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It's been my experience that chemists in general are pretty skeptical of the claims of the hard-core evolutionists. They make a good case when talking about the big picture but do a lot of hand-waving when it comes to the details.

If you think it's just "a lot of hand-waving when it comes to the details", then you clearly haven't been following the literature. Start spending some time in any well-stocked library browsing the dozens of journals which deal specifically with this topic, such as The Journal of Molecular Evolution:

I'm comfortable with the idea of, say, chimps and gorillas evolving from a common ancestor but the notion that complicated mechanisms such as blood clotting and vision "just happened" is a real stretch on the molecular level.

Odd you should say that, since the evolution of the blood clotting mechanism is pretty well understood now, and its "paper trail" has been extracted from cross-species DNA studies of the relevant genes.

See for example The Evolution of Vertebrate Blood Clotting, or The evolution of vertebrate blood coagulation as viewed from a comparison of puffer fish and sea squirt genomes. Excerpt from the latter paper:

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.

Also, Evolution of enzyme cascades from embryonic development to blood coagulation:

Recent delineation of the serine protease cascade controlling dorsal-ventral patterning during Drosophila embryogenesis allows this cascade to be compared with those controlling clotting and complement in vertebrates and invertebrates. The identification of discrete markers of serine protease evolution has made it possible to reconstruct the probable chronology of enzyme evolution and to gain new insights into functional linkages among the cascades. Here, it is proposed that a single ancestral developmental/immunity cascade gave rise to the protostome and deuterostome developmental, clotting and complement cascades. Extensive similarities suggest that these cascades were built by adding enzymes from the bottom of the cascade up and from similar macromolecular building blocks.

That was the abstract. An excerpt from the text:

The downstream protease of the vertebrate clotting cascade (Fig. 1d), thrombin, belongs to the same lineage as complement factors C1r and C1s. The upstream and middle proteases of the clotting cascade (factors VII, IX and X) belong to the most modern lineage, that of horseshoe crab clotting factor C. Therefore, the lineage of thrombin is parental to that of the upstream and middle proteases of the clotting cascade (Table 1) and distinguishes it from the other vitamin-K-dependent clotting proteases (factors VII, IX and X, and protein C). This conclusion agrees with sequence and species comparisons implying that thrombin was the ancestral blood-clotting protein [11]. It also suggests that vertebrate blood clotting emerged as a by-product of innate immunity, because the entire functional core of vertebrate clotting shares ancestry with complement proteases.

And if that's not enough, you could check these out:

Banyai, L., Varadi, A. and Patthy, L. (1983). “Common evolutionary origin of the fibrin-binding structures of fibronectin and tissue-type plasminogen activator.” FEBS Letters, 163(1): 37-41. Link: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=6685059&dopt=Abstract

Bazan, J. F. (1990). “Structural design and molecular evolution of a cytokine receptor superfamily.” Proceedings of the National Academy of Sciences of the United States of America, 87(18): 6934-6938. Link: http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=2169613

Blake, C. C. F., Harlos, K. and Holland, S. K. (1987). “Exon and Domain Evolution in the Proenzymes of Blood Coagulation and Fibrinolysis.” Cold Spring Harbor Symposia on Quantitative Biology: The Evolution of Catalytic Function, LII: 925-932. Link: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=3454300&dopt=Abstract

Crabtree, G. R. (1986). “The Molecular Genetics of Fibrinogen.” Journal of Cellular Biochemistry Supplement(10 PART A): 229.

Crabtree, G. R., Comeau, C. M., Fowlkes, D. M., Fornace, A. J., Jr., Malley, J. D. and Kant, J. A. (1985). “Evolution and structure of the fibrinogen genes: Random insertion on introns or selective loss?” Journal of Molecular Biology, 185(1): 1-20.

Di Cera, E., Dang, Q. D. and Ayala, Y. M. (1997). “Molecular mechanisms of thrombin function.” Cell Mol Life Sci, 53(9): 701-730.

Doolittle, R. F. (1985). “More homologies among the vertebrate plasma proteins.” Biosci Rep, 5(10-11): 877-884. Link: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=3938299&dopt=Abstract

Doolittle, R. F. (1990). “The Structure and Evolution of Vertebrate Fibrinogen A Comparison of the Lamprey and Mammalian Proteins,” in ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY: FIBRINOGEN, THROMBOSIS, COAGULATION, AND FIBRINOLYSIS. C. Y. Liu and Chien, S. New York, Plenum Press. 281. Link: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=2102616&dopt=Abstract

Doolittle, R. F. (1992). “A detailed consideration of a principal domain of vertebrate fibrinogen and its relatives.” Protein Science, 1(12): 1563-1577. Link: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=1304888&dopt=Abstract

Doolittle, R. F. (1992). “Early Evolution of the Vertebrate Fibrinogen Molecule.” Biophysical Journal, 61(2 PART 2): A410.

Doolittle, R. F. (1992). “Early Evolution of the Vertebrate Fibrinogen Molecule.” FASEB Journal, 6(1): A410.

Doolittle, R. F. (1992). “Stein and Moore Award address. Reconstructing history with amino acid sequences.” Protein Science, 1(2): 191-200. Link: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=1339026&dopt=Abstract

*Doolittle, R. F. (1993). “The Evolution of Vertebrate Blood Coagulation - a Case of Yin and Yang.” Thrombosis and Haemostasis, V70(N1): 24-28. Link: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=8236110&dopt=Abstract

Doolittle, R. F. and Feng, D. F. (1987). “Reconstructing the Evolution of Vertebrate Blood Coagulation from a Consideration of the Amino Acid Sequences of Clotting Proteins.” Cold Spring Harbor Symposia on Quantitative Biology: The Evolution of Catalytic Function, LII: 869-874. Link: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=3483343&dopt=Abstract

Doolittle, R. F., G., Spraggon and J., Everse S. (1997). “Evolution of vertebrate fibrin formation and the process of its dissolution.” Ciba Found Symp, 212: 4-17; discussion 17-23. Link: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=9524761&dopt=Abstract

Doolittle, R. F. and Riley, M. (1990). “The amino-terminal sequence of lobster fibrinogen reveals common ancestry with vitellogenins.” Biochemical and Biophysical Research Communications, 167(1): 16-19. Link: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=2310387&dopt=Abstract

Edgington, T. S., Curtiss, L. K. and Plow, E. F. (1985). “A linkage between the hemostatic and immune systems embodied in the fibrinolytic release of lymphocyte suppressive peptides.” Journal of Immunology, 134(1): 471-477.

Ghidalia, W., Vendrely, R., Montmory, C., Coirault, Y., Samama, M., Lucet, B., Bellay, A. M. and Vergoz, D. (1989). “Overall study of the in vitro plasma clotting system in an invertebrate, Liocarcinus puber (Crustacea Decapoda): Considerations on the structure of the Crustacea plasma fibrinogen in relation to evolution.” Journal of Invertebrate Pathology, 53(2): 197-205.

Hervio, L. S., Coombs, G. S., Bergstrom, R. C., Trivedi, K., Corey, D. R. and Madison, E. L. (2000). “Negative selectivity and the evolution of protease cascades: the specificity of plasmin for peptide and protein substrates.” Chemistry & Biology, V7(N6): 443-452.

Hewett-Emmett, D., Czelusniak, J. and Goodman, M. (1981). “The evolutionary relationship of the enzymes involved in blood coagulation and hemostasis.” Annals of the New York Academy of Sciences, 370(20): 511-527.

Holland, S. K., Harlos, K. and Blake, C. C. F. (1987). “Deriving the generic structure of the fibronectin type II domain from the prothrombin Kringle 1 crystal structure.” EMBO (European Molecular Biology Organization) Journal, 6(7): 1875-1880.

Jordan, R. E. (1983). “Antithrombin in vertebrate species: conservation of the heparin-dependent anticoagulant mechanism.” Archives of Biochemistry and Biophysics, 227(2): 587-595.

Kant, J. A., Fornace, A. J., Jr., Saxe, D., Simon, M. J., McBride, O. W. and Crabtree, G. R. (1985). “Evolution and organization of the fibrinogen locus on chromosome 4: Gene duplication accompanied by transposition and inversion.” Proceedings of the National Academy of Sciences of the United States of America, 82(8): 2344-2348.

Kornblihtt, A. R., Pesce, C. G., Alonso, C. R., Cramer, P., Srebrow, A., Werbajh, S. and Muro, A. F. (1996). “The fibronectin gene as a model for splicing and transcription studies.” FASEB Journal, 10(2): 248-257.

Laki, K. (1972). “Our ancient heritage in blood clotting and some of its consequences.” Annals of the New York Academy of Sciences, 202(4): 297-307.

Neurath, H. (1984). “Evolution of proteolytic enzymes.” Science, 224(4647): 350-357. Link: http://www.jstor.org/journals/00368075.html

Neurath, H. (1986). “The Versatility of Proteolytic Enzymes.” Journal of Cellular Biochemistry, 32(1): 35-50.

Neurath, H. (1986). “The Versatility of Proteolytic Enzymes.” Journal of Cellular Biochemistry Supplement(10 PART A): 229.

Oldberg, A. and Ruoslahti, E. (1986). “Evolution of the fibronectin gene: Exon structure of cell attachment domain.” Journal of Biological Chemistry, 261(5): 2113-2116.

Opal, S. M. (2000). “Phylogenetic and functional relationships between coagulation and the innate immune response.” Critical Care Medicine, V28(N9 SUPPS): S77-S80.

Pan, Y. and Doolittle, R. F. (1991). “Distribution of Introns in Lamprey Fibrinogen Genes.” Journal of Cellular Biochemistry Supplement(15 PART D): 75.

Pan, Y. and Doolittle, R. F. (1992). “cDNA sequence of a second fibrinogen alpha chain in lamprey: an archetypal version alignable with full-length beta and gamma chains.” Proceedings of the National Academy of Sciences of the United States of America, 89(6): 2066-2070. Link: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=1549566&dopt=Abstract

Patthy, L. (1985). “Evolution of the Proteases of Blood Coagulation and Fibrinolysis by Assembly from Modules.” Cell, 41(3): 657-664. Link: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=3891096&dopt=Abstract

Patthy, L. (1990). “Evolution of blood coagulation and fibrinolysis.” Blood Coagulation and Fibrinolysis, 1(2): 153-166. Link: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=2130927&dopt=Abstract

Patthy, L. (1990). “Evolutionary Assembly of Blood Coagulation Proteins.” Seminars in Thrombosis and Hemostasis, 16(3): 245-259. Link: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=2237446&dopt=Abstract

Patthy, L. (1999). “Genome evolution and the evolution of exon-shuffling—a review.” Gene, 238(1): 103-114. Link: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=10570989&dopt=Abstract

Roberts, Lewis R., Nichols, Lanita A. and Holland, Lene J. (1995). “CDNA and amino-acid sequences and organization of the gene encoding the B-beta subunit of fibrinogen from Xenopus laevis.” Gene (Amsterdam), 160(2): 223-228.

Sosnoski, D. M., Emanuel, B. S., Hawkins, A. L., Van Tuinen, P., Ledbetter, D. H., Nussbaum, R. L., Kaos, F. T., Schwartz, E., Phillips, D. and et al. (1988). “Chromosomal localization of the genes for the vitronectin and fibronectin receptors .alpha. subunits and for platelet glycoproteins IIb and IIIa.” Journal of Clinical Investigation, 81(6): 1993-1998.

Wang, Y. Z., Patterson, J., Gray, J. E., Yu, C., Cottrell, B. A., Shimizu, A., Graham, D., Riley, M. and Doolittle, R. F. (1989). “Complete sequence of the lamprey fibrinogen .alpha. chain.” Biochemistry, 28(25): 9801-9806.

Xu, X. and Doolittle, R. F. (1990). “Presence of a vertebrate fibrinogen-like sequence in an echinoderm.” Proceedings of the National Academy of Sciences of the United States of America, 87(6): 2097-2101. Link: http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=2315305

Zhang, Y. L., Hervio, L., Strandberg, L. and Madison, E. L. (1999). “Distinct contributions of residue 192 to the specificity of coagulation and fibrinolytic serine proteases.” Journal of Biological Chemistry, V274(N11): 7153-7156. Link: http://www.jbc.org/cgi/content/full/274/11/7153

Zimmermann, E. (1983). “[The evolution of the coagulation system from primitive defense mechanisms].” Behring Institute Mitteilungen, 82(73): 1-12.

And so on...

Similarly, there's a lot known about the evolutionary pathway of the vertebrate eye. And I'm not sure what you mean about the "complicated mechanisms" at the "molecular level" of the eye, since light-sensitive nerves are pretty straightforward, and a known variation on the chemistry of pre-existing non-photosensitive nerves. The rest of the eye is actually pretty simple on a molecular level.

Finally, I hope you understand that when you say "just happened", that that's an extremely poor description of what actually takes place when evolution is occurring.

Thanks. I give you a lot of credit for not accusing me of being a Bible-thumping ignoramus just because I -- like many other scientists -- have a lot of doubt as to all of the modern claims of evolution.

The rest of the eye is actually pretty simple on a molecular level.

We definitely disagree here. It's very simple if all the pieces are in the right place at the right time, but the process of seeing totally fails if even one of the pieces are missing.

Finally, I hope you understand that when you say "just happened", that that's an extremely poor description of what actually takes place when evolution is occurring.

Actually, I would argue that it's a rather good description. As an example, the link that you provided, The Evolution of Vertebrate Blood Clotting, invokes my phrase -- though in loftier language -- quite a bit. My comments are in red:

It turns out that thrombin itself exists in an inactive form called prothrombin. ("It turns out" = "it just happens") So it, just like fibrinogen, has to be activated before it can start the clotting process. What activates prothrombin? Here's where life gets really interesting. Prothrombin, a protease itself, is activated by another protease called Factor X which clips of part of the inactive protein to produce active, clot-forming thrombin. OK, so what activates Factor X? Believe it or not, there are still more proteases, two of them, actually, called Factor VII and Factor IX, that can switch on Factor X.
Blood clotting evolved there from two pre-existing proteins, normally found in separate compartments of the body, that had a fortuituous interaction when damage to a blood vessel brought them together. (Dang, we're lucky that this happened!)
... Remember, we're not starting from nothing. (Of course not -- it's more convenient when we don't start from nothing.) We're starting about 600 million years ago in a small pre-vertebrate with a low-volume low-pressure circulatory system. Just like any small inverterbate with a circulatory system, our ancestral organism would have had a full compliment of sticky white cells to help plug leaks. (Note how the author doesn't postulate how the organism got the circulatory system with a "full compliment of sticky white cells" in the first place. That's called "hand waving" and is the Wizard of Oz behind the curtain that we're not supposed to notice) ... That means, among other things, that all of a cell's internal signalling molecules are suddenly spilled out into the damaged vascular system. Included among the contents are a whole slew of internal signalling molecules, including prominent ones like cyclic adenosine monophosphate (abbreviated: cAMP), all dumped into the tissue surrounding a wound. (So how did the signalling components get there in the first place? Which came first, the circulatory system or the signalling components?)

...These spaces are laden with protein signals, insoluble matrix molecules, and extracellular proteases that cut and trim these molecules to their final shapes and sizes. In fact, such proteases constitute one of the major forms of extracellular signalling. So the tissues of our ancestral vertebrate would be laden with protein-cutting enzymes for reasons completely unrelated to clotting. (Fine, but how did these protein-cutting enzymes get there in the first place? This kind of answers my question about the signalling components but, in my opinion falls short. Perhaps more work is in order.)
...The fortuitious combination of a EGF sequence with the plasma protease changes everything. (There's that word "fortuitous" again. That's just a Latinized word for the phrase that I used: "just happened.")
...Could evolution take this rudimentary system and produce a multilayered cascade of factors? (The author begins to speak of evolution as some mysterious outside force. This is all too typical.) Most serine proteases, including trypsin and thrombin, are auto-catalytic. That means that some extent they can activate themselves, in many cases by cleaving a few amino acids to switch on their active sites. (How handy that the proteases that just happen to be laying around also happen to be auto-catalytic!)
But just as soon as the occasional clot becomes large enough to present health risks, natural selection would favor the evolution of systems to keep clot formation in check. And where would these systems come from? From pre-existing proteins, of course, duplicated and modified. (Of course, pre-existing proteins just happen to be hanging around, waiting for something to do. The dirty secret is that, according to classical Darwinian theory, for every useful protein in our bodies we should have dozens and dozens that aren't useful. That doesn't seem to be the case. Why should our bodies expend energy creating proteins that, at best, aren't useful and, at worst, are detrimental?)
... Next, if the clotting cascade really evolved the way I have suggested, the the clotting enzymes would have to be near-duplicates of a pancreatic enzyme and of each other. As it turns out, they are. Not only is thrombin homologous to trypsin, a pancreatic serine protease, but the 5 clotting proteases (prothrombin and Factors X, IX, XI, and VII) share extensive homology as well. (The author does have a very good point here.)

To sum it up, I'm an agnostic when it comes to "macro-evolution" (yes, I know that's a phrase that evolution advocates hate). I realize that the paper that you were kind enough to link me to wasn't intended to be a comprehensive treatise on the evolution of the blood clotting system. However, I also think that you would have to admit that his theory depends upon a lot of lucky circumstances. It's that "luck" and his basis of starting out with an organism that already has a rudimentary clotting system that makes me skeptical. If I win the lottery once, that's luck. If I win the lottery virtually every time I play, then there's probably something else besides luck that's behind my winnings.
What I'm curious about is how a single-celled organism evolved to a multi-celled organism complete with a circulatory system and a rudimentary clotting system. That's something that the author doesn't even try to answer. Evolution certainly exists in some form or fashion but it falls short on some awfully big questions.
Again, thanks for the time that you put into your answer. We both agree that evolution is a reality but differ in whether it explains all things (your position) or just some things (my position). In 20 years or so I might change my position.