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This article reminds me somewhat of Robert Laughlin's book, "A Different Universe" applied to origins of life/biology, instead of physics. In his book, he argues that the age of reductionism is about finished, and we are now intellectually entering into the age of emergent physical laws. Knowing fundamentally how matter works, gives you little or no information which can be used to predict collective behavior hierarchically. Maybe this is one of the BIG missing pieces of evolutionary theory. From nonliving to living, might be due to some sort of unknown chemical/biological phase boundary, with many other boundaries after that one (punctuated, abrupt new species). Perhaps the properties and behavior of living things just emerge, given some met (yet unknown) circumstance, and can't be discovered by knowing the fundamentals of evolution. But only by serendipitous observation. Robert Laughlin won the nobel prize in physics, and in the above mentioned book, he said this about evolution theory:

"Much of present-day biological knowledge is ideological. A key symptom of ideological thinking is the explanation that has no implications and cannot be tested. I call such logical dead ends antitheories because they have exactly the opposite effect of real theories: they stop thinking rather than stimulate it. Evolution by natural selection, for instance, which Charles Darwin originally conceived as a great theory, has lately come to function more as an antitheory, called upon to cover up embarrassing experimental shortcomings and legitimize findings that are at best questionable and at worst not even wrong. Your protein defies the laws of mass action? Evolution did it! Your complicated mess of chemical reactions turns into a chicken? Evolution! The human brain works on logical principles no computer can emulate? Evolution is the cause!"