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There is no subject called evolution physiology in university science. I ended up producing evolution physiology because of the extreme evolution of the yeast and mushroom which I studied. The study of extreme evolution required evolution physiology. Since there is no subject of evolution physiology elsewhere, there is an ocean of information that needs to be put together in that area. So that is what I do. The results clarify many elements of evolution which were left unexplained by the usual method of studying evolution through fossil evidence. Physiology is the interaction of biochemical processes. To study physiology requires studying two or more processes simultaneously to see how they interact. At the microbial level, change occurs so rapidly that dynamic systems must be studied at timed intervals to determine rates of change. None of that is possible anymore, because it requires timed measurements at short intervals (usually every 4 or 8 hours) while several processes are interacting in complex ways. I did some of that for a year in graduate school, but I was living a block from the laboratory and had nothing else to do. Otherwise, it never happens. So microbial physiologists turned to molecular studies. There is something in molecular studies for everyone. But it is not true physiology, because processes are not directly studied. Molecules imply a lot of things, but direct measurement is not quite the same as implication. But that is not the worst of the problems. Just as incompetent corrupters took over the social structures and turned them into power structures, the same thing happened in science. In fact, more easily so in science, since science is invisible to and unaccountable to the public. So there is a QAnon of science much like the QAnon of politics. It consists of reversing much of the established science from the past. Corrupters need falsehoods to prevail against rationality. So they systematically reversed all knowledge they could in science. The simplest example is claiming Yellowstone is a super volcano. It produced no lava. A super volcano without lava is like an ocean without water. Obviously, Yellowstone is an asteroid strike. More relevant is a planet that exploded between Jupiter and Mars creating the asteroid belt. Scientist have known that a planet exploded for more than a hundred years. But recently the claim is that there was no planet that exploded; instead the gravity of Jupiter caused rocks to orbit the sun where the asteroid belt is. The explanation is beyond absurd, but corrupters start at the desired end point and have little concern about credibility. Prove it. There is no such thing as proof beyond accepting the obvious as fact. That's why scientists do nothing but measure; they prove nothing. Nonscientists fail to grasp the origins of science. Nothing but measurements exist at the origins of science. Real scientists look at methods of measurement to determine what information is produced. Then there is the application of the resulting knowledge. Scientists who understand the measurements acquire an accumulation of established knowledge which evolved over 500 years. Nonscientists try to do something similar and become dupes to be exploited. Nonscientists are incapable of evaluating science. The complexities are over their heads. The most obvious example is Al Gore being duped into assuming carbon dioxide was over-heating the planet. He had no ability to evaluate that subject. Now days, the subject is imposed onto everyone so concertedly that no one is allowed to disagree or criticize. Conservatives supposedly disagree but have no knowledge of what they are disagreeing upon, which gives them no credibility. Evolution is mostly studied through fossil evidence. Persons who study fossils are not physiologists. So there is a large gap of missing reality in evolution physiology. Microbiology is studied as evolution, since microbes change so fast that they have to be studied as they are evolving. Laboratory conditions promote evolution type change being unnatural. But that type of study is short-term evolution. Long-term evolution is not easily studied by microbiologists. I got into evolution by studying microbes which are extremely unusual. They provide much information about evolution, particularly the evolution of physiology.
A dramatic starting point for evolution physiology is a bacterium called Pseudomonas fluorescens. It's one of the first identifiable bacterium to exist (in addition to vibrios which it would have evolved from), since it still has similar characteristics to what it had 600-700 million years ago. Being such an ancient bacterium, it prevailed over other bacteria in all of its major functions, which includes survival in usual water types, survival in soil and dissemination through the air in addition to evolving directly or indirectly into mitochondria. About 600 to 700 million years ago, P. fluorescens evolved two polar flagella for locomotion in water. What if the reverse could occur: spinning the proteins to energize ATP? That's what modern respiration is and it could only have evolved by reversing the spinning flagella proteins of P. fluorescens. The spinning moves reactants into place much more rapidly than diffusion. Rapid production of ATP is needed for animal motion. All biochemical reactions would benefit from spinning proteins moving reactants into place; but the process is too elaborate for anything but ATP production. There is no other possibility for the origins of modern respiration than the flagella proteins of P. fluorescens. Other biologists are clueless, because they don't study the related subject matter as physiology combined with evolution, not to mention the recent deterioration of science which is turning everything upside down including the description of respiration by incompetent biophysicists. The complexities of spinning proteins could not have evolved directly into a respiration process, because the cytoplasm of the cells would have been disturbed too radically. Cytoplasm is extremely structured. Every enzyme must be located in just the right place to allow reactants to move from one enzyme to the next with a minimum of space. Increase the space and diffusion increases. Diffusion of molecules in the cytoplasm would be total chaos, where thousands of processes must be occurring simultaneously. The evolution of physiology and micro-morphology are extremely demanding and do not rapidly occur, while macro-morphology easily evolves. This difference is shown with the morel mushroom, where visible morphological evolution was recent and dramatic. The morphology changes so easily that there are visible differences every few hundred miles between morel patches. Yet the micro-morphology and physiology are so resistant to change that the morel cannot improve upon numerous disadvantageous characteristics acquired from the yeast it evolved from.
The disadvantageous properties of the morel which it acquired from a yeast include the ascospores which are highly detrimental. Also, there is residual autolysis, which all yeast and bacteria depend upon for recycling nutrients but which is very disadvantageous for filamentous fungi, as they need long-term stability. What these examples of extreme evolution show is that macro-morphology evolves easily, since it is based on counting cells in each direction, but micro-morphology and physiology do not change easily, because the internal structure of the cell would be disrupted, while every molecule and reactant must be in just the right place to prevent chaos. What it means is that the rotating proteins had to evolve for spinning flagella, where they could be out of the way from cytoplasmic complexities. Then reversing the process was a minor step in the evolution of respiration. Simpler functions than respiration commonly are exchanged between organisms through horizontal gene transfer, where bacteria, viruses and molds move genes from one species to another including vastly different types of organisms. But respiration was apparently too complex to be moved from one species to another through horizontal gene transfer. Instead, a whole cell was implanted into the cells of different species as mitochondria. Biologists know that mitochondria had to originate as a cell of some species, but they cannot determine what the origins would have been. Since the respiration process began with P. fluorescens, it could have been that species that produced mitochondria. If not, there would need to have been a rapid evolution of P. fluorescens into some other species before it transformed into mitochondria. Regardless of how much change occurred in P. fluorescens before creating mitochondria, the process had to be not far removed from the starting point in P. fluorescens. A lot of drastic evolution occurred in a rapid manner at that point in time. The Cambrian explosion of life occurred 541 million years ago. Biologists do not know why it occurred. The physiology shows unmistakably what happened, how and why. The origins of animals shows up in the fossil evidence shortly before the Cambrian explosion. The fossils indicate a stationary form sitting on the bottom of seas. Motion was not possible until modern respiration existed to produce ATP in a rapid and abundant manner. At the same time, complexities could not evolve for plants or animals prior to the Cambrian explosion. The reason would have been an absence of minerals, and for plants, an absence of the clay needed for vascular structure.
The geology explains the problem. When planet Earth formed, it had no clay; but it had a lot of shale. Shale is chemically similar to clay, but the structure is different. The cause of the structural differences is beyond comprehension by scientists. But the shale had no significant complexity for minerals within it. Modern clay is loaded with essential minerals. Before the Cambrian explosion, complex minerals were precipitated out of the oceans, which left the oceans almost sterile. A lot of shale dissolved in the oceans and then precipitated out creating Precambrian sediments which are sort of shale-like. Those sediments have yellow and red streaks in them resulting from bacteria using sulfur and iron as energy sources. It shows that the iron and sulfur precipitated out of the ancient oceans with the shale. Calcium always saturates oceans and would have continuously done so as long as oceans existed. The reason is because the calcium is unlimitedly available for the purpose but it has low solubility. As it precipitates out of the oceans it causes other minerals and shale to precipitate with it. While it is soluble, it buffers the pH of the oceans at pH 8.1. There never would have been any other pH for the open oceans than 8.1 for that reason beyond limited environments. The same is true to this day, despite speculators claiming carbon dioxide is acidifying the oceans. pH 8.1 is somewhat basic, which causes precipitation of minerals. There is somewhat of an iron shortage in the oceans at this time limiting the production of algae. There could not have been any other restoration of minerals in the oceans than a planet exploding between Mars and Jupiter where the asteroid belt exists. The exploded planet also deposited a thin layer of clay onto planet Earth allowing vascular plants to evolve. Incompetents claim clay was formed by plant roots producing acid and dissolving rocks. The absurdity is beyond description. Plants with roots need to grow on clay, not rocks. Only the elemental composition of feldspars is similar to clay, and feldspars are not distributed as evenly as clay. The layer of clay on the surface of the earth is so thin that it had to fall from the sky after everything else was in place. The clay was apparently about 15 inches deep initially. A lot of it got moved around by glaciers and erosion. It could not have resided above the enormous amount of shale without being dropped down afterwards. Why clay in place of shale? At first, it would appear that the planet which exploded contained clay instead of shale. But that is probably not what happed. What probably happened is that the shale from the exploding planet entered the Earth's atmosphere as small particles and then precipitated in the atmosphere as clay. Precipitation in the atmosphere seems to have created the difference between shale and clay. A variety of minerals were necessary for complex life to evolve. It would have been the availability of minerals that created the Cambrian explosion of life. Minerals are needed as cofactors for demanding biochemical reactions. They are also needed in the porphyrin ring of modern respiration.
If iron, copper and cobalt are needed in porphyrin rings, how could modern respiration evolve without the minerals? It seems to have occurred because so little of such metals is needed in porphyrin rings compared to cytoplasmic metabolism. In fact, porphyrin rings evolved long before modern respiration. It was cyanobacteria (previously called blue-green algae) that evolved porphyrin rings over two billion years in stagnant water. Porphyrin rings are the most demanding and critical element of modern biology. They needed two billion years to evolve. Yet incompetent biophysicists left them out of their analysis of ATP synthesis. Biophysicists claim the kinetic energy of rotating proteins energizes ATP through "binding force." They don't know that kinetic energy can never be transformed into chemical energy. Kinetic energy is in nuclei, while chemical energy is in electrons. There is nothing that can be done to nuclei short of nuclear reactions that can influence the energy of electrons orbiting them. For that reason, only radiation can increase the energy of orbiting electrons as occurs with photosynthesis. Porphyrin rings are quasi aromatic. Aromatic means similar to the benzene ring, where each carbon atom has a double bond allowing electrons to flow linearly around the ring. Linearization of electron motion is the essence of aromaticity. The porphyrin ring has a metal atom in the center which serves as an electron exchange agent. The metal can put electrons into the ring and take them out as needed. As electrons flow linearly around the ring, they will have a variety of energy levels due to random effects. ATP synthesis can then draw out an electron of exactly the right energy level for high efficiency ATP production. With direct chemical reactions, there is always substantial difference between the starting energy level of the exchanged electrons and their later state. The difference is lost energy which creates heat. And the difference slows the rate of reactions. By contrast, taking an electron out of the porphyrin ring would be very rapid being just the right energy level. So the porphyrin ring speeds up the reactions in addition to increasing energy efficiency. In this way, a single electron from NADH can energize three ATP molecules. The total efficiency would be in the area of 95-98%. Nothing in biochemistry or technology comes close to that degree of efficiency. Incompetents claim electric motors produce higher efficiency but the stupidity is beyond description. No such transformation can get more than 40% efficiency except maybe some super conductors reduced in temperature to near absolute zero. The porphyrin ring would have entered P. fluorescens before the bacterium, directly or indirectly, formed mitochondria in eukaryotic cells.
Sometime near the origins of animal life, about 541 million years ago, E. coli created a symbiotic relationship to animal intestines. E. coli may have evolved directly from P. fluorescens or a slight intermediary offshoot may have been involved. E. Coli serves the purpose of breaking down genetic material that passes through the intestine of animals. Animals do not use genetic molecules as nutrients for many reasons. It's not easy to break down genetic material, as it is designed to be highly stable. Bacteria and yeasts break down their genetic material through autolysis using four enzymes: three to depolymerize and one to split off the phosphate. The phosphate has to be removed for metabolism, as it is quite toxic being strongly reactive. It's not easy to remove having a high energy bond. Animals would gain nothing trying to use genetic molecules as nutrients, as the molecules would not be easy to handle in the blood and would be quite disruptive moving through the cytoplasm of cells to get to the nucleus. When E. coli breaks down genetic material, it converts the sugar (ribose or deoxyribose) into carbon dioxide creating gas. Biologists don't know it. They are trying to produce a type of beans that are not gassy. They don't know they would have to remove the genetic material from beans to succeed.
P. fluorescens and E. coli are Gram negative bacteria. That means they have lipid in their cell walls which shows up with Gram's stain. Gram positive bacteria have totally different cell walls and they evolved much later—after the dinosaurs died out, 65 million years ago. Gram negative bacteria are the dread of biology. They are designed to chew through the cell walls of other organisms and feed upon the cells. Therefore, they look for nutrients which are high in nitrogen, while the Gram positive bacteria prefer nutrients which are high in carbohydrate. So some species, such as mushrooms and same vegetables, protect themselves from gram negative bacteria by selecting for gram positive bacteria on their surfaces. They would hypothetically excrete some form of carbohydrate to do that. But the morel mushroom hasn't had enough evolutionary time to produce that result; so the tissue of morels gets broken down by gram negative bacteria as it ages, and the result can make people sick from eating old morels. The cell wall material of Gram negatives is inherently toxic and said to be a form of endotoxin. Gram positive bacteria, however, are safe to eat and are found in some foods such as yogurt. Their cell walls are not toxic, though some have evolved as pathogens which excrete toxic substances such as the causes of strep throat and staph infections. Botulism is Gram positive and it produces one of the most potent toxins known which kills fish and birds in stagnant lakes.
The way it happened was that flowering plants took off when the dinosaurs died out, and much evolution occurred in the sugary substances produced by flowers. Streptomycetes evolved into Gram positive bacteria and filamentous fungi evolved into yeasts in the sugary substances of flower nectar. The cell wall composition of each shows the origins of the evolution.
Filamentous Fungi Filamenetous fungi are assumed to be the oldest form of biological life—even older than cyanobacteria. Of course, some demanding evolution is involved in creating the longevity. Their unique feature is the ability to survive on surfaces without drying out and start growing when humidity increases. The cell surfaces of filamentous fungi have demanding characteristics in avoiding dehydration and being hygroscopic. Mycologists have not determine the nature of the surface chemistry, as they don't significantly study physiology. Filamentous fungi cannot be studied in liquids as bacteria and yeasts can. And mycologists are not familiar with microbial physiology, as they work in botany departments rather than microbiology departments. The seeds of grains (very recent things) have phytates on their surface to absorb humidity from the environment for germination. Grain seeds do not germinate well in contact with water, because water seals out oxygen. So phytates might provide some clue as to the nature of the surface of filamentous fungi which have similar requirements for hygroscopicity. Phytates have six phosphate radicals surounding the six member ring of sorbitol. The large amount of oxygen would create hygroscopicity. Also attracted are metals. Metals are usually positive charged ions, at least when biologically active, which would be attracted to the oxygen much like water in the air. So the assumption of biologists is that phytates serve to attract metals. But the problem is, attracting metals on the surface is not a good thing. The rational is sometimes that phytates might be a method of storing metals. Biologists haven't noticed that the seeds need to be hygroscopic to germinate. The surface of filamentous fungi is certain to be much more elaborate in it's hygroscopic characteristics, but some sort of negatively charged ions would be needed to attract water from the air. The result is that those types of filamentous fungi (Some lost their ability to resist dehydration.) cannot pump excess hydrogen ions out of the cells to adjust their endogenous (internal) pH. When they absorb organic acids, they draw excess hydrogn ions into the cells and cannot expell them. So organic acids are a method of inhibiting the growth of filamentous fungi in the food industry by including small amounts of such acid homologues as benzoate, proprionate or citrate. But some filamentous fungi lost their ability to resist dehydration and they can pump hydrogen ions out of the cells and are not vulnerable to small amount of organic acids. One example is the common foot fungus. It gave up its ability to resist dehydration, since feet are sweaty. It's a truism of biology that functions which are not needed are rapidly lost. Cultures in microbiology often lose functions which are not needed under laboratory conditions. The result of the foot fungus losing its ability to resit dehydration is that good aeration of feet destroys it. For this reason, toes evolved a lot of space between them to promote drying. Therefore, the foot fungus can be eliminated most easily by using a hair dryer, if started soon enough before much tissue damage has occurred. However, there is more than one type of fungus that can infect feet.
Yeasts evolved from filamentous fungi in the nectar of flowers. Flowering plants exploded in numbers after the dinosaurs died out. Before then, they were extremely suppressed but were evolving. So yeast evolved after dinosaurs died out. Fossil evidence for yeasts only goes back 55 million years and the progression of evolution points to that evolutionary age. Flower nectar is a liquid, which means yeasts adapted to growth in liquid and usually gave up the ability to resist dehydration. Yeast usually die off when exposed to the atmosphere due to their inability to resist dehydration. Rhodotorula yeast adapted to harsh conditions including airborne dissemination. The yeast produces a red pigment. Wikipedia claims the red pigment serves to block out some light. That's not what pigments are for in yeasts and bacteria. Pigments serve to attract insects which feed on yeasts and bacteria and carry them around for dissemination, which would be the purpose with Rhodotorula. It's resistance to exposure would make it visible to insects, where other yeasts are not. The morel mushroom evolved from a yeast and does not tolerate dehydration, which makes it hard to manage on the surface of agar gel in a laboratory. Very high humidity is needed, and then morel mycelium grows so extensively that it will grow out of a laboratory container over time. Yeasts also had to combat bacteria trying to grow in flower nectar. Yeast won the battle being eukaryotic, while bacteria are prokaryotic. What yeasts did was excrete acetic acid and ethyl alcohol to kill the bacteria. Yeasts could tolerate the toxic substances better than bacteria being eukaryotic. In general, after yeasts use up the available glucose, they remetabolize the acetic acid and ethyl alcohol that they previously excreted. Inducible enzymes are used. They require a trace amount of glucose as an inducer while being derepressed by glucose. This physiology has only been tested in a few species. So yeast physiology is oriented around the production of acid and alcohol from sugary nutrients. The amount of acid and alcohol produced by yeasts is dependent upon phenotypic variation, as yeasts produce much more phenotypic variation than usual attempting to cope with challenging conditions and not being able to produce genotypic variation well being stuck in a solution without airborne spores. In addition to excreting acid and alcohol, yeasts attempt to use up sugars in their medium as rapidly as possible by metabolizing them and converting them into two carbon compounds. Acetic acid and ethyl alcohol are two carbon compounds. Storage fat is also made of the two carbon compounds. So yeast store a lot of fat in their attempts to get sugar away from competing organisms. Because of this type of metabolism, yeast evolved fat storage as an endogenous energy source. Up to 40% of yeast cell mass is often stored fat. Looking back at evolution before the existence of yeast, about 55 million years ago, there is no evidence of storage fat existing. Dinosaurs would have benefitted from storage fat, as they needed a lot of weight to tromp through the nonwoody brush. Elephants use a lot of fat to acquire the weight they need for tromping through brush. Notice the difference in body style. Dinosaurs are all bone and muscle—no evidence of fat. Elephants are blocky and solid, evidence of what storage fat does to give them weight. Similar proportionalities are visible in modern rodents. They are short and heavy due to storage fat, while their ancestors from dinosaur years were lean and longer legged. It means storage fat did not exist until it was evolved by yeasts. Structural fats did exist in cell membranes, but getting to storage fats required a stepwise process of evolution that only occurred in yeasts. After it existed in yeasts, it could be spread to other types of organisms through horizontal gene transfer.
Geologists claim fossil fuels originated with plant material. They base the claim on the fact that there are molecules with biological origins in fossil fuels. That logic is not how science works. Finding something tells almost nothing about its origins. It's like saying automobiles originated with rubber trees because they have rubber tires. The molecular structure and energetics of fossils fuels tell how they originated. Fossil fuels are called hydrocarbons because they have hydrogen attached to each carbon atom which forms long chains. Biological carbon is mostly carbohydrate, which means an oxygen atom and a hydrogen atom attach to each carbon atom, usually in six membered rings as sugars and their polymers.
The oxygen of carbohydrates is in a lower energy state than the hydrogen of hydrocarbons. There is no way to increase the chemical energy of carbohydrates to the energy state of hydrocarbons. Only radiation will increase chemical energy. Breakdown processes will not. Heat and pressure will not. Heat and pressure are related to kinetic energy in that they act upon the nuclei of atoms rather than the electrons orbiting nuclei. Where then did hydrocarbons come from? Scientists were acquiring such realities before incompetent power mongers took over science. Real scientists had determined that planet Earth began with a reducing atmosphere. That means a lot of hydrogen and no available oxygen. Hydrocarbons would have been stable under those conditions, at least after available oxygen got used up. It appears that planets form with a lot of hydrocarbons from the beginning. There is no visible process for creating hydrocarbons after the formation of planets. Lakes of hydrocarbons are seen on Jupiter's largest moon, Titan. It indicates that hydrocarbons were created as planets or their largest moons were created. On planet Earth, the most volatile hydrocarbons would have been oxidized by available oxygen; and apparently, some oxygen was released from perchlorates which created salt in the oceans. The oxidation of volatile hydrocarbons would have created much of the water and salt in the oceans and carbonates stored in various forms. Only later was oxygen restored to the atmosphere through photosynthesis. The liquid forms of hydrocarbons would have flowed into plant material forming coal. There was a lot of plant material available during the carboniferous era. Mountains were just beginning to form. As mountains formed, oil would have drained into lower areas where plant material existed. That was 300-360 million years ago. Since then, the coal got buried somewhat, but it tends to be not far from the surface.
In the not too distant past, only 10% of the DNA of higher organisms had a known function. The other 90% was sometimes called junk DNA. Not now days. More and more functions are being found for that other 90%. One of the purposes of the mysterious DNA is physiological regulation. There are patterns of physiology stored long-term and reused when necessary. One example is eating a raw food diet. Persons who eat that sort of diet notice that they feel highly energized, while fat disappears. Nutritionists (headed by bureaucrats) won't hear a word of it. They say a raw food diet is nothing more than fewer calories. How would they know? Bureaucrats use extremely reductionistic explanations as a cover for their incompetence. What a raw food diet does is trigger the physiology that early ancestors of humans had (otherwise known as monkeys). Monkeys needed to be feather weight and high in energy to live in trees. So they had a developed physiology that would give them that characteristic. That physiological pattern still exists to be activated when appropriate signals exist. Eating a raw food diet triggers that physiological pattern in humans. The evidence indicates that any number of previous physiological patterns exist to be activated when appropriate signals exist. Another example is that grains activate a fat storage physiology, because slave labor (as serfs) was needed in the fields. Slave laborers would work long hours with little food during the day. When they were eating the grains at night, they had to store enough fat to get through heavy work the next day. The tendency of grains to cause fat production is noticeable when carefully controlling and watching diets with some scientific understanding. Another type of food that promotes fat production is bananas. Monkeys could put on fat while eating bananas, because those types of palm trees have steps going up them due to the way the branches break away from the trunk of the trees. With steps going upward, fat was advantageous. Fat production caused by eating bananas is noticeable for humans. What these examples show is that physiological patterns are stored to be activated when the right signals exist in the physiology. My research on the morel mushroom shows this effect in a dramatic way. When growing morel mushroom mycelium on a surface, either agar gel or liquid, it differentiates into a tissue with some of the characteristics of the mushroom mixed into the tissue. This effect is an anomaly, as it does not occur under natural conditions; it only occurs when the mycelium is growing on a flat surface with optimum nutrition. Other mushroom scientists have not noticed this effect, because they do not optimize nutrition. Mycologists study in botany departments, which means cut off from microbiology at the research level, so they don't understand microbial nutrition.
These anomalies show morel mushroom tissue growing on a flat surface with characteristics of the mushroom mixed in and scrambled. A flat surface does that, because the morel evolved at the base of tress, which is a flat surface, while reaching down into the soil to feed on bacteria. The pattern of surface growth was stored in their DNA to be activated when growing on a surface with optimum nutrition. Physiological patterns are stored in the DNA to be repeated any time in the future when conditions produce the signal which activates that physiology.
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The flagella are like long corkscrews several times longer than the cell. The rotary motion is produced by about 18 proteins embedded in the cell wall. ATP provides the energy for spinning the works.
