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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.