Living systems are those which utilize energy to maintain themselves, grow, reproduce, move, respirate, feed, ect. Gibbs free energy is what drives these processes. dS isn't an important focus, because the reactions themselves are taking that Gibbs free energy. They are the most probable sink for the energy. They are the accessible states.
The use of Shannon entropy is for looking at the processes utilizing Gibbs free energy for productive purposes, those that are unique to life. There are also nonproductive channels, but they must consume less energy overall for life to continue. The accessible states for Shannon entropy are all possible states beforehand. Once energy has been expended, the result defines the state and is used to calculate the entropy. In the simplest case the before entropy is log(2)(a reaction might occur, or it might not), after the reaction it is log(1). As long as Gibbs energy flows though the Shannon "channels", this entropy is reduced.
Unlike energy release in bulk mixes, release in living cells occurs at collections of objects configured to capture that energy. The creation of each of those objects, their assembly and the function they serve, are all considered Shannon information. The information is ultimately coded in RNA and DNA. Once the Gibbs flow fails in key channels of information, the organism reverts to a bulk mix and Shannon entropy no longer applies. The organism is dead.
" The objection to evolution based on the Second Law of Thermodynamics will not be complete until we have thoroughly explained the thought experiment raised by betty boop on another thread:
Take a live albatross, a dead albatross and a 12 lb cannonball to the top of the Leaning Tower of Pisa and toss them over the side.
What happens next, i.e. the live albatross flying away, is what must be addressed before anyone can put the appeal to the Second Law of Thermodynamics in the "out" basket."
Bird's flap their wings and fly, or try to, when they sense the acceleration. The immune system is an unconscious reaction to life threats also. The organism begins shortly after birth to distinguish self from other, in terms of proteins and other antigens. Both reactions are coded in the DNA and involve feedback. The feedback and triggers are switches, rather than equilibrium. That is not common in chemical mixes.
It's the properties of RNA and DNA itself, the transcription reactions and their creation of catalytic machines that overcame the second law. If it can happen, it will.
The Gibbs free energy is just -T times the entropy change, at constant pressure. It's just a proxy for the total entropy.
The one thing I would like for Lurkers to keep in mind is that Shannon's is the Mathematical Theory of Communication. The content of the message being transmitted (which most people think of as "information") is completely beside the point to the theory - hence Shannon is applicable across the board to many disciplines.
Under Shannon, information is the reduction of uncertainty (entropy) in the receiver (or molecular machine) in going from a before state to an after state. It is the action, not the message. DNA, for instance, is a message.
For a graphic and more information, Lurkers might want to scan post 1791.
Hi spunkets! I missed this earlier. Hope it's not too late to reply!
It may well be that the bird's sense of the acceleration is what triggers the ensuing flight. But we were asking whether the bird was in fact a purely material system (in contradistinction to a living system); and as such, wholly subject to the physical laws. It seems to me that, if it were, then we would be able exactly to plot its path, once it is on the wing.
How would you propose to do this?