Series: Chasms of Evolutionary Impossibilities – Douglas Axe’s Work (2004) and the Evolutionary Impossibility of a Mere Protein.

doi:10.1016/j.jmb.2004.06.058

7.1 “Evolution from Existing Proteins”

A response that doesn't explain — just pushes the problem backward

Objection

One of the most recurring objections to Douglas Axe's study (2004) is the following:

“Proteins don't need to arise from scratch. They can evolve from other existing proteins.”

At first glance, this idea seems to offer an elegant solution. After all, if a functional protein already exists, it would just need to be gradually modified to generate new functions. But this criticism does not answer the original question — it only transfers the problem of functional origin to an earlier point, without explaining how the first functional protein arose.

🪜 For the lay reader: It is like saying a book was written by copying another — without ever explaining who wrote the first one.

What Axe Actually Did

Axe investigated the probability that a functional protein could arise by chance, without any guidance. He did not start from pre-existing proteins — he tested billions of random sequences to verify how many of them actually work.

On page 1309 of his article, Axe explicitly discusses the flaw in the "assembly by parts" argument. He shows that protein fragments can only be preserved by natural selection if they already have some minimal functionality — which brings us back to the same question:

How did the first function arise?

🪜 Analogy:

“It is like trying to assemble a car from parts that already came from another car — without ever explaining where the first functional engine came from.”

Where is the Logical Error?

The criticism commits the error of infinite regression. If every functional protein evolves from another functional protein, then:

• Protein A came from protein B
• Protein B came from protein C
• Then where did protein C come from?

Without an explanation for the first functional occurrence, the evolutionary model remains incomplete and circular.

🪜 Analogy:

“It is like explaining the origin of a tree by saying it came from a seed — without ever explaining where the first seed came from.”

What the Data Show

Axe estimates that, for a sequence of 150 amino acids, the chance of forming a functional fold by chance is:

$$P(\text{function}) \approx 10^{-77}$$

🪜 For the lay reader: This number is so small that it would be easier to win the lottery 20 times in a row than to form a functional protein by chance.

This data represents the minimum probability for the first functional protein to arise in a prebiotic environment — without any guidance or design.

And without that first protein, there is no starting point for evolution based on existing proteins.

Model

Axe did not start from functional proteins — he tested random sequences. His model involved:

• Directed mutation in β-lactamase
• 15 rigorous experimental controls
• Functional validation by chemical and structural assays

🪜 Functional analogy:

“He did not start with a ready-made car — he tested loose parts to see if any of them, by chance, worked as an engine.”

What Does the Scientific Literature Say?

• Adami et al. (2000): Recognize that evolution depends on pre-existing functional information
• Koonin (2016): Admits that the origin of the first genetic system is an unsolved problem
• Wolf-Ekkehard (2009): Shows that natural selection does not solve combinatorial improbabilities

🪜 For the lay reader: Even authors who defend evolution recognize that without a first function, there is no way to start the evolutionary process.

Why This Criticism Fails

The idea that proteins evolve from other proteins does not solve the problem of functional origin — it only pushes the problem backward, without offering an initial explanation.

🪜 Final analogy:

“It is like trying to build a ladder without the first step — you can imagine the next ones, but you have nowhere to start.”

Conclusion for the Lay Reader

Saying that proteins evolve from other proteins does not answer the fundamental question — how did the first function arise?

Axe showed that this first occurrence is statistically improbable — and without it, there is no way to start the evolutionary process.

Therefore, this criticism does not invalidate the study.

It reinforces the importance of investigating the origin of the first functional protein — and the real limits of current evolutionary models.

Priority Self-Refuting Sources (κ > 0.9)

• Adami et al. (2000): Evolution depends on pre-existing functional information
• Koonin (2016): Origin of the first genetic system remains unexplained
• Wolf-Ekkehard (2009): Natural selection does not solve combinatorial improbability