The Evolution of a Protein Transport Machine: Fazale Rana on Irreducible Complexity

Last year marked the 20th anniversary of Darwin’s Black Box, Michael Behe’s groundbreaking work on intelligent design. This month, the documentary Revolutionary: Michael Behe and the Mystery of Molecular Machines was made available online. It’s remarkably well made and is certainly required viewing for anyone interested in this topic. Behe’s ideas have been knocking around for more than 20 years now, and much has changed in the time that has passed. Revolutionary presents Behe’s argument in an updated and fresh form. In light of this focus on Behe’s work on design, I thought it would be fitting to write an article on irreducible complexity.

For the past few months, biochemist and old-earth creationist Dr.Fazale Rana has been posting ‘Question of the Week’ videos on his Facebook page (the videos are also available on YouTube), where he discusses various science and faith questions. Rana primarily focuses on topics surrounding the biological origins debate. I have followed much of his work in the past, primarily because he comes at the design debate from a different perspective. Though he does accept intelligent design, he doesn’t always agree with the way most ID theorists advance their arguments. Interestingly, one of his primary disagreements is with Behe’s argument from irreducible complexity and in one of his more recent videos he discussed the question ‘Is irreducible complexity a good argument for design?’.(1)

In the video, Rana begins by helpfully laying out some basic definitions and talks about how Behe’s work influenced him in the past. He then goes into a discussion about some of the usual responses ID critics use against Behe’s argument (co-option etc.). I was half expecting Dr. Rana to stop there and come down on the side of the critics, but I was pleasantly surprised. Rana recognises that the co-option response (at least with respect to the Type Three Secretory System) is completely misguided, and, as Behe and others have to point out continuously, it doesn’t begin to appropriately tackle this nagging biological perplexity. However, Dr. Rana brings up another example. In talking about his past enthusiasm for the argument he notes:

But all that changed for me in 2009 when a team of researchers from Australia and the UK published a paper in the Proceedings of the National Academy of Sciences, where they were looking at the evolutionary origin of what’s called the TIM23 protein import machine. This is an irreducibly complex protein transporter that is embedded in the inner membrane of mitochondria, that plays a role in mitochondria biogenesis, transporting proteins from the cytoplasm of the cell into the lumen of the mitochondria.(2)

You can read the full paper that Rana is referring to here.

Rana goes into a little more detail on the irreducible complexity of the mitochondrial machine that is in question, claiming that we can show experimentally that if one protein is removed from this complex, it will cease to function. For him, by demonstrating a plausible co-option scenario for the Darwinian development of this system, this paper essentially disproved Behe’s argument from irreducible complexity, though he does qualify the conclusions of the paper:

This work could be interpreted from a design framework where you could just simply argue that the similarity between the TIM A and TIM B, and the proteins that are part of the TIM 23 complex, is essentially a reflection of the modular design of biochemical systems, where you have components that can be pieced together in a variety of different ways to produce a number of different types of functional systems. Or you could view them as part of an archetypal design that a creator used to build different types of machines.(3)

Despite this, he thinks that the paper shows that irreducible complexity is a claim that can no longer be made because the researchers demonstrated a plausible stepwise pathway. Though he recognises that they hadn’t fleshed out all the details, and that it doesn’t definitively prove that the system emerged in the way they argue, to him they did succeed in presenting a plausible pathway.

Concerns About the Paper

Before moving on to some of Rana’s other points , I want to take a look at his reservations about irreducible complexity. I happen to disagree with his conclusions here, sensibly tentative though they are. Though the paper is now quite old (published in 2009), I did read the paper at the time and the media hype surrounding it. Various science news outlets picked up on it (4), asserting with smug triumphalism, intelligent design’s ignominious demise (yet again).

The main thing I’d like to do in this article is to draw attention to the other side of the argument. As I quoted above, though Rana charitably notes that the results of the paper in question can, conceivably, be interpreted in a design framework, I felt he wasn’t doing justice to the way various ID proponents have responded to the paper. Shortly after the paper was published, there were several noteworthy comments from various ID proponents, which cast serious doubt over the success of the paper in question. Here I will breifly outline some of them.

The first response was from Behe himself, though unfortunately he was predictably refused a ‘letters to the editor’ response to the paper. He subsequently posted his thoughts at Evolution News. Behe essentially points out that ‘the claims made in the paper far surpassed the data, and distinctions between such basic ideas as “reducible” versus “irreducible” and “Darwinian” versus “non-Darwinian” were pretty much ignored.'(5) The first questions to consider is whether the system is irreducibly complex or reducibly complex. And whether anyone claimed the system is in fact irreducibly complex in the first place. The authors of the paper, Clements et al, clearly think they are demonstrating that a previously postulated irreducibly complex system, is actually reducible. Yay for Darwin. They write:

Molecular machines have been described as being of irreducible complexity. But could a single component of the machine function in the absence of the others to provide even inefficient protein transport? Although searches of genomes have not found a species of eukaryote in which the LivH/Tim 23 type channel is present in the absence of Tim44 and Tim14 subunits, equivalent studies on the TOM complex in the outer mitochondrial membrane have provided just such proof of principle.(6)

However, Behe responds:

The authors intend to show that Darwinian processes can account for a reducibly complex molecular machine. Yet, even if successful, that would not show that such processes could account for irreducibly complex machines, which Clements et al cite as the chief difficulty for Darwinism raised by intelligent design proponents like myself. Irreducibly complex molecular systems, such as the bacterial flagellum or intracellular transport system, plainly cannot sustain their primary function if a critical mechanical part is removed. (2-4) Like a mousetrap without a spring, they would be broken. Here the authors first postulate (they do not demonstrate) an amino acid transporter that fortuitously also transports proteins inefficiently. They subsequently attempt to show how the efficiency might be improved. A scenario for increasing the efficiency of a pre-existing, reducible function, however, says little about developing a novel, irreducible function.(7)

Clearly, contrary to the assertion of the authors, and by extension Dr Rana, Behe argues that the mitochondrial machine is not irreducibly complex. More importantly, as Casey Luskin points out in his response ‘No ID proponent has ever claimed that this particular system is irreducibly complex, making this a straw man attack.'(8) Of course, the system still could be one that meets the standard criteria of an IC system, even if Behe and others never focussed on it, showing that there are plausible Darwinian pathways to such systems. Rana claimed that it had been experimentally confirmed that if one part is removed, the system crashes, but he neglected to elaborate on the details. If we look at the paper itself, we find no detailed support of this claim. Behe mentions a few other points, which you can read in the response, but concludes that:

…if these are the best “refutations” that leading journals such as PNAS and Science can produce in more than a decade, then the concept of irreducible complexity is in very fine shape indeed.(9)

To my mind, Behe’s response was a little brief, yet he managed to cast a few serious doubts about the paper. Aside from Behe’s comments, a more thorough and devastating rebuttal came from Casey Luskin. As mentioned, Luskin argues that the paper is a straw man, due to the fact that ID theorists haven’t claimed this system is irreducibly complex (10). Even apart from that, there are more serious problems with the arguments in the paper. One of the main problems with it, is their flippant and vague understanding of the IC challenge. Luskin references the work of philosopher Angus Menuge, who sharpened the challenge by laying out several necessary steps that an argument against IC must make. They are reproduced below:

For a working flagellum to be built by exaptation, the five following conditions would all have to be met:

C1: Availability. Among the parts available for recruitment to form the flagellum, there would need to be ones capable of performing the highly specialized tasks of paddle, rotor, and motor, even though all of these items serve some other function or no function.

C2: Synchronization. The availability of these parts would have to be synchronized so that at some point, either individually or in combination, they are all available at the same time.

C3: Localization. The selected parts must all be made available at the same ‘construction site,’ perhaps not simultaneously but certainly at the time they are needed.

C4: Coordination. The parts must be coordinated in just the right way: even if all of the parts of a flagellum are available at the right time, it is clear that the majority of ways of assembling them will be non-functional or irrelevant.

C5: Interface compatibility. The parts must be mutually compatible, that is, ‘well-matched’ and capable of properly ‘interacting’: even if a paddle, rotor, and motor are put together in the right order, they also need to interface correctly. (11)

Like most critics of Behe’s argument, Clements et al, only attempt to address C1 and as one can clearly see, this barely even scratches the surface of the problem. Luskin goes into quite some detail on other problems with the paper, such as the suspiciously easy appeal to ‘preadaption’, often using teleological language. You can read Luskin’s full response here.

The final response I’ll point to is one by Brian Thomas at The Institute For Creation Research. Despite the fact that I disagree with his theological stance, in the article he makes some legitimate points. Thomas criticises the reasoning of the authors and their preadaptation hypothesis:

…the very label “preadaptation” counters the authors’ claims. The idea admits that not-yet-evolved “proto-machines” are not subject to Darwinian selection of adaptations. Preadaptation is observed nowhere; it is a devised assumption “in keeping with Darwinian evolution.” The fact that non-functioning “machine parts” are invisible to Darwinian selection is exactly what design theorists have observed.(12)

There were two other responses made to the paper which are worth reading. One was by Clive Hayden at Uncommon Descent here, and Cornelius Hunter at his blog here.

In my view, the responses to the paper I have outlined provide some strong counter arguments to the claims made in the paper, removing Fazale Rana’s reason for having doubts about irreducible complexity.

Is Irreducible Complexity a Negative Argument?

Coming back to Rana’s video, there were some other comments he made that I’ll briefly touch on. One of Rana’s criticisms of Behe’s argument is that it’s framed in purely negative terms, and so risks a kind of “god of the gaps” reasoning. He sees the standard design argument this way:

The way in which, I believe Michael Behe, framed the argument…is in negative terms. That is evolution cannot explain the emergence of irreducibly complex systems, therefore these systems must be the product of a designer.(13)

I was disappointed to hear this comment made by Rana because it’s one of the weakest objections and the most common misunderstanding about the formal structure of design theory. I’m not going to bother responding in great detail to this claim, since it has been thoroughly dealt with in other publications. A good response to the god of the gaps charge can be found here. In short, as atheist Bradley Monton argues:

…I maintain that Behe’s irreducible complexity argument is not a God-of-the-gaps argument at all. Behe is not saying that we don’t know (or can’t know) how irreducibly complex systems like the bacterial flagellum could plausibly arise naturalistically. Instead, Behe is giving positive reasons that the sequence of events that would have to happen for irreducibly complex systems like the bacterial flagellum to arise via an undesigned process is an improbable sequence, and hence the design hypothesis should be taken seriously.(14)

Behe himself points out that:

…irreducibly complex systems such as mousetraps and flagella serve both as negative arguments against gradualistic explanations like Darwin’s and as positive arguments for design. The negative argument is that such interactive systems resist explanation by the tiny steps that a Darwinian path would be expected to take [because direct routes are impossible and indirect routes unlikely]. The positive argument is that their parts appear arranged to serve a purpose, which is exactly how we detect design.(15)

Rana complains that Behe and others don’t appeal to the positive designed qualities of biological systems, such as the information bearing properties, optimisation, and analogs to designed objects by humans. I find this a bizarre claim to make coming from anyone who has done even a cursory reading of Behe’s work, because even back in 1996, Behe’s argument appealed to all the things Rana accuses it of lacking.

One further point to make about Rana’s ‘god of the gaps’ charge is that ID doesn’t necessarily posit a god. It posits intelligence. The most one could accuse ID of doing is arguing for an ‘intelligence of the gaps’. This is not a problem if those gaps are features that positively require an appeal to intelligence. Rana worries that by doing this, one is backing into a vulnerable position, where all it takes is for someone to demonstrate one plausible Darwinian pathway, and the argument lies in tatters. That may be the case for particular molecular systems, but on the other hand, all it takes for naturalistic accounts to be falsified, is one single demonstration of a true irreducibly complex system. Famously, Darwin himself recognised this.(16) Essentially, Rana makes a straw man argument against the standard challenge from irreducible complexity, alleging that it makes a purely negative claim against evolution, but ID proponents have been crystal clear about the positive aspect of their theory, and so I conclude that Rana’s concerns here are misplaced.


Rana goes on to argue very strongly for design and I agree with all his comments about the richness of the design hypothesis. It’s just that he believes he is making a different type of argument to Behe’s and the rest of the standard ID model, when in fact he is merely making the same claims as standard ID theory. I’ll end this article by saying that I genuinely appreciate Rana’s work and his powerful case for biological design, I just think his reasons for rejecting Behe’s irreducible complexity challenge and his problems with the formal structure of the argument are very weak.

The dispute over irreducible complexity continues. What I aimed to do in this article was to address some of Rana’s concerns, especially surrounding this particular 2009 paper. Much more work has and is being done (17), and Behe’s provocative ideas continue to be written about in the philosophical and scientific literature.(18) As I mentioned at the beginning of this article, to get a clear and contemporary presentation of Behe’s ideas, I highly recommend giving Revolutionary a watch.


  1. Reasons to Believe (2017) Question of the Week: Aug 21, 2017 Is irreducible complexity a good argument for design?. Available at:
  2. Ibid.
  3. Ibid.
  4. Websites such as Softpedia, Wiredand ID critic Jack Scanlan picked up on the publication.
  5. Michael Behe, Reducible Versus Irreducible Systems and Darwinian Versus Non-Darwinian Processes, Evolution News (2009), Available at:
  6. Clements A, et al. (2009) The reducible complexity of a mitochondrial molecular machine. Proc Natl Acad Sci USA doi/10.1073/pnas.0908264106.
  7. Behe, op cit.
  8. Casey Luskin, PNAS Authors Resort to Teleological Language in Failed Attempt to Explain Evolution of Irreducible Complexity, Evolution News (2009), Available at:
  9. Behe, op cit.
  10. In Luskin’s article Molecular Machines in the Cell, he lists various molecular systems, some of which have been argued by scientists to be irreducibly complex. However, Luskin puts TIM and TOM systems in the category of machines ‘that may be irreducibly complex, but have not been studied in enough detail yet by biochemists to make a conclusive argument.’
  11. Angus Menuge, Agents Under Fire: Materialism and the Rationality of Science, (Rowman & Littlefield, 2004), p.104-105.
  12. Brian Thomas, Preadaptation: A Blow to Irreducible Complexity?, Acts & Facts (2009), 38 (11): 15.
  13. Reasons to Believe, op cit.
  14. Bradley Monton, Seeking God in Science: An Atheist Defends Intelligent Design (Broadview Press, 2009), p.115.
  15. Michael Behe, Darwin’s Black Box: The Biochemical Challenge to Evolution (New York: Free Press (2006), p.263-264.
  16. Darwin wrote ‘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. But I can find out no such case.’ (Charles Darwin, Origin of Species, (1872), 6th edition, (New York University Press, 1988), p. 154.
  17. For some of the most up-to-date work on mitochondrial transport systems I recommend reading Origin and Evolutionary Alteration of the Mitochondrial Import System in Eukaryotic Lineages.
  18. Many critics believe ID to be a dead theory. However Behe’s ideas, 20 years on, are still being studied to this day: Digital Irreducible Complexity: A Survey of Irreducible Complexity in Computer Simulations, A New View of Irreducible Complexity, The Argument from Irreducible Complexity, Michael Behe’s Challenge — Past, Present, and Future, Three Flagellum Updates Amplify Behe’s Challenge to Darwinism from Irreducible Complexity.

Peter S. Williams on Intelligent Design

Peter S. Williams is a philosopher I respect very highly. Being a Christian, most of his work falls within the realm of Christian apologetics, however, Williams is also an intelligent design proponent and has produced some valuable work on philosophy of science and intelligent design theory. In other articles, I would like to look at some of his specific writings in more depth. For now, I wanted to round up his work on ID. Here it is:

Peer Reviewed Papers

The Design Inference from Specified Complexity Defended by Scholars Outside the Intelligent Design Movement: A Critical Review,” Philosophia Christi (Vol. 9, Issue 2, 2007). Also available @

Atheists Against Darwinism



Christianity, Space & Aliens

Darwin’s Rottweiler and the Public Understanding of Scientism

The Definitional Critique of Intelligent Design Theory: Lessons from the Demise of Logical Positivism

Design and the Humean Touchstone

Designed or Desinoid: Dawkins, Science & the Purpose of Life

Focus on Intelligent Design: Some Advice on Avoiding Journalistic Embarrassment

Intelligent Design, Aesthetics and Design Arguments

Intelligent Design Theory – An Overview

If SETI is Science and UFOlogy Is Not, Which Is Intelligent Design Theory?

Playing Both Sides of the Pond: British and American Belief in Creation, Evolution and Intelligent Design

A Rough Guide to Creation & Evolution

Theistic Evolution & Intelligent Design in Dialogue

‘What do you believe is true even though you cannot prove it?’ – Comparing Dawkins’ Blind Faith to Flew’s evidence

A Critique of Intelligent Design Theory by Lawrence M. Krauss

The Big Bad Wolf, Theism and the Foundations of Intelligent Design: A Review of Richard Dawkins’ The God Delusion

On the Side of the Angels: Review of Richard Dawkins’ A Devil’s Chaplain

Part One

Part Two

Part Three

Undermining Richard Norman on “Why Science Undermines Religion

The War on Science: How Horizon Got Intelligent Design Wrong

A Response to Edward Turner’s Review of A Sceptic’s Guide to Atheism

A Response to Edward Turner’s Review of I Wish I Could Believe In Meaning: A Response to Nihilism

Dawkins Ad Hominem – Misrepresented Again?

Intelligent Designs on Science

‘Is Peter S. Williams a liar for God?’  One fallible human responds to another’s critique of ‘Darwin’s Rottweiler and the Public Understanding of Scientism’

Reviewing the Reviewers – Pigliucci et al on “Darwin’s Rottweiler & the public understanding of science”

God Questions – a dialogue-Carl Stecher and Peter S. Williams (Cosmological and Design Arguments)


Book Chapters

Peter has written about intelligent design in further detail in several of his books:

-In chapters 8 and 9 in I Wish I Could Believe in Meaning: A Response to Nihilism.

-In chapters 6 and 7 in A Faithful Guide to Philosophy: A Christian Introduction to the Love of Wisdom.



Peter S. Williams and AC Grayling Debate Fine-tuning

Peter S. Williams vs. Peter Hearty on ID

Faithful Guide To Philosophy 6: Paley, Hume & Design (Teleology I)

Faithful Guide To Philosophy 7: Intelligent Design (Teleology II)

Podcast Episodes

Thinking Through Creation & Evolution

Introduction to Intelligent Design Theory

A Rough Guide to Creation

Introduction to Intelligent Design Theory (2)

How Atheists Defend Intelligent Design Theory


Blog Posts

Peter often writes about ID on his excellent blog, ID Plus.


Peter S. Williams & Denis Alexander’s Dialogue on Intelligent Design

In this post, I wanted to draw attention to a particular written dialogue between ID advocate/philosopher Peter S. Williams and biologist/ID critic, Denis Alexander. Both Williams and Alexander are committed Christians (Williams being one of the UK’s foremost Christian philosophers and Alexander being the director of the Faraday Institute for Religion and Science), so in terms of their broader worldviews, they have much in common. Denis Alexander is a Christian neo-Darwinist, which would put his views pretty much in line with the Biologos crowd (in fact he is one of the bloggers at Biologos). Alexander has critiqued various aspects of ID in many publications¹

Back in 2006, Alexander had an article published on the website called Creation and Evolution?. In it he discusses theistic evolution, creationism, and ID. Subsequently, Peter S. Williams penned an interesting piece in the form of a hypothetical dialogue called Theistic Evolution & Intelligent Design in Dialogue. There are several characters in the dialogue who are coming from various perspectives in the origins debate. This article was written as some form of response to Alexander’s initial article. In response to this, Alexander wrote Designs on Science, an open letter to the characters in Peter Williams’ dialogue, which neatly summarizes some of Alexander’s criticisms of ID. Finally, in response to Alexander, Peter Williams wrote Intelligent Designs on Science: A Surreply to Denis Alexander. This was the concluding part of their dialogue.

It is well worth reading through the dialogue from start to finish. Both authors engage in a polite and cordial fashion throughout, and much ground is covered in great depth. In particular, Williams’ concluding response is very lengthy (25.000 words with almost 300 footnotes) and very well researched, and to my mind constitutes a devastating refutation of Alexander’s objections to design. In addition to this, Williams presents a strong positive case for ID. Of course, Williams doesn’t answer everything that Alexander has written on ID but he deals with the most salient points.

In future, I shall be writing my own response to some of Denis Alexander’s more recent publications on intelligent design.

  1.  Denis Alexander has critiqued ID extensively in books such as Creation or Evolution: Do We Have To Choose?The Language of Genetics: An IntroductionRescuing Darwin: God and Evolution in Britain TodayBeyond Belief: Science, Faith and Ethical ChallengesRebuilding the Matrix: Science And Faith In The 21St Century. On top of these, he has published many articles on the topic including Is Intelligent Design Biblical?Intelligent design is not scienceA Critique of Intelligent DesignA Response to Should Christians Embrace Evolution?


Jeffrey Koperski on Two Bad and Two Good Ways to Attack ID (Part 2): Two ‘Good’ Ways

In part one of this series looking at Jeffrey Koperski’s paper, Two Bad Ways to Attack Intelligent Design and Two Good OnesI focussed on the two arguments he thinks fail as good critiques of design. The first argument, if one could call it that, is the claim that ID is merely repackaged creationism. The second was the claim that ID fails to meet the criteria of science because it doesn’t adhere to methodological naturalism. I considered Koperski’s criticisms of those arguments and found them to be persuasive. In the second part of the paper, he takes a look at two more arguments. He sees these as being good reasons to reject ID. In this article I’ll be considering the two arguments put forward, suggesting that they fail as affective counter arguments, concluding that ultimately, the four arguments looked at in his paper all fall in to the category of bad arguments against design.

Soft and Hard Anomalies

After affirming the scientific status of design, Koperski explores the possibility of whether it is good science. He sees ID as having two main strands. The first strand includes ‘examples that are problematic for neo-Darwinism'(1) like concepts such as specified, and irreducible complexity, pioneered by William Dembski and Michael Behe. This description is partially accurate, however it neglects to include a crucial distinction, and that is that the arguments mentioned aren’t merely negative, problematic examples for neo-Darwinism, but they’re also advanced as positive confirmations of design. Formulating ID as a negative critique doesn’t do it justice. ID theorists recognise that neo-Darwinism’s failure is a necessary but not a sufficient condition for a scientific case for design. Michael Behe writes that ‘irreducibly complex systems such as mousetraps and flagella serve both as negative arguments against gradualistic explanations like Darwin’s and as positive arguments for design.'(2)

Focussing on specified and irreducible complexity, Koperski makes an interesting distinction between soft and hard anomalies. Soft anomalies are mysterious and improbable observations that are still consistent with the theory in question, despite them being puzzling. Hard anomalies are cases where theories are strictly contradicted by evidence and they ‘cannot be explained in terms of the reigning theory.'(3) His contention is that a theory should only be overturned if one encounters hard anomalies (data that defies possibility). This is essentially what Darwin himself argued when he wrote ‘If it could be demonstrated that any complex organ existed which could not possibly have been formed by numerous, successive modifications, my theory would absolutely break down.'(4) Koperski claims that cases of specified and irreducible complexity fall within the category of soft anomalies, and therefore don’t require us to adopt a new theory. 

My first response to this argument is to question the distinction between soft and hard anomalies. In theory and practise, what would a hard anomaly look like? Koperski draws on an example from physics when our models of the atom were proved to be deficient by black body radiation and the photoelectric effect. But we’re talking about biology here. What one considers a soft or hard anomaly seems highly subjective. If a soft anomaly is an observation that is improbable, yet not directly contradictory, how improbable does an observation need be to become a hard case? Of course, individually improbable and mysterious objects can be reconciled within a theory, but when many such cases accumulate and remain unexplained for a long period of time, with little hope of being resolved in the near future, scientists must begin to at least consider alternative explanations. And it seems that this is the situation we’re in with biology. Though I don’t wish to be too pessimistic about the progress of much research within modern evolutionary theory, it is no secret amongst more candid biologists that there are some grave explanatory deficiencies within the current paradigm, hence the need for an extended evolutionary synthesis and a ‘third way’ that has been receiving more attention in recent years.(5) I’m aware that this fact on its own does little to help ID, since those who are pushing for a reconsideration of evolutionary mechanisms still believe these anomalies can be accounted for in naturalistic terms, but as I will argue later, these attempts also encounter the same pitfalls as the classical neo-Darwinian accounts.

To draw a black and white distinction between soft and hard anomalies seems unrealistic in theory and practice, especially in biology. It is better to view biological systems as existing on a spectrum of probability. In responding to Darwin’s own claim that one must provide an examples of a system that “could not possibly” have been formed by natural selection, Peter S. Williams points out that:

…he was wrong to set the evidential bar quite so high (demonstrating the existence of a system that is highly unlikely to have been formed by numerous, successive – and unguided – modifications would cause a sufficiently catastrophic break down in his theory)… (6)

There comes a point when examples become sufficiently improbable to call into question the current theory, especially when multiple examples mount a cumulative case. This isn’t to say that there isn’t the possibility of a more direct disconfirmation within certain theories, but such knockdown observations are rare. Scientific theories need a greater sensitivity to evidence than such extreme categories as possibility and impossibility. In biology at least, it is difficult, to come up with examples of such theory-shattering hard anomalies that could conceivably be discovered. In practice, evolutionary biologists are remarkably adept at rationalising counter-evidence and explaining away anything that’s discovered. Cornelius hunter explains this point well:

Being an evolutionist means there is no bad news. If new species appear abruptly in the fossil record, that just means evolution operates in spurts. If species then persist for eons with little modification, that just means evolution takes long breaks. If clever mechanisms are discovered in biology, that just means evolution is smarter than we imagined. If strikingly similar designs are found in distant species, that just means evolution repeats itself. If significant differences are found in allied species, that just means evolution sometimes introduces new designs rapidly. If no likely mechanism can be found for the large-scale change evolution requires, that just means evolution is mysterious. If adaptation responds to environmental signals, that just means evolution has more foresight than was thought. If major predictions of evolution are found to be false, that just means evolution is more complex than we thought.(7)

Robert Laughlin makes a similar point when considering the ease with which biologists use theories of evolution to explain every possible outcome:

Your protein defies the laws of mass action? Evolution did it! Your complicated mess of chemical reactions turns into a chicken? Evolution! The human brain works on logical principles no computer can emulate? Evolution is the cause!(8)

Koperski is convinced that critics of design have shown that ‘although complex systems like the bacterial flagellum are improbable, they are still consistent with neo-Darwinism.'(9) This point depends upon the success of the replies Behe’s critics have made, but that’s a complex issue that requires an in-depth analysis of the biological data. From my reading of the literature at least, it’s far from clear that Behe has been adequately answered(10). The debate goes on. For the purposes of this article at least, it’s enough for me to assert that Behe and Dembski are arguing that the biological data, though perhaps theoretically/logically consistent, is practically inconsistent with modern evolutionary theories. The irreducibly complex structures that Behe talks about are special cases of specified complexity that block any logically direct Darwinian pathways. And though they leave open the possibility of indirect routes, these hopes lie beyond the reach of chance and exhaust the probabilistic resources of the universe. Critics often come back on this point and say that one or two exceptions to Darwinian accounts aren’t enough to warrant a drastic theory change. But we aren’t talking here of just one or two slightly puzzling systems that are exceptions to an otherwise successful explanatory theory, rather, as Dembski puts it’s a case of ‘global disciplinary failure…and gross theoretical inadequacy.'(11) Making a similar point he writes that, ‘It’s not just that we don’t know of such a (naturalistic) pathway for, say, the bacterial flagellum…It’s that we don’t know of such pathways for any such systems. The absence here is pervasive and systemic.'(12) Furthermore, the biological systems that tenaciously resist these naturalistic accounts bear all the hallmarks of design.

Heuristic Value and Peer-Review

The second strand in ID’s scientific case is its heuristic value. Much of the science that design theorists utilise to make their case, is often work that has been done by scientists that aren’t sympathetic to design. Their work just happens to make more sense within a design paradigm. As Koperski points out, they have focussed on things like the functionality of junk DNA and biomimetics. He argues that ’What critics rightly clamour for, however, is peer-reviewed research in which design has a more than heuristic role.’(13) Having said this, Koperski doesn’t fall in to the trap of claiming, as most critics do, that there are no peer-reviewed papers supporting design. He recognises that ‘To be fair, there are more published papers out there than most people realise.'(14) He’s also privy to the fact that many theorists who have tried to publish in journals have been discriminated against, taking away much of the incentive for further attempts. The bottom line is, ID critics have produced some substantial peer-reviewed work.(15) And though it can’t be denied that this output is meagre, the reasons for this seem to be combination of lack of incentive due to the possibility of damage to the scientists career and reputation, and the efforts of those hostile to design preventing its inclusion in journals. Nevertheless, Koperski puts some of the blame on the ID community for getting too distracted by the culture wars and focussing on public relations. Here I can agree, at least in part. It’s a balancing act. ID must maintain a healthy public appearance, but not before it has held its own in the scientific community. Sometimes certain ID advocates have emphasised the former over the later, primarily because they’re more interested in using ID as a means to an ideological end. Others, though, have been very clear about the primacy of ID’s scientific case over its broader cultural impact. Dembski makes this clear:

Unless intelligent design is an intrinsic good-unless it can be developed as a scientific research program and provide sound insights into the natural world-its use as an instrumental good for defeating ideologies that suffocate the human spirit becomes insupportable. Intelligent design must not become a noble lie for vanquishing views we find unacceptable.(16)

There is now a strong scientific core to ID, and a small group of dedicated researchers who are doing the theoretical and experimental benchwork. Granted, it’s a tiny minority. But it’s a growing minority. The main challenge for ID is to attract more scientists willing to work, despite the possibility of discrimination and ridicule. Though the peer-review output from ID folks is small, they have at least produced work that critics can grapple with, that isn’t, as Koperski puts it, merely heuristic, re-interpretive science. In 2005, the Biologic Institutewas set up, along with its ID friendly peer-reviewed journal, BIO-Complexity. A few years later, in 2007, the Evolutionary Informatics Lab also started. Most ID research has come from these two organisations, yet in his 2008 paper and 2015 book The Physics of Theism, he fails to mention these key developments in the ID community, yet they constitute the scientific core of design. There is plenty of scientific substance for critics to engage with. I’m not saying that the output from the ID crowd couldn’t and shouldn’t be more, but this depends on ID attracting more scientists  and a more open and gracious attitude on the part of those hostile to design with regard to it being allowed in journals.

The main complaint here is that there is little in the way of a research program. Even though he notes some possible lines of research outlined by Dembski, he laments that ID has failed to really get off the ground and that ‘the average design-friendly scientist still does not know quite what to do.'(17) Perhaps this is the case for some but overall I think most ID theorists know very well what to do, they just need more manpower and funding. And there have been many other detailed outlines of possible avenues of research in other books and papers.(18) But as I have already said, more research has been done then Koperski lets off and I’m convinced the ideas and potential are there for much more fruitful development, if more interest is gained. A further point he makes in The Physics of Theism is that design struggles to construct a research programme because ‘There is no way to know precisely how the Designer might have gone about his business. Turning out concrete predictions will therefore be difficult and perhaps impossible.'(19) This is a common objection to design, however it is a concern design advocates have wrestled with and they’ve formulated ways in which different aspects of ID can have predictive power. Though we can’t make blanket predictions about when, exactly, a designing intelligence acted, or might act in the future, we can make predictions about what sort of features we might find in living systems, were they designed. Before noting a dozen ID-inspired predictions, Stephen Meyer notes:

 …intelligent design hypotheses may generate several distinct types of predictions: predictions about causal powers, or lack thereof, of various mechanisms; predictions about the structure, organisation, and functional logic of living systems; predictions about what evidence will show about the history of life; and predictions about the causes of putatively bad design.(20)

Concluding my analysis of the Koperski’s argument that ID is at best a fringe science, I have argued that his distinction between soft and hard anomalies is too vague to be of much use, and sets the bar too high for falsification. Furthermore, ID theorists have brought to light sufficient cumulative evidence to put modern evolutionary theory into serious question, and make a good case for design. He underplays much of the more recent  scientific work done by design theorists (peer-reviewed work that isn’t merely heuristic science), and by extension underestimates the fruitfulness of a design framework and its potential as a research programme. I agree with him that much more work needs to be done, but I have argued that the main obstacle to ID’s fruitfulness is due to sociological   factors rather than a lack of scientific potential. In the end, this argument against design turns out to have little force.

Does ID Violate the Principle of Conservatism?

Though it has been established that ID’s alleged violation of methodological naturalism is of little consequence to its validity and scientific status, Koperski claims that there is another, more fundamental, shaping principle that ID violates, namely, scientific conservatism. This is the view that ‘when faced with anomalous data scientists prefer incremental change over more revolutionary change.'(21) The argument here is that ID is an unnecessarily radical proposal, and to accommodate anomalies in biology we needn’t make such a drastic change. The first aspect of this principle is epistemic conservatism, the view that unless a better explanation is available, one should remain within one’s current belief system. The other part of conservatism is Quinn’s principle of minimal mutilation which states that when accommodating new data one should make the smallest change possible. Here my aim isn’t to dispute the principle of scientific conservatism, because I believe it to be a sensible rule to adhere to. However, I will argue that ID doesn’t violate scientific conservatism.

With regard to epistemic conservatism, the idea of only changing theory if a better alternative is on the table, this is exactly what ID theorists are proposing. They are claiming that modern, naturalistic theories of evolution should be abandoned, or at least supplemented, because design offers a better explanation. Koperski’s main point though, is that ID ignores Quine’s minimal mutilation concept and goes a step too far. He notes that there is a live debate going on between biologists about the mechanisms of evolution. Though at first glance this provides support for the ID claim that neo-Darwinism is an inadequate theory, Koperski argues that this actually raises a serious problem for ID because it shows that there is a broader range of views to consider. The choice isn’t between Darwinism and design because there are many naturalistic, non-Darwinian proposals that have been advanced. Because these alternative proposals are said to explain the data that neo-Darwinism doesn’t, and still retain a naturalistic approach, these theories are to be preferred because they don’t introduce superfluous explanations of a different category. He points out that ‘Even if orthodox neo-Darwinism collapses, design obviously is not the only alternative.'(22) If one has a very specific definition of neo-Darwinism, then this is true. However many would argue that broadly speaking, neo-Darwinism is the only game in town, and no theory can be successful without natural selection being the primary mechanism. ID theorists such as William Dembski take a black and white approach to the options on the table. He writes ‘there are in fact two games in town…Darwinism and intelligent design.'(23), though to him the word ‘Darwinism’ is highly qualified. His contention is that any naturalistic biological theory must contain hereditary transmission, incidental change, and natural selection. These categories are broad enough to include novel ideas such as symbiogenesis, self-organisation, and genetic drift and various other mechanisms that have been proposed more recently. At the end of the day, it is natural selection that must be included in any theory for it to truly explain biological systems. This is a point that many neo-Darwinists would agree with. For instance Richard Dawkins proposes that ‘Darwinism is the only known theory that is in principle capable of explaining certain aspects of life.'(24) Ultimately this is down to a matter of how one defines neo-Darwinism. ID advocates do focus more on attempting to refute classical neo-Darwinism, mainly because it is historically and presently the most widely accepted theory. However they have still acknowledged the existence of alternative naturalistic theories, especially in more recent years. Koperski gives the impression that design advocates are ignorant of these views but this is not the case. Most alternative theories have been considered and rejected by ID theorists. In Darwin’s Doubt Stephen Meyer dedicates several chapters to examining alternative theories of evolution, finding them wanting. He concludes:

Clearly, standard evolutionary theory has reached an impasse. Neither neo-Darwinism nor a host of more recent proposals (punctuated equilibrium, self-organization, evolutionary developmental biology, neutral evolution, epigenetic inheritance, natural genetic engineering) have succeeded in explaining the origin of the novel animal forms that arose in the Cambrian period. Yet all these evolutionary theories have two things in common: they rely on strictly material processes, and they also have failed to identify a cause capable of generating the information necessary to produce new forms of life.(25)

Michael Behe writes that ‘A few scientists have suggested non-Darwinian theories to account for the cell, but I don’t find them persuasive.'(26) Other ID theorists have also surveyed the post-Darwinian world, and found it unsatisfactory to say the least. More recently many design proponents attended the widely reported ‘New Trends in Evolutionary Biology’ conference at the Royal Society, where evolutionary biologists debated different theories of evolution. Subsequently this provoked much discussion amongst ID theorists (27) I think it’s clear that they have a sufficient understanding of the various options out there. They argue that any theory of evolution that doesn’t include design is bound to fail, and that alternative naturalistic theories suffer similar problems to neo-Darwinism. Contrary to Koperski, these alternative proposals aren’t problematic for ID.

The main reason given for rejecting ID though, is not just that alternative views exist, but that they are more conservative. According to him ‘if any one of them is capable of resolving the problems posed by complex structures and macroevolution, ID is a more radical solution than is needed.'(28) This is of course true, but it depends on the ‘if’, and Koperski has not made the case that these theories succeed. More importantly, as I have pointed out, design theorists contend strongly that they don’t because they fail to account for the origin of complex specified information.

As to the claim that ID violates conservatism, I would argue that it is in a sense a scientifically conservative position, at the same time as being quite revolutionary. Marcus Ross argues that ‘ID is classified as a philosophically minimalistic position, asserting that real design exists in nature and is empirically detectable by the methods of science.'(29) As many have pointed out, ID is a broad tent, carrying with it very little metaphysical baggage, despite the fact that it might sit better within a theistic framework than a naturalistic one. Furthermore, ID does not require us to completely throw out the insights of evolutionary biology. Benjamin Wiker notes that ‘Darwinism is too small to fit the facts it claims to explain, and ID is large enough to include a modified form of Darwinism.’(30)

To say that scientists must make the smallest possible theory change to accommodate new data is not to say the change must necessarily be small. Though the jump from naturalism to design may be significant, it could be the case that this is the smallest possible change of theory we can make to successfully account for the data. Essentially, though naturalistic theories are more conservative, they turn out to be too conservative, sacrificing simplicity for explanatory adequacy. In a sense, scientific conservatism as a normative shaping principle is a form of Occam’s razor. Only in the case of all things being equal can we prefer the simpler hypothesis. In this case, all things aren’t equal because ID theory is the only theory that contains the essential ingredient necessary to accomplish the explanatory task. Though conservatism is a sensible approach to take, the history of science shows that sometimes science is forced to make drastic changes. The biological data us now pushing us to make the change from naturalism to design.

Coming to the end of his paper, Koperski advises scientists to frame biological mechanism in terms of an irreducible teleology. He points out that scientists use concepts of teleology quite freely now. Simon Conway Morris is one scientist that sees a purposeful pattern in evolutionary convergence for instance. Koperski contends that more modest, general theories of teleology are consistent with design, yet advocates refuse to include these ideas within their theories. I think proponents like Dembski would say that in principle they aren’t excluded, but they aren’t rigorous enough to tell us about design. Any view that holds that design is empirically detectable can be welcomed. But it is unclear how Conway Morris’s view can actually be said to detect design. He himself wouldn’t argue that it does either, only that it vaguely hints at some sort of teleology. Koperski complains that Dembski conceives of design too narrowly because he believes design must be empirically detectable. But surely for us to have a scientific theory of design it must be detectable by definition. Nonetheless, though Conway Morris and Dembski have their disagreements, they aren’t as opposed as they may seem.(31) Koperski writes that  ‘If ID really is about science, why not opt for a bigger tent, even if it is occupied with those of less conservative theology?'(32) ID doesn’t necessarily exclude theistic evolutionists, but it is often the case that the dissociation is wanted by theistic evolutionists themselves. Views like those of Simon Conway Morris are, as Dembski allows, perfectly consistent with ID, but consistency isn’t enough for a scientific theory. The tent is open, but whether or not theistic evolutionists like Conway Morris want to step inside is another question.


Koperski ends his paper with good and bad news. He recognises there is much more to ID than most critics think. However, to him the science is lacking sufficient bite and he finds alternative theories preferable to ID. I have argued that these reservations are misplaced and that design theorists have successfully formulated a broad scientific theory of design that just needs additional detail filling in with more interest and help. Though I agree with Koperski on many points, and think he offers a thoughtful and constructive critique of ID, I disagree that ID is little more than fringe science, and that shaping principles like conservatism and fruitfulness are problems for design. I conclude that on further inspection, the four arguments presented in his paper turn out to be bad ones. 


  1. Jeffrey Koperski, Two Bad Ways to Attack Intelligent Design and Two Good Ones(Zygon, vol.43, no.2 June, 2008),p.441.
  2. Michael Behe, Darwin’s Black Box: The Biochemical Challenge to Evolution (Free Press, 2006), p.263.
  3. Koperski, op cit, p.442.
  4. Charles Darwin, Origin of Species, (1872), 6th edition, (New York University Press, 1988), p. 154
  5. To keep abreast of the recent work by those focussing on the extended evolutionary synthesis I recommend the websites Extended Evolutionary Synthesis and The Third Way of Evolution.
  6. Peter S. Williams, Intelligent Design Theory – An Overview, Available at:
  7. Cornelius Hunter, Arsenic-Based Biochemistry: Turning Poison Into Wine, Available at:
  8. Robert B. Laughlin, A Different Universe (New York: Basic Books, 2005), pp. 168-169.
  9. Koperski, op citp.441
  10. Jonathan McLatchie, Michael Behe Hasn’t Been Refuted on the Flagellum, Available at:
  11. William Dembski, The Design Revolution: Answering the Toughest Questions About Intelligent Design (InterVarsity Press, 2004), p.214.
  12. ibid, p.296.
  13. Koperski, op cit, p.442
  14. Ibid, p.442
  15. Koperski’s article was published in 2008. Since then, many more peer-reviewed papers have been published since that year:
  16. Dembski, op cit, p.306
  17. Koperski, op cit, p.443
  18. Dembski has delineated several detailed research avenues in No Free Lunch and The Design Revolution. Also in Signature in the Cell, Stephen Meyer discusses many research questions in the epilogue and appendix.
  19. Jeffrey Koperski, The Physics of Theism: God, Physics, and the Philosophy of Science (Wiley-Blackwell, 2015),p.216
  20. Stephen C. Meyer, Signature in the Cell: DNA and the Evidence for Intelligent Design (Harper One, 2009), p.482-483.
  21. Jeffrey Koperski, Two Bad Ways to Attack Intelligent Design and Two Good Ones, p.443
  22. Koperski, op cit, p.444
  23. William Dembski, The Design Revolution: Answering the Toughest Questions About Intelligent Design (InterVarsity Press, 2004), p.266.
  24. Richard Dawkins, The Blind Watchmaker: Why the Evidence of Evolution Reveals a Universe without Design (Norton & Company, Inc, 1986), p.287.
  25. Stephen C. Meyer, Darwin’s Doubt: The Explosive Origin of Animal Life and the Case for Intelligent Design (HarperOne, 2013), p.337.
  26. Michael J. Behe, Darwin Under the Microscope (New York Times, 1996), Available at:
  27. At Evolution News there was extensive coverage of this conference.
  28. Koperski, op cit, p.444.
  29. Marcus Ross, Intelligent Design and Young-Earth Creationism: Investigating Nested Hierarchies of Philosophy and Belief,
  30. Benjamin Wiker, Does Science Point to God? Available at:
  31. Dembski and Conway Morris have had some correspondence and public interaction. And Dembski’s beef is not mainly theological: ‘Conway Morris’s fault is that he does not follow his position through to its logical conclusion. He prefers to critique conventional evolutionary theory, with its tacit materialism, from the vantage of theology and metaphysics. Convergence points to a highly constrained evolutionary process that’s consistent with divine design. Okay, but there’s more. If evolution is so tightly constrained and the Darwinian mechanism of natural selection is just that, a mechanism, albeit one that “navigates immense hyperspaces of biological alternatives” by confining itself to “thin roads of evolution defining a deeper biological structure,” then, in the language of conservation of information, the conditions that allow evolution to act effectively in producing the complexity and diversity of life is but a tiny subset, and therefore a small-probability target, among all the conditions under which evolution might act. And how did nature find just those conditions? Nature has, in that case, embedded in it not just a generic evolutionary process employing selection, replication, and mutation, but one that is precisely tuned to produce the exquisite adaptations, or, dare I say, designs, that pervade biology.’ (William Dembski, Conservation of Information Made Simple (2012), Available at: Dembski interacts further with Conway Morris’s work in Conway Morris’s Solution.
  32. Koperski, op cit, p.446.


Critic’s Corner: Kenneth Miller

Ken Miller is a cell biologist at Brown University. Miller is probably the most well known critic of ID, in part, due to his books Finding Darwin’s God and Only a Theory, his participation in the Dover trial, and his skill as an entertaining and charismatic science communicator.

Miller has vigourously sparred with many key ID proponents in print and in person for over a decade. Most of his response to ID has been directed at Michael Behe and his claims about the irreducible complexity of the bacterial flagellum, the blood clotting cascade, and the limits of neo-Darwinian mechanisms.

Miller’s criticisms of ID seem very strong on the surface, and are often cited as knockdown arguments. However, a closer examination of his critiques reveals a lack of substance and some deep misunderstandings.

Here are Miller’s published and recorded responses to ID, followed by responses to his work from ID theorists and others:
Finding Darwin’s God: A Scientist’s Search for Common Ground Between God and Evolution

Only a Theory: Evolution and the Battle for America’s Soul

Articles/Papers on ID 

YouTube Playlist: Ken Miller’s Lectures and Debates

Reasonable Doubts Podcast Episode: Darwin Day With Ed Brayton and Ken Miller

Testimony transcript from the Dover trial: Part 1/Part 2/Part 3/Part 4



A List of Selected Responses to Kenneth R. Miller

Responses to Ken Miller at Uncommon Descent

Responses to Ken Miller at Evolution News and Views

Responses from Cornelius Hunter

Responses from Answers in Genesis, Institute for Creation Researchand Creation Ministries International

Bradley Monton’s Responses to Ken Miller

Denyse O’Leary’s Responses

Michael Behe’s Responses

Kenneth Miller Resists Chloroquine Resitance

How Did We Get Here? (A written debate between Kenneth R. Miller and Philip E. Johnson)

Banana-Eating Moth Evolved in Less Than 1000 Years?

A Date With Ken Miller

Kenneth Miller’s Best Arguments Against Intelligent Design (accompanying lecture by Sean D. Pitman)

Truth or Dare with Dr. Ken Miller: A Lecture Guide to the Anti-Intelligent Design Claims by Dr. Kenneth Miller 

Mutilating Miller

Miller’s Meanderings: Only the Same Bogus Contentions

Dr. Kenneth Miller: Ignoring the Facts?

In addition to the above material, you can also find various points of response in most works of ID proponents.