Literature

Paper from the colloquium: In the light of Evolution

John Gerhart and Marc Kirschner offer a radical theory of variation: one that majors on the regulatory elements rather than on the genes themselves. Coming from the Evo-Devo school, this theory offers numerous novel avenues of thought.
First, there are real problems with many traditional models of phenotypic variation. The models work in a limited way with single traits, but they do not handle complex variations at all well. In such cases, selection has to act on several traits concurrently and mutations (the source of variation) just may not be forthcoming. Consequently, "evolution may be impeded".
Second, it is not widely realised that there is a remarkable "metazoan toolkit of conserved functional components and processes". These were all in place by the end of the Precambrian. These are referred to as "conserved core processes". "They comprise an enormous toolkit, and the genes encoding them comprise the majority of the genetic repertoire of the animal. They have changed very little in the course of animal evolution since the Cambrian, even though animal anatomy and physiology have changed."
Third, if the toolkit and the genes encoding them have not changed since the Precambrian, what has? The answer offered is the regulatory system. The metazoan toolkit was so powerful and versatile "that post-Cambrian animals could largely omit further functional innovation at the gene product level (protein and functional RNA evolution) and instead exploit regulatory innovation to diversify anatomy, physiology, and development." As an example, the authors point out (from genome analysis) that 79% of mouse genes retain Precambrian sequences.
Whilst the authors go on to discuss many aspects of this theory and point out some empirical data that appears to provide validation (but see comments from Wells on this), it is pointed out here (and by Wells) that this theory does not address the origin of complex specified information. All the essential genetic information existed in the Precambrian and is accepted by the authors almost as a gift bequeathed to Phanerozoic animals and plants. The Cambrian organisms possessed the innate capacity to vary. "If the capacity to develop large phenotypic differences already exists in the organism as self-inhibited alternate states, and these can be elicited by simple signals (weak linkage), then large evolutionary steps can be made with a modicum of genetic change. In such cases, the distinction blurs between evolutionary gradualism and saltation (the generation of significant traits by single mutations)."
Curiously, this paper can be read as a vindication of concepts developed by ID scholars: if you want to develop models of variation involving complex specified information, you must start out with complex specified information. For more on this, go here and here.

The theory of facilitated variation
John Gerhart and Marc Kirschner
Proceedings of the National Academy of Sciences USA, published May 9, 2007, 10.1073/pnas.0701035104

This theory concerns the means by which animals generate phenotypic variation from genetic change. Most anatomical and physiological traits that have evolved since the Cambrian are, we propose, the result of regulatory changes in the usage of various members of a large set of conserved core components that function in development and physiology. Genetic change of the DNA sequences for regulatory elements of DNA, RNAs, and proteins leads to heritable regulatory change, which specifies new combinations of core components, operating in new amounts and states at new times and places in the animal. These new configurations of components comprise new traits. The number and kinds of regulatory changes needed for viable phenotypic variation are determined by the properties of the developmental and physiological processes in which core components serve, in particular by the processes' modularity, robustness, adaptability, capacity to engage in weak regulatory linkage, and exploratory behavior. These properties reduce the number of regulatory changes needed to generate viable selectable phenotypic variation, increase the variety of regulatory targets, reduce the lethality of genetic change, and increase the amount of genetic variation retained by a population. By such reductions and increases, the conserved core processes facilitate the generation of phenotypic variation, which selection thereafter converts to evolutionary and genetic change in the population. Thus, we call it a theory of facilitated phenotypic variation.

See also:

Wells, J. What's New? Books & Culture, September/October 2006, Vol. 12, No. 5, Page 45