Experimental evidence for very long term processes

That is truly an absurd claim. False positives of “the design inference” date back to ancient beliefs attributing phenomena like lightning to the actions of gods such as Zeus or Thor. It also occurs pervasively in modern times with well-documented phenomena such as pareidolia. From an evolutionary perspective, it could be claimed that a bias towards false positives, rather than false negatives, in attributing agency is adaptive – as the cost of reacting to a rustle in the forest just caused by the wind is far lower than the cost of ignoring a rustle caused by a large predator.

You may claim that ID uses the term in a narrower sense, but then you’d have to (i) provide a rigorous definition of what it means in this sense, and (ii) demonstrate how ID’s use of it in this sense does not lead to false positives, in spite of the fact that their work has generally been debunked as being based on pervasive misrepresentation (e.g. presenting White’s assumption-laden guestimate as solid).


I don’t believe his model involves coordinated mutations (which I understand to be specific mutations occurring in the same individual). But the model does involve a number of arbitrary restrictions that make it not directly applicable to real life situations. Lynch openly admits this, and it is not a problem since his goal was not to model a real life situation. It was, rather, to demonstrate how utterly absurd Behe’s model was. The interesting thing is that Behe himself admitted that his model was just that, a model, and that other models were possible that showed there was no problem in evolving new proteins without the help of a god:

Our paper contains one simple result. When reasonable parameters are used with our model to estimate actual time scales or population sizes for the evolution of multi-residue (MR) protein features, they are unrealistically large. This implies that the model we chose, which is restricted to point mutations and assumes intermediate states to be deleterious, isn’t a plausible evolutionary pathway. One must therefore look about for a new model. We did not rule out such a possibility; in our original article, we explicitly stated, “we should look to more complicated pathways, perhaps involving insertion, deletion, recombination, selection of intermediate states, or other mechanisms, to account for most MR protein features."

Of course, he and his fellow ID’ers do not mention this when speaking to their acolytes.

A response to Michael Lynch - Behe - 2005 - Protein Science - Wiley Online Library


The greatest admission is in the original Behe & Snoke 2004 paper:

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 essentially undermines all versions of the “waiting time problem” proposed by ID-creationists. Behe and snoke here basically admit that all their calculations are worthless as arguments against historical evolution.

In the end this problem is still worse for “waiting time problem” proponents, because evolution is a biosphere-level phenomenon. The real question is, among all the species in an ecosystem, what is the probability that some feature will involve in some gene in some species.


But just watch. @Giltil will continue to insist til he is blue in the face that Lynch’s paper shows whales could not have evolved. It doesn’t matter how many experts explain to him that this is not what the paper shows. I hope I am wrong, but I wouldn’t bet anything on that.

It’s just like how another member is constantly referring to the “Lynch-Behe model” that, he believes, shows new proteins cannot evolve in animals.

In that sense, Behe’s paper has been a total success. It has given the DI fodder for their propaganda and fund-raising efforts.


This is an extraordinary claim. How on earth do you know that no trait in whale evolution required coordinated mutations?

I’m sorry, you claimed that they were all coordinated. And not just coordinated in twos or threes, but every single mutation coordinated with every single other.

Which is why, nearly a week ago, I asked:


What a bizarre response. It is as if you don’t understand your own position.

It is you who have accepted the ID claim that “coordinated mutations” are so improbable as to be practically impossible. (They may actually be correct about this.)

And you also agree that the evolution of whales would have required a whole lot of mutations.

The logical conclusion, then, is very few, if any, of these many mutations were “coordinated.”


It would be the logical conclusion only if your reasoning includes as the premise that whale evolution was produced by a process of random variations + natural selection. But because this premise is precisely the point of contention, you are guilty of circular reasoning here.

No, another is that there were lots of possible “sets” of coordinated mutations through which the ancestors of whales could have adapted.

Coordinated really just means that in order for a later mutation to have an adaptive effect, it must occur in an organism where a previous mutation has already exists that enables this adaptive effect.
If mutation B only is adaptive if mutation A has occurred first in the same individual, it is “coordinated”.

The issue with “coordinated” mutations only arise when there are very few possible alternatives, which makes finding the one solution that works very unlikely because the “wrong” enabling mutations have evolved first.

Most mutations are thought to epistatically interact with other mutations elsewhere in the genome, so a large fraction of mutations are probably “coordinated” in this way. But if B can be enabled not just by A, but by A1, A2, A3, A4, A5 etc, and not just B, but also B1, B2, B3, B4 etc. Suddenly despite the fact that the mutations all have co-dependencies, the fact that there are many possible alternatives means it’s not at all unlikely for a coodinated set to occur with regular frequency.

Proponents of the waiting time problem pick examples from the literature where there are only very few alternative sets (such as chloroquine resistance), they then pretend this is “normal” for any adaptation. It isn’t. There is lots of evidence for adaptations that also required coordinated sets, but where many more possible alternatives were available. That’s for example what this article shows:

It’s right there in the abstract already(my bolds):

To understand why molecular evolution turned out as it did, we must characterize not only the path that evolution followed across the space of possible molecular sequences but also the many alternative trajectories that could have been taken but were not. A large-scale comparison of real and possible histories would establish whether the outcome of evolution represents a unique or optimal state driven by natural selection or the contingent product of historical chance events1; it would also reveal how the underlying distribution of functions across sequence space shaped historical evolution2,3. Here we combine ancestral protein reconstruction4 with deep mutational scanning510 to characterize alternate histories in the sequence space around an ancient transcription factor, which evolved a novel biological function through well-characterized mechanisms11,12. We found hundreds of alternative protein sequences that use diverse biochemical mechanisms to perform the derived function at least as well as the historical outcome. These alternatives all require prior permissive substitutions that do not enhance the derived function, but not all require the same permissive changes that occurred during history. We found that if evolution had begun from a different starting point within the network of sequences encoding the ancestral function, outcomes with different genetic and biochemical forms would likely have resulted; this contingency arises from the distribution of functional variants in sequence space and epistasis between residues. Our results illuminate the topology of the vast space of possibilities from which history sampled one path, highlighting how the outcome of evolution depends on a serial chain of compounding chance events.


I think that the claim that particular coordinated mutations are vital to whale evolution, bears the burden of identification and demonstration here. As it stands, it is just a bald assertion.

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So, according to you, considering the whole biosphere, the probability that the process of random variation and natural selection can produce biochemical/morphological changes of the same amplitude than those observed for whale evolution from a pig-like ancestor is not small. In that case, you can certainly rise to Bechly’s challenge of the species pairs, can’t you?

I think I met that challenge with this post already.

For their divergence times within the last 10-50K years or so, I think the scale of differences we see between domesticated plants and animals, and their wild ancestors, are rather extreme. And they haven’t at all had another 4 million 950 thousands years to diverge further, and they’re already well on their way.

I could also again invoke the case of the selection of multicellularity from single-celled ancestors in laboratory evolution.

But we also had a thread on Bechly’s silly challenge here. There are many issues with Bechly’s framing of the challenge, such as the fact that he declares there’s “no conceivable reason” why we shouldn’t see a divergence of the sort of scale we see between fully aquatic whales and their terrestial ancestors happening all around us all the time.

Well how about the fact that evolution of that scale typically requires a radical change in lifestyle (switching to occupying a different niche), which generally don’t happen but following large mass extinctions where such niches open up where they were previously occupied? It’s extremely difficult to move into an already well-occupied niche full of highly adapted organisms and then start competing if you’re, well, 5 million years behind in the arms-race.

There’s also the issue of Bechly’s insistance that the interval is 5 milion years, when it could be as long as 20 million or even more.

I don’t think that’s what it means as either Gil or Behe use it. They are using it to mean neither mutation has an adaptive effect unless both are present.

That’s what I meant too.

The challenge is so vague that it’s impossible to know if you’ve satisfied it. What’s a new body plan, and how do you recognize one? It appears to be either the difference between a trilobite and a worm or the difference between a human and a chimp. That covers a whole lot of ground, and there can be no objective standard. It isn’t quantified in another way too: the distribution in time of these supposed sudden transitions is never measured. He only compares the past 5 million years to a single (again supposed) 5 million year period in the evolution of one taxon. Are such transitions evenly distributed in time? How often are they recorded? What’s the model used to decide the expected number for modern species? As science, this is hopeless.

Still, would any of the island radiations in birds count? I suspect not for Bechly, because the only differences as slight as those that would be credited would be the single case of chimps and humans.


The challenge is not to identify many such divergences but only one!!!

How do you measure “such”?

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For example, a divergence characterized by the appearance of a new functional system such as a sonar.

No, that can’t be it. Humans don’t have a new functional system. Also, “new functional system” is in the eye of the beholder. Is a leg a “new functional system” even if it’s just a slightly modified fin? Isn’t sonar just a refinement of voice and ears? Anyway, can I claim that the beak of an 'akiapola’au is a new functional system?



How does Bechly know the terrestial ancestors of whales weren’t already capable of some degree of sonar navigation? It’s not clear what distinguishes the degrees from each other so we say that now, here, it qualifies, and the immediate antecedent does not.

I think this dog’s entire face is a new functional system:

The whole thing works together. The flappy ears, the short fur, the long sloppy cheeks, even the white stripe across the face with the brown around the eyes. How well it’s able to control the muscles around the eyes to change expression.