Thursday, April 07, 2011

IDiots vs Francis Collins


Here's a video where several IDiots take on Francis Collins and his book The Language of God,. Jonathan Wells is prominently featured in this video and much of the attack is concerned with junk DNA. Wells makes his position very clear. He claims that modern scientific evidence has overthrown the "myth" of junk DNA and those of us who still believe in junk DNA are guilty of a "Darwin of the gaps" kind of argument. That's because, according to Welles, we don't have an explanation for junk DNA therefore we attribute it to Darwinian evolution (6.00 minute mark).

There is a lot of positive evidence that much of the DNA in our genome is non-functional. Wells is dead wrong about this. Furthermore, assuming that this junk DNA is non-functional and assuming that species share a common ancestor, we can explain many observations about genomes. IDiots can't do this. They have yet to provide an explanation for shared pseudogenes1 in the chimp and human genomes, for example. And I haven't heard any IDiot explain why the primate genomes are chock full of Alu sequences derived from a particular rearranged 7SL RNA sequence while rodent genomes have SINES from a different rearranged 7SL sequence and lots of others from a tRNA pseudogene [Junk in Your Genome: SINES].


Did Francis Collins use the existence of junk DNA as support for Darwin's theory of evolution? Here's what Wells says in the video (50 second mark).
If fact he relies on so-called junk DNA—sequences of DNA that apparently have no function—as evidence that Darwin's theory explains everything we see in living things.
I searched in the The Language of God for proof that Wells is correct. The best example I could find is from pages 129-130 where Collins describes the results from comparing DNA sequences of different organisms. He points out that you can compare coding regions and detect similarities between humans and other mammals and even yeast and bacteria. On the other hand, if you look at non-coding regions the similarities fall off rapidly so that there's almost no similarity between human DNA and non-mammalian genomes (e.g. chicken). This is powerful support for "Darwin's theory of evolution" according to Francis Collins. First, because you can construct phylogenetic trees based on DNA sequences and ...
Second, within the genome, Darwin's theory predicts that mutations that do not affect function (namely, those located in "junk DNA") will accumulate steadily over time. Mutations in the coding regions of genes, however, are expected to be observed less frequently, since most of these will be deleterious, and only a rare such event will provide a selective advantage and be retained during the evolutionary process. That is exactly what is observed.
I leave it as an exercise for Sandwalk readers to figure out how to explain this observation if the regions that accumulate fixed mutations aren't really junk but functional DNA. Your explanation should consist of two parts: (1) why the DNA is functional even though the sequence isn't conserved (provide evidence)2, and (2) why coding regions show fewer changes and why comparisons of different species lead to a tree-like organization.

I wasn't able to find where in Origin of Species Darwin discuss this prediction but I'm sure it must be there somewhere. Perhaps some kind reader can supply the page numbers?


1. Every knowledgeable, intelligent biologist knows that pseudogenes exist and they are junk. That's not in dispute. I haven't heard any Intelligent Design Creationists admit that there are thousands of functionless pseudogenes in our genome.

2. I can think of two or three possibilities but no evidence to support them.

45 comments:

  1. "There is a lot of positive evidence that much of the DNA in our genome is non-functional."

    Could you provide some links to material (articles, studies etc) that provides this "positive evidence" please?
    That would be exceptionally helpful.

    ReplyDelete
  2. "Second, within the genome, Darwin's theory predicts that mutations that do not affect function (namely, those located in "junk DNA") will accumulate steadily over time."

    But earlier (in Junk & Jonathan: Part 2) you said:
    "In fact, it [junk DNA] goes against any prediction of Darwinian evolution by natural selection."

    ReplyDelete
  3. There is a case I know of where pseudogenes do have a function: the vsg pseudogenes in the repetitive telomeric regions of trypanosomes. Many of the copies of the VSG have numerous stop codons and could not make a functional protein (nor are they expressed). However, they do serve as a source of sequence variation that can be recombined into the expressed VSG allele to make novel versions. Regardless, this is a special case where a pseudogene can serve a function and not a refutation of the point that IDiots cannot generally explain pseudogenes.

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  4. Dr Moran,

    I am a Geophysics major so I do not assume this correct. My guess is that psudogenes may be attributed to archaic functions no longer supported in the current form, they atrophied, and/or building blocks for future unspecified functions, and/or actual junk built up over deep time through replication error etc, or injected into the genome by invaders such as viruses. This is just my guess, any of it seem possible?

    Thanks

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  5. @Dennis,

    Yes, pseudogenes are the remnants of genes that used to be functional but for some reason have lost their function and now lie dormant in the human genome. We have thousands of them. Some of them are well-known like the gene that used to be required for making vitamin C. Others are olfactory receptor peudogenes left over from the time when we had a much better sense of smell.

    I've forgotten how the IDiots explain the existence of these pseudogenes. Can someone remind me?

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  6. One of the many anonymous readers wants some positive evidence of junk.

    Here are four examples.

    The genetic load argument emphasizes the fact that only a small percentage of our genome can have functional sequences otherwise we would be extinct.

    The deletion experiement is a direct test of whether sequences some non-codong are required. The results indicate they are not required.

    The fact that neither intron size nor sequence is conserved between species suggests strongly that most of it is junk.

    The widespread occurrance of human copy number variation affecting more than 10% of our genome suggests strongly that we can tolerate junk DNA.

    I've forgotten how the IDiots rationalize this data. Can someone remnd me how it's explained by postuating the existence of an intelligent designer?

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  7. Re Larry Moran

    Some of them are well-known like the gene that used to be required for making vitamin C.

    This is also strong evidence of the close relationship and common descent between the great apes and humans as the gene for making vitamin C is defunct in both.

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  8. Could it be that some of these genes that are called pseudogenes are the history of what the gene was. In other words the cell keeps the history just like we keep the history of changes we have made to something.

    That would seem a more intelligent thing to do than to just delete it.

    ReplyDelete
  9. Dr. Moran writes:

    Can someone remind me how it's [the presence of junk DNA] explained by postulating the existence of an intelligent designer?

    An antic sense of humor? An inordinate fondness for beetles? (Oh, wait, that's a different aspect of evolution.)

    I did see a Dembski article circa 2000-2001 or thereabouts recently where he said it was because the designer was intelligent but far from perfect. I presume he's since changed his tune to fit in more comfortably with his present company.

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  10. @ Anonymous Thursday, April 07, 2011 6:45:00 PM said...

    That would seem a more intelligent thing to do than to just delete it.

    The point is that the genome is not "intelligent". It just does stuff and either survives or does not. We only see the survivors, so what we see is biased, leading to design inference.

    @ Anonymous Thursday, April 07, 2011 12:46:00 PM

    More "Positive examples" of specific sections of true "junk" DNA are the thousands upon thousands of reported cases of
    defunct copies of the mitochondrial DNA found integrated into the nuclear DNA. Mitochondrial genes in animal cannot be translated by the nuclear system, as they like to use the UGA codon to mean trypophane, where the nucleaus would see this as a stop codon and terminate tranlation.

    Specific examples;
    In humans and primates (27 papers) http://www.ncbi.nlm.nih.gov/pubmed?term=primate%20AND%20nucmt
    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

    The only odd animals where these are not found are those where there seems to be selection against large amounts of non-coding DNA (like in Drosophila melanogaster)

    A review on the topic
    http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000834

    Sorry that you have to cut and paste the links, but I can't seem to get the link embedding to work on Blogger.

    ReplyDelete
  11. The 'designer' is intelligent - it's just not conscious. A mind can be both, but that should not force us to conclude that the two properties must always correlate and demand such a vehicle.

    Consistently sorting a collection (such as ... ooh, let's say the DNA in a population at any given time) - such that the better tends to remain and the worse tends to be eliminated is a triumph of intelligent design; no deity or aliens required.

    ReplyDelete
  12. "Second, within the genome, Darwin's theory predicts that mutations that do not affect function (namely, those located in "junk DNA") will accumulate steadily over time."

    But earlier (in Junk & Jonathan: Part 2) Moran said:
    "In fact, it [junk DNA] goes against any prediction of Darwinian evolution by natural selection."

    ReplyDelete
  13. A question for the other Jim or anyone else:

    Do these copies of the mitochondrial DNA (that are integrated into the nuclear DNA) regulate the expression of their "parent" gene in the nuclear DNA?

    By "parent" gene I mean the active gene that is very similar to the mitochondrial DNA.

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  14. Allan Miller, you would be very interested in the work of James Shapiro, Univ of Chicago (if you are not already familiar).
    There is an interesting discussion of this in the "Creationist Objects" thread.

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  15. @Allan Miller -

    'Intelligent' meaning 'effective' rather than 'telic' - interesting perspective, though not the ordinary usage of the word.

    Perhaps a bit adaptationist for some.

    ReplyDelete
  16. Could it be that some of these genes that are called pseudogenes are the history of what the gene was. In other words the cell keeps the history just like we keep the history of changes we have made to something.


    Why would a cell need to do that???

    ReplyDelete
  17. Posted earlier:
    "Could it be that some of these genes that are called pseudogenes are the history of what the gene was. In other words the cell keeps the history just like we keep the history of changes we have made to something.

    Why would a cell need to do that???"

    How about in case it needed to change back, if the environment changed. What do you think?

    ReplyDelete
  18. Anonymous said...
    Do these copies of the mitochondrial DNA (that are integrated into the nuclear DNA) regulate the expression of their "parent" gene in the nuclear DNA?

    By "parent" gene I mean the active gene that is very similar to the mitochondrial DNA.


    This is the last question I will answer, unless you actually do the background reading. It is obvious you did not by your question. Even a wiki search will tell you the problem with your question.

    To answer your question - No. Mitochondria are a completely separate DNA genome within our cells. The copy that works is the copy in the mitochondria.

    The copies in the nuclear DNA are complete junk. Even identical copies in the nuclear DNA do not work, because the nucleus misreads the tweaked genetic code of the mitochondria. In animal cells, there is no DNA or RNA movement into mitochondria (and trust me - this had been tried a lot). Mitochondria have their own ribosomes and tRNAs to express the genes they encode.

    There is no active gene similar to the the mitochondrial DNA.

    ReplyDelete
  19. From the evolution point of view, why are there non-functioning copies of the mitochondrial DNA in the nucleus?

    ReplyDelete
  20. Anonymous:

    Could it be that some of these genes that are called pseudogenes are the history of what the gene was. In other words the cell keeps the history just like we keep the history of changes we have made to something.

    Another Anonymous:

    Why would a cell need to do that???

    First Anonymous:

    How about in case it needed to change back, if the environment changed. What do you think?

    I think what the cell "needs" and the mutations that occur to the genes within it are two entirely different things. There'd be no use storing "history" in the form of junk, since mutations won't fix it to work again. Good thing, too, since anything that could mutate to work for good purpose would just as if not more likely mutate to foul things up. See Dr. Moran's "genetic load" discussion, linked in a comment he posted here.

    ReplyDelete
  21. From the evolution point of view, why are there non-functioning copies of the mitochondrial DNA in the nucleus?

    - The reason it's there is the same as the reason for any non-functional DNA: Mutation (from copying mistakes, duplication, mutagens, etc.) that isn't fixed by repair mechanisms.

    - For "adaptationists" who treat selection as an analog of design, junk is problematic, for the same reason it is problematic for design proponents or others who support a directed mutation concept, though not to the same extent. If selection operates to a high degree, one wouldn't expect to find much junk; for those supporting design or some other directed process, any junk at all is a refutation.

    - For other biologists, who think drift and contingency play large roles, accumulation of junk DNA isn't unexpected or surprising. It also provides some nice ways of showing evolution has occurred (e.g., shared "junk" showing shared ancestry; higher mutation rates in "junk" demonstrating the effect of natural selection).

    ReplyDelete
  22. From the evolution point of view, why are there non-functioning copies of the mitochondrial DNA in the nucleus?

    Because they are functionless, and do not negatively affect the fitness of the organism. So they are neutral genomic changes that fix under random genetic drift. The original post I had on this discussed the exception - in organisms that have very little non-coding DNA (like Dorosphila) they are eliminated. In those organisms, genome size seems to have mattered, so selection favoured those without the nucmts (the jargon term for these things).

    ReplyDelete
  23. Is this consistent with what the other Jim said:

    http://www.sens.org/sens-research/research-themes/mitosens
    "Mitochondria are very complex; they contain about a thousand different kinds of protein, each encoded by a different gene. But nearly all of those genes are not in the mitochondrial DNA at all – they are in the nucleus! The proteins are constructed in the cell, outside the mitochondrion, just like all non-mitochondrial proteins. Then, a complicated apparatus called the TIM/TOM complex hauls the proteins into the mitochondrion, through the membranes that make up its surface. Only 13 of the mitochondrion's component proteins are still encoded by its own DNA, and it's therefore only these 13 genes that remain vulnerable to the constant assault from free radicals produced during respiration (the life-giving reaction of oxygen and food by the mitochondria)."

    ReplyDelete
  24. @ Anonymous Saturday, April 09, 2011 9:39:00 AM

    No it's not. That's an over-simplified (to the point of being inaccurate) introduction to mitochondrial biology. It has nothing to do with numts.

    The wiki version is here, but you really should read the review paper I posted.

    http://en.wikipedia.org/wiki/Numt

    ReplyDelete
  25. the other Jim does not seem able to help. Anyone else?

    It seems there are three elements possibly involved.

    Active mitochondrial DNA in the mitochondria.

    Active genes in the nucleus that code mitochondrial-related proteins.

    Inactive genes also in the nucleus, that are like the active genes in the nucleus that code mitochondrial-related proteins.

    ReplyDelete
  26. You asked if two statements were compatible. The answer was no.

    If you want an into to mitochondrial biology, I would have pointed you to a number of links.

    http://www.kqed.org/quest/blog/2008/12/22/those-marvelous-mitochondria/

    http://micro.magnet.fsu.edu/cells/mitochondria/mitochondria.html

    ReplyDelete
  27. "If an outsider perceives 'something wrong' with a core scientific model, the humble and justified response of that curious outsider should be to ask 'what mistake am I making?' before assuming 100% of the experts are wrong." - David Brin

    Memorable quotes never prove a thing. But I think this one sums up well why there seems to be little in the way of "open hearts" towards certain anonymous posters. Some of us are post-docs or professors, who are specifically studying subjects at hand in this blog. It is honestly quite annoying when people with little or no knowledge on a subject seek to topple 30 years of work with their superficial critiques. I have yet to see an example where these hobby-level criticisms actually take into account the depth of knowledge that is actually out there.

    When we supply links to freely available papers or summaries, there is a reason. Your criticisms may be logical based on what you know. But once you know more, you will see that the basis by which you are forming these opinions is usually contradicted by the real data that is out there.

    Read the links, educate yourself, and we will discuss the issues with you, when you can come with an informed opinion

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  28. Anonymous:

    I am unwilling to accept the other Jim's frequent offers of help.

    There, fixed that for you.

    ReplyDelete
  29. I had posted that possibly there are::

    1. Active mitochondrial DNA in the mitochondria.

    2. Active genes in the nucleus that code mitochondrial-related proteins.

    3. Inactive genes also in the nucleus, that are like the active genes in the nucleus that code mitochondrial-related proteins.

    Since nobody has said otherwise, I am concluding that there are these 3 elements.

    ReplyDelete
  30. @anonymous Since nobody has said otherwise, I am concluding

    Since nobody has said otherwise, I am concluding that there are fairies at the bottom of my garden.

    ReplyDelete
  31. Here is the set of questions. Do people know the answers to these questions?

    1. Active mitochondrial DNA in the mitochondria.
    YES or NO?

    2. Active genes in the nucleus that code mitochondrial-related proteins.
    YES or NO?

    3. Inactive genes also in the nucleus, that are like the active genes in the nucleus that code mitochondrial-related proteins.
    YES or NO?

    ReplyDelete
  32. I think my reply got lost, so I'll try again...

    1. Active mitochondrial DNA in the mitochondria.

    Yes there are. 13 protein genes, 22 tRNAs and 2 rRNAs.

    2. Active genes in the nucleus that code mitochondrial-related proteins.

    Yes. There are ~1500 genes encoded in the nucleus that carry out function within the mitochondria. But the whole set of mitochondrial genes = ~1500 - (the 37 in 1). There are no nuclear "active backup copies" of the mitochondrial DNA.

    3. Inactive genes also in the nucleus, that are like the active genes in the nucleus that code mitochondrial-related proteins.

    These may exist, but I am not talking about those. I am talking about;

    4. Pieces of broken mitochondrial DNA that have integrated into the nuclear DNA. These are "inactive" junk.

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  33. From an evolution point of view, why would pieces of broken mitochondrial DNA have integrated into the nuclear DNA?

    ReplyDelete
  34. I swear I already answered this one.

    Evolution has nothing to do with the integration event.

    The fixation of the "accident" was due to the fact there was no fitness cost, and being lucky to fix by random genetic drift.

    ReplyDelete
  35. The question is why did DNA in the mitochondria leave there, transport over to the nucleus, enter the nucleus and integrate into the nucleus DNA?

    What is the explanation from an evolution point of view?

    Is everyone going to pretend not to get it?

    ReplyDelete
  36. Anonymous writes:

    The question is why did DNA in the mitochondria leave there, transport over to the nucleus, enter the nucleus and integrate into the nucleus DNA?

    To get to the other side?

    ReplyDelete
  37. anonymous asks,

    Is everyone going to pretend not to get it?

    No, not everyone. In fact, you seem to be the only person who is pretending not to get it.

    Why are you behaving like that? You've been told the evolutionary explanation several times.

    ReplyDelete
  38. Yes, "to get to the other side" is the evolution answer.

    This is actually the only answer you can give.
    And yet you still expect us to accept your evolution explanations.

    Do you not see how humorous that is?

    And I see that Dr. Moran is still pretending not to get it.

    For a change, why not take things like this seriously?

    Take a look at the work of Dr. James Shapiro if you are really serious about what is actually going on.

    ReplyDelete
  39. Anonymous asks:

    For a change, why not take things like this seriously?

    Take a look at the work of Dr. James Shapiro if you are really serious about what is actually going on.


    Why so coy, Anonymous? If you know a better explanation, why not just tell us what it is? (And show us the supporting evidence, of course!)

    Dr. Shapiro has a lot of publications, going back to 1966. (See the list at http://shapiro.bsd.uchicago.edu/publications.shtml). Do you want to be a bit more helpful in pointing out which work we should take a look at? And preferably, what you think it means?

    Or do you just want to troll?

    ReplyDelete
  40. qetzal seems to just be trolling.

    If anyone is serious about wanting to understand what is actually going on look into Dr. Shapiro.

    You can see in a minute what he has been focusing on for years.

    ReplyDelete
  41. http://en.wikipedia.org/wiki/James_A._Shapiro
    "James A. Shapiro is a Professor in the Department of Biochemistry and Molecular Biology at the University of Chicago. His research interests include natural genetic engineering or the ways by which organisms actively restructure their genetic material in response to environmental stresses. His view that it presents a 'third way' in evolution between what he calls "neo-darwinian orthodoxy" and creationism, has been challenged in a book review.[1]"

    VIDEO:
    http://www.youtube.com/watch?v=gZOkfjuXDg4

    ReplyDelete
  42. I wasn't able to find where in Origin of Species Darwin discuss this prediction but I'm sure it must be there somewhere. Perhaps some kind reader can supply the page numbers?

    Just to be clear. This is meant ironic, right?

    AnonToE

    ReplyDelete
  43. Would this be the James A. Shapiro to who you are referring ?

    "For those scientists who take it seriously, Darwinian evolution has functioned more as a philosophical belief system than as a testable scientific hypothesis. This quasi-religious function of the theory is, I think, what lies behind many of the extreme statements that you have doubtless encountered from some scientists opposing any critical analysis of neo-Darwinism in the classroom. It is also why many scientists make public statements about the theory that they would not defend privately to other scientists like me."
    — James A. Shapiro

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  44. steve oberski:

    Yes, that sounds like Dr. Shapiro.
    Have you had a chance to watch the video or read any of his scientific material.

    You might find it interesting.
    I am happy to discuss.

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  45. Well it seems to have gone quiet here when presented with the ideas and research of Dr. Shapiro. Which is a pity because he offers a form of evolutionism that does not require the supernatural. And it overcomes to obvious absurdities of the current evolution thinking.
    He is making out the future of evolution thinking.

    ReplyDelete