Joined: May 2002
Here is figure 5 from Jiang & Doolittle's article:
|Assembling the Scheme. |
It is thought that 50–100 million years separate the appearances of urochordates (which include the sea squirt) and vertebrates. During that time the machinery for thrombin-catalyzed fibrin formation had to be concocted by gene duplication and the shuffling about of key modular domains. The relative times of duplicative events can be estimated by various means, the most obvious being the presence or absence of a gene in earlier diverging organisms, although it must be kept in mind that lineages may lose genes. Another way to gauge events is from the relative positions of various gene products on phylogenetic trees, earlier branching implying earlier appearance. In this regard, (pro)thrombin invariably appears lower on the phylogenetic trees than do the other vitamin K-dependent factors (Fig. 2).
The order of events can also be inferred by considering the most parsimonious route to assembling the various clusters of peripheral domains. Nine of the proteases under discussion can be accounted for by six domain-swapping events (Fig. 5). Indeed, the presence of a multiple-kringle protease in the sea squirt genome provides a reasonable model for a step-by-step parallel evolution of the clotting and lysis systems. It should be noted that a serine protease with only one kringle has been found in the ascidian Herdmania momus (36). Although numerous scenarios have been offered in the past about how modular exchange was involved in generating these schemes (refs. 4, 12, and 37–41, inter alia), the new genomic data now provide a realistic set of starting materials.
The timing of duplicative events can also be approximated from ortholog–paralog comparisons. As an example, human and puffer fish factor V are 41% identical, and human and puffer fish factor VIII are 42% identical (not counting the variable B regions). On the average, the two factors themselves (in this region) are 38% identical, implying that the gene duplication that led to them occurred only a relatively short while before the common ancestor of fish and mammals. The difference is so small (42% vs. 38%) that it may turn out that the earlier diverging jawless fish will have only the preduplication gene. A genome study devoted to the lamprey or hagfish would settle the point.
Some of the previous articles on the evolution of blood clotting, referenced in the 2003 article:
4. Doolittle, R. F. & Feng, D. F. (1987) Cold Spring Harbor Symp. Quant. Biol. 52, 869–874.
12. Doolittle, R. F., Feng, D. F. & Johnson, M. S. (1984) Nature 307, 558–560.
37. Patthy, L. (1985) Cell 41, 657–663.
38. Doolittle, R. F. (1985) Trends Biochem. Sci. 10, 233–237.
39. Patthy, L. (1990) Semin. Thromb. Hemostasis 16, 245–254.
40. Krem, M. W. & Di Cera, E. (2002) Trends Biochem. Sci. 27, 67–74.
41. Gherardi, E., Manzano, R. G., Cottage, A., Hawker, K. & Aparicio, S. (1997) in Plasminogen Related Growth Factors, eds. Bock, G. R. & Goode, J. A. (Wiley, New York), pp. 24–41.
Many more articles on the topic (the inter alia, as it were) have been accumulated here:
AE reference thread on the evolution of the blood-coagulation cascade
So, when is Dembski going to retract the following?
The Argument from Personal Incredulity:
Miller claims that the problem with anti-evolutionists like Michael Behe and me is a failure of imagination -- that we personally cannot "imagine how evolutionary mechanisms might have produced a certain species, organ, or structure." He then emphasizes that such claims are "personal," merely pointing up the limitations of those who make them. Let's get real. The problem is not that we in the intelligent design community, whom Miller incorrectly calls "anti-evolutionists," just can't imagine how those systems arose. The problem is that Ken Miller and the entire biological community haven't figured out how those systems arose. It's not a question of personal incredulity but of global disciplinary failure (the discipline here being biology) and gross theoretical inadequacy (the theory here being Darwin's). Darwin's theory, without which nothing in biology is supposed to make sense, in fact offers no insight into how the flagellum arose. If the biological community had even an inkling of how such systems arose by naturalistic mechanisms, Miller would not -- a full six years after the publication of Darwin's Black Box by Michael Behe -- be lamely gesturing at the type three secretory system as a possible evolutionary precursor to the flagellum. It would suffice simply to provide a detailed explanation of how a system like the bacterial flagellum arose by Darwinian means. (italics original)