Monday, 17 September 2007

Re-Cell Cycling Front-loading Pt. I

Last week, my bestest friend DaveScot put up a post at Uncommon Descent (the intelligent design blog of William Demski and other illuminaries) about a paper on front-loading. This is an idea that DS is keen on - that there was an ur-cell that had all of the instructions necessary for all of life, and these were turned on at the right time to produce whatever The Designer wanted to appear. I thought it was worth having a look at the paper, if only to stave away boredom. This is the citation:

Sherman, M. (2007). Universal genome in the origin of metazoa. Cell Cycle 6: 1873-1877. Link

The paper advances a suggestion that goes totally against mainstream evolutionery biology, and is therefore nuts and wrong.

It's almost tempting to stop there, but I doubt anyone would get the joke. So, I'll use a different rhetorical strategy to Sherman, and if I make any grand statements, try to back them up with evidence and argument.

Before laying into it properly, I should state that the paper should never have been published in the form it was. The grammar is awful. I'll comment more on this after I've finished with the text - it makes me a bit suspicious about the whole thing. For the moment, it is enough to point out that the grammatical mistakes in the quotes are in the original, and if I were to acknowledge all of them with the usual sic, this post would look like a vomitorium.

The paper starts by laying out some facts that the author thinks need to be explained:

(1) seemingly simultaneous appearence of paleontological remains of all presently existing Metazoan phyla, both simple and advanced; (2) similarities of genomes among Metazoan phyla of diverse complexity; (3) seemingly excessive complexity of genomes of lower taxons; (4) similar genetics switches of functionally similar but non-homologous developmental programs.

Let's take these one by one:

(1) seemingly simultaneous appearence of paleontological remains of all presently existing Metazoan phyla, both simple and advanced. OK, this one is easy - it's boiler-plate creationism. CC300 and CC301 (go to the links for rebuttals).

(2) similarities of genomes among Metazoan phyla of diverse complexity. Grr, now I have to do some work. Sherman points out that some genes (or rather their orthologs) are found in diverse taxa, and not always doing the same thing. He states: does not expect to find genes responsible for development of bilateral organisms in primitive Metazoa with radial symmetry. Surprisingly, such genes, e.g., orthologs of hox genes, were found in Cnidaria, and furthermore they are expressed in Cnidaria in an asymmetric manner, as if to define segments in these radial organisms.

Why is this unexpected? Sherman does not explain. Perhaps he hasn't heard of common descent. Or co-option, where genes that have one function are used to do something else (any intelligent intelligent design supporter should know that the bacterial flagellum took some of its structure from the Type III Secretory System). Sherman does discuss genes changing function over evolutionary time:
A possible response to these arguments within the classical model would be a suggestion that the genes responsible for eye development in Arthropoda or vertebrates serve different functions in lower taxons (so-called gene sharing). In fact, several examples of gene sharing have been described, e.g., recruiting of small heal shock proteins to serve as crystallines. These examples, however, are exceptionally rare, and it is unclear whether they indeed can be responsible for making de-novo complex developmental programs serving unrelated functions.

So, Sherman, if this is exceptionally rare, why does Conway-Morris declare co-option to be "rampant" (pdf)? and redeployment are rampant both in a developmental
context (e.g. Eizinger et al., 1999; Heanue et al., 1999 (see also Relaix and Buckingham, 1999); Merlo et al., 2000; Damen, 2002; Locascio et al., 2002; Lowe et al., 2002; Fabrizio et al., 2003) and in related topics such as those concerned with enzymatic pathways (e.g. Peregrin-Alvarez et al., 2003).

Look, look! Conway-Morris acts like a fusty old academic and gives citations! Curse the man for making it so easy to check his assertion!

Of course, it could be that Sherman is unaware of this work, because he hasn't read this paper. Except ... it's cited in his paper. Not that that means much (find the Know-Thine-Own-Self Results).

It's around here that Sherman makes a comment so factually wrong even I spotted it. He writes
In fact, many of the regulatory genes were lost later in evolution, and are not present in Drosophila or C. elegans, e.g., hedgehog gene,5 indicaling that their presence is not necessay for development and life of vey complex Arthropoda.

Um, but hedgehog is found in Drosophila. It must be - it has the requisite silly name. Even funnier, it was discovered in the fruit fly! Oh, and the same page shows that there are genes similar to hedgehog in C. elegans.

Where were we? Oh, next point...

(3) seemingly excessive complexity of genomes of lower taxons; An immediate problem here is how one defines complexity. PZ Myers has a nice essay on this. But let us proceed. Sherman points out that the sea urchin, which apparently is primative (I guess this means it doesn't know how to eat spaghetti properly), has a whole suite of genes involved in eye development:
While the presence of the opsins could be explained by their possible function in a simple light sensing, sea urchin has the entire set of orthologs of major genes involved in the eye development ... Therefore, it appears that information on the eye development is encoded in the sea urchin genome, while no eye is actually developed, and thus the genetic information seems to be excessive.

He also points out that the sea urchin has the genes for an adaptive immune system.
Yet, sea urchin does not have antibodies, and possibly lacks adaptive immunity in general. Genes that are seemingly useless in sea urchin but are very useful in higher taxons exemplify excessive genetic information in lower taxons.

Or perhaps they exemplify our lack of knowledge about the sea urchin. Now, I know that Sherman is at Boston University Medical School, but I have no idea what he does there. I'm not, though, going to infer that he's useless. Or at least not on this basis.

One can't simply point at a gene and say "we don't know what it does in this organism, so it must be useless". In the paper Sherman cites about the presence of the adaptive immune system genes in the sea urchin, the authors point out that we know very little about the immune systems of most species. To nake his case, Sherman has to show that these genes are not used by the sea urchin, e.g. show that they are not expressed. Put the promotor next to GFP, transform it into the sea urchin, and watch to see when GFP is expressed (it glows green - very pretty). Perhaps the genes are active in the early part of the development of the visual sensory system, and this has been well conserved. Or, again, we could posit co-option of genes from one function to another. Just slap it in, and see when it glows!

There's a recurring theme in this paper - the author makes bold statements and utterly fails to back them up, with evidence, argument or citation. I'm not a developmental geneticist, so I don't want to follow all the claims up, although a few are certainly false (e.g. hedgehog above). Others may be correct, but how are we to know? Can we assume divine revelation?

Right, last point.

(4) similar genetics switches of functionally similar but non-homologous developmental programs. Oh, now the evo-devo people are going to love this:
A distinct set of data that call for a novel approach to evolution comes from comparison of genes that control functionally similar genetic programs in Chordata and Arthropoda. There appears to be a high degree of similarity in some of these genes. A classic example of such similarity is Pax6 gene that controls development of visual systems. According to all current accounts, a common ancestor of Chordata and Arthropoda was a very primitive organism that lacked eyes, and therefore the evolution of eyes in these groups was convergent.

All current accounts? Well, I guess Wiki isn't current then. Neither is Sean Carroll, who suggests a common ancestor had proto-eyes at least (p123 of From DNA to Diversity). Or perhaps Sherman is making a bold claim without any evidence. Again. Carroll et al. suggest that the development of the proto-eye that the common ancestor had was under control of Pax6, as it is so conserved. Sherman appears to be unaware of the idea of common descent. I hear it's a rather popular theory that's doing the scientific rounds.

So, to summarise where we've got to: Sherman has suggested that there is evidence for a problem, but has been unsuccessful in actually providing it. He goes on to suggest an alternative, which is a delight to snigger at. But that, dear fools who have gotten this far, is for another day.

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