Evolution: a different view (Introduction)

by David Turell , Thursday, April 21, 2016, 01:52 (3138 days ago) @ David Turell

This article takes from Andreas Wagner's work to show that evolution has amazing biochemical patterns to follow and this affects genes, and the search for new proteins in the landscape to fit new structures and functions, and it limits the number of functional RNA molecules to smaller number to be found in a search. It never wonders why this might be, and assumes it is all natural, while I see planning patterns to help evolution flow:-http://nautil.us/issue/20/creativity/the-strange-inevitability-of-evolution-"You don't have to be a benighted creationist, nor even a believer in divine providence, to argue that Darwin's astonishing theory doesn't fully explain why nature is so marvelously, endlessly inventive. “Darwin's theory surely is the most important intellectual achievement of his time, perhaps of all time,” says evolutionary biologist Andreas Wagner of the University of Zurich. “But the biggest mystery about evolution eluded his theory. And he couldn't even get close to solving it.”-"What Wagner is talking about is how evolution innovates: as he puts it, “how the living world creates.” Natural selection supplies an incredibly powerful way of pruning variation into effective solutions to the challenges of the environment. But it can't explain where all that variation came from. As the biologist Hugo de Vries wrote in 1905, “natural selection may explain the survival of the fittest, but it cannot explain the arrival of the fittest.” Over the past several years, Wagner and a handful of others have been starting to understand the origins of evolutionary innovation. Thanks to their findings so far, we can now see not only how Darwinian evolution works but why it works: what makes it possible.-***-"The trouble is that traits don't in general map so neatly onto genes: They arise from interactions between many genes that regulate one another's activity in complex networks, or “gene circuits.” No matter, you might think: Evolution has plenty of time, and it will find the “good” gene circuits eventually. But the math says otherwise.-"Take, for example, the discovery within the field of evolutionary developmental biology that the different body plans of many complex organisms, including us, arise not from different genes but from different networks of gene interaction and expression in the same basic circuit, called the Hox gene circuit. -***-"There are 20 different amino acids found in natural proteins, and for proteins just 100 amino acids long (which are small ones) the number of permutations is 10^130. Yet the 4 billion years of evolution so far have provided only enough time to create around 10^50 different proteins. So how on earth has it managed to find ones that work?-***-"And how does evolution find its way from an existing solution to a viable new one—how does it create? The answer is, at least in part, a simple one: It's easier than it looks. But only because the landscape that the evolutionary process explores has a remarkable structure, and one that neither Darwin nor his successors who merged Darwinism with genetics had anticipated.-***-"In the 1990s Schuster and his colleagues devised a computer program that could predict the simplest features of an RNA's shape (its secondary structure, which is how parts of the chain stick to other parts by pairing-up of bases) from its sequence. For an RNA of 100 bases, there are around 1023 possible shapes of this sort. But what was remarkable was the way these shapes and their sequences were related.-***-"E. coli consumes glucose and makes from it all 60 or so of the key molecular building blocks it needs to survive. But what if just one of those metabolic reactions was altered? Wagner and Rodrigues calculated and found that several hundred will also make do with glucose alone. In other words, E. coli's metabolic network is not finely tuned to run on glucose—lots of other variants will work too.-***-"These ideas suggest that evolvability and openness to innovation are features not just of life but of information itself....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."-Comment: Huge essay. I covered only a little. Why inevitability?