Denyse O'Leary wasn't impressed [The Latest From Lenski’s Lab]. She doesn't know very much about science so she has to rely on the opinions of other IDiots. In this case, she relies on Ann Gauger who published a comment on the website of The Biologic Institute [Inovation or Rennovation].
EXPERIMENTAL EVOLUTION, LOSS-OF-FUNCTION MUTATIONS,Behe's point is the same one that we've been hearing for decades; namely, that evolution cannot create new information or new genes. He proposed a basic rule-of-thumb that he calls The First Rule of Adaptive Evolution.
AND “THE FIRST RULE OF ADAPTIVE EVOLUTION”
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.
Break or blunt any functional coded element whose loss would yield a net fitness gain.Behe "predicted" that Lenski's citrate-utilizing bacteria would simply have evolved a way of expressing the citrate transporter gene (citT). He imagined that this would be a loss-of-function mutation ...
If the phenotype of the Lenski Cit+ strain is caused by the loss of the activity of a normal genetic regulatory element, such as a repressor binding site or other FCT [functional coded elements], it will, of course, be a loss-of-FCT mutation, despite its highly adaptive effects in the presence of citrate. If the phenotype is due to one or more mutations that result in, for example, the addition of a novel genetic regulatory element, gene-duplication with sequence divergence, or the gain of a new binding site, then it will be a noteworthy gain-of-FCT mutation.Behe was correct when he predicted that the mutation would involve the citT gene but the actual mutation(s) turned out to be "a noteworthy gain-of-FCT mutation" that did not conform to The First Rule of Adaptive Evolution [Lenski's long-term evolution experiment: the evolution of bacteria that can use citrate as a carbon source].
The results of future work aside, so far, during the course of the longest, most open-ended, and most extensive laboratory investigation of bacterial evolution, a number of adaptive mutations have been identified that endow the bacterial strain with greater fitness compared to that of the ancestral strain in the particular growth medium. The goal of Lenski’s research was not to analyze adaptive mutations in terms of gain or loss of function, as is the focus here, but rather to address other longstanding evolutionary questions. Nonetheless, all of the mutations identified to date can readily be classified as either modification-of-function of loss-of-FCT.
A few years ago, though, they published a paper describing the evolution of a “new” function in E. coli: the ability to use citrate as a carbon source for growth. Citrate had always been present in their minimal medium, but it was inaccessible to E. coli under normal lab growth conditions. After about 30,000 generations, though, the bacteria evolved the ability to take up and use the abundant citrate in the medium, thus allowing them to grow and reproduce faster. This announcement was splashed across headlines as evidence for the power of evolution to produce new adaptive traits.It's important to recognize what the IDiots are conceding. They admit that Lenski's long term evolution experiment does lead to evolution of a new strain of cit+ E. coli. This is a gain-of-function phenotype no matter how you try to spin it differently. The new function is the result of an entirely new gene formed from the fusion of two genes, rnk and citG. This, in turn, creates a new operon where a second copy of the citrate transporter gene (citT) is under the control of a second copy of the rnk promoter.
But how significant was this innovation? In his paper in Quarterly Review of Biology, Dr. Michael Behe pointed out that E. coli was already capable of using citrate for anaerobic growth (when no oxygen was available). He postulated that a change in gene regulation could turn on citrate transport and permit growth on citrate under aerobic conditions.
After an enormous amount of work, having sequenced the genomes of many clones along the lineages that led to the ability to use citrate, as well as lineages that never did, and testing the phenotypes of identified mutations, Blount et al. have now reported that Behe was largely right. The key innovation was a shift in regulation of the citrate operon, caused by a rearrangement that brought it close to a new promoter.
New genes and new information have been added to the genome while all of the old genes are still present. It's true that the new genes and new information arose from pre-existing bits of DNA that were already in the genome but that seems to be quibbling. So rather than admit that these new genes are really new information they fall back on a modified claim. The IDiots say that this is not really a "genuine innovation" (i.e. no true Scotsman). Here's how Ann Gauger puts it ...
But does this adaptation constitute a genuine innovation? That depends on the definition of innovation you use. It certainly is an example of reusing existing information in a new context, thus producing a new niche for E coli in lab cultures. But if the definition of innovation is something genuinely new, such as a new transport molecule or a new enzyme, then no, this adaptation falls short as an innovation. And no one should be surprised.What she says is correct. Lenski's group did not witness an entirely new gene poof into existence from thin air. Nobody should be surprised at that because the gods are very clever—they would never let anyone catch them in the act. They take care to make it look like evolution is a very natural process.
Did Ann Gauger, Michael Behe, and Denyse O'Leary really think that Lenski and his colleagues would discover evidence of god(s)' handiwork?
Behe, M. (2010) Experimental evolution, loss-of-function mutations, and "the first rule of adaptive evolution." Quart. Rev. Biol. 85:419-445. [PDF]