The Catechism Versus the Data (Part 5): When Did Neo-Darwinism Become a Dirty Word?

This is the fifth installment of a blog series responding to John Timmer's online review of the supplementary biology textbook Explore Evolution (EE). The first part is here, the second here, the third here, and the fourth here.

 

5. When Did Neo-Darwinism Become a Dirty Word?

Timmer objects to Explore Evolution's subtitle, "The Arguments For and Against Neo-Darwinism," claiming that "[d]uring the roughly 20 years I was directly involved in biology research, I'd never come across the term 'Darwinism.'" EE's subtitle actually uses the word "neo-Darwinism," not "Darwinism," but regardless, Timmer's complaint reveals more about his own ignorance than it does about any inaccuracy on the part of EE. Terms like "Darwinism" and "neo-Darwinism" (or similar cognates like "Darwinian," "neo-Darwinian," or "Darwinist") regularly appear in both the technical scientific literature and textbooks about evolution, and they are repeatedly employed by contemporary scientists and philosophers of science.

In a book published just last year, for example, University of Chicago evolutionary biologist Jerry Coyne repeatedly labeled the modern theory of evolution as "neo-Darwinism":

The modern theory of evolution, called neo-Darwinism in light of 150 years of post-Darwin research, has four parts... [p. 6] Neo-Darwinism, like the theory of chemical bonds, has graduated from theory to fact. [p. 6] Neo-Darwinism is thus a robust scientific theory, explaining a vast body of evidence, generating predictions that have been amply confirmed, and vulnerable to falsification, but showing itself more than capable of withstanding all scrutiny so far. [p.12] (Jerry Coyne, "Intelligent Design: The Faith That Dare Not Speak Its Name," in John Brockman, ed., Intelligent Thought: Science Versus the Intelligent Design Movement (New York: Random House, 2007), pp. 3-23.)

Coyne is far from an isolated example. The technical scientific literature is rife with terms such as "Darwinism" and "neo-Darwinism." Perhaps Timmer is unfamiliar with this literature, but even a brief search of leading scientific journals would have revealed hundreds of references to "Darwinism," "neo-Darwinism," and their cognates. Since 1980, there have been more than a thousand references to "Darwinism" and cognate terms in the journal Science alone. Another 1,549 references have appeared in the journal Nature.

The usage of these terms is also commonplace in textbooks on evolution. Douglas Futuyma's 2005 textbook Evolution defines "neo-Darwinism" as "[t]he modern belief that natural selection, acting on randomly generated genetic variation, is a major, but not the sole, cause of evolution." (Futuyma, 2005, p. 550) Donald Prothero's recent text, Evolution: What the Fossils Say and Why it Matters, similarly references "Neo-Darwinism," observing that it "extrapolates all larger evolutionary changes (macroevolution) as just microevolution writ large." (Prothero, 2007, p. 94) Strickberger's textbook Evolution equates "neo-Darwinism" with the "modern synthesis," defining it as "a change in the frequencies of genes introduced by mutation, with natural selection considered as the most important, although not the only, cause for such changes." (Strickberger, 2000 p. 649)

If terms like "Darwinism" or "neo-Darwinism" are unsavory to Timmer, then his beef is with his fellow evolutionists, not the writers of EE.

The Catechism Versus the Data (Part 4): The Origin of the Tetrapods

This is the fourth in a blog series responding to John Timmer's online review of the supplementary biology textbook Explore Evolution. The first part is here, the second here, and the third here.

4. Well, the Tetrapods are Monophyletic: Only "Ph.D." Malcolm Gordon Disagrees, Right?

Timmer accuses EE of what he calls the "find a Ph.D." approach: "if you look hard enough, you can find someone with a PhD who will say anything." In this instance, Timmer disparages the minority viewpoint of UCLA biologist Malcolm Gordon (a tenured professor, actually), who has argued that the tetrapods may have evolved polyphyletically (i.e., more than once).

It's the textbook catechism again: why bother with citing some lone dissenter like Gordon? Timmer counts noses, and the sum determines what is worthy of attention. Claim that the scientists cited in EE pale in numbers to those who support the catechismal view, and voilá, case closed. There is no controversy and we can all go home.

This is science by census. But does Timmer really want us to believe that numbers of scientists, and not the evidence and how best to interpret it, is what matters?

As it happens — to play along with Timmer's counting-noses game — Gordon developed his view with the late UCLA paleontologist Everett Olson (a former president of the Society of Vertebrate Paleontology), in Invasions of the Land: The Transitions of Organisms from Aquatic to Terrestrial Life (1995), a book published by Columbia University Press. More recently, Gordon articulated his ideas with the Australian paleontologist John Long. But, as Timmer says, these are just another couple of Ph.Ds — you know: find a Ph.D, he'll say anything.

So let's look at the evidence. A review of the literature shows that there is much more to this story than Timmer lets on.

Surveying the problem of the overall picture of tetrapod evolution, Gordon (1999, 338) writes:

Despite the large volume of publication, however, the underlying reality remains unchanged: everything we know is circumstantial and indirect, and what actually occurred remains unknown.

This sentiment was later confirmed in part by Takezaki et al. (2004). They compared sequences of 44 nuclear genes encoding over 10,400 positions in their attempts to resolve the phylogenetic relationships between the coelacanth, lungfish and tetrapod lines. They write:

Apparently, the coelacanth, lungfish, and tetrapod lineages diverged within such a short time interval that at this level of analysis, their relationships appear to be an irresolvable trichotomy. (2004, 1512)

These findings amplify what Gordon (1999, 339) said five years earlier:

Thus there are significant variations regarding conclusions derived from molecular biological data sets, and differences between various parts of the morphological and molecular data sets.

Gordon goes on:

The living lungfishes and the coelacanth represent tiny, randomly selected remnants of ancient groups that were numerous, varied, and widely distributed in the Devonian. One can only wonder at how accurate, or even relevant, the relationships that we estimate to exist between these organisms today may be with respect to the actual phylogenetic relationships of their basal groups. (1999, 340)

Gordon's main point is that the biogeographic distribution of the tetrapods in the Late Devonian, coupled with the incongruence of molecular data, coupled with a knowledge of the range of environments occupied by early tetrapods, support the contention that the tetrapods may have arisen polyphyletically. The assumed sarcopterygian progenitors in the Late Devonian had low offspring dispersal ranges and limited geographic ranges, yet the early tetrapods they supposedly evolved into also occupied separate and limited geographic ranges, and had limited dispersal. Many of the earliest tetrapods inhabited environments from shallow marine tidal areas to brackish environments to fresh (Blieck et al., 2007).

However, these groups were also widely separated without any apparent environmental continuity between them at the time of their evolution. Late Devonian tetrapod species are "highly endemic" (Clack 2006, 184), meaning that they are "restricted to the locality or region where they have been collected" (Blieck et al. 2007, 229). The fossils come from sites many thousands of miles apart.

Thus, the phylogenetic series reconstructed in familiar evolutionary cladograms include taxa rarely found together as fossils. Cambridge University paleontologist Jennifer Clack, an expert on this evidence, notes that "taking the tetrapods sites worldwide, one thing is obvious: they lie scattered over the globe in places that were remote from each, on separate continents, even in the Devonian" (2002, 99). "These forms," note other paleontologists working on the puzzle (Zhu et al. 2002, 720), "seem to have achieved worldwide distribution and great taxonomic diversity within a relatively short time." This paleo-biogeographical puzzle raises significant evidential difficulties for monophyletic (single origin) scenarios.

Weighing these paleo-biogeographic challenges, Clack (2002, 99) considers the possibility of polyphyletic tetrapod origins, but then dismisses that hypothesis as less likely than the monophyletic scenario:

The alternative, that tetrapods radiated independently from lobe-fins that had originally been euryhaline [salt-tolerating] and subsequently lost their salt tolerance, seems even more unlikely and countered by the detailed similaritthat are found in the tetrapods now known from over the world.

Here Gordon disagrees — and we have a case study in the fragility of the "consilience" of data lauded by Timmer.

Timmer argues that a "consilience" of different lines of evidence strongly favors the catechismal (monophyletic) tale, and faults EE for neglecting this consilience (e.g., the putatively mutually reinforcing molecular and anatomical data). He complains, for instance, that EE says nothing about the methods of cladistics, the approach within biological systematics that organizes taxa by shared characters: "A description of cladistic methods," he writes, "doesn't appear at all in EE."

But it is an open question whether molecules do reinforce morphology. Furthermore, as Gordon wryly observes (1999, 339) — and as is generally known among systematists — cladistic methods presuppose common ancestry:

First, since the analyses [of tetrapod relationships] were all done cladistically, the underlying phylogenetic model in all cases was monophyletic. A single "main line" of tetrapod evolution is assumed to have existed in all cases. Possible polyphyletic scenarios were methodologically and philosophically excluded as implausible.

The widely-used software packages that implement cladistic methods will try to arrange molecular and anatomical data (characters) into a monophyletic tree, come what may. Some of the characters will end up as homologies — i.e., as similarities caused by common ancestry — and others as homoplasies — i.e., as similarities not caused by common ancestry — but the assumption that a monophyletic tree exists somewhere in the data is not up for grabs. Cladistic methods generate monophyletic trees, because they can't help but make such trees: that's what the methods were designed to do.

As Gordon's skepticism about cladistics indicates, behind the public proclamations that molecules confirm morphology, which Timmer recites, is an extensive scientific debate about the dangers of circularity in systematic methods. These questions are well-known to working systematists.

Could students hear about these questions? Why not? Is the catechism really more important?

EE concerns itself, therefore, with the logically prior question of "How do biologists infer (know) that all organisms, or some group of organisms, share a common ancestor?" That's a question students need to be able to answer, weighing the evidence pro and con, before they take up the merits of cladistics (which assumes the truth of monophyly as a first principle).

Up next: When did "Neo-Darwinism" Become a Dirty Word?

References

Blieck, A., G. Clement, H. Blom, H. Lelievre, E. Luksevics, M. Streel, J. Thorez and G. C. Young. 2007. The biostratigraphical and palaeogeographical framework of the earliest diversification of tetrapods (Late Devonian). Geological Society, London, Special Publications volume 278. pp. 219-235.
Clack, Jennifer. 2002. Gaining Ground: The Orign and Evolution of Tetrapods. Bloomington, IN: Indiana University Press.
Clack, Jennifer A. 2006. The emergence of early tetrapods. Palaeogeography, Palaeoclimatology, Palaeoecology 232:167-189.
Gordon, Malcolm S. 1999. The Concept of Monophyly: A Speculative Essay. Biology and Philosophy 14:331-348.
Long, John A. and Malcolm S Gordon. 2004. The greatest step in vertebrate history: a paleobiological review of the fish-tetrapod transition. Physiol. Biochem. Zool. 77:700-19.
Takezaki, Naoko, Felipe Figueroa, Zofia Zaleska-Rutczynska, Naoyuki Takahata and Jan Klein. 2004. The Phylogenetic Relationship of Tetrapod, Coelacanth, and Lungfish Revealed by the Sequences of Forty-Four Nuclear Genes. Molecular Biology and Evolution 21:1512-1524.
Zhu, Min, Per E. Ahlberg, Wenjin Zhao, and Liantao Jia 2002. First Devonian tetrapod from Asia. Nature 420:760-1.

The Catechism Versus the Data (Part 3): The "Fact" of Evolution

This is the third in a blog series responding to John Timmer's online review of the supplementary biology textbook Explore Evolution. The first part is here, and the second here.

3. Open Your Catechism to Page One: The Fact of Evolution

So what is the "fact" of evolution? Timmer argues that "aspects of the theory [of evolution] can be safely treated as fact," and in support of this point, cites a paper by the Canadian geneticist T. Ryan Gregory, entitled "Evolution as Fact, Theory and Path."

Here is how Gregory (2008, 49) defines the "fact" of evolution:

The notion that species may change through time and that living organisms are related to one another through common descent—species have changed over time and are connected by descent from common ancestors.

Change through time, descent of organisms from common ancestors -- hey, that sounds familiar:

Evolution #1: "Change over time" First, evolution can mean that the life forms we see today are different than the life forms that lived in the past. (EE, p. 8) —we have to make an important distinction between the terms common descent and Universal Common Descent. You may think the terms mean the same thing. They don't. As we've just seen, it's possible to think that some organisms share a common ancestor without thinking that all organisms are descended from a single common ancestor. (EE, p. 10)

If the "fact of evolution" means simply change over time and common descent, then EE affirms the fact of evolution. But that's hardly surprising: so does almost any biologist, from the staff of the young-earth Institute for Creation Research to the curators of the American Museum of Natural History.

That's not what "the fact of evolution" means to most evolutionary biologists, however. The standard view is Darwin's single (monophyletic) tree, rooted in LUCA:

The millions of diverse living species we find around us in the modern world are descended from a common ancestor that lived in the remote past. (Ayala and Valentine 1979, 1)

Evolution asserts that the pattern of similarity by which all known organisms may be linked is the natural outcome of some process of genealogy. In other words, all organisms are related. (Eldredge and Cracraft 1980, 2)

It is important to realize at the outset that evolution is not "just a theory." It is, again, a theory and a fact—[N]ew forms of life are continually generated by the splitting of a single lineage into two or more lineages. This is known as "speciation." About five million years ago, a species of primates split into two distinct lineages: one leading to modern chimpanzees and the other to modern humans. And this ancestral primate itself shared a common ancestor with earlier primates, which in turn shared a common ancestor with other mammals. The earlier ancestor of all mammals shared an even earlier ancestor with reptiles, and so on back to the origin of life. Such successive splitting yields the common metaphor of an evolutionary "tree of life," whose root was the first species to arise and whose twigs are the millions of living species. Any two extant species share a common ancestor, which can in principle be found by tracing that pair of twigs back through the branches to the node where they meet. (Coyne 2005, 23; second emphasis added)

If "all organisms are related" (meaning "any two species share a common ancestor" in a universal evolutionary tree) because they "descended from a common ancestor," then the fact of evolution means Universal Common Descent, or Darwin's Tree of Life: "all the organic beings which have ever lived on this earth have descended from some one primordial form" (1859, 484).

Universal Common Descent is a "fact," however, coming under increasing skeptical scrutiny from evolutionary biologists, as Timmer saw first-hand at the Rockefeller University symposium on evolution this past May. Since the first edition of EE was published in 2007, prominent biologists such as Craig Venter, Eugene Koonin, and William Martin have added their doubts to those of Carl Woese, W. Ford Doolittle, Michael Syvanen, and the other evolutionary skeptics of Universal Common Descent cited in EE.

Consider, for instance, Eugene Koonin's "biological big bang" proposal:

—it is generally assumed that, in principle, the TOL [Tree of Life] exists and is resolvable although, in practice, full resolution might never be attained and, furthermore, might not even be particularly important for understanding the actual events that transpired during the respective transitional stages.

Here, I argue for a fundamentally different solution, i.e., that a single, uninterrupted TOL does not exist, although the evolution of large divisions of life for extended time intervals can be adequately described by trees. (2007, 3; reference numbers omitted)

Or Craig Venter:

We're just at the tip of the iceberg of what the [genetic] divergence is on this planet... One question is, can we extrapolate back from this data set to describe the most recent common ancestor. I don't necessarily buy that there is a single ancestor. It's counterintuitive to me. I think we may have thousands of recent common ancestors and they are not necessarily so common. (Brockman 2007, p. 42)

Or William Martin:

Traditional approaches to characterizing prokaryote genome evolution focus on the component of the genome that fits the metaphor of a tree. The issue is how large that component is over the fullness of evolutionary time. Although there can be little doubt that a considerable component of prokaryote genome evolution over recent evolutionary time scales is fundamentally treelike in nature, differences in gene content exceeding 30% among individual strains of E. coli demonstrate that LGT [lateral gene transfer] has substantial impact on genome evolution even at the species level. Our findings indicate that, over long evolutionary time scales, the cumulative role of LGT leaves almost no gene family among prokaryotes untouched....When all genes and genomes are considered, the tree paradigm fits only a small minority of the genome at best; hence, more realistic computational models for the microbial evolutionary process are needed. (Dagan et al. 2008, p. 10043; note numbers omitted)

Now this is a case where the catechism is going to lead students straight away from interesting puzzles, for reasons having nothing to do with intelligent design: both Koonin and Venter are on record as strongly opposing ID. When Carl Woese -- for what it's worth, another opponent of ID -- argues that "the time has come for Biology to go beyond the Doctrine of Common Descent" (2002, p. 8745), will students be allowed to learn about the molecular data motivating his argument?

Or will it be back to the catechism? Incidentally, Timmer fumbles Woese's argument, saying it "partly hinges on definitions, rather than some objectively apparent biological property." But Woese's case rests on objective molecular characters, their apparent incompatibility within a single common ancestor, and the non-homology of key proteins across domains (see Roberts et al. 2008). The Archaea, Eucarya, and Bacteria were defined on the grounds of molecular data, not verbal distinctions.

Fears about giving aid and comfort to ID advocates, no matter how misplaced those fears may be, will, if given their head, irreparably damage science education in America. Teaching the theory of evolution responsibly entails far more than giving students a familiar catechism to recite.

Up next: The Origin of the Tetrapods

References

Ayala, Francisco and James Valentine. 1979. Evolving: the theory and processes of organic evolution. Menlo Park, CA: Benjamin/Cummings Pub. Co.
Brockman, John, ed. 2007. Life: What A Concept! An Edge E-Book, available at http://www.edge.org/documents/life/Life.pdf.
Coyne, Jerry. 2005. The faith that dares not speak its name. The New Republic, 22/29 August 2005, pp. 21-33.
Dagan, Tal, Yael Artzy-Randrup, and William Martin. 2008. Modular networks and cumulative impact of lateral transfer in prokaryote genome evolution. PNAS 105:10039-10044.
Darwin, Charles. 1859. On the Origin of Species. London: John Murray.
Eldredge, Niles and Joel Cracraft. 1980. Phylogenetic Patterns and the Evolutionary Process. New York: Columbia University Press.
Gregory, T. Ryan. 2008. Evolution as Fact, Theory, and Path. Evolution: Education and Outreach 1:46-52.
Koonin, Eugene. 2007. The Biological Big Bang model for the major transitions in evolution. Biology Direct 2:21.
Roberts, E., A. Sethi, J. Montoya, C.R. Woese, and Z. Luthey-Schulten. 2008. Molecular signatures of ribosomal evolution. PNAS 105:13953-8.
Woese, Carl. 2002. On the evolution of cells. PNAS 99:8742-77.

The Catechism Versus the Data (Part 2): Much Ado About A Footnote Citing Christian Schwabe

This is the second in a blog series responding to John Timmer's online review of the supplementary biology textbook Explore Evolution. The first part is here.

2. Much Ado About A Footnote Citing Christian Schwabe

One theme of EE addresses differing views among evolutionary biologists about Darwin's Tree of Life, i.e., the theory of the universal common ancestry of all organisms on Earth: more precisely, the monophyly of terrestrial life, rooted in the Last Universal Common Ancestor, or LUCA. While the majority position within evolutionary biology endorses monophyly, a growing minority of workers argue for multiple independent origins, or polyphyly (see below). It's an important controversy, well worth the attention of textbooks.

But Timmer accuses EE of a "bait-and-switch" move in describing this controversy. By "lumping—together in a single footnote" several scientists with very different views about the overall pattern of life's history, he argues, EE tries for "borrowed credibility," misleading its readers about the true outlines of the current mono- versus polyphyly debate.

Timmer is particularly exercised by EE's inclusion of the ideas of Professor Christian Schwabe of the Medical University of South Carolina, whose publications he calls "borderline deranged." Given the space Timmer uses to criticize Schwabe, one might think that the latter's ideas receive significant attention in EE.

No, actually: the book mentions Schwabe exactly once, in a single footnote (which cites three of his papers). Timmer claims that EE lumps Schwabe together with other, better-known scientists, such as National Academy of Sciences member Carl Woese, as advocates of the polyphyletic view, without informing the reader about the different number of separate origins postulated by their respective theories.

But here is the actual EE footnote (p. 11):

Scientists who support a polyphyletic view differ on how many trees one should expect to find in the "orchard" of life. Some, such as microbiologist Carl Woese of the University of Illinois, argue that life on earth is descended "not from one, but from three distinctly different cell types" ("On the evolution of cells," Proceedings of the National Academy of Sciences 99 (2002):8742- 77; 8746). Others, including Malcolm Gordon of UCLA and Christian Schwabe of the Medical University of South Carolina, think there might be a greater number of separate trees.

And that's it. No misdirection or lumping: Woese says three independent origins; Schwabe and Gordon say more. Anyone who reads the EE footnote should grasp that scientific opinions about polyphyly differ.

Let's go back, however, to Timmer's charitable label for Schwabe, "borderline deranged," as it gives us our first opportunity to address the catechism versus data dilemma in more depth.

Timmer acknowledges that "every couple of years, [Schwabe] publishes a paper in which he argues in favor" of his "borderline deranged" ideas. These, however, "are not scientific controversies," Timmer claims, but "actually opinions that have barely registered within the wider scientific community."

Really? To see how Schwabe's research raises challenges to monophyly and universal common ancestry, consider this excerpt from one of his papers cited in EE:

Against this background of high variability between relaxins from purportedly closely related species, the relaxins of pig and whale are all but identical. The molecules derived from rats, guinea pigs, man and pigs are as distant from each other (approximately 55%) as all are from the elasmobranch's [shark's] relaxin. — Insulin, however, brings man and pig phylogenetically closer together than chimpanzee and man. (Schwabe 1994, 171-2)

According to Timmer's catechism, however, none of this is worth talking about, because Schwabe's ideas are just too crazy for serious consideration.

But someone forgot to tell journal editors and referees. Schwabe's "deranged" ideas -- coming from a tenured professor of biochemistry, and based in part on the puzzling features of relaxin (not "reflexin," as Timmer writes), and its phylogenetic distribution -- have cleared editorial review at the following journals:

• Christian Schwabe and Gregory Warr, "A Polyphyletic View of Evolution: The Genetic Potential Hypothesis," Perspectives in Biology and Medicine 27 (1984):465-85.

• Christian Schwabe, "On the validity of molecular evolution," Trends in Biochemical Sciences 11 (1986):280-3.

• C. Schwabe and E.E. B¸llesbach, "Relaxin: structures, functions, promises, and nonevolution," FASEB Journal 8 (1994):1152-60.

• Christian Schwabe, "Theoretical limitations of molecular phylogenetics and the evolution of relaxins," Comparative Biochemistry and Physiology 107B (1994):167-77.

• Christian Schwabe, "Genomic Potential Hypothesis of Evolution: A Concept of Biogenesis in Habitable Spaces of the Universe," The Anatomical Record 268 (2002):171-179.

• Christian Schwabe, "Chemistry and Biodiversity," Chemistry and Biodiversity 1 (2004):1584-9.

Were these papers ignored? No: the relaxin puzzles are well-known; as other biologists who study relaxin observe (Wilkinson et al. 2005, 3),

Relaxin evolution has confounded researchers for decades. High sequence variability in relaxins across closely related species is a well-known feature of this peptide, however startling similarities have been observed between very distant species such as pigs and whales.

Nor have Schwabe's heterodox ideas about the evolutionary process escaped critical notice. His 2004 paper in the journal Chemistry and Biodiversity was followed immediately -- in the very same issue -- with a critical reply, as was the case with Schwabe's 1999 FASEB Journal paper. Hafner and Korthof (2006) argue vigorously against Schwabe's position, and Wilkinson et al. (2005, 9) note that "relaxin evolution has been the centre of much controversy," which they believe their approach has been able to resolve.

"The centre of much controversy" -- but Timmer says (falsely) that no one cares, because it's all "borderline deranged" anyway. Thus, what might be an interesting case study, supported by multiple peer-reviewed publications, pro and con, about how to interpret molecular evidence in relation to the tree of life and its origin, would be tossed aside by Timmer, in favor of the catechism: the "fact" of evolution, never mind the data.

As we mentioned above, EE cites Schwabe in a single footnote. His name never appears in the main text. A reader who followed up the Schwabe citations, however, would find a rich controversy, likely to stimulate thinking.

And that's good, all worries about the complicated data notwithstanding.

Up next: The "Fact" of Evolution References

Hafner, Martin and Gert Korthof. 2006. Does a "500 million-year-old hormone" disprove Darwin? The FASEB Journal 20:1290-2.

Schwabe, Christian. 1994. Theoretical limitations of molecular phylogenetics and the evolution of relaxins. Comparative Biochemistry and Physiology 107B:167-77.

Wilkinson, Tracey N., Terence P. Speed, Geoffrey W. Tregear, and Ross A.D, Bathgate. 2005. Evolution of the relaxin-like peptide family. BMC Evolutionary Biology 5:14.

The Catechism Versus the Data: A Reply to John Timmer about Explore Evolution (part 1)

This is the first in a series of blog entries replying to John Timmer's online critique of the supplementary biology textbook Explore Evolution, posted by Paul Nelson on behalf of the book's production team.

1. Introduction: Sending Him the Book Didn't Help

On September 24, 2008, biologist and science writer John Timmer published an online review of the supplementary biology textbook Explore Evolution (EE). Timmer had previously written about EE without having read it, so Discovery Institute sent him a copy.

Alas -- having EE in his hands improved neither the quality of Timmer's writing about the book, nor indeed his coverage of the relevant science. In fact, Timmer so baldly misrepresents both the content of Explore Evolution, but especially the associated scientific evidence and controversies, that his review perfectly illustrates the need for a book like EE.

Our reply will reverse the order of Timmer's review. He starts by using nearly 1200 words to speculate about the motives of EE's authors. Since Timmer did not contact any of us, his speculations -- such as "the authors know precisely the sort of conclusions they'd like everyone to reach" -- cannot be better than groundless. We shall comment briefly in the last part of our reply, however, on a couple of his more philosophical points.

We want to focus on the science. Timmer's review reflects a deep dilemma that increasingly confronts educators in biology. The devil is in the details -- the data -- but if organizations such as the National Academy of Sciences, or the National Association of Biology Teachers, or the American Association for the Advancement of Science, don't want students to hear about the devil, namely, about challenges to accepted theory, then they will have to omit -- i.e., censor -- the data, namely, the evidence and how biologists variously interpret it.

Hence, many scientific publications that raise interesting questions about evolution will never see the inside of a classroom. The questions are too risky. Science education will become a catechism, diverging from science itself, because the questions now being raised by many evolutionary biologists cut ever closer to claims long held to be "fact."

This dilemma -- call it the catechism versus the data -- does not concern intelligent design, which has already found its way into public attention without science classroom endorsement. The dilemma concerns, rather, how evolution is taught. When students hear that "biologists today know that natural selection explains the origin of complexity," or "all biologists agree that every living thing descended from a single common ancestor" -- stock claims in many biology textbooks -- they are being miseducated about the actual state of the science.

And that is wrong.

In what follows, then, we rebut Timmer's hopelessly inaccurate construal of the contents of EE, and the evidence on which the book rests.

Up next: Much Ado About a Footnote Citing Christian Schwabe