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Science with a Sneer: A New Model for Scientific Papers?

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A recent paper published in PLOS ONE purports to have established Darwinian evolution and common ancestry beyond all questioning. Indeed, it says so right in the title: "Beyond Reasonable Doubt: Evolution from DNA Sequences." The researchers, W. Timothy J. White, Bojian Zhong and David Penny, have not so much provided a new model for explaining evolutionary theory as they have, perhaps, provided a new model for reporting research findings in peer-reviewed journals.

Both the tone and language of this paper convey sneering disrespect for anyone who would dare question the absolute truth of evolution. Such talk is expected in the blogosphere, but not in the body of what is supposed to be a sober scientific research paper.

The authors let loose their barbs from the very beginning in the abstract. After outlining their purpose and summarizing their findings, they observe: "It is time that researchers insisted that doubters put up testable alternatives to evolution." That's far from the normal voice of a scientific research paper. It gets worse. In the introduction they begin:

There are some areas of science where there is still strong resistance to basic scientific conclusions: anthropogenic climate change..., the reality of long term evolution..., the origin of life, and the safety and efficacy of vaccination programs are well-known examples. Thus we still require strong quantitative tests of our main scientific hypotheses, even if the conclusions appear obvious to most researchers.

The meaning can't be missed: anyone who doubts Darwinian evolution is simply in denial of the obvious. One can almost hear White, Zhong and Penny saying, "Can't believe we have to do this! It's such a waste of time, all this being so obvious, but we'll take one for the team and run these numbers one more time for the doubters still out there!" Not content with just that for an opening, they conclude the introduction with "This [their study and methodology] clearly does not 'prove' that yet unknown models are impossible, but the theory of evolution leads to extremely strong predictions, and so the onus is now on others to propose testable alternatives." Translation: "Case closed!"

They then get into their materials and methodology. The study is basically a phylogenetic analysis of similarities in protein sequences as markers of common ancestry (CA). The study assumes that such similarities are there due to CA because a design model would require too many decision points in the history of life for that to be a parsimonious explanation, if it's an explanation at all. It's not my purpose here to critique the study itself. I will leave that to others. Suffice to say that there seems to be little or nothing new in their approach.

What is new is how they report on their findings. Not content with laying out what they consider a strong case for evolutionary theory, they cannot resist direct jabs at critics and doubters. In the discussion they write:

So our conclusions are perhaps three-fold. Firstly we have provided a strong quantitative test rejecting a non-evolutionary model that amino acid sequences do not become more similar as we go back in time. Secondly, we have raised the problems of the number of parameters required of some alternatives, and finally we shift the requirement onto doubters to provide testable alternatives. On this third aspect, there does appear to also be a similar reaction from climate change advocates on placing responsibilities onto doubters. Other aspects of evolution have been tested and further aspects of evolution could be tested, perhaps especially the 'random' nature of mutations that occur without regard for any 'need' of the organism, but this is outside the scope of the present work. Indeed, there has always been excellent support for evolution from fossils and comparative morphology, and molecular data enables this to be quantitative. We can say that, as yet, no features of genomes have yet been found that are not understandable by 'causes now in operation'.

From the scientific point of view, there is no doubt that evolution has occurred, and there really were a continuous set of intermediates connecting individuals, populations, varieties, species, genera, families, etc. Nevertheless, as scientists we need to ensure that we have good quantitative tests available of all our favoured models. Given our results, we suggest that researchers need to be more assertive that evolution has both occurred, and continues to occur. It is essential that any person who does not accept the continuity of evolution puts forward alternative testable models. As we tell our first year undergraduates, 'belief is the curse of the thinking class'.

That last sentence is very telling. They are insinuating that anyone who doubts the Darwinian account of evolution could not possibly do so on scientific grounds and must therefore be under the influence of some personal belief, a "curse," so they say, to those that actually think. Even the term "thinking class" betrays a remarkable level of hubris on the part of the authors. It makes one wonder what the rules of entry to this "thinking class" might be. Obviously, not questioning Darwinian dogma would be one.

I also found it interesting that they use the phrase from Charles Lyell, "causes now in operation," that Stephen Meyer refers to significantly in his book Darwin's Doubt: The Explosive Origin of Animal Life and the Case for Intelligent Design, in his discussion of intelligent causation. It does appear that one of their purposes in this paper is to try to preemptively discredit Meyer -- the title ("Beyond Reasonable Doubt") suggests as much -- though they don't name him.

Additionally, I wouldn't expect to see a reference such as this in a scientific research paper: "Penny D (2011) Darwin's theory of descent with modification, versus the biblical Tree of Life. PLoS Biol 9: e1001096. doi: 10.1371/journal.pbio.1001096." Penny is one of the co-authors of this paper, so he is citing his own work. Apparently, contrary to the popular notion that ID or even "creationism" is un-scientific because it is untestable, the citation of this work in a peer-reviewed scientific research paper, and indeed the paper itself, are, in fact, testing a design/creation model...or at least the authors' notion of such a model. In their methodology they state:

Thus our non-evolutionary null model predicts that the similarity between the ancestral sequences is equal to the similarity between the extant sequences (that was calculated above in Step 7). When evolution from a common ancestor has occurred, the ancestral sequences will be significantly more similar than that predicted by the null model, and the null model will be rejected.

Later they challenge anyone who questions the evolutionary model to put up a testable model of his own, implying that there isn't one, even though they created their Null (that is non-evolutionary) model and rejected it, thus showing such a model is testable. So which is it? They write:

Our test is based on the expectation that, under evolution, the ancestral sequence of one natural group of taxa will be more similar to the ancestral sequence of a second natural group of taxa, than any sequence from the first group will be to any sequence from the second. In contrast, a variety of proposed non-evolutionary models either do not make this prediction, or require so many parameters that they cannot be said to make any testable predictions at all.

In reading the conclusion, you get the impression that the evolutionary model is the only model that makes testable predictions. But in their own description of the Null hypothesis it both makes a prediction and is tested and then rejected. Clearly, something here is amiss.

In any event, what is quite clear from this paper, particularly the abstract, introduction and discussion, is that the authors have no respect for anyone who would question or doubt evolution. "Contempt" might be the right word to describe what they actually communicate. In the standards that guide how scientific research reports are written, at least in the area of evolutionary biology, the language and tone they employ sets a new low.

Image credit: Jack Zalium/Flickr.