Friday, 30 May 2014

Evolutionary Creationism - A Guide for the Perplexed

The sheer volume of material available on the evolution-creation controversy is frankly overwhelming. In order to help the layperson wanting to come to grips with the main issues, I've compiled a list of article and papers on the main biblical and scientific issues.

While the scientific evidence for common descent is beyond dispute, many laypeople will simply reject this evidence if it clashes with their interpretation of the Bible. Therefore, emphasising the problems arising from a fundamentalist reading of the Bible as well as the recent, sectarian origins of the YEC exegetical paradigm is important to show that even without evolution, the YEC / OEC way of reading the Bible is incoherent.

Thursday, 29 May 2014

Understanding creationism: An insider’s guide by a former young-Earth creationist

David MacMillan, a technical writer and former YEC has started a series of articles at the Panda's Thumb blog explaining the self-deception required by YECs to dismiss evolution despite the overwhelming evidence in favour of it. In Part 1 he notes:
We understand the theory of evolution to be a series of conclusions drawn from over a century of research, predictions, and discoveries. This theory allows us to understand the mechanisms in biology and make further predictions about the sort of evidence we will uncover in the future. Its predictive power is vital to success in real-life applications like medicine, genetic engineering, and agriculture. 
However, creationists don’t see it the same way. Creationists artificially classify medicine, genetic research, and agriculture as “operational science,” and believe that those disciplines function in a different way than research in evolutionary biology. They understand the theory of evolution, along with mainstream geology and a variety of other disciplines, as a philosophical construct created for the express purpose of explaining life on Earth apart from divine intervention. Thus, they approach the concept of evolution from a defensive position; they believe it represents an attack on all religious faith. 
This defensive posture is reflected in nearly all creationist literature, even in the less overt varieties such as intelligent-design creationism. It dictates responses. When creationists see a particular argument or explanation about evolution, their initial reaction is to ask, “How does this attack the truth of God as Creator? What philosophical presuppositions are dictating beliefs here? How can I challenge those underlying assumptions and thus demonstrate the truth?” Recognizing this basis for creationist arguments is a helpful tool for understanding why such otherwise baffling arguments are proposed. (Emphasis mine)
I should point out that this applies to both young and old earth creationists. This instinctive special creationist belief that the basis of evolution is ultimatley an attack on theism can be seen in Andrew Perry's conflation of methodological naturalism and philosophical naturalism as highlighted in my recently concluded series of posts criticising his February 2014 article in The Testimony.

Future posts by David MacMillan will be linked to at my blog as they appear.

Wednesday, 28 May 2014

Human Evolution: Genes, Genealogies, and Phylogenies

Cell biologist and cancer researcher Graeme Finlay writes in today's BioLogos blog post how his research into oncogenes and retroviruses provided him with unarguable evidence for common descent from shared retroviral elements:
I became involved in cancer research, and in the early 1980s, read avidly to inform myself of dramatic developments in the genetics of cancers. It was then that I came across oncogenic retroviruses. These are a subtype of virus that had a cunning mode of propagating themselves, and they were revolutionizing our understanding of how cancers developed. They brought to light a class of genes known as oncogenes. I struggled to assimilate the deluge of data, totally focused on cancer biology, my professional interest. But to my enormous surprise, I was following a continuous track which led to the point where I found myself reading in the area of evolutionary biology. 
Retroviruses provided a way of demonstrating that many cancers are produced from a single abnormal cell. Counter-intuitive though it may seem, the billions of cells that may populate a tumour are the descendants of a single ancestral cell, so cancers are said to be monoclonal. And, almost unbelievably, retroviruses provided a way of showing that multiple species may be derived from a single progenitor species (indeed, ultimately from a single cell). Such related taxa of organisms are said to be monophyletic. 
As I read, I found that a large variety of genetic markers established both the monoclonal nature of tumours on the one hand, and the monophyletic nature of groups of species on the other. Humans, chimps, gorillas and orang-utans, for example, share millions of genetic markers that show – unambiguously – that the four species share a common history. The genetic principles applicable to cancer (or immunology or microbiology or whatever) and evolutionary phylogenetics were the same, thoroughly established and non-controversial.
Finlay is also a Christian who is active in showing that Christianity and evolutionary biology are not mutually exclusive. His BioLogos post is definitely worth reading, as well as a 2012 post co-authored with David Layzell on the same subject, which goes into more detail. Finally, Finlay's 2013 book Human Evolution: Genes, Genealogies and Phylogenies is arguably the final word in showing how the genomic evidence confirms the reality of human-ape common ancestry. I cannot recommend it highly enough. Anyone with an open mind who reads it will come away accepting that we share common ancestry with the apes.

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.

Sunday, 25 May 2014

Andrew Perry shows how not to discuss evolution and creation - 5

In October 2004, the Dover Area School District in Pennsylvania endorsed the teaching of Intelligent Design. This decision was challenged by eleven parents of students in the Dover Area district, and eventually reached the federal courts. On December 20th 2005, after a forty day trial in which ID luminaries such as Michael Behe testified, Judge John E Jones III declared that Intelligent design was merely another form of creationism and as such violated the Establishment Clause of the 1st Amendment to the US Constitution. [1]

Andrew Perry's attack on evolution unsurprisingly refers to intelligent design, but never mentions either the Kitzmiller v. Dover decision. In fact, he ignores the fact that the Intelligent Design movement is rooted in creationism, and asserts that OD advocates "dissociate themselves from religious creationism", a claim which is flatly contradicted by comments such as:
"Intelligent design is just the Logos theology of John's Gospel restated in the idiom of information theory" [2] 
made by ID advocate William Dembski, or by lawyer Phillip Johnson's remark in response to the question of whether he believed ID made 'Darwinists' more receptive to Christianity asserted:
"ID is an intellectual movement, and the Wedge strategy stops working when we are seen as just another way of packaging the Christian evangelical message. Christian workers and organizations sometimes have difficulty understanding why anything other than direct evangelism is worthwhile...The evangelists do what they do very well, and I hope our work opens up for them some doors that have been closed." [3]
This is common knowledge among those involved in the evolution-creation controversy, and for Perry to blithely assert that ID advocates are not defending the Bible but simply arguing that complexity in nature implies an intelligent cause indicates a poorly researched, tendentious argument.

Friday, 23 May 2014

Andrew Perry shows how not to discuss evolution and creation - 4

Perry continues by asserting that the debate exists because conceptually, creation and evolution do not look alike. Furthermore, he argues that the creation narrative is the language of appearance, ruling out any attempt to harmonise evolution and the Bible. Perry also dismisses any attempt to read Genesis 1 as ancient cosmology, asserting that it does not fit well with ancient cosmologies, and concludes his dismissal of any attempt to reconcile evolution and Genesis by claiming that literalist regard such harmonisation as rejecting Genesis and ignoring the centrality of Adam and Eve to Christian teaching.

The reality of an evolutionary natural history is of course the blunt fact that destroys Perry's argument. Evolution occurred, and human-ape ancestry is a fact. Perry - and other special creationists - have no credible option other than to retool their theology in the light of this reality. It is significant that even without evolution, then Perry's concordist approach is untenable. If we grant Perry's assertion that the Genesis narrative is the language of appearance, then as OT scholars recognise, Genesis describes a cosmology completely at variance with reality.

This shows that any attempt to harmonise evolution with the creation narratives is a flawed exegetical strategy as one is attempting to read the narratives in a way alien to how the original audience would have read it. Perry's bizarre claim that any claim Genesis 1 is ancient cosmology makes the details of the account irrelevant for the believer today ignores the need to contextualise the message of Genesis 1 for a modern audience. This is basic hermeneutics, and it is puzzling that Perry fails to grasp this elementary point.

Thursday, 22 May 2014

Andrew Perry shows how not to discuss evolution and creation - 3

What drives the evolution-creation debate is the fact that the interpretation of the creation narratives, as well as doctrinal positions inferred from interpretations of the Pauline corpus by fundamentalist Christian groups is flatly ruled out by an avalanche of scientific evidence which shows the reality of common ancestry, and the impossibility of universal human descent from two people living a few thousand years ago. Either the science is wrong, or the interpretation of the Bible is wrong. There are no other options. The scientific evidence as I have shown repeatedly is solid. Evolution is a fact, and on that point there is no further room for discussion.

Andrew Perry by his own admission is not in a position to comment on the science, but has shown a distinct reluctance to alter his interpretation of the Bible accordingly. Therefore, his strategy is to arbitrarily declare the problem a philosophical one. The justification he gives for this is anything but convincing, and at one point is based on quote mining a 2001 article by atheistic philosopher of science Michael Ruse. If arbitrarily redefining the terms of a debate is dubious, quote mining is intellectually dishonest.

Andrew Perry shows how not to discuss evolution and creation - 2

Perry's reference to 'harmonisation' betrays the fact that he is shaping any reconciliation of science and the Genesis narratives exclusively in terms of literalism or strong concordism: 
"If theistic evolution and young-earth creationism are polar opposites, old-earth creationism sits in the middle between these two extremes." 
This is incorrect. YEC and OEC take a literalist and strong concordist approach, respectively, to harmonising the narratives. The former view insists that a literal reading of the narrative describes exactly when ands how the universe was created. The latter sees the days either as consecutive day-age periods, a six day period of recent re-creation, days of proclamation, or intermittent creative epochs over geologic time. In both cases, the narrative is construed as making fact-statements about how and when creation occurred. A strong concordist view of TE, which seeks to harmonise evolution with the creation narrative is a view that does not enjoy wide support among those who reject YEC and OEC. Perry's spectrum fails because he is comparing TE, whose advocates almost completely reject strong concordism, with two views whose hermeneutical strategies are completely different.

Wednesday, 21 May 2014

Andrew Perry shows how not to discuss evolution and creation - 1

The philosophical analog to the imperial overreach exhibited by scientists who dismiss the value of philosophy to science is found in the philosopher who turns every single scientific problem he sees into a philosophical one, ignores the main scientific issues while tackling irrelevant philosophical side issues, then declares the problem solved. Christadelphian philosopher of religion and evolution denialist Andrew Perry has contributed to the February 2014 edition of The Testimony with his article "The creation versus evolution debate" which not only makes this mistake, but slides into naked fideism as the abstract indicates:
"The debate between biblical creation and the theory of evolution is argued in scientific terms - that is, on the scientists' home ground. The following article argues that the conflict is actually a philosophical one, reflecting the competing world views of the two sides. For believers in God and His revelation in the Bible, the changing theories of science must be subservient to the inspired Word of God." [1]
In one paragraph, Perry has conflated a theology of creation with an account of material origins, ignored the fact that many evolutionary biologists are also devout Christians active who do not fall into Perry's artificial and misleading dichotomy of creation versus evolution, and invoked fideism by declaring that the 'inspired Word of God" trumps scientific theories. 

To that one can add his conflation of human interpretations of the Bible with the original text, and a failure to recognise that evolution refers to fact and theory. While the modern synthetic theory, currently accepted theory of evolution like all theories is not final but subject to revision, the facts of common descent and large-scale evolutionary change which the modern synthetic theory seeks to explain completely rule out the special creation Perry seeks to defend.

Massimo Pigliucci schools Neil deGrasse Tyson on the value of philosophy

Biologist and philosopher Massimo Pigliucci has called out astrophysicist Neil deGrasse Tyson for his dismissal of the relevance of philosophy in his recent blog post Neil deGrasse Tyson and the value of philosophy. Tyson of course is not alone - Dawkins, Krauss, and Hawkins have in the past questioned the value of philosophy, but with the reboot of Cosmos positioning him as one of America's public scientific intellectuals, his attacks on philosophy would carry with them some gravity.

Pigliucci arguably gets the better of Neil deGrasse Tyson - as he points out, the philosophy of science has been incredibly useful for science:
You and a number of your colleagues keep asking what philosophy (of science, in particular) has done for science, lately. There are two answers here: first, much philosophy of science is simply not concerned with advancing science, which means that it is a category mistake (a useful philosophical concept) to ask why it didn’t. The main objective of philosophy of science is to understand how science works and, when it fails to work (which it does, occasionally), why this was the case. It is epistemology applied to the scientific enterprise. And philosophy is not the only discipline that engages in studying the workings of science: so do history and sociology of science, and yet I never heard you dismiss those fields on the grounds that they haven’t discovered the Higgs boson. Second, I suggest you actually look up some technical papers in philosophy of science  to see how a number of philosophers, scientists and mathematicians actually do collaborate to elucidate the conceptual and theoretical aspects of research on everything from evolutionary theory and species concepts to interpretations of quantum mechanics and the structure of superstring theory. Those papers, I maintain, do constitute a positive contribution of philosophy to the progress of science — at least if by science you mean an enterprise deeply rooted in the articulation of theory and its relationship with empirical evidence.
Significantly, even Jerry Coyne agrees with some of Pigliuccis's criticisms:
Further, philosophy helps scientists be rigorous, for the discipline teaches the logical tools that can help clarify scientific thinking. I, for one, have benefitted from reading the lucubrations of Dan Dennett about consciousness and about evolution, even if I don’t always agree with him. So on this count I think Tyson needed to be schooled.
Full article is here.

Tuesday, 20 May 2014

Tiktaalik roseae - an essay on creationism

Got a spare ten minutes? This video on Tiktaalik roseae gives both a quick rundown on its significance, as well as debunks the main special creationist attacks on its significance:

If you have an hour to spare, this lecture by Neil Shubin, one of the discoverers of this transitional fossil is well worth your time.

Those wanting more detail should consult this paper by Jenny Clack, one of the leading researchers in early tetrapod evolution. The fossil evidence for tetrapod evolution is beyond dispute. All that it needs is for the YEC to have the honesty and humility to read it, rather than arrogantly relying on their own distortion of the Bible, and in the process making an idol of their own ignorance.

Monday, 19 May 2014

Creation in six days, or a single day? Yet more reasons why young earth creationism is theological and scientific nonsense

Bernard Burt has asserted in a comment on my last post that Exodus 20:11 is proof that the universe was made in six days, and has obliquely implied that God will make this one of the criteria on which the faithful are judged. To quote another commenter, "I find this response a little worrying. If your belief matters more than the evidence, where do you draw the line?" Bernard's response is pure fideism which declares that reason and faith are mutually exclusive. 

Bernard, like all YECs is utterly inconsistent in his literal reading of the creation narratives. Genesis 1 clearly states that God created a solid firmament separating waters above from waters below, in which the sun, moon, and stars are set. The fact that there is no solid firmament above us alone should be enough to tell us that a literal reading of the creation narratives will result in error, a point that CC Walker, second editor of The Christadelphian recognised when he observed that "Moses’ testimony is not so “plain” that it cannot be misinterpreted or misunderstood." [1]

Saturday, 17 May 2014

Bryan College, fundamentalism, and the culture of fear

I'm sure that most who follow the evolution-creation controversy would be aware of the move by Bryan College in Dayton Tennessee to alter its statement of faith so that the part which refers to human origins: 
"that the origin of man was by fiat of God in the act of creation as related in the Book of Genesis; that he was created in the image of God; that he sinned and thereby incurred physical and spiritual death;" 
has now been altered to explicitly endorse monogenism: 
"We believe that all humanity is descended from Adam and Eve. They are historical persons created by God in a special formative act, and not from previously existing life forms." 

Friday, 16 May 2014

Bruce Waltke - Theistic evolution is the best synthesis of special revelation, general revelation, and science

The sidebar list of recommended reading isn't merely an affectation. It's a list of reference works that I have found useful in understanding how to create a grand synthesis of the books of divine revelation. One of the books on the list is "An Old Testament Theology: An Exegetical, Canonical, and Thematic Approach" by Bruce Waltke and Charles Yu.

Waltke is a respected evangelical OT scholar who (along with Michael Patrick O'Connor) literally wrote the book on biblical Hebrew syntax. [1] His synthesis? Evolutionary creationism:

Thursday, 15 May 2014

Junk DNA and the Onion Test - Most of our genome is non-functional

Genomics expert and evolutionary biologist TR Gregory has co-authored a paper with Alexander Palazzo in PLoS Genetics outlining the evidence which shows that most of the human genome is non-functional. I cannot recommend Palazzo and Gregory's paper enough as it concisely presents the case for junk DNA and acts as a corrective to the ENCODE hype which regrettably has been swallowed by many special creationists.

"20 scientific facts seldom taught to students" critically reviewed #13

It should be evident by now that John Collyer's '20 scientific facts seldom taught to students' serve only to emphasise the intellectual bankruptcy of his attacks on evolution. His thirteenth 'fact' is memorable for its utter mangling of molecular biology:
"The DNA helix in each cell requires twenty different proteins for its structure. These specific proteins can only be produced under the direction of the information in the DNA; therefore the whole complex system must have been formed complete from the beginning of life." 
DNA is not a protein, but a polymer made from four different nucleotides, adenine, guanine, cytosine, and thymine. Proteins are polymers of amino acids - the 20 standard amino acids are encoded by the genetic code which is encoded in DNA and messenger RNA sequences. It is painfully clear that Collyer has confused these two concepts.

Wednesday, 14 May 2014

"Fundamentalism robbed me of my Christianity"

At the always excellent God of Evolution blog is a guest article from Kevin Long, a former fundamentalist Christian. Unlike most former Biblical literalists whose faith was forever shattered by the struggle to reconcile a fundamentalist view of the Bible with the real world, Long has now rediscovered his Christianity, but the pathway was tortuous and painful:
Over the years, however, I became more and more aware that the evidence was stacked against a literal interpretation of scripture. I had to do intellectual backflips to allow myself to continue to learn, and maintain my viewpoint. Gradually, these backflips became more frequent, and more elaborate, and I had to do them while squinting, if you’ll allow the metaphor. In any event, this kind of continual conflict between facts and faith caused a great deal of psychological stress — as it does in pretty much everyone — and it just got worse over time. This was not healthy...

Three years into college, the breakdown came: Evolution. Was. True. There was simply no logical way around it. This then led to me completely losing my faith, and a brief, terrifying slide into atheism. Why? Because I had it drilled into me that if something wasn’t literally true, then it was a lie. My own fanaticism turned against me, I was forced to judge the Bible by that same standard, and I no longer believed anything.

But this, too, was a logical fallacy, of course, and I was eventually able to resolve it (I am a Christian, as I said at the start, so obviously, I got my faith back), but it was a long and arduous process that lasted decades. All that hell I put myself through for a small-minded, shallow interpretation of scripture that didn’t even logically proceed from the text. (Emphasis in the original)
This is the legacy of fundamentalism. This is how it creates atheism.This is the intellectual suffering that the zealots who read the creation narratives blindly and literally are inflicting on the next generation of believers. If the hermeneutical madness they promote does not rapidly become an embarrassing footnote in the history of Christian exegesis, there will be precious few generations to follow them.

"20 scientific facts seldom taught to students" critically reviewed #12

Collyer's twelfth point was the assertion that the "genetic information encoded in each cell in the DNA, if written out in detail, would require as many as 4,000 large volumes of closely printed text. This is no accident of nature."

Wrong. Collyer has ignored the fact that around 44% of the human genome is made up of mobile genetic elements  - DNA transposons, retrotransposons -  that copy and paste themselves into the genome randomly, often causing disease in the process. This is very much an unguided, random process. A significant fraction of the human genome owes its origin to ancient retroviral infection. In fact, there is more retroviral genetic material – the evidence of past retroviral infection – in our genome than there is direct protein coding material. Only a a small percentage of the human genome directly codes for protein or has specific regulatory function.

 A better analogy would be 4000 volumes consisting mainly of gibberish, spelling errors and random insertions of sentences from languages written in other languages, with at best 40 volumes of sensible information scattered randomly through the library.

"20 scientific facts seldom taught to students" critically reviewed #11

John Collyer's eleventh point was that  the "genetic code in every form of life is a precise set of information for the development and activity of that form of life, accompanied by elaborate transmission and duplication systems, without which life would cease. This complexity cannot be accounted for by chance, but testifies to intelligent design in every form of life."

Once again, Collyer has conflated abiogenesis and evolution. The former refers to the origin of life while the other explains how the diversity of life over time has emerged. They are separate disciplines and the problems with the former do not make the considerable evidence for the latter suddenly disappear. Furthermore, Collyer has once more invoked the argument from personal incredulity. Just because a layperson with no relevant background in origin of life studies cannot imagine how the genetic code evolved does not mean that a naturalistic origin for the genetic code will never be found.

Thursday, 1 May 2014

More on early Jewish views on cosmology and their implication for literalism

Rabbinic cosmology as Moshe Simon-Shoshan points out was a "dynamic synthesis of biblical texts, ancient Mesopotamian traditions, classical Greek scientific theories and methods, and the rabbis' own original speculations." [1] Recognising this is important in order to differentiate between biblical and non-biblical sources. However, there is no doubt that the Biblical contribution makes sense only when viewed against the ancient Near Eastern view of a flat world covered by a solid firmament. This cannot be stressed enough as it is the key to understanding why both YEC (literal) and OEC (strong concordist) readings of the creation narrative are untenable.