Two articles have been published by peer-reviewed journals with the title "Entropy and Evolution." One (Daniel Styer, American Journal of Physics, Vol. 76., No. 11, Nov. 2008) says that evolution does not violate the second law of thermodynamics and the other says it does (Granville Sewell, BIO-Complexity, 2013 (2):1-5, June 22, 2013).
The three main branches of physics are nuclear physics, dynamics, and thermodynamics. Nuclear physics is the study of the evolution of stars and the creation of elements. Dynamics studies the laws of nature and the creation of chemical compounds.
Thermodynamics is the study of liquids, solids, and gases. The zeroth law of thermodynamics is that temperature is measured with a thermometer in units called degrees. The 1st law defines heat and internal energy. The 2nd law is that heat flows from hot substances to cold ones. The 3rd law is that 454 degrees below zero is as cold as it gets. Thermodynamics has nothing to do with the operation of machines, biology, or the evolution of stars. A pendulum is not a thermodynamic system. A pendulum exists only in the minds of physicists, and it does not have a temperature or entropy. A pendulum and a Boeing 747 in flight obey the laws of dynamics, not thermodynamics.
Evangelists have the unintelligent but intelligible idea that evolution and the origin of life violate the 2nd law. The 2nd law can be expressed by saying entropy, which is measured in units of energy per degree, always increases. The evangelists are juxtaposing the fact that a sugar cube put in a cup of coffee will dissolve (2nd law) with the fact that proteins exist (evolution).
Entropy is related to the knowledge of the location of sugar molecules in Cartesian coordinates (x, y, z). The entropy of an un-dissolved sugar cube is less than the entropy of a dissolved sugar cube. Entropy is also related to probability calculations because there is the possibility that sugar molecules in a cup of coffee will drift towards one point and un-sweeten the coffee.
In trying to understand where proteins come from, biologists calculate the probability of getting a protein with the random selection of amino acids. There are 20 amino acids and an average protein contains 300 amino acids. The probability is very small because each amino acid has to be in exactly the right position relative to the other amino acids.
The evangelists are confusing the informational knowledge of the location of amino acids in a protein with the knowledge of the Cartesian coordinates of sugar molecules in a sugar cube. They are also confusing the probability calculation of biologists with the probability calculations of physicists. There is nothing improbable about a protein because proteins exist. It is quite improbable that a sugar cube will re-constitute itself in a cup of coffee.
Early in his article, Styer shows some understanding of this with the statement, "Disorder is a metaphor for entropy, not a definition for entropy." Sewell ignores this truism, as does Styer. However, Sewell squelches Styer with the following statement:
According to Styer, the Boltzmann formula, which relates the thermal entropy of an ideal gas state to the number of possible microstates, and thus to the probability of the state, can be used to compute the change in thermal entropy associated with any change in probability: not just the probability of an ideal gas state, but the probability of anything. (page 2)
Sewell formulates Styer's statements into a theory that he calls the "compensation argument." He then argues against the "compensation argument" instead of ridiculing it as unintelligible. Sewell is confusing the 1st law with the 2nd law.
Suppose you have two pieces of metal, one hot and the other cold, and you put them in thermal contact. According to the 1st law, the internal energy of the hot piece will decrease and the internal energy of the cold piece will increase. There will be no loss or gain of energy. The increase in the energy of the cold piece is "compensated" for, just like a merchant is compensated when you buy something.
However, the matter is entirely different with regards to entropy. There are two ways of looking at what happens. The first way is that the entropy of the cold piece increases and the entropy of the hot piece decreases. The second way is that the entropy of both pieces considered as one system increases. The idea that the increase in the entropy of one is "compensated" for by the decrease in the entropy of the other is nonsense.
This conflict between Sewell and Styer about the 2nd law is related to the cultural conflict about the theory of intelligent design, which is related to the cosmological argument for God's existence. Many people think mistakenly that the cosmological argument involves a "first cause" and is invalid because there can be an infinite regression of causes. In the context of this reasoning, the Big Bang, the origin of life, and evolution are thought of as evidence of the existence of an intelligent designer. The cosmological argument, according to Thomas Aquinas as explained by Etienne Gilson, is based on the existence of finite beings and the idea that an infinite being, not a "first cause," exists. The Big Bang, origin of life, and evolution is evidence that God does not exist because it is evidence that the universe is not intelligible.