By such a sentence not appearing anywhere in the result or conclusion.
Since it is a conclusion mistakenly drawn by creationists years after the paper’s publications, not by it’s authors.
Here on this very forum. In the various papers (by Michael Lynch and others) that have responded to Behe and others who have attempted to publish papers claiming such a limit. You should watch the video by evolutionary biologist @talkpopgen (Zach Hancock) I linked earlier.
In fact I can do better. Biochemist Michael Behe himself disagrees with it. In his first so-called waiting time paper (Behe & Snoke 2004) he writes(about the population sizes required to fix various numbers of individually deleterious mutations):
Such numbers seem prohibitive. However, we must be cautious in interpreting the calculations. On the one hand, as discussed previously, these values can actually be considered underestimates because they neglect the time it would take a duplicated gene initially to spread in a population. On the other hand, because the simulation looks for the production of a particular MR feature in a particular gene, the values will be overestimates of the time necessary to produce some MR feature in some duplicated gene. In other words, the simulation takes a prospective stance, asking for a certain feature to be produced, but we look at modern proteins retrospectively. Although we see a particular disulfide bond or binding site in a particular protein, there may have been several sites in the protein that could have evolved into disulfide bonds or binding sites, or other proteins may have fulfilled the same role. For example, Matthews’ group engineered several nonnative disulfide bonds into lysozyme that permit function (Matsumura et al. 1989). We see the modern product but not the historical possibilities.
This is Behe and Snoke admitting a colossal caveat with interpreting their results, and that the whole thing suffers from the hindsight thinking. Lynch 2005 demonstrated what happens for the waiting times if Behe and Snoke’s assumption of only a single set of mutations is violated (see figure 3).
Who cares what you think is fine? What matters is what was done in the actual experiment, not whether you are personally okay with some alternative possibility that wasn’t explicitly tested. LOL.
Cool, but then there are lots of examples of knock-out experiments where beneficial genes are knocked out, the organisms then evolve to compensate for the loss. Typically these involve completely deleting the gene encoding some enzyme specialized for a particular substrate conversion, and what happens is the population adapts by mutations causing upregulation of another enzyme that has some promiscuous activity on that same reaction. Here’s a recent example, open access:
In this paper we see how there are multiple routes by which the bacteria can compensate for the loss of two key enzymes (the strain is engineered both Δepd and ΔgapA). Generally, almost all involve ways of increasing the output of the sad gene. Either by gene duplications (more gene copies expressed = more enzymes), straightforward upregulation of expression, or mutations that increase the promiscuous activity, or some combination of two or all three. In fact the sheer number of ways there was for mutations to cause these compensatory changes was rather surprising, even including reductions in enzyme activity for enzymes active in other pathways (interesting how this biochemically led to increased sad expression btw.)
So what is the reason on special creation for forcing exactly the result (ancestral convergence) expected on common descent?
I mean, I assume you don’t think God is being intentionally deceptive by making the evidence look like common descent happened. So why does the evidence exhibit exactly the result expected on common descent?
Where is your model of the creation process that predicts ancestral convergence should result from it?
That entire sentence does not parse meaningfully into english. Try again please.
Something about the flood possibly being local. Okay. What does that have to do with how many species share common descent, and how much they have diverged in the time since the supposed flood? By the way, how many animals were on this ark and when did the flood happen? This is a serious problem you have to deal with. If you think two populations can have diverged by no more than two mutations, how can you think even two individual human beings can be related?
I already have, but seriously no that’s you who needs to do that. Handwaving in the direction of wind and local floods (wtf?) does not accomplish that. Dude wat?
Then it isn’t clear why there is a problem at all. If you allow the possibility of many equivalent mutational sets, then there is no reason to think there’s a two-deleterious-mutation barrier to evolution.
It’s clear already you’ve never truly thought about this issue at all and you’re just spewing apologetic nonse you don’t understand.
I predict I will have to explain your own argument back to you next to even get you to realize why the creationist authors you rely on (such as Behe) have suggested something like a two-mutation limit to evolution.
Now, recall: You have already admitted that Behe’s argument is based on the assumption that the trait requires two simultaneous mutations. This paper demonstrates no such thing and, in fact, shows that there are multiple pathways, each involving several mutations (as many as seven) to produce chloroquine resistance.
How did Behe and the rest of the DI respond? This video will demonstrate. Note that Behe and Luskin completely ignore that fact that the paper refutes Behe’s claim that it required two simultaneous mutations and instead lie about what his critics had said. They try convince their listeners that those critics had insisted that the trait required only one mutation.
At 3:39, they misquote Ken Miller as writing that Behe’s claim that it required two mutations was a “breathtaking abuse of statistical genetics.” Here is what, in fact, Miller actually wrote:
Behe cites the malaria literature to note that two amino-acid changes in the digestive-vacuole membrane protein PfCRT (at positions 76 and 220) of Plasmodium are required to confer chloroquine resistance. From a report that spontaneous resistance to the drug can be found in roughly 1 parasite in 1020, he asserts that these are the odds of both mutations arising in a single organism, and uses them to make this sweeping assertion:
“On average, for humans to achieve a mutation like this by chance, we would need to wait a hundred million times ten million years. Since that is many times the age of the universe, it’s reasonable to conclude the following: No mutation that is of the same complexity as chloroquine resistance in malaria arose by Darwinian evolution in the line leading to humans in the past ten million years.”
Behe, incredibly, thinks he has determined the odds of a mutation “of the same complexity” occurring in the human line. He hasn’t. What he has actually done is to determine the odds of these two exact mutations occurring simultaneously at precisely the same position in exactly the same gene in a single individual. He then leads his unsuspecting readers to believe that this spurious calculation is a hard and fast statistical barrier to the accumulation of enough variation to drive darwinian evolution.
It would be difficult to imagine a more breathtaking abuse of statistical genetics.
Behe and Luskin are lying. There is no two ways about it. Stick a pin in that for now.
Good. So you must also agree that that entire video is discredited. It does not demonstrate any the limitations to evolution they claim to have.
OK, so you are as ignorant and stupid as you appear to be. Thanks for clearing that up.
I have just provided video evidence of Behe lying. There is no other reasonable interpretation. In order to honestly mistaken, Behe would have to be unaware of what he had written in his own book. That is exceedingly unlikely.
I can produce more examples of DI mendacity if you wish.
That’s a serious accusation, on par with your accusation that I was impersonating a psychiatrist.
Do you have anything to back it up, as I have backed up my claim that Behe is a liar?
No, it is prohibitively unlikely. So what? Are there any examples of this actually happening?
So when I first asked for the qualifications on the two mutation limit, this was the answer I got.
All of the mutations in the papers I discussed from the video resulted in new function or were on the way to new function. But then you offered this further qualification.
That is a different scenario. Now we are talking about a set of multiple mutations that are only selectable when all are present. Fine. So then the question becomes: how do any of the experimental papers Tour & Stadler cited, apart from the Gauger et al paper, support this two mutation limit? If they all involve stepwise-selectable routes to new functions, that says nothing at all about what limits exist on non-selectable routes. They also say nothing about how often specified, nonselectable routes would have been necessary in the course of descent of all organisms from a common ancestor.
Close, except that experimental design was specifically looking for promoters, not functional proteins. The design for an experiment to look for functional proteins would look more like this, this or this. Or, conveniently, there are multiple threads here on such topics; I believe this is the most recent.
I would encourage you to look at the paper more closely. In broad strokes, the logic of the paper goes something like this. First, one can ask if ancestral sequences actually are more similar to each other, as we expect under common descent, and indeed that increased similarity (convergence) is observed. Second, one can ask if that would happen any time one applied ancestral reconstruction techniques to any random sequence data one came across, and the answer to that question is ‘very, very unlikely’ as indicated by the probabilities in the passage you quoted. Third, one can ask if separate origins–not random, but also not from a common ancestor–would produce the observed convergence. That’s the alternative model which is meant to reflect separate creation.
And I replied that you don’t get to be a biomedical engineer without knowing biology. Along with his engineering. Some people such as Stadler are multi-disciplinary people. And not being able to list the people who worked for Axe is not tantamount to lying, Axe did mention having people who worked for him, so there is evidence for that claim. Anything else, please?
Deception is done with a good motive? Not the kind of deception you are saying I’m doing.
Justified is not the opposite of malicious, though. And I didn’t add a qualifier, I just gave one, “malicious”. And no, I don’t speculate on peoples’ intents and motives here. You all, however…
Um, I’m still waiting for the relevant evidence. And I did check on Behe’s book where he answers his critics, that implies looking at Behe’s veracity, along with checking the soundness of his arguments. And I’ve read other peoples’ responses to what Behe wrote and said, notably Larry Moran on his Sandwalk blog.
I agree (and agreed) that multiple mutations were required, and certainly Behe didn’t mean all the mutations magically happened at the exact same moment. He had in mind that the various mutations did not confer a selective benefit, so they would not tend to be kept, unless they all had arrived.
Certainly, and I reviewed Behe’s explanation of a “CCC” in the course of this discussion, to make sure I got it right.
How about “Waiting on Two Mutations…” (Durrett and Schmidt, Genetics), where we read “Conclusion: Achieving two coordinated mutations in humans (where the first mutation does not confer a benefit) would take > 100 million years!”
Can you point to one of these papers, please? That was what I was asking for. And I did watch one of your videos by Zach Hancock over in the Royal Science Conference thread, and found it unsatisfactory. But I don’t see a video by Hancock in this thread, could you repost it?
Thank you! Comments follow.
First we read (in Lynch’s paper) “Although the authors claim to be evaluating whether Darwinian processes are capable of yielding new multi residue functions, the model that they present is non Darwinian (King and Jukes 1969). Contrary to the principles espoused by Darwin, that is, that evolution generally proceeds via functional intermediate states, Behe and Snoke consider a situation in which the intermediate steps to a new protein are neutral and involve nonfunctional products.”
Um, seriously? No one denies that evolution can reasonably be expected to proceed from step to selectable step, if the new fitness peak is nearby. And yes, Darwin expected such a progression, with lots of intermediate steps, but he admitted he didn’t know of any. And the gaps are still there! The expected continuous intermediates all along the path of life, have not been found. So the only real alternative is neutral steps, certainly everyone all agrees that harmful mutations are not a way to expect evolution to continue.
“Moreover, given that the authors restricted their attention to one of the most difficult pathways to an adaptive product imaginable, it comes as no surprise that their efforts did not bear much fruit.”
Right, evolution doesn’t work very well, even with a path of mostly neutral mutations. Just Behe and Snoke’s point.
Then Lynch points out:
“To stretch this statement to imply that all amino acid changes lead to nonfunctionalization is a gross mischaracterization of one of the major conclusions from studies on protein biology—most protein coding genes are tolerant of a broad spectrum of amino acid substitutions (Kimura 1983; Taverna and Goldstein 2002a,b).”
Then turning to Behe and Snoke, we read:
“… most mutations that alter the amino acid sequence of a protein effectively eliminate function (Reidhaar-Olson and Sauer 1988, 1990; Bowie and Sauer 1989; Lim and Sauer 1989; Bowie et al. 1990; Rennell et al. 1991; Axe et al. 1996; Huang et al. 1996; Sauer et al. 1996; Suckow et al. 1996).”
So it seems to be Lynch’s references against Behe and Snoke’s references! So which side is right? There seems to be an ongoing discussion, and Behe and Snoke would seem to be completely within their rights to say “we pick this side.”
Then Lynch says:
“under the assumption that all 20 amino acids are equally substitutable in the intermediate neutral state.”
Oops, I hope that didn’t mean like what it sounded he said. That seems extreme, if that is what he means, he didn’t say that earlier.
All this seems to cover the principles where Lynch said Behe and Snoke were mistaken, on to the problem with Behe and Snokes’ caveat!
Alright, in the caveat, they admit their estimate may be an underestimate in view of some considerations, or an overestimate based on other considerations! So hence the “colossal caveat”? It could even need both of these adjustments together! So I don’t see how they abandoned or discredited their results here. Certainly not in a colossal way.
And as far as hindsight thinking, I scanned the article looking in vain for this, could you post the pertinent quote?
Again, as I said (this gets tiresome), I conclude that any mutation restoring function would have been of interest, and would have been relevant in their results. Surely this is obvious. And you are the one proposing something that they almost certainly didn’t do: “search for two mutations which in combination renders a gene nonfunctional and where no other mutations can compensate, deliberately insert those two mutations, and then wait for those two and only those two to reverse.” That’s absurd, surely they ran the experiment to find out what happened, out of all possibilities.
Great, fine, that’s what I include in my view.
Um, you skipped all my reasons for doubting common descent, somehow! I think there are significant reasons to doubt common descent, and good reasons to believe in special creation. Therefore I reject common descent, and say the evidence for it is not persuasive, in that it doesn’t address critical concerns.
I claim my model of creation doesn’t predict that! The two models are quite different, and have different support for each, and the evidence needs to be evaluated. I think there’s a good choice here, and it’s not common descent. As per various concerns of the EES evolutionists.
Yes, sorry I blew a fuse somewhat.
Again, I don’t believe common descent is a good view at all, before or after the flood. But I do believe all the “kinds” (i.e. major groups of animals) were alive before humans arrived, so no need for more major divergence after humans.
I’m not sure why a count of animals is necessary, though, nor the date of the flood, or why these are serious problems. Bible readers have done just fine throughout without knowing this.
New function, new function, my friend! Think man, think! No one claims that at most any differences of two mutations are possible.
This wasn’t me concluding this, nor winds and waves, this was a paper in a journal. So back to it being your problem, not mine. Please explain how we got to humans, through millions of mutations, as I’ve heard it stated (I believe by Stadler), at such a slow rate…
Because the easiest task for evolution is if there are (let’s say) just two mutations to get to a function, this is a setup for evolution, can it do a slam dunk? Actually, it can, such as chloroquine resistance in mosquitoes, so we see it’s difficult, though, and I’ve tried to be careful and say “about two mutations”, and Behe sets the edge of evolution at what he terms a “double CCC”, or at four needed mutations to get to a new function. He claims that the barrier, the most we can expect from evolution.
I just going to say it sounds like you are saying neutral mutations get fixed basically as fast as they occur, i.e. all neutral mutations basically get fixed. If so, I don’t know what this has to do with our discussion here.
That’s fine, but as I mentioned to Rumraket, I can deduce some idea of what I think this means, but then I don’t see what it has to do with my discussion with him. Rumraket didn’t say anything about how this applied, neither, come to think of it, have you. I’m not inclined to go off learning a theory, until I can be shown how it’s relevant to the discussion I’m involved in.
IIRC, some ID’ers were questioning this on Uncommon Descent or some place like that. Sal Cordova, of all people, tried to explain to them that this was a finding too well supported by both mathematics and empirical data to seriously question.
Well it’s happened at least 6 times (by this paper) since we started keeping track (c.1950), and there could be more instances that were never observed. That is considerably more likely than once in 100,000,000 years, don’t you think?
OR are you the sort of person who thinks the more something happens the less likely it is to occur? (I know that sounds like a silly question, but it’s more common than you might think.)