Sunday, November 13, 2011

Jonathan Wells Talks About Genetic Load

Most people don't understand the positive evidence for junk DNA—this includes most scientists. Paulmc tried to convince the readers on Uncommon Descent that they had been misinformed about junk DNA. The fact that our genome has huge amounts of junk DNA is not just an argument from ignorance—an argument that most IDiots are familiar with—because there are several good reasons for concluding that most DNA has to be junk.

Wells addressed those arguments in: Jonathan Wells on Darwinism, Science, and Junk DNA.

Not Interested in How Much of Our genome Is Junk
Second, "paulmc" wrote that "there are a number of strong lines of evidence that suggest junk DNA comprises a majority of the human genome." The lines of evidence cited by "paulmc" included (1) mutational (genetic) load, (2) lack of sequence conservation, and (3) a report that "putative junk" has been removed from mice "with no observable effects." In addition, (4) "paulmc" wrote that "there is an active other side to the debate" about pervasive transcription. I’ll address these four points in order.

Before I start, however, I’d like to say that I’m not particularly interested in debates over what percentage of our genome is currently known to be functional. Whatever the current percentage might be, it is increasing every week as new discoveries are reported—and such discoveries will probably continue into the indefinite future. So people who claim that most of our DNA is junk, and that this is evidence for unguided evolution and evidence against ID, are making a “Darwin of the gaps” argument that faces the inevitable prospect of having to retreat in the face of new discoveries.
As I pointed out in my review, Wells really isn't interested in explaining to his readers how much of our genome is known to be functional. It would be embarrassing. Wells goes on and on about the discovery of little bits of functional DNA in a variety of species but he never says anything about how much functional DNA has been discovered, as a percentage of the total.

I figure that over the past twenty years or so there has been credible evidence that about 1% of putative junk DNA has a function in any given species. With that kind of "trend," we only have to wait 2000 years until all junk DNA has been found to be functional!

There's a very good reason why Wells doesn't want to tell his readers about percentages.

The other point I want to make about Wells' statement is that it's internally inconsistent. He opens with an admission that there really is positive evidence for junk DNA and closes with an accusation that it's all a "Darwin of the gaps" argument from ignorance.

Isn't that strange?

Genetic Load Is Just a Theory

The genetic load argument dates from the late 1960s when several experts in molecular evolution realized that humans could not survive if most of their genome was susceptible to mutation. They calculated that only small percentage could actually be functional and the majority had to be impervious to nucleotide substitutions and insertion/deletions [Genetic Load, Neutral Theory, and Junk DNA], Facts and Myths Concerning the Historical Estimates of the Number of Genes in the Human Genome].1

Theme
Genomes
& Junk DNA
The argument is based on the rate of mutation, which is largely due to DNA replication errors. The biochemistry is very well understood [Mutation Rates]. All recent data on genome sequencing confirms the mutation rate; the only scientific controversy is whether it could be as much as 2× higher than the biochemstry suggests. That dispute doesn't have any significant affect on the genetic load argument.

Wells correctly points out that the exact mutation rate is controversial. He then uses this as a way to discredit the genetic load argument because it's just "theoretical."
In other words, the first line of evidence cited by "paulmc" is not evidence at all, but a 40-year-old theoretical prediction based on questionable assumptions. The proper way to reason scientifically is not "Ohno predicted theoretically that the vast majority of our DNA is junk, therefore it is," but "If much of our non-protein-coding DNA turns out to be functional, then Ohno’s theoretical prediction was wrong."
Imagine that! The positive evidence for junk DNA is just "theory" based on mutation rates that aren't known exactly and on our understanding of genetics. The mutation rates are known facts so I assume Wells is questioning genetics. I guess that's why he didn't feel the need to tell his readers anything about the genetic load argument.2

BTW, does everyone appreciate the irony of Wells dismissing genetic load because it's "just a theory"? Even if it were true that genetic load is entirely a theoretical argument, why should Wells dismiss it? Isn't his whole book about supporting a "theory"?

The correct way to interpret the genetic load argument is ...
Everything we know about mutations tells us that a significant percentage are deleterious, or harmful. The evidence from decades of study on mutation rates tells us that the average human embryo will have over one hundred new mutations. Even if only a five percent of these are deleterious, it means that every new-born human will carry at least 5 new lethal mutations. At at that rate, the human species will go extinct in a very short period of time based on our understanding of population genetics.

However, if only a small percentage of our genome (~10%) is dependent on specific DNA sequences, then the number of lethal mutations falls below one per zygote and this is tolerable.


1. The Genetic Load argument doesn't preclude a function for most junk DNA. It could still have a function that's independent of sequence—like some form of "stuffer." What it rules out is the idea that large portions of our genome have sequence-dependent functions. Those are exactly the kind of functions that Wells emphasizes in his book.

2. The posting by Wells has all the hallmarks of a tentative position that he's not certain about. I strongly suspect that the reason why Wells "forgot" to describe genetic load in his book is because he didn't know about it. (He still doesn't seem to understand it.)

22 comments :

  1. Until you can remove all the alleged junk and have the organism develop correctly and have no issues at all, then you don't have any evidence for junk DNA.

    IOW Larry we are all waiting on you to support YOUR claim.

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  2. What claim have I not attempted to support to the best of my ability?

    I've presented abundant evidence for junk DNA over the past 21 years.

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  3. Joe G, your epistemology might benefit from http://lesswrong.com/lw/1ph/youre_entitled_to_arguments_but_not_that

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  4. @Joe G:

    So the only valid evidence for junk DNA would removing all of it? Nothing else counts?

    In that case, I guess you can show that removing any piece of DNA in an organism will cause it to develop incorrectly, right? Otherwise you don't have any evidence against junk DNA.

    Agreed?

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  5. Until you can remove all the alleged junk and have the organism develop correctly and have no issues at all, then you don't have any evidence for junk DNA.

    What part of that don't you understand?

    And if you don't have that ability then you don't have anything to support you claim.

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  6. Until you can remove all the alleged junk and have the organism develop correctly and have no issues at all, then you don't have any evidence for junk DNA.

    The claim isn't that junk DNA is something you can remove ENTIRELY and still have a functional organism. Did you not just read this post about genetic load? Junk DNA is still required as a buffer against deleterious mutations. This is a "function" of junk DNA, but it is a "function" that is independent of sequence.

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  7. anonymous says,

    Junk DNA is still required as a buffer against deleterious mutations.

    I don't believe that. It's an argument for function that makes absolutey no sense whatsoever.

    I mentioned "stuffer" DNA just as an examle of functional DNA that is independant of sequence. None of those kind of functions make sense. That's why I maintain that 90% of our genome is junk.

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  8. I find it very curious about how ID proponents treat Jonathan Wells. He is a self-confessed member of the Sun Myung Moon's organization, the Unification Church, which many regard as a cult. Some cult watch organizations regard it as particularly pernicious and dangerous, and classify it as of the "mind programming" variety.

    And most mainstream Christians too would also label the Unification Church as a cult, and as such lump it with other cults such as Scientology, Jehovah's Witnesses and even Mormons. Furthermore, many Christians regard these cults as manifestations of Satan. As an ex-Christian myself, I can guarantee that the local Baptist or Church of Christ congregation is not going to invite a Moonie to speak at their church anytime.

    Yet ID supports, who are of course predominantly evangelical Christians, seem to have none of these qualms. In fact Jonathan Wells is quite the hero among there midst. But there still remains the uncomfortable and awkward fact that if his dealings with them were on topics of religion or theology, Wells would be be treated like a pariah and even an "agent of Satan".

    So they are very curious bedfellows indeed, and I suspect that privately at least many ID supporters are less than comfortable with the arrangement. But given that they seem to have such a dearth of real qualified scientists, I suppose beggars cannot be choosers.

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  9. @Kartrev,

    You aren't religious? You think our universe was intelligently designed by a superior alien race from another universe? You have some letters after your name? Welcome new Senior Fellow! See everyone, ID is science, not religion.

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  10. Well, I am glad that Wells has taken the time to attempt a criticism of what I wrote on UD. I hope he'll join in for comments too.

    I am quite surprised by the lack of sophistication in his answers: he doesn't address the quantitative issues at hand - particularly around the mutational load argument. I am trying to continue the discussion there at UD.

    If anyone is interested, I will probably write about this elswhere, as comment threads on UD are not ideal. I've just started a blog in the last week, where I might write more. Apologies for the vulgar self-promotion.

    -- PaulMc(on UD) / Paul McBride.

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  11. Until you can remove all the alleged junk and have the organism develop correctly and have no issues at all, then you don't have any evidence for junk DNA.

    What part of that don't you understand?


    OK, you have made the position clear. You have to remove all of it before you have any evidence for any of it. Yet you're the one who says junk is also entirely compatible with design, so it doesn't bother you... The Denial is strong in this one. Shame about the grasp of fundamental logic.

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  12. Joe G said...

    Until you can remove all the alleged junk and have the organism develop correctly and have no issues at all, then you don't have any evidence for junk DNA.

    Just like you have to remove all the air from a bell jar or you don't have any evidence for the existence of a vacuum.

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  13. Kartrev, your points are good. The IDiots, especially at UD, will take any support they can get from anyone, no matter how crazy that person is. That they allow joe g to post his swill there is proof of that.

    joe, the muslim creationist and tick farmer, repairs toasters in his basement and likes to pretend that he's a scientist. He and wells make a fine pair.

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  14. Joe G:

    *cough* onion test/fugu *cough*

    There are excellent natural experiments of the sort you demand. No need for a lab experiment.

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  15. By the way joe, you said "we are all waiting...". Who's "we" and why do you IDiots constantly say "we" when you're only speaking for yourself? Do you think that just saying "we" gives your claims or questions more credibility?

    And speaking of claims, when are you IDiots going to support your claims with some real, positive evidence, instead of just a lot of religious gobbledegook, bald assertions, and Darwin bashing?

    Since you think that all putative junk DNA would have to be removed, and the organism would still have to function normally, to show that the removed DNA really is junk, then it should be just fine to turn that around and expect you to show that all DNA is required for an organism to function normally. After all, you IDiots do claim that there's no such thing as junk DNA.

    Maybe you can do some tests in your basement lab and get the evidence that supports that assertion? For a self proclaimed brilliant scientist like you it should be easy.

    Tell me joe, is there ANY junk DNA in any organism? If you say no, how do you know? If you say yes, then explain why it's there.

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  16. Direct evidence for junk DNA?

    1) pseudogenes:
    Mouse
    http://tables.pseudogene.org/Mouse60
    human
    http://pseudogene.org/human/index.php

    More species can be flipped through at the human link.

    2) Megabase deletions of mouse DNA
    http://www.nature.com/nature/journal/v431/n7011/full/nature03022.html

    The punchline being "We deleted two large non-coding intervals, 1,511 kilobases and 845 kilobases in length, from the mouse genome. Viable mice homozygous for the deletions were generated and were indistinguishable from wild-type littermates with regard to morphology, reproductive fitness, growth, longevity and a variety of parameters assaying general homeostasis".

    3)nucmts - nuclear copies of mitochondrial DNA fragments

    In dogs - http://www.ncbi.nlm.nih.gov/pubmed?term=PMID%3A%2012140679
    In bees - http://www.ncbi.nlm.nih.gov/pubmed?term=PMID%3A%2017404397
    In cats - http://www.ncbi.nlm.nih.gov/pubmed/7932781
    A general review
    http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000834

    I'll keep going if you come up with something better than a Russell's teapot argument.

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  17. The whole truth said...

    Who's "we" ... ?

    There are many voices in the heads of the Joes of this world, all struggling to get out.

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  18. 3)nucmts - nuclear copies of mitochondrial DNA fragments

    Not just fragments - a huge chunk (hundreds of thousands of bp) of the Arabidopsis mt genome can be found in the nuclear genome.

    http://www.nature.com/nature/journal/v402/n6763/full/402761a0.html

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  19. Thanks Arthur Hunt,

    I tend to search for "numts" as the keyword, so missed that one.

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  20. Numts aren't junk DNA. They have an important, sequence-dependent function: to annoy people who sequence mitochondrial genes.

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  21. Numts aren't junk DNA. They have an important, sequence-dependent function: to annoy people who sequence mitochondrial genes.

    Which definitely proves that there's an intelligent designer. The bastard.

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  22. Old 3-paper Jonny Wells:
    "Whatever the current percentage might be, it is increasing every week as new discoveries are reported—and such discoveries will probably continue into the indefinite future. So people who claim that most of our DNA is junk, and that this is evidence for unguided evolution and evidence against ID, are making a “Darwin of the gaps” argument that faces the inevitable prospect of having to retreat in the face of new discoveries."

    Was anyone else taken aback at the hypocrisy?

    Here:

    "Whatever the current evidence for evolution might be, it is increasing every week as new discoveries are reported—and such discoveries will probably continue into the indefinite future. So people who claim that evolution is false, and that this evidence for unguided evolution just doesn't count, are making a “IDer of the gaps” argument that faces the inevitable prospect of having to retreat in the face of new discoveries."

    ReplyDelete