Did Douglas Axe Disprove Evolution? Spoiler: No

[Rumraket (Mikkel R.)]

@lee_merrill

A quick Google search however, turned up Douglas Axe’s reply:

“the final two paragraphs of the discussion focus on what this value means for the evolution of new protein folds, concluding with this critique of the evolutionary model: “generating new folds from parts of old ones may be much less feasible than has been supposed.” [1]

Axe, in attempting to defend his 2004 paper against this objection (the objection that new proteins can evolve from parts of old ones), cites [1] which is … his 2004 paper.

I’d hate to play chess with Axe. “When your queen threatens my king, he just shoots a laser at her! Checkmate evolutionists!”

Well let me cite this post I wrote on a 2019 dissertation exploring this exact question to see if Axe 2004 somehow shows that generating new functional proteins from parts of other already functional proteins is “much less feasible than has been supposed”:

Protein chimeras are evidence against ID claims!

Here’s a small snippet:

Rather, given that Axe’s work is once again being cited and is doing the rounds in ID-creationist circles, I thought this would be as good a time as any to visit some work in experimental molecular biology that massively contradicts Axe’s number. And to not beat around the bush too much, we’re talking a 72 order-of-magnitude discrepancy between Axe’s frequency of 1 in 10⁷⁷ and what other experiments in probing protein sequence space reveal.

I will give an account of experiments done to probe a particular process of novel protein evolution, called gene fusion, which turned out to be able to find functional proteins at a rate of 1 in 3.3×10⁵. To put the magnitude of the discrepancy into context, it’s 1 followed by 72 zeroes, which is a number that seems to fit in the arena concerning things like the number of atoms in the observable universe (estimated at ~10⁸⁰). Quite a margin of error!

So we go from Axe estimating that new functional proteins require searching 10⁷⁷ on average before we find a single new one. And then an experiment using randomly fusing fragments of already existing proteins finds new functional ones at roughly 1 in ~300 000.

@lee_merrill

According to Hunt, I “molded a variant that would be exquisitely sensitive to mutation.” [2] Venema expressed the same concern, that the starting sequence I used was “intentionally ‘hamstrung’ with multiple mutations to render it far less functional than its natural counterpart.” [7]

Both Hunt and Venema seem to think the outcome would have been more favorable (i.e., functional sequences would have been more prevalent) had I used the highly proficient natural enzyme as a starting point rather than the handicapped version. Actually, as a demonstration will show, the opposite is true.”

This one is ridiculously false. Axe uses the example of a readable sentence to try to demonstrate this, which is so confused it’s difficult to resist the interpretation that he wrote it to obfuscate.

So let’s just correct his laughably inept example right here in a way that should be immediately comprehensible to any rational person that wants to understand.

So first of all, to calculate his final number, Axe calculates the “pass rate” (fraction of substitutions tolerated at a typical position) of his temperature sensitive enzyme mutants, raised to the 153th power (length of protein), multiplied by some hydropathic signature factor (which he estimates at 10-13), to get to his 10^-77 number.

In his experiment, using the temperature sensitive enzyme, he averages the pass rates for each segment and calculates the fraction of substitutions tolerated at a typical position to be 0.38.

So it’s 0.38¹⁵³ × 10^-13 = 10^-77

So the key number is 0.38. That’s the one his temperature sensitivity directly affects. By making it more sensitive to temperature, he has already mutated it, and made it less tolerant of further mutation. With this as the basis for his experiment he finds that 38% of substitutions at a typical position can still be tolerated and gives a functional enzyme.

He took the wild type sequence, which we can like Axe demonstrate with a sentence.
The “wild-type” sentence:
Did Douglas Axe Disprove Evolution? Spoiler: No

Then he created a highly degraded one that can barely even be read:
Dxd DoNglfs Ake Dispvuge EVolTtijn? SGoilah: No

I now pose the question: Which sentence can tolerate the most mutations before it entirely stops working - the wild-type, or the already mutated one?

This is like asking: What would be the passe rate for the wild-type enzyme? Would it be higher than 0.38, or lower than 0.38?

Had he not used the already degraded version, what per-position fraction of random mutants of the wild-type sentence would have retained readability?

Any thinking person can immediately see that the wild-type sequence should have a higher pass rate. More than 0.38. The already degraded, already mutated one can barely take any more before readability disappears entirely.

For forks sake, just think! Already mutating the wild-type sequence is how he got the temperature sensitive variant to begin with. He has already thrown mutations at the enzyme he uses in his experiment but doesn’t factor that into his calculation.

Even if we cannot by reason alone know how much higher than .38 that number would be if we used the wild-type sequence, we can see immediately just by looking at the sequences that obviously the wild-type sentence can tolerate more substitutions and retain readability.

Axe lies about what the result would be if he had used the wild-type protein in his experiment. It would NOT have made the result worse. That’s a BOLD FACED LIE and his explanation that purports to show this is deliberate obfuscation.