In the unpublished work of E.T Jaynes I came accross an interesting statement on muscle and thermodynamics, namely:
whereby Jaynes shows that in effect, the muscle is not violating the Second Law of thermodynamics because the work in a muscle is being performed on a very small scale using only one (in any event few) degree of freedom from a large molecule. Jaynes passed away in 1998 but he made a statement that his views on biology and thermodynamics would not be acknowledged until 20 years from the time he wrote his paper. This would be 2009.
Fuel powered muscles have already made the headlines (here) but they do not use large molecules to produce work. It is also interesting to note that some shape memory alloys metals (Ti-Ni) are considered for devising muscles . However since they are conductors, they are not, according to Jaynes' statement, optimal to provide the highest efficiency (since heat gets to spread easily). All this should point to a MEMS based solution.