Saturday, 19 April 2014

Neville Clark's attack on evolution - 1

Neville Clark is another Christadelphian who thinks that evolution is not only wrong, but must be eradicated from the Christadelphian community, even at the cost of excommunicating those who accept it. Clark asserts during a 90 minute long address and Q&A session that his talk will squash evolution flat in our community. Clark is seriously mistaken if he thinks that his talk will achieve that aim, as his address betrays insufficient knowledge of evolutionary biology, misrepresents evolutionary creationists, and fails to appreciate Genesis in its original context.

Clark does not differentiate between evolution as fact and evolution as theory

Clark begins by asserting that Darwin did not invent the idea of evolution, but rather described how evolution could occur. Here he makes his first mistake in forgetting that Darwin had two aims when publishing his book:
  1. Amassing evidence that evolution had occurred
  2. Proposing a plausible model for how evolution could occur
There is little excuse making this mistake as Darwin made the point at least twice. In 1863, he stressed that:
"[w]hether the naturalist believes in the views given by Lamarck, or Geoffroy St.-Hilaire, by the author of the ‘Vestiges,’ by Mr. Wallace and myself, or in any other such view, signifies extremely little in comparison with the admission that species have descended from other species and have not been created immutable; for he who admits this as a great truth has a wide field opened to him for further inquiry." [1]
Eight years later in The Descent of Man Darwin reiterated this point:
"Some of those who admit the principle of evolution, but reject natural selection, seem to forget, when criticising my book, that I had the above two objects in view; hence if I have erred in giving to natural selection great power, which I am very far from admitting, or in having exaggerated its power, which is in itself probable, I have at least, as I hope, done good service in aiding to overthrow the dogma of separate creations." [2]
Darwin provided considerable evidence from the biogeographical distribution of species, embryology and atavisms, and comparative anatomy to make his point that life shared a common ancestor and had diversified by a process of descent with modification. He was successful in convincing the scientific world that evolution had occurred, but his theory of natural selection, due to the lack of a robust theory of inheritance, did not win much support, and fell out of favour from the late 19th century to the early 20th century, when it returned as part of the modern synthetic theory of evolution. [3] Once again, the fact of evolution however was never seriously challenged as the evidence for it was regarded as overwhelming.

Evolution is not an atheist conspiracy

Support for evolution was found among both believing and unbelieving scientists, with some of Darwin's best supporters being theologically conservative Christians. Historian of science Michael Keas observes that some of the authors of The Fundamentals, the early 20th century series of essays defending conservative Christianity from modernism, were comfortable with aspects of evolution:
"In his “Science and Christian Faith” essay, [James] Orr also proposed a resolution to the apparent conflict between biological evolution and the Bible. Significant evidence points to “some form of evolutionary origin of species—that is some genetic connection of higher with lower forms,” but he thought that this change was limited (without specifying how limited). He also argued that God directs the mechanisms of evolution toward purposeful ends." [4]
David Livingstone, another historian of science reiterates the fact that some of Darwin's supporters were Christians, and did so because they realised the evidence supported evolution:
"Darwin’s cause in America was championed by the thoroughgoing Congregationalist evangelical Asa Gray, who set himself the task of making sure that Darwin would have “fair play” in the New World. Let us be clear right away that this cannot be dismissed as capitulation to the social pressure of academic peers. To the contrary, Gray had to take on one of the most influential naturalists in America at the time to maintain his viewpoint – none other than Louis Agassiz, a Harvard colleague who vitriolically scorned Darwin’s theory. But Gray was not alone. Many of his countrymen, associates in science and brothers in religion took the same stand. And indeed even those who ultimately remained unimpressed with if not hostile to Darwin were quite prepared to admit that evolution had occurred. It is surely not without significance that Christian botanists, geologists, and biologists – that is to say, those best placed to see with clarity the substance of what Darwin had proposed – believed the evidence supported an evolutionary natural history." [5]
The evidence for common descent is overwhelming and has been accepted for over a century

While the precise details of the mechanism of evolution are still a subject of active scientific debate today, the fact of common descent and large scale evolutionary change has not been seriously doubted for well over a century as the evidence is overwhelming. Genomics expert and evolutionary biologist T.R. Gregory notes:
"Over the past 150 years, this initial list [of evidence offered by Darwin] has been supplemented by countless observations in paleontology, comparative anatomy, developmental biology, molecular biology, and (most recently) comparative genomics, and through direct observations of evolutionary change in both natural and experimental populations. Each of thousands of peer-reviewed articles published every year in scientific journals provides further confirmation (though, as Futuyma…notes, “no biologist today would think of publishing a paper on ‘new evidence for evolution’ ... it simply hasn’t been an issue in scientific circles for more than a century”). Conversely, no 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." [6]
Just the evidence for common descent from comparative genomics alone is overwhelming

The evidence for common descent ranges across multiple disciplines including comparative anatomy, developmental biology, biogeography, palaeontology, and comparative genomics. A complete elaboration of this evidence would easily fill a book and go beyond the scope of this series. Arguably the most powerful evidence for common descent is comparative genomics, and a few points will readily demonstrate this to the disinterested observer. A brief overview of the genetic code will provide the background needed to understand this point.

The genetic code is a system in which the information required to code for proteins (complex molecules that have many functions including structural, signalling, regulatory, and enzymatic roles) is encoded in DNA and RNA. Proteins are complex polymers of simpler molecules known as amino acids. There are 20 standard amino acids in the human body, and each is encoded by one or more codons, consecutive sequences of three nucleotides:

A series of codons in part of an RNA molecule. Each codon consists of three nucleotides, usually representing a single amino acid. (Source: Wikipedia)
Due to the redundancy of the genetic code which has 64 possible codons to code for 20 standard amino acids and stop codons, there is more than one way to encode for each codon. On average, this amounts to approximately three codons per amino acid. 

This means that for a protein such as cytochrome c (involved in cellular respiration and programmed cell death) which is around 104 amino acids long, there are around 3^104 or around 4.1x10^49 possible ways to encode for the same cytochrome c protein. Another consequence of the redundant genetic code is that it is possible for each codon to tolerate point mutations without necessarily changing the amino acid for which it encodes. This can be readily seen in leucine, valine, serene, proline, threonine, alanine, and glycine, where any change in the third codon will not result in a change in amino acid.

The significance of this is readily seen when we look at what common descent would predict we would see in the cytochrome c gene of all life forms in which this gene appears. If all life shares a common ancestor, then we would expect to see that this vital gene would be highly conserved, with the amino acids sequence not varying by much at all, apart from the neutral changes mentioned above. Furthermore, any species which share a recent common ancestor would have cytochrome c genes that differ by only a few point mutations whereas those with a remote common ancestor would differ by more point mutations, as far more time has elapsed in the time since their ancestors separated. 

In fact, the situation is more complex than this as cytochrome c has functional redundancy in its amino acid sequence. This means that cytochrome c can tolerate changes in its amino acid sequence and still perform the same biological function. In fact, only around one third of its amino acid sequence cannot be changed. When we factor in both coding and protein redundancy, the total number of ways in which one can code for a functional cytochrome c gene is around 2.3 x 10^93 possible genes.

Finally, there is no reason that a particular animal needs a particular cytochrome c molecule. Genetic experiments have been done in which cytochrome c proteins from humans [7], fish, birds, insects, and mammals [8-9] functioned perfectly well in yeast cells which had their cytochrome c genes removed, showing that there is no biological reason why closely related species need to have similar or identical cytochrome c proteins. Common descent would be falsified if the cytochrome c sequences for closely related animals such as humans and chimps differed considerably.

What we see is in complete agreement with common descent. The cytochrome c amino acid sequences for humans and chimpanzees are identical. The cytochrome c genes for these primates differs by only four nucleotides out of 104, a difference of a little over 1%. Conversely, the amino acid sequence for the yeast Candida differs from humans by 51 amino acids. This has been appreciated for decades. Legendary geneticist Theodosius Dobzhansky, one of the scientists responsible for creating the modern synthetic theory of evolution noted:
The cytochrome C of different orders of mammals and birds differ in 2 to 17 amino acids, classes of vertebrates in 7 to 38, and vertebrates and insects in 23 to 41; and animals differ from yeasts and molds in 56 to 72 amino acids.
and observed that the multiple lines of evidence of this nature "make sense in the light of evolution: they are nonsense otherwise." [10]

Dobzhansky is needless to say correct. It is impossible to credibly explain why when we look at the coding sequences and amino acids for scores of proteins shared across all forms of life from yeast to mouse to man, we see that closely related species differ by fewer amino acids or nucleotides than more distantly related sequences, or why when we plot this information, the phylogenetic tree agrees remarkably well with the consensus tree. Common descent explains this perfectly. Special creation has no explanation other than to claim that 'God did it', which leaves open the question of why God is creating life in such a way as to simulate common descent right down to the genomic level.

Shared genetic errors - pseudogenes, retrotransposons and endogenous retroviruses

Compelling as this evidence is, there is an even more potent demonstration of the reality of common descent, and that is shared genetic 'errors' such as pseudogenes (genetic sequences resembling functional genes but which no longer work due to acquired errors), retrotransposons (genetic elements that copy themselves and randomly insert themselves through the genome) and endogenous retroviruses (decayed remnants of ancient retroviral infection which inserted themselves into the genome. There are many examples of identical genetic 'errors' which are found at exactly the same place in the genomes of related species, and the only credible explanation for this fact is that these genetic 'errors' first occurred in a common ancestor of these species, and was subsequently inherited.

An excellent analogy is that of plagiarism. If a teacher receives six term papers which have multiple identical paragraphs at the same place in these papers with identical spelling errors in the same words in the same sentences, with the identical paragraphs (minus the errors) coming from a previously published book on the subject, then the most likely conclusion is that one of the students plagiarised the book, making spelling errors in the process. That paper was then copied by five other students. The odds of the same six students independently writing paragraphs identical to a previously published book and independently making the same spelling errors in exactly the same place are so remote as to be discounted as a credible explanation.


Arguably the classic example is that of the enzyme L-gulonolactone oxidase which is the last enzyme in the ascorbic acid (vitamin C) biosynthetic pathway. In humans, the great apes, and monkeys, it is broken, which means these animals are unable to make their own vitamin C. Vitamin C is essential to life - if we do not get enough ascorbic acid in our diet, we will contract scurvy which is eventually fatal, as countless mariners discovered in the past. The GULO gene is crippled in exactly the same way in humans, apes, and monkeys. Common descent explains this perfectly: GULO was rendered non-functional in the common ancestor of these primates several million years ago, with the crippled gene subsequently inherited by the descendant species. Furthermore, we find that in primates with a recent common ancestor (such as humans and chimpanzees) the GULO pseudogene sequences differ by fewer point mutations than primates with a distant common ancestor (such as humans and monkeys).

Common descent explains this perfectly: GULO was rendered non-functional in the common ancestor of these primates several million years ago, with the crippled gene subsequently inherited by the descendant species. Once rendered non-functional, the GULO pseudogene picked up point mutations at the usual background rate, with species sharing a recent common ancestor differing by fewer point mutations than those with a remote common ancestor. 

Special creationists have no credible explanation for this fact, other than to assert:
  • God deliberated created humans, apes, and monkeys with a biosynthetic pathway for a critical trace nutrient that does not work
  • God created this crippled gene with exactly the same mutation in exactly the same place
  • God inserted the right sequence of point mutations in exactly the right way in the primates to simulate common descent
This makes God out to be a deceitful trickster at best. Even the intelligent design advocate Michael Behe, accepts that this is overwhelming evidence for common descent:
"Both humans and chimps have a broken copy of a gene that in other mammals helps make vitamin C...It's hard to imagine how there could be stronger evidence for common ancestry of chimps and humans." [11]
This is powerful evidence for common descent, but is only one single point of evidence among hundreds of other examples of shared identical genomic errors. Arguably the most powerful demonstration of common descent is the presence of endogenous retroviral elements in the same position in the genome of related species.

Endogenous Retroviruses

Retroviruses use RNA instead of DNA to encode their genetic information. When they infect a host cell, they can transcribe their genetic information to a DNA copy which is able to be inserted into the genome of a host cell. If this happens to be a sperm or egg cell, then the DNA copy of the retrovirus can be inherited like any other DNA element. When this happens, the genomic elements is referred to an an endogenous retroviral element.

John Coffin - an acknowledged expert in virology - notes that: 
Because the site of integration in the genome, which comprises some three billion base pairs in humans, is essentially random, the presence of an ancient provirus at exactly the same position in different, but related, species cannot occur by chance, but must be a consequence of integration into the DNA of a common ancestor of all the species that contain it. It evolution of retroviruses follows, therefore, that we can infer what viruses were present millions of years ago by examining the distribution of endogenous proviruses in modern species. [12] 
In a frequently cited paper, Coffin and his colleague Welkin Johnson pointed [13]  out how retroviral inclusions could be employed to reconstruct primate phylogenies or evolutionary family trees using the principle that retroviruses, once fixed in the genome of a species will be inherited by its descendants. 

Coffin and Johnson used human endogenous retroviruses - most of the HERV families are found in apes and Old World monkeys. The HERVs used in their study are: 
the result of integration events that took place between 5 and 50 million years ago, as indicated by the distribution of specific proviruses at the same integration sites (or loci) among related species. The evolution of primates has been the subject of intense study for well over a century, providing a well established phylogenetic consensus with which to compare and evaluate the performance of ERVs as phylogenetic markers. [14] 
What Coffin and Johnson are pointing out towards the end is that we have a fairly reliable evolutionary family tree based on physical characteristics which they used to see how well family trees constructed using ERV data compared with the consensus tree.

ERV inclusions as Coffin and Johnson point out [15] have three sources of information that can be used to construct phylogenetic trees: 
  • The distribution of ERV inclusions among related species 
  • Accumulated mutations in proviral sequences, which allow an estimate of  genetic distance 
  • Sequence divergence between the LTRs at each end of the ERV inclusion, which is a source of information unique to endogenous retroviruses. 
Both the huge size of the vertebrate genome and the  random nature of retroviral integration, it is highly unlikely that one will find multiple ERV inclusions at the same location. As the authors point out: 
Therefore, an ERV locus shared by two or more species is descended from a single integration event and is proof that the species share a common ancestor into whose germ line the original integration took place. Furthermore, integrated proviruses are extremely stable: there is no mechanism for removing proviruses precisely from the genome, without leaving behind a solo LTR or deleting chromosomal DNA. The distribution of an ERV among related species also reflects the age of the provirus: older loci are found among widely divergent species, whereas younger proviruses are limited to more closely related species. [16] 
The second point is fairly straightforward, as it is similar to the principle underlying other sequence-based phylogenetic analytical methods. As proviral sequences are selectively neutral, they will tend to accumulate mutations at the rate of their occurrence. Two species that have only diverged recently will only differ by a small number of mutations at their common proviral sequence, while those that diverged in the remote past will differ by a larger number of mutations.

Johnson and Coffin found that:
Three of the loci, HERV-KC4, HERV-KHML6.17, and RTVL-Ia, were detectable in the genomes of OWMs [Old World Monkeys] and hominoids [humans and apes], but not New World monkeys, and therefore integrated into the germ line of a common ancestor of the Old World lineages. HERV-K18, RTVL-Ha, and RTVL-Hb were found exclusively in humans, gorillas, chimpanzees, and bonobos, and thus are consistent with a gorilla/chimpanzee/human clade. None of the loci was detected in New World monkeys. [17] 
This data is perfectly explained by common descent. To reiterate an “ERV locus shared by two or more species is descended from a single integration event and is proof that the species share a common ancestor into whose germ line the original integration took place.” Johnson and Coffin found many loci shared by these primate species, some shared only by humans, chimps, bonobos and gorillas, some shared only by old world monkeys and hominoids (humans and great apes). This data is consistent with an evolutionary origin of these species, but impossible to explain by special creation unless God is consistently simulating common descent right down to simulating evidence of ancient retroviral infection inherited by humans and apes.

Given the fact that ERV insertion is random, the odds of just a single ERV being found at the same place at the genomes of humans and apes purely by chance is billions to one against. Even with around ten ERV elements at identical places, the odds of this occurring by chance are so unlikely as to be effectively zero. Having said that, being able to look at the whole genome to see what the entire pattern of ERV inclusions in humans and other primates shows would make an already unassailable case irrefutable. Cell biologist, evangelical Christian and cancer researcher Graeme Finlay notes that this has been done, and the results overwhelmingly confirm human-ape common ancestry just from the genomic  data: 
The ultimately rigorous test of the assertion that ERVs establish the truth of human evolution from remote primate progenitors requires the sequencing of entire genomes of multiple species, and a side-byside comparison of all the ERVs residing in them. This would allow every one of the 440,000 ERV and other LTR elements in the human genome to be checked against the equivalent sites of the genomes of other primates. At the turn of the century, whole-genome comparisons sounded like science fiction. But technological developments have been explosive. The first draft of the human genome sequence was published in 2001 – ahead of schedule and under budget. Analysis of draft sequences of the chimp and bonobo (or pygmy chimp) genomes followed in 2005 and 2012, respectively. Early returns on the gorilla genome, and sequence analysis of the orang-utan genome came in 2011, in quick succession. A first draft of the rhesus macaque (an OWM) genome came out in 2007. And, as already mentioned, sequences of two related archaic extinct humans – the Denisovan and Neanderthal hominins – have been added recently. Many more primate genome sequences are in the pipeline.

If one species had an individualistic collection of ERVs that bore no relation to the ERVs in supposedly related species, then the phylogenetic scheme would crash in a heap. This comparative genomic approach to delineating phylogenetic relationships is inherently very susceptible to falsification – an important criterion for pursuing real science. So what can be said of whole-genome comparisons of ERV content?

I have mentioned that there are four major classes of ERV and ERV-like inserts in primate DNA. In the case of three of them (types I, III and IV), it seems that essentially all inserts present in the human genome are shared by chimps and bonobos (Table 1.3). These types of retrovirus had stopped accumulating in the primate germ-line before the human and chimp lineages diverged. Only in the case of the ERV-K family are there human-specific members, and these are approximately 1% of the whole ERV-K complement. We can be confident that even for the ERV-K population of proviruses, the huge majority were inserted into the primate germ-line in individuals that were ancestors of humans and the two chimpanzee species. We can conclude on the basis of over 400,000 inserted markers of monoclonality that humans, chimps and bonobos are descended from common ancestors. Most of this lineage is shared also with gorillas and orang-utans. Full analysis of the orang-utan genome is not yet available. It seems that orang-utans have acquired some additional members of the ERV-E sub-family, but otherwise have inherited the same basic ERV complement that is possessed by humans, chimps and gorillas. 
Even with the much more distantly related rhesus macaque (an OWM), initial surveys found a high degree of sharing of the ERV population. The one detailed human–macaque comparison currently available involved a selection of those ERVs that have retained both LTRs in both species. This analysis showed that, depending on the category of ERV, between 19% and 65% of full-length ERVs and LTR elements are shared by these species (Table 1.3). Overall, of 3,781 such well-preserved inserts in the human genome, 1,369 (36%) are present also in the macaque – the same type of ERV at exactly the same location in the respective genomes. This is a colossal weight of evidence for common ancestry of humans and OWMs. One might also suppose that less well-preserved inserts would tend to be older, and that a higher proportion of them would therefore be shared by humans and OWMs. [18] (Emphasis mine)
The ERV data alone makes the case for human-ape common ancestry. Those who claim otherwise are grossly uninformed, deluded or lying. No credible special creationist explanation for this evidence exists. Just on this evidence, the evolution-creation debate has been lost by the special creationists. The only intellectually honest approach is to accept the science, examine the evidence, and humbly work out how to read the Bible in the light of this revelation from the book of nature. 


Neville Clark's attack on evolution was undermined at the outset when he neglected to point out that Darwin had two aims when publishing his thesis: outlining the evidence that evolution had occurred, and proposing a theoretical mechanism to explain it. The evidence for common descent just from the genomic data as I have summarised is beyond dispute, which makes anything Clark says from the opening minutes of his presentation irrelevant. Common descent and large-scale evolutionary change are facts, and no amount of misrepresentation of what evolutionary creationists believe, or creative exegesis of the creation narratives will change that fact. 

Clark is making the same class of mistake Cardinal Bellarmine in his dispute with Galileo in privileging flawed human interpretation of the Bible over the clear witness of creation. Bellarmine quoted the Bible to justify his opposition to heliocentrism. Bellarmine was wrong. Clark is likewise wrong in denying evolution. The danger is that by linking orthodoxy with the rejection of evolution, he is placing a stone of stumbling in the way of young Christadelphians who are unable to change their views as a precondition of fellowship. Quotes like these are depressing common:
“My own eldest son has decided he cannot be baptized because he has seen the evidence for evolution with his own eyes, and our ecclesia will not tolerate discussion on the subject. Unlike some young people, he is too honest to say he doesn’t believe it, just so that he can ‘pass the test’ and be baptized.”
“I will be spending most of this semester studying common descent and evolution in first year biology, and have done so through DNA and cells so far. It really is fascinating and very undeniable. There's also a young Christo girl from [X ecclesia] in the subject, and I am interested to know what she's thinking.”
That this is allowed to happen in our community is tragic. 

In the following posts in this series I will focus on Clark's misrepresentation of what evolutionary creationists believe, examine the real lessons from the Ralph Lovelock controversy, and consider a historically informed exegesis of the creation narratives. Those who possess a teaching role in the community need to be aware that James 3:1 holds those who teach to a higher example:
Not many of you should become teachers, my brothers and sisters, for you know that we who teach will be judged with greater strictness.


1. Darwin CR. Origin of species [Letter]. Athenaeum 9 May: 617; 1863.
2. Darwin C. The descent of man, and selection in relation to sex. London: John Murray; 1871.
3. To use Julian Huxley's term, this period is referred to as the 'Eclipse of Darwin'. During this time, alternative theories of evolution such as mutationism, orthogenesis, and neo-Lamarckianism held sway.
4. Keas M "Darwinism, Fundamentalism, and R.A. Torrey" Perspectives on Science and Christian Faith (2010) 62:37
5. Livingstone D.N. “Darwin’s Forgotten Defenders” (Eerdmans 1984) p xi-xii
6. Gregory T.R. "Evolution as Fact, Theory and Path" Evo Edu Outreach (2008) 1:46-52
7. Tanaka, Y et al , "Construction of a human cytochrome c gene and its functional expression in Saccharomyces cerevisiae." J Biochem (Tokyo) (1988) 103: 954-61.
8. Clements, J. M. et al "Expression and activity of a gene encoding rat cytochrome c in the yeast Saccharomyces cerevisiae." Gene (1989) 83: 1-14.
9. Hickey, D. R. et al (1991) "Synthesis and expression of genes encoding tuna, pigeon, and horse cytochromes c in the yeast Saccharomyces cerevisiae." Gene (1991) 105: 73-81
10. Dobzhansky T "Nothing in Biology Makes Sense Except in the Light of Evolution" The American Biology Teacher (1973) 35:125-129
11. Behe M "The Edge of Evolution: The Search for the Limits of Darwinism: (2007: Free Press) p 71-72 
12. Coffin JM “Evolution of Retroviruses: Fossils in our DNA” Proceedings of the American Philosophical Society (2004) 148:3, 264-280
13. Johnson WE Coffin JM "Constructing primate phylogenies from ancient retrovirus sequences" Proc. Natl. Acad. Sci. USA (1999) 96:10254-10260 
14. ibid p 10254
15. ibid p 10255 
16. loc cit
17. ibid p 10256
18. Finlay G “Human Evolution: Genes, Genealogies and Phylogenies” (2013: Cambridge University Press)