James,
thanks for your thoughtful comments.
>> I can understand your distinction between living systems and the inanimate, but the distinction is less crisp when you think of microorganisms and some new theories like Jeremy England's. Does a virus, bacteria, fungi or protozoa have a goal or purpose and does it grow, reproduce or metabolize?
I am not an expert on all these simple organisms/entities. A virus does not count as it is not self-sufficient. The others do all those things, I think. I must clarify that the statement by Hartwell et al I quoted in my essay about purpose is not I think meant to be a metaphysical statement about the meaning of life: it is a statement about all the physiological and developmental systems that underlie life, each of which does indeed have a purpose. Thus a bacteria has flagella because they enable it to move; a bird has wings because they enable it to fly.
>> Jeremy England's new theory regarding the second law of thermodynamics says the difference between the animate and the inanimate is that living things are much better at capturing energy from their environment and dissipating that energy as heat.
His thesis is very interesting but I think it is only part of the story. You can't capture the full nature of life by statistical mechanics methods alone, although they will be playing a significant role at the micro level. In particular what is missing is the element of genotype selection for phenotype advantage, with the key feature that a vast number of genotypes give the same phenotype outcome. This multiple realisability of higher level function is the key element discussed by Andreas Wagner in the book I mention, and cannot I think be encapsulated by statistical physics methods, because they do not refer to function.
>> "You start with a random clump of atoms, and if you shine light on it for long enough, it should not be so surprising that you get a plant," England said.
I don't think he can have seriously read the literature on the origin of life. No one knows how that happened. In particular we don't know if metabolism or information came first. Nor is it likely that life originated from plants. Indeed it did not, because the early atmosphere of the Earth had no oxygen.
>> Well done link of physics to logic, but is there also a cosmic or long-term link between physics and logic.
We don't understand that one. Roger Penrose writes nicely about it.
> What is the mixed-bag process of clouds of supernova elements forming into rocks vs microorganisms and are the latter alive or potentially alive but not the former?
Yes indeed.
Regards
George