Forum: OPEN FORUM: American Journal of Physics

Posts: 58

Sutherland,

I have a more fundamental problem with understanding the second law of thermodynamics.

In the free expansion of a gas, entropy increases. This is consistent with the second law of thermodynamics.

When you compress a gas and extract heat from it, the entropy of the gas decreases. This does not violate the second law because such a gas is not an isolated system.

However, there seems to be another theory or explanation for why the entropy of a compressed gas decreases. This theory is that the entropy of whatever caused the compression increased more than the entropy of the gas decreased. I can’t understand this explanation. It seems to be based on the idea that the entropy of the universe always increases.

Suppose, the universe consists of a large number of molecules attracted to each other by the force of gravity. The molecules will come together and form a star, no? Hence, the entropy of the universe has decreased.

Signature:
David Roemer

3/29/2012 at 6:59:22 AM GMT

S. Sutherland

Posts: 24

Hi Dave,

Not as good at stars as I am the atmosphere (mostly the math). Again I tread into an area I am distinctly under-qualified to go, but hopefully someone with greater expertise can correct any misconceptions I have.

I start with the assumption that entropy in the universe always increases (2nd Law). To wrap my head around how entropy works in the atmosphere I first think of it as a closed system with one boundary at the earth's surface and the other boundary with space (the place where earth's gravity loses it's influence over matter). With no tampering from outside the atmosphere it would reach uniform temperature, density, pressure and moisture inversely proportional by some factor to altitude--a state of maximum entropy. No life could be sustained in such an atmosphere.

But the entropy of the earth's atmosphere is sustained at a level significantly below maximum. I think about how external energy sources like solar radiation could make this happen. A majority of the solar radiation reaches the earth's surface where it is reflected or absorbed. Meanwhile, energy is being lost at the boundary with space. Each boundary becomes a transfer zone for energy into and out of the atmospheric system. Entropy in the universe increases at both the earth's surface and at the boundary with space but the increase is significantly less at the earth's surface, resulting in a net decrease of entropy inside the atmosphere. Also the heating of the earth's surface is uneven, more transfered to heat in some places than others, generally greater at the equator than the poles reducing the progress of entropy a bit more. This sets up systematic wind patterns the water cycle and a host of other activity including living organisms. All of these activities occur in the atmosphere because the system must move toward maximum entropy (2nd Law). It turns out that the increase in entropy within the system exactly equals the net decrease due to the differential of entropy flux at the boundaries plus, earth's rotation and uneven heating of the surface, etc. The heat entering the system sustains a level of overall order even though in the universe disorder continues to increase as the sun marches inexorably toward it eventual death.

The particular of rates of entropy flux in the atmosphere are impossible to measure precisely, they can only be estimated. I can't imagine how hard such calculations must be for living organisms.

Peixoto, et al (1991), Entropy Budget of the Atmosphere has been my go to article on the subject over the years (might need to update and get a more current one). I can understand the English and most of the math in this one. I appears to me that the math in the AJP article may bear a resemblance. Perhaps someone with more expertise can help me out here.

EDIT: Wanted to add a note about the "quality" of energy entering and leaving the atmosphere. The transfer of solar energy is much more orderly (has less entropy) than the energy lost into space, and more orderly than the energy contained in the atmosphere. Perhaps that help clarify the point about net loss of entropy within the atmosphere when entropy increases on the scale of the universe. The transfer of energy from the sun to the atmosphere via heating of the earth's surface increases entropy, but solar energy starts out quite focused and intense.

Last edited on 3/29/2012 5:18:36 PM GMT

3/30/2012 at 2:43:39 PM GMT
D. Roemer Posts: 58	Report Permalink
Hi Sutherland, Does this mean you agree that Eq. 3 in the first AJP article is absurd? Signature: David Roemer

4/7/2012 at 12:34:35 AM GMT

S. Sutherland

Posts: 24

Subject: RE:

D. Roemer said:

Hi Sutherland,

Does this mean you agree that Eq. 3 in the first AJP article is absurd?

Not ready to make that statement. I want to see if the math (including equation 3) and the math I already understand in the meteorological article are related. They seem similar to me and they both describe energy flux in open systems. Unfortunately that will take me a little time so I might not be able to work on it immediately. I would be happy if you or anyone else here were to take a look at it.

4/12/2012 at 5:30:41 AM GMT

Posts: 58

The editor of the AJP and the president elect of the AAPT suggested that I submit an article to the AJP explaining my approach to the issue. I didn’t feel qualified to write such an article, so I contacted a retired professor at New York University where I got my Ph.D. in quantum electrodynamics. This is what I said in the email to him (Robert Richardson):

"I am pretty sure that the entropy equations in the articles are nonsense, but I don’t know enough about statistical mechanics to explain why. They use the equation S = klogW, but there is no justification for the use of Boltzman’s constant for biological systems. Is there?
"If you are interested, I can email you my correspondence with the editor and publisher of the articles, and the pdf files of the two articles.”

Professor Richardson wrote back, and his answer confirmed what I told him about the equations:

"Hi David,
Nice to hear from you. The k in S = klogW is just a question of units and has no physical significance. logW is dimensionless and S has the dimensions of energy divided by temperature. k makes them match. In the "right” set of units k = 1. Please send me your work as I am always interested.”

I sent him my work and the articles. This is the uncharitable and absurd response I got:
"Hi David,
I have spent some time with your work but am not able to make an informed comment. I do sometimes testify as an expert in court. But my rate is $400/hr portal to portal. I doubt that you can afford a day of my time.”

I see the same kind of evasiveness in you and Randy Isaac. Emory Bunn, the author of the second paper, also said that he didn't have time to discuss the matter. It seems pretty simple to me. It makes as much sense to measure the temperature and entropy of a biological system with Boltzmann's constant as to measure the entropy and temperature of a deck of playing cards. The plastic the cards are made of have a temperature and entropy. The idea that an unshuffled deck of cards has a smaller entropy that a shuffled deck of cards is nonsense.

Signature:
David Roemer

4/13/2012 at 8:50:11 PM GMT

Posts: 80

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.

Randy

Last edited on 4/13/2012 8:50:59 PM GMT

4/14/2012 at 7:13:49 AM GMT

S. Sutherland

Posts: 24

Randy and David,

Randy, your statements support my initial impression that the entropy calculations in the meteorological article derived from the same equation. Usually in these cases I try to do a some mathematics to translate one into the other or at least identify correspondence between the values. Haven't had the time to do the work, and unfortunately I'm about ready for qualifying exams, so it may be a bit before I can address this.

David, would it be helpful to show how equations like the ones in the meteorological article, which are not in dispute, are similar to those in the AJP article? Perhaps that would either confirm your suspicion and provide support for an article, or it would explain what the authors of the AJP article mean and how it relates to a physical system. Physics really boils down to the math, at least for me.

On the surface I see similar reasoning in both articles, but I haven't checked the math. This isn't are area of expertise for me, so will will take some time to wrap my head around it. I want to be sure it will be helpful.

Wow, Randy. Sorry to hear about your brother. Will be praying for sure. --S

Last edited on 4/14/2012 7:18:43 AM GMT

4/14/2012 at 11:27:56 AM GMT

Posts: 80

Thank you very much, Scott. He's moving into hospice today.

David, I wonder if the discrepancy may be in how to apply their Eq 3 to a system of molecules in a gas? Did I understand you correctly that you thought this equation would predict a lower entropy when energy is added to that gas? Actually, the density of microstates would increase, hence the logarithm of the number of microstates increases, and the equation does predict an increase of entropy. All is well, don't you think?

Randy

4/16/2012 at 3:26:49 AM GMT

Posts: 58

Dear Randy and Scot,

I’m sorry to say I find you answer evasive because it is not responsive to my critique of the "Entropy and evolution” paper.

Equation (3) for entropy is S = k log W and it is analogous to the equation for temperature: KE = (3/2)kT. I am mentioning the temperature equation because the thermodynamic concept of temperature is easier to grasp than the concept of entropy, which is defined in terms of heat and temperature. If it was absurd for Styer to use the entropy equation, it is equally absurd to use the kinetic energy equation.

Your statements that biological systems follow the second law of thermodynamics and "all systems have a temperature” does not respond to my criticism of Equation (3). I am saying all systems do not have a temperature and entropy. All you are doing is contradicting me. You are not responding to my explanation of why Equation 3 does not apply to the biosphere evolving or a seed in the ground growing into a tree.

An example of a system that does not have a temperature is a three-legged stool. The four parts of the stool may have temperatures, but the stool itself does not.

Let me explain in another way why Eq. 3 is nonsense. Suppose you have a gas in a container with a cylinder at atmospheric pressure. You compress the gas with your arm muscle and extract heat from the gas, so that the entropy of the gas decreases. This does not violate the second law of thermodynamics because the gas is not an isolated system. It is connected to a human arm. Likewise, evolution and a seed growing into a tree do not violate the second law because they are not isolated systems of non-interacting particles.

What the Styer article does, by analogy, is calculate the increase in the arm’s entropy, using the Boltzmann constant, to prove that the increase in the entropy of the arm is greater than the decrease in the entropy of the gas, so that there is no violation of the second law. To justify Equation (3), I think you need to cite peer-reviewed papers which calculate the entropy of biological systems. Alternatively, you can explain to my why my reasoning is wrong.

As to your statement that biologists don’t calculate the probability of getting an English sonnet by the random selection of words and letters by a computer in order to understand evolution, I cite the following:

"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).

Signature:
David Roemer

4/17/2012 at 11:34:41 AM GMT

Posts: 80

David,

I'm truly puzzled by your thinking I'm being evasive. Let me try again. Eq. 3 does not need citations--it is the definition of entropy that all thermodynamicists know and it applies to all systems. No exception. I do not understand your argument of why it wouldn't apply. I'm not evading anything. Your argument just doesn't make sense to me. Your examples of compressing a gas with your arm is quite right and so is the argument they give in the paper. I see no contradiction whatsoever. Nothing to evade.

And the last quote you gave is surely correct--but no one writes sonnets that way and no biomolecule is created that way and no one calculates the probability of a biomolecule assembling in that way. It has no relevance to the situation.

4/18/2012 at 6:50:21 AM GMT

Posts: 58

Randy,

You say,

"And the last quote you gave is surely correct--but no one writes sonnets that way and no biomolecule is created that way and no one calculates the probability of a biomolecule assembling in that way. It has no relevance to the situation.”

Gerhart and Kirschner are mainstream biologists and this is a calculation made in an attempt to understand evolution. Because of this calculation and other considerations, natural selection only explains the adaptation of species to the environment. It does not explain the increase in the complexity of living organisms as they evolved from bacteria to mammals (common descent). The only theory that attempts to explain common descent is intelligent design (ID). However, there is no evidence supporting ID.

The connection between evolution and the second law is that biologists do the same kind of probability calculations that physicists do. Physicists label non-interacting entities No. 1, No. 2, etc. Biologists label amino acids a-No.1, a-No.2, b-No.1, b-No.2, etc. Your telling me this isn’t so makes sense only if you think Gerhart and Krishner are advocates of ID.

Based on this reasoning, I ridiculed Richard Dawkins for saying evolution does not violate the second law of thermodynamics because of the sun! Glen Branch, the Executive Director of the National Center for Science Education, squelched me by citing the two AJP articles, which use the equation (3) (S = klog W) to calculate the entropy of the biosphere.

Equation (3) only applies to thermodynamic systems. It does not apply, for example, to a Boeing 707. An airplane does not have a temperature or an entropy. Likewise, a seed planted in the ground and growing into a tree does not have a temperature or an entropy. A newly fertilized cell is much more complex than an airplane. Just as it is absurd to say the growth of a seed into a tree violates the second law, it is absurd to say calculations with the equation S = klog W can prove that the second law is not violated when a seed grows into a tree. The way I am interpreting your statement that equation (3) does not need a citation is that there is no citation that justifies applying the equation to biological systems.

I explained this to Emory Bunn, the author of the note improving on the first article by Daniel Styer, and to David Jackson, the editor of the AJP. They both said they didn’t have time to discuss the matter. David Jackson said I could submit an article to the AJP for publication. The correct procedure, I believe, would have been to forward my comments to Daniel Styer and Emory Bunn. Whether or not Jackson did this and what the response of Styer and Bunn was, I do not know. What this means is that you are the only one taking responsibility for equation (3). All we have is your statement that the equation applies to biological systems. We don’t have such a statement from Styer and Bunn because they have not responded to my explanation of why it is absurd to apply the equation to a biological system.

In the process of writing the article, I sent an email to Robert Richardson, a retired professor at New York University, asking for help. I said:

"I am pretty sure that the entropy equations in the articles are nonsense, but I don’t know enough about statistical mechanics to explain why. They use the equation S = klogW, but there is no justification for the use of Boltzman’s constant for biological systems. Is there?”

This was Richardson's initial response:

"Nice to hear from you. The k in   S = klogW is just a question of units and has no physical significance. logW is dimensionless and S has the dimensions of energy divided by temperature. k makes them match. In the "right” set of units k=1. Please send me your work as I am always interested.”

I sent him the articles and my ideas on the subject. This was his rude and uncharitable response:

"I have spent some time with your work but am not able to make an informed comment. I do sometimes testify as an expert in court. But my rate is $400/hr portal to portal. I doubt that you can afford a day of my time.”

In the article I submitted I included a link (http://www.evolutionnews.org/2011/10/more_philosophical_than_scient052441.html)
to the work of a mathematics professor, Granville Sewell, who criticized the AJP articles. There were two other links. It was obvious that I was not submitting the paper as something to be published. If the anonymous reviewer was honest, he would not have written the review. For all anyone knows, the reviewer could have been Styer or Bunn.

Let me summarize the things that I am saying with the suggestion that you ask a biologist about 1), and expert on thermodynamics about 2) and 4), and an editor of a scientific journal about 3).

1)   Natural selection only explains adaptation, not common descent.
2)   S = klog W does not apply to airplanes and biological systems.
3)   David Jackson’s behavior was unethical because he didn’t refer my criticisms to the authors.
4)   Robert Richardson’s behavior was disingenuous. He knows I’m right about equation (3), but he doesn’t want to get involved.

Signature:
David Roemer

4/20/2012 at 4:17:08 PM GMT

Posts: 58

I’d like to try to explain why the American Journal of Physics is so reluctant to publish a retraction its shocking articles. Saying that evolution violates the second law of thermodynamics is equivalent to saying that the theory of intelligent design is true. Intelligent design is the only theory that attempts to explain evolution, but there is no evidence supporting this theory. It is just a bright idea, like saying free will is an illusion.

Natural selection only explains the adaptation of species to their environment. It does not explain the increase in the complexity of life as it evolved from bacteria to mammals over a period of 3 billion years. Biologists understand this, but many laymen do not. What follows is an excerpt from a book by Kenneth Miller (Only a Theory: Evolution and the Battle for the American Soul) rebutting intelligent design and Michael Behe (The Edge of Evolution: The Search for the Limits of Darwinism).

In my opinion, Miller is being disingenuous. He never admits that there is a limit to the explanatory power of natural selection. If he said this, the book would not sell. A laymen reading this book might think that Behe says, "Natural selection does not explain the complexity of life” and Miller says, "Natural selection explains the complexity of life."

On page 67 Miller says: "A line in the sand is drawn, and on the other side of that line is intelligent design.” [Behe says that natural selection fails on the other side of the line. Whether or not intelligent design succeeds is a philosophical question, according to Behe.] The next paragraph says:

"How does Behe know where to draw that line? He takes a rough estimate from a 2004 clinical paper as to how often resistance to the antimalarial drug chloroquine has arisen in natural populations. ….1 chance in 10(20th power)…In fact he even invents a term for it, calling it …CCC…..To convert this number into an argument against evolution, Behe engages in a sleight of hand reminiscent of his argument for irreducible complexity.

"…….Given Behe’s estimate that fewer than 10 (40th power) cells have existed during the entire history of life on earth, that means that the evolution of even a moderately complex system of interacting proteins is far beyond the "edge” of what evolution can accomplish. He is so certain of this conclusion he calls it the two binding sites rule. Whenever we see two binding sites in a protein, he assures us, we see the hand of intelligent design. [Again, Miller attacks intelligent design instead of defending natural selection].

"….. Behe’s math requires that all of the mutations that produce a CCC must occur together, and they can be favored by natural selection only when all of these highly improbable events take place. ….Molecular studies of drug resistance in the parasite show that it is not the all-or-nothing one-chance-in-10(20th power) event he claims. Rather, full-blown resistance is preceded by a number of mutations that confer partial resistance, enabling natural selection to work at every step of the process. This means, as Nicholas Matzke wrote in his review of [i]The Edge of Evolution[/i], that chlorozuine resistance "is both more complex and vastly more probable than Behe thinks.

"….What he ignores, of course, is something that we already know to be true in the case of CCC, namely that natural selection can favor intermediate stages on the way to the evolution of the final, fully resistant organism."

The biological disagreement between Behe, Miller, and Matze is over Behe’s mathematics. My interpretation is that Behe is saying there are two evolutionary steps from species A to species B. Miller is saying there are 10 partial steps from species A to species B. Hence, the probability of getting from A to B is much less than what Behe says. Miller and Matze are not saying that the partial steps are the result of natural selection. They are saying that when a partial step occurs, natural selection acts upon that partial step.

Signature:
David Roemer

6/3/2012 at 8:21:23 PM GMT

Posts: 80

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.

Randy

6/4/2012 at 2:45:34 AM GMT

J. Bandstra

Posts: 4

Subject: entropy

I am new to this blog. In a closed system (i.e., no heat passing in or out, and no work done on the system) entropy (disorder) will always increase - and this happens in spite of, or maybe because of, random motion of atoms, say, in a diffusion situation. The earth is not a closed system, due to, at least, energy input from the sun (and energy radiating out to space). Thus, entropy can decrease on the earth, meaning that order can increase - I would assume, without any expertise in the area, that that could lead to higher order (less disordered) life forms. The entire universe, on the other hand, is (likely) a closed system and entropy must decrease in it - not meaning that entropy cannot decrease in parts of the universe. I take this to mean that order can increase on the earth, but overall, entropy is increasing in the universe. I do not know what this means in biological systems, but I do know that the overall increase of entropy (disorder) certainly suggests a Creator God. Also, the eventual effect (taking the really long view) is that the entire universe will be homogeneous - totally unlike the creation event. Not sure if this is relevant.

Jim Bandstra

6/4/2012 at 2:56:46 AM GMT
R. Isaac Posts: 80	Report Permalink
Well said, Jim! You understand it very well and stated it concisely. Thank you.

6/5/2012 at 5:15:05 AM GMT

Posts: 58

http://www.youtube.com/watch?v=qKaF8vX6HXQ

I am not a biologist and rely on authorities to get my understanding of evolutionary biology. My understanding is that natural selection explains only adaptation, not common descent. It explains why giraffes have long necks, but not how giraffes evolved from bacteria in only 3 billion years. This understanding comes from reading textbooks, peer-reviewed articles, scholarly works, and conversations with experts on evolutionary biology. I give some of those quotes in my attached YouTube video.

Like the Big Bang and the origin of life, the limitations of natural selection is a reason to believe in the Bible. It is a sign that God inspired the human authors of the Bible because the Bible says God created the universe from nothing. I don’t consider it evidence that God exists. We know God exists because we know humans are finite beings and finite beings need a cause.

I just got three long emails from Charles Kankelborg of Montana State University attempting to explain why the AJP article does not contain, as I am maintaining, a fraudulent equation. I did not find any of his comments helpful. I’v posted them at my blog at

http://newevangelist.me/2011/12/07/american-scientific-affiliation-2/

My main complaint is with equation 4c in the attached article which states that the entropy change of an organism over a period of 100 years is 9.53 X 10 (-23) J/K. This equation comes from applying the equation S = k log (W), where k is the Boltzmann constant and W is the thermodynamic probability. The change in thermodynamic probability is estimated to be 1000.

To me it makes no sense to calculate the entropy or temperature of an organism. It is like calculating the temperature and entropy of a Boeing 747 or a deck of cards. All Professor Kankelborg said was that I was wrong and that if I read more textbooks on statistical mechanics and thermodynamics I will see that this equation is not a hoax.

The other absurd thing about the article is that it implies that if you add heat to a system, the entropy will decrease. When you add heat to a system the entropy increases. For entropy to decrease there has to be a source of order. For example, if you compress a gas and extract heat, there is a decrease in entropy. However, we know the cause of the decrease: the work done by the compression.

I'v attached two more articles about evolution and entropy. One was published. The Applied Math Letters accepted the article, but decided not to publish it. Both articles argue that evolution is inconsistent with the second law of thermodynamics.

Attached Files:

AML_3497.pdf (273.24 KB)

AJPIAS_76_11_1031_1.pdf (63.13 KB)

D&NE040405f.pdf (601.41 KB)

Signature:
David Roemer

Last edited on 6/5/2012 9:18:20 AM GMT

6/5/2012 at 12:07:24 PM GMT

Posts: 58

The reference to the Boeing 747 is an allusion to the old model that evolution was like a tornado hitting a junkyard, picking up the remains of airplanes, and producing a Boeing 747 ready to fly. The new model is that evolution is like a computer generating an English sonnet by the random selection of letters or words. The AJP article calculates the entropy of a tornado (sun) and the entropy of an airplane (organisms) to prove that the assembly of an airplane by a tornado does not violate the second law of thermodynamics.

Signature:
David Roemer

6/5/2012 at 12:20:27 PM GMT

Posts: 80

Kankelborg is quite right.

And yes, organisms do have temperature and so does a 747. Just put a thermometer in them (or your mouth) and see!

No, I don't see where that article says that adding heat decreases the entropy. That would be peculiar

That defining equation of entropy is a universal and applies to everything in every situation.

Perhaps you need to read more biology textbooks. Reproduction with variation coupled with natural selection (interpreted broadly to include sexual selection, sweep selection, neutral selection, etc.) is adequate, in the opinion of almost all evolutionary biologists, to explain common descent from a few ancestral forms into all species of today. Yes, there are dissenters and you can certainly find them. Most of them complain because we don't have all the details of what happened in between. I don't know of any valid argument that such descent is not possible in principle.

Randy

6/5/2012 at 12:22:48 PM GMT
R. Isaac Posts: 80	Report Permalink
Again, any "new model" that claims evolution is simulated by a computer composing a sonnet by random assembly of notes is not accurate and does not even come close to reflecting what evolutionary biologists are talking about. Any model must reflect the basic concepts of reproduction with variation plus selection. That's missing in the "new model." Randy

6/5/2012 at 2:30:27 PM GMT

Posts: 58

The email exchange with Dr. Charles Kankelborg went like this:

David: 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.

Charles: A biological system is a thermodynamic system.

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

Charles: Certainly.

Your telling me Charles is right is just as pointless as Charles telling me I am wrong.

When a nurse takes a temperature, the temperature is of the fluid next to the thermometer. The idea that a human being is a thermodynamic system and has a temperature and entropy strikes me as being absurd.

We are having the same pointless conversation about the model of a protein biologists use to understand evolution. Why don’t we ask an expert on evolutionary biology? Perhaps he will be able to guide us to a scholarly work or textbook that explains why I am wrong and you are right.

If you want, I can start by assembling all of the quotes I have already given. I don't want to do it again because you might say I am taking them out of context, or you might say they are not mainstream biologists. I'm talking about the quotes from Krischner and Gerhart, Richard Dawkins, Kenneth Miller, Michael Behe, and Niel Campbell.

Behe is an advocate of ID, but the idea that there is a disagreement between him and Kenneth Miller about evolutionary biology is precisely what we disagree about. When it comes to ID, I agree with Kenneth Miller, not Michael Behe. Other people agree with Behe. Stop and think. Does it make sense that two professors of biology at major university have a disagreement about evolutionary biology such that the likes of you and me can figure out who is right?

I also have a great quote from Christine Kenneally, a PhD in linguistics, who thinks natural selection explains the complexity of life.

Signature:
David Roemer

Last edited on 6/5/2012 2:39:43 PM GMT

6/5/2012 at 7:40:02 PM GMT

Posts: 80

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.

Randy

6/5/2012 at 10:46:07 PM GMT

Posts: 58

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.

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David Roemer

6/5/2012 at 2:11:01 AM GMT

Posts: 80

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.

Randy

6/6/2012 at 4:40:15 AM GMT

Posts: 58

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).

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David Roemer

6/6/2012 at 4:48:37 AM GMT

J. Bandstra

Posts: 4