The Death Knell for ID?

A new paper has not only cast doubts on Michael Behe's assertions, it's run a freight train over the top of the ID arguments against evolution.

For a concise version see

http://www.nytimes.com/...us-learns-a-new-way-to-infect.html

The abstract can be found at

http://www.sciencemag.org/content/335/6067/428.abstract

Science 27 January 2012: Vol. 335 no. 6067 pp. 428-432

I don't have access to the full text, so would appreciate the input of people who have.

Briefly, it has been shown that a bacteriophage which infects E.coli via the LamB receptor was able to evolve a different mechanism to infect E.coli cells which had very few LamB receptors on the surface. Within only fifteen days there were phage particles using the OmpF protein, something the phage had never been known to do before.

DNA analysis showed that 4 separate mutations were needed for the phage to use OmpF. Of 96 lines, 24 developed the ability to use OmpF and the mutations were identical or almost identical.

This is something that, according to ID, is so improbable that it would either never happen or would take far too long to happen by random mutation and natural selection. The probability of all four mutations occurring simultaneously is approximately 1 in a thousand trillion trillion, so it seems likely that they were gained one at a time, something ID and Behe dismiss out of hand. Even if we accept their claim that stepwise mutations can't result in something bordering on irreducible complexity, they are left dealing with the fact that something with such a low probability of happening, happened within 15 days!

I'd like a very open discussion on this and would like to include those who can't post in the science fora, but I would like the emphasis to remain on the science so have no idea where this would go, since moderation may be required. Whatever Admin decides is fine with me.

Thread copied here from the The Death Knell for ID? thread in the Proposed New Topics forum.

Possible IDiot responses:

* "Yes, but this isn't an example of something else entirely which we also claim to be impossible, a claim refuted by different examples which, however, aren't examples of a third thing which we won't define clearly enough for you to find out whether they are or not."

* "This observation was made on organisms with such a short generation time that it was possible to make the observation. Therefore, like all such observations, it doesn't count."

* "That isn't irreducibly complex, because it evolved."

* "That isn't evolution, because it was an experiment done by a scientist in a laboratory, and is therefore an example of intelligent design. Of course, when we are talking out of the other side of our stupid faces, we claim that nothing counts as scientific knowledge unless it is the result of an experiment done by a scientist in a laboratory, because we are fucking morons."

* A resounding silence in which, in the far distance, one can here Behe's books being reprinted without emendation.

The Dover trial was probably already the death knell - particularly when they had to admit that they would have to consider Astrology a science to be consistent with their position.

More recently, we have old earth creationist Dembski switching to young earth creationism in order to keep his job.

I try to follow some of the ID blogs. There's almost nothing there that would count as an attempt to do serious science. It seems clear that they are just putting on a show, to make it look to creationists as if they have something.

Or, as Glenn R. Morton described it, when Dembski had at a conference repeated his criticism of genetic algorithms only to be met by a sea of hands raised by engineers who used genetic algorithms on a regular basis and knew for a fact that Dembski didn't know what he was pontificating about. Morton's description: "looking like a deer caught in the headlights."

Last I checked, that link was broken on Morton's site, but Google'ing I found this copy of it at http://asa.chm.colostate.edu/archive/asa/200004/0175.html

quote:

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William Dembski, Baylor University

This was the only talk I was unable to record. My new tape recorder refused to turn the tape. It took me an hour to figure out why. :-(( Fortunately, I have found a guy who said he would send me a copy of that talk on tape and on paper. All the biggies were there, Ernan McMullen, Paul Nelson, William Lane Craig, Michael Behe, John Baumgarder, Walter Bradley etc.

His talk was entitled "Can Evolutionary Algorithms Generate Specified Complexity?" In it he examined genetic algorithms and made many mistakes concerning their properties and the way they worked.

Life is complex and specified, Dembski said. A random sequence is complex and unspecified; a sonnet is complex and specified. [Thus he made the same error that Meyer made on day 2--ignoring the reality of spy codes which make a specified sequence appear random and unspecified. Specification is nothing more than an agreement between two individuals--it is semantics or meaning. And the second paragraph of Claude Shannon's seminal paper on information theory clearly states that information theory is incapable of dealing with meaning--grm] But Dembski drives on. Evolutionists haven't explained complex specified information (CSI) at the origin of life or the subsequent increase in CSI. Dembski used Dawkins 'me thinks it is like a weasel' example to claim that genetic algorithms have merely played a shell game in which they shuffle information around. He says that the fact that Dawkins put a target sequence into his program means that the information is already there and is being transferred to the string that is being randomly mutated. There is much truth in this. [assuming Dembski correctly described the program and I can't find my Blind Watchmaker to verify it--grm]. Dembski claims that once a letter in Dawkins program is correct, mutations cease at that location. [If so, it is like a poker hand being drawn. and one is indeed transferring info from the ideal sequence to the evolved sequence.--grm]

However, Dembski then goes on to assume that this is how all genetic algorithms work. He spoke of programs specifying a fitness function over the landscape and then using mathematical properties of the fitness function to find the ideal target. This is cheating because one must specify the info in the fitness function prior to searching for the target fitness. He called it the no free lunch theorem. [Of course genetic algorithms make no such assumption. We don't know the fitness function prior to writing a genetic algorithm and so can't use its mathematical traits to help us with our search. I was appalled at the poor understanding of genetic algorithms.--grm]

He then made a third mistake. He assumed that true fitness functions were flat except for the target which had a high fitness function. In a case like this, he claimed that it would be impossible to find the target because the target occupies too small a region of the sequence space for a random search to have a good shot at finding it. . [This is true but it entails an assumption which is questionable. While any of the laity in the room wouldn't understand the assumption that had just been slipped into them, it was clear to me and a few others. What Dembski is saying by defining such a fitness function is that there is one and only one molecular sequence which will perform a given function. The fact that cow enzymes are different from human which are different from slug enzymes, shows that more than one sequence performs a given function and that the target area in a sequences space is not as small as Dembski says--grm]

His fourth mistake was that he seemed to imply that genetic algorithms used a 20-questions approach to finding the target. The algorithm makes inquiries of the fitness function and gets a response like the game. The fitness function tells the program you are getting warmer, no you are getting colder, etc.[ He claimed that is teleology. It would be if that is what actually occurred with genetic algorithms.--grm]

He claimed that Stuart Kaufman agrees with him. [That would be an interesting thing to check on.--grm] He also claimed that there is only one known generator of specified complexity--an intelligent agent.

In the Q&A I raised the issue of biomolecular companies who use genetic algorithms to search for novel functionality. He claimed that it wasn't important and that such programs could never be used to design anything. Then much to my amazement, John Baumgardner said "'Glenn's point was exactly correct.' I nearly fell on the floor. He told Dembski that they were using genetic algorithms at Los Alamos to design lots of things. Two or three other people said the same thing. [One of these, a man named Eide Trotter, I later learned is a well connected Southern Baptist who goes to First Baptist in Dallas. He sat next to me and the next table on Thursday morning when I had breakfast with Paul Nelson, Mark Kalthoff and Tom Judson(?). After breakfast he said that he liked much of what I had said. Gerald Eichoefer, of Greenville College (don't know where that is) tried to come to Dembski's defense. He said that genetic algorithms were terrible inefficient search methods. He was shot down by a guy in the back who said that genetic algorithms vastly outperform a random search. and indeed a genetic algorithm isn't a random search. Later that day in the last session, Frank turned to me and said that Eichoefer claims to be a prophet of God. I must admit he looked like one which may explain why I took his name down off of his name tag.--grm]Hands were upraised all over the room. Dembski had the deer in headlights look. He turned it over to the next speaker.

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Blaise Pascal:
I have made this letter longer than usual, because I lack the time to make it short.

Slartibartfast:
I'm a great fan of science you know.

Share and enjoy!

quote:

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Possible IDiot responses.

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You guys are the idiots for believing that bacteria resistance or a virus infection proves how a bacteria can turn into a human being over millions of years. The evidence is so thrilling that it is enough to prove how evolution created everything.

You guys are the idiots for believing that bacteria resistance or a virus infection proves how a bacteria can turn into a human being over millions of years. The evidence is so thrilling that it is enough to prove how evolution created everything.

Presumably you have evidence for some alternate explanation?

The whole reason this paper is important is as follows

1. Behe and supporters of ID claim that this sort of thing can't happen, therefore ID is the only explanation.

2. It just happened in a lab in 15 days, not once, but many times.

Now either Behe is wrong and the foundation of the ID argument (they call it evidence) is fatally damaged

OR

The intelligent designer spent alot of time in the lab tinkering with the bacteriophages.

Do we know if the 3 intermediate mutations before the fourth really 'useful' one added any benefits of their own to the organism? It doesn't seem so from the article although it may be that no-one has looked for any yet.

If nothing useful for the intermediates is found, it's not obvious how natural selection can be claimed for them - or at least the story we tell for the evolution of complex structures like the eye is not an exact analogy.

So we're left with asking why something so apparently improbable happens so regularly - 24:96 or 1 roll of the dice in 4. The skeptic would say that on the evidence, something else is happening which we can't yet explain, but the obvious one is we got the odds wrong - ie the dice is loaded somehow. But we haven't yet shown how.

I agree that Dover should have put an end to the case for ID and I fully expected it to. However, Judge Jones showed much foresight when he said in the judgement that many would claim that it was a judgement of an activist court. Sure enough, this accusation is used time and again.

In the years since Dover, many bills have been introduced which show that ID is still trying to get a foot in the door by getting around the judgement using altered definitions and sleight of hand instead of dealing with the core finding of the judgement that ID isn't science. Behe's crucial claim, that certain things cannot happen by random mutation and natural selection, has been shown to be wrong, most notably in 2007 by Abie Smith (See Panda's Thumb and ERV's blog, I'll try to link later).

This paper in Science, however, is different, in that it doesn't compare isolates from 30 years ago to current isolates, but actually observed the "impossible" in real time, in an experiment, in a lab. Not only that, but it was observed happening multiple times. It seems to cover all the objections that ID followers put forward when confronted with this type of evidence.

Given that 4 mutations are involved in gaining the ability to use OmpF, it also makes inroads in the irreducible complexity argument, in real time, observed in a lab, again avoiding the criticism levelled at historical comparisons. This time the argument that "you weren't there to observe it so it's all guesswork" isn't going to work - the researchers were there, they did observe it and no guessing was involved.

Hope this helps, please forgive the huge cut and paste, but it was the easiest way to provide this information.

Nonetheless, there are several lines of evidence that selection drove their rise. First, all 248 independent mutations in the 51 sequenced J alleles were nonsynonymous, whereas the expected ratio of nonsynonymous to synonymous changes is 3.19:1 under the null model for the ancestral J sequence (16). This great excess is evident even if we include only the 82 nonsynonymous mutations in the 24 isolates that did not evolve the new receptor function. Second, the mutations are highly concentrated in the region of the J protein that interacts directly with LamB (18). Third, there was parallel evolution at the genetic level across the populations. For those phage that evolved to exploit OmpF, an average of 61%(4.06 out of 6.63) of mutations were shared across independently derived pairs (fig. S7), which greatly exceeds the fraction expected under a conservative randomization test (16) that used only the variable sites in J (P < 10−5). Pairs of phage that remained dependent on LamB shared on average 17% (0.58 out of 3.42) of their mutations (fig. S7), and this fraction is again significant under the same test (P < 10−5). Thus, it is clear that selection acted on the J protein even before the new capacity evolved. This selection presumably improved the interaction of the phage tail with LamB. From the Meyer paper

Hope this helps

Not much to me!

But it seems that this statement - if it could be explained and demonstrated in non-geek - may do the job.

Thus, it is clear that selection acted on the J protein even before the new capacity evolved. This selection presumably improved the interaction of the phage tail with LamB.

We need the word 'presumably' replaced by 'demonstrably' and then show why that is an advantage that would be selected for. Then we'd have a great story.

Do we know if the 3 intermediate mutations before the fourth really 'useful' one added any benefits of their own to the organism?

The original paper does touch on this, although it doesn't provide a definitive answer. They say ...

Meyer et al., 2012 writes: However, the all-or-none epistasis among the mutations means that selection for that new capacity per se was not responsible for the rise of the three prior mutations. Nonetheless, there are several lines of evidence that selection drove their rise.

They go on to describe evidence such as the ratio of synonymous to non-synonymous mutations, the distribution of those mutations in the protein principally being concentrated around the region which interacts with the LamB receptor and the fact that there is a much higher level of parallel evolution amongst the strains that evolved to utilise OmpF (61% in these as opposed to 17% in those that only utilised LamB).

It worth noting that while all of their evolved strains that could utilise OmpF did have 4 mutations they weren't all the same 4 mutations. In fact only 2 mutations were shared by all of the OmpF capable strains. The other 2 were slightly broader classes of mutations in one case all affecting the same amino and in the other being restricted between amino acids 990-1000 of the J protein. These distinctions would certainly heavily affect your probability calculations and it is highly likely that this is not a comprehensive catalogue of all the variations that give rise to the OmpF infection trait.

I would suggest that the fact that the intermediate forms seem to provide a selective advantage and the fact that the 4 mutations are not so highly specific are the most likely reasons an ID proponent might put forward for this not being a case that demonstrates the evolution of a truly irreducibly complex system, whatever one of those might really be.

TTFN,

WK

It's really quite simple: God wanted the phage to utilize the OmpF protein route.

/creo idiocy

You guys are the idiots for believing that bacteria resistance or a virus infection proves how a bacteria can turn into a human being over millions of years. The evidence is so thrilling that it is enough to prove how evolution created everything.

That would basically be response #1, with the addition of an explicit lie about your opponents --- which does not, I might add, make response #1 any smarter.