Monday, 26 August 2013

Scientific errors in Christadelphian attacks on evolution: The Testimony magazine - 4

The cover story "Uprooting Darwin's Tree" for the 24th January 2009 edition of New Scientist, "Uprooting Darwin's Tree" looked at the phenomenon of horizontal gene transfer, which means that at the microbial level the 'tree of life' is not an accurate description of the phylogenetic relationship between organism. The provocative cover for the issue which boldly proclaimed "Darwin was Wrong" was widely criticised by mainstream scientists for its potential to mislead, a point recognised by the magazine in its editorial which warned its readers to "expect to find excerpts ripped out of context and presented as evidence that biologists are deserting the theory of evolution en masse. They are not."

Regrettably David Burges, science editor of The Testimony in a  March 2009 article <1> likewise seized on this New Scientist cover story in an attempt to criticise evolutionary biology. Either he completely misunderstood the article on horizontal gene transfer, or he failed to read past the provocative cover. Either way, it yet again reflects poorly on the credibility of The Testimony.

Burges completely misunderstood the article, as his article indicates:
“DARWIN WAS WRONG”. No, not the words of this writer but a recent New Scientist cover headline relating to a feature article on the so-called ‘tree of life’. Remarkably, in this year of Darwin anniversaries, it reports that the consensus among biologists is moving away from one of Darwin’s key concepts. His tree of life, an imaginary branching structure mapping the evolution of one species into many, is being abandoned in favour of something far more complex, more like a web of life. In contrast, the Creator’s tree of life, representing the gift of eternal life in Jesus Christ, remains a foundation of the true gospel hope.
One of Darwin's 'key concepts' was the idea of descent with modification. That is not under dispute. Neither is the fact that when we look at the evolutionary relationship between multicellular organisms, a tree-like structure correctly models the evolutionary relationship between therm. Only at the level of single-celled organisms do we see a more complicated relationship, based on the concept of horizontal gene transfer. Burges completely missed the point, in his haste to misuse the New Scientist article to bolster his special creationism.

The New Scientist article, written by Graham Lawton, is a popular-level overview of horizontal gene transfer, and the implications it has for modern evolutionary biology. In short, horizontal gene transfer is the exchange of genetic material between species, sometimes between those that are only distantly related. While it is largely a feature of two of the three domains of life (Bacteria and Archaea), there is evidence that it takes place in multicellular life. While it shows that evolution is far more complicated than we had initially thought, horizontal gene transfer however does not mean that common descent has been invalidated. While the tree of life is better modelled as a net at its roots, at the eukaryotic level, the tree model is very much alive:

Source: New Scientist
Horizontal gene transfer and common descent are not mutually exclusive. In fact, horizontal gene transfer requires all life to have essentially the same genetic code, otherwise genetic material from one species would not be able to be transferred to another, and incorporated into its genome. To press a linguistic analogy, the presence of loan words from Hebrew and Arabic in English does not invalidate the fact that English, German and Dutch share a common ancestral language. 

One problem with bro. Burges' article is its implication that Darwin is the touchstone of modern evolutionary biology, when in reality, evolution has moved considerably over the last 150 years. Darwin was wrong about many things - his proposed mechanism of inheritance was utterly wrong - but his main thesis, that all life is interrelated and has emerged by the process of descent with modification remains robust. It is helpful to see what modern evolutionary biologists and life scientists are saying about horizontal gene transfer and its implications for evolution:
As Jan and I discussed, for the last three billion years of evolution the tree of life is a very good metaphor for evolution. Darwin was mostly right about that. On the other hand, the New Scientist article discusses some problems with the tree of life that extend beyond the early history. It makes several valid points that should make everyone skeptical of claims about evolution that are too simple. The tree isn't perfect. 
The bottom line is that it's unfair to say that Darwin was wrong. It's as unfair as saying the Newton was wrong because of Einstein. We need to recognize that modern evolutionary biology is an improvement over the view of the Victorian founder of the field, but a cover saying that Darwin was wrong conveys the wrong message. It suggests that up until recently scientists believed that Darwin was right about everything. 
A better headline might be: "More evidence that Charles Darwin didn't know everything there is to be known about evolution when he published his book in 1859."<2>
One of the fundamental problems with Burges' article is that is fails to recognise out that difficulties (real or imagined) with the modern synthetic theory do not invalidate the overwhelming evidence that evolution has occurred. None of the biologists who are working in the area of horizontal gene transfer believe evolution never occurred, and for bro. Burges' article to ignore this fact destroys its credibility. Lawton pointed out:
Nobody is arguing – yet – that the tree concept has outlived its usefulness in animals and plants. While vertical descent is no longer the only game in town, it is still the best way of explaining how multicellular organisms are related to one another – a tree of 51 per cent, maybe. In that respect, Darwin's vision has triumphed: he knew nothing of micro-organisms and built his theory on the plants and animals he could see around him. 
Even so, it is clear that the Darwinian tree is no longer an adequate description of how evolution in general works. “If you don't have a tree of life, what does it mean for evolutionary biology?” asks Bapteste. “At first it's very scary… but in the past couple of years people have begun to free their minds.” Both he and Doolittle are at pains to stress that downgrading the tree of life doesn't mean that the theory of evolution is wrong – just that evolution is not as tidy as we would like to believe. Some evolutionary relationships are tree-like; many others are not. “We should relax a bit on this,” says Doolittle. “We understand evolution pretty well – it's just that it is more complex than Darwin imagined. The tree isn't the only pattern.” <3>
Citing this article in order to buttress the allegation that "evolution is in crisis" is appalling scholarship. It is evidence that modern evolutionary biology is a live scientific discipline. It is not evidence that evolution never occurred, any more than the fact the currently accepted theory of gravitation - general relativity - does not explain quantum-level gravitation means objects don't fall to the ground or planets do not orbit stars. Difficulties in a theory do not mean the phenomena they attempt to explain do not exist. 

I mentioned earlier the controversial nature of the New Scientist article, which stemmed from the sensationalist cover which shouted "Darwin was Wrong." Unfortunately, many laypeople will (1) assume New Scientist is a scientific journal of authority on a par with Nature or Science and (2) simply read the cover and assume that evolution was wrong, without even looking at the article. The editorial for this edition made this very point:
Biology has been here before. Although Darwin himself, with the help of Alfred Russel Wallace, triggered a revolution in the mid-1800s, there was a second revolution in the 1930s and 1940s when Ronald Fisher, J. B. S. Haldane, Sewall Wright and others incorporated Mendelian genetics and placed evolution on a firm mathematical foundation. 
As we celebrate the 200th anniversary of Darwin's birth, we await a third revolution that will see biology changed and strengthened. None of this should give succour to creationists, whose blinkered universe is doubtless already buzzing with the news that "New Scientist has announced Darwin was wrong". Expect to find excerpts ripped out of context and presented as evidence that biologists are deserting the theory of evolution en masse. They are not.
Nor will the new work do anything to diminish the standing of Darwin himself. When it came to gravitation and the laws of motion, Isaac Newton didn't see the whole picture either, but he remains one of science's giants. In the same way, Darwin's ideas will prove influential for decades to come. 
So here's to the impending revolution in biology. Come Darwin's 300th anniversary there will be even more to celebrate. <4>
It is disappointing to see bro. Burges cite an article from a popular science magazine - an article that has been fiercely criticised by working biologists for its misleading nature - as proof that evolution is incorrect. He acknowledges that working scientists are not abandoning evolution, and refers to the editorial which warned creationists not to abuse the article for their own sectarian ends:
It must be stressed that biologists are in no way abandoning evolution, but have been forced to admit that one of the main planks of the theory has been found wanting. In the words of the New Scientist article: “The tree of life, one of the iconic concepts of evolution, has turned out to be a figment of our imagination”. That scientists are very sensitive about this conclusion is demonstrated by the editorial in the same issue, which solemnly warns, “None of this should give succour to creationists, whose blinkered universe is doubtless already buzzing with the news that ‘New Scientist has announced Darwin was wrong’”. <5>
One wonders why bro Burges did not take the advice of the editorial, or consider that if biologists are not abandoning evolution, then the theory is hardly one in crisis. The fact is that common descent - the theory that all life is interrelated via descent with modification - has not been seriously challenged for over 100 years. The genomist and evolutionary biologist TR Gregory points out that:
In The Origin of Species, published in 1859, Darwin cited independent lines of evidence such as the biogeographical distribution of species, homology of structure, the occurrence of vestigial organs and atavisms, and the already well established process of extinction as all pointing to a conclusion that species have changed over time and are connected by descent from common ancestors. Through the force of Darwin’s argument and the mass of supporting data he presented, it was not long before the contemporary scientific community came to acknowledge the historical reality of evolutionary descent. As A.W. Bennett summarized the situation in 1870,
The fascinating hypothesis of [descent with modification] has, within the last few years, so completely taken hold of the scientific mind, both in [Great Britain] and in Germany, that almost the whole of our rising men of science may be classed as belonging to this school of thought. Probably since the time of Newton no man has had so great an influence over the development of scientific thought as Mr. Darwin..
Over the past 150 years, this initial list 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 (1998) 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>
For those who are quite familiar with the evidence that evolution has occurred, as demonstrated from fields as disparate as embryology, palaeontology and molecular genetics, bro. Burges' assertion that the theoretical basis for evolution is under assault comes across as naive and uninformed. One would expect to see solid evidence from bro Burges that common descent is wrong. A superficial and biased reading of a popular science magazine does not constitute such evidence. 

Horizontal gene transfer does not invalidate common descent, but as mentioned before implies it, as horizontal gene transfer would not work without a common genetic code, which is one of the predictions of common descent. Of note is a recent paper <7> by Douglas Theobald, which places the theory of common descent under formal mathematical analysis.

Theobald notes <8> that the common ancestry of the higher taxa:
" now supported by a wealth of evidence from many independent sources, including: (1) the agreement between phylogeny and biogeography; (2) the correspondence between phylogeny and the palaeontological record; (3) the existence of numerous predicted transitional fossils; (4) the hierarchical classification of morphological characteristics; (5) the marked similarities of biological structures with different functions (that is, homologies); and (6) the congruence of morphological and molecular phylogenies."
Theobald acknowledges that this evidence does not address the question of whether all life, not merely the metazoa, are related:
However, the ‘universal’ in universal common ancestry is primarily supported by two further lines of evidence: various key commonalities at the molecular level (including fundamental biological polymers, nucleic acid genetic material, L-amino acids, and core metabolism) and the near universality of the genetic code. Notably, these two traditional arguments for UCA are largely qualitative, and typical presentations of the evidence do not assess quantitative measures of support for competing hypotheses, such as the probability of evolution from multiple, independent ancestors. <9>
Therefore, Theobald set himself the task of placing the theory of common descent under quantitative evaluation. His question was whether the three domains of life (Eukaryotes, Archaea and Bacteria) were unified by a common genetic relationship, or were three separate groups that arose in parallel and separately. (Note that the question of whether the Eukaryotes have common ancestry is a separate question, one which has long been answered in the affirmative, as Theobald reminded us earlier.)

Theobald approached this question in two ways, one which ignored the contribution of horizontal gene transfer, one which factored it in. When he examined the competing models (common descent versus parallel independent creation), common descent was overwhelmingly  favoured:
Among the class I models, all criteria select the UCA tree by an extremely large margin (score differences ranging from 6,569 to 14,057), even though nearly half of the proteins in the analysis probably have evolutionary histories complicated by HGT. For all model selection criteria, by statistical convention a score difference of 5 or greater is viewed as very strong empirical evidence for the hypothesis with the better score (in this work higher scores are better). All scores shown are also highly statistically significant (the estimated variance for each score is approximately 2–3). According to a standard objective Bayesian interpretation of the model selection criteria, the scores are the log odds of the hypotheses. Therefore, UCA is at least 102,860 times more probable than the closest competing hypothesis. Notably, UCA is the most accurate and the most parsimonious hypothesis. Compared to the multiple-ancestry hpotheses, UCA provides a much better fit to the data (as seen from its higher likelihood), and it is also the least complex (as judged by the number of parameters). (Emphasis mine) <10>
Even though in reality, there is a degree of horizontal gene transfer in all three domains, the sheer force of the support for common descent from the class I model is enough to show that this hypothesis is quite likely to be correct. Therefore, Theobald set out to factor in horizontal gene transfer and test the hypothesis of universal common descent. Again, common descent was overwhelmingly favoured over the alternatives:
The extraordinary strength of these results in the face of suspected HGT events suggests that the preference for the UCA model is robust to the extent of HGT. To test this possibility, the analysis was expanded to include models that allow each protein to have a distinct, independent evolutionary history. I refer to this set of models, which rejects a single tree metaphor for genealogically related taxa, as ‘class II’. Representative class II models are shown in Fig. 2. Within each set of genealogically related taxa, each of the 23 universally conserved proteins is allowed to evolve on its own separate phylogeny, in which both branch lengths and tree topology are free parameters... 
Nonetheless, as with the class I non-HGT hypotheses, all model selection criteria unequivocally support a single common genetic ancestry for all taxa. Also similar to the class I models, the class II UCA model has the greatest explanatory power and is the most parsimonious. (Emphasis mine) <11>
As Theobald shows, even when one factors in horizontal gene transmission, the common ancestry of all three domains of life is overwhelmingly favoured over alternative separate creation models. 


Horizontal gene transmission is a fascinating phenomenon, and promises to enrich out understanding of biology. However, it does not mean common descent is wrong. Far from it. David Burges' misleading and poorly researched article serves only to demonstrate the paucity of research invested in the story and the superficial nature of his understanding of the subject he deems himself qualified to dismiss. One would appreciate a correction in the Testimony to bro. Burges' article, given that it is freely available online, and remains on record as a sad reminder that in our community, ideology too often trumps evidence.


1. Burges D "Cutting down the 'tree of life'" The Testimony, March 2009 p 16-18
2. Moran L "Darwin was Wrong?" Sandwalk Thursday, January 22, 2009 
3. Lawton, ibid. p 39
4. Editorial: Uprooting Darwin's tree New Scientist 21st January 2009
5. Burges, ibid. p 16
6. Gregory TR "Evolution as Fact, Theory and Path" Evo Edu Outreach (2008) 1:46–52
7. Theobald D "A formal test of the theory of universal common ancestry" Nature (2010) 465:219-222
8. ibid, p 219
9. loc cit
10. Theobald, ibid. p 220
11. loc cit