It is often argued that the Second Law of Thermodynamics does not represent a valid argument against evolution. However I think such claims might not be valid because they ignore the following considerations from a research paper I found online:
[A] Adding energy to a system can overcome the Second Law’s “spontaneous tendency” and lead to increasing structure. However, the way in which energy is added is critical. Gasoline in the engines of construction equipment can construct a building out of raw steel and concrete, while the same gasoline in a bomb can reduce a building to a mass of raw steel and concrete.
[B] In the context of biomechanical systems, Kugler and Turvey  suggest that self-organization can be reconciled with second-law tendencies if a system includes multiple coupled levels of dynamic activity. Purposeful, self-organizing behavior occurs at the macro level. By itself, such behavior would be contrary to the second law. However, the system includes a micro level whose dynamics generate increasing disorder. Thus the system as a whole is increasingly disordered over time. Crucially, the behavior of elements at the macro level is coupled to the micro level dynamics.
Entropy and Self-Organization in Multi-Agent Systems
H. Van Dyke Parunak and Sven Brueckner
Proceedings of the International Conference on Autonomous Agents (Agents 2001), 124-130
My thoughts and questions:
The first paragraph above [A] shows that entropy can be decreased in an open system if there is a mechanism in place to import and harness external energy (gasoline in this case). In the absence of such a mechanism(s), the added energy will increase the entropy of the whole system. However the existence of such mechanisms is in itself problematic. Wouldn’t they require either: 1-an infinite regress of such mechanisms? Or 2-a self-organism of such an initial mechanism to a degree that can not be demonstrated by non-living results in nature or through experimental simulations?
The second paragraph suggests that organization could increase (an entropy decrease) within a part of a closed system without violating the Second Law of Thermodynamics, if the entropy increase in the remainder was large enough to produce a net increase. However wouldn’t the self-organization of a non-trivial system that could produce that require a mechanism which would also be subject to the caveats above?
The preceding is well “above my pay grade” so I’d welcome feedback from those who know a lot more about the issues in physics and biology.