A Response to David Gelernter’s Attack on Evolution

Let’s not even get to evidence and conclusions. Let’s start with his assumption–that stability is pretty much equal to function.

Do you believe that, Curtis? Where’s the evidence?

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Not a given protein, a given function.

We know that at such regions are frequent, given catalytic antibodies, which routinely find specific functions in sampling only 10^8 clones.

But you haven’t addressed those >5000 papers and their data. Why do you act like they don’t exist?

Indeed, but Doug Axe didn’t bother to measure enzymatic activity, which would have showed which of his mutants had low activity.

Since you are aware of this, how can you credibly claim that Axe’s work is generalizable, while ignoring catalytic antibodies?

Oh really Brian? That’s demonstrably false. What impression are we to gather from the following?

You write:

Indeed, Harvard mathematical biologist Martin Nowak has shown that random searches in sequence space that start from known functional sequences are no more likely to enter regions in sequence space with new protein folds than searches that start from random sequences. The reason for this is clear: random searches are overwhelmingly more likely to go off into a non-folding, non-functional abyss than they are to find a novel protein fold. Why? Because such novel folds are so extraordinarily rare in sequence space. Moreover, as Meyer explained in Darwin’s Doubt , as mutations accumulate in functional sequences, they will inevitably destroy function long before they stumble across a new protein fold. Again, this follows from the extreme rarity (as well as the isolation) of protein folds in sequence space.

Recent work by Weizmann Institute protein scientist Dan Tawfik has reinforced this conclusion. Tawfik’s work shows that as mutations to functional protein sequences accumulate, the folds of those proteins become progressively more thermodynamically and structurally unstable. Typically, 15 or fewer mutations will completely destroy the stability of known protein folds of average size. Yet, generating (or finding) a new protein fold requires far more amino acid sequence changes than that.

Your claim is that one protein superfamily can’t evolve into another protein superfamily by accumulating mutations, because you apparently think after 10-15 mutations the protein would become unstable and fail to function. And you reference Tawfik’s work to try to substantiate that point.

But his work doesn’t show that. On the contrary, it shows that under purifying selection it can continue to change while retaining function.

And then there’s another issue with your claim that one protein superfamily can’t change into another protein superfamily by this kind of incremental accumulation of amino acid substitutions. The issue is that it is a straw-man. Nobody claims they did. Biologists simply do not claim that the different superfamilies evolved into each other. Tawfik even states exactly that, when he says [speaking of structurally distinct superfamilies]: “… so basically we have no knowledge of how these are related, if at all.

That’s before we even start to consider your mistaken conflation of protein stability and protein function.

No he doesn’t. At no point in the talk does he say that enzymes “can only evolve within the confines of the same structure or architecture for the active site”. That’s just flat out false.

So I really think it’s you who should bother to watch Dan Tawfik’s presentation.

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And this false conflation is biophysical and biochemical, completely independent of whether these proteins evolved or were designed.

Where did you get this false assumption, @bjmiller?

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I’ve done it with a single substitution.

No, I’m not sure where you got the impression that I might.

I don’t see reasonable evidence supporting this position. I agree with you and @Rumraket on this particular issue.

My point was that stating @bjmiller is lying when he makes claims that we disagree with isn’t conducive to productive conversation.

I completely understand the frustration. Prior to this thread, @bjmiller has a track record here of dropping a few paragraphs of opinion (that I believe is unsupported by evidence) and disappearing again for months without dealing with any sort of contradictory evidence and argument. But accusations of lying go out of the boundaries of reasonable discussion.

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“Some time ago, paleontologists tried to explain the absence of soft-bodied ancestors in pre-Cambrian sediments as artifacts of preservation. No longer. This hypothesis has been refuted by evidence from fossil sites of the Burgess Shale type in Mongolia and China. They yielded nothing but fossil algae.”

This is a vomit inducing argument. Because one type of organism in one environment fossilized doesn’t mean therefore all soft-bodied organisms with fossilize. What preserves on type of remains may not preserve others. I mean this is taphonomy 101. And on top of that, the molecular evidence does suggest it’s an artifact of preservation.

But really, I’ve worked on fossils that are missing verts, phalanges, etc. Am I supposed to conclude that these specimens just have less verts than other specimens? I mean the others fossilized. Why didn’t these? That’s the kind of absurdities this argument leads to @bjmiller.

Also, why do you vanish during one conversation and then come back and start another one without finishing the previous one?

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Probably. Because they do this over and over and over.

These guys really know nothing about paleontology. They keep flaunting a 40-46 million year old basilosaurid as 49 million years old and are arguing that means evolution only had one million years to achieve that transition because Pakicetus comes in at around 50 mya. But NO ONE thinks Pakicetus is the oldest Pakicetid. NO ONE. There is just one problem. There are no Indian Paleocene mammal localities. There is no where to look for them! ID folks don’t know this. Or how to find and access localities. It’s hard not to laugh at them sometimes.

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Yeah that really makes no sense. So you find a fragmentary mammal fossil, and you’re supposed to conclude that was the total animal? Once upon a time, a mammal consisting of a jaw, a few ribs and vertebrae, and a toe, walked around? Oh gee I guess since the third rib didn’t fossilize, I can’t infer it ever existed?

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https://www.cell.com/current-biology/fulltext/S0960-9822(15)01177-X?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS096098221501177X%3Fshowall%3Dtrue

From the paper:
“The results of our study—which integrates fossil and molecular evidence to establish an evolutionary timescale—suggest that the Cambrian explosion is a phenomenon of fossilization, while biological diversity was established in the Neoproterozoic. Integrating all of the sources of uncertainty that we explore (Figure 6, Table 1) allows us to conclude that crown Metazoa originated 833–650 Ma, fully within the Cryogenian, while the component clades of crown Eumetazoa (746–626 Ma), crown Bilateria (688–596) Ma, crown Deuterostomia (662–587 Ma), and crown Protostomia (653–578 Ma) all diverged within a Cryogenian to early- or mid-Ediacaran interval.

The results of our analyses leads us to reject the hypothesis that metazoans, eumetazoans, bilaterians, protostomes, deuterostomes, ecdysozoans, lophotrochozoans, or, for that matter, any of the component phylum-level total groups, originated in the Cambrian.”

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What is the basis of your authority over Brian?

The argument from bad design. @swamidass would probably not be impressed by this.

One of the largest disconnections between theory and observation is the assumption that highly coordinated, specified changes in evolution could occur without coordinated, specified mutations. For instance, vocalization in humans and songbirds demonstrates remarkable similarities, including the reengineering of genes with the same amino acid substitutions. Therefore, major transformations do require specific, coordinated mutations:


Another example is the needed specificity in evolving new structures. For instance, the generation of a vertebrate lens requires an entire genetic network to direct its development.


The network requires highly specific changes. For instance, a gene launches multiple other genes through a specific transcription factor binding to TF binding sites in specific genes.

Bechly seems to think it’s anagenesis or bust for some reason

And punctuated anagenesis at that.

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My ability to read the paper Brian has incorrectly referenced multiple times. Read the post where I explain this Bill. It’s been linked.

Your “therefore” doesn’t actually follow. Straight up non-sequitur.

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Seem to misrepresenting this paper.
They say:
“This made the problem of the Cambrian Explosion even more acute: 550 million years ago there were no animals at all, and 537 million years ago there were already fully developed crown-group arthropods like trilobites with sophisticated compound eyes, exoskeletons, and articulated legs. Does anybody seriously believe that such an enormous transition within 13 million years is a piece of cake? Gelernter is right to be skeptical, and mainstream science supports his arguments.”

From the paper they cite:
These constraints come from the trace fossil record, which show the first evidence for total group Euarthropoda (e.g., Cruziana , Rusophycus ) at around 537 Ma. A deep Precambrian root to the euarthropod evolutionary lineage is disproven by a comparison of Ediacaran and Cambrian lagerstätten. BSTs from the latest Ediacaran Period (e.g., Miaohe biota, 550 Ma) are abundantly fossiliferous with algae but completely lack animals, which are also missing from other Ediacaran windows, such as phosphate deposits (e.g., Doushantuo, 560 Ma). This constrains the appearance of the euarthropod stem lineage to no older than 550 Ma.
So are they just ignoring the existence of stem Euarthropods? They certainly were around 550mya. They are making it sound like nothing then all the sudden crown groups.

Also, I disagree with a lot in that paper they cite.

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So your opinion is you understand the material better than Brian does. That does not mean he is wrong. You are labeling him as being wrong yet it is just your opinion.

Also, I’m a little behind on Cambrian dating but isn’t 550ma Precambrian… soooo