Posted by Andrea Bottaro on July 19, 2007 02:10 PM

Over at the Discovery Institute’s Media Complaints Division, Casey Luskin is keeping himself busy trying to fudge assert that the notion of “junk DNA” (which ID advocates consider erroneous, despite the fact that strong, independent lines of evidence indicate that a large fraction of genomic DNA in most eukaryotic organisms is phenotypically non-functional) was the result of application of Darwinian principles.

Several people (e.g. T. Ryan Gregory, Larry Moran and Steve Reuland, as well as myself ) have already pointed out that, on the contrary, a strict application of the Darwinian paradigm, also known as “panselectionism” or “adaptationism”, led many prominent evolutionary biologists to initially resist the idea that some DNA may be non-functional, an opposition which was later mostly lifted (sometimes partially, as we will see) by the progressive acceptance of neutralist views.

Indeed, as late as 2001 Ernst Mayr, one of the “deacons” of Darwinian adaptationism, thought it appropriate to state, in “What Evolution Is”:

A remarkably high proportion of DNA in the chromosomes seems to perform no obvious function, such as coding for RNAs and proteins. Such DNA, probably incorrectly referred to as “junk,” is estimated for humans to be as much as as 97 percent of the total DNA. […] There is widespread belief among Darwinians that such apparently unnecessary DNA wouldhave been eliminated long ago by natural selection if it did not have some, as of yet undiscovered, function.

(E. Mayr, 2001, What Evolution Is, Basic Books, p. 108)

[Note that for Mayr, never much the pluralist, true DarwiniansTM essentially included only strict followers of the Neo-Darwinian New Synthesis, with minor - ahem - adaptations.]

In “The Growth of Biological Thought” (1982), Mayr also rejected the idea that “junk DNA” may be largely composed of parasitic, “selfish” elements, which, while not strictly non-functional, only serve the goal of their own propagation. Such an idea, Mayr wrote:

is inherently distasteful to a Darwinian. Surely natural selection, a Darwinian would say, should be able to come up with a defense mechanism against such an expensive type of parasitism.(E. Mayr, 1982, The Growth of Biological Thought, Belknap Press, p 579; quoted by Maxine Singer in From Genomic Junk to Human Disease, Proc. Am. Phil. Soc. 138, 11-24, 1994)

In 1971, shortly after the seminal papers by Kimura, King and Jukes and others had formalized and begun to test the Neutral Theory, Mayr threw the gauntlet with words that would fit perfectly in the mouth of most of today’s ID advocates:

More and more sites even in the largest molecules are found to have specific functions. A “functionless site” is simply one the function of which has not yet been determined.

(E. Mayr, Populations, Species, and Evolution , 1971, Harvard University Press, p. 127; cited by Gert Korthof .)

So much for the claim that “junk DNA” was a direct consequence of Darwinian ideas.

But there is a far sweeter contradiction at play here.

On the one side, ID advocates certainly like to claim that the functionality of “junk DNA” is a direct and necessary consequence of the design approach. For instance, in a paper in the now defunct “peer-reviewed” ID journal PCID, Jonathan Wells says:

From an ID perspective, however, it is extremely unlikely that an organism would expend its resources on preserving and transmitting so much “junk.” It is much more likely that noncoding regions have functions that we simply haven’t discovered yet.

while on the other, they have expended significant amounts of effort countering what they claim is the fallacy of the “argument from optimal design”, which points out that biological “design” is at times clearly haphazard and inefficient, reflecting more the contingencies of an undirected evolutionary process than any foresight or intelligent planning. Thus, Bill Dembski wrote, in an article entirely devoted to this topic:

Nevertheless, taken strictly as a scientific theory, intelligent design refuses to speculate about the nature of this designing intelligence. Whereas optimal design demands a perfectionistic, anal-retentive designer who has to get everything just right, intelligent design fits our ordinary experience of design, which is always conditioned by the needs of a situation and therefore always falls short of some idealized global optimum.

[Incidentally, note that this article, written for a religious audience, is not shy at all about using the G-word, and while claiming that ID “refuses to speculate about the nature of this designing intelligence”, it eventually goes off the deep Biblical end:

This is a fallen world. The good that God initially intended is no longer fully in evidence. Much has been perverted. Dysteleology, the perversion of design in nature, is a reality. It is evident all around us. But how do we explain it? The scientific naturalist explains dysteleology by claiming that the design in nature is only apparent, that it arose through mutation and natural selection (or some other natural mechanism), and that imperfection, cruelty, and waste are fully to be expected from such mechanisms. But such mechanisms cannot explain the complex, information-rich structures in nature that signal actual and not merely apparent design–that is, intelligent design.

The design in nature is actual. More often than we would like, that design has gotten perverted. But the perversion of design–dysteleology–is not explained by denying design, but by accepting it and meeting the problem of evil head on. The problem of evil is a theological problem. To force a resolution of the problem by reducing all design to apparent design is an evasion. It avoids both the scientific challenge posed by specified complexity, and it avoids the hard work of faith, whose job is to discern God’s hand in creation despite the occlusions of evil.[8]

But this is another story.]

The problem of suboptimal design is so important in the ID advocates’ mindframe, that it deserved its own entry in their self-produced, unpretentiously named “Encyclopedia of Science and Philosophy”. Alas for Luskin, that entry readily concedes that “junk DNA” can not only exist, but is a predictable result of an intelligent design process analogous to human software design (the genome as bloatware, so to speak):

Dead code is code that was written into the program in high level programming language, either erroneously, or originally, for some now redundant purpose (such as testing other code), and remains in the program source code doing nothing. Modern compilers, programs that convert source code into computer-interpretable code, usually strip out
such unused code during the process of compilation, analogous to the way in which DNA polymerase excises introns (non-coding sequences) out of a gene and splices together its exons (coding sequences) when transcribing to mRNA. However, the dead code can happily sit in the source code (as perhaps can the ‘junk’ DNA stay in the DNA) forever - doing nothing but causing confusion to later intelligent observers - engineers who must update the program for example.

Sometimes software engineers will leave code that is not dead code, but does not perform a function, in the source code intentionally. Such code is sometimes called a stub, and is incorporated for the purposes of extensibility - extending the capabilities of the code later on. The code is correct and required effort to produce, was deemed unnecessary to the current version of the software, but is desirable to add functions to the next version, and therefore is purposefully left in - by design. Of course, depending on a number of factors - whether requirements for the next version of the software change or other software makes it obsolete before the next version - even code for extensibility might never be used. There are many other examples of code, that might never actually be used, being purposefully incorporated into software programs. Take interface code for example. Software engineers might build software A to talk to or interoperate with software B written by other software engineers. The source code that facilitates this interoperability is called interface code. However, if the software B project is cancelled, then the interface to B from A will likely never be used, but might never be removed. This is just another example of designed flaws or non-optimal design by intelligent designers.

It is also noteworthy that in computer science and engineering, what is actually considered optimal is contingent on many factors relating to the requirements for the design (what people need or want it to do) and how powerfully the design must implement functions to cater for those requirements. For example, the speed of a software module that runs a screensaver is likely to be considered optimal at a much lower bit-rate than one that renders visual radar feedback on the space shuttle.

Ultimately, of course, software engineers are imperfect designers with limited capabilities operating in imperfect conditions (budget, fatigue and delivery schedules etc.), and so no rational person expects their designs to be perfect, flawless, or even necessarily optimal (although they may converge on some of these some of the time). However, even a putatively perfect or superhuman intelligent designer - one capable of designing the biochemical underpinnings of life - is arguably not required to produce perfect, flawless or optimal designs.

So, Intelligent Design predicts efficient design and no “junk DNA”, except when of course it doesn’t. Ah, the power of having a heuristically empty theory!

Ultimately, I think ID’s current infatuation with the “no junk DNA” mantra, jumping on the bandwagon of some recent discoveries, is an altogether bad move for them, for several reasons:
- First, it puts them in the uncomfortable position of aligning themselves with ultra-Darwinian pan-selectionists, who not only have clear dibs on who first expressed skepticism at the existence of “junk DNA”, but also can explain why all DNA should be functional based on a much more elegant and parsimonious theory (based on straightforward, “micro-evolutionary” negative selection effects that even the most close-minded ID advocates would find hard to argue against).
- Second, it forces them into a contradiction with respect to the “argument from optimal design”: either design is optimized, in which case neither “junk DNA” nor our prostates and inverted retinas should exist, or it isn’t.
- Finally, and most importantly, it still leaves them facing the daunting task of explaining away the currently overwhelming evidence (from the c-value paradox, to the existence of large deletion polymorphisms, to the phylogenetic evidence for neutral “drift” of most stretches of intergenic sequence, etc) that much of genomic DNA in many eukaryotes has no phenotypic effect.

Of course, I don’t expect ID advocates to change course at this point, as their penchant for painting themselves into corners (see Behe’s testimony at the Dover trial for a masterpiece in the art) is now the stuff of legend. Still, it will be fun to see how they will cope when reality catches up with them.

[Note added in proof:
As I am re-editing this, I see Mike has made some of these points already in an independent post. Repetita iuvant, I guess.]

[UPDATE:
Casey Luskin has posted another piece at the Discovery Institute’s Media Complaints Division ominously entitled: “Is Panda’s Thumb Suppressing the Truth about Junk DNA?”, in which he alleges that I have suppressed a comment from one Andras J. Pellionisz, who seems to be a rather cranky biophysicist (“of Information Geometry of Nature”, according to his own self-description) who claims to have identified the function of “junk DNA” based on its “fractal geometrical” properties.

In fact, Dr. Pellionisz’s extensive comment has been posted on this blog since Friday morning, which is when I realized it was stuck in the pipeline awaiting authorization, simply because its unusually large number of links triggered our spam-detection system.

The real irony is that Luskin complains of a non-existing instance of censorship here while writing on a site that does not allow any comments whatsoever, and has systematically rejected track-backs from the Panda’s Thumb for years (I am sending one from this post, let’s see if it goes through).

Of course, the “Evolution News & Views” site has no interest in having its readers fairly and publicly evaluate its arguments, like we do at PT. Its goal is simply to administer the Discovery Institute’s Kool-Aid, without interference from uncomfortable questions or pesky facts. ]

[UPDATE II:
Luskin has added the following addendum to his original piece:

Update 8:00 am, July 23, 2007: Unsurprisingly, Dr. Pellionisz now reports that after my post went live, he discovered that Panda’s Thumb chose to post his comment.

Since the comment in question was in fact authorized for publication long before Luskin’s post went live with Pellionisz’s erroneous accusation, either Luskin or Pellionisz (or both) are still blatantly misrepresenting the truth. I’ll let them sort out between themselves who is in fact responsible for the falsehood; in the meanwhile, bets are open.]