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niiicholas



Posts: 319
Joined: May 2002

(Permalink) Posted: May 17 2002,22:00   

Hi,

Following my own suggestion, here is a thread devoted to collection material/links/references relevant to blood-clotting and the claims IDists make about it.  As there is not yet a single webpage anywhere that has gathered all of the relevant material in a single place, this might as well be it.  Perhaps at some point it could be edited into a FAQ, or could inspired someone to write a FAQ (since much of the hard work of finding the references, IDist quotes, etc., would be done).

Specifically relevant would be things like:

1) blood-coagulation/clotting (or hemolyph coagulation for you invertebrates out there), especially e.g. webpages/literature that describe the basics in an easily understandable manner such that a FAQ reader could be referred there

2) references to articles/lit. on the evolution of blood clotting

3) Links to/quotes of antievolutionist assertions regarding blood-clotting, with commentary on problems if you are inspired

4) Links to the various webpages already out there rebutting IDist claims.

Awhile ago I did a search and dug up a pretty good starting reference list, I'll post that in a moment.

nic

Edited by niiicholas on May 17 2002,22:00

  
niiicholas



Posts: 319
Joined: May 2002

(Permalink) Posted: May 17 2002,22:09   

These are the results of a computer search last year on terms like "evolution blood coagulation."  I was pretty careful checking abstracts etc. to avoid including "false hits" -- (e.g., "evolution" has a chemical meaning unrelated to biological evolution).

For fun, I added asterisks (*) to refer to papers that Behe referenced in Darwin's Black Box.  The others are the ones he missed, or that were published 1996 or later.

I'll quote the whole URL in code brackets, hopefully they'll fit.


Code Sample

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.  



Many of these articles are however tough to get (unless you're at UCSD, unsurprisingly), so I've only read a few.

Others are welcome to add stuff as they see fit.

Thanks, nic

Edited by niiicholas on May 17 2002,22:14

  
Wesley R. Elsberry



Posts: 4468
Joined: May 2002

(Permalink) Posted: May 18 2002,03:24   

Here's a reference that Ken Miller cited in the AMNH debate on 2002/04/23:

Quote
Robinson, A. Jean, Kropatkin, Mona, and Aggeler, Paul M.  1969.   Hageman Factor (Factor XII) Deficiency in Marine Mammals. Science 166:1420-1422.


Marine mammals lack one of the "parts" of the blood-clotting system whose absence supposedly renders the system non-functional.

Mark Todd pointed this one out to Miller, having heard about it from some of the veterinarians who I work with, too.  I don't think that they mentioned this bit around me.

--------------
"You can't teach an old dogma new tricks." - Dorothy Parker

    
niiicholas



Posts: 319
Joined: May 2002

(Permalink) Posted: May 24 2002,19:42   

Some good discussion and links on a bio.com article discussing the homology between a blood-clotting protein and a cone-snail venom protein (!!!) was posted on this II thread.

nic

Edited by niiicholas on May 24 2002,19:44

  
niiicholas



Posts: 319
Joined: May 2002

(Permalink) Posted: May 24 2002,20:25   

Some more stuff I've gathered on the mysterious missing Hagemann factor case:

1) I went and re-checked Darwin's Black Box and Behe does indeed include the component as part of the IC blood-clotting system.***

2) Here is the abstract of the Robinson et al. paper that Wes cited:

Quote

Robinson, A. Jean, Kropatkin, Mona, and Aggeler, Paul M.  1969.   Hageman Factor (Factor XII) Deficiency in Marine Mammals. Science 166:1420-1422.

Hematologic and coagulation studies were conducted on Atlantic bottlenose dolphins and killer whales. Hematologic values were similar to those in man. These animals differed from other mammals in that the Hageman factor (factor XII) was absent and this absence caused marked prolongation of coagulation. Levels of VIII and V were high and those of VII and X were low compared with levels in man.


The paper mentions at the end a longish list of birds, reptiles, etc. that don't have Hagemann factor either, surprise suprise, although it mentions that at least some of these have other factors that may compensate...

Also of interest are the names of the orcas: "Orky" "Snorky" "Corky". Don't see those names as headers in scientific tables every day...

3) The conclusions of the Robinson et al. (1969) paper are backed up by this recent paper:

Quote

Pubmend citation

Thromb Res 1998 Apr 1;90(1):31-7

Whale Hageman factor (factor XII): prevented production due to pseudogene conversion.

Semba U, Shibuya Y, Okabe H, Yamamoto T.


In Southern blot analysis of the Hind III-digested whale genomic DNA obtained from the livers of two individual whales, we detected a single band with a size of five kilobase pairs which hybridized to full length guinea pig Hageman factor cDNA. We amplified two successive segments of the whale Hageman factor gene by polymerase chain reaction (PCR), and sequenced the PCR products with a combined total of 1367 base pairs. Although all of the exon-intron assemblies predicted were identical to those of the human Hageman factor gene, there were two nonsense mutations making stop codons and a single nucleotide insertion causing a reading frame shift. We could not detect any message of the Hageman factor gene expression by northern blot analysis or by reverse transcription-polymerase chain reaction (RT-PCR) analysis. These results suggest that in the whale, production of the Hageman factor protein is prevented due to conversion of its gene to a pseudogene. The deduced amino acid sequence of whale Hageman factor showed the highest homology with the bovine molecule among the land mammals analyzed so far.


In other words, this is a classic textbook-style case of pseudogene production, as well as being yet another bit of evidence supporting the whale-artiodactyl connection that has been suggested by various molecular studies and supported by recently discovered transitional fossils, see J. G. M. Thewissen's whale evolution page here.

4) It should be pointed out that while Behe includes Hageman factor (= Factor XII) as part of the IC blood-clotting system in DBB, the likely ID defense will be to take the "eternally receding IC system" approach wherein they declare this part non-essential and therefore not "part" of the IC "system" (if it's not part of the system, what it is a part of?).  

According to this t.o. POTM, it is indeed questionable how necessary Factor XII is for blood-clotting:

Quote

In this view, 3 factors included in the older scheme
(Factor XII = Hageman, prekallikrein and HMK) are now excluded, since deficiencies do not cause clinical disease, although they are associated with long clotting times in vitro. The role of XI isn't clear, since deficieny isn't invariably associated with disease.


...although one wonders if "deficiencies" means "complete absense", as it is apparent that Factor XII does play some important roles, e.g. the introduction to Semba et al. (1998) states:

Quote

Hageman factor (factor XII) is an initiation factor of plasma protease cascades, such as the intrinsic blood coagulation pathway and the plasma kinin system [1 and 2]. Important roles of the plasma kinin system in inflammatory responses in infection have been demonstrated. Microbial proteases such as Pseudomonas aeruginosa elastase, and negatively charged bacterial components such as endotoxin are capable of activating Hageman factor and prekallikrein [3, 4, 5 and 6].


...sounds like a handy thing to have around for sure.  Certainly on the above quote we can say that Hageman factor is necessary for "Hageman factor-dependent cascade activation", which just goes to show that just about anything can be considered "essential for function" depending on where one draws the lines of the "system".  

An even better feature of Semba et al. (1998) is that they propose a hypothesis for why Hagemann factor has been lost in marine mammals:

Quote

Saito et al. reported that all marine mammals examined by them did not possess coagulation activities equivalent to Hageman factor and prekallikrein [8]. Their explanation of this observation is as follows: the lack of these initiation factors of the intrinsic blood coagulation pathway must be advantageous to the marine mammals in prevention of disseminated intravascular coagulation syndrome which might occur in the semi-static state of blood circulation in the skin and the lungs under high hydrostatic pressure.

[...]

3. Discussion
The present study demonstrates that the Hageman factor gene converted to a pseudogene by the point mutations in exons coding for the protease domain in the whale. This conversion explains the absence of Hageman factor in whale plasma [8]. Messenger RNA of whale Hageman factor was not also detected in the liver mRNA fraction even by Southern blot analysis of the RT-PCR products. This result suggests very high instability of whale Hageman factor mRNA. Since only the 3' half of the whale Hageman factor gene has been analyzed so far, final conclusions about the mechanism of the blocked expression of the whale Hageman factor gene message cannot yet be drawn.

Participation of the intrinsic blood coagulation pathway in the disseminated intravascular coagulation syndrome has been suspected. The whale may dive to depths of 1000 m, where a semi-static state of blood circulation in the skin and the lungs might occur due to the high hydrostatic pressure. The fact that the initiation factor of the intrinsic blood coagulation system is not produced in the whale would support the clinical suspicion about the participation of this system in the disseminated intravascular coagulation syndrome.

We have been postulating that Hageman factor and the plasma kinin system play important roles in the host defense of land mammals. However, our hypothesis does not explain why Hageman factor-deficient individuals are not suffering from infectious deseases. Therefore, there may be an opposite hypothesis: the plasma kinin system does not play an essential role in host defense. From a superficial point of view, the present study might support this opposite hypothesis. However, Saito et al. reported that a significant amount of high-molecular weight kininogen was present in whale plasma [8]. This concentration corresponds to 30% of that in human plasma. We presently confirmed this using dolphin plasma (data not shown). If we take into account that the significant amount of high-molecular weight kininogen is present even in whale plasma, we could speculate that the important roles of the plasma kinin system are compensated by an unknown system(s) in Hageman factor-deficient individuals as well as in the marine mammals.

The deduced amino acid sequence of whale Hageman factor closely resembles that of the bovine molecule including the Pro-rich region where almost no homology is observed among the human, guinea pig, and bovine molecules [16]. Recently, Shimamura et al. [19] described their opinion that whales (including dolphins and porpoises), ruminants (cows, chevrotains, deer, sheep), and hippopotamuses form a monophyletic group. This is based on their analyses of two retroposons in the genomes of 15 mammalian species. Our present data support their opinion.


So, we appear to have parts being lost, perhaps "parts" being replaced or compensated for, and generally a lot of evolution going on.  One wonders how any of this would be explained on a "IDdidit" just-so story.

nic

PS: Looking up 'related articles' in Pubmed reveals that decreased Factor XII activity is associated with increased miscarriage in humans:

Quote

PubMed link

Fertil Steril 2002 Feb;77(2):353-6

Coagulation factor XII activity, but not an associated common genetic polymorphism (46C/T),is linked to recurrent miscarriage.

Iinuma Y, Sugiura-Ogasawara M, Makino A, Ozaki Y, Suzumori N, Suzumori K.

Department of Obstetrics and Gynecology, Nagoya City University Medical School, Mizuho-ku, Nagoya 467-8601, Japan. iinuma@med.nagoya-cu.ac.jp

OBJECTIVE: To investigate whether a factor XII genetic polymorphism is associated with first-trimester embryonal loss. DESIGN: Prospective case-control study. SETTING; Nagoya City University Hospital. PATIENT(S): Eighty-three patients with a history of two or more unexplained first-trimester recurrent miscarriages and 67 controls with no obstetric complications or history of miscarriage. MAIN OUTCOME MEASURE(S): Plasma factor XII activity, a genetic polymorphism (46 C-->T) of factor XII, lupus anticoagulant, and beta(2)glycoprotein I dependent anticardiolipin antibodies. RESULT(S): Ten of the 83 patients and 1 of the 67 controls had decreased factor XII activity; the difference in frequency was statistically significant. Wild-type (CC), heterozygote (CT), and homozygote (TT) allele patterns were observed in 8, 36, and 39 patients, respectively, compared with 11, 20, and 36 of the patients and controls, respectively. The mean (+/- SD) corresponding factor XII activity was 154.8 +/- 44.8%, 112.7 +/- 30.2%, and 66.2 +/- 29.2% in patients and 164.6 +/- 26.7%, 114.3 +/- 28.1%, and 70.4 +/- 18.1% in controls. The two groups did not differ in the frequency of the T allele or categories of factor XII activity. CONCLUSION(S): Factor XII activity overall, but not the 46C/T common genetic polymorphism, is associated with recurrent miscarriage.
(bold added)

...which sure seems to imply that it is important for something.


Further support:

Quote

Pubmed link

Fertil Steril 2001 May;75(5):916-9

Factor XII but not protein C, protein S, antithrombin III, or factor XIII is a predictor of recurrent miscarriage.

Ogasawara MS, Aoki K, Katano K, Ozaki Y, Suzumori K.

Department of Obstetrics and Gynecology, Nagoya City University Medical School, Nagoya, Japan.

OBJECTIVE: To investigate whether a decrease in the values of protein C (PC), protein S (PS), antithrombin III (ATIII), factor XII (FXII), or factor XIII (FXIII) has predictive value for subsequent miscarriages. DESIGN: Prospective study. SETTING: Nagoya City University Medical School. PATIENT(S): A total of 536 patients with a history of two or more first-trimester miscarriages. INTERVENTION(S): One hundred and twelve patients treated with low-dose aspirin were excluded from the analysis. MAIN OUTCOME MEASURE(S): The subsequent pregnancy outcome of 424 patients was compared for abnormal and normal levels of each parameter. RESULT(S): There were no differences in the subsequent miscarriage rates between abnormal and normal values of PC, PS, ATIII, and FXIII. However, the rate with abnormal FXII is significantly higher than that with normal FXII. CONCLUSION(S): A decrease in FXII (but not in PC, PS, ATIII, or FXIII) predicts subsequent miscarriage in patients with a history of first-trimester recurrent miscarriages.



Here is another example of why missing Factor XII is not a good thing:

Quote

Ann Thorac Surg 2002 Jan;73(1):286-8

Huge left atrial thrombus with mitral stenosis in congenital factor XII deficiency.

Hasegawa T, Uematsu M, Tsukube T, Takemura Y, Okita Y.

Department of Surgery, Division II, Kobe University School of Medicine, Japan.

Factor XII deficiency has been reported to be a risk factor for thromboembolism as a result of inactivation of fibrinolysis. We describe a case of a huge left atrial thrombus with mitral stenosis, which was successfully removed surgically in a Factor XII deficient patient.

pubmed link


...and yet the ancestors of whales clearly had Hageman Factor, but lost it.  How is this possible unless Behe's argument about IC is fundamentally flawed?

nic


*** Added in edit, Dec. 2002:

Actually, Behe did not.  It looks like it is on pp. 82 and 84, but on p. 86 Behe limits the system to only four components.  This was pointed out to me by DNAunion here:

http://iidb.org/ubb....759&p=2

On p. 86, Behe writes,

Quote

”Leaving aside the system before the fork in the pathway, where some details are less well known, the blood-clotting system first the definition of irreducible complexity. … The components of the system (beyond the fork in the road) are fibrinogen, prothrombin, Stuart factor, and proaccelerin. Just as none of the parts of the Foghorn [Leghorn] system is used for anything except controlling the fall of the telephone pole, so none of the cascade proteins are used for anything except controlling the formation of a blood clot. Yet in the absence of any one of the components, blood does not clot, and the system fails.” (Michael Behe, Darwin’s Black Box: The Biochemical Challenge to Evolution, Free Press, 1996, p86)


(copying from DNAunion)

Ken Miller, here,

http://www.millerandlevine.com/km/evol/design2/article.html

...writes:

Quote

Consider, for example, the intricate cascade of proteins involved in the clotting of vertebrate blood. This has been cited as one of the principal examples of the kind of complexity that evolution cannot generate, despite the elegant work of Russell Doolittle (Doolittle and Feng 1987; Doolittle 1993) to the contrary. A number of proteins are involved in this complex pathway, as described by Behe:

When an animal is cut, a protein called Hagemann factor (XII) sticks to the surface of cells near the wound. Bound Hagemann factor is then cleaved by a protein called HMK to yield activated Hagemann factor. Immediately the activated Hagemann factor converts another protein, called prekallikrein, to its active form, kallikrein. (Behe 1996a, 84)

How important are each of these proteins? In line with the dogma of irreducible complexity, Behe argues that each and every component must be in place before the system will work, and he is perfectly clear on this point:

. . . none of the cascade proteins are used for anything except controlling the formation of a clot. Yet in the absence of any of the components, blood does not clot, and the system fails. (Behe 1996a, 86)

As we have seen, the claim that every one of the components must be present for clotting to work is central to the "evidence" for design. One of those components, as these quotations indicate, is Factor XII, which initiates the cascade. Once again, however, a nasty little fact gets in the way of intelligent design theory. Dolphins lack Factor XII (Robinson, Kasting, and Aggeler 1969), and yet their blood clots perfectly well. How can this be if the clotting cascade is indeed irreducibly complex? It cannot, of course, and therefore the claim of irreducible complexity is wrong for this system as well. I would suggest, therefore, that the real reason for the rejection of "design" by the scientific community is remarkably simple – the claims of the intelligent design movement are contradicted time and time again by the scientific evidence.


...the second quote is pretty clearly out-of-context and Miller should have noted that Behe left himself some wiggle room in DBB concerning everything "before the fork" -- most of the cascade.  Behe only explicitly includes four parts in the IC system.

Edited by niiicholas on Dec. 07 2002,23:41

  
niiicholas



Posts: 319
Joined: May 2002

(Permalink) Posted: May 24 2002,21:25   

A recent post on talk.origins by Dunk discussing some recent (2002) literature, with quotes:

Here is the google link

nic

  
niiicholas



Posts: 319
Joined: May 2002

(Permalink) Posted: May 24 2002,22:27   

An attempt to list the major relevant articles/books in the ID blood-clotting discussion:

Code Sample

Darwin's Black Box : The Biochemical Challenge to Evolution
by Michael J. Behe
http://www.amazon.com/exec/obidos/ASIN/0684834936/

Behe and the Blood Clotting Cascade (1997)
T.O. POTM on blood-clotting pointing out the sequence patterns
http://www.talkorigins.org/origins/postmonth/feb97.html

A Delicate Balance
by Russell F. Doolittle
http://bostonreview.mit.edu/br22.1/doolittle.html
Originally published in the February/ March 1997 issue of Boston Review

Behe Responds to the Boston Review
Letter to the Boston Review
by Michael J. Behe
(listed as copyright 1999, Behe originally posted the material to the Boston Review discussion bord in Spring 1997)
http://www.arn.org/docs/behe/mb_brrespbr.htm

Finding Darwin's God, Miller (1999)
Amazon.com link
http://www.amazon.com/exec/obidos/ASIN/0060930497/

In Defense of the Irreducibility of the Blood Clotting Cascade (July 31, 2000)
Response to Russell Doolittle, Ken Miller and Keith Robison
by Michael J. Behe
http://www.discovery.org/viewDB/index.php3?program=CRSC%20Responses&command=view&id=442

Design on the Defensive, (Fall (?) 2000)
Ken Miller's page responding to Behe's review of Miller's book
http://biocrs.biomed.brown.edu/Darwin/DI/Design.html

(Ken Miller evolution page: http://www.millerandlevine.com/km/evol/index.html)

Miller's response to Behe's (2000) "In defense of the IC of the Blood Clotting Cascade."
Introduction to Miller's argument on blood-clotting: http://www.millerandlevine.com/km/evol/DI/Clotting.html
...linked from Miller's 'Design on the Defensive' (http://www.millerandlevine.com/km/evol/DI/Design.html)

The Evolution of Vertebrate Blood Clotting
Miller's "original draft" (longer description than in the book) on the evolution of blood-clotting. Linked from the above reference: http://www.millerandlevine.com/km/evol/DI/clot/Clotting.html

Comments on Ken Miller's Reply to My Essays (Behe, January 2001)
A response to Ken Miller, but blood-clotting isn't mentioned.
http://www.discovery.org/viewDB/index.php3?program=CRSC%20Responses&command=view&id=579


There may be additional relevant online articles, I will add them if anyone suggests them.

Thanks, nic

Edited by niiicholas on May 24 2002,22:30

  
niiicholas



Posts: 319
Joined: May 2002

(Permalink) Posted: May 24 2002,23:28   

Here is a muddled page in support of Behe's IC blood-clotting argument, I list it as it draws heavily from Behe's chapter & gives a sense of Behe's specific arguments there (including Behe's inclusion of Hageman factor in the IC system):

Irreducible Complexity? Blood Clotting! at www.doesgodexist.org, by Robert Harsh

nic

  
niiicholas



Posts: 319
Joined: May 2002

(Permalink) Posted: May 24 2002,23:51   

A somewhat interesting but mildly confused article in Geology News, "Geoscience at the BA: Clots have been with us for 400 million years", reporting on a talk by Colin Davidson (Imperial College School of Medicine) on the evolution of blood-clotting, especially regarding the role of large (genome or chromosome) duplications.  I say the article is confused as punctuated equilibrium is invoked as having something to do with the situation, which AFAICT it doesn't, and as none of the connections of blood-clotting to more ancient protease cascade systems are discussed.  The interesting quotes concern gene duplication:

Quote

Evolution at molecular level

The basic tenets of molecular biology make understanding evolution at the molecular level possible. Genes are encoded by DNA, also known as nucleic acid, and composed of long strings of four biochemical units termed bases (shortened to A, G, C, and T). The linear order or sequence of these bases encodes special signals for starting and stopping as well code-script read in triplets for amino acids.

These chains of amino acids - of which there are 20 - form proteins and are the products of most (but not all) genes. We can, therefore, determine the determine the protein amino acid sequence of genes by decoding the triplet DNA sequences and compare it to any other gene. The more evolutionarily similar two organisms, the greater the similarity of amino acid sequences when comparing homologous genes. This is because there has been less time for the natural mutation process - such as inborn errors in DNA replication - to act on a gene's DNA sequence. When comparing most human and chimpanzee proteins one finds 98 to 100% identity, but the same proteins shared with bacteria the identity drops between 30 to 60% or less.

Proteins also exist in the genomes of most organisms that share a high degree of identity, and who share a common ancestor. The best understood mechanism of gene duplication occurs during the production of gametes in sexual organisms. This process is called meiosis in which the two sets of chromosomes - one from each parent - line up and the threads of DNA cross, break and rejoin so that DNA is exchanged between parental chromosomes - so generating diversity.

Usually this is an equal and reciprocal exchange, but occasionally the result is unequal and one of the chromosomes acquires a little more DNA containing an extra gene,or part of one. If the gamete with extra DNA acquires an entire gene it is referred to as "gene duplication by unequal crossover".

In blood clotting, two of the similar proteases, Factor VII (FVII) and X (FX), are within close proximity on chromosome 13 in humans indicating that unequal crossover played a role in the evolution of blood clotting.

Complete genome duplication

Another mechanism of gene duplication is through complete genome duplication. The entire genome of brewer's yeast Saccharomyces cerevisiae has been sequenced, and provides evidence of complete genome duplication by the genetic redundancy and conserved arrangement of the remaining duplicated genes. One way that genome duplication can occur is through polyploidy and subsequent degeneration back to a lower ploidy state. (Polyploidy is where the cell nucleus contains multiple sets of chromosomes.  Humans are diploid meaning we have two copies of each chromosome but the toad Xenopus laevis has four copies of each chromosome and therefore an additional two copies of each gene.)

Such duplicated genes can take one of two career paths. The majority of gene duplicates enter "early retirement" as the constant mutational pressure results in amino acid substitutions that render the protein non-functional. In the rare event that the amino acid substitution is beneficial, the duplicated gene can participate in natural selection and acquire a new function or interaction within an existing pathway - such as blood clotting.

" It appears that the physiologically important 'extrinsic' pathway as we know it mammals evolved by two rounds of genome or chromosomal duplication and one tandem duplication prior to a last common ancestor with fish ~400 MYA and after the origin of the vertebrates ~520 MYA. This brief window of evolutionary time indicates that a flurry of duplication events occurred to generate the clotting pathway and supports the theories of punctuated evolution.

"The evolutionary time frame of blood clotting evolution is supported by investigations into other gene families such as Hox genes and the genes of the MHC. Investigations in other systems support the two large-scale duplication of the ancestral vertebrate genome as well. The debatable issue is when both duplications occurred." says Davidson.


However, in the conclusion Davidson is also quoted as saying:

Quote

Fundamental evolutionary event

"Vertebrates are one of the planet's most diverse and successful group of animals colonizing both the water and land. Vertebrates share common developmental physiology, and anatomy and are distinguished from invertebrates by complex systems such as immune, nervous, endocrine and blood clotting systems.

"Since blood transports and mediates many of the above vertebrate innovations it seems certain that the protective function of blood clotting was a fundamental evolutionary event. A more primitive state of blood clotting than that found in jawless vertebrates is likely not present in any living creature and died with the primitive vertebrates in the Cambrian.

"The origin of vertebrate blood clotting, like the origin of life must have been a rare event, yet without protection from bleeding it would not have been possible for the radiation of vertebrates from fish to dinosaurs and ultimately humans."


I think it is a mistake to compare the origin of blood-clotting to the origin of life, or even to imply that it is rare: it is apparent that a similar system has arisen in arthropods at least (see Miller's (1999) discussion of the evolution of decapod blood-clotting), and it seems quite likely various clotting systems will be discovered in other complex metazoans (perhaps descended from a primitive ancestral system, but still with considerable independent evolution in each lineage, as e.g. with eyes).  One can even argue that the pitch of trees is a clotting system. Perhaps Davidson is a wee bit vertebrate-biased.

nic

  
niiicholas



Posts: 319
Joined: May 2002

(Permalink) Posted: May 25 2002,00:35   

An interesting paragraph from a recent article that continues the debate between Behe and Shanks & Joplin, regarding the (chemical) specificity necessary for ICness vs. "simple interactive" systems or what-have-you.

Niall Shanks and Karl Joplin, "Behe, Biochemistry, and the Invisible Hand," Philo, Volume 4, Number 1.

Link: http://www.philoonline.org/library/shanks_4_1.htm

Regarding blood-clotting & specificity, they write:

Quote

Behe bolsters his attack on the BZ reaction with a truly bizarre argument derived from the fact that the reagents in the BZ reaction have a wide variety of uses—in Behe’s terminology, they have low specificity. For example, one ingredient, sodium bromate, is a general purpose oxidizing agent, and ingredients other than the ones we mentioned can be substituted. In our reaction, we mentioned the use of cerium ions, but iron or manganese ions will work just as well. He points out that the reaction is easy to set up and runs over a wide range of concentrations.21

If this is the case, then mousetraps are not irreducibly complex either. The steel used in their construction has a wide range of uses, as does the wood used for the base. You can substitute plastic for wood, and any number of metals for the spring and hammer. Mousetraps are easy to make (which is why they are cheap) and will work with metals manifesting a wide range of tensile strengths. But the fact that they are easy to make does not mean they assemble just by chance. Mousetraps need a maker just as much as the BZ system needs chemical mechanisms governed by the laws of chemistry. Either the BZ system is an irreducibly complex system, or the complexity of mousetraps is not a model for irreducible complexity. Take your pick, for you cannot have it both ways.

This matter is made all the more acute because crucial components of Behe’s own examples of irreducible complexity have multiple uses and lack substrate specificity (interact with a wide variety of substrates). For example, plasminogen (a component of the irreducibly complex blood-clotting cascade) has been documented to play a role in a wide variety of physiological processes, ranging from tissue remodeling, cell migration, embryonic development, and angiogenesis, as well as wound healing.22 And though Behe tells us that plasmin (the activated form of plasminogen), “. . . acts as scissors specifically to cut up fibrin clots,”23 we learn in one of the very papers he cites that, “Plasmin has a relatively low substrate specificity and is known to degrade several common extracellular-matrix glycoproteins in vitro.”24

[...]

22. See Thomas H. Bugge, Keith W. Kombrinck, Matthew J. Flick, Cynthia C. Daugherty, Mary J. Danton, Jay L. Degan, “Loss of Fibrinogen Rescues Mice for the Pleiotropic Effects of Plasminogen Deficiency,” Cell 87 (1996): 709–19.

23. See Behe, Darwin’s Black Box, 88.

24. See Bugge, et al., “Loss of Fibrinogen Rescues Mice,” 709.



Blood-clotting comes up again here:

Quote

In our original article we pointed to the gene coding for the protein p53. Lab mice have been created in which this gene has been knocked out. In support of our claims about the existence of redundancy in biochemical systems, we pointed out that, though this protein was involved in a number of important biochemical and biological processes, its removal did not result in a catastrophic disruption of the developmental process. There was redundancy, and other proteins could conspire to do the work of the missing protein.

Behe acknowledges this case, but draws his reader’s attention to the blood-clotting cascade originally discussed in his book:

Yet contrast this case [p53] with that of mice in which the gene for either fibrinogen, tissue factor, or prothrombin has been knocked out. . . . The loss of any one of those proteins prevents clot formation—the clotting cascade is broken. Thus Shanks and Joplin’s concept of redundant complexity does not apply to all biochemical systems.41

Again, suppose this point is right. What is its relevance when the role of redundant complexity lies in its ability to account, in natural, evolutionary terms, for the origins of irreducible complexity? And origins, as Behe points out, is the central issue. Loss of functional genes reduces redundancy to yield an irreducibly complex system. All Behe’s example shows is that further losses at this point can catastrophically disrupt the system.

We also think, however, that Behe has oversold the irreducible complexity of the blood-clotting cascade. The cascade itself has features that manifest redundant complexity. The real situation is thus more complex than Behe’s carefully massaged description would lead you to believe. Plasminogen deficient (Plg-/-)—hence plasmin deficient—mice have been studied. As noted earlier, plasmin is needed for clot degradation (it cuts up the fibrin), yet:

Plasmin is probably one member of a team of carefully regulated and specialized matrix-degrading enzymes, including serine-, metallo-, and other classes of proteases, which together serve in matrix remodeling and cellular reorganization of wound fields. . . . However, despite slow progress in wound repair, wounds in Plg-/- mice eventually resolve with an outcome that is generally comparable to that of control mice. Thus an interesting and unresolved question is what protease(s) contributes to fibrin clearance in the absence of Plg?42

Behe cited this very paper, so we must assume that he, too, knows that parts of his clotting-cascade are redundantly complex. In this case, healing delayed is not healing denied!

[...]

41. See Behe, “Self-Organization and Irreducible Complexity,” 161.

42. See Bugge, et al. “Loss of Fibrogen Rescues Mice,” 717.


...Bugge et al. rides again!  (This was a paper which Doolittle misread, or at least oversimplified, in his Boston review article, which gave Behe an opportunity to dodge the real issue, namely how Doolittle has been able to predict the presence of blood-clotting proteins in various species (with simpler systems, no less) unless Doolittle's model for the evolution of blood-clotting has significant validity.)

Brief commentary on Shanks & Joplin: while they have introduced the useful notion of "redundant complexity", and in the above 2001 Philo paper have tied the concept to the "scaffolding" model for the origin of IC (i.e., reduce redundancy and you end up with IC), I don't think that they have a general solution to the origin of IC unless they incorporate cooption/change of function into their analysis.  I can only think of a few examples where "loss of scaffolding" explains the origin of an IC system, but many where cooption of a part/system to a new function explains it.  Perhaps more importantly, the processes are not mutually exclusive and so in some cases both processes might operate in succession.

nic

  
niiicholas



Posts: 319
Joined: May 2002

(Permalink) Posted: Dec. 07 2002,15:23   

bump

  
niiicholas



Posts: 319
Joined: May 2002

(Permalink) Posted: Dec. 08 2002,00:10   

Looks like this bit got nuked in the server crash.  The 1969 paper on Hagemann factor loss in whales has been cited, but there is an interesting 1998 paper:

Quote

http://www.ncbi.nlm.nih.gov/entrez....9678675

Thromb Res 1998 Apr 1;90(1):31-7
 
Whale Hageman factor (factor XII): prevented production due to pseudogene conversion.

Semba U, Shibuya Y, Okabe H, Yamamoto T.

Department of Clinical Laboratory Medicine, School of Medicine, Kumamoto University, Honjo, Japan.

In Southern blot analysis of the Hind III-digested whale genomic DNA obtained from the livers of two individual whales, we detected a single band with a size of five kilobase pairs which hybridized to full length guinea pig Hageman factor cDNA. We amplified two successive segments of the whale Hageman factor gene by polymerase chain reaction (PCR), and sequenced the PCR products with a combined total of 1367 base pairs. Although all of the exon-intron assemblies predicted were identical to those of the human Hageman factor gene, there were two nonsense mutations making stop codons and a single nucleotide insertion causing a reading frame shift. We could not detect any message of the Hageman factor gene expression by northern blot analysis or by reverse transcription-polymerase chain reaction (RT-PCR) analysis. These results suggest that in the whale, production of the Hageman factor protein is prevented due to conversion of its gene to a pseudogene. The deduced amino acid sequence of whale Hageman factor showed the highest homology with the bovine molecule among the land mammals analyzed so far.


...obvious implications concerning the origin of whales...

  
theyeti



Posts: 97
Joined: May 2002

(Permalink) Posted: Dec. 31 2002,15:25   

Just came across this recent article.  I haven't read the full-text, but according to the abstract it gives an account of the evolution of vertebrate coagulation factors from those of the invertebrates.

Blood Cells Mol Dis 2002 Jul-Aug;29(1):57-68

 Comprehensive Analysis of Blood Coagulation Pathways in Teleostei: Evolution of Coagulation Factor Genes and Identification of Zebrafish Factor VIIi.

Hanumanthaiah R, Day K, Jagadeeswaran P.


Quote
It is not clear how the complex mammalian coagulation pathways evolved from an entirely dissimilar invertebrate coagulation cascade. Comprehensive analysis of pro-coagulant factors and their regulators is lacking in early vertebrates to discern the mechanism of evolution of these genes from the invertebrates. To elucidate the coagulation pathways found in early vertebrates, zebrafish cDNAs/gene orthologues for major coagulant, anticoagulant, and fibrinolytic proteins were identified and characterized by homology to mammalian sequences. We found that zebrafish carry all hemostatic genes present in mammals, providing evidence that the coagulation system of teleosts is nearly identical to mammals. Zebrafish factor VII and X genes were identified and analyzed to reveal a novel factor VII-like gene flanked by the factor VII and factor X genes. This gene encodes a protein homologous to factor VII, but lacks critical residues for factor VII activity. Expression of the factor VII-like protein (named factor VIIi) demonstrated that it functions as an inhibitor of blood coagulation in biochemical assays using zebrafish or human plasmas. Analysis of intergenic DNA between the zebrafish VII/VIIi/X gene cluster and a Drosophila trypsin gene cluster revealed significant homology, and based upon these data, we propose a model for a rapid evolution of coagulation factors from the invertebrates.


theyeti

  
niiicholas



Posts: 319
Joined: May 2002

(Permalink) Posted: Dec. 31 2002,17:37   

Please give us your informed opinion when you get a chance to read it.  A freely online 2001 PNAS article (from related articles) provides something of a preview:

Quote

Sheehan J, Templer M, Gregory M, Hanumanthaiah R, Troyer D, Phan T, Thankavel B, Jagadeeswaran P.

Demonstration of the extrinsic coagulation pathway in teleostei: identification of zebrafish coagulation factor VII.

Proc Natl Acad Sci U S A 2001 Jul 17;98(15):8768-73

Department of Cellular and Structural Biology, South Texas Veteran's Health Care System, Audie Murphy Division, University of Texas Health Science Center, San Antonio, TX 78229, USA.

It is not known whether the mammalian mechanism of coagulation initiation is conserved in fish. Identification of factor VII is critical in providing evidence for such a mechanism. A cDNA was cloned from a zebrafish (teleost) library that predicted a protein with sequence similarity to human factor VII. Factor VII was shown to be present in zebrafish blood and liver by Western blot analysis and immunohistochemistry. Immunodepletion of factor VII from zebrafish plasma selectively inhibited thromboplastin-triggered thrombin generation. Heterologous expression of zebrafish factor VII demonstrated a secreted protein (50 kDa) that reconstituted thromboplastin-triggered thrombin generation in immunodepleted zebrafish plasma. These results suggest conservation of the extrinsic coagulation pathway between zebrafish and humans and add credence to the zebrafish as a model for mammalian hemostasis. The structure of zebrafish factor VIIa predicted by homology modeling was consistent with the overall three-dimensional structure of human factor VIIa. However, amino acid disparities were found in the epidermal growth factor-2/serine protease regions that are present in the human tissue factor-factor VIIa contact surface, suggesting a structural basis for the species specificity of this interaction. In addition, zebrafish factor VII demonstrates that the Gla-EGF-EGF-SP domain structure, which is common to coagulation factors VII, IX, X, and protein C, was present before the radiation of the teleosts from the tetrapods. Identification of zebrafish factor VII significantly narrows the evolutionary window for development of the vertebrate coagulation cascade and provides insight into the structural basis for species specificity in the tissue factor-factor VIIa interaction.

[...]

Discussion  
 
This investigation demonstrates the presence of coagulation factor VII in the zebrafish, providing molecular evidence for an extrinsic coagulation pathway in a nonmammalian species. Similarities between zebrafish and human primary protein sequence, domain organization (Gla-EGF-EGF-SP), and postulated three-dimensional structure suggest that this cDNA is orthologous to human factor VII. These sequence similarities include conservation of a single activation cleavage site, the cysteines participating in disulfide bonds, and residues that contribute to the formation of specific binding sites for sodium and calcium ions. The presence of the predicted protein was demonstrated in zebrafish plasma and liver with specific rabbit antisera vs. a unique zebrafish factor VII peptide. Immunodepletion of zebrafish plasma with the antipeptide antisera selectively inhibited thromboplastin-triggered thrombin generation. Finally, the zebrafish cDNA directed the expression of a secreted mature protein that was similar in size to human factor VII, which reconstituted thromboplastin-triggered thrombin generation in immunodepleted plasma. These structural and functional correlates reflect the conservation of factor VII gene function between zebrafish and man.

The coagulation serine proteases arose from the family of trypsin-like genes, characterized by protease domains that use the AGY codon for the catalytic serine {195}, and contain a specific sodium ion-binding motif, Tyr/Phe {225} (23, 27). The organization of the N terminus propeptide is unique to these proteases, composed of a ¦Ã-carboxylation (Gla) domain followed by two EGF or kringle domains. Although Gla, EGF, and SP modules exist in invertebrates such as Drosophila melanogaster, there is no evidence for this unique domain organization (28). Likewise, serine proteases responsible for hemolymph coagulation in Tachypleus tridentatus (Japanese horseshoe crab) and other invertebrates species differ significantly in N terminus domain content and organization from mammalian coagulation proteases (29¨C31). Evidence for prothrombin (which contains kringle domains) exists in the primitive jawless hagfish (Myxinidae) (11). However, zebrafish factor VII now provides the earliest known evolutionary appearance of the Gla-EGF-EGF-SP domain structure common to factors VII, IX, and X and protein C. Demonstration of both zebrafish prothrombin (18) and factor VII indicates that the relevant domain assembly for the coagulation proteases had occurred (presumably by exon shuffling) (32) at or before the time of the last common ancestor of humans and zebrafish, ¡Ö450 million years ago (33).

Significant species specificity exists in the tissue factor¨Cfactor VIIa interaction between mammalian species and appears relatively complete between zebrafish and man (15). The human soluble tissue factor¨Cfactor VIIa structure demonstrates three major intermolecular contacts involving the Gla, EGF-1, and EGF-2/SP domains, respectively (24). Inspection of homologous surfaces on the zebrafish factor VIIa model suggests that intermolecular interactions are conserved largely for the Gla and EGF-1 contact regions. In contrast, surface residues in the EGF-2/SP contact region are poorly conserved, suggesting that the intermolecular interactions with human tissue factor are largely disrupted. This disruption includes the protease insertion loop Leu-371¨CGlu-385 {170¨C178}, which appears to undergo a conformational change between the bound and unbound structures of human factor VIIa (25). In the zebrafish protein, this loop demonstrates a 5-aa deletion and replacement of a neighboring conserved Met with Arg-348 {164}. These differences in the EGF-2/SP intermolecular contact region between zebrafish and man suggest a structural basis for the observed species specificity in the tissue factor¨Cfactor VIIa interaction. Hybrid recombinant human/zebrafish factor VII proteins in which the EGF-2/SP intermolecular contact regions are exchanged could directly test their contribution to the species specificity of this interaction.

Identification of zebrafish factor VII has important implications for the relevance of this powerful genetic model to the study of hemostasis and thrombosis. The ability to trigger (and selectively inhibit) tissue thromboplastin-dependent coagulation in a species-specific manner provides indirect evidence for tissue factor in the zebrafish. Functional data also suggest the presence of a contact-activated coagulation pathway that is independent of factor VII and factor X-like activity in the zebrafish (15). Factor X-like activity (based on RVV-X activator) is not affected by immunodepletion of factor VII, demonstrating that these activities are distinct. The degree of similarity between zebrafish and mammalian coagulation suggests that the zebrafish is a relevant animal model for the study of genes that affect hemostasis. Phenotypic screens of mutagenized zebrafish may identify novel genes that regulate the initiation of coagulation.

In conclusion, the structural features of factor VII in the zebrafish suggest that domain assembly for the coagulation proteases occurred before radiation of the ancestral Actinopterygii (ray-finned fishes) and Sarcopterygii (lungfish and tetrapods). The gene structure (intron/exon boundaries) of coagulation factors VII, IX, and X and protein C indicates that these genes are paralagous, suggesting a common origin via gene duplication (34). Thus, it appears likely that the vertebrate coagulation cascade arose rapidly during proposed genome duplications between ancestral chordates and the development of jawed vertebrates (35¨C37). Given the functional and structural similarities to mammalian coagulation demonstrated thus far, the zebrafish should be a powerful model to identify novel genes involved in vertebrate coagulation.


Doolittle and Patthy are referenced, unfortunately little of Doolittle's and none of Patthy's blood-clotting stuff is in widely available online journals...they all seem to be down at UCSD however.

  
theyeti



Posts: 97
Joined: May 2002

(Permalink) Posted: Mar. 16 2003,13:08   

This one just came out.  Sure to be useful for blood-clotters.

Thromb Haemost 2003 Mar;89(3):420-8

Molecular evolution of the vertebrate blood coagulation network.

Davidson CJ, Hirt RP, Lal K, Snell P, Elgar G, Tuddenham EG, McVey JH.


Quote
In mammalian blood coagulation 5 proteases, factor VII (FVII), factor IX (FIX), factor X (FX), protein C (PC) and prothrombin act with two cofactors factor V and factor VIII to control the generation of fibrin. Biochemical evidence and molecular cloning data have previously indicated that blood coagulation involving tissue factor, prothrombin and fibrinogen is present in all vertebrates. Using degenerate RT-PCR we have isolated and characterized novel cDNAs with sequence identity to the blood coagulation serine proteases and cofactors from chicken and the puffer fish (Fugu rubripes). Sequence alignments, phylogenetic and comparative sequence analysis all support the existence of the Gla-EGF1-EGF2-SP domain serine proteases FVII, FIX, FX, PC and the A1-A2-B-A3-C1-C2 domain protein cofactors FV and FVIII in these species. These results strongly suggest that the blood coagulation network is present in all jawed vertebrates and evolved before the divergence of tetrapods and teleosts over 430 million years ago; and that vertebrate blood coagulation may have benefited from two rounds of gene or whole genome duplication. Sequences identified in Fugu coding for additional FVII-like, FIX-like and PC-like sequences support the possibility of further tandem and large-scale duplications in teleosts. Comparative sequence analyses of amino acid residues in the active site region suggest these additional sequences have evolved new and as yet unknown functions.


theyeti

  
niiicholas



Posts: 319
Joined: May 2002

(Permalink) Posted: Mar. 21 2003,03:03   

If anyone has text access and could send me the pdf of the previous article I'd be grateful.  I did a google search but no one has put it on the web yet.

Link:
http://www.ncbi.nlm.nih.gov/entrez....bstract

I did turn this up, though, dunno how I missed it before:

==========
A Scenario for the Evolution of Hemostasis
by Kevin O'Brien

http://home.tiac.net/~cri/1998/hemostasis.html

Quote

A Scenario for the Evolution of Hemostasis
by Kevin O'Brien


--------------------------------------------------------------------
This is a revised version of an article that originally appeared in the talk.origins newsgroup. It was composed in response to the following challenge:

Let's start with the clotting system. Tell us all how the IC core, consisting of fibrinogen, prothrombin, Stuart factor, and accelerin, could have evolved.

It is granted that prothrombin and the Stuart factor may have evolved from a common ancestor A by duplication and divergence, if A was autocatalytic.

References specific to talk.origins have been removed and slight editorial changes have been made. - Richard Harter, editor.


--------------------------------------------------------------------

==========

I've often thought that such an article could be written, I just didn't know who would do it.  But someone has.

I recommend we attempt to get some version of this on talkdesign.org if theyeti et al. consider it reasonable and if we can get permission (its a t.o. poster, I don't think that would be a problem).  

It would need a fair bit more editing though...

  
theyeti



Posts: 97
Joined: May 2002

(Permalink) Posted: June 18 2003,09:43   

Russel Doolittle has a new article out in PNAS.  Unfortunately, it's not available online yet.  But it's on PubMed.

Proc Natl Acad Sci U S A. 2003 Jun 13 [Epub ahead of print].

The evolution of vertebrate blood coagulation as viewed from a comparison of puffer fish and sea squirt genomes.

Jiang Y, Doolittle RF.

Quote
The blood coagulation scheme for the puffer fish, Fugu rubripes, has been reconstructed on the basis of orthologs of genes for mammalian blood clotting factors being present in its genome. As expected, clotting follows the same fundamental pattern as has been observed in other vertebrates, even though genes for some clotting factors found in mammals are absent and some others are present in more than one gene copy. All told, 26 different proteins involved in clotting or fibrinolysis were searched against the puffer fish genome. Of these, orthologs were found for 21. Genes for the "contact system" factors (factor XI, factor XII, and prekallikrein) could not be identified. On the other hand, two genes were found for factor IX and four for factor VII. It was evident that not all four factor VII genes are functional, essential active-site residues having been replaced in two of them. A search of the genome of a urochordate, the sea squirt, Ciona intestinalis, did not turn up any genuine orthologs for these 26 factors, although paralogs and/or constituent domains were evident for virtually all of them.


theyeti

  
niiicholas



Posts: 319
Joined: May 2002

(Permalink) Posted: June 24 2003,12:35   

Here is figure 5 from Jiang & Doolittle's article:

Quote
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?

Quote

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)

  
niiicholas



Posts: 319
Joined: May 2002

(Permalink) Posted: June 24 2003,13:04   

repost from my new ISCID thread:

New article on the evolution of blood-clotting
http://www.iscid.org/ubbcgi....=000006

Doolittle and an associate have just published a new article on the evolution of the blood-clotting cascade in PNAS:

Quote

Proc Natl Acad Sci U S A. 2003 Jun 13 [Epub ahead of print].
 
The evolution of vertebrate blood coagulation as viewed from a comparison of puffer fish and sea squirt genomes.

Jiang Y, Doolittle RF.

Center for Molecular Genetics, University of California at San Diego, La Jolla, CA 92093-0634.

The blood coagulation scheme for the puffer fish, Fugu rubripes, has been reconstructed on the basis of orthologs of genes for mammalian blood clotting factors being present in its genome. As expected, clotting follows the same fundamental pattern as has been observed in other vertebrates, even though genes for some clotting factors found in mammals are absent and some others are present in more than one gene copy. All told, 26 different proteins involved in clotting or fibrinolysis were searched against the puffer fish genome. Of these, orthologs were found for 21. Genes for the "contact system" factors (factor XI, factor XII, and prekallikrein) could not be identified. On the other hand, two genes were found for factor IX and four for factor VII. It was evident that not all four factor VII genes are functional, essential active-site residues having been replaced in two of them. A search of the genome of a urochordate, the sea squirt, Ciona intestinalis, did not turn up any genuine orthologs for these 26 factors, although paralogs and/or constituent domains were evident for virtually all of them.



Here is figure 5 (and discussion) from Jiang & Doolittle's article:

Quote
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.




What I find interesting is how this work is presaged on 20 years+ of literature on the evolution of blood-clotting.  For example, here are the references that Doolittle lists as some of the preceding work:

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

...and finally, several other recent articles advancing the discussion in the light of recently published genomes have also been published, e.g.:

Quote

Thromb Haemost. 2003 Mar;89(3):420-8.
 
Molecular evolution of the vertebrate blood coagulation network.

Davidson CJ, Hirt RP, Lal K, Snell P, Elgar G, Tuddenham EG, McVey JH.

Haemostasis Group, MRC Clinical Sciences Centre, The Faculty of Medicine, Imperial College, Du Cane Road, London W12 0NN, UK.

In mammalian blood coagulation 5 proteases, factor VII (FVII), factor IX (FIX), factor X (FX), protein C (PC) and prothrombin act with two cofactors factor V and factor VIII to control the generation of fibrin. Biochemical evidence and molecular cloning data have previously indicated that blood coagulation involving tissue factor, prothrombin and fibrinogen is present in all vertebrates. Using degenerate RT-PCR we have isolated and characterized novel cDNAs with sequence identity to the blood coagulation serine proteases and cofactors from chicken and the puffer fish (Fugu rubripes). Sequence alignments, phylogenetic and comparative sequence analysis all support the existence of the Gla-EGF1-EGF2-SP domain serine proteases FVII, FIX, FX, PC and the A1-A2-B-A3-C1-C2 domain protein cofactors FV and FVIII in these species. These results strongly suggest that the blood coagulation network is present in all jawed vertebrates and evolved before the divergence of tetrapods and teleosts over 430 million years ago; and that vertebrate blood coagulation may have benefited from two rounds of gene or whole genome duplication. Sequences identified in Fugu coding for additional FVII-like, FIX-like and PC-like sequences support the possibility of further tandem and large-scale duplications in teleosts. Comparative sequence analyses of amino acid residues in the active site region suggest these additional sequences have evolved new and as yet unknown functions.

[...]

Blood Cells Mol Dis. 2002 Jul-Aug;29(1):57-68.  
 
Comprehensive Analysis of Blood Coagulation Pathways in Teleostei: Evolution of Coagulation Factor Genes and Identification of Zebrafish Factor VIIi.

Hanumanthaiah R, Day K, Jagadeeswaran P.

ABSTRACT
It is not clear how the complex mammalian coagulation pathways evolved from an entirely dissimilar invertebrate coagulation cascade. Comprehensive analysis of pro-coagulant factors and their regulators is lacking in early vertebrates to discern the mechanism of evolution of these genes from the invertebrates. To elucidate the coagulation pathways found in early vertebrates, zebrafish cDNAs/gene orthologues for major coagulant, anticoagulant, and fibrinolytic proteins were identified and characterized by homology to mammalian sequences. We found that zebrafish carry all hemostatic genes present in mammals, providing evidence that the coagulation system of teleosts is nearly identical to mammals. Zebrafish factor VII and X genes were identified and analyzed to reveal a novel factor VII-like gene flanked by the factor VII and factor X genes. This gene encodes a protein homologous to factor VII, but lacks critical residues for factor VII activity. Expression of the factor VII-like protein (named factor VIIi) demonstrated that it functions as an inhibitor of blood coagulation in biochemical assays using zebrafish or human plasmas. Analysis of intergenic DNA between the zebrafish VII/VIIi/X gene cluster and a Drosophila trypsin gene cluster revealed significant homology, and based upon these data, we propose a model for a rapid evolution of coagulation factors from the invertebrates.



So, when is Dembski going to retract the following?

Quote

STILL SPINNING JUST FINE: A RESPONSE TO KEN MILLER

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)


This is what really gets the goat of scientists -- pronouncements of the failure of entire disciplines by IDists like Dembski, when it's clear that Dembski hasn't done the slightest bit of actual reading, let alone consideration, let alone informed critical discussion in peer-reviewed journals, or the relevant literature.  Sure, the origin of the flagellum is not yet well-understood (although there are number of plausible ideas and hints), but the IC argument was about a **class** of systems, called "IC systems", and when the literature on the evolution of *other* IC systems, like the immune system and blood-clotting system, is demonstrated, what is Dembski's response?  Did it "suffice" to show him the literature?  No, he just goes into denial mode.

Perhaps he will discuss it in his forthcoming book, but somehow I doubt it.  Let's get real, Dr. Dembski.

  
niiicholas



Posts: 319
Joined: May 2002

(Permalink) Posted: June 24 2003,13:11   

If this wasn't posted before:

EVOLUTION AND PHYLOGENY OF DEFENSE MOLECULES ASSOCIATED WITH INNATE IMMUNITY IN HORSESHOE CRAB
http://www.bioscience.org/1998/v3/d/iwanaga/3.htm

  
niiicholas



Posts: 319
Joined: May 2002

(Permalink) Posted: July 02 2003,15:43   

Check this out:

Quote

http://www.blackwell-synergy.com/links....abs

Journal of Thrombosis and Haemostasis
Volume 1 Issue 2 Page 227  - February 2003
doi:10.1046/j.1538-7836.2003.00062.x
 

REVIEW ARTICLE
Hemostasis and irreducible complexity
W. C. Aird

Summary. Coagulation evolved as a means to stem the loss of blood and to defend against pathogens. The complexity of the clotting cascade has been cited as evidence for the existence of divine intervention. The objective of this review is to draw on the debate between creationists and evolutionary biologists to highlight important evolutionary principles that underlie the hemostatic mechanism. I propose the following: (a) as with all biological systems, the hemostatic mechanism displays non-linear complexity; (b) the cellular response represents primary hemostasis owing to its place in the evolutionary time scale and functional importance; and © the rapid evolution of the hemostatic mechanism in vertebrates is testimony to the power and versatility of gene duplications and exon shuffling.

  
niiicholas



Posts: 319
Joined: May 2002

(Permalink) Posted: Dec. 19 2003,01:45   

Haven't read it yet:

Quote

Henri M.H. Spronk, José W.P. Govers-Riemslag, Hugo ten Cate. The blood coagulation system as a molecular machine.  BioEssays 25:1220-1228, 2003. Wiley, PubMed, DOI

Abstract
The human blood coagulation system comprises a series of linked glycoproteins that upon activation induce the generation of downstream enzymes ultimately forming fibrin. This process is primarily important to arrest bleeding (hemostasis). Hemostasis is a typical example of a molecular machine, where the assembly of substrates, enzymes, protein cofactors and calcium ions on a phospholipid surface markedly accelerates the rate of coagulation. Excess, pathological, coagulation activity occurs in thrombosis, the formation of an intravascular clot, which in the most dramatic form precipitates in the microvasculature as disseminated intravascular coagulation. Thrombosis occurs according to a biochemical machine model in the case of atherothrombosis on a ruptured atherosclerotic plaque, but may develop at a slower rate in venous thrombosis, illustrating that the coagulation machinery can act at different velocities. The separate coagulation enzymes are also important in other biological processes, including inflammation for which the rapid conversion of one coagulation factor by the other is not a prerequisite. The latter role of coagulation enzymes may be related to the old and probably maintained function of the coagulation machine in innate immunity.  

  
niiicholas



Posts: 319
Joined: May 2002

(Permalink) Posted: Mar. 17 2004,00:52   

I was just looking at some of the "related articles" on some of the other articles, I discovered this one:

C. J. Davidson, E. G. Tuddenham and J. H. McVey (2003). 450 million years of hemostasis Journal of Thrombosis and Haemostasis. Volume 1 Issue 7 Page 1487.

Quote
In this chapter we review the biochemical evidence, molecular cloning and sequence data indicating the structure of the blood-coagulation network in non-mammalian vertebrates and present an evolutionary scenario to account for possible evolution of what has been described as 'an irreducibly complex system that could not have arisen by a gradual step-by-step Darwinian process' [7]. [Ref #7 is: Behe MJ. Darwin’s Black Box. New York: The Free Press, 1996.]


They include a pretty detailed scenario and lots of pics.

Edited by niiicholas on Mar. 17 2004,00:53

  
niiicholas



Posts: 319
Joined: May 2002

(Permalink) Posted: Mar. 17 2004,01:33   

Looks like Davidson's PhD was on the topic:

Davidson CJ. Molecular evolution of haemostasis. PhD Thesis. London: University of London, 2001.

The alignments used in Davidson's article of the same name are available online here:

http://europium.csc.mrc.ac.uk/

For one of the articles:

Molecular evolution of the vertebrate blood coagulation network

Supplementary figures: Fig1pdf, Fig2pdf

Edited by niiicholas on Mar. 17 2004,01:37

  
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