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On Not Reading the Signature: Stephen C. Meyer’s Response to Francisco Ayala, Part II

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March 11, 2010 Tags: Design
On Not Reading the Signature: Stephen C. Meyer’s Response to Francisco Ayala, Part II

Today's entry was written by Stephen C. Meyer. Please note the views expressed here are those of the author, not necessarily of BioLogos. You can read more about what we believe here.

This is the second of the two part series by Stephen Meyer, the first of which was posted on March 8, 2010. Darrel Falk’s rejoinders to Part I and Part II have also been posted.

The closest that Ayala comes in his review to recognizing the central affirmative argument in the book is his rather clumsy attempt to refute the idea of intelligent design by insisting that existence of “nonsensical” or junk sequences in the human genome demonstrates that it did not arise by intelligent design. As he claims explicitly, “according to Meyer, ID provides a more satisfactory explanation of the human genome than evolution does.”

Again, I have to wonder whether Professor Ayala even cracked the pages of the book. My book is not about the origin of the human genome, nor about human evolution nor even biological evolution generally. It’s about chemical evolution, the origin of the first life and the genetic information necessary to produce it. In fact, I explicitly acknowledge in the epilogue that someone could in principle accept my argument for the intelligent design of the first life and also accept the standard neo-Darwinian account of how subsequent forms of life evolved. I don’t hold this “front-end loaded” view of design, but my book makes no attempt to refute it or standard accounts of biological evolution. For this reason, it’s hard to see how Ayala’s attempt to defend biological evolution and refute the particular hypothesis that intelligent design played a discernable role in the origin of the human genome in any way challenges the argument of Signature in the Cell.

Even so, it is worth noting that the argument that Ayala makes against intelligent design of the human genome based upon on the presence of “nonsensical” or so-called junk DNA is predicated upon two factually flawed and out-of-date premises. Ayala suggests that no designer worthy of the modifier “intelligent” would have allowed the human genome to be liberally sprinkled with a preponderance of nonsense DNA sequences and that the presence and apparently random distribution of such sequences is more adequately explained as a by-product of the trial and error process of undirected mutation and selection. According to Ayala, the distribution of a particular sequence (the Alu sequence), which he asserts contains genetic nonsense, suggests a sloppy, unintelligent editor, not an intelligent designer. As he argues:

It is as if the editor of Signature of the Cell would have inserted between every two pages of Meyer’s book, forty additional pages, each containing the same three hundred letters. Likely, Meyer would not think of his editor as being “intelligent.” Would a function ever be found for these one million nearly identical Alu sequences? It seems most unlikely.

Thus, in essence, Ayala claims that (1) a preponderance of nonsense DNA sequences and (2) the random distribution of these sequences shows that the human genome could not have been intelligently designed. But both of the factual claims upon which Ayala bases this argument are wrong.

First, neither the human genome nor the genomes of other organisms are predominantly populated with junk DNA. As I document in Signature in the Cell, the non-protein-coding regions of the genomes (of various organisms) that were long thought to be “junk” or “nonsense” are now known to perform numerous mission-critical functions. Non-protein-coding DNA is neither nonsense nor junk. On page 407 of Signature in the Cell, I enumerate ten separate functions that non-protein-coding regions of the genome are now known to play. (References to peer-reviewed scientific publications documenting my claims are there provided). Overall the non-coding regions of the genome function much like an operating system in a computer in that they direct and regulate the timing and expression of the other protein-coding genetic modules.

Further, the Alu sequences that Ayala specifically cites as prime examples of widely and randomly distributed nonsense sequences in the human genome are NOT non-functional or “nonsense.” Short Interspersed Nuclear Element (SINE) sequences of which Alu is one member, perform numerous formatting and regulatory functions in the genomes of all organisms in which they have been found. It is simply factually incorrect for Ayala to claim otherwise.

In general, SINEs (and thus Alus) allow genetic information to be retrieved in multiple different ways from the same DNA data files depending on the specific needs of different cell types or tissues (in different species-specific contexts). In particular, Alu sequences perform many taxon-specific lower-level genomic formatting functions such as: (1) providing alternative start sites for promoter modules in gene expression—somewhat like sectoring on a hard drive (Faulkner et al., 2009; Faulkner and Carninci, 2009); (2) suppressing or “silencing” RNA transcription (Trujillo et al., 2006); (3) dynamically partitioning one gene file from another on the chromosome (Lunyak et al., 2007); (4) providing DNA nodes for signal transduction pathways or binding sites for hormone receptors (Jacobsen et al., 2009; Laperriere et al., 2004); (5) encoding RNAs that modulate transcription (Allen et al., 2004; Espinoza et al., 2004; Walters et al., 2009); and (6) encoding or regulating microRNAs (Gu et al., 2009; Lehnert et al., 2009).

In addition to these lower-level genomic formatting functions, SINEs (including Alus) also perform species-specific higher-level genomic formatting functions such as: (1) modulating the chromatin of classes of GC-rich housekeeping and signal transduction genes (Grover et al., 2003, 2004; Oei et al., 2004; see also Eller et al., 2007); (2) “bar coding” particular segments for chromatin looping between promoter and enhancer elements (Ford and Thanos, 2010); (3) augmenting recombination in sequences where Alus occur (Witherspoon et al., 2009); and (4) assisting in the formation of three-dimensional chromosome territories or “compartments” in the nucleus (Kaplan et al., 1993; see also Pai and Engelke, 2010).

Moreover, Alu sequences also specify many species-specific RNA codes. In particular, they provide: (1) signals for alternative RNA splicing (i.e., they generate multiple messenger RNAs from the same type of precursor transcript) (Gal-Mark et al., 2008; Lei and Vorechovsky, 2005; Lev-Maor et al., 2008) and (2) alternative open-reading frames (exons) (Lev-Maor et al., 2007; Lin et al., 2008; Schwartz et al., 2009). Alu sequences also (3) specify the retention of select RNAs in the nucleus to silence expression (Chen et al., 2008; Walters et al., 2009); (4) regulate the RNA polymerase II machinery during transcription (Mariner et al., 2008; Yakovchuk et al., 2009; Walters et al., 2009); and (5) provide sites for Adenine-to-Inosine RNA editing, a function that is essential for both human development and species-specific brain development (Walters et al., 2009).

Contrary to Ayala’s claim, Alu sequences (and other mammalian SINEs) are not distributed randomly but instead manifest a similar “bar-code” distribution pattern along their chromosomes (Chen and Manuelidis, 1989; Gibbs et al., 2004; Korenberg and Rykowski, 1988). Rather like the distribution of the backslashes, semi-colons and spaces involved in the formatting of software code, the “bar-code” distribution of Alu sequences (and other SINEs) reflects a clear functional logic, not sloppy editing or random mutational insertions. For example, Alu sequences are preferentially located in and around protein-coding genes as befits their role in regulating gene expression (Tsirigos and Rigoutsos, 2009). They occur mainly in promoter regions—the start sites for RNA production—and in introns, the segments that break up the protein-coding stretches. Outside of these areas, the numbers of Alu sequences sharply decline. Further, we now know that Alu sequences are directed to (or spliced into) certain preferential hotspots in the genome by the protein complexes or the “integrative machinery” of the cell’s information processing system (Levy et al., 2010). This directed distribution of Alu sequences enhances the semantic and syntactical organization of human DNA. It appears to have little to do with the occurrence of random insertional mutations, contrary to the implication of Ayala’s “sloppy editor” illustration and argument.

Critics repeatedly claim that the theory of intelligent design is based on religion, not science. But in his response to my book, it is Ayala who relies on a theological argument and who repeatedly misrepresents the scientific literature in a vain attempt to support it. The human genome manifests nonsense sequences and sloppy editing ill-befitting of a deity or any truly intelligent designer, he argues. He also sees other aspects of the natural world that he thinks are inconsistent with the existence of a Deity. I’ll leave it to theologians to grapple with Ayala’s arguments about whether backaches in old age and other forms of generalized human suffering make the existence of God logically untenable. But on the specific scientific question of the organization of the human genome, I think the evidence is clear. It is Ayala who has been sloppy, and not only in his assessment of the human genome, but also, I must add, in his critique of my book.

Meyer's full bibliography for this essay can be downloaded here.

Stephen C. Meyer directs Discovery Institute’s Center for Science and Culture in Seattle, Wa. He received his Ph.D. in the philosophy of science from the University of Cambridge. He is the author of Darwin’s Doubt: The Explosive Origin of Animal Life and the Case for Intelligent Design (HarperOne, 2013) and Signature in the Cell: DNA and the Evidence for Intelligent Design (HarperOne, 2009) a Times (of London) Literary Supplement book of the year.

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Glen Davidson - #6554

March 11th 2010

I’ll leave it to theologians to grapple with Ayala’s arguments about whether backaches in old age and other forms of generalized human suffering make the existence of God logically untenable.

I won’t get into the whole “junk “DNA” issue much because I know little enough about it, and because there are rather more clear indications of unintelligent “design” than DNA that appears sloppy.  Of course ERVs and gene duplications, both of which are indicated within ours and other genomes, clearly cause there to be useless DNA in genomes, regardless of what is or is not made of them later.

But there is no evidence of foresight over the course of evolution, and concordant with that is the fact that both “good designs” and “poor designs” come from often very unlikely antecedents by any design principles.  Bird wings are very fine adaptations, yet they are modifications of birds’ ancestors terrestrial forelimbs, not modified pterosaur wings or first principles designs like any known intelligent designers would utilize (did in the case of the Wright brothers’ wings, and predecessors to that).

Glen Davidson

Glen Davidson - #6555

March 11th 2010

Continuing from #6554:

Then there are “bad designs,” some of which were mentioned by Ayala, like the narrow birth canal in humans, which could have been totally changed by any designer.  I could add the whole descent of the testes process, which leaves weak spots in male abdomens, and hardly compares favorably with the testes of birds which can effect spermatogenesis at rather higher temperatures than can those of mammals.

Obviously it’s not a question of theology at all when both the tell-tale evidence of “good” and of “bad design” in evolution just “happens to be” explained by evolutionary constraints, and have nothing at all to do with known design constraints.  That is the fact that IDists like Meyer continually fail to address, and no doubt will well into the future.

Nevertheless, it is not surprising when a theological apology like Meyer’s book is refuted according to certain theological understandings.  Ayala and the rest of us are well aware that Meyer is doing apologetics for a God who is supposed to have created with forethought and understanding.  Meyer hardly has reason to tell Ayala not to get into theology as a theist.

Glen Davidson

John VanZwieten - #6556

March 11th 2010

Is the first cell so evidently intelligently designed (specially created) that we should cancel any research into possible natural mechanisms?  Or would it be ok to try an experiment now and then in the off chance understanding those mechanisms simply eludes us so far?

Rick Mayo - #6592

March 12th 2010

Perhaps its just me but, it seems that anything that comes from the intelligent design end of the table is almost immediately subjected to “religious and theological biases.” There is little question or argument that this is true. Dr. Stephen Meyer has been very forthright that this (intelligent design) has nothing to do with a theistic inference. Further, many that are darwinists who are professed christians
are some of the loudest voices against anything that refers to intelligent design. Clearly, there is si something much bigger here at stake.

If I may take my liberty with this as one who is a novice to this entire issue….this sounds strangely historically familiar and reminds me of the Catholic church’s persecution of Galileo for his discovery
of heliocentric solar system. The Catholic church resisted the obvious…even threatened Galileo with inquisition, excommunication. What is so remarkable about all of this: is that Galileo was Catholic!

Could there be a sliver of a chance they were are witnessing a potential breakthrough that could shatter the “myth.” Interesting. Thumbs up to Stephen Meyer. They used to call this courage.

Glen Davidson - #6593

March 12th 2010

Oh, Stephen Meyer is sometimes forthright, although not where he’s most likely to be caught out on it.  On Dennis Miller’s program he says,

...the creator was not only capable of creating great beauty…


Later in the same program, when someone brings up the “possibility” that aliens did it, he states, among other things, that “the God hypothesis explains more.”  Explains more religion, but about equal “science.”

He tries to pretend that his faith is separate from his “science” (the truth is, apologetics), but of course it isn’t any more than when his CSC put out the Wedge Document.

I don’t doubt that Galileo is worth bringing up, since the IDists never cease from trying to force schools to teach religious apologetics in science classes at the expense of science.  Same old.

Perhaps there is courage in sticking up for evidence-free claims, but it’s nothing more than what we get from “theorists” about aliens.

Glen Davidson

Kendalf - #6606

March 12th 2010

Rick, while I agree in some respects with your parallel to Galileo and heliocentrism, I believe you are misrepresenting the complexities of the Galileo affair when you say that “the Catholic church resisted the obvious…” The evidence for heliocentrism was far from obvious during the time of Galileo’s trial, and in fact the immobility of the Earth was the “obvious” conclusion held by the vast majority of ~scientists~ (not theologians) during Galileo’s time.

This blog post (http://reasonableanswers.blogspot.com/2009/01/galileo-against-scientists-dispelling.html) may provide some helpful background to the Galileo affair.

It took almost a century before direct observational proof for heliocentrism was acquired. I would suspect that Meyer and other ID theorists would prefer not to wait that long…

Gregory Arago - #6616

March 12th 2010


I asked before, but now ask it again. It is clear that you are the resident ID-basher on this site, which is not mainly about ID, but rather about ‘science and religion’. But do you have any imput for building a constructive and cooperative dialogue between ‘science and religion’ to offer? Or do you think no such dialogue is possible?

You denied being a TE, EC or BioLogos supporter. Are you just here to derail conversations that would invite reasonable and tolerant voices to participate in better understanding how to live a life of religious faith in an era where ‘sciences’ are also powerful forms of knowledge? I don’t find much respect for ‘people who support ID’ in your tone, and it was a request by Dr. Darrel Falk himself, who likewise doesn’t accept the scientificity of ID, that people treat their ‘opponents’ with respect.


Rick Mayo - #6714

March 12th 2010

I have always wondered how evolutionists would account for morality in human beings. In a larger circle, this would also include ethics, principals, etc. The last 50 year has seen an incredible shift in morals in America. A case could be made that this represents a “de-evolution”. This process is described by Paul (I believe) in Romans chapter 1. According to this text, when humanity worshipped the creature more than the creator, it resulted in God responding by “turning them over’. As a theologian, this represents a real problem to moral relativists and even evolutionists in the sense that we see a “de-evolving” of humanity due to its denial of God and His proper place in the universe.

If this chapter is to be regarded literally, it would certainly explain the moral entropy that surrounds us. Where then, is evolution in the advancement of moral principals?

anair - #6853

March 15th 2010

The way science works is different evidence leads to different conclusions of different certainty.

Specified information in DNA as evidence for design, could be caused by an intelligent cause inside our cosmos as opposed to transcendent. But cosmological evidence (fine-tuning) is much more likely caused by a transcendent intelligence. And then historical evidence, and evidence from the presuppositional approach leads to Jesus of the Bible.

On one level Christian ID proponents can agree with Atheistic panspermia proponents, on other levels when taking in more evidence (of different kinds) looking at the big picture, different conclusions can be made: all of which require some level of faith (some more than others).

anair - #6855

March 15th 2010

continuing from #6853

To me one of the most amazing consequences of the ID theory is that it finally brings some more connection between aspects of human experience that have so long been compartmentalized. Being able to posit teleological reasons opens up new avenues with great potential for discovery in disciplines across the board. e.g. Cosmology, Abiogensis, Philosophy of Mind, Philosophy of Science, Ethics, Neuroscience, and even Art. Just as in the past we’ve made connections from Physics to Chemistry to Biology, now the hard sciences are making connections farther up. Sure this makes scientific inquiry more difficult, but much more powerful as well.

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