Science Literature

One of the lasting contributions of Professor Phillip Johnson has been his stress on clarifying the meaning of the word "evolution". He found a variety of definitions in common use, ranging from the "alteration in allele frequency" (which makes everyone an evolutionist), to the all-embracing concept of evolutionism (philosophical naturalism). Debates about the relevant science are muddied by people failing to use the word "evolution" in a consistent manner; for example, the industrial melanism of the peppered moth is often cited as proof of Darwin's theoretical model of evolution by natural selection. In his book, The Edge of Evolution, Professor Mike Behe put great stress on understanding Darwinian mechanisms at a molecular level. It is not good enough to talk about adaptation at a phenotypic level because the mechanisms relate to molecular changes at the genotypic level. When the evidence is examined from that perspective, it becomes clear that Darwinian mechanisms cannot build complexity. In a detailed review paper, Behe makes this point again and proposes the "First Rule of Adaptive Evolution" to summarise the findings of experimental evolution.

Phenotypic change does not necessarily map onto genotypic change (source here)

To qualify for Behe's review, experimental studies of evolution must have involved adaptation and must have included an analysis of genomic changes at the molecular level. He has set out to classify the mutations associated with adaptive change. Significant data matching these criteria relate to bacteria and viruses.

"Since species can evolve to gain, lose, or modify functional features, it is of basic interest to determine whether any of these tends to dominate adaptations whose underlying molecular bases are ascertainable. Here, I survey the results of evolutionary laboratory experiments on microbes that have been conducted over the past four decades. Such experiments exercise the greatest control over environmental variables, and they yield our most extensively characterized results at the molecular level."

The details of the review are of a technical nature and are best read in the paper. There is originality in the perspective Behe brings, because many of the researchers responsible for the experimental work have not discussed whether the mutations lead to a gain, a loss, or a modification of functional features. At this point it is worth referring to FCTs, which is the adopted acronym for Functional Coded elemenTs. Behe's analysis of both individual and aggregated findings represents a significant contribution to the literature.

"As seen in Tables 2 through 4, the large majority of experimental adaptive mutations are loss-of-FCT or modification-of-function mutations. In fact, leaving out those experiments with viruses in which specific genetic elements were intentionally deleted and then restored by subsequent evolution, only two gain-of-FCT events have been reported: the development of the ability of a fucose regulatory protein to respond to d-arabinose, and the antibiotic gene capture by f1."

This is a striking finding and it deserves to be formally labelled. Behe has obliged us by suggesting "the First Rule of Adaptive Evolution". This is a descriptive heuristic (rather than a prescriptive law). Adaptive evolution has the effect of breaking or blunting any FCTs whose loss would yield a net fitness gain.

"It is called the "first" rule because the rate of mutations that diminish the function of a feature is expected to be much higher than the rate of appearance of a new feature, so adaptive loss-of-FCT or modification-of-function mutations that decrease activity are expected to appear first, by far, in a population under selective pressure."

The key point to note here is that this Rule is driven by empirical data rather than by theory. The Rule expresses the findings of intensive research and it informs us about what actually happens. It is not a prediction deduced from theory.

"Except in cases where specific genetic features were first removed, as well as in the case of antibiotic gene capture by f1, all adaptive mutations in laboratory evolution experiments with viruses seem to be loss-of-FCT or modification-of-function mutations. Thus, in general laboratory evolutionary situations (that is, where a microorganism was under a general selective pressure rather than a specific one), adaptive loss-of-FCT or modification-of-function mutations were always available. This cannot be said for gain-of-FCT mutations."

For those familiar with The Edge of Evolution, this puts the spotlight again on the challenge of building complexity. These empirical results show that the great majority of cases of adaptive evolution involve either loss of functionality or a modification of an existing function. Adaptive evolution pre-supposes complexity. There is little evidence to support a model of the origin of species using the mechanisms of random mutation and selection (whether artificial or natural).

"Leaving aside gain-of-FCT for the moment, the work reviewed here shows that organisms do indeed adapt quickly in the laboratory - by loss-of-FCT and modification-of-function mutations. If such adaptive mutations also arrive first in the wild, as they of course would be expected to, then those will also be the kinds of mutations that are first available to selection in nature. This is a significant addition to our understanding of adaptation."

As this paper has been subjected to much critical scrutiny, it is appropriate to add some pointers to help general readers with their own appraisal of its significance. First, some complimentary comments from critics about the way the review has been conducted:

"My overall conclusion: Behe has provided a useful survey of mutations that cause adaptation in short-term lab experiments on microbes." (Professor Gerry Coyne, Department of Ecology and Evolution at the University of Chicago, source here).
"I read the paper in draft form some months ago and have not re-read it, but even then it exhibited an impressive command of the experimental evolution literature, at least the literature on adaptation of whole genomes of bacteria and phages (as opposed to the 'directed' evolution of genes on plasmids and of naked nucleic acids). I consider MB's characterization of most molecular evolution in these experiments as point mutations and/or deletions to be accurate. [. . .] My own view of the MB paper is that it has done a service to the study of evolution by pointing out where the next generation of experiments should focus." (Professor Jim Bull, Section of Integrative Biology, University of Texas at Austin, source here).

Numerous objections have been raised to Behe's analysis. It is claimed that the experimental evolution in laboratories does not represent the real world because there has not been enough time. It is claimed that studies of bacteria and viruses do not properly represent the incidence of 'gain-of-FCT mutations' in eukaryotes. It is claimed that mutations involving horizontal genetic transfer and gene duplication need to be considered to do justice to contemporary evolutionary theory. These objections are addressed here, here and here by Behe.

This blog started by pointing out the strong empirical emphasis which Behe brings to the field of evolutionary biology. There is typically a reluctance of researchers to get to the falsification stage of scientific enquiry. Often, theory is elevated above experiment, because the theory 'must be true'. What we now need are a set of review papers showing how theoretical ideas such as horizontal genetic transfer and gene duplication fare when they are analysed experimentally. Scientists should welcome this public scrutiny of favoured ideas - because this is the only way we can escape from 'normal science' in the Kuhnian sense. But for the present, we should digest the findings of Behe's review - here is his summary of the take-home message:

"The gist of the paper is that so far the overwhelming number of adaptive (that is, helpful) mutations seen in laboratory evolution experiments are either loss or modification of function. [. . .] Of course we had already known that the great majority of mutations that have a visible effect on an organism are deleterious. Now, surprisingly, it seems that even the great majority of helpful mutations degrade the genome to a greater or lesser extent."

Experimental Evolution, Loss-of-Function Mutations, and "The First Rule of Adaptive Evolution"
Michael J. Behe
The Quarterly Review of Biology, December 2010, 85(4), 419-445.

Abstract: Adaptive evolution can cause a species to gain, lose, or modify a function; therefore, it is of basic interest to determine whether any of these modes dominates the evolutionary process under particular circumstances. Because mutation occurs at the molecular level, it is necessary to examine the molecular changes produced by the underlying mutation in order to assess whether a given adaptation is best considered as a gain, loss, or modification of function. Although that was once impossible, the advance of molecular biology in the past half century has made it feasible. In this paper, I review molecular changes underlying some adaptations, with a particular emphasis on evolutionary experiments with microbes conducted over the past four decades. I show that by far the most common adaptive changes seen in those examples are due to the loss or modification of a pre existing molecular function, and I discuss the possible reasons for the prominence of such mutations.