Wesley R. Elsberry posted Entry 430 on August 24, 2004 05:56 PM.
Trackback URL: http://www.pandasthumb.org/cgi-bin/mt/mt-tb.fcgi/429

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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Commenters are responsible for the content of comments. The opinions expressed in articles, linked materials, and comments are not necessarily those of PandasThumb.org. See our full disclaimer.

Comment #6789

Posted by Pim van Meurs on August 24, 2004 6:19 PM (e)

Very Nice. Congratulations to all involved.

Comment #6795

Posted by Great White Wonder on August 24, 2004 7:16 PM (e)

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 7:23 PM (e)

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

Comment #6798

Posted by Pim van Meurs on August 24, 2004 7:28 PM (e)

Syntax Error: mismatched tag 'url'

Comment #6801

Posted by Pim van Meurs on August 24, 2004 8:12 PM (e)

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 8:42 PM (e)

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 9:29 PM (e)

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 9:32 PM (e)

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 9:54 PM (e)

Alan, Nick, Wesley, thanks for the article.

Comment #6811

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

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 1:40 AM (e)

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 8:48 AM (e)

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 (e)

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 (e)

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 2:12 PM (e)

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 2:16 PM (e)

Syntax Error: mismatched tag 'kwickxml'

Comment #6885

Posted by Steve Reuland on August 25, 2004 4:14 PM (e)

'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 4:38 PM (e)

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 4:41 PM (e)

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 4:51 PM (e)

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 6:53 PM (e)

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 7:03 PM (e)

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 7:04 PM (e)

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 7:10 PM (e)

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 (PubMedfreely 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 7:39 PM (e)

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 8:14 PM (e)

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 (e)

~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 (e)

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 1:17 PM (e)

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 3:58 PM (e)

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

Comment #6985

Posted by Marty Erwin on August 27, 2004 2:48 AM (e)

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 2:58 AM (e)

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 9:11 AM (e)

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 (e)

Maybe the paper is Closed for Renovation.

Comment #7005

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

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 (e)

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 (e)

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 4:41 PM (e)

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 4:45 PM (e)

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 9:06 PM (e)

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 Kpennock@discovery.org.) 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 9:34 PM (e)

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 (e)

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 (e)

Ah. That would explain a lot about the response.

Comment #7048

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

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 5:01 AM (e)

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 6:31 AM (e)

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 (e)

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 (e)

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 (e)

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 (e)

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 4:50 PM (e)

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 6:40 PM (e)

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 2:24 PM (e)

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 4:35 PM (e)

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 5:19 PM (e)

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 5:22 PM (e)

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 8:44 PM (e)

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 Kpennock@discovery.org ….) 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 Kpennock@discovery.org).

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 (e)

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 (e)

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 (e)

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 (e)

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

Comment #7195

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

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

Comment #7199

Posted by Mark A. Grobner on August 31, 2004 1:53 PM (e)

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 2:35 PM (e)

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 2:40 PM (e)

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 3:16 PM (e)

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 3:42 PM (e)

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 3:45 PM (e)

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 4:06 PM (e)

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 4:56 PM (e)

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 7:05 PM (e)

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 7:09 PM (e)

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 7:34 PM (e)

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 7:54 PM (e)

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 8:01 PM (e)

Syntax Error: mismatched tag 'quote'

Comment #7220

Posted by salvador on August 31, 2004 8:42 PM (e)

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 9:09 PM (e)

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 9:21 PM (e)

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 (e)

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 (e)

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 (e)

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 1:37 PM (e)

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 1:51 PM (e)

SAI: Specified Anti Information
The Finite Improbability Calculator

More Detail in Elsberry and Shallit

Comment #7234

Posted by RBH on September 1, 2004 3:19 PM (e)

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 3:39 PM (e)

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 4:32 PM (e)

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 4:47 PM (e)

“pseudoscientic”? Have we not spellchecked yet?

Comment #7243

Posted by Wesley R. Elsberry on September 1, 2004 4:54 PM (e)

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

Comment #7246

Posted by Steve on September 1, 2004 5:34 PM (e)

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 7:10 PM (e)

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 7:32 PM (e)

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 8:17 PM (e)

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 3:48 AM (e)

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 3:50 AM (e)

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 3:32 PM (e)

Is Protein Science a peer-reviewed journal?

Comment #7301

Posted by Russell on September 2, 2004 4:34 PM (e)

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 6:43 PM (e)

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 1:08 PM (e)

“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 1:33 PM (e)

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 1:52 PM (e)

Syntax Error: mismatched tag 'kwickxml'

Comment #7317

Posted by Dave S. on September 3, 2004 1:57 PM (e)

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 1:58 PM (e)

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 1:59 PM (e)

[…] 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 2:02 PM (e)

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 2:03 PM (e)

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 2:22 PM (e)

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 2:31 PM (e)

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 2:36 PM (e)

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 2:43 PM (e)

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 2:47 PM (e)

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 2:57 PM (e)

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 3:04 PM (e)

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 3:09 PM (e)

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 3:12 PM (e)

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 3:33 PM (e)

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 3:38 PM (e)

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 3:45 PM (e)

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

http://groups.google.com/groups?q=g:thl2830978445d&dq=&hl=en&lr=&ie=UTF-8&c2coff=1&safe=off&selm=brbt1u%24e0a%241%40geraldo.cc.utexas.edu

Comment #7340

Posted by Tom Schneider on September 3, 2004 4:11 PM (e)

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 4:15 PM (e)

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 4:30 PM (e)

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 (e)

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 1:15 AM (e)

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 2:17 AM (e)

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 (e)

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.iucc.ac.il&output=gplain

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 5:08 PM (e)

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 7:27 PM (e)

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 (e)

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 2:38 PM (e)

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.

Comment #7403

Posted by Pim on September 5, 2004 7:15 PM (e)

Jack on ARN comments:

I just read the article and it is not anti-evolution at all. Meyer questions the adequacy of random mutation and natural selection to account for all biological complexity. Like Simon Conway Morris, Meyer is making the case that evolution may be underpinned by a purpose. In other words, it’s teleological evolution versus non-teleological evolution.

Look at how the DI presents the argument

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.

Also note that 1) Meyer does not present ID as an (alternative) explanation in any scientific form or manner 2) teleology in evolution is not the issue either (see Ayala for instance who shows that evolutionary processes will inevitably give the appearance of teleology). But despite Meyer addressing teleology, he fails to develop an ID relevant argument.

It’s not just that Meyer fails to make any case for an ID hypothesis, but he can be observed making assertions about CSI and the Cambrian which remain either unsupported or contradicted by his own references (see Valentine for instance)

Meyer

Can neo-Darwinism explain the discontinuous increase in CSI that appears in the Cambrian explosion–either in the form of new genetic information or in the form of hierarchically organized systems of parts? We will now examine the two parts of this question

Interesting how the DI extrapolated the ‘can Neo-Darwinism explain’ to ‘no (current) materialistic theory of evolution can explain’.

But Meyer himself alludes to this

First, the possibility of design as an explanation follows logically from a consideration of the deficiencies of neo-Darwinism and other current theories as explanations for some of the more striking “appearances of design” in biological systems.

Of course this is neither logically nor even scientifically supportable as the review of omissions has shown. In other words, at best Meyer argues that his perception of a neo-Darwinian failure to explain information and complexity leads to a logical or at least plausibility of design. An argument which is logically and scientifically flawed. More ironic is that Meyer wants to argue that the unidentified ID hypothesis has a better explanatory power.
Until ID proponents can present an ID hypothesis (which is constrained) such claims have to be rejected based on logic and scientific argument.

But Meyer’s argument already fails with his basic premise that variation and selection cannot generate (complex specified) information. The lack of a relevant ID hypothesis will be unlikely resolved in the near future as long as ID revels in the darkness of gaps and ignorance.

However despite all these interesting problems, the critique by Gishlick focused on the many problems in Meyer’s arguments, pointing out that it is largely based on negative arguments.

Comment #7406

Posted by Salvador T. Cordova on September 5, 2004 9:06 PM (e)

Syntax Error: mismatched tag 'URL'

Comment #7407

Posted by Wesley R. Elsberry on September 5, 2004 9:24 PM (e)

Over on ARN, “Mike Gene” clarifies that his comment about “subtle character assassination” concerned Richard von Sternberg, not Stephen C. Meyer.

OK, fine.

The response still applies. We didn’t invent anything about Richard von Sternberg; everything we said concerning his background of involvement in creation issues is easily verifiable. As far as Sternberg’s involvement goes, we’re still just doing the post-mortem.

And we are still just wizards of subtlety here, at least compared to ID advocates having their say about biologists.

Comment #7409

Posted by Pim on September 5, 2004 10:09 PM (e)

I suggest that we take the discussion of Avida and Convergent evolution elsewhere but I would like to point out some of the problems with Sal’s somewhat blunt assertions and reality. Refering to Truman’s paper Sal states ‘the fantasy of Avida’ but ID proponents have been unable to explain away that CSI can be created using natural processes. Similarly he considers convergent protein to be evidence of CSI. Once again we notice like with Meyer a haphazard usage of the term CSI without much of any attempt to support the claims. In fact convergent evolution is not really a problem for evolutionary theory so if convergent evolution creates CSI we have yet another case of CSI arising naturally.
Of course CSI is a theoretically flawed concept, contradicted by actual fact and ultimately unable to live up to the expectations that some ID proponents seems to have.
Let me know when you present your ID hypotheses in a non begging the question manner. So far your contributions on ARN do not serve to help your claims much.
Your claims about Avida were corrected by RBH although you still seem to hold to some fallacies. Your claims about darwinian theory and phylogeny has also been shown to be erroneous, yet little seems to stop you from continuing your erroneous comments. It shows to me how ID is incapable of admitting that it was wrong, it shows me how ID will inevitably self destruct because it cannot make a positive case for ID and has to ignore much of the scientific knowledge to make its negative claims. It’s exactly this kind of conundrum which may explain the nature of Meyer’s paper.
Sal promised a while ago to show how Avida disproves phylogenies, we are still waiting. The same seems to apply with his claims of CSI and SAI. Mostly they seem to be based on Sal’s misunderstanding of the concepts.

Comment #7411

Posted by Pim on September 5, 2004 11:17 PM (e)

Remember that I posted the link to Creation Science News With Commentary by Dr. Richard Paley (see comment #7366). Dayton posted the reference on ARN with a wink and caught two fish

One was Jerry Don Bauer, the other one Mike Gene who apparantly missed the wink at the end of the posting and blurted

Mike Gene wrote:

LOL! Dayton is hoodwinked by a hoax! Look, when you rely on stereotypes as an intellectual crutch, you uncritically absorb anything that might seem to validate the precious stereotype. LOL!

Fascinating double irony

Comment #7413

Posted by Jack Krebs on September 5, 2004 11:41 PM (e)

Yes, and now Mike just claims he was playing with me - he knew all along I knew it was a hoax. Weird.

Comment #7417

Posted by Richard Wein on September 6, 2004 2:58 AM (e)

Wesley quoted Phil Johnson:

“[ … ] 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. [ … ]”

Most ID advocates (including, I believe, Sternberg and Meyer) are creationists in a much stronger sense than this. They believe in divine separate creation of “kinds”, not in gradual evolution from common ancestors.

Comment #7426

Posted by Phil on September 6, 2004 9:28 AM (e)

Hi,

Just an interested layman, so my comments may not be worth much at all, but here goes.

Didn’t Nilsson and Pelger [1994] use a computer algorithm to simulate the evolution of the eye without defining what the end result beforehand?

I am also quite sure I read about this in a Dawkins book, so it seems strange when this “scientific” paper uses “the Blind Watchmaker” and “Climbing Mount Improbable” so much that this is ignored.

Or maybe it is completely irelevant?

Comment #7427

Posted by andrea bottaro on September 6, 2004 10:25 AM (e)

Phil:
no, Nilsson and Pelger’s paper did not “simulate” eye evolution (not in the “forward” sense implied in your post, at least). What they did was to calculate, based on some physical properties of the eye and their effect on visual acuity, and under specific assumptions regarding selective pressures and mutation rates of the relevant parameters, how many generations would have been required for gradual evolution of the eye. They showed the time needed was surprisingly short.

It’s better not to refer to their model as an evolutionary simulation, because this seems to send ID advocates in a frenzy. David Berlinski went as far as accusing the entire scientific establisherment of conspiracy and cover-up based on this one paper. Seriously.

Indeed, now that you did, I expect them to show up here and start all over again. ;)

Comment #7445

Posted by Pim van Meurs on September 6, 2004 4:04 PM (e)

However Nilsson is working on a computer model for eye evolution see Computer modelling of eye evolution

A long standing question has been how variation and selection can produce an imaging eye. We have previously approached this question by theoretical modelling (Nilsson and Pelger, 1994: A pessimistic estimate of the time required for an eye to evolve. Proc R Soc Lond B 256: 53-58) which demonstrate that even with rather weak selection, the structures of a focused camera type eye can evolve in less than half a million generations. We now continue this line of research by computer simulations of eye evolution. These simulations are made to accurately mimic a realistic genetic control, and involves selection from populations of partially mutated offspring. The project has three principal aims: 1, to understand the conditions and criteria that select the fundamental optical types of eye (compound and simple etc) during early eye evolution; 2, to better understand the fine tuning of eyes to special visual requirements and habitat conditions; 3, to provide an insight into the mechanisms of genetic control required for evolution in general and eyes in particular. (Dan-Eric Nilsson, Lars Gislén)

Comment #7449

Posted by Steve on September 6, 2004 4:42 PM (e)

Has Meyer’s Hopeless Monster been the top entry on TPT for anyone else too?

Comment #7452

Posted by Reed A. Cartwright on September 6, 2004 5:08 PM (e)

Steve, we stickied it because of the press that it was getting.

Comment #7454

Posted by Steve on September 6, 2004 5:17 PM (e)

Ah, very good.

Comment #7470

Posted by Reed A. Cartwright on September 7, 2004 1:17 PM (e)

STATEMENT FROM THE COUNCIL OF THE BIOLOGICAL
SOCIETY OF WASHINGTON

The paper by Stephen C. Meyer in the Proceedings (“The origin of biological information and the higher taxonomic categories,” vol. 117, no. 2, pp. 213-239) represents a significant departure from the nearly purely taxonomic content for which this journal has been known throughout its 124-year history. It was published without the prior knowledge of the Council, which includes officers, elected councilors, and past presidents, or the associate editors. We have met and determined that all of us would have deemed this paper inappropriate for the pages of the Proceedings.

We endorse the spirit of a resolution on Intelligent Design set forth by the American Association for the Advancement of Science (www.aaas.org/news/releases/2002/1106id2.shtml), and that topic will not be addressed in future issues of the Proceedings. We are reviewing editorial policies to ensure that the goals of the Society, as reflected in its journal, are clearly understood by all. Through a web presence (www.biolsocwash.org) and contemplated improvements in the journal, the Society hopes not only to continue but to increase its service to the world community of taxonomic biologists.

The Council of the Biological Society of Washington
7 September 2004

Spotted on EvC Forum.

Comment #7472

Posted by Dave S. on September 7, 2004 1:39 PM (e)

I suspect the ID’ers have already gotten what they wanted, a paper published in a mainstream journal. That there is no positive case and no prospect of one put forth, and that it’s pretty poor even as a re-hash of existing refuted ideas is quite irrelevant. The mere fact that it exists is all that counts.

Objections, like the statement above, can be dismissed as caving under the pressure of the materialist mainstream community - who demand peer-reviewed publication and then whine when it’s presented. The just can’t be satisfied.

That’s how it’ll be presented I suspect.

Comment #7473

Posted by Gary Hurd on September 7, 2004 2:06 PM (e)

I think that Dave S. is certainly correct. At the same time, it becomes more and more clear that this wasn’t “peer reviewed” in the sense that competent biologists reviewed it. It smells like Sternbreg made a parting shot as editor to finally express himself as a creationst.

Comment #7474

Posted by Steve on September 7, 2004 3:25 PM (e)

Dave S is right. If you read the WorldNutDaily article linked below in the trackback section, you’ll see the numbnuts are using this to portray the fiction of Real Science Attacked by Hysterical Darwinists.

Comment #7477

Posted by Salvador T. Cordova on September 7, 2004 6:08 PM (e)

Syntax Error: mismatched tag 'URL'

Comment #7478

Posted by Great White Wonder on September 7, 2004 6:29 PM (e)

Salvador, any time you want to discuss the fundamental problems with your theory that it is possible to prove that life on earth was intelligently designed, please let me know.

The red herrings which consume your time would be laughable if they weren’t intended to deceive people who don’t know better (i.e., high school students who haven’t thought about the issues for more than an hour).

Even your red herrings are par-baked. You speak of this “problem” of “convergence in evolution both at the biochemical and morphological level” as if it is meaningful. What is the difference, in your “mind”, between the “biochemical” and “morphological level”?

Your inability to express yourself coherently or toss around irrelevant terms is hardly unique among ID apologists. C’mon, Salvador, see if you can bring your pointy head to rest here on earth for ten minutes and articulate your wonderful theories in such a way that a person with a mere Ph.D. in molecular and cellular biology can begin to understand what the hell you are raving about.

I’m assuming, of course, that you actually believe and understand the words that come out of your own mouth (an assumption that has bitten me in the ass more than once on this blog).

Comment #7480

Posted by shiva on September 7, 2004 8:11 PM (e)

I can anticipate what you have to say already:
“Salvador is confused, he doens’t understand, etc ….”>>>

Salvador does get one thing right after all!

Comment #7488

Posted by SL Page on September 8, 2004 8:06 AM (e)

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.

Actually, I recently read several of the “Occasional Papers of the BSG” and recent conference proceedings (conferences which, it appeared from the accompanying pictures, boasted an attendance of some 20 people, about 10-15 of whom were involved in organizing the conferences…). It seems that Wood and Cavanaugh have been busying themselves developing software for various types of analyses. A presentation at the last conference made the announcement of an amazing discovery - that equids form a baramin. That is, their amazing new software and ‘objective’ analyses have determined that horses and their relatives evolved from a horse-like ancestor.
Groundbreaking.

Comment #7490

Posted by Nick on September 8, 2004 11:51 AM (e)

As predicted in the original critique, the press releases have begun to fly:

NCSE Flip-flops As Controversy Over Peer-Reviewed Article Continues
Darwinists Like Peer-Review Except When They Don’t

By: Staff
Discovery Institute
September 8, 2004

SEATTLE, SEPT. 8 – For the past few years the Darwinian lobbyists at the National Center for Science Education (NSCE) have falsely complained that scientists who support the theory of intelligent design don’t publish peer-reviewed articles and don’t make their case at scientific conferences.

“Now an article has appeared in a biology journal that even the NCSE can’t find a way to spin out of existence,” responds Dr. John West, Associate Director of Discovery Institute’s Center for Science and Culture (CSC). “So what does it do? Claim the article shouldn’t have been published despite the fact it was approved by peer-review. Apparently politicians aren’t the only ones who do flip-flops.”

The article in question, “The Origin of Biological Information and the Higher Taxonomic Categories,” was written by CSC Director Dr. Stephen Meyer, and appears in the biology journal Proceedings of the Biological Society of Washington. The Proceedings is a peer-reviewed biology journal published at the National Museum of Natural History at the Smithsonian Institution in Washington D.C.

Dr. Meyer’s article argues that the theory of intelligent design explains the origin of the genetic information in early animal forms better than current materialistic theories of evolution.

“It’s too bad the Proceedings published it,” lamented anthropologist Eugenie Scott, executive director of the NCSE, last week. “… This article is substandard science.”

The editor of The Proceedings, Richard Sternberg, has two Ph.D.s in biology, forty peer-reviewed publications of his own, and has reviewed over 250 articles in his capacity as editor of the journal. In an interview with The Scientist, Sternberg confrimed that Meyer’s article went through the standard peer-review process and 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 U.S. public university, and another at a major overseas research institute.”

“Until a few days ago,” says Dr. Stephen Meyer, “Darwinists have argued that intelligent design isn’t science because it hasn’t been published in peer-reviewed journals. But now that an increasing number of scientists are making their case for design in scientific publications, Darwinists are ready to disown peer-review—temporarily, I’m sure.”

“The folks at the NCSE seem to embrace peer-review only when it confirms their pre-determined conclusions,” adds West. “Their goal isn’t peer-review, it’s censorship. They want to squelch the scientific debate. Fortunately, there are lots of scientists who still support free discussion.”

West also points out the spurious nature of the NCSE’s previous claim that supporters of intelligent design have not produced peer-reviewed publications. Mathematician William Dembski published a peer-reviewed monograph with Cambridge University Press, The Design Inference (1998). Biochemist Michael Behe has published his ideas recently in the peer-reviewed science journal Protein Science as well as previously in Philosophy of Science (2000) and And Stephen Meyer edited an entire volume of peer-reviewed articles with Michigan State University Press, Darwinism, Design, and Public Education (2003).

To interview Dr. Stephen Meyer contact Robert Crowther at rob@discovery.org.

[typos and weird formatting original as of Wed. morning]

Never mind the actual above critique, the bit in the first paragraph congradulating ID on getting an article in a peer-reviewed journal, or the recent developments (a week or two after the critique went up) indicating that the journal’s normal review procedures were not followed…

For those of you keeping score, here is my current count:

  1. Cries about creationism and peer-review: 5 (Meyer in The Scientist, Sternberg in The Scientist, Mike Gene, Salvador, and the current DI press release)
  2. Concessions that Meyer’s article was wrong on certain points: 0.5 (a partial from Salvador on the origin of genes)
  3. Substantitive responses to the above PT critique: 0
  4. Successful responses to the above PT critique: 0

Comment #7492

Posted by Dave S. on September 8, 2004 12:25 PM (e)

{sarcasm alert}Well you could have knocked me over with a feather. Who could possibly have guessed this would be the response??

Suffice it to say that not publishing in the relevant peer-reviewed literature is only one of the many problems with the current crop of ID arguments. Publishing one paper which has no positive arguments based on data, and offers no means to even obtain such arguments in the future doesn’t advance things very much in a useful direction.

No need to even mention that no IDist has yet applied him/herself to significantly addressing the array of problems specific to the “review”, only some of which are mentioned in the opening post of this thread.

Comment #7493

Posted by Keith Douglas on September 8, 2004 12:51 PM (e)

Notice again that the ID folks are using philosophy peer-review to claim “peer-reviewed” status for their publications. Arrrrrgggggg.

As a philosopher of science and technology, this is incredibly embarassing. My subspeciality is not in philosophy of biology or foundations of stats, though, so I am not au courant with the editorial policies in those areas.

Comment #7495

Posted by Wesley R. Elsberry on September 8, 2004 1:37 PM (e)

For those who thought that Meyer 2004 looked familiar, you were right. See my just-posted article on the already-published antecedent of Meyer 2004.

Comment #7508

Posted by Nick on September 8, 2004 6:49 PM (e)

Hey, folks, Panda’s Thumb and this critique just made Nature News (requires free registration to view).

PT traffic may be increasing further in the near future…

(DOI permalink to the story for future reference)

Comment #7509

Posted by Great White Wonder on September 8, 2004 7:24 PM (e)

The Nature article includes links to the Pandas Thumb and the Meyer thread.

Doctor Meyer has achieved infamy. He must be so proud.

Comment #7511

Posted by Steve on September 8, 2004 8:39 PM (e)

Infamy? That makes him kind of like The Notorious PZM.

Comment #7529

Posted by Nick on September 9, 2004 6:20 PM (e)

Just found out about this since it wasn’t TrackBacked, but someone has finally gotten up the gumption to respond to the above critique. See Joe Carter’s “Of Panda’s and Peers: Critiquing the Critics of Intelligent Design.”

My favorite line:

Joe Carter wrote:

[quoting Gishlick et al.] “Eighty percent loss of sequence identity is fatal to English sentences. Clearly proteins are much less specified than language.”

This is a rather bold claim. Is it really true that any protein sequence can lose 80% or more of the sequence similarity and retain the same structure and function? If so, then how is it possible for the sequences to convey information at all?

Yes Virginia, proteins really do work different than language. The same structure/function with sequence variability of 80% or more is the rule, not the exception (there are a few exceptions, such as histones). I even gave an example but anyone can find them by plinking around on Pubmed for a few minutes. Proteins have “information” in a sense, but there is no straightforward analogy to language, and proteins are not nearly as “specified” as Meyer and creationists-in-general think.

Strangely, Joe Carter doesn’t take this new important fact he just learned about proteins, and apply it to reassess Meyer’s paper, the ID literature Meyer cites, the calculations of protein “improbability” that creationists have been circulating for years, etc. He might find it surprising how quickly these arguments come unraveled when one compares them to how things actually work, rather than just assuming that inappropriate analogies to language, half-baked misapplications of information theory, and random-assembly calculations actually say something about biology/evolution.

Comment #7533

Posted by Great White Wonder on September 9, 2004 6:58 PM (e)

Oddly, Joe Carter abruptly terminated the addition of comments to that post.

Comment #7534

Posted by Joe Carter on September 9, 2004 7:26 PM (e)

GWW: Oddly, Joe Carter abruptly terminated the addition of comments to that post.

Actually, I didn’t realize that it was closed. I must have inadvertently closed it when I was cleaning up some spam. The thread is open again and comments are always welcome.

Nick: He might find it surprising how quickly these arguments come unraveled when one compares them to how things actually work, rather than just assuming that inappropriate analogies to language, half-baked misapplications of information theory, and random-assembly calculations actually say something about biology/evolution.

You have a point. I should have known better than to trust any analogy that originated with Daniel Dennett.

Comment #7535

Posted by RBH on September 9, 2004 8:08 PM (e)

Joe Carter wrote

You have a point. I should have known better than to trust any analogy that originated with Daniel Dennett.

Hm. That particular analogy is pretty old and widespread, and I don’t think Dennett can take credit (or blame) for it. For example, this from The Hindu doesn’t cite Dennett

Each of these letters is an amino acid. Proteins are long sentences strung using the 20 amino acids in sequence. In order for the cell to work and multiply, the instructions coded in the four-letter 64-word gene language need to be translated into 20-letter protein language. This translation is done through a set of RNA molecules.

and (perhaps not surprisingly) Duane Gish doesn’t credit Dennett:

Twenty different kinds of amino acids are found in proteins, so it may be said that the protein “language” has twenty letters. Just as the letters of the alphabet must be arranged in a precise sequence to write this sentence, or any sentence, so the amino acids must be arranged in a precise sequence for a protein to possess biological activity.

That’s been a pretty common analogy for some time. J. W. Ollers used it in a 1981 ICR Impact pamphlet, and he cites 1 1963 paper as apparently using it. Does Dennett’s use predate 1963?

RBH

Comment #7536

Posted by Wesley R. Elsberry on September 9, 2004 8:12 PM (e)

Joe Carter wrote:

You have a point. I should have known better than to trust any analogy that originated with Daniel Dennett.

Duane T. Gish, 1976 wrote:

Just as the letters of the alphabet must be arranged in a precise sequence to write this sentence, or any sentence, so the amino acids must be arranged in a precise sequence for a protein to possess biological activity.

http://www.icr.org/pubs/imp/imp-037.htm

Daniel Dennett making a linguistic analogy for proteins pre-dates 1976? Wow, that’s interesting to find out…

Comment #7537

Posted by Great White Wonder on September 9, 2004 8:15 PM (e)

You have a point. I should have known better than to trust any analogy that originated with Daniel Dennett.

Huh? When did Daniel Dennett analogize protein sequences to language? And was he really the first to do this?

The analogy obviously has some explanatory utility, at least in terms of start codons (they’re like some capital letters) and stop codons (they’re like some periods). But that’s about it. But that’s about it. You could analogize protein sequences to the grooves in a phonograph LP and get just as much (or as little) mileage out of the analogy (“We all know what happens when the record gets scratched, thus, evolution is based on a fraud.”)

I might as well reiterate my point again that Meyer’s argument with respect to the “language” of genes is SO naive and laughable that it begs the question of whether he thinks science is just a big joke where people just write down whatever pops into their head, slap a few citations after it, and move on the next paragraph. Certainly he acts as if that is the case. I would LOVE for him to act like a man and explain himself here but I suspect that his bosses at the Institute for Crap would never allow that to happen.

Comment #7543

Posted by RBH on September 9, 2004 8:48 PM (e)

Ha! I beat Wesley to the Gish piece by 4 minutes!

RBH

Comment #7614

Posted by Pasquale Vuoso on September 11, 2004 11:21 PM (e)

This is my first post here. I’ve been reading Meyer’s recent paper on the origin of ‘biological information.’ As I’ve read the critiques they seem to both address his main argument and to avoid it.

Meyer asks these questions:

Could a similar approach (referring to Conway Morris and the implications of convergence) shed explanatory light on the more general causal question that has been addressed in this review? Could the notion of purposive design help provide a more adequate explanation for the origin of organismal form generally? Are there reasons to consider design as an explanation for the origin of the biological information necessary to produce the higher taxa and their corresponding morphological novelty?

Now I think there are defects in the presentation (for example, Meyers invokes CSI in such a way that he presumes familiarity with it. Thus he doesn’t sufficiently contrast CSI with other theories of information–I’m thinking here of Shannon’s theory), but I think it is deserving of scientific evaluation. He seems to be dismissed, however, simply because he fails to see any explanatory power in the neo-Darwinian mechanism vis-a-vis biological complexity. Yet when he states the following–

…(W)e saw that natural selection lacked the ability to generate novel information precisely because it can only act after new functional CSI has arisen…. (W)ithout functional criteria to guide a search through the space of possible sequences, random variation is probabilistically doomed.

–isn’t this something that can be discussed?

I think this is a logically compelling dilemna, one that science should take seriously. The Latin root of science is ‘knowledge’; if the function of science is to acquire knowledge–and not simply doing something in a lab–then doesn’t this question deserve an answer?

I just finished looking at the latest issue of New Scientist. In their Book Review section there is a new book by James Valentine entitled ‘On the Origin of Phyla.’ This seems not only to contradict some of the criticism direted at Meyers, but to posit the very question that Meyers raises.

Here is what the review says:

Living animals, the descendants of the Cambrian explosion, are classified by zoologists into more than 30 phyla - nobody can agree exactly how many - each corresponding to a different body design. They are amazingly diverse yet share many features of morphology and genes, so there is no question that they descended step-by-step from a common ancestor.

The problem that James Valentine addresses is how to infer these hidden and mysterious evolutionary steps. How are animals related one to another? And why do they appear as fossils so suddenly, an event known as the Cambrian explosion?

The science is still a work in progress. But this book will be an essential tool for anyone who takes a serious interest in one of the most intractable episodes in our planet’s long history.

Meyers ends with:

An experience-based analysis of the causal powers of various hypotheses suggests purposive or intelligent design as a causally adequate–and perhaps the most causally adequate–explanation for the origin of the complex specified information required to build the Cambrian animals and the novel forms they represent. For this reason, recent scientific interest in the design hypothesis is unlikely to abate as biolgosits continue to wrestle with the problem of the origination of biological form and the higher taxa.

Shouldn’t this question preoccupy us?

Let me stop here–I have to run–and wait for some initial response and try out my URL formatting.

Comment #7615

Posted by Great White Wonder on September 11, 2004 11:50 PM (e)

Pasquale

Welcome to the Pandas Thumb! Since you’re new here, I’ll assume you aren’t a creationist troll and answer your question directly.

Shouldn’t this question preoccupy us?

If someone could come up with some scientific evidence which supported the existence of a collection of “intelligent designers” capable of designing all the life forms which ever existed on earth, then YES YES YES YES YES, that question should be near the top of the list!

Otherwise, the question definitely shouldn’t preoccupy us because it’s little more than a gap-filling argument from incredulous cooked up by Christians in order to get their “worldview” presented in science classrooms. It’s untestable. And it’s useless.

If Christians think they can write a program to prove that life was designed, you’d think it’d be easy pickins for them to write a program that can detect forged handwriting by the shape of the letters alone with 100% accuracy. With the latter program, they could earn themselves enough money to buy a whole lot more elections and then the whole issue of “Darwinism” would become moot.

Onwards!

Comment #7642

Posted by Nick on September 13, 2004 4:52 PM (e)

Dr. Stoltzfus, you wrote,

As an evolutionary biologist interested in novelty, it seems to me that you are missing the point when someone criticizes Darwinism for not explaining the origin of new genes. Scientific articles that report genes with i) an isolated distribution and ii) distinctive properties provide _prima facie_ evidence for a historically important process of the origin of new genes. However, they do not address the sufficiency of theories about the mechanism for this process. A theory about the mechanism of origin of features does not simply reiterate the historical inference that this or that specific thing happened.

Please go back up to the critique and read the articles on the origin of genes. Sometimes the origin of new genes is inferred based simply on phylogenetic comparison, basically, “Hey, critter A has gene X and sister critters B and C don’t”. This is what you focus on. But sometimes the origin of a new gene has been reconstructed in substantial detail, “caught in the act” of evolving. The individual mutation events – deletions, duplications, point mutations, etc. – have been reconstructed in great detail. These latter studies were the ones we prominently cited.

For example, Box 1 in Long et al. (2003), “The origin of new genes: glimpes from the young and old,” Nature Reviews Genetics 4, 865-875, reviews the geologically recent origin of the new gene jingwei amongst some African Drosophila species. Here is the summary diagram:

I submit that those who doubt the ability of mutation + selection to produce new genes are the ones “missing the point” if they ignore studies like the above.

The rest of your comment seems to assume a preposterously narrow view of neo-Darwinism that ignores all of the known mutational mechanisms (listed in Table 1 of Long et al. 2003) that every actual neo-Darwinist incorporates into evolutionary theory. The equation you cite applies essentially to situations at high levels of biological organization (e.g. whole organisms) where numerous genes interact to produce a quantitative polygenic trait, that trait varies in a population and has a measured mean, standard deviation, and heritability, and these quantitative changes can be tracked/predicted generation-to-generation. There is no reason to pretend that neo-Darwinians have to maintain this approximation at the level of DNA where the actual genes and specific mutational mechanisms are known.

It appears that your research focuses on non-adaptive changes in molecular evolution, such as mutation pressure. I’m sure this is fascinating stuff, but in the big picture of evolution I don’t see how these kinds of things are anything other than a explanatory supplement to the usual processes of mutation and selection for explaining the origins of new biological “information”.

While you’re here, Dr. Stoltzfus, and since you appear somewhat sympathetic to the Meyer paper, might I ask your opinion on a few points Meyer (2004) attempts to make?

1. Does the origin of new genes with new functions require the loss of old functions? Meyer (2004) says:

Meyer (2004) wrote:

Thus, although this second neo-Darwinian scenario [for the origin of new genes] has the advantage of starting with functional genes and proteins, it also has a lethal disadvantage: any process of random mutation or rearrangement in the genome would in all probability generate nonfunctional intermediate sequences before fundamentally new functional genes or proteins would arise.

But Long et al. (2003) say:

Long et al. (2003) wrote:

The creation of a new gene does not destroy previous functions.

2. Is the origin of new genes by mutation + selection really wildly improbable? Meyer (2004) says:

Meyer (2004) wrote:

Thus, whether one envisions the evolutionary process beginning with a noncoding region of the genome or a preexisting functional gene, the functional specificity and complexity of proteins impose very stringent limitations on the efficacy of mutation and selection. In the first case, function must arise first, before natural selection can act to favor a novel variation. In the second case, function must be continuously maintained in order to prevent deleterious (or lethal) consequences to the organism and to allow further evolution. Yet the complexity and functional specificity of proteins implies that both these conditions will be extremely difficult to meet.

But Long et al. (2003) say:

Long et al. (2003) wrote:

New genes can be created by the mechanisms discussed above, either individually or in combination, as in the case of jingwei, which was the first young gene to be described (Box 1, [box] 2). The origin of jingwei has highlighted the creative roles of several molecular processes acting in combination: exon shuffling, retroposition and gene duplication. In jingwei, all of these molecular mechanisms were identified by sequence and functional comparison, taking advantage of the similarity between jingwei and its parental genes.

This is not the only young gene system that has been directly observed. Other examples are the sphinx gene [23, 24] and the Sdic gene [22], which are both present in the single Drosophila species Drosophila melanogaster, and so are younger than the divergence time between D. melanogaster and its sibling species, no more than 3 million years ago. Like jingwei, sphinx was also created by retroposition, in this case from the ATP synthase F gene, which recruited nearby intron and exon sequences to form a standard chimeric structure. sphinx also evolved rapidly (Fig. 1). Besides exon shuffling and retroposition, a mobile element (S element) participated in the creation of a new splice site and coding region of the sphinx gene. Further examples of new genes in Drosophila and other organisms can be found in Table 2 Table 2 lists 22 examples]

[…]

Frequency of origin of new genes

The origination of new genes was previously thought to be a rare event at the level of the genome. This is understandable because, for example, only 1% of human genes have no similarity with the genes of other animals [59], and only 0.4% of mouse genes have no human homologues [60], although it is unclear whether these orphan genes are new arrivals, old survivors or genes that lost their identity with homologues in other organisms. However, it does not take many sequence changes to evolve a new function. For example, with only 3% sequence changes from its paralogues, RNASE1B has developed a new optimal pH that is essential for the newly evolved digestive function in the leaf-eating monkey [35]. Although it will take a systematic effort to pinpoint the rate at which new genes evolve, there is increasing evidence from Drosophila and mammalian systems that new genes might not be rare [61]. Patthy [62] compiled 250 metazoan modular protein families that were probably created by exon shuffling. Todd et al. [63] investigated 31 diverse structural enzyme superfamilies for which structural data were available, and found that almost all have functional diversity among their members that is generated by domain shuffling as well as sequence changes.

So, Dr. Stoltzfus, do you think:

  1. Is Meyer correct in these two instances?
  2. Should Meyer have cited Long et al. (2003) or something similar, even if he was going to disagree with mainstream conclusions?, and
  3. Based on your responses to the above questions, was Meyer (2004) a competent review on the topic “the origin of biological information”?

I would be very interested in your opinion on these questions.

Comment #7664

Posted by Ted Davis on September 15, 2004 8:33 AM (e)

I am a long-time NCSE member and am known as a critic of ID; I’ve been featured opposite Phillip Johnson in the NCSE Reports, for example. I also criticize ID opponents when I believe it appropriate. Some of the early rhetoric on this board merited criticism for its ad hominem flavor and I’m glad to see that has mainly stopped.

Politics does seem to influence both “sides” in this issue rather more than it should. I’ve been heavily critical of ID supporters for a number of things, and I’ve cautioned them esp about the kinds of things mentioned above in #7218, which is directly on the mark.

On the other hand, the official statement from the organization that owns the journal in question should also be criticized. Here it is:

“The paper by Stephen C. Meyer in the Proceedings (“The origin of biological information and the higher taxonomic categories,” vol. 117, no. 2, pp. 213-239) represents a significant departure from the nearly purely taxonomic content for which this journal has been known throughout its 124-year history. It was published without the prior knowledge of the Council, which includes officers, elected councilors, and past presidents, or the associate editors. We have met and determined that all of us would have deemed this paper inappropriate for the pages of the Proceedings.”

When read along with the fact that the journal’s editor and the peer reviewers are now coming under scrutiny and even personal attack, this does remind me of an aspect of the Galileo affair. Galileo sent the Dialogues to the appropriate Florentine censors, who approved it. Once his insult to the Pope at the end of the book was noticed (whether intentional or not we don’t really know, but it was clearly seen as insulting for good reasons), however, it hit the fan. The Pope took revenge on the censors and some others close to the process of publication; and also on Galileo.

Now the powers that be in this case clearly can’t bring Steve Meyer to Rome to answer charges of heresy. But they sure as heck can take revenge on the censors, for failing to exercise censorship. No doubt, those in the ID camp will hail this paper as evidence that they’ve finally gotten published in a refereed scientific journal. But their opponents do seem to overlook a certain circularity in the common claim that “They don’t publish in scientific journals so it isn’t science.” This incident does seem to underscore that circularity.

I recall hearing similar noises several years ago, when Dembski’s monograph The Design Inference was published by Cambridge University Press. Someone sent me a copy of an email from a leading scientist, in which he complained about the press having “finally let one past the goal,” or words to that effect.

My advice to both “camps” is this. Cool the rhetoric, dampen the politics. If the goal of this inquiry on both “sides” is truth, then keep the culture wars out of this. And don’t blame “the other guys” for starting it. I don’t see a monopoly on truth when I look in either direction.

Comment #7665

Posted by Dave S. on September 15, 2004 9:54 AM (e)

Ted Davis wrote:

When read along with the fact that the journal’s editor and the peer reviewers are now coming under scrutiny and even personal attack, this does remind me of an aspect of the Galileo affair.

Interesting.

So Ted, why then do you think this particular paper was published in a journal that has never published in that field before, and peer reviewed in a way quite different from the normal practice of that journal?

I fail to see where the personal Galileo-esque attack was in the cited statement. Isn’t it normal practice to reject papers off-topic? And it’s certainly normal practice to reject those found wanting in the science substance department.

But they sure as heck can take revenge on the censors, for failing to exercise censorship.

So you’re not even a teensy bit curious as to why all of a sudden their peer-review process changed for this one paper? Apparently at the behest of a single individual who seems to have acted as a departing deus ex mechina, much like a President trumping the courts and issuing pardons before leaving office.

I’ve had my own work disputed, sometimes harshly. It doesn’t feel pleasant I’ll tell you, but it helps one filter out the wrong paths. Complaining of persecution doesn’t help at all.

No doubt, those in the ID camp will hail this paper as evidence that they’ve finally gotten published in a refereed scientific journal.

Then how will they explain their statements that they’ve already published in the peer reviewed literature?

And if they believe that acceptence as a science merely requires publishing in the scientific journals and they have just now done so, then how do they reconcile this with their efforts to include their ideas to school boards and politicos before now?

Quite a nice rhetorical trick will be needed there.

But their opponents do seem to overlook a certain circularity in the common claim that “They don’t publish in scientific journals so it isn’t science.” This incident does seem to underscore that circularity.

Please provide a citation for the quoted statement. I know there have been complaints that they do not publish their ideas in the relevent scientific literature (e.g. biology, probability, information theory journals) as per the usual procedure, and there have been instances of where the lack of scientific methodology in ID is shown as strkingly apparent - but I don’t know of anyone in the professional community who seriously suggests that ID is not scientific simply because it’s proponants don’t publish in the journals.

My advice to both “camps” is this. Cool the rhetoric, dampen the politics. If the goal of this inquiry on both “sides” is truth, then keep the culture wars out of this. And don’t blame “the other guys” for starting it. I don’t see a monopoly on truth when I look in either direction.

I agree.

I’d be very interested in talking only about the evidence.

Unfortunately the “other side” keeps insisting on talking about ‘weaknessess in evolution’ or ‘evidence against evolution’ and refuses to provide a positive evidentiary case in support of their own “side”.

Comment #7671

Posted by Nick on September 15, 2004 2:05 PM (e)

Arlin,

You are arguing about the meaning of the term “neo-Darwinism”. Most people use it to describe the synthesis of Mendelian genetics and natural selection, and everything that followed in that tradition, including the molecular work. You are restricting it to mean that specific sub-claims about population genetics at the organismal level were meant to apply to all change at all organizational levels. This is a strawman of the first order.

Rather than have a pointless semantic battle, if you really feel strongly that the term “neo-Darwinism” should be restricted to what evolutionary theory said about quantitative change at the organismal level via population genetics processes circa 1966, then just use the term “Modern Evolutionary Theory” instead of “neo-Darwinism.”

The topic of this thread is Meyer’s paper. Meyer attacks “neo-Darwinism,” using the term in the general sense, not your specific sense. The question a hand is whether or not Meyer’s critiques of modern evolutionary theory are correct, well-informed, cite the relevant literature, etc. If you want to talk about that, then I suggest you answer the questions I put to you in my previous post:

  1. Is Meyer correct in these two instances? [new genes kill old function, the origin of new genes is so improbable that it is effectively impossible]
  2. Should Meyer have cited Long et al. (2003) or something similar, even if he was going to disagree with mainstream conclusions?, and
  3. Based on your responses to the above questions, was Meyer (2004) a competent review on the topic “the origin of biological information”?

I would be very interested in your opinion on these questions.

If you want to talk about something other than Meyer’s paper, then several other fora are available to you, such as talk.origins or the PT after the bar closes thread. It appears that you’ve been around the block on these definitional minutae before on the newsgroups (here is another extensive thread on the mutationist issue, just to save everyone some time).

Comment #7672

Posted by Ted Davis on September 15, 2004 2:43 PM (e)

Forgive me for not knowing how to put the fancy boxes around passages lifted from other posts. I don’t usually enter into this kind of online conversation. The formatting instructions are less than clear to me.

I’ll respond to some of Dave’s comments in post 7665:

“So Ted, why then do you think this particular paper was published in a journal that has never published in that field before, and peer reviewed in a way quite different from the normal practice of that journal?”

Well, Dave, I don’t know–do you have any special inside knowledge about the review process in this case? If so, I’d be interested to have that information.

You then write:
“So you’re not even a teensy bit curious as to why all of a sudden their peer-review process changed for this one paper? Apparently at the behest of a single individual who seems to have acted as a departing deus ex mechina, much like a President trumping the courts and issuing pardons before leaving office.”

Again–what specific information do you have, about the details in this particular case, that you can enlighten me with?

Next, this:
“I’ve had my own work disputed, sometimes harshly. It doesn’t feel pleasant I’ll tell you, but it helps one filter out the wrong paths. Complaining of persecution doesn’t help at all.”

We’ve had similar experiences, I gather, although sometimes referees filter out the things they shouldn’t. The finest essay I ever wrote, e.g., was declined by the editor of a leading journal in my field. He employed 12 referees instead of the usual 3 (I learned this directly from him later), trying actually to build a consensus to publish what was a frankly very unorthodox piece for that journal (no, it had nothing at all to do with ID). He decided to decline it. It’s been read more than anything else I have written, used in BBC programs, generates thousands of hits annually on the web. The editor has told me that this was his biggest editorial mistake.

I wasn’t persecuted. Why turn on the editor, giving the appearance of persecuting him for publishing Meyer’s article?

Finally, the little quotation in my paper was my own words, meant to convey a view I often hear. You say as much yourself, Dave, right here:
“I know there have been complaints that they do not publish their ideas in the relevent scientific literature (e.g. biology, probability, information theory journals) as per the usual procedure…”
That is all I was referring to, I was quoting no one in particular.

Comment #7674

Posted by Russell on September 15, 2004 3:34 PM (e)

It’s been read more than anything else I have written, used in BBC programs, generates thousands of hits annually on the web.

Not to cast aspersions on the piece in question, but the fact that Jonathan Wells is much more widely read than, say, Ernst Mayr does not do anything for his credibility (at least for me). Quite the contrary.

Comment #7675

Posted by Jason Donev on September 15, 2004 4:14 PM (e)

Very professional and well thought out response to a difficult situation. Kudos all around.

Prof. Jason Donev
University of Puget Sound Physics dept.

Comment #7688

Posted by Paul A. Nelson on September 16, 2004 2:50 AM (e)

Rick Sternberg just provided a website responding to the Meyer 2004 controvery:

Controversy and confusion surround the recent publication of the paper “The Origin of Biological Information and the Higher Taxonomic Categories” by Dr. Stephen C. Meyer in the Proceedings of the Biological Society of Washington. I was the managing editor of the Proceedings at the time of publication of the paper and I handled the review and editing process. The material on this website will clarify and resolve many of the disputes about the paper.

More here – www.rsternberg.net

Comment #7689

Posted by Pim on September 16, 2004 5:26 AM (e)

What I still do not understand is how Sternberg can argue

While Meyer presented a controversial alternative hypothesis, he did so in a scientific manner and in a way that advances understanding of why his view has reemerged as an option for some scientists

When in fact no alternative hypothesis was presented, certainly not in any scientific manner. The only way why ‘his view’ may have ‘re-emerged’ as an option for some is because Meyer argues for ignorance. But in this case, while there surely remains a lot science has to discover, Meyer’s ‘review’ paper in my opinion does not accurately and completely describe the current literature.

I am still curious how Meyer could reference a Valentine paper which seemed to argue the opposite for instance?

Sternberg also seems to miss the picture

The reaction to the paper by some extremists suggests that the thought police are alive and well in the scientific community.

While at first objecting to being referred to as a creationist, Sternberg now uses the term extremists to describe those who have pointed out the many flaws in the Meyer 2004 paper.

A side issue is how a paper which I believe should have been rejected by most reasonable standards (not because of its creationist arguments but rather because of its failure to accurately and completely review the current literature) managed to pass the peer review process described by Sternberg.

Comment #7696

Posted by Dave S. on September 16, 2004 12:49 PM (e)

Ted Davis wrote:

Forgive me for not knowing how to put the fancy boxes around passages lifted from other posts. I don’t usually enter into this kind of online conversation. The formatting instructions are less than clear to me.

It’s quite straightforward Ted (if I may call you Ted). Just type {quote} before the text and {/quote} afterwards, substituting square brackets for the curly ones. For italics, bold or underline, substitute ‘i’, ‘b’, or ‘u’ respectively for ‘quote’.

Well, Dave, I don’t know—do you have any special inside knowledge about the review process in this case? If so, I’d be interested to have that information.

I don’t know if you’d call it inside knowledge, but this journal has included in it’s submission guidelines, “Manuscripts are reviewed by a board of Associate Editors and appropriate referees.”

These are presuambly the same associate editors who appear in, “It was published without the prior knowledge of the Council, which includes officers, elected councilors, and past presidents, or the associate editors.” And it’s fair to inquire if the referees were appropriate.

Again—what specific information do you have, about the details in this particular case, that you can enlighten me with?

As above.

Maybe you have information that this is the sort of thing that journal does from time to time? If you do, it would seem to come as a surprise to the associate editors.

It’s an interesting side issue, but certainly not the main issue. The main issue is the response to the substantive criticism. But until Meyer does that, we have to settle with what we can get.

I’m cautiously optimistic there will be such a response and they won’t simply rely on rhetoric.

We’ve had similar experiences, I gather, although sometimes referees filter out the things they shouldn’t.

This is true.

The finest essay I ever wrote, e.g., was declined by the editor of a leading journal in my field. He employed 12 referees instead of the usual 3 (I learned this directly from him later), trying actually to build a consensus to publish what was a frankly very unorthodox piece for that journal (no, it had nothing at all to do with ID). He decided to decline it. It’s been read more than anything else I have written, used in BBC programs, generates thousands of hits annually on the web. The editor has told me that this was his biggest editorial mistake.

Glad you got it published in the end. This is a good example of an editor with an apparently personal agenda trying to circumvent the established process, and it shouldn’t be done. I’d like to read it sometime.

Once in a while, an editor will also publish something not because he/she thinks it advances knowledge in the field, but because it’s generated so much interest at the pre-publishing stage that publishing it is really the best way for everyone to see what the fuss is all about and examine the case for themselves.

Whatever the motives, no question the profile of this journal has been elevated substantially. For better or worse remains to be seen.

I wasn’t persecuted. Why turn on the editor, giving the appearance of persecuting him for publishing Meyer’s article?

Complaints of persecution in conjuntion with ignoring the specifics of the criticism are standard fare in pseudo-scientific circles.

If the Meyer article really has scientific merit, then that’s what the real issue is and I’d like to see his responses to the substance of the criticism.

I fail to see the merit yet, it looks like the same stuff we’ve seen ad nauseam that has convinced few but the true believers, but perhaps this merit will become apparent over time.

Finally, the little quotation in my paper was my own words, meant to convey a view I often hear. You say as much yourself, Dave, right here:
“I know there have been complaints that they do not publish their ideas in the relevent scientific literature (e.g. biology, probability, information theory journals) as per the usual procedure … “

Yes Ted, but I also say, which is in fact the completion of the very sentence you quoted but saw fit to omit, “… and there have been instances of where the lack of scientific methodology in ID is shown as strkingly apparent - but I don’t know of anyone in the professional community who seriously suggests that ID is not scientific simply because it’s proponants don’t publish in the journals.” Just so there is no missunderstanding, this is my view also, although I’m not counting myself as part of that community.

Publishing in the relevant peer-reviewed literature is a necessary, but not sufficient condition of any scientific enterprise. That’s the message that I get.

If the mere act of publishing was really the issue, then we’d have to accept cold fusion and all the works of Jan Hendrik Schon as valid scientific arguments too.

Publishing is the beginning of the peer review process, not the end.

Comment #7697

Posted by Andrea Bottaro on September 16, 2004 1:50 PM (e)

Syntax Error: mismatched tag 'URL'

Comment #7698

Posted by Andrea Bottaro on September 16, 2004 1:54 PM (e)

Syntax Error: mismatched tag 'URL'

Comment #7702

Posted by Wesley R. Elsberry on September 16, 2004 2:56 PM (e)

I’ve dumped some more comments to “The Bathroom Wall” that have diverged from discussion of Meyer 2004.

Comment #7739

Posted by Wesley R. Elsberry on September 17, 2004 10:44 AM (e)

A repeated comment already moved once to the Bathroom Wall has again been moved to the Bathroom Wall.

Fair warning: repeated messages that were moved for being off-topic are grounds for IP banning. We provide outlets for off-topic expression for a reason, to allow the main threads to remain topical.

Comment #7741

Posted by Nick on September 17, 2004 12:02 PM (e)

This just in!

Subject: Press Release - Scientific creation recognized officially as a scientific theory for the origin of life
From: “Raelian Movement”

SCIENTIFIC CREATION RECOGNIZED OFFICIALLY AS A SCIENTIFIC THEORY FOR THE ORIGIN OF LIFE

Press release, September 14, 2004 - The Raelian Theory about the creation of all life on Earth by intelligent beings has long been dismissed as unscientific despite the great number of scientists who have joined the Raelian Movement after having carefully reviewed the other available theories.

This “Raelian Theory” is also gaining more and more interest in the scientific community as a similar theory is being developed called the “Intelligent Design theory”, which hypothesizes that no new living entity can appear by chance.

On August 4th, 2004 an article by Dr. Stephen C. Meyer, Director of Discovery Institute’s Center for Science & Culture appeared in a peer-reviewed biology journal published by the National Museum of Natural History at the Smithsonian Institution in Washington D.C., the Proceedings of the Biological Society of Washington (volume 117, no. 2, pp. 213-239). In this article, entitled “The Origin of Biological Information and the Higher Taxonomic Categories”, Dr. Meyer argues that no current 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.

This article represents a major breakthrough as being published in a peer reviewed journal, it can be used as a reference and free the numerous scientists who were obligated to refer to evolution in explaining their discoveries.

Raelians are rejoicing over this event and will make sure that more articles are published in that domain so that biologists can look at living entities not as the result of random mutations but more as sophisticated creations in which every detail has been thought of and has a reason to exist.

“Biology will go so fast once biologists stop being blinded by the evolution theory and I am sure that in ten years from now scientists will look back and wonder why they accepted evolution for so long” said Dr. Boisselier, spokesperson of the Raelian Movement.

www.rael.org

Phil Johnson couldn’t have said it better himself…that last bit reminds me of a quote from Hitchhiker’s Guide to the Galaxy, describing someone-or-other as

A bunch of mindless jerks who will be the first against the wall when the revolution comes.

In other Raelian news,

Press Release
Raelian Movement

RAEL and three Raelians in the next Playboy issue!

MONTREAL, September 2004 – We are pleased to announce that an illustrated feature profiling RAEL and three beautiful and sensual Raelians will be published and announced on the cover of the October issue of the famous Playboy magazine.

Perhaps there will be a citation of Meyer (2004) for the DI to add to their citation list…

Comment #7742

Posted by Great White Wonder on September 17, 2004 12:31 PM (e)

Too funny.

The Raelians and the GCECCs are odd bedfellows, to say the least.

Comment #7775

Posted by Martin Neukamm on September 19, 2004 9:33 AM (e)

Congratulations! You refute not only the arguments of Meyer but also the most common arguments from the ID movement in your excellent review! ID explains everything and therefore nothing, because the designer always works in mysterious ways!

Let me add one argument against Meyer’s quotation of AXE (2004), whose article “shows” a very low probability of finding functional proteins among the sequence space (10^77): Meyer argues obviously selectively, because he never mentioned other studies, which came to a very different and much higher probabily. See for example the study of KEEFE und SZOSTAK (2001), who summarized after their experiments:

In conclusion, we suggest that functional proteins are sufficiently common in protein sequence space (roughly 1 in 10^11 ) that they may be discovered by entirely stochastic means, such as presumably operated when proteins were first used by living organisms.

Keefe, A.D.; Szostak, J.W. (2001): Functional proteins from a random-sequence library. Nature 410, pp. 715-718 (717).

Naturally, Meyer cites YOCKEY (1978) - one of the very rare articles of serious biologists who made the mistake and fell into the trap of anti-evolutionistic calculations. This argumentation is refuted since decades (e.g. in the german monograph from MAHNER (1986): Kreationismus - Inhalt und Struktur antievolutionistischer Argumentation. Pädagogisches Zentrum, Berlin.) This doesn’t prevent Meyer to cite Yockey.

Also, Meyer never mentioned the fact, that a whole industrial branch (“evolutionary biotechnology”) creates new molecules with definded new functions by in vitro-selection from random sequences. This would never be possible if Meyer were right! Here ist a small selection of (also german) literature which Meyer ignored and which invalidate his calculations and arguments against the probability of origin of new functional proteins:

Bailey, D.H. (2000): Evolution and Probability. Reports 20(4), 23-24.

Dorit, R.L.; Gilbert, W. (1991): The limited universe of exons. Curr. Opin. Genet. Dev. 1, 464-469.

Mahner, M. (1986): Kreationismus - Inhalt und Struktur antievolutionistischer Argumentation. Pädagogisches Zentrum, Berlin.

Schultes, E.A.; Bartel, D.P. (2000): One sequence, two ribozymes: implications for the emergence of new ribozyme folds. Science 289, 448-452.

Schuster, P. (1994): Molekulare Evolution an der Schwelle zwischen Chemie und Biologie. In: Wieser, W.(1994, ed.): Die Evolution der Evolutionstheorie. Von Darwin zur DNA Heidelberg. Spektrum, Berlin, Oxford, 63.

Schuster, P. (2001): Evolution in silico and in vitro: The RNA model. Biol. Chem. 382 (2001), 1301-1314.

Steiger, F. (1997): The Second Law of Thermodynamics, Evolution, and Probability. http://www.talkorigins.org/faqs/thermo/probability.html

And this is my homepage (in german)

Comment #8051

Posted by A Creationist Troll, apparently on September 28, 2004 7:37 AM (e)

Well, good to see that the evolutionist camp is so calm and rational. Personal abuse etc would so make it look as though your cages had been rattled. Also, I like the way that the NCSE’s role is “to defend evolution [the truth?] against attacks” - why pick that title - in essence an assertion of an objectively neutral role? Why not just say “National Campaign in Support of Evolution”? You wouldn’t even have to learn a new set of initials.

I’d be interested in comments on the responses to the factual inaccuracies that have been reported about this case by evolutionists and their rebuttal:
“Sternberg didn’t clear the article with the BSW Council” - when he didn’t have to and was a council member anyway;
“Meyer’s article was outside the scope of what the journal normally publishes” - it wasn’t;
“I doubt that any evolutionary biologists reviewed the paper” - Eugenie C. Scott no less making a false assertion, apparently!
“Sternberg didn’t show the paper to the journal’s board of associate editors” refuted by Sternberg;
“Sternberg didn’t show the paper to any of the associate editors” - Science.

Oddly enough with regard to the correspondence between language and genes - it wasn’t the creationists that started it - it was Dawkins, with METHINKSITISLIKEAWEASEL - which has been demonstrated to be a flawed analogy in various ways - firstly because the target sequence was designed - and secondly because as we can all now see, language is nothing like genes. So of course, you’ll be making sure that Dawkins doesn’t reproduce that analogy in future issues of “The Blind Watchmaker” and any instance where it is quoted will be clarified, in the same way that Haeckel’s embryos are not reproduced, and the peppered moth as case showing natural selection is identified as a flawed experiment, in all biology textbooks.

However, it is certainly within the realms of experimental possibility to assess the validity of the claims about mutations in proteins. Why not take a 200 aa protein (for example) and see how many proteins can be randomly changed before it loses some function - and how many before it loses all function? How many more before it gains an alternative function? And what the likelihood is of a change that is neutral vs one that is harmful? (as this will have a bearing on the possible validity of neutral evolution). Of course one protein doesn’t make an organism, but if we can see how it might work in one case, that would be a start.

Comment #8052

Posted by a Creationist Troll, apparently on September 28, 2004 8:02 AM (e)

With regard to functional proteins in the protein sequence space being “as common as 1 in 10^11” as reported above: can we tease out the implications of this a bit more?

1) What were the “stochastic means” that are talked about? Are we talking about organisms with the means of converting DNA to proteins producing random stretches of DNA? I would have thought that only getting one protein with what would effectively be random functionality (this not being specified - a functional protein is no use of an organism has no use for its function) for every 100,000,000,000 DNA bases would be a bit of a burden for the organism. In fact, such a big burden that I seriously doubt that there would be any selective advantage in an organism being able to “speculatively” have the wherewithall to generate these stochastic proteins.

2) Are there any means of “reverse-engineering” genes from proteins? Because without this you can’t really start from a useful protein and get the gene.

3) Assuming neither of the above, for a stochastic process to work, we need some means of having large amounts of free RNA or DNA floating around in some environment in which the molecular machinery is available to generate proteins from it - and then some way of the organism tagging what turned out to have been useful sequence so that it can “keep it for later” - there needs to be a selection process that will identify that one in 10^11 gene. Not just once, but over and over again until enough genes/proteins have been identified to do something useful.

4) I don’t think we’ve quite agreed how the mechanisms to produce key components of the system without which these stories about evolving proteins and genes are irrelevant - things like the RNA transcriptase etc. I bet the probability of randomly coming up with several proteins that can do this work isn’t within an order of magnitude of the 11 in 1 in 10^11.

Oh, by the way, you can call me names if it makes you feel better - it won’t bother me. I notice that name-calling posts aren’t reposted to the bathroom wall. Once you’ve got the name-calling out of your system, I am interested in your responses to these questions - and they ought to be sound, or the citation given above ought to be withdrawn. What you need is some creationist trolls doing the peer-reviewing.

Incidentally, given that Meyers’ was explicitly a review paper, why was there an expectation that it was going to add substantially to the body of material concerning ID? Oh, yes, I know - because then (since ID is regarded a priori as bad science) there would have been grounds to reject the paper at the outset!

Comment #8053

Posted by a Creationist Troll, apparently on September 28, 2004 8:14 AM (e)

I see from subsequent posts that Dawkins didn’t start the ball rolling with METHINKS - just gave a classic bad example. Mea Culpa.

Comment #8054

Posted by Russell on September 28, 2004 8:33 AM (e)

Syntax Error: mismatched tag 'b'

Comment #8055

Posted by Wesley R. Elsberry on September 28, 2004 10:04 AM (e)

R.v. Sternberg wrote:

In order to avoid making a unilateral decision on a potentially controversial paper, however, I discussed the paper on at least three occasions with another member of the Council of the Biological Society of Washington (BSW), a scientist at the National Museum of Natural History. Each time, this colleague encouraged me to publish the paper despite possible controversy.

Sternberg says he discussed the paper with a colleague. He does not say that he showed the paper to any member of the Council or an associate editor. Sternberg has not contradicted the statement of the BSW that no other Council member or associate editor had seen the manuscript before publication.

Comment #8060

Posted by a Creationist Troll, apparently on September 28, 2004 12:33 PM (e)

If somebody says, “I doubt that such and such happened”, and then it turned out that it did happen, then it is normally considered polite in proper debate to subsequently acknowledge, “Well, I was wrong - it did happen.”

Dr Scott said, “I doubt that any evolutionary biologists reviewed the paper.” (Am I correct in thinking that Dr Scott is actually an anthropologist?) However, not only is Sternberg an evolutionary biologist, but the three referees were “evolutionary and molecular biologists teaching at well-known institutions.” So Dr Scott’s doubts were unfounded. To set the record straight, it would be appropriate for NCSE to acknowledge this fact - otherwise Dr Scott’s unfounded doubts will become part of scientific mythology (like the Kansas board reducing the content of teaching on evolution, when it in fact increased it).

After all, you expect creationists to be entirely above board in the way they quote and cite - of course, you will be as well.

As far as the decision-making process for publication was concerned - the editor was not subject to the control of the council - but was apparently sufficiently concerned about the content of the paper to ask advice from colleagues on the council. Now, to me, this seems a prudent and reasonable approach. I don’t see on the basis of what I have been told about the scope of the paper that discussion about the origin of higher taxa lies beyond it - nor that the proposal of an alternative theory is inappropriate either.

Comment #8133

Posted by wildlifer on September 29, 2004 8:56 PM (e)

One Long Bluff:
The Gishlick, Matzke and Elsberry Response to Stephen Meyer’s Peer-Reviewed Article

According to the Nature report, “Meyer’s article has attracted a lengthy rebuttal on The Panda’s Thumb, a web site devoted to evolutionary theory.” The supposed rebuttal [3], titled “Meyer’s Hopeless Monster,” was written by Alan Gishlick, Nicholas Matzke, and Wesley R. Elsberry [hereafter GME], all of whom are staff members of the National Center for Science Education (NCSE), an organization that insists there is no evidence against neo-Darwinian evolution and that opposes any criticisms of Darwinian theory in public schools….
Third, GME do offer a potentially significant criticism. They claim that Meyer fails to discuss scientific literature that refutes his main claims. And, indeed, they provide a list of scientific citations that ostensibly solve the central problems that Meyer’s essay addresses, namely, the origin of genetic information and the origin of morphological novelty. As they put it, “Meyer’s paper omits discussion or even citation of vast amounts of directly relevant work available in the scientific literature.”

To someone unacquainted with the scientific literature, GME’s list of citations list might seem impressive. An actual reading of those citations, however, shows that they fail to support GME’s claims. Indeed, GME appear to be engaged in what might be called “literature bluffing.”

Literature bluffing is the indiscriminate citation of scientific papers and articles whose titles or abstracts may seem germane to the problem at hand, but which on careful reading prove not to settle the issue, or even not to have any relevance to it. Like a squid spewing out ink to confuse a pursuer, or a fighter jet dispensing chaff to deflect incoming missiles, a literature bluffer floods the discussion with citations to distract attention from the real issues.

Bibliographic search engines such as PubMed make it easy for literature bluffers to compile long lists of citations. The literature bluffer, however, rarely explains the arguments or evidence contained in the publications on the list. That would defeat the bluffer’s purpose, which is not really to address the merits of the case, but rather to overwhelm the reader with the apparent weight of scientific authority. The reader is then left with the work of actually studying the publications and assessing their relevance.

too funny

Comment #8135

Posted by wildlifer on September 29, 2004 9:02 PM (e)

One Long Bluff …

According to the Nature report, “Meyer’s article has attracted a lengthy rebuttal on The Panda’s Thumb, a web site devoted to evolutionary theory.” The supposed rebuttal [3], titled “Meyer’s Hopeless Monster,” was written by Alan Gishlick, Nicholas Matzke, and Wesley R. Elsberry [hereafter GME], all of whom are staff members of the National Center for Science Education (NCSE), an organization that insists there is no evidence against neo-Darwinian evolution and that opposes any criticisms of Darwinian theory in public schools….
Third, GME do offer a potentially significant criticism. They claim that Meyer fails to discuss scientific literature that refutes his main claims. And, indeed, they provide a list of scientific citations that ostensibly solve the central problems that Meyer’s essay addresses, namely, the origin of genetic information and the origin of morphological novelty. As they put it, “Meyer’s paper omits discussion or even citation of vast amounts of directly relevant work available in the scientific literature.”

To someone unacquainted with the scientific literature, GME’s list of citations list might seem impressive. An actual reading of those citations, however, shows that they fail to support GME’s claims. Indeed, GME appear to be engaged in what might be called “literature bluffing.”

Literature bluffing is the indiscriminate citation of scientific papers and articles whose titles or abstracts may seem germane to the problem at hand, but which on careful reading prove not to settle the issue, or even not to have any relevance to it. Like a squid spewing out ink to confuse a pursuer, or a fighter jet dispensing chaff to deflect incoming missiles, a literature bluffer floods the discussion with citations to distract attention from the real issues.

Bibliographic search engines such as PubMed make it easy for literature bluffers to compile long lists of citations. The literature bluffer, however, rarely explains the arguments or evidence contained in the publications on the list. That would defeat the bluffer’s purpose, which is not really to address the merits of the case, but rather to overwhelm the reader with the apparent weight of scientific authority. The reader is then left with the work of actually studying the publications and assessing their relevance.

too funny

Comment #8169

Posted by a Creationist Troll, apparently on October 1, 2004 7:18 AM (e)

Well, having read this thread and “One Long Bluff”, I know which party comes over as the more courteous and more careful with their logic. It will be interesting to see whether Discovery can demonstrate that GME are bluffing.

Jon Fleming wrote:

Claims that cumulative selection “does not provide a mechanism to allow macroevolution to occur” based on arm-waving and argument from ignotace is disputing the value of cumulative selection.

May I finish your sentence so that your reply makes some sense (albeit stating the obvious)? It is disputing the value of cumulative selection as an agency for macroevolution. I have already said that, if it is possible to demonstrate that a protein that is partially-specified (i.e. already doing in some measure what the protein will eventually do - in the example of prokaryotic RNA polymerase, having some catalytic effect on this process) will have a selective advantage under mutations, then cumulative selection would work as an evolutionary process for refining proteins. However:

1) Nobody seems to be saying how closely a proto-protein has to correspond to a “final” fully-specified protein as we might see it in an organism today for it to be “partially specified”. They are more concerned with picking semantic holes in my argument.

2) More importantly for evolution as an explanation, nobody seems to be saying where organisms get “random” DNA to make random polypeptide sequences, or how to get from a random polypeptide to a partially-specified protein - which is much the greater leap of improbability.

3) As yet unasked here, how often do mutations occur on a gene? What is the relative probability that a mutation on a gene will result in an increase in specification compared to it resulting in a decrease in specification? Especially given how conservative cellular processes are with DNA. If a gene is absolutely identical within a species - but there are differences in different species - it would suggest that the rate of mutation is so small that this would seriously undermine the credibility of this process as being able to generate new proteins or new features. Unless in some circumstances, mutation rates are higher (although if they are too high, then damage gets done quickly) … or some genes - perhaps ones which aren’t specifying proteins being used by the organism? - mutate more than others, giving kind of “active sites” for evolution.

It ought to be possible to research all of these things. Convincing answers to these questions would basically provide a mechanism for evolution - so not only would it explain the evidence (which is its current strength - though evolution as a theory has shown a great ability to adapt its explanations - see ReMine’s The Biotic Message) but be able to show how it works. Of course, I don’t think that it will be able to show this mechanism working - but if you want to win the argument against ID and creation, you have to show that unintelligent design can work.

Comment #8196

Posted by Steve on October 1, 2004 5:23 PM (e)

aCTa, you should probably at least read a textbook on molecular biology before you continue talking about these topics. You really don’t understand enough about them. That protein I mentioned is a yeast SNARE called SSO1. Typical protein. You have several mutants of it in yourself, actually. You could change about 220 of the 290 amino acids and get a functionally equivalent protein. Michael Behe has tried to make the same kind of argument as you, but with a lot more biochem knowledge, and failed.

Comment #8197

Posted by a Creationist Troll, apparently on October 1, 2004 5:28 PM (e)

:-) Glad to see it’s not only me who doesn’t always get Kwickcode quite right …… where’s the edit function when you need it?

Whilst I may have invented or mangled lots of other terms, the term “functional protein” was picked up from the citation of Keefe and Szostak given above. If you want to know what it means for a protein to have a function, ask them.

My understanding is that genes (amongst other things) code for proteins. So the function of a gene is linked to the function of the protein which it codes. So what I want to know is - if a gene codes a protein which has a specific function (or functions, if you like), how many changes can the gene undergo before the protein it codes starts to lose that function? Will any of that function remain if it has experienced 20% change?

I really don’t think that this is complex or confusing. It is an intuitive question that follows from the proposition that mutation of bases on the DNA allows new proteins to develop, which is necessary for an organism to code new features.

Comment #8205

Posted by Pasquale Vuoso on October 1, 2004 7:54 PM (e)

Syntax Error: mismatched tag 'u'

Comment #8218

Posted by Wesley R. Elsberry on October 2, 2004 5:38 AM (e)

I’ve moved a batch of comments not primarily about Meyer 2004b to the Bathroom Wall.

Comment #8219

Posted by Wesley R. Elsberry on October 2, 2004 6:45 AM (e)

Pasquale Vuoso,

A fundamental difference between Mattick and Meyer is that Mattick has proposed an explanation, that the necessary regulatory system he posits is fulfilled by the RNA transcribed from non-coding regions of the genome, including introns. Mattick also proposes that this RNA that functions as a regulatory system is subject to natural selection and is heritable through the DNA that gives rise to it. Mattick is proposing additional evolutionary mechanisms to account for observed complexity; he is not espousing a view that one must accept that biological phenomena require one or more intervening “intelligent designers” as does Meyer.

As I see it, there isn’t much in the way of parallel construction between Mattick and Meyer. Mattick is working within the framework of evolutionary biology and has perhaps identified a new mechanism of evolutionary change. Meyer dismisses all evolutionary explanations for certain phenomena and insists that “intelligent design” must be adopted instead in those cases. Mattick proposes that the necessary information for effective regulation of coding DNA is itself represented in the remainder of DNA, where noncoding DNA may have originated as “parasitic” DNA; Meyer says the origin of such information is an insoluble mystery under evolutionary biology and that one must invoke “intelligent designer(s)” to account for it.

In fact, Meyer’s argument by elimination of evolutionary alternatives is shown to be deficient because new evolutionary mechanisms, such as that of Mattick, are being proposed. The general problem posed is that Meyer is advancing an “ID of the gaps” argument, and advances in evolutionary biology, like this proposal by Mattick, tend to shrink the gaps that ID supposedly fills.

Comment #8243

Posted by Pim on October 2, 2004 4:09 PM (e)

And realize that the ‘regulatory information’ referred to by Mattick should NOT be confused with the meaningless term of complex specified information.

Comment #8247

Posted by Pasquale Vuoso on October 2, 2004 5:15 PM (e)

Syntax Error: mismatched tag 'i'

Comment #8248

Posted by Pasquale Vuoso on October 2, 2004 5:26 PM (e)

Syntax Error: mismatched tag 'kwickxml'

Comment #8250

Posted by Pasquale Vuoso on October 2, 2004 5:44 PM (e)

Syntax Error: mismatched tag 'kwickxml'

Comment #8252

Posted by Frank J on October 2, 2004 7:03 PM (e)

Pasquale Vuoso wrote:

Why is all this important? Why the discussion? Well, to me, it boils down to this. If I believe that the neo-Darwinian mechanism is ‘truly’ explanatory of the great preponderance of biological phenomenon, then I will employ this methodology, this model, when attacking biological phenomenon in the laboratory. What this means is that I will be looking for a mechanism that ‘gradually’ builds up complexity through ‘intermediate’ forms, etc. But, if my working model is Intelligent Design, then from this perspective I should be looking for something altogether different.

I’m not sure what you mean by “the neo-Darwinian mechanism,” but AIUI, it does not exclude the possibility of genetic changes that may be radically different than ones documented so far. You mention Margulis, so you may have heard of others like Stuart Kauffman, who criticize the “the neo-Darwinian mechanism” in its narrowest definition, but propose testable alternatives that that they (reluctantly?) admit are still within a general Darwinian evolutionary framework. The problem is that those whose “working model” is Intelligent Design do not look for anything except contrived incredulity arguments against “Darwinism.” Is your “working model” different? Are you actually looking for a testable mechanism? Does it conclude that common descent is more likely than independent abiogenesis? Does it suggest that the mechanism is more evolutionary than saltational? Is it consistent with the general timing and events of natural history that are arrived at by several different scientific disciplines? Does it challenge anti-evolutionary positions that differ from its own?

As for “world view,” this non-biologist’s humble opinion is that biologists with both theistic and non-theistic world views both overemphasize the role of natural selection. But that seems more a function of the fact that the molecular mechanisms have been harder to study (though getting less so) than of any world view. The world view that bothers me is the “postmodern” one that thinks that we should stop questioning the what, when, and how of biological history and just misrepresent the answers we have, however incomplete they may be.

Comment #8257

Posted by Pasquale Vuoso on October 2, 2004 8:16 PM (e)

I’ve had a couple of long posts the last couple of days, so I’m determined to be brief here.

Frank J wrote:

The world view that bothers me is the “postmodern” one that thinks that we should stop questioning the what, when, and how of biological history and just misrepresent the answers we have, however incomplete they may be.

Frank, I think this is the crux of Meyer’s paper. He’s saying that ID has greater “explanatory power” than neo-Darwinian mechanisms. (It’s hard to define what “neo-Darwinian” mechanisms are, but I’m thinking of the Modern Synthesis type stuff, although, as you point out, there are variations). Meyer means that when one tries to “explain” what one sees when looking at the ‘what’ and ‘when’ of ‘biological history’, that ID gives a better “explanation” of the ‘how.’ Now this is obviously something that can, and is being, argued. But what I tried to point out in my last post is that one’s methodology is necessarily affected by one’s working “paradigm”.

I’m Catholic. I have no problem with common descent. I have no problem with evolution. But when one looks at the fossil record, the better interpretation–from my perspective–seems to be a “saltationist” one. Yet this begins to pull the rug out from underneath Darwinism in general. And, from what I’ve studied, the ‘Modern Synthesis’ isn’t a compelling enough mechanism to come to the aid of the MS. That’s why I think it’s well time that the ‘how’ of evolution be re-examined. And, as the quotes from Mattick suggests, considerable ‘rethinking’ may need to be done. And, as I also tried to point out, ID is not an alternative ‘how’ ‘explanation’ that is completely indifferent to the methods experimenters choose to employ. Thus, if it is indeed correct, it can help us explore the ‘how’ of evolution in a more efficient way.

P.S. Twice I’ve gotten a message saying that I couldn’t post, and to try later–which I then did; only to find out that my post was posted twice. So, sorry for the repetitive posts.

Comment #8258

Posted by Flint on October 2, 2004 9:29 PM (e)

He’s saying that ID has greater “explanatory power” than neo-Darwinian mechanisms.

I don’t understand this. Supernatural claims “explain” anything and everything. One need only say “God did it” (via whatever locution seems to disguise direct religious motivation) and the explanation is complete. One doesn’t even need to know WHAT is being explained; no target is required, no evidence is required, no knowledge is required. Yet the “explanation” remains complete. The only problems are that this approach is of no practical utility.

As for whether the fossil record shows evidence of saltation, how should this be determined? I thought our knowledge of the fossil record, along with how it was produced, failed to support this proposition. Certainly genetic and molecular methods also fail to support saltation..

The “how” of evolution is constantly being examined, and further examination lends ever-stronger support. In my reading, the only motivation for a re-examination is that current explanations conflict with doctrine, not with evidence.

Comment #8260

Posted by Flint on October 2, 2004 9:32 PM (e)

He’s saying that ID has greater “explanatory power” than neo-Darwinian mechanisms.

I don’t understand this. Supernatural claims “explain” anything and everything. One need only say “God did it” (via whatever locution seems to disguise direct religious motivation) and the explanation is complete. One doesn’t even need to know WHAT is being explained; no target is required, no evidence is required, no knowledge is required. Yet the “explanation” remains complete. The only problems are that this approach is of no practical utility.

As for whether the fossil record shows evidence of saltation, how should this be determined? I thought our knowledge of the fossil record, along with how it was produced, failed to support this proposition. Certainly genetic and molecular methods also fail to support saltation..

The “how” of evolution is constantly being examined, and further examination lends ever-stronger support. In my reading, the only motivation for a re-examination is that current explanations conflict with doctrine, not with evidence.

Comment #8274

Posted by Wesley R. Elsberry on October 3, 2004 6:52 AM (e)

Pasquale Vuoso wrote:

To my ear this sounds like a ‘chicken and the egg’ problem: which came first? Simply to propose a new mechanism doesn’t solve the much greater problem of ‘how it arose in the first place.’

I suggest re-reading the Mattick article. He did propose how the regulatory system he talks about arose. You may not agree with his hypothesis, but you cannot simply overlook the fact that he did give one. And it wasn’t, “Poof, an ID did it.”

As for the supposed “parallels” you see between Mattick and Meyer, my hypothesis is that you are willing to engage in strained and spurious over-analysis of Mattick in a desperate attempt to validate Meyer’s work.

While Meyer does indeed go on and on about “neo-Darwinism”, the fact of the matter is that his basic argument has to be broader than that in order to conclude, “therefore ID”. He has to eliminate not just natural selection, but any sort of evolutionary process. That’s why Meyer has sections in which he dismisses structuralism and self-organization. That fact that more evolutionary processes are being proposed and researched all the time should be worrisome to you if you are relying on the way Meyer has framed his argument.

Pasquale Vuoso wrote:

On the other hand, ‘complex specified information’ has some meat to it. It is a way of ‘carving out’ an area in probability space that then becomes suggestive. It also becomes something that can be helpful when we go ‘looking’ for possible answers (as I stated at the end of my last post.)

I couldn’t disagree with you more. Let’s see you provide even one citation to published work where a “probability space” has been “carved out” fully, completely, and correctly according to Dembski’s “generic chance elimination argument” as given in chapter two of No Free Lunch and which uses the “universal small probability” as Dembski stipulates in The Design Revolution. We’ll wait. And wait. And wait.

You see, no one has “done the calculation” as Dembski urged others to do back in the closing pages of The Design Inference. “Specified complexity” as rendered by Dembski has turned into a shibboleth of the ID community, a phrase that signifies nothing in the real world. Its pseudo-mathematics do nothing for anyone. Even its creator has only attempted four calculations, none of which succeeded. In the time since the publication of The Design Inference, no one else has even tried to utilize Dembski’s “rigorous” framework to accomplish any useful task in science. Dembski’s dismissal of Gell-Mann is a much more appropriate observation of his own work: it “resists detailed application to real-world problems”.

Comment #8361

Posted by Pasquale Vuoso on October 4, 2004 5:27 PM (e)

Syntax Error: mismatched tag 'b'

Comment #8362

Posted by Great White Wonder on October 4, 2004 5:53 PM (e)

If I were a biologist investigating this, I would treat the genetic code as a “highly sophisticated computer program” and try to “break it down” into its constituent “subroutines”.

But you’re not a biologist investigating anything. Instead, you are a boring hack parroting creationist drivel on a blog. Remember?

Why don’t you write all your grand ideas down and self-publish them? Then, when the history books are written, you’ll be remembered in the same way that Dembski et al are remembered.

Won’t that be nice? You are so lucky.

Comment #8363

Posted by Wesley R. Elsberry on October 4, 2004 6:17 PM (e)

Pasquale Vuoso wrote:

In my reading (and re-reading) of the article, I can’t find any evidence that Mattick did, indeed, propose “how the regulatory system” arose. He simply suggests that “introns’ have a role in the said “regulatory system”, and that the ‘introns’ found in eukaryotes might have precursors in “self-splicing mobile genetic element(s)”. But this isn’t the same as “explaining” where, or how, this “regulatory system” came about.

pp.63-64, the section headed “From Parasites to Parallel Controls”. You seem to have an unrealistic view of the level of detail that should go into a popular article, and a hypocritical view if you don’t demand of Meyer and comrades to explain “where, or how” their “intelligent designer” came about. Mattick proposes that the rise of the eukaryotic spliceosome permitted the parallel evolution of introns. “If this hypothesis is true, its meaning may be profound,” says Mattick on that page. This goes significantly beyond your characterization in the quote above. That is, a reader relying solely upon your account would be misinformed concerning the content of Mattick on this subject. You need to develop a consistent standard of detail that you expect of hypotheses, as for Mattick’s hypothesis and its level (or lack) of detail, and apply that to the conjectures that you appear to prefer from ID advocates as well. Mattick says he has a hypothesis, and it is not, “Poof, an ID did it.”

Comment #8372

Posted by Pim on October 4, 2004 7:01 PM (e)

Pasquale Vuoso wrote:

Now, as to the relevancy of ID, may I ask you this question? Do you know of any “computer program” that isn’t the work of human intelligence, namely, an “intelligent agent”? Doesn’t the presence of a “program” directly imply the presence of a “programmer”?

And here lies the problem. As Wesley Elsberry has shown, Dembski cannot really exclude Darwinian mechanisms such as selection as the programmer/designer. Or in other words, the teleology observed in biology (function) may very well be explained in natural terms. The suggestion that intelligence is required or even a possibility is an interesting one but ID presents no hypotheses that allow us to test their claims beyond the usual appeal to ignorance. As you state, criticizing and comparing pathways and hypotheses is scientific but the conclusions that ‘thus design’ are lacking in positive hypotheses, theoretical foundations and practical applicability.

When Wesley points out the lack of much relevant research Pasquale responds

But maybe this should change. Isn’t that exactly what Meyer is arguing?

As far as I can tell, this is not what Meyer is arguing. His argument is basically an attempt to eliminate a few hypotheses, ignore a few others, and then state well ID can explain it. But no real details beyond the claim of possibility.

ID theory seems like a “better steering mechanism” along the road of fruitful future experimental procedures.

Why? So far nothing ID has produced has shown that ID is a better steering mechanism. THere is a big difference between the inflated claims about ID and its practical relevance which is minimal, especially in the area of science.

Comment #8408

Posted by Pasquale Vuoso on October 5, 2004 2:42 PM (e)

Wesley R. Elsberry wrote:

pp.63-64, the section headed “From Parasites to Parallel Controls”. You seem to have an unrealistic view of the level of detail that should go into a popular article, and a hypocritical view if you don’t demand of Meyer and comrades to explain “where, or how” their “intelligent designer” came about…. You need to develop a consistent standard of detail that you expect of hypotheses, as for Mattick’s hypothesis and its level (or lack) of detail, and apply that to the conjectures that you appear to prefer from ID advocates as well.

The problem I have with what Mattick is proposing isn’t that it lacks ‘detail’, but that it seems to be circular reasoning–which cannot be helpful.

If eukaryotes (even simple ones) have “information systems”, then “embedded networking” must already be present or else you don’t have a “system”. So, if you say the rise of the “splicesome” now “frees” introns to take over other functions than transcription, allowing them to “evolve” into “microRNAs” that have a “network” function, then it’s fair to ask: How can “future” evolution account for what is “already” present. It seems illogical.

It seems more “logical” to admit your dealing with a “designed” “information system” (who designed it doesn’t really matter, so long as their ‘mind’ works like your ‘mind’) and to begin analyzing this “information system” in the same way as you would a ‘microchip design’. You’d ask: What are the component parts here, and how might they have been assembled? Again, you’d expect ‘subroutines’, etc, etc. The example I gave of evidence that two “prokaryotic” genomes fused to form one “eukaryotic” genome fits in with the picture of ‘subroutines’ being part of larger ‘routines’, which themselves are part of larger routines, etc.

If “eukaryotes” came about by “fusion” of “prokaryotes”, then how did “multicellular” organisms come about? Did two “eukaryotes” “fuse” themselves together to form some new form of life? Is “fusion” a very integral part of biological evolution? I just think this is a more logical, and hence likely more productive, way of proceeding.

Comment #8411

Posted by PvM on October 5, 2004 3:48 PM (e)

Pasquale wrote:

If “eukaryotes” came about by “fusion” of “prokaryotes”, then how did “multicellular” organisms come about?

An accidental experiment may help understand this. Let me paraphrase and get the details later. A predator was accidentally released in a tank with single cellular algae I believe (Volvox or something). Under predation pressure some inventive solutions were found such as the generating 8 cell structures. These colonies initially had no specialized functions but there is some good literature on how these specializations may have arisen as well. If you are really interested let me know and I get you the details.

Aha I got the basics right and the specifics wrong

Glenn Morton reports

The reference to the bacteria which became colonial is Boraas, M.E. The
induction of algal clusters by flagellate predation EOS, Tran. Amer. Geophy. Union, 64:1102 It is now in the species Coelosphaerium which is in a different family from the original Chlorella vulgaris. It began with colonies ranging from 4 to 32 cells in size but then settled down to an even 8.

and the abstract

Predation was a powerful selective force promoting increased morphological complexity in a unicellular prey held in constant environmental conditions. The green alga, Chlorella vulgaris, is a well-studied eukaryote, which has retained its normal unicellular form in cultures in our laboratories for thousands of generations. For the experiments reported here, steady-state unicellular C. vulgaris continuous cultures were inoculated with the predator Ochromonas vallescia, a phagotrophic flagellated protist (‘flagellate’). Within less than 100 generations of the prey, a multicellular Chlorella growth form became dominant in the culture (subsequently repeated in other cultures). The prey Chlorella first formed globose clusters of tens to hundreds of cells. After about 10–20 generations in the presence of the phagotroph, eight-celled colonies predominated. These colonies retained the eight-celled form indefinitely in continuous culture and when plated onto agar. These self-replicating, stable colonies were virtually immune to predation by the flagellate, but small enough that each Chlorella cell was exposed directly to the nutrient medium.

Comment #8413

Posted by Steve on October 5, 2004 4:44 PM (e)

To my untrained mind, I would think that quorum sensing is an obvious route to multicellularity.

Comment #8501

Posted by Neil Johnson on October 7, 2004 2:06 PM (e)

The papers I have reviewed have always required two copies of my comments: one copy for the authors, another for the journal’s files. Unless I have missed something (an always possible occurrence!), shouldn’t there be a paper trail in the offices of the PBSW of the reviews of the Meyer manuscript? Assuming, of course, that the PBSW follows the same procedure for manuscript handling.

If, as Dr. Sternberg asserts, the manuscript was reviewed by three reasonably appropriate people, then the comments would be (even anonymously) available, which would support his case.

OTOH, if copies of the reviewers’ comments cannot be found, that would be additional clear evidence that normal editorial policies were ignored in this case. It might also indicate that the veracity of Dr. Sternberg’s account of the handling of the manuscript could not be independently verified…

Comment #8708

Posted by Pasquale Vuoso on October 12, 2004 4:57 PM (e)

I see the “fellows” at the Discovery Institute have published their rebuttal to GME’s article. It’s kind of quiet out there. Anybody home?

Comment #8715

Posted by Pete Dunkelberg on October 12, 2004 5:44 PM (e)

Pasquale and others: Read the new topic –
The DI Strikes Back.

Comment #8716

Posted by PvM on October 12, 2004 5:47 PM (e)

Link