Wednesday, September 21, 2005

Understanding Evolution

Berkely has launched their new and improved Understanding Evolution page. It's colourful, inviting, uses a tasteful number of flash animations, and still looks professional. It's very easy to navigate, but they really ought to put the beef near the top. A guided tour through evolution is what people need to see.

Unfortunately, there are a couple problems I see with this site. It spends too much time presenting the formulation of evolution. That is, it presents too much about how "we think" evolution works. I agree this is important, because creationists have done such a fine job of creating straw men out of age-old public misconceptions. Unfortunately, much of what I see will re-inforce creationist prejudices that we are just spoon-feeding them an "alternate truth" to the one they were initially fed. Which "truth" do you think they'll go for?

The presentation of homology as evidence for evolution is, I'm sorry to say, bad, bad, bad. I'm going to give some credit here to creationists in order to point out why this is bad. First, the Berkely site starts with the classic example of tetrapod limbs. While I agree it's a very ostensible example, one must remember that an evolution-weary mind is approaching this with doubts and reservations. Creationists already have a response to this and this new presentation makes no pre-emptive strikes..

Here's the problem, the skeptical student (doubful, but interested in knowing more about evolution) is faced with a dichotomy:
similar structures are caused by a common ancestor
similar structures are caused by a common designer

Why is one of these statements better than the other?

To most biologists, it's clear why the first is a better explanation. It actually offers a reason to expect the pattern, whereas the second relies on some statement about the capriciousness of the deity. To the general (and perhaps somewhat skeptical) reader, this is not so clear. In fact, both of the above statements could be viewed as begging the question (i.e. "circular reasoning").

The important issue is not simply one of similarity, but rather of similarity distributions. To which animals do these sorts of limbs belong? Why don't flies or starfish have limbs with these bones in them? Such limbs always belong to special subset of vertebrate animals. The emerging picture is one of a nested hierarchy which really is the key issue. Since nested hierarchies are a mathematically necessary consequence of any branching process (i.e. common ancestry) we have a priori reasons to expect such a pattern to emerge. This is the actual theoretical framework that is the other half of the agument. The reasons for expecting this.

In the context of a nested hierarchy, the distribution of limb skeletons is precisely and explicity predicted by a theory of common ancestry. What students are never presented with first is a picture of nested hierarchies. They're thus not presented with a picture of the evidence for common ancestry. Instead, they're first presented with a picture of a tree (the inference) and a bunch of characters mapped on (the evidence). To a naïve and dubious young student, this looks as tenuous as any crackpot seminar or tract booklet. It's easily charicatured as selective data usage and has become a favourite of creationist attacks on evolution education. Show the kids the evidence first, then show them how the conclusions came from that evidence.

If you're going to present limb homologies to students, then you have to have other evidence to re-inforce your conclusion. Otherwise, you're just going to get the "common designer" crap in return. The theory of evolution is far too elegant to be in competition with such an illogical argument.
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Tuesday, September 20, 2005

Little Piggies of Urodeles

A recent set of exchanges between myself and a friend brought me upon this Answers in Genesis article. In it, Jonathan Sarfati (an acid-tongued spokesperson for AiG) claims that the digit development of frogs is completely different from that of all other tetrapods. In it, he claims, frogs grow their digits from developing buds. PZ Myers responded to Sarfati's claims about bird/dinosaur digit homology and amphibian digit development.

A minor correction is worth publishing. In the article Myers states:
We’ve got a pretty good handle on the outline of limb development in multiple tetrapod lineages now, and they all use the same tools. Contrary to Sarfati’s implication, they all have apical ectodermal ridges (with some rare exceptions in a few highly derived, direct-developing frogs) and zones of polarizing activity, they all use the same set of molecules, including FGF-4 and FGF-8 and the same Hox genes and retinoic acid and BMPs. If there’s one thing we know, it’s that limb development is dazzlingly well conserved.

Despite the fact that I think most of Myers's article is a wonderful vulgarization of limb development, this last part is an overstatement.

It is true that many aspects of limb and digit development in tetrapods is remarkably well conserved throughout tetrapods, but it is not true that all tetrapods have an AER, it is also not true that they all use apoptosis to create the interdigital spaces. All salamanders that have so far been studied grow their digits from buds and lack an AER, much like Sarfati explained for frogs (only Sarfati attributes it to the wrong animal). Apoptosis has only been detected in the developing digits of one salamander Desmognathus and its role in limb development is not clear (Franssen et al. 2005). It is also the case that salamanders begin digit development with digit 2, which is also in stark contrast with the majority of other tetrapods which develop digit 4 first. This is an interesting and perplexing problem for developmental biologists.

So does this mean that Sarfati is right? Does this mean that the limbs of salamanders cannot be homolgous to those of other tetrapods? The problem comes from this statement by Sarfati which exemplifies a rather deep ignorance of developmental biology (and I'm not even an expert!):
If the birds evolved from dinosaurs, then one would expect common genes. These in turn would code for a common development in the embryo.

This is both overly simplistic and fallacious, since we already know that most of the "genetic toolkit" for animal development is highly conserved. The fact is, the same genes are used in nearly all tetrapods. In fact, vast numbers of the same genes are involved in similar processes in all animals. Some genes have been duplicated and modified to produce different functions -- which is precisely how animal form evolves!

As Myers points out beautifully, and what is the most important point here, is that the patterning mechanisms are conserved. We know that developing tetrapod limbs use a special hierarchical pattern of Hox genes that lay out the "construction zones" in a developing embryo. We see remarkable conservation in both the Hox genes and the placement of special region known as the zone of polarizing activity (ZPA) which plays a role in setting up anterior-posterior polarity of the developing limb.

The emerging picture of salamander limb development is that there are a striking number of "mechanical" differences in the way the construction takes place. The order of digit development and many of the processes that make the digit protrusions are different. However, what doesn't appear to have changed, is precisely what we would expect if the digits are homologous: the genes that control the identity of the digits.

Animal development doesn't work in the same way as humans construct buildings. It's not as logical as we would think it is. In fact, it's rather perplexing and enigmatic and often proceeds along seemingly very illogical courses. The process of making a digit (as in, a protrusion of the distal part of a limb) is under different controls from the process that says what those digits are (the thumb vs. forefinger, etc.). Sarfati's oversimplification is academically irresponsible. It is flat-out wrong making the entire thesis of his argument baseless.

Franssen, R.A., Marks, S., Wake, D. and Shubin, N. 2005. Limb chondrogenesis of the seepage salamander (Desmognathus aenus(Amphibia: Plethodontidae). Journal of Morphology 265:87-101
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Welcome to The Lancelet!

Add one more biology blog to the list, here comes The Lancelet! Here you'll find the random musings and deluded ramblings of a palaeontology graduate student.

Why "The Lancelet"? This is the common name for an animal sometimes known as Amphioxus (Branchiostoma) - a primitive chordate that has long functioned as a living archetype for the ancestor of all vertebrates... maybe that will be a post for later this week: the history of The Lancelet... but I'm sure there are a number of those on the web.

Books I'm reading:
The Vertebrate Body by A.S. Romer and T. Parsons. Because I never received any formal training in anatomy while I was an undergraduate, I now have to spend my time teaching these important lessons to myself.

From DNA to Diversity S. Carroll et al. Because, when one reads about anatomy they want to know "how the hell did this evolve!?" Carroll and co-authors have bring the complex answers to this question down to lowly wannabe anatomist like me. I recommend it for anyone with a working knowledge of molecular biology.

In the meantime, I'll try to get some news up that the other science bloggers aren't already crawling all over.
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