American Scientific Affiliation

Open Forum Topic: American Journal of Physics posted on 1/24/12

http://www.youtube.com/watch?v=qKaF8vX6HXQ
On the website of the Skeptics Society, in a moderated blog topic (“Evolution and Religion”), I said Richard Dawkins was wrong when he said this:

When creationists say, as they frequently do, that the theory of evolution contradicts the Second Law of Thermodynamics, they are telling us no more than that they don’t understand the Second Law (we already knew that they don’t understand evolution). There is no contraction, because of the sun! (Richard Dawkins, The Greatest Show on Earth: The Evidence for Evolution, p. 415)

The Deputy Director of the National Center for Science Education, Glenn Branch, said that I was wrong and cited an article by Emory F. Bunn titled, “Evolution and the second law of thermodynamics,” published in American Journal of Physics [(2009) 77(10):922-925]. This article does indeed present calculations involving the sun showing that evolution does not violate the second law.

I think the American Journal of Physics erred in publishing this article it for two reasons.The first reason is that the insight evolution violates this law comes from biologists, and only biologists are qualified to discuss it competently. The second reason is that the author has an understanding of the second law that is different from my understanding of it. One of us must be wrong.

If a gas in a container is connected with a valve to a vacuum and the valve is opened, the gas will flow into the empty container. There is more knowledge of the location of the gas molecules in the small volume than in the large volume. There is an increase in disorder or a decrease in complexity. Entropy is another word for order. Entropy always decreases in nature, according to the second law.

If a gas in a container has a piston that can compress the gas, an animal can increase the complexity of the gas by pushing the piston. This does not violate the second law because the gas is not an isolated system. The idea that the complexity of the gas increases because the complexity of the animal decreases by a greater amount strikes me as being flat out wrong. The idea of calculating the decrease of the entropy of the animal and showing it is greater than the increase of the entropy of the gas strikes me as absurd. I don’t see any difference between such a calculation and the calculation offered by Emory F. Bunn.

Statistical mechanics explains why a gas will fill up a container. If a gas consists of N molecules, there are N! = N x (N – 1) x (N – 2)… possible ways the molecules can be distributed in the container. The chance of getting any particular distribution is 1 in N!. I don’t know how to complete the proof. But I know Maxwell’s distribution of velocities in a gas and the bell-shaped curve are derived using Stirling’s approximation: log N! = Nlog N.

The primary structure of a large protein can have 600 amino acids. There are 20 different kinds of amino acids. Biologists imagine that the 600 amino acids are non-interacting particles, just like in a gas. Just as in statistical mechanics, biologists ask how many different ways there are of arranging 600 amino acids? The answer is 600 to the 20th power instead of N!. Thus, it is impossible to get a protein by random chance since there is only 3 billion years available for the protein to evolve. This is why biologists say evolution violates the second law. It is the same kind of reasoning that explains why a gas will fill up the entire container.

Reply by Randy Isaac on 1/29/12
David, I think a few clarifications are in order. You said “Entropy always decreases in nature, according to the second law.” I think you mean “…always increases in a closed system…” Of course, in open systems with an energy flux, entropy can increase or decrease, according to the second law.

Also, you said “Entropy is another word for order.” Yes, the two are related but it isn’t always easy to quantify the two. Entropy is really defined by the number of possible states or configurations.

When you say “It is perfectly reasonable to say evolution violates the second law of thermodynamics because they both use probability calculations,” I would caution that they use probability very differently and it does not follow that evolution violates the second law. As Chuck rightly points out, no biologist I know thinks that. Probability calculations are useful in assessing various paths for natural processes but none that I know of says that evolution couldn’t have or didn’t happen.

Your comment that “…natural selection explains the increase in the complexity of life” isn’t quite complete. While the selection process is an important part, one must also include the source of variation, in which, usually through energy influx, there is replication with variation as the source of increased information and complexity, with selection as the vital feedback constraint. Rather than being pseudo-science, it’s a very successful and thriving area of science, seems to me.

Scot M. Sutherland says on 3/25/12: Perhaps you can see why I have not been labeled a humanist.
Yes, I can see why you are not labeled a humanist. However, that does not mean you are not a humanist as I understand the term. There are many people who don’t believe in the Westminister Confession, but they keep it to themselves and they give religion to their children. Such people are not humanists. When asked about their lack of faith they will say, “God hasn’t given me the gift of faith.”

A humanist thinks hoping for personal fulfillment based on human experience by being united with a transcendent reality after we die is irrational or unenlightened. In their view, rational people strive for “self-realization” and the welfare of their fellow man. Being a humanist doesn’t mean denying that God exists. This quote is from the humanist John Dewey:

The idea that “God” represents a unification of ideal values that is essentially imaginative in origin when the imagination supervenes in conduct is attended with verbal difficulties owing to our frequent use of the word “imagination” to denote fantasy and doubtful reality. But the reality of ideal ends as ideals is vouched for by their undeniable power in action.

These considerations may be applied to the idea of God, or, to avoid misleading conceptions, to the idea of the divine. The idea is, as I have said, one of ideal possibilities unified through imaginative realization and projection. But this idea of God, or of the divine, is also connected with all the natural forces and conditions—including human associations—that promote the growth of the ideal and that further its realization. We are in the presence neither of ideals completely embodied in existence nor yet of ideals that are mere rootless ideals, fantasies, utopias. For there are forces in nature and society that generate and support the ideals. They are further unified by the action that gives them coherence and solidarity. It is this active relation between ideal and actual to which I would give the name “God.” I would not insist that the name must be given. http://www.harvardsquarelibrary.org/philosophers/john_dewey.php

As you said, humans are superior to angels. But, not because we don’t have the duty to serve God in the hope of personal salvation. It is because humans possess sanctifying grace and angels don’t. My guess is that you try to disabuse people of this belief. To you, humans are superior to angels because we can serve our fellow man.

I think the Executive Council of American Association of Physics Teachers, who I have been contacting, is not taking responsibility for the pseudo-scientific articles because they are humanists. The articles were written with the goal of discrediting belief in Heaven and Hell. If the authors apologize and recant, that will promote religious faith. This will make the American Association of Physics Teachers very unpopular with their fellow humanists.

Reply by Randy Isaac on 3/27/12
David,The second law of thermodynamics is not limited to a gas of non-interacting particles. It is a much broader, all-encompassing law that applies to all physical systems. The law says, quite simply, that the Gibbs free energy is minimized in every event. That applies everywhere. In the general case, adding heat to a system may or may not decrease the entropy. For a non-interacting system of molecules, the entropy would increase but in the general case of more complex systems, it may lead to a lower entropy. The second law doesn’t preclude that.

As for probability, I think it is important to note that biologists do not calculate the probability of a protein in the manner you suggest. Proteins do not assemble that way. As in every complex multi-step chemical reaction, the detailed steps in formation of any molecule must be considered when assessing probabilities. We simply do not know all those steps adequately to be able to calculate any probability at all. We do know, however, that they are not assembled in one step of amino acids condensing into a chain, a la a deck of cards. Hence, the probability you suggest is not relevant.

You are right that in science we can do the study and analysis and usually determine what is the correct answer. Many scientists have considered this issue in detail and it is rather clear that evolution is not at all precluded by the second law of thermodynamics. Again, your extrapolation to the assessment of spiritual status is unwarranted and out of order, as well as inaccurate.
I said the second law does not apply to biological systems. I didn’t say it only applies to systems of non-interacting particles. This is the equation (see equation 3) in “Entropy and evolution” (AJPIAS_76_11_1031) I consider absurd:

Entropy of biological system = Boltzmann’s constant × thermodynamic probability

This is like saying: Temperature of a biological system = (3/2)Boltzmann’s constant × average kinetic energy of molecules.

A biological system doesn’t have a temperature. The only things that have temperatures are gases, liquids, and solids. Temperature is a macroscopic concept that we understand because of our sense of touch and because we can measure it with a thermometer. We can also measure the average kinetic energy of the molecules in a system and find out that the two are related by Boltzmann’s constant.

Let me try to explain it another way. The chance of shuffling a deck of cards and getting them back in the original order is 1/52! Does this mean the entropy of the deck of cards is Boltzmann’s constant divided by 52!?

The other unbelievably wacky thing about the article is the implication that adding heat to a system can decrease its entropy.

Biologists do probability calculations on sonnets to explain why natural selection can’t explain the evolution of the primary structure of a protein:

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)

Kirscher and Gerhart reduced the “millions of years” to a “short time” by taking into consideration natural selection and facilitated variation. However, they never told us how long it would take a computer to generate a sonnet. The reason is that nobody cares. Only laymen think that natural selection explains the complexity of life.

Reply by Randy on 4/13
David, I’m sorry for being slow to respond. I’m dealing with my brother’s terminal illness and it is very difficult.

But let me jump in here. You seem to think I’m being evasive, so let me be very very clear:

1. Equeation 3 in that article is precisely correct. It says that entropy is Boltzmann’s constant times the natural log of the number of microstates. That is in fact the definition of entropy and it certainly is not absurd.

2. ALL systems and ALL phenomena without exception follow the second law of thermodynamics, whether biological systems or systems of gases or whatever. There is no system of any kind to which the second law does not apply. And yes, all systems do have a temperature.

3. Adding energy to a system does generally increase the entropy, as the authors of that article actually do specify, but the second law doesn’t specify that–it specifies only that the Gibbs Free energy will decrease, where that energy includes the energy source. Normally the entropy does increase.

I hope that’s clear. The article is not deceptive and it is not wrong. Evolution does not in any way contradict the second law of thermodynamics. And no, biologists don’t calculate probabilities like that. Not at all.

I hope that wasn’t evasive.

Reply by Randy on 6/3/12
Dave, I’m sorry for the long delay. My brother has now gone on to be with the Lord and the memorial services and related activity are finally over. I’m slowly returning to something close to normalcy.

As for the Kirschner and Gerhart quote, I do not know them nor have I read the context of their work. But in any case, in science the validity of an assertion is not based on who says it but on the evidence supporting it. If they purport to be simulating evolution, then I would like to see the evidence for it. As far as I know, it does not simulate any evolutionary process advocated by virtually all biologists.

You make many assertions that I believe are false but it would take too long to address all of them. Let’s focus simply on the most basic one.s The equation to which you object is the fundamental definition of entropy and is known to apply to all systems, with no exception. The reason is not the use of probabilities by biologists, as you suggested. Rather, it is a fundamental aspect of physics which applies to every living cell and every Boeing 747. If you have some evidence why it should not apply, please provide it. The equation is not absurd in any sense that I know. The only retraction needed is not from AJP.

As for your assertion that natural selection does not explain common descent, I suppose it depends on how you are defining your terms. Common descent depends on both reproduction with variation and natural selection. With that clarification, the connection is rather clear.

I will not comment on your other two assertions about who said what or who is unethical. Let’s focus only on the ideas and the evidence and logic supporting them.

Reply by Randy Isaac on 6/5/12
Quotes aren’t helpful, Dave. Focus on the logic and rationale and evidence underlying the concepts.

ALL systems are thermodynamic systems, whether they be persons or trees or airplanes. I am having difficulty understanding why you would call such a statement absurd. Temperature has to do with the kinetic energy of the atoms in the system. That’s why it makes sense to apply to any system composed of atoms. If you are running a fever, all the atoms in your body will have a slightly elevated kinetic energy, varying somewhat according to their location, whether it be external or internal, etc. We can measure the temperature in all systems because kinetic energy of the atoms in the system will flow to a thermal sensor put in contact with it, bringing it to equilibrium.

Similarly, the second law of thermodynamics is universal, applying to ALL systems, without exception. And entropy, including its definition depending on the logarithm of the density of states, is a universal concept, applying to ALL systems.

And not a single one of the models that have independent probabilities of occurrence for each base pair or each amino acid, is a valid simulation of the process of evolution of a protein of any kind. I know you can find quotes for zillions of such claims, but they are all wrong. Why? Because no gene and no protein ever assembles in that manner nor is it proposed that they do so. Each one is an increment from a previous biochemical system. That’s what we see in every cell reproduction event and every organism reproduction and we extrapolate that back to a common ancestor, though we cannot do so in detail.
Temperature is macroscopic variable measured with a thermometer. A Boeing 747 in flight does not have a temperature. You can measure the temperature of different parts of the airplane, but there is no meaningful way to average out the temperatures to get a single temperature for a plane. Likewise, you can’t measure the temperature of a single fertilized egg of an animal. A fertilized egg has many more parts than a Boeing 747. The parts are so small that you can’t even measure the temperature of the different parts. If you put a tiny thermocouple into the egg, you are not measuring the temperature of a biological system. You are measuring the temperature of a bunch of chemicals.

A fertilized egg will develop into a multi-cellular animal, just as a biosphere of bacteria grew into a biosphere with animals. The idea of proving that the second law of thermodynamics is not violated in these two processes by attributing a temperature and entropy to these biological systems and by writing down equations using the Boltzmann constant is absurd.
The other absurd thing about the paper is that is says heat energy caused the entropy of the biosphere to decrease. When you add heat to a gas, the entropy of the gas increases. This is how the AJP paper puts it:
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.
If each of these organism were evolving at the rate assumed in Eq. (2), the change in entopy of the biosphere each second would be -302 J/K. In contrast we found earlier that a lower bound for the Earth’s entropy throughput each second is about 420 X 10(12) J/K. In other words, at a minimum the Earth is bathed in about one trillion times the amound of entropy flux requred to support the rate of evolution assumed here.
The model biologists use to understand the evolution of the primary structure of a protein is the English sonnet, just as the model physicists use for a gas is a deck of playing cards. This is the real connection between evolution and thermodynamics.
Because of this model, as well as the complexity of molecular machinery and genetic engineering, natural selection only explains the adaptation of species to the environment, not the increase in the complexity of life. I speak with more authority on this topic than most people because I can lawfully teach biology in New York State if there is no biology teacher available.

Reply by Randy Isaac on 6/5/12
It seems you are saying that a system cannot be a thermodynamic system if you cannot measure or somehow determine the average temperature of that system. But that’s not the criterion for being a thermodynamic system. All systems are thermodynamic systems both microscopically and macroscopically.

You state that “The idea of proving that the second law of thermodynamics is not violated in these two processes by attributing a temperature and entropy to these biological systems and by writing down equations using the Boltzmann constant is absurd.” It is a basic thermodynamic principle that temperature and entropy exist for all systems and that all systems obey the second law of thermodynamics. It does not matter whether or not you understand how to determine such a temperature–it does exist and can be shown both experimentally and theoretically. I’m at a loss to understand why you object to Boltzmann’s constant. Simply asserting that something is absurd is not sufficient. You do not have valid arguments for systems not having temperature or entropy.

Then you state “The model biologists use to understand the evolution of the primary structure of a protein is the English sonnet,” No, they do not. I have only seen anti-evolutionists use such a model when they attempt to show evolution didn’t happen. Of course it didn’t happen in that way. But no evolutionist suggests it either. This is an unrealistic scenario and is meaningless.

In science, authority is of little value. It all rests on the evidence and the logic underlying the assertions. Authorities can simply be authoritatively dead-wrong.
For a gas, there is a temperature and an entropy variable related to the average kinetic energy and the thermodynamic probability via the Boltzmann constant.

 For a deck of playing cards there is no thermodynamic probability because there is no temperature and no thermodynamic system. The probability of shuffling a deck of cards and getting them in factory order is 1/52! It makes no sense to say the entropy of a deck of cards when it comes from the factory is S = k log 1/52! I don’t see any difference between this absurd equation and equation (4b): S = k log 10 (-3).
The theory of evolution was invented to explain the existence of fossils, and a considerable amount of evidence supports this theory. This gives rise to the question of what caused life to evolve from bacteria to mammals in 3 billion years. The only theory that explains this is intelligent design (ID), but there is no evidence for ID. To make this theory look better, advocates of ID compare it with the theory of natural selection. Natural selection is supported by the evidence, but only explains the adaptation of species to the environment, not the increase in the complexity of life. Atheists go along with this misinformation because they don’t want to admit that there is no scientific explanation for evolution at the present time.
My guess is that you did not get your ideas about evolutionary biology from textbooks, peer-reviewed articles, and scholarly works, but from reading popular literature. I suggest that you discuss the matter with a biology professor and watch my video titled “The Truth About Evolution and Religion” (http://www.youtube.com/watch?v=qKaF8vX6HXQ).

Reply by David Roemer on 6/6/12 @Jim Bandstra
I thought of another way of explaining why equation 4(b) in “Entropy and evolution”  is absurd. Suppose you have a big box filled with ping pong balls. If you shake the box up, the balls will bounce around inside the box like the molecules in a gas. Does it make sense to use the equation: KE = 3/2 kT to determine the temperature of the box of ping pong balls?

The answer is no. The reason is that a box of ping pong balls does not have a temperature. A box of ping pong balls is not a thermodynamic system. The only thing that has a temperature is the plastic the ping pong balls are made of.

The suggestion that I am not thinking intelligently because of anxiety over religion is very pertinent to this discussion. Inhibition is a defense mechanism for anxiety and people can be inhibited from thinking intelligently when it comes to religion. This quote is from a famous psychoanalyst:

Let us consider for example, a person listening to a paper and having critical thoughts about it. A minor inhibition would consist in a timidity about expressing the criticism; a strong inhibition would prevent him from organizing his thoughts, with the result that they would occur to him only after the discussion was over, or the next morning. But the inhibition may go so far as not to permit the critical thoughts to come up at all, and in this case, assuming that he really feels critical, he will be inclined to accept blindly what has been said or even to admire it; and he will be quite unaware of having any inhibitions. In other words, if an inhibition goes so far as to check wished or impulses there can be no awareness of its existence. (The Neurotic Personality of Our Time, Karen Horney, M.D., New York: Norton, 1937, p. 55 )”

I am not an advocate of intelligent design. I do not think the Big Bang, the origin of life, or evolution is evidence of God’s existence. We know God exists because we have free will. Free will means we possess a center of action that makes us unified with respect to ourselves and different from other humans. Hence, we are finite beings and an infinite being exists. In the west, we call the infinite being God.

The Big Bang, the origin of life, and evolution, however, is evidence that God has communicated Himself to mankind because the Bible says God created the universe from nothing.

An example of irrational thinking is the theory that free will is an illusion. Many atheists believe this theory even though there is very little evidence supporting it. Atheists don’t even realize it is a theory. Atheists can’t even grasp the idea that humans are embodied spirits. The only concepts atheists grasp concerning the human mind is dualism and materialism.

This is why Randy Isaac is so misinformed about evolutionary biology. He gets his information from listening to atheists and advocates of intelligent design shouting at each other.

Reply by Randy Isaac says 6/6/12
Boltzmann’s constant is the proportionality between energy and temperature. It is the proportionality factor between entropy and the density of states.
This is true only for a thermodynamic system. A box of ping pong balls, a living organism, and a Boeing 747 is not a thermodynamic system.

If you shake a box of ping pong balls really hard, the average kinetic energy of each ball will be less than 1 joule. If the equation KE = 3/2 kT is applicable, the temperature of the ping pong balls will be about 10,000,000,000,000,000,000,000 degrees. This makes no sense. Equation 5, which says that the change in entropy of the biosphere each second is 302 J/K, is just as absurd.

Reply by Randy Isaac on 6/10/12
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) I don’t see the relevance of the Gibbs free energy to this topic. That variable just takes into consideration a system with chemical reactions.The second law does not say that entropy must always increase. An example of entropy decreasing is when hydrogen molecules under the force of gravity come together to form a star. I know that it is frequently said that when the entropy of a system decreases there is a greater increase in the entropy of the environment. However, I don’t understand this at all. All I understand is the thermodynamics and statistical mechanics of an isolated gas. In a gas, the molecules will fill up the entire container because that is the most probable distribution. The density of the gas is uniform except for small fluctuations over small periods of time. To calculate those fluctuations and time intervals, physicists assign a label to each atom: No. 1, No. 2, etc. In other words, the model of a gas is a deck of playing cards. The model Krischner and Gerhart use for a protein is an English sonnet.

2) The kinetic energy or vibrational energy of molecules is not relevant either. Kinetic energy is a microscopic variable and temperature is a macroscopic variable.
3) It most certainly is necessary to bring biologists into this disagreement between you and me about whether the AJP should retract the article by Daniel Styer. The article is about evolutionary biology and creationism, not physics. The editor of the AJP, David Jackson, should have referred my comments to Styer for rebuttal. If Styer told me that a fertilized egg had a temperature, I could write to the college he works for and explain that he is not qualified to teach physics.
Instead of doing this, Jackson, with the approval of the American Association of Physics Teachers, told me to submit my own article. An anonymous reviewer said I was mistaken, just like you. The AJP and the AAPT are using this review to justify not publishing the retraction. The leaders at the American Institute of Physics and the American Association for the Advancement of Science are also not taking responsibility. The only organization taking responsibility for the article is the American Scientific Affiliation through you and all the members who are not supporting my efforts to get the AJP to retract the article. My correspondence with the AIP and AAAS as well as with the AJP and AAPT and an expert on thermodynamics at New York University is here:
http://newevangelist.me/2012/02/22/physics-department-of-new-york-university/
http://newevangelist.me/2012/02/02/american-journal-of-physics/
http://newevangelist.me/2012/02/23/american-association-of-physics-teachers/
http://newevangelist.me/2012/05/06/american-institute-of-physics/

Reply by Randy Isaac on 6/13
David, 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 think I understand the Gladyshev article well enough to realize that it supports the Styer article in only one respect. He states on page 57,

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.

This is what Styer is implying: Heat flows into and out of of Earth is what caused the biosphere to become more complex. This is absurd for two reasons: 1) We don’t know what caused the biosphere to increase in complexity during evolution. 2) Natural selection only explains how species adapt to the environment, not how mammals evolved from bacteria in 3 billion years.

Creationism is irrational, but the idea that the sun caused evolution is downright stupid.

The article does not support the absurd equation in Styer for the entropy of the biosphere: S = 9.53 X 10 (-23) J/K (4c). What is absurd is not the estimate of the probabilities, but the use of the Boltzmann constant, instead of 1 J/K, to calculate the entropy. The Gladyshev article doesn’t say anything about the Gibbs function for an organism. It speaks only about subsystems within an organism. In an earlier article (“On the Thermodynamics of Biological Evolution”, J. theor. Biol. (1978) 75, 425-441), Gladyshev has the equation G = sum of G(i). A biological system contains chemical reactions and if you have enough subsystems you can meaningfully talk about the Gibbs function of those subsystems, I suppose. But nowhere in the article does Gladyshev use the Boltzmann constant to calculate the Gibbs function or the entropy of a subsystem or the organism as a whole.

Reply by Randy Isaac on 6/14/12
David, 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.

Reply by David Roemer on 6/15/12
I agree that there is no point in discussing thermodynamics any further. As I said to the editor of the American Journal of Physics, it should be possible for two PhDs in physics to come to an understanding of what the second law of thermodynamics means, but apparently not.

That leaves open only the question of whether natural selection explains the complexity of life. The only theory that explains the complexity of life is the theory of intelligent design, but atheists don’t like to admit this. What is wrong with the theory of intelligent design is that there is no evidence for it. There is no evidence that living organisms are “irreducibly complex.” ID is just a bright idea.

The following quote is from a PhD in linguistics, not biology. Pinker is Steven Pinker who has a PhD in linguistics and Bloom is Paul Bloom who has a PhD in psychology. What we have in this quote is three laymen disagreeing with the expert, Charles Darwin:

They [Pinker and Bloom] particularly emphasized that language is incredibly complex, as Chomsky had been saying for decades. Indeed, it was the enormous complexity of language that made is hard to imagine not merely how it had evolved but that it had evolved at all.

But, continued Pinker and Bloom, complexity is not a problem for evolution. Consider the eye. The little organ is composed of many specialized parts, each delicately calibrated to perform its role in conjunction with the others. It includes the cornea,…Even Darwin said that it was hard to image how the eye could have evolved.

And yet, he explained, it did evolve, and the only possible way is through natural selection—the inestimable back-and-forth of random genetic mutation with small effects…Over the eons, those small changes accreted and eventually resulted in the eye as we know it. (Christine Kenneally, The First Word: The Search for the Origins of Language, pp. 59–60)

Reply by Randy Isaac on 6/15/12
David, Perhaps an analogy will help illustrate why your critique of Styer misses the mark. Suppose Alice and Bob are discussing an ice maker.

Bob: When ice freezes, the entropy decreases. Therefore it violates the second law of theromdynamics.

Alice: No, it doesn’t! The ice maker works by plugging it into the electrical outlet and the power from the electric power source provides more entropy than the water/ice system loses, so the second law of thermodynamics is preserved.

Bob: FOUL! You just said that energy from the electric power source causes a decrease in entropy of the ice which is absurd.

Alice: Of course not! The electrical power runs the motor which runs the compressor which transfers the heat from the water to the environment.

 In that analogy, Bob made exactly the same mistake you’ve made. Styer’s argument is just like Alice’s–looking at the thermodynamics of the entire system, not needing to comment on the kinetics of the compressor and pump that transfer the entropy from the water to the environment. Similarly, Styer didn’t need to deal with the kinetics of how the entropy is transferred, only that the total entropy flow is consistent with the second law. Gladysheve rightly articulates the distinction between theromdynamics and kinetics.
I don’t understand why the decrease in the entropy of a system has to be accompanied by a greater increase in the entropy of the environment. When hydrogen atoms come together under the force of gravity to form a star, the entropy of the hydrogen gas decreases without any increase in the entropy of the environment.

The way I understand the idea of Styer and Gladyshev about entropy and evolution is this. There is a sense in which evolution does violate the second law of thermodynamics rooted in the lack of understanding of what caused the complexity of life to increase. Fighting creationists and advocates of intelligent design, atheists cry out in a panic: “The second law about complexity always decreasing only applies to a closed system. The earth is not a closed system because of the sun. The second law of thermodynamics is not violated.”

Reply by Randy Isaac on 6/15/12
The entropy of a star does increase. It heats up, doesn’t it? The second law does state the entropy will increase in a closed system and indeed that has never been violated to our knowledge.

Your characterization of anyone (and it’s not just atheists but also Christians who understand science) responding in panic is rather far off the mark. The response is usually one of exasperation towards people who ought to know better but keep insisting wrongly that evolution violates the second law of thermodynamics. It doesn’t at any level of the hierarchy, as Gladyshev rightly points out. In every case, those who argue that evolution violates the second law have in some way misunderstood or misstated thermodynamic principles.

You in particular failed to see that the basic concepts of temperature and entropy apply to more than gases but also to solids and liquids and biological systems. And you wrongly accused Styer of claiming the sun’s heat was a mechanistic cause of the reduction of entropy in evolution.
I don’t think hydrogen atoms spread far apart in outer space is a gas. You can calculate the averages kinetic energy of each atom, but to convert the KE to a temperature with the Boltzmann constant doesn’t make sense to me because you can’t measure the temperature of such a rarefied gas with a thermometer.

As the gas atoms come closer together, the volume occupied by the atoms decreases. I suppose there comes a point in the evolution of a star when it becomes meaningful to say it has a temperature. However, long before that point, the complexity of the system has decreased because there is more knowledge about the location of the gas atoms. Likewise, the increase in the complexity of life during evolution does not violate the second law of thermodynamics. It does not violate the second law because the second law is absolutely true. Creationists show bad judgment on this point. The idea that evolution does not violate the second law because the earth is not a closed system strikes me as being absurd.
We should get off the topic of thermodynamics and focus on the question of whether natural selection acting upon innovations explains the complexity of life. Thermodynamics is getting us nowhere. By discussing evolutionary biology, we can get the input of biologists who should understand the limits of natural selection.
Reply by Randy Isaac on 6/15/12
I’m sorry. I thought you understood at least atoms and gases in a thermodynamic sense but I was mistaken. I think at this point I will advise you to continue your discussion with a different group.
Reply by David Roemer on 6/16/12
I am a Catholic and think that creationism and intelligent design are irrational. Darwinism, the idea that humans evolved from animals, is pseudoscience because only the bodies of humans evolved from animals, not their souls. Intelligent atheists think the human soul is just an idea, but rational people know that the human soul is spiritual. Less intelligent atheists think the human soul is spiritual by definition.

An example of pseudoscience promoted by atheists and Protestants is that natural selection explains common descent. Natural selection only explains how giraffes got long necks, not how giraffes evolved from bacteria in 3.5 billion years.

I’v been trying to explain this to Randy Isaac on the Open Forum by quoting from peer-reviewed articles and scholarly works. Randy’s responses are inane. No member of the ASA is supporting me in my efforts to get the AJP to retract its absurd article titled “Entropy and evolution.” You are the first ASA member that seems to be a real Christian, not a liberal Christian. Real Christians believe in Heaven and Hell.

I just started reading Biology’s First Law: The Tendency for Diversity and Complexity to Increase in Evolutionary Systems whose co-author Daniel W. McShae is an associate professor of biology at Duke University. He is not an advocate of intelligent design. What follows is the opening paragraph of the book. I was happy to find it because it gives me another quote to throw into the face of people who believe in evolution instead of believing in the Bible.

The history of life presents three great sources of wonder. One is adaptation, the marvelous fit between organism and environment. The other two are diversity and complexity, the huge variety of living forms today and the enormous complexity of their internal structure. Natural selection explains adaptation. But what explains diversity and complexity?

My YouTube video titled, “The Truth About Evolution and Religion” is at http://www.youtube.com/watch?v=qKaF8vX6HXQ.

Email exchanges starting on 6/4/2012 with Charles Kankelborg. Subject: Pseudoscience in the American Journal of Physics
Dear Dr. Kankelborg,
I started a topic on the open forum of the ASA about the attached article. The article uses a fake equation to prove evolution does not violate the second law of thermodynamics. I am trying to get the AJP to retract the article.

Scientists invented the theory of evolution to explain the existence of fossils, and a considerable amount of evidence supports this theory. This gives rise to the question of what caused life to evolve from bacteria to mammals in 3 billion years. The only theory that explains this is intelligent design (ID), but there is no evidence for ID. To make this theory look better, advocates of ID compare it with the theory of natural selection. Natural selection is supported by the evidence, but only explains the adaptation of species to the environment, not the increase in the complexity of life. Atheists go along with this misinformation because they don’t want to admit that there is no scientific explanation for evolution at the present time. Saying evolution does not violate the second law of thermodynamics is way of promoting this scam.

My correspondence with physicists about this issue is at

http://newevangelist.me/2012/02/22/physics-department-of-new-york-university/

http://newevangelist.me/2012/02/02/american-journal-of-physics/

http://newevangelist.me/2012/02/23/american-association-of-physics-teachers/

See also my explanation at

http://www.catholictruthscotland.com/MAYnewsletter12.pdf

Dear Mr. Roemer,
At your request, I have reviewed some of your correspondence, including that with AJP editor David Jackson, regarding the AJP article on the thermodynamics of evolution. The equation S = k log(Omega), which you question in correspondence with Prof. Richardson, is foundational to statistical mechanics and is a totally appropriate tool for evaluating the entropy of a complex physical system, including any biological system. Every good statistical mechanics textbook (Reif, Huang, etc.) develops this equation and some of its applications in detail. The quotations you have extracted from other literature (Kirschner & Gerhart, Kenneally) to support your point appear to be addressing unrelated topics, and serve only to cloud the issue.

You have questioned the use of the Boltzmann constant in calculating the entropy from the configuration of a biological system, but it is required in the equation for the units to work out. If k is omitted, you don’t have an entropy in the thermodynamic sense, dS = dQ/T. To perform a valid computation of thermodynamic entropy based on configuration of playing cards, dice, amino acids, atoms, or any other physical objects, you need the k.

Regarding the AJP article, it is a straightforward exercise that I would expect students of our undergraduate thermo course to understand well enough to repeat the calculations for themselves. This exercise shows clearly that evolution, including the growing complexity of life since the time of its origin on Earth, does not violate the second law of thermodynamics. There is no pseudoscience here, and in fact there is nothing surprising. Thermodynamically, the increase in biological organization represented by the development of life on Earth, from zero to all of today’s biological diversity, is recapitulated in every generation as DNA is copied and cells multiply and whole new organisms are born. But the entropy decrease entailed by this growth, which is much more rapid than that due to evolution, still does not violate the second law. The net entropy introduced to the universe by absorption of sunlight and subsequent infrared radiation from Earth is more than sufficient to satisfy the second law, so that the entropy of the universe increases monotonically.

As the AJP article points out, the second law of thermodynamics permits but does not require evolution. If you are committed to the proposition that belief in macroevolution and Christian faith cannot coexist (I do not share this opinion with you, but Richard Dawkins does), the 2nd law is of no help to your quest. You are barking up the wrong tree.

Finally, As a brother in Christ, I ask you to consider more carefully the statements you make in public. You have played into a trap set by Richard Dawkins and other prominent atheists who have mounted an attack on Christian faith by making unwarranted extrapolations from science. I think we can both agree that Dawkins, PZ Myers, and others like them are trading on their scientific credentials to paint Christianity and the bible as anti-intellectual. Your persistent, public, and unjustified criticism of the AJP article, and of the journal editor who indulged you by sending out your own article for peer review, tends to confirm this atheist slur in the eyes of scientifically educated people who do not know Jesus. You have followed up with harrassment of AIP and AAPT officials, and have questioned their professional integrity even while they acted appropriately in the sight of the whole world. This is amply documented on your own blog. The people you have treated in this manner were made in the image of God. Please, please apologize to them.

Dear Dr. Kankelborg,
I interpreted Dr. Richardson’s email to me as confirmation that the equation: S = k log(Omega) only applies to thermodynamic systems. It does not apply to biological systems. I suppose it makes sense to say the entropy of an un-shuffled deck of playing cards is log (1/52!)joules/degree. But I think it is nonsense to say the entropy is k log (1/52!). A deck of playing cards, a Boeing 747, and a seed planted in the ground don’t have a temperature or an entropy.

You are the second person who has staked his professional reputation on the AJP article by saying the article is okay. The first was Randall Isaac who responded to my topic on the ASA forum. Emory Bunn, the author of a note that improved on the calculations in the Daniel Styer article, said that he didn’t have the time to discuss the matter. Randall promised to “walk me through it,” but never did.

The editor, David Jackson, should have referred my criticism to Styer, who wrote the article. Styer has a reputation to protect and a conscience to follow. Instead, Jackson told me to submit an alternative article. I protested to the AAPT, but submitted an article anyway. The anonymous reviewer said that I didn’t know what I’m talking about. The AJP is using this anonymous review to justify not printing a retraction.

As I said to Emory Bunn, it should be possible for two PhDs in physics to come to an agreement about the second law of thermodynamics. I have ter Haar’s “Elements of Statistical Mechanics,” Zemansk’s Heat and Thermodynamics, and an advanced book by Huang.

I do not believe in intelligent design or creationism. I know perfectly well that evolution does not violate the second law of thermodynamics. What I am going to do is restate my explanation of why the article should be retracted on the ASA forum. I will address any comments or criticism of my reasoning, as I always have. If you have a better suggestion for determining who is right or wrong about evolution and entropy, I would like to hear it.

Dear David,
Dr. Richardson’s email is correct “if you use the right units”, which would mean measuring temperature in energy units. Some texts do that, because it is more natural for statistical mechanics. In that case, k=1. That does not change the result of the calculation, only the units. A biological system is a thermodynamic system. So it is quite correct to give the entropy of, say, a protein or a genome or a deck of cards in joules/K.

In the article you sent to David Jackson, you say “It is equally irrational to try to prove evolution doesn’t violate the second law by performing entropy calculations on living organisms. It is like calculating the entropy of a deck of playing cards with Boltzmann’s constant. A deck of playing cards has neither entropy nor temperature.” This makes no sense to me as a physicist. It seems perfectly natural to test the second law against any observed process, in biology or otherwise. First, it is perfectly reasonable to calculate entropy for a living organism (or, in this case, for a subset of that organism as represented by information carried in its DNA or protein sequences). Likewise for a deck of cards. This does not depend on evaluating the temperature of such a thing. Temperature is only well defined when something is in  thermodynamic equilibrium, but entropy can be calculated in a broader range of circumstances. The second law also applies to non-equilibrium systems (if it did not, then we wouldn’t talk of applying it to the universe as a whole, which is clearly far from equilibrium). So, what is wrong with the AJP paper?

I think that Jackson acted properly. I don’t think he is required to contact his authors in response to non-peer-reviewed criticism (but how do you know that Jackson did not contact Styer? And why should Styer respond?) So far as I can tell, you didn’t provide any evidence that there was something wrong with the article. Jackson went the extra mile and lined up a reviewer for your article, and so you have yet another opinion from another physicist that weighs against your arguments.

Dear Charles,
I don’t understand why the difference in the entropy of an organism over a hundred year period is 9.53 X 10 (-23) J/K (Equation # 4c).

I don’t understand why a biological system is a thermodynamic system. Is a Boeing 747 a thermodynamic system? Is a deck of cards a thermodynamic system? A thermodynamic system has a temperature. Since it has a temperature and heat can enter or leave the system, it has entropy. Talking about the entropy or temperature of a deck of playing cards or a biological system makes no sense to me, as a PhD in physics. Your telling me it makes sense to you doesn’t help me at all.

If one insists on calculating the entropy change of the organism, I would say the entropy change was log 10 (-3) J/K = -6.91 J/K not 9.53 X 10 (-23) J/K.

By the way, Stephen M. Barr, who is Roman Catholic physicist and prominent enough to be in Wikipedia, said I was wrong. He claims to have read my article in the Catholic Truth, but he did not address my arguments and explanations. He associates anti-evolutionism with Protestants and tarred me with those two brushes.

David Jackson is certainly guilty of wrong doing if I am right. The article may have been written in good faith, but now that I have told them about the error they should correct it. If I am wrong, Professor Richardson should have explained it to me. I got my PhD at NYU and Richardson was recommended to my by a personal friend of both of us. His behavior towards me was rude and uncharitable. I consider this evidence that when religion is involved people lose their ability to behave properly and think reasonably.

I’v attached two articles about evolution and entropy, one of which was published. The other was accepted for publication by Applied Mathematics Letters, but they changed their mind.

Hello again David,

On 2012 Jun 04, , at 5:54 PM, David Roemer wrote:

I don’t understand why the difference in the entropy of an organism over a hundred year period is 9.53 X 10 (-23) J/K (Equation # 4c).

I think the authors explained their assumptions fairly clearly. A bit arbitrary, but they are trying to make conservative estimates. It is in the spirit of a Fermi calculation.

I don’t understand why a biological system is a thermodynamic system. Is a Boeing 747 a thermodynamic system?

Certainly.

Is a deck of cards a thermodynamic system?

Yes.

A thermodynamic system has a temperature.

Not true in general. The next level of complexity is a thermodynamic system that has several components of differing temperatures. Most stat mech books stop there. But there are also thermodynamic systems that, in a more fundamental sense, do not have a well-defined temperature. An example from my own field would be the upper solar corona, which has an anisotropic and non-maxwellian distribution of velocities. Equipartition is broken in the corona because of waves that preferentially add kinetic energy to certain ions in the directions perpendicular to the magnetic field. Actually, we can treat it pretty well by associating temperatures with the various pieces and parts. For example, the “perpendicular temperature” of a given ion will differ from its “parallel temperature”, and the temperatures of the various ionic species are different from one another and from the electron temperature, which itself is a bit goofy because the electron distribution is non-maxwellian (there are fat, nonthermal tails in the velocity distro). Nevertheless, we can talk about equivalent microstates in the same way you would for an ideal gas. It’s just a little messier. And so the entropy such a system can be discussed in a sensible way. Because equipartition is broken in a systematic way, the entropy is lower, for example, than the entropy of a plasma without these strange anisotropic and species-dependent effects. Sorry, that was a bit of a tangent. But there’s an extensive and rapidly literature out there on nonequilibrium thermo; I would confess to knowing only a tiny bit of it.

Since it has a temperature and heat can enter or leave the system, it has entropy. Talking about the entropy or temperature of a deck of playing cards or a biological system makes no sense to me, as a PhD in physics. Your telling me it makes sense to you doesn’t help me at all.

For thermodynamic systems with definite temperature, you can calculate changes in entropy of dS = dQ/T. That’s handy for lots of things, but it’s not the most fundamental definition available. The configuration-based definitions (Huang, eqs. 6.27-29) are more fundamental. Of course, in that context Huang is trying to rederive classical equilibrium thermo.

If one insists on calculating the entropy change of the organism, I would say the entropy change was log 10 (-3) J/K = -6.91 J/K not 9.53 X 10 (-23) J/K.

Sorry, I am not following your numbers. Why would you say that?

By the way, Stephen M. Barr, who is Roman Catholic physicist and prominent enough to be in Wikipedia, said I was wrong. He claims to have read my article in the Catholic Truth, but he did not address my arguments and explanations. He associates anti-evolutionism with Protestants and tarred me with those two brushes.

David Jackson is certainly guilty of wrong doing if I am right. The article may have been written in good faith, but now that I have told them about the error they should correct it. If I am wrong, Professor Richardson should have explained it to me. I got my PhD at NYU and Richardson was recommended to my by a personal friend of both of us. My thesis advisor is still there. His behavior towards me was rude and uncharitable. I consider this evidence that when religion is involved people lose their ability to behave properly and think reasonably.

Well, neither Barr, nor Jackson, nor Richardson, nor even your advisor at NYU has a moral obligation to take to explain why you are wrong. They are certainly not obliged to explain it to your satisfaction. Calling them uncharitable really does not help matters. I am attempting to sort through your arguments in my poor way, but my resources (in terms of time, at least) are limited.

I’v attached two articles about evolution and entropy, one of which was published. The other was accepted for publication by Applied Mathematics Letters, but they changed their mind.

I can’t do justice to these articles. The Sewell article looks pretty suspicious. I haven’t verified his equations (though I’d like to come back to them at some point), but sections 3-4 seem to diverge from the mathematical treatment and deal in rather vague generalities. That’s too bad, because he could have applied his equations to the Earth and evolution in particular. I would note that, at least at a conceptual level (with a more standard treatment), the AJP letter did address Sewell’s conceptual point: It is not merely that the entropy of the overall system has increased, but that there is a demonstrated coupling between earth and its environs that is used to derive that increase. So they are not guilty of the superficiality Sewell seems to be talking about.

David, I have to focus on some thing over the next couple weeks (am headed to a conference and need to finish my talk!). If you are still wanting to talk about these things, could you contact me again after June 20?

Email from Robert Kaita on 7/19/12. Subject: Clarification on Publications and Directory Use

Dear Dr. Roemer: It has been called to my attention that you have been asking the American Scientific Affiliation (ASA) for support in getting the American Journal of Physics (AJP) to retract an article entitled “Entropy and Evolution.” First, retractions are the prerogative of the authors, and not the journal or any readers who might disagree with them. The authors must themselves conclude that what they have published is invalid. For those who are not authors but disagree with their results, the standard procedure is for them to publish an article that explains why. We recommend that you submit an article to the AJP or other journal, so that both positions become part of the record that enables readers to compare the merits of the opposing views. Second, the membership directory of the ASA is meant for ASA activities only, and for private individual member use for ASA networking. It is not intended to be a means for solicitations of any kind. This includes support for a particular cause, so we respectfully ask that you refrain from using it in this way. We appreciate your passion, and hope that you can use the various forums and other means that are available to express it.

Sincerely,
Robert Kaita, Ph. D.
President, ASA
Dear Dr. Kaita,
An organization called The Catholic Truth of Scotland endorsed my cause of getting the “Entropy and evolution” article retracted. A Word version of the published letter explaining why the article is wrong is attached. Retractions of peer-reviewed papers by scientific journals are common when there is fraud or wrong doing involved in the writing of the article. Such is the case with this article.

The paper may have been written and published in good faith. There is a lot of similar nonsense about entropy and evolution in the literature. The source of this nonsense is the idea that evolution violates the second law of thermodynamics and the idea that it does not violate the second law of thermodynamics because of the sun. What makes this article egregious is that it actually writes down an incorrect equation (4c) proving that the second law is not violated by evolution.

This article promotes the misinformation that natural selection explains the complexity of life. Natural selection only explains how giraffes got long necks, not how giraffes evolved from bacteria in 3.5 billion years. Like the Big Bang, and the origin of life, this is a reason to believe in the Bible because the Bible says God created the universe from nothing. The Big Bang, etc., is a sign that God inspired the human authors of the Bible.

I submitted documentation explaining this to the American Journal of Physics (AJP). They should have referred the matter to the author for rebuttal. The author has a reputation to protect and a conscience to follow. Instead, the AJP gave the documents to an anonymous reviewer who said I was wrong. The AJP is using this anonymous review to justify not printing a retraction.

What I suggest is that you initiate a moderated discussion about the article on the Open Forum. I will explain why I think the article is absurd step by step. A moderator will make sure all comments are relevant and reasonable. As I said to the editor of the AJP, two PhDs in physics should be able to come to an agreement about what the second law of thermodynamics says and doesn’t say.

I’v also attached two peer-reviewed articles that discuss entropy and evolution rationally. There are a lot of quotes and arguments about the article on the Open Forum of the ASA.

The following are links to my correspondence with physicists about the article:

http://newevangelist.me/2012/02/22/physics-department-of-new-york-university/

http://newevangelist.me/2012/02/02/american-journal-of-physics/

http://newevangelist.me/2012/02/23/american-association-of-physics-teachers/

http://newevangelist.me/2012/05/06/american-institute-of-physics/

My YouTube video titled “The Truth About Evolution and Religion” (http://www.youtube.com/watch?v=qKaF8vX6HXQ) also sheds light on this issue.

This is the link to my letter to The Catholic Truth of Scotland:

http://www.catholictruthscotland.com/MAYnewsletter12.pdf

Email to Emily Bunnel on 6/22/12. Subject: God and Nature Submission
What do you think of the article apart from its suitability for the ASA? It is no small thing when a peer-reviewed journal publishes nonsense with religious overtones and implications.

 I’v been trying to explain why the article should be retracted on the Open Forum of the ASA, but Randy Isaac is swearing up and down that I am wrong. His comments are inane and non-responsive.
I think I found some support from Robert Kaita. He sent me an email advising me not to use the ASA membership information for inappropriate reasons. But when I explained to him why the article was absurd, he asked for more time to consider the matter. He will be on vacation until July 2.
My request is that he assign a moderator to conduct the discussion on the Open Forum. I will explain why the AJP article is absurd step-by-step to scientists who don’t understand evolutionary biology and thermodynamics. A good idea would be to invite the author of the article and the AJP  to defend their refusal to publish a retraction. They have not defended themselves so far in an honest manner.  If they do attempt a defense, it will just be dirty work, unless I am mistaken. They are using people like Randy Isaac and the ASA to do their dirty work for them.
Message to Dr David R Bowman on 7/2/12
What is egregiously absurd and is an outright mistake is equation 4b. The nonsense starts when Styer states that the “statistical definition of entropy” is S = k log Omega. This applies only for thermodynamic systems, like a gas. For non-thermodynamic systems, like a deck of playing cards, this equation should be S = log Omega, without the Boltzmann constant. This equation is called the Shannon equation, I believe, and plays a role in information theory. Just because you have a probability estimate doesn’t mean you can convert it to joules per degree using 1.38 X 10 (-23).

The second absurdity is not so bad that the article should be retracted. It is a common error found in many articles and books. This is the idea that evolution does not violate the second law of thermodynamics because the earth is not a closed system. The scientifically informed reason is that the second law only applies to non-interacting particles. Hydrogen gas in outer space, for example, forms stars. A gas does not always fill up the entire container it is in.

For the purpose of understanding evolution, the earth is a closed system. It is true that the sun is bathing it with energy, but heat energy tends to increase disorder, as when ice melts. Heat causes entropy to increase. I’v attached an article published in Physics Today which makes this mistake. However, the article doesn’t attempt to calculate the entropy of the biosphere using the Boltzmann constant. In fact the paper says:

“The probability that at ordinary temperatures a macroscopic number of molecules is assembled to give rise to the highly ordered structures and to the coordinated functions characterizing living organisms is vanishingly small.”

Email to Istvan Kolossvary on 7/3/12. Subject: Pseudoscience in the American Journal of Physics
Dear Istvan,

I am very happy to get your supportive letter.

1) In my opinion, saying that evolution is guided by God’s providence is an injudicious presentation of doctrine (Matthew 7:6—cast not your pearls before swine). Atheists and Protestants think the Big Bang, the origin of life, and evolution are evidence that God exists. They also do not understand that humans are embodied spirits. The only mind-body theories they grasp are dualism and materialism. I consider the Big Bang evidence that God does not exist. These phenomena, however, are evidence that God inspired the human authors of the Bible. According to John 1: 1, God created the universe from nothing. The Big Bang and evolution are a sign or a reason to believe in revelation.

2) I am aware of the fact that thermodynamic textbooks say that entropy always increases. This is related, I believe, to the idea that natural processes are always irreversible. However, I recall reading that there is or was some controversy over whether biological processes are irreversible. In any case, I don’t understand this. All I understand is that in the free expansion of a gas entropy increases. When a gas is compressed and heat is extracted, the entropy of the gas decreases.

3) An important book for me is Bernard Lonergan’s Insight. He explains that the human mind is structured like the scientific method. The lowest level is observations, which requires paying attention. At the next level humans ask questions about what they observe. They want to know the cause of things, the relationship between things, and the unity between things. This is the level of inquiry and requires intelligence. Extremely intelligent people invent answers or theories. This brings us to the level of reflective judgment where humans marshal the evidence and decide whether a theory is true or probable. This requires being rational. The fourth level is deciding what to do with our bodies. This requires being responsible. In other words, humans are attentive, intelligent, rational, and responsible animals. None of these adjectives can be defined or explicated. This is one of the reasons there is no evidence supporting the theory of intelligent design.

Email to Robert Kaita on July 6, 2012. Subject: PSCF submission.
Dear Dr. Kaita,

I’v attached an article titled “Evolution and the culture war” for publication in the PSCF. It is a retreatment of an article published in the Catholic Truth of Scotland and a review of Biology’s First Law: The Tendency for Diversity and Complexity to Increase in Evolutionary Systems on Amazon.com.

I sent those two prior articles to James Peterson, editor of the PSCF. His response was that the PSCF doesn’t publish things that have already been published.

I think you should know that I got an email from ASA member Istvan Kolossvary (istvan@kolossvary.hu). His line of research has to do with “entropy, free energy and proteins.” Also, he is writing a long essay on the topic and is planning to submit it to the PSCF in the fall.

I was glad to hear from him because he said:

You are absolutely right, using the particular numerical value of k_B in Eq. 3 and 4 is ludicrous. More than ludicrous, it is dangerous and damaging to students who are subjected to learning physics from teachers who try using numerology in defense of an agenda. This particular value of k_B is for ideal gas in SI units. It is so elemental, I am embarrassed to point it out. Even the name says it, this particular k_B value multiplied by Avogadro’s number is the ubiquitous gas constant ‘R’ that appears in every single page of every single introductory text to thermodynamics. The author of this paper, therefore, implicitly proclaims that evolution can be quantified/modeled as ideal gas. Now, show me another journal in the scientific world that would allow a paper to be published on modeling evolution as ideal gas. Even if one could make an intelligible statement about evolution in the ideal gas context, WHERE IS THE ARGUMENT? In this paper, the author does not bother giving any argument, but willingly or unwillingly feeds numerology to science students. This is clearly wrong.

Email to Robert Kaita and James Peterson on 7/6/12. Subject: PSCF submission.  Dear Dr. Kaita,

Your idea that I submit an article to PSCF has been squashed.

My goal has always been to get the American Journal of Physics to retract the article by Daniel Styer. I explained to David Jackson, the editor of the AJP, why the article was absurd. He should have forwarded my criticisms to Styer for rebuttal. Styer has a reputation to protect and a conscience to follow. If Professor Styer attempted to defend the article, I would have explained to his employers that he was not fit to teach physics.

Instead, Jackson told me to submit an article of my own. I did so, and an anonymous reviewer said I was wrong. Jackson is now using this anonymous review to justify not printing a retraction. No one at the AJP or the American Association of Physics Teachers is taking responsibility for the article.

The only physicist saying publicly the article is okay in the light of my critique is Randy Isaac. He is supporting the article in the Open Forum of the ASA at the topic “Pseudoscience in the American Journal of Physics.” My suggestion is that you assign a moderator to a new Open Forum discussion. The moderator can insure that both of our comments about article are clear and to the point. If Isaac refuses to participate, he should be discharged from his position as Executive Director of the ASA.

Email to James Peterson, Robert Kaita, and Emily Ruppel on 7/9/12. Subject: PSCF Submission.
The reason the article I submitted to the PSCF is not publishable in a peer-reviewed journal is that it says another article in a peer-reviewed journal is absurd. You should give my paper to David Jackson, the editor of the American Journal of Physics, with the explanation that the Styer article puts you in a morally ambiguous situation: If you reject my article, it makes it look like you approve of Jackson’s refusal to publish a retraction. If you accept my article, your readers will wonder why Jackson did not retract the Styer article?

I’v attached an updated version of the article, “Entropy and the culture war.”

Very truly yours, David Roemer

Email sent to Francis Collins on 7/19/12. Subject: Pseudoscience in the American Journal of Physics
Dear Dr. Collins,
I am trying to get the American Journal of Physics to retract the attached article titled “Entropy and evolution.” The article uses the Boltzmann constant to calculate the entropy of the biosphere in order to refute the idea that the second law of thermodynamics doesn’t apply to evolution. Like you, I am a member of the American Scientific Affiliation. I’v also attached an essay explaining why the AJP article is absurd. A version of this essay was published by the Catholic Truth of Scotland newsletter.

By action and inaction Randy Isaac, Executive Director of the ASA, Robert Kaita, Vice President of the ASA, and James Peterson, editor of Perspectives on Science and Christian Faith are supporting the unjustifiable behavior of the AJP. I have a Ph.D. in physics from New York University, and Dr. Isaac is saying on the Open Forum of the ASA that I don’t understand the second law of thermodynamics.

The inability of science to explain the Big Bang, the origin of life, and evolution is evidence that God inspired the human authors of the Bible. I consider creationism and intelligent design pseudoscience, but this article is actual nonsense. The least you should do is publically resign your membership with the American Scientific Affiliation.

Very truly yours, David Roemer

Email sent to Robert Mann on 7/25. Subject: Essay Submission

Dear Dr. Robert Mann,

My essay (“Evolution and the culture war”) explains why the American Journal of Physics should retract the attached article (“Entropy and evolution”). It contains an absurd equation purporting to calculate the entropy of the biosphere in joules/second. The Catholic Truth of Scotland published a version of my essay (http://www.catholictruthscotland.com/MAYnewsletter12.pdf)

My primary goal is to put pressure on the AJP to retract the article. Randy Isaac, Executive Director of the American Scientific Affiliation, and Stephen M. Barr, a prominent Catholic physicists associated with First Things, are on record as supporting the AJP article, throwing into question their integrity.

The editor of the AJP, David Jackson, is managing to avoid taking responsibility for the article. This puts all other editors of scientific journals in a morally compromising situation. If you publish my essay, your readers will wonder why the AJP didn’t retract its article. If you don’t publish my essay, I can accuse you of promoting misinformation about evolution and the second law of thermodynamics.

Very truly yours, David Roemer



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