Literature

Austin Hughes does not mince his words in describing a "major hindrance to progress" in understanding the evolutionary past. He claims that a major factor has been "confusion regarding the role of positive (Darwinian) selection". This addresses some fundamental issues in evolutionary biology because, for many, any evidence of adaptation is automatically interpreted as natural selection favouring adaptive mutations. But yes, just in case you think Hughes might qualify his charge elsewhere, read on and find that he makes it even more explicit!

"To biologists schooled in Neo-Darwinian thought processes, it is virtually axiomatic that any adaptive change must have been fixed as a result of natural selection. But it is important to remember that reality can be more complicated than simplistic textbook scenarios."

"If you have variation, differential reproduction, and heredity, you will have evolution by natural selection as an outcome. It is as simple as that." (Source here)

The problem is not one that can be easily corrected, because it is endemic. According to Hughes: "Thousands of papers are published every year claiming evidence of adaptive evolution on the basis of computational analyses alone, with no evidence whatsoever regarding the phenotypic effects of allegedly adaptive mutations." The researchers have adopted a mindset which blinds them to alternative approaches to handling the data. The problem relates to codon-based methods of testing for positive selection. We do not need here to go over the theory behind these methods, nor follow how Hughes arrives at the view that there has been an "unwarranted generalization" from one case to all cases. However, we can note this conclusion:

"Yet, despite their shaky foundations, numerous publications have used these methods as the basis for claims of positive selection at the molecular level."

The trigger for the alarm bells sounding is a paper by Yokoyama et al (blogged here). Hughes sees this paper as a model of its kind, establishing the genetic basis for variation and devising tests for positive selection which allow conventional thinking to be scrutinized.

"It is to be hoped that the work of Yokoyama et al. will help put an end to these distressing tendencies. By incorporating experimental evidence regarding the phenotypic effects of reconstructed evolutionary changes, this study sets a new standard for studies of adaptive evolution at the molecular level."

The take-home message is that (bad) theory has dominated empirical analysis for too long in evolutionary biology. It is time to put things in order. We need less reliance on the deductive framework provided by neo-Darwinism, and more attention to empiricism and induction. (For a previous blog related to this, go here). Hughes calls for a new standard in research:

"In recent years the literature of evolutionary biology has been glutted with extravagant claims of positive selection on the basis of computational analyses alone, including both codon-based methods and other questionable methods such as the McDonald-Kreitman test. This vast outpouring of pseudo-Darwinian hype has been genuinely harmful to the credibility of evolutionary biology as a science."

With these thoughts in mind, it may be worth revisiting topics (here, here and here) that have been discussed previously: drawing attention to the way theory dominates the interpretations placed on data, and how researchers are curiously blind to alternative approaches to handling the same data. This is Kuhnian "normal" science. It preserves the paradigm - but at what cost?

The origin of adaptive phenotypes
Hughes, Austin L.
Proceedings of the National Academy of Sciences, 105(36), 13193-13194, September 9, 2008 | doi: 10.1073/pnas.0807440105.

First Paragraph: Sequences of DNA provide documentary evidence of the evolutionary past undreamed of by pioneers such as Darwin and Wallace, but their potential as sources of evolutionary information is still far from being realized. A major hindrance to progress has been confusion regarding the role of positive (Darwinian) selection, i.e., natural selection favoring adaptive mutations. In particular, problems have arisen from the widespread use of certain poorly conceived statistical methods to test for positive selection. Thousands of papers are published every year claiming evidence of adaptive evolution on the basis of computational analyses alone, with no evidence whatsoever regarding the phenotypic effects of allegedly adaptive mutations. But it would be a mistake to dismiss Yokoyama et al.'s study, in this issue of PNAS, of the evolution of visual pigments in vertebrates as more of the same. For, unlike all too many recent papers in the field, this study is solidly grounded in biology.

See also:

Coppedge, D.F. How Not to Prove Positive Selection (Creation-Evolution Headlines, Sept 5, 2008).