Posted by Wesley R. Elsberry on August 24, 2004 05:56 PM

Review of Meyer, Stephen C. 2004. The origin of biological information and the higher taxonomic categories. Proceedings of the Biological Society of Washington 117(2):213-239.

by Alan Gishlick, Nick Matzke, and Wesley R. Elsberry

[The views and statements expressed here are our own and not necessarily those of NCSE or its supporters.]

“Intelligent design” (ID) advocate Stephen C. Meyer has produced a “review article” that folds the various lines of “intelligent design” antievolutionary argumentation into one lump.  The article is published in the journal Proceedings of the Biological Society of Washington.  We congratulate ID on finally getting an article in a peer-reviewed biology journal, a mere fifteen years after the publication of the 1989 ID textbook Of Pandas and People, a textbook aimed at inserting ID into public schools.  It is gratifying to see the ID movement finally attempt to make their case to the only scientifically relevant group, professional biologists.  This is therefore the beginning (not the end) of the review process for ID.  Perhaps one day the scientific community will be convinced that ID is worthwhile.  Only through this route — convincing the scientific community, a route already taken by plate tectonics, endosymbiosis, and other revolutionary scientific ideas — can ID earn a legitimate place in textbooks. 

Unfortunately, the ID movement will likely ignore the above considerations about how scientific review actually works, and instead trumpet the paper from coast to coast as proving the scientific legitimacy of ID.  Therefore, we would like to do our part in the review process by providing a preliminary evaluation of the claims made in Meyer’s paper.  Given the scientific stakes, we may assume that Meyer, Program Director of the Discovery Institute’s Center for Science and Culture, the major organization promoting ID, has put forward the best case that ID has to offer.  Discouragingly, it appears that ID’s best case is not very good.  We cannot review every problem with Meyer’s article in this initial post, but we would like to highlight some of the most serious mistakes.  These include errors in facts and reasoning. Even more seriously, Meyer’s paper omits discussion or even citation of vast amounts of directly relevant work available in the scientific literature. 

Summary of the paper

Meyer’s paper predictably follows the same pattern that has characterized “intelligent design” since its inception: deny the sufficiency of evolutionary processes to account for life’s history and diversity, then assert that an “intelligent designer” provides a better explanation. Although ID is discussed in the concluding section of the paper, there is no positive account of “intelligent design” presented, just as in all previous work on “intelligent design”.  Just as a detective doesn’t have a case against someone without motive, means, and opportunity, ID doesn’t stand a scientific chance without some kind of model of what happened, how, and why.  Only a reasonably detailed model could provide explanatory hypotheses that can be empirically tested.  “An unknown intelligent designer did something, somewhere, somehow, for no apparent reason” is not a model.

Meyer’s paper, therefore, is almost entirely based on negative argument.  He focuses upon the Cambrian explosion as an event he thinks that evolutionary biology is unable to account for. Meyer asserts that the Cambrian explosion represented an actual sudden origin of higher taxa; that these taxa (such as phyla) are “real” and not an artifact of human retrospective classification; and that morphological disparity coincides with phyletic categories.  Meyer then argues that the origin of these phyla would require dramatic increases in biological “information,” namely new proteins and new genes (and some vaguer forms of “information” at higher levels of biological organization).  He argues that genes/proteins are highly “complex” and “specified,” and that therefore the evolutionary origin of new genes is so improbable as to be effectively impossible.  Meyer briefly considers and rejects several theories proposed within evolutionary biology that deal with macroevolutionary phenomena.  Having rejected these, Meyer argues that ID is a better alternative explanation for the emergence of new taxa in the Cambrian explosion, based solely upon an analogy between “designs” in biology and the designs of human designers observed in everyday experience.

The mistakes and omissions in Meyer’s work are many and varied, and often layered on top of each other.  Not every aspect of Meyer’s work can be addressed in this initial review, so we have chosen several of Meyer’s major claims to assess.  Among these, we will take up the Cambrian explosion and its relation to paleontology and systematics. We will examine Meyer’s negative arguments concerning evolutionary theories and the origin of biological “information” in the form of genes.

An expanded critique of this paper is in preparation.

Playing with Dynamite: The Cambrian Explosion

The Cambrian explosion is a standard topic for antievolutionists. There are several reasons for this: many taxa make their first appearance in the Cambrian explosion; the amount of time within the period of the Cambrian explosion is geologically brief; and we have limited evidence from both within and before the Cambrian explosion on which to base analysis. The first two factors form the basis of an antievolutionary argument that evolutionary processes are insufficient to generate the observed range of diversity within the limited time available. The last factor is a general feature of the sorts of phenomena that antievolutionists prefer: not enough evidence has yet accrued to single out a definitive scientific account, so it is rhetorically easy for a pseudoscientific “alternative” to be offered as a competitor. In Meyer’s closing paragraph, he mentions “experience-based analysis.”  The consistent experience of biologists is that when we have sufficient evidence bearing upon some aspect of biological origins, evolutionary theories form the basis of explanation of those phenomena (an example where much evidence has become available recently is the origin of birds and bird flight; see Gishlick 2004).

Problems with Meyer’s discussion of the Cambrian Explosion:

1. Meyer tries to evaluate morphological evolution by counting taxa, a totally meaningless endeavor for investigating the evolution of morphology. Most paleontologists gave up taxa-counting long ago and moved on to more useful realms of research regarding the Cambrian (see Budd and Jensen 2000). This is perhaps why most of Meyer’s citations for this section are to his own articles (themselves not in relevant scientific journals).

2. Meyer repeats the claim that there are no transitional fossils for the Cambrian phyla. This is a standard ploy of the Young-Earth Creationists (see Padian and Angielczyk 1999 for extended discussion of this tactic and its problems). Meyer shows a complete lack of understanding of both the fossil record and the transitional morphologies it exhibits (even during the Cambrian explosion; for a recent example of transitional forms in the Cambrian explosion see Shu et al. 2004) as well as the literature he himself cites. (This topic has been dealt with before, as with DI Fellow Jonathan Wells. See Gishlick 2002 at http://www.ncseweb.org/icons/icon2tol.html.)

3. Meyer attempts to argue that the “gaps” in the fossil record reflect an actual lack of ancestors for Cambrian phyla and subphyla.  To support this, Meyer cites some papers by University of Chicago reasearcher Mike Foote.  However, of the two papers by Foote cited by Meyer, neither deals with the Cambrian/Precambrian records (one concerns the Middle and Late Paleozoic records of crinoids and brachiopods, the other the Mesozoic record of mammal clade divergence), or even transitional fossils. Foote’s papers deal with issues of taxonomic sampling: How well does a fossil record sample for a given time period reflect the biodiversity of that period?  How well does a given fossil record pinpoint divergence times? Foote’s conclusions are that we have a good handle on past biodiversity, and that divergence times probably match appearance in the fossil record relatively closely. But Foote’s work utilizes organisms that are readily preserved.  It doesn’t deal with organisms that aren’t readily preserved, a trait that almost certainly applies to the near-microscopic, soft-bodied ancestors of the Cambrian animals.  According to Meyer’s argument, which doesn’t take into account preservation potential, microscopic metazoans such as rotifers must have arisen recently because they entirely lack a fossil record. Neither of Foote’s papers supports Meyer’s contention that the lack of transitional fossils prior to the Cambrian indicates a lack of ancestors.  Lastly, it appears that fossils of the long-hypothesized small, soft-bodied precambrian worms have recently been discovered (Chen et al. 2004).

Information and Misinformation

For some, “information theory” is simply another source of bafflegab. And that appears to be the only role Meyer sees for “information theory”. After brief nods to Shannon and algorithmic information theory, Meyer leaves the realm of established and accepted information theoretic work entirely.

1. Meyer invokes Dembski’s “specified complexity”/”complex specified information” (SC/CSI) as somehow relevant to the Cambrian explosion. However, under Dembski’s technical definition, CSI is not just the conjoint use of the nontechnical words “specified” (as in “functional”) and “complexity”, as Meyer erroneously asserts.  According to Dembski’s technical definition, improbability of appearance under natural causes is part of the *definition* of CSI.  Only after one has determined that something is wildly improbable under natural causes can one conclude that something has CSI.  You can’t just say, “boy, that sure is specific and complicated, it must have lots of CSI” and conclude that evolution is impossible.  Therefore, Meyer’s waving about of the term “CSI” as evidence against evolution is both useless for his argument, and an incorrect usage of Dembski (although Dembski himself is very inconsistent, conflating popular and technical uses of his “CSI,” which is almost certainly why Meyer made this mistake.  See here for examples of definitional inconsistency.).

2. Meyer relies on Dembski’s “specified complexity,” but even if he used it correctly (by rigorously applying Dembski’s filter, criteria, and probability calculations), Dembski’s filter has never been demonstrated to be able to distinguish anything in the biological realm — it has never been successfully applied by anyone to any biological phenomena (Elsberry and Shallit, 2003).

3. Meyer claims, “The Cambrian explosion represents a remarkable jump in the specified complexity or ‘complex specified information’ (CSI) of the biological world.” Yet to substantiate this, Meyer would have to yield up the details of the application of Dembski’s “generic chance elimination argument” to this event, which he does not do. There’s small wonder in that, for the total number of attempted uses of Dembski’s CSI in any even partially rigorous way number a meager four (Elsberry and Shallit, 2003).

4. Meyer claims, “One way to estimate the amount of new CSI that appeared with the Cambrian animals is to count the number of new cell types that emerged with them (Valentine 1995:91-93)” (p.217). This may be an estimate of something, and at least signals some sort of quantitative approach, but we may be certain that the quantity found has nothing to do with Dembski’s CSI. The quantitative element of Dembski’s CSI is an estimate of the probability of appearance (under natural processes or random assembly, as Dembski shifts background assumptions opportunistically), and has nothing to do with counting numbers of cell types.

Of Text and Peptides

1. Meyer argues that “many scientists and mathematicians have questioned the ability of mutation and selection to generate information in the form of novel genes and proteins” (p. 218).  He makes statements to this effect throughout the paper.  Meyer does not say who these scientists are, and in particular does not say whether or not any of them are biologists.  The origin of new genes and proteins is actually a common, fairly trivial event, well-known to anyone who spends a modicum of effort investigating the scientific literature.  The evolution of new genes has been observed in the lab, in the wild, inferred in great detail between closely-related modern species, and reconstructed in hundreds of cases by comparing the genomes from organisms sequenced in genome projects over the last decade (see Long 2001 and related articles, and below).

2. Meyer compares DNA sequences to human language.  In this he follows Denton’s (1986) Evolution: A Theory in Crisis.  Denton (1986) argued that meaningful sentences are isolated from each other: it is usually impossible to convert one sentence to another via a series of random letter changes, where each intermediate sentence has meaning. Like Denton (1986), Meyer applies the same argument to gene and protein sequences, concluding that they, like meaningful sentences, must have been produced by intelligent agents.  The analogy between language and biological sequence is poor for many reasons; starting with the most obvious point of disanalogy, proteins can lose 80% or more of their sequence similarity and retain the same structure and function (a random example is here). Let’s examine an English phrase where four out of five characters have been replaced with a randomly generated text string.  See if you can determine the original meaning of this text string:

Tnbpursutd euckilecuitn tiioismdeetneia niophvlgorciizooltccilhseema er [1]

Eighty percent loss of sequence identity is fatal to English sentences. Clearly proteins are much less specified than language.

3. Meyer cites Denton (1986) unhesitatingly.  This is surprising because, while Denton advocated in 1986 that biology adopt a typological view of life, he has abandoned this view (Denton 1998).  Among other things, Denton wrote, “One of the most surprising discoveries which has arisen from DNA sequencing has been the remarkable finding that the genomes of all organisms are clustered very close together in a tiny region of DNA sequence space forming a tree of related sequences that can all be interconverted via a series of tiny incremental natural steps.” (p. 276)  Denton now accepts common descent and disagrees with the “intelligent design” advocates who conjecture the special creation of biological groups, regularly criticizing them for ignoring the overwhelming evidence (Denton 1999).

4. Meyer’s case that the evolution of new genes and proteins is essentially impossible relies on just a few references from the scientific literature. For example, Meyer references Taylor et al. 2001, a paper entitled “Searching sequence space for protein catalysts” and available online at the PNAS website.  But Taylor et al.’s recommendation for intelligent protein design is actually that it should mimic natural evolution: “[A]s in natural evolution, the design of new enzymes will require incremental strategies…”.

There is a large mass of evidence supporting the view that proteins are far less “specified” than Meyer asserts.  Fully reviewing this would require an article in itself, and would be somewhat beside the point since Meyer’s claim is categorically disproven by the recent origin of novel genes by natural processes.  (Another way in which “experience-based analysis” leads one to conclusions other than those Meyer asserts.) However, some idea of the diversity of protein solutions to any given enzymatic “problem” is given at the NCBI’s Analogous Enzymes webpage, which includes hundreds of examples.  There is more than one way to skin a cat, and there are many more ways to evolve a solution to any given functional “problem” in biology.

The origin of novel genes/proteins

Meyer makes his case that evolution can’t produce new genes in complete neglect of the relevant scientific literature documenting the origin of new genes. 

1. A central claim of Meyer’s is that novel genes have too much “CSI” to be produced by evolution. The first problem with this is that Meyer does not demonstrate that genes have CSI under Dembski’s definition (see above). The second problem is that Meyer cites absolutely none of the literature documenting the origin of new genes.  For example, Meyer missed the recent paper in Current Opinion in Genetics and Development with the unambiguous title, “Evolution of novel genes.” The paper and 183 related papers can be found here.  Many other references can be found linked from here.

It is worth listing a few in-text to make crystal-clear the kinds of references that Meyer missed:

Copley, S. D. (2000). “Evolution of a metabolic pathway for degradation of a toxic xenobiotic: the patchwork approach.” Trends Biochem Sci 25(6): 261-265. PubMed

Harding, M. M., Anderberg, P. I. and Haymet, A. D. (2003). “‘Antifreeze’ glycoproteins from polar fish.” Eur J Biochem 270(7): 1381-1392. PubMed

Johnson, G. R., Jain, R. K. and Spain, J. C. (2002). “Origins of the 2,4-dinitrotoluene pathway.” J Bacteriol 184(15): 4219-4232. PubMed

Long, M., Betran, E., Thornton, K. and Wang, W. (2003). “The origin of new genes: glimpses from the young and old.” Nat Rev Genet 4(11): 865-875. PubMed

Nurminsky, D., Aguiar, D. D., Bustamante, C. D. and Hartl, D. L. (2001). “Chromosomal effects of rapid gene evolution in Drosophila melanogaster.” Science 291(5501): 128-130. PubMed

Patthy, L. (2003). “Modular assembly of genes and the evolution of new functions.” Genetica 118(2-3): 217-231. PubMed

Prijambada I. D., Negoro S., Yomo T., Urabe I. (1995). “Emergence of nylon oligomer degradation enzymes in Pseudomonas aeruginosa PAO through experimental evolution.” Appl Environ Microbiol. 61(5):2020-2. PubMed

Ranz, J. M., Ponce, A. R., Hartl, D. L. and Nurminsky, D. (2003). “Origin and evolution of a new gene expressed in the Drosophila sperm axoneme.” Genetica 118(2-3): 233-244. PubMed

Seffernick, J. L. and Wackett, L. P. (2001). “Rapid evolution of bacterial catabolic enzymes: a case study with atrazine chlorohydrolase.” Biochemistry 40(43): 12747-12753. PubMed

2. Meyer cites Axe (2000) as a counter to the evolutionary scenario of successive modifications of genes leading to new protein products. But Axe (2000) is not in any sense about “successive modifications”; Axe modified proteins in several locations at a time.  ID advocates love to cite certain Axe papers that indicate that functional proteins are rare in sequence space, but not others that indicate the opposite (Axe et al., 1996).  Axe apparently said in 1999 that his work had no relevance to intelligent design.

3. Meyer portrays protein function as all-or-nothing. But protein function is not all-or-nothing. Recent research highlights several evolutionary mechanisms “tinkering” with existing genes to arrive at new genes (Prijambada et al. 1995; Long 2001). But you won’t learn about that from Meyer.

4. As far as we can tell, Meyer uses the word “duplication” or something similar only twice in the entire 26-page article.  One of these usages is in the references, in the title of an article referring to centriole duplication.  The other is on p. 217, where Meyer introduces the genes-from-unnecessary DNA scenario. However, he subsequently ignores duplicated functional genes in this section and focuses on the origin of genes from noncoding DNA. Duplication really belongs with Meyer’s section on the second evolutionary scenario, the origin of genes from coding DNA.  There, Meyer argued that the origin of new genes from old genes was impossible because such a process would mess up the function of the old genes.  If he had put it there, he would have revealed the existence of the extremely simple, and already well-known, solution to the problem that he posed, namely, gene duplication (Lynch and Conery, 2000, 2003).

5. Meyer relies heavily on a new paper by Axe published in the Journal of Molecular Biology. Meyer alleges that Axe (2004) proves that, “the probability of finding a functional protein among the possible amino acid sequences corresponding to a 150-residue protein is similarly 1 in 10^77.” But Axe’s actual conclusion is that the number is “in the range of one in 10^77 to one in 10^53” (Axe 2004, p. 16). Meyer only reports the lowest extreme. One in 10^53 is still a small number, but Meyer apparently didn’t feel comfortable mentioning those 24 orders of magnitude to his reader.  A full discussion of Axe (2004) will have to appear elsewhere, but it is worth noting that Axe himself discusses at length the fact that the results one gets in estimating the density of functional sequences depend heavily on methods and assumptions.  Axe uses a fairly restricted “target” in his study, which gives a low number, but studies that just take random sequences and assay them just for function — which Meyer repeatedly insists is all that matters in biology — produce larger numbers (Axe 2004, pp. 1-2). [2]

We would like to pose a challenge to Meyer.  There are a large number of documented cases of the evolutionary origin of new genes (again, a sample is here).  We challenge Meyer to explain why he didn’t include them, or anything like them, in his review.  We invite readers to wait to see whether or not Meyer ever addresses them at a later date and whether he can bring himself to admit that his most common, most frequent, and most central assertion in his paper is wildly incorrect and widely known to be so in the scientific literature.  These points should not be controversial: even Michael Behe, the leading IDist and author of Darwin’s Black Box, admits that novel genes can evolve: “Antibiotics and pesticide resistance, antifreeze proteins in fish and plants, and more may indeed be explained by a Darwinian mechanism.” (Behe 2004, p. 356)

If we might be permitted a prediction, Meyer or his defenders will respond not by admitting their error on this point, but by engaging in calculated obfuscation over the definition of the words “novel” and “fundamentally.”  They will then assert that, after all, yes, evolution can produce new genes and new information, but not “fundamentally new genes.”  They will never clarify what exactly counts as fundamental novelty.

Morphological novelty

The origin of morphological novelty is also a large topic with an extensive literature, but unfortunately we can only discuss a limited number of topics in any depth here.  To pick two issues, Meyer fails to incorporate any of the work on the origin of morphological novelties in geologically recent cases where evidence is fairly abundant, and Meyer also fails to discuss the crucial role that cooption plays in the origin of novelty.  Below is a small sampling of the kinds of papers that Meyer would have had to address in this field in order to even begin to make a case that evolution cannot produce new morphologies:

Ganfornina M. D., Sanchez D. 1999. “Generation of evolutionary novelty by functional shift.” Bioessays. 21(5):432-9. PubMed

Mayr, E. 1960. “The Emergence of Evolutionary Novelties.”  in Evolution After Darwin: Volume 1: The Evolution of Life: Its Origin, History, and Future, Sol Tax, ed.  The University of Chicago Press, Chicago, IL. pp. 349-380.

Pellmyr, O. and Krenn, H. W., 2002. “Origin of a complex key innovation in an obligate insect-plant mutualism.” PNAS. 99(8):5498-5502. PubMed

Prum, R. O. and Brush, A. H., 2002. “The evolutionary origin and diversification of feathers.” Q Rev Biol. 77 (3), 261-295. PubMed

True, J. R. and Carroll, S. B., 2002. “Gene co-option in physiological and morphological evolution.” Annu Rev Cell Dev Biol. 18, 53-80. PubMed

Mayr’s paper in particular is a well-known introduction to the topic.  He emphasized the important role of change-of-function for understanding the origin of new structures.  In his conclusion he wrote,

“The emergence of new structures is normally due to the acquisition of a new function by an existing structure.  In both cases the resulting ‘new’ structure is merely a modification of a preceding structure.  The selection pressure in favor of the structural modification is greatly increased by a shift into a new ecological niche, by the acquisition of a new habit, or by both.  A shift in function exposes the fully formed ‘preadapted’ structure to the new selection pressure.  This, in most cases, explains how an incipient structure could be favored by natural selection before reaching a size and elaboration where it would be advantageous for a new role.” (p. 377-378)

Mayr wrote this in 1960, at the sprightly age of 56, but it applies rather well to discoveries about the origin of new genes and new morphological structures made in the last few decades.  Most new genes and new structures are derived by change-of-function from old genes and old structures, often after duplication.  Many other terms are used in the evolutionary literature for this process (Mayr’s “preadaptation”, replaced by “exaptation” by Gould; cooption; functional shift; tinkering; bricolage; see e.g. the commonly-cited essay by Jacob 1977 for a discussion of the “tinkering” analogy for evolution), but none of them appear in Meyer’s essay. 

The Power of Negative Thinking

Negative argumentation against evolutionary theories seems to be the sole scientific content of “intelligent design”. That observation continues to hold true for this paper by Meyer.

1. Meyer gives no support for his assertion that PE proponents proposed species selection to account for “large morphological jumps”. (Use of the singular, “punctuated equilibrium”, is a common feature of antievolution writing. It is relatively less common among evolutionary biologists, who utilize the plural form, “punctuated equilibria”, as it was introduced by Eldredge and Gould in 1972.)

2. Meyer makes the false claim that PE was supposed to address the problem of the origin of biological information or form. As Gould and Eldredge 1977 noted, PE is a theory about speciation.  It is an application of Ernst Mayr’s theory of allopatric speciation — a theory at the core of the Modern Synthesis — to the fossil record.  Any discussion of PE that doesn’t mention allopatric speciation or something similar is ignoring the concept’s original meaning.

3. Meyer also makes the false claim that PE was supposed to address the origin of taxa higher than species. This class of error was specifically addressed in Gould and Eldredge 1977.  PE is about the pattern of speciation observed in the fossil record, not about taxa other than species.

4. Meyer makes the false claim that genetic algorithms require a “target sequence” to work. Meyer cites two of his own articles as the relevant authority in this matter. However, when one examines these sources, one finds that what is cited in both of these earlier essays is a block of three paragraphs, the content of which is almost identical in the two essays. Meyer bases his denunciation of genetic algorithms as a field upon a superficial examination of two cases. While some genetic algorithm simulations for pedagogy do incorporate a “target sequence”, it is utterly false to say that all genetic algorithms do so. Meyer was in attendance at the NTSE in 1997 when one of us [WRE] brought up a genetic algorithm to solve the Traveling Salesman Problem, which was an example where no “target sequence” was available.  Whole fields of evolutionary computation are completely overlooked by Meyer. Two citations relevant to Meyer’s claims are Chellapilla and Fogel (2001) and Stanley and Miikkulainen (2002). (That Meyer overlooks Chelapilla and Fogel 2001 is even more baffling given that Dembski 2002 discussed the work.) Bibliographies for the entirely neglected fields of artificial life and genetic programming are available at these sites:

http://users.ox.ac.uk/~econec/alife.html
http://www.cs.bham.ac.uk/~wbl/biblio/gp-bibliography.html.

A bibliography of genetic algorithms and artificial neural networks is available here.

On the Other Hand: the View Meyer Fails to Consider

When Meyer states that a massive increase in information is required to create all the body plans of the living “phyla” he is implying that evolution had to go from a single celled creature to a complex metazoan in one step, which would be impossible. But the origin of metazoans is not a case of zero to metazoan instantly. Rather, it involves a series of incremental morphological steps.  These steps become apparent when the evolution of the major clades of metazoan life is viewed in a phylogenetic context. The literature using this phylogenetic perspective is extensive if Meyer wanted to investigate it (for example see Grande and Rieppel eds. 1994, Carroll 1997, Harvey et al. eds. 1996). Certainly an acknowledgment of such literature is crucial if one is going to discuss these topics in a scholarly article, even if it was to criticize it. No discussion of an evolutionary innovation would be complete without reference to the phylogeny, and yet we find not one in Meyer’s 26 page opus.

Perhaps the glaring absence of phylogenies owes to Meyer’s lack of acceptance of common descent, or perhaps it is because when the relationships of the ‘phyla’ are seen in a phylogenetic context, one readily sees that all of the complex developmental and morphological features that diagnose the extant clades need not arise simultaneously. Rather, they are added incrementally. First one cell type, then three, multiple body layers, and bilateral symmetry. At this point you have a “worm” and all the other bauplans are basically variations on the worm theme. There are worms with guts, and worms with muscles, worms with segments, worms with appendages, and even worms with a stiff tube in them (this last would be us).

Missing from Meyer’s picture is any actual discussion of the origins of metazoan development. Reading Meyer, one would think that it is a giant mystery, but the real mystery is why Meyer does not reference this huge area of research.

Meyer implies that the lack of specificity of development in genes is a surprising problem for evolution, yet it is well known and it is widely recognized that development is coordinated by epigenetic interactions of various cell lineages. Meyer treats this fact as if it were some mysterious phenomenon requiring a designer to input information. But, just as the ordered structure of convection cells in is boiling pot of water is not a mystery to physicists even though it is not specified by the shapes of the component water molecules, neither are developmental programs to biologists. The convection cells are an emergent property of the interactions of the water molecules, just as the growth of organismal form is an emergent property of the interactions of cell lineages.

It is thought that metazoan development arose by competition between variant cell lineages that arose during ontogeny, and thus its organization remains in the epigenetic interactions of the various cell lineages (Buss 1987). This was extensively documented by Leo Buss in 1987, but Meyer somehow failed to mention this seminal work on the origin of metazoan development.

Understanding the interactions of lineages and their various reciprocal inductions is crucial to understanding the evolution of metazoan development and bodyplans. The study of this forms the basis for the entire field of evolutionary and developmental biology, Meyer acts like this field doesn’t even exist, while citing sparingly from some of its works. Also absent is any discussion of the difference between sorting and selection (see Vrba and Gould 1986). The difference is crucial: sorting at one level does not imply selection, but rather may be the result of selection at an entirely different level of the organismal hierarchy.  Meyer appears to be completely unaware of this distinction when criticizing the inability of selection to create new morphologies. In some cases novelty at one level in the hierarchy may result when selection occurs somewhere else in the hierearchy: the emergent morphology may actually be the result of a sorting cascade, rather than direct selection. The evolution of metazoan bodyplans involved an exchange between selection at the level of the individual and at the level of the cell lineage, which was sorted through developmental interactions (Buss 1987) .

Finally, any discussion of development and evolution would not be complete without dealing with the effects of heterochrony on form, and here too we find relevant citations glaringly absent despite the prominent place of heterochrony in the literature going back to de Beer. This is 60 years of research missed by Meyer. (The oversight is worse when one considers various contributing ideas in development that date back to von Baer.)

Meyer repeatedly appeals to the notion of an ur-cell metazoan ancestor that had all the genetic potentiality of the different metazoan bauplanes. The reference to this hypothetical super-ancestor is as popular with creationists as it is erroneous to biologists. While biologists have at times proposed a need for such an ur-cell, this is no longer particularly in vogue, because the recognition of hierarchy and epigenetic processes and has removed the need for an all-encompassing ancestor.

There are many hierarchies that need to be separated. There is the phylogenetic hierarchy (the order of character acquisition in time), the developmental hierarchy (the order of cell differentiation) and the structural hierarchy (the position of various parts in an organism). Meyer muddles all of these together and treats them like they are all the same thing, but they are not. 

A Long Walk Off a Short Peer Review

The Proceedings of the Biological Society of Washington (PBSW) is a respected, if somewhat obscure, biological journal specializing in papers of a systematic and taxonomic nature, such as the description of new species. A review of issues in evolutionary theory is decidedly not its typical fare, even disregarding the creationist nature of Meyer’s paper. The fact that the paper is both out of the journal’s typical sphere of publication, as well as dismal scientifically, raises the question of how it made it past peer review. The answer probably lies in the editor, Richard von Sternberg. Sternberg happens to be a creationist and ID fellow traveler who is on the editorial board of the Baraminology Study Group at Bryan College in Tennessee. (The BSG is a research group devoted to the determination of the created kinds of Genesis. We are NOT making this up!) Sternberg was also a signatory of the Discovery Institute’s “100 Scientists Who Doubt Darwinism” statement. [3] Given R. v. Sternberg’s creationist leanings, it seems plausible to surmise that the paper received some editorial shepherding through the peer review process. Given the abysmal quality of the science surrounding both information theory and the Cambrian explosion, it seems unlikely that it received review by experts in those fields. One wonders if the paper saw peer review at all.

Although this critique has focused on the scientific problems with Meyer’s paper, it may be worth briefly considering the political dimensions, as the paper is likely to become part of the ID creationists’ lobbying machine.  The paper has been out since early August, so it is somewhat puzzling that the Discovery Institute and similar groups have yet to publicize this major event for ID theory. Are they embarrassed at its sub-par (even by ID standards) content, or are they are waiting to spring it on some unsuspecting scientist at a future school board meeting or state legislature hearing?  Regardless, once the press releases start to fly, responses to the paper should be careful to not assume facts not in evidence (such as the review, or lack thereof, of Meyer’s paper), and should be careful to distinguish between issues that are scientifically important and unimportant.  Whether or not editorial discretion was abused in order to enable “intelligent design” to make a coveted appearance in the peer-reviewed scientific literature is not currently known, and is at any rate not the most important issue. The important issue is whether or not the paper makes any scientific contribution: does it propose a positive explanatory model?  If the paper is primarily negative critique, does it accurately review the science it purports to criticize?  The fact that a paper is shaky on these grounds is much more important than the personalities involved.  Intemperate responses will only play into the hands of creationists, who might use these as an excuse to say that the “dogmatic Darwinian thought police” are unfairly giving Meyer and PBSW a hard time.  Nor should Sternberg be given the chance to become a “martyr for the cause.”  Any communication with PBSW should focus upon the features that make this paper a poor choice for publication: its many errors of fact, its glaring omissions of relevant material, and its misrepresentations of the views that it does consider.

The ultimate test of the value of a peer-reviewed paper is whether it spawns actual research and convinces skeptics. Applicability and acceptance in science, not in politics, is the ultimate test of proposed scientific ideas. As we have stated before, all ID advocates have to do is demonstrate to scientists that they have something that works. They need a positive research program showing scientists that ID has more to offer than “Poof, ID did it.”

Conclusion

There is nothing wrong with challenging conventional wisdom — continuing challenge is a core feature of science.  But challengers should at least be aware of, read, cite, and specifically rebut the actual data that supports conventional wisdom, not merely construct a rhetorical edifice out of omission of relevant facts, selective quoting, bad analogies, knocking down strawmen, and tendentious interpretations.  Unless and until the “intelligent design” movement does this, they are not seriously in the game. They’re not even playing the same sport.

Postscript

As we have said, the errors in this paper are too numerous to document more than a few here.  We invite readers to find more mistakes and misrepresentations in this work and add them to our comments section, and/or email them to us to add to the full online critique.

Endnotes

1. The original phrase was: “The origin of biological information and the higher taxonomic categories”, the title of Meyer’s paper.  The random text was generated at the random text generator webpage: http://barnyard.syr.edu/monkey.html…

2. Page numbers for Axe (2004) in this section refer to the in press, pre-publication version of Axe’s paper availabe on the JMB website: http://dx.doi.org/10.1016/j.jmb.2004.06.058.

3. As mentioned previously, Meyer is the directory the Discovery Institute’s Center for Science and Culture. Meyer’s reported affiliation on the PBSW paper is to Palm Beach Atlantic University, which requires all faculty to affirm the following statement:

To assure the perpetuation of these basic concepts of its founders, it is resolved that all those who become associated with Palm Beach Atlantic as trustees, officers, members of the faculty or of the staff, must believe that man was directly created by God.

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Trackback URL: http://www.pandasthumb.org/cgi-bin/mt/mt-tb.cgi/429

Comment #6789

Posted by Pim van Meurs on August 24, 2004 06:19 PM

Very Nice. Congratulations to all involved.

Comment #6795

Posted by Great White Wonder on August 24, 2004 07:16 PM

My favorite example which shows what a moron Mr. Meyer is can be found at http://www.discovery.org/scripts/viewDB/index.php?command=view&id=1090, where he writes

First, the genetic code is neither universal (as PBS claimed), nor “nearly universal” (as Pond claims). There are now—count them—at least 15 known variants from the standard genetic code that determines amino acid assignments from DNA “codons” during the process of protein synthesis in different living organisms. Whitworth students who wish to verify this claim might check the following website maintained by the National Institutes of Health at: http://www.ncbi.nlm.nih.gov/…

Secondly, and more importantly, the existence of these variant codes is not consistent with a key prediction derived from Darwin’s theory of universal common ancestry. To see why, imagine typing on a keyboard in which the assignment between the keys and the letters that appear on your screen have been secretly changed. When you hit a specific letter such as an “n,” a different letter such as “t” appears. Or, imagine that every time you hit, say, an “o,” a period and a double space appears on your screen. Now envision submitting such a paper to a professor (without any information about the special new code that your computer used). Will your paper make sense? Will you get a good grade? I doubt it.

Kudos to you guys for your extensive (and yet incomplete!) review, although it is far, far, far too kind to the simple-minded faker and promulgator of bull-hockey who refers to himself as Dr. Meyer.

As usual, the lack of integrity on the part of the pseudoscientific fraudster is only alluded to between the lines.  So I am left wondering what the difference is between a “lie” and a “false claim,” especially when the “false claim” is made by someone who cannot reasonably argue that he was unaware of the falseness of his claim and who is clearly motivated not to tell the truth.

Comment #6797

Posted by Reed A. Cartwright on August 24, 2004 07:23 PM

So are y’all working on submitting a response to PBSW?

Comment #6798

Posted by Pim van Meurs on August 24, 2004 07:28 PM

For some scientific papers that help one understand the evolution of genetic code see:

Recent evidence for evolution of the genetic code.

The genetic code, formerly thought to be frozen, is now known to be in a state of evolution. This was first shown in 1979 by Barrell et al. (G. Barrell, A. T. Bankier, and J. Drouin, Nature [London] 282:189-194, 1979), who found that the universal codons AUA (isoleucine) and UGA (stop) coded for methionine and tryptophan, respectively, in human mitochondria. Subsequent studies have shown that UGA codes for tryptophan in Mycoplasma spp. and in all nonplant mitochondria that have been examined. Universal stop codons UAA and UAG code for glutamine in ciliated protozoa (except Euplotes octacarinatus) and in a green alga, Acetabularia. E. octacarinatus uses UAA for stop and UGA for cysteine. Candida species, which are yeasts, use CUG (leucine) for serine. Other departures from the universal code, all in nonplant mitochondria, are CUN (leucine) for threonine (in yeasts), AAA (lysine) for asparagine (in platyhelminths and echinoderms), UAA (stop) for tyrosine (in planaria), and AGR (arginine) for serine (in several animal orders) and for stop (in vertebrates). We propose that the changes are typically preceded by loss of a codon from all coding sequences in an organism or organelle, often as a result of directional mutation pressure, accompanied by loss of the tRNA that translates the codon. The codon reappears later by conversion of another codon and emergence of a tRNA that translates the reappeared codon with a different assignment. Changes in release factors also contribute to these revised assignments. We also discuss the use of UGA (stop) as a selenocysteine codon and the early history of the code.

Or the vaste resources at the Freeland lab

such as [rul=http://www.evolvingcode.net/documents/rewiring.pdf…]”Rewiring the keyboard: evolvability of the genetic code[/url]” (2001), R.D. Knight, S. J. Freeland and L. F. Landweber, Nature Reviews Genetics, 2(1):49-58

Remember also that Meyer has a degree in philosophy of science. But please calling someone a moron/fraudster is not very productive for a discussion. This posting is too good to have it be derailed by such comments.

Comment #6801

Posted by Pim van Meurs on August 24, 2004 08:12 PM

From Palm Beach Atlantic website we read

As University Professor, Dr. Meyer consults with faculties within the University on the integration of faith and learning. He, also, consults with the Director and faculty of the Supper Honors Program in curriculum development. Annually, Dr. Meyer assists in the planning and coordination of a conference on intelligent design as a plausible explanation from scientific evidence for the origin of life. Dr. Meyer teaches a course each year in Christian Apologetics in the School of Ministry. He came to PBA after having served on the faculty of Whitworth College in Spokane, Washington for the past 12 years.

Comment #6802

Posted by RBH on August 24, 2004 08:42 PM

Gishlik, Matzke, and Elsberry quoted one of Meyers’ arguments,

4. Meyer claims, “One way to estimate the amount of new CSI that appeared with the Cambrian animals is to count the number of new cell types that emerged with them (Valentine 1995:91-93)” (p.217). This may be an estimate of something, and at least signals some sort of quantitative approach, but we may be certain that the quantity found has nothing to do with Dembski’s CSI. The quantitative element of Dembski’s CSI is an estimate of the probability of appearance (under natural processes or random assembly, as Dembski shifts background assumptions opportunistically), and has nothing to do with counting numbers of cell types.

It appears that the ID creationists can’t even keep their own metrics straight.  That sounds more akin to  Paul Nelson’s (as yet undefined) “Ontogenetic Depth” than to Complex Specified Information or Specified Complexity. 

However, it has been four months since Nelson claimed (Comment #731)

Posted by Paul A. Nelson on April 7, 2004 04:45 AM

I’m lecturing at the University of Maine (Orono) today, but will try to post the reply when I return to Chicago tomorrow.  It’s pretty long: I think I’ll put it up at ISCID and link from here.

Hello?  Anyone there, Paul?

RBH

Comment #6804

Posted by ~DS~ on August 24, 2004 09:29 PM

I can’t get the original from that link. It comes back No Abstract Available

Comment #6805

Posted by Pim van Meurs on August 24, 2004 09:32 PM

Meyer may have given up on waiting for Nelson to provide the long awaited and promised details and have chosen another measure from Valentine.

He should have waited…

Comment #6806

Posted by Steve on August 24, 2004 09:54 PM

Alan, Nick, Wesley, thanks for the article.

Comment #6811

Posted by Nick on August 24, 2004 11:27 PM

Posted by ~DS~ on August 24, 2004 09:29 PM

I can’t get the original from that link. It comes back No Abstract Available

DS,

The paper actually has no abstract (one of, um, a few peculiarities).  The link just has the reference information, etc. (PBSW doesn’t really have a webpage and online PDFs like most journals, just the table of contents at the publisher webpage).

Comment #6815

Posted by Ian Musgrave on August 25, 2004 01:40 AM

Thanks to Wesley, Nick and Alan for this review

Wesley et al., wrote:

5. Meyer relies heavily on a new paper by Axe published in the Journal of Molecular Biology. Meyer alleges that Axe (2004) proves that, “the probability of finding a functional protein among the possible amino acid sequences corresponding to a 150-residue protein is similarly 1 in 10^77.”

As Wesley et al., note a fuller treatment of the Axe paper is coming, but I would like to note that neither Axe nor Yockey (who Meyer also invokes. Meye also ignores Yockey’s more favourable bound of 1 in 10 ^43 [Yockey 1992, pg 328]) were talking about finding any possible function as Meyer implies. They were specifically talking about finding an enzyme with a given core structure and a given mechanism, which is a very different (and less likely) thing. As the analogous functions page Wesley et al., link to points out, there is more than one way (often several ways) to get the same function via structurally and mechanistically different enzymes. Thus the figures Meyers quotes are irrelevant to the point he is trying to make.

Meyers use of these figures are also irrelevant, as we can see from this example:

Meyers wrote:

Other considerations imply additional improbabilities. First, new Cambrian animals would require proteins much longer than 100 residues to perform many necessary specialized functions. Ohno (1996) has noted that Cambrian animals would have required complex proteins such as lysyl oxidase in order to support their stout body structures. Lysyl oxidase molecules in extant organisms comprise over 400 amino acids. These molecules are both highly complex (non-repetitive) and functionally specified. Reasonable extrapolation from mutagenesis experiments done on shorter protein molecules suggests that the probability of producing functionally sequenced proteins of this length at random is so small as to make appeals to chance absurd, even granting the duration of the entire universe.

However, no evolutionary biologist suggests that lysyl oxidase (around 250 aa’s not 400 aa’s) was produced by random searches through sequence, rather that they were produced by duplication and divergence of simpler ancestral enzymes. Lysyl oxidases are copper amine oxidases which cross link collagen into strong filaments (Kagan & Li, 2002). Copper amine oxidases are a diverse enzyme family which are present in prokaryotes, and unicellular eukaryotes such as yeast where they are involved in amine metabolism. Indeed several yeasts have a lysly oxidase (Duff et al., 2003), which while structurally unrelated to the metazoan lysly oxidases, show that generation of metazoan lylysl oxidases by duplication and divergence of ancestral copper amine oxidases (or other copper containing enzymes) is quite feasible. Furthermore, lysyl oxidases have roles in gene expression (via oxidizing lysines in the histones that package the genes in the nucleus (Kagan & Li, 2002)) so it is likely that proto lysyl oxidases could have been present well before they were needed as collagen cross-linking proteins (as they are in some yeasts). Metazoan lyslyl oxidases are relatively old enzymes, and appear to have been in place by around 600 Mya, at least 40 Mya before the start of the Cambrian (Krawetz 1994, Exposito 2002).

To conclude, to generate a modern lysyl oxidase by a random search of sequence space may take as long as the age of the Universe to complete, but the generation of a primitive lysyl oxidase by duplication and divergence from preexisting amine oxidases is certainly achievable in a 40 Mya time frame. As the model proposed by evolutionary biology is the duplication and divergence model (which ironically was first carefully articulated in it’s modern form by Ohno, who Myeres cites as someone saying new genes can’t evolve) Meyers spends a large amount of time beating up a straw man.

Duff AP,et al, The crystal structure of Pichia pastoris lysyl oxidase.Biochemistry. 2003 Dec 30;42(51):15148-57.
Exposito JY, Cluzel C, Garrone R, Lethias C. Evolution of collagens. Anat Rec. 2002 Nov 1;268(3):302-16.
Krawetz SA. The origin of lysyl oxidase. Comp Biochem Physiol Biochem Mol Biol. 1994 May;108(1):117-9.
Kagan HM, Li W. Lysyl oxidase: properties, specificity, and biological roles inside and outside of the cell. J Cell Biochem. 2003 Mar 1;88(4):660-72.
Ohno S.  The notion of the Cambrian pananimalia genome.Proc Natl Acad Sci U S A. 1996 Aug 6;93(16):8475-8.
Yockey, H. P Information theory and molecular biology. Cambridge University Press, Cambridge, United Kingdom. 1992. chapters 9 and 12, see esp page 328

Comment #6828

Posted by charlie wagner on August 25, 2004 08:48 AM

the major organization promoting ID, has put forward the best case that ID has to offer.

This is not the best case for intelligent input. I wish people would spend as much effort trying to debunk my theory as they do with these obviously flawed inferiors. I guess it’s easier to do. No serious challenges to Nelson’s Law have ever been put forth, so as far as I’m concerned, intelligent input is an absolute requirement for the evolution of living organisms.

Comment #6852

Posted by gish on August 25, 2004 11:57 AM

Here’s yet another example of the genetic controls involved in the origination of morphological novelty that we did not put in our review.

Wagner,G P. and C-H Chiu. 2001. The tetrapod limb: A hypothesis on its origin. Journal of Experimental Zoology 291:226-240.

Abstract:

The tetrapod limb is one of the major morphological adaptations that facilitated the transition from an aquatic to a terrestrial lifestyle in vertebrate evolution. We review the paleontological evidence for the fin-limb transition and conclude that the innovation associated with evolution of the tetrapod limb is the zeugopodial-mesopodial transition, i.e., the evolution of the developmental mechanism that differentiates the distal parts of the limb(the autopodium, i.e., hand or foot) from the proximal parts. Based on a review of tetrapod limb and fish fin development, we propose a genetic hypothesis for the origin of the autopodium. In tetrapods the genes Hoxa-11 and Hoxa-13 have locally exclusive expression domains along the proximal-distal axis of the limb bud. The junction between the distal limit of Hoxa-11 expression and of the proximal limit of Hoxa-13 expression is involved in establishing the border between the zeugopodial and autopodial anlagen. In zebrafish, the expression domains of these genes are overlapping and there is no evidence for an autopodial equivalent in the fin skeleton. We propose that the evolution of the derived expression patterns of Hoxa-11 and Hoxa-13 may be causally involved in the origin of the tetrapod limb.

Comment #6855

Posted by Steve F on August 25, 2004 12:10 PM

It seems like there is an awful lot wrong with this paper, yet it was able to pass peer review (admitedly in a relatively minor journal).  How was this possible given the above arguments.  Peer review isn’t perfect, but you’d think given the implications of this work that they would be thorough in their reading of it.

A YEC geologist (Brandt I think) published in either GSA or Geology, on an alleged subaqueous setting for Dino tracks in the Coconino sandstone.  This article (later roundly panned I believe) comes with a note after from the editor, that runs along the lines of ‘this is a novel interpretation’ (i.e. its from a wacko cretinist).  Do we have such a qualifier in this journal?  Did they just put it in in the hope of generating a bit of controversy?

Comment #6874

Posted by Wesley R. Elsberry on August 25, 2004 02:12 PM

I moved a bunch of comments not directly related to the content and criticism of Meyer 2004 to the “Bathroom Wall”.

Comment #6875

Posted by ~DS~ on August 25, 2004 02:16 PM

David Heddle wrote:

They sweep our good fortune (for having just the right vacuum energy to make our universe livable) under the rug.

On the anthropic quantum/cosmological IDC supposition[s]; how would one falsify it? To falsify the propisition that the universe was designed for life on a nano-microscopic level, i.e. that physical parameters of particles/bosons/Calabi-Yau Metrics, whatever, etc. were purposely and precisely chosen so that life, based on chemical molecular interaction arising from underlying quantum properties, would be possible within that universe, what would be needed?

It seems like one way to possibility would to show the universe was not designed for life to exist in it, would be to find life existing in a/the universe in which it cannot exist. That’s the only direct way I can envision and clearly that raises a problem as far as validity, and incidentally would be pretty damn good evidence for some kind of non-human, intelligent, funny business.

I’m not trying to take anyone off track here. It’s just that I’ve seen this argument advanced in various forms on several venues and I’ve seen it advertised as a scientific argument in favor of IDC, but I’ve never seen a set of testable predictions that flows from it. Myabe that topic would be worth a future post.

Comment #6885

Posted by Steve Reuland on August 25, 2004 04:14 PM

Da Boyz wrote:

2. Meyer compares DNA sequences to human language.  In this he follows Denton’s (1986) Evolution: A Theory in Crisis.  Denton (1986) argued that meaningful sentences are isolated from each other: it is usually impossible to convert one sentence to another via a series of random letter changes, where each intermediate sentence has meaning. Like Denton (1986), Meyer applies the same argument to gene and protein sequences, concluding that they, like meaningful sentences, must have been produced by intelligent agents.  The analogy between language and biological sequence is poor for many reasons; starting with the most obvious point of disanalogy, proteins can lose 80% or more of their sequence similarity and retain the same structure and function (a random example is here). Let’s examine an English phrase where four out of five characters have been replaced with a randomly generated text string.  See if you can determine the original meaning of this text string:

Tnbpursutd euckilecuitn tiioismdeetneia niophvlgorciizooltccilhseema er [1]

Eighty percent loss of sequence identity is fatal to English sentences. Clearly proteins are much less specified than language.

I would be careful about how you put this.  It’s fairly certain that if you replaced 80% of a protein’s sequence at random, then you’d end up with a functionless protein (or at least one that lost its original function).  The chances of remaining within the functional sequence space (for that particular protein) are slim. 

However, it’s also fairly certain that you could make incremental changes, preserving function at each step, and end up with 80% sequence divergence.  And because we see highly divergent protein homologues, highly similar ones, and everything in between, we can be confident that this is a general phenomenon:  A given protein function (with a given architecture) is highly distributed throughout sequence space, with various nodes connected by neutral networks.  And that’s enough to put Meyer’s claim to rest.

Of course I don’t know what a good English analogy would be, but it’s not really proper to compare protein sequence divergence to a random change in English characters.

Comment #6886

Posted by Great White Wonder on August 25, 2004 04:38 PM

I would be careful about how you put this.

I’m not sure that it matters how carefully Meyer’s “argument” is addressed.  It is such a hopelessly naive and stupid argument that a “careful” examination only opens the door so others may wonder if there is any credibility to it.  “Da Boyz” did fine.

Another perfectly solid rebuttal to the argument might go like this:  Proteins aren’t sentences.  Among thousands of differences which could be named, there are no genetically encoded “questions” or “subjects” or “adverbs” or “prepositional phrases” or “direct objects”.  Furthermore, there is no way to determine a priori from the amino acid sequence of a protein whether a newly identified protein is “spelled correctly”.  There being NO true inherent relationship between grammatical sentences and proteins, the argument is dead.  And rotting. 

A good question we might ask is: what is the character of a person who obviously goes to great lengths to present such arguments to the public in an effort to disparage the hard work of genuine scientists?  How should such people be treated by other scientists when they are exposed as having passing such garbage for truth?

Comment #6887

Posted by Steve Reuland on August 25, 2004 04:41 PM

This is kind of nit-picky, but FYI:

Da Boyz wrote:

But Taylor et al.’s recommendation for intelligent protein design is actually that it should mimic natural evolution: “[A]s in natural evolution, the design of new enzymes will require incremental strategies…”.

(emphasis added)

I don’t know what term Taylor uses, but the standard term in protein engineering is rational design — the term refers to methods that rely on structural and functional information, with predicted consequences for specific mutations, as opposed to directed evolution techniques.  (Directed evolution techniques are generally superior, even though according to what Meyers says about proteins, they shouldn’t work at all.) 

Not terribly important, but I find it somewhat amusing that had the IDists known anything about the protein engineering literature, they would have called themselves the Rational Design movement.  They missed a chance to piggyback on a term already ubiquitious in the literature.

Comment #6889

Posted by Steve Reuland on August 25, 2004 04:51 PM

GWW wrote:

I’m not sure that it matters how carefully Meyer’s “argument” is addressed.  It is such a hopelessly naive and stupid argument that a “careful” examination only opens the door so others may wonder if there is any credibility to it.  “Da Boyz” did fine.

Da Boyz certainly did do fine, and they’re 100% correct about why English sentences are a terrible analogy to protein sequences. 

But never underestimate the propensity for ID/creationists to harp on a minor and irrelevant issue in order to distract people away from the main argument.  I can easily picture Meyer, or one of his surrogates, claiming that since changing 80% of a protein’s sequence at random would almost certainly destroy its function, then Da Boys’ rebuttal was false and effectively refuted.  Of course this would be a gross distortion, but it would require another round of rebuttal in order to point out the error, at which point the main goal of obscuring the issue with sheer volume will have been achieved.

Comment #6895

Posted by Nick on August 25, 2004 06:53 PM

Steve (Reuland),

Thanks.  Point taken on the random replacement vs. progressive replacement issue.  In order for the analogy to be more exact we would need:

1. Some version of “conservative substitution” for english letters, analogous to conservative substitution with amino acids

2. Some simulation of progressive change, with only “functional” changes being retained in the phrase.

Producing #2 with a text string in a way analogous to a protein string would require changing the rules of english such that they were as flexible as proteins — but the different flexibility is exactly the point.

We can try #1, however.  Let’s take the original string:

“The origin of biological information and the higher taxonomic categories”

…and modify 4/5 letters, only keeping vowels for vowels and consonants for consonants, to simulate conservative substitutions. And just to be sporting I’ll keep all the spaces unchanged also:

“Tpu epinac av byidigekin ivlicmupein irl ghi pethih sexoladir mocemigiep”

Still looks pretty unreadable to me.  Conclusion?  English is far less flexible than amino acid sequence.

Comment #6897

Posted by Frank J on August 25, 2004 07:03 PM

Pim van Meurs wrote:

Perhaps when ID proposes its hypothesis rather than a negative argument, it may gain some respectability.

But a prominent IDer, Michael Behe, has proposed a hypothesis. In “Darwin’s Black Box” (1996) he suggested that the first cell had all the biochemical complexity required for subsequent species. I haven’t read Meyer’s article, but from the review I cannot figure whether he agrees or disagrees with Behe. He uses the incredulity arguments against common descent that Behe mostly avoids, but in typical ID fashion, it is not clear whether he is proposing (designer assisted) independent abiogenesis for the Cambrian phyla or not. Also, where and when, exactly, is CSI inserted, per the Meyer hypothesis? Behe has told us. Has Meyer, and if not, will he?

If this is truly the beginning of ID publishing instead of a publicity stunt, we should expect to see some forceful restating, and testing of course, of Behe’s hypothesis. If there are disagreements among IDers, we should expect to see the leading anti-Behe hypotheses spelled out, and some heated debates among IDers. At the very least, the “what happened and when” of each ID position should be detailed and tested. Behe says “old earth,” Paul Nelson apparently says “young earth.” Deferring this question has fooled the public, but there’s nowhere to hide now. Publishing in a real scientific journal (albeit a minor one) will put this question front and center. If this is to be the beginning for ID, it has to be the beginning of the end for the big tent.

Comment #6898

Posted by Pim van Meurs on August 25, 2004 07:04 PM

Certain aspects make english ‘robust’ to change. As long as the first and last letter of each word remain the same the order of the intermediate letters can be randomized, and yet we can interpret words relatively easily

Link

Although this means that all the letters are still there, just scrambled.

Comment #6899

Posted by Nick on August 25, 2004 07:10 PM

Steve (Reuland) writes,

I don’t know what term Taylor uses, but the standard term in protein engineering is rational design — the term refers to methods that rely on structural and functional information, with predicted consequences for specific mutations, as opposed to directed evolution techniques.  (Directed evolution techniques are generally superior, even though according to what Meyers says about proteins, they shouldn’t work at all.)

Taylor et al. 2001 (PubMed —  freely online) conclude with the following paragraph:

“Our estimate of the low frequency of protein catalysts in sequence space indicates that it will not be possible to isolate enzymes from unbiased random libraries in a single step. The required library sizes far exceed what is currently accessible by experiment, even with in vitro methods (31, 35). Instead, as in natural evolution, the design of new enzymes will require incremental strategies in which, for instance, a suitable scaffold is first generated, binding and catalytic groups are subsequently added, and the ensemble is optimized in an iterative fashion. Our two-stage approach to binary-patterned mutases and work on the redesign of existing enzymes (36–38) demonstrate the power of stepwise and modular procedures for directing the course of evolution. By iteratively combining combinatorial mutagenesis and selection with intelligent design, it may also prove possible to create novel protein scaffolds, unknown in nature, and to endow them with tailored catalytic activities.”

The bit about “intelligent design” is undoubtedly why Meyer cited the article, but if one actually reads the paragraph, it’s pretty clear that Long et al. are saying that human intelligent designers shouldn’t use random search, they should mimic evolution with incremental mutation + selection approaches.

Comment #6902

Posted by Jack Krebs on August 25, 2004 07:39 PM

Frank J writes,

Deferring this question [of the age of the earth] has fooled the public, but there’s nowhere to hide now. Publishing in a real scientific journal (albeit a minor one) will put this question front and center. If this is to be the beginning for ID, it has to be the beginning of the end for the big tent.

This is a good point.  Really, encouraging the IDists to publish is what we should do, because then they either have to start trying to act like scientists or the fact that they don’t try to act like scientists will become apparent to an even larger group of people.  But if they do try to act like scientists, then they will have to put lots of stuff on the line - the age of the earth, common descent, the power of genetic change to produce “new information,” etc.

Comment #6904

Posted by Steve on August 25, 2004 08:14 PM

We’ve seen now at least a dozen attempts at ID Protein Math. But anyone who knows anything about proteins can tell you that there are several sets of amino acids which are interchangeable for certain situations. This summer I spent a fair amount of time using a mutagenesis kit to switch serines and cystines. With no effect on the protein shape. Every time I see creationists do their calculations, they assume the given sequence is the only functional sequence of every possible combination of that length. That’s a stupid assumption. If they were honest, they’d admit that even with new modeling tools, there’s no way to estimate what percentage of the possible protein space have any or a given functionality.

Comment #6916

Posted by David Wilson on August 26, 2004 10:42 AM

~DS~ (Comment #6804) wrote:

I can’t get the original from that link. It comes back No Abstract Available.

A pdf copy of the paper is available at the Discovery Institute’s Centre for Science and Culture’s website here.

If what I have read of it so far is any guide,  Gishlick et al’s review has only scratched the surface of how truly dreadful it is.

Alan Gishlick et al wrote:

Meyer argues that “many scientists and mathematicians have questioned the ability of mutation and selection to generate information in the form of novel genes and proteins” (p. 218).  He makes statements to this effect throughout the paper.  Meyer does not say who these scientists are, ….

Well he does at least nominate a few candidates (Denton, Eden, Schützenberger and Løvtrup) in the second paragraph of the second column on p.218.  One might perhaps argue about whether Schützenberger, and perhaps Eden as well,  were really “scientists”.  But the paper is so full of so much more egregious rubbish that the issue of  whether Schützenberger or Eden were not really scientists seems to me to be a relatively minor quibble in comparison.

Comment #6923

Posted by Adam Marczyk on August 26, 2004 11:24 AM

Regarding genetic algorithms and the alleged necessity of target sequences, more information can be found here:

Genetic Algorithms and Evolutionary Computation

Comment #6935

Posted by Mark Perakh on August 26, 2004 01:17 PM

Of course there are many examples of targetless genetic algorithms. The same Dawkins, for example, besides the much discussed wiesel algorithm (which is indeed targeted) also developed and used a “biomorph” algorithm which is targetless - see my chapter (ch 11)in Why Intelligent Design Fails.
Also, Meyer points to inadquacies of random mutations and natural selection for evolution to happen. In regard to mutations it is the improbability and in regard to selection it is its inability to innovate as it has to work only on existing species. OK, let us accept these inadequacies. The point Meyer obfuscates is that while each of the two components (mutations and selection) is incapable of causing evolution alone, what makes evolution working is the combination of these two mechanisms. This combination gives rise to abilities absent in each of the components separately (as becomes obvious from the success of genetic algorithms). Since ID advocates are much in favor of “emergentist” view as opposed to “reductionist” view (see, for example the anthology From Complexity to Life edited by Gregresen), they (including philosopher Meyer) should have appreciate the emerging evolution-causing property of the combination of mutations and selection vs. inability of each of these mechanisms to do it alone.  Meyer glosses over that point.

Comment #6950

Posted by Wesley R. Elsberry on August 26, 2004 03:58 PM

A few more comments have been shifted to a more appropriate place.

Comment #6985

Posted by Marty Erwin on August 27, 2004 02:48 AM

The link to the Meyer article on the Discovery Inst. website posted by David Wilson (comment #6916) now links to a map to Adobe’s Seattle campus. Its on the DI website but does not link to the pdf of the Meyer article.

Comment #6986

Posted by Marty Erwin on August 27, 2004 02:58 AM

The link to the Meyer article on the Discovery Inst. website posted by David Wilson (comment #6916) now links to a map to Adobe’s Seattle campus. Its on the DI website but does not link to the pdf of the Meyer article.

Comment #6996

Posted by Wesley R. Elsberry on August 27, 2004 09:11 AM

Yes, the DI seems to be having some “technical difficulties” in delivering the PDF of the Meyer 2004 paper.

Comment #7000

Posted by Steve on August 27, 2004 10:16 AM

Maybe the paper is Closed for Renovation.

Comment #7005

Posted by Nick on August 27, 2004 11:40 AM

There is now a new link at the DI, apparently the paper will be up at 5 pm…

New DI link

The Origin of Biological Information and the Higher Taxonomic Categories
By: Stephen C. Meyer
Proceedings of the Biological Society of Washington
August 25, 2004

The Origin of Biological Information and the Higher Taxonomic Categories is a paper authored by Stephen C. Meyer and recently published in the peer-reviewed journal “Proceedings of the Biological Society of Washington.” It will be available in its entirety at this link after 5pm on Friday, August 27.

Comment #7006

Posted by Pim van Meurs on August 27, 2004 11:42 AM

Now the page states

The Origin of Biological Information and the Higher Taxonomic Categories is a paper authored by Stephen C. Meyer and recently published in the peer-reviewed journal “Proceedings of the Biological Society of Washington.” It will be available in its entirety at this link after 5pm on Friday, August 27

Comment #7010

Posted by Reed A. Cartwright on August 27, 2004 12:22 PM

What I find interesting is that none of the CRSC Fellows, who keep track of this blog, have popped on to support Meyer.

Comment #7026

Posted by Marty Erwin on August 27, 2004 04:41 PM

One of the things I see being missed here is the real intent of this publication. The DI does make use of rhetorical strategy in long-term planning. I predict that publication and post-publication critical review of Meyer’s paper will be transformed, by capable DI “spinmeisters” such as Campbell, into some type of claim that the scientific community is so biased in regards to ID that it is incapable of rendering an objective evaluation of ID.

The arguments for ID are essentially philosphical arguments and DI probably recognizes that it is easier to win the hearts (ethos and pathos) of the population than it is to win their minds (logos). This is cultural warfare and we should never expect the other side to play by any established set of rules.

Comment #7027

Posted by Great White Wonder on August 27, 2004 04:45 PM

This is cultural warfare and we should never expect the other side to play by any established set of rules.

I propose a new term for characters like Campbell and Meyer: Swift Boat Creationists.

Comment #7043

Posted by Nick on August 27, 2004 09:06 PM

This appeared on the DI website somewhere around 6 pm:

The Origin of Biological Information and the Higher Taxonomic Categories

By: Stephen C. Meyer
Proceedings of the Biological Society of Washington
August 25, 2004

On August 4th, 2004 the Proceedings of the Biological Society of Washington, a peer-reviewed biology journal, published an extensive review essay by Dr. Stephen C. Meyer, Director of Discovery Institute’s Center for Science & Culture. The article entitled “The Origin of Biological Information and the Higher Taxonomic Categories” appears in the current issue of the Proceedings (volume 117, no. 2, pp. 213-239).

In the article, Dr. Meyer argues that no current materialistic theory of evolution can account for the origin of the information necessary to build novel animal forms. He proposes intelligent design as an alternative explanation for the origin of biological information and the higher taxa.

On August 26th, a critique of the article authored by Alan Gishlick, Nick Matzke and Wesley Elsberry appeared on the Pandas Thumb website. For this reason, we have decided to make Dr. Meyer’s article available now in HTML format on this website. (Off prints are also available from Discovery Institute by writing to Keith Pennock at .) We trust that the Pandas Thumb critique of Meyer’s article will seem a good deal less persuasive, and less substantive than . Meyer’s article itself, once readers have had a chance to read Meyer’s essay. Dr. Meyer will, of course, respond in full to Gishlick et al. in due course.

In the meantime, enjoy!

Here is the link to the above, with an HTML version of the paper just posted to the site, which I encourage everyone to read (although interestingly the DI page doesn’t similarly link to the PT critique…).

Comment #7044

Posted by Wesley R. Elsberry on August 27, 2004 09:34 PM

Nick,

All in all, an interesting response.

We’ve got Stephen C. Meyer speaking in the third person of the persuasiveness of … Stephen C. Meyer.

While Meyer asserts that our critique “appeared” on PT on August 26th, he fails to note that it also “appeared” here on August 25th, and August 24th. To date, the full critique page has garnered 1,818 page views.

I trust that our critique will be considered just as persuasive by those in possession of it and Meyer’s paper — at least to those without an ideological precommitment to “intelligent design”. As Dembski notes, you can’t hope to convince certain classes of people.

The critique here is just the start of our examinations of Meyer 2004. We have by no means yet inventoried all the crud in Meyer’s Augean stable of a paper.

Comment #7045

Posted by Glenn Branch on August 27, 2004 10:24 PM

We’ve got Stephen C. Meyer speaking in the third person of the persuasiveness of … Stephen C. Meyer.

Probably the by-line is intended to be attached to the article, not the three paragraphs of explanation.

Comment #7046

Posted by Wesley R. Elsberry on August 27, 2004 10:31 PM

Ah. That would explain a lot about the response.

Comment #7048

Posted by Wesley R. Elsberry on August 28, 2004 12:10 AM

One wonders at the confidence of the DI CSC… they “trust” that readers will find Dr. Meyer’s paper more persuasive and more substantive than our critique, yet one will note, as Nick did, that they fail to provide a direct link to the critique. Hmmm.

We have no problem linking to their page. On the contrary, I’ve long been an advocate of disseminating the work of antievolutionists. That material makes the very best argument for antievolution being a pseudoscience. (This goes back years to when I ran a BBS system and offered various creationist essays in addition to the scientific responses.) I just posted the DI link for the Meyer 2004 paper on the Antievolution.org discussion board, and I would be willing to host an unaltered copy of the DI page on Meyer 2004 on the AE site if the DI CSC is willing to give permission for me to do so.

Comment #7049

Posted by Reed A. Cartwright on August 28, 2004 05:01 AM

Nick wrote:

although interestingly the DI page doesn’t similarly link to the PT critique

Why would they?  That would ruin their entire slight of hand argument.

Comment #7051

Posted by Frank J on August 28, 2004 06:31 AM

Reed A. Cartwright wrote:

Why would they?  That would ruin their entire slight of hand argument.

Note the contrast. The Talk Origins Archive links to the sites of all of its major critics, representing all of the mutually contradictory anti-evolution strategies. Nothing to hide there.

Comment #7052

Posted by Mark Perakh on August 28, 2004 10:36 AM

In comment 6923, Adam Marczyk refers to his post to TalkOrigins of April 2004. I have opened it - it is a very fine and detailed discussion of genetic algorithms which may serve as a good primer for non-experts in this area, and also is a fine addition to anti-Dembskiana, dissecting the Great Bill’s rudimentary approach to evolutionary algorithms where he is as much an expert as in Renyi divergence. Thank you, Adam!  Mark Perakh

Comment #7054

Posted by Pim van Meurs on August 28, 2004 12:16 PM

So far most creationists who have seen the Elsberry et al rebuttal of Meyer’s paper seem to have been somewhat embarassed. Guess Elsberry, Matzke and Gishlick managed to be persuasive. And their paper only addresses only the more obvious problems.

Comment #7055

Posted by Pim van Meurs on August 28, 2004 12:18 PM

From the DI “He [Meyer] proposes intelligent design as an alternative explanation for the origin of biological information and the higher taxa.”

But Meyer does not really present ANY evidence that ID is an alternative explanation.

Comment #7056

Posted by Reed A. Cartwright on August 28, 2004 12:40 PM

But Meyer does not really present ANY evidence that ID is an alternative explanation.

Of course not, that would take effort.  It is much easier to sit in a lazy-boy and criticize modern biology than actually take part in it.

Comment #7062

Posted by Marty Erwin on August 28, 2004 04:50 PM

Crikey… Meyer’s article (as posted on the DI website) isn’t a journal article, its a testimonial to a lack of editorial oversight in publication. When the length (in pages) of normal research articles (and corresponding publication costs) is considered, this tome is either a failed book or an attempt to take posthumous revenge on Gould for publishing The Structure of Evolutionary Theory.

Comment #7070

Posted by steve on August 28, 2004 06:40 PM

Of course not, that would take effort.  It is much easier to sit in a lazy-boy and criticize modern biology than actually take part in it.

It’s also pretty easy to make up terms, then say they revolutionize science.

Comment #7134

Posted by Wesley R. Elsberry on August 30, 2004 02:24 PM

In the discussion board at Internet Infidels, it was pointed out that Richard von Sternberg is a featured speaker at an upcoming ID conference in Finland.

Here’s the relevant bits from the web site…

Ph.D. Richard v. Sternberg
Staff scientist at the National Center for Biotechnology Information (GenBank)
National Institutes of Health
Richard Sternberg has a doctorate in biology from Florida International University and in systems science from Binghamton University. He is responsible of all invertebrate and fish DNA database decisions for NCBI-GenBank, EMBL and DNA Data Bank of Japan. Areas of specialization: Genome evolution and analysis of genomic data, function of repetitive DNA elements and macroevolutionary transitions.

A 21st Century View of Genomes
Richard Sternberg

The genomes are highly nonrandom, hierarchical, data-storage organelles that are used by cellular information-processing systems. Examples will be given of the complexity of gene organization, cells that construct genes de novo, and the functionality of “noncoding DNA”. The talk will emphasize that genes themselves are irreducibly complex structures, and pitfalls in common neoDarwinian models of gene evolution.

Fluid Genomes: Information-Generating or Information-Shuffling?
Richard Sternberg

All known genomes are highly plastic in terms of content, organization, and size. This fluidity is due to the operation of DNA modification pathways that alter chromosomes in a highly specific manner. The idea that genome fluidity results in new information is examined in light of the evidence. Based on the data available, it is suggested that genome fluidity shuffles and rearranges existing information. Like in workplaces where flexible, movable partitions can be used to rapidly reorganize office spaces without necessitating deep architectural changes, so too genome plasticity has a role in deploying and fine-tuning existing information.

Comment #7160

Posted by David Heddle on August 30, 2004 04:35 PM

Wesley wrote:

…I’ve long been an advocate of disseminating the work of antievolutionists. That material makes the very best argument for antievolution being a pseudoscience.

Interesting, for similar reasons I am in favor of my sons studying evolution in school.

Comment #7166

Posted by Pim on August 30, 2004 05:19 PM

Indeed, studying evolution makes for another good example of arguments for antievolution being a pseudoscience. I thought we already agreed on that though?

Comment #7167

Posted by Pim on August 30, 2004 05:22 PM

Indeed, studying evolution makes for another good example of arguments for antievolution being a pseudoscience. I thought we already agreed on that though?

Comment #7173

Posted by Pim van Meurs on August 30, 2004 08:44 PM

And the Discovery Institute’s website keeps evolving. Now it does not mention anything about Gishlick’s critique nor that Meyer in due course will respond to Gishlick.

Some days earlier

On August 26th, a critique of the article authored by Alan Gishlick, Nick Matzke and Wesley Elsberry appeared on the Pandas Thumb website. For this reason, we have decided to make Dr. Meyer’s article available now in HTML format on this website. (Off prints are also available from Discovery Institute by writing to Keith Pennock at ….) We trust that the Pandas Thumb critique of Meyer’s article will seem a good deal less persuasive, and less substantive than . Meyer’s article itself, once readers have had a chance to read Meyer’s essay. Dr. Meyer will, of course, respond in full to Gishlick et al. in due course.

As of today August 30, 2004 we read:

On August 4th, 2004 the Proceedings of the Biological Society of Washington, a peer-reviewed biology journal, published an extensive review essay by Dr. Stephen C. Meyer, Director of Discovery Institute’s Center for Science & Culture. The article entitled “The Origin of Biological Information and the Higher Taxonomic Categories” appears in the current issue of the Proceedings (volume 117, no. 2, pp. 213-239).

In the article, Dr. Meyer argues that no current materialistic theory of evolution can account for the origin of the information necessary to build novel animal forms. He proposes intelligent design as an alternative explanation for the origin of biological information and the higher taxa.

Due to an unusual number of inquiries about the article and because the article is presently not available on line elsewhere, Dr. Meyer, the copyright holder, has decided to make the article available now in HTML format on this website. (Off prints are also available from Discovery Institute by writing to Keith Pennock at ).

I understand that the DI would not want to attract too much attention to Gishlick et al’s substantial critique or worse commit to a promise that Meyer will address ‘in due time’ the critique.

Comment #7188

Posted by Reed A. Cartwright on August 31, 2004 11:15 AM

Dr. Meyer, the copyright holder, has decided to make the article available now in HTML format on this website.

Don’t journals usually require you to sign the copyright to them?  I wonder if the DI is playing right on this?  Does anyone have a copy of a PBSW to see what their instructions to authors are?

Comment #7190

Posted by Russell on August 31, 2004 11:34 AM

Due to an unusual number of inquiries about the article …

I wonder if Wesley and Panda’s Thumb can claim credit for what must be an unusual flurry of interest in an obscure journal?

Comment #7192

Posted by Wesley R. Elsberry on August 31, 2004 12:32 PM

Creationist article stirs debate

Oakland, CA, Aug. 30 (UPI) — A paper by a creationist group, published in a little-known scientific journal, is creating concern among evolutionary biologists.

NCSE was mentioned, as the apparent trigger for this article was an NCSE news item emailed to the NCSE News list. “Panda’s Thumb” was not mentioned.

Comment #7193

Posted by Reed A. Cartwright on August 31, 2004 12:32 PM

The Washington Times has an article about Meyer’s paper.

Comment #7195

Posted by Reed A. Cartwright on August 31, 2004 12:39 PM

Double post!  That’s what I get for previewing.

Comment #7199

Posted by Mark A. Grobner on August 31, 2004 01:53 PM

Hearing that an ID paper was published in the Proceedings of the Biological Society of Washington I informed a colleague that routinely publishes there of the apparent change in editorial policy.  Upon hearing this, she immediately contacted several individuals and found that the paper was not sent to any of the associate editors as is the usual procedure.  Also, the editor in question is no longer in charge.  Also, there will be an explanation and a condemnation of the article being published in the next issue.

Comment #7200

Posted by Reed A. Cartwright on August 31, 2004 02:35 PM

So it appears that our suspisions were correct that proper procedures were not followed.  It will be interesting to read a more detailed account of what happened in the next issue.  Hopefully, the BSW will allow some place like NCSE, TO, or TD to also publish the explaination.

Comment #7201

Posted by Pim on August 31, 2004 02:40 PM

On ARN, Salvador’s spin is making me dizzy. If Salvador wants to defend Meyer’s paper, he is encouraged to post on PT. But given the imho poor quality of Meyer’s arguments, I doubt that many ID proponents will come to his defense. In fact DI has dropped any promise of Meyer addressing the critiques.
As far as Peer Review is concerned, this indeed appears to be a  failure of peer review in the sense that it made it into the publication but luckily peer review is not restricted to such and Gishlick et al have shown how peer review does work.
At a minimimum Meyer’s paper will serve as a reminder of the lack of scientifically viable ID hypotheses. It’s encouraging that the peer review process seems to work and that an explanation/update will be printed.

Comment #7202

Posted by Reed A. Cartwright on August 31, 2004 03:16 PM

What I’d really like to see is an entire issue of PBSW devoted to debunking Meyer’s “review.”  There is surely enough errors in there and enough data correcting them for atleast five papers in response.

Comment #7207

Posted by Steve on August 31, 2004 03:42 PM

Cold Fusion / Free Energy nuts have made an effort in the last decade to get jobs in the USPTO, to advance their agenda. Don’t be surprised if the DI types do the same.

Comment #7208

Posted by Steve on August 31, 2004 03:45 PM

Cold Fusion is like physics’s ID movement, but without the religious zeal, so the net effect is they also fail in the scientific arena, but don’t bother trying to introduce it in public school curricula. If you look at the proponents of both, they sound very much like each other.

Comment #7209

Posted by Pim on August 31, 2004 04:06 PM

Teach the “controversy” I’d say. :-) Of course when at the receiving end of so much criticism, one may experience a certain sense of discomfort.

Meyer’s paper will serve as an important reminder as to the lack of scientific relevance of ID.

Comment #7211

Posted by Steve on August 31, 2004 04:56 PM

To be specific, though, by ‘the same’, I didn’t mean the IDiots would get jobs with the USPTO. In their case it would be jobs at journals.

Comment #7214

Posted by Pim on August 31, 2004 07:05 PM

What surprises me to at least some extent is the total absence AFAIK of any ID proponents coming to Meyer’s rescue. Other than describing without much detail Gishlick et al’s in depth review in some negative terms.
Come on guys… This is your chance to show what ID has to offer scientifically.

Comment #7215

Posted by Pim on August 31, 2004 07:09 PM

I was wrong Jazzraptor on ARN wrote

I skimmed the paper, and I have to say that Meyer deserves some great praise for his scholarship. The paper is a very good summary of current state of knowledge in biology.

followed by a later posting

I plan to read the paper a time or two again, and then read the critique. I’ll comment again after that.

Perhaps there is some hope for a response? I wonder why Jazz made the comment that ‘Meyer desrves some great praise for his scholarship’? Is this sarcasm or something? What am I missing?

Comment #7216

Posted by Steve on August 31, 2004 07:34 PM

ID seems to have two faces. The one presented to science is somewhat cautious. They at least partially admit that their various Capitalized Creationist Terms (IC, CSI, OD, EF etc) are busted, but believe they are of some value, promise future revisions and corrections, and so on.
  The face presented to the public claims evolution is on the way out, ID has been successful, ‘Darwinism’ has been mortally wounded, etc.

AFAICT.

Comment #7218

Posted by Frank J on August 31, 2004 07:54 PM

Steve wrote:

ID seems to have two faces. The one presented to science is somewhat cautious…The face presented to the public claims evolution is on the way out, ID has been successful, ‘Darwinism’ has been mortally wounded, etc.

And the gap is apparently widening. In the early days Johnson criticized YEC, and Behe publicly accepted not only an old earth but common descent too. More recently, the more technical articles all but admit that evolution is how the designer did it, yet Behe and Dembski have been backpedaling from common descent, and YEC criticism is off the table. Much of what the public hears is not from the major ID players, though, but second-hand from sympathizers who fill in the blanks with more classic creationist-friendly terminology. The major ID players, however, do nothing to correct the misconceptions.

Comment #7219

Posted by Wesley R. Elsberry on August 31, 2004 08:01 PM

Jazzraptor wrote:

I skimmed the paper, and I have to say that Meyer deserves some great praise for his scholarship. The paper is a very good summary of current state of knowledge in biology.

That needs to be amended slightly to make it not obviously false:

I skimmed the paper, and I have to say that Meyer deserves some great praise for his scholarship. The paper is a very good summary of the current state of knowledge Intelligent Design advocates have of biology.

Comment #7220

Posted by salvador on August 31, 2004 08:42 PM

Pim mentions me,

I’m flattered.  I think you guys have your biases, but Wesley and company try to give a fair review.

One thing I agree with is the objection to Meyer’s appealing to the fact novel genes arising in nature.  Such instances do not negate the ID inference, but it should not be used by IDists at this time.  Novel genes may arise because of pre-programmed ability as James Shapiro is investigating.  Therefore, although it does not negate the ID inference, Meyers is not arguing from a position of strength.

As far as the continued appeals to Elsberry and Shallit 2003, I’m disappointed Wesley will not come to ARN under his real name.  I responded to his invitation 8 months ago to come to his site. I always felt some reciprocity was in order.  No matter, I’m in no rush, and to his credit he has always been gentlemanly and respectful and has responded to my questions.  Thank you Wesley.

My rebuttals of the uncharitable representations in that paper and outright gaffes will continue.  His TSPGRID argument has a hole in it which is rather hard to explain to the non IT types. I’m trying to find a way to do so.  I actually did cite his error already, to which he offered an incorrect response.  It’s the difficulty of demonstrating to people who are non-IT types, that is the challenge.  His appeal to simple-computational processes is also flawed, and I’m combing through his bibliography as I have time.  Wesley and company appeal to Quantum Computers and cellular automata to generate CSI. Simiple computational process, by simple computational quantum computers :-)

I rather liked the fact Wesley’s SAI is appearing in the equidistance of molecular sequence divergences of cytochrome-c.  Nice simple computational process at work, eh?  Right along with a bunch of molecular clocks to boot.

In the meantime, I hope Stephen Meyers will read these reviews and learn.  I can confidently say he can ignore any challenges offered by the “Elsberry and Shallit 2003” paper.  I don’t mind you guys building your case on it though. It’ll just be that more of an embarassment to see it all collapse when that paper is refuted.

Oh well.  I’ll pull a “Bill Dembski drive by posting” before I get jumped.

cheers,
Salvador
PS
I see Cornelius Hunter responding to Jason Rosenhouse over at ISCID, I hope Dr. R. shows up. 

On a side note, Dr. Rosenhouse wrote a rebuttal to one of the student’s “letters to the editor” in the JMU campus newspaper.  You see, 3 letters to the editor in 2003-2004 by students were published in the campus newspaper attacking Darwinism.  I had nothing to do with that (unfortunately, otherwise they’d have been better written letters).  Nonetheless it shows the increasing sympathies towards ID in Dr. R’s own secular college campus. Ain’t it heart warming. 

In Dr. R’s own school, more and more students refuse to bow the knee to Darwin.  Dang, in his own back yard!!! Oh, I suspect there are some ID sympathizers in the faculty too.  YIKES!

I should say, I’m pleased to have helped his JMU kids see the light of ID.  Some of the best science students at JMU are (gasp) up-and-coming IDists. Wooohooo!

I would have advised the student in question not to have written the article which Dr. R rebutted.  Andrew is young and learning, thus I will teach him better arguments.  I’m pleased to say I helped a few JMU students become creationists and intend to help a few more see the light.

Dembski’s Publisher is InterVarsity Press.  I saw, oh, about 500 students at ISAT at an InterVarsity meeting on Friday Night. 

If Dr. R would care to politely have a recorded debate at JMU, I am amenable to that.  He can maybe put a stop to what’s going on.  Maybe.  How about 90 minutes?  30 minutes each for stating our positions, 15 for rebuttals or further commentary and then offering of lists of relevant literature.  We won’t solve all the issues, but maybe at least raise a little awareness of what is at stake.  I want a civil presentation by each side.

Oh, and “hi” to my friend RBH.  Avida 1.6 will reflect my fix to their misleading documentation because of his help to me.  Pim will be amused I pelted Avida organism with enough cosmic rays to incinerate a turkey and those things still kept replicating.  I love Avida.

Comment #7222

Posted by Wesley R. Elsberry on August 31, 2004 09:09 PM

Salvador T. Cordova wrote:

As far as the continued appeals to Elsberry and Shallit 2003, I’m disappointed Wesley will not come to ARN under his real name.  I responded to his invitation 8 months ago to come to his site. I always felt some reciprocity was in order.  No matter, I’m in no rush, and to his credit he has always been gentlemanly and respectful and has responded to my questions.  Thank you Wesley.

My rebuttals of the uncharitable representations in that paper and outright gaffes will continue.  His TSPGRID argument has a hole in it which is rather hard to explain to the non IT types. I’m trying to find a way to do so.  I actually did cite his error already, to which he offered an incorrect response.  It’s the difficulty of demonstrating to people who are non-IT types, that is the challenge.  His appeal to simple-computational processes is also flawed, and I’m combing through his bibliography as I have time.  Wesley and company appeal to Quantum Computers and cellular automata to generate CSI. Simiple computational process, by simple computational quantum computers :-)

I prefer my own discussion board for hosting my replies to stuff. At least there, if it “disappears”, it’s my own fault for not backing up.

I don’t recall any “outright gaffes” being documented yet. As for “uncharitable”, I think I have quite a bit of leeway if one agrees to compare the level of charity afforded by myself and Dr. Dembski to the objects of our criticisms.

I don’t recall offering an incorrect response on TSPGRID. I do recall mentioning the critical difference between deterministic and non-deterministic algorithms, and how TSPGRID is non-deterministic.

I do appreciate the effort that Salvador is putting into this, although somewhat more documentation and somewhat less meta-talk would get us further.

Comment #7223

Posted by Wesley R. Elsberry on August 31, 2004 09:21 PM

Salvador T. Cordova wrote:

In the meantime, I hope Stephen Meyers will read these reviews and learn.  I can confidently say he can ignore any challenges offered by the “Elsberry and Shallit 2003” paper.  I don’t mind you guys building your case on it though. It’ll just be that more of an embarassment to see it all collapse when that paper is refuted.

It doesn’t matter if “the paper” is “refuted”; what matters is whether the particular claims made are supported and true. Here are the claims again:

2. Meyer relies on Dembski’s “specified complexity,” but even if he used it correctly (by rigorously applying Dembski’s filter, criteria, and probability calculations), Dembski’s filter has never been demonstrated to be able to distinguish anything in the biological realm — it has never been successfully applied by anyone to any biological phenomena (Elsberry and Shallit, 2003).

3. Meyer claims, “The Cambrian explosion represents a remarkable jump in the specified complexity or ‘complex specified information’ (CSI) of the biological world.” Yet to substantiate this, Meyer would have to yield up the details of the application of Dembski’s “generic chance elimination argument” to this event, which he does not do. There’s small wonder in that, for the total number of attempted uses of Dembski’s CSI in any even partially rigorous way number a meager four (Elsberry and Shallit, 2003).

In order to demonstrate that Elsberry and Shallit 2003 is incorrect on point (2), all one has to do is produce a citation in the published literature (dated prior to our paper) showing a complete and correct application of Dembski’s GCEA to a biological system such that “CSI” is concluded. Thus far, I’m unaware of any such instance. The only thing that makes any moves in that direction at all is Dembski’s section 5.10 of “NFL”, and we were careful to make clear why that one was both incomplete and incorrect.

In order to demonstrate that Elsberry and Shallit 2003 is incorrect on point (3), all one has to do is produce citations in the published literature (dated prior to our paper) showing the attempted application of Dembski’s GCEA to more than four cases. I’m unaware of any further examples that have been published, but I’m perfectly open to revising our number to account for all the instances.

Until and unless those citations are forthcoming, the braggadacio about how the Elsberry and Shallit 2003 paper can be safely ignored seems somewhat out of place.

Comment #7224

Posted by Pim van Meurs on August 31, 2004 10:33 PM

Salvador also claimed that Elsberry had accepted that there were problems with his arguments and that he would revise it.

He [Elsberry] ‘s already offered to revise one part on my objection.

But all I have been able to find is

Since I am working on a shorter version of the paper for publication, working out potential issues is quite useful. I appreciate comments that shed light on whether we’re hitting the marks we set or not. I’m still thinking that TSPGRID demonstrates some problems in the argument for LCI, but it’s possible that we’ve overlooked something. If that’s the case, we’ll have to revise the discussion of TSPGRID or abandon it.

I’m not convinced yet that it’s time to man the lifeboats, though.

I am sure that Salvador understands the differences between ‘offering to revise’ and ‘offering to revise based on relevant objections’. So far Salvador’s arguments seem to not be very convincing.

Seems there are some problems with reading comprehension here.

Sal on ISCID argued

I spent hours trying to refute one of Elsberry’s counterexamples called TSPGRID. In the end I don’t think either side made a convincing case about CSI, and I ended up assenting to Elsberry’s SAI.

Lars figured it all out

The point with the TSPGRID program is not that it doesn’t contain any CSI from start - it most likely does, and that CSI comes from an intelligent source. The point is that the amount of CSI that the program outputs is much larger than the amount of CSI that was in the program and its input from the beginning.  Hence, large amounts of CSI that weren’t there before have been generated. This clearly contradicts the LCI.

The problem with Sal’s argument is that it also disproves that the prime number example quoted by Dembski exhibits CSI. But Sal is arguing a deterministic example, not a stochastic one. Rock clarified that in the same thread.

Let X=PrimeUpto(Y), make Y=100 and X becomes the first one hundred primes

Sal even abandons LCI

I should clarify.

A system can acquire information: like a space probe, there is information increase as it gathers information. LCI is not violated as its ‘thermodynmic’ information boundary is opened. The system can adapt and reconfigure itself based on the data it acquires.

Which is contrary to Dembski’s argument. In other words, variation and selection can generate CSI in the genome since it is an open system.
I appreciate that Sal responded on this thread, as Dembski’s personal ‘grenade catcher’[1] and ARN cheerleader, supporting ID is surely made harder if ID proponents write a paper like Meyer.

[1]

Dembski has been accused of not responding to his critics, and Salvador has eagerly expressed (and in public, no less) his willingness to take a “grenade” for Dembski so that Dembski can continue to not respond to critics. Who is that supposed to fool?

To claim that there are outright gaffes in Elsberry and Shallit’s paper is one thing, supporting it is quite something else.

Comment #7228

Posted by Salvador T. Cordova on September 1, 2004 11:52 AM

PvM has rightly spotted my past reluctance to embrace CSI.  The reluctance is there, and it has lessened over the past 8 months.

Wesley’s SAI is a very sound definition, and I will argue it is a subset of CSI.  SAI is a very usable concept and is less controversial.  I have often said Wesley’s SAI is gift to ID, and IDists should offer holiday in honor of it’s inventor.

What Meyers achieved really in referencing Dembski (even if the definition of CSI is still being examined and possibly evolving), is that Dembski can now claim his work was referenced in a biology peer-reviewed paper (now it is a sacred writing so to speak having been peer-reviewed).  However, the more general concept of functional information (as in functional DNA) is implicity accepted.  Meyer’s did a nice conflationary move to sneak our man Bill into the scientific community.  Well done Stephen. hehehe.

I am certainly amenable to making retractions and withdrawals publicly of my provisional beliefs, as I have no reputation to defend, and can afford to make errors publicly. I am armed with the knowledge however, that there are biology facutly and biologist who reject Darwinian evolution.  For example, two creationist biology professors graduated from my alma mater, GMU, (Timothy Standish and Gordon Wilson) and this is the same school where Morowitz taught.  ID sympathies are there, but sympathies are not science.  We’ll see how all this plays out.  I will be offering a list of scientifically falsifiable postulates.  One of them will actually incorporate Wesley’s SAI concerning erosion of sequence divergences.

I also don’t necessarily tow the party line on irreducible complexity (mayby 95% but not completely).  I’m willing to voice my breaking ranks with my ID comrades because I do not wish they argue from anything but the strongest positions.

Ok.  Wesley, thank you for your clarifications, and you can expect me to visit your website.  I will be slow in posting there as I want to be methodical and exact and respectful of your time.

respectfully,
Salvador

Comment #7230

Posted by Pim on September 1, 2004 12:47 PM

Sal wrote:

Wesley’s SAI is a very sound definition, and I will argue it is a subset of CSI.  SAI is a very usable concept and is less controversial.  I have often said Wesley’s SAI is gift to ID, and IDists should offer holiday in honor of it’s inventor.

Wesley is indeed a gift to ID since his comments and suggestions quickly expose the major problems with ID hypotheses. The algorithm room, which up to this day remains unaddressed by Dembski or other ID proponents was a fascinating insight which led to the self destruction of the CSI concept. Similarly, Wesley’s observation that Dembski’s description of how to infer the ‘designer’ could not eliminate natural selection as an intelligent designer was bordering on genius.

Sal quickly comes to the real issue namely that Meyer’s paper serves to show that CSI is references in a peer reviewed paper. But like cold fusion, CSI seems to be suffering from many problems and the fact that it was quoted without much elaboration as to how to measure CSI does not help its cause much. While Sal may be right, Meyer used a conflationary move to sneak Bill into the scientific community, science seems to have rejected the idea quickly. And the rejection was well supported by a scathing critique.
I understand that Sal’s hope is in ID sympathizers but there are/were cold fusion sumpathizers as well. The cold hard reality was that it was shown to be wrong. I am looking forward to a scientifically meaningful ID hypothesis, but somehow I am not holding my breath. I have seen some ad hoc claims that ID can be falsified but really, without explaining how an Intelligent Designer can be constrained, ID has nothing to offer beyond the usual eliminative argument of appeal to ignorance.
Since you suggest that you are amenable to making retractions of your provisional beliefs, is it time to admit you were wrong about nested hierarchies and evolution? Or does that require some more time to sink in?

Comment #7231

Posted by Russell on September 1, 2004 01:37 PM

For those of us trying to follow along, but not already immersed in this discussion: SAI = ? (and what’s the original reference to it?

Thanks.

Comment #7233

Posted by Pim on September 1, 2004 01:51 PM

SAI: Specified Anti Information
The Finite Improbability Calculator

More Detail in Elsberry and Shallit

Comment #7234

Posted by RBH on September 1, 2004 03:19 PM

Salvador claimed

Oh, and “hi” to my friend RBH.  Avida 1.6 will reflect my fix to their misleading documentation because of his help to me.  Pim will be amused I pelted Avida organism with enough cosmic rays to incinerate a turkey and those things still kept replicating.  I love Avida.

See here for what really happened.  (And it was ver 1.3, Sal, not 1.6).

RBH

Comment #7235

Posted by Pim on September 1, 2004 03:39 PM

RBH, thanks for the details. Seems Sal confused replication with random drift. I thought by now Sal had come to realize this. Guess that it may take some time to publicly make retractions :-)

Comment #7237

Posted by Great White Wonder on September 1, 2004 04:32 PM

Cold Fusion / Free Energy nuts have made an effort in the last decade to get jobs in the USPTO, to advance their agenda.

Steve, are you telling us that some people are so desperate that they ignore the well-known fact that the USPTO is a horribly mismanaged outfit which generates unassertable patents at ever-increasing rates?

If so, you are right.

On the other hand, it might be fun (becuase the IDiots and their followers are so clueless) to attempt to patent some ID-inspired method.  I could request the most competent Examiner I know of to tear it to shreds, provide him with all the resources, and give it a decent “public” airing which might make it into the news (at least in the backs of some of the bigger science journals, e.g., Nature Biotechnology or something like that).

Hmmm. Yes.  If only I didn’t have a job.  And if I wasn’t a hedonist.  Ah, I can’t wait until my reincarnation as an independently wealthy owner of vast reserves of land!  It’ll be sweet.

Comment #7240

Posted by Bill Gascoyne on September 1, 2004 04:47 PM

“pseudoscientic”? Have we not spellchecked yet?

Comment #7243

Posted by Wesley R. Elsberry on September 1, 2004 04:54 PM

No, apparently we had not. Let me know if you spot others…

Comment #7246

Posted by Steve on September 1, 2004 05:34 PM

GWW: heh. Patent The Controversy!

It would be amusing to get a patent on “generating and utilizing capitalized scientific-sounding terms for the purpose of selling religious fiction.” But I think the DI has some prior art.

The Free Energy people sound just like the creationists. We’re being suppressed, lots of scientists secretly believe us, but fear for their careers, unfair playing field…

Comment #7255

Posted by Bill Gascoyne on September 1, 2004 07:10 PM

The literature using this phylogenetic perspective is extensive if Meyer wanted to investigate it (for example see Grande and Rieppel eds. 1994, Carroll 1997, Harvey et al. eds. 1996) certainly an acknowledgment of such literature is crucial if one is going to discuss such topics in a scholarly article, even if it was to criticize it. No discussion of an evolutionary innovation would be complete without reference to the phylogeny, and yet we find not one in Meyer’s 26 page opus.

A new sentence should begin after the parenthetical comment.

Comment #7258

Posted by Bill Gascoyne on September 1, 2004 07:32 PM

But, just as the ordered structure of convection cells in is boiling pot of water is not a mystery to physicists

…in a boiling pot…

The study of this forms the basis for the entire field of evolutionary and developmental biology,

This should be a separate sentence (change , to .).

Finished reading; no more corrections forthcoming. Good job!

Comment #7262

Posted by Great White Wonder on September 1, 2004 08:17 PM

Sal wrote

I would have advised the student in question not to have written the article which Dr. R rebutted.  Andrew is young and learning, thus I will teach him better arguments.  I’m pleased to say I helped a few JMU students become creationists and intend to help a few more see the light.

Sal, what did you tell this young Andrew that convinced him that becoming a “creationist” was the right thing to do?  Or did you accomplish your goal using some form of non-verbal communication and/or prayer?

Comment #7271

Posted by Richard Wein on September 2, 2004 03:48 AM

In the article, Dr. Meyer argues that no current materialistic theory of evolution can account for the origin of the information necessary to build novel animal forms. He proposes intelligent design as an alternative explanation for the origin of biological information and the higher taxa.

The author of this blurb has made the same mistake as Meyer in assuming that Dembski’s so-called “information” (which is actually improbability with respect to all possible natural processes) really means “information”. It makes no sense to talk about “the origin of the [improbability] necessary to build novel animal forms”. Then again, perhaps the author of this blurb is Meyer.

Comment #7272

Posted by Richard Wein on September 2, 2004 03:50 AM

P.S. Sorry if I’m starting to sound like a broken record on this point, but, as long as the IDologists keep playing this game of equivocation, it’s necessary to keep pointing it out.

Comment #7299

Posted by T. Russ on September 2, 2004 03:32 PM

Is Protein Science a peer-reviewed journal?

Comment #7301

Posted by Russell on September 2, 2004 04:34 PM

T.Russ: Is Protein Science a peer-reviewed journal?

yes, it is. Some of us have noted that ID advocate Michael Behe recently published a paper there - the first one in the serious scientific literature, I believe, in which he explicitly addresses the question of evolution, as a “skeptic”! Mind you, it’s not really an “ID” paper, in that it never addresses that hypothesis, but it does present some interesting mathematical modeling.

Comment #7305

Posted by Wesley R. Elsberry on September 2, 2004 06:43 PM

Let’s keep focused on Meyer 2004 here. I’m sure that Behe’s paper will shortly be receiving close attention in another thread.

Comment #7314

Posted by Wesley R. Elsberry on September 3, 2004 01:08 PM

“The Scientist” has an article that mentions the Gishlick et al. review of Meyer 2004:

http://www.biomedcentral.com/news/20040903/04/…

Comment #7315

Posted by David Heddle on September 3, 2004 01:33 PM

When Sternberg said on the link referenced by Wesley is so true:

Sternberg said he was concerned that some in the science community have labeled him and Meyer as creationists. “It’s fascinating how the ‘creationist’ label is falsely applied to anyone who raises any questions about neo-Darwinian evolutionary theory,”

As I can attest to from my experience on this site, there is a near reflexive name-calling and generalization response to anything that deviates from accepted dogma.

Comment #7316

Posted by Gary Hurd on September 3, 2004 01:52 PM

[quote]As I can attest to from my experience on this site, there is a near reflexive name-calling and generalization response to anything that deviates from accepted dogma.[quote]

Except you seem to overlook the obvious fact that they are creationists, and “intellegent design” is merely creationism.  What I find even worse is that ID creationism lacks the honesty of say the American Science Affiliation which acknowledges their theological roots, and does a better job of integrating science and the Bible than anything churned out by the Discovery Institute.

Comment #7317

Posted by Dave S. on September 3, 2004 01:57 PM

David Heddle wrote:

As I can attest to from my experience on this site, there is a near reflexive name-calling and generalization response to anything that deviates from accepted dogma.

Probably this is due to the fact that our experience is that most of the time the anti-evolutionist is a creationist. And this often turns out to be the case even after the person so designated complains about the assumption. It’s hardly “fascinating” IMO, but a reasonable if sometimes (i.e. rarely) mistaken assumption.

Comment #7318

Posted by Pim on September 3, 2004 01:58 PM

Notice the stark difference between

The article was the subject of a detailed critique on Panda’s Thumb, a Web log that focuses on issues in evolutionary science. The critique calls Meyer’s article “a rhetorical edifice out of omission of relevant facts, selective quoting, bad analogies, and tendentious interpretations.”

“It’s too bad the Proceedings published it,” Scott said. “The article doesn’t fit the type of content of the journal. The bottom line is that this article is substandard science.”

Focusing on the scientific merrits or lack thereof of the paper and Sternberg’s ‘response

Sternberg said he was concerned that some in the science community have labeled him and Meyer as creationists. “It’s fascinating how the ‘creationist’ label is falsely applied to anyone who raises any questions about neo-Darwinian evolutionary theory,” he said. “The reaction to the paper by some [anti-creationist] extremists suggests that the thought police are alive and well in the scientific community.”

And finally the pinnacle of irony: Meyer himself

Meyer said: “I have received a number of private communications from scientists expressing their agreement or intrigue with the arguments that I develop in my article. Public reaction to the article, however, has been mainly characterized by hysteria, name-calling and personal attack.” Labels, he said, “are ultimately a diversion.”

Who is creating the diversion here by focusing on the labels such as ‘creationism’, ‘hysteria’ and name-calling when in fact most of the objections are all about the lack of scientific merrit of the paper.

Funny how the ID proponents now seem to lament the peer review process for calling attention to the problems with the paper.

Finally based on nothing but a hunch and Sternberg’s comment

Richard Sternberg, a staff scientist at the National Center for Biotechnology Information who was an editor of the Proceedings at the time, told The Scientist via E-mail that the three peer reviewers of the paper “all hold faculty positions in biological disciplines at prominent universities and research institutions, one at an Ivy League university, one at a major US public university, and another at a major overseas research institute.”

I predict that the Major Overseas Research Institute will turn out to be: The Max Planck Institute.

Comment #7319

Posted by Wesley R. Elsberry on September 3, 2004 01:59 PM

[…] Persons who believe that the earth is billions of years old, and that simple forms of life evolved gradually to become more complex forms including humans, are “creationists” if they believe that a supernatural Creator not only initiated this process but in some meaningful sense controls it in furtherance of a purpose.  […]

— PE Johnson, Darwin On Trial (2nd Ed.), 1993, p.4 (footnote)

David,

Perhaps you would care to address the substantive issues that we raised in our critique of Meyer 2004?

Comment #7320

Posted by Andrew on September 3, 2004 02:02 PM

If we could find one ID apologist who wasn’t a creationist, maybe this would be “name-calling” instead of “applying an accurate synonym.”  If ID apologists didn’t spend their time on “The Bible Answer Man,” maybe this wouldn’t be name-calling.  Etc.

Comment #7321

Posted by Pim on September 3, 2004 02:03 PM

As I can attest to from my experience on this site, there is a near reflexive name-calling and generalization response to anything that deviates from accepted dogma.

Don’t confuse your ‘experience’ with reality David. Gishlick’s et al article focuses on the scientific merrits (or lack thereof). It’s the DI and others who seem to be focusing on ‘creationism’ as a label to detract from the real issue namely the paper itself and the critique. Not surprisingly few have come to the defense of the paper. Would you care to explain your position on Meyer’s paper?

Comment #7322

Posted by David Heddle on September 3, 2004 02:22 PM

If we could find one ID apologist who wasn’t a creationist, maybe this would be “name-calling” instead of “applying an accurate synonym.”

This is fatuous in many ways. First of all there are many who see evidence for design in cosmology but do not believe in creationism—they simply find the evidence intriguing.

Let me say it again, there are many, many, (much more than the “one” you requested) that see evidence of design but are not creationists. See, for example, the list of quotes I provided in the Bathroom wall.

Then there are many IDers who are not young earth creationists. In fact, on the physics side, ID is antithetical to young earth creationism.

Wesley wrote

Perhaps you would care to address the substantive issues that we raised in our critique of Meyer 2004?

It’s your blog, but if you were intellectualy honest I would expect to see the “substantive issues” plea used universally. For example, how does Seteve’s comment on this thread:

ID seems to have two faces. The one presented to science is somewhat cautious. They at least partially admit that their various Capitalized Creationist Terms (IC, CSI, OD, EF etc) are busted, but believe they are of some value, promise future revisions and corrections, and so on.
  The face presented to the public claims evolution is on the way out, ID has been successful, ‘Darwinism’ has been mortally wounded, etc.

rise to the level of “address[ing] the substantive issues that we raised in our critique of Meyer 2004”

Comment #7323

Posted by T. Russ on September 3, 2004 02:31 PM

ID theorist’s are creationists just as are theistic evolutionists. But ID theorist are not “creation scientists.”
When people at pandasthumb and other anti-ID sites use the word “creationist,” do they mean creation scientists? Often times that seems to be what they are going for.

The main reason why so many IDers are opposed to being labled “creationists” has much to do with the reckless usage of that term “creationist” when employed by their zealous opponents.

T. Russ (a philosophical creationist and proponent of the intelligent design hypothesis as a leading causal explanation for the existence of specified complexity)

Comment #7324

Posted by Pim on September 3, 2004 02:36 PM

David wrote:

It’s your blog, but if you were intellectualy honest I would expect to see the “substantive issues” plea used universally. For example, how does Seteve’s comment on this thread:

Shame on you for asserting that Wesley is not intellectually honest. I still notice any absence of attempts to address the critiques raised in the paper. That IS obvious, and to be honest it does not come as a real surprise to me. I notice you did not address Wesley’s quote of Johnson nor his request to address the substantive issues in their critique of Meyer.

Comment #7325

Posted by David Heddle on September 3, 2004 02:43 PM

Look Pim, HE placed a link in a comment, and I responded with a comment that dealt with the content referred to. If what was at the end of the link wasn’t fair game for discussion, then why provide it?

Comment #7326

Posted by Wesley R. Elsberry on September 3, 2004 02:47 PM

David,

Tu quoque, anyone?

So you’re saying you have no aspirations to perform better than “Steve”?

That’s OK, I was just surprised that you would admit that in public.

The lack of response on the substantive issues from anyone in the ID camp is interesting, I think.

Comment #7328

Posted by David Heddle on September 3, 2004 02:57 PM

Wesley,

Look, I have been following this thread with interest, and after some initial comments which you (understandably) moved  to the bathroom wall I did so quietly—because I have neither the time nor expertise to make substantive comments on the merits of Meyer’s paper or the review—it is far out of my field. But as I just wrote, I simply responded to a link you provided, and you slammed me, if I may paraphrase, for being irrelevant. So I simply picked a single comment out (I could have picked more than one,  I picked Steve’s almost at random—if you feel the urge to insult him that is your business) that did not address Meyer’s paper or the review, and even less reason to be here (I, at least, was responding to the link) and yet you flamed me. It’s the old even playing field, I suppose.

Comment #7329

Posted by Steve on September 3, 2004 03:04 PM

In my own defense, I do occasionally talk about scientifically substantive things

http://www.pandasthumb.org/pt-archives/000468.html#c7306…

Though it’s true, most of my comments relate to dishonesty and incoherence within the various creationist fringes. The reason? I’m interested in the nuances of self-deception and irrationality, social dynamics, “lying for God’, etc. If anything, I don’t think I should be held to David’s standard, because I don’t allege unfairness and misbehavior on the part of TPT contributors. Indeed, I value them, and tell them so.

Comment #7331

Posted by Les Lane on September 3, 2004 03:09 PM

In search of a higher impact factor.

The Proceedings of the Biological Society of Washington seems to have additional difficulties.  I’d be curious to know more about the Biological Society.  There doesn’t appear to me much info on the web.

Comment #7332

Posted by Steve on September 3, 2004 03:12 PM

Here’s some good substance on Meyer from Jim Balhoff:

The story gives the last word to Meyer, who comments, “Public reaction to the article, however, has been mainly characterized by hysteria, name-calling and personal attack.”  It is worth pointing out that the Panda’s Thumb critique “Meyer’s Hopeless Monster” spends about 6000 words
patiently explaining the scientific shortcomings of the paper.

Comment #7335

Posted by Wesley R. Elsberry on September 3, 2004 03:33 PM

David,

Wesley,

Look, I have been following this thread with interest, and after some initial comments which you (understandably) moved  to the bathroom wall I did so quietly—because I have neither the time nor expertise to make substantive comments on the merits of Meyer’s paper or the review—it is far out of my field. But as I just wrote, I simply responded to a link you provided, and you slammed me, if I may paraphrase, for being irrelevant. So I simply picked a single comment out (I could have picked more than one,  I picked Steve’s almost at random—if you feel the urge to insult him that is your business) that did not address Meyer’s paper or the review, and even less reason to be here (I, at least, was responding to the link) and yet you flamed me. It’s the old even playing field, I suppose.

We have David’s bit:

As I can attest to from my experience on this site, there is a near reflexive name-calling and generalization response to anything that deviates from accepted dogma.

And my response:

Perhaps you would care to address the substantive issues that we raised in our critique of Meyer 2004?

The point, perhaps missed by David, is that the critique we made is not primarily either “name-calling” or “generalized”. It is quite specific on matters of the science. This was not an issue raised by Steve, but it was raised by David.

I didn’t say David’s original comment was “irrelevant”. What I did (rather obliquely) point out was that our critique did not match the remainder of the comment David made. Apparently, I wasn’t quite clear enough on that.

Yep, the playing field is still level. The players coming out to do their thing on it, though, are quite “differently-abled”.

Comment #7337

Posted by Wesley R. Elsberry on September 3, 2004 03:38 PM

David Heddle wrote:

[…] and yet you flamed me. […]

Perhaps we’re using different connotations of “flame”. I don’t understand how what I said in response was in any way “toasty”.

I could provide examples of what a “flame” would be in my reckoning…

Comment #7339

Posted by Wesley R. Elsberry on September 3, 2004 03:45 PM

For reference, the following link contains a “flame”:

http://groups.google.com/groups?q=g:thl2830978445d&dq=&hl=en…

Comment #7340

Posted by Tom Schneider on September 3, 2004 04:11 PM

See this paper, which should have been cited by Meyer:

http://www.lecb.ncifcrf.gov/~toms/paper/ev/…

@article{Schneider.ev2000,
author = “T. D. Schneider”,
title = “Evolution of Biological Information”,
journal = “Nucleic Acids Res”,
comment = “Second issue in the month, July 15,
  release date July 10”,
volume = “28”,
number = “14”,
pages = “2794-2799”,
year = “2000”}

Comment #7341

Posted by Wesley R. Elsberry on September 3, 2004 04:15 PM

T. Russell Hunter wrote:

When people at pandasthumb and other anti-ID sites use the word “creationist,” do they mean creation scientists? Often times that seems to be what they are going for.

Still haven’t caught up on your reading, Russ?

http://www.antievolution.org/people/wre/essays/ea.html…

If I mean “creation science”, I’ll say SciCre specifically.

Comment #7342

Posted by Glenn Branch on September 3, 2004 04:30 PM

Steve wrote:

Here’s some good substance on Meyer from Jim Balhoff…

Balhoff was presumably forwarding NCSE’s broadcast message of September 3.

Comment #7365

Posted by Pim on September 4, 2004 12:57 AM

Mike Gene on ARN also misses the point it seems link

I have not been following this debate nor have I read the Meyer paper. But upstairs, Sal was talking about Rosenhouse’s blog, so I checked it out. I see Alan Gishlick, Nick Matzke, and Wesley Elsberry have a reply. Rosenhouse posted an excerpt that caught my eye:

….

Okay, for years the critics complain there are no peer-reviewed papers about ID. One appears, and now they are complaining there is an ID paper in the peer-reviewed literature!

I find the above excerpt to be quite deplorable. Once again, the critics resort to subtle character assassination.

Note that 1) Mike Gene has not read the paper by Meyer 2) Mike Gene has not read the Gishlick critique (Rosenhouse posted an excerpt that caught my eyes) and yet Mike claims that “they are complaining that there is an ID paper in the peer-reviewed literature”. Thus totally missing the point namely that the authors are focusing on the poor quality of the paper and wondering how such a paper may have passed initial peer review. Of course, Mike has to suggest that the critics resort to subtle character assasination. Perhaps so subtle that only Mike can observe it?

What is quite telling to me is that Mike Gene like others who complained before, have little to say in defense of the paper. Of course Mike could claim that since he has not read the article he has little to offer in response but that did not prevent him from having an opinion on the critics and their motivations. 
So far the best Mike seems to have to offer is an accusation (so far unfounded) of subtle character assasination and a tu quoque argument (Pennock). Of course Mike Gene misses the point (hint: is the article described/hyped as ‘peer reviewed’, hint: is the article represented as presenting (the best) case for ID hint: Did Pennock claim that there was evidence of CSI in the Cambrian but somehow failed to present the evidence?)?

See DI press release

On August 4th, 2004 an extensive review essay by Dr. Stephen C. Meyer, Director of Discovery Institute’s Center for Science & Culture appeared in the Proceedings of the Biological Society of Washington (volume 117, no. 2, pp. 213-239). The Proceedings is a peer-reviewed biology journal published at the National Museum of Natural History at the Smithsonian Institution in Washington D.C.

In the article, entitled “The Origin of Biological Information and the Higher Taxonomic Categories”, Dr. Meyer argues that no current materialistic theory of evolution can account for the origin of the information necessary to build novel animal forms. He proposes intelligent design as an alternative explanation for the origin of biological information and the higher taxa.

Is there anyone willing to stand up in Meyer’s defense I wonder? Will Mike Gene visit the Pandathumbs blog to read the actual article so that he can read the whole article in proper context? Soon on a blog in your neighborhood… Or not…

Comment #7366

Posted by Pim on September 4, 2004 01:15 AM

Is this for real?

Evolutionists Forced By Preponderance Of Evidence To Finally Publish Intelligent Design Paper In Peer-Reviewed Journal
  (8/25/2004) The origin of biological information and the higher taxonomic categories by Stephen C. Meyer of the Discovery Institute, an important paper in the history of Science on par with Watson and Crick’s paper on the structure of DNA which demolishes all the false icons of Evolutionism and breaks open Darwin’s black box by showing that only the Intelligent Design of the Lord can account for the origins of the bauplans of the higher taxa, has been published in the highly-respected journal Proceedings of the Biological Society of Washington (Vol. 117, No. 2, pp. 213-239).

Read more at Turn to OBJECTIVE for an objective Christian perspective

Please tell me it’s a clever spoof. Either way, it’s funny

Comment #7367

Posted by RBH on September 4, 2004 02:17 AM

C’mon, Pim.  “Dr. Richard Paley”?  A link to Landover Baptist Church?  And this hoot of a bio on the Mall Mission link?

Wendy Tullar was once a shopper who succumbed to Secular Consumerism until the Light of Jesus showed her the way to Salvation. She now works as a Consumer Rehabilitator and Mall Missionary for Fellowship Baptist.

RBH

Comment #7371

Posted by Wesley R. Elsberry on September 4, 2004 11:51 AM

Mike Gene wrote:

I find the above excerpt to be quite deplorable. Once again, the critics resort to subtle character assassination.

Some time ago on talk.origins, “Dave” expressed a perspicacious rejoinder to another instance of this sort of talk.

Dave wrote:

McCoy’s character wasn’t assasinated, it committed suicide in another thread.  This thread is a post-mortem.

http://groups.google.com/groups?selm=b49s8v%24r4j%241%40news…

When someone makes as many errors as we have documented Stephen Meyer does, one naturally does wonder about his scholarship and character. But we didn’t invent these problems in Meyer’s work; he did that to himself. As “Dave” says, we’re just doing the post-mortem.

In general, ID advocates seem to hold biologists to a standard of discussion that the ID advocates come nowhere close to using themselves. See the AE Discussion Board thread on invidious comparisons deployed by ID advocates. One thing that can be said of that is that the ID advocates certainly aren’t guilty of subtlety there.

Comment #7378

Posted by Pim on September 4, 2004 05:08 PM

Things are getting better. While Mike Gene still seems to not have read the paper (and Gishlick’s et al’s response) he make the following comment

From the paper Mike Gene quotes:

Given R. v. Sternberg’s creationist leanings, it seems plausible to surmise that the paper received some editorial shepherding through the peer review process. Given the abysmal quality of the science surrounding both information theory and the Cambrian explosion, it seems unlikely that it received review by experts in those fields. One wonders if the paper saw peer review at all.

Mike Gene: This is exactly the type of slime we’ve come to expect from our critics.

Remember, Mike Gene has not read the Meyer paper, he seems to be mostly unaware of the Gishlick rebuttal wich exposes a long list of fallacies, shortcomings etc in Meyer’s article yet he focuses on a post mortem analysis of what may have happened and considers this to be ‘the slime we have come to expect from our critics’.

Sure Mike. Why don’t you come to the defense of the Meyer paper or address the Gishlick et al comments in context?

I do understand what seems to me to be a level of frustration. When ID finally gets an opportunity to present its scientific case it not only fails to present a scientific hypotheses of ID but it also seems to be full of holes in how it addresses scientific knowledge.

The flagellum is not doing much better either.

Comment #7380

Posted by T.Ikeda on September 4, 2004 07:27 PM

So Sternberg is associated with the “Baraminology Study Group”. Hmm… Several years ago I wrote, “Baraminology is ‘Kinds for the ’90s’”. And there is no hint that they’ve made one iota of progress since.

I should probably trademark that phrase…
Of course, there’s some ambiguity about whether it was the 1990s or the 1790s.

Comment #7392

Posted by Tom Schneider on September 5, 2004 11:34 AM

Meyer’s main point is that he thinks that
information cannot be gained by biological
systems.  The paper I mentioned above

Evolution of Biological Information
http://www.lecb.ncifcrf.gov/~toms/paper/ev/…

which was published in the standard scientific literature, demonstrates clearly:

1.  How to measure information in biological
systems using bits as Shannon did;

and

2.  How the information is gained by pure
Darwinian mutation and selection.

I have added some more comments at

http://www.lecb.ncifcrf.gov/~toms/paper/ev/#Meyer…

They explicitly demonstrate four major failures
in Meyer’s paper.

Comment #7395

Posted by Bill Ware on September 5, 2004 02:38 PM

I see  here, that  Richard Sternberg sits on the editorial board of the Baraminology Study Group at Bryan College.

“Baraminology is an entirely invented field of study peculiar only to creationists; the sole purpose of it is to determine the makeup of the “created kinds” found in biblical text.”

Yes that’s Bryan College (Motto: We’re here to educate. Not indoctrinate.) named after William Jennings Bryan who was the prosecutor at the Scope’s Monkey Trial, right here in lovely  Dayton, TN.

It’s nice that my community is getting the recognition it so well deserves.

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