The scientific study of evolution is filled with controversies. That was one of the messages coming out of a two-day symposium on the latest in research from the field that was hosted by Rockefeller University last week. I'll discuss the scientific details of some of the talks separately, but it's worth analyzing these controversies in light of the "academic freedom" bills that are being considered by a number of states, which purport to protect teachers who discuss controversies regarding evolution.

Nationwide, nearly half a dozen states are considering variants of such bills, some of which throw in the origin of life and climate change for good measure. Legislators in Florida recently introduced such a bill in response to new educational standards that were the first to formalize the teaching of evolution. Althought two incompatible bills passed the state House and Senate, they died when the legislature went out of session; similar measures are still pending in other states. These bills appear to have originated at the pro-Intelligent Design thinktank the Discovery Institute, and constitute part of its latest effort towards reducing the teaching of evolution in public schools.

Manufacturing controversies

So, might Discovery actually be on to something here? It's worth doing a comparison of the controversies they'd like to see taught with the topics that are considered controversial within the actual scientific community. It's pretty easy to get a sense for what Discovery thinks is a controversy by looking at Explore Evolution, the textbook they have created in the hope of encouraging schools to teach it. Those ostensible controversies fall into three major groups: existence of common descent, power of natural selection, and the existence of proteinaceous machines.

Common Descent: Discovery presents common descent as controversial exclusively within the animal kingdom, as it focuses on embryology, anatomy, and the fossil record to raise questions about them. In the real world of science, common descent of animals is completely noncontroversial; any controversy resides in the microbial world. There, researchers argued over a variety of topics, starting with the very beginning, namely the relationship among the three main branches of life.

Russ Doolittle presented an analysis based on individual folds in proteins that clearly resolved the Bacteria, Archaea, and Eukaryotes, while a distant relative, Ford Doolittle, argued that the prevalence of horizontal gene transfer at the bacterial level made any such trees questionable, or at best uninformative. Meanwhile, Thomas Cavalier-Smith argued forcefully that gene-based trees miss out on significant evolutionary events, such as the transition that gave the Archaea a radically different membrane chemistry. Almost anyone who touched on the subject (and there were several speakers that did) gave a confused picture of what the genome of a Eukaryote looked like before it first took a mitochondrion on board.

These are areas of real controversy; Cavalier-Smith seemed to introduce half his slides by pointing how they showed where others had gone wrong. But it's worthwhile noting that there is essentially no overlap with the areas that Discovery would like to pretend are controversial. Ford Doolittle, in fact, made repeated reference to the fact that there were areas that phylogenetic trees made sense for tracing common descent, and that the animal kingdom was one of them.

Natural Selection: Explore Evolution seems to think a reply can be made to the arguments in favor of natural selection. Based on the symposium, the scientific community clearly doesn't. Selective pressure made appearances in nearly every session. Selection for self-replicating RNAs and for enclosing biochemical precursors within membranes were central to the origin of life work of Gerald Joyce and Jack Szostack, respectively. At the other end of the spectrum, the researchers exploring human evolution (Katherin Pollard, Bruce Lahn, and Svante Pääbo) spoke of the challenges of identifying signs of selection amidst the genetic drift that's occurred within the genomes of mammals in general and primates in particular.

Here, it was clear that there simply is no controversy. In contrast to the arguments over bacterial trees and the origin of eukaryotes, none of the researchers felt compelled to explain or justify their focus on the role of mutation and selective pressure. Concerns, when they arose, were simply focused on identifying the consequences of selection. As such, Discovery's focus on presenting a controversy here seems hallucinatory.

Molecular Machines: Michael Behe, a Discovery fellow, has advanced the argument that some aspects of cellular life are analogous to machinery, and thus must have required the same attentive design that a machine does. This proposal is flawed on a number of levels, and has not gained enough traction within the biological community to rise to the level of anything beyond a distraction. But items Behe might consider molecular machines did appear in the talks, and their role was informative.

The proteasome is one complex of dozens of proteins that was mentioned in a couple of talks. Despite the enormous complexity and large number of specialized proteins in a proteasome, evolution readily explains its origins through gene duplication and specialization. Simplified forms, with fewer proteins, exist in Archaea and Bacteria. Not only are these simple versions of the proteasome an indication of its evolution, the gradual increase in its complexity allowed researchers to use it to infer evolutionary relationships among the three branches of life.

Similar analyses were performed with actin and tubulin, essential components of the complex skeletons that support Eukaryotic cells. Structural relatives of these genes appear in Bacteria and Archaea, where they appear to act to separate cell components even in the absence of a complex skeleton. An essential component of some Eukaryotic RNA interference systems also shows up in Archaea, where it does something completely unrelated to RNA interference. In all of these cases, parts of the supposedly designed machinery exist elsewhere, where they perform more limited but often related roles. Their use in determining evolutionary relationships didn't so much as elicit a blink from an audience of scientists.

Taking controversy to the classroom

Other controversies within the evolutionary field popped up in the discussion. Bruce Lahn reiterated his controversial proposal that an allele of a key gene in human brain development came via Neanderthals. Andrew Roger suggested that secondary and tertiary endosymbiosis may have scrambled parts of the eukaryotic family tree. Peter Holland, who works on amphioxus, described some confusion about the precise location of the base of the chordate tree, while Ulrich Technau mentioned that the single axis that exists in Cnidarians may not be equivalent to either of the two axes of bilaterians.

Evolution clearly has no shortage of controversies. But none of those controversies involve the basic principles of evolution, and all of them operate within a framework where random mutation and selection play a key role in creating diverse species that are related by common descent. It's clear that the Discovery Institute is trying to introduce controversies that don't exist, while ignoring those that do. That's why the academic freedom bills it's promoting are such dangerous things; while supposedly promoting intellectual analysis, they're actually an attempt to pave the way for misinformation to enter the scientific classroom.

Is there room for the real controversies in the classroom of public schools? Maybe, but I'm not in any way convinced. I would be pleasantly surprised if the average high school student left knowing what horizontal gene transfer is, what the proteasome does, or the significance of the Archaea. Understanding how those things play out within the current scientific understanding of evolution is going to be beyond all but the most advanced students. Teaching even the real controversies may simply be bad pedagogy.