The world’s foremost atheist (not much of an accomplishment) and most famous writer on evolution is Richard Dawkins. In a recent interview, he was asked,
Out of all the evidence used to support the theory of evolution, what would you say is the strongest, most irrefutable single piece of evidence in support of the theory?
Dawkins replied that it is difficult to pick out the best evidence, since there is so much of it, but he eventually settled on genetic evidence, the sort that we examined in part 1 of this post, in which proteins or genes of different organisms are compared:
There’s an enormous amount of evidence, from all sorts of places, and it’s hard to pick one strand which is more important than any other… I think to me perhaps the most compelling evidence is comparative evidence, from modern animals – particularly biochemical comparative evidence, genetic, molecular evidence.
After briefly explaining the methodology, Dawkins presents his conclusion:
So, you can take any pair of animals you like – kangaroo and lion, horse and cat, human and rat – any pair of animals you like, and count the number of differences in the letters of a particular gene, and you plot it out, and you find that it forms a perfect branching hierarchy. It’s a tree, and what else could that tree be, but a family tree.
Well… baloney. As we’ve seen, evolutionary trees constructed on the basis of genes contradict each other all the time. So it’s time to let Dr. Jekyll speak again. Churakov et al., discussing precisely the example mentioned by Dawkins, found that five genes supported a pattern in which human and armadillo are most closely related; nine genes supported a contradictory history, where human and elephant are most closely related, and eight genes supported a third (hi)story, where elephant and armadillo were closest relatives. And writing in the journal Evolution and Development , researchers entitled their paper Conflicting phylogenetic signals at the base of the metazoan tree, and wrote in the summary that “… analyses of… sequences fail to resolve the relationships… We demonstrate that… conflicts in the phylogenetic signal contained in different amino acid sequences obscure the phylogenetic associations among the early branching Metazoa. These factors raise concerns about the ability to resolve the phylogenetic history of animals with molecular sequences.”
Genes vs. Bones
The journal Nature weighed in with a review article that spoke about evolution wars. This was not a reference to conflict between biologists and critics of evolution. It was a reference to wars within biology. One problem, as we have seen, is that there is a huge discrepancy between different trees-of-life, depending on which protein or gene you use. But there is also a divergence between tree-of-life models when you contrast those made from anatomical evidence and those made on the basis of genetic evidence. It’s as if you compare two computers. If you look at the hard-drive, the evidence indicates that one computer came from South Korea and the other from Taiwan. But if you look at the motherboard, you conclude that one computer came from Oshkosh and the other from Tierra del Fuego. The widespread disagreement between molecule-based evolutionary trees and anatomy-based evolutionary trees led the Nature writer to comment that “Evolutionary trees constructed by studying biological molecules often don’t resemble those drawn up from morphology [the study of the structure and anatomy of the organism].”
Despite these clear statements in the professional literature, evolutionary biologists persist in overselling their brand. Notwithstanding the research that contradicts their absolutist claims, they often insist, when writing for the broad public, that molecular studies confirm anatomical studies. For example, in his book Galileo’s Finger, Oxford University scientist Peter Atkins boldly states, “The effective prediction is that the details of molecular evolution must be consistent with those of macroscopic evolution.” He then adds, “That is found to be the case: there is not a single instance of the molecular traces of change being inconsistent with our observations of whole organisms.” Yet a variety of reports clearly recognize that these studies frequently conflict with one another. One authoritative review paper by Darwinian leaders in this field stated, “As morphologists with high hopes of molecular systematics, we end this survey with our hopes dampened. Congruence between molecular phylogenies is as elusive as it is in morphology and as it is between molecules and morphology.” Another set of pro-evolution experts wrote, “That molecular evidence typically squares with morphological patterns is a view held by many biologists, but interestingly, by relatively few systematists. Most of the latter know that the two lines of evidence may often be incongruent.” And despite consistent attempts by apologists to portray developments in this area of biology as something less than a crisis for evolutionary theory, the news is finally making its way into the popular press. In 2009, for example, The Telegraph reported that, “Charles Darwin’s tree of life is ‘wrong and misleading’”.
In July 2010, a Johannesburg educator contacted a distinguished American geneticist and posed a number of questions about evolution to him. The educator has no training in science and little knowledge of biological evolution. He was caught in the cross-fire of the controversy regarding the teaching of evolution in Torah schools and was seeking some enlightenment. In his response, the American biologist played the perfect Mr. Hyde:
There is overwhelming evidence for evolution. The more we learn and the more powerful our technologies become, the greater our insight is into the relationship of all living organisms, past and present.
This statement came with no qualification: nothing about contradictions, difficulties, wars, absurd classifications, incongruities, “burial” or “annihilation” of the tree of life. Just that we have overwhelming evidence for evolution on the basis of advanced research into relationships between organisms. To say that the professor was selling lokshen to the teacher is to insult pasta.
The typical reader, confronted with this material, might think that with so many setbacks, evolutionary biologists would at least countenance a different view of reality. The typical reader, alas, is not familiar with the mechanics of scientific paradigms. Thomas Kuhn was arguably the most influential philosopher of science in the twentieth century. In The Structure of Scientific Revolutions, first published a half-century ago, Kuhn did a marvellous job in describing how the most productive work done by the vast majority of scientists is in solving puzzles within the regnant ideology. Little attention is paid to all the loose ends – those parts of the paradigm which are not explained and, indeed, unexplainable. It is only when the difficulties accumulate to the point where the theoretical structure of the theory collapses that the bulk of the community of scientists acknowledges the problems.
In other words, paradigms are much like flypaper: once stuck, it’s hard to leave. The flood of counter-evidence has not caused biologists to desert the evolutionary paradigm en masse. The lingo changed – where before biologists spoke of the Tree of Life, they now often speak of the web of life or the bush of life  or the mosaic of life. Or rather, when they speak to each other they use the new terminology. In pronouncements to the public or in textbooks, it’s the same old story: the tree-of-life is this impossibly gorgeous, perfectly consistent research programme that confirms the Darwinian worldview without a wrinkle.
Paradigms often take at least a generation to overturn. In a trenchant insight into the workings of modern science, the great physicist Max Planck, the father of quantum mechanics, remarked:
A new scientific truth does not triumph by convincing its opponents and making them see the light, but rather because its opponents eventually die, and a new generation grows up that is familiar with it.
Still, there is hope. In the New Scientist article cited above, evolutionary biologist Eric Bapteste writes, “If you don’t have a tree of life, what does it mean for evolutionary biology? At first it’s very scary – but in the past couple of years people have begun to free their minds.” And philosopher of biology John Dupré adds that it is all “part of a revolutionary change in biology. Our standard model of evolution is under enormous pressure.” The belief that all species are related and evolved from common ancestors is sacrosanct among many biologists. No doubt, many will stick to the dogma like a tattoo to a biker. But the Tree of Life has fallen with such a thunderous thud that it is forcing some biologists to consider different possibilities. A paper published in August 2011 by four European evolutionary biologists argues that the Tree of Life is “becoming increasingly implausible.” Although the Tree of Life “has been stretched to fit the data” in various ways, “given our knowledge of the data, it seems that the elastic limit of the original hypothesis has been passed.” Some even go so far as to acknowledge that the whole field has made little progress in the past century: a review article in the journal BioEssays reported that despite a vast increase in the amount of data since Darwin’s time, “our ability to reconstruct accurately the tree of life may not have improved significantly over the last 100 years.”
It is quite entertaining to watch researchers swinging from tree to tree, first concluding that they have found The One True Tree, and then, after obtaining contrary results, ditching the first tree and replacing it with a quite different specimen. We could continue to discuss the crises befalling the Tree of Life paradigm, but perhaps it’s best to end by noting that in Stevenson’s novel, the affable Dr. Jekyll is the awful Mr. Hyde. He is so tormented by his inability to stop metamorphosing into his monstrous alter ego that, in desperation, he finally commits suicide.
Those who jump into the evolution debate often drown under the claim that there is overwhelming evidence for evolution. It is a claim that is meant to preclude any possibility of challenging the validity of evolutionary biology. Any instance of counter-evidence is brushed aside, often without careful consideration, because, “Hey, there is overwhelming evidence for evolution.”
My experience has been that those who claim that there is overwhelming evidence for evolution are like the schoolyard bully who always threatens to open up with a machine gun but, when push comes to shove, produces a pea-shooter. The invincible evidence for evolution – when actually chewed rather than swallowed – is far more vulnerable than is made out to be.
Richard Dawkins, widely considered the most influential spokesman for evolutionary biology, stated that genetic analysis constitutes the strongest, most irrefutable evidence for evolutionary biology. The expectation, going back several decades, was that common descent would be smoothly vindicated by genetic data. It would corroborate (or clarify, as the case may be) evidence from anatomy and palaeontology regarding the relationships between all organisms, and would once and for all convince everyone that we are all descendents of bacteria.
This expectation has turned out to be wrong. In a classic case of piling one epicycle atop another, researchers committed to the evolutionary paradigm twist themselves into loops trying to morph trees into bushes, and bushes into webs, and webs into mosaics or whatever the latest metaphor happens to be. The truth is that genetic analysis is a Rorschach test. Evolutionary biologists see relationships because they want to see relationships. The exercise starts within the Darwinian paradigm, and pre-supposes that all organisms are biologically related. But when you allow yourself to look past the evolutionary horizon, you see that the genetic data does not support a picture of common descent. Evolutionary biology is a sartorially-challenged emperor. It’s time to depose him.
Retrieved 13th February 2011.
 See http://www.evolutionnews.org/2011/02/for_darwin_day_false_facts_and043691.html.
Retrieved 12th February 2011.
 Mosaic retroposon insertion patterns in placental mammals, Gennady Churakov, Jan Ole Kriegs, Robert Baertsch, Anja Zemann, Jürgen Brosius, and Jürgen Schmitz. Genome Research, Cold Spring Harbor Laboratory Press, March 2009. The article can be viewed here: http://genome.cshlp.org/content/19/5/868.abstract.
Retrieved 13th February 2011.
 EVOLUTION & DEVELOPMENT 5:4, 346–359 (2003). See the article here: http://people.vanderbilt.edu/~antonis.rokas/pdfs/2003_Rokas_etal_Choanos_EvolDev.pdf.
Retrieved 13th February 2011.
 Trisha Gura, “Bones, Molecules or Both?,” Nature, Vol. 406:230-233 (July 20, 2000).
 Peter Atkins, Galileo’s Finger: The Ten Great Ideas of Science, page 16 (Oxford University Press, 2003).
 Patterson et al., “Congruence between Molecular and Morphological Phylogenies,” Annual Review of Ecology and Systematics, Vol 24, page 179 (1993).
 Masami Hasegawa, Jun Adachi, Michel C. Milinkovitch, “Novel Phylogeny of Whales Supported by Total Molecular Evidence,” Journal of Molecular Evolution, Vol. 44, pages S117-S120 (Supplement 1, 1997).
Retrieved 15th July 2012.
 See https://torahexplorer.com/2010/07/04/readers-feedback-professor-james-shapiro-rabbi-blue/.
Retrieved 6th August 2012.
 Thomas Kuhn, The Structure of Scientific Revolutions, third edition, The University of Chicago Press, 1996.
 Here is one example of the genre. An article in Trends in Ecology and Evolution concluded, “the wealth of competing morphological, as well as molecular proposals [of] the prevailing phylogenies of the mammalian orders would reduce [the mammalian tree] to an unresolved bush…” W. W. De Jong, “Molecules remodel the mammalian tree,” Trends in Ecology and Evolution, Vol 13(7), pages 270-274 (July 7, 1998).
 Planck (1949) Scientific Autobiography, pages 33-34.
 See http://www.biology-direct.com/content/6/1/41/abstract.
Retrieved 5th September 2011.
 Matthew A. Wills, “The tree of life and the rock of ages: are we getting better at estimating phylogeny,” BioEssays, Vol. 24: 203-207 (2002), reporting on the findings of Michael J. Benton, “Finding the tree of life: matching phylogenetic trees to the fossil record through the 20th century,” Proceedings of the Royal Society of London B, Vol. 268: 2123-2130 (2001).