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Thread: Nice defense of Evolution

  1. #51
    tWebber lee_merrill's Avatar
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    Quote Originally Posted by Seeker View Post
    Eventually, we have a system like our blood clotting, which has several proteases which are almost equal but slightly different...
    Source: Michael Behe

    As I wrote in Darwin's Black Box (Behe 1996, 86), the problem of blood clotting is not in just forming a clot--any precipitated protein might plug a hole. Rather the problem is regulation. The regulatory problems of the clotting cascade are particularly severe since, as pointed out by Halkier (1992, 104), error on either side--clotting too much or too little--is detrimental. As irreducible complexity would predict, Kenneth Miller's scenario has no problem postulating a simple clot (the initial nonspecific aggregation) but avoids the problem of regulation.

    Source

    © Copyright Original Source



    So blood clotting is a particularly difficult problem for evolution to solve. I agree that enzymes can evolve, as in the arrival of nylonase by a few selectable mutations, but traversing protein space to a new function by a random walk seems to be prohibitive, and most mutations will degrade an enzyme or be neutral.

    Blessings,
    Lee
    "What I pray of you is, to keep your eye upon Him, for that is everything. Do you say, 'How am I to keep my eye on Him?' I reply, keep your eye off everything else, and you will soon see Him. All depends on the eye of faith being kept on Him. How simple it is!" (J.B. Stoney)

  2. #52
    tWebber HMS_Beagle's Avatar
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    Quote Originally Posted by lee_merrill View Post
    Source: Michael Behe

    As I wrote in Darwin's Black Box (Behe 1996, 86), the problem of blood clotting is not in just forming a clot--any precipitated protein might plug a hole. Rather the problem is regulation. The regulatory problems of the clotting cascade are particularly severe since, as pointed out by Halkier (1992, 104), error on either side--clotting too much or too little--is detrimental. As irreducible complexity would predict, Kenneth Miller's scenario has no problem postulating a simple clot (the initial nonspecific aggregation) but avoids the problem of regulation.

    Source

    © Copyright Original Source



    So blood clotting is a particularly difficult problem for evolution to solve. I agree that enzymes can evolve, as in the arrival of nylonase by a few selectable mutations, but traversing protein space to a new function by a random walk seems to be prohibitive, and most mutations will degrade an enzyme or be neutral.

    Blessings,
    Lee
    LOL! Good one lee! An almost 20 year old hand-wave by Behe as your "evidence". How will evolutionary biology ever survive your intellectual onslaught?

  3. Amen Seeker amen'd this post.
  4. #53
    tWebber shunyadragon's Avatar
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    Quote Originally Posted by lee_merrill View Post
    Source: Michael Behe

    As I wrote in Darwin's Black Box (Behe 1996, 86), the problem of blood clotting is not in just forming a clot--any precipitated protein might plug a hole. Rather the problem is regulation. The regulatory problems of the clotting cascade are particularly severe since, as pointed out by Halkier (1992, 104), error on either side--clotting too much or too little--is detrimental. As irreducible complexity would predict, Kenneth Miller's scenario has no problem postulating a simple clot (the initial nonspecific aggregation) but avoids the problem of regulation.

    Source

    © Copyright Original Source



    So blood clotting is a particularly difficult problem for evolution to solve. I agree that enzymes can evolve, as in the arrival of nylonase by a few selectable mutations, but traversing protein space to a new function by a random walk seems to be prohibitive, and most mutations will degrade an enzyme or be neutral.

    Blessings,
    Lee
    Quoting the ameteur Behe Hehe! is the death of your argument among scientists.

    Source: https://www.ncbi.nlm.nih.gov/pubmed/19667012



    Step-by-step evolution of vertebrate blood coagulation.

    Doolittle RF1.
    Author information

    Abstract
    The availability of whole-genome sequences for a variety of vertebrates is making it possible to reconstruct the step-by-step evolution of complex phenomena such as blood coagulation, an event that in mammals involves the interplay of more than two dozen genetically encoded factors. Gene inventories for different organisms are revealing when during vertebrate evolution certain factors first made their appearance in or, on occasion, disappeared from some lineages. The whole-genome sequence databases of two protochordates and seven nonmammalian vertebrates were examined in search of approximately 20 genes known to be associated with blood clotting in mammals. No genuine orthologs were found in the protochordate genomes (sea squirt and amphioxus). As for vertebrates, although the jawless fish have genes for generating the thrombin-catalyzed conversion of fibrinogen to fibrin, they lack several clotting factors, including two thought to be essential for the activation of thrombin in mammals. Fish in general lack genes for the "contact factor" proteases, the predecessor forms of which make their first appearance in tetrapods. The full complement of factors known to be operating in humans does not occur until pouched marsupials (opossum), at least one key factor still absent in egg-laying mammals such as platypus.

    © Copyright Original Source



    This is legitimate peer reviewed science where Behe has not published his ID religious agenda concerning blood clotting.
    Last edited by shunyadragon; 11-12-2019 at 05:47 PM.
    Glendower: I can call spirits from the vasty deep.
    Hotspur: Why, so can I, or so can any man;
    But will they come when you do call for them? Shakespeare’s Henry IV, Part 1, Act III:

    go with the flow the river knows . . .

    Frank

    I do not know, therefore everything is in pencil.

  5. Amen HMS_Beagle amen'd this post.
  6. #54
    tWebber
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    Quote Originally Posted by Seeker View Post
    On the other hand, mutations which make the other copy more efficient at degrading the clot than to activate the phrotrombin will also be advantageous and give advantage to other mutations which regulate when and where each enzyme is copied. And so on.
    In the bold section I should have said ''where each enzyme is made'' and not ''copied''. I will correct the mistakes in the technical response to Lee as I ''spot'' them.

  7. #55
    tWebber TheLurch's Avatar
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    Quote Originally Posted by lee_merrill View Post
    Yet function implies a fold, does it not?
    One, the answer is no. Look into intrinsically disordered proteins.

    Second, it doesn't address the problems I described: the protein could have adopted some other fold, and Axe wouldn't be able to tell. As a result, his experiment is about adopting this one particular fold, and not folds in general. And, as his earlier paper showed, what he's finding with this fold doesn't even apply to others.

    Quote Originally Posted by lee_merrill View Post
    Are you saying he should have tested for all possible activities?! That would be prohibitive.
    Agreed that it would be prohibitive. But what i'm saying is that he shouldn't have drawn general conclusions about protein functional folds when he doesn't have equally general data to back those conclusions up. Because, you know, that's how science should work.

    Quote Originally Posted by lee_merrill View Post
    Well, see above...
    I have seen above. Nothing you said there addresses this issue.

    Quote Originally Posted by lee_merrill View Post
    Well, I can't get to the article to see how he drew his conclusions, but apparently he was onto something:

    Source: Science Direct

    The accepted paradigm that proteins can tolerate nearly any amino acid substitution has been replaced by the view that the deleterious effects of mutations, and especially their tendency to undermine the thermodynamic and kinetic stability of protein, is a major constraint on protein evolvability—the ability of proteins to acquire changes in sequence and function.

    Source

    © Copyright Original Source

    .
    Or not, if you'd bothered to quote through to the end of the abstract.
    .
    We describe ways of predicting and analyzing stability effects of mutations, and mechanisms that buffer or compensate for these destabilizing effects and thereby promote protein evolvabilty, in nature and in the laboratory..
    Or even bothered to read the stuff you're quoting thoroughly:

    Source: Evolution News

    In the study, after 5-10 mutations, roughly 2 in 3 mutations inactivate a protein.]Source[/URL]

    © Copyright Original Source


    So, you have to have massive mutational damage before it starts becoming sensitive to additional mutations, and even then there are known biological mechanism that "buffer or compensate" for the damage.

    Sounds like proteins can explore a huge range of sequence space with little difficulty.
    Last edited by TheLurch; 11-13-2019 at 09:53 AM.
    "Any sufficiently advanced stupidity is indistinguishable from trolling."

  8. Amen shunyadragon amen'd this post.
  9. #56
    tWebber lee_merrill's Avatar
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    Quote Originally Posted by shunyadragon View Post
    Source: https://www.ncbi.nlm.nih.gov/pubmed/19667012



    Step-by-step evolution of vertebrate blood coagulation.
    The main problem with this simple scenario has to do with the kinds of subsidiary domains found in thrombin.

    © Copyright Original Source

    So it's a simple scenario for a complex system, with acknowledged problems. In addition, his figure 6 ("Time-line phylogeny for appearance (and disappearance) of various clotting factors during the course of vertebrate evolution.") has only 6 of the factors, and one step labeled "Period of invention."

    So not a complete scenario, by any means.

    Blessings,
    Lee
    "What I pray of you is, to keep your eye upon Him, for that is everything. Do you say, 'How am I to keep my eye on Him?' I reply, keep your eye off everything else, and you will soon see Him. All depends on the eye of faith being kept on Him. How simple it is!" (J.B. Stoney)

  10. #57
    tWebber shunyadragon's Avatar
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    Quote Originally Posted by lee_merrill View Post
    So it's a simple scenario for a complex system, with acknowledged problems. In addition, his figure 6 ("Time-line phylogeny for appearance (and disappearance) of various clotting factors during the course of vertebrate evolution.") has only 6 of the factors, and one step labeled "Period of invention."

    So not a complete scenario, by any means.

    Blessings,
    Lee
    There are other peer reviewed scientific articles on the subject Dis you read the article? I will post more.

    What are your qualification to judge a peer reviewed article? Please enlighten us on specifics of the problems you see.

    Behe has not peer reviewed published his claims. He had to print his own book.

    Source: https://www.pnas.org/content/100/13/7527



    The evolution of vertebrate blood coagulation as viewed from a comparison of puffer fish and sea squirt genomes
    Yong Jiang and Russell F. Doolittle
    PNAS June 24, 2003 100 (13) 7527-7532; https://doi.org/10.1073/pnas.0932632100

    Abstract
    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.

    © Copyright Original Source

    Last edited by shunyadragon; 11-13-2019 at 04:55 PM.
    Glendower: I can call spirits from the vasty deep.
    Hotspur: Why, so can I, or so can any man;
    But will they come when you do call for them? Shakespeare’s Henry IV, Part 1, Act III:

    go with the flow the river knows . . .

    Frank

    I do not know, therefore everything is in pencil.

  11. #58
    tWebber lee_merrill's Avatar
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    Quote Originally Posted by TheLurch View Post
    One, the answer is no. Look into intrinsically disordered proteins.
    Well, interesting. Yet in the case of the protein Axe worked with, function and folds do seem related.

    Source: Douglas Axe

    ... given the importance of hydrophobic interactions to protein folding, it seems likely that the sample space can be restricted to sequences carrying the hydropathic signature of a known fold.

    © Copyright Original Source



    ... the protein could have adopted some other fold, and Axe wouldn't be able to tell.
    Though as far as I can see, Axe was attempting to measure one function to get an idea how other functions would respond to mutations.

    Source: Douglas Axe

    The prevalence of low-level function in four such experiments indicates that roughly one in 1064 signature-consistent sequences forms a working domain.

    © Copyright Original Source


    Surely the editors would have caught it if his work only applied to one fold.

    And, as his earlier paper showed, what he's finding with this fold doesn't even apply to others.
    Though I think these results may be consistent, given that a number of mutations are generally required to disable function, as you yourself say: "So, you have to have massive mutational damage before it starts becoming sensitive to additional mutations..."

    Or not, if you'd bothered to quote through to the end of the abstract.
    Yet the conclusion still stands, that "the deleterious effects of mutations, and especially their tendency to undermine the thermodynamic and kinetic stability of protein, is a major constraint on protein evolvability..."

    Sounds like proteins can explore a huge range of sequence space with little difficulty.
    Yet Tokuriki and Tawfik it seems, confirm Axe's results:

    Source: Evolution News

    In the study, after 5-10 mutations, roughly 2 in 3 mutations inactivate a protein. Therefore, 1 in 3 amino acids at each position on average would correspond to a functional sequence. The rarity would then be less than 1/3 to the power of the sequence length. This estimate closely matches the result from Axe’s 2004 β-lactamase experiment that only 1 in 1077 sequences corresponds to a functional fold/domain within the protein.

    Source

    © Copyright Original Source



    Blessings,
    Lee
    "What I pray of you is, to keep your eye upon Him, for that is everything. Do you say, 'How am I to keep my eye on Him?' I reply, keep your eye off everything else, and you will soon see Him. All depends on the eye of faith being kept on Him. How simple it is!" (J.B. Stoney)

  12. #59
    tWebber shunyadragon's Avatar
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    More on the evolution of blood cloting.

    Source: https://academic.oup.com/mbe/article/31/11/3040/2925737



    Positive Selection during the Evolution of the Blood Coagulation Factors in the Context of Their Disease-Causing Mutations
    Pavithra M. Rallapalli, Christine A. Orengo, Romain A. Studer, Stephen J. Perkins Author Notes

    Abstract
    Blood coagulation occurs through a cascade of enzymes and cofactors that produces a fibrin clot, while otherwise maintaining hemostasis. The 11 human coagulation factors (FG, FII–FXIII) have been identified across all vertebrates, suggesting that they emerged with the first vertebrates around 500 Ma. Human FVIII, FIX, and FXI are associated with thousands of disease-causing mutations. Here, we evaluated the strength of selective pressures on the 14 genes coding for the 11 factors during vertebrate evolution, and compared these with human mutations in FVIII, FIX, and FXI. Positive selection was identified for fibrinogen (FG), FIII, FVIII, FIX, and FX in the mammalian Primates and Laurasiatheria and the Sauropsida (reptiles and birds). This showed that the coagulation system in vertebrates was under strong selective pressures, perhaps to adapt against blood-invading pathogens. The comparison of these results with disease-causing mutations reported in FVIII, FIX, and FXI showed that the number of disease-causing mutations, and the probability of positive selection were inversely related to each other. It was concluded that when a site was under positive selection, it was less likely to be associated with disease-causing mutations. In contrast, sites under negative selection were more likely to be associated with disease-causing mutations and be destabilizing. A residue-by-residue comparison of the FVIII, FIX, and FXI sequence alignments confirmed this. This improved understanding of evolutionary changes in FVIII, FIX, and FXI provided greater insight into disease-causing mutations, and better assessments of the codon sites that may be mutated in applications of gene therapy.

    © Copyright Original Source


    Molecular Biology and Evolution, Volume 31, Issue 11, November 2014, Pages 3040–3056,
    Glendower: I can call spirits from the vasty deep.
    Hotspur: Why, so can I, or so can any man;
    But will they come when you do call for them? Shakespeare’s Henry IV, Part 1, Act III:

    go with the flow the river knows . . .

    Frank

    I do not know, therefore everything is in pencil.

  13. #60
    tWebber lee_merrill's Avatar
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    Quote Originally Posted by shunyadragon View Post
    What are your qualification to judge a peer reviewed article?
    Well, you deemed it worthy of posting, to support your point--what are your qualifications to judge a peer reviewed article, may I ask in reply?

    Please enlighten us on specifics of the problems you see.
    I did, now please respond to my points--instead of posting more articles.

    Behe has not peer reviewed published his claims. He had to print his own book.
    Please see "Simulating evolution by gene duplication of protein features that require multiple amino acid residues" by Behe and Snoke.

    Source: https://www.pnas.org/content/100/13/7527



    The evolution of vertebrate blood coagulation as viewed from a comparison of puffer fish and sea squirt genomes
    Yong Jiang and Russell F. Doolittle
    PNAS June 24, 2003 100 (13) 7527-7532; https://doi.org/10.1073/pnas.0932632100

    Abstract
    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.

    © Copyright Original Source


    So why exactly are you citing this paper? It seems to be much less comprehensive than the first one you cited, which I did read. It's a lot of work to read these papers, so if you're not going to tell me what you got from them, I'm going to think you're just spraying papers at me without consideration.

    Blessings,
    Lee
    "What I pray of you is, to keep your eye upon Him, for that is everything. Do you say, 'How am I to keep my eye on Him?' I reply, keep your eye off everything else, and you will soon see Him. All depends on the eye of faith being kept on Him. How simple it is!" (J.B. Stoney)

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