Scott H Mullins Jun0793 08:10AM Protein and amino acid sequences A creationist with whom I

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Scott H Mullins Jun-07-93 08:10AM Protein and amino acid sequences Organization: Purdue University Engineering Computer Network From: smullins@author.ecn.purdue.edu (Scott H Mullins) Message-ID: Newsgroups: talk.origins A creationist with whom I am debating has recently brought up supposed problems with protein sequences. He has cited the following evidence: In cytochrome-C sequences the following percentage of divergence (measured as a percentage of difference between the sequences in the total number of amino acid sites) are found between the species given in line A and each of the species in line B: A: Rhodospirillum rubrum (a bacterium) B: human (66%), pig (64%), turtle (64%), tuna (66%), sunflower (69%) silkworm (65%), lamprey (66%), wheat (66%), Baker's yeast (69%) A: screw-worm fly B: kangaroo (22), lamprey (26), penguin (22), dog(19), pekin [sic] duck (20) A: baker's yeast B: horse (42), dog (41), pigeon (41), tuna (43), lamprey (45), sunflower (43) castor bean (42) A: carp B: horse (13), rabbit (13), chicken (14), turtle (13), frog (13) Now for hemoglobin (I don't know if it is alpha or beta hemo) A: snail B: lamprey (85), carp (87), frog (87), chicken (85), kangaroo (85) The first, third, and fourth sets of sequence data make sense to me because the last ancestor for all those in group B with the the species in A is the same (I am not entirely sure for yeast in the third data set). My problem is that I don't know where the lamprey falls in the classification scheme or really exactly where the fly or yeast goes either. Is the lamprey a vertebrate? From the data it is hard to tell if it is a fish or what. Another question: Is the degree of divergence among frogs as great as that among mammals? Why might this be? He has also given the following data on "relaxin" (I don't even know what that is) again in percent variation: A: human B: pig (46), rat (46), shark (46), skate (34) A: pig B: rat (54), shark (50), skate (31) A: shark B: pig (50), rat (37), skate (42) This data looks extremely odd to me so I have requested his references. My request to t.o'ers. Does anyone out there know the answers to these question and/or have good references that I should look at? These are specific questions from a creationist (what a surprise) and I would love to be able to expand on my previous answer to him but I simply don't have the background for it. Thanks for any help you can provide. Scott smullins@ecn.purdue.edu ================================================================== Loren I. Petrich Jun-07-93 12:24PM Protein and amino acid sequences Organization: LLNL From: lip@s1.gov (Loren I. Petrich) Message-ID: <1v085j$e9h@s1.gov> Newsgroups: talk.origins : A creationist with whom I am debating has recently brought up supposed : problmes with protein sequences. He has cited the following evidence: Well, I'm sure that L.A. Moran or Stan Friesen might know more about molecular evolution than I do, but that's one of my amateurish interests, so I'll take it on. : In cytochrome-C sequences the following percentage of divergence (measured as : a percentage of difference between the sequences in the total number of amino : acid sites) are found between the species given in line A and each of the : species in line B: : : A:Rhodospirillum rubrum (a bacterium) : B: human (66%), pig (64%), turtle (64%), tuna (66%), sunflower (69%) : silkworm (65%), lamprey (66%), wheat (66%), Baker's yeast (69%) : : A: screw-worm fly : B: kangaroo (22), lamprey (26), penguin (22), dog(19), pekin [sic] duck (20) : : A: baker's yeast : B: horse (42), dog (41), pigeon (41), tuna (43), lamprey (45), sunflower (43) : castor bean (42) : : A: carp : B: horse (13), rabbit (13), chicken (14), turtle (13), frog (13) : : Now for hemoglobin (I don't know if it is alpha or beta hemo) I may add that sequences have been found for both alpha and beta; they appear to be descended from a common ancestral molecule. : A: snail : B: lamprey (85), carp (87), frog (87), chicken (85), kangaroo (85) : : The first, third, and fourth sets of sequence data make sense to me : because the last ancestor for all those in group B with the the species : in A is the same (I am not entirely sure for yeast in the third data set). : My problem is that I don't know where the lamprey falls in the classification : scheme or really exactly where the fly or yeast goes either. Is the lamprey : a vertebrate? From the data it is hard to tell if it is a fish or : what. A lamprey is indeed a vertebrate: it is a jawless fish, like the first fish to appear on this planet. Jaws are derived from the first gill bars. As to where yeast would fall, it appears that molecular-evolution studies like this one are able to answer this question, extrapolating from their success where independent evidence is available. What one really wants is a table of _all_ the values, not just "one vs. the others" as shown here. Here is a family tree, from various sources of data: _Rhodospirillum rubrum_: a purple bacterium Mitochondria of: Animals: Insects: screwworm fly silkworm moth Vertebrates: Jawless fish: lamprey Bony fish: carp tuna Land ones: frog turtle Birds: pigeon chicken duck penguin Mammals: kangaroo rabbit pig horse dog human Plants: sunflower castor bean wheat Fungi: yeast : Another question: Is the degree of divergence among frogs as great as that : among mammals? Why might this be? Why are all the divergences approximately the same? That's one of the key results of molecular evolution, the "neutral theory", which states that much of molecular-level evolution is driven by genetic drift between equally-capable possibilities. This means that, aside from alteration by natural selection and statistical effects, one will see the same molecular distance between all pairs of species sharing the same youngest common ancestor. "Stage of evolution" is totally irrelevant. Indeed, it is interesting to see a revival of the 19th-cy. concept of orthogenesis in the form of the statistics of molecular evolution. : He has also given the following data on "relaxin" (I don't even know what : that is) again in percent variation: : : A: human : B: pig (46), rat (46), shark (46), skate (34) : : A: pig : B: rat (54), shark (50), skate (31) : : A: shark : B: pig (50), rat (37), skate (42) : : This data looks extremely odd to me so I have requested his references. It may be that this protein is under so little selective constraint that its non-critical parts are effectively randomized. Or else these may be molecules with two different ancestries serving the same function in different species. The family tree: Cartilaginous fish: shark skate Mammals: rat pig human : My request to t.o'ers. Does anyone out there know the answers to these : question and/or have good references that I should look at? These are : specific questions from a creationist (what a surprise) and I would : love to be able to expand on my previous answer to him but I simply don't : have the background for it. : : Thanks for any help you can provide. -- /Loren Petrich, the Master Blaster /lip@s1.gov From: Loren I. Petrich To: All Msg #80, Jun-07-93 02:58PM Subject: Re: Protein and amino acid sequences Organization: LLNL From: lip@s1.gov (Loren I. Petrich) Message-ID: <1v0h5s$h1l@s1.gov> Newsgroups: talk.origins In article smullins@author.ecn.purdue.edu (Scott H Mullins) writes: [a lot of stuff...] I forgot to present estimated divergence dates. Here is the family tree and the dates: [Format: Parent, then all the branches, then the date; unfortunately, I cannot draw family trees very well in text form] Purple bacteria / mitochondria: _Rhodospirillum rubrum_ (a purple photosynthetic bacterium) Eukaryotic mitochondria in ancestral protists 1500 my [Proterozoic] Ancestral protists: Animals Plants Fungi (yeast) 1000 my [Proterozoic] Animals: Insects Mollusks (snail) Vertebrates 600 my [Base of Cambrian] Insects (with pupa phase): silkworm moth screwworm fly 100-200 my [Mesozoic] Vertebrates: Jawless Fish (lamprey) Jawed Fish 500 my [early Paleozoic] Jawed Fish: Elasmobranchs Bony Fish Land Vertebrates 400 my [mid-Paleozoic] Elasmobranchs: shark skate [I don't know for sure] Bony fish (teleosts here): carp tuna 100 my [Late Mesozoic?] Land Vertebrates: Amphibians (frog) Reptiles 350 my [Late Paleozoic] Reptiles: Turtles Birds Mammals 250 my [Permian] Birds: duck chicken penguin pigeon 65 my [late Mesozoic / early Cenozoic] Mammals: Marsupials (kangaroo) Placentals 100 my [late Mesozoic] Placentals: pig horse dog rabbit rat human 65 my [late Mesozoic / early Cenozoic] Plants (flowering): Dicots Monocots (wheat): 100-150 my [late Mesozoic] Dicots: sunflower castor bean 50-150 my [late Mesozoic / early Cenozoic] =============================================================== Cornelius Krasel Jun-08-93 12:47AM Protein and amino acid sequences Organization: InterNetNews at ZDV Uni-Tuebingen From: zxmkr08@studserv.zdv.uni-tuebingen.de (Cornelius Krasel) Message-ID: Newsgroups: talk.origins I am not very familiar with sequence analysis (yet), but I will give it a try... In smullins@author.ecn.purdue.edu (Scott H Mullins) writes: >A creationist with whom I am debating has recently brought up supposed >problmes with protein sequences. He has cited the following evidence: [Cytochrome C will be considered in a later post] >He has also given the following data on "relaxin" (I don't even know what >that is) again in percent variation: This is from the SwissProt entry RELX_PIG (which contains the sequence for pig relaxin): FUNCTION: RELAXIN IS AN OVARIAN HORMONE THAT ACTS WITH ESTROGEN TO PRODUCE DILATATION OF THE BIRTH CANAL IN MANY MAMMALS. It is (with this definition) surprising that sharks and skates also have relaxins, but as far as I can remember at least sharks have live offspring (so it's not so surprising any more). Relaxin has also been found in the spiny dogfish (squalus acanthias) which is oviparous. Hence, its function there is not known. Relaxins usually consist of two amino acid chains which are connected by disulfide bonds. The B chain is about 30-40 amino acids long, the A chain seems to be a bit shorter. Relaxins are made as preprohormones, that is, when synthesized, the chains are connected by a peptide on which selective pressure is probably quite low. This peptide is cut out during processing. There is also a leader peptide which channels preprorelaxin into the secretory pathway. These leader peptides are quite similar for all secreted proteins since they fulfil a common signaling function (namely, marking the protein for secretion). Generally, short proteins are very unsuitable for constructing evolutionary trees if they have a function because most of the amino acids cannot be replace d without loss of function. This is assumed to be a smaller problem with bigger proteins (with hundreds of amino acids). For example, the A chain of whale relaxin is identical to the A chain of pig relaxin. If you nevertheless make a cluster analysis with the GCG program PILEUP with the A and B chains just concatenated, you get the following picture: (approximately ASCII figure) --------------------------- ! ! ------- ! ! ! --------------------------- ! ! ! ! ! ! ---------- ! ! ! ! ! ! ! ! ! ! -------------------- ! ! ! ! ! ! ! ! ! ------- ! ! ! ------ ! ! ! ! ! ! ! ! ! ! ! ! ---------------- ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ----------- ! ! ! ! ! ! ! ! ! ! A B C D E F G H I J A: Raja Erinacea (Little Skate) B: Squalus Acanthias (Spiny dogfish) C: Odontaspis Taurus (Sand tiger shark) D: Rat E: Rhesus monkey F: Human G: Horse H: Balaenoptera acutorostrata (Minke whale) I: Pig J: Balaenoptera edeni (Bryde's whale) Although the near relationship between Bryde's whale and pig is not really convincing :-) the rough relations between groups are not that wrong... (Data were taken from SWISSPROT Release 24.0 and aligned with PILEUP by UWGCG. Connecting and leader peptides were removed before aligning in the human, the monkey, the pig and the rat sequence.) BTW: does anybody know of a good introductory text into evolutionary analysis of sequences? --Cornelius.

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