This article was originally posted on September 29, 2004.
The September 9, 2004 issue of Nature reported the publication of an article advocating the theory of intelligent design in a peer-reviewed scientific journal. The article, written by Discovery Institute Senior Fellow Stephen C. Meyer and titled "The Origin of Biological Information and the Higher Taxonomic Categories," was published in the Proceedings of the Biological Society of Washington (PBSW). [1, 2]
The mere fact that the article was published has generated intense controversy. Many in the Darwinist establishment have criticized the editor of PBSW for even considering an article advocating the theory of intelligent design. Except for one essay posted on the Internet, however, there has not been much in the way of actual scientific critique of the article's contents. This posting is the first of several responses to that one essay.
According to the Nature report, "Meyer's article has attracted a lengthy rebuttal on The Panda's Thumb, a web site devoted to evolutionary theory." The supposed rebuttal , titled "Meyer's Hopeless Monster," was written by Alan Gishlick, Nicholas Matzke, and Wesley R. Elsberry [hereafter GME], all of whom are staff members of the National Center for Science Education (NCSE), an organization that insists there is no evidence against neo-Darwinian evolution and that opposes any criticisms of Darwinian theory in public schools.
Since Nature has given prominence to this hastily written essay, we will respond to it fully, in a series of installments over the next days and weeks. This posting constitutes the first installment and provides a road map to our detailed critique of GME and defense of Meyer.
In this introductory installment we describe the overall tactics of GME's response to Meyer’s article. Before doing so, however, it will help to summarize Meyer’s argument and catalogue GME’s main objections to it.
The argument of Meyer's article can be summarized in eight statements:
(1) The origin of morphological novelty during the history of life is increasingly recognized as a fundamental and unsolved problem in theoretical and evolutionary biology.
(2) The problem of the origin of biological form is a manifestation of the problem of the origin of biological information.
(3) Biological information can be distinguished from Claude Shannon’s purely mathematical conception of information. Whereas Shannon's classical information theory provides a mathematical measure of the complexity (or improbability) of a string of characters, biological information refers to strings or structures that are both complex and functionally specified. As such, biological information constitutes an example of “specified complexity,” or what William Dembski calls “Complex Specified Information” [hereafter CSI] -- a term he and others have used to distinguish functionally specified information from mere Shannon information or information-carrying capacity.
(4) The Cambrian Explosion constitutes a paradigmatic example of the origin of functionally specified biological information (CSI). During the Cambrian many novel animal body plans appear to have arisen during a geologically short interval of 5-10 million years. Whether the Cambrian Explosion was this abrupt or not, the emergence of these new body plans would have required the origin of large amounts of genetic and epigenetic biological information.
(5) Neo-Darwinism [hereafter ND] cannot account for the origin of the many novel genes and proteins that arise during major episodes of biological innovation such as the Cambrian explosion. Thus, ND cannot account for the origin of the genetic information necessary to build new animal body plans.
(6) Constructing novel body plans such as those that arose during the Cambrian Explosion also depends upon new epigenetic (as opposed to just genetic) morphological information. Natural selection acting on random genetic variations alone cannot produce the necessary epigenetic morphological information. For this reason, neo-Darwinian mechanisms cannot -- in principle -- account for the origin of novel body plans such as those that emerged during the Cambrian Explosion.
(7) No other current materialistic evolutionary theory solves the problem of the origin of biological information exemplified by the Cambrian Explosion.
(8) The need for new biological information suggests actual, not just apparent, design in the history of life. Indeed, the theory of intelligent design [hereafter ID] provides a causally adequate explanation for the origin of the information necessary to build novel animal forms.
GME criticize Meyer's article on several grounds. Their main criticisms, keyed to specific propositions in Meyer’s argument, are as follows:
A. (Contra 3) Meyer misunderstands information theory and the work of mathematician William Dembski. Further, Dembski’s work, which Meyer appropriates, fails to offer a non-question begging definition of specified complexity or CSI.
B. (Contra 4) Meyer's interpretation of the Cambrian Explosion is flawed. In particular, recent scientific discoveries suggest that animal body plans did not emerge as abruptly as previously thought. In any case, recent scientific literature suggests that the Cambrian Explosion is merely an artifact of our classification system.
C. (Contra 5) Current evolutionary theory does account for the origin of new genes. Meyer fails to cite numerous scientific papers that make this clear.
D. (Contra 6) Current evolutionary theory does account for the origin of morphological novelties. Meyer again fails to cite numerous scientific papers establishing this point.
E. (Contra 7) Meyer fails to consider some recent variants of neo-Darwinian theory that solve the problems he discusses.
F. (Contra 8) Meyer relies solely on "negative argumentation" and fails to provide a positive evidential basis for the theory of intelligent design.
Before examining GME's criticisms in detail, it will be helpful to ask: What would it take to rebut Meyer's arguments? A serious critic would have to begin with a clear understanding of Meyer's arguments and the evidence he adduces to support them. Furthermore, to succeed scientifically a critic would have to counter Meyer's arguments with evidence, not merely disparaging comments or contrary opinions.
But what have GME actually given us?
First, their supposed rebuttal begins with -- and is characterized throughout by -- a condescending tone and personal attacks on Meyer's motives.
Second, GME claim that Meyer's article contains "serious mistakes" that include "errors in facts and reasoning.” Yet, as we will show, GME misunderstand and/or misrepresent important aspects of Meyer's argument. This calls into question the relevance of some of their critiques and their overall judgment about the quality of Meyer’s reasoning.
Third, GME do offer a potentially significant criticism. They claim that Meyer fails to discuss scientific literature that refutes his main claims. And, indeed, they provide a list of scientific citations that ostensibly solve the central problems that Meyer’s essay addresses, namely, the origin of genetic information and the origin of morphological novelty. As they put it, "Meyer's paper omits discussion or even citation of vast amounts of directly relevant work available in the scientific literature."
To someone unacquainted with the scientific literature, GME’s list of citations list might seem impressive. An actual reading of those citations, however, shows that they fail to support GME's claims. Indeed, GME appear to be engaged in what might be called "literature bluffing."
Literature bluffing is the indiscriminate citation of scientific papers and articles whose titles or abstracts may seem germane to the problem at hand, but which on careful reading prove not to settle the issue, or even not to have any relevance to it. Like a squid spewing out ink to confuse a pursuer, or a fighter jet dispensing chaff to deflect incoming missiles, a literature bluffer floods the discussion with citations to distract attention from the real issues.
Bibliographic search engines such as PubMed make it easy for literature bluffers to compile long lists of citations. The literature bluffer, however, rarely explains the arguments or evidence contained in the publications on the list. That would defeat the bluffer's purpose, which is not really to address the merits of the case, but rather to overwhelm the reader with the apparent weight of scientific authority. The reader is then left with the work of actually studying the publications and assessing their relevance.
Doing that work is time-consuming, but useful nonetheless. Sifting through a pile of citations can teach us one of three things:
i. There is evidence of which we were unaware that challenges our understanding of a scientific problem or theory.
ii. There is evidence of which we were unaware that supports our understanding.
iii. The pile of citations is nothing more than a bluff, and the bluffer may not even have read or understood the publications.
We will show in the coming installments that GME’s list of citations constitutes a bluff. The term "bluff" may seem harsh, but as we shall see it aptly describes the strategy adopted by GME. Their pile of citations is analogous to a stack of poker chips. Like poker players, literature bluffers want us to fold before they show us their cards. "Just look at all these references and citations! Do you really want to challenge all this scientific expertise?" But science, properly understood, is not a game of accumulating citations and using them to bluff others into silence.
In the interest of good science, we are calling GME's bluff.
One fact that will emerge from our analysis is that most of the articles that GME cite contain little more than inferences based on neo-Darwinian theory. Making inferences based on a theory is a valid exercise, but it must not be confused with testing the theory against the evidence. When the truth of the theory itself is at stake -- as it is here -- the theory cannot be defended by inventing just-so stories that presuppose its truth. No scientific theory can be tested without explicit and serious consideration of the possibility that it might be false. To think otherwise is to abandon science for story-telling.
In several installments over the next few days and weeks we will focus primarily on the scientific aspects of this controversy. In the process we will show that GME misunderstand Meyer's arguments in significant respects, and that the evidence they adduce to rebut those arguments does nothing of the sort.
 Jim Giles, "Peer-reviewed paper defends theory of intelligent design," Nature 431 (2004): 114.
 Stephen C. Meyer, "The Origin of Biological Information and the Higher Taxonomic Categories," Proceedings of the Biological Society of Washington 117 (2004): 213-239.
 Alan Gishlick, Nick Matzke, and Wesley R. Elsberry, "Meyer's Hopeless Monster," The Panda's Thumb (posted August 24, 2004), http://www.pandasthumb.org/pt-archives/000430.html
Part II: Neo-Darwinism's Unsolved Problems