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As I noted previously, where one draws the system boundary is critical in this analysis. I agree that the contribution of energy released during polymerization needs to be considered as well.If the result depends on where you draw the boundary would that not be an indication that there's something wrong with the analysis.
However, let's define our initial local system not as a set of activated nucleotide monomers but inactivated versions. In this case, energy must first flow into the system from the surroundings for activation, and then flow out again during polymerization. I'm not sure what the net effect of this is precisely, but clearly a much small net change to the system, if not close to zero. This then allows configuration entropy to be significant.--
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