Microbiology is studied as evolution, because microbes change as they are being studied. After publishing my graduate research on an unusual yeast, Nadsonia fulvescens, I got a letter from a scientist saying I must have misidentified the species, because all laboratory cultures of N.f. lost their ability to sporulate, and it hadnít been isolated from the wild since 1918. It took me ten years to get the work published, moving around a lot, and apparently laboratory cultures lost their ability to sporulate during that time. Microbes lose genes while being handled due to a selection process. Genes which are not used under laboratory conditions disappear quite rapidly. Pathogens tend to become non-virulent under laboratory conditions, and they are sometimes used as ďlaboratory attenuatedĒ vaccines.
This yeast, Nadsonia fulvescens, is extremely informative of yeast evolution. The evolution of yeast has been a mysterious subject, because very little is known of the natural habitat of yeasts. A lot of yeast species have been only located by extracting them from the gullets of insects, and where they exist in the wild is not known. Yeasts have a lot of similarity in appearances, and very little is known about their differences beyond appearance.
Nadsonia evolved on tree sap. Most yeasts love tree sap, but they canít evolve on it, because trees tend to exude sap for a short amount of time, and rain washes the sap away quite often. Nadsonia adapted to the problem by forming a spore when separated from the nutrients in tree sap. To do this, it had to form a spore without nutrients being available. Forming a spore from internal reserves results in a lot of shrinkage of cell mass, which required moving the cell mass into a smaller chamber where the spore forms. Nadsonia is the only yeast known to form a spore in a chamber alongside the original cell, which indicates that it is the only yeast that forms a spore without nutrients available.
Yeasts must avoid dehydration
Another species of Nadsonia clarifies a lot about the process. Itís Nadsonia elongata. The cells are about 5 times longer than cells of N. fulvescens. The difference in habitat tells the whole story of yeast evolution. N. elongata is found on Birch trees. Birch doesnít exude, but it has a loose bark. It means N.e. can find protection from dehydration under the loose bark, while liquid nutrients accumulate there in some form. Elongation is promoted by surface growth, as molds demonstrate. So there is a lot of surface growth for N.e. without much liquids under Birch bark.
Most scientists did not notice that yeasts do not tolerate dehydration, as molds do. Nadsonia dramatically shows the need for protection from dehydration by yeasts. N.f. had to form a spore when separated from liquid sap, and N.e. had to find protection from dehydration under loose bark.
The ability of molds to tolerate dehydration is an extremely demanding property involving highly unusual surface properties. Because of this cell surface, a small amount of organic acids will kill molds, and propionic acid or citric acid is often used as a mold inhibitor in foods. No one knows why molds are intolerant of organic acids, as the cell surface of molds is mysterious. Since yeasts grow in sugary liquids, they would have rapidly lost the demanding properties of dehydration tolerance.
Studying evolution biology
After completing my masters work at the University of Arizona, I studied for a year at the University of California at Davis. Davis was a world center for evolution biology at that time. Robert Hungate, who wrote the book on bacterial metabolism, would hand out stacks of papers on pathways for energy metabolism by bacteria. Mortimer Starr, a taxonomist, taught microbial evolution. He would hand us stacks of material on recent structures and functions, and we would go over to his house, a block away, and discuss the evolution that produced them. H.J. Phaff had thousands of collected yeast cultures, a small percent of which we would evaluate. The differences and diversity are the story of evolution.
I dropped out of Ph.D. studies after taking courses for a year because of mental pain. Mental pain is caused by memories of pain being too close to the surface and contacted by distractions in the environment. I then moved onto the vacated farm where my grandparents used to live in central South Dakota and did mushroom research. The nondistracting environment reduced the mental pain. Since my yeast research showed the basic physiology of mushroom formation, I thought about studying the common mushroom, but a nearby professor was studying the morel mushroom, and he talked me into studying it.
The morel mushroom
The morel was extremely mysterious. It forms spores within cells on the surface (called ascospores), which only yeasts have a reason to do. Yeasts are basically single-celled, and they form spores within the cell for efficiency. Fungi never do. So why does the morel form ascospores? I soon found that the morel has the same physiology of yeasts. This physiology is very unique and is extremely impractical for other species. It therefore meant that the morel evolved so recently from a yeast that it had not yet changed its physiology.
Physiology is resistant to change
The morel shows that morphology can evolve very easily, but physiology cannot. Morphology is counting cells in various directions, which can be easily changed in response to need. Physiology is webbed into strict relationships to extreme complexities which cannot be easily changed. For this same reason, micro-morphology cannot easily evolve, as the position of everything inside the cell is extremely important. A cell is like a multidimensional assembly line, where metabolites move a minimal amount of distance from one reaction to the next. Change the locations just slightly, and the reactants do not get where they are supposed to be. Changing the shape of the cell is changing the locations, which is extremely difficult to do.
This type of evolution, the micro-morphology of fungi, occurred hundreds of millions of years ago, and it does not so easily occur now days. Long ago, there was less specialization and less competition. These factors allowed whimsical evolution to occur. The clamp connection of molds shows this. Itís a channel from one cell to another which goes around a cell wall separating them. Why? There is not a very good reason why, but there are a lot of variations on it.
The fact that clamp connections are still around shows another major element of evolution. Unless there is a good reason for something to change, it is held in place forever after. There has to be a selective advantage for change, otherwise destructive change including bad mutations are prevented. There are at least two methods of preventing unnecessary change. One is that mutations are often cut out and repaired. The other is that proteins surround or protect areas on the chromosome where change is not supposed to occur.
An example of this resistance to change is in two dots below the front teeth on the human jaw. Those dots can be felt with the tongue. They are the remnants of hooks used by ancient fish to catch prey about 400 million years ago. Mammals evolved from ancient fish, as recent fossils show that the human wrist evolved from fish fins. The ancient hooks evolved down to two dots, and there is no selective advantage for them to evolve away further. Evolution can only see advantage or disadvantage. With no further disadvantage, the dots have been held in place for hundreds of millions of years.
Humans store physiological patterns
The importance of this resistance to change shows up in human nutrition. There are patterns in physiology which go a long ways back. Those patterns are turned on and off through control mechanisms which are triggered by various conditions. For example, persons who eat a raw food diet notice that they get thin. The idiots in nutrition say the persons simply get fewer calories. They wouldnít know how many calories a person is getting. There is a physiological pattern that goes with a raw food diet. It not only makes a person thinner, it makes one highly energized. This pattern of physiology would have been developed by monkeys which needed to be very light to climb trees. That physiological pattern is still in place to be triggered when eating a raw food diet.
Nutritionists are locked onto a formula which says fat equals calories consumed minus calories burned up, and therefore more exercise is needed to lose weight. Fat production is under numerous, complex control mechanisms. Persons who work outdoors find that exercise causes them to put on weight. The obvious reason why is because ancestors who did hard work did not eat very often and needed to store a lot of fat. The simple-minded assumption that there is no place for energy to go but being burned up or producing fat defies the complexity and raises the wrong questions. Forcing people to eat less and get more exercise could damage health trying to defy laws of physiology.
Morel evolution follows ice age cycles
The age of the morel mushroom is highly visible in its characteristics and its ecology being locked into the cycle of ice ages. The morel re-evolves during each ice age cycle. There are other weird mushrooms which produce ascospores, and they are assumed to always be cup fungi. The morel is called a cup fungus for that reason, even though it does not have a cup shape. Change the word cup to apothecium, and then call the pits on the surface of the morel apothecia, and abracadabra, the morel becomes a cup fungus. There certainly is a close relationship between the morel and cup fungi. The surface of the spores from the larger cup fungi are said to be a finger print for the surface of morel spores. Instead of connecting them through terminology, how about a biological connection. Various evolutionary trees show some sort of connection, never the same with modern phylogenetics. That still doesnít explain the biology.
The biology of cup fungi is that the fleshy ascomycetes must evolve into the cup shape for survival. The morel isnít there yet, but it must evolve into the cup shape to survive through an ice age. Since there are two large cup fungi, they apparently evolved through two ice age cycles. Surviving with ascospores is so difficult for fungi that they never go through very many ice age cycles. Ice ages have been cycling at 100 thousand year intervals. There are small molds with a cup shape which appear to be very old. But the mold-like fungi find stable micro-niches that allow them to survive for a long time.
The reason why fleshy ascomycetes must evolve into a cup shape is shown with the morel. The morel has much difficulty coping with water, rain and humidity. Since it will not tolerate dehydration, being physiologically a yeast, it can only grow in sandy soil or something similar such as mountain humus. Fine textured soil draws moisture to the surface through capillary action causing it to dry out fast. After the morel emerges, it must not dry out too fast, or spores do not completely form. It takes 3 to 5 days for spores to form. Then the morel needs to dry out, because shrinkage of tissue is needed to force the spores out of the ascus. The spores are heavy and project for much distance.
The weather is seldom ideal for allowing morels to stay hydrated for a few days and then drying. Therefore, the cup shape is an improvement in allowing different parts of the tissue to dry at different rates. Near the outer rim, the tissue dries fast, as needed during wet years. Farther down, the tissue dries slow, as needed during dry years. Obviously, this strategy is a losing battle for long term survival, where weather extremes are a certainty.
Scope and perspective are missed at universities
In studying these unusual species, a person looks back in time quite a ways and needs to consider a large part of the complexity in environmental conditions, which of course is evolution biology of the type that evaluates complexities. Laboratory scientists do not do this. They study laboratory procedures and are tied up in technical complexities which do not allow the luxury of studying removed complexities. They therefore get an awful lot wrong in drawing conclusions on natural conditions.
Morel scientists at the universities claim that the morel has a conidial stage, previously identified as the leaf mold, Costantinella cristata. Conidia are microscopic stalks with exposed spores on themóthe most common way for molds to form spores. That type of evolution ended about 100 million years ago. Numerous other micro-structures are found with the leaf mold including rosettes and croziers. Tacking such structures onto the morel shows a complete absence of a concept of what the morel mushroom is, if not a complete absence of a concept of how fungi have been evolving. The basis for the false assumptions is that the leaf mold appeared when attempts were made to grow morels on compost covered with leaves.
Other scientists have never noticed that morels only grow in sandy soil and therefore follow river basins. Sand is needed, because it does not dry out through capillary action, while morel mycelium will not tolerate dehydration being physiologically still a yeast. Mycelium cannot grow on dead leaves without drying rapidly between rains. The mycelium would also have to be a decay organism to grow on leaves, while yeasts are not decay organisms. Of course, morel scientists at the universities do not know the morel evolved from a yeast, but how could they make assumption in contradiction to the biology from a basis of real science? Science is supposed to build upon established knowledge, not ignorant assumptions.
This shows the inability of laboratory scientists to go beyond their technicalities in evaluating biology in the wild. For this reason, evolution biology does not generally go beyond the study of bones or DNA to evaluate total biology and its relationship to environmental influences through time. It takes a lot of study of a lot of complexities to evaluate biology through time.
The nature of soil is missed outside agriculture
One of the critical factors is understanding soil, as biology is intricately related to the soil. Only agriculture scientists study soil, biologists do not. Even geologists who heavily study soil do not look at the biological significance but primarily the chemistry. Itís strange that they could be claiming that soil was produced by the breakdown of rocks, when the chemical composition is not the same for soil and rocks. Clay is high in aluminum, while many types of rocks have little aluminum in them. The chemical composition cannot be different, when one transforms into the other.
It appears that shale was the closest thing to soil that formed while the earth was being created. Clay was added later when a planet exploded in the asteroid belt between Mars and Jupiter. One major bit of evidence is that the clay is layered on top of everything else, while shale goes very deep. Another bit of evidence is in the biology. Biology on land was held back until clay was layered over the surface, which occurred 543 million years ago resulting in the ďCambrian explosion of life.Ē Along with the clay, critical minerals were added to the surface of the earth, which allowed diversification of the biology.
In studying these subjects including starting college in agriculture, I didnít realize that I was becoming an evolution biologists. A major reason why I became an evolution biologist is because of a huge void of information and a lot of false information in this area. I look into subjects which others are not studying or are getting wrong. This includes the largest part of the subject of natural, wild evolution which can only be studied outside of laboratories.
Wildflowers on the plains
I started photographing wildflowers with an old-style camera simply because they were pretty. The smallest wildflowers have the most complexities and beauty, but it is hard to grasp without photography. This process brought a lot of stark evolution to the surface. Prairie wildflowers are strongly shaped by visible environmental influences. The harsher the environment, the larger the differences between variants. The most visible factor acting upon the evolution of prairie wildflowers is whipping grass which strips leaves. Wildflowers adapt by protecting leaves, often drawing them close to the stem and making them small and waxy. Sometimes the leaves are close to the ground, as with dandelions or cone flowers. Sometimes, the leaves are too large and heavy to be damaged, as some milkweeds. Then a variant of milkweed is found around the shoreline of lakes, where unlimited water is available, and whipping grass does not exist. Guess what its name is: Asclepias incarnata, the incarnate milkweed. The leaves and flowers are huge and luxurious. The scent is a complex vanilla. A few feet away, surrounded by grass, is the closest relative, which is small with tiny leaves and a flower about four millimeters across.
One of the most visible elements of the evolution of wildflowers is phenotypic variation. This adaptation is also extremely noticeable in the morel mushroom. The wildflowers and mushrooms show the extent and variations in dramatic ways. Yet this phenomenon is almost unstudied in science. Most scientists do not understand the variations when they encounter them. With the morel, phenotypic variations are so extreme that scientists usually assume there are different species involved. They miss an awful lot about evolution and ecology. There can never be similar species occupying the same environmental niche. One will always prevail against the others. The variants near each other must be phenotypic and not genotypic. Temporary mixing is found with invasive species, such as weeds, but over time, one genotype will prevail over the others.
Grass shaped modern biology
To look a few months back in evolution is to be stuck with the other four billion years. Itís all connected. The most dramatic and important element of biological evolution was totally missed by university scientists. Itís the transition from reptilian biology to modern mammalian biology which occurred 65 billion years ago, as the dinosaurs died out. Scientists assume that an asteroid killed the dinosaurs and, ho hum, not much else happened. Most of what we see in biology happened at that time. An asteroid doesnít do all of that. Grass does. You would probably have to study a lot of agriculture to understand what grass did 65 million years ago.
The transition began before dinosaurs died out. A recently found dinosaur fossil, called Anzu wyliei, has long legs and looks like a chicken. It would have gotten that way by walking through grass. Other dinosaurs were extremely heavy, because they had to walk through heavy brush which covered their entire ecosystem. You have to tromp through a lot of thick brush to understand that. Before Oregon was stripped of its old-growth forests, it was the perfect place to study such ecology. I spent a lot of time doing that during the seventies.
Anzu wyliei was the last known dinosaur to evolve before they were all wiped out. It means grass was significantly developed before the dinosaurs died off. If an asteroid killed the dinosaurs, it would have only been the trigger, while grass shaped the result. I think it was a volcano that triggered the die off, because volcanoes produced a longer-lasting effect than an asteroid would.
Recently, another dinosaur was found to have evolved just before dinosaurs died out. It was a flightless, winged dinosaur called Tongtianlong limosus. (Original Article: http://www.ed.ac.uk/news/2016/dinosaur-casts-light-on-late-burst-of-evolution) This dinosaur would have required a lot of open space, which again indicates that grass was significantly established before dinosaurs died out. Grass would have evolved on hills, while the nonwoody brush which most dinosaurs were eating would have been located in low areas.
Grass replaced the overwhelming brush of nonwoody plants which were holding back all evolution. Biologists try to explain how and why mammals replaced dinosaurs. Mammals didnít replace dinosaurs. Grass destroyed dinosaurs, and grass promoted mammals. Dinosaurs needed nonwoody brush for food. When grass destroyed the nonwoody brush, dinosaurs had no food. There were conifers on the hills during dinosaur years, and they were designed by the need to prevent dinosaurs from eating them. The result was the aromatic chemistry of conifers, woodiness and sharp, small leaves. After the dinosaurs were gone, broadleaf trees were possible.
Flowering plants and mammals were slowly evolving during dinosaur years, but their numbers were reduced so much that they were almost invisible in fossil evidence. After the nonwoody brush was destroyed by grass, flowering plants and mammals thrived in the grass.
This biology and evolution cover extremely broad subject matter. Professional scientists donít study such broad subjects, because they get paid to do more specific and narrow things. Only an independent scientist wandering through a diversity of subjects can study science in such a broad way.
Terrestrial life began shortly after the Cambrian Explosion of 543 million years ago. Why not earlier? It would have been clay covering the shale on the surface that allowed plants to move onto land. The shale would have been too hard. Also, valuable minerals were added at that time. Even the oceans were depleted of minerals through oxidation and biology. With minerals and soft clay on the land, plants moved onto land.
One of the first things terrestrial plants did was evolve modern photosynthesis. Before then, cyanobacteria were producing crude photosynthesis. They were immersed in water, which prevented photosynthesis from evolving in an efficient way. The reason is because gases do not move through water easily. So once plants moved onto land and out of the water, they could exchange gases with the environment much more easily. With rapid exchange of gases, photosynthesis became much more efficient.
This transition shows up in a phenomenon called "SPICE" (Steptoean Positive Carbon Isotope Excursion). During Cambrian times, the oxygen level got very low, and about 500 million years ago, oxygen levels went up drastically. The cause of the oxygen reduction would have been an increase in biological activity in the oceans and lakes, while cyanobacteria could not produce enough oxygen. When plants began to grow on land, they modernized photosynthesis producing larger amounts of oxygen.
Pseudomonas fluorescens (P.f.) is 600-700 million years old. Evolutionary age is not highly definable, since all species branch infinitely all the way back to pre-life chemicals. But a concept of age exists based upon recognizable characteristics that go back in evolution. P.f. has recognizable characteristics that go back that far. Its polar flagella would be that old. Before that, the bacterium would have existed in some form for at least a billion years.
The age of the polar flagella of P.f. can be determined from the evolution of modern respiration. There are a group of rotating proteins that speed up respiration allowing animals to move faster than they could with simple diffusion supplying the energy. Those rotating proteins evolved from the polar flagella of P.f. This relationship can be stated as an unquestionable fact of evolution due to the similarities and physiology. One state must evolve from the other state, no options about it. The reason is because polar flagella were free to evolve without interference; while respiration proteins could not have evolved on their own due to demanding physiology. The physiology of respiration is locked into cell structure and requirements for energy which left no room for screwing around with alternatives. On top of that, the new form of respiration did not work its way into the old form of respiration. Instead it entered the cell as whole bacteria which transformed into mitochondria. This addition to cell structure allowed the new form of respiration to be added to the old form and then replace the old form after getting refined.
Since P.f. has a history of at least a billion years as a bacterium, the evidence of its age is unmistakable. A lot of evidence of age builds up over a billion years. P.f. is the most versatile bacterium in existence beating all others by a mile. It produces two pigments, while other bacteria which need a pigment cannot afford such a luxury. P.f. has numerous forms allowing it to adapted to several major environments. It is the best adapted bacterium to fresh water, where it produces two polar flagella. It is the best adapted bacterium to the soil (ignoring Streptomycetes), where it recycles nutrients from thawing ice. It is the best adapted bacterium for blowing in the wind, where it forms a spore-like state contaminating laboratory cultures more ubiquitously than mold spores.
As P.f. adapted to various environments, it branched off into all of the other gram negative bacteria while leaving the original state as the main stem of gram negative evolution. All of the diversity of gram negative bacteria traces back to P.f., which probably includes Escherichia coli (E. coli) which entered the intestines of animals from their beginning, which would be about 500 million years ago. Since P.f. is much older than E. coli, E. coli probably evolved from it.
Yet there is the whimsical claim by some persons that the gram positive bacteria are older than the gram negatives. Those persons do not give a credible explanation, which goes to show how out of contact with reality most scientists are when looking at broad-scale subjects such as evolution. No one gets paid to do broad-scale studies, because it takes life-times of endless observations to make any progress in doing so. Workers get paid by the hour, not by the lifetime, which leaves a lot of emptiness in their contact with broad subjects.
Gram positive bacteria clearly evolved with modern biology beginning 65 million years ago with the die-out of dinosaurs. Two major indicators are the simplicity of their characteristics and their affinity for carbohydrates. Biologists are totally unfamiliar with the transition that occurred 65 million years ago. They don't know that there were no storage molecules before then including starch, fats or free sugars. Circumstantially, there could have been traces of such evolution beginning in obscure locations such as flowers of rare plants, but this physiology was not spreading to other species to influence other organisms. When flowering plants began to produce sugary substances after the transition, 65 million years ago, the result was the evolution of yeasts and gram positive bacteria.
Gram positive bacteria have an affinity for carbohydrates, while gram negatives have an affinity for nitrogen containing molecules. The reason is very obvious. Before the transition 65 million years ago, bacteria had to destroy other cells for nutrients, and gram negatives are designed to do that. Their cell walls chew through other cells upon contact, which makes them the dread of biology. Gram positives don't do that. They feed upon readily available nutrients of the carbohydrate type which are released by dead vegetation. Some of them later became pathogens, which might not look like a vegetarian diet, but other similarities show the same origins.
Microbiologists are not aware of this difference in nutrition, because they don't study broad enough subjects. You have to be looking and asking the right questions to see such evidence. Here is a major source of information which has been out of view of microbiologists: Many plants and most mushrooms protect themselves from the scourge of gram negative bacteria by causing gram positive bacteria to form on their surface. A highly visible example is green beans. After sitting around for awhile, they get coated with a buttery substance on their surface. It's edible and doesn't have much flavor. It would be a coating of gram positive bacteria, probably Bacillus cereus, though I have not tested it to find out what species it is. Microbiologists do not know what the evolutionary habitats are for B. cereus and B. subtilis, but circumstantially, those similar bacteria would have evolved on the surface of plants being promoted as protection from gram negative bacteria, while variants would have evolved on decaying vegetable matter.
A highly informative bit of evidence is the morel mushroom. It has no such protection having evolved from a single-celled yeast a few months ago. As the morel ages, gram negative bacteria invade the tissue. Persons who eat old and deteriorating morels get sick from them, as the invading gram negative bacteria have an endotoxin in the cells walls. That type of toxicity never occurs with other mushrooms, as they protect themselves from gram negative bacteria, though some of them produce their own toxin for protection against predators.
There are some very complex gram positive bacteria, such as Listeria, which appear to go back in evolution farther than the other gram positives. Listeria probably evolved from Streptomycetes, since it has a soil-adapted stage.
Streptomycetes are filamentous bacteria which are highly specialized in breaking down cellulose in soil. They have been breaking down cellulose in the soil for 450 million years. They would have been the evolutionary source of the gram positive bacteria which evolved on carbohydrates after the biological transition 65 million years ago. If Streptomycetes started as gram negatives, evolving from Pseudomonas fluorescens, their gram negative cell walls would have evolved into gram positive cell walls, since the primary function of gram negative cell walls is to invade other cells, which would have been no longer necessary in breaking down cellulose in the soil.