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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216 Comments
Pim van Meurs · 24 August 2004
Very Nice. Congratulations to all involved.
Great White Wonder · 24 August 2004
Reed A. Cartwright · 24 August 2004
So are y'all working on submitting a response to PBSW?
Pim van Meurs · 24 August 2004
Pim van Meurs · 24 August 2004
RBH · 24 August 2004
~DS~ · 24 August 2004
I can't get the original from that link. It comes back No Abstract Available
Pim van Meurs · 24 August 2004
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...
Steve · 24 August 2004
Alan, Nick, Wesley, thanks for the article.
Nick · 24 August 2004
Ian Musgrave · 25 August 2004
charlie wagner · 25 August 2004
gish · 25 August 2004
Steve F · 25 August 2004
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?
Wesley R. Elsberry · 25 August 2004
I moved a bunch of comments not directly related to the content and criticism of Meyer 2004 to the "Bathroom Wall".
~DS~ · 25 August 2004
; how would one falsify it? To falsify the propisition that the universe was designed for life on a nano-microscopic level, i.e. that physical parameters of particles/bosons/Calabi-Yau Metrics, whatever, etc. were purposely and precisely chosen so that life, based on chemical molecular interaction arising from underlying quantum properties, would be possible within that universe, what would be needed? It seems like one way to possibility would to show the universe was not designed for life to exist in it, would be to find life existing in a/the universe in which it cannot exist. That's the only direct way I can envision and clearly that raises a problem as far as validity, and incidentally would be pretty damn good evidence for some kind of non-human, intelligent, funny business. I'm not trying to take anyone off track here. It's just that I've seen this argument advanced in various forms on several venues and I've seen it advertised as a scientific argument in favor of IDC, but I've never seen a set of testable predictions that flows from it. Myabe that topic would be worth a future post.Steve Reuland · 25 August 2004
Great White Wonder · 25 August 2004
Steve Reuland · 25 August 2004
Steve Reuland · 25 August 2004
Nick · 25 August 2004
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.
Frank J · 25 August 2004
Pim van Meurs · 25 August 2004
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.
Nick · 25 August 2004
Jack Krebs · 25 August 2004
Steve · 25 August 2004
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.
David Wilson · 26 August 2004
Adam Marczyk · 26 August 2004
Regarding genetic algorithms and the alleged necessity of target sequences, more information can be found here:
Genetic Algorithms and Evolutionary Computation
Mark Perakh · 26 August 2004
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.
Wesley R. Elsberry · 26 August 2004
A few more comments have been shifted to a more appropriate place.
Marty Erwin · 27 August 2004
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.
Marty Erwin · 27 August 2004
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.
Wesley R. Elsberry · 27 August 2004
Yes, the DI seems to be having some "technical difficulties" in delivering the PDF of the Meyer 2004 paper.
Steve · 27 August 2004
Maybe the paper is Closed for Renovation.
Nick · 27 August 2004
Pim van Meurs · 27 August 2004
Reed A. Cartwright · 27 August 2004
What I find interesting is that none of the C
RSC Fellows, who keep track of this blog, have popped on to support Meyer.Marty Erwin · 27 August 2004
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.
Great White Wonder · 27 August 2004
Nick · 27 August 2004
Wesley R. Elsberry · 27 August 2004
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.
Glenn Branch · 27 August 2004
Wesley R. Elsberry · 27 August 2004
Ah. That would explain a lot about the response.
Wesley R. Elsberry · 28 August 2004
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.
Reed A. Cartwright · 28 August 2004
Frank J · 28 August 2004
Mark Perakh · 28 August 2004
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
Pim van Meurs · 28 August 2004
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.
Pim van Meurs · 28 August 2004
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.
Reed A. Cartwright · 28 August 2004
Marty Erwin · 28 August 2004
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.
steve · 28 August 2004
Wesley R. Elsberry · 30 August 2004
David Heddle · 30 August 2004
Pim · 30 August 2004
Indeed, studying evolution makes for another good example of arguments for antievolution being a pseudoscience. I thought we already agreed on that though?
Pim · 30 August 2004
Indeed, studying evolution makes for another good example of arguments for antievolution being a pseudoscience. I thought we already agreed on that though?
Pim van Meurs · 30 August 2004
Reed A. Cartwright · 31 August 2004
Russell · 31 August 2004
Wesley R. Elsberry · 31 August 2004
Reed A. Cartwright · 31 August 2004
The Washington Times has an article about Meyer's paper.
Reed A. Cartwright · 31 August 2004
Double post! That's what I get for previewing.
Mark A. Grobner · 31 August 2004
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.
Reed A. Cartwright · 31 August 2004
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.
Pim · 31 August 2004
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.
Reed A. Cartwright · 31 August 2004
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.
Steve · 31 August 2004
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.
Steve · 31 August 2004
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.
Pim · 31 August 2004
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.
Steve · 31 August 2004
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.
Pim · 31 August 2004
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.
Pim · 31 August 2004
Steve · 31 August 2004
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.
Frank J · 31 August 2004
Wesley R. Elsberry · 31 August 2004
salvador · 31 August 2004
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.
Wesley R. Elsberry · 31 August 2004
Wesley R. Elsberry · 31 August 2004
Pim van Meurs · 31 August 2004
Salvador T. Cordova · 1 September 2004
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
Pim · 1 September 2004
Russell · 1 September 2004
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.
Pim · 1 September 2004
SAI: Specified Anti Information
The Finite Improbability Calculator
More Detail in Elsberry and Shallit
RBH · 1 September 2004
Pim · 1 September 2004
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 :-)
Great White Wonder · 1 September 2004
Bill Gascoyne · 1 September 2004
"pseudoscientic"? Have we not spellchecked yet?
Wesley R. Elsberry · 1 September 2004
No, apparently we had not. Let me know if you spot others...
Steve · 1 September 2004
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...
Bill Gascoyne · 1 September 2004
Bill Gascoyne · 1 September 2004
Great White Wonder · 1 September 2004
Richard Wein · 2 September 2004
Richard Wein · 2 September 2004
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.
T. Russ · 2 September 2004
Is Protein Science a peer-reviewed journal?
Russell · 2 September 2004
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.
Wesley R. Elsberry · 2 September 2004
Let's keep focused on Meyer 2004 here. I'm sure that Behe's paper will shortly be receiving close attention in another thread.
Wesley R. Elsberry · 3 September 2004
"The Scientist" has an article that mentions the Gishlick et al. review of Meyer 2004:
http://www.biomedcentral.com/news/20040903/04/
David Heddle · 3 September 2004
Gary Hurd · 3 September 2004
Except you seem to overlook the obvious fact that they are creationists, and "intellegent design" is merely creationism. What I find even worse is that ID creationism lacks the honesty of say the American Science Affiliation which acknowledges their theological roots, and does a better job of integrating science and the Bible than anything churned out by the Discovery Institute.
Dave S. · 3 September 2004
Pim · 3 September 2004
Wesley R. Elsberry · 3 September 2004
Andrew · 3 September 2004
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.
Pim · 3 September 2004
David Heddle · 3 September 2004
T. Russ · 3 September 2004
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)
Pim · 3 September 2004
David Heddle · 3 September 2004
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?
Wesley R. Elsberry · 3 September 2004
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.
David Heddle · 3 September 2004
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.
Steve · 3 September 2004
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.
Les Lane · 3 September 2004
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.
Steve · 3 September 2004
Wesley R. Elsberry · 3 September 2004
Wesley R. Elsberry · 3 September 2004
Wesley R. Elsberry · 3 September 2004
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
Tom Schneider · 3 September 2004
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"}
Wesley R. Elsberry · 3 September 2004
Glenn Branch · 3 September 2004
Pim · 4 September 2004
Pim · 4 September 2004
RBH · 4 September 2004
Wesley R. Elsberry · 4 September 2004
Pim · 4 September 2004
T.Ikeda · 4 September 2004
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.
Tom Schneider · 5 September 2004
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.
Bill Ware · 5 September 2004
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.
Pim · 5 September 2004
Salvador T. Cordova · 5 September 2004
Avida has been used to supposedly show that biological information is evolvable. It done no such thing without invoking fantasy world conditions.
The Fantasy of Avida
If there any convergent protein evolution we have a case of CSI. See
Problem of Convergent Evolution
Nice SAI relationships between the proteins of two different unrelated creatures, evolving independently, eh?
[edited to correct links]
Wesley R. Elsberry · 5 September 2004
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.
Pim · 5 September 2004
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.
Pim · 5 September 2004
Jack Krebs · 5 September 2004
Yes, and now Mike just claims he was playing with me - he knew all along I knew it was a hoax. Weird.
Richard Wein · 6 September 2004
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.
Phil · 6 September 2004
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?
andrea bottaro · 6 September 2004
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. ;)
Pim van Meurs · 6 September 2004
Steve · 6 September 2004
Has Meyer's Hopeless Monster been the top entry on TPT for anyone else too?
Reed A. Cartwright · 6 September 2004
Steve, we stickied it because of the press that it was getting.
Steve · 6 September 2004
Ah, very good.
Reed A. Cartwright · 7 September 2004
Dave S. · 7 September 2004
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.
Gary Hurd · 7 September 2004
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.
Steve · 7 September 2004
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.
Salvador T. Cordova · 7 September 2004
Great White Wonder · 7 September 2004
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).
shiva · 7 September 2004
<<"Salvador is confused, he doens't understand, etc . . . .">>>
Salvador does get one thing right after all!
SL Page · 8 September 2004
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.
Nick · 8 September 2004
Dave S. · 8 September 2004
{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.
Keith Douglas · 8 September 2004
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.
Wesley R. Elsberry · 8 September 2004
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.
Nick · 8 September 2004
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)
Great White Wonder · 8 September 2004
The Nature article includes links to the Pandas Thumb and the Meyer thread.
Doctor Meyer has achieved infamy. He must be so proud.
Steve · 8 September 2004
Infamy? That makes him kind of like The Notorious PZM.
Nick · 9 September 2004
Great White Wonder · 9 September 2004
Oddly, Joe Carter abruptly terminated the addition of comments to that post.
Joe Carter · 9 September 2004
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.
RBH · 9 September 2004
Wesley R. Elsberry · 9 September 2004
Great White Wonder · 9 September 2004
RBH · 9 September 2004
Ha! I beat Wesley to the Gish piece by 4 minutes!
RBH
Pasquale Vuoso · 11 September 2004
Great White Wonder · 11 September 2004
Nick · 13 September 2004
Is Meyer correct in these two instances?
Should Meyer have cited Long et al. (2003) or something similar, even if he was going to disagree with mainstream conclusions?, and
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.Ted Davis · 15 September 2004
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.
Dave S. · 15 September 2004
Nick · 15 September 2004
Ted Davis · 15 September 2004
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.
Russell · 15 September 2004
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.
Jason Donev · 15 September 2004
Very professional and well thought out response to a difficult situation. Kudos all around.
Prof. Jason Donev
University of Puget Sound Physics dept.
Paul A. Nelson · 16 September 2004
Pim · 16 September 2004
Dave S. · 16 September 2004
Andrea Bottaro · 16 September 2004
The link to Sternberg's page posted above by Pim is messed up (go here[/URL)]. I really think all the attention paid to the peer review process of Meyer's article only distracts attention from the main issue, which should be to detail its many fundamental flaws, as highlighted by Gishlick et al.
I do believe (until proven otherwise) that Sternberg acted in good faith, if with poor scientific judgement, in overseeing the review of Meyer's paper. If anything, the events as he describes them show that, if the pool of peer reviewers he contacted is somewhat representative of scientists as a whole, scientists would by and large err on the side of accepting a controversial manuscript which they do not agree with, rather than suppressing it, despite significant flaws. In general, and in my experience, I think this is indeed often the case - a partially flawed paper expressing mainstream ideas would in general be accepted for publication less readily than an equally flawed but unorthodox and "challenging" paper. So much for "thought police" and "censorship systems".
I guess the real question is how much flaw is acceptable in a scholarly journal (as opposed to a book, web site paper, etc), as there must be a threshold below which a manuscript is just an expression of muddled thinking and/or ignorance which does not deserve the "institutional" recognition provided by the peer-review system. Many seem to think Meyer's paper is below that threshold, while Sternberg and his reviewers, at least partially, disagree. At this point, only time will tell (it doesn't look promising that the arguments found in Meyer's paper, which are certainly not new, have not had any impact on the scientific community at large, since they were originally proposed).
----------------------
As a side note, Dr. Sternberg's explanation for his participation in the Baraminology Study Group also seems understandable. However, I think that his web page should also acknowledge, for the record, his more-than-casual, ongoing activities related to ID "theory" and its advocates, dating back at least to his participation in the ID http://www.iscid.org/rapid/schedule.html"Research and Progress in Intelligent Design" conference, held in 2002 at Biola University. While Dr. Sternberg may define himself as a process structuralist, he seems in fact to have taken significant steps from the more "classical" forms of structuralism (D'Arcy-Thompson's, for instance) toward outright Intelligent Design, and, in the interest of full disclosure, should probably openly say so.
Andrea Bottaro · 16 September 2004
Dang, looks like I made a mess of the links as well. Sorry.
Here is von Sternberg's page again: http://www.rsternberg.net
Wesley R. Elsberry · 16 September 2004
I've dumped some more comments to "The Bathroom Wall" that have diverged from discussion of Meyer 2004.
Wesley R. Elsberry · 17 September 2004
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.
Nick · 17 September 2004
Great White Wonder · 17 September 2004
Too funny.
The Raelians and the GCECCs are odd bedfellows, to say the least.
Martin Neukamm · 19 September 2004
A Creationist Troll, apparently · 28 September 2004
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.
a Creationist Troll, apparently · 28 September 2004
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!
a Creationist Troll, apparently · 28 September 2004
I see from subsequent posts that Dawkins didn't start the ball rolling with METHINKS - just gave a classic bad example. Mea Culpa.
Russell · 28 September 2004
Calm down, Mr. Troll. Your post was a bit incoherent; I'm doing some interpreting here to figure out what you're trying to say.
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:
If you're interested in rebuttals to the inaccuracies that "evolutionists" have reported, probably your best source is v. Sternberg himself.
"Sternberg didn't clear the article with the BSW Council" - when he didn't have to and was a council member anyway;
I suppose the BSW can have whatever rules they choose. I don't know what they are. Do you? Now, being a member of my family, do I get to make decisions for my family? How about my community? Gosh! I'm feeling ... empowered!
"Meyer's article was outside the scope of what the journal normally publishes" - it wasn't;
According to Mr. Troll, apparently. But then, why couldn't they find reviewers to catch the obvious gaffes described in the post above?
"I doubt that any evolutionary biologists reviewed the paper" - Eugenie C. Scott no less making a false assertion, apparently!
Oh? Do you have reason to believe that Dr. Scott does not doubt that? I also doubt it. Am I making a false assertion, too?
"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.
With all due respect, it's v.Sternberg's credibility that's the question here. I'm more interested in hearing what the associate editors have to say than in what v.Sternberg says.
Wesley R. Elsberry · 28 September 2004
a Creationist Troll, apparently · 28 September 2004
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.
wildlifer · 29 September 2004
wildlifer · 29 September 2004
a Creationist Troll, apparently · 1 October 2004
Steve · 1 October 2004
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.
a Creationist Troll, apparently · 1 October 2004
:-) 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.
Pasquale Vuoso · 1 October 2004
Wesley R. Elsberry · 2 October 2004
I've moved a batch of comments not primarily about Meyer 2004b to the Bathroom Wall.
Wesley R. Elsberry · 2 October 2004
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.
Pim · 2 October 2004
And realize that the 'regulatory information' referred to by Mattick should NOT be confused with the meaningless term of complex specified information.
Pasquale Vuoso · 2 October 2004
Pasquale Vuoso · 2 October 2004
To Pim:
You write:
But to my way of looking at what we have before us, the term 'regulatory information' is meaningless. It's about the same as "dark matter" or "dark energy". It's no more than a surmise, a reflection more of how much we don't know than how much we doknow.
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.)
Pasquale Vuoso · 2 October 2004
To Pim:
You write:
But to my way of looking at what we have before us, the term 'regulatory information' is meaningless. It's about the same as "dark matter" or "dark energy". It's no more than a surmise, a reflection more of how much we don't know than how much we doknow.
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.)
Frank J · 2 October 2004
Pasquale Vuoso · 2 October 2004
Flint · 2 October 2004
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.
Flint · 2 October 2004
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.
Wesley R. Elsberry · 3 October 2004
Pasquale Vuoso · 4 October 2004
Great White Wonder · 4 October 2004
Wesley R. Elsberry · 4 October 2004
Pim · 4 October 2004
Pasquale Vuoso · 5 October 2004
PvM · 5 October 2004
Steve · 5 October 2004
To my untrained mind, I would think that quorum sensing is an obvious route to multicellularity.
Neil Johnson · 7 October 2004
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...
Pasquale Vuoso · 12 October 2004
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?
Pete Dunkelberg · 12 October 2004
Pasquale and others: Read the new topic --
The DI Strikes Back.
PvM · 12 October 2004
Link