A Rejoinder to Part II of Stephen C. Meyer’s Response to Francisco Ayala

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March 11, 2010 Tags: Design

Today's entry was written by Darrel Falk. You can read more about what we believe here.

A Rejoinder to Part II of Stephen C. Meyer’s Response to Francisco Ayala

In Part 2 of Stephen Meyer’s response to Francisco Ayala’s critique of the Intelligent Design movement in general, and of Signature in the Cell in particular, Meyer focuses primarily upon Ayala’s statement that, “there are lots and lots of DNA sequences that are nonsensical.”

First, I would like to note that one cannot help but be impressed with how current Meyer is with regard to this literature. He cites ten articles from 2009 and three from this year. Clearly he and his colleagues are keeping up with the literature. This is just one example of why I have come to conclude that the ID movement ought to be considered a scientific movement.

Another example is Meyer’s book itself. In the book, Meyer, quite eloquently in my opinion, demonstrates that his approach fits within the bounds of how historical science is done. The fact that he spends time carefully analyzing the scientific literature for evidence of function is further indication that they are doing science. Their Intelligent Design model predicts that the DNA in the human genome (and other organisms) is fully functional, and Meyer and his colleagues are carefully scrutinizing the scientific literature to see if it is.

Although I am convinced they are wrong on many counts, I appreciate that they are doing science (however good or bad it is) and I hope the scientific community will engage them on the basis of that science and not on the basis of rhetoric (theirs and ours!). Elements of their work are clearly rhetorical, and I alluded to one example of that in yesterday’s post. Regretfully, there are times when I slip into that mode as well. I am trying my best to stay focused on the issues—if you catch me doing otherwise, you should feel free to call me on it.

Since Meyer used technical language unfamiliar to many non-scientists, I want to refer readers to an excellent new book, Inside the Human Genome: A Case for Non-Intelligent Design, by leading evolutionary biologist, John Avise. Like Ayala, Avise argues that biology informs theism, and most certainly does not negate it. If there is any one science-related book I would urge our audience to read in the upcoming year it would be this one. Avise clearly lays out the philosophical and theological work we Christians have yet to do, based on detailed but accessible descriptions of genomic data.

Meyer spends considerable time disputing what he calls “Ayala’s claim” that Alu1 sequences are distributed randomly. I’ve reread Ayala’s post several times trying to find what makes Meyer think Ayala claimed this. Put simply, he doesn’t say it nor does he imply it. He does say that on average there are about 40 copies of Alu sequences between every two genes, but this is simply a fact. Meyer spends considerable time trying to show Ayala is wrong about something he didn’t say. I don’t know why he does this and don’t consider to be helpful to the discussion.

There are about a million Alu sequences (see footnote) scattered around the human genome. They constitute about ten percent of all letters in the DNA code. Meyer points out that a number of functional regions have been discovered within Alu sequences. He’s right. But this comes as no surprise to biologists—evolutionary theory certainly predicts that some portion of these sequences would take on useful functions over time.

However, there is no question that many Alu sequences really have no function. As Avise explains in his book, and as Ayala mentions in his post, most of these elements are almost certainly of no value to cells. On the contrary, these extra sequences can cause serious problems. In Avise’s words, “To the best of current knowledge, many if not most of these repetitive elements contribute not one iota to a person’s well-being. They are well-documented however to contribute to many health disorders.”

Alu is only one of many kinds of repetitive elements in the genome. The actual number of DNA letters devoted to all mobile elements (those which move from one location in the genome to another) is at least 1.3 billion! That’s 45 percent of the genome. In addition, non-mobile elements represent another huge portion.

For sure, plenty of magnificent “sense” is scattered throughout the genome, coding for absolutely marvelous things—like how to make the brain, for example—but this still doesn’t negate the fact that almost certainly much, if not most, of the DNA plays no role, and in many cases can be harmful.

Since many of our readers are not experts and they depend upon authorities, I would like to conclude with a request. If you hold a faculty position in molecular biology at a research university (or you know of someone who does), and you think that my portrayal (or Avise’s and Ayala’s) of the current state of our knowledge about this is inaccurate, please send an email to info@biologos.org. We will post the names of any dissenting molecular biologists who hold faculty positions in research universities on our website. I am aware that ID folk will simply say that such scientists will not respond because of the need to be clandestine in order to protect their careers. However, my experience is that tenured faculty are not afraid to say what they think; indeed it is that quality that especially distinguishes the faculty I have known over the years.

1. Alu is a short stretch of DNA code. There are three billion letters of code in the human genome. One Alu sequence is about 300 letters long. There are about a million copies of this short sequence scattered throughout the genome.


Darrel Falk is former president of The BioLogos Foundation. He transitioned into Christian higher education 25 years ago and has given numerous talks about the relationship between science and faith at many universities and seminaries. He is the author of Coming to Peace with Science.

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Harry - #6557

March 11th 2010

I have always considered unitary pseudogenes to be the best evidence for common descent. Mainly because in my view the question of function vs non-functional is largely irrelevant. When you see huge numbers of pseudogenes that have the same inactivating mutations in the same places in different organisms’ genomes there really is no alternative explanation other than common descent. Even if it can be shown that some of these pseudogenes have acquired new functions, I still don’t see how that would in any way undermine the overpowering evidence they provide for common ancestry.

I would recommend the work of Steve  Matheson and T. Ryan Gregory on this specific topic of junk DNA.


Glen Davidson - #6558

March 11th 2010

Although I am convinced they are wrong on many counts, I appreciate that they are doing science (however good or bad it is) and I hope the scientific community will engage them on the basis of that science and not on the basis of rhetoric (theirs and ours!).

I would like to see evidence that Meyer is doing science.

I do not doubt that science is being done by certain IDists, however.  What I still lack is any evidence that they are doing any science truly based on ID.  Attempts to counter evolutionary theory do occur, without much success, yet those should be considered to still be based in evolutionary theory itself, which actually makes entailed predictions.  IDists make predictions, I know, but their “functional DNA prediction” is discordant with their claims that “nonfunctional” and “poor” types of “design should not count against ID.

Glen Davidson
http://tinyurl.com/mxaa3p


Glen Davidson - #6559

March 11th 2010

Continuing from #6558:

Meyer ought at least to explain the DNA which codes for basically useless biological processes and structures like gooseflesh and the coccyx in humans, and teeth in young platypuses and baleen whales.  We have a good explanation.

And why does the human X chromosome have a homolog in platypuses which is not a sex chromosome in them?  This isn’t a matter of “bad design,” it is something that is highly explainable via evolutionary divergence and contingency, and which is without any meaningful explanation in ID at all.

Glen Davidson
http://tinyurl.com/mxaa3p


Harry - #6560

March 11th 2010

Interestingly creation biologist Todd Wood has an recent blog post on transposable elements. He most definitely disagrees with Meyer.

“it is misleading to say that transposable elements are “functional” or “essential.” The vast majority of transposable elements in the human genome are nonfunctional copies that have been damaged(?) by point mutations. To my knowledge, there is no evidence of essential function for most of these transposable elements. Indeed, some eukaryotes (like baker’s yeast) that have comparatively few transposable elements.”


Harry - #6561

March 11th 2010

...

“the argument for the common ancestry of chimps and humans depends in no way whatsoever on the functionality of transposable elements. The argument is more compelling if the sequences are purely parasitic, but the overwhelming similarity still implies that chimps and humans could have shared a common ancestor, even if transposable elements had an essential cellular function. In my chimp genome paper, I challenged myself and my fellow creationists to account for biological similarity in a creationist context. To date, the challenge has not been met.”

“McClintock herself proposed an important functional role for transposable elements. Functionality was not the exclusive prediction of creationists. It is definitely false to claim that evolutionists did not propose functions for transposable elements.”


Mike Gene - #6562

March 11th 2010

The Alu sequences fit very well within the hypothesis of front-loaded evolution.  This is explained in detail here:

http://designmatrix.wordpress.com/2009/11/23/the-srp-alu-elements-and-nudging/

These elements (derived from an ancient component associated with the ribosome) are a nice example of a preadaptation that has facilitated the evolution of primates/humans.


Mike Gene - #6563

March 11th 2010

Harry, quoting Todd Wood:

“it is misleading to say that transposable elements are “functional” or “essential.” The vast majority of transposable elements in the human genome are nonfunctional copies that have been damaged(?) by point mutations.”

But this is a myopic perspective. Specific transposable elements may not be functional or essential to the existence of a particular organism, but if we step back, it is easy to argue that they have functioned to facilitate evolution.  In fact, they were essential for the evolutionary emergence of human beings.  Without transposable elements, humans would not have evolved.


Mike Gene - #6565

March 11th 2010

“McClintock herself proposed an important functional role for transposable elements.”

Yes, and let’s not forget what she said:

In the future, attention undoubtedly will be centered on the genome, with greater appreciation of its significance as a highly sensitive organ of the cell that monitors genomic activities and corrects common errors, senses unusual and unexpected events, and responds to them, often by restructuring the genome.

In other words, genomes are not passively shaped by random events and selection.  They actively participate in their own evolution.  This is a view that gets close to teleology, for it is a shift from evolution as something that just happens because of imperfect replication in a contingent environment to evolution as a *function* to cope with the contingent environment.  James Shapiro, from the University of Chicago, is someone who has been advocating this view for some time now.  You can read many of his papers here:

http://shapiro.bsd.uchicago.edu/index3.html?content=genome.html


Chris Massey - #6572

March 11th 2010

I imagine Meyer standing on the edge of a city dump. “Why look over here, this broken fridge is now a home for a family of rats. The dirt in this old wheelbarrow has sprouted a variety of plants. And this old tire is collecting rainwater from which the rat family drinks! This is no dump. It was clearly designed as a nature preserve!”

Yes, I take the analogy too far. The human genome has many wonderful, functional components (which most dumps do not). But Meyer’s laundry list of functions that have been found for various pieces of non-coding DNA does nothing to refute the basic argument that the human genome is littered with functionless sequences. That the genome has co-opted some of it for useful purposes doesn’t mean the overall issue of junk DNA and psuedogenes disappears.


Mike Gene - #6575

March 11th 2010

Hi Darrel,

You write, “He’s right. But this comes as no surprise to biologists—evolutionary theory certainly predicts that some portion of these sequences would take on useful functions over time.”

Which would mean that evolutionary theory also predicts some other portion would not have taken on a useful function.  In other words, all bases are covered.  If evolutionary theory predicts some sequences would have a function and others would not, that’s not a very impressive prediction.


Glen Davidson - #6576

March 11th 2010

Which would mean that evolutionary theory also predicts some other portion would not have taken on a useful function.  In other words, all bases are covered.  If evolutionary theory predicts some sequences would have a function and others would not, that’s not a very impressive prediction.

That doesn’t logically follow, since logically it could be that all sequences could eventually take on a function, leaving at most a negligible amount of “junk DNA.”  Indeed, bacteria have very little “junk DNA,” and a number of scientists who strongly favored selection during the course of evolution thought that there should be very little useless DNA.

More importantly, evolutionary theory has never been thought to predict how much “junk DNA” there might be, at least not at earlier and current levels of knowledge.  So no such “prediction” was ever held to be “impressive.”  Evolution was established based upon largely selected features long before “junk DNA” became any kind of an issue.

And yes, Meyer continues to fail to explain why the patterns of life fit the predictions of natural selection, and do not conform to known design constraints.

Glen Davidson
http://tinyurl.com/mxaa3p


Nick Matzke - #6594

March 12th 2010

“Which would mean that evolutionary theory also predicts some other portion would not have taken on a useful function.  In other words, all bases are covered.  If evolutionary theory predicts some sequences would have a function and others would not, that’s not a very impressive prediction.”

This is like saying meteorological theory is not impressive because it isn’t a magical oracle telling you which way the wind is blowing while you sit in your bathrobe munching on cereal in the morning.

Over here in actual science, overarching theories function, and are tested, by making if-then statements.  I.e. if there is high pressure in the west and low pressure in the east, then the wind will blow east.  With junk DNA, here are some statements evolutionary theory ACTUALLY makes: (1) if DNA chunk X is well-conserved between species/clades/whatever then it is very likely it has a function; if not conserved, then not likely; (2) similar more detailed statements can be made about dN/dS ratios and the like; (3) if the mutation rate is (input observed mutation rate), then the amount of the genome which has some sequence-specific function cannot be much higher than Y;


Nick Matzke - #6595

March 12th 2010

(4) if DNA chunk X has no known reason for existing other than organismal function (e.g. most genes), then it probably has function, but if DNA chunk X could well have been produced by something other than selection for function—e.g. repetitive elements—then we have to take seriously the possibility that it has no function; (5) if organisms of the same or less complexity as humans exist with 10x less or 10x more DNA as humans (which is true), and the differences in DNA are mostly due to repetitive elements (which is true), then there is something deeply, wildly wrong with the blind assumption that it is obvious that most of the DNA in most organisms is functional.

Meyer just ignores all this and jams virtually any piece of data into the “it all has function” paradigm.  Often he is being ridiculous.  E.g. the fact that Alus do not follow a flat uniform random distribution of locations in the genome is not evidence of function, it could just be evidence of some bias in Alu insertion induced by some biochemical peculiarity.  Or it could be evidence of nonfunction, i.e. selection excludes Alus from functionally key regions (this is true for e.g. the Hox clusters).


Nick Matzke - #6596

March 12th 2010

And Meyer and other IDers are totally insensitive to the important differences between “the element has a nonrandom distribution”, “the element has some detectable biochemical effect”, “the element has some detectable biochemical effect that has some biological relevance”, “the effect has some meaningful biological function”, and “the element has some meaningful biological function that could not be fulfilled just as well by dozens of other similarly trivial mechanisms, as e.g. gene regulation can be influenced by anything from chromosomal position to the regional tightness of DNA packing to minor point mutations influencing the strength of binding of regulatory proteins to whatever else you can think of.”


Nick Matzke - #6597

March 12th 2010

And then the whole idea of Alus or other elements having “evolutionary functions”—i.e. “their function is in helping species to evolve”—is, at the very least, tremendously controversial, even though it is popular with various excitable scientists who haven’t read enough evolutionary biology to know that panselectionism is bad and we always have to consider non-adaptive hypotheses along with adaptive hypotheses for organismal feature X.  The criteria for deciding what even constitutes an “evolutionary function” are not clear, the concept of selection on clades rather than organisms is at least a challenging thing to make workable, due to the low population size of clades relative to organisms (thus drift is much more powerful for low population size), and, most importantly, it is very very easy for people to confuse “X had no important evolutionary effect” with “X had an evolutionary effect” with “X had an evolutionary function.”  In every single instance, a prosaic null hypothesis should be considered.


Nick Matzke - #6598

March 12th 2010

Amongst the excitables in science, this is often not done, and it gets even worse in the science journalism and press-releases, and even worse still in the mining of this stuff by the IDists/creationists.  Ironically, they end up even more extreme uncritical functionalists than the naive panselectionists who are their worst enemies!


Dennis Venema - #6612

March 12th 2010

Hi Darrel,

You’ve been very kind with your words here, which is commendable.

Meyer’s approach is a very common one in anti-evolutionary literature re: repetitive DNA - find a rare example where the repetitive DNA in question has picked up a function, and then attempt to portray all such sequences as similarly functional. Of course, to a biologist, this is manifestly silly - but biologists are not the target of ID literature like Meyer’s book.

It is for this reason that I tend to focus on unitary pseudogenes when I present to non-specialists - especially examples like those devoted to non-mammalian life (e.g. the vitellogenin pseudogene in the human genome - click my name above for a link to a paper on this pseudogene). These examples seem have a greater qualitative impact in that their implications can be readily grasped by laypersons; also, the “appeal to function” argument is more readily seen as hollow.

Dennis


Mike Gene - #6632

March 12th 2010

Hi Nick,

“This is like saying meteorological theory is not impressive because it isn’t a magical oracle telling you which way the wind is blowing while you sit in your bathrobe munching on cereal in the morning.”

No it’s not.  I did not say evolutionary theory was not impressive (as your analogy would depend on); I pointed out that the prediction Darrel cited - “evolutionary theory certainly predicts that some portion of these sequences would take on useful functions over time” - was not impressive.  If someone claimed that meteorological theory predicts in some places the wind would blow, would that be an impressive prediction?


Nick Matzke - #6693

March 12th 2010

“I did not say evolutionary theory was not impressive”

OK fair enough, I was over-interpreting.

“I pointed out that the prediction Darrel cited - “evolutionary theory certainly predicts that some portion of these sequences would take on useful functions over time” - was not impressive.”

What I was reacting against was the implication—perhaps you didn’t mean this—that evolutionary theory should be able to predict from scratch exactly what proportion of DNA will be functional, without any input data etc., and that this is a flaw if it can’t.  This is what I think is like asking meteorological theory to tell you which way the wind is blowing without any inputs.


Nick Matzke - #6694

March 12th 2010

But even if we are just talking about this prediction: “evolutionary theory certainly predicts that some portion of these sequences would take on useful functions over time”—I don’t think that’s a bad/unimpressive prediction.  Given what we think we know about cooption and evolution’s propensity for bricolage and tinkering, this does indeed give the expectation that, if you have a whole bunch of typically functionless elements, over millions of years some of them will acquire some function.  This prediction is “surprising” from the point of view which says that all junk everywhere is functionless, which is the strawman depiction of evolution put up by the ID movement.


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