Exposing the evolution theory. Part 2

Yes, that is correct. Your language is better here. 'Account for' is preferred to predict. Well that is not true. I doubt anyone would claim design for a totally random process. Not so. ID doesnt claim to be able to predict anything or everything. I suppose a prediction on an experiment depends on the experiment. But nothing was predicted regarding the outcome of Axe's experiment.Take Junk DNA as another example. Darwinian evolution predicted that junk DNA would be prevalent, most of the content of DNA. 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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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.

Why would nobody claim design for a totally random process? Your designer can't flip coins?It is nice that you acknowledge that ID makes no predictions. Thank you. Therefore ID is ubfalsifiable and not science.But then you claimed ID predicted little or no junk DNA. How is that derived without lots of assumptions about the designer's abilities and motives? Do you contend that your designer was constrained to produce life with little or no junk DNA? If so, how? Edited by JonF, : No reason given.Edited by JonF, : No reason given.

"cdesign proponentsists" exposes the lie that creationists and IDists are different. All they did was (try to) change " creationist" to "design proponent". Nothing else in the book was changed. Yes it does. There is no controversy in science about evolution.

You need to read more carefully. Rarity is not the thing in dispute. Hunt doesn't dispute Axe's numbers per se.If one part, Hunt is complaining that the sample is too restrictive in function as to lead to those numbers, but Axe pointed out in his response (his Objection 3) to Hunt's posting that Hunt is looking at it backwards. Essentially, in the search space, Axe picked a functional spot lower on the hill. Hunt seems to think that is a problem and characterized that low spot as new spikey hill. But Axe pointed out in his response that Hunt (and Stephenson, Venema) objections are misplaced. Axe's low spot allows for function to be found at any other low spot along that hill as well as higher up the peak, which allows for a whole lot more positives than Hunt is accusing Axe of allowing. But according to Axe, even that more generous allowance of function still is a small island in a large sea.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)With respect to Hunt pointing out other studies, he give a range between 10^10 - 10^63 (in the apples to apples comparison, Axe's figure was 10^64). So Axe's results were not much outside the range of other studies, and Hunt did not indicate Axe was exaggerating with regards to his number). But note Hunts last paragraph in that section 3 of his response: Axe's approach was the "reverse" one. As to the assumptions Hunt is saying that are not warranted, those are the objections above that Axe dispelled in his response, which would make Axe's numbers OK (barring some other objection). But the as to the 'forward' method, the one that lead to a 10^10 result, Hunt admits that the numbers might be too high essentially being a false positive (the "have no biological relevance" remark). So at the very least, between that wide range, it leans more in the direction of Axe's numbers.

Cars, paintings, buildings, and other human designs have common designers. Those designs do not fall into a nested hierarchy. Obviously, it is you who doesn't understand what a nested hierarchy, nor do you understand intelligent design. Then show how designed things fall into a nested hierarchy based on shared derived characteristics. I have yet to see an ID supporter do this. Echolocation is a behavior, not an anatomical structure. The structures that dolphins and bats use for echolocation are entirely different as we would expect for adaptations that evolved independently in two different lineages. That is entirely false. The theory of evolution predicts a nested hierarchy independently of the data. This is standard scientific testing.What do you think a scientific hypothesis is? How do you think science tests a hypothesis? Please show that a phylogeny based on parts found in Corvettes produces the same statistically significant phylogenetic signal found in life. Otherwise, you are just blowing smoke.

Axe used the gene sequence from two modern species which are both derived sequences. Modern species don't evolve from other modern species. Modern species evolve from a common ancestor who lived in the past. Both of the genes that Axe used had accumulated mutations since common ancestry, and neither gene represented the ancestral sequence that both of them evolved from. Therefore, Axe didn't model evolution because he didn't mutate the ancestral sequence. There are other functions that proteins can have, DUH!!! You can't test for one single function out of possible millions and claim that a protein has no function, DUH!!! Then Axe should have tested for functions other than beta-lactamase activity that could have served as an island, BUT HE DIDN'T!! He also didn't use the ancestral sequence that could have contained those islands, DUH!!Edited by Taq, : No reason given.Edited by Taq, : No reason given.

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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,

Darwin died before DNA was discovered, so what you describe is a fantasy.What we can say is that only evolution can be used to accurately predict which parts of a genome have function. When we see sequence conservation across species this tells us that those sequences most likely have function. ID makes no such prediction, as shown by the insistence that massive amounts of non-conserved sequence in the human genome is claimed to have function according to ID supporters. The evidence still points to 90% of the human genome not having function that affects fitness.

I'm beginning to think you have a problem with logical language.
Axe is defending against the criticism of his method by showing that the criticism is without merit. Essentially the criticism is wrong because the charge is backwards in thinking. And he used an analogy to demonstrate that.Hunt in the first section in describing what Axe did properly indicated that Axe didnt use the wild-type enzyme specifically because it would be too resistant to mutations. In other words, the wild-type enzyme has built in protections that would prevent the likelyhood of any mutations. In order to even be able to do the experiment, Axe instead used a molded enzyme that was less blocked from mutations occurring, which also set the bar lower for functionality compared to the wild type.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.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? 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?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. Huh? Normal english please.
Do you mean "ratched up his argument" and "indirect routes"? If so, I still don't know what you are saying I don't think you understand his experiment. Axe wasn't purely assembling proteins from a wholly random sequence. He was remaining in the TEM-1 penicillinase family and modifying an enzyme in amino acid blocks (because single point mutations is prohibitive to research, as the space of results in count would be well beyond the number of atoms in the universe), and to an extent restricting where mutations would occur that would not automatically wreck the basic folding structure. The whole point was to break down what is a impossibly huge effort (getting a functional protein by assembling a random sequence) and breaking that problem down into a smaller chunk (TEM-1 family of protein folds) and then even narrowing it down smaller (his 10-block amino acid changes) to even approach an estimate that could be extracted out to something useful.
Perhaps you're not aware, but this isn't the only enzyme or protein that has been looked at. Axe chose this one because it was a small-moderate length protein (153 AAs) and his actions was further refining experiments done previously by himself and other scientists.
Your characterization of what he was doing is way off. 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. Humans alone have 20,000+ proteins, and the average size is roughly 480 AAs. Axe was looking at one enzyme (not in Humans) that would be considered moderate to small in size, that is 153 AA's long. Just the possible combinations of AA's for a protein of that size are greater than 10^199. (Just to give an comparison, it is estimated there are about 10^80 atoms in the universe). Nobody can search that much space. You have to break it down into more manageable chunks, which is what Axe was trying to do.Axe was limiting his search to the same domain of the TEM-1 penicillinase family, which even within those constraints the search space is prohibitive. And if proteins do evolve through small changes, limiting your results within a family is being generous to evolution because you are limiting your search space to an area that is likely where evolution works. You want to expand that further, go ahead. It will only handicap the case for evolution even more.If you're so keen on search, how would you explore that space?

Because design is: to do or plan (something) with a specific purpose or intention in mind. Kinda opposite to random. I did no such thing. Which you even demonstrate with your next line.... ... ID doesn't comment on the abilities and motives of a designer outside of the base definition (so at least an intelligence and capability to do something according to a purpose). ID acknowledges all demonstrated natural processes, including Natural Selection. Allowing for known natural processes to be available, one would not expect that there could never be something akin to 'junk' (no function) in DNA. But design principles would suggest that in a designed semiotic system, there would likely not be a majority or a significantly high amount of junk.

Please define what a nested hierarchy is. I think we have different ideas of this.
To me, in it's simplest form, it is groups within groups. Or a defined set that contains other defined sub-sets.So for example, of all nested hierarchies, there would be a subset of hierarchies based on "shared derived characteristics". But that doesnt mean that all nested hierarchies are based on "shared derived characteristics"

People have designed random number generators that are truly random, based on when radioactive isotopes decay or random electrical noise. Hard to believe your designer can't.From your Message 121 "ID doesnt claim to be able to predict anything or Everything." seems to me that means it can't predict anything.

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one would not expect that there could never be something akin to 'junk' (no function) in DNA. But design principles would suggest that in a designed semiotic system, there would likely not be a majority or a significantly high amount of junk.

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Why? You claim you don't "comment on the abilities and motives of a designer outside of the base definition (so at least an intelligence and capability to do something according to a purpose)." Yet you claim to know its motive in re junk DNA. How do you know it would not include junk DNA for some reason you don't know or on a whim or its idea of a joke or...Sure seems inconsistent to me.Edited by JonF, : No reason given.

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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,