Meyer’s Hopeless Monster

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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:

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.

References

Axe D. D., Foster N. W., Fersht A. R. 1996. “Active barnase variants with completely random hydrophobic cores.” PNAS 93(11):5590-4. PubMed

Axe, D. D. 2000. “Extreme functional sensitivity to conservative amino acid changes on enzyme exteriors.” Journal of Molecular Biology 301(3):585-95. PubMed

Axe, D. D. 2004. “Estimating the Prevalence of Protein Sequences Adopting Functional Enzyme Folds.” Journal of Molecular Biology 341(5):1295-1315. PubMed – In press: http://dx.doi.org/10.1016/j.jmb.2004.06.058

Behe, M. 2004. “Irreducible complexity: obstacle to darwinian evolution” in Debating Design: From Darwin to DNA. Edited by W. A. Dembski and M. Ruse. Cambridge University Press, pp. 352-370. Amazon

Budd, G. E. and S. E. Jensen. 2000. A critical reappraisal of the fossil record of the bilaterian phyla. Biological Reviews of the Cambridge Philosophical Society 75:253-295. PubMed

Buss, L. W. 1987. The evolution of individuality. Princeton University Press, Princeton. 201p. Amazon

Carroll, R. L. 1997. Patterns and Processes of Vertebrate Evolution. Cambridge Paleobiology Series #2. Cambridge University Press, New York. Amazon

Chellapilla, K. and Fogel, D. B. 2001. “Evolving an Expert Checkers Playing Program without Using Human Expertise.” IEEE Transactions on Evolutionary Computation, 5:4, pp. 422-428. http://www.natural-selection.com/Li[…]EEE-TEVC.pdf

Chen, J-Y., Bottjer, D. J., Oliveri, P., Dornbos, S. Q., Gao, F., Ruffins, S., Chi, H., Li, C.-W., and Davidson, E. H. 2004. “Small Bilaterian Fossils from 40 to 55 Million Years Before the Cambrian.” Science 305(5681):218-222. JournalPubMed

Davis, P., and Kenyon, D. H. 1989. Of Pandas and People: The Central Question of Biological Origins. Haughton Publishing Company.

Denton, M. J. 1986. Evolution: A Theory in Crisis. Woodbine House.

Denton, M. J. 1999. “The Intelligent Design Movement: Comments on Special Creationism.” in Darwinism Defeated? The Johnson-Lamoureux Debate on Biological Origins. Regent College Publishing, pp. 141-153.

Denton, M. J. 1998. Nature’s Destiny : How the Laws of Biology Reveal Purpose in the Universe. Free Press.

Dembski, W. A. 2002. No Free Lunch. Rowman & Littlefield.

Eldredge, N., and Gould, S. J. 1972. “Punctuated equilibria: an alternative to phyletic gradualism.” In: Models In Paleobiology. Edited by T. J. M. Schopf. Freeman, Cooper, San Francisco. pp. 82-115. Amazon

Elsberry, W. R. and Shallit, J. O. 2003. Information Theory, Evolutionary Computation, and Dembski’s “Complex Specified Information”. http://www.antievolution.org/people[…]sdembski.pdf

Foote, M. 1997. “Sampling, taxonomic description, and our evolving knowledge of morphological diversity.” Paleobiology 23:181-206.

Foote, M. Hunter, I. P., Janis, C. M. & Sepkoski, J. J. 1999. “Evolutionary and preservational constraints on origins of biologic groups: Divergence times of eutherian mammals.” Science 283:1310-13 14.

Gishlick, A. 2004. “Evolutionary Paths to Irreducible Systems: The Avian Flight Apparatus.” in Why Intelligent Design Fails: A Scientific Critique of the New Creationism. Young, M. and Edis, T., eds. Rutgers University Press. pp. 58-71. Website

Gould, S. J., and Eldredge, N. 1977. “Punctuated equilibria: the tempo and mode of evolution reconsidered.” Paleobiology 3(2):115-151. JSTOR

Grande, L. and O. Rieppel, eds. 1994. Interpreting the hierarchy of nature: from systematic pattern to evolutionary process theories. Academic Press, San Diego. 298p.

Harvey, P. H., Leigh Brown, A. J., Maynard Smith, J., and Nee, S., eds. 1996. New Uses for New Phylogenies. Oxford University Press, New York. 349p.

Jacob, F., 1977. Evolution and Tinkering. Science 196 (4295), 1161-1166. JSTORPubMed

Long, M. 2001. “Evolution of novel genes.” Curr Opin Genet Dev 11(6):673-80. PubMed

Lynch, M. and Conery, J. S. 2000. “The evolutionary fate and consequences of duplicate genes.” Science 290(5494): 1151-1155. PubMed

Lynch, M. and Conery, J. S. 2003. “The evolutionary demography of duplicate genes.” J Struct Funct Genomics 3(1-4): 35-44. 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.

Moore, R. C. and Purugganan, M. D. 2003. “The early stages of duplicate gene evolution.” PNAS 100(26): 15682-15687. PubMed

Padian, K., and Angielczyk, K. D. 1999. Are there transitional forms in the fossil record? In P.H. Kelley, J.R. Bryan, and T.A. Hansen eds. The Evolution-Creation Controversy II: Perspectives on science, religion, and geological education. Paleontological Society Papers 5:47-82.

Prijambada ID, 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

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

Shu, D.-G., Conway Morris, S., Han, J., Zhang, Z.-F., and Liu, J-N. 2004. “Ancestral echinoderms from the Chengjiang deposits of China.” Nature 430:422-428.

Stanley, K. O. and Miikkulainen, R. 2004. “Competitive Coevolution Through Evolutionary Complexification.” Journal of Artificial Intelligence Research 21: 63-100, 2004. Abstract

Taylor, S. V., Walter, K. U., Kast, P. and Hilvert, D., 2001. “Searching sequence space for protein catalysts.” PNAS 98 (19), 10596-10601. PubMed

Vrba, E. S. and S. J. Gould. 1986. “The hierarchical expansion of sorting and selection: sorting and selection cannot be equated.” Paleobiology 12:217-228.

27 TrackBacks

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Dr. Jonathan Wells Jonathan Wells is a Senior Fellow at The Discovery Institute's Center for the Renewal of Science and Culture who holds two Ph.D's, one in Molecular and Cell Biology from the University of California at Berkley, and... Read More

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Liars from Deinonychus antirrhopus on January 17, 2005 12:57 PM

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216 Comments

Very Nice. Congratulations to all involved.

My favorite example which shows what a moron Mr. Meyer is can be found at http://www.discovery.org/scripts/vi[…]&id=1090, where he writes

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

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

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

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

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

Syntax Error: mismatched tag at line 11, column 122, byte 2147 at /usr/local/lib/perl5/site_perl/5.12.3/mach/XML/Parser.pm line 187

From Palm Beach Atlantic website we read

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

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

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

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

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

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

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

Hello? Anyone there, Paul?

RBH

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

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…

Alan, Nick, Wesley, thanks for the article.

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

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

DS,

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

Thanks to Wesley, Nick and Alan for this review

Wesley et al., Wrote:

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

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

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

Meyers Wrote:

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

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

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

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

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

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

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

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

Abstract:

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

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?

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

Syntax Error: mismatched tag at line 9, column 2, byte 1390 at /usr/local/lib/perl5/site_perl/5.12.3/mach/XML/Parser.pm line 187

'Da Boyz Wrote:

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

Tnbpursutd euckilecuitn tiioismdeetneia niophvlgorciizooltccilhseema er [1]

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

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

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

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

I would be careful about how you put this.

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

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

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

This is kind of nit-picky, but FYI:

'Da Boyz Wrote:

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

(emphasis added)

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

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

GWW Wrote:

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

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

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

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.

Pim van Meurs Wrote:

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

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

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

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.

Steve (Reuland) writes,

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

Taylor et al. 2001 (PubMedfreely online) conclude with the following paragraph:

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

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

Frank J writes,

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

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

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.

~DS~ (Comment #6804) Wrote:

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

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

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

Alan Gishlick et al Wrote:

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

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

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

Genetic Algorithms and Evolutionary Computation

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.

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

Pasquale Wrote:

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

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

Aha I got the basics right and the specifics wrong

Glenn Morton reports

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

and the abstract

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

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

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…

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?

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

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This page contains a single entry by Wesley R. Elsberry published on August 24, 2004 5:56 PM.

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