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On the Relationship between Design and Evolution

Discovery Institute, Seattle, WA 98104, USA
Author to whom correspondence should be addressed.
Religions 2023, 14(7), 850;
Received: 24 May 2023 / Revised: 24 June 2023 / Accepted: 24 June 2023 / Published: 28 June 2023
(This article belongs to the Special Issue Exploring Science from a Biblical Perspective)


A longstanding question in science and religion is whether standard evolutionary models are compatible with the claim that the world was designed. In The Compatibility of Evolution and Design, theologian E. V. Rope Kojonen constructs a powerful argument that not only are evolution and design compatible, but that evolutionary processes (and biological data) strongly point to design. Yet Kojonen’s model faces several difficulties, each of which raise hurdles for his understanding of how evolution and design can be harmonized. First, his argument for design (and its compatibility with evolution) relies upon a particular view of nature in which fitness landscapes are “fine-tuned” to allow proteins to evolve from one form to another by mutation and selection. But biological data run contrary to this claim, which poses a problem for Kojonen’s design argument (and, as such, his attempt to harmonize design with evolution). Second, Kojonen appeals to the bacterial flagellum to strengthen his case for design, yet the type of design in the flagellum is incompatible with mainstream evolutionary theory, which (again) damages his reconciliation of design with evolution. Third, Kojonen regards convergent evolution as notable positive evidence in favor of his model (including his version of design), yet convergent evolution actually harms the justification of common ancestry, which Kojonen also accepts. This, too, mars his reconciliation of design and evolution. Finally, Kojonen’s model damages the epistemology that undergirds his own design argument as well as the design intuitions of everyday “theists on the street”, whom he seeks to defend. Thus, despite the remarkable depth, nuance, and erudition of Kojonen’s account, it does not offer a convincing reconciliation of ‘design’ and ‘evolution’.

1. Introduction

A perennial question in discussions about biological origins is whether or not design is compatible with evolutionary theory. Are the two friends or foes? Was Richard Dawkins correct when he claimed that “Darwin made it possible to be an intellectually fulfilled atheist” (Dawkins [1986] 1991, p. 6)? Or is evolution simply the means by which a Creator brought about his divine plan? These are important and challenging questions for those interested in the intersection of science and faith.
Yet a more difficult question concerns whether mainstream evolutionary theory is compatible with biology-based design. Is it possible, say, that the wing of a hummingbird and the blush of an orchid provide empirical evidence for design, while at the same time being fully explained by natural selection, random mutation, and other natural processes? Can one have full-blooded versions of both design and evolution simultaneously?
These are much more difficult questions. A host of fine thinkers past and present have weighed in on one side or the other. In 2005, for example, 38 Nobel Laureates signed a statement which declared that evolution is “an unguided, unplanned process of random variation and natural selection” (Elie Wiesel Foundation 2005). Yet other scientists disagree, including those who state that “evolution is not in opposition to God, but a means by which God providentially achieves his purposes. Therefore, we reject ideologies that claim that evolution is a purposeless process or that evolution replaces God” (BioLogos Foundation n.d.) Indeed, the co-discoverers of natural selection—Charles Darwin and Alfred Russell Wallace—held opposing views about the relationship between design and evolution.
Adjudicating this long-standing disagreement is no easy matter. But progress can be made by analyzing in detail the best current treatment available. Such a treatment has been rendered by E. V. Rope Kojonen, a theologian at the University of Helsinki, in a thoughtful and serious book, The Compatibility of Evolution and Design (hereafter, CED), published by Palgrave-MacMillan/Springer-Nature (Kojonen 2021). Kojonen argues that evolution and design can be harmonized. Indeed, he contends that mainstream evolutionary biology is fully compatible with design arguments (or design perceptions) that are based on biological phenomena. The wing of the hummingbird displays evidence of design even while being the product of natural selection, random mutation, and other processes—all without the need for divine intervention or supervision per se.
We will explore Kojonen’s view in more detail below. For now, it is important to note that his analysis is formidable and wide-ranging, covering literature across several subdisciplines of biology and philosophy. Philosophically, the work is remarkably sophisticated, engaging current discussions of causation, explanation, determinism, theodicy, and so on. Kojonen also ably engages current scientific discussions, from the bacterial flagellum to fitness landscapes to evolutionary convergence; he is also highly conversant in the literature of proponents of intelligent design (ID). Throughout the book, Kojonen offers nuanced arguments, appropriate qualifications, and respectful engagement with both mainstream evolutionary theory and contemporary notions of design. In short, CED is a fine work of scholarship.
Indeed, we regard CED as the best current treatment of the compatibility of design and evolution from a theistic evolutionary point of view. A careful analysis of this work is highly relevant to making headway on the broader question of the relationship between evolution and design. Thus, our analysis here will have wider application to the literature as a whole, mutatis mutandis.
To this end, we provide an extended examination of CED. While the strengths of the book are remarkable, we nonetheless contend that the book’s overall thesis is flawed: Kojonen’s attempt to draw together mainstream evolutionary theory with a biology-based design argument (or perception) does not succeed.
Our analysis proceeds in four steps. First, we provide a summary of CED. Second, we argue that the success of Kojonen’s proposal depends in part on the scientific details in question. Third, we give an extended analysis of these scientific details and argue that they run contrary to Kojonen’s model; we focus in particular on protein evolvability, the bacterial flagellum, and convergent evolution. Finally, we round out our article by raising epistemological concerns about Kojonen’s fundamental understanding of how to detect design in the natural world.
Importantly, in this article, we do not contend (or assume) that evolutionary theory is false or implausible per se. Even in our examination of scientific details, our point is either to critique Kojonen’s view of ‘design’ or to illuminate tensions between ‘design’ and ‘evolution’ in his model. Thus, in this article, we are interested in Kojonen’s view of design and its compatibility with evolution rather than the truth or falsity of evolutionary theory itself. (We should note, however, that because of the way Kojonen frames the matter, our criticisms of his view of design do have negative implications for the feasibility of evolutionary theory as he understands it. But, as we will see, this is an implication of our argument based on his own framing. It is not the focus of our argument itself).

Definitions and Qualifications

A definition or two will help keep matters straight along the way. The word ‘evolution’ has been defined in many different ways (Meyer and Keas 2003). In some contexts, it means ‘change over time’, whereas in others, it means ‘common ancestry’. Elsewhere, it refers to the mechanism of natural selection acting on random mutations. Still elsewhere, it means the selection-mutation mechanism plus supplemental natural processes such as genetic drift (neutral evolution), natural genetic engineering, phenotypic plasticity, niche construction, and so on. In this article, we follow Kojonen’s use of the term to refer to mainstream evolutionary theory, which is a combination of common ancestry, the mutation-selection mechanism, and other natural processes (as necessary).
In general, by ‘design’, we mean an intentional act of an agent in accord with a plan, pattern, or purpose. Having said that, our use of the term ‘design’ in this paper will usually refer to Kojonen’s particular version of design rather than to a general idea of design (as just defined). The context in each case will make clear which definition is in use. Kojonen’s version of design is a strain of ‘intelligent design’, the idea that (i) certain features of the natural world are best explained by mental agency rather than by mindless processes or forces, and (ii) the design of these features is detectible, whether through direct intuitive perception or careful scientific analysis. In short, design is real and detectable. As noted, Kojonen is particularly interested in ID in biology.
It is important to mention that there is much controversy surrounding the notion of ‘intelligent design’. There is also much ferment about its relationship to evolutionary theory. Strictly speaking, ID minimally holds that at least one physical feature of the universe is best explained by mental agency (as opposed to mindless causes), and that the design of this feature can be empirically detected. As defined, ID is compatible with many definitions (or versions) of evolution. For example, ID is compatible with ‘evolution’ defined as ‘change over time’, ‘change in the frequencies of alleles in a population’, ‘common ancestry of a certain taxonomic group’, or ‘universal common ancestry of all (or most) taxonomic groups’. ID is also broadly compatible with the idea that evolutionary mechanisms (e.g., natural selection acting upon random mutation) can explain at least some features of the universe. Importantly, ID is incompatible with the idea that all features of the universe can be explained by non-mental causes or that, even if some features are caused by mental agency, such agency is not detectable from apprehension of the effects (or features) in question.
Having clarified this point, we emphasize that the aim of this article is not to provide a definitive statement about ID and evolution, but rather to evaluate Kojonen’s specific proposal on these matters. As noted, in our view, Kojonen’s model stands as the finest current model on offer from an evolutionary point of view. Future discussions will need to grapple with Kojonen’s careful account.

2. Summary of The Compatibility of Evolution and Design

In their simplest form, CED’s main theses are as follows (Kojonen 2021, pp. 6–10, 205–13):
  • Evolutionary theory, properly understood, is both scientifically correct and compatible with a certain type of biological design argument.
  • The biological world itself provides notable grounds for belief in a purposeful Creator, and evolutionary theory does not defeat these grounds.
  • For those worried about so-called natural evil, there is a way to join evolution with a biological design argument that actually adds credibility to evolution-based theodicies, rather than raising additional hurdles for them.
In order to defend these primary claims, Kojonen carefully constructs an argument for the harmony of evolution and biological design. We will refer to this argument as Kojonen’s evolution-friendly biological design argument (or KEBDA). Importantly, one of the unique features of Kojonen’s proposal is his contention that, even with the acceptance of standard evolutionary theory (and, hence, no need to appeal to design-based alternatives to evolution), biological phenomena still provide notable grounds for belief in a Designer (see point 2 above). Kojonen argues that this is true not just for a scholar who can follow the nuances of KEBDA, but even for an everyday theist (the “theist on the street”) who relies on intuition and common sense to apprehend design in biological phenomena (Kojonen 2021, pp. 32, 145–204). Thus, in Kojonen’s evolutionary vision, flora and fauna don’t simply reveal God ‘through the eyes of faith’ but rather in a more robust and substantial way.1
This is a unique and provocative contribution to the literature on this topic, and Kojonen has broken new and stimulating ground. We will return to this interesting feature of CED in due course. For now, however, we will focus on summarizing the first thesis above—the compatibility of evolution with design—which forms so much of the impetus behind, and substance of, Kojonen’s endeavor in CED.
As is evident, Kojonen is clear from the outset that his argument takes mainstream evolutionary theory as a given (Kojonen 2021, pp. 7, 98, 105). He states, for example, that “the validity of the essential scientific claims of evolutionary biology will be accepted as the starting point of my inquiry” (Kojonen 2021, p. 7).2 On this view, there are no causal ‘gaps’ in evolutionary processes, and as such, no divine interventions are needed.3 Evolution is a settled matter. Accordingly, CED does not seek to provide a scientific defense of evolution per se but rather to give a philosophical account of how evolution and design are (or can be) compatible (Kojonen 2021, pp. 5–8). Supposing that full-orbed evolutionary theory is true, does it dovetail with detectable biological design?
Having taken evolution as a starting point, Kojonen carefully builds his case for its compatibility with design. The details of his proposal are manyfold, but the basic idea is straightforward: the locus of design is at the origin of the cosmos (or the laws of nature) (Kojonen 2021, pp. 164–67). God acts at the beginning of the universe, granting to it all that is necessary for biological complexity to eventually unfold. The deity creates the laws of physics and chemistry, which then give rise to preconditions—including “the library of forms”—that enable evolution to produce complex entities.4 Random mutations and natural selection alone are insufficient for the emergence of biological complexity; preconditions are required, and God ultimately stands behind these preconditions (Kojonen 2021, pp. 97–143).

2.1. Why Bother with Design?

Naturally, a critic might wonder, “Why bother with design if Kojonen has already granted evolutionary theory? That is, if evolutionary explanations are fully adequate to explain biological diversity and complexity—as Kojonen assumes—then what is left for design to explain?” As Kojonen himself puts it, “Evolutionary processes are supposed to provide an explanation for precisely the same features of biology that design arguments also attempt to explain—therefore making design unnecessary”. (p. 9).
Kojonen recognizes the power of this objection. The worry, in short, is that a critic might claim that Kojonen’s model violates Ockham’s razor. As David Glass puts it:
In most cases design is compatible with the alternative explanation, but if this is so, why not accept both design and the alternative explanation? The obvious answer is that there is no need to infer two explanations when one will do. When I learn that my children were playing in the study, the hypothesis that there has been a burglary becomes redundant as an explanation for the untidiness.
Kojonen draws upon a number of resources to respond to this objection. Indeed, one of the very fine features of CED (and Kojonen’s other writings) is his use of “conjunctive explanations” in this regard (Kojonen 2021, pp. 148–55, 2022a).5 He notes that his burden is to show that the conjunction of ‘design and evolution’ has greater explanatory value (or goodness) than simply ‘evolution’ on its own. Given that ‘design and evolution’ are less simple than ‘evolution’ (and so are a prima facie violation of Ockham’s razor), Kojonen recognizes the need to show that the conjunction of ‘design and evolution’ provides an offsetting benefit that ‘evolution’ alone lacks. Kojonen’s task is to show that the conjunction has enough explanatory gain so that ‘design’ is a helpful—rather than superfluous—addition to evolution’s explanation of biological complexity and diversity (Kojonen 2022a).6
Kojonen takes up this challenge directly. He ultimately cites an array of considerations—the origin of proteins, the complexity of the bacterial flagellum, evolutionary algorithms, and the like—to show that it is implausible to think biological diversity and complexity ultimately arose without a designing mind. As he summarizes: “The cosmos must be special indeed to allow for the evolution of the kind of complex teleology and the large variety of creatures that we observe. And this feature of the cosmos… is explained better by a theistic view than by supposing that this feature is due to chance” (Kojonen 2021, p. 162, see also pp. 97–143). So, biological complexity and diversity are best explained by (ultimate) design rather than by random processes. In this sense, Kojonen believes that adding ‘design’ to ‘evolution’ provides an important explanatory gain over and above ‘evolution’ alone. Without designed preconditions, one cannot fully account for the extraordinary complexity and diversity of biological life.
One of Kojonen’s thought experiments may help illuminate his line of reasoning. He asks readers to suppose that the first photos of the moon showed the text of John 3:16 written in craters on the surface (Kojonen 2021, p. 165). Suppose further that there was a natural explanation for each crater (and asteroid). Suppose also that we could trace these natural explanations all the way to the big bang. “In this case”, writes Kojonen, “it seems that natural explanations simply do not explain the intelligibility of the pattern, even though they explain each individual crater”. (Kojonen 2021, p. 165) The evidence of design remains clear, even if that design occurred at the beginning of the universe and was transmitted by natural processes across time and space. So it is in biology, he argues. The complexity of flagellar motors and other biological phenomena point directly to design; the fact that proximal (evolutionary) causes are in play does not preclude God as the ultimate cause. Indeed, positing a designer adds explanatory value: the appeal to a natural explanation to account for John 3:16 is not at all convincing on its own.
Note that Kojonen does not want to add just any ‘design’ hypothesis to ‘evolution’. In fact, he wants to add a hypothesis that has three key elements: (i) biological design (Kojonen 2021, pp. 132, 157–74), that is (ii) empirically detectible (Kojonen 2021, pp. 132, 157–74),7 and (iii) came about without divine intervention (Kojonen 2021, pp. 28, 109, 122, 146, 184, 185, 192). So, even though evolutionary theory is correct, there is still a real design argument here—one that is based on biological phenomena, not data from cosmology or physics per se. And this design argument does not include divine interventions; instead, organic creatures arise from the laws of nature over time—what one might call a full-throated “front-loaded” view of design.8 It is this view of ‘design’ that Kojonen believes adds explanatory value to ‘evolution’.
Notably, under Kojonen’s model, evolution per se is not ultimately responsible for the impressive complexity and diversity of life we observe on Earth—at least not any more responsible than natural processes are for spelling out John 3:16. In the John 3:16 analogy, natural processes on their own are recognized to be impotent to spell out the message, and this is why we recognize that a Mind must have crafted the laws of nature (and initial conditions of the universe). In a similar way, Kojonen contends that evolution on its own is impotent to create much of the observed complexity and diversity of life, and what gives evolution its impressive creative powers are the “preconditions” that ultimately derive from the laws of nature (and initial conditions) that God designed at the beginning of the universe.

2.2. Which Version of Evolution?

Of course, careful thinkers will note that much of the discussion hinges on what the term ’evolution’ means. It is one thing to say that God’s initial creative act eventually produced biological diversity and complexity; it is quite another to claim that all of this is compatible with standard evolutionary theory, properly understood. Kojonen is well aware of this difficulty. In response, he canvasses an array of interpretations of evolution—everything from Stephen Jay Gould’s ‘contingency’ view to Simon Conway Morris’s ‘directional’ view—and argues that each legitimate version is compatible with front-loaded design. He summarizes:
If evolution is directional… then this directionality is contingent on the laws and constants of nature allowing this directionality. If evolution is highly contingent, so that running the “tape of life” again would cause a very different result, then this makes it surprising that such valuable outcomes have in practice been reached.
He explains that, on the contingency side, the appeal to design (rather than to cosmic chance) explains the general possibility and existence of purposive organisms in biology, as well as the preconditions for both. On the directionality side, the appeal to design (rather than to undesigned processes) explains how evolution is able to instantiate platonic “laws of form”, which in turn enable convergence and subsequent evolutionary outcomes. Either way, the (resulting) complexity of biological organisms makes more sense from a design perspective than from a non-design perspective (Kojonen 2021, pp. 152–53, 194).9
In this fashion, then, Kojonen has argued that evolution and design are not mutually exclusive, but rather can be harmonized. Indeed, evolution actually needs design (in the form of precise preconditions and fine-tuned natural laws), so evolution is not simply compatible with design but actually supportive of it.
We hope this brief summary draws attention to the considerable strengths of The Compatibility of Evolution and Design. As mentioned, Kojonen’s treatment is nuanced, thoughtful, clear, and fair-minded. It is a model of fine scholarship and deserves serious attention in current and future discussions of the relationship between design and evolutionary theory.
Even so, we have significant concerns. We explore these in Section 4, Section 5, Section 6 and Section 7 below.

3. Why Scientific Evidence Is Crucial

But first, the issue must be framed in the proper way. In particular, one must be clear about what Kojonen needs to do to succeed. In this section, we argue that, although KEBDA is philosophical argument, it nonetheless rises or falls in part on scientific evidence. In order to successfully harmonize ‘design’ and ‘evolution’, Kojonen needs to show that his case for design is strong and does not conflict with his acceptance of evolution. In Section 4 and Section 5, we will argue that Kojonen’s argument for design is scientifically implausible and also in tension with evolutionary theory. As a result, KEBDA is fundamentally flawed. For the moment, however, we contend that Kojonen’s philosophical reconciliation of evolution and design hinges in part on scientific data, whatever that data happen to be.

3.1. Design and the “Preconditions” of Evolution

As mentioned, Kojonen attempts to show that the conjunction of ‘design and evolution’ has greater explanatory merit than ‘evolution’ alone. Given his particular version of design, Kojonen must show that ‘evolution and empirically-detectible biological design that came about without divine intervention’ help explain life in a way that ‘evolution’ on its own does not. He must show that this type of ‘design’ adds something helpful. Kojonen sees all of this clearly (Kojonen 2021, pp. 149–56). KEBDA is his attempt to rise to this challenge.
How does Kojonen go about this daunting task? In chapter four, Kojonen marshals various arguments to show that the preconditions of evolution must be designed if evolution is to be successful (as he believes it to be).10 The deck must be stacked in advance. In particular, fitness landscapes must be finely tuned ahead of time in order for evolutionary processes to successfully produce biological complexity and diversity. Kojonen believes that it is implausible to think that evolutionary processes can account for flora and fauna without these special preconditions. To make his case, Kojonen cites the work of Andreas Wagner, William Dembski, and others on protein evolution, evolutionary algorithms, structuralism, and the like. For Kojonen, these thinkers’ arguments powerfully show that evolutionary processes need prior “fine-tuning” of fitness landscapes (Kojonen 2021, pp. 97–143, esp. pp. 109–23). Thus, ‘evolution and design’ is superior to ‘evolution alone’.
But two problems bubble up with Kojonen’s depiction of design. The first is that scientific evidence strongly indicates that fitness landscapes are not “fine-tuned” in the way required by Kojonen’s model. The work of ID theorists Douglas Axe, Ann Gauger, Stephen Meyer, and others is especially relevant in this regard (Axe 2000, 2004, 2016; Meyer 2009, 2013, 2021; Gauger et al. 2010; Gauger and Axe 2011; Reeves et al. 2014). We will analyze this research (and Kojonen’s response) in the next section. Our basic argument will be that, on Kojonen’s view, one of the key ways that ‘design’ adds explanatory value to ‘evolution’ is by setting up fine-tuned fitness landscape that enable evolution to search and find biological forms.11 But if empirical evidence indicates there are no such landscapes, then Kojonen’s conception of ‘design’ is poorly grounded and, thus, has little explanatory benefit to add to evolution.
The second problem also concerns Kojonen’s case for design. He supports his case by citing biological phenomena that, upon closer inspection, actually display a type of design that is incompatible with mainstream evolutionary theory. This harms his philosophical attempt to harmonize ‘design’ and ‘evolution’. In particular, Kojonen cites the bacterial flagellum, a molecular propulsion apparatus that propels bacteria through liquid. Yet, as we will argue, the type of design found in the flagellum runs contrary to evolutionary theory, which (again) hampers Kojonen’s attempt to harmonize ‘design’ and ‘evolution’. We will examine the bacterial flagellum (and Kojonen’s response) in more detail below.
Thus, in summary, the landscape is as follows: in order for Kojonen to succeed at showing that the conjunction of ‘evolution and design’ is explanatorily superior to ‘evolution’ alone, he needs to show that adding ‘design’ increases evolution’s explanatory value in a way that offsets the liability of violating Ockham’s razor. Two explanatory entities are better than one only in certain conditions. What kind of ‘design’ does Kojonen believe fits these conditions? The kind of design he has in mind is the type in which God created the laws of nature, which ultimately lead to fine-tuned “preconditions” (including smooth fitness landscapes) that enable evolution to occur. Kojonen gives several lines of evidence for this view, including research on fitness landscapes, the bacterial flagellum, evolutionary algorithms, structuralism, convergence, and so on. His task is to show that this evidence makes his view of ‘design’ sufficiently robust and plausible to add explanatory merit to ‘evolution’.
By way of response, we will focus on the critical question of whether Kojonen’s articulation and justification of design is convincing. Though we do not have space to examine every line of evidence that Kojonen raises, we will analyze three key areas: fitness landscapes, the bacterial flagellum, and convergence.12 With respect to these areas, Kojonen must accomplish the following: First, he must justify his empirical claim about fitness landscapes. Without smooth landscapes, his concept of ‘design’ cannot augment ‘evolution’ in a way that helps explain evolution’s ability to search and find viable biological forms. ‘Design’ would thus add little explanatory value on this score. Second, Kojonen must show that the bacterial flagellum counts as evidence for ‘design’ but in a way that does not conflict with ‘evolution’. If the flagellum manifests a type of design inconsistent with evolution, then, in effect, Kojonen would have accepted evidence that creates an internal tension in his conjunction of ‘design and evolution’. Third, Kojonen must similarly show how convergence supports his view of ‘design’ in a way that also avoids conflict with ‘evolution’. Thus, in sum, Kojonen needs to articulate and justify his conception of design in a way that augments the explanatory value of evolution rather than undercuts it.
We take up these matters in the next section. But before doing so, it is crucial to realize that the point of our (upcoming) scientific analysis is not to criticize evolutionary theory per se. Although we believe that the scientific evidence in question counters mainstream evolution, we nonetheless set this aside for the sake of the argument. Instead, our criticisms are aimed at Kojonen’s conception of design. We will contend that he does not offer sufficient empirical support for it—and so it adds little explanatory merit to ‘evolution’—and that some of the evidence he does offer actually conflicts with his commitment to evolution. (Of course, it ought to be noted that, because Kojonen concedes that evolution needs the help of design, our criticisms of his view of design have broader implications for whether evolution, as he understands it, can successfully produce biological complexity. But that particular implication follows from his way of framing the issue; it is not the focus of our argument itself.)

3.2. The Importance of Scientific Evidence

Why make such a big deal about scientific evidence? Here’s why this point is worth emphasizing: in the face of scientific criticisms of Kojonen’s model, proponents of Kojonen’s view may be tempted to defend it in the following ways:
  • Kojonen’s proposal is a philosophical model, not a scientific one. Scientific evidence is of secondary importance.
  • KEBDA is primarily an exercise in harmonizing two distinct views (‘design’ and ‘evolution’), not in the evaluation of the empirical evidence for these views, whether individually or jointly.
  • Kojonen’s model shows that evolution and design are compatible, whatever the scientific details may be. Having established this harmony, it is now just a matter of working out the details over time.
It is true that KEBDA 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?
Scientific data are also crucial to assessing the internal harmony of Kojonen’s conjunction of ‘design and evolution’. For example, do empirical studies show that the bacterial flagellum embodies a type of design that is in tension with Kojonen’s acceptance of evolution or not?
These empirically oriented questions help determine whether Kojonen’s conception of ‘design’ adds explanatory value to ‘evolution’ in a way that makes his model plausible. This is why scientific evidence is essential to assessing Kojonen’s ’philosophical’ design argument. Philosophically, KEBDA has many strengths indeed. But the great temptation here is to think that its philosophical merits carry the day, and that KEBDA is basically a success because of its impressive conceptual and epistemological content. (Having said that, we do have significant epistemological concerns, which we will explain in Section 7 below.) Yet in any case, if the scientific data do not support KEBDA, then it suffers a serious blow. It struggles to meet its own standard of showing that ‘design and evolution’ are superior to ‘evolution’ alone.
So, what do the scientific data indicate?

4. Scientific Problems for Kojonen’s View of Proteins

Unfortunately, the scientific evidence runs strongly contrary to KEBDA. In what follows, we argue that empirical challenges posed by Axe, Gauger, Meyer, and others severely damage Kojonen’s account of design. In Section 5, we contend that research on the bacterial flagellum likewise raises difficulties for Kojonen’s reconciliation of design and evolution. If we are correct, then the scientific details—so important to the justification of Kojonen’s model—damage the central thesis of his book.
First, we begin with proteins, which are the subject of the research of Axe and others.

4.1. Rarity and Isolation of Proteins

4.1.1. The Work of Andreas Wagner

As noted, Kojonen proposes that divinely created laws of nature ultimately gave rise to “preconditions”, a “library of forms”, and the like, which eventually enabled natural selection and random mutation (and other natural processes) to produce all manner of flora and fauna. With this preset advantage, evolutionary processes can find viable biological forms, including—most notably—new proteins.13 The key question, then, is whether there is good empirical evidence that proteins (or ‘primitive’ proteins of whatever kind) can evolve into other proteins, including into more complex proteins. Or are viable proteins too different to allow an evolutionary transition from one to another? Following Wagner (2014, p. 100), Kojonen notes that if “viable protein forms” are like “stars in our universe, islands separated by vast expanses of dark empty space”, then “we would be in the situation described by…ID proponents, and evolution by natural selection would be impossible” (Kojonen 2021, p. 121). So, are proteins isolated from each other? Or are they connected by evolutionary bridges?
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 multi-dimensional map of all possible amino acid sequences.14) 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.
Kojonen states:
If functional forms are close to one another, then producing a new protein form or function would not require evolution to search through the entire vast realm of all possible arrangements of amino acids. Rather, evolution would only need to search through the adjacent space of possible forms to find viable new forms. This is a far easier task, and if functional forms are arranged in such a way, then this would explain how evolution is possible despite the rarity of functional forms.
Kojonen justifies this assertion by citing the research of Andreas Wagner (and his team).15 Wagner claims to have demonstrated that proteins can evolve into one of their nearest neighbors through a tractable number of mutations. Every protein in biology is thus interconnected through a continuous series of traversable steps.

4.1.2. Limitations of Wagner’s Research

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. 2017, 2018; Oxford Academic 2017). 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) (Ferrada and Wagner 2010). 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.

4.1.3. Axe, Gauger, and Others on Protein Rarity and Isolation

Though Wagner’s own research is insufficient to answer whether natural processes can give rise to proteins, other scientific research does address this question. This research strongly indicates that proteins are rare and isolated, and that viable evolutionary pathways between them are highly unlikely.
To appreciate the centrality of this problem, consider, first, the importance of proteins to life on earth. The advent of new complex proteins occurs in major transformations throughout organic history. These transformations include the origin of life, the origin of eukaryotic cells, the origin of complex animal body plans, and the origin of new plant phyla. Each of these events requires the genesis of highly complex novel proteins (Hutchison et al. 2016; Paps and Holland 2018; Heger et al. 2020). So, explaining biological complexity and diversity requires explaining the origin of many new complex proteins.
Second, empirical evidence indicates that proteins are rare, isolated, and difficult to achieve by evolutionary means. Kojonen’s own way of framing the matter helps make this clear. He writes:
The more crucial point that needs to be made in response [to Axe et al.] is that what matters is not just the rarity of functional forms, but also their closeness in the “biological hyperspace” of functional forms, meaning the “distance” in mutations that is required to traverse between these forms.
So, in Kojonen’s view, a “crucial” issue is the “distance” in mutations from one functional protein to another. That is, protein evolution hinges in part on how many mutations must be changed to produce a new function, the rate at which mutations can occur, the probabilities of the required number of mutations arising in the amount of time available, and the like. Current research provides striking data on this score. For example, Axe (2010) performed a population genetics study which found that when a feature requires more than six mutations before giving any benefit, this feature is unlikely to arise in the whole history of the Earth—even in the case of bacteria that have large population sizes and rapid generation times. Additional research by Gauger and Axe (2011) found that merely converting a particular metabolic enzyme to perform the function of a closely related enzyme—the kind of conversion that evolutionists claim can readily happen—would require a minimum of seven mutations. Yet this exceeds the limits of what Darwinian evolution can produce over the Earth’s entire history, as calculated by Axe (2010). A follow-up study by Gauger, Axe, and biologist Mariclair Reeves bolstered this finding by attempting to mutate additional enzymes to perform the function of a closely related protein (Reeves et al. 2014).16 After inducing all possible single mutations in the enzymes, and many other combinations of mutations, they found that evolving a protein to perform the function of a closely related protein would take over 1015 years—over 100,000 times longer than the age of the Earth. Collectively, this research indicates strong barriers to protein evolution, and that evolving a protein from a similar protein often requires more time (and mutations) than is available. Evolutionary processes simply have neither the time nor resources to ‘search’ and find the right mutations to produce even a basic transformation, much less the hundreds of thousands of transformations necessary to produce all known proteins in organisms on Earth. Once again, viable proteins appear to be as isolated as stars in the universe.
Moreover, the empirical data on protein rarity poses a quantifiable challenge to KEBDA. Several studies demonstrate that, for many proteins, functional sequences occupy an exceedingly small proportion of physically possible amino acid sequences. For example, Axe (2000, 2004)’s work on the larger beta-lactamase protein domain indicates that only 1 in 1077 sequences are functional—astonishingly rare indeed. Such rarity presents prima facie evidence that many proteins are very difficult to evolve by a blind evolutionary process of random mutation and natural selection.
Of course, a common rejoinder to this data is to claim that ‘protein rarity’ is only true for select proteins; many others are not so rare. That is, many proteins might have sequences with functions that are more common in sequence space and are thereby easier to evolve. As Kojonen (2021, p. 119) puts it, “others argue that functional proteins are much more common”. He specifically cites Tian and Best (2017) as a rebuttal to Axe (2004) on this point. Similarly, Venema (2018) objects to Axe (2004)’s research because he believes “functional proteins are not rare within sequence space”. Importantly, Kojonen is correct that some proteins are easier to evolve than others, and this point is pressed by some scientists17—but nonetheless, a very large proportion of proteins seems beyond the reach of mutation and selection.
Indeed, Tian and Best (2017) present much data that actually support Axe’s general thesis for protein rarity. They reported that the functional probabilities for ten protein domains range from 1 in 1024 to 1 in 10126. Yet even if we grant generous assumptions towards evolution, additional research indicates that only three of the ten domains studied by Tian and Best could have possibly emerged through an undirected evolutionary search of sequence space. Specifically, Chatterjee et al. (2014) calculated that there are at most 1038 trials available over the entire history of life on Earth to evolve a new protein. Therefore, if a protein domain has a probability of less than 10−38, then it is unlikely to emerge via a process of random mutation and natural selection. Seven of the ten domains studied by Tian and Best (2017) had probabilities below 10−38. Thus, even though Kojonen (2021, p. 119) cites Tian and Best (2017) to argue that the “specificity required for achieving a functional amino acid sequence” may be less for some proteins, their research provides strong empirical evidence that many proteins have functional sequences that are so rare as to be beyond the reach of standard evolutionary mechanisms.
Kojonen (2021, p. 119) also cites Taylor et al. (2001) to counter (or mitigate) Axe’s results on protein rarity. Taylor et al. (2001) reported that the probability of evolving a chorismate mutase enzyme is 1 in 1023, which Kojonen (2021) takes to suggest that functional protein sequences can be “more common than in the case of the protein studied by Axe”. Yet the fact that chorismate mutase represents less rare sequences is unsurprising given that its function requires a simpler fold than typical enzymes such as beta-lactamase studied by Axe (2004).18 Could chorismate mutase evolve? If it could, this still does not demonstrate the feasibility of Kojonen’s thesis: the possibility that some simpler proteins could evolve does not mean that all (or even most) more complex proteins could evolve. But for KEBDA to succeed, evolutionary mechanisms must be up to the task in all cases, not just some.
The possibility of evolving relatively simpler proteins, however, raises another objection. Hunt (2007) asks: If a simple protein could evolve in the first place, might it also evolve further into a more complex protein? More specifically, if one assumes that a comparatively simple protein such as chorismate mutase could evolve, why could it not also evolve into a more elaborate protein, including one with a functional sequence that is as rare as those studied by Axe?19 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.20 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.
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.21 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.22
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.

4.2. The State of the Field

Stepping back, broader trends in the field of protein science have confirmed this formidable picture. In particular, protein evolution studies have consistently demonstrated that the evolvability of complex proteins is highly constrained, contrary to evolutionary expectations. Consider, for example, the perspective of Dan Tawfik, a leading researcher in this field until his recent death. Tawfik (2016) summarized the field as follows:
  • An enzyme could only be altered experimentally to perform a new function if its structure and active site were not substantially changed. Such “micro-transitions” could never accumulate to transform an enzyme into something fundamentally different.
  • Proteins in different superfamilies have no connection to those in other superfamilies in terms of their sequences and structures. The different superfamilies represent “isolated galaxies”. (A “superfamily” is one of the broadest categories under which one can group similar proteins.)
  • Researchers have “zero knowledge” of how the superfamilies are related or could have originated.
Yet an even more compelling result from Tawfik’s own research shows the isolation of fundamentally different protein structures, called “protein folds”.23 (The generation of a stable “protein fold” is a necessary condition for protein function.) Tawfik’s experiments showed that between 3 and 15 mutational changes destroyed the structural and thermodynamic stability of numerous kinds of protein folds (Tokuriki and Tawfik 2009; Tokuriki et al. 2007; Meyer 2021, pp. 319–20). But to transform a given protein fold into another one requires many more than just 15 mutations. Thus, as mutations accumulate, they will destroy the stability of a protein fold long before a novel protein fold arises. In short, degradation occurs more rapidly than innovation. This implies that there are no evolutionary pathways between fundamentally different protein folds. Mutating one stable protein fold into another generates thermodynamically unstable intermediates. These intermediates cannot perform any function and thus will not be preserved by natural selection. This experimental result once again highlights the isolation of viable protein structures from each other.
Tawfik himself operated within the philosophic framework of scientific materialism, so he simply assumed that novel proteins must have evolved through some undirected evolutionary process. He proposed models for their origin but acknowledged that he could not justify the plausibility of any of these models. In an article for the American Society for Biochemistry and Molecular Biology, molecular biologist Rajendrani Mukhopadhyay interviewed Tawfik, who said:
“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.”
Currently, the field of protein evolution lacks plausible, solid hypotheses about how natural processes transformed random sequences of amino acids (peptides) into the sophisticated entities that we recognize today as proteins. Until that happens, the origin of proteins will remain, as Tawfik says, “something like close to a miracle” (Mukhopadhyay 2013).
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 himself noted that if “viable protein forms” are like “stars in our universe, islands separated by vast expanses of dark empty space” then “we would be in the situation described by…ID proponents, and evolution by natural selection would be impossible” (Kojonen 2021, p. 121). This is exactly what the empirical evidence indicates.
Yet the point here is not to criticize evolutionary theory—although clearly, there are formidable problems with Kojonen’s understanding of protein evolution. Instead, for present purposes, our target is Kojonen’s account of design. Recall that, in his proposed model, preconditions (and smooth fitness landscapes) are fine-tuned so that evolution can successfully search and build viable biological forms. Yet empirical evidence shows that no such preconditions or fine-tuned fitness landscapes exist. Kojonen’s view of design is, thus, at odds with the data itself. As such, it is poorly situated to add explanatory value to evolution.

5. Scientific Problems for Kojonen’s View of the Bacterial Flagellum

Recall our earlier (brief) discussion of the famed bacterial flagellum, a microscopic rotary engine that helps propel bacteria through an aqueous environment. Kojonen believes that the flagellum actually strengthens his model. He holds that the complexity of the flagellum shows that there must be fine-tuned “preconditions” that ultimately point to design in the laws of nature (Kojonen 2021, p. 122). The bacterial flagellum not only indicates design, but Kojonen believes it does so in a way that is fully compatible with mainstream evolutionary theory. He contends that the organelle arose by a stepwise process of exaptation and so is fully consistent with evolution. All told, then, the flagellum not only fits with evolution but also bolsters the case for design. Thus, in Kojonen’s hands, the bacterial flagellum shows that ‘evolution and design’ is better than ‘evolution’ alone.
We will argue below, however, that type of design embodied in the bacterial flagellum is incompatible with mainstream evolutionary theory. This harms Kojonen’s philosophical attempt to harmonize ‘design’ and ‘evolution’. In effect, Kojonen’s conjunction of ‘evolution and design’ is at odds with itself: one of the conjuncts undermines the other. That is, the bacterial flagellum provides evidence of ‘design’ in a way that damages ‘evolution’. To show this, we first define “irreducible complexity”. Next, we illuminate the underlying engineering and design principles of the bacterial flagellum, showing its astonishing complexity. Third, we raise problems with Kojonen’s account of the bacterial flagellum, arguing that its particular design contradicts evolutionary theory. This analysis shows, once again, that the scientific details do not support Kojonen’s model, and that it is internally conflicted in a significant way.

5.1. Irreducible Complexity Defined

An initial definition will start matters. In his 1996 book, Darwin’s Black Box, biochemist Michael Behe defines “irreducible complexity” as follows:
In The Origin of Species Darwin stated: “If it could be demonstrated that any complex organ existed which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down”. A system which meets Darwin’s criterion is one which exhibits irreducible complexity. By irreducible complexity I mean a single system composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease functioning.
Behe provides a mousetrap illustration that is helpful in this regard. He notes that a mousetrap is an irreducibly complex system: it is composed of five parts (a platform, spring, hammer, catch, and trigger), each of which is essential for the trap to work. A mousetrap with 80% of the parts does not catch 80% as many mice. Without a hammer, for example, the trap catches no mice. It simply does not work. All parts have to be in place for the trap to be functional.

The Irreducible Complexity Argument in a Nutshell

Behe’s broader argument is that IC systems are best explained by a mind rather than by mindless physical processes. We know from our repeated experience that intelligent agents create irreducibly complex systems—they can bring together an array of parts in order to achieve a particular outcome, whether that be a radio to catch soundwaves or a rocket ship to travel to space. By contrast, we know that stepwise physical processes, such as natural selection, must move towards immediate function (or else they wander stochastically, or perhaps even fail). For a process like natural selection to build some new feature, each step must confer a functional advantage that enhances the organism’s survival and reproduction. If not, the step is “blind” to natural selection, and there is no selective way to pass the trait on to the next generation. So, in human experience, gradual natural processes do not produce IC systems. But intelligent agents do. Thus, intelligent agency is a superior explanation for the origin of irreducibly complex systems.
Of the many examples of irreducible complexity that Behe cites, the most prominent is the bacterial flagellum. This organelle is a “true rotary engine” (Minnich and Meyer 2004) that propels a bacterium through liquid by rapidly spinning a whip-like tail. It operates much like an outboard motor. Indeed, both comparative biology and knockout experiments on the flagellum show that it requires many coordinated protein parts in order to function (Macnab 1987; Pallen and Matzke 2006). A machine of this intricacy—in which all essential parts must be in place prior to any function—requires explanation. Kojonen sees the power of Behe’s argument:
Since the core function of an irreducible complexity emerges only after all necessary parts are in place, it cannot plausibly be evolved in this direct way. After all, natural selection cannot select for a function that emerges only after all of the parts are in place, because selection cannot look to the future. Instead, the gradual evolution of the parts of a system like the flagellum would have to be favored by natural selection for some other reason, not because of increases in mobility.
Moreover, Kojonen acknowledges that even the claim of “indirect” evolution of the bacterial flagellum faces severe challenges and would even require some measure of “serendipity”:
Behe admits that an irreducibly complex system could in principle evolve in the tinkering, indirect fashion that Behe’s critics point to. However, he claims that, as the complexity of the system increases, the probability of such evolutionary accounts decreases. Because the proteins must fit together, the parts must be modified before serving in the new function. Thus, “analogous parts playing other roles in other systems cannot relieve the irreducible complexity of the new system; the focus simply shifts from ‘making’ the components to ‘modifying’ them” (Behe 2006, pp. 112–13). Orr (1996), who is otherwise critical of Behe’s work, surprisingly agrees with this criticism: “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”. Here, the appeal to our common human experience of designing things supports the inference that creating complex teleological order is difficult. There is, indeed, quite a bit of serendipity in parts useful for one purpose being so easily adaptable to another role.
How does Kojonen rise to the challenge? In the main, he cites protein homology, co-option (or exaptation), and protein evolvability. We will analyze each of these below.
But to appreciate the type of design manifest in the flagellum—and whether or not it is compatible with evolution, as Kojonen believes it to be—let us first consider the exquisite characteristics of this organelle.

5.2. The Exquisite Bacterial Flagellum

5.2.1. General Features

Harvard biologist Howard Berg has deemed the bacterial flagellum “the most efficient machine in the universe” (quoted in Dembski 2004, p. 324). It is not difficult to see why. It is a true machine, having some 35–40 protein parts, each of which has an individual function, and which together perform an integrated function—complete with short-term memory, self-assembly, and an efficiency that surpasses human engineering. The flagellum has a highly efficient proton-powered rotary engine that operates at up to 100,000 rpm. It is one of the best understood molecular machines in science (Minnich and Meyer 2004).

5.2.2. The Engineering Logic of the Bacterial Flagellum

The engineering logic of the bacterial flagellum has been detailed by engineer and computer scientist Waldean Schulz (2021a, 2021b, 2021c). He has demonstrated that rotary propulsion requires several tightly integrated systems: a flagellar motor and a filament, part delivery mechanisms, an assembly process, and a navigation system. Each is essential for the flagellum to function, each is composed of multiple proteins, and each must meet very tight constraints dictated by an overarching design logic.
Subsystems of the flagellum include:
Numerous articles have been written on the ingenuity of each of these mechanisms, some of which have even served as models for human innovation (Mohammadi et al. 2017; Jiang et al. 2021; Tachiyama et al. 2022). One biologist observed that, “…the flagellum is so well designed and beautifully constructed by an ordered assembly pathway, even I, who am not a creationist, get an awe-inspiring feeling from its ‘divine’ beauty” (Aizawa 2009).
Recall Kojonen’s earlier statement that the “crucial” issue concerning the evolution of proteins turns on “mutations”, including the number, timing, and rate needed to traverse from one functional protein to another. The challenge increases dramatically when assessing the origin of even one of the essential flagellar subsystems. For instance, undoubtedly, many mutations would be required for the ‘evolution’ of the flagellum’s navigation system (aka chemotaxis). To yield a functional system that provides an advantage to the organism, either all of these mutations would have to occur simultaneously—akin to a miracle—or each mutation (or set of mutations) would have to confer a functional advantage (or at least inflict no harm) at every step toward a fully operational system. Of particular note, the proteins composing the navigation system serve no other purpose in the bacterium, nor do they closely resemble any other proteins (see below). A partially materialized propulsion/navigation system, on the other hand, would not simply be “neutral” but rather disadvantageous to the cell given that the production of malformed proteins or some non-functional system would require energy to produce, yet would provide no offsetting benefit. In fact, because useless parts or proteins provide no advantage to the organism, they would likely be quickly degraded if not deleted (Gauger et al. 2010).
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.
So, just how does co-option plausibly explain the origin of the most efficient machine in the universe?

5.3. Indirect Evolution, Co-Option, Exaptation

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
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.
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’.

5.3.1. Co-Option on Its Own Terms

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.

5.3.2. Problem 1: Confusing Sequence Similarity with an Evolutionary Pathway

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 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.

5.3.3. Problem 2: Overstating Protein Homology

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 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% 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%.

Excursus on T3SS

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.
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.
Moreover, further 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.

5.3.4. Problem 3: Assembly Not Required?

Yet 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. 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.
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.
Like many of his evolutionary colleagues, Kojonen simply elides this problem.
Stepping back, it is important to reiterate that our main point in this section is not to critique evolutionary theory per se. Though Behe’s irreducible complexity argument does challenge mainstream evolution, our point instead is to critique Kojonen’s conjunction of ‘design and evolution’. Recall that Kojonen believes that complexity of the bacterial flagellum adds to his case for joining ‘design’ to ‘evolution’ (see esp. Kojonen 2021, p. 122). But Behe’s argument shows that the type of design manifest in the bacterial flagellum runs contrary to evolution. Thus, 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.

6. Convergent Evolution

We now turn briefly to convergent evolution which, in our estimation, serves as the basis for Kojonen’s most powerful positive argument for the laws of form (or “library of forms”). In Kojonen’s model, these forms are a key element of the preconditions that make evolution possible. Notably, he regards them as “an emergent consequence of the laws of chemistry and physics” (Kojonen 2021, p. 123). That is, they arise from the laws of nature. Recall that in Kojonen’s model, the laws of nature are designed. So, the laws of form play an important role in his conception of design and its explanatory value: evolution can only happen under certain conditions, and chief among these conditions are the laws of form, which are themselves the direct result of God’s design of natural laws. Thus, the laws of form connect design and evolution in a way that shows the added explanatory merit of design to assist evolutionary searches.
As noted, we regard “convergent evolution” as the most formidable argument that Kojonen provides for the existence of the laws of form. In what follows, we argue that Kojonen’s account of convergence drives a wedge between his acceptance of ‘design’ on the one hand and ‘evolution’ on the other. Once again, internal conflict comes to the fore.
To see this, some background on convergence is helpful. In Kojonen’s view, convergence itself “refers to the independent evolution of the same biological outcome in two or more different lineages, beginning from different starting points” (Kojonen 2021, p. 125). He observes, for example, that “dolphins and sharks have similar streamlined bodies and dorsal fins, even though dolphins are mammals and sharks are fish”. He also points out that paddle-shaped limbs for swimming “have evolved independently seven times, and a structure as complex as the eye has evolved independently 49 times…” (Kojonen 2021, p. 125). Kojonen interprets convergence as evidence for preconditions or, more specifically, that laws of form “play a significant role” in helping evolutionary processes cluster around similar solutions (Kojonen 2021, p. 125). He notes that the presence of similar features in the natural world, which are not explained by common ancestry, suggests to some thinkers that natural selection acting on random mutation may be directional or forced to move along certain fortuitous evolutionary pathways. Somewhat more modestly, Kojonen himself concludes that convergence shows “the evolution of Earth-like life is heavily influenced by functional constraints” (Kojonen 2021, p. 127). Put in the form of a rhetorical question, then, the general thought seems to be: if the same solutions independently arose over and over, doesn’t that suggest that the deck was likely stacked to allow evolution to succeed? (Kojonen 2021, p. 125)
Unfortunately, notable problems arise for Kojonen’s appeal to convergence. First, convergence relies on a great many improbable events. It not only requires the evolution of certain complex proteins, traits, and systems but the evolution of these things independently more than once. As just noted, Kojonen claims that the eye, in one form or another, independently evolved dozens of times. This means that the probabilities about protein rarity and isolation (described in Section 4) apply with even greater force. If the probability is prohibitively low of evolving even a single short protein one time in the entire history of the Earth, then, all things being equal, the probability of evolving this protein multiple times is proportionally greater.34 So much the more with entire systems of proteins, cell types, tissues, and organs. So, Kojonen’s appeal to convergence runs headlong into an a fortiori argument.35
Notably, this is a problem for Kojonen’s case for design: on his view, convergence points to the laws of form, and these laws in turn arise directly from the designed laws of physics and chemistry. So, convergence is indirect evidence of design. Yet if an evolutionary origin of convergence is implausible, then Kojonen’s case for design likewise suffers.
Second, and at a deeper level, Kojonen’s model falls prey to the horns of a troubling dilemma. This dilemma is a version of what philosopher of biology Paul Nelson has deemed “Sober’s Paradox” (Nelson 2022). The basic problem is that Kojonen’s beliefs about common ancestry conflict with his belief in convergence. His attempt to accept both claims fractures the unity of his model.
To see this, consider the first horn of the dilemma. If Kojonen retains evolutionary convergence, then he de-fangs his co-option response to Behe’s irreducible complexity argument. This is because co-option depends for its plausibility on similar protein parts in other systems serving as good candidates for modification into the specialized parts needed for the bacterial flagellum. As Kojonen explains about the flagellum, “The existence of similar parts in other systems, for example, does provide supporting evidence for evolvability” (Kojonen 2021, p. 118). But with ‘convergent evolution’, highly complex parts or systems—even more complex than the bacterial flagellum—can arise without similarity or common ancestry. Yet if that is plausible, what force does the co-option really have?
Moreover, Kojonen also undercuts his argument for protein evolution. His account hinges on mutation and selection’s ability to traverse from one functional protein to another. Presumably, it is easier for evolution to forge a new protein from a similar one rather than from a vastly different one. Otherwise, if it is just as plausible to claim that evolution can produce major innovations as it can minor changes, why bother to talk about gradual change from one similar functional protein to another? The force of the argument has been lost.
More generally, Kojonen’s acceptance of evolutionary convergence harms the justification of common ancestry in standard evolutionary thought. The received view is that similar structures are best explained by a common ancestor who also had a similar structure. On this view, it is more parsimonious to claim that a complex feature evolved once rather than twice. Whether this reasoning is correct or incorrect is irrelevant; the point is that it runs contrary to convergent evolution. If complex features are just as likely to arise independently multiple times as they are a single time, then it is extremely difficult to make the case for common ancestry (Luskin 2017). Once again, Kojonen has accepted a claim that renders his model internally unstable.
Matters do not get easier on the other side of the dilemma. If Kojonen retains his account of protein evolution, his co-option response to Behe, and the standard justification for common ancestry, then he harms the justification of evolutionary convergence. As we have seen, this is because each of these lines of argument (or reasoning) presupposes that it is more probable for biological complexity to have evolved once rather than multiple times independently. This crucial presupposition cuts the ground out from evolutionary convergence, which is committed to the idea that independent evolutionary lineages have produced similar features.
Moreover, Kojonen clearly regards convergence as important. Recall that he believes “[e]xamples of convergence are ubiquitous in biology” (Kojonen 2021, p. 125, emphasis added). The reason that these examples are said to be ‘convergent’ is because, in general, multiple lines of evidence—typically from genetics, paleontology, biochemistry, systematics, and the like—indicate that it is difficult to form a coherent phylogenetic account of their origin from a given common ancestor. These data count as anomalies under common ancestry. That is why evolutionary biologists regard them as the result of convergent evolution. Yet if Kojonen opts for the ‘common ancestry’ horn of the dilemma, then he must eschew convergence. But convergence is arguably his best argument for the laws of form and, indirectly, for the locus of design in the laws of physics and chemistry. This loss damages a significant feature of his model.36
In short, Kojonen is caught between a rock and a hard place. A familiar refrain sounds again: Kojonen’s understanding of (and justification for) ‘design’ conflicts both with his own reasoning (about co-option, etc.) as well as with the justification of common ancestry, a mainstay of ‘evolution’. His model is internally fragmented.
One of the most interesting features of Kojonen’s treatment of design is his exploration of the laws of form. But this particular argument for them—perhaps the best of the book—comes at a very steep price.

7. Design Detection Damaged

In this final part of our argument, we raise concerns about the epistemology underlying Kojonen’s model. In brief, our concerns are twofold: First, Kojonen’s proposal severely damages his own design argument. And second, his model also significantly damages the legitimacy of an everyday theist’s intuitive apprehension of design. This latter point is notable because Kojonen is keen to show that his model generally supports (or at least does not harm) the “theist on the street” who intuitively perceives design in the biological world (Kojonen 2021, pp. 32, 156, 162–64, 206).
In what follows, we first summarize key elements of Kojonen’s view of design detection. Second, we explain why these elements are problematic both for the justification of Kojonen’s biology-based design argument and for the “theist on the street”.

7.1. Kojonen’s View of Design Detection

In chapter five of CED, Kojonen lays out his views on design detection. He cites with approval the work of philosopher of science Del Ratzsch:
According to Ratzsch (2001), design detection typically works by first identifying artifactuality through identifying counterflow, properties that are contrary to what would be expected based on natural processes. However, when analyzing artifactual objects, features like complex teleology then function as secondary markers identifying intentional production, as opposed to what can also be accidental artifactual products, such as footprints. Here Ratzsch identifies both mind correlative order, which suggests design, and mind affinity, which almost inescapably suggests mind. He then argues that while design is typically detected by first observing counterflow, these secondary marks of design can actually provide grounds for design beliefs even in the absence of counterflow.
(Kojonen 2021, pp. 164–65, original emphasis)
This is a complex paragraph, but the basic idea is as follows: First, Kojonen seems to agree with Ratzsch that detecting design usually happens through a process that begins with “counterflow”. In this context, “counterflow” is, to use Kojonen’s language, that which runs “contrary to what would be expected based on natural processes”. (For a formal definition, see Ratzsch 2001, p. 5.) The idea is that a key step in detecting design typically involves understanding what nature would do when left to its own devices and then contrasting that with what one actually sees. For example, we know that it is unlikely that nature on its own would produce a forest with trees lined up in perfectly straight rows. If we find such a thing, we can justifiably conclude that some kind of mind was at work. Kojonen seems to accept Ratzsch’s point here.
But Kojonen also goes on to agree with Ratzsch that, even without counterflow, one can still reliably detect design. In some cases, we can justifiably say that something is designed even if it is the result of normal natural processes. This is why Kojonen speaks of “secondary marks” that include “mind correlative order” and “mind affinity”. (Mind affinity is simply a special case of mind correlative order. Both are characterized by a special stamp of ‘mind’—roughly, a deep connection with what minds do, operate, or produce (Ratzsch 2001, pp. 3–4, 14–15, 61–69, 134).) The basic idea is that, when a given object in nature exhibits a deep correlation with what minds (uniquely) do, a person can reliably believe that the object is designed—even if it is a product of nature’s normal operation.
As noted earlier, Kojonen illustrates this idea with a ‘moon crater’ scenario, also from Ratzsch. Kojonen asks readers to suppose that the first photos of the moon showed the text of John 3:16 written in craters on the surface (p. 165). Suppose further that there was a natural explanation for each crater (and asteroid). Suppose also that we could trace these natural explanations all the way to the big bang. “In this case”, writes Kojonen, “it seems that natural explanations simply do not explain the intelligibility of the pattern, even though they explain each individual crater” (Kojonen 2021, p. 165). The evidence of design remains clear, even if that design occurred at the beginning of the universe and was transmitted by natural processes across time and space. So, even when nature is acting in her normal way (with no interruptions or counterflow), we can still detect design in certain cases.
This allows Kojonen to say that his proposal still preserves our ability to detect design despite the fact that, in his model, the locus of design is at the origin of the laws of nature (e.g., Kojonen 2021, pp. 164–67). Both the professional biologist and the “theist on the street” can discern God’s handiwork even if nature has never been disrupted since its initial creation. In other words, if biological complexity arose via the laws of nature, we can still look at a given organism and reliably believe that it was designed—even if it is the direct result of unbroken laws going back to the big bang. In particular, this means that mainstream evolutionary theory’s appeal to only physical causes poses no threat to a biological design argument or to the direct intuitive apprehension of design enjoyed by everyday theists.

7.2. A Looming Epistemological Conflict

But this account is flawed. Kojonen’s understanding of design detection runs contrary to his acceptance of evolutionary theory and his placement of the locus of divine activity at the creation of the laws of nature. The tension is so significant that it undercuts his design argument and defense of the theist on the street.
To see this, consider how Kojonen replies to a key objection to his account of design detection. This objection asks: just how would we detect biological design if Kojonen’s model were correct? That is, if God created the laws of nature (along with the initial conditions), and this led to all subsequent physical, chemical, and biological phenomena, how exactly can we say that biological phenomena point to design more so than mere physical objects do? How can we claim, say, that the eye of the eagle provides better evidence of design than a couple of rocks on the ground? The whole point of Kojonen’s model is to show that biological design fits nicely with evolutionary theory.
Kojonen perceptively articulates the objection to his view as follows:
Why, then, should we think that there is something special about biology that gives grounds for the perception of design, as opposed to ordinary rocks, which also require the existence of a Creator?
Kojonen’s reply to this objection draws on his foundational understanding of how humans detect design. He provides several resources in this regard. One resource is, of course, his extended argument in CED. That is, Kojonen observes that someone who understands KEBDA can appeal to it in order to understand how biology in particular can evince design in a special way. In other words, if his long argument is correct, then biology points to design in a particular way because the biological data uniquely show the need for fine-tuned preconditions. And these preconditions are best explained by a Designer.
Of course, the problem with this response is that it only succeeds if Kojonen’s argument itself succeeds. Insofar as one has reason to doubt Kojonen’s argument, one likewise has reason to doubt his response to the objection. If our criticisms in this article are correct, then this line of reasoning is unconvincing.
Yet Kojonen also gives broader grounds for design detection. Notably, these grounds are available not just to specialists—who can follow the nuances of KEBDA’s use of fine tuning in biology—but also “theists on the street” who apprehend design by direct intuition or perception. In particular, Kojonen writes:
It seems to me that even if we did not know about the fine-tuning evidence, our experience of creating things, and observing the properties of life, should make us suspect that our cosmos must be fine-tuned to allow for the evolution of such properties. Assume a further principle that what requires most ability also best demonstrates the existence of that ability. Then, given that the production of complex biological organisms requires far more fine-tuning than the existence or something like rocks, biological organisms better demonstrate the fine-tunedness of the cosmos.
So, the basic idea is that when we notice the complexity of biological life, our own experience of making things (including, presumably, complex things) should make us suspect that the complexity of life likewise requires fine-tuning. And if biological organisms require more fine-tuning than, say, rocks, it is reasonable to hold that these organisms manifest design in a more robust way.
Elsewhere, Kojonen states the matter more simply: “we can know based on our own experience (and through the testimony of others) that it is difficult to produce this type of [biological] order, and that designing an automated process [analogous to evolution] to produce such order is more difficult still” (Kojonen 2021, p. 163). Once again, he refers to “our own experience” as well as that of other human beings. We know based on our first-person experience, and the reports of others, that it takes a mind to create certain things. One does not produce iPhones by waiting until nature gets around to it. Instead, it takes work, creativity, and a lot of fine-tuning.
Kojonen also adds a final element to his account of design detection (and reply to the objection)—namely, that human’s basic apprehension of design is grounded in certain prima facie intuitions. He writes in the next sentence:
Moreover, as Nagel (2012, p. 6) points out, the design intuition (and resistance to Darwinism as an unguided process) is often based on an “untutored reaction of incredulity to the reductionist neo-Darwinian account of the origin and evolution of life. It is prima facie implausible that life as we know it is the result of a sequence of physical accidents together with the mechanism of natural selection”.
Here, Kojonen seems to say that our “design intuition” often arises from a basic sense that unguided evolution cannot create the complexity of life we see around us, and that there must instead be a mind behind it all.
Thus, the key aspects of design detection in Kojonen’s model (and in his reply to the objection above) include: (i) our observations about the properties of life (including, presumably, its complexity), (ii) our own experience of creating things, including complex things, (iii) the experiences of others along these same lines, (iv) common sense reasoning about what it takes to build complex rather than simple things, and/or (v) our intuition of design in biology, which often arises from a basic sense of the creative limits of unguided nature. Put in the simplest way, these points collectively hold that, in our experience as agents, complex things require greater resources than simple things to make, and that nature can only explain so much. The complexity of life is better accounted for by mental agency rather than unguided nature—especially when it comes to, say, an eagle’s eye rather than simple rocks on the ground.

7.3. Mind over Matter

At the heart of these points is the common-sense idea that humans can exercise creativity (and produce fine-tuned systems) in a way that nature cannot. Indeed, Kojonen’s own design argument hinges on a similar idea. He writes, for example, “The cosmos must be special indeed to allow for the evolution of the kind of complex teleology and the large variety of creatures that we observe. And this feature of the cosmos… is explained better by a theistic view than by supposing that this feature is due to chance” (Kojonen 2021, p. 162). Theism explains complex teleology and biological diversity better than chance does. God’s agency is a better explanation than chance, because agents can create things that nature (and its contingency) cannot.
This general line of reasoning lies at the center of Kojonen’s attempt to unite ‘design’ and ‘evolution’. As we have seen, Kojonen argues extensively that evolution on its own cannot search and find viable biological forms. It requires preconditions of just the right kind—a Goldilocks arrangement. He writes, for example, about “the kind of fine-tuning of the landscape of forms that seems to be required to evolve the kind of biological order described by Behe” (Kojonen 2021, p. 122).37 And these ’fine-tuned’ preconditions are best explained by a Designer. This whole line of thinking presupposes that some phenomena are beyond the reach of unaided nature but can only be explained by a mind. Agents have powers to create (or fine tune) in ways that nature does not.
A similar presupposition informs the other cognitive resources that undergird Kojonen’s understanding of design detection. He notes that “design intuition” is often based on deeper intuition about the limits of physical accidents and natural selection—the limits of nature acting on its own, more or less. A similar presupposition underlies Kojonen’s appeal to “our experience” of building complex things, rather than simple ones. We know it takes mental effort to do so. And Kojonen believes this fact, coupled with our realization of nature’s complexity, should lead us to suspect that there is a mind behind it all. Why? Because we know that minds can do things nature cannot.
Kojonen’s own moon crater analogy nicely illustrates this point. Recall that the illustration was supposed to show that we can detect design even when we encounter unaided nature. That is, even without disruptions in the course of cosmic history, we can still reliably detect the activity of an original Designer. The analogy makes us think, “Yes, there would have been a mind that caused the message”. Why? Because we have a lot of reliable experience of agents who have abilities different from (and beyond) the abilities of nature. We know that natural laws do not create messages. That is why we say the John 3:16 message is not fully explicable by natural law. We also know that agents possess the unique power to write messages. That is why we immediately recognize design. In our experience, only minds do that sort of thing, not nature. The analogy succeeds to the extent that we are justified in maintaining that minds exercise greater creative powers than nature does.
A similar point can be made about Kojonen’s other analogies, illustrations, and metaphors about design and its detection (including the detection of indirect design). These include the VCR factory analogy, castle-building metaphor, Mats Wahlberg’s fugues analogy, analogy to human technology, Asa Gray’s mechanical loom, and so on. (Kojonen 2021, pp. 157–74, esp. 164–74; Kojonen 2022a). In all cases, the detection of design, including indirect design, depends upon the fundamental insight that the creativity of minds exceeds that of nature. The apprehension of complexity only reliably triggers a belief in (or inference to) design if minds can create complexity that nature cannot.
Collectively, then, Kojonen’s formal argument, cognitive resources, and key illustrations all rest on the basic insight that minds have creative powers greater than that of nature. This is the heart of his understanding of design detection.

7.4. Kojonen’s Model Undercuts Itself

But Kojonen’s own model undercuts this pivotal insight. His particular views of ‘design’, along with his acceptance of mainstream ‘evolution’, harm his own understanding of design detection. His model damages the very foundation upon which it rests. Notably, our critique does not presuppose that evolution is false or that it occurs without design (see Kojonen 2021, pp. 145–46). Instead, we will assume for the sake of argument that Kojonen’s model is correct in the sense that (i) evolution is true, and (ii) design is located at the origin of the laws of nature. From this vantage, we raise three epistemological worries, which collectively build on each other.38

7.4.1. Element 1: Direct vs. Indirect Design

The first concern centers on the distinction between ‘direct design’ and ‘indirect design’. The former is due to the immediate action of an agent, whereas the latter is due to action of an agent that has been (or is) mediated by some other process, entity, or event. Direct design occurs when God creates a type of organism by His own hand; indirect design is when He organizes the big bang and lets natural laws take it from there, for example.
In our lived experience, humans readily attribute direct design to various types of biological phenomena. (This is not only true of “theists on the street”, for example, but also of some other people as well.) For example, consider a person who sees a hummingbird for the first time. A natural reaction is to think that this type of bird was directly designed. (“Wow! That’s spectacular. Somebody made that!”) In fact, humans often experience things like hummingbirds as distinct entities—what Axe (2016, pp. 65–86, esp. 71) calls “busy wholes” or what one might call “natural kinds”. That is, humans often experience an entity like a hummingbird as a certain type of thing, and they naturally believe that this type is the result of direct design. By contrast, it is rarely the case that, upon seeing a hummingbird for the first time, a typical person would say, “Wow! That’s specular. Somebody indirectly created that by a process of secondary causes over millions of years”. Instead, many people believe that a designer directly crafted the first instance of a given specimen or feature. (“God made the first hummingbirds, then they reproduced”.) Whether rightly or wrongly, human beings routinely apprehend (or infer) direct design when they encounter the power, beauty, and complexity of organisms or organs.
Yet in Kojonen’s model, these beliefs in direct design are uniformly false. In his view, there is no direct design of biological phenomena. All biological diversity and complexity are the result of indirect design. The locus of design was billions of years prior to the advent of life on Earth. (Indeed, even if Kojonen were to locate direct design at the origin of life, all subsequent flora and fauna would still be the result of indirect design.) This simply follows from Kojonen’s understanding of design (and of evolution). So, if Kojonen’s proposal were true, human beings who accepted his view would have a serious defeater for their ‘direct design’ beliefs about biological organisms and features. They would realize that they have little or no grounds to trust their minds in this context. Indeed, if they had an intuitive belief, based on biological data, that the human species was directly designed, they would likewise be mistaken. Humans and their array of unique capacities ultimately came from the same event that gave rise to rocks and stardust. Again, a person in this situation would have a defeater for her belief in direct design.
Something similar is true of the common intuition that an eagle’s eye appears to be more designed than a couple of rocks. But in Kojonen’s model, both are the result of the same event. The eye of the eagle seems directly designed, but it is not any more so than a mere rock. This, too, is a defeater for such a belief.
But then how would a person in this general situation know that the laws of physics and chemistry were directly designed, as Kojonen believes them to be? Recall that his argument for design is supposed to be based on biological phenomena. But if his model were correct, humans would have no cases of biological things that seemed to be directly designed actually turning out to be directly designed. So, if there are no such cases—and these cases are the basis for believing that the laws of nature are directly designed—then the ground for believing that the laws are directly designed is very poor indeed. If a baseball player strikes out in his first 23 plate appearances, what basis does he have to believe that he will get a hit at his next at-bat?39
In effect, Kojonen’s model undermines its own design argument. To succeed, Kojonen needs some basis in biology to say that the laws of nature were directly designed. (If he appeals to the big bang model in cosmology or fine-tuning in physics, as opposed to the data of biology, then he has essentially cast aside the heart of his model. See Kojonen (2021, pp. 131–32).) Unfortunately, in Kojonen’s own proposal, biology itself ends up providing defeater after defeater for ‘direct design’ beliefs. This undercuts the basis for his claim that the laws of nature are directly designed.
This is our first concern. Two other concerns (below) build on this one and cover other aspects of Kojonen’s account, including other resources he has for design detection.

7.4.2. Element 2: Continuity of Non-Agent Causes

In the previous section, we offered a counter to Kojonen’s claim that, in his model, an informed person can know, based on apprehension of biological things, that the laws of nature are directly designed. In what follows, we expand our concern to whether a similarly informed person would know that biological phenomena were designed (again, granting Kojonen’s model for the sake of argument). This second problem builds on the first problem. If Kojonen’s model were true, not only would all cases of ‘direct design’ beliefs about biological phenomena be false, but a person who accepts the model would also believe that non-agent causes are proximately sufficient to bring about any given biological phenomenon. (In this case, ‘non-agent’ causes would include evolutionary causes but not be limited to them. It would also include other physical causes as well as the causal effects of platonic “laws of form”, appropriately interpreted, if any. A ‘non-agent’ cause does not reject agent causes per se; it simply does not invoke them.40) For example, if Kojonen’s model were true, a person who accepted the model would believe that, despite her ostensible prima facie belief that, say, a designer directly crafted an eagle’s eye or the first hummingbirds, it is actually the case that each of these phenomena are proximately explained by non-agent causes. For each biological organism or feature, there would be continuity of non-agent causes from before that entity’s existence that led up to (and through) the advent of that entity. Indeed, this continuity would extend all the way back in time. (In fact, there might not be any particular reason, based in biology, to think there was a big bang.) A person who accepted this model would believe that non-agent causes gave (proximate) rise to case after case of biological complexity. The same would be true for human beings, too. An unbroken chain of non-agent causes from the ancient past would extend up to (and through) the rise of the first humans, whoever they happened to be.
The question, then, is: on what grounds would a person in this position believe that biological phenomena were designed? Or, put differently, on what grounds would a person in this situation believe that non-agent causes are insufficient to explain biological complexity? What grounds are there to invoke a designer? The continuity of non-agent causes from the inorganic realm to (and through) the organic realm makes this a difficult question. By contrast, discontinuity from the inorganic to organic realms (or from episode to episode in organic history) might suggest that a designing agent added new information or direction. But according to Kojonen, there is no such discontinuity.
Of course, Kojonen might point out that the whole point of KEBDA is to show that evolution on its own is insufficient to search and find viable biological forms. It needs fine-tuned preconditions, and these are best explained by a designer. But this response misses the point. What this response fails to consider is that, even if evolutionary processes as such are insufficient, in his model, there is still continuity of unbroken, non-agent causes from ancient cosmic history through the origin of life and through the advent of all instances of biological complexity, including of human beings. Evolutionary causes are only one type of ‘non-agent’ cause. There are other processes that are in play; all of these are non-agent causes. None of them are the direct action of an agent. A human being who apprehended and accepted this unbroken continuity would have no reason per se to believe that biological phenomena were the result of a designing agent at any time in the past. In fact, the strong continuity of non-agent causes might in fact suggest the opposite. (And again, to try to counter this by appealing to big bang cosmology or fine-tuning in astrophysics is to miss the point of Kojonen’s biology-based model.) To be sure, on Kojonen’s view, biological phenomena (and evolution) ultimately depend on a Designer. But even when we grant this claim, it does not follow that a person in this situation would have sufficient evidence to believe that (Kojonen 2021, pp. 145–46).41

7.4.3. Element 3: The Foundations of Design Detection

Despite our arguments above, a critic might wonder: “But what about Kojonen’s other resources for detecting design, including the human experience of creating complex things? And doesn’t the sheer complexity of biological phenomena justify design beliefs in some way, despite the negative implications Kojonen’s model has for ‘direct design’ beliefs? For example, doesn’t the moon crater illustration show that certain kinds of complexity reliably trigger design beliefs (or inferences to these beliefs) despite the concerns noted above?”
Alas, the answer is no. It is true, of course, that Kojonen’s various illustrations are helpful and stimulating in this regard. These include the VCR factory analogy, castle-building metaphor, Mats Wahlberg’s fugues analogy, analogy to human technology, Asa Gray’s mechanical loom, and so on. (Kojonen 2021, pp. 157–74, esp. 164–74; Kojonen 2022a). And Kojonen’s sophisticated KEBDA argument is also stimulating on this front as well. But Kojonen’s illustrations, as well as his design argument itself, are based on his more fundamental view of design detection. And his model undercuts this very foundation.
Recall that Kojonen’s view of design detection was anchored on five elements: (i) our observations about the properties of life (including, presumably, its complexity), (ii) our own experience of creating things, including complex things, (iii) the experiences of others along these same lines, (iv) common sense reasoning about what it takes to build complex rather than simple things, and/or (v) our intuition of design in biology, which often arises from a basic sense of the creative limits of unguided nature. Collectively, these points hold that, in our experience as agents, complex things require greater resources than simple things to make, and that nature can only explain so much; design is needed to account for the complexity of life. These are the fundamental resources (and insights) that Kojonen marshals as the basis for humans’ ability to detect design. But Kojonen’s model raises problems for each of these resources.
To see why, note first that (i) above (about life’s complexity) serves as the explanandum. It is not itself an explanation. The remaining four points attempt to provide an explanation. Second, consider points (ii) and (iii) above, humans’ experience of creating complex things. As we have seen, a person who accepts Kojonen’s view would lack evidence that humans were directly designed. Instead, they would believe that human beings and their cognitive abilities arose from the seamless continuity of non-agent causes that extend billions of years in the past. As such, it would be difficult to know whether human creativity (and design) is a legitimate category of explanation above and beyond the powers of natural processes and non-agent causes. For all one could tell, human creativity is simply another manifestation of non-agent processes that extend back indefinitely in time. ‘Human creativity’ could be suitably different than the ‘creativity of non-agent causes’, but the evidence of organic (and inorganic) history would not necessarily suggest anything of the kind.
For many human beings (including “theists on the street”), their creative experience helps show the limits of unguided nature as well as the need for a designer. Yet this is precisely what ‘continuity’ obscures: biological history (and inorganic history prior to it) no longer offer reason to think that nature (or non-agent causes) is limited in this way. As a result, for a person who accepts Kojonen’s model, the idea that ‘minds have creative powers that nature lacks’ no longer has a substantial basis. For all she can tell, human creativity is simply a product of mindless forces, which extends back indefinitely. So, one’s experience of creating complex things does not give her any particular reason to believe that design is necessary to explain complexity in biology.
Similarly, point (iv) above also falters: humans’ commonsense reasoning about what it takes to build complex things would no longer serve as a strong basis to infer (or apprehend) design. That is because, again, a person who accepted Kojonen’s model would realize that every case of the emergence of biological complexity in organic history is preceded by non-agent causes that, for all one could tell, are sufficient to account for the entity in question. For all one could tell, proximate non-agent causes have produced biological complexity that includes—and exceeds—the feats of human engineering. Our commonsense reasoning that ‘complexity requires a mind’ would not per se find support in organic (and inorganic) history.
Once again, the alleged merit of KEBDA is beside the point. Even if evolution on its own is insufficient, Kojonen still holds that non-agent causes run in continuity from the inorganic to the organic, and then through every episode in organic history. There is no discontinuity, and so it is unclear—based on biology—whether a designer is required.
Moreover, this same reasoning undercuts Kojonen’s final element of design detection: a person who accepts Kojonen’s model would no longer have grounds for her intuitive belief that unguided natural processes have only limited creative power. This is for the same reasons as those we have just explored. After all, her view of the organic world is one in which non-agent causes seem to account for complexity after complexity. They even apply to human beings and their unique cognitive and creative powers. The evidence available to her would not indicate, in itself, that nature is limited. Indeed, ‘continuity’ might rather suggest just the opposite.
This cuts the ground out from beneath Kojonen’s many metaphors and illustrations of design and its detection (including indirect design and its detection). These include the moon crater example, Wahlberg’s fugues, the VCR factory analogy, the castle-building metaphor, the analogy to human technology, Asa Gray’s mechanical loom, and so on. In all cases, these examples depend upon one or more of the principles above, including the experience of creating complex things, common-sense reasoning about what it takes to make a complex (or fine-tuned) system, or intuitions about the creative limits of unguided nature. But Kojonen’s model erodes these very foundations.42

7.5. Brief Conclusion

Thus, Kojonen’s model harms each of the elements of his account of design detection, including humans’ own experience of creating complex objects. If Kojonen’s view of design (and of evolution) is true, then a person who accepts it is in trouble: the model undermines the very grounds it relies on. Kojonen’s proposal undercuts the epistemological resources that it needs to enable design detection.
Moreover, a person who accepted Kojonen’s model would have defeaters for her (intuitive) belief that the laws of nature are directly designed, biological organisms and organs are designed, and that some biological phenomena, such as the eye of an eagle, display greater evidence of design than simple rocks do. Whether such a person is a seasoned expert or an everyday “theist on the street”, this same set of limitations applies to whoever accepts Kojonen’s view.

7.6. The Theist on the Street and a Helpful Design Detection Analogy

An important goal of Kojonen’s proposal is to affirm the rationality of “theists on the street” regarding their intuition that life was designed. Yet his model undercuts that intuition. To further appreciate why, consider this question: What if the universe really were as Kojonen describes? That is, what if humans (including theists on the street) were born into such a world and developed their cognitive abilities in it? Would they actually have the dispositions and beliefs that Kojonen thinks undergird our current ability to detect design? There are good reasons to believe the answer is “no”.
An analogy may help in this regard. Imagine a jury being asked to try a court case about an allegedly fraudulent casino that was accused of rigging slot machines to yield winning jackpot combinations far less than they should, statistically speaking. On these particular slot machines, there are four reels with 10 symbols on each reel. The machines will pay out a jackpot when the symbols on all four reels line up with an identical symbol—a cherry—something that should happen, on average, 1 in every 104 spins, or 1 in every 10,000 spins.
The prosecution presents evidence that the casino’s machines are producing jackpots far less than they ought to. In fact, the prosecution’s team of experts tested the slot machines and found they only pay out a jackpot 1 in every 100,000 spins—an order of magnitude less frequently than they should.
The defense then takes its turn and makes a counterargument: “Actually, we live in a very special universe where the physical laws that govern slot machines (and their statistical odds) are fine-tuned such that things always happen about an order of magnitude less frequently than you’d expect. In fact, the ‘weird’ behavior of these slot machines proves our theory is true!”.
But how did the defense know that in our “special” universe, “things always happen about an order of magnitude less frequently than you’d expect”? They could only know this based upon background knowledge of how often things ought to happen (in this case, that there ought to be a win 1 in every 10,000 spins) and then, on this basis, compare the behavior of the slot machines to show that winning was occurring actually far “less frequently than you’d expect”.
The problem for the defense’s argument is that if we if we really lived in their universe, then all our knowledge of physical laws and statistics and slot machines would be based upon our experience in that universe. And if the defense’s argument was true then, based upon our experience in that universe, we should “expect” a win 1 in every 100,000 spins—not 1 in every 10,000 spins—and thus the slot machines at stake in the case should appear to be behaving perfectly normal. Thus, in the defense’s universe, we could never know that things were happening “an order of magnitude less frequently than you’d expect”.
The defense must answer this question: If we lived in their universe, how could they possibly “know” that the slots were producing wins less likely than they should? In their universe, the slot machines should behave exactly as experience would suggest—so they could never argue that things were behaving in a weird way. But the fact that the slots are behaving weirdly suggests that the defense’s “fine-tuned universe” argument cannot be true.
This analogy invites us to consider the epistemological effects of living in a universe described by Kojonen’s model (in which evolution is true, design is confined to the advent of the laws of nature, and biological data are in view). In this universe, it is not clear that humans (including theists on the street) would have the basic epistemological dispositions or beliefs that Kojonen believes undergird our ability to detect design in biology. For example, people who grew up in this universe would not likely believe that nature (i.e., non-agent processes) have only limited ability to build biological complexity. After all, in this universe, the continuity of non-agent processes across the advent of everything from bacteria to blue whales seems to suggest that non-agent causes are quite creative. Similarly, people who grew up in this universe would not likely believe that our own experience of creating complex things is at all relevant to the claim that ‘minds have greater creative power than nature does’. Instead, they would likely believe that our minds are simply a manifestation of nature’s creativity (or the creativity of non-agent causes). A similar line of thinking applies to the other elements of design detection discussed above. The bottom line is that human cognition would likely be significantly different in Kojonen’s universe than we actually experience it to be. Conversely, the fact that we have the particular cognitive dispositions and beliefs that we currently possess—instead of the ones we’d have in Kojonen’s universe—suggests that we live in a world notably different than captured in Kojonen’s model. Thus, in a particular sense, Kojonen’s model is inconsistent with the lived experience of some humans, including some theists on the street. This seriously harms the plausibility of his proposal, including its defense of everyday theists.

8. Summary and Conclusions

We have come at last to the end. The salient question in this article is one that Kojonen himself addresses: Are two explanatory appeals better than one? Why bother with ‘design’ if one already accepts ‘evolution’? Kojonen’s task is to show that the conjunction of ‘evolution and design’ is explanatorily superior to ‘evolution’ alone. To succeed, he needs to show that adding ‘design’ increases evolution’s explanatory value in a way that offsets the liability of violating Ockham’s razor. Kojonen holds that the kind of ‘design’ that fits the bill is the type in which God created the laws of nature, which ultimately lead to fine-tuned “preconditions” (and smooth fitness landscapes) that enable evolution to occur. Kojonen gives several lines of evidence for this view, including research on fitness landscapes, the bacterial flagellum, evolutionary algorithms, convergence, and so on. His task is to show that this evidence makes his view of ‘design’ sufficiently robust and plausible to add explanatory merit to ‘evolution’.
In this article, we argued that Kojonen’s account of design is flawed. It requires fine-tuned preconditions (and smooth fitness landscapes) so that evolution can successfully search and build viable biological forms. Yet empirical evidence shows that no such preconditions or fitness landscapes exist. At precisely the place we would expect to find evidence of Kojonen’s type of ‘design’, we find no such thing. Accordingly, his view of design is at odds with the evidence itself. As such, it is poorly situated to add explanatory value to evolution.
We also contended that Kojonen’s conjunction of ‘design’ and ‘evolution’ is internally fragmented. Recall that Kojonen believes that the complexity of the bacterial flagellum adds to his case for joining ‘design’ to ‘evolution’. Yet Behe’s irreducible complexity argument shows that the type of design manifest in the bacterial flagellum runs contrary to mainstream evolution. Thus, the very system that provides strong evidence of design also undercuts evolution. In effect, this drives a wedge between the two. Kojonen’s conjunction of ‘design and evolution’ is at war with itself.
We also highlighted the internal tension in Kojonen’s attempt to join ‘design’ and ‘evolution’ with respect to convergent evolution. Kojonen draws on convergence as a key argument for the “laws of form”, which are an important element of fine-tuned preconditions and, thus, his case for design. Yet convergent evolution conflicts with Kojonen’s use of co-option and approach to protein evolution. It also conflicts with the general justification of common ancestry. Thus, this element of Kojonen’s case for design chaffs against his own reasoning as well as mainstream evolutionary thought. Internal discord surfaces once again.
In each of these criticisms, we have not targeted evolutionary theory itself. Although we believe that the scientific evidence we have covered counters mainstream evolution, we have set this concern aside in this article. Instead, our criticisms are aimed at Kojonen’s conception of design. We have contended that he does not offer sufficient empirical support for it—and so it adds little explanatory merit to ‘evolution’—and that some of the evidence he does offer actually conflicts with his commitment to evolution, producing incoherence within his model. (We should note, however, that because of the way Kojonen frames the matter, our criticisms of his view of design do have negative implications for the feasibility of evolutionary theory as he understands it. But this is an implication of our argument based on his own framing. It is not the focus of our argument per se. We will return to this point momentarily.)
Finally, we raised epistemological concerns aimed at the fundamental basis of Kojonen’s understanding of design detection. If our concerns are correct, then they cut deeply against Kojonen’s design argument as well as his defense of the theist on the street. In a nutshell, our worry is that a person who takes Kojonen’s model seriously—or who lived in such a universe—would either have defeaters for her biology-based design beliefs or might not have the cognitive dispositions and beliefs that (in our experience) are foundational to the formation of such beliefs in the first place. Kojonen’s reliance on evolution (and non-agent causes) undermines his basis for design detection, in short.
Stepping back, it is important to reiterate, once again, the many strengths of Kojonen’s treatment. The extensive review we have given here is a credit to a book of remarkable sophistication, precision, and erudition. Only a venerable fortress is worthy of a long siege. The Compatibility of Evolution and Design is the best of its class.
Even so, we bring this article to a close on a poignant note: Kojonen’s model may have devastating implications for mainstream evolutionary theory. Recall that the heart of his proposal is that evolution needs design (in the form of fine-tuned preconditions). Evolution on its own is insufficient to produce flora and fauna. But if we are correct that Kojonen’s conception and justification of design are flawed, then it follows—by his own lights—that evolution is impotent to explain biological complexity. Kojonen’s own account of the efficacy of evolution depends upon the success of his case for design. But if the latter stumbles, then so does the former. In a startling way, Kojonen has set the table for the rejection of evolution. If he has failed to make his case for design, then he has left readers with strong reasons to abandon mainstream evolutionary theory. The full implications of this striking result warrant further exploration.

Author Contributions

All authors contributed to all sections of this paper but the most significant contributions are as follows: Abstract, C.L. and S.D.; Introduction, S.D.; Summary of The Compatibility of Evolution and Design, S.D.; Why Scientific Evidence Is Crucial, S.D.; Scientific Problems for Kojonen’s View of Proteins, B.M. and C.L.; Scientific Problems for Kojonen’s View of the Bacterial Flagellum, C.L. and S.D.; Convergent Evolution, S.D. and E.R.; Design Detection Damaged, S.D. and C.L.; Summary and Conclusions, S.D. All authors have read and agreed to the published version of the manuscript.


Funding provided by the Discovery Institute.

Institutional Review Board Statement

Not applicable.

Informed Consent Statement

Not applicable.

Data Availability Statement

No new data were created or analyzed in this study. Data sharing is not applicable to this article.


The authors would like to acknowledge the reviewers of this paper for their helpful feedback.

Conflicts of Interest

The authors declare no conflict of interest.


All of this depends, to a notable extent, on a given person’s background beliefs.
To elaborate, for example, Kojonen writes: “[I]f the salvaging operation is to be successful, the evidence of biological teleology needs to be shown to provide at least some support for the rationality of religious belief, even while accepting evolutionary explanations as true or probably true” (Kojonen 2021, p. 5, emphasis added). And: “the biological design argument developed here should be understood as a primarily philosophical argument, rather than a scientific one” (Kojonen 2021, p. 6). “However, in this book, the validity of the essential scientific claims of evolutionary biology will be accepted as the starting point of my inquiry. I invite proponents of ID, as well, to assume the plausibility of evolution for the sake of the argument, and to join me in asking if the falsity of the conclusion of design really follows from it” (Kojonen 2021, p. 7, emphasis added).
As we understand him, Kojonen does not exclude divine interventions from organic history in the sense of prohibiting them or even as a supplement to evolutionary processes per se. Instead, he is simply interested in building an account that does not require any such inventions. See Kojonen (2021, pp. 28–30, 145–204) and Kojonen (2022b).
Kojonen states that the “preconditions” of evolution, including the “library of forms”, are “an emergent consequence of the laws of chemistry and physics” (Kojonen 2021, p. 123).
For more on conjunctive explanations and (also) explanatory goodness, see Glass (2012, 2022), Glass and McCartney (2014), (Glass and Schupbach, forthcoming), and Glass (2017).
Kojonen (2022b) outlines the problem and his general solution:
Evolution is commonly understood to explain teleology (or the appearance of teleology) itself via reference to a non-teleological process. It is understood as an attempt to reduce teleology to non-teleological causes, and in this way explain the very same evidence that was the given as grounds for inferring design. Thus, once we already have an explanation for biological teleology by way of Darwinism, it is then argued that we no longer have a need for any further explanations. The traditional Darwinian claim is that the question “what processes are responsible for the apparent teleology of biological nature” has already been definitely answered by the theory of evolution, with no need for further explanations. However, if evolution is understood to depend on “laws of form” and to act more as a search engine than as an independent creator like the architect, then it seems to me that Darwinism pushes back the question of the general origin of biological teleology to the laws of nature, and does not yet fully explain this teleological order. If natural selection works, then it can be asked whether its functionality is better explained by reference to design or by reference to chance. This would leave room for a theistic conjunctive explanation of teleology, following Gray’s line of argument on the dependence of evolution on design.
Kojonen believes that the detectability of design can be discerned by rigorous argument, common sense, and/or intuitive apprehension, given certain background beliefs and other considerations.
See Footnote 3.
Kojonen also holds that his model allows for elements of both contingency and directionality together in complementary ways (Kojonen 2021, p. 131).
Kojonen also cites the work of Wagner and others in support of his view (Kojonen 2021, pp. 123–35). See our discussion below.
Kojonen (2021, p. 122) frames the matter as follows: “It seems, then, that defending the power of the evolutionary mechanism requires assuming that the landscape of possible biological forms has some fairly serendipitous properties…. The ability of evolution to generate teleology appears to depend on teleology…” So, the need for preconditions, smooth fitness landscapes, and the like is part of Kojonen’s case for design or “teleology”. It is precisely the ‘design’ of these “serendipitous properties” that allows ‘evolution’ to succeed. But if empirical evidence shows that no such “properties” exist, then Kojonen’s appeal to design (in this instance) does not add explanatory benefit to his account of how evolution can find biological forms.
A brief word about Kojonen’s analysis of evolutionary algorithms is in order. Kojonen draws on the work of ID thinkers, such as William Dembski, to argue that evolution on its own is insufficient to explain the rise of biological complexity and diversity (Kojonen 2021, pp. 97–115). In his response to Kojonen’s account, Jeavons (2022) focuses on Kojonen’s argument that biological fitness landscapes were fine-tuned so that evolutionary searches would achieve predetermined outcomes. Although Jeavons (2022) does not frame it as such, his insightful analysis of evolutionary algorithms poses severe challenges to Kojonen’s premise that the landscapes could have been sufficiently fine-tuned solely due to fine-tuning of the laws of physics and the universe’s initial conditions. Jeavons (2022) states that “additional feedback mechanisms must generally be added to modify the properties of the evolutionary algorithm in a goal-directed way during a run, based on some information about its current performance”. He then states that the adjustments must be based on such variables as the current population and individuals’ current fitness. Consequently, no fitness landscape resulting solely from the initial fine-tuning would allow for an effective evolutionary search in every biological context. For example, if a search was performed effectively for large populations of ants in the late Cretaceous period in one environment, it would likely not allow for successful evolutionary searches in many other contexts, such as the evolution of the first cetaceans. Instead, multiple infusions of new information would have been required to continuously tailor evolutionary searches to achieve desired outcomes. Jeavons (2022) states, “to achieve significant results, an evolutionary algorithm must be carefully tailored to the problem in hand, and the problem itself must have appropriate properties”. Somewhat curiously, neither Kojonen (2022b) nor Jeavon himself acknowledge or solve these difficulties for Kojonen’s model.
Proteins carry out the large majority of the work in a given cell, so they are crucial for virtually all forms of biological life.
More fully, ‘sequence space’ is roughly all the possible ways that amino acids can be linked together. Of these many different ways, only a small percentage actually produce a functional protein. By way of analogy: There are many ways that letters in the English alphabet can be arranged in, say, a one-hundred-letter sequence. But of all these ways, only a tiny fraction will form meaningful English sentences. Similarly, only a tiny fraction of the ways that amino acids can be combined will actually produce functional proteins. In short, it is a needle-in-a-haystack scenario.
Elsewhere in CED, Kojonen cites in support of his view of the “laws of form” the work of Michael Denton and others (Kojonen 2021, pp. 123–25). He also explores convergent evolution, drawing in particular on the work of Simon Conway Morris (Kojonen 2021, pp. 125–28). Our discussion below also applies to the work of these thinkers, mutandis mutatis.
Other experiments by Gauger et al. (2010) broke a gene in the bacterium E. coli required for synthesizing the amino acid tryptophan. When the bacteria’s genome was broken in just one place, random mutations were capable of “fixing” the gene. But when just two mutations were required to restore function, Darwinian evolution became stuck, unable to restore the full function.
For example, Venema (2018) cites intrinsically disordered proteins (IDPs), noting they “do not need to be stably folded in order to function” and therefore represent a type of protein with sequences that are less tightly constrained and are presumably therefore easier to evolve. Yet IDPs fulfill fundamentally different types of roles (e.g., binding to multiple protein surfaces) compared to the proteins with well-defined structures that Axe (2004) studied (e.g., crucial enzymes involved in catalyzing specific reactions). Axe (2018) also responds by noting that Venema (2018) understates the complexity of IDPs. Axe (2018) points out that IDPs are not entirely unfolded, and “a better term” would be to call them “conditionally folded proteins”. Axe (2018) further notes that a major review paper on IDPs cited by Venema (2018) shows that IDPs are capable of folding—they can undergo “coupled folding and binding”; there is a “mechanism by which disordered interaction motifs associate with and fold upon binding to their targets” (Wright and Dyson 2015). That paper further notes that IDPs often do not perform their functions properly after experiencing mutations, suggesting they have sequences that are specifically tailored to their functions: “mutations in [IDPs] or changes in their cellular abundance are associated with disease” (Wright and Dyson 2015). In light of the complexity of IDPs, Axe (2018) concludes:
If Venema (2018) pictures these conditional folders as being easy evolutionary onramps for mutation and selection to make unconditionally folded proteins, he’s badly mistaken. Both kinds of proteins are at work in cells in a highly orchestrated way, both requiring just the right amino-acid sequences to perform their component functions, each of which serves the high-level function of the whole organism.
Venema (2018) also argues that functional proteins are easy to evolve. He cites Neme et al. (2017), a team that genetically engineered E. coli to produce a ∼500 nucleotide RNA (150 of which are random) that encode a 62 amino-acid protein (50 of which are random). The investigators reported that 25% of the randomized sequences enhance the cell’s growth rate. Unfortunately, they misinterpreted their results—a fact pointed out by Weisman and Eddy (2017), who raised “reservations about the correctness of the conclusion of Neme et al. that 25% of their random sequences have beneficial effects”. Here is why they held those reservations: the investigators in Neme et al. (2017) did not compare the growth of cells containing inserted genetic code with normal bacteria but rather with cells that carry a “zero vector”—a stretch of DNA that generates a fixed 350 nucleotide RNA (the randomized 150 nucleotides are excluded from this RNA). Weisman and Eddy (2017) explain how the zero vector “is neither empty nor innocuous”, since it produces a “a 38 amino-acid open reading frame at high levels” of expression. Yet since this “zero vector” and its transcripts provide no benefit to the bacterium, its high expression wastes cellular resources, which, as Weisman and Eddy (2017) note, “is detrimental to the E. coli host”. The reason the randomized peptide sometimes provided a relative benefit to the E. coli bacteria is because, in some cases (25%), it was probably interfering with production of the “zero vector” transcript and/or protein, thus sparing the E. coli host from wasting resources. As Weisman and Eddy (2017) put it, it is “easy to imagine a highly expressed random RNA or protein sequence gumming up the works somehow, by aggregation or otherwise interfering with some cellular component”. Axe (2018) responds to Neme et al. (2017) this way:
Any junk that slows the process of making more junk by gumming up the works a bit would provide a selective benefit. Such sequences are “good” only in this highly artificial context, much as shoving a stick into an electric fan is “good” if you need to stop the blades in a hurry.
In other words, at the molecular level, this random protein was not performing some complex new function but rather was probably interfering with its own RNA transcription and/or translation—a “devolutionary” hypothesis consistent with Michael Behe’s thesis that evolutionarily advantageous features often destroy or diminish function at the molecular level (Behe 2019). In any case, what Neme et al. (2017) showed is that a quarter of the randomized sequences were capable of inhibiting E. coli from expressing this “zero vector”, but they provided no demonstrated benefit to unmodified normal bacteria.
Finally, Venema (2018) cites Cai et al. (2008) to argue for the de novo origin of a yeast protein, BSC4, purportedly showing that “new genes that code for novel, functional proteins can pop into existence from sequences that did not previously encode a protein”. However, the paper provides no calculations about the rarity of the protein’s sequence nor its ability to evolve by mutation and selection. Rather, the evidence for this claim is entirely inferred, indirect, and based primarily upon the limited taxonomic range of the gene, which led the authors to infer it was newly evolved. Axe (2018) offers an alternative interpretation:
The observable facts are what they are: brewers’ yeast has a gene that isn’t found intact in similar yeast species and appears to play a back-up role of some kind. The question is how to interpret these facts. And this is where Venema and I take different approaches. … Other interpretations of the facts surrounding BSC4 present themselves, one being that similar yeast species used to carry a similar gene which has now been lost. The fact that the version of this gene in brewers’ yeast is interrupted by a stop codon that reduces full-length expression to about 9 percent of what it would otherwise be seems to fit better with a gene on its way out than a gene on its way in.
The function of chorismate mutase is to catalyze the conversion of chorismate to prephenate through amino acid side chains in its active site, thereby restricting chorismate’s conformational degrees of freedom. Essentially, it is merely providing a chamber or cavity that holds a particular molecule captive, thereby limiting that molecule’s ability to change. In contrast, beta-lactamase requires the precise positioning and orientation of amino acid side chains from separate domains that contribute to hydrolyzing the peptide bond of the characteristic four-membered beta-lactam ring. This function requires a more complex fold compared to chorismate mutase. Axe (2004) specifically compares beta-lactamase to chorismate mutase and notes that the beta-lactamase fold “is made more complex by its larger size, and by the number of structural components (loops, helices, and strands) and the degree to which formation of these components is intrinsically coupled to the formation of tertiary structure (as is generally the case for strands and loops, but not for helices)”.
For example, Hunt (2007) argues that relatively short peptides that perform simple functions could first evolve, which could then in turn evolve into more complex proteins that have rarer sequences. Research has shown that some short polypeptides derived from a random library can frequently perform simple functions (see e.g., Keefe and Szostak 2001). However, their ability to further evolve into complex enzymes appears extremely improbable, because functional paths in sequence space would not likely extend to regions containing even modestly complex proteins. The planet analogy in the main text illustrates why: suppose a tiny region around one pole of our hypothetical planet contained a high percentage of traversable land. Even so, a continuous path to the other pole still would not likely exist if a much larger region around the other pole contained a miniscule percentage of traversable land.
Axe (2011) replies to this objection as follows:
It’s kind of like insisting that the height from which a person has an accidental fall has nothing to do with their chance of surviving because it’s the speed of impact that really matters. One could equally insist that the speed of impact is irrelevant—it’s the force of rapid deceleration that really matters. In truth they all matter, and they do so for closely related reasons. The confusion comes from overlooking the causal links between them. Yes, the Darwinian mechanism requires that the different protein folds and functions not be isolated, and yes the rarity of functional sequences has a great deal to do with whether they are isolated.
This objection is further rebutted by the planet analogy in the main text, which shows that extreme rarity directly correlates with isolation.
The area comparisons for the planet were calculated by comparing the proportion of functional sequences for each protein by the percolation threshold in sequence space as defined in percolation theory. The percolation threshold represents the proportion of randomly distributed occupied sites in a lattice below which long continuous paths of neighboring occupied sites become rare. The threshold has been identified for multi-dimensional lattices as approximately the reciprocal of the number of a site’s nearest neighbors (Gaunt et al. 1976). In the context of protein sequence space, it is approximately the reciprocal of the average number of sequences accessible in a single mutation, which is typically less than 10,000. The planet’s traversable land divided by the traversable land corresponding to the percolation threshold of a two-dimensional lattice was set equal to the protein’s proportion of functional sequences divided by its percolation threshold.
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 (Miller 2017; Footnote 12). 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.
Proteins are chains of amino acids that fold into stable three-dimensional shapes determined by molecular interactions between their constituent amino acids. These “protein folds” determine the specific function that a given protein is then able to perform in the cell (Dobson 2003; Onuchic and Wolynes 2004; Dill et al. 2008). Due to their importance in determining biological functions, protein folds can be considered “the smallest unit of structural innovation in the history of life” (Meyer 2013, p. 191).
The paragraph concludes with the sentence: “The existence of similar parts in other systems, for example, does provide supporting evidence for evolvability (Musgrave 2004; Pallen and Matzke 2006)”. We will take up this particular claim below. Note also Kojonen (2021)’s appeal to co-option in his response to Behe on page 122.
Behe (2007, p. 95) likewise notes: “modern Darwinists point to evidence of common descent and erroneously assume it to be evidence of the power of random mutation”. See also a more recent discussion in Behe (2019, pp. 287–91).
The proteins are: FlgD, FlgH, FlgI, FlgJ, FlgM, FlgN, FlhE, FliB, FliD, FliE, FliL, FliO, FliS, FliT, FliZ.
The proteins are: FlhDC.
The proteins are: FliK, FliJ, FliG.
The proteins are: FlgE, FlgK, FlgL, FlgBCFG.
The proteins are: FlhA, FlhB, FliF, FliP, FliQ, FliR, FliH, FliI, FliM, FliN, FliC.
The proteins are: FliM, FliN, FliC.
The four proteins are FlgH, FlgI, FliS, FliT.
To elaborate, the injectisome is found in a small subset of gram-negative bacteria that have a symbiotic or parasitic association with eukaryotes. Since eukaryotes evolved over a billion years after bacteria, this suggests that the injectisome arose after eukaryotes, relatively late in the history of life. However, flagella are found across the range of bacteria, and the need for chemotaxis and motility (i.e., using the flagellum to find food) is thought to have arisen very early—perhaps being present as early as the last bacterial common ancestor. Most certainly, the need for chemotaxis and motility preceded the need for parasitism, which means we would expect that the flagellum long predates the injectisome. Indeed, given the narrow distribution of injectisome-bearing bacteria, and the very wide distribution of bacteria with flagella, parsimony suggests the flagellum long predates injectisome rather than the reverse.
Presumably, the probabilities are independent in each case. The whole point of convergent evolution is that independent evolutionary lineages led to the same outcome in organic history.
Of course, Kojonen could reply by trying to dissipate these probabilities by appealing to deeper laws of nature, laws of form, or other fundamental features of matter. If the deep structure of nature constrains the development of life by causing it to ‘cluster’ around similar biological forms, then perhaps the probability of the repeated emergence of these forms is higher than expected. But this response is problematic in two ways. First, it plainly runs against actual data we have on protein rarity and isolation, including the rates and time needed for mutations or other changes to produce new proteins. Second, Kojonen cannot take this line of thinking very far if he also wants his model to be compatible with versions of evolution that allow (significant) for contingency. Recall that, though Kojonen himself emphasizes the laws of form (and laws of nature that underlie them), he is nonetheless keen to claim that his model is compatible with mainstream interpretations of evolutionary theory, including ones that allow for a notable degree of contingency and chance.
Of course, it is possible for Kojonen to reply that some clusters of similarities, such as nested hierarchies, are better explained by common ancestry, whereas other similarities, which appear to be isolated, are better explained by convergent evolution. But the problem with this possible reply is three-fold. First, it does not take seriously Kojonen’s own claim that convergence is “ubiquitous”. To the extent that Kojonen accepts the pervasiveness of convergence in biology is likewise the extent to which the proposed reply is untenable. If convergence is persuasive, is it plausible that convergent similarities never include similarities that are part of a nested hierarchy, for example? Second, the possible reply above also does not solve a deep problem in the other direction: to the extent that similarities are due to common ancestry is also the extent to which convergence does not explain these similarities. But this is a problem, because Kojonen’s view of convergence is ultimately rooted in his understanding of design—it arises from the laws of form, which are themselves the result of designed laws of nature. So, to the extent that Kojonen wishes to use common ancestry to explain similarities (such as those in nested hierarchies) is also the extent to which his use of ‘design’ does not add explanatory value to ‘evolution’. Third, and more generally, the burden is on Kojonen to make these matters clear. He assumes that similarity implies common ancestry (in his view of protein evolution and reply to Behe), yet at other times, he seems to think (other?) similarities point to convergent evolution (and design). Kojonen should resolve this tension by providing a principled ground to demarcate the two that does not damage the explanatory value of ‘design’ and that also avoids internal tension between ‘design’ and ‘evolution’.
The full quote is helpful. Kojonen (2021) writes:
According to this view, then, the possibility of evolution depends on the features of the space of possible forms, where all the forms must be arranged in a way that makes an evolutionary search through it possible. This argument shows how the preconditions for the working of the “blind watchmaker” of natural selection can indeed be satisfied by nature in the case of protein evolution, despite an extreme rarity of functional forms. According to this view, then, the possibility of evolution depends on the features of the space of possible forms, where all the forms must be arranged in a way that makes an evolutionary search through it possible. This argument shows how the preconditions for the working of the “blind watchmaker” of natural selection can indeed be satisfied by nature in the case of protein evolution, despite an extreme rarity of functional forms. Behe (2019, p. 112) argues that Wagner does not yet solve the puzzle of evolving irreducible complexity, arguing that “it doesn’t even try to account for the cellular machinery that is catalysing the chemical reactions to make the needed components. “ However, suppose that, in the case of the bacterial flagellum, though the vast majority of possible arrangements of biological proteins are non-functional, there nevertheless exists a series of possible functional forms, little “machines” that happen to contain increasing numbers of the flagellum’s vital parts while still serving some other function. This then would allow for the seamless transition from no flagellum to a flagellum over time, through small successive steps. In this manner, by moving through such a suitable library of forms, the blind process of evolution would have the ability to produce even the most complex structures without the intervention of a designer. This is the kind of fine-tuning of the landscape of forms that seems to be required to evolve the kind of biological order described by Behe.
It seems, then, that defending the power of the evolutionary mechanism requires assuming that the landscape of possible biological forms has some fairly serendipitous properties. (Kojonen 2021, p. 122, emphases added)
Kojonen (2021) elsewhere writes:
Suppose for the sake of the argument that Behe is partially correct: complex machinery exists in nature and is difficult to evolve. Nevertheless, suppose that his critics are also correct, and the evolution of such complexity through Darwinian mechanisms actually happened. Given these premises, a theistic evolutionist could well argue that the irreducible complexity argument merely shows how demanding the conditions for evolvability are, and how much fine-tuning evolution actually requires. In a universe designed to allow for evolution, such serendipity could be expected, rather than being unlikely. Hence, Behe’s argument could simply reveal the extent to which fine-tuning is required by evolution.
Pretty clearly, we will not assume that Kojonen’s argument for design (KEBDA) is correct given that such an assumption would beg the question at issue. Our epistemological concerns target ways of knowing that make this argument possible in the first place.
Kojonen draws on Mats Wahlberg’s argument (or analogy) of “computer-generated fugues in order to argue that the products of a design process incorporating random elements can still evidence design” (Kojonen 2021, p. 169). Even if human agents were to listen to such a fugue and mistakenly believe that every element of it was designed (when, in fact, some elements are randomly generated), they are still correct that “the sounds they hear are expressive of intelligence and intent” (Kojonen 2021, p. 170). So, this example apparently shows that design might still be detectable even if humans are mistaken about certain aspects of it. Perhaps, then, Kojonen can reply to our argument by saying that even if humans are mistaken about ‘direct design’, they can still be said to reliably detect design in some notable sense. By way of reply: First, we will show below that Kojonen’s model undercuts humans’ ability to detect design in the way required by Wahlberg’s argument (or analogy). Second, it is arguably the case that, relative to the justification of design beliefs, ‘direct design beliefs’ (“Someone made hummingbirds!”) are more fundamental than ‘detailed design beliefs’, as we might call them (“Someone made every detail of hummingbirds!”). Thus, permissible mistakes about the latter may not be relevant to the epistemic permissibility (and troubling implications) of mistakes about the former. Third, it is not entirely clear that, in Wahlberg’s example, fugues are “random” in a sense that would be relevant to the current discussion.
An ‘agent’ cause, by contrast, is the direct action of an agent.
Accordingly, our argument does not fall prey to Kojonen’s critique of Dawkins’s claim that evolution can produce design without a designer and is thus a “consciousness-raiser” that ought to prompt a person to be wary of design (see Kojonen 2021, pp. 145–46). Kojonen (2021, p. 145) responds to Dawkins by saying, “Suppose for the sake of argument that a divine designer is actually responsible for the laws of form (and other environmental factors) that enable evolution. In that case, evolution would be dependent on design, and therefore evolution would not actually show us that evolution can produce design without a designer”. But this critique of Dawkins does not apply to our argument. First, Kojonen’s line of thinking fails to address the larger points we are making about (i) the implications of evolution for ‘direct design’ beliefs and (ii) the broader continuity of non-agent causes that would be apparent to a person who accepted Kojonen’s model. Second, in the quote above, Kojonen seems to move illicitly from ontology to epistemology: from the fact that there is a designer (and design of the type he proposes), it does not follow that evolution itself would not point human observers in the other direction. It is entirely possible that, in some notable sense, evolution might obscure the signal of design. The fact of design does not entail evidence of design. (Similarly, the fact of design likewise does not entail the lack of defeaters to evidence of design.)
Of course, each of Kojonen’s illustrations is not (simply) given to show that humans can detect design directly or indirectly. Kojonen deploys them for an array of purposes. But our point here is that, insofar as these illustrations support the idea that (on Kojonen’s model) human beings can reliably detect design based on biological phenomena, these illustrations are instead undercut by the fact that Kojonen’s model actually damages the foundational dispositions or beliefs involved in design detection that undergird (this use of) these illustrations. Moreover, Kojonen’s illustrations do not seem to address our points about direct design and non-agent continuity. Biological complexity could in principle be designed (or compatible with design), but that does not mean there would be sufficient evidence of such, especially given some of the key elements of Kojonen’s proposal. So, too, with Kojonen’s view of human technology and the need for fine-tuning to make it possible (Kojonen 2021, p. 173–74). Even if such fine-tuning did exist, a person who accepted Kojonen’s key claims (about evolution, non-agent causes, and so on) would likely have little evidence of it. Interestingly, in his discussion of human technology, Kojonen seems to move away from biological data and, instead, openly cites data from other areas, including mathematics and commonsense physics. Perhaps this is a tacit admission of one of our key points: in Kojonen’s model, the biological evidence on its own may not in fact point to design.


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