Replication generates far-from-equilibrium structures

How can living systems form by natural processes opposing the second law of thermodynamics? Devine 2018, book Chap 10 .

Given one bacterium in a soup of nutrients, the bacterium and its descendants will replicate until the system reaches it carrying capacity.  In a resource rich environment, replicated structures are more likely to be observed than alternatives because the probability of replication increases with the number N of existing structures. The system can be maintained against death and decay in a homeostatic state by accessing nutrients to continually replicating while rejecting high entropy waste.  But if there is no flow through of nutrients, the bacterial system experiences death and decay under the second law of thermodynamics.

The AIT perspective sees natural replication process as computations on a real-world UTM that are able to generate ordered repeats of structures, having low algorithmic entropy, forming a far-from-equilibrium system.  The nutrients used by the replicating system are natural structures carrying instruction bits and stored energy, analogous to the behaviour of computational automata.  The instructions in the DNA of the replicating cell, access the instruction and the stored energy bits that enter the system to generate repeats of the cell structure.  The process separates the heat and degraded species from the ordered regions to be ejected by natural processes.  Much if not all, of the self-organising capability of life on earth, or of a system of cells, would seem to be a consequence of the evolution of replicating structures.
Replication processes, can self-regulate

Consider a replicating system existing in a viable macrostate, e i, consisting of many microstates all with the same provisional entropy H( e i). The degradation programme can be represented on the real-world UTM U by; U(p2law, e i)--> ηj.  Here p2lawis the algorithm representing second law degradation processes and ηj characterises a state outside the macrostate and includes history bits that embody the instructions to maintain reversibility. Hence H(ηj) = H( e i) +H(p2law) as all bits are tracked.  

If however, homeostasis is maintained by resource bits H(σj), (specifying the configuration σj) that enter the system, and instruction bits, H(prepl), where prepl is the replicating programme that regenerates an equivalent microstate, the energy carried in must equal energy out.  Also, the bits carried in (including instruction bits) must equal H(waste) the bits ejected by the system as the temperature adjusts to force both these equalities. This conservation identifies the requirements for homeostasis, i.e.
H(waste) = H(p2law) + H(prepl) + H(σj).
The extraction of heat or waste from the system by the action of physical laws, is in effect a transfer of order into the system from the environment.

Variation in replicating structures Devine 2018, book Chap 10 .
Variation in a system of replicated structures provides a natural mechanism to stabilise the system against a changing environment as the most efficient structures having lower entropy throughputs, dominate.  Where resources are shared between different replicating system because of variation, inter-dependent structures emerge by selection processes as the inter-dependence uses resources more efficiently.  Because of the variations, inter-dependant replicating systems over time can adapt to a changing environment as new configurations emerge.

Observationally it appears that, in comparison to simpler structures, a system of interconnected and nested systems (such as a forest ecology nesting species, with species nesting organs, and organs nesting cells) is more viable far from the equilibrium set, as the waste of one part of the system is the resource input for another as demonstrated by the predator prey relationship. It seems that life is more efficient in maintaining the system further from the most probable set of states than no life, but at the cost of needing to pump out more waste, hastening the heat death of the universe. Indeed, Schneider and Kay (1994) show that, an ecology  of myriads of inter-dependent self-replicating units, where species lower in the food chain consume the waste of higher species, the overall degradation of the system is greater than would be the case for a non-living system, or even a simpler living system.