Friday, July 11, 2014

Here’s That Protein-Protein Interaction Problem

Evolutionists Don’t Know What They’re Doing

In Chapter 7 of The Edge of Evolution, Michael Behe explained why protein-protein interactions are a problem for evolution. Here is a summary of the problem. First, protein-protein interactions are important. Proteins often work in teams where half a dozen or more proteins may be interacting with each other to form a molecular machine. Protein-protein interaction is ubiquitous throughout life—so ubiquitous that we now have a name for the collective set of such interactions: the interactome. You can’t do much without protein-protein interactions. It is not as though protein-protein interactions are a convenient extra that makes cells a bit more efficient or bequeaths a few nice-to-have functions. Protein-protein interactions are fundamental to life, and are fundamental at all levels. Evolution must have been creating protein-protein interactions throughout evolutionary history as new species and capabilities arose.

And yet it is difficult to get two proteins to interact in a meaningful way. Such interactions must not be too strong or too weak. Imagine that you had two proteins that you needed to bind meaningfully to each other. If you randomly selected the amino acids at the binding patch on the surface of one of the two proteins, then meaningful binding would be unlikely. In fact, you would have to repeat the experiment millions of times before you could expect to get a good result.

But evolution does not have such resources. It cannot conduct millions of evolutionary experiments in order to luckily find amino acid sequences on protein surfaces that are required for important biological functions. And even if it could, that would only be the first step, because molecular machines are often comprised of multiple proteins, interacting with each other at multiple sites. So evolution would have to luckily find several sequences, in multiple proteins, and get them to arise in similar time frames, so the molecular machine would function.

But that is not all, for molecular machines often work in conjunction with other molecular machines. Having a molecular machine without its neighbors would often not help much.

And yet even with all this there remain more problems. For instance, most proteins are not highly modifiable. You can’t just randomly go about swapping in different amino acids. Protein function typically degrades rapidly with amino acid substitutions. So it is challenging for very much interaction site experimentation to take place in the first place. And of course another problem is that it is astronomically difficult for evolution to evolve a single protein to begin with, let alone meaningful interaction sites.

Simply put, from a scientific perspective protein-protein interaction is another problem for evolution.

218 comments:

  1. Cornelius Hunter: In fact, you would have to repeat the experiment millions of times before you could expect to get a good result. But evolution does not have such resources.

    Of course it does.

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  2. Zachriel,

    Cornelius Hunter: "In fact, you would have to repeat the experiment millions of times before you could expect to get a good result. But evolution does not have such resources."

    Zachriel: "Of course it does."

    It does? Please explain where and how evolution has the resources to conduct repeated experiments. I sure hope you're not equating blind, purposeless, random processes with experimentation. Somehow I think you are.

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    1. A natural experiment is an empirical study in which individuals (or clusters of individuals) exposed to the experimental and control conditions are determined by nature or by other factors outside the control of the investigators, yet the process governing the exposures arguably resembles random assignment.

      --- http://en.wikipedia.org/wiki/Natural_experiment

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    2. CH: But evolution does not have such resources. It cannot conduct millions of evolutionary experiments in order to luckily find amino acid sequences on protein surfaces that are required for important biological functions.

      Wow. What about those random mutations and selection pressure? Isn't that what it's all about? Didn't they teach you in grad school, Cornelius?

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    3. "Millions of times"? There are millions of millions of bacteria in the average human gut.

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    4. Zachriel,

      "Millions of times"? There are millions of millions of bacteria in the average human gut."

      And so,...?

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    5. Nic: And so,...?

      "Millions of times" is a very small number in the history of life. Furthermore, evolution posits that complex interactions evolved from simpler interactions.

      As Bilbo points out, "Behe agrees that organisms with very large population sizes (microbes and perhaps insects) are able to "experiment" at the required level to obtain new proteins. He argued that the 'edge' or 'limit' of what they could produce was two proteins." Where Behe goes wrong is not understanding how a simpler system can evolve into a more complex system incrementally. He stakes his claim on irreducibility, but it's easy to show how irreducibility is a natural byproduct of optimization.


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    6. Zachriel,

      "Where Behe goes wrong is not understanding how a simpler system can evolve into a more complex system incrementally. He stakes his claim on irreducibility, but it's easy to show how irreducibility is a natural byproduct of optimization."

      Actually this is where you equate the statement 'this is where Behe goes wrong' with the statement 'you don't agree with him'. Two radically different things, I'm afraid.

      You, nor anyone else over the last 200 years has even remotely demonstrated a simpler system evolving into a more complex system to the degree required to justify common descent.

      So, the question begs to be asked. Who has less understanding, Zachriel, or Behe? I know where I would place my bet.


      If it is so easy to show irreducibility is a natural by product of optimization why don't you enlighten us. Of course, that would require a definition of optimization in this context.

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    7. Zachriel said

      "but it's easy to show how irreducibility is a natural byproduct of optimization."

      But optimizatonis a goal directed process not a ramdom process. And no reproductity succescannot be the e goal of all the optimization process we see in life forms, as there are process optimized to a level where the cost of optimization is greater than the reproductive advantage they provide.

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    8. Nic: You, nor anyone else over the last 200 years has even remotely demonstrated a simpler system evolving into a more complex system to the degree required to justify common descent.

      Of course they have. Creationists just wave their hands when examples are provided.

      In any case, common descent is independently supported by the nested hierarchy and the fossil succession.

      Nic: Who has less understanding, Zachriel, or Behe?

      If you are going to appeal to authority, then keep in mind that the vast majority of biologists reject Behe's contentions.

      Blas: But optimizatonis a goal directed process not a ramdom process.

      No. Many natural processes work towards the most efficient path, such as rivers cutting channels to the sea.

      Blas: But optimizatonis a goal directed process not a ramdom process.

      Does a river have a goal?

      Behe's claim is that the evolution of irreducible complexity is implausible. We have only to show a plausible sequence with each step providing a selectable benefit.

      If have a structure A with function F, it may happen that the presence of structure B may enhance function F, perhaps B binds a reactant needed by A. Over time, A may lose the ability to bind the reactant, while B becomes more efficient at binding, so the combination A-B becomes more efficient than the original A alone, and A-B is now irreducible. Repeat this process to A-B-C to A-B-C-D. Now, it is plausible that C may become redundant as functions are spread among the other structures, so that we end up with A-B-D, even though A-B-D couldn't have evolved directly.

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    9. Z: Behe's claim is that the evolution of irreducible complexity is implausible. We have only to show a plausible sequence with each step providing a selectable benefit.

      J: No, you have to show that there is a historical sequence of mutations that EXPLAIN the existence of every organism that you posit has existed at the TIME that you posit it existed. That's why Behe knows it's implausible. Because that isn't doable even if UCA is true.

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    10. Actually, Z, you have to show more than that. You have to show that geology, taphonomy, ecology, etc imply the fossil succession that exists. That's undoable too, at this time. It probably will always be undoable. And we don't even know what the fossil succession is. We modify stratigraphic ranges all the time by new fossil finds.

      UCA and SA histories are just that--posited histories. They are NOT explanations of the events entailed IN those histories. Fossil succession alone prevents us from explaining either using the data set accepted by both parties.

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    11. Jeff: No, you have to show that there is a historical sequence of mutations that EXPLAIN ...

      The negation of implausible is plausible. That's all that has to be shown.

      Jeff: UCA and SA histories are just that--posited histories.

      Yes, common descent is a hypothesis, meaning it has testable implications which have been repeatedly verified.

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    12. oleg:

      Wow. What about those random mutations and selection pressure? Isn't that what it's all about? Didn't they teach you in grad school, Cornelius?

      Well that is part of the problem. You are fighting selection as protein function drops off rapidly as you start randomly substituting new amino acids into the sequence.

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    13. Axe et al., A search for single substitutions that eliminate enzymatic function in a bacterial ribonuclease, Biochemistry 1998: "The broad picture that has emerged from studies of this sort is one of functional tolerance of substitution."

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    14. CH: Well that is part of the problem. You are fighting selection as protein function drops off rapidly as you start randomly substituting new amino acids into the sequence.

      That's a quantitative question, CH. Not a simple yes/no question.

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    15. Z:

      There are millions of millions of bacteria in the average human gut.

      Yes, with millions and millions of protein-protein interactions. Your argument is circular--you are starting with the thing that you are arguing evolved.

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    16. Cornelius Hunter: Yes, with millions and millions of protein-protein interactions.

      Quite a difference between "millions of millions" and "millions and millions".

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    17. Z: Quite a difference between "millions of millions" and "millions and millions".

      J: And yet that difference doesn't change the fact that you're starting with what you have to prove. You need to read up on deductive logic. Seriously.

      Z: The negation of implausible is plausible. That's all that has to be shown.

      J: That isn't relevant. Inductive criteria apply ONLY to explanations. Thus, inductive plausibility criteria don't even APPLY to mere posited histories. So what you mean by plausibility amounts to your own version of personal credulity.

      Z: Yes, common descent is a hypothesis, meaning it has testable implications which have been repeatedly verified.

      J: No one can even articulate the number of axioms required to IMPLY/EXPLAIN how a human evolved from a non-human species or organism. You're utterly confused. You need to read up on deductive logic.

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    18. J1: No one can even articulate the number of axioms required to IMPLY/EXPLAIN how a human evolved from a non-human species or organism.

      J2: That is to say, the only way you can do it is to just disregard the current theory that morphologies and phenotypes are conditioned in part by DNA sequences, epigenetic information, etc. If you wanna dump those theories for variation explanation, then you can probably pull off a 2-year-old's explanation for the evolution of a human species from a non-human.

      And that doesn't begin to deal with explaining the relevant fossil succession and the posited gaps. If you wanna dump geology, taphonomy, ecology, etc to account for the currently-inferred fossil succession (which changes all the time, anyway) relevant to your hypothesis, then you can probably pull of a 2-year-old's explanation for the relevant fossil succession.

      But induction doesn't work that way. Per induction criteria, you don't dump your best explanatory theories to salvage a hypothesis in LastThursdayIsm fashion that has virtually zero value to humans in the first place. But granted, 2-year-old's do that all the time.

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    19. Then again, maybe 2-year-old's don't confuse what is actually just their own manner of story-telling with explanation.

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    20. Jeff: And yet that difference doesn't change the fact that you're starting with what you have to prove.

      The question presupposes the existence of life, which provides millions of millions of possible tests, contrary to Cornelius Hunter's claim.

      Jeff: That isn't relevant.

      You need to read up on deductive logic. Seriously. To contradict "it's not plausible", we only have to show plausibility.

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    21. Z: The question presupposes the existence of life, which provides millions of millions of possible tests, contrary to Cornelius Hunter's claim.

      J: But the vast majority of UCA'ists don't agree with you that it's plausible that the origin of a universal common ancestor occurred in an a-causal way. Why should CH take you more seriously than them? If UCA depends, per the majority of UCA'ists, on a causal abiogenetic origin of the UCA, then of course the plausibility or implausibility of abiogenesis is married to the plausibility of implausibility of UCA. They are one history in that case.

      Z: To contradict "it's not plausible", we only have to show plausibility.

      J: Again, inductive plausibility apply ONLY to explanations, NOT stories. So in that sense, a mere story has no plausibility as a description of or inference about reality, historical or otherwise. And you have yet to define what else you're meaning by "evidence," "plausibility," etc other than your own version of personal credulity.

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    22. Rather, " inductive plausibility CRITERIA apply ONLY to explanations ..."

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    23. Call it a-plausible instead of implausible. The point is the same. There is nothing PLAUSIBLE about claiming a posited history occurred if that history isn't explicable in terms of anything we can even posit about causality in an enumerable list of propositions. All we can do when that's the case is ask if UCA or SA contradicts our other inductively derived theories. Short of that, reason doesn't touch the question yet.

      If you wanna say UCA is self-evident to you, then a posteriori evidence has nothing to do with your belief in UCA in the first place.

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    24. Jeff: If UCA depends, per the majority of UCA'ists, on a causal abiogenetic origin of the UCA

      That is incorrect. Common ancestry does not depend on any theory of the origin of life.

      Jeff: Again, inductive plausibility apply ONLY to explanations, NOT stories.

      Again, simple deduction is that the negation of implausible is not implausible.

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    25. Z: That is incorrect. Common ancestry does not depend on any theory of the origin of life.

      J: The only way that could be true is if all historical events aren't caused such that the UCA just popped into existence without a cause. Otherwise, there is no evolutionary history apart from a pre-evolutionary history that served as necessary conditions of the evolutionary history.

      Z: Again, simple deduction is that the negation of implausible is not implausible.

      J: Again, there is no relative plausibility criteria for mere stories other than one's own version of personal credulity. And personal credulity has no relevance to rational debate between 2 or more persons.

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    26. Jeff: The only way that could be true is if all historical events aren't caused such that the UCA just popped into existence without a cause.

      That is incorrect. For instance, if life was seeded by an interplanetary source, the evidence would still support common descent.

      Jeff: And personal credulity has no relevance to rational debate between 2 or more persons.

      What you mean is we will continue to provide an argument, and you will continue to wave your hands. We already knew that.

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    27. Z: That is incorrect. For instance, if life was seeded by an interplanetary source, the evidence would still support common descent.

      J: And that posited pre-evolutionary history of events would constitute what you posit to be the necessary conditions of the evolutionary history IF you're claiming ALSO that events are caused. But positing histories and showing that an entailed event at some time t is necessary for one or more posited events future to them requires positing CAUSAL capacities in the initial conditions of the history. This is how deduction can work AS explanation, which are oblivious to.

      Z: What you mean is we will continue to provide an argument, and you will continue to wave your hands. We already knew that.

      J: No. What I mean is that you will continue to pontificate your own version of personal credulity wrongly assuming all the while that it must be the equivalent of reasoning since your ego compels you to believe that. In fact, you start in mid-air constantly as if those mid-air claims are self-evident when they're not even remotely self-evident. Worse, you then admit they're not self-evident and yet repeat that mistake OVER and OVER again. You can't even learn from mistakes.

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    28. Jeff: And that posited pre-evolutionary history of events would constitute what you posit to be the necessary conditions of the evolutionary history IF you're claiming ALSO that events are caused.

      Except the Theory of Evolution doesn't require a theory of how life originated. No scientific theory explains everything, or must explain everything, for it to be a valid theory. The Theory of Evolution explains how life evolves, and the history of that evolution.

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    29. Jeff: No. What I mean is that you will continue to pontificate your own version of personal credulity wrongly assuming all the while that it must be the equivalent of reasoning since your ego compels you to believe that.

      We provided what we consider a plausible scenario. Instead of addressing that scenario and explaining why you don't find it plausible, you go off on your usual disconnected rant.

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    30. Z: We provided what we consider a plausible scenario.

      J: Right, with a meaning of plausibility and evidence that has nothing to do with inductive reasoning. Nor are you doing deductive reasoning since you've never articulated enough hypothetico-deductive axioms to imply the events you posit. You can't even model the relative temporal ORDERING of those events since cladograms never match the currently inferred fossil succession (which is ever changing with new finds, anyway). That's why they have to posit, in LastThursdayIsm fashion, all the ghost lineages required to rule out a falsification. And that's just another way of saying that naive falsification is impossible once you posit the fallibility of human belief-generation modes. That alone, leaves all hypotheses sitting equal at the starting gate. We need induction to advance us from there. You ain't got no inductive evidence, because you don't HAVE a deductive explanation yet.

      Z: Except the Theory of Evolution doesn't require a theory of how life originated. No scientific theory explains everything, or must explain everything, for it to be a valid theory.

      J: There's no theory that EXPLAINS a UCA history. If you're saying a cladogram here and a cladogram there models this or that lineage, fine. But that still leaves SA standing per the only hypothesis rejection criteria that is rational--i.e., INDUCTIVE criteria. What's hard about that? If your own version of personal credulity compels you to extrapolate beyond what there is evidence for, fine. But there's still no INDUCTIVE EVIDENCE to support that extrapolation.

      In the first place, cladograms are only hypothesized to model relative temporal ordering of origin events. They don't explain WHY those events happened or even THAT they were caused. As such, they have no predictive value until you can use some finite set of assumptions to model past and future events of some class of biological events.

      But this isn't possible in the first place since cladograms don't tell us which portions of fossil succession have to do with relative temporal ordering of species origins vs. those portions of fossil succession which are due to contingencies of erosion, taphonomical conditions, population density, geographical extent, fossil discovery, etc.

      You need WAY more premises than those entailed in a cladistic algorithm to IMPLY a particular novel observation of the relevant kind.

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    31. Jeff: There's no theory that EXPLAINS a UCA history.

      We weren't discussing "UCA history". Not everything is about your idiosyncratic epistomology.

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    32. Jeff:

      But that still leaves SA standing per the only hypothesis rejection criteria that is rational--i.e., INDUCTIVE criteria.

      How does that work? Would it be too much trouble for you to provide the reasoning that led you to that conclusion? As it stands, it's one of your oft-repeated claims that looks as idiosyncratic to me as it does to Zachriel.

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    33. From what we understand, Jeff thinks that for common descent to be a valid scientific explanation, it has to be able to predict every case of cladogenesis. If not, he counts each supposed case of cladogenesis as an ad hoc assumption of the explanation.

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    34. That might be so. I'm just curious to learn whether his proprietary epistemology has been patented.

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    35. Z: We weren't discussing "UCA history".

      J: That's what this blog is about. CH nor anyone else denies descent with modification.

      Pedant: How does that work? Would it be too much trouble for you to provide the reasoning that led you to that conclusion?

      J: Inductive reasoning is detailed in any standard logic text used in universities. It's not some big secret.

      Z: From what we understand, Jeff thinks that for common descent to be a valid scientific explanation, it has to be able to predict every case of cladogenesis.

      J: Not a "valid" explanation, but AN explanation. That which is unexplained is not an explanation. No one denies common descent of some degree. For crying out loud, even Ken Ham believes there's common descent of wolves, foxes, jackals, dogs, etc. But a cladogram involves assumptions that have nothing to do with what DNA sequences, etc are necessary conditions of WHAT phenotypes, morphologies, etc. And even then they contradict currently-inferred fossil succession such that lots of ghost lineages have to be inferred in LastThursdayism fashion.



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    36. The real question is, where do treatises on logical reasoning say that story-telling can be more or less plausible as histories, and what criteria is used for that, per those treatises?

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    37. J: Inductive reasoning is detailed in any standard logic text used in universities. It's not some big secret.

      So you've been bluffing. You won't or can't tell us what inductive criteria and process you used to conclude, for example, that:

      But that still leaves SA standing per the only hypothesis rejection criteria that is rational--i.e., INDUCTIVE criteria

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    38. Since induction relies on evidence, how does your inductive process leading to separate ancestry as an explanation deal with the fossil succession in geologic time?

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    39. The real question is, where do treatises on logical reasoning say that story-telling can be more or less plausible as histories, and what criteria is used for that, per those treatises?

      Please define "story-telling" and demonstrate how you distinguish story-telling from testable hypotheses.

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    40. There is no inductive evidence for an SA history. That's not what I mean by SA left "standing." I mean that since there is no EXPLANATION for either a UCA history or an SA history, there is no inductive evidence for either kind of history. Hence, neither is rejectable via induction applied to the same data set.

      But regardless of the fact that there is no inductive evidence for either, at least one of those types of histories seems to be true if the world is as regular as we think it is.

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    41. ... Moreover, I never hear ID'ists arguing against using the UCA hypothesis as a working hypothesis. They typically argue against the claim that there is "overwhelming evidence" for UCA or this or that "common ancestry" even though there is no explanation for them nor applied sound genetics in the cladistic modelling. We don't know enough about what sequences, etc condition what phenotypes/morphologies/etc to even do that yet.

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    42. But regardless of the fact that there is no inductive evidence for either, at least one of those types of histories seems to be true if the world is as regular as we think it is.

      WHY? You need to explain what you say.

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    43. Jeff: That's what this blog is about.

      No, the post is or was about the evolution of protein-protein interactions.

      Jeff: Inductive reasoning is detailed in any standard logic text used in universities.

      That's not an answer.

      Jeff: That which is unexplained is not an explanation.

      The Theory of Evolution doesn't explain every case of historical cladogenesis. Rather, it identifies common mechanisms. It also places limits on possible histories.

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    44. Pedant: WHY? You need to explain what you say.

      J: Why, what? Why is there no inductive evidence for a UCA history? Because there is no explanation or predictive model for such a history. Why do we think the world is pretty regular? Because so much is predictable on that assumption.

      Z: No, the post is or was about the evolution of protein-protein interactions.

      J: So do the math for us. Show us how all the protein-protein interactions could have arisen from a UCA in the posited time-frame.

      Z: The Theory of Evolution doesn't explain every case of historical cladogenesis. Rather, it identifies common mechanisms. It also places limits on possible histories.

      J: That doesn't change the fact that there are UCA'ists who claim there is evidence for a UCA history. But there is no INDUCTIVE evidence for such a history, so it's no clear what they mean by evidence apart from their own version of personal credulity.

      Z: That's not an answer.

      J: I've stated basically what the logic texts say over and over. Since Pedant doesn't believe it, he can read a inductive logic chapter for himself. They deal with predictive heuristics, calculable probabilities (using observed frequencies, etc), and rejection criteria for explanations. A UCA history is not even in the ball park in terms of any of these. Of course neither is an SA history.

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    45. Jeff: I've stated basically what the logic texts say over and over.

      You might want to either post it again, or link to the answer.

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    46. I'll hunt down one of my logic books.

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    47. Pedant: Please define "story-telling" and demonstrate how you distinguish story-telling from testable hypotheses.

      J: Story telling in this context is the positing of historical events that are not explicable in terms of anything we know about causality or expressible in an enumerable list of hypothetical propositions about causality. Where the former fails, the latter tends to be impossible or impractical. But without such explanations or predictive heuristics, inductive hypothesis-rejection criteria don't even come into play.

      E.g., is a UCA history was explicable and an SA history wasn't, we'd reject the SA history, and vice versa. If both types of histories were explicable, we'd reject one in terms of parsimony or explanatory breadth. But when neither are explicable or predictable via a model or heurisitc, neither is in the ball park of rejection yet.

      We don't even have observed frequencies that can be used to do probability calculations for comparison. The histories, both biological and geological, are so riddled with contingencies and the resulting uncertainties that we can't even begin to deal with the complexities to do realistic probability calculations.

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    48. Jeff: I'll hunt down one of my logic books.

      Ah yes. Here it is. Jeff: By "our theories," I mean our hypothetico-deductive explanations. So,

      Hypothesis: Branching descent with modification
      Prediction: Nested hierarchy of traits
      Observation: Nested hierarchy of traits
      The observation supports the hypothesis.

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    49. Zachriel said:
      "No. Many natural processes work towards the most efficient path, such as rivers cutting channels to the sea."

      How do you define the mos efficient path? Is it cutting channels? Is that an optimization process?

      No. Many natural processes work towards the most efficient path, such as rivers cutting channels to the sea.

      Zachriel said:
      "Does a river have a goal?"

      No. Optimization processes do. Darwinists need goals for the optimization process of protein binding.

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    50. Blas: How do you define the mos efficient path?

      Rivers work to minimize potential energy.

      Blas: Is that an optimization process?

      Yes.

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    51. Zachriel said:

      "Rivers work to minimize potential energy."

      No. Rivers do not work. Matters tend to the state a minimum energy. They take the path minimize more the next point and they cut channels following this physical law. It is more or less efficient only in regard of the definition efficiency .

      "Blas: Is that an optimization process?
      Zachriel:Yes."

      Amen.

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    52. Blas: Rivers do not work.

      W = Fs

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    53. Zachriel

      W = Fs

      You forgot the part "to minimize potential energy".

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    54. Blas: You forgot the part "to minimize potential energy".

      You said "Rivers do not work." Can we agree that work is involved as river waters move towards the sea? And that the work minimizes the gravitational potential energy?

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    55. Jeff:

      But that still leaves SA standing per the only hypothesis rejection criteria that is rational--i.e., INDUCTIVE criteria.

      There is no inductive evidence for an SA history. That's not what I mean by SA left "standing." I mean that since there is no EXPLANATION for either a UCA history or an SA history, there is no inductive evidence for either kind of history. Hence, neither is rejectable via induction applied to the same data set.

      What data set? Do you mean the fossil succession in geologic time? Do mean the enormous data set showing that "life comes from life.?

      Are you claiming that such data have NO BEARING WHATSOEVER on the hypotheses of separate or continuous ancestry? That they are not suggestive of any testable hypothesis?

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    56. Jeff:

      I'll hunt down one of my logic books.

      Are you saying that you can't remember how you derived the claim:

      But that still leaves SA standing per the only hypothesis rejection criteria that is rational--i.e., INDUCTIVE criteria.

      ???

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    57. Zachriel said

      "You said "Rivers do not work.""

      Yes, I intended to say they are not an agent that make an optimization process. Water do not have a goal. Water is not improving the way it fall.

      "Can we agree that work is involved as river waters move towards the sea? And that the work minimizes the gravitational potential energy?"

      Yes.

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    58. Blas: Water is not improving the way it fall.

      Actually, it can, by cutting a channel through softer rock.

      Blas: Yes.

      Minimizing work is another way to say optimizing.

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    59. Zachriel said

      "Actually, it can, by cutting a channel through softer rock.

      Minimizing work is another way to say optimizing. "

      Well as you should know the work made but the falling water is independant of the path and is equal to the difference of the potential energy change. What change with the path is the power. Are you going to define optimizing increasing or reducing the power needed?

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    60. Blas: Well as you should know the work made but the falling water is independant of the path and is equal to the difference of the potential energy change.

      Slower paths generally mean more potential energy stored in a larger volume of water. Shorter paths reduce potential energy more quickly, while having lower energy costs.

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    61. Zachriel said

      "Slower paths generally mean more potential energy stored in a larger volume of water. Shorter paths reduce potential energy more quickly,"

      And where is the optimization process?


      " while having lower energy costs. "

      What do you mean by energy costs? Always the variation of energy is the mass per g per the variaton of the height.

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    62. Blas: And where is the optimization process?

      Following or making the path that reduces potential energy the most.

      Blas: Always the variation of energy is the mass per g per the variaton of the height.
      What do you mean by energy costs?


      Some is lost to friction and other forces, though some is also used to carve more efficient channels.

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    63. Zachriel said

      "Following or making the path that reduces potential energy the most."

      Zachriel, all the path reduces the potential energy the same. m x g x delta h

      "some is also used to carve more efficient channels. "

      Channels are carved at the expenses of the cinetic energy the mass of wate acquire during the fall. The potential energy change is always the same.

      If the water perform an optimizaton process you have to define wich is the optimun in the view of water. Good luck.

      Blas: Always the variation of energy is the mass per g per the variaton of the height.
      What do you mean by energy costs?

      Some is lost to friction and other forces, though some is also used to carve more efficient channels.

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    64. Blas: Zachriel, all the path reduces the potential energy the same. m x g x delta h

      Blas, a fast moving river has less mass than one that is not moving or moving very slowly (given the same headwaters).

      Blas: Channels are carved at the expenses of the cinetic energy the mass of wate acquire during the fall. The potential energy change is always the same.

      Friction and mechanical forces reduce the speed of the river, slowing the release of potential energy. However, some of this mechanical energy tends to create a more efficient channel.

      Blas: If the water perform an optimizaton process you have to define wich is the optimun in the view of water.

      We already did. Rivers work to minimize potential energy.

      Delete
    65. Zachriel said

      "Blas, a fast moving river has less mass than one that is not moving or moving very slowly (given the same headwaters)."

      ???

      Zachriel said:

      "Friction and mechanical forces reduce the speed of the river, slowing the release of potential energy. However, some of this mechanical energy tends to create a more efficient channel."

      What do you mean by a more "efficient" channel?

      Zachriel said:
      "We already did. Rivers work to minimize potential energy."

      You are saying that the optimization process is find the faster way to reduce its potential energy?

      Delete
    66. Blas: What do you mean by a more "efficient" channel?

      One that can best reduce the potential energy of the river by moving the mass of water to a lower level.

      Blas: You are saying that the optimization process is find the faster way to reduce its potential energy?

      To reduce its total potential energy. With a given headwater, the faster the river can move water downhill, the lower its potential energy.

      Delete
    67. Zachriel said:
      "To reduce its total potential energy. With a given headwater, the faster the river can move water downhill, the lower its potential energy."

      No. The potential energy is independant of how fast the river move.

      Delete
    68. Blas: The potential energy is independant of how fast the river move.

      Let's try a thought-experiment. We have a river flowing to the sea. Some obstruction occurs, and the river stops flowing, resulting in a large lake. Once the lake fills, the river resumes its previous flow. Which has more potential energy, before or after the obstruction?
      http://static.flickr.com/26/53644574_3ce98ae58c_b.jpg

      Delete
    69. Zachriel said
      "Let's try a thought-experiment. We have a river flowing to the sea. Some obstruction occurs, and the river stops flowing, resulting in a large lake. Once the lake fills, the river resumes its previous flow. Which has more potential energy, before or after the obstruction?"

      The potential energy is exactly the same:

      m x g x delta h

      Delete
    70. What's the "m" stand for?

      Delete
    71. Blas: mass

      That's right. So which has more mass? The river with a large lake, or the same river without a large lake?
      http://static.flickr.com/26/53644574_3ce98ae58c_b.jpg

      Delete
    72. The system with the lake has more mass and more potential energy, but that is still independant of "the faster the river can move water downhill".

      Delete
    73. Blas: The system with the lake has more mass and more potential energy, but that is still independant of "the faster the river can move water downhill

      You had said "The potential energy is exactly the same". We're making progress!

      Now, take a river which falls almost directly into the sea, and a slow winding river that ten times as long and twice as wide. Which has more mass? Then we'll try to put it all together.

      Delete
    74. Zachriel said:
      "Now, take a river which falls almost directly into the sea, and a slow winding river that ten times as long and twice as wide. Which has more mass? Then we'll try to put it all together."

      I do not know. It can be either way. It will depend of the flow rate of the source. I suppose that we are starting with the same source and the water "optimice" the way it goes down in one case falling directly into the sea and in the other making a ten times long and twice wide.

      Delete
    75. Blas: I suppose that we are starting with the same source and the water "optimice" the way it goes down in one case falling directly into the sea and in the other making a ten times long and twice wide.

      So the answer to Which has more mass?

      Delete
    76. Wich river has more mass the Po or the Rio de la Plata?

      Delete
    77. See you decided to side-step the question.

      Blas: Wich river has more mass the Po or the Rio de la Plata?

      The Rio de la Plata has more mass, much of which is seawater. It has low potential energy because it is virtually at sea level.

      Our example used the same headwaters. Take a river which falls almost directly into the sea, and a slow winding river that ten times as long and twice as wide. Which has more potential energy?

      Delete
    78. To determine the potential energy you have to determine at the same instant the mass of water at each altitude and then you can compare the potential energy at that instant of both systems.
      Let aside this example , then for you optimization is "searching" for the lower energetic level.

      Delete
    79. Blas: To determine the potential energy you have to determine at the same instant the mass of water at each altitude and then you can compare the potential energy at that instant of both systems.

      That's right. From the same headwaters, take a river which falls almost directly into the sea, and a slow winding river that ten times as long and twice as deep and wide. Which has more potential energy?

      Blas: then for you optimization is "searching" for the lower energetic level.

      Lowest potential energy. Rivers work by converting potential energy into kinetic energy.

      Delete
    80. Zachriel said
      "Blas: then for you optimization is "searching" for the lower energetic level.

      Lowest potential energy. Rivers work by converting potential energy into kinetic energy. "

      River works converting potential energy into kinetic energy in order to reach the lower potential energy status. That is optimization.

      Delete
  3. Pedant,

    "A natural experiment is an empirical study in which individuals (or clusters of individuals) exposed to the experimental and control conditions are determined by nature or by other factors outside the control of the investigators, yet the process governing the exposures arguably resembles random assignment.

    --- http://en.wikipedia.org/wiki/Natural_experiment"

    And you think this answers the question how?

    ReplyDelete
    Replies
    1. And why do you think it doesn't answer the question?

      Delete
    2. Pedant.

      "And why do you think it doesn't answer the question?"

      "A natural experiment is an empirical study in which individuals (or clusters of individuals) exposed to the experimental and control conditions are determined by nature or by other factors outside the control of the investigators, yet the process governing the exposures arguably resembles random assignment."

      Translation:Stuff happens.

      I suppose you would think the phrase a metal, spirally threaded, fully slotted, manually implemented, fibre intrusive securing device, is describing something other than a wood screw.

      Delete
    3. Translation:Stuff happens.

      What a silly thing to say. If you had read and understood the article, you might have learned that patterns in historical data can be detected and analyzed to provide useful information. As in the case of the Soho cholera outbreak which John Snow was able to ascribe to contaminated water. New knowledge at the time, with profound consequences for public health.

      Delete
    4. Pedant,

      Analyzing historical data and experimentation are not the same thing, Pedant. And in case you forgot, experimentation was the topic.

      Delete
    5. Nic: Analyzing historical data and experimentation are not the same thing

      The former is called a natural experiment, while the latter is called direct experimentation. Biological organisms actually conduct direct experimentation over generations.

      Nearly all of astronomy is based on natural experiments, for instance. It's not like they make a million suns for in the lab.

      Delete
    6. So, Nic, what do you think of astrophysics? There are no experiments there, just observations. Is it not a scientific discipline?

      Delete

    7. "The former is called a natural experiment, while the latter is called direct experimentation."

      And they are fundamentally different.

      "Biological organisms actually conduct direct experimentation over generations."

      No, they do not. Experimentation, by definition, requires intelligent input and interpretion. This type of linguistic nonsense is all too common in evolutionary thinking.

      Delete
    8. Oleg,

      "So, Nic, what do you think of astrophysics? There are no experiments there, just observations. Is it not a scientific discipline?"

      This is typical of you, Oleg. Distort what a person has said and then attack him for it. I never said interpreting historical scientific data was not scientific. I said it was not experimental in nature, which it is not.

      Seriously Oleg, you really need to develop some integrity.

      Delete
    9. Nic: Experimentation, by definition, requires intelligent input and interpretion.

      We're using the term in the sense used in the original post. "If you randomly selected the amino acids at the binding patch on the surface of one of the two proteins, then meaningful binding would be unlikely. In fact, you would have to repeat the experiment millions of times before you could expect to get a good result"; random mutation and selection for function.

      Delete
    10. Distort what a person has said and then attack him for it.

      You weren't attacked, you were corrected.

      You really need to grow up.

      Delete
    11. Zachriel,

      Nic: "Experimentation, by definition, requires intelligent input and interpretation."

      Zachriel: "We're using the term in the sense used in the original post. "If you randomly selected the amino acids at the binding patch on the surface of one of the two proteins, then meaningful binding would be unlikely. In fact, you would have to repeat the experiment millions of times before you could expect to get a good result"; random mutation and selection for function."

      And how does this counter what I said?

      Delete
    12. Pedant,

      Nic: "Distort what a person has said and then attack him for it."

      Pedant: "You weren't attacked, you were corrected."

      And where did I ever claim interpreting historical data was unscientific which would require I be corrected? The answer is nowhere. No, Pedant, Oleg tried putting words in my mouth and he got called on it.

      Those who need to grow up are the ones who spout tired rhetoric and expect everyone to fall for it.

      Delete
    13. Nic: And how does this counter what I said?

      You quibbled over semantics. We pointed out we were using it in the sense of the original point being raised, and elaborated it so you might understand the response.

      Delete
  4. In his book, The Edge of Evolution, Behe agrees that organisms with very large population sizes (microbes and perhaps insects) are able to "experiment" at the required level to obtain new proteins. He argued that the "edge" or "limit" of what they could produce was two proteins. If the complex needed three or more proteins to function, then he argued that would be over the "edge." Behe argued that for smaller populations, such as mammals, producing more than one protein would be over the "edge."

    ReplyDelete
  5. Of course, such interactions are a problem for evolution. The idea that a monkey at a typewriter would eventually produce Shakespeare presumes the monkey would keep at it after hitting a few keys. Even if the monkey typed "To be or not to be..." the monkey wouldn't know it and would stop to peel a banana, scratch itself or go to sleep. Evolution, if there was such a thing, would stop after one protein: mission accomplished.

    ReplyDelete
    Replies
    1. Glenn: Evolution, if there was such a thing, would stop after one protein: mission accomplished.

      We know that's not true because ongoing evolution is something we can directly observe.

      Delete
    2. Zachriel,

      Glenn: "Evolution, if there was such a thing, would stop after one protein: mission accomplished."

      Zachriel: "We know that's not true because ongoing evolution is something we can directly observe."

      Here you go again, spouting your unsupportable rhetoric about observable evolution. I know I've asked this of you before, but we'll try one more time. How about supplying some examples of observable evolution which would support the concept of common descent.

      Delete
    3. Nic: Here you go again, spouting your unsupportable rhetoric about observable evolution.

      Here you go again, conflating different claims. Glenn claimed that evolution would stop after one protein. That has little to do with common descent, but the general evolutionary process.

      The primary evidence for common descent is the nested hierarchy and fossil succession, though observations of evolution have to be consistent with common descent, of course.

      Delete
    4. Zachriel,

      "Here you go again, conflating different claims. Glenn claimed that evolution would stop after one protein. That has little to do with common descent, but the general evolutionary process."

      Come now, Zachriel, you made a claim for observable evolution in defence of the idea evolution continues onwards and upwards unabated in response to Glenn's statement that it would cease after one protein.

      "The primary evidence for common descent is the nested hierarchy,..."

      Seriously, you're still going to try the nested hierarchy routine? We went through this before, remember? Don't you remember you could not even supply a rudimentary definition of what constituted a nested hierarchy or provide any examples of same?

      You just spout rhetoric, continually. Please, try to present some sound logical arguments for a change. If you wish I'll give you another opportunity to define a nested hierarchy, give some examples and explain why it is evidence for evolution. You utterly failed to do so in the past, but as I said, I'll give you another opportunity to present your case.

      Delete
    5. Nic: Come now, Zachriel, you made a claim for observable evolution in defence of the idea evolution continues onwards and upwards unabated in response to Glenn's statement that it would cease after one protein.

      Why would it cease? We directly observe organisms in the process of evolving. The claim doesn't make any sense.

      Nic: Don't you remember you could not even supply a rudimentary definition of what constituted a nested hierarchy or provide any examples of same?

      Huh? You must be thinking of someone else. A nested hierarchy is a hierarchical ordering of nested sets. Dewey Decimal is a nested hierarchy.

      Uncrossed branching with variation produces a nested hierarchy of traits, and we observe such a nested hierarchy. It leads to predictions concerning what we will find in rocks to molecules.

      Delete
    6. Zachriel,

      "Why would it cease?"

      Why would it continue?

      "We directly observe organisms in the process of evolving. The claim doesn't make any sense."

      You keep saying that, but continually fail to provide any kind of solid evidence, just continual rhetoric.

      Nic: Don't you remember you could not even supply a rudimentary definition of what constituted a nested hierarchy or provide any examples of same?

      Zachriel: "Huh? You must be thinking of someone else."

      Nope, it was you.

      "A nested hierarchy is a hierarchical ordering of nested sets."

      Well, that's hardly circular.

      "Dewey Decimal is a nested hierarchy."

      The Dewey Decimal system is not likely to have any effect on biological evolution, so I really don't think it qualifies as an example. Feel free to try again

      "Uncrossed branching with variation produces a nested hierarchy of traits, and we observe such a nested hierarchy. It leads to predictions concerning what we will find in rocks to molecules."

      AN EXAMPLE! And why does it provide evidence for evolution? You're just spouting the same nonsense as last time.

      Delete
    7. Nic: Why would it continue?

      Because of variation and fecundity.

      Nic: You keep saying that, but continually fail to provide any kind of solid evidence

      E. coli Long-term Experimental Evolution Project Site
      http://myxo.css.msu.edu/ecoli/

      Nic: Well, that's hardly circular.

      A nested hierarchy is an ordered set such that each subset is contained within its superset. Even more precisely, S is a nested hierarchy if S is a partially ordered collection of sets by inclusion such that given X∈S and Y∈S and Z∈S, if X⊆Y and X⊆Z, then Y⊆Z or Z⊆Y.

      Nic: The Dewey Decimal system is not likely to have any effect on biological evolution, so I really don't think it qualifies as an example.

      You asked for an example. It's an example.

      Nic: AN EXAMPLE!

      Uncrossed branching with variation produces a nested hierarchy of traits, and we observe such a nested hierarchy when we classify biological organisms.
      http://en.wikipedia.org/wiki/Phylogenetic_tree

      Delete
    8. Zachriel,

      Nic: "Why would it continue?"

      Zachriel: "Because of variation and fecundity."

      Both of which do nothing for the argument of common descent, unless of course you add overwhelming amounts of conjecture and extrapolation. So, that hardly answers the question, does it?

      Nic: "You keep saying that, but continually fail to provide any kind of solid evidence."

      Zachriel: "E. coli Long-term Experimental Evolution Project Site
      http://myxo.css.msu.edu/ecoli/"

      So, here we go again with bacteria remaining bacteria as evidence for evolution from a common ancestor. So I'll ask the same question again. How does bacteria remaining bacteria qualify as evidence for evolution from a common ancestor?

      Nic: "Well, that's hardly circular."

      Zachriel: "A nested hierarchy is an ordered set such that each subset is contained within its superset. Even more precisely, S is a nested hierarchy if S is a partially ordered collection of sets by inclusion such that given X∈S and Y∈S and Z∈S, if X⊆Y and X⊆Z, then Y⊆Z or Z⊆Y."

      A BIOLOGICAL EXAMPLE, PLEASE!

      Nic: "The Dewey Decimal system is not likely to have any effect on biological evolution, so I really don't think it qualifies as an example."

      zachriel: "You asked for an example. It's an example."

      Okay, it's an example. Now, provide a biological equivalent to the Dewey Decimal System and demonstrate how this biological Dewey Decimal System is evidence for evolution.

      As the great Yogi Berra said, 'it's deja vu all over again'.

      Nic:" AN EXAMPLE!"

      Zachriel: "Uncrossed branching with variation produces a nested hierarchy of traits, and we observe such a nested hierarchy when we classify biological organisms.
      http://en.wikipedia.org/wiki/Phylogenetic_tree"

      So, in your thinking, repeating what you have already said; which is not an example of a nested hierarchy, or an explanation as to how it is evidence for evolution; and tacking on a reference to wikipedia regards the phylogenetic tree; which is not an example of a nested hierarchy, or an explanation as to how it is evidence for evolution; is answering my request for a biological example of a nested hierarchy, and an explanation as to how it is evidence for evolution? I'll retire to bedlam.

      Really, Zachriel, it's like I'm talking to a wall. Do you really not see the fact you never provide an answer? You just keep going around the same circle. Don't you ever get dizzy?

      Delete
    9. Nic: Both of which do nothing for the argument of common descent, unless of course you add overwhelming amounts of conjecture and extrapolation.

      Why do you keep conflating the issues. We were discussing whether evolution would continue after a single protein evolved.

      Nic: So, in your thinking, repeating what you have already said; which is not an example of a nested hierarchy

      Indeed, biological organisms do generally sort by trait into a nested hierarchy.

      Delete
    10. Zachriel,

      Nic: "So, in your thinking, repeating what you have already said; which is not an example of a nested hierarchy"

      Zachriel: "Indeed, biological organisms do generally sort by trait into a nested hierarchy."

      So you keep saying. And I keep asking you for a biological example of such a hierarchy. And yet again you provide absolutely nothing. You really don't realize the fact you never provide an answer, do you?
      Absolutely unbelievable.

      Delete
    11. To be clear on the first point: There is a distinction between evolution as the change in heritable characteristics of population (such as the evolution of new protein interactions), and common descent which depends on cladogenesis.

      To be clear on the second point: We have provided a precise definition of a nested hierarchy. We have also provided two examples; Dewey Decimal and biological taxonomy. While the former is arbitrary (and there are many other equally rational library classifications), the latter is due to the observed pattern of traits (there is only one objective overall pattern).

      The interesting thing about a nested hierarchy is that any non-trivial subset of the nested hierarchy also forms a nested hierarchy. That follows directly from the definition above. With Dewey Decimal, 500 is the sciences, with subsets including astronomy, physics, chemistry, life sciences, and so on. With the biological nested hierarchy, mammals is a subset of the nested hierarchy, and also forms a nested hierarchy, with subsets including Monotremata, Eutheria, and Marsupialia.

      Delete
    12. Nic: And I keep asking you for a biological example of such a hierarchy.

      Not sure if your question is even coherent. A single organism can't be a nested hierarchy. It's the pattern of traits among the various organisms that constitute a nested hierarchy.



      Delete
    13. Perhaps this will help. Cat, dog, trout, form a very simple nested hierarchy: {{cat, dog}, {trout}}

      Delete
    14. Zachriel,

      "We have provided a precise definition of a nested hierarchy."

      Really, where?

      "We have also provided two examples; Dewey Decimal and biological taxonomy."

      I just can't believe you. The Dewey Decimal System is an absolute joke as an example when the discussion revolves around biological systems. I'll ask again for probably the 100th time. What are these observed patterns of trait?

      "mammals is a subset of the nested hierarchy, and also forms a nested hierarchy, with subsets including Monotremata, Eutheria, and Marsupialia."

      "Perhaps this will help. Cat, dog, trout, form a very simple nested hierarchy: {{cat, dog}, {trout}}"

      Now, how is this evidence for evolution?

      "A single organism can't be a nested hierarchy."

      Okay. Can it contain a nested hierarchy?

      Delete
    15. ZAchriel,

      "Perhaps this will help. Cat, dog, trout, form a very simple nested hierarchy: {{cat, dog}, {trout}}

      Nic: "Now, how is this evidence for evolution?"

      That should read; Now, what makes this particular grouping a nested hierarchy and how is this evidence for evolution?

      Delete
    16. Zachriel: We have provided a precise definition of a nested hierarchy.

      Nic: Really, where?

      You quoted it yourself.

      S is a nested hierarchy if S is a partially ordered collection of sets by inclusion such that given X∈S and Y∈S and Z∈S, if X⊆Y and X⊆Z, then Y⊆Z or Z⊆Y."

      Zachriel: The Dewey Decimal System is an absolute joke as an example when the discussion revolves around biological systems.

      It's an example of a nested hierarchy, which is what you asked. Unless you understand the pattern under discussion, you're not going to understand how that relates to common descent.

      Nic: how is this evidence for evolution?

      Uncrossed branching with variation produces a nested hierarchy of traits, and we observe such a nested hierarchy.

      But you really need to try to understand the pattern first. For instance, we keep providing the definition of a nested hierarchy, and you keep asking for the definition of a nested hierarchy.

      Delete
    17. We misattributed one of the statements above. The "absolute joke" comment is Nic's, of course.

      Zachriel: Cat, dog, trout, form a very simple nested hierarchy: {{cat, dog}, {trout}}

      Nic: Now, what makes this particular grouping a nested hierarchy

      As written, it's a nested hierarchy by definition. The reason we grouped it the way we did is because cat and dog share more traits than either does with trout.

      Delete
    18. "Nic: how is this evidence for evolution?

      Uncrossed branching with variation produces a nested hierarchy of traits, and we observe such a nested hierarchy. "

      Don't forget you also need extinction of the species near the borders that small incremental evolution would result in. And you also need to explain away things like all those conflicting signals. e.g. DNA tree not matching morphological trees. And the problem of connecting the branches to the trunk. And you also have to explain why the hyrax looks more like a rodent, and the aardvarks looks like an anteater, but both are more closely related to the elephant. And then there is the group, shark ,trout human, or maybe trout, lungfish human, or how about crocodile, komodo monitor, sparrow? And humans are suppose to be close to chimps, but some of our DNA is closer the the gorilla, and some is closer to the rhesus monkey. There is even someone who suggested that. since some details of human anatomy, are so close to the pig, that humans are actually chimp/pig hybrids. Evolution has got to explain all this stuff.

      Delete
    19. natschuster: Don't forget you also need extinction of the species near the borders that small incremental evolution would result in.

      Do you think if we looked real hard, we might find evidence of extinction?

      natschuster: And you also have to explain why the hyrax looks more like a rodent, and the aardvarks looks like an anteater, but both are more closely related to the elephant.

      Convergence. See Darwin 1859.

      natschuster: And humans are suppose to be close to chimps, but some of our DNA is closer the the gorilla, and some is closer to the rhesus monkey.

      Incomplete lineage sorting, which is a direct implication of population genetics.

      Delete
    20. Interesting how all the species near the borders became extinct.

      So convergence means that the nested hierarchy applies expect where it doesn't.

      And is incomplete lineage sorting really an adequate when the DNA evidence gives conflicting trees that are all over the place?

      Delete
    21. natschuster: Interesting how all the species near the borders became extinct.

      Well, if you did look, you would find evidence that the vast majority of all species have gone extinct.

      natschuster: So convergence means that the nested hierarchy applies expect where it doesn't.

      As Darwin noted, it's unlikely that "the descendants of two organisms, which had originally differed in a marked manner, should ever afterwards converge so closely as to lead to a near approach to identity throughout their whole organisation." In other words, you have to take more than a superficial look.

      natschuster: And is incomplete lineage sorting really an adequate when the DNA evidence gives conflicting trees that are all over the place?

      You went from a specific to a generality. There are many reasons for conflicting trees. Incomplete lineage sorting, as we pointed out, is a direct implication of population genetics, and predicts that some genes in humans will be closer to chimpanzees than to gorillas.
      http://biologos.org/blog/evolution-basics-incomplete-lineage-sorting-and-ancestral-population-sizes

      Delete
    22. Z: will be closer to chimpanzees than to gorillas

      And visa versa.

      Delete
    23. It looks like the extinctions were kinda selective, wiping out those species near the border and leaving those in the middle realtively unscathed.

      And are you sure that if you take more than a superficial look at a tenrec, it will look more like an elephant than than it does an insectivore, or that a golden mole will look more like an elephant than a mole? Or how about an aardvark? Will it look more like an elephant than an anteater? Will the hyrax look more like an elephant than it does a rodent? That's an awful lot of convergence.

      Delete
    24. natschuster: It looks like the extinctions were kinda selective, wiping out those species near the border and leaving those in the middle realtively unscathed.

      Do you have a statistical analysis which shows that?

      natschuster: And are you sure that if you take more than a superficial look at a tenrec, it will look more like an elephant than than it does an insectivore

      Insectivore just means an organism that eats insects. However, molecular evidence places tenrecs in Afrotheria, along with aardvarks and elephants. There's also fossil and morphological evidence. See Tabuce et al., Early Tertiary mammals from North Africa reinforce the molecular Afrotheria clade, Proc. R. Soc. B 2007; and Asher et al., The new framework for understanding placental mammal evolution, BioEssays 2009.

      In any case, the overall nested heirarchy is supported despite some problematic cases. In other words, pointing to problematic cases doesn't make the overall pattern disappear.

      natschuster: That's an awful lot of convergence.

      See Darwin 1859.

      Delete
    25. Zachriel,

      Nic: "Now, what makes this particular grouping a nested hierarchy"

      Zachriel: "As written, it's a nested hierarchy by definition. The reason we grouped it the way we did is because cat and dog share more traits than either does with trout."

      Well, what a surprise, Mammals have more in common with each other than they do with fish, who would have thought that to be the case?

      Okay, for the sake of moving on I'll skip the definition of nested hierarchy and focus on the important question. How is it evidence for evolution?

      Delete
    26. Nic: Mammals have more in common with each other than they do with fish, who would have thought that to be the case

      They're mammals because they have traits characteristic of the group we call mammals.

      Nic: I'll skip the definition of nested hierarchy

      No, don't skip the definition, otherwise, the evidence will make no sense.

      Nic: How is it evidence for evolution?

      Uncrossed branching with variation produces a nested hierarchy of traits, and we observe such a nested hierarchy.

      Delete
  6. Hi Zachriel,

    If you're the same Zach who was at TT before he was banned, it's good to see you. Behe would agree with you that organisms with large enough populations can produce up to two proteins, even if they don't have a function. But he argues that we shouldn't expect them to produce three or more functionless proteins. So if new complexes can be built by adding one or two proteins at a time, then neo-Darwinian evolution can accomplish it. If new complexes can only be built by adding three or more proteins at a time, then some other mechanism must be at work. Behe doesn't try to show that new complexes must be built by adding three or more proteins at a time. He does, however, point out that most proteins function in complexes of six or more. So he hasn't proven ID, but he has shown that neo-Darwinism has a significant challenge to overcome before we should accept it.

    I should also add that Behe not only accepted common descent, he even argued for it in EoE. He just thought there had to be some other mechanism besides natural selection working on random mutation to explain it.

    ReplyDelete
    Replies
    1. Bilbo: If you're the same Zach who was at TT before he was banned, it's good to see you.

      http://telicthoughts.com/

      Delete
    2. Bilbo: Behe would agree with you that organisms with large enough populations can produce up to two proteins, even if they don't have a function.

      Sure. In response to Cornelius Hunter, there's millions of millions of trials.

      Bilbo: He does, however, point out that most proteins function in complexes of six or more.

      Sure, but the process of adding proteins to an existing functional complex is not that mysterious. One method is through division of labor and optimization.

      Delete
    3. Yes, and that is why we should Behe's argument not as a refutation of neo-Darwinism, but as a stiff challenge to it. Have all or most of the multi-protein complexes arisen in such a stepwise manner? Before we can affirm that, I think much more research would be needed.

      Delete
    4. If a mutation occurs, for example in one out of a million organisms, then an adaptation that requires one mutation while happen in one in a million organisms. If an adaptation requires two mutations then we need one million squared organisms, If it requires three mutations, then we need one million to the third power. Pretty soon, we more organisms than are available.

      Delete
    5. ""Bilbo: He does, however, point out that most proteins function in complexes of six or more."

      Sure, but the process of adding proteins to an existing functional complex is not that mysterious. One method is through division of labor and optimization"

      Behe said that metabolic pathways are irreducibly complex because each step produces something that is functional, so it isn't hard in that sense to add another step and produce something else. But the problem is that proteins have to bind to each other to work as a complex. They need a rather precise fir. Specific amino need to be there in a specific alignment. Getting that by accident is hard. Even evolving from another, preexisting protein is hard because of the precision needed. and the fac that changing the arrangement of amino acids, can cause the protein to loose stabilty. You need simultaneous, compensatory changes. or you get a floppy, useless protein.

      Delete
    6. natschuster: If a mutation occurs, for example in one out of a million organisms, then an adaptation that requires one mutation while happen in one in a million organisms.

      The rate is about one mutation per thousand bacterial replications, or in complex animals, a few hundred mutations per each replication. In bacteria, the rate can actually be much higher when under environmental stress. In primordial organisms, the rate would probably be even higher.

      natschuster: If an adaptation requires two mutations then we need one million squared organisms

      That's not actually how you would calculate it, but per your own arithmetic, it would be "If an adaptation requires two mutations then we need one thousand squared organisms." There are about a hundred million million organisms in the average human gut.

      Delete
    7. I guess I wasn't clear. I didn't mean any mutations. I meant specific mutations that will lead to an new adaptation. Most mutations are either harmful or neutral, so they won't have much of an effect. And even if, for a specific mutation happens once per 1000 replications, an adaptation that requires sevem mutation would require 1000^7 organism. That is a lot of organisms. Eventually, the numbers begin to work against you.

      Delete
    8. "Behe said that metabolic pathways are irreducibly complex because each step produces something that is functional, so it isn't hard in that sense to add another step and produce something else"

      Should say, "not irreducibly complex." Sorry, my bad.

      Delete
    9. natschuster: Most mutations are either harmful or neutral, so they won't have much of an effect.

      That's right, but some are beneficial.

      natschuster: That is a lot of organisms. Eventually, the numbers begin to work against you.

      Yes, it's very unlikely that many independent mutations will results in a complex adaptation. On the other hand, many beneficial changes can occur with only one or two mutations. These can then become predominant in a population, leading to additional beneficial mutations, like a ratchet.

      natschuster: Behe said that metabolic pathways are {not} irreducibly complex because each step produces something that is functional, so it isn't hard in that sense to add another step and produce something else

      That's right. And therefore it can lead to increasing levels of complexity, and sometimes a 'scaffold' can be removed leaving a Roman Arch.
      http://upload.wikimedia.org/wikipedia/commons/e/e2/Ancient_Roman_triumphal_arch_of_Medinaceli-Spain.jpg

      Delete
    10. "Yes, it's very unlikely that many independent mutations will results in a complex adaptation. On the other hand, many beneficial changes can occur with only one or two mutations. These can then become predominant in a population, leading to additional beneficial mutations, like a ratchet."

      So, how does it happen. if an adaptation requires a whole lot of mutations for there to be any benefit, or to compensate for loss of stability, or some other harmful side effect.

      Delete
    11. natschuster: So, how does it happen. if an adaptation requires a whole lot of mutations for there to be any benefit, or to compensate for loss of stability, or some other harmful side effect.

      Evolution generally works by incremental adaptation.

      natschuster: if an adaptation requires a whole lot of mutations for there to be any benefit, or to compensate for loss of stability, or some other harmful side effect.

      If it can't evolve, it won't evolve. Most possible structures are outside the scope of evolution.

      Delete
    12. Zachriel,

      Zachriel:"Evolution generally works by incremental adaptation."

      Zachriel: "Do you have a statistical analysis which shows that?"

      Well?

      Delete
    13. Nic: Well?

      You might start with Lenski's E. coli Long-term Experimental Evolution.
      http://myxo.css.msu.edu/ecoli/

      After that, you might want to look at various fossil sequences, such as for the mammalian middle ear.


      Delete
    14. Zachriel,

      Nic: Well?

      Zachriel: "You might start with Lenski's E. coli Long-term Experimental Evolution.
      http://myxo.css.msu.edu/ecoli/"

      Really, that's what you give me? Bactera remaining bacteria is your idea of a statistical analysis showing incremental adaptation leads to common descent?

      "After that, you might want to look at various fossil sequences, such as for the mammalian middle ear."

      And what would be your evidence that these differences are incremental adaptations, one leading to the next, and simply not variations in the hearing structures of the various creatures?

      Delete
    15. Nic: Bactera remaining bacteria is your idea of a statistical analysis showing incremental adaptation leads to common descent?

      You asked about evolution working by incremental adaptation, not common descent.

      Nic: And what would be your evidence that these differences are incremental adaptations, one leading to the next, and simply not variations in the hearing structures of the various creatures?

      Because there is a temporal succession. At one time, there were no land tetrapods at all. Then there were. At one time, there were tetrapods without mammalian ossicles. Then there were. We can find fossil transitional structures of the progression. This progression was predicted from studies of embryos long before fossil transitionals were found.

      Delete
    16. Zachriel,

      "You asked about evolution working by incremental adaptation, not common descent."

      So are you saying common descent is not a result of the accumulation of incremental adaptations?

      Nic: And what would be your evidence that these differences are incremental adaptations, one leading to the next, and simply not variations in the hearing structures of the various creatures?

      "Because there is a temporal succession. At one time, there were no land tetrapods at all. Then there were."

      How do you know that?

      "We can find fossil transitional structures of the progression."

      And you know these were simply not creatures unique onto themselves, but in fact transitions, how?

      Delete
    17. Nic: So are you saying common descent is not a result of the accumulation of incremental adaptations?

      Cladogenesis (branching) may or may not entail adaptation.

      Nic: How do you know that?

      From the fossil evidence. Or is geology now wrong too?

      Nic: And you know these were simply not creatures unique onto themselves, but in fact transitions, how?

      Of course they're unique unto themselves. That doesn't mean they don't exhibit transitional features. But you seem to be hung up on geology now. Is there any science you accept?

      Delete
    18. Zachriel,

      Nic: "So are you saying common descent is not a result of the accumulation of incremental adaptations?"

      Zachriel, "Cladogenesis (branching) may or may not entail adaptation."

      So, are you saying an accumulation of incremental adaptations may lead to common descent on some occasions but not on others?

      Nic: 'How do you know that?'

      Zachriel: "From the fossil evidence. Or is geology now wrong too?"

      Why would you ask if I believe geology is wrong? Is there only one way to interpret geology, and that way is your way?

      Nic: And you know these were simply not creatures unique onto themselves, but in fact transitions, how?

      Zachriel: "Of course they're unique unto themselves. That doesn't mean they don't exhibit transitional features."

      Why are they 'transitional features'? What makes them 'transitional'?

      Delete
    19. Nic: So, are you saying an accumulation of incremental adaptations may lead to common descent on some occasions but not on others?

      Sure. A population may evolve adaptively without cladogenesis, while a population may divide into separate species without adaptation, which is actually pretty common.

      Nic: Why would you ask if I believe geology is wrong? Is there only one way to interpret geology, and that way is your way?

      Geologists have established quite a few basic facts about geological history, such as the great age of the Earth, and the ordering of strata. Do you dispute their findings?

      Nic: Why are they 'transitional features'?

      They have characteristics intermediate between the primitive and derived forms. Knuckle-walking is considered an intermediate adaptation between quadrupedalism and bipedalism. See Richmond et al., Origin of Human Bipedalism:
      The Knuckle-Walking Hypothesis Revisited, Yearbook of Physical Anthropology 2001.

      Gorillas are knuckle-walkers, so they exhibit the transitional feature. That doesn't imply humans are descended from gorillas, nor does it imply that knuckle-walking is inferior.

      Delete
    20. Zachriel,

      Nic: So, are you saying an accumulation of incremental adaptations may lead to common descent on some occasions but not on others?

      Zachriel, "Sure. A population may evolve adaptively without cladogenesis, while a population may divide into separate species without adaptation,..."

      So whatever happens it happens because of evolution?

      Nic: Why would you ask if I believe geology is wrong? Is there only one way to interpret geology, and that way is your way?

      Zachriel: "Geologists have established quite a few basic facts about geological history, such as the great age of the Earth, and the ordering of strata."

      And how did they establish the great age of the Earth and the ordering of the strata?

      Nic: Why are they 'transitional features'?

      Zachriel: "They have characteristics intermediate between the primitive and derived forms. Knuckle-walking is considered an intermediate adaptation between quadrupedalism and bipedalism."

      So they've been given the label of transitional? That's all this statement is actually saying. "Knuckle walking is considered an intermediate adaptation,..." It's not known to be, it's only considered to be.

      "Gorillas are knuckle-walkers, so they exhibit the transitional feature. That doesn't imply humans are descended from gorillas, nor does it imply that knuckle-walking is inferior."

      Could it be that Gorillas are knuckle walkers because they were meant to be? If not, why not?

      Delete
    21. Nic said:

      "Why would you ask if I believe geology is wrong? Is there only one way to interpret geology, and that way is your way?

      I know geology from standard courses in Uni, which interpretation are you referring to? In other word, what is your accepted interpretation?

      Delete
    22. Nic: So whatever happens it happens because of evolution?

      All sorts of things happen that are not evolution. Not sure what you're trying to say.

      Nic: And how did they establish the great age of the Earth and the ordering of the strata?

      It's one of the great scientific stories! Like Galileo. or Darwin.

      The history of geology stretches back to ancient times, but modern geology can be said to have been founded by James Hutton's Theory of the Earth in 1785 wherein he proposed that the Earth must be very old to account for the erosion of mountains and the deposition of sedimentary layers. Of course, geology is much more advanced today, and overlaps that of astronomical theories of star and planet formation.

      Nic: So they've been given the label of transitional?

      It's considered transitional because it has "characteristics intermediate between the primitive and derived forms".

      Nic: It's not known to be, it's only considered to be.

      The evidence support knuckle-walking as a transitional adaptation.

      Nic: Could it be that Gorillas are knuckle walkers because they were meant to be?

      Gorillas are well-adapted to their own environment. That doesn't mean knuckle-walking isn't transitional.

      Delete
  7. "Simply put, from a scientific perspective protein-protein interaction is another problem for evolution."

    Couldn't we say the highly specified purpose of each protein contradicts the evolutionary myth? The causation of each protein is not random.

    ReplyDelete
    Replies
    1. Sure Marcus, there are all kinds of scientific contradictions to evolution, including the mere evolution of proteins, let alone their interactions. But this post focuses on the interactions. If you're saying that we don't need any more "problems," because the theory is already a big flub then I could hardly argue with you, except that more scientific findings can't hurt.

      Delete
    2. Marcus: Couldn't we say the highly specified purpose of each protein contradicts the evolutionary myth?

      Functional structure is exactly what Darwin proposed evolution to explain. Saying the existence of functional structures contradicts his theory is incoherent.

      Delete
    3. Zachriel: "The broad picture that has emerged from studies of this sort is one of functional tolerance of substitution."

      The ONLY previous sentence is, "Exhaustive-substitution studies, where many amino acid replacements are INDIVIDUALLY TESTED at all positions in a natural protein, have proven to be very valuable in probing the relationship between sequence and function."

      Protein neutrality is reasonably characterized at around 33% chance of destabilization per substitution by a number of papers now.

      Delete
    4. Guo et al., Protein tolerance to random amino acid change, PNAS 2004: "the probability that a random amino acid replacement will lead to a protein's functional inactivation ... was found to be 34% ± 6%."

      Delete
    5. So do you still claim he mischaracterized the data? It's clearly exponential decay.

      Delete
    6. John: So do you still claim he mischaracterized the data?

      Who mischaracterized the data?

      John: It's clearly exponential decay.

      If you're referring to protein mutation; yes, multiple independent mutations in the absence of selection are likely to disable a protein.

      Delete
    7. Zachriel: "Who mischaracterized the data?"

      CH at July 12, 2014 at 9:10 AM?

      Zachriel: "If you're referring to protein mutation; yes, multiple independent mutations in the absence of selection are likely to disable a protein."

      You should probably clarify what you mean by "in the absence of selection". Are you talking about fixation in a population? I'm pretty sure that mutagens don't stop to check if they are going to destroy a protein before having their effect.

      Delete
    8. John: CH at July 12, 2014 at 9:10 AM

      Okay.

      John: You should probably clarify what you mean by "in the absence of selection".

      True. It wasn't clear.

      Obviously, if there are multiple mutations, it will eventually disable a protein. On the other hand, some mutations are neutral or nearly neutral, and these can potentiate beneficial changes.

      Delete
  8. I was researching the ccr4-not complex the other day while reading about polyadenylation. I thought, that sounds like it's doing basically the same things to RNA that the ubiquitination process does to proteins.

    I did not know that both processes were actually performed at different sectors of the same machine. Now the processes are obviously analogically related in the human mind. But I don't see why evolution would "consider" them to have anything to do with each other. I bet they share information somehow.

    ReplyDelete
    Replies
    1. This comment has been removed by the author.

      Delete
  9. ""natschuster: if an adaptation requires a whole lot of mutations for there to be any benefit, or to compensate for loss of stability, or some other harmful side effect".

    If it can't evolve, it won't evolve. Most possible structures are outside the scope of evolution."

    So how did something like the flagellum evolve. How did all those extremely complex protein complexes evolve.
    They required a whole ot of mutations at all those binding sites and such.

    ReplyDelete
    Replies
    1. natschuster: So how did something like the flagellum evolve.

      It's not known with certainty, but many of the components have other uses within the cell.

      natschuster: How did all those extremely complex protein complexes evolve.

      You do realize that complex things can evolve, just not all complex things (or even many simple things).

      natschuster: They required a whole ot of mutations at all those binding sites and such.

      Protein space is rich in possibilities well-within the range of evolutionary processes. Even random sequence peptides can be functional.

      Delete
  10. "t's not known with certainty, but many of the components have other uses within the cell."

    But you have to change them in very specific wats so that they fit together they write way and works as a flagellum.

    "You do realize that complex things can evolve, just not all complex things (or even many simple things)."

    If complexity means there's a lot of stuff there, yeah. If you need very precise, specified complexity that's a different
    story.

    And it's precise function we are talking about in those protein complexes. Just one misaligned amino acid can throw the whole thing off.

    ReplyDelete
    Replies
    1. natschuster: But you have to change them in very specific wats so that they fit together they write way and works as a flagellum.

      Not really. You can get minimal motility fairly easily, improved step-wise.
      http://www.sfu.ca/colloquium/PDC_Top/EoC/can-complex-systems-evolve-or-be-modified-by-evolution-/bacterial-flagella-and-secretory-systems.html

      natschuster: If complexity means there's a lot of stuff there, yeah.

      Specified complexity is not always well-defined. However, if you have a complex structure that has a function, even if it works in a roundabout way, it's probably has specified complexity.
      http://www.rubegoldberg.com/

      natschuster: And it's precise function we are talking about in those protein complexes. Just one misaligned amino acid can throw the whole thing off.

      It might, but proteins are fairly tolerant of mutation.

      Guo et al., Protein tolerance to random amino acid change, PNAS 2004: "the probability that a random amino acid replacement will lead to a protein's functional inactivation ... was found to be 34% ± 6%."

      Delete
    2. That doesn't seem very tolerant given that most proteins are over a hundred amino acids in length.

      Delete
    3. John: That doesn't seem very tolerant given that most proteins are over a hundred amino acids in length.

      The original claim concerns beneficial changes that require two or more mutations. Two or even three mutations are well-within plausibility based on a "33% chance of destabilization per substitution".

      Delete
    4. he was talking about a flagellum. Do you have a path on continuous mutations that can turn it into something else? After all, you have a 2/3 chance of keeping it to try something else.

      Delete
    5. John: Do you have a path on continuous mutations that can turn it into something else?

      Some of the components already have other functions.

      Delete
    6. Zachriel: "Some of the components already have other functions."

      That's a clever answer, but the original goalposts were destabilization of the protein itself, not how it could be used the way it is in different complexes. I think his point was that not every protein is the same and so they had to come from somewhere. But yes, there are many different uses of the same protein parts... often within the same organism! So again you now have more patterns that are independently specified and matched or "preferentially attached" to.

      What about the life we don't know John? Any hand of cards is just as unlikely John!

      Delete
    7. John: That's a clever answer, but the original goalposts were destabilization of the protein itself, not how it could be used the way it is in different complexes.

      Your question was "Do you have a path on continuous mutations that can turn it into something else?" While we don't have a clear pictures of the exact mutational pathway, the fact that these structures have other uses shows that such a pathway is not implausible, and a stepwise, selectable path seems available.
      http://www.sfu.ca/colloquium/PDC_Top/EoC/can-complex-systems-evolve-or-be-modified-by-evolution-/bacterial-flagella-and-secretory-systems.html


      Delete
  11. I understand specific complexity to mean tat the all stuff has to arranged in a specifc way, or I doesn't work.



    "It might, but proteins are fairly tolerant of mutation."

    I'm not talking about a protein losing function. I'm talking about a protein acquiring the ability to fit in with other proteins in a complex. Even if they are evolved from other proteins, you need to make some very specific changes. If you need to change number of amino acids, then it may very well not be enough organism

    ReplyDelete
  12. natschuster: I'm not talking about a protein losing function. I'm talking about a protein acquiring the ability to fit in with other proteins in a complex.

    Yes, and as long as those changes occur in selectable steps, then specified complexity can increase.

    ReplyDelete
  13. How do you the changes can happen in specified steps, if you need a bunch of steps before you get the function in question?
    And. by the way, how much much tolerance to proteins have for two amino acid changes? Any way to figure that out? Would it be the tolerance of one amino acid change squared. The loos of stability caused by amino acid changes does happen.

    ReplyDelete
    Replies
    1. natschuster: How do you the changes can happen in specified steps, if you need a bunch of steps before you get the function in question?

      Complex structures have to occur in selectable steps.

      natschuster: by the way, how much much tolerance to proteins have for two amino acid changes?

      It depends on the protein. For thymidine kintase, with an average 2.4 mutations, the survival fraction was 32%. For DNA polymerase l with an average of 3.8 mutations, the survival fraction was 4%. See Guo 2004.


      Delete
  14. How are the steps selectable if they are all necessary for the thing to work?

    And is four the maximum numbers of mutations that proteins can tolerate. That doesn't seem like a whole lot. Don;t you have to sometimes change more than that to get a new function?

    ReplyDelete
    Replies
    1. natschuster: How are the steps selectable if they are all necessary for the thing to work?

      Because they may have minimal function, or have other functions, or enhance other functions.

      natschuster: And is four the maximum numbers of mutations that proteins can tolerate.

      No. It depends on the specific mutations.

      natschuster: Don;t you have to sometimes change more than that to get a new function?

      If it takes a lot of very specific mutations and there are no intermediate steps, then it probably won't evolve. However, there is substantial evidence of the evolution of many complex structures.

      Delete
  15. Do we have any idea what those function might be?

    And since we re dealing with a large number of proteins, just about the whole organism, averages are significant. If the average number of mutations they can tolerate is four, and a lot of adaptations require more than four, then we won't get enough to make an organism.

    And is the evidence that complex structures evolved the fact that they are here?

    ReplyDelete
    Replies
    1. natschuster: Do we have any idea what those function might be?

      It depends on the specifics. Here's an example of step-wise evolution.
      http://www.sfu.ca/colloquium/PDC_Top/EoC/can-complex-systems-evolve-or-be-modified-by-evolution-/bacterial-flagella-and-secretory-systems.html

      natschuster: And is the evidence that complex structures evolved the fact that they are here?

      We have the nested hierarchy, the fossil succession, studies of embryonic development, direct evolution experiments, etc.

      Delete
  16. the nested hierarchy has lots of anomalies that have to be explained away, and falls apart when you try to connect the main branches to the trunk.

    The fossil succession, since it doesn't actually show one species evolving into another, y'know evolution, looks just like a museum display of the development of technology.

    And the differences in embryonic development, at the blastula stage and the gastrula stage should be considered evidence against evolution. You can;t have it both ways.

    And to the best of my knowledge direct experiments only go so far, so hat is how far the evidence goes.

    Now, every organism has lots of extreme complexity at every level, We know from experience how hard it is to make complex things like cells without design. So that should be evidence for design.

    ReplyDelete
    Replies
    1. natschuster: the nested hierarchy has lots of anomalies that have to be explained away, and falls apart when you try to connect the main branches to the trunk.

      Are we making progress then? So the nested hierarchy is largely supported, but there are some problem areas. So we have problems sometimes resolving the distinction between closely related organisms, different sorts of mammals, for instance.

      natschuster: The fossil succession, since it doesn't actually show one species evolving into another, y'know evolution, looks just like a museum display of the development of technology.

      Except for artifacts don't form into a nested hierarchy. And they don't reproduce.

      natschuster: And the differences in embryonic development, at the blastula stage and the gastrula stage should be considered evidence against evolution.

      How so?

      Delete
  17. "Are we making progress then? So the nested hierarchy is largely supported, but there are some problem areas."


    Well, you need another mechanism to explain why we don't see the smooth gradation between groups that incremental evolution would result in. And the anomalies are all over the place. And you need to explain the fact that lots of molecular evidence goes against the morphological evidence. so you need more mechanisms like horizontal gene transfer. So you could say that there is sort of something that could be considered something that looks like some people might consider it a nested hierarchy, but how strong that is as evidence for evolution, I'm not sure.

    "Except for artifacts don't form into a nested hierarchy. And they don't reproduce."

    If you tried hard you could put artifacts into a nested hierarchy, You just have a lot of mixing and matching. But organism also have lots of mixing and matching. And it looks like you are mixing two things up. There's nested hierarchy, then there's fossil. And I'm not sure what reproduction has to do with anything.

    And if similarities in embryonic development are evidence for evolution, then difference should be evidence against evolution. especially since it is really hard to make random, changes in embryonic development, y'know, by random mutations, and not actually kill the embryo.

    ReplyDelete
    Replies
    1. natschuster: Well, you need another mechanism to explain why we don't see the smooth gradation between groups that incremental evolution would result in.

      There are many excellent fossil series that show smooth gradation, such as for cirripedia. Also, evolution isn't necessarily smooth, but varies considerably in rate.

      natschuster: you need more mechanisms like horizontal gene transfer

      Turns out we can observe mechanisms of horizontal gene transfer.

      natschuster: So you could say that there is sort of something that could be considered something that looks like some people might consider it a nested hierarchy, but how strong that is as evidence for evolution, I'm not sure.

      About as close to a nested hierarchy as the Earth's orbit is elliptical. In any case, it's an easily detectable pattern.

      natschuster: If you tried hard you could put artifacts into a nested hierarchy

      It's not hard at all! It's just that when examining objective character traits, there are many different equally reasonable classifications. There's no reasonable classification that puts bats with birds instead of mammals, even though they both have wings.

      natschuster: especially since it is really hard to make random, changes in embryonic development, y'know, by random mutations, and not actually kill the embryo.

      Every human baby has a couple of hundred mutations. They're all mutants!

      Delete
    2. natschuster,

      Why are you here asking questions that you could answer yourself by doing a little research? It's not hard. There's plenty of information freely available on the Internet and in libraries.

      Do you feel that your religious beliefs are threatened by science?

      Delete

  18. ""natschuster: especially since it is really hard to make random, changes in embryonic development, y'know, by random mutations, and not actually kill the embryo."

    Every human baby has a couple of hundred mutations. They're all mutants!"

    Jus try a mutation that effects early embryonic development.


    Pedant:

    I do try to keep abreast of the science. It's just that the problems the evidence for evolution is so spotty, and the problems are huge. For example, incremental evolution would not produce the nested hierarchy, rather it would produce a smooth continuum between groups, you need to bring in another process, the extinction of the species near the borders. And you to explain away all the anomalies. And you need to explain why the DNA so often contradicts the morphology. That's hardly parsimonious. And the fossil record does not actually show species evolving one onto another. If that is what happened why didn't it get caught in the fossil record? We need more apologetics like punc ek.

    And the evidence for design is obiquitous in life. There's fantastic complexity and really real good designs everywhere.

    I do admit that sometimes, I do feel a little uneasy when someone with letters after their name claims that they found some more evidence for evolution.

    ReplyDelete
    Replies
    1. natschuster: For example, incremental evolution would not produce the nested hierarchy, rather it would produce a smooth continuum between groups, you need to bring in another process, the extinction of the species near the borders.

      We responded to this already. We have evidence of extinction. The vast majority of species have gone extinct.

      natschuster: And you need to explain why the DNA so often contradicts the morphology.

      Do you have specifics in mind?

      natschuster: That's hardly parsimonious. And the fossil record does not actually show species evolving one onto another.

      We responded to this already too. There are many excellent fossil series.

      Delete
    2. All the transitions I've read about show transition between major groups, not form one species to another.

      Delete
    3. I should have not said "all." There are a few that show what might be species to species evolution, but they are so few, and might very well represent intraspecies variation.

      Delete
    4. Here's a review that you might find informative.
      http://www.somosbacteriasyvirus.com/speciation.pdf

      Delete
    5. "Do you have specifics in mind? "
      There's this:

      Graham Lawton, "Why Darwin was wrong about the tree of life," New Scientist (January 21, 2009)

      Then there's the hyraxes and aardvarks mentioned above mentioned above. There's the fact that some of our DNA is closer to that of the gorilla than the chimp. There's those seaslugs that have plant DNA for making chlorophyll.


      Delete
    6. I found this in the article you linked in the part about terrestrial mammals:

      "However, detailed records of gradual
      speciation events do not exist, suggesting that
      ALLOPATRIC SPECIATIONmight be the norm"

      I admit I didn't read the article thoroughly. I do have a life outside of blogging.


      And the changes that I did see in the diatoms and such may very well just have been intra-species variety., they were so tirvial

      Delete
    7. natschuster: Graham Lawton, "Why Darwin was wrong about the tree of life," New Scientist (January 21, 2009)
      Not sure where the article indicates a discrepancy between morphology and genetics.

      natschuster: Then there's the hyraxes and aardvarks mentioned above mentioned above.

      Well, let's agree that they nest within eukaryotes, metazoa, chordates, vertebrates, tetradpods, amniotes, mammals, eutheria, afrotheria.

      natschuster: There's the fact that some of our DNA is closer to that of the gorilla than the chimp.

      Incomplete lineage sorting. That's straight arithmetic, given population genetics.

      natschuster: There's those seaslugs that have plant DNA for making chlorophyll.

      The sea slugs incorporate the organelles into their cells. It's not a mystery. Some of the genes have even been incorporated into sea slug genorme, but we can clearly determine their origin.

      What is your point exactly? That the nested hierarchy isn't perfect? That's been known since Darwin.

      natschustser: And the changes that I did see in the diatoms and such may very well just have been intra-species variety., they were so tirvial

      The difference between humans and chimpanzees is also rather trivial really. Same basic body plan.

      Delete
    8. I found this in the article:

      "The problems began in the early 1990s when it became possible to
      sequence actual bacterial and archaeal genes rather than just RNA.
      Everybody expected these DNA sequences to confirm the RNA tree, and
      sometimes they did but, crucially, sometimes they did not. RNA, for
      example, might suggest that species A was more closely related to
      species B than species C, but a tree made from DNA would suggest the
      reverse.

      Which was correct? Paradoxically, both--but only if the main
      premise underpinning Darwin's tree was incorrect. Darwin assumed
      that descent was exclusively "vertical", with organisms passing
      traits down to their offspring. But what if species also routinely
      swapped genetic material with other species, or hybridised with
      them? Then that neat branching pattern would quickly degenerate into
      an impenetrable thicket of interrelatedness, with species being
      closely related in some respects but not others."

      I understand that diatoms have a great deal of intraspecies variation. So the examples may be just that. There isn't that much overlap between humans and chimps. Anyway, the differences in the diatoms do seem much more trivial, just one part of the test was a little biiger or smaller, than that between chimps and monkeys.

      Anyway, if there are so many problems that require so much apologetics with the nested hierarchy, then maybe evolution is not the best explanation.

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  19. I did a little research about barancles. I would expect to see a smooth continuum from barnacles to something like shrimp because presumably they had a common ancestor. What I found is that the barnacles showed up fully formed as barnacles in the Cambrian

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    1. natschuster: I did a little research about barancles.

      The earliest barnacles are preceded by crustaceans and crustaceans are preceded by arthropods.

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    2. Is there a smooth transition from proto barancles to barnacles? If not, why not?

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  20. And I neglected to mention above that the numbers begin to work against you when you have to do something like make a number of random changes in a protein to do something like make a new binding site.

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    1. natschuster: And I neglected to mention above that the numbers begin to work against you when you have to do something like make a number of random changes in a protein to do something like make a new binding site.

      How so? Keep in mind that many mutations are neutral or nearly neutral, while others may provide some benefit towards a different function. Also, because environments often change cyclically (hot-cold, wet-dry), many structures have considerable evolutionary flexibility. They evolve to be evolvable within limits, that is, to find the sweet spot between best function and most flexibility.

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    2. So while a protein is developing, say ten mutations to create a new binding site, each still has some function? And you don't loose stability?

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    3. natschuster: So while a protein is developing, say ten mutations to create a new binding site, each still has some function?

      If it takes ten independent mutations to form a new binding site, it may not be plausible. However, many proteins have weak secondary functions, so if selection for the primary function is relaxed (such as after a gene duplication), the secondary function may evolve more precisely.

      Furthermore, point mutations are not the only mechanism of new protein evolution. Proteins are made up of motifs, and changing these motifs allows the rapid evolution of new functions.

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  21. Anyway. I just read that the status of the greenish warbler, as a ring species has been called into question. This just keeps on happening with the evidence for evolution. Coincidence? I think not.

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    1. So? The study strongly supports speciation. It'sfo just not the smooth pattern of the canonical ring species.

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