Let’s take a look at Mike Behe’s first rule of adaptive evolution, which states that most examples of adaptation in evolutionary experiments involve a loss of function, or a modification of an existing function. Not new functionality.

The paper was published in the Quarterly Review of Biology. I found it on PubMed.

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.

By far the most common adaptive changes in the examples we have are due to loss of function or modification of pre-existing function?

Evolution News has a post up about the paper.

Excerpt:

After reviewing the effects of mutations upon Functional Coding ElemenTs (FCTs), Michael Behe’s recent review article in Quarterly Review of Biology, “Experimental Evolution, Loss-of-Function Mutations and ‘The First Rule of Adaptive Evolution’,” offers some conclusions. In particular, as the title suggests, Behe introduces a rule of thumb he calls the “The First Rule of Adaptive Evolution”: “Break or blunt any functional coded element whose loss would yield a net fitness gain.” In essence, what Behe means is that mutations that cause loss-of-FCT are going to be far more likely and thus far more common than those which gain a functional coding element. In fact, he writes: “the rate of appearance of an adaptive mutation that would arise from the diminishment or elimination of the activity of a protein is expected to be 100-1000 times the rate of appearance of an adaptive mutation that requires specific changes to a gene.” Since organisms will tend to evolve along the most likely pathway, they will tend to break or lose an FCT before gaining a new one. He explains:

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.(Michael J. Behe, “Experimental Evolution, Loss-of-Function Mutations and ‘The First Rule of Adaptive Evolution’,” Quarterly Review of Biology, Vol. 85(4) (December, 2010).)

Behe argues that this point is empirically supported by the research reviews in the paper. He writes:

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

After asking “Why is this the case?” Behe states, “One important factor is undoubtedly that the rate of appearance of loss-of-FCT mutations is much greater than the rate of construction of new functional coded elements.” He draws sound and defensible conclusions from the observed data:

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. … In general, if a sequence of genomic DNA is initially only one nucleotide removed from coding for an adaptive functional element, then a single simple point mutation could yield a gain-of-FCT. As seen in Table 5, several laboratory studies have achieved thousand to million-fold saturations of their test organisms with point mutations, and most of the studies reviewed here have at least single-fold saturation. Thus, one would expect to have observed simple gain-of-FCT adaptive mutations that had sufficient selective value to outcompete more numerous loss-of- FCT or modification-of-function mutations in most experimental evolutionary studies, if they had indeed been available.

But this stark lack of examples of gain-of-functional coding elements can have important implications:

A tentative conclusion suggested by these results is that the complex genetic systems that are cells will often be able to adapt to selective pressure by effectively removing or diminishing one or more of their many functional coded elements.

Behe doesn’t claim that gain-of-function mutations will never occur, but the clear implication is that neo-Darwinists cannot forever rely on examples of loss or modification-of-FCT mutations to explain molecular evolution. At some point, there must be gain of function.

Now, there was a response to this paper from Jerry Coyne on his blog, and then a rebuttal from Mike Behe in a separate article on Evolution News.