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Proteins Are Rare and Isolated — And Thus, Cannot Evolve

Photo: Curiosity rover on Mars, by NASA/JPL-Caltech/MSSS.

Were the laws of physics and chemistry fine-tuned to allow proteins to evolve easily? This claim is a key element in a conception of design advocated by theologian Rope Kojonen. He believes, in effect, that God designed the laws of nature so that proteins and other biological phenomena can evolve. In a previous post, I discussed an article, “On the Relationship between Design and Evolution,” that I wrote with Stephen Dilley, Casey Luskin, and Emily Reeves. Both in the article and in a series at Evolution News, we have been critiquing Kojonen’s book The Compatibility of Evolution and Design, which argues that evolutionary theory can be reconciled with the belief that life demonstrates evidence of design. Here, I will expand my previous argument about proteins, showing functional proteins are rare and isolated — and thus, cannot evolve. If my account is correct, then Kojonen’s view of design is fatally flawed.

The Relationship Between Rarity and Isolation

Kojonen acknowledges that many proteins correspond to such rare sequences that they could not have emerged through a random search. Yet he argues that rarity does not necessarily entail isolation. We summarize the argument as follows: 

Like Kojonen, other thinkers (e.g., Hunt 2007; Venema 2010; Matheson 2010) have argued that rarity in sequence space does not necessarily imply isolation in sequence space to a degree that would pose a barrier to evolution. This line of thinking accepts (or allows) a continuous path of functional sequences from a simple protein to a more complex protein. Under this view, even if proteins are rare, they are (or could be) clustered together. As such, the mutation-selection mechanism would not need to search a large region of sequence space; it would only need to find the continuous pathways close at hand.

A Spacecraft Seeks a Clear Path

We respond to this argument as follows:

Yet a simple analogy shows why this objection is wrong. Imagine a spacecraft lands on the north pole of a planet, and the astronauts wish to drive to the south pole. Their ability to do so depends on the percentage, p, of the planet’s surface that is navigable. If p is 70.0%, a continuous path likely exists between the poles. If p is 0.1%, a path most likely would not exist. The lower the percentage, the less likely a path.

Let us now consider how this analogy would apply to the evolution of new proteins. The rarity of the beta-lactamase domain studied by Axe (2004) would correspond to a planet the size of our entire galaxy, and the total amount of navigable land would correspond to the surface area of an atom. If we extend our analogy to a protein whose rarity is 1 in 1023, this would still be akin to a planet the size of Jupiter with a total area of traversable land the size of a postage stamp. A navigable path from one pole to the other would almost certainly not exist. In other words, even for the protein that Kojonen claims has a sequence probability that is “more common”, the possibility of a continuous functional path leading from it to a typical protein is exceedingly remote. 

Complex proteins appear to be overwhelmingly isolated, including from simple amino acid sequences that can perform basic functions. Collectively, the data show that proteins of typical complexity are beyond the reach of natural selection, random mutation, and other standard evolutionary mechanisms.

Could the laws of physics have been fine-tuned to enable such narrow paths? It seems not:

Kojonen tries to overcome this problem by arguing that the physical properties of proteins are “finely-tuned” to bias the clustering of functional sequences such that a very narrow path could extend to complex proteins with rare functional sequences. The biasing would result in the prevalence of functional sequences along a path to a new protein being much higher than in other regions of sequence space. But such biasing could not possibly assist the evolution of most proteins. Biasing in the distribution of functional sequences in sequence space due to physical laws is arguably subject to the same constraints as the biasing in play in the algorithms employed by evolutionary search programs. Consequently, protein evolution falls under “No Free Lunch” theorems that state that no algorithm will in general find targets (e.g., novel proteins) any faster than a random search. An algorithm might assist in finding one target (e.g., specific protein), but it would just as likely hinder finding another. Thus, although Kojonen acknowledges that proteins are sometimes too rare to have directly emerged from a random search, he fails to appreciate the extent to which rarity necessitates isolation and why this must often pose a barrier to further protein evolution. Different proteins have completely different compositions of amino acids, physical properties, conformational dynamics, and functions. Any biasing that might assist in the evolution of one protein would almost certainly oppose the evolution of another. In other words, the probability of a continuous path leading to some proteins would be even less likely than if the distribution of functional sequences were random.

Rare Functional Sequences Entail Isolation

We summarize our general argument as follows:

In the end, evolving new proteins is quite difficult to envision under known laws of nature. This is because a continuous path of functional sequences in sequence space is not plausible — primarily due to both the rarity of functional sequences and the isolation of proteins with entirely different structures and functions. A key point here is that extremely rare functional sequences entail isolation in sequence-space. This hurdle poses a fundamental challenge to Kojonen’s thesis that nature was designed to evolve life. Proteins, like stars, are separated by vast distances. 

Recall that Kojonen’s model holds, in effect, that God designed the laws of nature so that proteins can evolve. This is a key element of Kojonen’s design hypothesis. This hypothesis is testable: is there empirical evidence that known laws of nature allow for proteins to evolve? Or do the data indicate impassable hurdles between functional proteins? The data clearly favor the latter. Functional proteins sequences are rare and isolated, with vast chasms of non-functionality between them.

The unavoidable connection between protein rarity and isolation not only overturns Kojonen’s thesis about design, but also overturns mainstream evolutionary theory in its entirety. Although our primary target is Kojonen’s account of design, the scientific data clearly raise additional troubling problems for evolution.