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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 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
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?
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.
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.
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.