Thursday, June 14, 2007

Catherine Shaffer Responds to My Comments About Her WIRED Article

 
Over on the WIRED website there's a discussion about the article on junk DNA [One Scientist's Junk Is a Creationist's Treasure]. In the comments section, the author Catherine Shaffer responds to my recent posting about her qualifications [see WIRED on Junk DNA]. She says,
You might be interested to learn that I contacted Larry Moran while working on this article and after reading the archives of his blog. I wanted to ask him to expand upon his assertion that junk DNA disproves intelligent design. His response was fairly brief, did not provide any references, and did not invite further discussion. It's interesting that he's now willing to write a thousand words or so about how wrong I am publicly, but was not able to engage this subject privately with me.
Catherine Shaffer sent me a brief email message where she mentioned that she had read my article on Junk DNA Disproves Intelligent Design Creationism. She wanted to know more about this argument and she wanted references to those scientists who were making this argument. Ms. Shaffer mentioned that she was working on an article about intelligent design creationism and junk DNA.

I responded by saying that the presence of junk DNA was expected according to evolution and that it was not consistent with intelligent design. I also said that, "The presence of large amounts of junk DNA in our genome is a well established fact in spite of anything you might have heard in the popular press, which includes press releases." She did not follow up on my response.
His blog post is inaccurate in a couple of ways. First, I did not make the claim, and was very careful to avoid doing so, that “most” DNA is not junk. No one knows how much is functional and how much is not, and none of my sources would even venture to speculate upon this, not even to the extent of “some” or “most.”
Her article says, "Since the early '70s, many scientists have believed that a large amount of many organisms' DNA is useless junk. But recently, genome researchers are finding that these "noncoding" genome regions are responsible for important biological functions." Technically she did not say that most DNA is not junk. She just strongly implied it.

I find it difficult to believe that Ryan Gregory would not venture to speculate on the amount of junk DNA but I'll let him address the validity of Ms. Shaffer's statement.
Moran also mistakenly attributed a statement to Steven Meyer that Meyer did not make.
I can see why someone might have "misunderstood" my reference to what Myer said so I've edited my posting to make it clear.
Judmarc and RickRadditz—Here is a link to the full text of the genome biology article on the opossum genome: Regulatory conservation of protein coding and microRNA genes in vertebrates: lessons from the opossum genome. We didn't have space to cover this in detail, but in essence what the researchers found was that upstream intergenic regions were more highly conserved in the possum compared to coding regions, but also represented a greater area of difference between possums and humans.
This appears to be a reference to the paper she was discussing in her article. It wasn't at all clear to me that this was the article she was thinking about in the first few paragraphs of her WIRED article.

Interested readers might want to read the comment by "Andrea" over on the WIRED site. She He doesn't pull any punches in demonstrating that Catherine Shaffer failed to understand what the scientific paper was saying. Why am I not surprised? (Recall that this is a science writer who prides herself on being accurate.)
So, yes, this does run counter to the received wisdom, which makes it fascinating. You are right that the discussion of junk vs. nonjunk and conserved vs. nonconserved is much more nuanced, and we really couldn't do it justice in this space. Here is another reference you might enjoy that begins to deconstruct even our idea of what conservation means: “Conservation of RET regulatory function from human to zebrafish without sequence similarity.” Science. 2006 Apr 14;312(5771):276-9. Epub 2006 Mar 23. Revjim—If you have found typographical errors in the copy, please do point them out to us. The advantage of online publication is that we do get a chance to correct these after publication.
Sounds to me like Catherine Shaffer is grasping at straws (or strawmen).
For Katharos and others—I interviewed five scientists for this article. Dr. Francis Collins, Dr. Michael Behe, Dr. Steve Meyers, Dr. T. Ryan Gregory, and Dr. Gill Bejerano. Each one is a gentleman and a credentialed expert either in biology or genetics. I am grateful to all of them for their time and kindness.
I think we all know just how "credentialed" Stephen Meyer is. He has a Ph.D. in the history and philosophy of science. Most of us are familiar with the main areas of expertise of Michael Behe and none of them appear to be science.

14 comments :

  1. I find it difficult to believe that Ryan Gregory would not venture to speculate on the amount of junk DNA but I'll let him address the validity of Ms. Shaffer's statement.

    He must answer that himself of course, but in his interview with for Sci Am on the ENCODE work he certainly speculated (and it seems the work support his numbers). Here is an excerpt from his email:

    How much of what was identified is likely to be functional?

    - 5% of the genome sequence is conserved across mammals, and for about 60% of this (i.e., 3% of the genome) there is additional evidence of function. This includes the protein-coding exons as well as regulatory elements and other functional sequences. So, at this stage, we have increasingly convincing evidence of function for about 3% of the genome, with another 2% likely to fall into this category as it becomes more thoroughly characterized.


    And here is an excerpt from the article:

    The consortium found that 5 percent of the studied sequence has been conserved among 23 mammals, suggesting that it plays an important enough role for evolution to preserve while species have evolved. But of all the new ENCODE sequences identified as potentially important, only half fall into the conserved group.

    ( http://genomicron.blogspot.com/2007/06/more-about-encode-from-scientific.html )

    He expanded on this in yesterdays post:

    Evidence currently available suggests that about 5% of the human genome is functional. The least conservative guesses put the possible total at about 20%. The human genome is mid-sized for an animal, which means that most likely a smaller percentage than this is functional in other genomes. None of the discoveries suggest that all (or even more than a minor percentage) of non-coding DNA is functional, and the corollary is that there is indirect evidence that most of it is not.

    ( http://genomicron.blogspot.com/2007/06/function-non-function-some-function.html )

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  2. What he said.

    I probably was not willing to say "it's all non-functional" or even "it's mostly non-functional" with certainty because we don't have all the data yet. But based on what we currently know, I think 5% is clear, 10% is reasonable, and 20% (Mattick's bet) is probably a tad high.

    On another point, I have stayed far away from the "framing" kerfuffle, but if it involves stating things with certainty without solid data, then I won't be doing it.

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  3. "But of all the new ENCODE sequences identified as potentially important, only half fall into the conserved group."

    From NHGRI press release: "However, the ENCODE effort found about half of functional elements in the human genome do not appear to have been obviously constrained during evolution...."

    What do "functional" and "potentially important" mean as used (misused?) above, and can someone give a clearer explanation of what's being summarized in the above quotes?

    Thanks.

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  4. I do want to make a note that Ms. Shaffer did ask interesting questions, and that my interaction with her was positive. I think some of the issue is that Wired wanted a discussion of "junk DNA" and creationism, and that some of the more scientific content was cut during editing. Whatever the situation, the piece has certainly engendered some interesting discussion.

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  5. Shaffer's reply clearly shows that she still doesn't get it. The Genome Biology paper is clearly about promoter regions of microRNA and protein coding genes. And yet early in her article she wrote this:

    "The opossum data revealed that more than 95 percent of the evolutionary genetic changes in humans since the split with a common human-possum ancestor occurred in the "junk" regions of the genome."

    That's simply wrong - not just bad editing. She didn't understand the paper, and she apparently still doesn't understand that her statement is wrong.

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  6. Larry,
    I wonder whether or not Catherine Shaffer is a closet "Creationist". If she is, she may bear watching. I see this as a disturbing trend. A pseudo- science writer unable or unwilling to understand the science and being a type of shill for the IDiots.

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  7. I just heard on the radio that 'junk DNA" is going to be discussed today on Talk of the Nation Science Friday

    Science Friday's web page

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  8. Just to clarify my earlier comment - I intended to say that Shaffer is wrong to confuse junk DNA with the promoter regions that were the focus of the GB paper.

    I did not mean to say that she was wrong to claim that 95% of the sequence differences between human and opossum fall in 'junk' regions.

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  9. "I have stayed far away from the "framing" kerfuffle, but if it involves stating things with certainty without solid data, then I won't be doing it."

    Right, I was uncomfortable with Larry's "framing" of "speculate" here, so I shouldn't have run with it.

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  10. "I have stayed far away from the "framing" kerfuffle, but if it involves stating things with certainty without solid data, then I won't be doing it."

    Right, I was uncomfortable with Larry's "framing" of "speculate" here, so I shouldn't have run with it.


    I was actually referring to some other post I read somewhere that one should say everything with certainty.

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  11. This debate is about "Junk DNA" and "Creationism"?

    I'd say "Junk Creationism" and "DNA" is more like it.

    What possible purpose -- "intelligent design" -- could there be for junk DNA?

    I am a software engineer by trade and I can tell you that I rarely (if ever) "design" junk into my programs. In fact, i would have to say that I find the idea a bit distasteful -- nay, absurd.

    Sometimes my programs contain a little junk by accident (and on rare occasions, turn out to be almost pure junk) -- but that's another matter entirely. :-)

    --jim




    -- Jim

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  12. Interested readers might want to read the comment by "Andrea" over on the WIRED site. She doesn't pull any punches in demonstrating that Catherine Shaffer failed to understand what the scientific paper was saying. Why am I not surprised? (Recall that this is a science writer who prides herself on being accurate.)


    Andrea is he not she.

    Pete

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  13. Oh-- I just wrote an extremely hateful email to WIRED after I read that article. I was feeling particularly impatient after we just went through this with SciAm.

    Thanks Larry, and TR, for having the patience to address this article properly :)

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