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

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?

Boltzmann's constant is the proportionality between energy and temperature. It is the proportionality factor between entropy and the density of states.

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.

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

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.

 

By comparison, if we question how long it would take a high-speed computer to write randomly a specific Shakespearean sonnet, we are asking that all the letters of the words of the sonnet will come up simultaneously in the correct order. It is an impossible task, even if all the computers in the world today had been working from the time of the big bang to the present. Even to compose the phrase, "To be or not to be,” letter by letter, would take a typical computer millions of years.” (Marc W. Kirschner and John C. Gerhart, The Plausiblity of Life: Resolving Darwin's Dilemma, page 32)

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

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

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

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

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