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6/6/2012 at 10:01:03 AM GMT
Posts: 60
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. 



David Roemer


6/6/2012 at 10:24:23 AM GMT
Posts: 60
Jim Bandstra, 

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. 



David Roemer


6/6/2012 at 11:09:27 AM GMT
Posts: 130

Dave,

  Accusations of anyone's qualifications or their background are neither accurate nor appropriate in this forum. Continued violations will lead to suspension. Please focus on the ideas.

  Your analogy of ping pong balls leads you to the wrong conclusion. Yes, the box of balls has a total internal energy, it has a temperature and it has an entropy, all of which can, in principle, be measured or calculated. You have not given any reason why not. All subcomponents as well as the whole system are thermodynamic.  There is nothing in that box that would exclude it from any thermodynamic considerations.

Randy



6/6/2012 at 11:20:05 AM GMT
Posts: 60
I agree that you can calculate the average kinetic energy of the ping pong balls in a shaking box. But can you calculate the temperature of the box of ping pong balls using Boltzmann's constant?

David Roemer


6/6/2012 at 11:46:41 AM GMT
Posts: 130
Boltzmann's constant is the proportionality between energy and temperature. It is the proportionality factor between entropy and the density of states.


6/6/2012 at 12:20:47 PM GMT
Posts: 60
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.  


David Roemer


6/8/2012 at 12:40:10 AM GMT
Posts: 130
Dave, perhaps it would help to consider the terms of the various thermodynamic variables. The key one that is relevant for this discussion is Gibb's Free Energy. G = U - TS + PV plus other specialty terms such as those related to magetism, stress and strain, etc. The internal energy U is composed of both kinetic energy (like that of ping pong balls) and the internal thermal energy of the atoms. No, you would not convert the kinetic energy of the ping pong balls into temperature in the way you described. Of course, kinetic energy of macroscopic movement can be converted into thermal energy but that's not how you treat these systems. The temperature T of the system relates to the thermal energy portion (the atoms) of the internal energy. So the Gibb's free energy can indeed be defined (though harder to calculate!) for any system, be it ping pong balls, 747's, or biological system. The second law of thermodynamics in its complete form simply says that the Gibb's free energy will be minimized. That's all. That's enough. It applies to EVERYTHING! So please do not repeat again the false assertion that these systems are not thermodynamic systems. I can understand your concern if you thought the macroscopic kinetic energy components had to be converted to the temperature T. But they don't.


6/8/2012 at 3:00:41 AM GMT
Posts: 60
http://www.youtube.com/watch?v=qKaF8vX6HXQ

We agree that it is wrong to convert the kinetic energy of a group of ping pong balls into temperature. When I say that a collection of ping pong balls is not a thermodynamic system, this is what I mean. What is the relevance of the idea that a group of ping pong balls is a thermodynamic system? 

Daniel Styer states, "Suppose that, due to evolution, each individual organism is 1000 times ‘more improbable’ than the corresponding individual was 100 years ago." He then plugs this number into the equation S = k log (omega). If it is irrational and ignorant to convert the kinetic energy of ping pong balls into a temperature, why is it not irrational and ignorant to convert the probabilities associated with organisms into entropy? 

Let us say the temperature of a fertilized egg in a human is 98.6 degrees. Is this the temperature of a mass of chemicals or is it the temperature of a structure more complex than a Boeing 747? Do you think that a Boeing 747 has a temperature? Do you think that a fertilized egg has a temperature? 

Temperature is the most fundamental variable in thermodynamics. It is measured with a thermometer, and gives rise to the variables called heat and entropy. The Gibbs function is defined in terms of temperature, heat, and entropy. We should first come to an agreement about temperature before tackling the more difficult concepts.

You have not responded my post # 32, where I argue that the article says heat from the sun caused the entropy of the biosphere to decrease. Generally, heat causes entropy to increase. Isn't it nonsense to say heat decreases entropy? 

The model of evolution in the 1950s was that it was like a tornado hitting a junk yard, lifting up the scrap metal, and creating a Boeing 747. Now, the model of evolution is that it is a computer generating an English sonnet in 3 billion years from the random selection of letters and words. Because of the impossibility of a computer doing this, natural selection explains only adaptation, not common descent. According to you, this is just the position of advocates of intelligent design. According to me, this is mainstream biology. Do you think we can reach an agreement about what is taught in biology textbooks, scholary works, and peer-reviewed articles? 
 
I'v attached two peer-reviewed articles about the connection between evolution and entropy. I'v also pasted on the URL for my YouTube video titled "The Truth About Evolution and Religion."



David Roemer

 Attached Files: 
D&NE040405f.pdf (601.41 KB)
,
AML_3497.pdf (273.24 KB)

6/8/2012 at 5:45:02 PM GMT
Posts: 130

All systems are thermodynamic systems and can be characterized by Gibbs Free energy and changes to it as governed by the second law of thermodynamics. Whether one knows how to accurately calculate the respective components of kinetic energy and temperature and entropy is another matter, and entirely irrelevant to the question of whether it is a thermodynamic system. Yes, you can calculate temperatures and entropies of systems. It's not easy and usually one deals with partial derivatives while hold all but one or two variables constant. Net: all biological systems follow the second law of thermodynamics.

 

Yes, I did respond to your concern that Styer claimed adding heat caused a decrease in entropy. I stated that he said just the opposite. Consider his sentence "The Sun emits heat and hence decreases in entropy, while outer space absorbs
heat and hence increases in entropy." He is absolutely correct. The sun lost heat and decreased in entropy while the heat from the sun was transferred to outer space which incrased in heat and also in entropy. So your fears are assuaged--he does not claim that an increase in energy will cause a decrease in entropy.

If you have any evidence or examples of mainstream biology papers or textbooks advocating that evolution is properly simulated by a tornado in a junk yard creating a 747 (note that they didn't exist in the 50's!) or of a computer composing a sonnet at random, please let me know. I would suggest that they are either anti-evolution propaganda or they are not evolution advocates in any way. From Darwin till the present, evolutionary theory is predicated on some form of gradualism--replication with variation and selection. WIthout that, it isn't evolution. That is not simulated by a tornado or a random set of elements. The methods and degree of gradualism have changed radically since Darwin but the core concept remains the same.

 



6/8/2012 at 8:19:14 PM GMT
Posts: 60
So, we agree that it is irrational to say heat from the sun decreased the entropy of the biosphere. Our disagreement is over whether or not Styer says this in the article. Is this correct? 

This is the quote that likens evolution to a computer generating a sonnet:

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)

Kirschner and Gerhart modified the "millions of years” to "a short time” by taking into consideration natural selection and facilitated variation. They did this by stopping the computer when it got "to” and generating the remainder of the phrase. They also randomly selected dictionary words instead of letters. 

The significant thing is that they did not say how long it would take a computer to generate a sonnet using this more realistic algorithm. Kirschner and Gerhart don’t say because nobody cares. Nobody thinks natural selection explains the complexity of life. Every body knows that the primary structure of a protein does not even begin to describe the complexity of life. There are four levels of complexity in a protein. There is molecular machinery. There is genetic engineering, where cells read what is in the environment and constructs the right proteins. There is cell differentiation, which is the development of a single fertilized egg to a multicellular organism. There is instinctual behavior in animals. 

The second quote is not about evolution, but about the need for DNA to assemble the amino acids in the blood stream. A sonnet has 600 letters, and the calculation here concerns a smaller than averaged size protein. I’m including this quote to show how the probability of getting a protein is calculated. Also, no where in this textbook used by 65% of biology majors in the US do Campbell and Reece deny that this calculation puts a limitation on natural selection.

Each of the four identical polypeptide chains that together make up transthyretin is composed of 127 amino acids…The primary structure is like the order of letters in a very long word. If left to chance, there would be 20 to the 127th power different ways of making a polypeptide chain 127 amino acids long. (Campbell and Reece, Biology, 7th edition, page 82)


The calculations done in this Nature article were not on proteins but on DNA. The article reports calculations on a protein with 300 amino acids. Hence the probability of getting the protein through random selection of amino acids is not 20 to the 300th power, but 4 to the 1200th power.

Title: Natural Selection and the Complexity of the Gene (Nature, Vol. 224, 1969, p. 342)

Subtitle: Conflict between the idea of natural selection and the idea of uniqueness of the gene does not seem to be near a solution yet.

First paragraph: Modern biology is faced with two ideas which seem to me to be quite incompatible with each other. One is the concept of evolution by natural selection of adaptive genes that are originally produced by random mutations. The other is the concept of the gene as part of a molecule of DNA, each gene being unique in the order of arrangement of its nucleotides. If life really depends on each gene being as unique as it appears to be, the it is too unique to come into being by chance mutations. There will be nothing for natural selection to act upon. 

Let me conclude with another quote which sheds light on the Styer article. The author is not saying evolution violates the second law of thermdynamics. He is just referring to the fact that the probability calculations in statistical mechanics are similar to the probability calculations done by biologists: 

Considered thermodynamically, the problem of neo-Darwinism is the production of order by random events. (Ludwig von Bertalanffy, "Chance or Law,” in Beyond Reductionism: New Perspectives in the Life Sciences, The Macmillan Company, 1969, page 76)



David Roemer


Last edited Friday, June 08, 2012