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Page numbers from my personal copy
p.1 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.
[JLJ - The 1904 de Vries quote was actually written by a Mr. Arthur Harris in "a friendly criticism" of de Vries' views, which de Vries subsequently quoted in his own work. On a side note, it appears that both variation and evolution are more properly conceptualized as emergent effects of a complex, interacting, and networked process - rather than "things" unto themselves that can be deconstructed in infinite detail. When you deconstruct a creative process you get a lot of things that, networked together in the appropriate way, just 'work'. One simply specifies the process of reproduction, development, selection and reproduction etc. - evolution and variation are emergent network effects of this process.]
p.2 How on earth did evolution manage to rewire the Hox network of a Cambrian fish to create us?
[JLJ - Actually very little rewiring was needed. The robust fish that evolved into mammals was already pre-adapted to land (see Mayr, 1960, p.368 http://johnljerz.com/superduper/tlxdownloadsiteWEBSITEII/id505.html) - it crawled along the sea floor with primitive limbs, and breathed through both lungs and gills. Evolution then took over.]
p.2 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.
[JLJ - The same thing applies for games pieces on a game board - the job they do is more a property of the network in which they are embedded.]
p.3 How does evolution find workable solutions when it lacks the means to explore even a small fraction of the options? 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.
p.3-4 To act as a catalyst, an RNA molecule needs to fold into the right shape... Naively, you might expect RNAs with a similar shape... to share a similar sequence... Instead, RNAs with the same shape could vary very widely in sequence. You could get the same shape, and therefore potentially the same kind of catalytic function, from very different sequences... RNAs with the same kind of shape were connected in a network that weaved its way throughout pretty much the whole of sequence space. You could go from one sequence to another with the same shape (and thus mush the same function) via a succession of small changes to the sequence, as if proceeding through a rail network station by station. Such changes are called neutral mutations, because they are neither adaptively beneficial nor detrimental.
p.5 So this is why the RNAs are evolvable at all: not because evolution has the time to sift through the impossibly large number of variations to find the ones that work, but because there are so many that do work, and they're connected to one another.
[JLJ - It is difficult to understand is what is meant by connection and network: The author considers RNA to be connected in a network if functionally identical organisms can trace a "path" through their RNA that vary by one mutation. I would consider such an abstract collection a related set, because modern definitions of the word network imply a physical connection, as in a computer network. But Wagner is the famous biochemist and I am not, so what do I know?]
p.6 This suggests that evolvability, and the corollary of creativity or innovability, is a fundamental feature of complex networks like those found in biology.
p.6 Evolution sends vast numbers of organisms off to explore this intricately ordered library, seeking good answers to life's problems.
p.7 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.
p.7 These findings uncover a property of biological systems even deeper than the evolutionary processes that shape them. They reveal the landscape on which that shaping took place, and they show that it was only possible at all because the landscape has a very specific topology, in which fundamentally similar combinations of the component parts... are connected into vast webs that stretch throughout the whole of the multidimensional space, each intricately woven amidst countless others.
p.8 These ideas suggest that evolvability and openness to innovation are features not just of life but of information itself.
p.8 Yet the question that remains is: Why does the space of evolutionary options have this essential, robust structure? ...Jesse Bloom of the Fred Hutchinson Cancer Research Center in Seattle, a specialist on protein evolution... "One could posit that evolution is only able to work effectively if this property exists, and so the things that ended up evolving have this property," he says.
[JLJ - Perhaps missing the point. Maybe evolution as we know it itself emerged from multiple, possible ways for an advanced organism to develop. What we see in evolution today is perhaps the winner among millions of ways it could have been done.]
p.9 for electronic components that carry out logic functions... "The more complex they are, the more rewiring they tolerate," says Wagner. Not only does this open up possibilities for electronic circuit design using Darwinian principles, but it suggests that evolvability, and the corollary of creativity or innovability, is a fundamental feature of complex networks like those found in biology.
[JLJ - Ummm... as an electronic circuit designer I can relate that the parts used are normally robust enough as they are. Circuits called "quads" already partially implement this idea and they are used where reliability is favored over circuit complexity.]
p.9 [Manrubia] "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."
p.9 Nobel laureate chemist Manfred Eigen... 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.
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