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5/22/2013Discussion group, Lexington, MA
5/25/2013“Jesus: Liar, Lunatic, Legend…or Lord?” London, England
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Accusations of anyone's qualifications or their background are neither accurate nor appropriate in this forum. Continued violations will lead to suspension. Please focus on the ideas.
Your analogy of ping pong balls leads you to the wrong conclusion. Yes, the box of balls has a total internal energy, it has a temperature and it has an entropy, all of which can, in principle, be measured or calculated. You have not given any reason why not. All subcomponents as well as the whole system are thermodynamic. There is nothing in that box that would exclude it from any thermodynamic considerations.
All systems are thermodynamic systems and can be characterized by Gibbs Free energy and changes to it as governed by the second law of thermodynamics. Whether one knows how to accurately calculate the respective components of kinetic energy and temperature and entropy is another matter, and entirely irrelevant to the question of whether it is a thermodynamic system. Yes, you can calculate temperatures and entropies of systems. It's not easy and usually one deals with partial derivatives while hold all but one or two variables constant. Net: all biological systems follow the second law of thermodynamics.
Yes, I did respond to your concern that Styer claimed adding heat caused a decrease in entropy. I stated that he said just the opposite. Consider his sentence "The Sun emits heat and hence decreases in entropy, while outer space absorbsheat and hence increases in entropy." He is absolutely correct. The sun lost heat and decreased in entropy while the heat from the sun was transferred to outer space which incrased in heat and also in entropy. So your fears are assuaged--he does not claim that an increase in energy will cause a decrease in entropy.
If you have any evidence or examples of mainstream biology papers or textbooks advocating that evolution is properly simulated by a tornado in a junk yard creating a 747 (note that they didn't exist in the 50's!) or of a computer composing a sonnet at random, please let me know. I would suggest that they are either anti-evolution propaganda or they are not evolution advocates in any way. From Darwin till the present, evolutionary theory is predicated on some form of gradualism--replication with variation and selection. WIthout that, it isn't evolution. That is not simulated by a tornado or a random set of elements. The methods and degree of gradualism have changed radically since Darwin but the core concept remains the same.
By comparison, if we question how long it would take a high-speed computer to write randomly a specific Shakespearean sonnet, we are asking that all the letters of the words of the sonnet will come up simultaneously in the correct order. It is an impossible task, even if all the computers in the world today had been working from the time of the big bang to the present. Even to compose the phrase, "To be or not to be,” letter by letter, would take a typical computer millions of years.” (Marc W. Kirschner and John C. Gerhart, The Plausiblity of Life: Resolving Darwin's Dilemma, page 32)
Each of the four identical polypeptide chains that together make up transthyretin is composed of 127 amino acids…The primary structure is like the order of letters in a very long word. If left to chance, there would be 20 to the 127th power different ways of making a polypeptide chain 127 amino acids long. (Campbell and Reece, Biology, 7th edition, page 82)
Title: Natural Selection and the Complexity of the Gene (Nature, Vol. 224, 1969, p. 342)Subtitle: Conflict between the idea of natural selection and the idea of uniqueness of the gene does not seem to be near a solution yet.First paragraph: Modern biology is faced with two ideas which seem to me to be quite incompatible with each other. One is the concept of evolution by natural selection of adaptive genes that are originally produced by random mutations. The other is the concept of the gene as part of a molecule of DNA, each gene being unique in the order of arrangement of its nucleotides. If life really depends on each gene being as unique as it appears to be, the it is too unique to come into being by chance mutations. There will be nothing for natural selection to act upon.
Considered thermodynamically, the problem of neo-Darwinism is the production of order by random events. (Ludwig von Bertalanffy, "Chance or Law,” in Beyond Reductionism: New Perspectives in the Life Sciences, The Macmillan Company, 1969, page 76)
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.
There's a helpful article written by Georgi Gladyshev in Entropy that addresses appropriate ways of thinking about entropy in evolution. You can find it at http://www.mdpi.org/entropy/papers/e1040055.pdf and I attach it for convenience
I'm afraid the article was over my head. I sent an email to Professors Granville Sewell and Andy McIntosh with the Gladyshev article asking for help. Sewell and McIntosh wrote the articles I attached on June 5.
If that's over your head, you should not be asking a journal to retract a paper on the basis of thermodynamics. As you admitted in a pervious post, your understanding of thermodynamics is limited to a gas in a box. The theromdynamic concepts, however, do apply to liquids, gels, solids and ensembles of those objects and you may be interested in learning how it does.
I appreciate your references to the papers by Sewell and McIntosh but I find neither paper persuasive. Those papers, take us in a very different direction from your assertions. They are focused on a discussion of the mechanisms of entropy change, if I may state it in those terms. You took the approach that thermodynamic parameters are not valid for biological systems, an assertion not supported by anyone, as far as I know.
On the whole, one may assert that both internal factors (characteristics of the biosystem) and external factors (characteristics of the environment) determine the trend of biological evolution, whose progress is, of course, possible thanks to the inflow of solar energy and energy from other sources.
Keep studying the article until you understand all of it. It's good. Note especially the distinction he emphasizes between kinetics and thermodynamics. This is something that Sewell misses as well. Styer is not talking about kinetics and saying anything like what you are attributing to him. He is talking thermodynamics and showing that total entropy is increasing. That is, while the entropy may be decreasing ever so slightly with evolution, properly taking the entire system into account with the energy flow, the overal entropy still increases and the second law is not violated. That is a result independent of the kinetics of what drives the evolution.
Yes, yes, yes, Boltzmann's constant is involved in relating the density of states to the entropy which is in the Gibb's function which is in Gladyshev's article. If you still cannot understand how temperature and entropy apply not only to gases but also to solids and liquids, then we'll just have to stap this conversation. I've repeated it often enough and explained it thoroughly. Maybe one more hint since you seem to think only in terms of gases contained in a box. Perhaps you might think of each atom in a solid body, or a liquid systems, or the like, as being in a box by itself where the box is formed by the neighboring atoms in a nearly fixed fashion. Yes, it all has a temperature and its entropy is calculated through Boltzmann's constant.