Exposing the evolution theory. Part 2

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Secondly, as to published research and evidence for ID, you appear to be quite unaware. There is quite a lot of research a out there (including peer-reviewed papers), as well as a number of books, websites, talks, etc.

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There really isn’t that much compared to the output of evolutionary science. Their vanity journal only publishes a few papers a year.

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One was linked in the first post of this thread. More recently, there was a major mathematical paper released

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In their vanity journal. And what I can see of it doesn’t look promising. Axe’s paper is pretty useless for supporting ID, too.

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The amount is kinda irrelevant. All that really matters is whether it is true or not.

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Productivity is important. If ID is scientifically sterile then it will be shunned for a paradigm that makes more sense of observations. Not that ID publications are exactly known for being true.

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Aside from that, there are papers being released just about every week that by implication are more supportive of the ID perspective than the Darwinian one, without directly mentioning either.

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In my experience the ID people say that, but it is rarely - if ever - true.

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ID itself is an idea, and thus doesnt have a "journal' of its own, any more than "evolution" has its own journal. If though you are referring to the Discovery Institute having its own journal, it does but that is irrelevant. ID topics are not only published there, as the Axe paper referenced in the first comment are.

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The Discovery Institute crowd are the heart of the ID movement. So in fact I do count their journal as an ID journal.And the few papers the ID group get to pusblish elsewhere are generally unhelpful to ID, as Axe’s paper is.

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And how can you say the Axe paper is useless?

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I say that it is useless for supporting ID because it doesn’t contain any results that really support ID. I guess that it isn’t as bad as The Design Inference or Darwin’s Black Box turned out to be, but it’s still not much use.

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Or it may be shunned because it is not philosophically preferred and it has nothing to do with the science.

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As evolution was, until Darwin and Wallace made their case.

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Whether it is "scientifically sterile" is yet to be demonstrated. What example can you provide that something said with regards to ID is not true?

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How about Axe’s estimate of the proportion of protein sequences exhibiting enzymatic activity, since you listed that paper. And that’s one of the better pieces of ID work. See the critique [url=https://pandasthumb.org/archives/2007/01/92-second-st-fa.html]here (though it is linked on the first page of this thread so you have had the chance to see it already.)The idea that irreducible complexity cannot evolve is another common error (and one that Dembski has made). Behe didn’t make that mistake in Darwin’s Black Box, but he came very close to it.As to the scientific sterility I have already pointed out the lack of papers. And really ID is so vague - encompassing everything from Young Earth Creationism to Behe’s naturalistic evolution with occasional help from God it really can’t offer the same understanding of nature that evolution succeeds in providing.

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So you claim. But how about a recent article Parenteau, J. et al. (2019), Introns are mediators of cell response to starvation, Nature. that is more supportive of an ID view of things and puts another nail in the coffin for the 'Junk DNA' view that is common to Darwinian evolution.

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The idea of Junk DNA is alive and well (and hated by some supporters of Darwinian evolution - hence the ENCODE fiasco). A small function for some introns doesn’t really do much to change that.

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Then I guess you do not understand at all what Axe's paper is about. His paper provided a challenge to how Darwinian evolution is supposed to act. It estimates how rare amino acid sequences are that generate functional protein folds, and as a measure of the content of specified complexity within enzymes that is very relevant to questions of ID.

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Since the estimate is orders of magnitude too low and since it isn’t actually useful for probability calculations in many evolutionary scenarios it isn’t as useful as you think.

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So your saying that in 150 years ID will be the reigning paradigm?

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No, I’m saying that a sufficiently strong case can overcome any philosophical bias. ID hasn’t much of a case and shows no sign of developing one. The ID movement hasn’t even agreed on a theory that could potentially replace evolution yet.

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I also find it interesting that Wallace, co-discoverer of evolution by natural selection, ended up effectively siding with ID. He is considered by some to be a founding father for the modern ID movement.

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Except he wasn’t really. The real founders were the Of Pandas and People crowd. Needless to say he never came up with a strong scientific case for those views (which may have stemmed from his adoption of Spiritualsm).

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It hasnt been demonstrated that Axe is wrong. In the critique you cite, Hunt is not really arguing with Axe over the science, but just his conclusions based on the science. He really is just quibbling over a possible difference between rarity and isolation of protein sequences that lead to a functional protein fold.

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But the rarity was the precise point I made. And when I read Axe’s response his attempt to deal with that is laughable. Written language is not the same as proteins.

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Shown how?

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For a start, Behe said as much in Darwin’s Black Box. Are you saying that Behe was wrong in that ?
Note also that Behe tried adopting a very different definition of irreducible complexity, and later dropped the idea. Hardly a sign of confidence in his argument.

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I think you need to go look at again what "Junk DNA" is supposed to be. Introns having any function (I note how you added the adjective "small") means they are not Junk DNA.

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Some introns having a function in one organism - that happens to have very few introns - is not much of a case against junk DNA, not least for the fact that it doesn’t touch the main arguments for it.

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The orders of magnitude is debatable, but I don't think you can just assert they are too low

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See the already cited article. Axe’s response offers no valid defence, so I am not simply asserting it - and you haven’t even successfully countered the arguments.

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Sure, they do not apply to "many evolutionary scenarios", but it isn't claimed that they do. Just the formation of protein enzymes, which just happen to be in EVERY cell of EVERY living thing and are necessary for life.

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It doesn’t apply for many scenarios involving the evolution of enzymes either. It can only be safely applied when a completely random sequence is generated. Which is not typical of evolution at all.

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Again, I don't think you are understanding the paper. The response to Axe written by Arthur Hunt was not really questioning the rarity either. So rarity is NOT the point

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Since we are explicitly disagreeing about rarity, since Hunt explicitly points out that other studies show much less rarity and since Hunt also argues that Axes methods would exaggerate the rarity it seems that it very much is the point.

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So rarity is NOT the point. Isolation is! To make it as simple as possible for you to understand, what hunt is trying to say is that there is no necessary relation between isolation and rarity, whereas Axe is demonstrating that saying there is no relation is silly.

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Note that Axe is also defending the criticism of his method. Except that there is no demonstration.

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Of course the written language is not the same as proteins, and Axe wasn't saying so. If you read his response more clearly, Axe is using an analogy with words to describe how the level of function he was looking for (to get positives in his search) was low, which actually helps the case for evolutionary processes because he was not setting the bar high to exclude it. Nevertheless, the rarity number was still astronomically high despite a low threshold for evolution to overcome. Understand now?

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I understand that I was correct. Axe attempted to defend against the criticism of his experiment - which would exaggerate the rarity - by using an alleged analogy that was nothing of the sort.

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I'm confused. Behe did or didn't....do what? I know Behe didn't say an IC "cannot evolve" at all, but he did suggest that the best option would be co-option, but the more parts you add with that route the complexity goes up exponentially, and you soon are at a probability that is realistically prohibitive. Who pro-ID has supposedly said otherwise?

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You certainly are confused, since you were asking how it was shown that irreducible complexity could evolve. I notice that you mention nothing about changes in parts (causing a reliance on other parts that was not previously present) or loss of parts which would also be reasonable elements in any explanation.

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I'm not buying this, but please do explain.

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Why not ? Isn’t it true that Behe never latched up his argument to deal with opindirect routes and is working on quite different arguments now ?

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So introns, while they were once thought to be junk, genetic debris left over from millions of years of evolution, are now showing evidence of function. So that is one part of the Junk DNA paradigm that is done with. What other "main arguments" did you have in mind?

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Some introns in one organism. But the main arguments would involve the onion test, mutation rates and the effects of too many mutations. Both the latter indicate that large parts of DNA is not under selective pressure with regard to sequence.

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This makes no sense. How can you say it doesn't apply?

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Because you would have to assume a uniform distribution and we know that isn’t true. The odds of getting a functional protein from a minor modification of an existing functional protein are much higher than getting a functional protein by assembling a random sequence.

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I think you are getting mixed up with a simulation vs an estimation of the rarity of sequences leading to functional folds. Axe wasn't simulating evolution. But his estimates do have implications on the search space for function that evolution would have to traverse to.... evolve!

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Then you don’t understand search. The structure of the search space is important. A search mechanism that is able to take advantage of that structure will do better than a random search.

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Take Junk DNA as another example. Darwinian evolution predicted that junk DNA would be prevalent, most of the content of DNA

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It certainly did not. That discovery was a surprise. And one that some Darwinists still object to. Evolution was expected to remove junk DNA.

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ID predicted that though there could be some junk, most DNA would prove to be functional. An lo and behold, as more evidence mounts the ID position is proving to be the correct one.

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More accurately, despite the evidence remaining strongly against them ID supporters are desperately pretending otherwise.

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You need to read more carefully. Rarity is not the thing in dispute. Hunt doesn't dispute Axe's numbers per se.

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As you admit below, he does.

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Hunt's other objection was related to isolation (not rarity). HE thinks that functional sequences along the same domain might be closer together in the sea of possibilities. Axe didn't directly address this in his experiment, but there is no evidence of a lack of isolation with respect to rarity, so rarity should still (to some extent) factor into determining functional fold possibilities. (Axe's response on Objection 2)

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You seem to have missed the fact that Hunt specifically addresses isolation: I note also that you omit the fact that the forward approach is associated with the very highest figures. To say that those figures are too high does not give us much reason to think that figures at the very lowest end of the range are correct.Finally Axe’s objections raised in his point 2 rest on an alleged analogy with absolutely nothing to show that it is valid. Does chemistry work the way Axe needs it to ? He doesn’t give the slightest reason to think it does,

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I'm beginning to think you have a problem with logical language.

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Hardly. I think you have a problem with the facts.

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Axe is defending against the criticism of his method by showing that the criticism is without merit.

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But he doesn’t show any such thing.

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Essentially the criticism is wrong because the charge is backwards in thinking. And he used an analogy to demonstrate that.

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An analogy can’t demonstrate anything unless it accurately represents the problem. Hunt talks about the actual question and gives references. Axe talks about his supposed analogy without giving any references that provide empirical support.

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Hunt (and others) seemingly think that this less that optimal functioning starting point is too restrictive, but as Axe pointed out they are missing the point. By using this modified enzyme to start with, Axe wasn't picking a fixed low point on the hill (as illustrated by Hunt) to restrict positives too, but instead he was picking a lower position on the hill as a starting point that would be much easier to move away from (via mutations) and anything at the same elevation or higher (in relation to the starting point) would be a positive.

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I disagree. Moving in a random direction is more likely to retain function if at the centre of the distribution (only moving too far can lose function). The further from the centre, the more likely a random move is to lose function. But neither point is found in Hunt or Axe.Axe’s actual objection doesn’t seem to make sense either. Nobody is suggesting that using a low level of function as the criterion is a mistake. Hunt actually says that Axe looked for some measure of function - not equal function to the originally protein. In suggestion otherwise Axe is the one suggesting that he set the bar too high.Hunt actually objects that Axe chose a variant unusually sensitive to mutation - which would be more likely to lose function.

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I'm not sure if you just have a problem with Axe using an analogy to describe it. But if so, then why don't you also have a problem with Hunt (and others) using an analogy to criticize it. What else do you think all the talk and pictures of hills that Hunt uses are?

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This is where we see the problem is in your lack of understanding. Hunt’s drawings are to illustrate points - they aren’t actual arguments. The support for the points is elsewhere. Axe, on the other hand uses his alleged analogy as an argument - but the analogy seems to be invalid and THAT is my objection.Are you seriously going to suggest that if I accept the use of illustrative diagrams I must accept any alleged argument by analogy even if there is no reason to think that there is a valid analogy there? That would demonstrate a real problem with logical thought.

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It was you who originally said: "The idea that irreducible complexity cannot evolve is another common error". And then you said something about Behe not making that mistake. I then asked you how so? To which you responded that Behe did say "as much", which I take it the "as much" to be "irreducible complexity cannot evolve". So which is it?

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Behe stated that irreducible complex structures could evolve. This supports the assertion that the idea that they cannot is an error.

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And it's not clear what you are referring to as to parts changing, relians, or loss of parts. I could talk about IC all day, but you gotta be clear in what you are stating/asking before I comment further.

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I listed ways other than cooption that irreducible complexity structures could evolve. That you failed to understand doesn’t bode well for discussion. (And I bet you don’t know when a scientist first argued that evolution would produce irreducible complex structures either)

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I don't think you understand his experiment. Axe wasn't purely assembling proteins from a wholly random sequence.

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And I didn’t say that he was. What I am saying is that the headline figure of 10^-77 is only useful in that scenario. And that is because I understand the importance of the distribution of functional proteins in sequence space. This is why Axe’s claims about isolation are much more important and the fact that his case amounts to speculation and highly dubious analogies is such a major weakness.

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And you don't comprehend what the size of the search space is? Searching the entire space is prohibitive by time and technology. If you are talking about the entire search space for proteins in general, you are out of your mind.

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Of course i’m not and if you had any understanding of my point you would know that. The point is that the search space is structured such that stepwise refinement starting from a good point - for something close enough, not necessarily the desired function - is a lot, lot better than random search,

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Reading comprehension is a problem for you, isnt it.

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On the contrary. You claimed that there is no evidence of a lack of isolation with respect to rarity - but Hunt actually cited such evidence - and I quoted it. So unless you are complaining that I correctly comprehended Hunt’s point the problem seems to be yours.

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Hunt has a problem with the rarity numbers because he thinks they may be exaggerated for the various reasons he gave. Axe responded to his charges of 'exaggerated' just fine.

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Obviously he did not.

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If you don't like the analogy, that is your problem. You don't seem to have any problem with Hunt's analogy. I wonder why.

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Axe gives no reason to think that his alleged analogy is valid and neither do you. Hunt, in contrast does not rely on argument by analogy and his illustrations do appear to be valid.Again, the problem is clearly yours.

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Hmm. I quote Hunt regarding the "foward" method comparison, then comment directly about his highest number of 10^10 i the following paragraph. Nope, don't seem to have omitted it at all.

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Ok, I’ll give you that one. But the idea that if the highest extremes are likely exaggerated then the lowest extremes are likely correct is hardly a good argument, not when there are more than 50 orders of magnitude involved. The mere fact that Axe’s figure is at the lower extremes is reason to suspect it is too low. So you still missed the significance of the forward method only supplying the highest end - its likely. flaws do not taint figures produced by other methods at all.

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You're either hyper-sensitive or using a double standard. Using a graph image as Hunt does and presenting the experiment in terms of search space, islands of function, and his hill diagram, are just as much an analogy of the experiment as what Axe is analogizing with respect to the use of a lower-level functioning enzyme.

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Your inability to answer my points hardly means that there is something wrong with me.Hunt uses images to illustrate points which stand without the images. Axe’s demonstration is entirely based on the supposed analogy - but neither he nor you have offered any reason that suppose that the analogy is valid. No hyper-sensitivity, no double standard just plain sense.

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You may call one "Hunt talks about the actual question and gives references" and then say that Axe is using "supposed analogy" and giving no references (he does give references in his response, and don't forget he has the references from his paper that are directly involved too). Sounds like special pleading to me.

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I said that Axe doesn’t offer any references that give empirical support for his analogy - or his claims of isolation.

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Funny, but the actual science doesn't support that. If you start at the center/top of distribution, you only have one way to go - down.

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And another failure of reasoning on your part. We are not concerned with changes in the level of function, only whether the changed protein is in the part of sequence space where some level of function is found. And so by applying an irrelevant criterion you miss a simple and obvious point.

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That is what Axe's analogy was demonstrating.

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If you wan to claim that Axe made the same mistake as you, that is your problem. Hunt is (correctly) concerned with whether the new sequences have some measure of activity - not whether the level increased or decreased.

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Hunt is not saying the bar is too low per se, but he is saying the bar is restricted to a narrow area (or small spikey hill as in his diagram) as to the tested enzyme variety Axe uses. Hunt seems to think the function area is restricted to the black box that Axe uses as a starting point

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I think you have misunderstood Hunt’s point. In fact Hunt says the small spikey hill So, in fact it represents sensitivity to mutation.

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Yes, Hunt does say that in relation to it being a "temperature sensitive variant". But Hunt doesn't provide any references to that specifically and neither does Axe comment on the temperature side of things (outside of his paper).

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As quoted above Hunt claims that the temperature sensitivity makes the variant chosen by Axe more sensitive to mutation.That sensitivity to mutation naturally makes it easier to lose function (that’s the point of it). That is why the hill is small and spikey.Hunt does note that the enzyme chosen by Axe is inactive at the temperatures at which E Coli is usually grown but does not make a point of it.

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Well Behe qualified how an IC system could evolve. So unless you are including that, I'm not sure where or who said it cannot.

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William Dembski did - in one of his books where he was attempting to apply his Explanatory Filter to the evolution of a flagellum.

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And where did you do that? Is that supposed to be where you said: " I notice that you mention nothing about changes in parts (causing a reliance on other parts that was not previously present) or loss of parts...", cause that is a lot of unintelligible nothing.

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I’m sorry that you didn’t understand but those are ways in which irreducible complex systems could evolve.

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I understand the concept of search space just fine. But I don't understand what you are saying here.

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I understand up to when you say "starting from a", but not past that. What is "a good point - for something close enough, not necessarily the desired function" supposed to mean?

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I mean that if your initial sequence either has some of the desired function or a similar function it helps a lot in finding a sequence that is good at the desired function.

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LOL, are you for real? "Images" were an analogy that Hunt used to "illustrate points" that was also part of his analogy. Just because you don't want to characterize it that way doesn't make it so. And Hunt didn't provide references for his analogy.
Touche!

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Oh, we’ve reached the point where you resort to outright lying ?

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And neither did Hunt use references for his analogy. Axe wasn't the one making claims of isolation. That was Hunt.

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Wrong again. Hunt said that functions weren’t isolated. And he produces a reference to support it Knox et al, 1996; Adediran et al., 2005.

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Hunt says (no references) that Axe's enzyme was too sensitive to temperature. Here's a picture I made to visualize that. (No reference either).
So I guess to you, if a critic makes up some picture that he says demonstrates some unsubstantiated claim, it's gotta be so!

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Yawn. Hunt does not produce a diagram to show temperature sensitivity, it’s not an important point and neither you nor Axe have actually denied it.Let us also note that you wouldn’t be making these ridiculous accusations if you actually could show that Axe’s analogy was valid. It’s all just bullying and a smokescreen for your inability to address the real issue.

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For the moment I'm not trying to dispute whether IC systems can or cannot evolve. What I am saying is that your statements: "I notice that you mention nothing about changes in parts (causing a reliance on other parts that was not previously present) or loss of parts..." doesnt make sense in an English sense. I cannot figure out what you are saying, not on a technical level or a pro/against IC sense, but what the hell does that mean in normal English.

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The problem seems to be that Behe’s terminology is a problem for you. He’s the one that expressed IC in terms of parts. So, or rephrase, one or more of the parts making up a system may change such that their operation becomes dependent on one or more other parts of the system

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Still a little confused with your language. What are you meaning by "desired function" vs "similar function" and how are those distinct from "good at desired function"?

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That seems to be definitely your problem.
The desired function is the function being searched for.
A similar function is a function similar to the desired function
Being good at the function refers to how well the sequence performs the function.

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Dear Lord! You apparently cannot see the obvious.
Hunts diagrams (figures 1-3 and probably 4 too) are pictures Hunt made up. They are not based on numbers or data from Axe's paper or anywhere else. They are merely images to help describe something he is talking about. They relate to his analogizing Axe's paper by describing it in terms of hills and topography in sequence space. So his description is an analogy, and the pictures that relate to the description is analogy too. Figures 1-3 had no references, and were the subject of what Axe responds to as his Objection 3.

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The diagrams illustrate what Hunt is talking about - that is my point. The pictures aren’t arguments, simply illustrations of Hunt’s points.
Thus the analogy isn’t the argument.

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I think your getting your objections mixed up.
The question of isolation is what Axe deals with in his labeled Objection 2, but it is Figure 4 (and added reference) in Hunt's response. The picture really isn't anything more than a visual aid again referencing his analogy he employed before. The reference is used to support that proteins are not necessarily isolated, but has little if any direct link with Hunt's picture.

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In other words the picture is used to illustrate the point - and the actual point is supported by the reference. It’s so good that you’re agreeing with me.

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You haven't demonstrated that Axe's analogy was bad. All you have said is that since it was a 'word' analogy, and proteins are not words, then it is a bad analogy. Well, Hun't analogy is a 'hill' analogy, and proteins are not hills. So then by your standards Hunt's analogy and diagrams should be a bad analogy as well. If you don't think that, then double standard by you.

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You mean that - with regard to isolation - I should rely on points supported by references and not analogies ? Amazingly that is exactly what I did ! As I keep pointing out the diagrams are illustrations, not the actual argument. So there goes your claims of a double standard.As to whether Axe’s claimed analogy is good or not - well there is no obvious reason to think it is and neither you nor Axe seem to offer any.

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I have no problem with Behe's terminology. But you haven't exactly mentioned his terminology beyond saying "change of parts", "other parts", "loss of parts" without any logical connecting words or context that in any way refers to something Behe said. Behe has said a lot of stuff. Quote something for God's sake so we have some clue what you are referring to.

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(Wikipedia citing Darwin’s Black Box)Does that satisfy you ?

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Do you mean: "So, to rephrase..."?

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Yes.

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"one or more of the parts making up a system" - I will assume you mean an IC system. If not, please correct me.

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Since I am speaking of how a system can become IC, I obviously include systems that are not (yet) IC. Even without that consideration I see no good reason why you would assume that I meant only IC systems.

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"may change" - OK. But I might need to you flesh out how they are supposed to change (trust me, it's important)

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That is going to be specific to the sort of system you are looking at.

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"such that their operation" - I am assuming you mean the function of the part.

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I mean what the part does.

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"becomes" - this implies a new state of the part. As in a new function, yes?

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Generally not a new function - performing the same function but in a slightly different way would be more typical.

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"dependent on one or more other parts of the system" - OK. But the parts within an IC system are already dependent on one or more parts. So what is changing? Is it a change in how they depend on each other?

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It is an additional dependency. After all I am describing how IC systems can evolve, remember ? The creation of dependencies between existing parts has rather obvious relevance to that

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Can you really do that and retain the function of the part?

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I can’t see any reason why not.

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If it has a new function, it isn't doing the original function, and thus the IC system fails.

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Good job I wasn’t talking about parts changing function in an IC system then.

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The question really lies in what you mean, specifically, by "may change". If you can relate this to something Behe (or any one else defining IC) actually says (quote preferred) that would help immensely. Or give an example (or analogy *hehe*) if possible.

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Not really. The details have to be specific to the system. A system where the parts are individual molecules would be different from a system where the parts are bones, for instance. The nature of the parts and how they interact is critical.

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"if your initial sequence either has some of the [function being searched for] or a [function similar to the desired function] it helps a lot in finding a sequence that is [how well the sequence performs the function]

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Try:“If the start point has some level of function or a related function it makes it easier to find an end point with the required level of function.”

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Ya. So? You're still not clear on what is being looked for in the search space

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When we are talking about search in a very generic sense, that is normal and expected.

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...but if I had to guess I think you might be suggesting (like a lot of others) that we should be looking for new function (which I assume is what "similar to the desired function" is supposed to be. But how one would do that and is it feasible? And again.... in the case of Axe's experiment it wasn't what he was looking for, nor did he have a reason to.

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But we aren’t discussing Axe’s experiment - we are talking about the significance of the 10^-77 figure. Specifically the point is that you can’t use it as the probability of evolving a new functional protein because evolution is not the same as random search.

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But even that is not much help for evolution.

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Well, unless Axe has a better argument for isolation than an alleged analogy - that he can’t even show is valid - it isn’t exactly a problem for evolution. And even then, so long as figures many orders of magnitude higher are reasonable possibilities it isn’t even of great significance.

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Yes it does. But that quote is NOTHING like what you said. Your statement used English words, but it was rambling and incoherent. Glad you stepped up and produced something understandable. Now maybe we can proceed.

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By which you mean that you were unfamiliar with Behe’s definition of IC - which I quoted - and therefore unable to follow an informal discussion of the subject.

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Well which is it? If you are not talking about an IC system, then what is the point? A non-IC system is irrelevant to our discussion.

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You are, of course, completely wrong. Since the point of the discussion is how evolution can produce IC systems it would be pointless to start with a system that is already IC.

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BUT.... I'm getting a feeling you may not understand what IC is. Behe's quote is not talking about evolving an IC system, but he is describing what an IC system is...assuming it exists.

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This is an amusing piece of idiocy. Are you imagining that the terminology in the definition is only applicable to IC systems ? That only an IC system can have “parts” ? I can see no other reason for such foolishness.

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For example, lets assume we have an IC system that is made of 100 parts. That 1 IC system has a function. The 100 parts have a 'sub-function', that when combined in their particular configuration, produce the function of the IC system (In Behe's quote that is the "that contribute to the basic function"). Now if you have 2 of the parts present, you do not have 2% of the IC function available. If you have 99 of the parts present, you do not have 99% of the IC function available. In both cases, you have 0% of the IC function availalble, and thus you have no IC system, nor an 'almost' IC system.

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This is unrelated to any point I have made. My points are about changing or removing parts. If you have a non-IC system with 100 parts it must - by the definition of IC - have at least one part that may be removed without ceasing to function. And if a part changes it still has the same number of parts.

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So if you truly are talking about how a system can become IC (evolving IC?), then realize that the concept of (yet) IC might be problematic.

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Only to someone who fails to understand that a system becoming IC means that the system was not originally IC.

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I have to assume that any "dependency", whether current or new, refers to the sub-function of any part in how it interacts with the sub-function of one or more other parts. So any existing 'dependency' is one part well-matched and interacting with other part(s). Adding an "additional dependency" I suppose could be allowed, but it would also have to be well-matched and interacting with another part(s) and could NOT interfere with the sub-function of any of the prior existing parts. That in itself would be highly unlikely to occur.

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Since the parts are already functioning in a system they are already interacting with other parts. Also, they must be adequately “well-matched”. Of course if this is not true then a system with “ill-matched” parts could become IC just by becoming better matched.

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So that is all possible, but not probable. Adding another dependency just complicates what is already working, and NS would tend to weed that out unless it somehow improves function (not new function) of the IC system. But then, so what? It does nothing to explain how the IC system came about in the first place.

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It is not intended to be an explanation of how a system evolves, simply a sketch of how a system might acquire the feature of being IC.Now a new dependency might be a consequence of improved function, but it is not necessary to have any benefit. Neutral changes can and do spread through drift.

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What do you mean? Of course evolution is doing a random search. (Random search or blind search, however you want to describe it)

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No, evolution is more like a hill-climbing search. I.e. it perturbs a parameter and moves to that value if it is higher, then it perturbs again and so on. A random search simply chooses completely random points until it hits the target with no feedback at all. [/quote] Anything other than a blind search means you have information added to filter the search parameters. But evolution is unguided, purposeless, so it has no thought, no target, and cannot set filter information as to what it is searching for. Navigating the search space is done by mutations, which are random/blind. Natural selection is the selector, but it has no power over how it traverses search space. [/quote]Natural selection does provide guiding information. See above.

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That is why Hunt brought up the point about isolation. That objection doesn't dispute the 10^77 number in general, it just says that maybe all the positives are clusted together. If it turns out proteins are not isolated (which is supported by work since the 2004 paper we've been covering), then Hunt's point loses any punch. (And that is to a great extent what Axe's analogy was demonstrating. If no isolation, the search space is too big to realistically cover by evolution)

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You mean that if it turns out that proteins are not isolated Axe’s point loses any punch.And that they were not isolated was supported by work before 2004. One of the papers Hunt cited was published in 1996.You also misunderstand Axe’s “analogy”. It was meant to show that rarity entails isolation which is obviously false - and not something that can be shown by anything less than a genuine analogy - and Axe gave us no reason at all to believe that his “analogy” was genuine.

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I understand the Behe quote just fine

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I didn’t say otherwise. My point is that you needed me to quote it.

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You're not making sense.

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On the contrary. My argument would be nonsense if it started with an IC system. Do try thinking about it.

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Look again at your statement, the second one I was breaking down for understanding. The "system" in that context is an already complete, functioning system made up of 'parts'. We are talking about IC systems I thought.

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We are talking about how we can GET an IC system without running foul of Behe’s argument. Obviously it makes no sense to start with a system that is already IC.

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You're not getting it. If we are talking about an IC system, then YES!!!, the terminology is only applicable to an IC system. It doesn't apply to a non-IC system. The terminology isn't just "have parts", it also relates to what those parts do.

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I’m “not getting it” because it is obviously stupid. The terminology is applicable to systems in general. If it didn’t you couldn’t use the definition to see if a system was IC - you’d have to know if the system was IC before you could even think about it.

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Lets say you have an IC system, and you have a non-IC system. Yes, they both can have parts, but so what? That is not what the terminology is saying. How does the terminology differentiate those two systems???

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The question only makes sense if the terminology applies to both systems. So a non-IC system can have parts (it’s not a system if it doesn’t). They can even be well matched. If you want to be pedantic it can even lose function if any part is removed. It just has to fail to meet the definition in at least one respect.

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OK, fine. But I thought we were trying to speak about IC systems, not non-IC systems. Your non-IC system with 100 parts is.... non-IC. Add a part, it is still non-IC. Take away a part, still non-IC. so what?

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Really ? If you take away all the non-essential parts you will have an IC system, certainly in the important sense that taking away any part will stop the system from functioning.

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No. You're not getting what IC means. *sigh*

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Wrong, as usual.

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Becoming an IC system is not a matter of a having a non-IC system and then adding/changing a part (unless you are talking about the creation of the whole IC system from scratch, but I don't think you are going there).

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Subtracting - not adding - a part can make a system IC. Changing a part so that it or another part become essential to the system’s function can make a system IC. This is not difficult.

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If a non-IC system is functioning, taking a part away, by definition, will not necessarily crash the function.

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Congratulations on understanding one of the essential points of my argument.

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When you say "ill-matched", what does that mean? From the sound of it, though, 'ill-matched' would indicate the parts are not contributing as a whole to the system function. So you wouldn't have a functioning system.

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I mean not-well-matched, of course. And if the parts of any functioning system are automatically well-matched then that part of the definition of IC is redundant. (Not that that is a bad thing, it does Behe’s argument more harm than good anyway)

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Ok, but it seems like you are weaseling on definitions. If something is 'dependent', than it is not 'neutral'. That is a contradiction in terms.

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Wrong again. I simple mean “neutral” as opposed to “beneficial” or “deleterious” (which should be obvious from the context).

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You're assuming a lot about the landscape of the search space.

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No, I’m not. Describing an algorithm says nothing about the search space.

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In your hill-analogy, the only way Darwinism works is if the landscape is a smooth, gradual sloping up the whole way. But you are not taking into account any peaks or valleys, the steepness of a slope, nor that function lives on islands in a vast ocean, which is more accurate a description of the topology.

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Again you are wrong. Peaks and valleys are not an issue. And the idea that function “lives on islands in a vast ocean” is so,etching you have yet to demonstrate.

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The randomness relates to the mechanism of change - mutations. NS cannot guide those. NS can pick the best of whatever is provided to it, but that is not accounting for whether it is presented with an upward option

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If it isn’t presented with an upward option it stays where it is. And that’s pretty common.

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What does NS do when it reaches a peak? It doesn't know that there is another, higher point in the vicinity. Unless you have very smooth transition from one to the other, NS gets stuck.

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In the simplified version I gave you, yes. In reality it isn’t so simple.

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But if proteins families/superfamilies are isolated even a little, then Axe's point is fine. And with more recent information, that does appear to be the case.

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I note that you have yet to give any such information. I also note that despite Axe responding to Hunt he said nothing about Hunt’s more general point:

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The citation in Hunt's paper only relates to the TEM-1 and DD-peptidases having some related structures. But that similarity doesn't extend to across all proteins.

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It doesn’t have to extend across all of them. I don’t think that it makes any sense to assume that all proteins are derived from a single ur-protein. More likely by the time genes came along life was already using multiple proteins.But I will add the fact that the functions overlap is certainly evidence against complete isolation, and certainly a problem for the assertion that rarity strongly implies isolation as Axe claimed in his response.

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No, I didnt need help to understand Behe. I needed help to understand you. Your words were not Behe's

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And quoting Behe's definition was part of the help you needed.

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Ok, I understand now what you meant by "applicable". You're using in more of a manner of "to test by". I was taking that more as "confers the property to".

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The real issue is your failure to understand “terminology”. When you said that theterminology didn’t apply you were claiming that at least some of the words in the definition could not be used to describe systems that were not IC.

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Yes, I get that. But this is the reverse of 'building' up an IC system. So how does building up an IC system work?

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But I was never talking about building a system. I was talking about how the system gets to be IC. That, after all, is the important issue.

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Umm, ok. But before you 'subtract' a part, the system is already IC + some part. So you haven't shown how to make IC yet.

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Really ? The original system is not IC, the system without non-essential parts is IC. That looks like “making IC” (sic) to me.

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No. The part(s) are ALREADY essential to the system if it is IC. You cannot 'change' part(s) to become essential.

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Since the system is not IC the first point doesn’t apply. Even if the second point is true it is certainly true that a part can change so that it needs one or more of the other parts,

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Aye. But again, this is not talking about building up an IC system. Your talking about breaking or building down to something that is already there.

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I never intended to - or need to - discuss how systems evolve. The only point that matters is how systems get to be IC. That is the problem Behe posed. After all if there was a case that non-IC systems couldn’t evolve there wouldn’t be much point in singling out IC systems.

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Perhaps. But then again, it could be there to prevent someone trying to say "ill-matched" parts are functioning. The basic idea is the parts work with each other. Ill-matched implies the opposite of that.

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No. That restriction is there to rule out some simple working systems where the parts interact usefully. If an alleged “part” doesn’t do something for the system there is no way in which it can be seen as a part of the system.