Vowles and Amos - the issue of convergent DNA sequences

But that's not what science does. Science is the process by which we construct models about the natural world, and you claim to be doing science.As I said, you clearly don't even understand your own models. You understand them so poorly that you don't even recognize them as models. How can a discussion with you proceed? No, that's you, remember? Yours is the position that all evidence must be taken to support the model of individual, separate creation of species, not mine. You've made it quite clear that no amount of evidence could convince you that common descent was accurate; thus it is you trying to inflate scant evidence into a hollow model. Nonsense. That's exactly what you have. No matter what the evidence supports you come to it from a presupposition that common descent can't be true. You've demonstrated that over and over and over again.Now how about you actually respond to my post? You haven't addressed a single one of my points.

Nope, that's a total straw man you're creating. I am open it creationism, Intelligent Design, and theistic evolution.I believe that an unfortunate process occurred in the way evolution was taught and believed, and much of that process still remains, and basically that the theory was believed and dogmatically asserted as true long before the evidence was understood, and that this same wrong approach continues today.That's why evolutionists will argue against data, in these debates, if presented by someone open to creationism, and yet the same data would be supported by them if an evolutionist was arguing evolution using the data. For the evolutionist, the theory precedes and governs the data, not the other way around, imo. That's my opinion of what I have observed in discussions with evolutionists.

You are not taking time to understand posts before responding to them.I never said that you were unaware that mutation was non-random. That is obvious from our discusssion, and if I didn't realize it, I would indeed be an idiot.What I was addressing was your apparent claim that the V&A paper was the one to reveal this, and that the fact that they were claiming non-random mutation was the reason that evolutionists are squirming at your comments. (When in fact all evolutionists in the discussion have agreed that mutation is non-random.)V&A didn't reveal non-random mutation, it has been known and accepted for a long time that mutation is non-random. You seem to think that the following quotes from the paper suggest that they are claiming to have provided the first real evidence for non-random mutation - but you've simply shown your own misconceptions: True, but that in no way implies that those models are so constructed because evidence for non-random mutation is not accepted. Instead, it is a hell of lot simpler to model DNA evolution with an assumption of randomness; and modeling such evolution accurately with non-random considerations is a daunting task. And that's okay, for the time being. Models aren't claims of reality, they are a simplification of reality that serves as a framework for further studies. I believe they are referring to formalizing anecdotal evidence (from developing genetic markers for mapping studies) regarding mutation bias flanking microsatellites, not anecdotal evidence about non-random mutation in general. No, I am not. It's simply that you don't understand their usage of those terms - they are referring to assumptions made when constructing models, not assumptions made while evaluating evidence.The fact that V&A cite a dozen or so references regarding non-random mutation in their introduction should clue you that they are not claiming to have discovered non-random mutation. They are claiming to have found a mutational bias in sequences flanking (AC)n microsatellite repeats - nothing more, nothing less. It is a form of non-random mutation, but it is not the first time non-random mutation has been shown.Do you understand? But that simply isn't the case - you are making up your own terms that I can only assume that you don't understand, since you've used them inconsistently and refused to provide a definition though asked multiple times.But, I'll try again anyway - what is "convergent DNA"? That term is not used a single time in the V&A paper or the review article; but has been used by you probably a hundred times in our discussions.Also, your responses are becoming more and more absurd - whenever anybody questions one of your ideas or asks you a question, you tell them that they need to read the paper - which again suggests to me that you don't fully understand the paper, otherwise you'd be able to answer.If I recall correctly, when I asked for you to clarify the "convergent DNA" term, you told me I really needed to read the paper. Since the paper never uses that term, I'm not sure how rereading the paper would have helped. But that seems to be all you do; or you have an extremely short memory. One example: We all had a discussion, and WK, TimChase, EZscience, and myself all agreed that the mutational bias described by V&A would indeed confound phylogenetic analysis.SO, when you claim that we act "as if only an ignoramous could envision" such, are you misrepresenting, forgetting, or did you never understand in the first place? Randman, it appears to me that you "have just not read" any of our posts, "nor considered [their] intent and finding", yet you "have the gall to blast" us for the exact opposite of the arguments that we have made, since we all spent a page or two worth of posts discussing how the V&A findings would impact phylogenetic analysis.Some constructive criticism:
- Take your time.
- Read things until you understand them.
- If you still don't understand them, ask for clarification.
- Don't respond to things you don't understand.
- Don't argue for the sake of arguing.
- Don't accuse ignorance or conspiracy if others disagree; actually defend your arguments.
- We're not "out to get you".On a number of occasions you've argued rabidly with people that were agreeing with you. That should be enough to make you stop and think about your posting style.

Where am I claiming that? I am claiming that in context, evolutionists do base their models on the assertion of random mutation, and the paper discusses the same. No one said anything about the first real evidence. You inserted that, but the paper does claim the following: They are specifically addressing the assumption of independent and random mutations as a basis for models of DNA sequence evolution, and mention how that can adversely affect phylogenetic analysis.They add later: So they acknowledge that there is evidence prior, They also reference elsewhere earlier studies and some non-anecdotal evidence, imo, but maybe they consider that anecdotal.Regardless, evolutionists do indeed frequently refer to "random" mutations, and quite specifically do so arguing there against any directional mechanism.For example, evolutionists will argue phylogentic analysis based on the idea that non-coding DNA would only be shared via a common ancestor since the mutations are random and highly unlikely to occur independently.This paper asserts there are directional elements that could be problematic for such claims in phylogenetic analysis.I agree that evolutionists are aware that that mutations are not random, but whether they are yet willing to consider that their claims may be incorrect if based on models that assume random mutation is something I am not so sure of, yet. You keep going back to this, but I never argued that, nor beleived that. In fact, WK and I covered that point awhile back on a differenrt thread, one I believe he linked to, which perhaps you should read.I am not misunderstanding their paper. You are applying wrong assumptions about what I have written. That's wrong actually because they are making claims that this finding could affect phylogenetic analysis, and there is an obvious implicit claim, which you seem to be running from which is we need to understand this more to understand how this could work with other areas of DNA. That term is used elsewhere, but not in the paper. Nevertheless, convergent evolution of DNA is used in the paper, which is the same idea.Convergent evolution of DNA, and convergent DNA, I would have thought would be clear to you as the same concept, but I guess I was wrong. Is there some other way to interpret the phrase "convergent DNA"? When medical journals use that term, are they using it differently or something? I did notice WK agreeing to that, but the other comments on this thread and the one prior suggested especially suggested disagreement. EZ and you suggested that coding DNA would not be affected, and though that is peripheal to convergent sequences for non-coding DNA, the idea for phylogenetic analysis of coding DNA was thus somewhat summarily ruled out, imo, on the earlier thread which did in fact derogatorily dismiss my comments.But you did respond to WK's point, although he had made a similar general assertion before. Nevertheless you added something I consider blatantly misrepresenting my argument. How could you honestly argue that when in reality we had a fairly long discussion acknowleding natural selections role, but debating the timing effect, in selection for traits?This just looks like you bashed the whole idea that any coding DNA sequences could be affected, and then when WK says what I have said, which is it can have an effect, you say, well, that is interesting but what randman "seems to have said."Pardon me, but that's BS.In fact, the language of "predisposition" that I used early on, which you guys bashed as ignorant and wrong, was at WK's suggestion. It was her term he offerred to clarify and earlier claim. He qualified an assertion saying a "prediposition" is a better way to look at it. Now, I am not saying WK and I agree here on a lot, nor that he thinks the emphasis I am putting on this is correct, but honestly, you guys bashed me for saying there was a predisposition, WK's word, not mine.

So scaryfish, what is your take on the term "random" in "random mutations?"This has always confused me. I had a discussion with my professor last year and we decided that it meant "without respect to fitness" or something along those lines. This is because we recognized that each portion of the genome probably has a bias with regard to how much mutation occurs (hotspots) and what type of mutations occur (transitions more often than tranversions), not to mention this new study which indicates that microsatellites bias flanking sequence mutations.

You actually claim that in your post. (Yep, the same one containing the above quote...)You claim that V&A provide the first non-anecdotal evidence for non-random mutation, and that they interpreted previous non-anecdotal evidence as really being anecdotal.This is your incorrect interpretation of their statements (see below). And you are wrong in that claim.They ARE NOT basing their models on "the assertion of random mutation".They ARE assuming random mutation in their models, even though they know that mutation has a non-random component.I already explained that. True. In fact, I directly explained that to you in the post you were responding to.Again, you are arguing against me for something we agree upon.Doesn't that make you stop and think? Do you really wonder why I keep telling you to take time to read the posts? No. They are referring specifically to anecdotal evidence regarding non-random mutation around microsatellites. The anecdotal evidence refers to trends seen during genetic marker design around microsatellites.There is plenty of non-anecdotal evidence for non-random mutation as a general characteristic. They reference that non-anecdotal evidence. Funny, a few posts ago you disagreed. You obviously still have not grasped what a "model" is, why assumptions would be made in that model, or how scientists remain tentative about the results of that model.Here is an example: We want to model how tall a 100-story building, but we are constrained in what techniques we can use. One technique we are allowed to use is to directly measure the height of a story with a measuring tape. We have a crane that only allows us access to the first five floors, so we measure those and determine an average story height. Now, we make the assumption that all stories are roughly the same height, so we model the height of the building as the number of stories multiplied by the average height of the lower stories. When we provide the results of our model, we do so tentatively, stating: assuming a uniform story height, our model tells us that the height of the building is approximately x units high.That number is unlikely to be a perfectly accurate height, but it doesn't need to be. It the result of a model, not a true measurement of reality. By definition, a model is a simplified representation of reality, so it will necessarily contain assumptions.Try to grasp that. No. That is supposition, which is why you wrote that it "could" confound analysis. They have direct evidence of mutational bias in sequences flanking (AC)n sequences. They have no evidence revealing the confounding effect on phylogenetic analysis, though it is likely.Which is why most of us agree that such is probably the case. Wrong. I am completely, with ever fiber of my being, in favor of understanding the molecular genetics of DNA as fully as possible.What I am "running from" is your presupposition that you already have an understanding of what the results of further studies will be, and that such results will have an enormous negative (if not falsifying) impact on the theory of evolution.You have been far too eager to apply the findings of V&A universally to DNA. Well, you still haven't really given me a definition, since you've used "convergent DNA" in a way that is distinct from "convergent evolution of DNA".Will you ever supply a definition?You have experience with medical journals using "convergent DNA"? Can you supply a reference? No, you simply, didn't understand; and your usual argumentative style where you see things as black and white worked against you again.I never suggested that it would not be affected. In fact, I was the one who challenged WK's assertion that it was highly unlikely that it would affected. I provided a reference in support of that challenge.I have made the supposition that coding or non-coding sequence under natural selection will be less effected than sequence not under selection, in an evolutionary sense. That is very different than saying it won't be effected at all, especially give I was the one who spoke out the firmest saying it would be effected. Because our long argument on "timing effect" was a separate argument. (And your "timing effect" hypothesis was inexorably logically flawed.) I have no idea what you are talking about - where did I bash the use of the word "predisposition"?Not only that, the word "predisposition" can be used correctly or incorrectly. Based on V&A's work; that the flanking sequence has a "predisposition" to a certain mutation or evolution is correct; that the flanking sequence has a "predisposition" to evolve towards coding sequence is incorrect. That's absolute bullshit, I agree; given I was the one who pointed it out to WK, not the other way around.See? You are arguing with me on a point we agree on. Doesn't that make you think about your discussion style? At all?

I tend to take it as random as in not mutating towards an ultimate goal. In other words mutation is blind to the outcome, like you said. As you've said it is clear that the types of mutations that occur can be biased, and the areas in which mutation occur can also be non-random. But I do think that natural selection can favour genomes that produce fewer deleterious mutations, by things like codon bias. I guess that is still pretty much random, the process that causes the mutations and the type of mutations that occur are random, it's just skewing the odds away from mutations that are likely to have a major impact by changing what you're starting with.And of course there are some special cases where mutation is very specific and targeted, such as Repeat Induced Point mutation (RIP) in Neurospora

Absolutely false. Your position has consistently been one of opposition to common descent. You can try to lie about it now but you're not going to fool anybody. You're the only one here who has been arguing against data. The rest of us are simply rebutting your erroneous conclusions. Nonsense. Remember it was creationists who devised the theory of evolution, and who gathered the data on which it was originally built. So of course the data preceeded the theory. Your assertion is patently false.Now, for the third time, are you able or willing to respond to the substantive points of my posts?

Uh, wrong, and you cannot show that. In fact, I claimed the opposite they referenced prior studies indicating non-random mutations in the paper. That's just semantics. If you are confused over what I wrote, fine, but I clearly referred to the models. I also think you fail to accept that "random mutations" is a basic assertion within ToE. I agree it is a false assertion, and that evolutionists probably know it's false, but they still try to use it. OK, but they do then refer to other non-anecdotal studies in the paper. No kidding, and that's exactly my point. This study shows that the oversimplification in assuming "randomness" is probably incorrect, that there is some sort of directional aspect to mutations. Thanks for "though it is likely" which indicates the current state of evidence needs to be reinterpreted in light of what is likely and not likely, and thus claims about what is not likely or highly unlikely based in prior faulty models are incorrect, exactly as I have been claiming all along. It's the exact opposite. I am merely looking at what we know rather than we think we know, and recognizing that evolutionists are making claims about DNA without really knowing the facts.Evolutionists have long made claims that mutations are random. Now, I realize that the they recognize they are not completely random, but they make the claim anyway.Perhaps you can explain what they mean?What do they mean by "random mutation"?Now, I suppose you mean mutations not specifically adaptive or something along those lines, but we don't know that yet.For all we know, there are predispositions embedded that are overall adaptive. This would support a sort of theistic evolution or maybe something closer to naturalistic ID.Creationists usually hold, it seems, that the mutations are the opposite, not beneficial overall.My point is that we really just are in the beginning stages of knowing why mutations occur, the type and frequency of mutations, and whether they even can explain all the diversity of life that has developed.I suspect if common descent is true, we will see that the nature of physics and chemistry is such that there was a predisposition that played a major role in evolution, and that it was not strictly random, even in the adaptive sense.But seeing the random claim is sort of tossed out there without much backing it up, you tell me?

I am oppossed to overstatements in common descent claims, and thus think that is a myth, but almost always add when I speak of "myth" that the myth could be true, but evolution has proceeded more along myth-making lines, imo.

randman-Myself, and apparently everybody else that converses with you, are tired of your backtracking, semantics, misrepresentation, and apparent lack of desire to try to understand or have a decent discussion. You are inappropriately argumentative to the point that you make up things to argue about, claiming that people have said the exact opposite of what they had said and referenced repeated times. Every decent point that someone makes is ignored or misrepresented.Very tiring.In response to your ramblings about random and non-random, I'll simply reference my earlier post on the subject, since I have tired of repeating myself.A pertinent line: The first time you responded it, you ignored all of the substantive points, so I'm not even sure why I bother... I guess I keep hoping you'll mature in your discussion style.

Where is the evidence for this significant random component? I am not necessarily denying it, just asking if the assumption has really been tested and understood.ToE does assert non-random mutation. If mutations are not random, then does that make the ToE wrong?In what way are mutations "random"?But really, and I'd have to reread here, but the issue, imo, goes to more detailed and specific claims. For example, if we say, look here, there are similar sequences between humans and chimps so they must have a common ancestor at some point, and diverged at some point.But what if we find that the genetic similarities between chimps and humans are partly due to similar anatomy, and then find that non-coding similarities evolve via convergent DNA patterns embedded in the functional DNA?We don't know so making claims which are based on the assumption of random mutations are wrong. Maybe the appearance of similar non-coding DNA is not due to common ancestry, but common mutations brought on by the nature of DNA and it's chemical properties.Until we understand the causes of convergent DNA, we just cannot assert that common ancestry is the only valid explanation.Can you not see that?Why do you think that is unreasonable?

Like "it's the most accurate model that explains the diversity of life on Earth"? If you're opposed to statements that common descent is accurate, as you continually have been, then one of two things is true:1) You hold the incoherent position of believing that common descent is accurate, but are opposed to stating that it is accurate;
2) You don't believe in common descent.Don't try to play me, Randman. It's insulting, and you're not very good at it.

It's not playing you. I've been very clear all along. Years ago I believe in evolution, and was challenged by someone to look into the evidence for myself. This was in the 80s.What I found was most of what I was taught was bogus in one form or another.Take the use of Haeckel's drawings in depecting recapitulation via a phylogenetic stage. It was clearly false. I am not a scientist, and I heard the evidence it was wrong from a science professor at NC State university (not at the university but he was speaking at a meeting at a nearby university).Nevertheless, in 1997, it pretty much took a paper by some evolutionists to finally address this false claim, or at least in some measure.So my approach is to try to carefully look at each piece of evidence.Frankly, at this stage I do not beleive conclusions should be made. I think the idea that evolutionary theory was a valid theory 100 years ago when the data used back then to support it was erroneous is incorrect.I think genetic evidence is at least some real support for common descent instead of bogus claims such as recapitulation, but at the same time, I don't think we understand it all yet, and I am waiting to see how it emerges.There are days I swing more towards creationism, and other days towards ID, and I am open to theistic evolution, or something between that and ID.I definitely don't think the way evolution is taught is correct, and I think the evolutionist camp treats it more as pseudo-faith approach, but I am not dogmatic on any one form or model of how it happened. The more I look at universal common descent, the more unlikly it seems, so much so that I would think it a miracle and evidence for God if it is indeed true.This message has been edited by randman, 06-27-2005 06:17 PM

Come on. This is what I'm talking about. It's like saying that "the more I think I'm my father's son, the more unlikely it seems." Of course you're the decendants of your parents. And of course common descent is no less likely than an organism having decendants.Only a dogmatic opposition to common descent, that rejects any and all evidence for it without review, would cause you to say something so foolish.