Before starting on about the second law of thermodynamics, I am not using the second law of thermodynamics nor am I saying that abiogenesis is thermodynamically impossible. What I am saying is that it does have thermodynamic issues.
First of all, the energy applied to any prebiotic soup is going to be more likely to break down the organic compounds that produce them. This problem gets worse the more complex those organic compounds become.
Second, many aspects of a living cell do not result from chemical necessity. The arrangement of the nucleotides in DNA is a perfect example of this problem. The arrangement of the nucleotides in DNA is not compelled by chemistry but it is based on the information that it holds. The DNA can be arranged as needed to hold that information. The point is that there are many aspects of a cell necessary for life that cannot simply be produced by chemical processes but are easily broken down by thermodynamic processes.
There is actually a principle that deals with open systems and how the application of energy affects the entropy of the system. Put simply, when energy is supplied to a system, that energy tends to drive the entropy of the system towards the entropy of the applied energy. This principle actually explains why the second and third laws of thermodynamics work the way they do. Entropy increases in a closed system because the heat of the system increases the entropy of the system. With the third law the molecular forces are able to apply energy in a more organized matter as the system cools down towards absolute zero, eventually reaching a minimum level of entropy.
Consequently, abiogenesis cannot be considered even remotely scientific unless a process exists that can overcome these problems on the thermodynamic end of things. No solution has ever been proposed. In fact, most evolutionists just simply assume adding energy is all that is necessary in that magically it produces living cells, despite the fact that it is akin to nuking a junkyard and expecting to get fully functional airplanes.
