On the Relationship between Design and Evolution

Round 1

Reviewer 1 Report

This article presents a timely and needed evaluation of Kojonen’s argument in his recent book “The Compatibility of Evolution and Design”. The author(s) first present Kojonen’s argument, then go on to critically analyse it. The author(s) argue Kojonen’s model depends on the viability of evolutionary explanations, which they go on to criticize. They also have some philosophical criticisms of Kojonen’s arguments.

This is an interesting paper, but there are also problems and potential objection the authors should address before publication. Generally, The authors should engage throughout the paper with prior literature on Kojonen’s argument, such as the articles featured in the Zygon December 2022 issue. The authors should mention the concept of “conjunctive explanation”, important to Kojonen’s argument, as well as other ways Kojonen explains his argument in addition to the proximate/ultimate distinction. Here, the volume Conjunctive Explanations in Science and Religion, particularly Kojonen’s article in that volume, “Asa Gray vs. Charles Darwin”, would be helpful in getting a more precise picture of Kojonen’s views at several points. Engagement with prior responses to Kojonen is also needed to help identify the precise novel contribution of the present paper.

I will now give some critical commentary section by section.

In 1-2, the author’s summary of Kojonen’s argument seems mostly accurate, if missing some central parts, as mentioned previously. The authors should take these into account and reference previous summaries. This would also help make clearer what precisely is “unique” about Kojonen’s proposal, given some other arguments for the compatibility of design intuitions and evolution (such as Plantinga and Ratzsch, or Asa Gray’s account).

In addition, there is need to clarify similarities and differences between Intelligent Design and Kojonen's ideas. The design arguments of the ID movement seem distinct from Kojonen’s approach, particularly due to Kojonen’s claims regarding the compatibility of mainstream Darwinian evolutionary biology and design arguments. Kojonen also does not present the design argument as a scientific argument.

In 3-5 and 6.2, the authors scientifically evaluate portions of Kojonen’s proposal. They argue, for example, that it is not plausible that nature allows evolution and that convergence undercuts common descent. I have concerns about the applicability of this critique against Kojonen’s argument. A potential objection is that criticisms of evolutionary explanations are just critiques of evolution, rather than the compatibility of evolution and design as such. For example, the authors argue that it is implausible that there exists an evolutionary pathway for the stepwise evolution of the bacterial flagellum, whereas Kojonen’s starting assumption requires affirming that such pathways must exist. Arguably, the critic of the thesis of compatibility of evolution and design (rather than just evolution) would need to adopt the same assumption for the sake of argument. The same applies to the argument that there are no pathways to evolve proteins due to the rarity of functional proteins, and to the author’s opposition between convergence and common descent. These are arguably not issues with the thesis of compatibility between design and evolution, but critiques of the reliability of evolutionary biology.

In order to show that Kojonen’s thesis is wrong, it would seem that a more promising line might be to argue that the evolution of life’s complexity can happen without fine-tuning, rather than that such evolution cannot happen. Kojonen’s claim seems to be simply that the most plausible responses to alleged problems with evolutionary explanations (such as irreducible complexity) would themselves provide evidence of fine-tuning.

There is value in showing where Kojonen has failed to properly cite his source, such as in the case of how many parts of the flagellum are homologous. This 90% figure for homologous flagellum parts might derive from Sarkar’s Doubting Darwin?, where p. 113 claims that 80-88% are now known to have homologs. The book is cited by Kojonen in his earlier The Intelligent Design Debate and the Temptation of Scientism, p. 64. So it may be that Kojonen has simply failed to cite his example of an ID critic arguing for this precise number. But he is correct that a figure close to 90% has been claimed by some ID critics - perhaps this would be fair to state although it is a minor detail.

Sections 3-5 are liable to many potential objections, since there is plenty of further literature responding to the ID movement’s criticisms and discussing issues like distinguishing convergence and homology. If the authors wish to keep these sections in the paper, then in fairness to evolutionary biology, it would be good to cite some further responses in addition to the ones cited by Kojonen. For example, although new understanding of the evolution of the T3SS makes earlier estimates of homologies problematic (as components homologous to parts of the T3SS should probably not be counted), the idea that only 10% of components are homologous seems quite low and unnecessary for the author’s arguments.

The lines of criticism in chapters 6.1 and 6.3 are more promising, in that these do not assume the falsity of evolutionary explanations and so might be able to show inconsistencies in Kojonen’s project itself.

In 6.1, the authors also argue that Kojonen fails to conceptualize a valid way in which the outcomes of evolution could be determined or influenced by fine-tuning the starting conditions. The authors argue that there is no reason to think that laws of nature by themselves are causally efficacious. A potential reply might be that Kojonen’s argument for the compatibility of evolution and design does not require that life is a deterministic outcome from the Big Bang and the early conditions of the cosmos. Darwinian evolutionary explanations commonly begin with the origin of life, so Kojonen might also begin with the origin of life, and argue that starting from this point, the pathways that life could evolve on are determined by the laws of nature.

There are additional issues that the authors might press Kojonen on here: Kojonen does not write much about the origin of life in his book, and seems to allow for some indeterminism within evolution. It seems that in his view, as long as the possibility of certain evolutionary outcomes is better explained by design, then these outcomes will testify of design even if they were not determined by the laws. In his response to David Glass in Zygon, Kojonen even allows that his design argument could allow divine guidance of mutations with certain caveats.

The authors should also further consider the major answers to this given by Kojonen, such as the idea that the laws of nature and the environment determine what sort of evolutionary pathways are available, what kind of structures are easier or more difficult to evolve, and so on. The authors also do not consider precursors to such ideas such as structuralism (such as Michael Denton’s ideas), Conway Morris’ and other’s interpretations of convergence, and Kojonen’s use of evolutionary algorithms and other indirect methods of design as analogies of how this could work.

In 6.3, The authors develop the objection that Kojonen’s model undercuts the basis of design intuitions.  They argue that if we live in a universe where natural processes do produce evolution, this would undercut the experience that intelligent agents are able to design certain types of order. However, this objection seems to be the same as the Dawkinsian objection to design intuitions that Kojonen does discuss on pages 145-146 of his book. Kojonen’s response is that this objection is guilty of circular reasoning: the critic cannot just assume that evolution produces such order without design. But if this is not assumed, then evolution is not a counterexample to our normal intuitions about design. Thus, Kojonen would likely respond that the authors have not shown any reason why the idea of designed evolution would generally undercut design perceptions or design arguments.

I hope these criticisms are helpful in improving the author's valuable contribution for publication.

Author Response

Please see our uploaded reply. Many thanks for your helpful comments and suggestions.

Author Response File: Author Response.pdf

Reviewer 2 Report

The article is a critical review of Rope Kojonen's book "The Compatibility of Evolution and Design", in which, for the sake of the argument, Kojonen accepts that "mainstream" evolution is a true explanation for the diversity and complexity of life (from now on I will simply call this "evolution" for brevity), but argues that even then design is still needed at some level. It is not clear to me whether Kojonen himself actually does believe that evolution is true, but for the sake of the argument of his book, he simply grants that it is. The point of his book is not to defend evolution, but to develop a design argument on the premise that it is true. 

Much of this critical review is seeking to show why "mainstream" evolution cannot be a true explanation for the diversity and complexity of life, and it provides a clear and concise summary of modern arguments against the explanatory power of evolution. In itself, this is a useful summary of the case by someone who is clearly a proponent of intelligent design. However, this seems to miss Kojonen's point, as it is attacking an axiom that he concedes for the sake of the argument that he is building, rather than his argument itself.

Having said that, it may be that Kojonen does muddy the waters a little himself within his book, providing statements apparently in favor of evolution that can be legitimately critiqued. 

Even if this review does miss the main point of Kojonen's book, it has value in that any "theist on the street" who is weighing up Kojonen's case will at some point also need to weigh up the evidence for evolution before coming to a fully thought-through position on the wider topic of orgins. 

I hope that the journal editors will invite Kojonen to provide his own response to this piece. 

Author Response

Many thanks for your instructive feedback. Please see our uploaded reply.

Author Response File: Author Response.pdf

Reviewer 3 Report

This paper reviews and criticizes Kojonen’s theory of origins which combines evolution and design. My comments are below:

 

10. Sp. “Strengthen”

 

36. “full-blooded”? What does that mean? Suggest a different phrase.

 

246-247. Why is that true if he presupposes evolution to be true? If your argument entails that he must prove what he presupposes (that is, evolution), then you should state that more clearly.

 

262. Split infinitive.

 

292-300. Seems unnecessary.

 

305. Not only is smoothness not sufficient (simple example, a smooth, flat, landscape does not help evolution), but it is not difficult to construct an evolutionary explanation not requiring smoothness. For example, perhaps two simultaneous substitutions are occasionally required (due to a rugged fitness landscape). However, it is required that all native structures must be reachable across a relatively broad region of sequence space, for example via gradually increasing, even if not all smooth, landscapes leading to native structures, without too many false local maxima in the way.

 

330. Typo. “turn”

 

334-372. Again, this seems verbose, pedantic, and unnecessary.

 

422-442. “Instead … structures.” Suggest you move this to an endnote. You are confusing normal science with theory-neutral science. Both Kojonen and Wagner assume evolution is true. Wagner’s conclusions fall into normal science. Those interested in the details can see the endnote.

 

475-476. “That is, protein evolution hinges in part on how many mutations must be changed to produce a new function.” This is nonsensical.

 

495. Should use double quotation marks.

 

621. Wandering is probably the best case. More likely, they would fail.

 

622-623. This conflates adaptive change with neutral change. Not harming is not equivalent to conferring a functional advantage.

 

624-625. This denies neutral evolution and the inheritance of neutral changes. Yes, it is not “selected,” but that is not equivalent to not passed along.

 

712. Use double quote.

 

714. Deleted? Or degraded?

 

788-789. You are equating “homology” with “sequence similarity.” This is not correct. Sequence similarity is one metric used to infer whether two molecules are or are not homologous. Beyond that, they are not the same thing. Moreover, this passage is confusing because you have not explained exactly how the hypothetical co-option mechanism is supposed to work. For example, in this mechanism the concept of homology is different than how the term is typically used. Typically, it refers to structures sharing a common ancestor by virtue of speciation events. In co-option, presumably one protein is related to another by virtue of a gene duplication event. Speciation is not required or implied. Gene duplication is a much less heroic hypothesis than speciation.

 

789-790. No, this does not suggest common ancestry, as explained in previous comment.

 

792-793. Why not explain Kojonen’s mistake in equating homology with sequence similarity? The parenthetical in his quote is false. Similarity does not imply homology. At least not in the way these terms of art are typically used. Also 819.

 

812a. No. The parenthetical is false. Homology is not equivalent to similarity.

 

812b. No, homology as a term of art does indicate an evolutionary origin. You’d have to turn back to clock to early-mid 19^th century, such as Richard Owen, to use homology as mere similarity, but even then it is a particular type of similarity.

 

824ff. Your continued use of the term “homology” as mere similarity plays into the false argument you are attempting to deconstruct (EG, 836-7 and elsewhere).

 

837. The use of “homology” here, as a matter of degree, is also false. Homology is not a continuous measure. It is a binary, yes/no, indicator. Two structures are either homologous, or not homologous.

 

842. If the sequence similarity is not a consequence of “some evolutionary pathway,” then they are not homologues, as described.

 

860-861. Suggest delete.

 

862ff. The Dembski quote works against you, as it supports Kojonen’s thesis.

 

882-883. I didn’t know a functional relationship was a premise of the co-opted hypothesis.

 

979-980. Seems like a questionable and unnecessary claim. What about regulatory sequences? What about other information outside of the genome? What about the periodic table? Etc. This claim that protein-coding sequences is a “true” building block of life raises questions. Are other sources of information false?

 

978-979. Use of the word “code” may cause confusion with the genetic code.

 

980. ? This seems vague.

 

981. To what “code” is the sentence referring?

 

996. One could argue it is not a tiny number (all relative). Might be safer to say tiny fraction.

 

997. Since you are focusing on protein-coding sequences, one could argue it is not “precise” given the redundancy in the genetic code.

 

1044. I thought option 1 was IC+laws, not merely laws.

 

1048. Meyer already mentioned.

 

1247ff. Valid criticism, but it might be more apparent and powerful if it is framed as “having it both ways.”

 

1269-1277. Seems like valid criticism, though evolutionists will argue that there is no tension between convergence and common ancestry, because convergence is most important in instances where the observed convergence is not sufficiently substantial to have overlap with common ancestry. For example, the streamlined body form of dolphins and sharks. Yes there is a similarity, but it could not be due to common ancestry given that the example is of a mammal and a fish.

 

1478ff. This sort of argument is effective against determinism and atheism, but deployed here against Kojonen theory seems weak. Why couldn’t he lean on the initial conditions part of his hypothesis to steer evolution in the desired direction?

Author Response

Thank you for your careful reading of our manuscript. We have made a number of changes in light of your comments. Please see our uploaded reply.

Author Response File: Author Response.pdf

Round 2

Reviewer 1 Report

The paper is much improved and is an interesting contribution to the discussion. It could still be improved by considering potential replies further.

1. The authors contend that they merely mean to point out inner contradictions in Kojonen's position, rather than criticize evolutionary explanations as such. This still does not seem convincing. Kojonen is arguing that the most plausible understanding of mainstream evolutionary theory requires fine tuning for evolutionary processes to produce life's complexity. In opposition, the authors argue that the scientific evidence shows there is not sufficient fine tuning for evolution to occur, or to explain features like irreducible complexity which Kojonen discusses. A potential reply would be that to demonstrate the incompatibility of evolution and design, the authors should rather argue that evolution can happen without fine tuning, rather than that evolution cannot occur. As long as the most plausible version of evolution is one that combines evolution with fine tuning (or other forms of design), it seems Kojonen's argument for compatibility would go through. It seems to be a separate question whether evolution actually can occur in this way.

2. In their replies to reviewers, the authors contend that it is not necessary for them to discuss standard ways of harmonizing convergence and common descent, since Kojonen does not discuss these. However, it would improve the paper to briefly discuss these standard harmonizations, and consider whether Kojonen can make use of them. The authors argue that Kojonen cannot plausibly argue that some similarities are better explained by common descent than by convergence, since fine-tuning can make the same features evolve multiple times without common descent. However, it is not clear why Kojonen could not hold that some clusters of similarities such as nested hierarchies are better explained as the result of common descent, while isolated similar properties are better explained as convergence?

3. In their discussion of the frequency of functional proteins, the authors would do well to also discuss common criticisms of the papers by Axe and Gauger, as Kojonen also references a broad range of estimates for the frequency of functional proteins.

4. On the issue of whether Kojonen's argument undermines the logic of the design argument, the authors would do well to consider the replies to this objection that are present in Kojonen's book further. This includes Kojonen's reply to the Dawkinsian argument for evolution as a "consciousness-raiser", and Kojonen's use of the analogies by Asa Gray (the mechanical loom) and Mats Wahlberg (the automated music generation) to argue that design intuitions are still fundamentally correct even if the people with these intuitions have incorrect beliefs on the directness of design.

5. On the author's argument that the design of fine-tuning underlying evolution might also be indirect, there are potential replies that the authors could consider. For example, one could utilize Occam's razor and argue that the supposition of a further process beyond that does not add any explanatory value. Or one could argue that the chain of processes would still have to end with direct design at some point, or we would no longer be dealing with a design hypothesis. Yet another possibility would be to claim that the design evidence does not have to stand alone or prove everything about the designer, but could be combined with other considerations, such as cosmological arguments.

I am looking forward to seeing the author's stimulating contribution in print.

Author Response

Reviewer Comment

"In their discussion of the frequency of functional proteins, the authors would do well to also discuss common criticisms of papers by Axe and Gauger, as Kojonen also references a broad range of estimates for the frequency of functional proteins." 

 

Our Response

We altered the text and added new material and endnotes to highlight that our analysis of protein rarity and isolation directly addresses the research Kojonen cites, such as Taylor et al. (2001) (in addition to Tian and Best (2017) which we had already addressed).

 

We would be happy to also address critics of Axe and Gauger, but no to our knowledge criticisms of their research appear in peer-reviewed literature. There are however quite a few responses to Axe in the popular literature. We have therefore added responses to those critics’ substantive arguments and cited literature. These include the following critics of Axe:

 

• Hunt, Arthur. 2007. Axe (2004) and the evolution of enzyme function. PandasThumb. January 14. Available online: https://pandasthumb.org/archives/2007/01/92-second-st-fa.html (accessed on 21 June 2023).

 

• Matheson, Steve. 2010. Bread and circus: Signature in the Cell at Biola (Part II). Quintessence of Dust. May 27. Available online: https://sfmatheson.blogspot.com/2010/05/bread-and-circus-signature-in-cell-at_28.html (accessed on 21 June 2023).

 

• Venema, Dennis. 2010. Seeking a Signature. Perspectives on Science and Christian Faith 62: 276-283.

 

• Venema, Dennis 2018. Intuitions, Proteins, and Evangelicals: A Response to Undeniable. Sapientia. February 5. Available online: https://henrycenter.tiu.edu/2018/02/intuitions-proteins-and-evangelicals-a-response-to-undeniable/ (accessed on 21 June 2023).

 

We engage with the arguments of each of these critics in the newly added material.

 

In addition, we have also added new material that addresses each of the reviewer's other points (on convergence, design detection, and so on).