July 6, 2023

Biology is like a box of puzzle pieces dumped onto the floor and not put together. That's because scientists study by looking through a straw. They are so absorbed in the details of what they do that they don't look at surrounding realities. When looking at surrounding realities, the pieces fit together in unmistakable forms.

There are two major concepts recently revealed that are essential to understanding evolution. One is horizontal gene transfer and the other is phenotypic variation as an adaptation mechanism.

Horizontal gene transfer was discovered as a result of genetically modified organisms (GMOs). The genes injected into crops would show up in nearby weeds. The genes were being transferred to unrelated organisms being carried by bacteria, fungi and viruses.

This concept totally changes how evolution is evaluated. The previous concept required genes to flow from parents to offspring only, called Mendelian inheritance. There was too much of a stretch to explain everything that way.

An example is the state flower of South Dakota, the Pasque. It's like a blue tulip for flower petals, while everything else is like a dandelion. The leaves hug the ground like a dandelion; and the seeds float away like umbrellas. What sort of parental type does that? Big flower petals like tulips don't exist on the upper plains. It wasn't until horizontal gene transfer was elucidated that the unusual combination could be explained. The tulip petal genes would have been transferred from an unrelated species.

Phenotypic variation as an adaptation mechanism continues to throw biologists into confusion. The unusual variations are assumed to be genotypic and used for classification, but there are too many variations which confuses the subject.

The morel mushroom produces extreme variations with phenotypes, which clarifies the subject. Most, if not all, of the enzymes of morels take form as several phenotypes. When the TCA enzymes were separated by gel electrophoresis, three to five variants were found for each enzyme. That means there are so many phenotypes of morels that no two morels would be exactly the same.

But morel scientists were not aware of phenotypic variation of that type and tried to use the variants for classification. It didn't work. No one can agree on what species should be for morels.

All organisms use phenotypic variation as a method of coping with varied demands. Older species, such as the puffball, which hasn't changed much in 300 million years, reduced it's phenotypes to four. But the morel has not had enough time to sort out phenotypes; so every morel is a different phenotype and ninety percent of them in the upper plains environment, where conditions are harsh, are not functional in producing spores.
 

 
Biologists know that the mitochondria that generate energy in a cell originated as a microbe such as a bacterium; but they don't know what it was or when it took form. Putting together the pieces of evolution physiology clarifies the subject.

Mitochondria modernized ATP production, which made animal motion possible. The metabolism of animals is focussed on producing ATP, because large amounts of ATP are needed for motion. Animals borrow complex molecules from plants including vitamins and proteins, which frees up animal metabolism for producing ATP.
 

 
ATP production became highly efficient and rapid, about when animals took form. Strange forms were sitting on the bottom of lakes or sea floors to become animals, but they could not acquire motion until ATP production was made fast and efficient for the purpose.

Two extremely demanding process were required to create the respiration process that animals required. One was rotational motion; and the other was the porphyrin ring. Rotational motion allowed a much faster process than diffusion; and the porphyrin ring created close to one hundred percent efficiency in transferring energized electrons to ATP.

Rotational motion was needed to speed up reactions, because diffusion through cell cytoplasm is extremely slow and encumbered. Enzymes must be attached to membranes for exact locations, so reactants can move from one enzyme to the next with minimum diffusion. But that process still leaves a problem in getting reactants into place and out of the way. Rotational motions speeds up that process by picking up reactants, bringing them together and moving them out of the way. But doing that is so demanding that it only occurs for ATP production in mitochondria.

That process could not evolve in the cytoplasm, because any disturbance would create havoc with the extremely ordered arrangement. Evolution of physiology is extremely slow for that reason. Changes in the cytoplasm are too disruptive to allow very much alteration to occur.

So the new form of ATP production evolved out of the way near the cell walls. That's were flagella form in creating motion. There are two types of flagella for bacteria: peritrichous flagella cover the surface of bacteria such a Vibrio; and polar flagella are at one end, such as with Pseudomonas.

Vibrio would be the oldest identifiable bacterium. It would have evolved with the cyanobacteria in stagnant waters. It exists in stagnant water creating cholera.

As some of the Vibrios ended up in cleaner water, more rapid motion would have been needed to find nutrients. So polar flagella evolved for faster motion resulting in Pseudomonas evolving from Vibrio.

The cyanobacteria can be traced back about 1.5 billion years. Pseudomonas are not directly identifiable in fossil evidence, but their physiology would have taken form about 700-800 million years ago.

The polar flagella of Pseudomonas use about 18 proteins to create rotational motion. ATP provides the energy. So that process could be reversed in using rotational motion to generate ATP in a rapid form. About 21 proteins are used to create rotational motion for ATP production.

Since animal evolution began round the "Cambrian explosion of life," 543 million years ago, the use of the rotational proteins to synthesize ATP would have been available at that time. The process would have entered animal cells as mitochondria originating as Pseudomonas fluorescens or a near offshoot.

Pseudomonas fluorescens excels in bacterial ecology unlike any other bacterium. It is the most common bacterium (other than cyanobacteria) in fresh water, where it produces a blue-green fluorescent pigment for attracting insects to carry it around. Pigments are extremely valuable for bacteria in attracting insects for dissemination; but pigments are so hard to produce that very few bacteria can afford the luxury. P. f. has two pigments. In addition to the water-soluble pigment, it produces a pink pigment, after recycling nutrients through autolysis with ideal nutrition.

P.f. blows in the air like mold spores. It is one of the most likely bacteria to contaminate cultures from the air. That means it tolerates drying and rehydration.

P.f. is also the most prevalent of the non-filamentous bacteria in some soil. It grows on cell debris when ground thaws in the spring and then releases the nutrients to plants through autolysis, which reduces proteins to amino acids and genetic material to nucleosides. Can plant roots absorb amino acids and nucleosides? Some roots are probably adapted to do so, since they grow extremely rapidly under the conditions which provide nutrients from P.f. Now days there are a lot of variants that branch off from main-stem species such as P.f.

The Porphyrin Ring

The porphyrin ring creates close to 100% efficiency in the production of ATP. Biologists don't know why the porphyrin ring exists; and the biophysicists who revamped the mechanisms of ATP synthesis left out the porphyrin ring claiming the energy is transformed from kinetic energy, an impossibility.

Perhaps it's necessary to study electronics to understand the porphyrin ring. The porphyrin ring is a super-aromatic structure. That means alternate double bonds between carbon atoms allow linearized electrons to rotate around the ring. Aromatic molecules produce linearized motion of electrons.

In the center of the porphyrin ring is a metal atom. Iron first, then copper and then cobalt in the chain of three porphyrin rings. The metal atoms absorb and release electrons, as an external source of high energy electrons, NADH, adds an electron and the ATP being produced exchanges an electron.

The linearized electrons flowing around the ring will have some random variation in energy; and the metal atom probably influences the amount of energy in the linearized electrons, which is why there is more than one type of metal atom.

Therefore, an electron which has just the right amount of energy can enter the ATP molecule, which reduces heat as energy loss to almost zero. The net result is that one high energy electron provided by NADH can energize three ATP molecules.

The porphyrin ring would have evolved in cyanobacteria over a billion years as a means of promoting photosynthesis. The demanding characteristics of the porphyrin ring would have taken a long time to evolve; and the only thing evolving in a suitable manner at that time was cyanobacteria.

Modernization Of Biology

Dinosaurs evolved for 225 million years. Such a long time supposedly means they were well adapted. They weren't. Nonwoody brush covered the lowlands and held up all evolution except on the hills which were taking form, where conifers evolved. Between the brush and conifers a few flowering plants evolved including grass which slowly took form to replace the nonwoody brush.

Grass was getting significantly established by the time the dinosaurs were exterminated by the asteroid strike, as indicated by the newest dinosaur, Anzu wyliei. Anzu wyliei looked like a large chicken with long legs. The long legs means it was adapted for grass.

Grass modernized all biology. It allowed broadleaf trees and other flowering plants to evolve and created space for mammals to evolve. Flower nectar allowed yeasts to evolve from filamentous fungi and a new type of bacteria (Gram-positives) to evolve from Streptomycetes, which are filamentous bacteria that grow in soil. The Gram-positive bacteria have cell walls similar to Streptomycetes.
 

 
The older type of bacteria are called Gram-negatives. That's because the Gram-stain attaches to the lipid in the cell walls of the older bacteria, while the newer bacteria do not have lipid in their cell walls.

Gram-negative bacteria are the dread of biology. They chew through the cell walls of plants and animals to feed on cell contents. Gram-positive bacteria do not. They adapted to growing on carbohydrate, at first competing with yeasts in flower nectar; and then when losing that battle, moving on to other forms of carbohydrate that became available through flowering plants.

So Gram-negative bacteria are adapted to growing on high nitrogen nutrients characterized by cell contents; and Gram-positive bacteria are adapted to growing on carbohydrate, though some have became pathogens and adapted to the high nitrogen of cell material.

Mushrooms and some vegetables protect themselves from Gram-negative bacteria by promoting the growth of Gram-positive bacteria on their surface. That's why mushroom caps get viscid when wet. Raw green beans will get a coating on them if sitting out for a while. That coating would be Gram-positive bacteria promoted to protect against Gram-negative bacteria. Just theorizing, the bacteria on mushrooms and green beans would be Bacillus cereus and Bacillus subtilis. Which is on which, I don't know.

Gram-positive bacteria are good to eat, if they are not pathogens, while Gram-negative bacteria are never good to eat, because the lipid in their cell walls is always toxic. It is called endo-toxin.

Yeasts defeated Gram-positive bacteria in flower nectar by excreting acetic acid and ethanol. Since yeasts are eukaryotic and bacteria are prokaryotic, yeasts could tolerate higher concentrations of acetic acid and ethanol than bacteria could.

So yeasts absorbed sugars as fast as possible to keep them away from the bacteria. But there was often still more sugars available after producing the maximum tolerable amount of acetic acid and ethanol; so the yeasts converted some of the carbohydrates to fat. After the sugars are gone, yeasts re-absorb the acetic acid and alcohol and use them as energy sources.

All three of those substances, acetic acid, ethanol and fat are produced from two carbon compounds resulting from the breakdown of sugars. Acetyl Coenzyme-A takes the two carbon compounds from sugars and channels them into acetic acid, ethanol and fat.

Fats did not exist, until yeasts evolved their production in flower nectar. Dinosaurs would have benefited from fat, because they needed a lot of weight to plow through nonwoody brush, which they ate. Elephants have fat, and their structure is quite different from that of dinosaurs.

Of course, it was horizontal gene transfer that spread the genes for fat production from yeasts to plants and animals.

The earliest broadleaf trees had very small seeds, which means they did not have the ability to store fat. The fossil evidence for yeasts goes back to 50 million years ago. Presumably, some of the broadleaf trees already acquired their characteristics by then. The primary examples at this time are willows and cottonwoods. They have roots in water near streams, which created such a stable ecology that they could continue to prevail into modern times.

Another property of willows and cottonwoods is that their branches do not taper. Modern broadleaf trees measure stress forces and thicken the wood where stress is greatest, which means where branches attach to the trunk of the trees. Conifers also do not taper their branches. They began evolving 300 million years ago in response to hills forming, as tectonic plates thickened resulting in some buckling.

Evolution was much more whimsical early on, because there was less competition then. Filamentous fungi produced a lot of structures 200-300 million years ago including clamp connections and stalks with spores. A clamp connection is a tube that grows out of one cell and into the next cell. Various things would happen in the clamp connection including spore formation. Some of the clamp connections still exist, because evolution does not get rid of structures when there is no selective advantage doing so.

Evolution is much more difficult now days. All biology will become extinct in 2-10 million years due to extreme complexities which created interdependencies which will not tolerate change in adapting to varying environmental conditions. Humans evolved on top of maximum complexities (differentiation), which results in a lot of contradictions. No one can produce ideal nutrition because of the contradictions.

(The numbers used for evolution are constantly changing due to rounding, guessing and being obnoxious [a corrupter's version of precision]. So old numbers vary slightly on web sites.)