Monday, July 16, 2007

Casy Luskin Gets it Wrong (Again)

 
This is getting to be really annoying. What is it about the concepts of junk DNA and Darwinism that confuse the IDiots? It's not rocket science.

In today's posting on the Discovery Institute anti-science website, Casey Luskin leads off an anti-evolution posting with,
It’s beyond dispute that the false “junk”-DNA mindset was born, bred, and sustained long beyond its reasonable lifetime by the neo-Darwinian paradigm.
Let me try and make this simple for the IDiots.
  1. Junk DNA is here to stay. It's a lie to claim that the concept has been abandoned by scientists. True, there are some stupid scientists who don't understand what's going on but they do not represent the consensus.

  2. The concept of junk DNA is anti-Darwinian. There's no possible way that a true Darwinist could accept junk DNA. It is incredibly ignorant to claim that the idea of junk DNA was "born, bred, and sustained" by the neo-Darwinian paradigm. On the contrary, it has helped overturn that paradigm, replacing it with a more pluralistic approach to evolution.
It goes without saying that Intelligent Design Creationists think they have a better "paradigm" than real scientists. Luskin is amazed by recent discoveries that some heritable diseases are caused by mutations in regulatory sequences, which he, in his ignorance, thinks are equivalent to junk DNA.
How much earlier might these non-coding “junk” DNA causes of disease have been recognized had scientists operated under an intelligent design paradigm rather than a Neo-Darwinian one?
Me, me, me (pumping his hand in the air). I know the answer ...

12 comments :

  1. I saw the title and thought this was an old post. The last quoted remark is, well, remarkable in its idiocy. What aspect of Intelligent Design Creationism does Mr. Luskin fancy explains such diseases, and how might an explanation have been derived?

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  2. Mark asked what aspect of ID creationism explains genetic diseases. That's easy. The designer did it, just as in his new book Behe explicitly says that malaria was designed. That designer is one mean bastard.

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  3. In the North American form of ID/creationism, the designer, the Christian god, is not a mean bastard at all, but is instead a loving god who is punishing us (reluctantly) for the (supposed) transgressions of some (alleged) people he (allegedly) created thousands of years ago (possibly earlier). In their view, they deserve the diseases their god has inflicted them with, and therefore worship the being who saddled them with those diseases.

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  4. Larry, could you explain a bit further, why do you think junk DNA is anti-Darwinian? Yes, it goes against some tenets of the Modern Synthesis, but is it in your opinion incomaptible with the original principles that Darwin articulated?

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  5. dolphin asks,

    Larry, could you explain a bit further, why do you think junk DNA is anti-Darwinian? Yes, it goes against some tenets of the Modern Synthesis, but is it in your opinion incomaptible with the original principles that Darwin articulated?

    In the modern era, Darwinism refers to evolution by natural selection. Although the Modern Synthesis originally incorporated random genetic drift the hardening that followed the centenary of the publication of Origin in 1959 saw an increased emphasis on adaptation as the only real mechanism of evolution. Neo-Darwinism reflects this hardening, although there's controversy about the real meaning of "neo-Darwinism."

    The presence of large amounts of junk DNA in a genome cannot be explained if your view of evolution is exclusively Darwinian. If it's there it should have a function and if it has no function it should have been eliminated. It is incompatible with strict Darwinism but perfectly compatible with other views of evolution.

    One can search through Darwin's works and come up with several instances where Charles Darwin admitted the possibility of nonadaptive evolution. That's not the issue. When I say that something is anti-Darwinian I don't mean that is is completely contrary to anything Charles Darwin ever thought about. That's not a proper use of the term "Darwinian." Darwinian refers to evolution by natural selection and junk DNA evolves by accident.

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  6. Another fine post, Larry.

    While we visitors to Sandwalk can see that Luskin is just a fart in a hurricane, those paying his six-figure Disco salary through direct contributions are nowhere near as insightful. Sadly, the unfortunate minions coughing up the cash to fuel Luskin's ignorance-mongering propaganda and misinformation machine lack the intellectual wherewithal to comprehend either the void in their own understanding or the tragic public disservice perpetuated by the DI, so they will keep the dollars flowing.

    On a peripherally related, but still biochemically relevant, note, Larry, here is the reference to an April 2007 talk on the site http://www.fora.tv/ dealing with the origin of life as a natural consequence of geochemistry.

    Inevitable Life?
    Santa Fe Institute - Santa Fe, NM
    Inevitable Life? with Eric Smith and discussant David Krakauer.

    http://www.fora.tv/searchresults.php?keywordsearch=eric+smith&x=10&y=11&page=1

    When the page comes up just click the "Launch Fora Player" button.

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  7. Larry, you say:
    The presence of large amounts of junk DNA in a genome cannot be explained if your view of evolution is exclusively Darwinian.

    But isn't this kind of view axiomatically assuming, that "junk DNA" is - as its name would imply - indeed completely functionless, even in evolutionary perspective? As far as I know, there are no comprehensive (or any kind) of studies, that would look at how the "junk DNA"-less individuals of a given species compare fitness-wise, to the wild-types. (Okay, there was a Nature paper couple of years ago, where they deleted a 2 Mb(?) chunck of the genome and the mice seemed fine. But that was an artificial setting, and they were looking only to basic phisiology.) And though technologically is not yet feasible to address such questions, shouldn't we remember our "know unknowns" ;-)?

    Also, in your opinion, isn't our current use of "function" (usually referring to genes wich can be related easily to phenotypes) limiting now? Especially, now post-ENCODE, when we know that "the human genome is pervasively transcribed, such that the majority of its bases are associated with at least one primary transcript and many transcripts link distal regions to established protein-coding loci"?

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  8. dolphin asks,

    But isn't this kind of view axiomatically assuming, that "junk DNA" is - as its name would imply - indeed completely functionless, even in evolutionary perspective?

    Yes, that's the point. If it really is junk then it's a problem for Darwinists. That's probably why they're spending so much time trying to argue that junk DNA doesn't exist.

    Also, in your opinion, isn't our current use of "function" (usually referring to genes wich can be related easily to phenotypes) limiting now? Especially, now post-ENCODE, when we know that "the human genome is pervasively transcribed, such that the majority of its bases are associated with at least one primary transcript and many transcripts link distal regions to established protein-coding loci"?

    I'd be willing to bet that the vast majority of that transcription is spurious and artifactual. Just because a large percentage of the genome might be accidentally transcribed once in a blue moon does not mean that it has a function.

    Would you like to take me up on that bet?

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  9. "I'd be willing to bet that the vast majority of that transcription is spurious and artifactual."

    I certainly agree with that. But does that mean, the organism would be better off (or equally good) without those transcripts and/or the DNA it is derived from? My gut feeling says "no", but then we have to wait until there's data about it.

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  10. dolphin says,

    But does that mean, the organism would be better off (or equally good) without those transcripts and/or the DNA it is derived from? My gut feeling says "no", but then we have to wait until there's data about it.

    My gut feeling is that the transcripts don't mean anything at all. But it's soemthing more than a "gut feeling." It's consistent with everything else I know about molecular biology and biochemistry.

    It's hard to have a "gut feeling" about something that's outside of your worldview so I assume that your perspective is close to the adaptationist position where the idea that something might be useless (junk) is unsettling.

    We'd all like to have real data to settle this question but we're faced with an unusual dilemma in many of these cases. When a researcher advances a case for something it's usually supported by some data—in this case abundant detectable transcripts.

    That puts the skeptics in a difficult position. We're asked to prove a negative; namely that all the transcripts have no function. As you know, that's an impossible demand. All we can do is to show that in some specific cases it's extremely unlikely that a transcript has any purpose but the proponents of function can always say we just haven't tried hard enough.

    For the foreseeable future this will be a debate about ideas, concepts and how to interpret data in the absence of proper controls. It's not a debate that will be decided by data.

    What I'd really like is for reviewers to demand that researchers publish data on the abundance or frequency of transcripts and not just on their identification. Would it make a difference to you if you knew that a transcript of "junk" DNA had only been detected once in one library and that was from HeLa cells growing in culture? Why aren't we given that information in the papers?

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  11. "Would it make a difference to you if you knew that a transcript of "junk" DNA had only been detected once in one library and that was from HeLa cells growing in culture?"

    This is an important point, and yes it makes a huge difference (to me certainly), whether an in vitro observation can be applied to in vivo situations as well.

    However, I don't mean that all those transcripts that were found by the ENCODE people (if real) have to have some function (as I said, I agree with you, that most of them probably don't). But the DNA that codes them could be an excellent substrate for cis-regulatory evolution, and thus over time (especially in an often changing enviroment) it could become important, who has those sequences and who doesn't.
    That said I agree, this kind of thinking has roots in my own biases, as a developmental biologist.

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  12. dolphin says,

    But the DNA that codes them could be an excellent substrate for cis-regulatory evolution, and thus over time (especially in an often changing enviroment) it could become important, who has those sequences and who doesn't.

    Only if the DNA was transcribed on a regular and predictable basis. If it's just random accident that occurs only in only one or two cells over the lifetime of an organism then it's no different from all the rest of the DNA in the genome.

    Given enough time, all of it will be transcribed at least once by accident.

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