The Nature of Mutations

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Enard W, Przeworski M, Fisher SE, Lai CS, Wiebe V, Kitano T, Monaco AP, Paabo S.
Molecular evolution of FOXP2, a gene involved in speech and language.
Nature. 2002 Aug 22;418(6900):869-72.

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Britten RJ, Rowen L, Williams J, Cameron RA.
Majority of divergence between closely related DNA samples is due to indels.
Proc Natl Acad Sci U S A. 2003 Apr 15;100(8):4661-5.

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Britten RJ.
Divergence between samples of chimpanzee and human DNA sequences is 5%, counting indels.
Proc Natl Acad Sci U S A. 2002 Oct 15;99(21):13633-5.

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Lenski RE, Winkworth CL, Riley MA.
Rates of DNA Sequence Evolution in Experimental Populations of Escherichia coli During 20,000 Generations.
J Mol Evol. 2003 Apr;56(4):498-508.

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"M"...I have recently discovered NCBI and I will check there to see if I can get access to any of these. I will get back to this as soon as I can.And I apologize for it taking so long in between posts, as I have read about it earlier. As I said before, I am subject to call-in and recall five days a week, and then I have little ones that take up most of my time at home. Again, I apologize and I hope that you guys / gals (?) understand.Phos...

I think we still need to agree on a definition of mutation. We proposed this one: --Percy

Slight qualifacation on that definition. For our purposes should we restrict it to heritable changes. A somatic change (say cancer is a mutation) but not of interest in this discussion.

If you're going to reject our explanations as soon as we say the word "evolution", how could we possibly do that?But, I'll try. I'll present some data and we'll try to come up with a theory that generalizes the data through natural processes (a requirement of science).1)Population studies. Long-term observation of populations shows changes in trait frequencies with a correllation to trait usefulness in the environment. Offspring tend to resemble their parents in certain predictable ways (as shown by Mendel). Sometimes new traits seem to appear from nowhere - an organism has a trait that none of it's ancestors had. The change in trait ratios could be explained by a hypothetical "selection" process where organisms with beneficial traits are "rewarded" with more offspring, and organisms with detrimental traits are eliminated.2) Similarity of organisms: Organisms demonstrate an apparent, loose hierarchy of forms - particularly vertebrate life. In particular, the most similar but yet still distinct species tend to be geographically close to each other. One explanation for this is that if a population is split into separated groups, new traits accumulate in those populations until the populations could be classified as different species.3) The fossil record: Fossil organisms display sorting by apparent sophistication over depth of strata. One explanation for this is the gradual emergence of taxonomic forms over geologic time. This would be concurrent with an explanation of common descent for all modern life.I'm sure I've left something out; the point is that the ToE (like any scientific theory) isn't confirmed by one "smoking gun" evidence, but rather inferred from a vast weight of data. That's how science is done.But if you're just going to assert that this researcher or that one "assumes" evolution, you've got a bullet-rpoof way to reject any data that doesn't appear to support your position. In that's the case, why argue with you? You may reject the conclusion of the researcher (which is totally fine) but data is data, no matter what assumptions were held by those who uncovered it. If you have a better theory to explain the above data, let's hear it. Recourse to supernatural entities, however, isn't a hypothesis worth our time. Supernatural entities have no place in science because they're not accessable to science, by definition. Therefore how can any predictions be made about their behavior?

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Hi PLG..An even better review of epigenetics and evolution...unfortunately Nature Reviews Genetics requires a subscription...but you can get it in most university libraries with a bio department.

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Hi Math...hey, is there some way that I could access some of these papers/journals through a university library via the web? I don't even know if it is possible, just shooting in the dark.Tnx for any info! As you can probably guess, the only access I have had to journals is my local public library which I cannot take home. Most of my information that I have taken in is from those and biology textbooks that I have bought and read on my own.As far as education goes (some of you are going to love this, so I hesitate even saying it), I have studied biology texts but never had the money nor the time to take courses. All of my main education was work related that they paid for, and that is all in evidence, its accumulation, processing and presentation. This is where I suppose that I get my unique view regarding the "evidence" for evolutionary theory and its presentation.As far as that goes, to be honest, I see evolutionary theorists (not those who claim to be evolutionists from the "work" theorists do) as people who have purposefully done one of two things. They either pruned their papers to highlight certain things that gave credence to their pet theory, or they honestly assumed certain things in order to procede with their investigations...but then failed to cease assuming those things when the evidence dictated that they were not possibilities. Like any investigation, if there is no peripheral supporting evidence for an assumption, then that assumption is not warranted and most likely not even a possibility.Greetings!This message is a reply to:
Message 127 by Mammuthus, posted 05-06-2003 04:25 AM
Replies to this message:
Message 202 by Percipient, posted 05-19-2003 02:46 PM
Message 209 by SLPx, posted 05-19-2003 03:23 PM
Message 218 by Fedmahn Kassad, posted 05-19-2003 05:58 PM[This message has been edited by Adminnemooseus, 07-09-2003]

From Percipient, 5-19-2003, 02:24 PMPhospho writes:
Because the author believes that evolution has been proven (because he has been unwittingly duped into the bogus terminology and word-games that evolutionary theorists dish out), it is not his fault, he just got caght up into it. Does this make any sense to you?I understand what you're saying, but can see no basis for it. It's interesting that you think terminology has something to do with the acceptance of the evidence supporting evolution (it's more accurate to say it this way than to say "proven"), because your approach has been primarily terminological. You carefully define your terms so that there's no term for "beneficial mutation", then claim that therefore there's no such thing. Meanwhile people have been showering you with examples of beneficial mutations, and there's a running score on discussion of some of those mutations if you've seen Message 180.You can take each supposed beneficial mutation one by one and argue that it isn't really beneficial based upon your special definition of beneficial, but meanwhile the process of evolution effecting environmental adaptation continues to be observed in the world around us.--PercyThis message is a reply to:
Message 195 by PhospholipidGen, posted 05-19-2003 01:56 PM[This message has been edited by Adminnemooseus, 07-09-2003]

From Percipient, 5-19-2003, 02:46 PM It seems that you view laborers in the field of evolution as inherently dishonest people who latch onto the theory of evolution for philosophical or anti-religious reasons and then adhere to it in spite of the lack of supporting evidence and the presence of falsifying evidence. But people don't dedicate their careers to the pursuit of something they believe false, and such a situation as you describe would result in a host of whistleblowing former evolutionists who could finally bear the duplicity no more. Or it would force you to believe in a massive conspiracy where no scientist every breaks the code of silence about the bankruptcy of evolution.As Crashfrog just explained, evolutionary theory explains the available evidence. It is accepted because of the evidence, not in spite of it. The purpose of any theory is to provide a framework of understanding for natural phenomena, and evolution does this for biology. The explanatory and predictive framework it provides has immense value, and this is why it is accepted nearly universally by scientists.As much as Creationists like to believe otherwise, there is no competing theory to evolution. If you think there is, then try providing alternative scientific explanations for the evidence in Crashfrog's Message 199.--PercyThis message is a reply to:
Message 200 by PhospholipidGen, posted 05-19-2003 02:20 PM[This message has been edited by Adminnemooseus, 07-09-2003]

From PhospholipidGen, 05-19-2003 02:47 PM"Q"...

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Well, then, why did you start by playing games? Your whole argument has been, so far, that beneficial mutations aren't really "beneficial" in the strictest sense of the word. If that's not a word game, what is?

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I don't remember saying that. What I remember saying is, though a mutation may carry with a beneficial side-effect, it still remains carrying with it the original deleterious affect.You say that this is not a consideration because that means that I must assume purpose, and you see a cosmos without purpose, only chance and natural selection. This is your paradigm, not mine. So then we must get back to what the facts of nature state. i beleive that I have read about a paper describing the results of tampering with the specificity of proteins, and the paper described the fact that certain areas of the protein was not affected by substitutions and the like, for they did not change the protein's conformation.Yet other mutations did have an effect, and every effect that they had on other areas (particularly regarding the pritein's active site) did change the protein. It rendered it useless, or nearly useless, for carrying out its function. I believe that this demonstrates that, contrary to what some think, the entire genome of organisms was not put together by successive mutations over millions of years.Before I can believe this in a logical and cohesive manner, it must first be demonstrated to me. Do you know of any experiments where an entire and unique genome is being put together from nothing? OK, maybe that a bit out there, how about starting from the basic nucleotides, on up to some kind of organism?To date, I have not seen any evidence, aside from pure speculation worded as "matter-of-fact" statements, of the kind of genetic change that evolutionary theory needs to codify itself. In other words, making some kind of specific change in an organism, creating phenotypic novelties which did not exist before the mutation took place.In other words, please give me something besides speculation to show that mutations of any kind could give something that wasn't coded for before...a fin where before there was none, changing that fin into a leg, changing that leg into your right arm, complete with hand, finger and thumb.I just realized something, perhaps I have been targeting the wrong thing. Irregardless of our argument concerning mutations' standing as beneficial or not, really what the question is, is whether they can produce the diversity on this planet that we behold today.All of the arguments to date have been over what mutations ARE, not what they are capable of doing (to a certain point). Resistance does not change an organism from a single celled organism into something else. Neither does a new copy of a gene.So what can?Greetings!This message is a reply to:
Message 136 by crashfrog, posted 05-08-2003 02:03 PM
Replies to this message:
Message 204 by Percipient, posted 05-19-2003 02:57 PM
Message 207 by Percipient, posted 05-19-2003 03:15 PM[This message has been edited by Adminnemooseus, 07-09-2003]

From Percipient, 05-19-2003 02:57 PMHi Phospho,I appreciate that you're busy, and I can see that you want to be thorough and not miss any posts, but I doubt this discussion can make much progress if you're always replying to two week old messages. It might work better if you could read forward to the present and then reply to those messages that seem most apropos. Just a suggestion...--PercyThis message is a reply to:
Message 203 by PhospholipidGen, posted 05-19-2003 02:47 PM[This message has been edited by Adminnemooseus, 07-09-2003]

From PhospholipidGen, 05-19-2003 02:58 PM

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How do you define "naturalistic paradigm"?

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As I understand it is an approach that uses exactly that for which there is "evidence" and excludes anything else. And by evidence I mean all the different forms of input that science uses and that it is repeatable as needed to produce a broad consensus of both skeptical and "friendly" observers.

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If you think you have "evidence" that suggest that the naturalistic paradigm need revision please tell us.

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My point is this, there are truths, reality, facts that cannot be experimentally reproduced in a lab, and then some not even reproducible out in the field. Yet they exist none the less.You believe in wind currents, do you not? Yet they are unpredictable as to their details. Watch your local weather man today, his predictions about the weather tomorrow, and then watch tomorrow when he shows the stats and compare how good he called it. they are hardly ever right, and even when they are close, they never come close to the details (wind speed, etc.)There are forces in this world that cannot be seen by the human eye, just as certain frequencies of sound cannot be heard by the human ear, yet animals can see them, and hear them as well.When a door opens and slams shut repeatedly, seemingly all by itself...when things fly across the room seemingly all by itself...and when apparitions of people appear out of thin air at their will...these are all things that cannot be repeated experimentally, yet they occur.Please don't start with the nonsense, be adults. I have never taken drugs nor was involved with any kind of cult group, yet I have seen these things, and more. Just because you have never had the experience does not mean that these things did not, nor could not take place.And no, I do not use these things as a spring board for my arguments, they are all from a scientific point of view. As Mayr has stated, the arguments are never concerning the facts of science, but the interpretations of those facts of science.Greetings!This message is a reply to:
Message 139 by NosyNed, posted 05-08-2003 02:32 PM[This message has been edited by Adminnemooseus, 07-09-2003]

From PhospholipidGen, 05-19-2003 03:10 PM

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Begging the question: Where did all those different eggs come from? There's way more alleles in the human population than could ever have been stored in the genetics of two people.

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Negative, I do not believe that this is the case. I wish I had access to my papers right now, but I do remember reading somewhere that the genetic capabilities of just one man and one woman coming together, allelically speaking, is staggering. And yes, I beleive that the human population has a whole lot of variational capabilities.

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The thing is we've come a little farther (understatement) with the theory these days, due to the introduction of knowledge of genetic mechanisms and population studies.

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This was my argument before. Darwinism is dead, and the synthetic theory (Neo-Darwinism) came about because certain key theorists couldn't stand to lose their pet theory. The genetic mechanisms you refer to are the very ones we argue here today. You say that you believe that they are capable of producing a human from a single-celled organism, and I say that this belief is unsubstantiated by the facts.The facts demonstrate that you can change an organism, you can put a leg where an antennae is supposed to be. You can change the genetics of a fly and make its halters full fledged wings, but none of this gave the organism something novel or new, it just changed the area from where it is suppose to be to where it was not suppose to be. This is change, not evolution.When you can produce wings for a horse, or for any other non-flying organism, then you will have demonstrated that evolution is a possibility. Until then, you have no clear-cut evidence, which is why theorists play these word-definition-games. I have already posted about population genetics, they mean nothing to evolution.Greetings!This message is a reply to:
Message 140 by crashfrog, posted 05-08-2003 02:43 PM
Replies to this message:
Message 211 by crashfrog, posted 05-19-2003 03:58 PM
Message 215 by SLPx, posted 05-19-2003 04:35 PM[This message has been edited by Adminnemooseus, 07-09-2003]

From Percipient, 05-19-2003 03:15 PM This is pretty much what Crashfrog means by word games. If a mutation permits an organism to produce more progeny in the existing environment than an unmutated organism, then that mutation is beneficial. Your hairsplitting about "side-effects" and "deleterious effects" is mere word games. The mutation is beneficial if it provides a reproductive advantage, and surviving long enough to reproduce is a pretty big part of this. A mutation that causes an organism's descendents to be a larger proportion of the population some generations down the road must obviously be a beneficial mutation. It's really as simple as that.i beleive that I have read about a paper describing the results of tampering with the specificity of proteins, and the paper described the fact that certain areas of the protein was not affected by substitutions and the like, for they did not change the protein's conformation.Yet other mutations did have an effect, and every effect that they had on other areas (particularly regarding the pritein's active site) did change the protein. It rendered it useless, or nearly useless, for carrying out its function. I believe that this demonstrates that, contrary to what some think, the entire genome of organisms was not put together by successive mutations over millions of years.It of course makes no sense to generalize from these examples that all mutations have no effect or only deleterious effects. It's probably been said many times now that most mutations have no effect or are harmful. But some mutations are beneficial.Do you know of any experiments where an entire and unique genome is being put together from nothing? OK, maybe that a bit out there, how about starting from the basic nucleotides, on up to some kind of organism?These are interesting questions, but off-topic. This thread is about mutations, not about abiogenesis.To date, I have not seen any evidence, aside from pure speculation worded as "matter-of-fact" statements, of the kind of genetic change that evolutionary theory needs to codify itself. In other words, making some kind of specific change in an organism, creating phenotypic novelties which did not exist before the mutation took place.You've seen the evidence, you're just still in denial. The ball for the discussion about specific beneficial mutations is in your court again. See Message 180.--PercyThis message is a reply to:
Message 203 by PhospholipidGen, posted 05-19-2003 02:47 PM[This message has been edited by Adminnemooseus, 07-09-2003]

From PhospholipidGen, 05-19-2003 03:17 PMRe: Evidence

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Yeah, totally, PPG. I'd love to hear your evidence that the naturalistic paradigm is incomplete. Of course, never mind the fact that if the existence of supernatural entities could be inferred by their actions in the natural world they would cease to be supernatural, wouldn't they?

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No, they wouldn't. Where do you come up with that illogical conclusion? And, yes, supernatural entities can not only be inferred from their actions, they at times can be witnessed in the act. Whether you can see them or not at that moment is another story.

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"Slap in the face to reality"? Reality as I perceive it contains no supernatural entities. You'll have to show evidence to the contrary that can't be explained by naturalistic means. Of course, no one ever has...

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First off, Frog, just because you have never experienced them doesn't mean that they don't exist. If you choose to live your life by what you can and cannot see, you will never mature.Secondly, plenty of people have gathered evidence of supernatural activity. Whether you choose to believe it or not is another story, but in the end, reality will always win.Enough of this. I would like to start another thread, but as you can see, I have a difficult enough of a time just trying to keep up with this one.Greetings!This message is a reply to:
Message 141 by crashfrog, posted 05-08-2003 02:46 PM
Replies to this message:
Message 212 by crashfrog, posted 05-19-2003 04:08 PM[This message has been edited by Adminnemooseus, 07-09-2003]

From SLPx, 05-19-2003 03:23 PM

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All of my main education was work related that they paid for, and that is all in evidence, its accumulation, processing and presentation. This is where I suppose that I get my unique view regarding the "evidence" for evolutionary theory and its presentation.

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By 'unique' I can only conclude that the true meaning used here is "irrelevant."

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As far as that goes, to be honest, I see evolutionary theorists (not those who claim to be evolutionists from the "work" theorists do) as people who have purposefully done one of two things. They either pruned their papers to highlight certain things that gave credence to their pet theory, or they honestly assumed certain things in order to procede with their investigations...but then failed to cease assuming those things when the evidence dictated that they were not possibilities.

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Those are some serious charges.
I suggest you proviude some supporting documentation or retract such inflammatory claims.
Which reminds me, I am still waiting for support for your earlier claims...

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Like any investigation, if there is no peripheral supporting evidence for an assumption, then that assumption is not warranted and most likely not even a possibility.

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Pity then that evolution does not conform to your criteria for rejection.This message is a reply to:
Message 200 by PhospholipidGen, posted 05-19-2003 02:20 PM[This message has been edited by Adminnemooseus, 07-09-2003]

From PhospholipidGen, 05-19-2003 03:35 PM

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Not in dispute. I never claimed that any particular part of a living organism was without function, only without purpose.

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If you use a screwdriver to pound a nail, it has the function of a hammer. That doesn't mean that it has the purpose of a hammer. There's no way to connect function and purpose, without assuming that the purpose and function of something are the same. But, that's just an assumption.

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And this is an argument with little intelligence behind it. I have seen it on every board that I have ever posted on and it is nothing more than another semantic word-game. Purpose is most definitely connected by function, only evolutionists deny this.

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Anyway, irreducable complexity is child's-play to refute. Consider a stone arch - irreducibly complex in that the removal of any stone will topple the arch. Ergo, it could not have been built stone by stone, right?

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Wrong, obviously. Arches are built stone by stone. How does this work? We put up a scaffold to support the arch as we build it. Is the scaffold as efficient or useful as the arch? No, not at all. But the scaffold is sufficiently simple that it can be built piece by piece, used to construct the "irreducibly complex" arch, and then taken away, leaving only the beautifully efficient arch.

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I was not using this as an argument. A point, but not an argument. And there is only one thing wrong with your ill thought out, regurgitated rebuttal, as with all that use this ridiculous charade of an argument. You totally ignore the fact of the origin of the so-called "scaffolding", and this destorys your whole story.

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Perfectly? Have you talked to women about this? The clitoris is located outside of the vagina, where it becomes rather hard to stimulate with the penis.

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Again, not that I am going off topic here, but...if you know what you are doing, this is not a problem................

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Me...
How is it that, in a world prevously of asexual organs only, could sexual organs ever even get a start, and most importantly, why?

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"Q"...
Because sexual reproduction is great for the adaptation of species.

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You make all the same mistakes. Now you are advocating conscience into evolutionary theory. You are now making evolutionary theory a theory of metaphysical advancement. Please, make up your mind.

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Genitals just evolved to match. They wouldn't have to have evolved from scratch for any animal, much less humans. They simply would have decended with modification, like anything else.

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More "just-so" story telling. Unlike you, I need evidence that this is possible. I will not just take your, or anyone else's word for it, because that is how this whole mess got started anyway. "Darwin said it...it sounds like it would work...it must be real!" Darwin never produced any hard evidence, which is why Darwinism failed. Neo-Darwinism never produced any hard evidence, but was born out of certain assumptions before they could even be verified as being based upon factual information."Genitals just evolved to match" doesn't tell me anything scientific. That is your opinion made in a "matter-of-fact" statement. You are following in the illegitimate shoes of your evolutionary forefathers.Greetings!This message is a reply to:
Message 144 by crashfrog, posted 05-08-2003 03:13 PM
Replies to this message:
Message 214 by crashfrog, posted 05-19-2003 04:24 PM
Message 219 by John, posted 05-19-2003 07:13 PM
Message 223 by salty, posted 05-20-2003 09:50 AM[This message has been edited by Adminnemooseus, 07-09-2003]