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Life has a metabolism: food molecules are broken down to release energy that the organism then uses. This is very different than anything a rock or crystal would do. A burning candle is perhaps somewhat closer, but I will argue that the combustion process is not regulated, and the energy released is not used by the candle to do anything.As far as the cambrian explosion: If you read the wikipedia article https://en.wikipedia.org/wiki/Cambrian_explosion (not just the intro), it doesn't seem like a significant blow to the theory of evolution...
Two other aspects of the living state, that are not mentioned in any definition of life, is life builds up energy value as it grows. If we burn a large tree, versus burning a smaller version of the same species of tree, the larger tree has more energy value. This is same is true of animals. Growth in life, adds chemical energy to the life form. Animate matter tends to drift toward a state of lowering energy. When living things die, other critters lower their once stored energy, via metabolism. Another aspects of the living state is its bulk structures represent a lowering of entropy; order. If we take a snap shot of any level of the living state, we see a wide range of ordered structures. When something dies, it structures follow the way of inanimate matter, with the entropy increasing; decompose. But while alive, life does the opposite of decompose. It absorbs higher entropy starting materials, and then polymerizes these and turns this into lowered entropy ordered structures. Life also generates a lot of entropy, through dynamic processes such as metabolism, so there is net increase in entropy consistent with the second law. However, the continuous high rate of entropy increase; metabolism, is made possible because of the extensive low entropy structures that life creates. These create an entropy deficit, requiring a high entropy offset. Metabolism is an entropy offset. The Cambrian explosion, by resulting in diversity, reflects a type of high entropy offset. This would have due to the something that had changed in structuring, that caused the structural entropy to fall. In my opinion, the best choice would be connected to the brain, nervous system and better cellular differentiation control. This lowered the multicellular structural entropy, enhancing the need for offset entropy; genetic diversity. Natural selection would then select high metabolic potential life; vitality, leading to stabilization of species.
Are you sure you wrote this all out of your own head or is there a little copy and paste going on , anyway you long post has nothing to do with evolution or the mystery of the Cambrian explosion? And I do not need a tutorial on the subject of entropy. Maybe you should try to keep to the topic of the thread?Alan
Quote from: Alan McDougall on 14/06/2016 01:51:17Are you sure you wrote this all out of your own head or is there a little copy and paste going on , anyway you long post has nothing to do with evolution or the mystery of the Cambrian explosion? And I do not need a tutorial on the subject of entropy. Maybe you should try to keep to the topic of the thread?AlanI don't mean to be rude or disrespectful. These are ideas I have developed over the past few years, connected to some of the practical needs of the water side of life, that is taboo to mention. This does link to the Cambrian Explosion. Several years ago, based on need, I noticed no definition of life ever seems to include life is a state of matter that gains energy value as it grows, nor does anyone mention that life structurally lowers entropy, as it grows, by turning small molecules into large ordered structures, which have perfect folds unaffected by randomness. The bias of the random traditions would have no need to look for this. In spite of this observation, discussions of entropy still get bogged down, since the concept of entropy has different meaning in chemistry and information theory. So I needed to figure out a way to settle this, by separating cellular entropy into its fixed and dynamic aspects. Most people lump the two, causing the cause and affect to appear random; more in line with the premises of the random philosophy. If you look at structural entropy as the cause for dynamic entropy; enzymatic reactions, this allows you to explain the Cambrian Explosion. The Cambrian explosion forms so many species that natural selection seems to be put on hold, because almost everything becomes selected. It was almost like nature becomes PC based, instead of competition based. The reason has to do with chemical selection in water. Structural entropy lowering is very intimately connected to water. The result is a need for a new offset; dynamic entropy goes up. Selection changes from macro-nature of Darwin, to the needs of nano-scale selection in the water. This is still Darwinian but at the nano-scale, not at the level of macro-scale species. From this beginning, I developed a way to explain how this works, in simple way, using the simple ideal system of water and oil. If we start with the ideal system of oil and water, these will want to separate into two layers. You can try this at home with cooking oil and water. The phase separation lowers system free energy, but it creates an entropy potential; adds order. To increase the entropy of this two layer system; 2nd law, we need to figure out a way to make them blend in a more permanent way; solution. This can be done with an extraction, by the oil or water, of things such as alcohols, so the water and oil can better blend using a third component. This can also mean extracting proteins into each phase. If can also mean chemically modifying the oil or the water, so each is more conducive to the other. Water is simple and so there is little room for change. The oil is more conducive to change, due to all the carbon able to form four bonds. In evolution, the organics will be modified, with the entropy potential of two layers; fix lowered entropy, providing drive for the needed change; induced dynamic entropy. Where life is slick is the energy value of life increases as it grows. The big tree or animals has more caloric value. The ideal system of oil and water represents an energy rich organic phase and a very low energy water phase. This means since life gains energy value, as it grows, it sort of perpetuates and even amplifies, the oil-water affect; entropy deficit, so life has a constant need for change; evolution, and dynamic entropy offset. As a practical example, obesity adds energy value to the body; fats since fats have more energy value than muscle. This amplifies the oil-water analogy in the body, which separates layers, adding structural entropy potential. This can lead to dynamic entropy changes; health problems. The large size of many dinosaurs was connected to evolution using the energy side to generate enhanced oil-water entropy lowering. The result will be more dynamic entropy. Warm blooded mammals burn more food, which means mammals has a higher dynamic entropy offset; metabolism. Mammals are more stable and outlasted the dinosaurs. There is a logic to evolution; water-oil, energy and entropy, fixed and dynamic entropy, entropy is a state variable.
For example, over 50 years ago it was discovered that proteins fold with exact folds. This was not predicted by the statistical assumptions of biology, that were getting popular. Even though this has been demonstrated as an experimental fact, these observations still can't be explained with statistical thinking.
I see two aspects of entropy being involved in the Cambrian Explosion. As you point out, there was external environmental entropy, such as caused by asteroids and weather. This increase in entropy can change the environmental parameters that life sees, and thereby impact the parameters of the selection process. If it got cold for several years, big fir fur animals become selected more. There is also internal entropy potential, within life itself, due to its own internal chemical environment. Given a chance, life will spread to fill in a geographical area. For example, bacteria can be killed with antibiotics; asteroid to the body. Once this new environment is set, internal entropy, genetic changes, can lead to some bacteria who are resistant to antibiotics. If we do nothing, usually the good bacteria have a selective advantage and will prevent the proliferation of the harmful bacteria.The bad bacteria need an asteroid or an external entropy change, to be given a chance at selection. For example, over 50 years ago it was discovered that proteins fold with exact folds. This was not predicted by the statistical assumptions of biology, that were getting popular. Even though this has been demonstrated as an experimental fact, these observations still can't be explained with statistical thinking. This was an example of an internal entropy change in science; innovation discovery of protein folding. The question becomes, why didn't this have natural selection, seeing this observation could have been the basis for a new state of the art? The answer is the external scientific environment was setting a potential against it; bias of traditions. The needed change of environment may require an external entropy increase, like a symbolic asteroid, to break up the biased environment. Once that happens, a wide range of research and innovation will suddenly appear, based on water, that even cures cancer in an inexpensive way; Cambrian explosion of science. Relative to the Cambrian explosion, internal changes, induced by chemical equilibria within water, created a potential for the future; need for higher entropy offset. However, the old environment was limiting and inhibiting. Natural selection can become a rigged system based on the environment. What was needed was a change in the environment, such as by asteroids, which increased the entropy of the natural selection system, so the internal entropy potential could be more fully expressed. All of a sudden, all the pent up potential seems to appear at once. In terms of another example, the dinosaurs were huge and strong and had an advantage over smaller animals that turned out to be more fit in the long term. However, the system was rigged based on environmental conditions designed for the theme that might was always right. An asteroid was needed to create more entropy in that environment; change the parameters of for selection, leading to the new and more adaptive life being selected. Relative to internal entropy, water causes structural entropy to lower. This can be amplified as organics evolve to the potentials set by the water. This sets an internal entropy potential, which then needs a high entropy offset. An asteroid, by increasing the environmental entropy, plays into the hands of this new life, and acts as the catalyst for the needed offset. The needs of adaptation, in a wide open environment, will require higher levels of internal entropy; metabolism and trial and error adaption that makes more use of the body and mind in new ways.
I disagree with idea of proteins being bound to the the law of thermodynamics!
Quote from: Alan McDougall on 15/06/2016 15:03:54I disagree with idea of proteins being bound to the the law of thermodynamics!The laws of thermodynamics are among the most tested, and best established theories of any science.So far there are NO systems that have EVER been observed to violate the Laws of thermodynamics. Proteins, like everything else in the universe that we can observe, appear to be bound by these laws.What, if I might ask, about proteins doesn't appear to obey the laws of thermodynamics?
Quote from: chiralSPO on 15/06/2016 16:35:06Quote from: Alan McDougall on 15/06/2016 15:03:54I disagree with idea of proteins being bound to the the law of thermodynamics!The laws of thermodynamics are among the most tested, and best established theories of any science.So far there are NO systems that have EVER been observed to violate the Laws of thermodynamics. Proteins, like everything else in the universe that we can observe, appear to be bound by these laws.What, if I might ask, about proteins doesn't appear to obey the laws of thermodynamics?. I should have said, "I disagree that the evolution of life by single proteins folding can effected by the laws of thermodynamics." As an Engineer who spent most of my working life in the Electric Generating field in South Africa, I am well aware that the laws of thermodynamics cannot be violated in any closed system and had to deal with Entropy as it directly effected the productivity of the colossal boiler generator systems that we had to keep at the minimum level of entropy as possible.
Proteins follow the laws of thermodynamics. However, proteins are not bound by the laws of statistics. Proteins fold with exact folds, held together with the equivalent of only a few hydrogen bonds. Due to this weak binding energy, and the energy available at ambient conditions, statistics predicts an average fold, which is not observed. The confusion about thermodynamics, may be due to misunderstanding created by the statistical traditions. If we teach people that proteins are under the laws of statistics, which they are not, the required black box approach makes it hard to analyze reality in a rational way; this is taboo. This can make it appear like protein, on occasion, violate the laws of thermodynamics. It is more of a magic trick. In Chemistry, there is a relationship called the Gibb's Free Energy equation; G = H-TS, where G is the free energy, H is the enthalpy which is a measure of internal energy, T is temperature and S is entropy. The key variable is the free energy G, which is the sum of internal energy (enthalpy), and entropy. As long as the free energy is favorable, entropy can go up or down. Even though the second law says that the entropy of the universe has to increase, in chemical systems, entropy can spontaneously decrease, as long as the enthalpy changes, in such a way, that the free energy change is favorable. Free energy decides, not entropy or enthalpy. In the case of proteins in water, the entropy of the protein can lower into exact folds, not under statistics, because the internal energy change of the water-protein system is dominate. This makes free energy favorable. The push is supplied by the water and protein, which lowers internal energy to such a degree, entropy can decrease into a stable phase with probability of 1.0. Water is not an ideal solution composed of random water molecules. Rather water will lower entropy, from random, to form order, driven by the formation of hydrogen bonding; lowers internal energy. Each water molecule can form up to four hydrogen bonds. When you place organics in water; oil-water analogy, lowering the enthalpy of the hydrogen bonds of water, still has priority, due to the strength of this bonds and their large numbers in the dominant water phase. The water will force organics into ordered shapes, that can lower organic entropy, because this is how you minimize system free energy; maximize the needs of water. Information entropy is not the same as chemical entropy. There is no Gibbs free energy equation for computer based information, where free energy changes can allow entropy to decrease. However, neural and cellular information is different and is prioritized based on a free energy scale, allowing information to crystalize as chemical structuring. The creative process is where scattered information or data; starts at higher entropy, can crystalize into a low entropy relationship, driven by free energy changes. In computer memory, the media is not set up with the information stored based on a chemical potential scale. This would be where high priority info is chemically hotter than lower priority info, such that the Gibb's free energy equation applies. If this was the case, the media would try to lower free energy and in doing so will rearrange the memory; new idea. This is another way to create AI; mimic life. Right now the media for computer memory is based on a uniform media, where free energy applies to the media, but the media is separate from information entropy, due to no connection in terms of chemical priority. The Cambrian Explosion was began with natural selection optimized to a way of life. However, the free energy of all of life was evolving; decreasing. The result was entropy was lowering internally to the needs of water, but the entropy offset was optimize to the old in that fixed environment. Once the environment was disrupted, the 2nd law had a means of expression. Physical expression is a form of information, governed by free energy, since it can be traced to chemicals; water.