The 2nd Law of Thermodynamics and evolution

I thought that critics of Darwinism long ago gave up arguments based on the 2nd Law of Thermodynamics, but such arguments were recently posted on Answers in Genesis:

The principles of thermodynamics, even in open systems, do not allow a new functional biological structure to be achieved without new machinery already being in place.

Let’s put a bit more detail in here. The laws of thermodynamics have one law in particular—the Second Law of Thermodynamics—which says that in a closed system the amount of energy that is no longer available for useful work is increasing. This is energy “lost” to the system per unit degree of temperature, and it is called the entropy of the system. The principle of energy loss for useful work still applies in an open system, since there is no benefit unless there is a machine to use the energy added.

Energy is defined as the ability or capacity to do work. Energy can be added to an open system without regard to the availability of a machine to convert that energy into useful work.

Boeing 777s cannot be made in a car factory by adding loads of sunlight or electricity unless the machinery is available to use that energy to build Boeing 777s. Similarly the human brain cannot be formed from simpler machines just by adding energy if there is no machinery available to do this. Spontaneously forming of such machinery will not happen.

The conversion of a car factory to produce Boeing 777's concerns a purposeful macroscopic arrangement of parts, whereas the 2nd Law of Thermodynamics does not concern such an arrangement of parts. In the 2nd Law of Thermodynamics, energy in a substance is uniformly distributed at the atomic or molecular level, as in the kinetic energy in the atoms or molecules of gases.

. . . .unlike macro machines, chemical machinery at the molecular level involves setting up proteins of hundreds and usually thousands of polypeptide bonds linking a string of amino acids. And each of these bonds is in a raised energy state such that, left to itself, it would break down and not stay in that state. To suggest, as some are saying, that the raised energy state would be maintained while natural selection favored, over many generations, single random mutations, one by one, to finally bring together the full complement of necessary amino acids is, frankly, thermodynamically absurd. This is never observed and is contrary to all thermodynamic principles of energy transfer.

DNA is generally stable and shows no particular tendency to spontaneously decay.

The 2nd Law of Thermodynamics is often stated in ways that have nothing to do with biology, e.g.,

Kelvin statement: It is impossible to construct an engine, operating in a cycle, whose sole effect is receiving heat from a single reservoir and the performance of an equivalent amount of work.

Clausius statement: It is impossible to carry out a cyclic process using an engine connected to two heat reservoirs that will have as its only effect the transfer of a quantity of heat from the low-temperature reservoir to the high-temperature reservoir

I think that a good illustration of the effect of the 2nd Law of Thermodynamics is a closed system with two finite reservoirs at different temperatures plus an engine -- say, a Carnot engine -- that performs work by operating in a cycle in which heat is received from the hot reservoir in one stage of the cycle and heat is transferred to the cold reservoir in another stage. As the work is performed, the hot reservoir becomes cooler and the cold reservoir becomes warmer, and as a result of these temperature changes the engine becomes increasingly less efficient (in a Carnot engine with an ideal gas as the working substance, the efficiency is defined as the ratio of (1) the temperature difference of the reservoirs to (2) the absolute temperature of the hot reservoir). Eventually a point is reached where the temperature difference between the two reservoirs is so small that practically no work can be performed at all. However, according to the First Law of Thermodynamics, the total internal energy of the closed system is the same as it was at the beginning. What has changed is that this energy is no longer capable of performing work inside the system because that energy is now uniformly scattered in the form of a uniform temperature throughout the system whereas a difference in reservoir temperatures is required to perform work. The system has changed from an ordered system -- where higher-energy gas particles in the hotter reservoir are separated from lower-energy gas particles in the colder reservoir -- to a disordered system where the gas-particle energy is uniformly distributed throughout the system. This increase in disorder is represented by an increase in the total entropy of the system.

Wikipedia discusses efforts to use the "Gibbs free energy" concept to relate living things to the 2nd Law of Thermodynamics:

In recent years, the thermodynamic interpretation of evolution in relation to entropy has begun to utilize the concept of the Gibbs free energy, rather than entropy. This is because biological processes on earth take place at roughly constant temperature and pressure, a situation in which the Gibbs free energy is an especially useful way to express the second law of thermodynamics. . . .

. . . .In the popular textbook 1982 textbook Principles of Biochemistry by noted American biochemist Albert Lehninger, it is argued that the order produced within cells as they grow and divide is more than compensated for by the disorder they create in their surroundings in the course of growth and division . . . .

In 1998, noted Russian physical chemist Georgi Gladyshev, in his book Thermodynamic Theory of the Evolution of Living Beings, argues that evolution of living beings is governed by the tendency for quasi-equilibrium, semi-closed, hierarchical living systems to evolve in the direction that tends to minimize the Gibbs free energy of formation of each structure. Variations of the Gibbs function of formation of a thermodynamic system at any stage of the evolution, for instance ontogenesis and phylogenesis, such as a social system, according to Gladyshev, "can be calculated by means of thermodynamic methods." Gladyshev calls this a form of sociological thermodynamics.

Similarly, according to the chemist John Avery, from his recent 2003 book Information Theory and Evolution, we find a presentation in which the phenomenon of life, including its origin and evolution, as well as human cultural evolution, has its basis in the background of thermodynamics, statistical mechanics, and information theory. The (apparent) paradox between the second law of thermodynamics and the high degree of order and complexity produced by living systems, according to Avery, has its resolution "in the information content of the Gibbs free energy that enters the biosphere from outside sources."

So some scientists have turned the tables by using thermodynamics to argue in favor of evolution, and it looks like some of their arguments are really bad -- for example, Gibbs free energy has no "information content." Personally, I don't feel that thermodynamics can be a good argument either for or against evolution.

Anyway, thermodynamics is a very abstruse subject. Thermodynamics is a very important subject in mechanical engineering but though I am a mechanical engineer I admit that I feel that I never completely understood it.