less about what is being discussed. When you are told that a person has a car, you know that they have a vehicle, specifically, a car. But if you are told merely that they have a vehicle, you know that they have a vehicle, but not what type of vehicle. So you know less than if you were told that they had a car, because "vehicle" is less specific than "car". The fact that the definition (in your example) lists several different types of vehicles doesn't mean that it has more information; it means that you know less about which type of vehicle is being referred to.
Philip J. Raymentdiscuss 08:20, 31 October 2011 (UTC)
[ec, but still to the point] Try to remember, Philip, that your job is not to explain to us what information really is. You just need to explain how you and other creationists choose to use the term in the context of genetics, in particular to make the argument for creation. You've jumped around a good bit in the land of analogies, but as far as I can make out, what you have been trying to say is that a description has more information if it has more detail, and, I believe, that a set of instruction has more information if it specifies more detail in the product. We have been pointing out that that definition does not always coincide with our intuitive concept of information when applied in analogy land. Perhaps we react oversensitive because we don't like your presumption that you know more about the proper use of everyday concepts than we do. No matter. It's your argument, you can define your terms any way you want. Because of that, it is fruitless to fight over analogies. When are you going to expound on your definition of genetic information as the set of instructions that describe the construction and operation of living organisms, in particular Let's just hear how you think you can determine increase or decrease in the amount of genetic information? You may think you have told us already, but you haven't. Or maybe it's just that your thoughts are muddled. Here you say that the significance [of genetic information] to the role of creating and maintaining a living being is important, but elsewhere you have said Whether or not the instruction is correct/helpful/useful/less likely to save your life is a separate issue to the number of instructions/amount of information. So far, my claim that the operational definition of "species" is a thousand times more precise than the creationists' definition of "genetic information" is holding up real fine. --Awc 08:40, 31 October 2011 (UTC)
a description has more information if it has more detail, and, I believe, that a set of instruction has more information if it specifies more detail in the product. That's pretty close.
We have been pointing out that that definition does not always coincide with our intuitive concept of information when applied in analogy land. I've had these sorts of instructions before numerous times, and often it's been a case of the critic thinking of "information" only in a statistical sense, such as Shannon information. So I've tried to get them them to see that creationists are talking about "information" in that sense (which is, incidentally, not to suggest that the data can't also be looked at that way), by pointing out that what we are talking about is much closer to the normal, everyday, meaning of the word. What I have not meant to suggest is that the normal, everyday, meaning of the word will give you a complete understanding, or will allow you to distinguish increases or decreases in every single case. It's a starting point, which, as I've said before, I wish people would acknowledge before moving on to special or difficult cases. But even lately on this page, so much of the argument has been along the line that living things do not contain information in any sense other than statistical, or at least that analogies with non-genetic information are so completely nonsensical that they can't be used.
Because of that, it is fruitless to fight over analogies. Does that mean that you'll accept their applicability? Or does "not fight" mean "reject and ignore"?
Some of each. "Fruitless" means it doesn't matter anyway. —Awc 14:19, 1 November 2011 (UTC)
When are you going to expound on your definition of genetic information as the set of instructions that describe the construction and operation of living organisms... I already have, even if it's scattered over numerous conversations.
... in particular Let's just hear how you think you can determine increase or decrease in the amount of genetic information? You may think you have told us already, but you haven't. I have. You can (in principle, assuming you know enough detail) determine such by comparing the "before" and "after" and seeing if it adds new function or ability. There may be some borderline cases, such as Lenski's bacteria that added a "new" ability that they already had(!), but that doesn't change the principle that a new function or ability would be an increase in information.
Or maybe it's just that your thoughts are muddled. Or maybe it's just that you are not really coming to grips with the concept. Although everyone understands what "information" means, in the sense that they know a book contains information but a blank sheet of paper doesn't, one aspect that is profound is that, to quote from information, information "has been described as the third fundamental quantity of the universe, alongside matter and energy". That is, information is not a property of the physical, but something completely different. That takes a bit of pondering to fully appreciate.
That information is not a physical property is OK. I hope I don't have to believe the gibberish about information being "the third fundamental quantity of the universe" to follow your argument. —Awc 14:19, 1 November 2011 (UTC)
Here you say that the significance [of genetic information] to the role of creating and maintaining a living being is important, but elsewhere you have said Whether or not the instruction is correct/helpful/useful/less likely to save your life is a separate issue to the number of instructions/amount of information. Those two comments are not inconsistent with each other.
Very helpful. I see them as inconsistent. Are you saying you understand why I see them that way but there is an aspect I haven't considered, or are you saying you don't understand why iI see them that way? —Awc 14:19, 1 November 2011 (UTC)
So far, my claim that the operational definition of "species" is a thousand times more precise than the creationists' definition of "genetic information" is holding up real fine. Not at all.
Philip J. Raymentdiscuss 04:34, 1 November 2011 (UTC)
information is not a property of the physical, but something completely different. so information is an intangible thing that is NOT a property of anything physical ? so the phrase "bite me !" contains no information in itself ? How then does the ethereal information connect to the physical construct ? and is that why the same physical construct can attach to different information at different times ?
Hamster 05:02, 1 November 2011 (UTC)
so information is an intangible thing that is NOT a property of anything physical ? Correct.
so the phrase "bite me !" contains no information in itself ? Your question is incorrect. Assuming black text on a white screen, the black pixels that display that phrase on the screen contain no information of themselves. Rather, the information is carried in the arrangement of those black pixels. Use of the word "phrase" implies a reference to the meaning rather than the pixels.
How then does the ethereal information connect to the physical construct ? By the arrangement of the physical, as I've said numerous times.
and is that why the same physical construct can attach to different information at different times ? "Attach to"?? I don't understand your question.
Philip J. Raymentdiscuss 05:25, 1 November 2011 (UTC)
so arrangement of pixels ? ok what of a carved sign ? the arrangement of atoms in the material in which the word is carved ?
how about different fonts , does sans serif contain different information than serif or script , considering the quantity and arrangement of the pixels is different Hamster 05:32, 1 November 2011 (UTC)
what of a carved sign ? the arrangement of atoms in the material in which the word is carved ? In a sense, yes, but it would be better to say the arrangement of the cuts, which remove some atoms and leave others.
how about different fonts , does sans serif contain different information than serif or script , considering the quantity and arrangement of the pixels is different No, not every arrangement carries different information; there is redundancy. I'm sure that you are aware that there are different ways of saying the same thing. That is, a different arrangement of words can (not "will") convey the same meaning. Similarly, a different arrangement of pixels can convey the same information.
Philip J. Raymentdiscuss 07:41, 1 November 2011 (UTC)
so the arrangement of pixels need not be precise because a different arrangement can "not will" convey the same meaning ? So a DNA strand which reads differently with say a deviation of 10% can convey the same information ? How does one decide if it does or does not ? If you see an l and a 1 these convey totally different meanings but have almost precisely the same pixel pattern.(lower case l and numeric 1) Hamster 08:06, 1 November 2011 (UTC)

How far have we gotten?

  1. Genetic information is the set of instructions that describe the construction and operation of living organisms.
  2. If the end products of two sets of instructions are identical, except one of them possesses an additional function or ability, then the instructions producing that one have more genetic information.

That sounds reasonable, but there must be more to it because we continually come to different conclusions when considering concrete examples. Perhaps you could explain the finer principles by application to a few cases.

  • Why do you equivocate on whether nylonase is a new ability?
  • Why is the new protein coat of the flu virus every season not a new function?
  • Why is the development of antibodies against a new disease not a new function?
  • If an enzyme is modified to become, say 1000 times more efficient, does that involve no increase in information because the ability existed in some form before?
  • If an enzyme is modified to react with (e.g. digest) an additional substrate, without affecting the reaction with the primary substrate, is that an increase in information, even though the specificity of the enzyme has decreased?

There's probably more, but getting an answer to these questions should help. —Awc 14:19, 1 November 2011 (UTC)

I should probably call attention to the fact that the specification you gave refers only to the end result, not to any details of the instruction set leading to that result. Is that what you intended? I mention it because I perceive—probably unjustly—this as one of the points you waffle on. —Awc 20:27, 1 November 2011 (UTC)

That information is not a physical property is OK. I hope I don't have to believe the gibberish about information being "the third fundamental quantity of the universe" to follow your argument. What makes it "gibberish"? And I think it probably does help to understand that.
Are you saying you understand why I see them that way but there is an aspect I haven't considered, or are you saying you don't understand why iI see them that way? The latter.
You made these two statements, and you don't understand why I see them as contradictory:
  • [The] significance [of genetic information is determined by its] role of creating and maintaining a living being. (You introduced the concept of significance in the context of a statue, where you claimed that the information content was only in the position of the surface, not the position of all the atoms.)
  • Whether or not the instruction is correct/helpful/useful/less likely to save your life is a separate issue to the number of instructions/amount of information.
One time you say you have to know what the instructions are good for in order to quantify their information content. The next time you say that's irrelevant. —Awc 21:17, 5 December 2011 (UTC)
so the arrangement of pixels need not be precise because a different arrangement can "not will" convey the same meaning ? I don't like the "need not be precise" bit. Rather, there is more than one arrangement that will convey the same meaning.
So a DNA strand which reads differently with say a deviation of 10% can convey the same information ? Yes (can, not will).
How does one decide if it does or does not ? By whether or not they have the same meaning.
If you see an l and a 1 these convey totally different meanings but have almost precisely the same pixel pattern.(lower case l and numeric 1) Correct. Which is why it would be wrong to say that a small difference will convey the same information. But compare "dog" and "dog". The pixel arrangements vary, but the meaning—the information—is the same.
I should probably call attention to the fact that the specification you gave refers only to the end result, not to any details of the instruction set leading to that result. Is that what you intended? The specification? You mean your points 1 and 2 above? They might not refer to the details of the instruction set, but they do refer to the instruction set, not just the end result. No. 1 is "Genetic information is the set of instructions...". No. 2 is less clear, but still refers to the instructions themselves.
A reason for referring to the outcome is because that's what the meanings of the instructions are. If a recipe is defined as a set of instructions for making a pie, then does that definition refer to the instructions or the outcome? The instructions are described in terms of the outcome that they produce. Of course, one could also describe the instructions in terms of ingredients, temperatures, and actions. But how many people would understand what three cups of self-raising flour, 80g of butter, and one cup of milk makes? Some would, but for most people it would be better to describe the product (scones).
Similarly with genetic instructions, one could list the actual genes, or the amino acids, or the proteins produced by those instructions. But it may be simpler to mention the product. However, it's still the "ingredients" that are the key.
With the scones, if a new batch has an extra crispy crust, is that due to a new instruction, or simply a higher temperature in the oven? What if the crust has no crispness at all, making it easier to eat by people without teeth? Did that require new instructions, or was it simply not cooked enough? The point is that the change in the instructions are key, but unless you understand the change and how it works, you have to fall back on the change in the outcome to try and get a handle on what's happening.
Furthermore, you need to determine if the change in instructions is more or less specific. In another post on this page that I've made in the last 24 hours, I've pointed out the difference between new information and a virus gaining a new protein coat.
2. If the end products of two sets of instructions are identical, except one of them possesses an additional function or ability, then the instructions producing that one have more genetic information. I'm going to disagree with this one a little. This would normally be the case, but there could be exceptions. One, which we've discussed before, is where an organism loses something (e.g. eyes), then a mutation later reintroduces eyes. The point here is that the instructions for eyes were there all along, but were turned off. You could try arguing that the switch being turned on amounts to more information, but even if so, it's a trivial amount; the key is that the (much larger set of) instructions for eyes are not new. So "an additional function or ability" could be due not to new information, but to existing information being turned on.
Of your five bullet points, I've answered the first two in other posts in the last 24 hours.
Why is the development of antibodies against a new disease not a new function? It may be, depending on how you define "function". But the important questions are, does it amount to new information, and, if so, what is the source of that information? It well might, for example, be an intelligently-programmed algorithm for coming up with new proteins.
If an enzyme is modified to become, say 1000 times more efficient, does that involve no increase in information because the ability existed in some form before? Again, it depends on the information behind it. If a machine is modified to become a 1000 times more efficient, is that due to a simple change such as the amount of lubrication, or due to some new, complex, component that makes it more efficient?
If an enzyme is modified to react with (e.g. digest) an additional substrate, without affecting the reaction with the primary substrate, is that an increase in information, even though the specificity of the enzyme has decreased? A reduction in specificity would suggest that there is no more information.
Philip J. Raymentdiscuss 23:38, 4 December 2011 (UTC)
After all that waffling, where are we? Back at square one:
  1. Genetic information is the set of instructions that describe the construction and operation of living organisms.
I am unable to find any consistent criteria in the things you are saying. If there are any, you will have to extract them yourself. If you can do that, please write them down here ...
—Awc 21:29, 5 December 2011 (UTC)
One time you say you have to know what the instructions are good for in order to quantify their information content. The next time you say that's irrelevant. I didn't say either. That is, I didn't say that you have to know what the instructions are good for in order to quantify their information content, and I didn't say that know what they anything is irrelevant. In the latter case, I said that was a separate issue.
Let's go over what was said. I said that "there is nothing significant about the position and identity of all the atoms. Whereas there is something significant about the 3-D surface of the statue." Note that I was talking about the significance of atoms and shapes, not of information. What is significant about a shape is whether or not it conveys information. Consider the sentence "I have coins in my pocket". The arrangement of letters making up that sentence is signifant because it conveys information. The actual information conveyed by that arrangement of letters is not itself significant (in this conversation at least). So you can have an arrangement of material that is significant (in that it carries information) without the information itself being significant.
So let's go back to this comment of yours:
One time you say you have to know what the instructions are good for in order to quantify their information content. I was not talking about quantifying the information content of "instructions" (i.e. information). I was talking about determining whether an arrangement of matter constitutes information.
After all that waffling… That wasn't waffling.
Philip J. Raymentdiscuss 06:30, 21 April 2012 (UTC)

Items needed for meaningful discussion.

a clear definition of information, meaning , how each is measured and quantified.
if Philip has provided these a ref or diff link should be easy
an end to english language analogies Hamster 04:33, 1 November 2011 (UTC)
a clear definition of information, meaning See information.
how each is measured and quantified I have said numerous times that although you can compare to see if there is less or more, measurement is not (yet) possible.
an end to english language analogies Because you say so? Because they make the creationist point so well? Because...? No, as I have pointed out before, language analogies are used by geneticists[1] and are completely legitimate. Why do anti-creationists continue to deny the evidence? Why do they continue to demand that discussion has to be on their terms? If you want to constrain the discussion to your terms and your way of thinking, go somewhere else like Wikipedia that will accommodate you. This site exists to be sensible, not to constrain discussion.
Philip J. Raymentdiscuss 05:17, 1 November 2011 (UTC)
no analogies are NOT completely legitimate in all cases, only when trying to introduce broad concepts. Find me a working biologist who talks about the effects of gene duplication as applied to disease in terms of cars and boats, or the length of text strings. When you see a doctor do you say, my pain is like the chirping of starving sparrows, or do you say, I have a pain in the elbow joint of my left arm, on the anterior aspect ?
I have said numerous times that although you can compare to see if there is less or more, measurement is not (yet) possible. and once more you assert that you can compare something you cant measure. If you can compare a length you have defined what length means and could measure it even if you invent units to do it. How do you compare a wooden dowel with a apple ?

Hamster 07:58, 1 November 2011 (UTC)

The only "definition" as it is is the lead section: "knowledge or data. It may form part of a message, it may be constituted by knowledge held by an individual or it may even exist as data held in storage. More technically, information can be described as a message transmitted by a message sender and received and understood by a message receiver." Nothing there about more or less. And the quantification section deals with Shannon, which you say isn't what you mean, and Kolmogorov complexity, which really isn't a measurement. So your continued citation of the article is unhelpful at resolving the situation, nor are your one sentence comebacks. Sterile 13:01, 1 November 2011 (UTC)
PS Analogies may be a proxy for the real thing in an explanation, but they are not the real thing, especially in a quantifiable case. Imagine if we explained momentum in terms of an analogy. Very unproductive. Sterile 13:03, 1 November 2011 (UTC)
no analogies are NOT completely legitimate in all cases, only when trying to introduce broad concepts. I didn't say that they were legitimate in "all cases", but why can they only be legitimate for broad concepts?
Find me a working biologist who talks about the effects of gene duplication as applied to disease in terms of cars and boats, or the length of text strings. I provided one in the link in the post that you were replying to! There are none so blind as those who will not see.
When you see a doctor do you say, my pain is like the chirping of starving sparrows, or do you say, I have a pain in the elbow joint of my left arm, on the anterior aspect ? It depends on what the doctor asks, but certainly not just the latter. If I did, he would want to know how bad it is on a scale of one to ten. Also (and more to the point), it's likely that someone (not me) would describe it by comparing it to the pain of childbirth. So yes, analogies are used in that circumstance.
and once more you assert that you can compare something you cant measure. Yes, and I've explained numerous times how there is nothing wrong with this.
If you can compare a length you have defined what length means and could measure it even if you invent units to do it. You need more than units; you need a way to measure those units. If we didn't have thermometers, we could still compare temperatures (is this hotter than that?). You could even invent a unit (e.g. degrees Celsius), but unless you have some way of determining how many of those degrees there are (the thermometer), you still can't measure temperature.
How do you compare a wooden dowel with a apple ? So you object to my English-language analogies, but are happy to use other (inappropriate) analogies when it suits you?
Nothing there about more or less. I don't see why there needs to be anything about more or less. They are commonly-understood terms.
Analogies may be a proxy for the real thing in an explanation, but they are not the real thing, especially in a quantifiable case. Imagine if we explained momentum in terms of an analogy. Very unproductive. Of course they are not the real thing. That's why they are analogies! I don't see the problem in explaining momentum in terms of an analogy, assuming you could find an appropriate one.
Philip J. Raymentdiscuss 23:59, 4 December 2011 (UTC)
If we wanted to validify that momentum is conserved, would we use an analogy?
I don't see why there needs to be anything about more or less. If you are trying to develop an argument that everyday processes don't create information, an argument about a trend, but you have no way to establish the trend, then you have no argument. Sterile 03:47, 9 December 2011 (UTC)
If we didn't have thermometers, we could still compare temperatures (is this hotter than that?) how would that work without a measuring device of some kind ? you could stick your finger in it , but thats a measuring device itself. Hamster 06:10, 12 December 2011 (UTC)
If we wanted to validify that momentum is conserved, would we use an analogy? Of course not, and I'm not claiming that. But neither would we "validify" that energy is conserved without understanding what we are talking about.
If you are trying to develop an argument that everyday processes don't create information, an argument about a trend, but you have no way to establish the trend, then you have no argument. But you do have a way to establish the trend: see if there is more or less! Your objection was that we didn't explain what was meant by more or less, and I merely said that we didn't need to. That is, we don't need to explain it; I didn't say that we don't need to make use of the concept.
how would that work without a measuring device of some kind ? you could stick your finger in it , but thats a measuring device itself. Only if you are happy to call something that compares temperatures a "measuring" device. If you are happy to do that, you should be happy to call our eyes and brains a measuring device for measuring information, because, as I've always said, you can compare two sets of information and see if one has more or less. The problem is that you people keep asking for a measuring device that doesn't involve relative "measurements".
Philip J. Raymentdiscuss 06:44, 21 April 2012 (UTC)

ervs

how many do humans have ? well quite a few , same as chimps Hamster 07:10, 1 November 2011 (UTC)

Relevance? Philip J. Raymentdiscuss 07:49, 1 November 2011 (UTC)

Missing references

There are a few references in the article to (at least) Spetner, as in "Spetner (2002)" and "(2004)" which are not listed in the bibliography or references. Philip J. Raymentdiscuss 07:51, 1 November 2011 (UTC)

Also Batten (2003) is not properly linked. The Spetner bibliographic info can be found, albeit indirectly, on the research page. That should be fixed. That I didn't do it properly to begin with you can chalk up to laziness, or, as I prefer to think of it, efficient allocation of resources. —Awc 13:34, 1 November 2011 (UTC)
I'm not sure what you mean by "properly linked". Batten (2003) is a reference to Batten in the bibliography. There is no reference to Spetner for 2002 or 2004 in the bibliography. Philip J. Raymentdiscuss 00:01, 5 December 2011 (UTC)
I've tracked down the missing references and added them. Only one of the two was in the Research page. Philip J. Raymentdiscuss 13:14, 21 April 2012 (UTC)

Richard Dawkins

What's really sad is it does nothing to help the argument that no meaningful information can be created. It's not engaging in the ideas of genetic information, and is really just a distraction. It's an argument from authority in a sense. But hey, if that's the article you want.... And yes, "claims" is a weasel word, whether you chose to believe it or not. Who's claiming it? Citation please. Sterile 23:51, 1 November 2011 (UTC)

If evolutionists could provide examples of genetic information being formed naturalistically, then they would be quick to cite them. So not being able to cite any is relevant.
It's an argument from authority in a sense. As I've pointed out before, a fallacious argument from authority is when the persons is not an authority. Are you suggesting that Dawkins is not an authority on evolution?
And yes, "claims" is a weasel word, whether you chose to believe it or not. It's not a weasel word if it's known who claimed it.
Who's claiming it? You, for one! You changed it to say that information increases have been found! That's your claim! Why you would ask who's claiming it when you are claiming it beggars belief!
Philip J. Raymentdiscuss 00:45, 5 December 2011 (UTC)
Sure, he is, and he's written a lot on genetic information. For some reason, you don't admit to that. I'm not sure if I'm using information in the same sense as you. Sterile 03:23, 6 December 2011 (UTC)

I removed this paragraph:

In a controversial documentary, Richard Dawkins was asked "Can you give an example of a genetic mutation or an evolutionary process which can be seen to increase the information in the genome?", and was unable to provide one such example.

and Philip returned it with the reasons

  1. "he has never answered the question, and"
  2. "his excuse for the pause has been shown to be wrong."

The first reason is imply untrue: http://www.skeptics.com.au/publications/articles/the-information-challenge/. The second would require knowing what was going on inside his head. I'll change it back, but I'll take my time to calm any incipient edit warring. Better would be if Philip changes it back. —Awc 11:28, 18 April 2012 (UTC)

The question was asking him to provide examples. His article you linked to talked at length about information, but still didn't provide examples. Ergo, he has not answered the question.
You don't need to know what was going on in his head. His excuse was that it was then he realised that he was being interviewed by creationists. But he had already realised this earlier, so no, his excuse is shown to be wrong, and that didn't require knowing what was going on in his head.
Philip J. Raymentdiscuss 12:35, 18 April 2012 (UTC)

I have started From a Frog to a Prince, which is the place to go into details and decide what the incident reveals about CMI and Dawkins. Independent of that, I am concerned about the purpose of reporting the incident in this article. Could you tell me clearly how this helps the reader understand the concept genetic information? What is the point of quoting Dawkins, and not somebody else? Of all the things Dawkins has said about genetic information, why is this quote the most enlightening? —Awc 20:43, 18 April 2012 (UTC)

Of all the things Dawkins has said about genetic information, why is this quote the most enlightening? Perhaps because this is the most enlightening. Everything else is theoretical; this is practical.
Could you tell me clearly how this helps the reader understand the concept genetic information? The question is misplaced because the article doesn't need to be just about the concept, but also how it relates to the creation/evolution question. It helps the reader understand that genetic information is contrary to evolution, because evolution can't explain it.
Philip J. Raymentdiscuss 07:42, 21 April 2012 (UTC)

Enzyme specificity

I'm truly puzzled by the statement, "Finally, creationists argue that the specificity of the enzyme produced must increase. While evolutionists may argue that specificity is either hard to define unambiguously or is not a good surrogate for genetic information, the evolutionary paradigm holds that the first cells produced enzymes with less specificity than present organisms, and it is hard to imagine evolution occurring without specificity increasing at least sometimes." What biochemists call specificity has been observed to increase. If it is a "surrogate for genetic information" by creationists as this statement implies, then genetic information has been shown to increase. %Sterileevolutionist story telling! 11:06, 29 August 2013 (UTC)

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