Tuesday, 27 May 2014

Andrew Perry shows how not to discuss evolution and creation - 6

Perry's admission that he has not studied science past the secondary level has already been amply demonstrated by his rejection of common descent, one of the best-attested facts in modern science. It also means he is simply not in a position to critically appraise the claims made by the ID community. This is apparent when he asserts, without providing any justification for his statement, "It is well known that complex coded information and complex functional systems are the result of intelligent agency, including those produced by scientists in biology laboratories." [1] This is false, and shows that Perry  is merely regurgitating the factually inaccurate assertions made by the ID community which he would have realised were wrong had be bothered properly researching the subject.

The ability of natural selection acting on random mutations is more than capable of creating complex structures. The field of evolutionary computation shows how computer algorithms that simulate evolution are perfectly capable of creating complex structures. [2] Complex behaviour in robots such as altruism, cooperation, and deception appeared when they were programmed to evolve. [3] Finally, the evolution of complex biochemical systems has been reconstructed, showing that contrary to what he alleges, evolution is more than capable of producing complexity. Bridgham, Carroll, and Thornton point out that:
"According to Darwinian theory, complexity evolves by a stepwise process of elaboration and optimization under natural selection. Biological systems composed of tightly integrated parts seem to challenge this view, because it is not obvious how any element’s function can be selected for unless the partners with which it interacts are already present. Here we demonstrate how an integrated molecular system—the specific functional interaction between the steroid hormone aldosterone and its partner the mineralocorticoid receptor—evolved by a stepwise Darwinian process. Using ancestral gene resurrection, we show that, long before the hormone evolved, the receptor’s affinity for aldosterone was present as a structural by-product of its partnership with chemically similar, more ancient ligands. Introducing two amino acid changes into the ancestral sequence recapitulates the evolution of present-day receptor specificity. Our results indicate that tight interactions can evolve by molecular exploitation—recruitment of an older molecule, previously constrained for a different role, into a new functional complex." (Emphasis mine) [4]
Again, none of this is difficult to find. Arguments specifically refuting the ID argument that complexity cannot arise from evolutionary processes have been in the literature for well over a decade. Digital evolution has been particularly useful in exposing the vacuity of the ID argument:
A long-standing challenge to evolutionary theory has been whether it can explain the origin of complex organismal features. We examined this issue using digital organisms—computer programs that self-replicate, mutate, compete and evolve. Populations of digital organisms often evolved the ability to perform complex logic functions requiring the coordinated execution of many genomic instructions. Complex functions evolved by building on simpler functions that had evolved earlier, provided that these were also selectively favoured. However, no particular intermediate stage was essential for evolving complex functions. The first genotypes able to perform complex functions differed from their non-performing parents by only one or two mutations, but differed from the ancestor by many mutations that were also crucial to the new functions. In some cases, mutations that were deleterious when they appeared served as stepping-stones in the evolution of complex features. These findings show how complex functions can originate by random mutation and natural selection. (Emphasis mine) [5]
That Perry maintains his patently false assertion that "complex functional systems are the result of intelligent agency" despite the clear evidence refuting him once again highlights the poorly researched, tendentious nature of Perry's anti-evolution article.

As Perry's assertion that intelligent agency is needed for the creation of complex systems is false, the inference he draws from this assertion can be dismissed. It is not 'reasonable to infer an intelligent cause (God) for at least some specified complexity in nature. In fact, the term 'specified complexity as philosopher of science John Wilkins pointed out over a decade ago  owes its origins to origin of life researcher Leslie Orgel:
In fact, it comes from a book published in 1973, by Leslie Orgel, entitled The Origins of Life: Molecules and Natural Selection. It is odd to think that this notion, which is supposed by Dembski to demonstrate that life, or LIFE as he like to refer to it in his The Design Inference of 1998, cannot be the result of natural selection, was coined in the context of a discussion how it actually could. [6]
Physicist Matt Young attacks Dembski's assertion that natural processes are incapable of creating specified complexity, concluding:
The definition of entropy in information theory is precisely the same as that in thermodynamics, apart from a multiplicative constant. Thus, Dembski's claim that you cannot increase information beyond a certain limit is equivalent to the claim that you cannot reverse thermodynamic entropy. That claim, which has long been exploited by creationists, is not correct. The correct statement is that you cannot reverse entropy in a closed or isolated system. A living creature (or a coin-tossing machine) is not a closed system. A living creature thrives by reversing entropy and can do so in part because it receives energy from outside itself. It increases the entropy of the universe as a whole as it discards its wastes. Dembski's information-theoretical argument amounts to just another creationist ploy to yoke science in support of a religious preconception. [7]
Tom Schneider, a biologist with a research interest in molecular information theory has shown, using a computer model Ev, that natural processes can indeed create what Behe calls 'complex specified information', neatly rebutting the ID assertion:
According to Dembski, the existence of "specified complexity" always implies an "intelligent" designer. The question then is where, who or what is the designer? Is it me, Tom Schneider? No, that can't be right. I did set up the program - true - but I didn't make the complexity. When I set it up the parameter file, I only specified the size of the genome, the number of sites and a few other items. Well! The size of the genome and number of sites determines the information Rfrequency! But wait. At the first generation the sequence is RANDOM and the information content Rsequence is ZERO. So I didn't make the "complex specified information", as measured by Rsequence after 2000 generations. It must be created by Ev. Nor did I make the 'right' ("specified") pattern match the weight matrix gene to the binding sites. Only after I took my hands off the parameter file was the random sequence generated and the evolutionary process started. When I was involved there was no correlation between the two. Ev must have made the correlation. (Emphasis in original) [8]
Again, it is clear that Perry, is hopelessly out of his depth in this technical subject, but that's not the point. Perry has uncritically relied on ID arguments, and is either ignorant of, or has elected not to mention the copious mainstream scientific refutations of the ID position. Either option is damning.

It is also clear that Perry's knowledge of what ID proponents assert is rudimentary, let alone his understanding of mainstream science. He asserts:
"Regardless of this use of the intelligent-design argument, however, ID theorists see the increasing complexity of nature in biological understanding as the driver for a move away from naturalism to intelligent causation in biological explanation - and this is the significant claim - not any argument for God's existence" [9]
As written, this is disingenuous nonsense. We've already seen that Intelligent Design was a political and rhetorical strategy by special creationists to get around the ban on teaching special creationism in public schools after the 1987 Edwards v. Aguillard Supreme Court decision. We're seen that the ID community is almost exclusively comprised of theists, with some being explicit in their linking of intelligent design and the God of Christianity. In other words, this explicit linking of God with intelligent causation means that their claim is effectively an argument for God's existence. Furthermore, we've seen that natural processes are perfectly capable of producing complexity. Finally, his blithe reference to 'ID theorists' ignores the fact that there is no such thing as a theory of intelligent design, that  is, something with predictive and explanatory powers. This admission comes from Paul Nelson, one of the leading figures in the ID community:
Easily the biggest challenge facing the ID community is to develop a full-fledged theory of biological design. We don’t have such a theory right now, and that’s a problem. Without a theory, it’s very hard to know where to direct your research focus. Right now, we’ve got a bag of powerful intuitions, and a handful of notions such as ‘irreducible complexity’ and ‘specified complexity’ - but, as yet, no general theory of biological design. [10]
Nothing has changed in the ten years since he made this admission.

The problem with the creation-evolution dispute, pace Perry is not a lack of common ground between the two parties, but rather a failure of special creationists to recognise that literalism and strong concordism are failed approaches to interpret the creation narratives. Even if evolution is excluded and an old-earth progressive creation model employed, the sequence of creation events in Genesis 1 is flatly contradicted by what we know from the fossil record. Genesis 1 asserts that flowering plants appeared  before mammals. This cannot be reconciled with the fact that some of the earliest mammal-like animals [11] appeared at least 205 million years ago while flowering plants appear in the fossil record around 130 million years old. [12] Furthermore, as has been explained many times in detail, a literal reading of the creation narratives clearly shows evidence of a pre-scientific cosmogeography, including a solid firmament in which sun, moon, and stars were set. That the sky is not solid is something that even YECs recognise. By failing to recognise that strong concordism is not a viable exegetical option, Perry is merely creating problems with science where none should exist for interpreters of the creation narrative. 

At the risk of some simplification, science seeks to explain natural phenomena using natural explanations. Perry's attack on evolutionary biologists for a priori excluding the hand of a creator not only betrays his ignorance of the epistemological basis of modern science, but also allows any science denialist to attack any branch of modern science for excluding God:
The scriptural idea of God as a Creator working through His angels (that is, the fact of divine agency) affects what scientists may claim to know. Science textbooks do not present naturalistic evolution as 'possibly true' but as a fact. But the fact of divine agency is opposed to the philosophy of naturalism that informs the theory of evolution. For example, a scientist works with the 'fact' of spontaneous change, but a religious apologist will offer the idea of a change 'initiated' by God as an explanation for what has happened. This is an unwelcome adjustment to the rules of the game for a scientist. [13]
Again, there is the failure to differentiate between evolution as fact and evolution as theory which automatically negates his entire premise. More importantly,  the philosophy of naturalism informs all scientific endeavour, as it should. Science by definition is the study of natural explanations of natural phenomena. Does Perry criticise developmental biologists or meteorologists when they appeal to natural processes to explain embryogenesis, or thunderstorm formation? Appealing to his idea of 'divine agency' would oblige Perry, if he was consistent, to declare these two disciplines null and void as the Bible explicitly declares that both embryogenesis and thundercloud formation are acts of God:
Did you not pour me out like milk and curdle me like cheese? You clothed me with skin and flesh, and knit me together with bones and sinews. [14] 
When he utters his voice, there is a tumult of waters in the heavens, and he makes the mist rise from the ends of the earth. He makes lightnings for the rain, and he brings out the wind from his storehouses. [15]
Perry appears to conflate what some have called methodological naturalism (the idea that natural events have natural causes) with philosophical naturalism (the belief which a priori excludes the existence of the supernatural by defining the natural world as the only thing that exists). Whether this is due to confusion on his part, or a deliberate rhetorical strategy is impossible to tell, but yet again undermines his credibility on this subject. Perry's implicit attack on evolutionary biology for excluding divine agency is merely special pleading if he does not expand his attack to all branches of science.


Perry, in trying to redefine a scientific problem to a philosophical one, is merely following the well-worn path trodden by special creationists who, having had their arguments against evolution thoroughly refuted by scientists, are desperately trying to change the terms of the game in order to buy their way into the debate. As Michael Ruse observes:
...perhaps realizing that a straight frontal scientific approach will not succeed…the new creationists are making much of the claim that the essential difference between evolutionists on the one hand and creationists or "theists" (as they prefer to call themselves) on the other hand is one of conflicting philosophies. [16]
and in doing so, they are deliberately simplifying a complex picture:
Philosophically, those of us who would separate atheism and evolutionism suggest that simply using a catch-all term "naturalism" conceals subtleties in peoples' approaches. Once these subtleties are uncovered, the clash between evolution and creationism is no longer seen to be the simple black and white philosophical matter that the creationists claim. [17]
Perry's use of naturalism as a catch-all term is painfully apparent at the end of his article, where he asserts that popular evolution writing has a 'philosophical layer' embedded in it which conflicts with religion, which he terms the 'philosophy of naturalism', one which he believes can be dismissed 'on philosophical grounds' to render the theory of evolution impotent to exclude from a special creationist point of view:
There is a philosophical layer embedded in popular evolution writing, and the conflict with religion lies in this layer. This is the philosophy of naturalism. Once this is rejected on philosophical grounds, the theory of evolution cannot exclude either special creation or divine agency. Consequently, a fairly literal view of Genesis can be defended." [18]
This is the core of Perry's thesis, and it betrays both a profound ignorance of scientific epistemology, as well as the unsophisticated use of naturalism about which Ruse warns earlier, which blurs the ground between methodological naturalism and philosophical naturalism. Is Perry rejecting the former? Given the extraordinary power of the scientific method to generate knowledge about the natural world, the burden of proof lies on him to show how an overtly theistic scientific epistemology would be superior to one that always looks for natural causes. If it is the latter, then his argument collapses completely, as both militant atheists and theists who accept evolution share the same assumptions about the naturalistic basis of scientific epistemology, in which one looks for natural causes for natural phenomena.

Perry's argument also falls apart when one considers the less than carefully hidden special pleading in attacking evolutionary biology alone, despite the fact that the same methodological naturalism underlies not just evolutionary biology, but science itself. As mentioned earlier, the Bible uses fairly emphatic language to describe God's involvement in meteorology and embryology. Do we reject those disciplines because they provide entirely naturalistic explanations for embryogenesis and thunderstorm formation? By Perry's logic, we do, yet he is conspicuously silent in denouncing 'theistic developmental biologists' and 'theistic meteorologists'.

The reference to 'popular evolution writing' fairly damns Perry's argument (if only as a surrogate marker for the paucity of detailed research in his article) as the evidence for evolutionary biology stands or falls not on any philosophical presuppositions of the authors of these popular books, but on whether one can find evidence to support common descent in the mainstream scientific literature. As evolutionary biologist TR Gregory observes: reliable observation has ever been found to contradict the general notion of common descent. It should come as no surprise, then, that the scientific community at large has accepted evolutionary descent as a historical reality since Darwin’s time and considers it among the most reliably established and fundamentally important facts in all of science. [19]
If Perry wants to argue for special creation, then he is obliged to show how special creation is a better fit for the evidence for common descent found in disciplines as disparate as comparative genomics, biogeography, and palaeontology, and that obliges him to make his argument in the scientific domain, rather than take pot-shots against imagined naturalistic bias in popular scientific writing, something which is painfully evident in his penultimate paragraph:
The conflict with religious thinking is philosophical when evolutionists make their view exclusively true - when they exclude special creation, reject Genesis, or deny divine agency at work in various ways throughout the known history of the universe. [20]
It is hard to know where to begin given the multiple unspoken assumptions which he simply takes as given, without justifying them:

  • Evolutionary biology does not conflict with religious thinking, but with special creationism. Perry has conflated religious thinking with antievolutionism without recognising that he needs to justify this presupposition, rather than taking it as axiomatic.
  • Assuming that rejecting a literal reading of the creation narratives is the same as rejecting Genesis. In asserting this, Perry is flying in the face of a considerable body of Old Testament scholarship. 
  • Once again, conflating evolution as fact with evolution as theory, and ignoring the fact that evolutionary biologists have every right to assert that common descent is true, given the overwhelming evidence in its favour
  • Conflating methodological naturalism and philosophical naturalism by asserting that evolutionary biologists a priori deny the possibility of divine agency, implying that the former implies the latter.
The most damning thing about Perry's entire thesis is that even though he tries to change the rules of the game from science to philosophy, as the last point shows, he fails to make a convincing case on philosophical grounds.



1. Perry A "The creation versus evolution debate" The Testimony (2014) 84:69-72
2. Marcyzk A "Genetic Algorithms and Evolutionary Computation" TalkOrigins Archive April 23 2004
3. Floreano D et al (2007). Evolutionary Conditions for the Emergence of Communication in Robots. Current Biology (2007) 17:514-519
4. Bridgham JT, Carroll SM, Thornton JW. "Evolution of hormone-receptor complexity by molecular exploitation" Science  (2006) 312:97–101.
5. Richard E. Lenski RE, Ofria C, Pennock RT, Adami C "The Evolutionary origin of complex features" Nature (2003) 423: 139-144
6. Wilkins JS "CSI, the original series…" Panda's Thumb 27 March 2004
9. Perry, op cit p 71
10. Nelson P Touchstone Magazine 7/8 (2004): pp 64 – 65. Cited here.
11. Kermack KA, Mussett F, Rigney HW, "The skull of Morganucodon" Zoological Journal of the Linnean Society (1981) 71: 1-158
12. Lawton-Rauh A, Alvarez-Buylla, ER, Purugganan, MD  "Molecular evolution of flower development". Trends in Ecology and Evolution (2000) 15:144–149.
13. Perry, op cit p 72
14. Job 10:10-11
15. Jer 10:13
16. Ruse M "Methodological Naturalism under Attack" in Intelligent Design Creationism and Its Critics: Philosophical, Theological, and Scientific Perspectives Ed. Pennock RT (2001: MIT Press) 363-385
17. ibid, p 365
18. Perry, op cit p 72
19. Gregory TR "Evolution as Fact, Theory, and Path" Evo Edu Outreach (2008) 1:46-52
20. Perry, op cit p 72