Pharyngula

Scientists…in disagreement!

Yesterday, I reposted an article on homology within the neck and shoulder, which describes an interesting technique of using patterns of gene expression to identify homologous cellular pools; the idea is that we can discern homology more clearly by looking more closely at the molecular mechanisms, rather than focusing on final morphology and tissue derivation. Trust me, if you don’t want to read it all—it’s cool stuff, and one of the interesting points they make is that they’ve traced the fate of a particular bone not found in us mammals, but common in our pre-synapsid ancestors, the cleithrum. They argue from a common cellular origin that this bone has been reshaped into a ridge on our shoulder blade, the scapular spine.

As many readers might know, though, the word “homology,” especially when coupled with a novel technique for its determination, is always good for an argument. This one is no exception.

I won’t get too much into the details of the disagreement, but I just want to point out a very common phenomenon: every scientist is presenting ideas and evidence for hypotheses, and it is expected that other scientists will respond by trying to argue against them. It’s what makes for a healthy science, that there is vigorous debate. Sometimes this goes on in private communications back and forth, sometimes it occurs at meetings, and sometimes it works its way into print, and you can find the argument enshrined in the pages of the science journals.

Here’s a good example: after the publication of the Matsuoka et al. paper that I described, Sánchez-Villagra and Maier wrote a three-page rebuttal and published it in Evolution and Development. They make a strong case that perhaps the comparative descriptions are oversimplified, minimizing the great variation found in musculoskeletal organization, and that fossil and phylogenetic evidence shows an absence of both the cleithrum and the scapular spine, making the homology dubious.

It is possible that Matsuoka et al. (2005) have found ev-
idence that the population of cells that give rise to parts of the
scapular spine of therian mammals is homologous to the
populations of cells that give rise to the cleithrum of basal
gnathostomes. But homology at the cellular level does not
necessarily imply homology at higher levels of the hierarchy. So the cleithrum does not “survive as the scapular spine in living mammals” (Matsuoka
et al. 2005, p. 347)—it has been extinct in synapsids for more
than 250 million years! If no traditional homology of the
cleithrum was challenged by Matsuoka et al. (2005), then this
needs to be explicitly stated, otherwise the readers are misled.

Ahlberg and Koentges have their own reply to the rebuttal. It’s also three pages long, and is rich with detail and ideas—it’s also good science. Here’s a short excerpt:

S.-V. & M.’s point
that the cleithrum has been extinct in synapsids for more
than 250 million years and cannot “survive” as the scapular
spine is moot. We are not claiming that the scapular spine is
a remnant of the cleithrum ossification, but we do infer that
it is made from the same cell populations that once made the
leading edges of that cleithrum ossification. At that inter-
section between two seemingly contradictory homology
statements emerges a mechanistic explanation of evolutionary change: the cleithrum has been lost through the re-specification of cell fate within a stable cell population map. We
provide evidence for genes involved in imparting such skeleton-muscular connectivity and find that these genes (part of
the Hox gene network) have been expressed in neural crest

I’m not going to resolve the argument here, of course. I will say that Sánchez-Villagra and Maier are making a perfectly reasonable argument from structure, while Ahlberg and Koentges are making a perfectly reasonable argument from the developmental process…and my personal bias is to find the logic of how a structure develops to be more persuasive than what it ends up looking like, so I’m inclined to favor the Ahlberg and Koentges explanation. What I look forward to, though, is the continuing exploration of the problem, and the appearance of further data to support one or the other position…or something else altogether. This is how science works.

One other thing: both papers have pleasant acknowledgments.

We thank Per Ahlberg and G. Koentges for their prompt and in-
formative response to our communication with them, leading to this
paper, and for generously engaging on an open discussion about the
issues at hand. We also thank S. Kuratani for discussion of ideas.

We thank Marcelo Sánchez-Villagra and Wolfgang Maier for their open and collegial approach to this discussion.

I just wanted to bring this up to illustrate a few important points. When I summarize a paper here, I’m often simplifying and skipping over colossal amounts of deep background—these explanations are not definitive, final answers! Also, if you want to see some dissenting opinions on that last paper, now you have some sources to trace down. And finally, much as my bias in evolution leans towards the process side, I have the same bias in valuing science: the important part isn’t so much the final answer, but how you get to it.


Sánchez-Villagra MR, Maier W (2006) Homologies of the mammalian shoulder girdle: a response to Matsuoka et al. Evolution and Development 8(2):113-115.

Ahlberg P, Koentges G (2006) Homologies and cell populations: a response to Sánchez-Villagra and Maier. Evolution and Development 8(2):116-118.