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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.
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.
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.
Does this mean you agree that Eq. 3 in the first AJP article is absurd?
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.
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
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.
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."
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.
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.
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.
I can't imagine why you think a Boeing 747 is not a thermodynamic system. Of course it is. The fact that you (and I) do not know how to average the temperature correctly is irrelevant. For one thing, the existence of an airplane is a perfect example, in the bigger picture, of a decrease in entropy due to work/heat. It seems to me that you are trying to use this as an example that God is the Creator. Of course He is. But that has nothing to do with this example. I don't get it.