Anatomy of an Oyster Shell

Some Pacific oysters on a plateWe’re still on the same (4 October) edition of Nature today as we were on Friday, with Jeffrey Tomkins and Brian Thomas collaborating to produce Oyster Genome Confounds Mollusk Evolution.

Most evolutionists who study fossil mollusks believe these creatures evolved from a hypothetical ancestor that had no shell. How could nature, with no intelligent input, coax imagined soft-bodied ancestors to blindly construct the hard shells of oysters, which research now shows contain over 250 different proteins?

The paper is The oyster genome reveals stress adaptation and complexity of shell formation (open access; a Science Daily article can be found here), and does indeed mention that they “identified 259 shell proteins.” In their article Tomkins and Thomas take the popular “if it’s complex the it must be designed/can’t have evolved” line, with little further evidence offered. Let’s take a tour.

First, gene count:

Perhaps one of the most amazing aspects of the oyster genome is its vast gene repertoire. Humans have about 21,000 genes, but the team found that oysters use over 28,000 genes. When compared to seven other animal genomes, the researchers found 8,654 genes that only oysters have.

The abstract to the paper states that molluscs are “one of the most species-rich but genomically poorly explored phyla” – in translation, it’s a big group that is also poorly studied. Indeed, phylum refers to body plan, and at this level humans are in the same (sub)phylum as hagfish. I bring this up for two reasons. First, this is a little too broad for a baraminological “kind,” which is a bit of a pity as some the arguments being put forward by T&T would benefit if that were not the case. Second, the paper does not compare their organism – the Pacific oyster, Crassostrea gigas – with any other mollusc genome. What this means is that many of these 8,654 genes could and will be shared by the many thousands of other mollusc species. The features described in this paper need not be all or nothing – yet that is what the ICR is relying on.

Next, environmental adaptation:

Because oysters are not highly mobile creatures and live in challenging and fluctuating environments—like estuaries and intertidal zones—they need a large suite of genes that allow them to adapt to changes in air exposure, toxins, temperature, and salinity. Indeed, the researchers identified 7,938 genes that contribute to genetically programmed environmental adaptation, which is a key component of the creation biological origins model.

The “creation biological origins model” – not elaborated upon or referenced here – seems to be the concept that I have termed “Guliuzzism.” However, the genes very much seem to be involved in the “acclimatisation” sense of adaptation, which should by rights have nothing to do with the creationists’ evolution alternative.

Then we have something about shell formation:

Traditional thought suggests that adjacent cells excrete the proteins and minerals that build oyster shells. But one of the least expected discoveries from the project was the complicated biology of shell formation. Of the 259 proteins found to play a structural role in oyster shells, 84 percent were not excreted proteins. How could the shell be excreted if its proteins were not excreted?

In oyster shell construction, 61 proteins appear to be deposited in “budded vesicles”—special membrane-surrounded, protein-containing portions—at the shell-forming interface. The other proteins are products of oyster cell biochemical pathways. The whole scenario of shell-forming looks like a very complicated biological process.

The paper itself says, however:

The involvement of cells in shell formation is further supported by the functional diversity of proteins detected in shells. Many housekeeping proteins, such as elongation factor 1α and ribosomal proteins, were found in the shell; indeed, most oyster shell proteins are not structural proteins but are distributed in diverse metabolic pathways (Fig. 4c and Supplementary Table 25). This functional diversity of shell proteins mirrors that of cells, which is unexpected under the matrix model. Furthermore, 84% of the 259 shell proteins identified are not classical secreted proteins (Supplementary Text H3.4 and Supplementary Table 24); they may be part of cells or deposited by exosomes. Supporting the presence of exosomes, 61 of the 259 shell proteins matched proteins in the exosome database. Cells and exosome-like vesicles containing calcite crystals have been observed at the mineralization front, although their significance in shell formation is debated. This study provides molecular evidence for their presence inside shells and their probable participation in shell formation.

There are some notable differences between what the paper says here and what T&T said. While they say that the 84% of proteins “were not excreted,” the paper really says that they were not normally excreted, suggesting some alternative mechanisms. (Also worth noting is that it seems that many of the 259 have other jobs and would be present shell or no.) When T&T go on to ask “How could the shell be excreted if its proteins were not excreted?” they assume a bit much. The same goes for the 61 proteins in the vesicles – those are merely the ones already known to be associated with exomes, and there could be more or even less (for all we actually know) involved in that function. The paper isn’t even as ready to jump to the vesicle conclusion as the ICR article is either. Given that, should we really trust these two when they say that evolution can’t evolve something they can’t even accurately retell?

Geologic time is next:

Not only does all of this unexpected biological and genetic complexity stand at odds with evolutionary origins, but it also conflicts with deep evolutionary time scales. Mollusks are at the bottom of the rock column. Fossil authority Donald Prothero once wrote, “All the major classes of mollusks (except scaphopods) [tusk shells] were established in the Cambrian.”

The book cited is given as “Prothero, D. 2004. Bringing Fossils to Life. New York: McGraw-Hill, 282.” Tomkins and Thomas do not explain why a Cambrian origin of the phyla is problematic – the (50 million year long) Cambrian is a long way from the “bottom of the rock column,” even when it comes to fossil-bearing rocks. My reading suggests that the origins of molluscs are not well pinned down, with some of the very earliest being controversial – whether or not they are truly molluscs are debatable, transitional form style.

Finally, extinction:

Prothero also wrote, “About 8,000 to 15,000 living [mollusk] species are known, but many more are known from the fossil record (about [40,000]).” Since there are fewer mollusks today than in the past, it appears that they have not been evolving at all, but simply going extinct.

If molluscs have been around 500 million years then it is only to be expected that there would be more extinct than extant species – but not so if they had only existed for 6000. But I’m glad they brought this up. The true purpose of the study was to give a starting point for investigating how climate change induced ocean acidification could impact oyster shells. Not being all that fond of climate science – Tomkins recently reposted a rather amusing screed on his website related to it – our two authors have tip-toed around the issue. But, truth be told, molluscs probably are going to take a hit whether or not that is a trend that predates the industrial revolution.

T&T conclude:

Both the genetics and the fossils agree with the Bible. Mollusks were expertly formed from the beginning and have not evolved since.

They are a very long way from proving this. The last sentence actually suggests species immutability, which is quite a silly thing to claim in this day and age. In order to have a hope of showing that molluscs did not evolve a proper analysis of many mollusc species and relatives would have to be conducted, with an eye for shared genes and shell morphology and construction. Sharp all-or-nothing differences between easily separable groups would at least suggest that something is amiss, if not prove it outright. Time to get sequencing, Jeff.

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One thought on “Anatomy of an Oyster Shell

  1. If the oyster shell isn’t “excreted”, then how does it develop? God must be present shortly after the hatching of each and every oyster to place on the shell himself.

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