Page 5 of 10 FirstFirst ... 34567 ... LastLast
Results 41 to 50 of 97

Thread: Nice defense of Evolution

  1. #41
    tWebber TheLurch's Avatar
    Join Date
    Jan 2014
    Location
    Northeast USA
    Faith
    MYOB
    Gender
    Male
    Posts
    1,402
    Amen (Given)
    91
    Amen (Received)
    574
    So, a bit of meta-discussion about Doug Axe.

    Most of the Discovery Institute crew are pretty obviously a bit bonkers when it comes to science. Mike Bene is a bit like the black knight, continuing to insist he's right even as valid criticisms of his work pile up. Jon Wells seems to think that a few problems in out-of-date textbooks somehow invalidates the theory the textbooks are describing. Paul Nelson is a young earth creationist that somehow stumbled into a science argument. Steven Meyer is a geologist who's mystified by biology. Dembski i similar but with a math background.

    The one unifying feature they have is an intense dishonesty. It may not be conscious, but they change their presentations to suit their needs (ID may be science or religion depending on their audience), misinterpret research so consistently that there's no way it could be accidental or stupidity, etc. They're almost certainly lying to themselves to convince themselves about what they're doing (maybe even unconsciously), but they're also lying to everyone else in the process.

    Axe at least once upon a time seemed to be doing biology, and basing his arguments on his own research. So, i'd kind of given him the benefit of doubt. His arguments were dumb, and based on an unjustified extrapolation of his work, but i figured he's at least trying to put some substance behind it. But looking over his stuff in more detail thanks to Lee has made it clear that he's no better than the rest of them.

    One of the truisms about science is that you have to go where the data leads you. That seems to be the exact opposite of what Axe is doing. As far as i can tell, he set out to conclude that functional proteins were rare, and he's adjusted his research to try to fit that conclusion. That's why he started by making random mutations and then, when that mostly left function intact, he's moved on to making large numbers of mutations, simply because that's what he needs to do in order to inactivate the protein. He then uses this to leap to conclusions about the existence of functional proteins in general, even though he never tests for anything other than the original function of the protein he's working with.

    In other words, once i've been compelled to look more closely, it's become clear that Axe is no better than the rest of them.
    "Any sufficiently advanced stupidity is indistinguishable from trolling."

  2. Amen shunyadragon, HMS_Beagle, Roy amen'd this post.
  3. #42
    tWebber lee_merrill's Avatar
    Join Date
    Jan 2014
    Location
    Durham, NC
    Faith
    Christian
    Gender
    Male
    Posts
    1,248
    Amen (Given)
    421
    Amen (Received)
    229
    Quote Originally Posted by TheLurch View Post
    Once again, no he did not show that. He showed that multiple mutations designed specifically to disrupt the structure of the protein produced non-functional proteins. That's it.
    So he hoodwinked the editors of the Journal of Molecular Biology? What you just stated would not seem worthy of publication.

    Targeting multiple random changes (10 of them in the paper you cited!) at the sites within a protein that are most likely to be structurally significant doesn't actually tell you anything about how frequent other structures are.
    Sure it does, varying the areas of structure in the protein would be the way to find out how the structure can vary, this seems almost self-evident.

    Source: Douglas Axe

    Since tertiary structure is needed for a typical enzyme active site to form, one way to obtain this estimate is to measure the prevalence of sequences supporting a working active site.

    © Copyright Original Source



    But i'll take you changing the subject to be a tacit acknowledgement that, as i claimed:
    a) most mutations are neutral or alter function rather than eliminating it.
    b) that fact proved a barrier to Axe's early attempts to get the results he wanted, so he had to change his methods.
    Well, I disagree, but I don't think every point needs disputing. Most mutations are neutral or deleterious, for instance, correct?

    Axe was not measuring new function; he was testing the same function that the protein already performed—read the abstract you yourself linked.
    Yes, but his work provides a way to estimate the prevalence of protein sequences adopting functional enzyme folds. Just quoting from the title. This gives us an idea of the distance to new function.

    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)

  4. #43
    tWebber lee_merrill's Avatar
    Join Date
    Jan 2014
    Location
    Durham, NC
    Faith
    Christian
    Gender
    Male
    Posts
    1,248
    Amen (Given)
    421
    Amen (Received)
    229
    Quote Originally Posted by Roy View Post
    False. Multiple mutations that enhance the existing functionality may be selected for.
    I think that's compatible with what I said--I agree.

    False. Axe didn't show anything at all about new function, or about genetic distance.
    See above, in my reply to The Lurch.

    Quote Originally Posted by lee_merrill
    Though you have to get to new function in order for multiple mutations to be selected positively, and Axe shows that new function is generally far away. So the mutations are probably independent.
    False. Even if the preceding two claims were correct, this would not follow.
    Well, if it's a long way to new function, with multiple mutations, then the mutations are probably not positive together. Thus they are probably neutral or deleterious, and thus independent.

    Blessings,
    Lee
    Last edited by lee_merrill; 11-06-2019 at 06:30 PM.
    "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)

  5. #44
    tWebber lee_merrill's Avatar
    Join Date
    Jan 2014
    Location
    Durham, NC
    Faith
    Christian
    Gender
    Male
    Posts
    1,248
    Amen (Given)
    421
    Amen (Received)
    229
    Quote Originally Posted by shunyadragon View Post
    An interesting example of evolution in regions of uniform environment over time is the tropical rain forests. A large variety of diversification of varieties, subspecies, and varieties of species develop without the necessity of selecting for function.
    Surely function was being selected for throughout! A uniform environment does not mean that selection ceases.

    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)

  6. #45
    tWebber shunyadragon's Avatar
    Join Date
    Jan 2014
    Location
    Hillsborough, NC
    Faith
    Agnostic
    Gender
    Male
    Posts
    14,341
    Amen (Given)
    1567
    Amen (Received)
    970
    Quote Originally Posted by lee_merrill View Post
    Surely function was being selected for throughout! A uniform environment does not mean that selection ceases.

    Blessings,
    Lee
    Simply no. function has not been selected throughout. Genetic drift results from mutations creating genetic diversity throughout the history of life does not necessarily relate to function. Genetic diversity for evolution is greatest in many environments that do not change over hundreds of thousands if not millions of years like rainforests. Adaptive function does arise from the genetic diversity due to mutations.
    Last edited by shunyadragon; 11-06-2019 at 09:04 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.

  7. #46
    tWebber shunyadragon's Avatar
    Join Date
    Jan 2014
    Location
    Hillsborough, NC
    Faith
    Agnostic
    Gender
    Male
    Posts
    14,341
    Amen (Given)
    1567
    Amen (Received)
    970
    Quote Originally Posted by lee_merrill View Post
    Surely function was being selected for throughout! A uniform environment does not mean that selection ceases.

    Blessings,
    Lee
    I would like to get back to the real problem with Axe and other scientists(?) with the Discovery Institute that The Lurch has explained this in detail, and I have brought in every thread with references, and that is the unethical dishonest use of probability and statistics to justify the Intelligent Design agenda. Your statement 'function was being selected for throughout' is inaccurate in the relationship between genetic mutations, development of genetic diversity through genetic drift over time, and the role of selective change that results in the evolution of species, but it is not the BIG ISSUE of the elephant in the room.
    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.

  8. #47
    tWebber TheLurch's Avatar
    Join Date
    Jan 2014
    Location
    Northeast USA
    Faith
    MYOB
    Gender
    Male
    Posts
    1,402
    Amen (Given)
    91
    Amen (Received)
    574
    Quote Originally Posted by lee_merrill View Post
    So he hoodwinked the editors of the Journal of Molecular Biology? What you just stated would not seem worthy of publication.
    I don't know what was involved in the decision to publish. But i do know that you're not well enough versed in this topic to determine what's worth publishing.

    Quote Originally Posted by lee_merrill View Post
    Targeting multiple random changes (10 of them in the paper you cited!) at the sites within a protein that are most likely to be structurally significant doesn't actually tell you anything about how frequent other structures are.
    Sure it does, varying the areas of structure in the protein would be the way to find out how the structure can vary, this seems almost self-evident.
    That's wrong on multiple levels. To begin with, Axe never tested whether the mutant proteins adopted some other structure - he has absolutely no idea whether there's a structure there or not. He simply tested for a single enzymatic activity. The protein could have adopted a different structure and a different enzymatic activity, and Axe would never be able to tell, because he didn't bother to look.

    Do you not know that because you didn't read the paper, or because you are incapable of understanding it?

    The second issue here is that Axe had tried this earlier with a different protein, and it didn't work. He completely randomized the internal hydrophobic residues, and found that as long as he used a hydrophobic replacement, he could swap them all out and the enzyme would still work. So his results on this protein aren't even generally true, and therefore can't be used to draw general conclusions.

    (Sidenote: another indication that Axe is simply shopping for results that let me say what he wants to.)

    Quote Originally Posted by lee_merrill View Post
    Source: Douglas Axe

    Since tertiary structure is needed for a typical enzyme active site to form, one way to obtain this estimate is to measure the prevalence of sequences supporting a working active site.

    © Copyright Original Source

    .
    Yes, it's an inaccurate and error prone way of estimating it, given that it gives different results with different proteins.

    Quote Originally Posted by lee_merrill View Post
    Yes, but his work provides a way to estimate the prevalence of protein sequences adopting functional enzyme folds. Just quoting from the title. This gives us an idea of the distance to new function.
    This is going to be redundant with the above, but let me just make everything as clear as possible.

    1) You cannot know whether mutagenesis has disrupted a protein's folding without measuring whether it's folded, because many mutations inactivate enzymes without disrupting their function. Axe has never measured this.
    2) You cannot know how distant other folds are without determining whether your mutated protein has adopted a different fold. Axe has never measured that either.

    If you think this work tells us what you're claiming it does, you have to show that both of those statements are wrong.
    "Any sufficiently advanced stupidity is indistinguishable from trolling."

  9. Amen shunyadragon amen'd this post.
  10. #48
    tWebber TheLurch's Avatar
    Join Date
    Jan 2014
    Location
    Northeast USA
    Faith
    MYOB
    Gender
    Male
    Posts
    1,402
    Amen (Given)
    91
    Amen (Received)
    574
    Two errors in that post that i noticed too late to edit:
    "another indication that Axe is simply shopping for results that let him say what he wants to"
    "many mutations inactivate enzymes without disrupting theirstructure"

    As always, my apologies for typing carelessly.
    "Any sufficiently advanced stupidity is indistinguishable from trolling."

  11. Amen Seeker amen'd this post.
  12. #49
    tWebber lee_merrill's Avatar
    Join Date
    Jan 2014
    Location
    Durham, NC
    Faith
    Christian
    Gender
    Male
    Posts
    1,248
    Amen (Given)
    421
    Amen (Received)
    229
    Quote Originally Posted by TheLurch View Post
    Axe never tested whether the mutant proteins adopted some other structure - he has absolutely no idea whether there's a structure there or not. He simply tested for a single enzymatic activity.
    Yet function implies a fold, does it not?

    Source: Douglas Axe

    Since tertiary structure is needed for a typical enzyme active site to form, one way to obtain this estimate is to measure the prevalence of sequences supporting a working active site.

    © Copyright Original Source



    The protein could have adopted a different structure and a different enzymatic activity, and Axe would never be able to tell, because he didn't bother to look.
    Are you saying he should have tested for all possible activities?! That would be prohibitive.

    The second issue here is that Axe had tried this earlier with a different protein, and it didn't work. He completely randomized the internal hydrophobic residues, and found that as long as he used a hydrophobic replacement, he could swap them all out and the enzyme would still work. So his results on this protein aren't even generally true, and therefore can't be used to draw general conclusions.
    Actually, he talks about the prevalence (not rarity) of low-level function, so maybe he got similar results?

    Source: Douglas Axe

    The prevalence of low-level function in four such experiments indicates that roughly one in 10(64) signature-consistent sequences forms a working domain.

    © Copyright Original Source



    1) You cannot know whether mutagenesis has disrupted a protein's folding without measuring whether it's folded, because many mutations inactivate enzymes without disrupting their structure.
    Well, see above...

    2) You cannot know how distant other folds are without determining whether your mutated protein has adopted a different fold. Axe has never measured that either.
    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



    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. The actual rarity is much more extreme, since almost no sequences are functional after 10 percent of a protein randomly changes.

    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)

  13. #50
    tWebber
    Join Date
    Nov 2018
    Faith
    Unspecified
    Gender
    Male
    Posts
    164
    Amen (Given)
    119
    Amen (Received)
    10
    Lee,

    Can evolutionary processes make enzymes evolve, or increase their specificity?

    Yes, clearly. An example is the blood clotting enzymatic cascade. To put it simply, there are several enzymes, all serine proteases, which are enzymes that cut the peptide bond in the proteins using a serine in its catalytic center.

    Picture that in an ancestral species a protease like this existed and was responsible for the activation of the clotting proteins, like thrombin and fibrinogen, which usually are in an inactive state and are activated cutting a piece of the protein. After activated, these proteins interact to form clots, and eventually, also have to be degraded by the protease.

    If you have only one protease which does all that, it isn't going to work well. It may do, but the same enzyme that is activating the clotting proteins is also degrading them as well and the process isn't going to be very efficient.

    Now suppose that there is a mutation which duplicates the protease gene. This is relatively common, because it is an error in the DNA copy where a strand of DNA is copied twice. Now we have two copies of the same protease, which doesn't help any. But it allows each copy to accumulate mutations independently of the other. So mutations which make one of the copies more efficient at activating the prothrombin than to degrade the clot will allow a faster activation of the blood clotting. 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.

    Eventually, we have a system like our blood clotting, which has several proteases which are almost equal but slightly different, and which differences correspond to mutations which makes them more efficient in a specific step of the cascade reaction and less efficient in the rest of the steps. That is, MORE SPECIFIC. And all that cannot only be explained by the conjunction of mutations with natural selection, but it is evident when we consider the sequences of proteases and their localization in the genome, which is what we would expect of a process like this of duplication and differentiation of genes.

    Does that answer your question of whether enzymes evolve?
    Last edited by Seeker; 11-12-2019 at 01:47 PM.

Posting Permissions

  • You may not post new threads
  • You may not post replies
  • You may not post attachments
  • You may not edit your posts
  •