No Justice for the watchmen? II

 

Exaptation cannot reduce irreducible complexity

 Co-Option and Protein Homology Don’t Explain the Evolution of the Flagellum

Casey Luskin

Critics of intelligent design have not taken arguments for irreducible complexity (IC) sitting down. In a recent post I described how our new peer-reviewed paper, “On the Relationship between Design and Evolution,” in the open-access journal Religions, details the elegant design of the bacterial flagellum. My co-authors (Brian Miller, Stephen Dilley, and Emily Reeves) and I explain why its irreducible complexity poses a challenge to Darwinian evolution. Critics have replied that IC systems can evolve via indirect evolutionary pathways (often called exaptation). That’s where a system might start with one function but then evolve to acquire a new function along the course of its history. Vital to indirect evolutionary pathways is the concept of co-option, which holds that proteins can be borrowed from other systems in the cell, and then modified and retooled to perform entirely new functions in some new system. 

Our article is a response to Rope Kojonen’s book The Compatibility of Evolution and Design. We start by reviewing just what needs to be explained — and ask what is needed to show that such models are plausible.

More generally, a plausible evolutionary explanation of the bacterial flagellum must explain not just the flagellum-chemotaxis propulsion/navigation system but its array of other characteristics, including its delivery system of individual parts, maintenance cycle, feedback loops, and performance efficiencies. In particular, indirect evolutionary accounts (such as co-option or exaptation) must explain how the 35–40 protein parts of the flagellum evolved from parts that originally served different functions in the cell. It must also account for their assembly instructions. The insurmountable barrier to any scenario is the numerous tight constraints identified by Schulz (2021a, 2021b, 2021c) that must be met before the system could function at all. Recall H. Allen Orr’s assessment of co-option (cited by Kojonen above):

“We might think that some of the parts of an irreducibly complex system evolved step by step for some other purpose and were then recruited wholesale to a new function. But this is also unlikely. You may as well hope that half your car’s transmission will suddenly help out in the airbag department. Such things might happen very, very rarely, but they surely do not offer a general solution to irreducible complexity.” (Orr 1996)

So, just how does co-option plausibly explain the origin of the most efficient machine in the universe?

We then note that Kojonen — a very thoughtful critic of ID, who takes ID arguments seriously — endorses such indirect / exaptation / co-option models of flagellar evolution. We explain why this is a question that must be addressed via the scientific evidence:

Kojonen takes the challenge of irreducible complexity head-on. He frames the problem as follows:

“Draper (2002) homes in on the crucial question: Are the requirements for each individual part really as strict as Behe claims? If biological parts are more malleable than Behe assumes, so that less specificity is required for fulfilling their roles, then Behe’s argument against co-option fails. Debunking Behe’s argument, then, depends on the details of how proteins work and how difficult it is to transition from one form to another, somewhat similar, form. Then, a continuous series of functional forms, leading from no flagellum to a flagellum, must exist so that no change is too large for natural selection to cross, and all modifications can be made. As with Dembski’s argument, it does seem plausible that evolving such complex systems is difficult, and the existence of such an evolutionary pathway has stringent conditions. But difficult or not, it is possible that nature does allow it. Behe thinks that the existence of such pathways is unlikely, but the existence of such pathways is fundamentally an empirical question.24” (Kojonen 2021, p. 118)

Notice two key elements of this passage. First, Kojonen states that the matter is “an empirical question”. Indeed, it is. Once again, the scientific details are paramount. Is there evidence of smooth evolutionary pathways between viable forms or not? This is a fundamentally scientific question. Kojonen’s model hinges in part on empirical evidence.

Protein Rarity Challenges Co-Option

Second, Kojonen also states that “[d]ebunking Behe’s argument, then, depends on the details of how proteins work and how difficult it is to transition from one form to another, somewhat similar, form”. So, Kojonen believes that successfully countering Behe’s argument depends on how proteins work and the prospects for a protein-to-protein transformation. This makes sense. The flagellum, for example, is made of protein parts. The function of each part, as well as the likelihood of a given part evolving into its present form from an ancestral form, is highly relevant. In short, Kojonen believes that his counter to Behe — an attempt to show that the flagellum’s ‘design’ is compatible with mainstream ‘evolution’ — rests upon the plausibility (or implausibility) of protein evolution.

This is significant. We have already examined strong evidence against fine-tuned preconditions and fitness landscapes that are ‘designed’ to enable proteins to evolve. This means that the calculations above (Section 4) directly impact the viability of Kojonen’s response to Behe. If these calculations are correct, then it is safe to say — by Kojonen’s own lights — that he has not met the challenge of irreducible complexity. The flagellum, thus, appears to display a type of design that conflicts with evolution. Thus, to the extent that Kojonen accepts the bacterial flagellum as evidence of ‘design’, he faces an internal coherence problem for his conjunction of ‘design and evolution’.

What Co-Option Must Explain

So what exactly is needed to yield a viable model of indirect evolution / co-option? Some excellent work has been done on this question by folks within the ID community, as we recount: 

Having raised this crucial challenge to Kojonen’s reply to Behe, we will now take co-option on its own terms for the sake of argument. Yet even on these terms, it still fails to be plausible. Kojonen cites authorities that invoke exaptation (also called “co-option” or “indirect evolution”) to explain the evolutionary origin of the bacterial flagellum. Under this model, evolution proceeds by borrowing parts from different systems, retooling them to change their functions, and then combining them into a new system to perform a new function. Philosopher Angus Menuge lists five elements that any co-option account must provide to explain an irreducibly complex system:

Availability of parts.

Synchronization, in which parts are available at the same time.

Localization, in which parts are available at the same location.

Coordination, in which part production is coordinated for assembly.

Interface compatibility, in which parts are “mutually compatible, that is, ‘well-matched’ and capable of properly ‘interacting’”. (Menuge 2004, pp. 104–5)

Typically, exaptation or co-option accounts do not explain anything beyond part of element (1). In this vein, Kojonen claims that 90% of flagellar parts have homologues that perform functional roles outside the flagellum. As we will see, this is an inaccurate claim — and co-option/exaptation accounts of the evolution of the flagellum face this and additional obstacles.

Kojonen thus follows in the footsteps of many co-option advocates in only assessing the first element of any successful co-option-based model of evolution, and we thus focus our critique there asking the question of whether sequence similarity between flagellar proteins and other proteins helps us solve the problem of its origin. We recount three main problems with such co-option-based evolutionary model of the flagellum.

Problem 1: Mere Sequence Similarity Is Not Evidence of an Evolutionary Pathway

The first main point we make is that merely establishing that two proteins have similar sequences is not sufficient to show that there is an evolutionary pathway to go from one sequence to the other:

In the context of biochemical evolution, the primary evidence for homology between two proteins is typically said to be similarity between amino acid sequences. An initial mistake made by proponents of co-option is therefore to confuse sequence similarity between two proteins with evidence for an evolutionary pathway. Even if other systems have proteins similar to each component of an irreducibly complex system, at most, this suggests homology, which might reflect common ancestry. Mere sequence similarity does not constitute a stepwise evolutionary explanation. Kojonen seems to miss this important nuance. He states that “parts of the flagellum are similar (or homologous) to parts that have other uses, and this gives grounds for constructing a plausible evolutionary explanation for its evolution” (Kojonen 2021, p. 117). He also writes, “The existence of similar parts in other systems, for example, does provide supporting evidence for evolvability” (Kojonen 2021, p. 118). But similarity does not itself indicate a viable evolutionary pathway. As Behe explains:

“Although useful for determining lines of descent… comparing sequences cannot show how a complex biochemical system achieved its function — the question that most concerns us in this book. By way of analogy, the instruction manuals for two different models of computer put out by the same company might have many identical words, sentences, and even paragraphs, suggesting a common ancestry (perhaps the same author wrote both manuals), but comparing the sequences of letters in the instruction manuals will never tell us if a computer can be produced step-by-step starting from a typewriter… Like the sequence analysts, I believe the evidence strongly supports common descent. But the root question remains unanswered: What has caused complex systems to form?25” (Behe 1996, pp. 175–76)

Behe points out that a single author (or mental agent) could be the cause of two different manuals. Accordingly, mere similarity is not evidence that mindless processes can bring about the system in question.

Problem 2: Useful Flagellar Protein Homology Is Not as Widespread as You’d Think

What we often find when evaluating protein similarity is that not all proteins are similar to other proteins — especially in a manner that is useful for constructing evolutionary explanations. We go through the literature and find what it really shows about flagellar protein homology to non-flagellar systems:

But the problem runs deeper than incorrect reasoning about sequence similarity: many parts of the bacterial flagellum are dissimilar to parts of other biological systems. Thus, a second problem facing the co-option model of evolution is that biological parts are often unique and unavailable to be borrowed from other systems (Khalturin et al. 2009; Beiko 2011). But Kojonen claims this is not a problem for the flagellum:

“Though a complete evolutionary explanation for the bacterial flagellum is still missing, critics of Behe have argued that approximately 90% of the parts of the flagellum are similar (or homologous) to parts that have other uses, and this gives grounds for constructing a plausible evolutionary explanation for its evolution. The type III secretion system, for example, has been argued to represent a viable precursor system to the flagellum. (Musgrave 2004; Pallen and Matzke 2006).” (Kojonen 2021, p. 117)

Kojonen cites two sources for his claim that 90% of flagellar parts are homologous to “parts that have other uses”. (Presumably, he is referring to parts that exist elsewhere besides the flagellum itself.) But this claim is highly problematic. One of his sources, Musgrave (2004, p. 81), provides no comprehensive analysis of flagellar homologues but simply asserts, via citations to other sources, that “between 80 and 88 percent of the eubacterial flagellar proteins have homologs with other systems, including the sigma factors and the flagellins” — but those sources (discussed below) do not substantiate this claim. Kojonen’s other source, Pallen and Matzke (2006), does provide a comprehensive study of flagellar proteins that are homologous to other proteins, but they too do not substantiate a claim that “90%” of flagellar proteins are homologous to proteins outside of the flagellum.

According to Table 1 of Pallen and Matzke (2006), 15 of the 42 flagellar proteins they studied did not have known homologues.26 So, at best, they only identified homologues for only about 64% of the flagellar proteins they studied (27 out of 42) — significantly less than 90%. Moreover, the vast majority of the remaining 27 proteins for which they reported homology are highly suspect and/or do not support an evolutionary pathway leading to a flagellum:

Two of the claimed flagellar proteins with detected similarities to other proteins are regulatory proteins with unsurprising similarity to other regulators, yet they are not structural components of the flagellum that contribute to its motility function.27

Three of the allegedly homologous proteins had only slight sequence similarity; they were claimed to be homologous based on “structural or functional considerations”.28 Yet because evolution proceeds by modifying sequences of DNA and proteins, a lack of sequence similarity suggests these other proteins are not a viable source that could have been utilized via an evolutionary pathway.Seven of claimed homologous proteins are strictly homologous to other flagellar proteins,29 what might be called “intraflagellar homology”. One cannot explain the initial evolution of the flagellum by claiming it evolved from itself, so these examples are entirely unhelpful towards explaining the how the flagellum first arose from “parts that have other uses” (Kojonen 2021, p. 117) or from “similar parts in other systems” (Kojonen 2021, p. 118), as Kojonen puts it. This tenuous argument may have been derived from Musgrave (2004, p. 81), who argues that flagellar proteins find homologues in “other systems” including “flagellins”—but flagellin is a strictly flagellar protein that only forms a subunit of the flagellum’s propellor.

Eleven of the claimed homologous proteins were similar to proteins in the Type Three Secretory System (T3SS),30 three of which were also claimed to show intraflagellar homology.31 As quoted above, Kojonen cites the T3SS as a potential “viable precursor system to the flagellum”, but this argument has been long-criticized by intelligent design proponents (Illustra Media 2003) as well as by other scientists. More on this below.

Kojonen’s other source for his 90 percent statistic, Musgrave (2004), provides two citations for his claim that “between 80 and 88 percent of the eubacterial flagellar proteins have homologs with other systems” — Aizawa (2001) and Ussery (2004). Ussery (2004) does not discuss homology for flagellar proteins outside of the flagellum; he merely compares sequence diversity across other flagellar proteins that fulfill the same flagellar function in different species of bacteria. Aizawa (2001) does identify some non-flagellar homologues for flagellar proteins, but only finds homologues for four flagellar proteins that were not also identified by Pallen and Matzke (2006).32 All four of these homologues are proteins used in the T3SS. Although there is clear homology between various flagellar proteins and the T3SS, we will explain below that such data are of limited value to account for the evolution of the flagellum.

Adding the four additional flagellar homologues identified by Aizawa (2001) to those identified by Pallen and Matzke (2006) brings the total to 31 out of 42 flagellar proteins that show sequence similarity to other proteins — 74% — which is again moderately less than 90%. But as noted above, the vast majority of these homologues are unhelpful in constructing some kind of an evolutionary pathway. In the end, Kojonen’s citations (and the sources of his citations) reveal at best only 4 out of 42 flagellar proteins (9.5%) are homologous to “similar parts in other systems” which could have potentially served as “precursors” to the flagellum, as Kojonen says. Nine-and-a-half percent is strikingly less than his claimed statistic of 90%.

More on the Type 3 Secretory System (T3SS)

Because the T3SS is so often cited as a potential “precursor” to the flagellum, it’s worth devoting some time to that topic specifically. In our paper we elaborate on various reasons why the T3SS could not have been an evolutionary precursor to the flagellum:

Because quite a few (perhaps up to 15) flagellar proteins appear homologous to proteins in the T3SS, the latter is often cited as a possible evolutionary precursor (or close relative) to the flagellum (Musgrave 2004; Miller 2008, p. 59). It is therefore worth exploring further why the T3SS could not serve as “a viable precursor system to the flagellum”, as Kojonen believes it to be. The T3SS is part of the flagellum itself and is used to pump proteins from inside the cell to outside the cell where they self-assemble into the flagellum. For this function, the T3SS is simply a molecular pump involved in flagellar assembly. Even granting that it could have been co-opted for some function, it is nonetheless unrelated to the flagellum’s motility function and so is unlikely to have been ‘co-opted’ to produce motility, the core function of the flagellum.

Once the flagellum is assembled, the T3SS provides an additional function: a structural component that anchors the flagellum in the cell membrane. Yet even here, it is not part of the motor portion of the assembled flagellum, but could be viewed as something akin to the bracket on an outboard motor. Again, the T3SS is a poor candidate for co-option (and modification) into the proteins that comprise the flagellum’s propulsion function.

Notably, a different molecular machine (called an “injectisome”) uses the T3SS as well (Diepold and Armitage 2015). In the injectisome, the T3SS is involved in both assembling the injectisome and in the injectisome’s function. (The injectisome is used by certain predatory bacteria to inject toxic proteins into eukaryotic cells, which then kill the eukaryotic cells so they can be ingested by the bacterium.) But it is doubtful that the injectisome and its T3SS are useful in explaining the origin of the flagellum. First, there are ecological and phylogenetic considerations that strongly imply the flagellum predates the T3SS and the injectisome and, thus, could not have evolved from these systems (Abby and Rocha 2012a, 2012b; Deng et al. 2017; Coleman et al. 2021).33 As New Scientist reported:”

One fact in favour of the flagellum-first view is that bacteria would have needed propulsion before they needed T3SSs, which are used to attack cells that evolved later than bacteria. Also, flagella are found in a more diverse range of bacterial species than T3SSs. “The most parsimonious explanation is that the T3SS arose later”, says biochemist Howard Ochman at the University of Arizona in Tucson.” (Jones 2008)

Second, even if the T3SS could have served as a precursor to the flagellum, it is not clear that this would provide anything close to a viable evolutionary pathway — a “continuous series of functional forms, leading from no flagellum to a flagellum”, as Kojonen puts it. William Dembski nicely captures the essence of the evolutionary leap required to explain how a flagellum evolved from the T3SS:“[F]inding a subsystem of a functional system that performs some other function is hardly an argument for the original system evolving from that other system. One might just as well say that because the motor of a motorcycle can be used as a blender, therefore the [blender] motor evolved into the motorcycle. Perhaps, but not without intelligent design. Indeed, multipart, tightly integrated functional systems almost invariably contain multipart subsystems that serve some different function. At best the T[3]SS represents one possible step in the indirect Darwinian evolution of the bacterial flagellum. But that still wouldn’t constitute a solution to the evolution of the bacterial flagellum. What’s needed is a complete evolutionary path and not merely a possible oasis along the way. To claim otherwise is like saying we can travel by foot from Los Angeles to Tokyo because we’ve discovered the Hawaiian Islands.” (Dembski 2005, p. 52)

Thus, even if the T3SS were a precursor to the flagellum, it would not necessarily help its evolution. But we further observe that “research indicates that the T3SS and flagellum are so distinct that they may in fact have independent origins (Tan et al. 2021) — a generally unexpected result on an evolutionary view.”

Problem 3: Not Addressing Flagellar Assembly

We further point out in the paper that “even if all the necessary parts were available and co-opted so that they could be constructed in the form of a flagellar motor, co-option does not explain the assembly instructions needed to construct complex systems.” Explaining the assembly of IC systems is something that Behe has called “Irreducible Complexity Squared” — and it is a vital aspect of molecular machines that almost always goes unaddressed by evolutionary models:

It is not just a matter of getting the parts; it’s also putting them together in the right sequence, at the right time, and in the right orientation. Simply having all the ingredients for chocolate cake is not in itself sufficient to produce a cake. Something similar is true for a Corvette engine. So much the more for the most efficient machine in the universe. Microbiologist Scott Minnich and philosopher Stephen Meyer explain this challenge:

“[E]ven if all the protein parts were somehow available to make a flagellar motor during the evolution of life, the parts would need to be assembled in the correct temporal sequence similar to the way an automobile is assembled in a factory. Yet, to choreograph the assembly of the parts of the flagellar motor, present-day bacteria need an elaborate system of genetic instructions as well as many other protein machines to time the expression of those assembly instructions. Arguably, this system is itself irreducibly complex.” (Minnich and Meyer 2004)

From beginning to end, the flagellar assembly process is “tightly controlled and regulated in a sequential genetic hierarchy mirroring organelle assembly from the inner membrane to the outer cell surface” (Minnich and Meyer 2004). Indeed, Behe has deemed the origin of flagellar assembly equivalent to “Irreducible Complexity Squared” (Behe 2007, p. 93), because, as he puts it, “not only is the flagellum itself irreducible, but so is its assembly system. The assembly process and the flagellum together constitute irreducible complexity piled on irreducible complexity” (Behe 2019, p. 286).

Yet in his most recent book, Darwin Devolves, Michael Behe observes that when it comes to explaining the evolutionary origin of the flagellum’s assembly, one continues to hear very little from the evolutionary biology community:

“In 1996 [in Darwin’s Black Box] I showed that, despite thousands of papers in journals investigating how that fascinating and medically important molecular machine worked, there were no papers at all that tested how the bacterial flagellum might have arisen by a Darwinian process. The scientific literature was absolutely barren on the topic…. Twenty years on, there has been a grand total of zero serious attempts to show how the elegant molecular motor might have been produced by random processes and natural selection.” (Behe 2019, p. 287; see also Behe 2007, pp. 267–68)

We close this section of our paper by observing that “Like many of his evolutionary colleagues, Kojonen simply elides this problem.” Now this is not necessarily Kojonen’s fault — it’s really just the fact that there is virtually nothing in the mainstream scientific literature trying to explain the evolution of flagellar assembly. 

In the end, we find that the bacterial flagellum contains a form of complexity that challenges not just Darwinian evolution but also co-option-based indirect models of evolution. Rope Kojonen wants us to appreciate the design of the flagellum but also to believe that this form of design can evolve. His project is to harmonize evolution and design (as he envisions them). He wants to count the flagellum as designed, but also wants to ignore the fact that the type of design it displays — irreducible complexity — poses a major problem for evolution. Thus, he wants to join “design and evolution,” but only by setting aside some of the main features of the flagellum. This harms his attempt to reconcile evolution and design in a coherent fashion. As we put it in our article, “Kojonen’s marriage of ‘evolution and design’ has a major problem: the very system that provides strong evidence of design also undercuts evolution. One part of the model saws off the branch upon which the other side sits. Kojonen’s model is internally conflicted.” 

Please read our open-access paper, here, for more details including endnotes and citation information.