Did Douglas Axe Disprove Evolution? Spoiler: No

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So we could start with Wikipedia’s definition of body plan, which you said you agree with: “This term, usually applied to animals, envisages a “blueprint” encompassing aspects such as symmetry, layers, segmentation, nerve, limb, and gut disposition.” I would add organs, which Bechly seems to include.

Bechly remarks: “Whales are thought to be nested in and derived from artiodactyl ungulates. The fossil record shows that the transition from quadrupedal whale ancestors similar to Raoellidae (such as Indohyus) and Pakicetidae to fully marine pelagicete whales like Basilosauridae happened in just 4.5 million years. This implies that the body plan transition from a pig-like animal to a dolphin-like animal happened within the lifespan of a single species. Of course, this does not exclude the possibility of several successive speciation events within this time period, but it is still a fact that illustrates the biological abruptness of this major anatomical re-engineering.”

So he says this is considered and example of a body plan change in this timeframe, and also remarks that this is surprising, if this happened.

Yes, I would concur.

Well, I would call flippers new limbs, referencing what was said above about definition of body plans, and thus a new body plan.

I do realize that these are different, so we need to know if someone is a reliable witness. I have no evidence that they would be likely to mispresent what Bechly said. And I addressed this apparent discrepancy in Bechly’s view, do we need to rehash this?

Yes, that is my aim.

Noted, and I would only add organs, as mentioned above.

If it’s a reasonable question, then it needs an answer. That can be a valid reply to a claim, and a counterargument.

I think your view unlikely, as I said previously, since there seems to be an easier approach, that was not taken. Why didn’t the people at Peaceful Science, when they made their counterexamples, not see this easier way to refute Bechly? Art Hunt for one, Roy and Rumraket for others, you can check with them.

Agreed.

Well, from Wikipedia: “The model of a tree is still considered valid for eukaryotic life forms. Trees have been proposed with either four[25][26] or two supergroups.[27] There does not yet appear to be a consensus; in a 2009 review article, Roger and Simpson conclude that "with the current pace of change in our understanding of the eukaryote tree of life, we should proceed with caution. ” This does not seem to correspond with what you said.

That’s great! Glad to hear your response to this quote from Oxford Academic: “The assembly of a comprehensive and dated Tree of Life (ToL) remains one of the most formidable challenges in evolutionary biology. The complexity of life’s history, involving both vertical and horizontal transmission of genetic information, defies its representation by a simple bifurcating phylogeny.”

Sounds like we’re not nearly done yet.

But without intermediates! And is about 10-15 million years not sudden, in the history of life? I believe it is. Why else would they call it “The Cambrian Explosion”?

Bechly did say he believed every organism had a parent organism, but he also spoke of input from outside natural processes. As I mentioned, I don’t think we need to postulate undetectable miracles, as Bechly and Behe do, I’m fine with obvious miracles giving rise to new forms of life.

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I agree that you can give an extreme example, where the bounds of sensible variability in sensitivity are exceeded. I would claim Axe’s procedure does not exceed reasonable bounds of sensitivity.

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You have no idea if that is true.

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I’m not sure what you mean in your challenge here, we wouldn’t sample variable regions for activity, we would instead check the whole enzymes for function, correct?

It’s actually low, by design, in order to favor the Darwinian view, as Axe said: “Having understood this, we now see that Objection 3 has things inverted. In the work described in the 2004 JMB paper, I chose to apply the lowest reasonable standard of function knowing this would produce the highest reasonable value for P, which in turn provides the most optimistic assessment of the feasibility of evolving new protein folds. Had I used the wild-type level of function as the standard, the result would have been a much lower P value which would present an even greater challenge for Darwinism. In other words, contrary to Objection 3, the method I used was deliberately generous toward Darwinism.”

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I do have reason to believe that, the reviewers thought his threshold was reasonable, for one. And a lot of discussion here has not resulted in showing how this is false.

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Like I said you have no reason to believe it is true. I bet Axe knows it’s not true, though. That’s why he has stayed silent on the question for seven years.

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[quote=“lee_merrill, post:385, topic:17458”]

You’re not sure what anyone means here, particularly Axe.

No, we would, in the context of the constant immunoglobulin regions flanking them. The variable regions are the ones selected and refined to bind antigens. They are a pool of random sequences.

We would check the immunoglobulin chains for enzymatic function. We already know the constant regions lack beta-lactamase activity, so any activity would come from the variable regions.

Axe’s extrapolation makes a crystal-clear prediction, as does your claim that he was telling the truth about his silly binary assay. You seem to lack faith in Axe here. Why?

Axe lied. There’s a simple way to assess Axe’s veracity. How much money would you be willing to bet?

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This is Axe’s claim. Is it true, Lee?

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It is obvious.

You are claiming both that birds can have new systems (penguins) and that something that is a bird can’t have new systems (honeycreepers). Even though you seem to have no idea what honeycreepers are.

Your ignorance is obvious, your double-standard is obvious, your hypocrisy is obvious, your goalpost-shifting is obvious, your evasion is obvious and your dishonesty is obvious.

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I have read that section of Axe’s post several times, and I honestly cannot see any coherent argument there. If just seems like a bunch of bafflegab. I don’t mean it is an argument that commits a logical error or two, or misstates a couple facts. It just comes across like the Chewbacca defense:

What am I missing?

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I don’t think you’re missing anything. It really is nonsense.

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I don’t think you’re missing anything. To me it reads like skilled obfuscation. And I’ve really tried my best to give it as charitable an interpretation I can come up with.

When he writes that he set up the experiment “to favor Darwinism”, and I then look at what happens in his experiment, to give him a charitable interpretation I have to ignore that he claims that, because the two don’t square.

When he writes that using TEM-1 would have made the results worse for evolution, I can’t make sense of that. Trying to imagine he did the experiment with TEM-1, at the ~10 ug/ml MIC of the temp-sensitive enzyme, would unavoidably have given a more favorable result to evolution. The TEM-1 enzyme is more resilient than the temp-sensitive version he made. He would have unavoidably found higher per-position tolerance to mutation over 38%.

So what could he mean instead? Well maybe he means that, had he used the TEM-1 at it’s own MIC of ~5200 ug/ml, that would have produced a per-position tolerance to mutations that was less than 38%? But he has no basis for claiming that. Such a result is not reported anywhere in his paper, and it’s not clear why wild-type TEM-1 would be more sensitive to mutations at ~5200 ug/ml, than the temp-sensitive enzyme would be at ~10 ug/ml. That’s why I say the most generous interpretation I can give him is that his claim is without basis. Baseless.

In that case, what Axe should have said had he been honest, was that “It’s not clear that using wild-type TEM-1 instead of my temp-sensitive enzyme, under equally stringent conditions, would have made the result better for evolution.”

But that’s not what he says. He claims it would be worse for evolution, and then gives his analogy to explain why. But if his analogy had any basis in fact, it would instead just mean that the result we got would be invalid. That if we had used wild-type TEM-1 at the temp-sensitive MIC, we would (according to Axe) have produced a result that implied the enzyme could tolerate more mutations than it actually could. That we would have obtained a result that merely looked more favorable to evolution, but would be produced through an invalid experiment.

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He does explain that. Because his method of “scaling up” errors in a phrase produced a serious overestimate of the number of legible alternatives he has to compensate by inventing the arbitrary rule that any variant that performs worse than the start version should be rejected. Which makes no sense but it’s what he says.

Following that rule - which doesn’t really address the problem he identified - if he started with TEM-1 he’d “have” to reject any mutant version that didn’t perform as well as TEM-1. Therefore starting with a lower performing variant supposedly favours “Darwinism” because it lowers the threshold of functionality.

The idea that he should just have chosen a more sensible method of “scaling up” apparently didn’t occur to him.

The whole thing really is nonsense. Whether Axe believes it or is cynically counting on the extreme gullibility of ID supporters is impossible to say. Either discounts him as anyone worth talking to in the issue.

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That’s fine, but it seems easier to just check the enzyme as a whole, instead of delving into the active parts, and testing them individually. Like the diffusion test with antibiotics, the researchers don’t pick the bacteria apart, and test the pertinent pieces.

Because it’s defensible? I’ve explained again and again why a binary assay does seem reasonable, and calling his assay silly is not a refutation.

Please explain. And I’m not here to get rich…

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Yes, I think I can see why he said that.

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No, that’s not what I’m saying. I hold that some birds can have new systems, and that the various honeycreepers, don’t. And I did look up honeycreepers, to know what they were.

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Why would the P value be lower? Explain.

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Thank you for addressing Axe’s points! And I think he meant what you described in your previous paragraph: “Trying to imagine he did the experiment with TEM-1, at the ~10 ug/ml MIC of the temp-sensitive enzyme, would unavoidably have given a more favorable result to evolution. The TEM-1 enzyme is more resilient than the temp-sensitive version he made. He would have unavoidably found higher per-position tolerance to mutation over 38%.”

Why do you reject that as his meaning? And then propose different scenarios, and reject them?

No, his analogy is to show that the results would be skewed if he had used the wild-type variant: “The remedy is to use a different starting sequence. Specifically, we need the starting sequence to be of the same quality that we intend to require of mutant sequences in order for them to be accepted. Otherwise the mismatch in quality will skew our results.”

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Once again, Bechly’s implied definition is incompatible with the one you found on Wikipedia. You don’t seem to get this. Anyway, what organs do whales have that cows don’t?

Two main problems here: first, it’s not a body plan transition under the definition you have just presented. Second, there is nothing to show that the transition happened in the time period Bechly claims.

I suppose there’s a third too, that the transition didn’t happen all at once as Bechly’s ideas of saltation would see to require, since there are many intermediate fossils, which he for some reason fails to mention.

And we’re left to find a definition of “body plan” under which this is true, even ignoring the part about the timeframe.

Under what definition of “body plan” do all birds have the same, especially if penguins are claimed to be different?

How can you consider flippers to be new limbs, when they’re just wings stripped of flight feathers? Aren’t they, if anything, just slightly modified limbs? And yet you consider the beaks of palila and akiapola’au (and, I suppose also, eagles and flamingos) to be the same.

So which is true? DI misrepresented what Bechly said, or Bechly contradicted himself?

You addressed nothing.

Try harder.

It’s not clear what you mean by this or how it relates to whales or penguins. Once more: the Wikipedia definition applies to phyla. Under that definition all mammals, in fact all vertebrates, have the same body plan. How can you reconcile this with Bechly’s claims?

So it’s not an argument. No, a question isn’t a counterargument. Nor was it a valid reply.

Why should the easier approach always be taken?

Why don’t you check with them? And perhaps it’s late to ask, but why should we care?

That’s because you don’t understand it. You’re just googling until you find a snippet that, free of all context, seems to work for you. Nobody says our knowledge of the tree is yet perfect or that there aren’t exceptions, including horizontal transfer, hybridization, and incomplete lineage sorting. But the big picture is of a single tree with some local exceptions. What it most certainly is not is a forest of separate, unrelated “kinds”.

Another snippet. I would agree with the addition of one word: “defies its complete representation by a simple bifurcating phylogeny”. As I said, there are local exceptions, but that doesn’t obscure the general picture. You will note that your snippet is part of the introduction to a journal issue that features various sorts of progress and advances in recovering the actual tree of life, or various bits of it.

No, but we’re done enough to spot the pattern, which is universal common descent. There are no separate “kinds”. If there were, they should have been easy to identify. Bet you can’t identify just one.

Didn’t you read the parts where I told you there were lots of intermediates?

Is it? But of course the Cambrian explosion was considerably longer than that.

You understand that the name was applied long before we had a detailed idea of its length, right?

Great. What’s your evidence for this? And what sort of miracles do you mean? Separate creation, de novo, ex nihilo? Doesn’t fit the data and silly even theologically.

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Because Axe says this:

A much lower P value.

Why does Axe think the P value would be lower? He doesn’t here say invalid, he says lower. Much lower. Why would he say that?

He also says his results “Favor Darwinism”, also implying using TEM-1 would have produced a result with a lower P-value. But he then goes on to argue, with his analogy, that the results would have produced a misleading result.

These statements are in contradiction with each other.