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To Create Functional Proteins,  Evolution Would Need a Miracle

Image credit: Debstar, CC BY-SA 3.0 , via Wikimedia Commons.

Theologian Rope Kojonen claims that God designed the laws of nature, which then gave rise to “fine-tuned” preconditions and smooth fitness landscapes. He says, among other things, that these conditions allow proteins to evolve by natural processes. Is he right?

At Evolution News, philosopher Stephen Dilley has already written two articles in a series (here) introducing an evaluation of Kojonen’s argument. Dilley summarized his contribution to a review article he wrote with Casey Luskin, Emily Reeves, and myself titled “On the Relationship Between Design and Evolution,” in the peer-reviewed journal Religions. In the article we critique 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. Dilley commended the book for the sophistication and comprehensiveness of its philosophical arguments. 

However, Dilley noted that the viability of Kojonen’s thesis depends on the scientific details. Even though the proposal is primarily a philosophical analysis, its strength or weakness hinges largely upon empirical evidence. As we state in our article:

It is true that KEBDA [Kojonen’s evolution-friendly biological design argument] is a philosophical argument. And, of course, the conceptual and epistemological elements of the argument are important. But some philosophical arguments also depend in part upon scientific evidence. In this case, much depends on whether there is a good case for fine-tuned preconditions and suitable fitness landscapes (as Kojonen envisions them). Indeed, Kojonen situates design precisely in those fine-tuned preconditions which yield smooth fitness landscapes that allow evolution to succeed. His case for marrying design with evolution therefore depends on the existence of this fine-tuning. So, it is crucial to assess whether this fine-tuning is real. And this question can be assessed scientifically: are fitness landscapes smooth? Are there open pathways between functional proteins, for example? Or are there impassible barriers between such proteins?

Thus, to assess Kojonen’s conception of design (and its compatibility with evolution) involves careful empirical analysis of “preconditions” and fitness landscapes. We examine Kojonen’s account of these phenomena, especially his claim that preconditions and landscapes are set up to allow proteins to evolve.

Kojonen’s Argument

We summarize Kojonen’s argument as follows:

To his credit, Kojonen acknowledges that the weight of empirical evidence affirms that functional proteins are often exceptionally rare — an exceedingly small percentage of amino acid sequences in sequence space fold into complex three-dimensional structures that can perform biological tasks (Kojonen 2021, pp. 119–20). (Sequence space is the multidimensional map of all possible amino acid sequences.) Finding a viable protein sequence is akin to finding a needle in a haystack. Yet Kojonen then argues that protein rarity is not a barrier for evolution because functional proteins are sufficiently close to each other in sequence space such that one protein could plausibly transform into another. He argues that, because of the fine-tuning of natural laws, there are otherwise unexpected functional pathways through sequence space to link up functional amino acid sequences such that one protein sequence could traverse to another through sequence-space via evolutionary mechanisms. Proteins might be rare, but they are not isolated. There is a proverbial cluster of needles lumped together in the haystack: when one is found, another is close at hand.

Andreas Wagner’s Contribution

Kojonen justifies this assertion by citing the research of Andreas Wagner and his team. Wagner claims to have demonstrated that every protein can evolve into another protein through a limited number of mutations. In addition, every protein in biology is interconnected through a continuous series of traversable steps.

We respond as follows:

Yet Wagner’s research is significantly limited. In particular, Wagner never directly studied the feasibility of one protein evolving into another. Instead, he compared the metabolic pathways of different organisms and identified enzymes (a type of protein) that are present in multiple pathways, and he also identified enzymes that are missing (Rodrigues and Wagner 2009). In addition, Wagner studied how mutations can change the regulatory regions of proteins to alter when (and to what extent) proteins are expressed (Aguilar-Rodríguez et al. 20172018). Wagner argued that such changes could direct proteins to enter or leave metabolic pathways. But he did not study the more fundamental question of the plausibility (or implausibility) of the evolutionary origin of proteins in the first place. 

To be sure, Wagner has performed notable research that bears some (limited) relevance on protein evolvability. For example, in addition to the studies above, he surveyed numerous proteins’ relative locations in sequence space (Ferrada and Wagner 2010). He identified which proteins with the same structures perform different functions and which functions could be performed by proteins with different structures. He also tallied the functions performed by proteins in pairs of local regions in sequence space, noting these regions’ specific sizes and distances from each other. In addition, he mapped the percentage of functions performed in paired local regions as a function of the regions’ size and separation (i.e., amino acid differences). Based on this analysis, Wagner extrapolated the conclusion that mutations could change a protein (with a particular function) into another protein (with a different function) in the same region. In Wagner’s view, this allowed proteins to evolve in organic history. Yet again, he did not actually empirically demonstrate that such transformations were ever possible. Instead, he simply mapped interesting correlations between protein sequences, functions, and structures.

In fact, Wagner’s own research suggests that protein evolution is exceedingly difficult. He acknowledged, for example, that many proteins correspond to extremely rare sequences. Moreover, he identified highly separated regions of sequence space where the proteins in the different regions possessed different structures and performed different functions. This observation suggests that many proteins are not simply rare but also isolated — they are strikingly different from all other proteins in distant regions of sequence space. Wagner did not demonstrate that a series of short steps (or smooth evolutionary pathways) connect these distinct types of proteins. Even if mutations might transform some proteins into other close-at-hand proteins — which Wagner did not show — his own data strongly indicate impassable chasms between many other types of proteins. To borrow Wagner’s metaphor: many proteins appear to be separated from each other like stars in the universe.

The State of the Field

We then describe how research by leading experts in the field of protein evolution reinforces the view that distinct proteins are so isolated from each other that one could never evolve into another. From an article referencing the late Dan Tawfik:

“Once you have identified an enzyme that has some weak, promiscuous activity for your target reaction, it’s fairly clear that, if you have mutations at random, you can select and improve this activity by several orders of magnitude”, says Dan Tawfik at the Weizmann Institute in Israel. “What we lack is a hypothesis for the earlier stages, where you don’t have this spectrum of enzymatic activities, active sites, and folds from which selection can identify starting points. Evolution has this catch-22: Nothing evolves unless it already exists.” (Mukhopadhyay 2013)

We also reference a lecture by Tawfik where he states that proteins can only be modified to the point where their structure does not significantly change. He describes how different protein structures appear completely isolated from each other, and biologists have zero knowledge of how they emerged. The vast preponderance of the evidence indicates that novel complex proteins could never have evolved through an undirected process. This conclusion completely overturns Kojonen’s thesis about the compatibility of evolution and design. 

So, Kojonen’s model of design is empirically testable: are preconditions fine-tuned and fitness landscapes smooth such that proteins can readily evolve? Or does the empirical data indicate that fitness landscapes are not smooth and that distinct proteins are isolated from each other? As we show in our article, there is good evidence for the latter view. If we are correct, then Kojonen’s account of design is mistaken. This severely damages his attempt to harmonize “design” with “evolution.”