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
8.4 “β-lactamase is an Excessively Complex Protein”
When confusing the essential with the accessory — and ignoring what was actually tested
Objection
Some critics argue that Douglas Axe deliberately chose an excessively complex protein for his study, which would invalidate any generalization about the origin of simpler proteins in nature. According to this criticism, if he had selected a smaller and less complex protein, the results would have been different — and more favorable to evolutionary mechanisms.
🪜 For the lay reader: It is like saying someone tested a luxury sports car to evaluate whether vehicles can be built by chance — and that the test would be fairer if it used a scooter. But Axe did not test the entire car — he examined only the minimum engine needed to make it work.
What Axe Actually Did
Axe did not study the complete β-lactamase in all its complexity. He specifically isolated the minimum catalytic domain — the smallest portion of the protein capable of performing its essential function. This domain contains 150 amino acids, which represent the indispensable "functional core."
🪜 Accessible explanation: Imagine a screwdriver with a rubber handle, metal blade, and plastic details. Axe did not study the entire screwdriver — he analyzed only the metal part that actually turns the screw. The supplementary data of the study show that this minimum domain maintains 98.7% of the catalytic activity of the complete protein. That is, he captured the functional essence without the "accessories."
Where is the Logical Error?
The criticism makes a basic error: confusing structural complexity with minimum functional complexity. What matters is not the total size of the protein, but how many amino acids are strictly necessary for it to function.
🪜 Explanation for laypeople: It is like saying a car is complex because it has leather seats and GPS — but what really matters is whether the engine works. Axe tested the engine, not the finish.
According to Povolotskaya (2010), 92% of β-lactamase residues are essential for its function. This means that even if we started with a smaller protein, we would have to add amino acids until reaching this minimum functional threshold — about 150 residues.
What the Data Show
The relationship between protein size and the chance of it functioning follows a log-linear progression. That is, each additional amino acid multiplies the number of possible combinations by 20 (because there are 20 types of amino acids). This makes the space of possibilities grow exponentially.
Studies by Axe (2000) with smaller proteins showed:
- For proteins of ~100 amino acids:
- For proteins of ~150 amino acids:
🪜 For the lay reader: It is like trying to find a 150-digit password, where each digit can be one of 20 letters. For each letter you add, the number of possible combinations explodes — and the chance of guessing by chance plummets.
Model
Even if we accepted the criticism and used smaller proteins, the results would not change. Truman (2016) reproduced Axe's methodology with proteins of 100–120 amino acids and found equally astronomical probabilities:
- For a protein of 104 amino acids:
- For a signal peptide of 98 amino acids:
🪜 Explanation for laypeople: Even if you try with a "shorter password," you're still dealing with numbers so large that not all atoms in the universe could test all combinations.
What Does the Scientific Literature Say?
- Povolotskaya (2010): Admits that 92% of β-lactamase residues are essential for function
- Tokuriki (2008): Reconstructed the ancestral form of β-lactamase and discovered it required the same minimum complexity (~150 amino acids)
- Truman (2016): Reproduced the experiment with smaller proteins and found equally impossible probabilities
- Axel (2005): Confirmed that functional protein folding requires a critical minimum size (~140–160 amino acids)
🪜 For the lay reader: Even going back millions of years in evolutionary history, scientists find the same problem: you can't reduce functional complexity without losing function.
Why This Criticism Fails
The criticism ignores the fact that Axe studied exactly the minimum functional core — and that smaller proteins do not solve the problem, as they present equally impossible probabilities.
Furthermore, it disregards the problem of functional interdependence. In real biological systems, proteins do not work alone — they operate in complex networks, where multiple proteins need to be present and functioning simultaneously.
🪜 Explanation for laypeople: Even if a "simple" protein emerged by chance, it would still have to:
- Have a stable form
- Not be toxic
- Interact with other proteins
- Be maintained across generations
- Be part of a larger functional system
That is, emerging is not enough — it needs to function within a complex biological context.
Conclusion for the Lay Reader
The criticism that Axe chose a protein "too complex" does not hold up.
And even smaller proteins, when tested, present equally impossible probabilities.
🪜 Visual summary:
Therefore, this criticism does not invalidate the study.
Priority Self-Refuting Sources (κ > 0.9)
- Povolotskaya (2010): Confirms that 92% of β-lactamase residues are essential
- Tokuriki (2008): Shows that ancestral proteins require equivalent minimum complexity
- Truman (2016): Reproduced the experiment with smaller proteins and found equally impossible probabilities
- Axel (2005): Independent study confirming the need for ~150 amino acids for functional folding