Adding information to the genome.

Hi Kaichos Man,Your misinterpretation of that Kimura quote has been explained to you how many times now? And you're still asking the exact same question instead of going back to the explanations you've already been provided and seeking clarification or more detail? In reply to the very message where this precise behavior on your part was described?I'll try to repeat, but in a little more detail, the same explanation that Wounded King already gave you many posts ago. The four nucleotides of DNA are adenine, cytosine, guanine and thymine, abbreviated as A, C, G and T. The amino acids that are the building blocks of proteins are specified by DNA nucleotide triplets called codons, like ATC (adenine, thymine, cytosine) or TGT (thymine, guanine, thymine).There are 64 different codons but only 20 amino acids, so there's lot's of redundancy. For example, the amino acid isoleucine is specified by ATT, ATC or ATA. The amino acid leucine is specified by CTT, CTC, CTA, CTG, TTA or TTG. Here's a nice table I found: Just look at all the redundancy. The TCT codon creates serine, but so do TCC, TCA, TCG, AGT and AGC. That means that a mutation could change TCT into TCC or into TCA or into TCG and it would still code for the same amino acid as before the mutation, serine. Or AGT could mutate into AGC and it would still code for serine. Such mutations would cause no change at all. This high degree of redundancy is one reason why Kimura said that most change at the molecular level (i.e., in the DNA and proteins) is not caused by selection, because a mutation that causes no phenotypic change cannot be selected for (that's not quite true because some nucleotides are more easily constructed and therefore more available than others, but that's a relevant detail we need not consider in this discussion).But there's yet another reason why Kimura said this. The amino acids that DNA codons represent are combined into proteins by the cell's internal machinery, but changing just one or a few amino acids in a protein often results in a protein that behaves identically or very similarly to the original. This means that many mutations that change the codon to program for a different amino acid still end up producing a protein that does pretty much the same thing as the original protein. Once again there is no change at the phenotypic level, only at the molecular level, and so there can be no selection. So proteins are another place where molecular change can occur without selection.And there's still another reason why Kimura said this. Kimura's neutral theory includes both neutral and near neutral mutations. A mutation or accumulation of mutations that causes DNA to produce a protein that behaves differently than the original, thereby causing a change in the phenotype, could still be neutral if the change provides no change or nearly no change in selection. This is the random drift due to neutral or near neutral mutations that Kimura talks about.And so it is for those three reasons, redundancy at the codon level for producing amino acids, redundancy at the amino acid level for constructing proteins, and neutral or near neutral phenotypic changes, that Kimura was able to accurately say that most change at the molecular level is not a result of Darwinian selection.But these changes due to random drift are not adaptive like those driven by selection. Most change at the phenotypic level, which is under genetic control and results from mutations (and allele remixing in sexual species) is a result of adaptive forces driven by selection, which is why Kimura goes on to say: So when you see a hummingbird with a tongue long enough to reach to the base of a deep flower, that's adaptive evolution caused by selection of mutations favorable to a sufficiently long tongue. When you see a male peacock's tail on display, that's adaptive evolution caused by selection of mutations favorable to a tail that appeals to peahens, thereby increasing the probability of reproduction allowing the peacock to contribute its genes to the next generation.Any questions that aren't just a repeat of your original question?--PercyEdited by Percy, : Clarify 3rd to last paragraph.

This would require you doing us the favor of not acting like one. We all go through phases of patient explanation. Everyone has their limit. In WK's last post (Message 161) he echoes what everyone has been telling you, that you're just repeating the same questions over and over again, or in WK's words in response to your claim that the rebuttals were ineffective, "But he [meaning you] should also explain why he doesn't find your argument effective, not merely restate his own." It's like you're trying as hard as you can to not comprehend anything. There's no explanation so carefully crafted, so studiously composed, so carefully researched, that you can't misinterpret or ignore it in a way such that, apparently, the only thing you can think to do is state your question yet again.--Percy

Yes, I know. But WK went to the trouble of commenting on your exchanges with others, saying the same thing that everyone else is, that you ignore rebuttals and just keep repeating your original questions. In other words, the guy with whom you're currently having a productive discussion can still see how poorly you're still handling your discussions with everyone else.The key to understanding is learning how to ask good questions. In one of the religious threads a stupid question in a discussion about Jesus might be, "Are you saying that Jesus Christ is Santa Claus?" A better question might be, "In what tangible ways does Jesus Christ respond to prayers?"--Percy

Well, yes, the principle is true, but I wouldn't call it "the most important reason." For one thing, "functionally less important" is not a synonym for junk DNA, though it certainly includes it. For another, it is now generally believed that in the past we overestimated the proportion of DNA and proteins that were non-functional. For example, many regions of junk DNA are still transcribed into snippets of RNA, and recent work indicates that these RNA snippets play a significant role.But while arguing that Kimura believes that natural selection plays only a minor role in evolution you seem to have quoted Kimura contradicting you: Steps 3 and 4 require natural selection. This sequence of four steps is pretty much what Drosophila described to you in an earlier post.No biologist in his right mind would ever reject the role of natural selection, and Kimura was a biologist of the highest rank. The evidence for natural selection surrounds us everywhere in every adaptive feature of every organism from bacteria to whales. Neutral theory is not why white rabbits evolve in the arctic and not in the tropics, or why fish that can crawl between ponds evolve in regions that experience frequent drought, or why new strains of flu evolve every year. These are all examples of adaptive evolution as a result of natural selection.So you have somehow misinterpreted as supportive a passage where Kimura directly contradicts you. You know what you believe, and you apparently interpret any passage you don't understand as supporting what you believe.If it were true that Kimura actually rejected natural selection as having a significant role in evolution then he would be an enormously controversial figure within biology, but he didn't and he's not. What he proposed is that neutral and near neutral mutations also play a significant role in evolution. He wasn't trying to replace natural selection as the main actor in evolution, he was only trying to place another actor on the stage along side natural selection.--PercyEdited by Percy, : Change list to Roman numerals.

What two roles for selection do you think you see? This might be key to your misunderstanding.It's interesting to see those quotes you provided from a 1973 BBC documentary (Perspectives on Molecular Evolution), but Kimura's ideas as they developed in the years after that (the "nearly neutral" variation of the theory came after that documentary) are not considered controversial today. Kimura's neutral theory now has wide acceptance within biology and has proved particularly useful in population genetics.You can quote mine Kimura to your heart's content trying to make him seem to consider natural selection as playing a minor role in adaptation, but as I keep telling you, no biologist in his right mind could ever believe that. The evidence for natural selection is in every adaptive feature of every organism.Kimura's 1973 statement about hemoglobin seems crafted as an illustration to aid public understanding. It doesn't reflect any actual research findings and isn't true. In fact, just as the hemoglobin of high and low altitude creatures differs to take advantage of different oxygen levels, so does the hemoglobin of fish (subject to increasing pressure with increasing depth and a whole host of other factors) differ from that of land animals, and these differences are due to natural selection. Kimura's hemoglobin example was likely successful in getting his point across to laypeople, but biologists both then and today would role their eyes at such a naively incorrect statement.Kimura's neutral theory makes claims about the causes of variation at the molecular level, and that hemoglobin is a well know molecule probably explains why he chose it for an example, and undoubtedly some proportion of hemoglobin variation is neutral, but just as undoubtedly a significant proportion has been driven by adaptive selection due to environmental pressure. Kimura understands this when he provides his step 4 that you cited earlier: Notice that Kimura says that selection is responsible for adaptive evolution. When he's talking about neutral variation dominating over selected variation he's talking about the molecular level.When Kimura says: He was only saying what we're already telling you is true and that we all agree with. Many changes at the molecular level are neutral with regard to selection. But adaptation requires selection, Kimura knew this, and he was not saying that chance plays a greater role in adaptation than natural selection. He was saying that at the molecular level chance plays a greater role. You keep forgetting the "at the molecular level" part of what he's saying.--PercyEdited by Percy, : Add clarifications.Edited by Percy, : Grammar.

Well, duh! No biologist sees natural selection as a source of variation. Random mutation is the source of variation.Every year thousands of aspiring artists put their wares before the public. The artists are the source of variation. Which artists succeed and which eventually decide that maybe some other line of work might be more remunerative is decided by the public, who performs selection. Artists provide the variation, the public performs selection.In an analogous way, variation in the genome is supplied by random mutation, and selection is performed by constraints imposed by the environment that control whether any particular combination of random mutations is passed on to the next generation, otherwise known as natural selection.--PercyEdited by Percy, : Improve phrasing.

Hi Kaichos Man,You have a long list of misunderstandings about evolution, and it seems to be getting worse. Maybe evolution isn't something you're ever going to grasp.--Percy

I think maybe the problem is that you've delved into an area that requires a better understanding of basic evolution before you can make some relatively subtle distinctions.Keeping this simple, the source of variation is mutations.Some mutations propagate through a population due to drift, causing observable patterns of variation.And some mutations propagate through a population due to selection, causing other observable patterns of variation.Some patterns of variation are best explained by drift, others by selection.The vast majority of biologists, and that includes Kimura, believe that selection plays a significant role in the process of evolutionary change, adaptation in particular. He states it explicitly and without ambiguity in his step iv: "Intergroup competition" is one form of selection. "Individual selection" is another way of saying intragroup competition. Kimura appears to think of the environment as providing the context in which competition for contributing one's genes to the next generation takes place.We await your next garbling of our explanations. --PercyEdited by Percy, : Improve explanation.

I share your frustration. I've started a subthread over at Message 182 in the Peanut Gallery thread.--Percy

No one here who doesn't have your reading comprehension problems sees any significant conflict between Kimura's views and evolutionary theory.--Percy

Hi Kaichos Man,In case it helps you figure out where you're going wrong, here's a couple problems in the way you're looking at things.First, the phrase "functionally less important molecules" is not a synonym for junk DNA.Second, here's a significant contradiction in your views. First you make a statement that acknowledges that what Kimura would term "functionally important molecules" do evolve, just not as fast as "functionally less important molecules." Then you contradict yourself by claiming that Kimura thought that evolution could only take place in junk DNA: So your understanding of Kimura's views is contradictory. You have him knowing that evolution could take place in both functionally important and functionally less important molecules, but at different rates. And you also have him knowing that evolution could only take place in functionally irrelevant molecules, what you're calling junk DNA. I think if you work to resolve this contradiction in your understanding that it will help you discover what Kimura was really saying.--Percy

As we've told you many times, everyone agrees that advantageous mutations are rare.In the passage you quote (which is from Retrospective of the last quarter century of the neutral theory on page 522) Kimura takes advantage of that fact to make an approximation in the math for neutral mutations that ignores advantageous mutations. Certainly if some small number like one out of a million mutations are advantageous then this is a valid approximation.But however rare advantageous mutations might be, they do occur, and they are selected for, regardless where they occur on the scale from functionally important down through functionally less important to functionally irrelevant.In other words, your reading comprehension problems are still showing. The perversity of explaining with the written word where your problems comprehending the written word are leading you astray is apparent to me.--PercyEdited by Percy, : Typos.

And you should have said "functionally less important," because that's what Kimura said. Kimura did not use the term "junk DNA." And once you say things right it doesn't support your position at all. I can tell that you're under the impression that this Kimura quote somehow advances your position, but not being able to misinterpret Kimura with your flair and panache I have no idea why.Seriously, dude, get a clue. Why don't you read and reread and reread again that Kimura paper you're quoting from in its entirety until you actually understand him, being careful to note when he's talking about evolution at the molecular versus phenotypic level, and trying to avoid making mistaken misinterpretations about passages that mention advantageous mutations. Here's the link again: Retrospective of the last quarter century of the neutral theoryOf course it will take you longer to understand the paper than other people. You're in same position as Linus from the Peanuts strip. One night Charlie Brown sees Lucy and Linus looking up at the stars, and Lucy is telling Linus all kinds of nonsense. Charlie Brown comments, "Poor Linus. He's going to have to go to school twice as long as everyone else because he has to unlearn everything Lucy tells him."--Percy

As Percy no, I'm not a moderator. Admin, my linked account, is a moderator. I'm not playing a moderator role in this thread. But if you feel like you're experiencing problems in a thread then you should raise your issues at Report discussion problems here: No.2 and devote your attention in this thread to responding to the points people make, just as we are doing for the points you make. I will describe my points again.Kimura never uses the term "junk DNA." He instead says "functionally less important." And he's talking about variation at the molecular level, not the phenotypic level. We've told you this many times in this thread.The other point I'll just repeat: In case it isn't clear, this is where instead of evasion you explain how this Kimura quote supports your point.--PercyEdited by Percy, : Grammar.

You've lost the thread of the conversation. What you said that I objected to was, "It therefore made sense to Kimura that the only place the variation needed by evolution could take place was in the junk DNA." This is, of course, false.Reread my Message 218 where I describe how you were making two contradictory claims about what Kimura believed. You were claiming that he both acknowledged and rejected that evolution could occur in functionally important DNA.There's no substitute for knowing what you're talking about, and you clearly don't. After more than 200 posts you're still making the same mistakes you started with. I again suggest you read and reread the paper you've been quoting from until you understand it: Retrospective of the last quarter century of the neutral theory. Keep a dictionary of genetics terminology close by and refer to it often.--Percy