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I'll answer the rest later, due to time constraints right now, but let me focus on the first issue. You wrote "So, we agree that it is irrational to say heat from the sun decreased the entropy of the biosphere. Our disagreement is over whether or not Styer says this in the article. Is this correct?"
I'm saying it is correct to say that when heat is added to a system, the entropy will generally increase and not decrease. Styer is correct in his statement. He says the sun loses heat as it radiates heat. Therefore the sun decreases in entropy. Then he says that the surrounding "outer space", meaning the solar system area excluding the sun, increases in entropy due to heating from the sun. Styer is therefore quite consistent with the concept that more energy increases entropy. My disagreement is with your claim that Styer made a mistake.
II. ENTROPY FLUX THROUGH THE EARTHThe Sun heats the Earth through electromagnetic radiation largely in the visible and near-infrared bands. The Earth radiates electromagnetic radiation largely in the far-infrared band into outer space, where it eventually joins the cosmic microwave background. The Earth itself remains almost constant in temperature, so the incoming radiant energy from the Sun must balance almost exactly the outgoing radiant energy into space. In short, the Sun heats the Earth and to a nearly equal extent the Earth heats outer space. Each of these "heatings” is accompanied by an entropy change. The change of entropy for a system at constant absolute temperature T, gaining heat Q quasistatically, is (Delta)S = Q/T.………..If each of these organisms were evolving at the rate assumed in Eq. 2, the change in entropy of the biosphere each second would be − 302 J/K.
ACKNOWLEDGMENTSTwo anonymous referees made valuable suggestions that improved this article significantly.
I'm afraid you're wrong on all three counts.
1. No, Styer is NOT "saying that heat added to the biosphere causes the entropy of the biosphere to decrease 302 J/K every second." He is saying that a calculation of the configurational entropy of organisms alone would amount to 302 J/K and then he points out that this is offset by heat from the sun. He does NOT state that this decrease is caused by the influx of heat. He goes on to point out that "In other words, at a minimum the Earth is bathed in about one trillion times the amount of entropy flux required to support the rate of evolution assumed here." He is very clear that the heat from the sun increases the entropy of the earth many times more than the decrease from the increased order in evolution.
2. The use of Boltzmann's constant is accurate. You have not yet given any reason otherwise. Boltzmann's constant is the correct proportionality factor between the density of states (you erroneously reprhrase that as 'probabilities'--it's not quite the same thing) and entropy. Styer has not made a mistake on this point.
3. I''m afraid it's not Styer who doesn't understand the relationship between entropy and evolution. He nailed it. Your comment, however, is neither plausible nor an accurate statement of evolution or of what biologists do.
I"ve looked into your quotes on random assembly of proteins more deeply. Not a single one of your quotes says what you interpret it to mean. Note particularly the phrase "If left to chance," Each one of these authors is pointing out the vast number of possibilities and how a random process like that simulated by a computer composing a sonnet with each note selected at random, could not possible solve the problem. Not a single one says that this is how evolution works and that this is a legitimate simulation of evolutionary process.
Like you did with Styer, you have misinterpreted all of these works and then accused them of saying things they haven't been saying. If it doesn't have reproduction with incremental variation, it's not evolution.
1. Styer is pointing out that the second law of thermodynamics is not violated by the decrease in entropy in the evolutionary process because the total entropy is still increasing. He does not say that the energy from the sun causes the decrease in entropy in the biosphere. In this article Styer does not comment on what mechanisms caused the decrease in entropy in the biosphere.
2. It is not absurd at all to say that there is a temperature of a fertilized egg. It is perfectly accurate. It reflects the average atomic kinetic energy in the entire egg which is typically in near equilibrium with its surroundings. Boltzmann's constant is part of the definiton of entropy and is the correct way to calculate it from the density of states (different from the probabilit function).
3. My request for quotes was for you to show evidence that the majority of standard textbooks simulate evolution as computers composing sonnets by random selection of each note. Your selections showed your claim to be false. As for natural selection not explaining common descent, quotes don't suffice--and you didn't provide any--because you still need basic logic and data. I think by now every single concern of your about the Styer article has been proven to be false. AJP has no need to retract anything but I think you do.
1. The second law of thermodynamics just says the Gibb's Free energy must decrease, not the entropy. The latter (which is what most people think is the second law) holds only for the systems where internal energy (and temperature) is constant. So when water freezes, the entropy of the water decreases but the total entropy of the water plus the environment increases. Same with evolution. THe biosphere itself has a decrease in entropy but the total entropy of the system (biosphere plus its environment) increases so the second law is preserved.
2. David, we're talking average kinetic energy of the atomic nuclei within each molecule, the vibrational energy. Yes, this is well-defined in any collection of molecules, whether it be a fertilized egg or a 747 or anything else.
3. That 'disagreement' has long been resolved by every biology professor I know. I could name the ones I have talked with in a long list but there's no need to pull them into public. There is one angle where there could be a discussion, namely, the extent of the evidence. There are some who claim there isn't enough evidence for common descent because too many details are missing. It is true that much information is missing--historical records are gone for much of our history. So those who make such a requirement could say that common descent is not adequately explained. But given the wealth of evidence that does exist, such demands seem inappropriate. Just talk with leaders of genetic sequencing programs like the human genome project!
1. Then you don't understand thermodynamics or the second law at all. The second law is expressed in its full form through Gibbs free energy. Your example of a box of atoms in a gas form is only one simplified way of explaining things. Understood more fully, thermodynamics refers to all physical systems.
2. Then you don't understand temperature, perhaps because you're only thinking of a gas while I'm a solid-state physicist. Temperature is precisely connected to the vibrational energy of the atomic nuclei in any solid, liquid, or molecular submstance.
3. Biologists have already weighed in and the matter is settled.
Styer's article is correct and in claiming that it should be retracted you have shown a deep misunderstanding of thermodynamics.