Jonathan,
“In fact, it is fairly clear that the existance of a structured search space (which is precisely what a non-Darwinian mechanism is) leads directly to the idea that the structuring was done by an intelligent agent.”

This entire comment is off-tangent. However, I will answer this specifically. A structured search space is not an evolutionary or nonevolutionary trait, it is the most usual search space. Natural slection for example looks at local gradient in fitness, there the fitness depends on the organisms possibility to answer to the current environment. Nothing unnatural is ‘doing the structuring’.

“False. (a) a binding site was there. (b) it already bound to aldosterone.”

There was no aldosterone produced in the original organism. The binding ability to aldosterone was incidential. This is how evolution proceeds, it can make use of available resources.

From the IC perspective neither aldosterone or its receptor existed. Thus, according to IC definition, this was an irreducible chicken-and-egg situation.

“In addition, since this did not test IC, I don’t see why they would have tried this experiment.”

My proposal was to test IC formulations. It is your concern how to do it.

” it would only be a _partial_ refutation.”

There is nothing in IC that distinguishes between 2 or more “irreducible components”. Thus the whole concept was falsified.

“Had this not been publicized by a big PR push, and allowed discussion in the scientific community before calling the NY Times, noone would be calling foul.”

So we can call everything of ID foul by its own PR practices.

“Again, I refer you to evolutionary theory and the Big Bang if you want to talk about “goalpost moving”.”

Evolutionary theories and Big Bang theories are much more elaborated than ID is. Details have changed and the theories have grown. However, IC refuses to meet experiments, see above. Since IC, even though it is only partly covering ID, is refuted all the assumed predictive parts of ID are falsified. (SCI is a non-starter.) It is a theological question whether ID is refuted or not; the assumed predictive parts are.

Freawaru,
“you are confusing ID with creationism”

ID trivially implies creationism, and vice versa.

Salvador,
“IC does pose a very formidable and substantial barrier to Darwinian evolution”

You have to prove this, it is unsubstantiated.

“1 amino acid substitution is piddling, 2 is somewhat piddling, however because of exponenial growth, once one gets to 8 or more, it’s starts to no longer be piddling.”

Your definition of IC makes it a bad indicator of design. Further it makes it unpredictive and unfalsifiable.

Yes, Dembski ‘corrected’ some of the flaws with Behe’s definitions and Behe never provided any evidence to support his claims about indirect routes. Now we find out that Darwinian routes and evolutionary routes (remember IC only focuses on Darwinian routes), can in fact generate IC. Which means that IC is not a reliable indicator of design after all. As such, IC has lost much of any relevance unless it can be saved by some positive hypotheses but that’s what ID seems to want to avoid at all cost (remember how Dembski considered such requests pathetic?)

Both myself and Mike Gene believe it is too difficult of a position to say that ALL IC systems can not evolve via Darwinian means, but IC does pose a very formidable and substantial barrier to Darwinian evolution, and that the abundance of certain IC systems would be sufficient to put design as legitmate alternative to naturalistic evolution.

That said, I think Behe is right to call this a piddling example and this paper is knocking down a strawman.

The examples Andrew cites with Behe deals with the exponentially difficult correlation of the number of amino acid positions to the number of trials required to achieve a protein with an appropriate characteristic. The examples that Behe and Snoke explored attempted to quantify the improbability when there were a number simultaneous changes needed and when there was low to negative selective advantage to the intermediates. 1 amino acid substitution is piddling, 2 is somewhat piddling, however because of exponenial growth, once one gets to 8 or more, it’s starts to no longer be piddling. Thus they helped to clarify the idea of what it means to have “SEVERAL well matched parts”, rather than just some vague notion of what SEVERAL means. Behe’s definition uses the phrase, “several well matched parts”.

In my book, 2 amino acid residues do not constitute “several well matched parts”, but that is what the supposed rebuttal dealt with. 2 amino acid components! A crude worst case search to find the combination is 1 out of 20^2 = 400, which is quite achievable.

Consider that I wanted to break a password that had only 2 alphabetic characters. That would be feasible, I need 26^2 trials. However, to imply that because one can resolve a password with 2 alphabetic characters that therefore a password of 10 characters would easily be achieveable is misleading. In the same way, the researchers have abused the idea of what “several” means in the definition of IC.

Further, Musgrave misrpresented Behe by implying Behe contradicted himself by rejecting the rebuttal because it dealt with a single protein, when the reason was the system lacked several well matched components. Of course, one might argue that 2 amino acids are “several well match parts”, but that is quite a stretch!

Behe might have argued his case better by comparing it to the proteins he and Snoke were describing, where the conception of the word SEVERAL was a quantified in greater detail.

I agree that it might not have been most accurate to call the results “piddling”; but then again, though they reflected a significant amount of work and looked at an interesting question, the results were extremely minor compared to the billing (think commentary in Science, NYT…)

Moreover, your comment:

No one is saying that the Bridgham et al. paper refutes all of intelligent design. (That’s not even conceptually possible, since an omnipotent God can do whatever he wants. That’s why it’s fun to be omnipotent.)

The paranoid mindset of the creationist is amusing, if sad. I don’t “want this to be a win for Darwinism,” nor am I part of some vast Darwinist conspiracy to suppress contrary ideas, as you suggested earlier. (If that were so, Stephen Jay Gould would have been shot down in his infancy.) I just care when otherwise-intelligent people say demonstrably false things.

Actually, the Science commentary _does_ in fact say that. If you think that this is an over-reaching statement, you should join me in criticism of that.

Here’s what the Adami perspective article says:

“such studies solidly refute all parts of the intelligent design argument.”

“So your efforts to resusciate ID”

What resuscitation? Nothing has been refuted.

“They’re not talking about rejecting teleological explanations, so it’s just not relevant.”

Perhaps you missed the part of the discussion where we talked about why Darwinism is an important part of the formulation.

“the paper takes a biological structure Behe previously characterized as irreducibly complex”

False. As pointed out many times above, Behe never characterized this as irreducibly complex.

“But can’t we at least agree on the obvious — that Behe looks like an idiot and a liar now for characterizing the Bridgham et al. paper as “piddling?””

No. Obviously you missed all of the conversation above and ignore all of the actual claims of both parties. Just because you _want_ this paper to be a win for Darwinism doesn’t change the fact that this paper does not in any way test irreducible complexity.

As Adami said, the information presented is “intrinsically interesting to biologists” — I agree with that completely. However, it is not of relevancy to the ID argument because it is not a system which Behe claims are irreducibly complex. How is this a difficult subject for people to grasp?

No one is saying that the Bridgham et al. paper refutes all of intelligent design. (That’s not even conceptually possible, since an omnipotent God can do whatever he wants. That’s why it’s fun to be omnipotent.)

So your efforts to resusciate ID based on “teleological explanations” and “structured search spaces” don’t even rise to the level of red herrings. They’re not talking about rejecting teleological explanations, so it’s just not relevant.

Rather, the paper takes a biological structure Behe previously characterized as irreducibly complex and shows an evolutionary pathway for the evolution of that structure.

Believe ID if you want. I’m sure I can’t convince you otherwise and I won’t bother trying. But can’t we at least agree on the obvious — that Behe looks like an idiot and a liar now for characterizing the Bridgham et al. paper as “piddling?”

False. (a) a binding site was there. (b) it already bound to aldosterone. Interestingly, the evolution of aldosterone (which I believe would _need_ a specialized binding site _before_ it would be useful [thus inhibitting both the selection of it and its receptor]) was not considered.

So, with all of your premises incorrect. No.

“If any ID proponent had been doing research for the last ten years they would have easily tested each and everyone of these formulations and perhaps selected one that survived initial tests.”

That would require major funding, and, last time I checked, there was not a large funding supply for ID. In addition, since this did not test IC, I don’t see why they would have tried this experiment.

“disprove _one_ of Behe’s formulations. Thereby the concept of IC is refuted.” [emphasis mine]

Even if this were true (which, as I pointed out above, it isn’t), it would only be a _partial_ refutation. If science proceeded on this basis, we would have rejected evolution long ago. Do you view the fact that Darwin was wrong about a lot of things as a total failure of his theory?

“The experiments they could have used should of course start with such simple systems as the current research looked at. To suggest that one should, or must, start with more complex systems is to not understand how science is done.”

I didn’t suggest that. What I did suggest was that taking the small bite is not the same as taking the big bite. They are taking the small bite (and, as many have shown, not even been successful at that) and _pretending_ to have taken the big bite. You do it in your own post. Had this not been publicized by a big PR push, and allowed discussion in the scientific community before calling the NY Times, noone would be calling foul. Behe would submit a response, clarifying his concepts and pointing out how the experiment did not meet them, and everybody would move on. But to treat such tiny claims as if they were huge, sweeping claims seems to be characteristic of the Darwin-pushers.

“That the rest of us take home is that ID is moving its goalposts according to evolution progress, just as religion has always moved its goalposts according to science progress”

That’s a huge case of the pot calling the kettle black. Again, I refer you to evolutionary theory and the Big Bang if you want to talk about “goalpost moving”. The fact is that all ideas must be reformulated with time. I don’t know of _any_ idea from _any_ arena of life which has not been. To say that this is restricted to ID and theology is simply being disingenuous.

It depends on what you mean by mainstream. IC is no obstacle to the same kind of processes by which ID is no obstacle to. However, the people who are screaming about ID are usually the ones (such as Leshner and Scott) which are committed to Darwinian paradigms. In fact, it is fairly clear that the existance of a structured search space (which is precisely what a non-Darwinian mechanism is) leads directly to the idea that the structuring was done by an intelligent agent. See:

http://www.4truth.net/site/apps/nl/content3.asp?c=hiKXLbPNLrF&b=784461&ct=1742245

According to the Berkeley website on evolution:

http://evolution.berkeley.edu/evosite/evo101/IIIC1aRandom.shtml

“In this respect, mutations are random—whether a particular mutation happens or not is generally unrelated to how useful that mutation would be.”

And this idea that organismal change is unrelated to organismal need has been exactly what has caused people to doubt teleological arguments. This is precisely the basis for Dawkins climb up Mount Improbable. Now that we know that organisms heavily rely on a mutation space that is structured to give beneficial, sensical mutations based on need, teleology is clearly implied, and the refutations of teleology is clearly refuted. This is why the “Darwinian” adjective is critical. This is why ID’s main aim has been Darwinian evolution. Other forms of evolution are perfectly inline, and actually support, ID ideas.

So, if you are willing to grant that the “mainstream evolution” supports ID, then I will concede that “mainstream evolution” is not a challenge to IC. If you at least continue to admit that non-Darwinian evolution is a major part of current evolutionary theory, then we can perhaps work together in getting objections to Darwinism heard in the classroom, since we can both agree that this is part of mainstream science. Currently, the Darwinian version is the only part of the story being told. If the Darwinian version is no longer mainstream, we can at least work together to get directed/assisted/whatever-you-want-to-call-it evolution into schoolbooks rather than the outdated Darwinian version.

“Okay, so we can all agree that IC as it is presently formulated by Behe is no obstacle to evolution as currently understood by mainstream science?”

This is patently false. I suggest you take the time to actually read the biological literature and see how Darwinian and neo-Darwinian is used. It is usually used exactly as ID’ers describe it, AND as a positive thing.

As a quick example, when deciding how to characterize certain genetic changes, this paper had a discussion about whether or not certain characterizations were neo-Darwinian, with the implication that they clearly preferred Darwinian explanations. In fact, in review articles discussing adaptive mutagenesis, the question of whether or not such processes can be accomodated by Darwinian paradigms are of great concern.

Also, in this paper, the author pleads with his audience that a given observation is compatible with Darwinism.

The fact is, that the “old guard” in science (the ones who are in charge of peer-review, for instance) are very strict Darwinists, and people have to bend over backwards to point out that what they are saying can be fit in with the Darwinian paradigm that it is very amusing. For example, see the abstract of Chance Favors the Prepared Genome:

“Rejecting entirely random genetic variation as the substrate of genome evolution is not a refutation, but rather provides a deeper understanding, of the theory of natural selection of Darwin and Wallace.”

It doesn’t matter how irrational it is, we _have_ to align ourselves with Darwin! If someone figures out that Darwin doesn’t matter, then Dawkin’s will lose his security blanket! Oh the horror!

I repeat, the original organism and its different hormone-receptor systems lacked aldosterone and it’s receptor, including the aldosterone binding site. You are thinking of the ancestral state receptor, which was a different cortisol/DOC binding site.

To get from this situation to the aldosterone-MR receptor is an irreducible complex chicken and egg situation *according to Behe’s ‘multiple parts’ original IC definition*. (And furhermore according to Behe, the way this paper showed evolution did it, should not be happening.)

“Nowhere that I am aware of does Behe list increase or decrease in selectivity as being irreducibly complex.”

No, the point was that he tried to explain away the experiment by stating “Nothing new was produced in the experiment; rather, the pre-existing ability of the protein to bind several molecules was simply weakened.” which Musgrave show is false. The selectivity for aldosterone was produced. The sensitivity was perfectly as it should be.

“I have to take Behe’s side on this — after ten years, this is the best they can do?”

The point is that no ID research has proved IC, but that this paper, looking at an evolutionary process, happened by chance disprove one of Behe’s formulations. Thereby the concept of IC is refuted.

One of its problems is that there are several formulations, see Musgraves post at Panda’s Thumb that I linked to. If any ID proponent had been doing research for the last ten years they would have easily tested each and everyone of these formulations and perhaps selected one that survived initial tests.

The experiments they could have used should of course start with such simple systems as the current research looked at. To suggest that one should, or must, start with more complex systems is to not understand how science is done.

ID hasn’t done its basic homework, so the field is pushed further into obscurity. That the rest of us take home is that ID is moving its goalposts according to evolution progress, just as religion has always moved its goalposts according to science progress, and “that IC as it is presently formulated by Behe is no obstacle to evolution as currently understood by mainstream science” as Andrew remarked.