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Thread: "No Predictive Theory in Biology or History" Carl

  1. #101  
    Forum Cosmic Wizard spuriousmonkey's Avatar
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    I gave somewhere evidence for the emergence of a totally new functional protein.

    It was ignored.
    "Kill them all and let God sort them out."

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  2. #102  
    Forum Cosmic Wizard SkinWalker's Avatar
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    Quote Originally Posted by spuriousmonkey
    I gave somewhere evidence for the emergence of a totally new functional protein.

    It was ignored.
    Ignoring evidence that contradicts superstition is what creationists do best.
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    Quote Originally Posted by marnixR
    Quote Originally Posted by cypress
    Sorry, that's not true. Past moderator practices provide good heuristics on this point.

    ....

    Actually I have previously learned it would only have to conform to the prior commitments of the moderators or conform to the opinions of talkorigns. Whether or not it had explanatory power is secondary.
    i see that we've finally arrived at the point where most conspiracy theorists end up: the reason why no-one listens to me isn't because my point of view doesn't have any scientific merit, but because there's a worldwide conspiracy to suppress the truth
    On the contrary. I am only pointing out the practices of this board. I don't consider this a conspiracy. This board and its moderators have policies that they maintain. I can live within those rules.
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    Quote Originally Posted by spuriousmonkey
    I gave somewhere evidence for the emergence of a totally new functional protein.

    It was ignored.
    If I recall, the evidence didn't include how it was formed. There are many examples of novel proteins appearing in organisms when the need arises. Fruitfly species contain more that twenty unexplained novel proteins. Another good example is T-urf13 (if I remember) in some corn. I was looking for an example of a novel proein formed by mutation and selection by a multi-step pathway. Your example did not fit the criteria (they rarely if ever do).

    Novel proteins exist throughout the phyla, The problem is that mutation and selection does not offer a demonstrated mechanism to derive them. This is another example where the facts (emergence of novel proteins) doe not conform to Darwinian prediction of a stepwise path to these proteins.
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  5. #105  
    Forum Cosmic Wizard spuriousmonkey's Avatar
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    The example stated that the novelty was derived by means of evolution.

    I'm quite sure I would have remembered if they had stated pink elephants created a new protein for fun.
    "Kill them all and let God sort them out."

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    Quote Originally Posted by cypress
    Can a blind mechanism ever be expected converge on the same solution in face of the innumerable permutations available?
    Yep. By Darwinian evolution. for example.
    Quote Originally Posted by cypress
    The problem is that mutation and selection does not offer a demonstrated mechanism to derive them.
    What's wrong with Darwinian evolution?
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  7. #107  
    WYSIWYG Moderator marnixR's Avatar
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    Quote Originally Posted by iceaura
    Quote Originally Posted by cypress
    Can a blind mechanism ever be expected converge on the same solution in face of the innumerable permutations available?
    Yep. By Darwinian evolution. for example.
    the answer as to why is (1) embryology and (2) the limited number of viable solutions
    "Reality is that which, when you stop believing in it, doesn't go away." (Philip K. Dick)
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    Quote Originally Posted by spuriousmonkey
    The example stated that the novelty was derived by means of evolution.

    I'm quite sure I would have remembered if they had stated pink elephants created a new protein for fun.
    yet they only observed the outcome. They did not observe the process. They are only guessing. Their only evidence is their prior commitment. Pretty weak.
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    Quote Originally Posted by marnixR
    Quote Originally Posted by iceaura
    Quote Originally Posted by cypress
    Can a blind mechanism ever be expected converge on the same solution in face of the innumerable permutations available?
    Yep. By Darwinian evolution. for example.
    the answer as to why is (1) embryology and (2) the limited number of viable solutions
    In other words they are just guessing .... A pattern is emerging.
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  10. #110  
    WYSIWYG Moderator marnixR's Avatar
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    in other words you're putting your own spin on things - again
    "Reality is that which, when you stop believing in it, doesn't go away." (Philip K. Dick)
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    Quote Originally Posted by marnixR
    in other words you're putting your own spin on things - again
    All sides put their own spin on things. You do too. The key is to distinguish between fact and inference. Direct observation is very close to fact. Inferences are guesses no matter how educated they are. Those who use inference to reach conclusions and then call those conclusions "fact" can only do so if they have a prior commitment that their belief is true. Honestly Max, do you have a prior commitment that is used as a framework to drive your inferences?
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    Quote Originally Posted by cypress
    Inferences are guesses no matter how educated they are. Those who use inference to reach conclusions and then call those conclusions "fact" can only do so if they have a prior commitment that their belief is true.
    Or they use words like "fact" in a normal, native English speaker sort of way, in which the possibility that it's all a dream, or the antibiotic resistance that showed up in the test tube was put there by secret genetic engineers, or there never was a world a billion years ago but instead a special creation on the year 6538 BC, or the laws of the universe snapped into their current configuration only recently, and so forth, are taken for granted as background noise until further notice;

    and only a lack of evidence or presence of counter-evidence, significant counter-argument, contradiction of more reliable inferences, etc etc, are taken into account fro the present issues.
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  13. #113  
    WYSIWYG Moderator marnixR's Avatar
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    Quote Originally Posted by cypress
    Honestly Max, do you have a prior commitment that is used as a framework to drive your inferences?
    at least i don't try do distort other people's words to mean something they haven't said
    "Reality is that which, when you stop believing in it, doesn't go away." (Philip K. Dick)
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  14. #114  
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    All sides put their own spin on things. You do too. The key is to distinguish between fact and inference. Direct observation is very close to fact. Inferences are guesses no matter how educated they are. Those who use inference to reach conclusions and then call those conclusions "fact" can only do so if they have a prior commitment that their belief is true. Honestly Max, do you have a prior commitment that is used as a framework to drive your inferences?
    It is fact, because it happened before their very eyes. What is not 100% fact is how it is thought to happen, something you will not hear any of your debate opponents claim. The point is that the change was caused by evolution, not by a microscopic elf with a spanner.

    Again: Evolution is a fact, but how it happens is still being researched. Finding new mechanisms enhances our knowledge of evolution, it does not undermine it.
    Disclaimer: I do not declare myself to be an expert on ANY subject. If I state something as fact that is obviously wrong, please don't hesitate to correct me. I welcome such corrections in an attempt to be as truthful and accurate as possible.

    "Gullibility kills" - Carl Sagan
    "All people know the same truth. Our lives consist of how we chose to distort it." - Harry Block
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    Quote Originally Posted by KALSTER
    All sides put their own spin on things. You do too. The key is to distinguish between fact and inference. Direct observation is very close to fact. Inferences are guesses no matter how educated they are. Those who use inference to reach conclusions and then call those conclusions "fact" can only do so if they have a prior commitment that their belief is true. Honestly Max, do you have a prior commitment that is used as a framework to drive your inferences?
    It is fact, because it happened before their very eyes. What is not 100% fact is how it is thought to happen, something you will not hear any of your debate opponents claim. The point is that the change was caused by evolution, not by a microscopic elf with a spanner.
    Before their very eyes? Can you send me a reference that it (emergence of a novel protein) happened in real time under observation.

    Again: Evolution is a fact, but how it happens is still being researched. Finding new mechanisms enhances our knowledge of evolution, it does not undermine it.
    If you define evolution broadly enough (or narrowly enough) I would also agree it is fact. this kind of statement is not very useful because it only states the obvious. It conveys very little information but allows for a great deal of misinformation.

    Do you claim this statement is fact? "All biological diversity occured by the Darwinian process of stepwise mutation along with selection".
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    Quote Originally Posted by cypress
    Before their very eyes? Can you send me a reference that it (emergence of a novel protein) happened in real time under observation.
    Antibiotic resistance. This makes the fourth or fifth time this bogus request of yours has been fulfilled nevertheless, two or three with multiple links.

    And it makes no difference. Even if it hadn't happened in the lab, there's plenty of evidence of it having occurred in the world. It's like acorns growing into oak trees - he "seed" theory of oak tree generation is well confirmed, even though no one has observed the process happening in real time before their very eyes.
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  17. #117  
    Administrator KALSTER's Avatar
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    If you define evolution broadly enough
    There is only one definition of evolution. The change of the genes of populations of organisms over time. Whenever something more is implied by a given definition, you start talking about mechanisms.

    It conveys very little information but allows for a great deal of misinformation.
    It conveys only what it is supposed to convey. What do you mean it allows for a great deal of misinformation? How? Are you claiming intent to obfuscate the understanding of non-scientists? To what end?

    Do you claim this statement is fact? "All biological diversity occured by the Darwinian process of stepwise mutation along with selection".
    I don't think so. What do you mean by "stepwise"? Do you think evolutionary biologists claim all mutation is stepwise, as in directed towards a goal?
    Disclaimer: I do not declare myself to be an expert on ANY subject. If I state something as fact that is obviously wrong, please don't hesitate to correct me. I welcome such corrections in an attempt to be as truthful and accurate as possible.

    "Gullibility kills" - Carl Sagan
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    Quote Originally Posted by iceaura
    Quote Originally Posted by cypress
    Before their very eyes? Can you send me a reference that it (emergence of a novel protein) happened in real time under observation.
    Antibiotic resistance. This makes the fourth or fifth time this bogus request of yours has been fulfilled nevertheless, two or three with multiple links.

    And it makes no difference. Even if it hadn't happened in the lab, there's plenty of evidence of it having occurred in the world. It's like acorns growing into oak trees - he "seed" theory of oak tree generation is well confirmed, even though no one has observed the process happening in real time before their very eyes.
    antibiotic resistance is not an example of emergence of novel protein function. It is an example of modificaton by damaging existing function. It is also silly to say that we don't observe growth of an oak tree. Sorry but your analogy is a farce.
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    Quote Originally Posted by KALSTER
    If you define evolution broadly enough
    There is only one definition of evolution. The change of the genes of populations of organisms over time. Whenever something more is implied by a given definition, you start talking about mechanisms.
    A very modest and uninteresting definition.

    It conveys very little information but allows for a great deal of misinformation.
    It conveys only what it is supposed to convey. What do you mean it allows for a great deal of misinformation? How? Are you claiming intent to obfuscate the understanding of non-scientists? To what end?
    Many people interpret that to mean very different things. It does not eliminate any posibilities for how genes change. By your definition genetic engineering is an evolutionary porcess. I don't make any claim about intent. I simply note that it tends to misinform. I find it very confusing.

    Do you claim this statement is fact? "All biological diversity occured by the Darwinian process of stepwise mutation along with selection".
    I don't think so. What do you mean by "stepwise"? Do you think evolutionary biologists claim all mutation is stepwise, as in directed towards a goal?[/quote]

    Stepwise in the sense that Darwin described where single steps make small changes that accumulate into new form and function. Stepwise in that the process does not suddenly skip past any typical steps defined by a known process. I think that most biologists do believe mutation occurs in steps that accumulate into large scale changes. While some biologists may think some changes are directed, I don't thank many would say that mutation is goal driven.

    Do you have any example of an emergent novel protein that happened in observable time? If so, has the process been identified?
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    Quote Originally Posted by cypress
    antibiotic resistance is not an example of emergence of novel protein function. It is an example of modificaton by damaging existing function
    No, it isn't. I have already linked, for you, an explicit description of four different kinds of mechanisms known to have evolved in organisms thereby acquiring resistance to antibiotics, none of the four limited to damage of existing function of any protein.

    You are reduced to asserting blatant factual falsehoods, easily debunked. At this point, rethinking of your overall argument is overdue.

    Quote Originally Posted by cypress
    It is also silly to say that we don't observe growth of an oak tree.
    No human has ever directly observed the process of growth of an oak tree from acorn to full adult. It is a matter of mere inference, reason, or - as you say - unproved guesswork.
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    Quote Originally Posted by iceaura
    Quote Originally Posted by cypress
    antibiotic resistance is not an example of emergence of novel protein function. It is an example of modificaton by damaging existing function
    No, it isn't. I have already linked, for you, an explicit description of four different kinds of mechanisms known to have evolved in organisms thereby acquiring resistance to antibiotics, none of the four limited to damage of existing function of any protein.

    You are reduced to asserting blatant factual falsehoods, easily debunked. At this point, rethinking of your overall argument is overdue.
    I'm sorry Iceaura, you are simply incorrect. B-Lactamases and similar enzymes that cleve antibiotics have been around for an unknown period of time. We do not know how they originated. The remaining examples involved point mutations to existing genes that damaged existing funtion and created no new function. The damage prevented the antibiotic from exploiting it's designed chemic pathway.

    Quote Originally Posted by cypress
    It is also silly to say that we don't observe growth of an oak tree.
    No human has ever directly observed the process of growth of an oak tree from acorn to full adult. It is a matter of mere inference, reason, or - as you say - unproved guesswork.
    You just reduce your own credibility when you say such nonsense. Biological development is generally understood. Suit yourself.
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    Quote Originally Posted by cypress
    B-Lactamases and similar enzymes that cleve antibiotics have been around for an unknown period of time. We do not know how they originated. The remaining examples involved point mutations to existing genes that damaged existing funtion and created no new function.
    Apparently you never bothered with those links and stuff, like this one: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1113838/ , that others have found for you.

    The many mechanisms that bacteria exhibit to protect themselves from antibiotics can be classified into four basic types (fig ​(fig1).1Figure 1). Antibiotic modification is the best known: the resistant bacteria retain the same sensitive target as antibiotic sensitive strains, but the antibiotic is prevented from reaching it. This happens, for example, with β lactamases—the β lactamase enzymatically cleaves the four membered β lactam ring, rendering the antibiotic inactive. Over 200 types of β lactamase have been described (table). Most β lactamases act to some degree against both penicillins and cephalosporins; others are more specific—namely, cephalosporinases (for example, AmpC enzyme found in Enterobacter spp) or penicillinases (for example, Staphylococcus aureus penicillinase)
    - - - - - - -
    Genes either exist in nature already or can emerge by mutation rapidly. Rapid mutation has been seen with (a) the TEM β lactamase, resulting in an extension of the substrate profile to include third generation cephalosporins (first reported in Athens in 1963, one year after the introduction of ampicillin) and (b) the IMI-1 β lactamase (reported from a Californian hospital before imipenem was approved for use in the United States).15
    But carry on, as seems your mission.
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    Quote Originally Posted by iceaura
    Quote Originally Posted by cypress
    B-Lactamases and similar enzymes that cleve antibiotics have been around for an unknown period of time. We do not know how they originated. The remaining examples involved point mutations to existing genes that damaged existing funtion and created no new function.
    Apparently you never bothered with those links and stuff, like this one: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1113838/ , that others have found for you.

    The many mechanisms that bacteria exhibit to protect themselves from antibiotics can be classified into four basic types (fig ​(fig1).1Figure 1). Antibiotic modification is the best known: the resistant bacteria retain the same sensitive target as antibiotic sensitive strains, but the antibiotic is prevented from reaching it. This happens, for example, with β lactamases—the β lactamase enzymatically cleaves the four membered β lactam ring, rendering the antibiotic inactive. Over 200 types of β lactamase have been described (table). Most β lactamases act to some degree against both penicillins and cephalosporins; others are more specific—namely, cephalosporinases (for example, AmpC enzyme found in Enterobacter spp) or penicillinases (for example, Staphylococcus aureus penicillinase)
    - - - - - - -
    Genes either exist in nature already or can emerge by mutation rapidly. Rapid mutation has been seen with (a) the TEM β lactamase, resulting in an extension of the substrate profile to include third generation cephalosporins (first reported in Athens in 1963, one year after the introduction of ampicillin) and (b) the IMI-1 β lactamase (reported from a Californian hospital before imipenem was approved for use in the United States).15
    But carry on, as seems your mission.
    iceaura. These are examples of existing function. B-Lacamases previously existed. I figured you would consider the mutations of B-Lactamases as I do which are modifications or adaptations of existing function. We talked about adaptations before as well. They combat the slight differences in antibiotics always performing the same function. Namely to cleave the antibitic and render it impotent.

    This is not new function. It is slight modification of a prexisting function. I have always acknowledged the power of evolutionary processes to produce slight modifications to existing functions. We have talked about many in the past.
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    Quote Originally Posted by cypress
    iceaura. These are examples of existing function. B-Lacamases previously existed.
    Not the ones that cleave these new antibiotics - they have function not seen before in any protein.
    Quote Originally Posted by cypress
    I figured you would consider the mutations of B-Lactamases as I do which are modifications or adaptations of existing function.
    The"modifications" or "adaptations" result in new function - capabilility not present in the former enzyme, or earlier versions of the organism.

    And that is just one particular instance of one small corner of the world of evolved antibiotic resistance.
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    Now you are simply redefining what new function is to fit your presupposition.
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  26. #126  
    Forum Cosmic Wizard spuriousmonkey's Avatar
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    Quote Originally Posted by cypress
    Now you are simply redefining what new function is to fit your presupposition.
    Aren't you doing the same?
    "Kill them all and let God sort them out."

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  27. #127  
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    Quote Originally Posted by cypress
    This is not new function. It is slight modification of a prexisting function.
    And if we make a slight modification of that function? And a slight modification of that again? That's how exaptation and indeed evolution often works- surely you know that? When the function change is drastic and single-step it is usually because of a loss of the original function entirely. However we would of course expect the alteration of original function to produce a similar new function to be more gradual.

    Alteration of function is new function, however slight that alteration may be. Iceaura's example couldn't even be called slight but rather significant- but that's irrelevant. Alter a function and you have a new function. You're just arguing semantics- badly.
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    Quote Originally Posted by TheBiologista
    Quote Originally Posted by cypress
    This is not new function. It is slight modification of a prexisting function.
    And if we make a slight modification of that function? And a slight modification of that again? That's how exaptation and indeed evolution often works- surely you know that?
    I don't think anybody actually knows this. It is the prediction. But it has not been confirmed by any direct mechanism. When we compare something absent a particualr function to something with that function and then speculate a stepwise progression from one to the other, there clearly comes a point where the particular function does not exist and then next when it does. Your slight modification concept makes logical sense, but when examined in detail does not substitute or cover for my objection that new function is not the same as modification of existing function.

    When the function change is drastic and single-step it is usually because of a loss of the original function entirely. However we would of course expect the alteration of original function to produce a similar new function to be more gradual.

    Alteration of function is new function, however slight that alteration may be. Iceaura's example couldn't even be called slight but rather significant- but that's irrelevant. Alter a function and you have a new function. You're just arguing semantics- badly.
    In the case we were discussing, an enzyme that cleaves a particular class of chemicals (antibiotics) with particular combinations of binding sites designed to penetrate bacteria membranes and then bind to another class of protein that effectively ends a key metabolic process. Here the enzyme is modified by one point change to be active for a slightly different antibiotic that was not cleaved by the unmodified enzyme. But the function is the same. It cleaves molecules that have a particular group of binding sites.

    It is difficult to see how one could consider this new function unless you are predisposed to see it that way.

    A good example of new function is the frame shift modification that seems to have generated the nylase enzyme but this was a case of a single point mutation, that is new function in one fell swoop, not the many small steps you describe. Another clear example is the flagellum example you raised before where there are no fewer than 30 novel proteins with no known precursors. Another example is the T-URF enzyme ( a novel protein) giving certain corn varieties fungal resistance again not something that occurred through multiple slight modifications. None of these follow the multistep slight modifications path Darwinian evolution proposes.
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    Quote Originally Posted by spuriousmonkey
    Quote Originally Posted by cypress
    Now you are simply redefining what new function is to fit your presupposition.
    Aren't you doing the same?
    No, I don't think I am.

    New: Not previously experienced.
    Function: The physiological activity of a molecular system.

    In this case the function is to cleave molecules with a particular partial shape and set of binding sites.
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    Quote Originally Posted by cypress
    Quote Originally Posted by TheBiologista
    Quote Originally Posted by cypress
    This is not new function. It is slight modification of a prexisting function.
    And if we make a slight modification of that function? And a slight modification of that again? That's how exaptation and indeed evolution often works- surely you know that?
    I don't think anybody actually knows this. It is the prediction. But it has not been confirmed by any direct mechanism.
    We know it by inference from natural examples such as these and from experimentation with mutagenesis and artificial selection. These are mechanistically identical to the natural process but are directed so that the process can be dismantled. There are analogous natural processes too. Somatic hypermutation, for example.

    We know by experimentation with random, non-directed mutation that it can alter protein's specificity for a ligand, be it protein or otherwise, that it can alter a protein's shape, mechanical characteristics and so forth. We know by observation that the very same mutations occur in nature and at what rates. So we can infer that mutation in nature can do what mutation in the lab does. Because there's no actual difference between the two. Ditto selection. There's no mechanistic difference between artificial selection and natural selection. One could be said to merely be a subset of the other in fact.

    Quote Originally Posted by cypress
    When we compare something absent a particualr function to something with that function and then speculate a stepwise progression from one to the other, there clearly comes a point where the particular function does not exist and then next when it does.
    The modified function is the new function. The transition has occurred in a single step. It's just not the extent of a transition that you want.

    Quote Originally Posted by cypress
    Your slight modification concept makes logical sense, but when examined in detail does not substitute or cover for my objection that new function is not the same as modification of existing function.
    Take the word TEND. Make a very slight modification and make it TREND. We can say that the word and its meaning have been modified. We can also say the word is new or has a new meaning. Both sets of assertions are true. Your objection is nonsense.

    Quote Originally Posted by cypress
    When the function change is drastic and single-step it is usually because of a loss of the original function entirely. However we would of course expect the alteration of original function to produce a similar new function to be more gradual.

    Alteration of function is new function, however slight that alteration may be. Iceaura's example couldn't even be called slight but rather significant- but that's irrelevant. Alter a function and you have a new function. You're just arguing semantics- badly.
    In the case we were discussing, an enzyme that cleaves a particular class of chemicals (antibiotics) with particular combinations of binding sites designed to penetrate bacteria membranes and then bind to another class of protein that effectively ends a key metabolic process. Here the enzyme is modified by one point change to be active for a slightly different antibiotic that was not cleaved by the unmodified enzyme. But the function is the same. It cleaves molecules that have a particular group of binding sites.
    Sure, if your labelling of the function is as broad as "cleaves antibiotics" then the function cannot be said to have been altered. But the function is far more specific than that. It is "cleaves antibiotic A at site X" and indeed we could go into more detail than this. Even if this were altered via mutation to "cleaves antibody A at site Y", this would constitute a new function with potentially many new implications, not least of which would be novel catabolites. In Iceaura's example the change is larger, a switch to a new substrate. That we classify the new substrate into the same broad category as the original is not relevant.

    All you've done is be vague enough about how you define function so that you can say it has not changed, or it least that it has not changed sufficiently to cross some imaginary line into "new function".

    Quote Originally Posted by cypress
    It is difficult to see how one could consider this new function unless you are predisposed to see it that way.

    A good example of new function is the frame shift modification that seems to have generated the nylase enzyme but this was a case of a single point mutation, that is new function in one fell swoop, not the many small steps you describe.
    You'll note that I previously mentioned that drastic changes in function are "usually because of a loss of the original function entirely". This is typically the case for frame shift mutations, that you've pointed out one exception does not make a lie of that "usually". There are many similar examples of function following a major mutation such as a frame shift or large deletion, but these are hugely outnumbered by the examples of functional mutations due to incremental change.

    Quote Originally Posted by cypress
    Another clear example is the flagellum example you raised before where there are no fewer than 30 novel proteins with no known precursors.
    I've never heard of this before. In which bacterial species is this? The template, "classical" flagellum researchers like to study is the one from Salmonella. There are, last I read about it, two proteins without known homologues in that system. Can you give me a recent journal reference on this?

    Quote Originally Posted by cypress
    Another example is the T-URF enzyme ( a novel protein) giving certain corn varieties fungal resistance again not something that occurred through multiple slight modifications. None of these follow the multistep slight modifications path Darwinian evolution proposes.
    Never said that "multistep slight modifications" paths were all there was to evolution, just that this appears to be what we see most commonly. On the contrary, l have brought up exceptions numerous times. Giving more examples of these exceptions doesn't move things forward much.

    T-urf is a mitochondrial gene, isn't it? If it is non-novel to a species known to have undergone endosymbiosis or which is capable of some other form of LGT, then it's plausible that it was introduced to the maize species via a lateral transfer event. That does not mean that the gene was not derived from an ancestor gene via mutation and selection, it just means that once derived via familiar processes in an unrelated species, it was transferred into a new species. Whereupon it continued to undergo selection. Darwin would not have envisioned the LGT event, but then he also didn't know anything about mutations or vertical gene transfer. I think we can let him off the hook.

    Does T-urf have no known homologues in any species? If that's the case then please give me a reference of that too. Mind you, that would still constitute little more than an appeal to ignorance. Given that it is just one modestly-sized gene, it's entirely plausible that it could have come into maize via LGT from an uncharacterised species. Show me a set of say five novel genes which work together in a eukaryotic species. That'd be tough to explain.
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    Quote Originally Posted by TheBiologista
    Quote Originally Posted by cypress

    I don't think anybody actually knows this. It is the prediction. But it has not been confirmed by any direct mechanism.
    We know it by inference from natural examples such as these and from experimentation with mutagenesis and artificial selection.
    Inference can lead us to suspect or to believe a process accounts for an outcome. Knowledge of a fact is quite different than suspicion or belief.

    These are mechanistically identical to the natural process but are directed so that the process can be dismantled. There are analogous natural processes too. Somatic hypermutation, for example.
    Good examples of adaptation or modification, but not novel function.

    We know by experimentation with random, non-directed mutation that it can alter protein's specificity for a ligand, be it protein or otherwise, that it can alter a protein's shape, mechanical characteristics and so forth. We know by observation that the very same mutations occur in nature and at what rates. So we can infer that mutation in nature can do what mutation in the lab does. Because there's no actual difference between the two. Ditto selection. There's no mechanistic difference between artificial selection and natural selection. One could be said to merely be a subset of the other in fact.
    I do not dispute this. But it is not an example of new function.

    Quote Originally Posted by cypress
    When we compare something absent a particualr function to something with that function and then speculate a stepwise progression from one to the other, there clearly comes a point where the particular function does not exist and then next when it does.
    The modified function is the new function. The transition has occurred in a single step. It's just not the extent of a transition that you want.
    Since when is modified and novel the same? We are not debating the extent of modification. Even under the scenario you propose, at some step we reach a point where previously a function is not being performed and does not exist and then it does. If your model holds you would not have to speak vaguely about gradual modifications leading to new function. Instead you would point out the step where the new function first becomes apparent. Let's take a real example. Evolutionary theory predicts that whales evolved from a land mammal. To do this a multitude of new functions are required. One example is the counter current heat exchangers and blood flow control system used to maintain the internal testes below body temperature. This is new function. The theory predicts this new system was derived by numerous slight modifications, but clearly there becomes a point where previously there is no counter current exchanger and now there is. There previously is not a feedback controller and variable flow restrictor and now there is. Let's not get balled up in definitions.

    Clearly these represent new function whereas a modification that allows an enzyme to bind to and cleave a particular type of chemical undergoes a single point mutation so that it has a different shape pattern and binding affinity so that it now cleaves a slight variation of the chemical is clearly not new function. If at some point this enzyme mutates to bind to another protein which is incorporated into a cellular transport system, that would be new function. Why is your bias so strong that you are unwilling to see this?

    Quote Originally Posted by cypress
    Your slight modification concept makes logical sense, but when examined in detail does not substitute or cover for my objection that new function is not the same as modification of existing function.
    Take the word TEND. Make a very slight modification and make it TREND. We can say that the word and its meaning have been modified. We can also say the word is new or has a new meaning. Both sets of assertions are true. Your objection is nonsense.
    I have not argued that stepwise modification of letter patterns are incapable of generating new words. Had I made this argument, with this example, you would have proved me wrong. Use an example from cell biology. If the predictions from Darwinian evolutionary theory are correct you would literally have millions of examples.

    Sure, if your labelling of the function is as broad as "cleaves antibiotics" then the function cannot be said to have been altered. But the function is far more specific than that. It is "cleaves antibiotic A at site X" and indeed we could go into more detail than this. Even if this were altered via mutation to "cleaves antibody A at site Y", this would constitute a new function with potentially many new implications, not least of which would be novel catabolites. In Iceaura's example the change is larger, a switch to a new substrate. That we classify the new substrate into the same broad category as the original is not relevant.

    All you've done is be vague enough about how you define function so that you can say it has not changed, or it least that it has not changed sufficiently to cross some imaginary line into "new function".
    The problem you have in defending the predictions of evolutionary theory is that even if I were to improperly grant that modification of a function to produce a variation of the same function is actually "novel" function, your predicion goes much much further than this. The theory also predicts that this same process applies to the very clear cases of novel function that I am speaking of. For this prediction to be born out, you still need to demonstrate that this process actually does produce clearly novel functions. The cases where the 30 novel proteins in the flagellum.

    Quote Originally Posted by cypress
    It is difficult to see how one could consider this new function unless you are predisposed to see it that way.

    A good example of new function is the frame shift modification that seems to have generated the nylase enzyme but this was a case of a single point mutation, that is new function in one fell swoop, not the many small steps you describe.
    You'll note that I previously mentioned that drastic changes in function are "usually because of a loss of the original function entirely". This is typically the case for frame shift mutations, that you've pointed out one exception does not make a lie of that "usually". There are many similar examples of function following a major mutation such as a frame shift or large deletion, but these are hugely outnumbered by the examples of functional mutations due to incremental change.
    Then why do you have such difficulty,no why are you unable to provide even one progression leading to new function?

    Quote Originally Posted by cypress
    Another clear example is the flagellum example you raised before where there are no fewer than 30 novel proteins with no known precursors.
    I've never heard of this before. In which bacterial species is this? The template, "classical" flagellum researchers like to study is the one from Salmonella. There are, last I read about it, two proteins without known homologues in that system. Can you give me a recent journal reference on this?
    Sure I'll get back to this in a few days. Sorry but I am busy right now. I suspect we will get into a debate about what constitutes a homologues structure. Please provide a definition so we don't have to argue about moving the goal post.

    Quote Originally Posted by cypress
    Another example is the T-URF enzyme ( a novel protein) giving certain corn varieties fungal resistance again not something that occurred through multiple slight modifications. None of these follow the multistep slight modifications path Darwinian evolution proposes.
    Never said that "multistep slight modifications" paths were all there was to evolution, just that this appears to be what we see most commonly. On the contrary, l have brought up exceptions numerous times. Giving more examples of these exceptions doesn't move things forward much.
    Except these appear to be the rule, not the exception. I can go on and on with these examples and you have yet to provide even one example of your supposedly numerous multiple stepwise pathways to novel function. The T-URF example is not a modification of existing function, it is novel. It did not exist and now it does, and it performs a new role without disturbing previous function.

    T-urf is a mitochondrial gene, isn't it?
    Yes it is.

    If it is non-novel to a species known to have undergone endosymbiosis or which is capable of some other form of LGT, then it's plausible that it was introduced to the maize species via a lateral transfer event.
    It is not known except in a particular corn variety. There is no homologous gene. It appears to be kit bashed together from several disparate areas of the mitochondrial DNA structure.

    That does not mean that the gene was not derived from an ancestor gene via mutation and selection, it just means that once derived via familiar processes in an unrelated species, it was transferred into a new species. Whereupon it continued to undergo selection.
    Interesting and typical speculations. The trademark of your entire discussion. How is speculation science? Why do you not grant the same level of speculation from your opponents? When your opposition speculates it gets labeled as pseudo-science. Can you say bias?


    Does T-urf have no known homologues in any species? If that's the case then please give me a reference of that too. Mind you, that would still constitute little more than an appeal to ignorance.
    Once again you will have to define homologue. Except I am not making any apeal at all. I am pointing out that novel functions often appear rapidly without any hint of Darwinian stepwise pathways. I don't offer any explanation for this observation. I do not speculate how it came to be. I can continue to offer example after example of this. You on the other hand claim these are exceptions to the rule but then you never offer any example of the rule. Let's return to the countercurrent blood to blood heat exchanger in whales. That is novel function and includes several novel gene functions, gene expression controls, and developmental controls. Darwinian theory predicts emergence of this in about 9 million years through stepwise mutation. We can return to the discussion of Population Genetics modeling to predict the number of generations and therefore years to derive this system by a darwinian pathway. Any guess as to what we might conclude?

    Given that it is just one modestly-sized gene, it's entirely plausible that it could have come into maize via LGT from an uncharacterised species. Show me a set of say five novel genes which work together in a eukaryotic species. That'd be tough to explain.
    Before we can declare LGT plausible, we first have to establish that LGT occurs other than by goal driven processes at any reasonable frequency between muticellular organisms other than as an attempt to explain away the contradictions in molecular systematics. I agree that bacterial and viral genes are infrequently transfered to eukaryote organisms,but this is only a small part of the required explanation, and not the part I am objecting about. Even by this mechanism we still need to generate novel proteins in bacteria first. You are only moving the problem around like a street hustler and "find the pea".

    I think the countercurrent heat exchanger in whales is a good example. Flagellum continues to be another. Please be sure to define homologous and provide observed cases of LGT of novel genes so we can proceed. Direct observation and repeatability are the hallmarks of good science.
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  32. #132  
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    Quote Originally Posted by cypress
    Quote Originally Posted by TheBiologista
    Quote Originally Posted by cypress

    I don't think anybody actually knows this. It is the prediction. But it has not been confirmed by any direct mechanism.
    We know it by inference from natural examples such as these and from experimentation with mutagenesis and artificial selection.
    Inference can lead us to suspect or to believe a process accounts for an outcome. Knowledge of a fact is quite different than suspicion or belief.
    That's not what inference is. It is not speculation, nor even hypothesis. It is a logical extension. That aside, our inferences have testable implications. If our tests are successful, then we can be satisfied that our inference was good.

    Quote Originally Posted by cypress
    These are mechanistically identical to the natural process but are directed so that the process can be dismantled. There are analogous natural processes too. Somatic hypermutation, for example.
    Good examples of adaptation or modification, but not novel function.

    We know by experimentation with random, non-directed mutation that it can alter protein's specificity for a ligand, be it protein or otherwise, that it can alter a protein's shape, mechanical characteristics and so forth. We know by observation that the very same mutations occur in nature and at what rates. So we can infer that mutation in nature can do what mutation in the lab does. Because there's no actual difference between the two. Ditto selection. There's no mechanistic difference between artificial selection and natural selection. One could be said to merely be a subset of the other in fact.
    I do not dispute this. But it is not an example of new function.
    Again, this is just semantics. What you're asking for is modification sufficient to satisfy your definition of novel function. The point at which the old function is gone and a new function is in place. That point is immediate. As soon as a function changes, the old function is probably gone (unless the protein has dual or multiple functions in which case it becomes more complicated). Your problem seems to be that in most examples ascribed to mutation and selection, the old function and the new function are similar. This is what is predicted by that method. At each step there should be similarity with the prior step. What you seem to be asking us for is an outcome from mutation and selection which resembles the outcome you'd get from some other process. Then you're complaining that our failure to do so somehow disproves that process.

    To return to an analogy I used before, we're saying that we know that a man A was present at his home at time t=0. He was later found at his local shop at time t=100. We have observed him continuously moving via a process we call "walking" towards the shop between times t=4 and t=10. Again at times t=30 and t=35 and then again on several similar occasions prior to t=100. Each time we observed him walking, he reached a novel, albeit only slightly different, location. We put the man on a treadmill in a lab and, under a directed experiment, we had him "walk" for a time of 20. In that time, he covered roughly the distance we hypothesise he covered by walking between times t=40 and t=60 in our natural observations. The total time he took to go from home to shop suggests that the rate of movement matches observations both in nature and in the lab, from which we infer that the process by which the man moved the full distance was "walking".

    It is very much possible that other forms of movement were involved, and we are open to evidence on that matter.

    You are telling us that we haven't shown man A can move to a novel location via walking, whilst defining "novel location" differently to the way that we do and simultaneously denying that we can infer the possibility of walking long distances in a plausible time based on these shorter observations and experimental evidence.

    Quote Originally Posted by cypress
    Quote Originally Posted by cypress
    When we compare something absent a particualr function to something with that function and then speculate a stepwise progression from one to the other, there clearly comes a point where the particular function does not exist and then next when it does.
    The modified function is the new function. The transition has occurred in a single step. It's just not the extent of a transition that you want.
    Since when is modified and novel the same?
    They're not equivalent, nor did I claim they were. One is a logical subset of the other. That's been the case since logic required that a thing gain something novel to it, and/or lose something, in order to be describable as "modified". "Gain/novelty" and "loss" are logical subsets of "modified".

    Quote Originally Posted by cypress
    We are not debating the extent of modification. Even under the scenario you propose, at some step we reach a point where previously a function is not being performed and does not exist and then it does. If your model holds you would not have to speak vaguely about gradual modifications leading to new function. Instead you would point out the step where the new function first becomes apparent. Let's take a real example. Evolutionary theory predicts that whales evolved from a land mammal. To do this a multitude of new functions are required. One example is the counter current heat exchangers and blood flow control system used to maintain the internal testes below body temperature. This is new function. The theory predicts this new system was derived by numerous slight modifications, but clearly there becomes a point where previously there is no counter current exchanger and now there is. There previously is not a feedback controller and variable flow restrictor and now there is. Let's not get balled up in definitions.
    Science relies heavily on precision of meaning, so it's pretty important that we clarify meaning wherever it is ambiguous. In the case of the whale evolution, I'd need to know more about the specifics to comment properly, but my general point about function changing and being novel at every step still holds. From the perspective on any one gene involved there is no such line over which we suddenly see "novelty" by your definition of the word. There is a point where, from our perspective, this or that emergent function appears, but if you get right down to the mutation that made it happen, it will most often be one of those slight modifications of one of the genes involved, a small change of function that will not in itself satisfy your definition of "novel".

    Quote Originally Posted by cypress
    Clearly these represent new function whereas a modification that allows an enzyme to bind to and cleave a particular type of chemical undergoes a single point mutation so that it has a different shape pattern and binding affinity so that it now cleaves a slight variation of the chemical is clearly not new function. If at some point this enzyme mutates to bind to another protein which is incorporated into a cellular transport system, that would be new function. Why is your bias so strong that you are unwilling to see this?
    Lets go back to the antibiotic resistance gene for a moment as a possible example. Gene A cleaves antibiotic N and produces metabolite X. A point mutation causes gene A (now called gene Ai) to instead cleave antibiotic O which results in a metabolite Y. A slight change you would not call "novel". Gene A is selected for because antibiotic O is used heavily. Generations later gene B (now called gene Bi) undergoes a point mutation which gives it a specificity for metabolite Y, which is structurally similar to the molecule it used to bind. B was previously a signalling molecule which tells a transcription factor to make more of several genes including gene Ai. On the gene scale, there have been two mutations which do not satisfy your definition of "novel function". But on the organism scale, we've seen resistance to a new antibiotic, production of a new metabolite (which you would also consider not a "novel function"), a new receptor and overall a new feedback chain which causes the bacterium to increase production of a resistance gene in response to high levels of metabolite. That broad function appears by your definition to be novel, and a superficial examination would suggest the line of novelty was in the last step, but when we look closer there was no such line and your criteria were never actually satisfied. That being because your criteria are not a test of evolution by mutation and selection at all.

    Quote Originally Posted by cypress
    Sure, if your labelling of the function is as broad as "cleaves antibiotics" then the function cannot be said to have been altered. But the function is far more specific than that. It is "cleaves antibiotic A at site X" and indeed we could go into more detail than this. Even if this were altered via mutation to "cleaves antibody A at site Y", this would constitute a new function with potentially many new implications, not least of which would be novel catabolites. In Iceaura's example the change is larger, a switch to a new substrate. That we classify the new substrate into the same broad category as the original is not relevant.

    All you've done is be vague enough about how you define function so that you can say it has not changed, or it least that it has not changed sufficiently to cross some imaginary line into "new function".
    The problem you have in defending the predictions of evolutionary theory is that even if I were to improperly grant that modification of a function to produce a variation of the same function is actually "novel" function, your predicion goes much much further than this. The theory also predicts that this same process applies to the very clear cases of novel function that I am speaking of. For this prediction to be born out, you still need to demonstrate that this process actually does produce clearly novel functions. The cases where the 30 novel proteins in the flagellum.
    Well I hope the hypothetical outline above helps to illustrate how observations and valid inference allow us to go further in our assertions. Do dig up that reference on the 30 novel proteins in the flagellum if you get a chance.

    Quote Originally Posted by cypress
    Quote Originally Posted by cypress
    It is difficult to see how one could consider this new function unless you are predisposed to see it that way.

    A good example of new function is the frame shift modification that seems to have generated the nylase enzyme but this was a case of a single point mutation, that is new function in one fell swoop, not the many small steps you describe.
    You'll note that I previously mentioned that drastic changes in function are "usually because of a loss of the original function entirely". This is typically the case for frame shift mutations, that you've pointed out one exception does not make a lie of that "usually". There are many similar examples of function following a major mutation such as a frame shift or large deletion, but these are hugely outnumbered by the examples of functional mutations due to incremental change.
    Then why do you have such difficulty,no why are you unable to provide even one progression leading to new function?
    Because your definition of "new function" does not match what we are claiming evolution can do via mutation and selection alone. It is a definition based on a misapprehension of "function" as well as "novelty". Our theory does not predict an observable change that would satisfy your definition of novel function, so in effect you're asking us to give examples which violate the theory.

    Quote Originally Posted by cypress
    Another clear example is the flagellum example you raised before where there are no fewer than 30 novel proteins with no known precursors.
    I've never heard of this before. In which bacterial species is this? The template, "classical" flagellum researchers like to study is the one from Salmonella. There are, last I read about it, two proteins without known homologues in that system. Can you give me a recent journal reference on this?
    Sure I'll get back to this in a few days. Sorry but I am busy right now. I suspect we will get into a debate about what constitutes a homologues structure. Please provide a definition so we don't have to argue about moving the goal post.[/quote]

    You're asking me to provide a definition of a term you used in one of your claims? Why don't you tell me what you meant, rather than have me put words in your mouth?

    Quote Originally Posted by cypress
    Quote Originally Posted by cypress
    Another example is the T-URF enzyme ( a novel protein) giving certain corn varieties fungal resistance again not something that occurred through multiple slight modifications. None of these follow the multistep slight modifications path Darwinian evolution proposes.
    Never said that "multistep slight modifications" paths were all there was to evolution, just that this appears to be what we see most commonly. On the contrary, l have brought up exceptions numerous times. Giving more examples of these exceptions doesn't move things forward much.
    Except these appear to be the rule, not the exception. I can go on and on with these examples and you have yet to provide even one example of your supposedly numerous multiple stepwise pathways to novel function.
    No, we keep providing examples of stepwise modification but your definition of novelty leads you to reject them. That's a problem because your definition of novelty is not relevant to the theory of evolution.

    [quote="cypress"][quote]
    Quote Originally Posted by cypress
    The T-URF example is not a modification of existing function, it is novel. It did not exist and now it does, and it performs a new role without disturbing previous function.

    T-urf is a mitochondrial gene, isn't it?
    Yes it is.

    If it is non-novel to a species known to have undergone endosymbiosis or which is capable of some other form of LGT, then it's plausible that it was introduced to the maize species via a lateral transfer event.
    It is not known except in a particular corn variety. There is no homologous gene. It appears to be kit bashed together from several disparate areas of the mitochondrial DNA structure.
    Well the recombination from more than one gene is rather easily explained. Though it is not "several" disparate areas in the case of T-urf. It's one. A piece of one gene ended up in the sequence coding for a transmembrane protein. Recombination events like this happen every time we produce a new sperm or ovum. Homologous chunks of our chromosomes swap over, in effect swapping alleles, though the break points may sometimes occur in the middle of a coding sequence. It also goes wrong quite frequently and in the vast majority of cases that means a broken gene. But in very rare cases it means a new positively select coding sequence. I'm not sure whether the same holds for mitochodria (they're unicellular and asexual) but we know they can perform a similar function. Any of these processes would account for that element of the evolution of T-urf. Like general LGT and endosymbiosis, it's a rare event- or at least in the case of recombination it is rare that it results in a beneficial mutation.

    Now, what does help you is that there appears to be a third, unique element to T-urf. It's a very small part of the gene but it's not clear where that part of the sequence came from. The most that can be said about that is that we don't know it's origins and don't have the evidence to determine if it arose by a known process. Likeliest explanation is lateral transfer from a species which infects mitochondria- probably a virus. But to confirm this, we'd need to find a homologue of that sequence, and not just that but find it in a species which could plausibly make a transfer into mitochondria.

    What is your proposition as to how that little bit of DNA got in there?

    Quote Originally Posted by cypress
    That does not mean that the gene was not derived from an ancestor gene via mutation and selection, it just means that once derived via familiar processes in an unrelated species, it was transferred into a new species. Whereupon it continued to undergo selection.
    Interesting and typical speculations. The trademark of your entire discussion. How is speculation science? Why do you not grant the same level of speculation from your opponents? When your opposition speculates it gets labeled as pseudo-science. Can you say bias?
    You're not making speculations, you're just telling us how impossible something is and offering us no alternatives. Nor are you presenting your views as speculations, you're telling us as a fact that evolution can't explain this or that and then accusing us of speculating when we use evolution to put forward a plausible explanation.

    Rather than label my responses and suggest I don't allow you to do this or that, why not counter my posts with logic or evidence?

    Quote Originally Posted by cypress
    Given that it is just one modestly-sized gene, it's entirely plausible that it could have come into maize via LGT from an uncharacterised species. Show me a set of say five novel genes which work together in a eukaryotic species. That'd be tough to explain.
    Before we can declare LGT plausible, we first have to establish that LGT occurs other than by goal driven processes at any reasonable frequency between muticellular organisms other than as an attempt to explain away the contradictions in molecular systematics.
    When you see a chunk of DNA with no homologue in a given species A, then find that same chunk of DNA in a species B which frequently infects A, then show that B can insert it's DNA into cells of A in the lab at a measurable frequency, that it can do it in an in vivo model of same, then find that the frequency of insertion makes an insertion plausible during the time that A and B have associated in nature- how in the hell is that a mere attempt to explain away a contradiction? You really think this is all guesswork, don't you?

    You finish by asking me to provide more evidence and laughably enough, to define the terms that you are using. No. Do this. Make a claim, back it up. Stop telling us what's impossible and show us the alternative.
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    Quote Originally Posted by TheBiologista

    Again, this is just semantics. What you're asking for is modification sufficient to satisfy your definition of novel function. The point at which the old function is gone and a new function is in place. That point is immediate. As soon as a function changes, the old function is probably gone (unless the protein has dual or multiple functions in which case it becomes more complicated).
    In the specific cases we have discussed these past months we have a hormone receptor mutated to be more or less selective for .... hormones. Not new function. We have membrane gateways being broken... Not new function, just broken old function. So far, with the exception of the lists I provided, which are rapid development of new function with no known evolutionary pathway, we simply don't have an example of what you are describing here.

    Your problem seems to be that in most examples ascribed to mutation and selection, the old function and the new function are similar. This is what is predicted by that method. At each step there should be similarity with the prior step. What you seem to be asking us for is an outcome from mutation and selection which resembles the outcome you'd get from some other process. Then you're complaining that our failure to do so somehow disproves that process.
    No the problem is that I am not disputing this mechanism of modification of existing function to similar function. I don't acknowledge it because I don't dispute it. However, if this mechanism actually leads to novel form as function as the theory predicts, then you would be able to offer a verified example of it. This is what true science is all about. This is why you and the other moderators classify other theories that cannot offer verifiable, testable predictions as pseudo science. Yet you stubbornly refuse to admit your prior commitments are void of observation.


    To return to an analogy I used before, we're saying that we know that a man A was present at his home at time t=0. He was later found at his local shop at time t=100. We have observed him continuously moving via a process we call "walking" towards the shop between times t=4 and t=10. Again at times t=30 and t=35 and then again on several similar occasions prior to t=100. Each time we observed him walking, he reached a novel, albeit only slightly different, location. We put the man on a treadmill in a lab and, under a directed experiment, we had him "walk" for a time of 20. In that time, he covered roughly the distance we hypothesise he covered by walking between times t=40 and t=60 in our natural observations. The total time he took to go from home to shop suggests that the rate of movement matches observations both in nature and in the lab, from which we infer that the process by which the man moved the full distance was "walking".
    You only use analogies because you don't have a real verified example from biology. Your analogy fails when we make it more realistic by adding the caveat that we don't know if this is the same man we are observing. We see a man but not the man. Furthermore the treadmill analogy fails too because when we put evolutionary theory on the treadmill, it proceeds far to slowly. See my new post broken from this one on Whale Evolution.

    More later.
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    Quote Originally Posted by cypress
    For this prediction to be born out, you still need to demonstrate that this process actually does produce clearly novel functions. The cases where the 30 novel proteins in the flagellum.
    You are making the favorite creationist argument again - we don't know about something, therefore it is impossible/nonexistent etc.

    No one was looking for precursor proteins of the standard flagella arrangements (there are several) until recently. In the short time of research, several have been found for most of the major flagellar setups, and there is even debate now about which evolutionary narrative is more likely (rather than a blank where none is indicated);

    the notion that there are 30 different proteins each unrelated to any other proteins known, in any bacterial flagellum, is an error. Even Wikipedia can get you better than that.
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    Quote Originally Posted by iceaura
    Quote Originally Posted by cypress
    For this prediction to be born out, you still need to demonstrate that this process actually does produce clearly novel functions. The cases where the 30 novel proteins in the flagellum.
    You are making the favorite creationist argument again - we don't know about something, therefore it is impossible/nonexistent etc.

    No one was looking for precursor proteins of the standard flagella arrangements (there are several) until recently. In the short time of research, several have been found for most of the major flagellar setups, and there is even debate now about which evolutionary narrative is more likely (rather than a blank where none is indicated);

    the notion that there are 30 different proteins each unrelated to any other proteins known, in any bacterial flagellum, is an error. Even Wikipedia can get you better than that.
    Well you are simply mistaken. I used flagellum because biologista used the example some time ago to try to argue stepwise modification leading to novel proteins. His article was way of the mark and these recent studies proposing protein precursors for many of the flagellum proteins are also a joke. One of them, probably the one you are thinking of suggests that 26 somehow came from the same unidentified precursor. The difficulty here is in defining how one determines what a likely precursor is. I did not answer biologista's objection to this because your researchers define homologues so loosely we can get nearly anything to be its precursor. We need to be much more rigorous that this. Define for me how we determine what qualifies as a precursor and I will happily answer your objection.
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    Quote Originally Posted by cypress
    I did not answer biologista's objection to this because your researchers define homologues so loosely we can get nearly anything to be its precursor. We need to be much more rigorous that this. Define for me how we determine what qualifies as a precursor and I will happily answer your objection.
    What are you talking about? What would a "loose definition" of "homologue" have to do with something being a precursor protein?
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    Quote Originally Posted by cypress
    Quote Originally Posted by TheBiologista

    Again, this is just semantics. What you're asking for is modification sufficient to satisfy your definition of novel function. The point at which the old function is gone and a new function is in place. That point is immediate. As soon as a function changes, the old function is probably gone (unless the protein has dual or multiple functions in which case it becomes more complicated).
    In the specific cases we have discussed these past months we have a hormone receptor mutated to be more or less selective for .... hormones. Not new function.
    Not sure which case you're referring to, but if specificity has changed by widening, narrowing or shifting then it is very much a new function. Your argument relies on you failing to elaborate on "hormones". That's just a categorisation that we use, hormones may vary greatly in structure. For example, some are proteins, others are small molecules. So a shift in specificity for "hormones" could be quite a profound change in function. Even if we're talking about some sort of specificity shift between steroid hormones, it's still a new function. Again, this is all about your self-serving definitions.

    Quote Originally Posted by cypress
    We have membrane gateways being broken... Not new function, just broken old function.
    Misunderstanding of "function". If the "broken" gene undergoes positive selection, it's not broken and we can say that it has some function.

    Quote Originally Posted by cypress
    So far, with the exception of the lists I provided, which are rapid development of new function with no known evolutionary pathway, we simply don't have an example of what you are describing here.
    Rubbish. We don't have an example of what you want, because what you want is an example that evolution cannot provide.

    Quote Originally Posted by cypress
    Your problem seems to be that in most examples ascribed to mutation and selection, the old function and the new function are similar. This is what is predicted by that method. At each step there should be similarity with the prior step. What you seem to be asking us for is an outcome from mutation and selection which resembles the outcome you'd get from some other process. Then you're complaining that our failure to do so somehow disproves that process.
    No the problem is that I am not disputing this mechanism of modification of existing function to similar function. I don't acknowledge it because I don't dispute it. However, if this mechanism actually leads to novel form as function as the theory predicts, then you would be able to offer a verified example of it.
    We have done so and you've re-defined novelty so that our examples don't count.

    Quote Originally Posted by cypress
    This is what true science is all about. This is why you and the other moderators classify other theories that cannot offer verifiable, testable predictions as pseudo science. Yet you stubbornly refuse to admit your prior commitments are void of observation.
    I don't think you have much of an idea what science is all about.

    Quote Originally Posted by cypress
    To return to an analogy I used before, we're saying that we know that a man A was present at his home at time t=0. He was later found at his local shop at time t=100. We have observed him continuously moving via a process we call "walking" towards the shop between times t=4 and t=10. Again at times t=30 and t=35 and then again on several similar occasions prior to t=100. Each time we observed him walking, he reached a novel, albeit only slightly different, location. We put the man on a treadmill in a lab and, under a directed experiment, we had him "walk" for a time of 20. In that time, he covered roughly the distance we hypothesise he covered by walking between times t=40 and t=60 in our natural observations. The total time he took to go from home to shop suggests that the rate of movement matches observations both in nature and in the lab, from which we infer that the process by which the man moved the full distance was "walking".
    You only use analogies because you don't have a real verified example from biology.
    No, I'm using this analogy because you have not recognised the examples given as being valid. I'm trying to illustrate to you the logic we apply to make the claims we do, based on the evidence we have.

    Quote Originally Posted by cypress
    Your analogy fails when we make it more realistic by adding the caveat that we don't know if this is the same man we are observing. We see a man but not the man.
    I was trying to simplify things by using an analogy. But you've misunderstood the analogy. I have to admit I'm at a loss at where to go from here.

    The distance walked was an analogy for the observed change in a gene, under the assumption that change has indeed occurred. You and I do not dispute that this change occurs (at least we are not talking about it right now), but rather the mechanism responsible, the analogy for which in this case was walking. We're arguing about the capacity of the mechanism to produce the a result which agrees with observations, when we make the starting assumption that the man is the same man. The possibility that the man may not be the same man is not relevant to a discussion on the capacity of the mechanism to match observation unless the observation is not matched, in which case we proponents of the mechanism would be hoping that it wasn't the same man.

    Quote Originally Posted by cypress
    Furthermore the treadmill analogy fails too because when we put evolutionary theory on the treadmill, it proceeds far to slowly.
    No it doesn't, the only examples you've given from observation have been explicable by other known evolutionary mechanisms. I could introduce cars and trains and planes into my analogy and talk about the constraints on each and the testable implications of each but it seems likely you will not see my point.
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    Novel function can be found in the AFGP protein of ice-fish. A very rare example, to be sure.

    The evolution of new proteins with new functions does not work by simply creating them from scratch. The toolkit available is: exon shuffling, domain shufflling, gene fusion, gene divergence, gene duplication, mobile element recruitment etc. Lots of "new" genes are known. For example, in Drosophila you have genes like jingwei, Sdic, sphinx, Cid, Dntf-2r and Adh-Finnegan - all of them arising from any of the standard mechanisms I just listed.

    New proteins with novel functions simply don't need to evolve out of "nothing", for there already exists tried and tested methods for generating new function from preexisting function. Evolving a new protein entirely from the ground up would be a very surprising thing to discover - and quite probably impossible.
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    Quote Originally Posted by Zwirko
    Novel function can be found in the AFGP protein of ice-fish. A very rare example, to be sure.

    The evolution of new proteins with new functions does not work by simply creating them from scratch. The toolkit available is: exon shuffling, domain shufflling, gene fusion, gene divergence, gene duplication, mobile element recruitment etc. Lots of "new" genes are known. For example, in Drosophila you have genes like jingwei, Sdic, sphinx, Cid, Dntf-2r and Adh-Finnegan - all of them arising from any of the standard mechanisms I just listed.

    New proteins with novel functions simply don't need to evolve out of "nothing", for there already exists tried and tested methods for generating new function from preexisting function. Evolving a new protein entirely from the ground up would be a very surprising thing to discover - and quite probably impossible.
    Cypress will probably love that last statement.

    I suspect if we could trace back through related functions all the way to the very first replicators we would find the first "functions" to be simple things such as replication efficiency, replication fidelity, sequence stability and so forth. They're no more "functions" than any of the other examples given, but they undergo positive or negative selection which is all that is actually relevant.
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    Quote Originally Posted by Zwirko
    Novel function can be found in the AFGP protein of ice-fish. A very rare example, to be sure.

    The evolution of new proteins with new functions does not work by simply creating them from scratch. The toolkit available is: exon shuffling, domain shufflling, gene fusion, gene divergence, gene duplication, mobile element recruitment etc. Lots of "new" genes are known. For example, in Drosophila you have genes like jingwei, Sdic, sphinx, Cid, Dntf-2r and Adh-Finnegan - all of them arising from any of the standard mechanisms I just listed.

    New proteins with novel functions simply don't need to evolve out of "nothing",

    Right, novel function is not from scratch, and it has not been shown to occur by stepwise progressions either. Certainly we can and should invoke these tools to explain individual steps. The fruit fly genes are also good examples of novel genes, but once again these examples seem to lack a stepwise explanation. The intermediate steps don't seem to exist as one would normally expect by evolutionary predictions.


    for there already exists tried and tested methods for generating new function from preexisting function. Evolving a new protein entirely from the ground up would be a very surprising thing to discover - and quite probably impossible.
    Agreed. In addition evolving them from a series of stepwise alterations where two or more consecutive steps are neutral or deleterious would also be a very surprising thing to discover. Not impossible but the frequency is estimated at less than 1 in 10^18 occurances for just one neutral intermediate.
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    You don't really need a step-by-step explanation. You can't get one either because that level of detail in the evolutionary history has been long since lost in the mists of time, and there is little or no hope of ever recovering it. We can only work with what is around today and attempt to piece together a history.
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    Quote Originally Posted by cypress
    Not impossible but the frequency is estimated at less than 1 in 10^18 occurances for just one neutral intermediate.
    Whose idiotic estimate was that? Looks like another one of those "and then you multiply together all the probabilities I pulled out of my ass and declared to be of independent events" bits of howler calculation.
    Quote Originally Posted by cypress
    The fruit fly genes are also good examples of novel genes, but once again these examples seem to lack a stepwise explanation. The intermediate steps don't seem to exist as one would normally expect by evolutionary predictions.
    Now you are denying lab evolution - events observed under controlled circumstances.
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    Quote Originally Posted by iceaura
    Quote Originally Posted by cypress
    Not impossible but the frequency is estimated at less than 1 in 10^18 occurances for just one neutral intermediate.
    Whose idiotic estimate was that? Looks like another one of those "and then you multiply together all the probabilities I pulled out of my ass and declared to be of independent events" bits of howler calculation.
    Quote Originally Posted by cypress
    The fruit fly genes are also good examples of novel genes, but once again these examples seem to lack a stepwise explanation. The intermediate steps don't seem to exist as one would normally expect by evolutionary predictions.
    Now you are denying lab evolution - events observed under controlled circumstances.
    Can you provide an example of multistep "lab" evolution in fruitflies, leading to a novel gene, I am not aware of any.

    To Zriko's point, there is plenty of opportunities to observe individual steps in a pathway in the lab. that we don't is the issue.
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  44. #144  
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    The techniques that would allow such lab observations have only existed for a short period of time. The Drosophila genome has only been sequenced in the last 10 years, for example. It is not surprising that there is no "mutli-step lab evolution" sequences known; nor would one really expect to see such a thing on such a short time scale. How would we recognise such small evolutionary changes if they were happening? We'd have to sequence every single fruit fly in the lab, every generation.

    Research you might find interesting is the work of Richard Lenski's lab at Michigan State University who is studying the long-term evolution of an organism in real time. He's studied 12 populations of E.coli for something like 45,000 generations over 20 years. One of the 12 populations evolved the ability to metabolise citrate; other populations have underwent minor changes. The exact mechanisms that led to the ability to utilise citrate are currently beiing studied and should reveal the step-by-step sequence of events that took place.
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    Quote Originally Posted by Zwirko
    The techniques that would allow such lab observations have only existed for a short period of time. The Drosophila genome has only been sequenced in the last 10 years, for example. It is not surprising that there is no "mutli-step lab evolution" sequences known; nor would one really expect to see such a thing on such a short time scale. How would we recognise such small evolutionary changes if they were happening? We'd have to sequence every single fruit fly in the lab, every generation.
    It was surprising relative to evolutionary predictions to find ths number of novel genes in presumptivly closely related species in such a short evolutionary time window. This is particularly surprising given the number of changes that would be postulated by traditional evolutionary mechanisms (including the ones you described) with no hint of residual intermediates. this of course is in contradiction to the presumed mechanisms. As far as a research program that could explain this, one could postulate an evolutionary pathway, and then desgn and test the efficacy of these intermediates for selective advantage. It is not necessary that everymutation is observed.

    Research you might find interesting is the work of Richard Lenski's lab at Michigan State University who is studying the long-term evolution of an organism in real time. He's studied 12 populations of E.coli for something like 45,000 generations over 20 years. One of the 12 populations evolved the ability to metabolise citrate; other populations have underwent minor changes. The exact mechanisms that led to the ability to utilise citrate are currently beiing studied and should reveal the step-by-step sequence of events that took place.
    I have been following his work for some time now. It is interesting to note that E. coli already has the ability to digest citrate but it simply lacks a mechanism to transport it into the cell in the presence of oxygen. Lenski said this: “The only known barrier to aerobic growth on citrate is its inability to transport citrate under oxic conditions.” This capability had been reported at least two time previously in the past few decades. In one instance, a protein that transports citrate in the abscence of oxygen was overexpressed allowing it to grow on citrate in oxygen.

    The primary point though is that it took trillions of cells and over 30,000 generations to develop it, and only one of the 12 lines succeeded, but only those in that line that were more than 20,0000 generations old indicating that an intermdeiate neutral change was first required. This fits exceptionaly well with the point I have been making that changes of greater than two steps happen exceedingly slowly. Those requiring three are likely out of reach for organisms with lower populations than bacteria and other micro-organisms. It will be interesting to see how many steps were involved.
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    Quote Originally Posted by cypress
    The primary point though is that it took trillions of cells and over 30,000 generations to develop it, and only one of the 12 lines succeeded,
    No. Other less dramatic changes were observed, in the other lines. They "succeeded" too.

    Given a natural mixing and recombination between lines, statistically there would now be individuals with most or all of the changes found in any of the lines, if they provided any advantage (and maybe if they didn't). That would happen in two or three generational steps.
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    [quote="iceaura"]
    Quote Originally Posted by cypress
    The primary point though is that it took trillions of cells and over 30,000 generations to develop it, and only one of the 12 lines succeeded,
    No. Other less dramatic changes were observed, in the other lines. They "succeeded" too.

    Succeeded in the sense of the purpose of the research. The bacteria was exposed to large quantities of citrate and just a little sucrose. Success was defined as the ability to injest citrate in an oxygen rich environment.

    Given a natural mixing and recombination between lines, statistically there would now be individuals with most or all of the changes found in any of the lines, if they provided any advantage (and maybe if they didn't). That would happen in two or three generational steps.
    I doubt it would occur in 3 generations (a couple days) but your point does not seem relevant anyway.
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  48. #148  
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    incredulity isn't a scientific argument.
    "Kill them all and let God sort them out."

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    cypress, I'm not too sure why you keep referring to "two or three" steps as being some kind of statistically unlikely event. Clearly, it isn't unlikely enough to support your argument.
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    Quote Originally Posted by spuriousmonkey
    incredulity isn't a scientific argument.
    Just so stories about dog-like creatures evolving into whales through illdefined and undescribed processes is not science.

    By contrast, appplying accepted techniques from population genetics and experimental biology to the known and observed processes of mutation and selection to demonstrate that those processes in particular operate too slowly to fit the available timeframe given the relatively low population size and known mutation rates. Thus the predicion that whales evolved by these processes seems falsified. That is hardly an apeal to incredulity.

    Note that I have not made any actual argument from incredulity. I have not said "therefore whales did not evolve from dog-like mammals" I have only said that one particular prediction is wrong. Now if you have some information to indicate i am wrong, I am happy to discuss it.
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    Quote Originally Posted by Zwirko
    cypress, I'm not too sure why you keep referring to "two or three" steps as being some kind of statistically unlikely event. Clearly, it isn't unlikely enough to support your argument.
    I don't find it clear at all. Keep in mind that I am speaking of three or more differences that impact binding afinity or tertiary structure. I am not talking about the inconsequential changes to primary seqence that have little or no impact on protein form or functional characteristics. I am quite awar that nearly 40% of the amino acid sequnce of many proteins can be altered with no change in form or function. but since these changes are inconcequetal, for this discussion we need not consider them.
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  52. #152  
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    Just so stories about dog-like creatures evolving into whales through illdefined and undescribed processes is not science.
    What nonsense and ignorance! You are making it sound as if they had a big hat with pictures of fossils in it and then proceeded to choose two at a time and declaring them descendants of each other. How do you think they arrived at their knowingly intrinsically tentative conclusions?

    You keep labouring under the delusion that because we don't fully understand all the mechanisms of evolution yet that it is not an established fact. The interrelatedness of animals is an observed fact, just as much as the observed fact of gravity is.

    By contrast, appplying accepted techniques from population genetics and experimental biology to the known and observed processes of mutation and selection to demonstrate that those processes in particular operate too slowly to fit the available timeframe given the relatively low population size and known mutation rates. Thus the predicion that whales evolved by these processes seems falsified. That is hardly an apeal to incredulity.
    Sure it is! It is NOT falsified simply because we perhaps don't know exactly how it happened? What an astonishingly ignorant thing to say. That is what research is for.
    Disclaimer: I do not declare myself to be an expert on ANY subject. If I state something as fact that is obviously wrong, please don't hesitate to correct me. I welcome such corrections in an attempt to be as truthful and accurate as possible.

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  53. #153  
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    Many examples - including a couple that I mentioned previously - involve major and or profound changes in tertiary structure and can not be described as "inconsequential changes to primary sequence".

    The evidence you seek can be seen if you take any particular protein family as a starting point. I'd take the serine-protease super-family as an example, specifically the mammalian chymotrypsin-like proteases. Look at the active sites and look at the varied reactions that they catalyse.
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    Quote Originally Posted by KALSTER
    Just so stories about dog-like creatures evolving into whales through illdefined and undescribed processes is not science.
    What nonsense and ignorance! You are making it sound as if they had a big hat with pictures of fossils in it and then proceeded to choose two at a time and declaring them descendants of each other. How do you think they arrived at their knowingly intrinsically tentative conclusions?
    I'm not sure why you misiterpret my words. I am not arguing common descent as unsupported by evidence, but to say things are related does not tell us how they changed rom one to the other. I am pointing out that declaring that these changes happened through undescribed processes that have not been observed or validated is a just so story.

    You keep labouring under the delusion that because we don't fully understand all the mechanisms of evolution yet that it is not an established fact. The interrelatedness of animals is an observed fact, just as much as the observed fact of gravity is.
    The similarity and progression is an observed fact. That they are direct descendents of the others is not something that can be tested or observed so it is not anywhere near as established as the fact and laws of gravity. I don't understand hoy you see them as the same. Clearly you personally observe the extent of gravity capability but even one with a prior commitement about common descent understands the uncertainty introduced by absence of direct observation and inability to do repeatable tests.

    By contrast, appplying accepted techniques from population genetics and experimental biology to the known and observed processes of mutation and selection to demonstrate that those processes in particular operate too slowly to fit the available timeframe given the relatively low population size and known mutation rates. Thus the predicion that whales evolved by these processes seems falsified. That is hardly an apeal to incredulity.
    Sure it is! It is NOT falsified simply because we perhaps don't know exactly how it happened? What an astonishingly ignorant thing to say. That is what research is for.
    One postulated process is falsified (unless by repeated testing, an error is discovered and cpability by that process is revivied), other untested processes are still an option. This is the process of elimination.
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  55. #155 Nine Months Later I Reply 
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    I have not been to this thread for nine months. This thread, which I initiated nearly a year ago now, has really taken-off. I think I might just say thanks to everyone who participated. I'll go to some other topic now at this site.-Ron 8)
    married for 37 years; teacher for 30; living in Australia for 33 years; Baha'i for 45 years. Writer of poetry for 25 years.
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  56. #156 Re: "No Predictive Theory in Biology or History" C 
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    Quote Originally Posted by RonPrice
    PREDICTABILITY

    There is as yet no predictive theory of biology, just as there is not yet a predictive theory of history. These subjects are too complicated for us.
    -Carl Sagan, Cosmos, Futura, 1983, p.57.

    No suspicion, no theory, no expert, no Kremlinologist had the least idea that that vast superstructure was going to collapse. The best of academics were as ignorant as you and I. It would seem we are routinely unable to predict what will happen; our best seers are regularly humbled. What could The time for the destruction of the world and its people hath arrived1 possibly mean? Surely we are beginning to get some idea in a world which largely did not exist when these words were spoken with a tempest that keeps blowing and continues sweeping the face of the earth.
    I found this old message (posted by Ron Price) by accident. It is true that exact predictions are often difficult. But a farmer knows what to expect in the fall (on the basis of what has been done several months earlier). His predictions, however, can not be exact, due to atmospheric conditions, etc. Most often they are confirmed. But occasionally results are better or worse than expected. The same is probably true in history. Hitler predicted victory of fascism, Stalin predicted victory of communism, etc. Even in physics predictions are often often probabilistic rather than exact. Yes, I am thinking about quantum mechanics.
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  57. #157 Re: "No Predictive Theory in Biology or History" C 
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    Quote Originally Posted by RonPrice
    PREDICTABILITY

    There is as yet no predictive theory of biology, just as there is not yet a predictive theory of history. These subjects are too complicated for us. ...
    ===========

    Predictions of some biological theories are very reliable. For example, a prediction that a person exposed germs of tuberculosis has a a very high chance of "catching the disease."
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  58. #158 Thank You All 
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    I have enjoyed reading what has become one of the most extensive threads initiated by one of my posts. The value of this thread, to me anyway, is that it has made me examine that quotation of Sagan's and see it as a much more complicated statement than I had originally envisaged it. Thank you all again for your participation.-Ron Price, Tasmania 8)
    married for 37 years; teacher for 30; living in Australia for 33 years; Baha'i for 45 years. Writer of poetry for 25 years.
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  59. #159 Re: Thank You All 
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    Quote Originally Posted by RonPrice
    I have enjoyed reading what has become one of the most extensive threads initiated by one of my posts. The value of this thread, to me anyway, is that it has made me examine that quotation of Sagan's and see it as a much more complicated statement than I had originally envisaged it. Thank you all again for your participation.-Ron Price, Tasmania 8)
    It was my pleasure.
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