Genome and evolvability (Introduction)

by David Turell , Friday, January 09, 2015, 20:18 (3394 days ago)

A review of Wagner's book, Arrival of the Fittest which explains Wagner's concepts, and foolishly tries to make evolution seem easy. There is no explanation for the start of life, but it does show pattern networking in the genome which can realistically make the whole process easier. The concluding paragraph raised the question of the information necessary, and no explanation of where the info came from.-"And gene circuits? Same story. Wagner has collaborated with physicist Olivier Martin to explore the space of hypothetical gene regulatory networks. They searched for different networks that, by mutually regulating the activity of the constituent genes, would produce the same overall patterns of gene expression— that is, the same phenotype.4 To take a trivial example, in a network of three genes A, B, and C, the same result of switching off expression of gene B could be achieved by either A or C inhibiting B. Even for just a dozen or so genes the number of possible networks of interactions becomes too vast for an exhaustive search, and so the researchers could examine only a tiny region of the space. But the outcome was clear: On the one hand, circuits typically have dozens to hundreds of neighbors with the same phenotype, while on the other hand circuits that differed in more than 90 percent of their “wires” could still produce the same expression pattern.-"This helps to explain a puzzling aspect of gene circuits: their robustness. In the late 1990s a team of researchers at Stanford University created around 6,000 mutants of brewer's yeast, each of them lacking a different single gene, and found that many of them thrived just as well as the unmutated yeast did.5 The same proves to be true for many other organisms: You can obliterate many of their individual genes to no obvious effect. But this is no surprise if there are plenty of similar gene circuits that do much the same job as the original one. Looked at this way, robustness is complementary to innovation: Any network that can evolve new features and forms among a vast array of alternatives must necessarily be robust against small changes, because it almost certainly has an alternative on hand that performs equally well. This realization offers an antidote to an excessively deterministic view of genes: Exactly which genes you have may not matter so much (within reason), because the job they do is more a property of the network in which they are embedded.-........-"Manrubia agrees that complexity is the key. “It seems clear that efficient navigability can only be achieved in genotype spaces of high dimensionality,” she says. That simply puts more options in reach—because you have more directions to reach in. “As the number of possible neighbors of a sequence increases, the likelihood that some of those neighbors has a viability comparable to the original one grows.” One consequence, she says, is that there could be an adaptive imperative favoring larger genomes, at least for organisms inhabiting varying environments: That way, you gain more in robustness than you lose in the labor of replicating and maintaining a lot of DNA.-"These ideas suggest that evolvability and openness to innovation are features not just of life but of information itself. That is a view long championed by Schuster's sometime collaborator, Nobel laureate chemist Manfred Eigen, who insists that Darwinian evolution is not merely the organizing principle of biology but a “law of physics,” an inevitable result of how information is organized in complex systems. And if that's right, it would seem that the appearance of life was not a fantastic fluke but almost a mathematical inevitability."-http://nautil.us/issue/20/creativity/the-strange-inevitability-of-evolution