Monday, May 23, 2011

Junk & Jonathan: Part 5—Chapter 2


This is part of my review of The Myth of Junk DNA. For a list of other postings on this topic see the link to Genomes & Junk DNA in the "theme box" below or in the sidebar under "Themes."

Chapter 2 is Junk DNA: The Last Icon of Evolution? It's mostly an explanation of how the concept of junk DNA fits into evolution. According to Wells, Darwin's theory of evolution by natural selection explains how living things descend with modification from a common ancestor. (Recall that Wells rejects common ancestry.) Wells explains that Darwin's original idea has been extended with the discovery of DNA. He describes "neo-Darwinism" like this ...
According to neo-Darwinism, traits are passed on by genes that reside on microscopic thread-like structures in the cells called chromosomes, and new traits arise from accidental genetic mutations.
In order to clear up any confusion, Wells tells us that, "... I will use "Darwinism" in the rest of the book to mean both Darwin's theory and neo-Darwinism" (p. 19). This is important since it's clear that he's talking about the theory of natural selection when he talks about Darwinism or neo-Darwinism.

Wells describes how Ohno coined the term "junk" DNA in 1972 then quotes Richard Dawkins as a supporter of junk. He states his belief that a couple of papers on selfish DNA in 1980 were taken as evidence of junk. He concludes that ...
... some biologists were skeptical of the notion of "junk DNA" from the very beginning—though most accepted it.
Wells fails to distinguish between those biologists who recognize the existence of junk DNA (e.g. pseudogenes) and those who thought that most of our genome is junk. I still believe that only a minority of biologists think that most our genome is junk. I also think that many biologists make a distinction between "junk" and "selfish." I know I do. In my mind "selfish" DNA, such as active transposons or endogenous retroviruses, isn't junk.

Next comes a couple of pages under the subheading "Using Junk DNA as Evidence for Darwinism and Against Intelligent Design." The usual suspects are mentioned. He quotes Ken Miller, Douglas Futuyma, Michael Shermer, Francis Collins, Phil Kitcher, Jerry Coyne, and John Avise. Although their emphasis varies, they all make the point that the presence of junk DNA in our genome is not consistent with intelligent design. It is, however, consistent with evolution (but not natural selection).

Theme

Genomes
& Junk DNA
It's important to note that biologists don't, with rare exceptions, claim that the presence of junk DNA is evidence for Darwinism or evolution. It's consistent with our understanding of modern evolutionary theory but compact genomes with no junk would also be consistent with evolution, especially evolution by natural selection.

Most of these writers are pointing out how difficult it is for Intelligent Design Creationists to make their case in light of massive amounts of junk in our genome. They are mostly arguing against design and not for evolution.1 This point will come up again in Chapter 10.

Wells concludes with ...
The arguments by Dawkins, Miller, Shermer, Collins, Kitcher, Coyne and Avise rest on the assumption that most non-coding DNA is junk, without any significant biological function. Yet a virtual flood of recent evidence shows that they are mistaken: Much of the DNA they claim to be "junk" actually performs important functions in living cells.
The stage is set. In the rest of the book, Jonathan Wells will try and convince us that most of the DNA in our genome is not junk. Pay attention 'cause it's important to keep the main focus of the dispute in center stage. What the scientists are saying is that there's a lot of junk in our genome and, in order to blunt that attack on design, Wells has to show that there's not very much junk DNA (perhaps none). It won't be sufficient to show that a few percent here and there aren't junk. Any amount of junk DNA is a threat to the basic concept of intelligent design. That's why the IDiots are so worried.


1. I often make the same argument against adaptationists. Some of them see design by natural selection as the dominant feature of evolution but that's not what our genome tells us. There's no illusion of apparent design in our genome sequence.

45 comments :

  1. I'm going to go ahead and guess what the Iders overall strategy is going to be: after pointing out the ~1% or so of examples of non-coding DNA that was assumed by many to not have a function until it was discovered to have some sort of role...they'll say the other 99% has a function as well..its just that no one has discovered it yet. No matter what tests of a particular sequence have been done, they can always say scientists just havent done the proper tests. This may not be sound scientific reasoning buts its enough for their followers

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  2. Dr. Moran:
    "It's important to note that biologists don't, with rare exceptions, claim that the presence of junk DNA is evidence for Darwinism or evolution. It's consistent with our understanding of modern evolutionary theory but compact genomes with no junk would also be consistent with evolution, especially evolution by natural selection."

    It must be nice to have a theory that is so flexible that junk or no junk it is still correct.

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  3. anonymous says,


    It must be nice to have a theory that is so flexible that junk or no junk it is still correct.


    It's a mark of a good theory that it be consistent with the data. If natural selection was the only mechanism of evolution then the existence of genomes with huge amounts of junk DNA would be difficult to understand. But modern evolutionary theory can account for junk DNA.

    Modern evolutionary theory can also explain why bacterial genomes have so little junk DNA.

    Intelligent Design Creationism, on the other hand, doesn't explain anything.

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  4. Anonymous writes of evolution:

    It must be nice to have a theory that is so flexible that junk or no junk it is still correct.

    And it must be an absolute bitch to have a theory (ID) that demands no junk, a series of nasty, well-corroborated facts that show lots of junk, and the likes of Jonathan Wells left to make excuses (like "front loading," which is kind of like the Second Coming - if it's not doing what it's supposed to the first time, why then that must mean it'll come back later and do it the second time).

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  5. I predict a rather Woodmorrappe-esque unwarranted and illogical re-definition/extrapolation.

    For those unfamiliar with Woody, he is a classic YEC apologist/shyster. He wrote a paper roundabout 1998 in which he first re-defined virtually all noncoding DNA as pseudogenes, then pointed out that a couple of pseudogenes had been identified as having functions, therefore all pseudogenes(i.e., all noncoding DNA) have functions, therefore they cannot be evidence for evolution.

    The logic is impeccable.

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  6. Dr. Moran:
    "It's a mark of a good theory that it be consistent with the data."

    Evolutions just add new stories to the theory so that any contradictory data is covered by the new story.
    We all know that. There is really no use in even arguing this point.

    The bottom line is that what we observe is the result of directed development.

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  7. "I also think that many biologists make a distinction between "junk" and "selfish." I know I do. In my mind "selfish" DNA, such as active transposons or endogenous retroviruses, isn't junk...."

    That is truly a distinction with a difference. Perhaps some discussion regarding exactly what is accepted as "junk" DNA would be in order? Pseudogenes-- i.e., now-disfunctional remnants of loci that presumably provided some selective benefit in the past-- would certainly qualify, but absent evidence that they affect the phenotype of our species, I'm not ready to confer non-junk status on them. The reductio ad adsurdum is that any bp which connects functional units is, per se, useful and therefore not junk.

    Where do we draw the line?

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  8. Evolutions just add new stories to the theory so that any contradictory data is covered by the new story.

    Welcome to the wonderful world of science. That's how Newton's theory of gravitation, for example, (which still works wonderfully well in most circumstances) was extended by Einstein to become general relativity - a new story (warping of space-time) was added to the theory so that it covered the contradictory data (bending of light by gravity).

    Directed development, on the other hand, has the "advantage" of being a single absolutely unchanging story in the face of any and all contradictory data.

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  9. "Flexible" theories are also inherently unfalsifiable.

    Intelligent design theory and creationism allows for degeneration in genomes due to the fact that natural selection cannot prevent the inevitable accumulation of deleterious mutations and noise.

    However, ID is interested in the possibility that much of "junk DNA" is functional and has been designed. IDers have "curious minds" whereas Moran just wants to kill off any investigation and research because he is not curious.

    I regard Larry as a paragon of anti-science.

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  10. Jud is wrong in thinking that Einstein's theory "extended" Newton's theory.
    Einstein's theory was a new paradigm that replaced Newton's theory.
    In the same way, the old paradigm that the sun goes around the earth, was replaced by the new paradigm that the earth goes around the sun.
    People need to acquaint themselves with the ideas of Thomas Kuhn.

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  11. @Bozo IDers have "curious minds"

    I think you confuse curious with credulous or perhaps just plain dishonest.

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  12. Anonymous writes:

    Jud is wrong in thinking that Einstein's theory "extended" Newton's theory.
    Einstein's theory was a new paradigm that replaced Newton's theory.


    Ah, so e=mc^2 contradicts and thus replaces F=ma?

    Please do try to learn some math and science before you post again.

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  13. I'm amazed that clever advocates should have such a hard time finding explanations for junk DNA that "confirm" intelligent design. The disigner could have needed a matrix. Or (s)he was prescient and hided the coding passages of DNa in lost of junk in order to protect them against ionicing radiation or this or that.

    It seems rather foolish on both sides to cook this up into decisive evidence. Because the next step is of course some IDist to claim that junk is good as junk and therefore designed. Or some IDiot goes into the workshops of creative peoples looking into their dustbins finding lots of junk et voila - junk is a signature of design.

    Be warned. Don't be so foolish to get caught in that cheap trap.

    joe

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  14. Jud: And it must be an absolute bitch to have a theory (ID) that demands no junk...

    It doesn't actually:

    "Why does the genome have junk?"

    "Because G... er, um, the Intelligent Designer designed it that way."

    ID is compatible with literally any data. It explains everything, and therefore it explains nothing. You can see examples of this when IDiots rebut the argument from bad design. Or when IDiots (a la Behe) move the goal posts every time their candidates for "irreducibly complex" systems get debunked.

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  15. Reginald Selkirk writes:

    ID is compatible with literally any data. It explains everything, and therefore it explains nothing. You can see examples of this when IDiots rebut the argument from bad design. Or when IDiots (a la Behe) move the goal posts every time their candidates for "irreducibly complex" systems get debunked.

    I'm in general agreement with your concept, but I'd express it a little differently.

    Evolutionary theory, like any scientific theory, must change its explanations to fit changes in data (for example ideas on inheritance changing from those of Darwin to fit the facts of genetics).

    ID must change the data to fit the explanation (the "bottom line," as one commenter put it) of a Deit- err, Designer.

    Thus the popularity of "front loading," which removes the necessity that DNA have any contemporaneous utility - the Designer's just keeping it on inventory for the future, right? (Why a Designer would need to do this is of course never explained or even questioned.) Or the morphing of "irreducible complexity" into "complex specified information." Why go to the trouble of proving the information's been specified by a Designer when you can just put "specified" right in your definition? QED!

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  16. @Anonymous

    "It must be nice to have a theory that is so flexible that junk or no junk it is still correct."

    Blowfish have barely any noncoding DNA. We have a ton. Evolution has little problem with either situation; IDers must hem and haw about how the Designer has good days and he has bad days and the blowfish was one of the good days when he really had time to go over his designs with a fine-toothed comb. Also, the Designer works in mysterious ways.*

    "Because the next step is of course some IDist to claim that junk is good as junk and therefore designed."

    Ha, they already do that.

    Why do we die? Because the Designer wants us to.*

    Why do our eyes have a blind spot? Because the Designer didn't want us seeing there.*

    Why are some people born with horrible diseases? Because the Designer wants them to suffer.*

    *Any similarities between the Designer and a malevolent God are purely coincidental.

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  17. On junk vs. selfish DNA. I would think of junk DNA as any sequence that's evolving neutrally. Since transposons and ERVs in general are evolving neutrally, I'd call them junk.

    We have to make a distinction between individual insertions and families. The insertions are not under selection, that is their sequences are in no way conserved within the genome (except for those rare sequences that have acquired a function in the individual). But families are under a sort of selection, since copies that have lost the ability to cause new insertions no longer reproduce. But this needs to be clearly distinguished from selection on individual copies.

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  18. John Harshman says,

    On junk vs. selfish DNA. I would think of junk DNA as any sequence that's evolving neutrally. Since transposons and ERVs in general are evolving neutrally, I'd call them junk.

    I'm talking about active transposons and functional endogenous retroviruses (ERVs). Since they are still functional I don't call them junk. They have to be functional to be selfish genes.

    I agree that most functional transposons and ERVs will soon mutate to pseudogenes. That's when they become junk DNA and that's when they stop being selfish DNA.

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  19. My attempted point was that even active transposons are evolving neutrally, and so I would consider them junk. Their sequences are not conserved; they're just brand new junk.

    But of course it's a matter of personal preference.

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  20. John, I am not an expert on this, but I think your definition of junk is too strong. For example, I think the ITS spacer evolves more or less neutrally, yet it appears to have a function. It serves as a spacer, so that its actual code is almost irrelevant, hence not conserved. But this does not exactly make it "junk". Am I missing something about your definition?
    Lou

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  21. Atheistoclast, you claim here that:

    "Intelligent design theory and creationism allows for degeneration in genomes due to the fact that natural selection cannot prevent the inevitable accumulation of deleterious mutations and noise."

    Yet in the thread for Part 4 - Chapter 1, you claimed:

    "Selection is all-pervading. If 50% of the genome were really useless, selection would whittle it down, as it has done in countless examples where even something functional imposed too high a metabolic cost on the organism."

    So 50% junk couldn't persist because natural selection is too strong to allow it, but genomes can accumulate mutations and noise because natural selection is too weak to prevent it? How interesting!

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  22. One Of The Anonymouses wrote:

    People need to acquaint themselves with the ideas of Thomas Kuhn.

    I laugh my frigging socks off when creationist-types invoke Kuhn. The Kuhnian revolution already happened when the previous paradigm, extracted from a 2,000-year-old book of myths and moral advice, was replaced by something with vastly more explanatory power and consistency: evolutionary theory. Of course, we can't rule out that another revolution may occur - but going back a step is not what Kuhn meant at all.

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  23. Perhaps the funniest part of all of this is that the people Dr. Moran is arguing with actually believe that a snake told a woman to eat an apple, and caused everyone to be a sinner, until the zombie son of god freed them from their sin.

    Now I may not know what junk DNA does, but I know if you start with a story like that, you're an idiot.

    I understand that this topic is of great interest to the Doctor, but seriously - don't you have some cool experiments you could be doing that will tell us more about the world we live in than arguing with zombie-worshipers?

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  24. Anonymous said: "It must be nice to have a theory that is so flexible that junk or no junk it is still correct."

    This is a sarcastic reference to a common misunderstanding by creationists of the falsifiability standard. The standard is that one's theory must, at least in principle, produce predictions in some experiments of what one will and will not find, thus leaving it open to falsification. The creationists like our Anonymous friend above want to change the "some" to "all", thus claiming a nonfalsifiability foul if evolution fails to produce such predictions in each and every situation. It's akin to rejecting the theory of bird flight because it can't predict with exact accuracy where a particular bird will go.

    Of course, ID gets a total pass at making any predictions. Funny that.

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  25. It must be nice to have a theory that is so flexible that junk or no junk it is still correct

    if anyone could suggest an observation that could possibly contradict ID I would be surprised.

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  26. flies posted:
    "if anyone could suggest an observation that could possibly contradict ID I would be surprised."

    Can you suggest an observation that could possibly contradict evolution theory?

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  27. Looks like nobody can think of an observation that would contradict evolution theory.

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  28. Anonymous writes:

    Looks like nobody can think of an observation that would contradict evolution theory.

    I can think of a couple off the top of my head; took all of 5 seconds. Pretty darn poor that ID proponents couldn't do the same.

    - The classic "fossil rabbits in the Cretaceous."

    - More specifically along the lines of what we've been discussing, genetic relationships between current species and ancestral species that do not take the form of a nested heirarchy.

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  29. Why would fossil rabbits in the Cretaceous contradict evolution theory?

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  30. I have seen this statement about fossil rabbits in the Cretaceous.
    How does that contradict evolution theory?

    Is it because there is no ancestor line found that would lead to a rabbit at that time?

    But if a rabbit were found then evolutionists would simply say that that proves there must be such a line and it has not been found yet.

    Right?

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  31. Looks like we won't be getting a response to my post about a fossil rabbit in the Cretaceous.
    Pity.

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  32. Anonymous writes:

    Why would fossil rabbits in the Cretaceous contradict evolution theory?

    Anyone with the most elementary understanding of the theory of evolution and the multiple lines of scientific evidence corroborating it would know the answer. Because you lack any understanding of evolution, you don't even know what you're attempting to criticize.

    But if a rabbit were found then evolutionists would simply say that that proves there must be such a line and it has not been found yet.

    Your attempted criticism is so wrong as to verge on pathetic. That is not an insult, it is a simple, accurate statement of fact.

    Most folks here have simply stopped responding to you, because they are tired of having to do your intellectual work for you. Not knowing evolutionary theory is absolutely understandable. Refusing to learn anything about it and expecting other people to do your work for you is fairly close to what I'd call sin.

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  33. Jud, as I said, there is no point talking to you.

    At this point, nobody has said how a fossil rabbit in the Cretaceous would contradict evolution theory.

    Can anyone answer that question?

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  34. Anonymous writes:

    At this point, nobody has said how a fossil rabbit in the Cretaceous would contradict evolution theory.

    Can anyone answer that question?

    Sigh. If you really demand that someone spell out something so simple -

    It's an anachronism. It would place rabbits prior in time to animals from groups ancestral to them - i.e., it would present the same logical impossibility as you being born before your grandparents.

    Flipping these around: If you are born before someone, that person can't be your grandparent. And if rabbits lived prior to animals that the various forms of evidence on which evolution is based - genetic, morphological, paleontological, geological, etc. - say are ancestral to rabbits, then that evidence and the evolutionary theory it supports would be incorrect.

    Any anachronism would do, the more dramatic the better - humans riding dinosaurs as in Ken Ham's "museum," for instance.

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  35. Jud doesn't get it.
    Can someone work out what evolutionists could say if a fossil rabbit was found in the Cretaceous?
    Evolutionists are exceedingly good at just so-stories.
    Does anyone honestly think that you could not work out some story to explain the rabbit fossil?
    Of course you could!
    Stop pretending.

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  36. Since the folks here don't know evolution theory ideas too well, let me help you.
    Think "ghost lineages".
    Think how you currently deal with a "temporal paradox".
    You can make up some story.

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  37. Anonymous writes:

    Think "ghost lineages".

    Think how you currently deal with a "temporal paradox".

    Ah, the typical sequence.

    1- "You can't think of any evidence that would falsify evolution."

    - Two types of evidence presented.

    2. Since Anonymous can't even figure out what one of cited types of evidence is, he fastens on the other and demands (repeatedly) "Explain it to me!"

    - Explanation given in simple, easy-to-understand terms.

    3. Anonymous cries, "You would not accept this evidence as falsifying evolution, neener, neener, neener!" (OK, I added the last 3 words myself.)

    So, about Anonymous' latest distractions:

    "Ghost lineages" are "missing links" - no fossils in the record to verify lineages evolutionary biologists believe to have existed. The history of ghost lineages is a history of evolutionary biologists predicting such lineages and later finding fossil verification. In other words, they are predictions of evolutionary theory that have been verified as correct when the fossils have been found (e.g., the fossils in the whale lineage). This doesn't involve anachronism, so it isn't relevant to my point.

    "Temporal paradox" - This has to do with the ancestry of birds, specifically that there are bird-like feathered dinosaur fossils younger than Archaeopteryx.

    Wikipedia says "Numerous researchers have discredited the idea of the temporal paradox." One basis is that the younger bird-like fossils are not thought to be in the Archaeopteryx ancestral lineage. Another is that there are fossils (rare, but there) of these bird-like dinosaurs that are older than Archaeopteryx.

    However, Anonymous has actually identified a live scientific controversy (though it was considerably hotter before there was so much evidence showing birds did indeed evolve from dinosaurs), and should be given credit for that. There is some genetic work going on with dinosaur DNA, and if that would ever show a true anachronism - that Archaeopteryx did indeed live before animals that are genetically its ancestors - this would qualify as evidence falsifying current evolutionary theory.

    Sounds like something the Disco Institute and like-minded folks should be spending research dollars on.

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  38. As I have said, talking to you Jud is a waste of time.
    But I am glad I have been able to give you an evolution theory education.

    So we see that if a rabbit was actually found in the Cretaceous, evolutionists would dig deep to come up with a just-so story to cover it.

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  39. Your speculation is baseless, since nothing like that has been found, and scientists do not behave as you suggest. Relying on "just-so" stories is what IDers do, which is why they are so criticized. Ditto for evolutionary psychologists, if you'd like a more mainstream example.

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  40. It is funny that evolutionists have no problem recognizing the just-so stories from evolutionary psychologists but do not recognize their own just-so stories.

    Will anyone acknowledge that?
    Or will you try that classic deflection technique of claiming that those you disagree with suffer from that tendency but you don't.
    What blindness!

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  41. If your claim was true then evolutionary scientists would be getting criticism en masse from academics in other fields, such as math and physics. Yet they don't. When chemists claimed to have found cold fusion, physicists jumped all over them. Not so with evolution. The reason is obvious, and the blindness is yours.

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  42. Got to give ScienceAvenger credit for a creative attempt to distract.

    Evolutionists recognize other people's just-so stories. But not their own.

    If a rabbit fossil were found, evolutionists would just come up with yet another just-so story.

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  43. It's not *Cretaceous* rabbits, -- the original quote (from Haldane) was a "*PreCambrian* rabbit.

    We already have eutherian mammals in the Cretaceous --- not modern placentals but the oldest rabbit-like forms are only about 10 million years younger than the end of the Cretaceous. A Cretaceous rabbit would be surprising, but not impossible (the molecular biologists who think that placentals diverged way before the fossil record evidence might think this quite likely).

    No, we need to have a PreCambrian rabbit, i.e. from more than half a billion years ago, before evidence for the first vertebrate. (Actually a Jurassic rabbit might do--- before the split between marsupials and placentals, but Cretaceous is not improbable enough)

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  44. Jud was the one who posted:
    "The classic "fossil rabbits in the Cretaceous.".

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  45. Yes, I know I misremembered the original quote, sometimes attributed to Haldane. But it works anyway - it's not "rabbit ancestors a few million years after the Cretaceous," it's rabbits, full-fledged Peter Cottontails, hopping around with T Rexes overhead, that would pose an insuperable problem for evolutionary theory as we currently know it.

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