On <em>Signature in the Cell</em>, Robert Saunders Still Doesn't Get It - Evolution News & Views

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On Signature in the Cell, Robert Saunders Still Doesn't Get It

At his Wonderful Life blog, geneticist Robert Saunders has responded to my recent take down of his "critique" of Stephen Meyer's arguments for intelligent design, offered and defended in Signature in the Cell. Of course, it wouldn't be an anti-ID article without its share of condescending rhetoric. Saunders claims that I "have absorbed a typical strategy beloved of Intelligent Design creationists: of devising neologisms that don't correspond to normally used science terminology, and combined this with ignorance of biology." I have no doubt that Dr. Saunders is informed about his discipline but the arguments he presents here are weak.

Saunders proceeds to quote what I wrote concerning the arbitrary nature of the ordering of nucleotide base pairs along the spine of DNA's sugar-phosphate backbone. Meyer observes that "there are no chemical bonds between the bases along the longitudinal axis in the center of the helix. Yet it is precisely along this axis of the DNA molecule that the genetic information is stored" (SITC, p. 242). On this, Saunders writes,

This paragraph just baffles me. [...] I'm not clear why this "fundamental property" bothers Jonathan M -- he seems to have a major comprehension failure at this point.
Who said I was "bothered" by it? The point here is actually quite simple, and it surprises me that Saunders still doesn't get it, despite my explaining it to him in my previous blog post. It is the arbitrary nature of nucleotide sequencing that allows DNA to have information-bearing properties. The nucleotides do not align by virtue of some sort of chemical affinity. As I stated previously, any sequence is possible but only some sequences are biologically meaningful.

Saunders subsequently quotes my rebuttal to the charge that ID is a "god-of-the-gaps" argument. He responds

Oh, for goodness' sake, this ( "x is complex; therefore, x is designed,") is exactly what Meyer is saying. He cannot envisage a mechanism giving rise to the genetic code, so he invokes a supernatural entity.
But I explained in the very section he quotes why this is emphatically not the case. ID is based on standard principles of scientific methodology. When dealing with past events, scientists conventionally use the historical (abductive) method of inference to the best explanation. In order to reconstruct what happened in the remote past, scientists allow their present experience of cause and effect to guide their search for the best explanation. Thus, it follows that intelligence is the best -- most causally adequate -- candidate explanation for the information intrinsic to the hereditary molecules of DNA and RNA. I am having difficulty seeing how this can possibly be construed as a "god-of-the-gaps" argument.

Saunders continues,

And, yes, we have clearly demonstrable mechanisms by which genetic information can grow in both quantity and complexity. I even see this happening in the lab in experimental timescales. Jonathan is ignorantly regurgitating ID creationist neologisms, to invoke a supernatural entity.
If Saunders were to provide specific examples, we could talk about those. Furthermore, Stephen Meyer's book is concerned with the origin of life. Processes of mutation, gene duplication, polyploidy, genetic drift, natural selection, etc., by definition only occur after the emergence of the first life. So such mechanisms can be ruled out as candidate explanations for the event in the history of life with which Meyer's book is concerned.

Saunders subsequently quotes what I wrote regarding the irrelevance of polyploidy to the origin of the first life. He writes

This is Jonathan wiffly-waffling around a subject he doesn't seem to have a strong grasp of. It's often stated in ID creationist circles (such as the C4ID) that there is no known source of "information" other than from an intelligent mind. This is clearly nonsense, as Simon knows: gene and genome duplication provides the raw material for whole families of diverged genes to arise. What is "specified complexity"? Is it the genetic code itself? The mere existence of heritable material? Is this the same as Meyer's undefined "specified information"?
Specified complexity can be defined as an extremely improbable phenomenon (factoring in the probabilistic resources at one's disposal) which conforms to an independently given pattern. Millions of bases in a sequence-specific order qualifies as specified complexity, as does the molecular machinery under-girding flagellar assembly, as do the carvings on mount Rushmore. The crystal lattice structure of an ice crystal, on the other hand, would not qualify as specified complexity.

And gene duplication does not provide new genetic information. Sure, duplicated gene copies subsequently mutate and diverge and explore combinatorial sequence space in search of novel utility. But it is not at all clear that a blind search can find the bases of those functional fitness peaks within a plausible time frame -- especially when multiple non-adaptive mutations are required to facilitate an innovation in function. And this problem is only further accentuated when regulatory sequences also have to be altered.

Regarding my points about ID's predictions, Saunders writes,

OK, here is why I think this is just so much nonsense:

"it predicts the presence of complex and functionally specific information in the cell" -- This is a quite bizarre claim. The Intelligent Design variant of creationism arose in the 1990s. At that time, the presence of large amounts of genetic "information" in cells was well known. In what way is the presence of information a sensible prediction? And as far as I can tell, this whole "complex and functionally specific information" remains remarkably ill-defined ... and in particular is inconsistent with conventional information theory. If we're now going to think of the origins of life and the genetic systems we see around us today, all ID creationists are saying is that they cannot understand how it happened, and in their religiously motivated world-view prefer to fall back on supernatural intervention rather than taking a genuinely scientific approach to the problem. How is complex and functionally specific information defined?

Okay, let's explain this one more time. ID provides an explanatory filter for detecting the products design in nature. If feature x is designed, says the theory of ID, we expect to find specified complexity associated with the system -- because specified complexity is one of the effects that intelligent agents often leave behind as indicative of their activity. I have already explained what ID theorists mean by "specified complexity." And the concept of "specified complexity" is not unique to ID proponents. Indeed, the concept has been entertained by information theorists such as Hubert Yockey. As Bernd-Olaf Kuppers has observed, "the problem of the origin of life is clearly basically equivalent to the problem of the origin of biological information."

Saunders continues,

"it predicts the already-alluded-to rarity of functional protein folds in amino acid sequence space." This is quite interesting, particularly given Axe's background as a post-doc in Alan Fersht's lab in Cambridge. But as far as I can see, this boils down to the usual incredulity argument. For Axe, with a pedigree of working in a prestigious lab in Cambridge, I would have thought a more prestigious outlet for this review might have been possible. As it is, he's reduced to publishing in the Biologic Institute house journal, with the not-so-impressive archive of 7 papers over its two years of existence, all authored by members of the editorial board (all of whom appear to be creationists of one variety or another).
Actually, the demonstration of the rarity of protein folds in sequence space reveals that a quantity and quality of information that meets the definition of "specified complexity" is necessary in specifying innovation in enzymatic domains. So, if proteins are detectably designed, this is exactly what we should be expecting to see.

Regarding Bio-Complexity, the quality of people on the editorial board is top-notch and could compete with just about any other journal out there. And not all of those who review the papers submitted to the journal are advocates of ID. Bio-Complexity is a quality journal.

Saunders also doesn't get my point about patterns of the fossil record and, specifically, the pattern of morphological disparity preceding diversity. Neo-Darwinian evolution conversely predicts that the major distinct animal body plans will arise after numerous small-scale speciation events -- that is, we ought to observe small scale differences adding up to big differences. The actual fossil record, however, reveals the exact opposite of that -- with the major taxonomic groups (phyla) appearing first, and the minor taxonomic groups (e.g. genus, species) arising only later.

Saunders further raises questions regarding the notion that ID predicts function for so-called "junk DNA." Indeed, this is one area where I think ID offers significant heuristic value. Where Darwinian thinking expects us to find junk and waste wherever we look in the cell, ID predicts the opposite -- that is to say, we should expect to find function and meaning. It seems unlikely that a designer would fill our genomes with millions of bases of nonsensical "filler." If ID is correct, therefore, it is to be expected that much of this "filler" will be found to be functional (though granting that various scenarios may well have resulted in the accumulation of some level of genuine junk).

On the issue of fine tuning, Saunders appeals to the famous anthropic argument, noting,

The fine-tuning argument has always seemed to me to be somewhat tautologous. Had the constants been different, we would not be here to look at the Universe and its physical constants. We have a sample size of 1. Exactly 1.
William Lane Craig has effectively countered this argument:
[S]uppose you are dragged before a firing squad of 100 trained marksmen, all of them with rifles aimed at your heart, to be executed. The command is given; you hear the deafening sound of the guns. And you observe that you are still alive, that all of the 100 marksmen missed! Now while it is true that

5. You should not be surprised that you do not observe that you are dead,

nonetheless it is equally true that

6. You should be surprised that you do observe that you are alive.

Since the firing squad's missing you altogether is extremely improbable, the surprise expressed in (6) is wholly appropriate, though you are not surprised that you do not observe that you are dead, since if you were dead you could not observe it.

To conclude, Saunders has offered us nothing substantive and demonstrates an apparent lack of familiarity with the arguments employed by proponents of ID. As Casey Luskin recently observed, if anti-ID advocates had any more substantive objections to make, you can bet that we would have heard them by now.


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