Monday, July 30, 2012

Darwinists Don't Believe in Junk DNA

The "news" on Uncommon descent continues to amaze me. Today they put up a post with an ironic title: Sometimes, one runs into ID opponents who are just so confused ….

It caught my attention because my name was mentioned. Apparently some "ID opponent" read my take-down of Jonathan Wells' book The Myth of Junk DNA. This prompted the following response from "news" (lawyer, Barry Arrington).
"The Myth of Junk DNA" is actually quite easy to read. We’ve excerpted a number of passages here at UD. The interesting part is that Darwinists thought that the presence of huge amounts of junk DNA was evidence for their position.
If Barry Arrington had bothered to read my review of Wells' book he would know that this is a lie. You can read the entire series of posts at: The Myth of Junk DNA by Jonathan Wells but I want to draw your attention specifically to my comments on the history of the controversy: Junk & Jonathan: Part 1—Getting the History Correct] [Junk & Jonathan: Part 2— What Did Biologists Really Say About Junk DNA?].

In those posts I specifically addressed the claim by Jonathan Wells that Darwinists believed in junk DNA back in the early 1970s. This claim is totally wrong (i.e. a lie) in several respects.

First, "Darwinists" are evolutionary biologists who think that natural selection is the only significant force in evolution (adaptationists). Junk DNA has no function and this is anathema to real Darwinists. They opposed the concept of junk DNA, preferring to think that eventually we would find functions for this DNA.

Second, even if you generously assume that "Darwinists" is a euphemism for "evolutionary biologists, Wells and Arrington are wrong. Most evolutionary biologists were not fans of junk DNA back then and even today it is not supported by a large percentage of evolutionists. I even posted the results of a poll to show this. I recently attended a meeting of evolutionary biologists and I'm pretty sure that the majority still don't feel very comfortable with the idea that 90% of our genome is junk.

The truth is that the concept of junk DNA was put forth by a minority scientists who were pluralists in the sense that they understood the importance of neutral alleles and random genetic drift. Some of the best evidence (genetic load) came from population geneticists at a time when most evolutionary biologists had no time for that subject.

The vast majority of evolutionary biologists thought that junk DNA was a problem for evolutionary biology—the exact opposite of what Wells claims. Barry Arrington would know this if he had bothered to read any serious reviews of The Myth of Junk DNA but it's quite obvious that he has no intention of exposing his beliefs to critical analysis.

I don't fault Barry Arrington for not understanding genomes and junk DNA; after all, he's a lawyer, not a scientist. However, I do fault him for parroting the opinion of Jonathan Wells and for not making the attempt to find out for himself whether Wells is correct. It wouldn't take much for Arrington to check his facts (Google is your friend.)

In my opinion, the evidence for massive amounts of junk DNA in our genome is overwhelming but I struggle to convince other scientists of this. It's not surprising that creationists aren't convinced.

What is surprising is that they (creationists) don't recognize that this is a scientific controversy that still hasn't been settled. That's why Arrington can say ...
Now that it turns out that much, probably most, of it isn’t junk, is that evidence against the Darwinist’s position?
Creationists think the issue has been settled by scientists and the intelligent design creationist position has been confirmed—your genome really has been designed by God. Not only that, they believe this refutes the idea that natural selection is responsible for junk DNA. They believe this in spite of all the evidence in the scientific literature showing that the debate is still raging and natural selection has nothing to do with the presence of junk DNA.

Isn't that strange?


36 comments :

  1. Darwinists do actually believe that evolution by natural selection is a wasteful and inefficient process. But they are indeed less inclined to believe that organisms would accumulate so much extra DNA that does impose a metabolic and even spatial cost (huge in some plants), and likely contributes to disease. It goes against all what we know about life.

    Larry's own views on "Junk DNA" are not based on any serious analysis of the evidence (he ignores all that I present here), but on his own misconceptions. For example, he thinks that "defective/inactive" retrotransposons must be useless even though countless papers have suggested that they do influence gene expression or DNA replication/repair despite not being able to move around the genome.

    He fails to appreciate that he is the big and healthy hulk of man because his African ancestors lost the ability to produce eumelanin in their skin, when they migrated to Ireland ,by availing of a defective melanin receptor. This allowed them to absorb more Vitamin D that afforded them good teeth and bones.

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    1. @Atheistoclast:

      he [Moran] thinks that "defective/inactive" retrotransposons must be useless even though countless papers have suggested that they do influence gene expression or DNA replication/repair

      No, Larry Moran thinks quantitatively and you don't think quantitatively, if you think at all. Moran points out that only a small percentage (maybe 8-9%) of nucleotides in our genome are known to be constrained by biochemical function. That is a quantitative fact.

      IDologues who have lied through their teeth about the Myth of Junk DNA refuse to make quantitative statements. Instead we get vague gobbledygook like this:

      countless papers have suggested that they [retrotransposons] do influence gene expression or DNA replication/repair

      Notice that our creationist friend does not quantify his statement-- he does not say what fraction of nucleotides in what fraction of transposons have been found to have function, and how much does that function constrain the identity of the nucleotides. Creationists avoid equations, math and numbers, instead preferring meaningless terms such as "much DNA will turn out to be functional." Oh, what does "much" mean? 150 million nucleotides? Out of 3 billion, that's still a minority.

      That kind of thing--"Much DNA"-- impresses the Muggles, it doesn't impress scientists.

      Let's ask our creationist friend the Four Questions about Junk DNA that all creationists evade and weasel out of answering.

      1. You claim there are “hundreds”, or “thousands”, of creation scientists. Can you name 10 base pairs of non-coding DNA (out of 3 billion) with a novel function discovered by any one of those “hundreds” of creation scientists? Just 10 base pairs? Out of 3 billion?

      2. What fraction of all nucleotides in the human genome are right now experimentally known to be functional—not just transcribed—but biochemically constrained as to sequence, due to function?

      3. Under ID theory, what fraction of all nucleotides in the human genome would you predict to be biochemically constrained—and how do you compute that fraction from ID?

      4. Under evolutionary theory, what fraction of all nucleotides in the human genome would you predict to be biochemically constrained—and how do you compute that fraction from evolution?

      Let the weaseling out begin!

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    2. I think both yourself and Larry suffer from a basic incomprehension of the English language. What Larry has established is that about 9% of the human genome is essential. But what he has utterly failed to demonstrate in any way is whether the remaining 91% is in fact "junk", or whether it is functional but non-essential.

      I maintain that we are far from being able to quantify exactly how much of the genome is functional. We just need to do a lot more research and this takes time. But a multitude of observations made over the past 20 years indicate that Larry's premises are unjustified. For example, his insistence that a retrotransposon is "junk" because its ability to move about has been disabled is flat out wrong - this can easily be falsified by citing examples of long-distance regulation by inactive retrotransposons.

      But if I had to speculate, I would estimate that at least 75% of the genome does have some functional role, however subtle and unobvious this may be.

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    3. But what he has utterly failed to demonstrate in any way is whether the remaining 91% is in fact "junk", or whether it is functional but non-essential.

      In fact, I've given lots of evidence that a substantial portion of our genome is junk.

      There is DNA that is functional but non-essential—some members of gene families are examples—but that isn't a significant fraction of our genome.

      We just need to do a lot more research and this takes time.

      We've been at it for 45 years and so far the original hypothesis ("mostly junk") has held up.

      But a multitude of observations made over the past 20 years indicate that Larry's premises are unjustified.

      What "premises" are those? Are they the ones that are figments of your imagination?

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    4. No you don't! You have so far used three criteria:

      1. If a retrotransposon is inactive, it must be useless.

      2. If a sequence of DNA is not conserved, it must be useless.

      3. If I can't think of a potential use, it must have none.

      That really has been it, Larry.

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    5. 1. I never said that all defective transposons are junk. In fact, I've mentioned several papers showing that some have acquired a new function in some species.

      2. I've given examples of some nonconserved sequences that have an essential function and I've discussed, and refuted, the speculations that MOST nonconserved DNA might have a function.

      3. If, after 45 years of trying, nobody has come up with a reasonable potential function for most of our genome then it's perfectly legitimate to tentatively conclude that it has none. It is not scientifc to conclude that it must have some completely unknown function just becaues you don't want it to be junk.

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    6. Larry admits that many inactive transposons have indeed acquired a new function (through "co-option") since their insertion and subsequent disabling by mutation. He also admits that many non-conserved sequences are functional, but that these are exceptions to the rule rather than the norm. But that is isn't exactly what he mentioned in "What's in your genome?": (he regards most intergenic DNA as junk on account that it is not conserved):

      http://sandwalk.blogspot.co.uk/2011/05/whats-in-your-genome.html

      However, in order to support his claim, he would have to actually *demonstrate* that large swathes of the genome really are junk. But in order to do this, he would have to exhaust all the possibilities that they do have some use.

      It would also be productive for him to define what he really thinks is "functional". Many Alu elements are implicated in silencing functional genes - but that might have an adaptive effect that he doesn't realize. In fact, most evolutionary biologists would regard the proliferation of Alu elements as crucial to the evolution of primates.

      The fact is, as Jonathan Wells has often stated, that almost every week a new paper comes out describing the function of some transposon, or some ERV or other region of ncDNA. Larry's advice to the researchers involved would have been "don't bother investigating this as there is nothing interesting at all in these repetitive sequences of DNA!" It is a quintessentially anti-scientific position that Dr. Moran is assuming but he can't see it.

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    7. I predicted atheistoclast would weasel out of answering the simple questions I asked him, and he weasled out just like a creationist.

      They raise the issues like "junk DNA" and they pretend like they care about the data. You ask them to quantify the very issues they raise and present as key-important-relevant-crucial-critical, and without exception creationists weasel out and dismiss the issues they themselves raised as unimportant-irrelevant-forgettable-trivial.

      Atheistoclast: We just need to do a lot more research and this takes time.

      What do you mean "we" Kemosabe? Don't say "we" creationist, say "you" or "they". Creationists are not scientists. Such discoveries are made by evolutionists without exception.

      I asked Clast to name 10 nucleotides, just 10 nucleotides, that are non-coding and have a novel function discovered by a creationist or ID proponent. Just 10 nucleotides out of 3 billion in the human genome.

      Creationists say there are hundreds of creation scientists, and yet those alleged "hundreds" could not find function in 10 non-coding nucleotides out of 3 billion in the human genome.

      So Atheistoclast must say "you" or "they" when referring to any discoveries, past or future, about function in non-coding DNA.

      The fact is, as Jonathan Wells has often stated, that almost every week a new paper comes out describing the function of some transposon, or some ERV or other region of ncDNA.

      The facts are:

      1. Jonathan Wells and Casey Luskin lied through their teeth when they said that molecular biologists said that non-coding DNA was a subset of non-functional DNA. No molecular biologist ever said this. Scientists said non-functional DNA was a subset of non-coding DNA--not the same. Wells and Luskin are pathological liars.

      Do not mention their names again until they have published a grovelling apology for the lying slanders they directed at the scientific community.

      2. None of these discoveries are made by creationists or ID proponents. Only evolutionists make scientific discoveries in biology.

      3. As for non-coding DNA, Jacques Monod & co-workers got the Nobel in 1965 and Jack Szostak & co-workers got the Nobel in 2009 for finding functions in non-coding DNA. Evolutionists all. Creationists have gotten no Nobels for finding function in non-coding DNA.

      4. All of these discoveries about transposons, ERVs. etc. collectively make up a tiny fraction of their respective classes/types of DNA (a minority of transposons, of ERVs, etc.) and in most cases, only a small fraction of nucleotides within them are biochemically constrained.

      I asked Clast four simple questions in my last post, predicted he would weasel out, and he behaved as all creationists do.

      To this I will add two further, fifth and sixth questions.

      5. I have scar tissue on my knee. It is biological. Must it be functional? I have a pretty good hypothesis about how the scar tissue formed. If something is a product of observed, ongoing biological processes, why should we assume it is functional by default?

      Is a dead tree lying on its side functional? Is a rock that apparently rolled down from the top of a rocky hill functional? When we observe the ongoing processes that make things, and they are ongoing and observed, why should we assume by default that everything is functional?

      6. And if it were functional, how do you know the function is organism-level function? As opposed to a transposon or ERV's function simply serving itself. How is a transposon different from an internal parasite? If an internal parasite may serve itself and not its host, why should we assume a transposon's or ERV's function is different and must serve its "host"?

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    8. By your reasoning, and that of Larry's, 90% of the homeobox domain is effectively a waste of space because only 6 residues actually bind to recognition sites in DNA.

      Likewise, plants that are "octoploid" (i.e have 8 copies of their genome) are equally profligate since they need only 1 copy to survive. But it has never occurred to either yourself or Larry that this "extra baggage" may contribute to their robustness and versatility as studies show.

      Science is not easy. It is hard stuff. Those who put their hands up in the air and give up trying to find difficult answers to vexing problems, and who make unwarranted assertions, have no place within science.

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    9. Atheistoclast has succinctly described the reason why ID proponents and creationists like Atheistoclast and Casey Luskin will never be scientists:

      Those who put their hands up in the air and give up trying to find difficult answers to vexing problems, and who make unwarranted assertions, have no place within science.

      I agree: that perfectly explains why ID proponents and creationists have no place in science. That is exactly what creationists an ID proponents do: creationist throw their hands up in the air and give up trying to find solutions to difficult problems.

      All the functions found within non-coding DNA in the last 47 years have been found by evolutionists without exception. No creationist or ID proponent has found any novel functions in any non-coding DNA.

      Creationists and ID proponents threw up their hands and didn't even try or make any attempt to find any novel functions in any non-coding DNA, which includes about 2.7 billion bp in the human genome.

      The creationist "contribution" to science was to make up the execrable lie that some molecular biologists believed all non-coding DNA was a subset of non-functional DNA.

      This is a damn lie. Atheistoclast's creationist authorities all promote it. Does Atheistoclast criticize this? No.

      Molecular biologists said non-functional DNA is a subset of non-coding DNA-- not the same thing at all.

      To repeat: evolutionist Jacques Monod & co-workers got a Nobel Prize for finding novel functions in non-coding DNA in 1965. Jack Szostak & co-workers got a Nobel for finding novel functions in non-coding DNA in 2009.

      That's two Nobels for evolutionists and ZERO for creationist thumbsuckers.

      I asked Atheistoclast (and Casey Luskin, and many other creationists flat out to name 10 base pairs, just 10 base pairs, of non-coding DNA with a novel function discovered by creationists or ID propoenents.

      All creationists, including Atheistoclast and Casey Luskin, weasel out of answering that simple question: just 10 nucleotides. Out of 3 billion. 10 nucleotides.

      Don't weasel out Atheistoclast, answer a damn question just for once in your miserable anti-scientific career, just answer the damn question just once. Answer the damn question you weasel. Answer it you weasel, it's not that hard.

      I'm not asking you something hard, like who created the Intelligent Designer? This is the easiest question I can possibly ask a creationist, and they all weasel out. Name just 10 nucleotides. Out of 3 billion. 10 nucleotides you weasle, 10 nucleotides, list the nucleotides you lying anti-scientific little weasel. Answer the question you weasel, answer it. ANSWER IT WEASEL, ANSWER IT.

      Creationist have no place in science and they never will because they are lying little weasels who cannot answer difficult questions nor even easy questions, they just
      weasel weasel weasel you lying little weasel.

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  2. I am an evolutionary biologist, but not a Darwinist in the sense as described by Larry. I do study adaptive processes, and think that most interesting traits are shaped by natural selection in some way or other, but do of course know that many parts of the genome are neutrally evolving (drifting). Further, I don't know what percentage of the human genome is junk, but would have absolutely no "problem" believing it could be as much as 90%.

    Just wanted to get that off my chest.

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  4. Larry, that was a "News" item at UD. Doesn't that make the author Denyse O'Leary rather than Barry Arrington?

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    1. No, I don't think so. They both publish as "news" but this has to be Arrington because it's too well-written to be Denyse.

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    2. Comments 5 and 6 at that thread at UD are an exchange between the two and suggest to me that Denyse was the author.

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    3. To me, those comments indicate that Barry Arrington is the author.

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  5. You must not be one of them there Darwinists if'n you don't think all DNA is essential and necessary and functional and adaptive and whatever. Welcome to the ID camp.

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  6. I'm not so sure about your negative opinion of evolutionary biologists. Surely I cannot remember ever talking to a colleague who expressed any doubts about the fact that coding region are swimming in a vastly larger sea of junk DNA. On the other hand, people are quick with an adaptationist explanation for the lack thereof in bacteria, but that makes sense to me.

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    1. I agree. I hardly know any evolutionary biologists who don't agree that the great majority of the DNA is junk. Back in the 1950s and 1960s population geneticists noticed that there was just too much DNA in the genome to have it all be functional, since that would lead to a mutational load that was much higher than we observed (and higher than the organism could tolerate). So they suspected something funny was going on. After Ohno's 1969 book most population geneticists and many other evolutionary biologists agreed with him about that. There had been panselectionists (mostly in the U.K.) who held out a bit, but by now almost all of them are agreed.

      Molecular biologists were a bit more skeptical, because they tend to view the cell as an elaborate machine, and if all the DNA is functional, think of the large number of grants that can be applied for to study it. But the discovery of transposons, SINEs, LINEs, and short tandem repeat sequences has impressed on them that most DNA is junk, and since about the 1980s they have taken that view.

      And of course all of this was a surprise to "Darwinists". Far from wanting to believe in junk DNA they had to swallow hard. Now about the only believers that there is no junk DNA are creationists. They like to claim that this is a prediction from "ID theory" but none of the major "ID theorists" talked about it (not Dembski, not Behe, for example). In fact it is a prediction from theology, about what a Designer would intend. They don't want to admit that.

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    2. Unfortunately, knowledge about junk wasn't too comon amongst those genome sequnecing guys (remember prdictions of way too high gene numbers) and the same can be observed in the emerging field of systems biology. I guess much of this is due to the fact that people without a proper training in genetics and evolutionary biology are entering the field.

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    3. The too-high gene numbers continued long after almost everybody agreed that most DNA was junk. Even if there had been 100,000 genes there that still would leave the great majority of DNA without function. So I don't think reluctance of people to accept that there was junk DNA was the reason for the too-high gene numbers.

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    4. The only people who continue to assert that 90% of the genome is "junk" are ideologues like Moran and Felsenstein who aren't prepared to carry out serious research into investigating why so much ncDNA has accumulated in the genome (no serious person can claim it has always existed from the outset). The fact is that most evolutionary biologists regard "junk DNA" as a kind of "dark matter" of the genome that will yield important revelations and already has done.

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    5. No creationist, scientists do not call "junk DNA" "dark matter". "Dark matter" is non-coding DNA. "Junk DNA" is non-functional DNA.

      For example, in Sean Carroll's Endless Forms Most Beautiful he is very clear that non-coding DNA is what he calls "Dark Matter."

      Carroll describes Jacques Monod & co-workers research into finding functions in non-coding DNA for which they received the Nobel Prize in 1965. Evolutionists obviously, no creationist or ID proponent has ever discovered novel functions in even one base pair of the billions of non-coding DNA base pairs in the human genome.

      Scientists believe

      (A) Non-functional DNA is a subset of non-coding DNA.

      But lying creationist weasels like Atheistoclast, Casey Luskin and Jonathan Wells lie and and say that molecular biologists believe

      (B) Non-coding DNA is a subset of non-functional DNA.

      (A) and (B) are not the same. Creationists and Intelligent Design proponents are liars.

      Again, I will ask creationist weasels to answer these four simple questions, which no creationist has ever even attempted to answer:

      1. You claim there are “hundreds”, or “thousands”, of creation scientists. Can you name 10 base pairs of non-coding DNA (out of 3 billion) with a novel function discovered by any one of those “hundreds” of creation scientists? Just 10 base pairs? Out of 3 billion?

      2. What fraction of all nucleotides in the human genome are right now experimentally known to be functional—not just transcribed—but biochemically constrained as to sequence, due to function?

      3. Under ID theory, what fraction of all nucleotides in the human genome would you predict to be biochemically constrained—and how do you compute that fraction from ID?

      4. Under evolutionary theory, what fraction of all nucleotides in the human genome would you predict to be biochemically constrained—and how do you compute that fraction from evolution?

      Let the weaseling out begin!

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    6. Dark matter of the genome

      The search for more and more functional ncDNA, previously regarded as being junk, is now a major part of finding cures for genetic diseases.

      http://www.guardian.co.uk/science/blog/2011/sep/14/dark-matter-of-the-genome

      Now stop libeling me with false claims that:

      1. I am a creationist.
      2. I believe there are thousands of creationist scientists.
      3. I am in a position to know the function of every DNA fragment. Nobody is.
      4. I am in a position to predict the functional constraint of all DNA sequences. Nobody is.

      I believe that the accumulation of ncDNA, like retrotransposons, just like gene/genome duplication, is a natural process. I just don't agree with Larry that this process is accidental in nature, but has shaped the genome and made it more robust and versatile. I endorse Shapiro's view that these transposons are a form of "natural genetic engineering" that facilitate adaptation.

      Like I say, I don't know any evolutionary biologist who claims that the explosion Alu elements has not beneficially affected primate evolution. Show me one who rejects this.

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    7. @Atheistoclast:

      Now stop libeling me with false claims that...:

      3. I am in a position to know the function of every DNA fragment.


      You're a liar, but not a good one. At no point did I ever ask you, or any creationist, to describe the function of every DNA fragment.

      I asked you to describe:

      (A) just 10 nucleotides of non-coding DNA with a novel function whose function had been discovered by a creationist or ID proponent. That's 10 out of 3 billion, or 0.0000003% of the human genome.

      Instead, you assert that I asked you to describe.

      (B) the function of every DNA fragment.

      What a lying little weasel-- did you think I wouldn't notice the difference between 10 and 3,000,000,000!?

      The difference between what I said, and what you said I said, is only off by a factor of 300 million, or 30 billion percent. True, creationists consider that a small error.

      I am in a position to predict the functional constraint of all DNA sequences.

      I never asked you, nor any creationist, to predict the functional constraint of all DNA sequences. I repeated my question to you several times so you know exactly what I asked. You know it wasn't that.

      I asked you for the fraction of nucleotides in the genome that are biochemically constrained by function. A fraction, a percent, is one number.

      If you ask most scientists that, they'll either give you a percent or say, "I don't know but I know how to look it up."

      You ask a lying creationist that, and he twists it around into something completely different, such as:

      I am in a position to predict the functional constraint of all DNA sequences.

      I have never asked a creationist a difficult question. I only ask them simple, simple, simple, infantile questions that are direct and which they refuse to answer.

      Creationists are not lying little weasels because they can't answer hard questions. They're lying little weasels because they refuse to answer easy, simple questions relevant to the topics they themselves raise.

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  7. "I don't fault Barry Arrington for not understanding genomes and junk DNA; after all, he's a lawyer, not a scientist."

    Even lawyers can use science as a way of knowing, so I can certainly find fault with someone who doesn't take the trouble to understand that about which he pretends to speak authoritatively.

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  8. @Diogenes, you seem...angry, frustrated, perturbed. Your use of incredulous labels (pathological liars, thumbsuckers, lying little weasels etc..) on those you disagree with is rather detestable and detracts from your argument.

    Try toning it down a bit, view those you disagree with as other human beings who may simply be more or less mistaken than you are. Disagree, challenge, debate, but please abandon the rhetoric.

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    1. When it comes to Atheistoclast/Joseph Esfandiar Hannon Bozorgmehr, the labels applied by Diogenes do not even begin to do this creationist wackjob justice.

      Keep up the good work Diogenes.

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    2. Except that I am not a creationist. I am actually a vitalist, but you wouldn't understand what I mean by that.

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    3. I don't think this is about disagreement, but about IDiocy. Thus the words are mere descriptors. The most appropriate for the IDiots.

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    4. So you are a vitalist wackjob ?

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    5. @Anonymous:
      you seem...angry, frustrated, perturbed.

      Wow, with your incredible powers of deduction, you should work for Scotland Yard. It boggles the mind. How could you possibly deduce that just from my repeated use of the phrase "You lying little weasel." Your preternatural powers of perception are astounding. You could be a TV psychic with powers like that.

      Your genius super-powers are like those of Counselor Deanna Troy on Star Trek. The Borg are shooting 10,000 photon torpedoes at the Enterprise, and she uses her super-powers of empathy to say: "Captain, I thenth hothtility." Gee, ya think?

      Your use of incredulous labels (pathological liars, thumbsuckers, lying little weasels etc..) on those you disagree with

      Hold on there Kemosabe. I call people liars if they disagree with known facts-- not because they disagree with me-- when they contradict known facts, and do not correct themselves when the error is pointed out, but instead double down on their lies.

      Not because they disagree with me. Did you think that bit of sophistry, "just because they disagree with you", would slide past without being noticed? Nice try.

      If you make a mistake and correct it, hey no problem, we're all human.

      But if you spout a falsehood, it is proven to be false, and you pile a worse falsehood on top, you're a pathological liar.

      The phrase "thumbsucker" describes non-scientists who assert they know more about science than scientists, after it has been shown they are ignorant or dishonest about scientific facts. (The origin of the phrase is from police work; "thumbsucker" describes policemen who push papers but never pound the pavement.)

      As for "lying little weasel" it is appropriate when someone 1. raises a subject they present as key-crucial-critical; 2. refuses to quantify or specifically define the key aspects of the topic they have raised; 3. when asked specific questions that are crucial to quantifying or measuring key aspects of the topic they have raised, proceeds to change the subject, weaseling out. This is a strategy employed by creationists. Never let them change the subject.

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    7. @Atheistoclast:

      Except that I am not a creationist. I am actually a vitalist, but you wouldn't understand what I mean by that.

      Oh! Here I thought you were a creationist, so I thought you hypothesize an invisible, intangible "mysterious force" whose interactions with matter cannot be quantified, and which cannot lead to testable predictions, and thus whose existence can only be supported by any contrived and fictional "problems" or "failures" of evolution.

      In fact, you're a vitalist, so you hypothesize an invisible, intangible "mysterious force" whose interactions with matter cannot be quantified, and which cannot lead to testable predictions, and thus whose existence can only be supported by any contrived and fictional "problems" or "failures" of evolution.

      Now that's completely different. Wow, was I off base.

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  9. I don't fault Barry Arrington for not understanding genomes and junk DNA; after all, he's a lawyer, not a scientist.

    I would fault Mr. Arrington for pontificating on a subject which he is totally incompetent to discuss. The same applies to IDiots David Klinghoffer and Casey Luskin. They are no more qualified to pontificate on junk DNA then they are to pontificate on string theory.

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  10. "Darwinists" are evolutionary biologists who think that natural selection is the only significant force in evolution (adaptationists). Junk DNA has no function and this is anathema to real Darwinists. They opposed the concept of junk DNA, preferring to think that eventually we would find functions for this DNA.

    This is historically true. There were evolutionary biologists who thought that, and they did prefer to think that eventually we would find functions for most DNA.

    But it does not have to be true. It's possible to believe that natural selection is the only significant force in evolution and still accept that there could be lots of DNA which has no current function, and believe that this junk DNA is not significant in evolution. And the forces which created it are not significant in evolution. That's a point of view which is quite consistent with an adaptationist stand. It's likely to be wrong, but it fits. Similarly, a lot of mutations could be neutral mutations, and it could be argued that those mutations are irrelevant to adaptive evolution. If you define "evolution" as "any change in DNA-sequence frequency" then they are not completely irrelevant since when they randomly change they result in changes in DNA-sequence frequency. But if you argue that some changes don't matter, then it's all jake.

    The truth is that the concept of junk DNA was put forth by a minority scientists who were pluralists in the sense that they understood the importance of neutral alleles and random genetic drift. Some of the best evidence (genetic load) came from population geneticists at a time when most evolutionary biologists had no time for that subject.

    I'm not sure quite which timeframe you're talking about, but I was doing molecular biology somewhere around that time, and in my own experience it was particularly biochemists who were quick to label DNA as junk. I vividly remember one woman who explained about her research, she had extracted an E Coli plasmid and used it to synthesize mRNA in vitro, and mapped some of the genes. About 70% of the plasmid DNA did not produce anything for her, and she said it was all junk. I suggested they might possibly be repressed, and she said no, she only had the transcription machinery from normal E coli cells there and the plasmid couldn't make any repressors. I didn't ask her about the possibility of active control because she was sort of flirting with me and I didn't want to get her upset. But I didn't get anywhere with her regardless, and so even today I regret not asking her about it.

    It's just another face of reductionism. On the one side you have people who think there must be things happening that we don't understand and may not even know about. On the other side you have people who say that if we don't know about it by now then it must not exist. I think it's better to be skeptical about both of those positions.

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