Origin of Life, Molecular Biology, Natural & Human Evolution

The Origin of Life, Molecular Biology, Natural & Human Evolution

The Origin of Life

Molecular Biology

Natural Evolution, Human Evolution

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This essay is only Part 2 of a larger essay.

Read the full essay by going to “Evolution: Understanding Physical and Mental Existence”

That essay is now available in the following separate sections:

1. Cosmogony, Cosmic Evolution, Evolution of Earth

2. Origin of Life, Molecular Biology, Natural Evolution, Humans (this essay)

3. The Evolution and Function of the Human Mind

4. Evolution and Functions of Societies and Cultures

5. “Intelligent Design Theory” as opposed to Natural Evolution

6. Extraterrestrial Intelligence? What could it Mean to Us?

7. The Future and Expected End of Mankind and the Universe

8. Closing Comments and Conclusions

Content of “Origin of Life, Molecular Biology, Natural & Human Evolution”:

Introduction

1. The Origin of Life

1.1. Habitable Zones

1.2. The Origin of Life

2. Molecular Biology

2.1. DNA, RNA, Ribosomes, Enzymes, Proteins, Lipids, Carbohydrates, ATP

2.2. Cell Evolution: Genomics, Proteomics,

Computational Biology, Epigenetics, Death

3. Natural and Human Evolution

3.1. The Changing of the Oceans and Atmosphere. Organisms. The Tree of Life

3.2. Oxygen, Life Feeding on Life, Mobility, New Functions,

the Brain, Complex “Systems”, Ecological Communities

3.3. Advances in Animal Development, Mammals, Homo Sapiens

3.4. The Human Brain

3.5. The Virus – the Sneaky, the Parasite, the Drop-Out

4. Further Changes and Interruptions – the Extinctions and New Beginnings

5. Singularities in Natural Evolution and Anomalies in Nature

Introduction:

When we pause for a moment in our busy life – at lunch, during a holiday, on vacation – we can perceive the wonderful and sometimes cruel existence we live in – the universe, nature on this planet Earth, our surroundings, our body, our mind. In trying to understand this existence, we find that everything in our world is evolving – has always been evolving and will continue to do so. If we want to understand our existence, we should attempt to understand this evolution.

Not too many years ago, one of the early NASA space projects provided the very first and rather beautiful pictures of Earth as seen from outer space. Astronomic telescopes had already provided excellent pictures of distant galaxies. Now we could visualize how our own “Milky Way” galaxy would look with the tiny spot of our Sun as one of a billion others somewhere in its outer reaches – and a still smaller, blue planet, "Earth”, whirling around that tiny sun – about four billion times already since its appearance. That small Earth is our only home, but our brains that evolved only a few ten thousand years ago allow our minds to span the universe in time and space. What were the starting conditions, principles, laws, and forces of nature that let this evolution occur?

Recent progress in astronomy has taught us how our universe originated in one spot some 14 billion years ago and has been expanding in all directions ever since. What happened in time and space that, out of the original burst of energy at that time, finally we humans, with all our exceptional talents, came to exist and live on this tiny planet where we now are – and to develop the mental capabilities we now have?

A few key aspects of Creation and evolution appear to be fundamental to the understanding of what occurred. They are especially surprising and impressive [1].

Come along on a mental voyage – to explore the existence which we live in – from the vastness of the universe to submicroscopic molecular life, the virtual phenomena of the mind, and unfolding civilizations – from an origin in the distant past to an expected end in the distant future!

This essay is only on part (Part 2) of a larger overview of all of existence in the essay “Evolution: Understanding Our Physical and Mental Existence”, to be found on the website www.schwab-writings.com in the Section on “Science and Evolution”.

1. The Origin of Life and Natural Evolution

1.1. Habitable Zones

Only certain zones in the universe – within a galaxy and within a solar system – are suitable for the formation of higher forms of life as we know it. They are called “habitable zones” by the sciences. Primarily, they require the presence of suitable materials – a suitable mix of the light and heavy elements – a sun as a suitable energy supply, and the absence of or shielding against destructive radiation. [2] Additionally, due to the long time required for the development of higher forms of life, those areas must have a low density of collision-threatening comets or large meteorites – or must be shielded against them.

This indicates that such habitable zones can be found only within galaxies, since gas clouds outside galaxies are too cold and lack energy sources. Within galaxies, their central areas, with their higher density, are thought to have too much radiation, possibly in connection with central black holes, as well as too many supernovae resulting in the projection of too much radiation. Too far out in a galaxy, the opposite may be the case, resulting in too little quantities of heavy materials from past supernovae. This leaves a certain band of certain galaxies as a habitable zone where solar systems could harbor life.

Within individual solar systems, great proximity of planets to their central sun would result in excessive surface heating – with life basically restricted to the very narrow band between 0 and 50^oC surface temperature on planets – for the availability of liquid water and a heat level below destructiveness for large organic molecules (except for extremophile bacteria). A large distance of planets from the central sun would not provide enough heat from this energy source. Depending on the size and age of a star – and its consequent heat-radiating intensity – the habitable zone for its planets would be closer to or farther away from the central star, possibly shifting with the age and radiation of the star. The early Earth demonstrates that atmospheric greenhouse effects allow for the extension of the habitable zone to an area of lower heat reception. This allowed Earth to become habitable at an early time when the Sun had only 70% of its present luminosity. The habitable zone of our solar system, including atmospheric influences, begins beyond Mercury and includes the region from Venus by way of Earth to Mars. Beyond that area, there are not enough heavy elements and an excess of water content (beyond the Asteroid Belt). The outer planets are too cold (distance from Sun), largely gaseous, and, therefore, not considered habitable for life as we know it – except possibly some of their moons that may be kept warm through extreme tidal deformation. In sum, our Earth is in a very habitable zone of the universe, being about 60% of our galaxy’s radius away from its center and, within our solar system, about one hundred times the diameter of our specific sun away from it.

The assessment whether “habitable zones” are fairly plentiful in the universe and, consequently, whether we humans are a highly unusual phenomenon in the universe, or whether much other intelligent life can be expected in the universe, is a subjective one. Depending upon the individual scientist and the general trend in the sciences at any one time, the glass is either half full or half empty. In times past, plenty of other intelligent life had been expected in the universe. The SETI project [3] was started to discover and communicate with that supposed life. Then, a more critical view arrived and publications [4] pointed out how unlikely any other higher forms of life – specifically, intelligent life – in the universe would be (but not denying the possibility for extensive bacterial life). Lately, the discovery of “extremophile” bacteria deep under ice, at very hot deep-sea vents, or deep within rocks, has opened a view allowing for larger “habitable zones” and, therefore, greater probabilities. But the expected, randomly repetitive large catastrophes remained as the limiting factor, possibly not allowing enough time for the slow development of higher forms of life. But do we really know whether higher evolution must always be slow?

On the other hand, the recognition of the great resilience of Earth’s atmosphere and the resurgence of ever higher forms of life after each of the past catastrophes should allow for the acceptance of higher comet or meteor risks in the environment and, consequently, larger habitable zones or higher probabilities for advanced forms of life in the universe to develop in the available time. The fact that life on Earth easily survived many passages through the galaxy’s spiral arms and the many reversals in the magnetic field, with consequent higher radiation levels during transition times, should allow for more radiation risks.

The assumption that higher forms of life have required billions of years to develop on Earth should be put in perspective with the arrival of large quantities of oxygen only some 600 million years ago. This oxygen, consequently, led to the oxidizing of biomaterials as a source of energy and, therefore, required mobility, then leading to nerves and, finally, the brain as the main characteristic of what we call “higher” form of life.

Life’s development in the last 600 million years was quite rapid, especially during the last 65 million years, after the demise of the dinosaurs. Why could another Earth-like planet in the universe not have shown even faster mammal development? It could have occurred, for example, in lieu of dinosaur development after an earlier catastrophe, hundreds of millions of years earlier in evolution than on Earth.

In sum, this author assumes a somewhat more temperate position, seeing the very special character of Earth as a harbinger of life in the vastness of the universe, but also seeing the probability for other Earth-like planets in other solar systems and in other galaxies to harbor higher forms of life – with enough shielding against radiation and impacts and with atmospheres with enough resilience, like our own, to overcome catastrophes. This would allow for considerably more intelligent life in the universe than has recently been assumed – specifically in consideration of the very large number of existing galaxies (several billions) and the very large number of solar systems within them (several billions in each of them).

After all, the product of an exceptionally large number and a small probability still allows for the result to be anything, but possibly also a large number.

1.2. The Origin of Life

Living beings are composed of molecules. Certain molecules are called “organic” by scientists, because they were found to appear mainly in combination with, or as products of, processes of living organisms. Later, it was found that some of these organic molecules – they should be called “proto-organic” – existed before life arose on Earth and were the precursors of life. The designation “organic” is misleading. Those molecules – mainly complex compositions of carbon, hydrogen, nitrogen, and oxygen – often containing the famous Kekule-discovered “benzene” hexagonal ring of six carbon atoms – did not originate in the universe in connection with any organic life. Later, however, as life arose, these molecules actually did occur in life processes and became the dominant form of molecules in living beings – hence their group designation as “organic” molecules.

The question arises why carbon became the key atom in all organic molecules and, consequently, all living organisms – though combined with hydrogen, nitrogen, oxygen, phosphorus, and many spurious materials. Atoms consist of a nucleus composed of positively charged protons and neutrons. They attract negatively charged electrons in a number equal to the protons. The electrons can be visualized as circling the atomic nucleus on a sphere or “shell”. But when more than two electrons are needed for the nucleus, the first shell is full and the extra electrons circle on an additional shell. More electrons are added for heavier nuclei, until, at eight electrons, that second shell is full and another one has to be started – and so on. Electrons can be shared with other atoms, thereby establishing bonds with those other atoms. Two hydrogen atoms, with only one electron each, can establish bonds with an oxygen nucleus requiring two electrons to complete its second shell – thereby forming H₂O, water. Carbon has four electrons in its second shell that could hold eight and, thereby, can establish four bonds in all directions with all kinds of other atoms (nitrogen, the next most important atom in organic chemistry, can have only three bonds and oxygen only two). Those electrons, being of an inner shell, are very stable. This makes carbon a versatile and strong building block for complex structures or chains. In other words, it is the regularity of the electron shell structure of atoms that led to the combinatorial bonding of atoms and that let carbon become the key element of organic composition and consequent natural evolution.

As described above, simple “organic” but not “living” molecules – such as methane and some amino acids [5] – had already been constructed in cosmic space from the ejecta of collapsed stars by means of ultraviolet light and radioactivity in the universe and were floating around in space before Earth was formed. Consequently, when the origin of Earth took place as it “accreted” (coagulated) in its band of gas and dust around the Sun, such proto-organic molecules became part of Earth and may have survived this forming process, at least at high altitudes of the atmosphere and, less likely so, in some niches of the surface crust, possibly at some depth. On the other hand, Earth reached extremely high temperatures upon accretion, early formation, and under early comet impact and may have become sterilized thereby.

A different theory concerning the origin of life on Earth appears more promising. During the violent time of Earth’s formation and thereafter, asteroids and comets consisting of ice impacted Earth [6]. Four significant factors came together in these comets: dust particles, an icy surface on those particles (or dust on icy surfaces), inclusions of proto-organic molecules in those icy surfaces as available in space, and ultraviolet light. The dust particles that accreted to form the comets consisted of mineral or metallic material. “Cosmic” ice [7] had formed in outer space on these dust particles (or dust particles had accumulated on the ice) and contained already complex organic molecules as available in space – as one knows from the recent investigation of comets. The combination of a catalytic effect of the mineral or metallic surfaces of the dust particles – with the energy provided by ultraviolet radiation as available in space and the effect of the ice to hold the proto-organic material, to give it yet some limited mobility – facilitated the formation of more complex molecules, especially since cosmic ice goes through transformations into different states (amorphous, cubic, hexagonal, and liquid).

Four resulting organic formations of dust in or on cosmic ice were detected and are of special significance: nitrile, chinon (so named in the related paper, commonly called quinone), adenine, and formaldehyde.

- Nitriles (for example, Propionitrile CH₃CH₂CN) consists of carbon, hydrogen, and nitrogen atoms. When immersed in water, as when cosmic ice temporarily melts under the influence of radiation or when it hits an ocean on Earth, it is transformed into a lipid acid. Certain lipids (for example, phospholipids and other amphipathetic lipids) can spontaneously form “micelles”. Micelles are hollow spheres or bubbles organized in a double layer of fatty acids, like cell membranes. They permit “protected” chemical evolution in their inner space.

- Quinone can be formed in comets or cosmic ice from the already existent methane, ammoniac, and carbon dioxide. Quinone has certain chemical similarities to chlorophyll [8]. On the one hand, it can transform absorbed radiation into chemically stored energy. On the other hand, it protects other proto-organic molecules from the destructive radiation that exists in space and existed on early Earth even before Earth’s final atmosphere was formed.

- Adenine is formed from carbon, hydrogen, and nitrogen atoms. Not only is it one of the nucleo-bases that are the key elements of RNA and DNA as carriers of genetic information, it is also a precursor of adenosine tri-phosphate (ATP) which plays a key role as energy carrier in cellular dynamics.

- Formaldehyde (H₂CO) is the forerunner of ribose or desoxyribose, the sugar backbone of RNA and DNA, both formed out of a polymerization of 5 formaldehyde molecules.

Some icy comets, as also some rocky comets, do not fully vaporize upon entry into Earth’s atmosphere. Icy comets that do not fully vaporize have the additional advantage of keeping their inner temperatures moderate, thereby allowing the complex proto-organic substances to survive.

It is known that some of the cosmic proto-organic molecules lead immediately to more complex molecules as they enter the water of Earth’s oceans.

Calculations indicate that any comet that hit Earth may have deposited 10²⁴ dust particles into the early oceans!

A more detailed discussion would indicate the specific significance of ultraviolet radiation for the promotion of chemical reactions leading to more complex molecules (or the maintaining of a balance between “right-handed” and “left-handed sugars” in the evolution-feeding original organic soup on Earth – or the contribution of ultraviolet radiation to RNA formation).

In sum, the icy comets may have been the source not only of water for Earth but also of the organic evolution on Earth and the origin of life. This may explain why life originated so quickly, within only 50 million years after Earth had cooled and stabilized.

Organic molecules found a favorable environment in the early atmosphere and oceans, as well as deep underground, shielded from the effects of the numerous meteor impacts, radiation, and the intense volcanism of the early Earth.

A famous experiment by scientists shows that additional quantities and types of “organic” material could appear naturally in this environment when lightning hit waters rich in basic proto-organic molecules. More likely, such formations occurred when early organic molecules accumulated on clay or pyrite surfaces or at underwater volcanic vents (“hot-spots”) rich in iron and sulfur efflux [9]. Clay and pyrite surfaces are electrostatically attractive to such proto-organic molecules. In environments rich in such molecules, these can form a dense layer on the surfaces of those clays in shallow ponds or pyrites at deep-sea volcanic wells, keeping the individual basic molecules somewhat immobile in close proximity to each other.

This immobility, however, is not total stillness, since elevated temperature indicates a corresponding amount of “Brownian” movement appearing as a constant “wiggle” of all atoms or molecules within whatever space is available – resulting in corresponding collisions between adjacent molecules. Furthermore, radiation will cause further collisions and will partially impact the electron layers of the molecules – possibly damaging some electron “shells” and dissolving some bonds, but also possibly rendering them receptive to linkage with neighboring other molecules. Actual linkage, then, is a matter of probability and the right temperature, one high enough to permit forceful Brownian and electron-based interaction between molecules, but not too high to immediately destroy newly formed molecules again.

Considering the “astronomical” number of interacting molecules on all the potentially suitable clay or pyrite surfaces of Earth and the millions of years until DNA appeared on Earth as it cooled down, it is not surprising that critical conditions were reached at one point where RNA or DNA fortuitously formed and remained stable on a clay surface. In a shallow pond – or, more likely, at an underwater hot-spot or “vent” – RNA could have formed first, subsequently forming DNA.

Anthony Mellersh – in his Origins of Life and Evolution of the Biosphere (23, 261-274), 1993, indicates that an RNA strand adheres to a solid surface in an undulated way. Each of the folds of this undulation happens to be just three RNA bases long, permitting the fitting of certain amino acids into those folds. Could this have been the original process of one being formed from the other, amino acids from RNA or RNA from amino acids – with the rule that three RNA bases are needed for the definition of each amino acid upon translation – thereby being established? Inversely, could the aboriginal amino acids have formed minute bits of RNA on their surface that, when attached next to each other on a clay surface, formed these longer undulating chains and, hence, RNA? Then, only 100 genes on DNA/RNA were necessary to form primitive living organisms [10].

Luke Lehman (at Scripps, in La Jolla, 2004) demonstrated that extraterrestrial amino acids reaching volcanic underwater vents could combine with carbonylsulfide gases to form peptide chains, the beginning of proteins.

Günter Wächtershauser of Munich University suggests that it was an iron/nickel/sulphur surface as found at hydrothermal vents that produced amino-acids and proteins. Trevor Dale of Cardiff University expanded this theory indicating that proteins could crystallize in the form of long fibers (amyloid) acting as a catalytic surface for the origin of RNA. Charles Cockell of Open University, U.K., indicated that the numerous impact craters occurring during the violent early phase of Earth often generated hydrothermal springs leading to some of the above processes. Upon cooling, further evolution of organic molecules could occur.

The present status of science indicates that RNA was the first molecule that was self-replicating, utilized resources from its environment and was leading to evolution, therefore called a “living” molecule. But, while all precursor organic molecules could be synthetically produced by now, it was not yet possible to simulate the natural starting conditions sufficiently to produce RNA synthetically and prove any of the theories of its origin.

RNA is a very complex molecule – with a complex composition and structure, not flat as shown in chemical formulas on paper, but with a complex, three-dimensional shape. RNA is used by nature to produce amino acids, the building blocks of proteins. Amino acids did occur in outer space and, as indicated, were present on the early Earth or were transported there at a later time. Most, if not all, chemical processes can work in both directions. Consequently, could natural, aboriginal amino acids, some early nucleo-base, and cosmic formaldehyde have led to the formation of the first pieces of RNA? As pointed out in a later chapter, the translation of RNA into amino acids is not simple and commonly utilizes some facilitating proteins. Did some primitive proteins and nucleotides facilitate the back-translation of amino acids into RNA pieces? This may be the bottleneck for synthetic replication of RNA generation and may be providing for the uniqueness of its appearance in the first place.

One must assume that synthetic production of RNA should be possible in the future through ingenuity or fortuitous circumstances. This leads to the thought of “creating” a new, man-made start of natural evolution based on a variant of RNA. Such evolution could be controlled, in laboratories. But what if some of that new RNA escapes or is exposed to a natural environment somewhere on Earth? What would or could evolve from it over time? Possibly less than science fiction expects – since most niches for survival are filled. But the phenomenon of invasive species taking over new territories tells another story – and so does the precaution of NASA not to expose other celestial bodies with our organisms or Earth to possible organisms from other celestial bodies.

In any event, it appears as a miracle and singularity of Creation that only RNA appeared, only once, about 3.9 billion years ago as a self-replicating molecule leading to evolution – and, consequently, as the source of life. There is evidence that RNA is self-replicating and can also synthesize DNA (see, for example, the work done by Walter Gilbert, Sidney Altman). DNA is a much more stable molecule, capable of forming long and stable chains by linking multiple molecules like segments of a string together (by means of phosphorus linkage atoms). DNA can reproduce new RNA.

For these reasons, DNA may have prevailed at that early time over any other possible self-replicating molecules – possibly in the competition for scarce resources – for example, phosphorus – or in competing for favorable territories – for example, the areas with just the right temperature and availability of chemical compounds, as well as sufficiently undisturbed to allow nature to experiment with the formation of those molecules over some period of time. Some scientists believe that it may have taken 10 million years to produce DNA. But, as said, it has not been possible so far to synthetically reproduce any such “living” molecules.

It is equally difficult to understand why no other self-replicating and evolving molecule, different from RNA or DNA and their derivatives, has ever appeared subsequently in the course of the last 3.9 billion years. Theoretically, other forms of life along the lines of DNA should have become viable, even though propagating less efficiently than the one that prevailed. So many later microbes, plants, and animals have found niches to avoid predators and evolve – but no other “living” molecule ever found a niche in which to appear and start a different, surviving strain of life from that which we know and are made of. This must be counted among the mysterious singularities in evolution, as will be pointed out in a later chapter of this essay [11].

A much discussed scientific theory indicates that RNA or DNA may have arrived within a meteorite, possibly from Mars, from where many large meteors arrive all the time and many more arrived during the early phase of our solar system [12]. This would not solve the problem of the origin of life – it would just antedate and relocate the problem. The same can be said about the “Panspermia” theory, indicating that RNA or DNA may have arrived from outer space beyond our solar system and may be found in many areas of outer space [13].

There is a new conjecture indicating that the formation and multiplication of DNA were specifically favored on the early Earth by the existence of the Moon [14]. At that early time, the Moon was much closer to Earth, as described earlier. Consequently, the tidal waves were enormously larger, washing over wider areas and then leaving them to dry out again. This left more salt in the tidal areas. It is known that the double-stranded DNA helix tends to break up in one condition, only to form a new double helix in the other condition thereafter. Consequently, under the most favorable circumstances, there could have been a doubling of DNA with each tidal cycle, quickly leading to dominance. The problem consists in the fact that this assumes the existence of the Moon close to Earth at the time of the origin of DNA, some almost 4 billion years ago. As indicated above, in the chapter on the origin of the Moon, there are some serious problems with this assumption.

After all, it appears as if the availability of precursor organic compounds for life’s formation as evolved in cosmic space and deposited on icy comets, then their swift variation or expansion in the early oceans, as described above, may have been the prime candidate for the explanation of the RNA-based origin of life on Earth – and, possibly, in a similar way on other celestial bodies.

What we describe as life is a self-organizing system of complex molecules – taking on a life and evolution of its own in accordance to its own rules. This is another example of the “Combinatorial Principle,” but also of the “Basic Principle of Evolution”, as explained in Chapter 1.1.5, indicating that the universe evolves as possible at any one time or place in accordance with the then and there given starting and boundary conditions – with evolution being driven by probabilistic or random variations, and finding viability in accordance with opportunity.

If the origin of a “living” molecule, RNA, was a highly unusual event and occurred only once on Earth, can one say that all natural life on Earth descended from that one single molecule?

2. Molecular Biology

2.1 DNA, RNA, Ribosomes, Enzymes, Proteins, Lipids, Carbohydrates, ATP

In considering the further evolution of life from its mysterious beginning about 4 billion years ago [15], one has to look at the most important organic compounds allowing cells or organisms to live and evolve, described by their scientific designations as nucleic acids, nucleotides, codons, ribosomes, enzymes, amino acids, proteins, lipids, carbohydrates, and adenosine triphosphate, or “ATP”, for short.

Both RNA and DNA are called “nucleic acids” (DNA = deoxyribonucleic acid and RNA = ribonucleic acid). A preceding chapter presented a discussion on why RNA is assumed to be the source of life on Earth. But RNA itself is not very stable, and any strands of it easily break up into smaller pieces. RNA, however, is thought to have been capable of forming DNA – a much more stable molecule, allowing the formation of very long strands with superb multiplication capability. Thus, DNA is the molecule that became the repository, or archive, of our genetic foundation. RNA remained as the linkage between DNA and amino acids – by creating the amino acid strings that form proteins.

DNA is formed by two almost identical, twisted strings constituting the famous “double helix”. The individual segments of the DNA strands, the so-called nucleotides described below, consist of sugar molecules with attached “nitrogenous bases”. Each nucleotide along the nucleic acid string is linked to the next one by a “phosphate group”, a single oxidized phosphorus atom. The phosphorus links may allow – with all the necessary stability of those DNA molecules – the introduction of minor variations in the DNA strands under special external influences (chemical- or radiation-related). Such variations can lead to the mutations necessary for evolution, which in turn lead to different or higher forms of life at an acceptable rate. The variations must be slow enough to allow for the development of large colonies of viable living beings. On the other hand, the variations must be fast enough to allow for evolution to use opportunities and avoid risks connected with climatic changes, ecological changes, and the limited lifetime of our Sun and Earth – ultimately to reach the development of higher civilizations in the time between major catastrophes, as described in a later chapter.

The length of DNA may be only a few hundreds or thousands of nucleotides in simple organisms, but it reaches almost 3 billion of such nucleotide segments in humans. Such a long strand (about 2 meters long, if fully extended) is not left loose in the cell. It is set in a very tight spiral, then, in eukaryotic cells, wound around very small cores (nucleosome particles consisting of four histone proteins) produced in the cell, with just 1.8 windings or 140 base pairs of DNA per core (this DNA section then being called a nucleosome). The nucleosomes are separated by 20 to 100 base pairs of DNA and the whole spiral is then once more formed into a super-spiral. It is intriguing to notice that the spiraling is done in such a fashion as to leave important “addresses” (regulatory elements of the genetic helix) for later transcription accessible on the outside. The still very long spiral of a spiral can then be coiled and formed, upon fertilization or cell division, into some larger species-specific patterns, the so-called chromosomes, including the famous X-shaped and Y-shaped chromosomes of humans.

Along either of the two helix-intertwined DNA strands, the sugar molecule of each nucleotide is provided with a small protrusion – a “nitrogenous base” in chemical language – consisting of one or two hexagonal or pentagonal rings of carbon and nitrogen atoms with outward-reaching, additionally attached nitrogen or hydrogen atoms. These protruding molecules are connected to the corresponding (and protruding) molecules on the other one of the two twisted DNA strands. The connection is made by two or three hydrogen atoms as bonds at the end of those connecting protrusions, depending on how they are formed (their chemical nature).

An individual subunit of DNA, the combination of a sugar molecule with its nitrogenous base, is called a “nucleotide”. There are only four different kinds of nucleotides, according to the only four types of attached nitrogenous bases they may possess (called A, C, G, and T or, within RNA, U). When linking one strand with the other along DNA, only certain linkages of bases (or letters, as indicated) from one strand to the other are possible due to the very different configurations of the ends of those bases that have to meet and link between the two strands of DNA – and also to complement each other in their different sizes, thereby keeping the double DNA helix at relatively constant width.

Subgroups of three adjacent nucleotides along a DNA string are called a “codon”, because it always takes one such codon group of three nucleotides to let the subsequent messenger-RNA produce one specific amino acid as a building block of proteins. The type of amino acid that results is determined by the types and sequence of bases in the codon being expressed. The sequence of codons on DNA results in a corresponding sequence on the messenger RNA and, consequently, in a specific sequence of amino acids in the outgoing string of those amino acids, which is then called a protein.

A significant string of many codons, resulting in the expression of a protein, is called a “gene”. So far, about 20,000 human genes have been identified and 5,000 more are expected to be identified in the future, for a total of possibly even less than 25,000 human genes. This is just about the number of genes some fishes have and just 25% more than the number of genes for some worms. The difference comes from the capability of the human genome for gene splicing and control. Thereby, the same number of genes can express a vastly larger number of proteins, theoretically in the trillions [16], which is a much larger number than that of some plants and other organisms with larger number of genes but which are not capable of splicing. Additional differences may come from variations in gene coiling (or condensations, compressions) in the chromosomes, providing or inhibiting gene expression (see the new field of epigenetics discussed below).

RNA is similar to DNA, but consists of only one strand of somewhat different nucleotides. The nucleotide designated by the letter “T” in DNA is replaced by the nucleotide designated by the letter “U” in RNA. Three types of RNA are produced through transcription of DNA. Messenger RNA, the mRNA, is the agent in the creation of amino acids and their chain-like assembly into protein molecules, the main actors of life in the cells. Some amino acids do appear naturally in cosmic space out of the material available from earlier star explosions, transformed by the radiation permeating space. But most of the specific amino acids needed in organisms must be produced by those organisms themselves, beginning with the material that is available in their seed or egg cell. This is accomplished by mRNA based on the code found on DNA.

Another kind of RNA transcribed from DNA is called “rRNA”. Its transcription from DNA is facilitated by specific molecules called RNA-polymerases. The “rRNA” strings form “ribosomes”. They consist of a combination of several “rRNA” molecules and an additional accumulation of specific protein molecules. Ribosomes are large molecules that facilitate the transcription of mRNA into amino acid sequences, the new proteins.

Additionally, there is “tRNA”, the “transport RNA”. Its function in transcription is explained later.

Enzymes: “Enzymes” is the name of the group of proteins that act as catalysts – for example, the above-mentioned RNA polymerase (there are three types of those), facilitating transcription of DNA into RNA.

Amino acids: The core cluster of an amino acid consists of a nitrogen atom with two or three attached hydrogen atoms (an “amino group”) that is connected to a carbon atom with two attached oxygen atoms (a “carboxyl group”) by way of an intermediate carbon atom. Attached to this core cluster is one of 20 possible chains that define the specific type of the 20 naturally existing amino acids, all designated by a letter (in four groups, containing either D, E, K, R, H, or S, T, Q, N, Y, or A, V, L, I, M, F, W, or G, C, P) [17]. These chains consist of as few as one hydrogen atom (in Glycine, designated by the letter “G”) to a chain of six links (in Arginine, designated by the letter “R”), or a combination of a pentagonal plus a hexagonal arrangement of carbon and hydrogen atoms (in Tryptophan, designated by the letter W), and more [18].

Proteins, also called polypeptides: Proteins consist of chains of amino acids – with the core groups of the different amino acids being linked and their side chains remaining outside. The specific sequence of amino acid types being produced by mRNA transcription is indicated by the sequence of codons on the genome of the DNA that is being transcribed via that mRNA, as described before. The proteins do all the work in any living unit [19] – from the smallest proteins forming “picornaviruses” to the largest knots of proteins in the cells of the human body.

Protein strings can be up to many hundreds or even thousands of amino acids long.

Most proteins, specifically the larger ones, do not stay in an extended state but, after being formed, quickly fold into complex shapes. Each type of protein assumes a specific shape. These shapes are composed of spirals (α-helices), bands (β-sheets) and some loose ends, all lumped together in a specific way. The total form may be quite compact, but may also include certain niches where actually most of the protein’s action on, or sensitivity to, its environment takes place.

There may be 10,000 different types of proteins in a human cell at any one time (up to 50% of its mass) and possibly many hundreds of thousand different types in the human body at different times.

Lipids are a diverse group of molecules including fats used by the body for energy storage and lipid bilayers used in the cell as membranes. Lipid bilayers can naturally form spherical arrangements (bubbles) – so-called “liposomes” – providing excellent protection for the inside space within those bubbles.

The first lipid bubbles may have become available from the nitriles arriving on Earth with icy comets. But, once DNA and the secondary proteins were able to form lipids, it was only a matter of time until this capability led to ongoing production of protective bubbles around the DNA and its associated protein factory – an arrangement we now call “cells”.

Lipid acids, more commonly now called fatty acids, are chains of, typically, 14 to 20 carbon atoms, each with two attached hydrogen atoms. Their high carbon content explains their energy content when used in the form of fats as nourishment. Fats are three lipid acid chains connected at their end by a combination of a few carbon, hydrogen, and oxygen atoms. Lipid bilayers are double sheets of small interconnected molecules, each having two lipid acid chains attached, but all directed toward the intermediate space between two sheets forming the bilayer.

Carbohydrates: Carbohydrates include the various forms of sugars and larger molecules composed of sugars. The simple sugars (fructose and glucose) contain short chains of carbon atoms, with attached hydrogen atoms to one side and oxygen-hydrogen atom combinations, on the other, as well as more complex configurations of atoms at the end of the chain. These end-configurations determine the difference between the various sugars. Some sugars can form three-dimensional hexagonal rings out of their chains. Carbohydrates provide an easily accessible energy supply to the body – by way of oxidation in the mitochondria – providing heat and forming ATP – the latter transferring energy to wherever it attaches itself to.

Glucose, the main energy source for the body, is formed in the liver from various food materials absorbed by the intestines and can be stored in modest amounts in the muscles (in the form of glycogen). Plants store their energy surplus in a multi-molecular form of sugar called “starch” (e.g. in potatoes and cereals).

Sugar molecules also serve as the structural element of larger molecules, as in cellulose and cotton and when forming the supporting strings of DNA and RNA. Cellulose may be the most abundant organic material on Earth, with high energy content, but animals lack the enzyme needed to break it up and absorb it as food [20]. Sugar molecules also can form “chitin”, a plastic-like material used as supporting structure (armor) by the invertebrates.

ATP: The small molecule adenosine triphosphate (ATP) plays a key role in the cell wherever energy is needed – for example, in the formation of proteins through transcription and in the deformation of proteins as in working muscles. ATP consists of a complex head formed by a couple of hexagonal or pentagonal rings of carbon and nitrogen atoms with an attached tail of three phosphorus atoms, coupled by oxygen atoms and with oxygen atoms to their sides. The last of these phosphorus atoms can be shed with an explosive effect, driving the ATP head or third phosphorus link, and whatever it is attached to, forward. This may serve for the firm attachment of a smaller molecule to a larger one by overcoming the mutual repulsion provided by their electron orbits. It may also help molecules to move forward against fields of electric potential as when moving through openings (“channels”) in a cell wall. Finally, it may serve to bring a protein molecule to a different folding pattern, with different geometric aspects resulting, for example, in the movement of muscle fibers relative to each other. That can result in a “shortening” of a packet of muscles on the body.

ATP is produced or reconstituted in the mitochondria of a cell with the assistance of an electron-donor molecule (NAD, resulting from the vitamin niacin) and the components and energy from sunlight in plants or, in animals, from oxidizing carbohydrates (glucose, a hexagonal ring of carbon atoms with attached hydrogen atoms, then becoming carbon dioxide and water) and fats (fatty acids, ultimately also becoming carbon dioxide and water). There may be a million ATP molecules in a single cell at any one time, being replenished by the mitochondria as needed.

One cannot leave this section without marveling how the few basic atoms – carbon, oxygen, hydrogen, and phosphorus (why phosphorus, and no other?) – arranged in a few interconnected simple patterns – in simple hexagonal and pentagonal rings or just in more or less extended strings – can result in so many different molecules with such widely different and important functions in the human body (or in any other organism), thereby providing the phenomenon of life.

All of these phenomena of origin of organic molecules, their interaction, and life can be seen as another demonstration of the Combinatorial Principle that was presented in connection with cosmic evolution as facilitating and driving the amazing evolution in the universe – whereby individual particles are capable of combination in such a way that the resulting larger components present totally different types of characteristics from their constituent parts. Carbon dioxide, water, and some other small molecules were able to form proteins, lipids, and carbohydrates – that were able to form living cells – that were able to form organisms – that ultimately had brains – and formed civilizations.

One can also marvel at the shapes that folded DNA and proteins can assume – the art of nature – so different from our art and, yet, so intriguing.

2.2. Cell Evolution: Genomics, Proteomics, Computational Biology, Epigenetics, Death

Upon the origin of life, the formation of “cells” was the most important innovation after the appearance of RNA and DNA, possibly occurring simultaneously out of self-forming lipid bubbles protecting their interior space where undisturbed proto-organic evolution could have taken place. The original living and multiplying cells may have contained little else but DNA, RNA, some proteins, and a nutrient solution of water.

It was the most important accomplishment of the following three billion years of slow evolution, prior to the appearance of complex organisms, to develop some advanced cells, the “eukaryotic” cells [21], with a number or important internal structures and functions – setting the stage for the subsequent explosive evolution of higher forms of life. These internal structures of cells, also called “organelles” – some possibly symbiotically acquired by absorbing other micro-organisms – include (organized by their function):

- A major internal separation:

o Nucleus: An inner membrane includes the DNA, now subdivided into chromosomes, and provides protected space for the transcription of DNA into RNA

- Structures serving the controlled transport of materials

o Endoplastic Reticulum: a complex structure surrounding the nucleus providing surfaces for directed molecular transport

o Golgi apparatus: Membrane enclosed spaces for the transport and processing of lipids and proteins

o Lysosomes: Membrane enclosed spaces for transport and digestion of imported materials

- Structures serving the energy household of the cell

o Chloroplasts (only in plants): Membrane-enclosed spaces for photosynthesis

o Mitochondria: Membrane-enclosed sub-units, now believed to be symbiotically incorporated basic bacteria with their own DNA, providing oxidation of organic materials resulting in either heat or production of ATP for subsequent processes requiring energy (muscle movement, formation of proteins, and more)

- Structures for the physical stabilization of the cell and material transport within

o Cytoskeleton: consisting of various fibers providing structural support for the cell and placement of organelles or RNA when in translation into proteins, but also serving as path for molecular movement within the cell, and, finally, serving to divide recently split chromosomes in the process of cell division

and more. All of these structures or “organelles” function in a complex way of chemical, molecular, or just electron processes as studied and described by “molecular biology” [22].

The essence of life and the core of a living cell is the DNA double helix. It has a surprisingly simple structure – but the dynamic world of all the many thousands, if not many millions, of molecules within a cell is astonishingly complex. All molecules are in constant movement, in either a slight wiggle at a given place or in a zigzag movement under the influence of perpetual collisions with neighboring particles. Some of those movements follow certain surfaces of structures within the cell; others occur in the three-dimensional space of the cell liquid, the cytoplasm. This movement is the energetic expression of heat and is called “Brownian” movement, sensed by us as temperature. Equally important are movements of certain molecules that are guided by electric potentials along the outside of larger molecules, as when providing the translation of DNA and RNA or when passing through “gates” in the cell membranes. Between these erratic Brownian movements and the guided progressions, the choreography of molecules in a cell is a strange combination of random events and strictly regulated progressions – a dichotomy that was already described in cosmic evolution and appears as a basic principle of all natural evolution – and that can still be found in human thought and human societies in their progression.

To understand the dynamics of the world of molecules in a cell, one has to look at the atomic forces at play. Positive and negative charges attract and neutralize each other, but two positive or two negative charges repel each other. As discussed before, atomic nuclei are composed of protons that are being held together by neutrons. Each proton has one positive charge, consequently capturing one electron with its negative charge. The electrons “circle” the nucleus at a certain distance, not unlike planets. The all negative electron spheres, also called “shells”, of adjacent atoms repel each other, keeping the atoms or molecules apart. But when an electron is missing in the outer shell of an atom, the forcing together of adjacent atoms, as in collisions, can lead to the sharing of an electron. This provides a permanent bond between those two atoms. Consequently, the Brownian zigzag movement of all the molecules within a cell result from those particles being bounced off the electron shells of other molecules, but this movement can also lead to new bonds, resulting in “chemical reactions” of the molecules among each other.

There is one additional energy source for molecular events in the cell -- ATP (adenosine triphosphate). This is a small organic molecule with an attached tail of three oxidized phosphorus atoms, as described above. The separation of the last of these three phosphorus atoms (called “hydrolysis”, due to the need for the presence of water) is an almost “explosive” event, setting energy free for motion or chemical bonding. ATP is produced in large quantities by the mitochondria in the cell, utilizing the carbohydrate food intake or fat storage of the body and oxygen as supplied by the bloodstream. Subsequently, the energy from freshly formed or reconstituted ATP can be used through hydrolization to facilitate chemical reactions in the cell or just for the folding of proteins, motions of molecules against electrostatic fields, or deformations, as in muscles.

If one were able to shrink oneself – to the size of a molecule within a cell, – one would be in a large room comparable to, say, 20 feet length, width, and height (if one equates one foot to 1 micrometer, which is one-millionth of a meter). The organelles described above would appear as bulky furniture distributed within it and, in the case of the lysosomes, moving three-dimensionally through the cell. There would be plenty of water molecules floating around, constituting as much as 70% of the cell content (“cytoplasm”), each about one-thousandth of an inch wide (corresponding to a few Angstroms or to 10^-10 meters). The very numerous ATP molecules (up to a million within a cell) are about ten times larger than the water molecules, in our presentation about one-hundredth of an inch wide (less than 100 Angstroms). The thousands of proteins in a cell (constituting up to 40% of the cytoplasm in some cells) are about one-tenth of an inch wide (less than 100 nanometers, 10^-9 m), but would be up to several inches long if they were not coiled up in little balls a few tenths of an inch in diameter. The chromosomes that appear only upon cell division would be short of a foot tall (less than a micron), but if the human DNA string were ever extended, it would be about 1.3 miles long in this visualized miniature world [23].

The above indicates that the larger molecules and organelles are imbedded in a very fine quicksand of water and ATP molecules, which constantly wiggle and move around. This lets even the largest molecules move erratically, as they themselves move and are being pushed by surrounding molecules in Brownian movement. Diffusion figures at the level of cells are difficult to come by and are contradictory. Indications vary from diffusion rates of 6 microns (1 micron = 1 millionth of a meter) per minute to 400 microns per second. This indicates that protein molecules may need several minutes or only small fractions of a second to move from one end of a cell to the other (possibly as little as one-thousandth of a second, especially the smaller molecules when they move along the surfaces of the flat cell structures, the organelles, described above) [24]. This lets the innards of a cell appear not just like a boiling stew, but like a most dramatic convulsion of the thousands of types of molecules that are on the loose in the cytoplasm, with the flat surfaces of internal cell structures exhibiting swiftly moving molecular layers like oil slicks on pavement.

The need for this dynamic behavior becomes apparent when one looks at the process of generating new proteins through translation of RNA, specifically during rapid cell division. Some bacteria cells can multiply in less than 20 minutes under favorable circumstances.

Compared to this random convulsion, the motions of directed molecules following prescribed paths appear calm and determined. Take, for example, the duplication of DNA upon cell division or the transcription of DNA into RNA or the translation of RNA into proteins. A special protein (the “initiator” protein in the case of DNA duplication, a specific “transcription factor” in the case of selective DNA transcription, or a “ribosome” in the case RNA translation into proteins) begins the process either at the end of the DNA or RNA or at a specific “address” site on the DNA or RNA as given by the transcription factor. These special molecules are created by the cell upon the need for certain proteins or under the influence of neighboring cells, thereby controlling the destiny or role of a cell in the body in the formation of whole tissues or patterns (including surface colorations of flowers and butterflies). There are other proteins that continue the process of transcription. In the case of DNA being transcribed to RNA, it is RNA polymerase; in RNA translation into proteins, it is ribosome. There are at least 30 different types of protein involved in the complete transcription and translation.

In the case of RNA translation into proteins, each codon on the RNA has to ascertain that a specific amino acid is added to the nascent protein in the proper sequence. This is accomplished by “transfer RNA modules”, one for each kind of amino acid, that capture the required amino acid from within the cytoplasm (by means of a special enzyme) and guide it to the ribosome to be attached to the nascent protein in its turn, under control of the ribosome. While the ribosome proceeds with the attachment, with energy provided by ATP (and GTP), it is already guiding the next specifically required amino acid by means of its transfer RNA to its place next in line.

The transcription or translation proteins slide along the respective DNA or RNA string like a sequence of pearls, guided by their shape and driven by field potentials at the point of their action and by energy supplied by ATP when shedding one of its phosphorus atoms.

The progress of translation can be in the order of hundreds of nucleotide steps per second. This is even more impressive if one considers that, at this rate, matching the type of nucleotides of the string to be translated with the proper nucleotide material from the cytoplasm has to be accomplished in the proper combinations(!). This explains, to some extent, the need for the great quantity and great mobility of the molecules in the cytoplasm that have to become available at the small points of action in the cell at the right time. Furthermore, one has to consider that not only one transcription or translation takes place in the cell at a time; multiple DNA genes can be transcribed at the same time. The same gene (or part or combinations thereof) can be transcribed several times. A piece of mRNA can be translated simultaneously by a substantial number of ribosomes into a stream of identical output proteins.

This lets a cell appear as a humming factory for the mass production of proteins – when highly active, as in growth phases. There are other phases – when the organism is at rest, in hibernation, or in segments of the organism – that are not in an active state. Even a resting human body, however, has ongoing respiration, digestion, circulation, minimal muscle movements, and brain functions – plus the continuing growth of skin, hair, and nails – all requiring ongoing cell functions, including translations and protein activities.

Transcribing DNA or RNA and producing proteins is not all that a cell does. Once the proteins are formed and properly folded, assisted by a group of many other proteins, they enter a very complex network of interactions of molecules. At any one time, there may be thousands of types of proteins in some cells and some hundreds of thousands or even millions of types of proteins (including the many antibodies) within a human individual. Of these, many are formed by the 25,000 human genes or their splicing and combinations in transcription. Others are provided by protein interactions in post-translational modifications, thereby contributing to protein diversity. Some special ones are provided by food intake (for example, vitamins and medications).

Modern science has been able to trace the network of protein interactions for some important cell functions. On paper, they look like strange line patterns with many intersections and back-and-forth progressions across the picture, some repetitive or circular. Considering the fact that the human genome can produce tens of thousands of proteins, there are many such network patterns of protein interactions that are active at any one time in the cell. All this must be visualized not only in chemical, but also in physical terms as the wild motion of molecules in erratic diffusion or guided paths, thereby perpetually combining, unfolding, refolding, and separating – with the addition of the large number of explosive ATP hydrolizations providing the required energy. The discovery and understanding of all the possible networks of protein interactions may well be the main task of molecular biology and “proteomics” in the foreseeable future.

One may want to look at ATP (adenosine triphosphate) in greater detail. The human energy source is food, digested and distributed throughout the body to each cell. Within each cell, there are domains called “mitochondria” – possibly the remnants of once-independent organisms that were symbiotically incorporated into more advanced cells when the cycle of energy from the Sun through chlorophyll was replaced by energy gained through the oxidizing of organic material through evolutionary steps some 600 million years ago (possibly beginning already some 1.5 billion years ago).

Mitochondria’s main function within a cell is the production of ATP from glucose and fats. The amount of mitochondria in a cell or tissue varies with the function and need of the cell or tissue. Depending upon demand in the cell, a more or less copious stream of ATPs emanates from the mitochondria into the cytoplasm that obviously can store only a limited amount of these molecules.

The “burned out” ATP molecule, having lost one of its phosphorus atoms, now in the form of ADP (adenosine diphosphate), returns to the mitochondria, where it is reconstituted into ATP.

Another dynamic effect results from openings in the cell membranes. There are either “gates” for the transfer of materials or merely some protruding proteins poking partway through the membranes for signaling between cells and their surroundings, as for controlled cell growth or behavior. Such molecular signals let the cell realize its specific function within the texture of the body. This leads not to total DNA replication but to the transcription of only those parts of DNA into RNA and translation into proteins that are required for the cell’s function at its specific place and time. The gates transfer not only signals and nutrients into the cell and waste product out of the cell, but also transfer substances for cell metabolism or, in the case of glands, transfer necessary substances from the cell into the organism’s body.

The enormous complexity of simultaneous and alternative molecular activities in the cell can no longer be analyzed or influenced by conventional laboratory processes. Increasingly, computer analyses and models are utilized. Potential processes are computer-modeled, even the folding of large proteins. The models are increasingly refined and have now reached a high degree of accuracy. Interdisciplinary molecular biology supported by computer scientists utilizing large computers (“computational biology”) is the most advanced form of research at this time, concentrated mainly on “proteomics”, the field of science related to proteins, their composition (their amino acid sequences), their folding into specific shapes, and their great variety of interactions [25].

The large variety of proteins in the cell and the very complex molecular interactions must have evolved over a long period of time after the origin of life. At first, RNA and some primary proteins may have given origin to life on the basis we know. Subsequent DNA and chance enlargements of its molecular chain through attached nucleotides [26] may have given origin to new proteins, some useful and retained in superior cells, others not, leading to cellular “birth defects” and the disappearance of those cells. Could the large number of unusable nucleotides (introns) on the human genome partially be witness to that? [27] Life existed for more than 3 billion years on the monocellular level before complex organisms arose. If one counts possibly two cell divisions per day in the most prolific areas on Earth, there were about a trillion generations for the evolution of cellular complexity – and many trillions of cells were evolving in parallel – resulting in trillions time trillions of nature’s experiments.

It is interesting to note that it was the complexity of the above described molecular dynamics that permitted an increasing diversification of cells and, later, of the swiftly evolving organisms. Diversification and evolution required at least some changes in the DNA-RNA-Protein sequences. More often, it required the addition of new steps on the genome, genome splicing and control of expression, and, thereby, the production of additional types of proteins, specifically as the rise of complex organisms required a great variety of different cells to develop out of the same seed or egg cell.

To explain the swiftness of some important hereditary adaptations to the environment in biological evolution only by the theory of random changes in the genome has left some scientists dissatisfied. While religious people look for divine interference in genetic evolution (see the Intelligent Design Theory, discussed later), these scientists recently began to look for another scientifically provable mechanism of genetic change. The field of Epigenetics [28] investigates the occurrence of heritable changes in gene expression without changes in the DNA sequence. Specifically, DNA methylation, histone acetylation, and RNA interferences are being investigated. This leads to the consideration that the very complex multiple gene coiling in chromosomes may possibly become influenced by environmental factors. This can lead to the covering of expression addresses on the genome and, hence, expression inhibition – and possibly other factors.

While this effect of gene expression modification is understandable, it still is not automatically heritable. Only if the new form of gene coiling (or compression, condensation) becomes part of the egg cell and is propagated, would this environmentally triggered effect become hereditary. A permanently not-expressed gene could subsequently deteriorate without being rejuvenated (lacking random failure elimination) through selection and end up in the junk genome. Furthermore, gene over-expression or inhibition is known to be a factor in cancer. Furthermore, this concept seems to lend itself more for the explanation of gene suppression and less for the explanation of gene modification or creation.

It is a mysterious fact of nature that cells do not live eternally. The limited life and ultimate death of all complex organisms, including humans, is based on molecular circumstances on the level of cells. For one, there can be pathological events in consequence of invasions by bacteria or viruses. There also can be errors on the genome leading to the production of erroneous, “toxic”, or non-functional key proteins that result in the cell not being able to continue its function. The whole organism may not be able to survive, as when excessive cancerous growth occurs in the brain.

On the other hand, there are various molecular circumstances that lead only to aging and age-related death of the cell [29]. For example, in animal cells, the tail end of the genome, the “telomere”, deteriorates with successive cell divisions, finally leading to the cell’s dysfunction. At that time, the cell initiates its own termination, a form of cellular suicide. The debris of a single or a few cells is quickly removed from the body. A dead body, returned to earth, quickly returns to the cycle of materials and energy in nature and may be taken up again by other organisms [30]. While this leads to the conclusion that all cells are mortal, the egg cell of an organism, forming a new organism in the next generation, actually survived. Consequently, there is a form of “permanent” life for one strand of cells through all generations. This is even more apparent in monocellular organisms propagating by simple cell division.

From the human point of view, one must marvel at the dynamic world of the molecules in the cell – not only as the carriers of our lives and minds – but also leading us to ask an existential question of our existence: what, or who, are we if our component parts are constantly changing, new ones arriving in our bodies, old ones disappearing from us such that, at the end, possibly none of the original parts we were born with is still within us – yet, we are still the same individual. Is the essence of living beings not in their physical substance, but only in their configuration (“Gestalt”)? [31]

In sum, it is the dynamic world of the proteins and other molecules in the cells that provides for the evolution and functioning of all life, even in the largest and most sophisticated organisms. Of course, a protein does not “know” what it does; it just appears to follow the given circumstances in adherence to the natural laws of physics and chemistry. When a nerve impulse reaches a certain cell, the fibers within it are moved by the action of released calcium that activates ATP (by hydrolysis), and a muscle contracts – with whatever consequences for the organism. But when a certain pattern of neurons in the brain are activated in connection with a “thought visualization”, some cells in the body may produce large amounts of adrenalin, activating the whole organism, leading to whatever beneficial or catastrophic consequences for the whole organism. In other words, the molecules in the cell do not merely follow blind laws of physics and chemistry. There can be a controlling – or, at least, somewhat influencing – mind far beyond the cells. We will see more of this in the discussion of the brain and mind in later chapters.

In the course of evolution, it was first the cosmic evolution that produced its great variety of phenomena and structures and is now moving on for many more billions of years toward its ultimate exhaustion and dissolution. But subsequent to this physical evolution, the origin of life on Earth – and most likely on other planets in the universe well before – produced another evolution of new phenomena in existence, namely, in the cells. This new natural, biological evolution may appear less powerful but it became at least equally if not more complex, at least equally if not more dynamic than the cosmic evolution – leading to a new dimension of existence in the molecular life of cells – and, later, to organisms and the human mind.

3. Natural and Human Evolution

3.1. The Changing of the Oceans and Atmosphere. Organisms. The Tree of Life

Life requires the input of energy to transform the basic materials of simple carbon compounds, water, nitrogen, and others into the organic materials of proteins, sugars, lipids, and more. Two sources of energy were available on early Earth, volcanism and the Sun. The most dependable source of volcanic heat combined with material for organic processes was presented at the fissures where continental plates slowly separated over hundreds of millions of years, deep under the oceans at deep sea vents. In contrast, the most favorable areas for availability of the Sun’s energy and material for organic processes were in shallow waters or directly under the surface of the oceans. Consequently, nascent life split rather early into those two directions. The undersea life of Archaea bacteria and a resulting deep sea food chain as well as the variety of primitive microbes living deep within rocks [32] will not be further discussed in this essay, even though they may well constitute a large portion of the mass of all living organisms on our planet. It was the other direction, of Sun-based life, that ultimately evolved into human life and that will be the object of further discussion.

The early atmosphere of Earth consisted mainly of nitrogen, carbon dioxide, methane (CH₄), spurious other elements, and only a minor percentage of oxygen. Early life, in the form of monocellular plankton or algae, had developed some very significant processes. It was able chemically to combine the dissolved calcium in the oceans, augmented by influx from the erosion of early land masses, with carbon dioxide from the atmosphere (that became dissolved in the oceans) to form structural and protective shells. Upon the death of those monocellular beings, their shells fell to the ocean floor and formed limestone – or, in its purest form, marble. Furthermore, the process of photosynthesis appeared, allowing those forms of early life to utilize solar energy for the production of bio-substances, thereby absorbing even more carbon dioxide in order to extract the carbon for use in biological compounds. This left oxygen as a by-product that was released to the oceans and, later, to the atmosphere.

The original oceans on Earth contained large amounts of dissolved iron, augmented mainly by submarine volcanic activity and the influx of sediments. The dissolved oxygen from the original atmosphere and any other oxygen subsequently formed by algae photosynthesis, as just mentioned, were quickly depleted in forming insoluble iron oxides that resulted in deposits of banded iron formations and red clays at the bottom of the oceans. Only after all iron had been deposited out of the oceans could oxygen accumulate in any significant quantity in the oceans and atmosphere. This began about 2.5 billion years ago. Oxygen availability has increased steeply since that time as a product of increasing biological activity.

Beginning about 800 million years ago – and more rapidly about 550 million years ago – the abundance of oxygen in the atmosphere and oceans facilitated the appearance of a new energy cycle for the growth and reproductive needs of early forms of life by utilizing the oxidation of already existing organic material as the source of energy. This had a number of significant evolutionary consequences:

- The era of “complex organisms” began. The concept of “complex organism” shall be used here to describe composite beings consisting of large numbers of connected cells with differentiated functions in specifically structured arrangements. At first, those arrangements may have been just tubes, evolving beyond the earlier occurring algae strings of identical cells. The formation of these tubes floating in water facilitated the capture and digestion of other biological material (plankton or simple algae). Only later did one end of the tube become a mouth, and the other a restriction to retain the captured material until digested by means of emitted enzymes. Enzyme production and food absorption may have become delegated to suitably located cells. Extensions of strings of cells may have evolved into food-capturing tentacles – and these later into limbs.

- The internal cell structures (organelles, as discussed) and the digestive system appeared and mitochondria became incorporated in the cells to serve energy conversion (by way of ATP production for the formation of more complex proteins or for muscle contraction, see earlier chapters, or for body heat in warm-blooded animals).

- Larger size and different functions were an advantage in the competition with other bio-material-consuming organisms for food sources.

- Larger size and functional differentiation could also be a defense against being consumed by other organisms – with high propagation rate being another defense of some species against being extinguished.

- Differentiation allowed the utilization of ecological niches in an increasingly crowded world – ultimately leading to the population of the dry land of the continents. Speed of differentiation or of evolutionary adaptation allowed early occupation of niches.

- Larger size and the accumulation of specialized cells increasingly required coordination and control within the organisms – at least in balanced growth and balanced function – as known to be largely accomplished by inter-cell and intra-cell control mechanisms on the level of proteomics, facilitated by an increase in the number of types of proteins and their interaction. In other words, the increasing complexity of organisms went hand in hand with the increasing complexity of protein functions.

The consequence was an “explosion” of genetic evolution and, more so, a consequential substantial increase in protein complexity leading to basically new structures of life and ever new varieties of species in the oceans, in wetlands, on or under dry land, and in the air – even at submarine hot-spot vents or under snow and ice.

Evolutionary biology has traced this evolution and has developed a pictorial presentation in the form of the “phylogenetic tree of living organisms” – with the earliest beings at the root and the later beings forming the trunk, branches, and twigs of that evolutionary “tree” – humans commonly being shown at the top.

Strangely enough, it is not possible to indicate the earliest root of the evolution of life with any degree of certainty. The genetic material of the earliest cells that appeared about 3.9 billion years ago was not retained in fossil materials. Should one assume that there were even simpler forms of life at an earlier time when RNA may have been the starting molecule of life’s origin about 4 billion years ago?

Subsequently, a very early split into two branches of cells – the undersea cells living at submarine hot-spot vents and the earliest cells living in shallow surface waters – allow the assumption that either one of the two was the earlier form of life with the other being a derivative.

Even later, as life branched into various forms and higher forms of life appeared, it is often not possible to indicate precisely the sequence of evolutionary development. There is discussion concerning the correct presentation of the main trunk of evolution. Should it be the line that ultimately leads to the highest form of life, humans – leaving the now-disappeared dinosaurs on a side branch? What if humans will be exterminated in the next global catastrophe and even higher life would evolve from a different branch than mammals, leaving humans as an abandoned side branch?

There is one valid comparison with a tree – the lower branches of life’s development are wider spread, are quantitatively larger, and arrived at greater diversification than the top branches – possibly on account of more time having been available, but also on account of the shorter reach of smaller organisms and their faster multiplication.

There is another mystery with the evolution of life: The “phylogenetic tree” obviously is not a “tree”. Trees appear as multiples in forests. On any tree, the same leaves and fruit sprout on each branch. On the phylogenetic tree there is no repetition. All branches, twigs, and their endings are different. Why is there only one tree and all branches are singular? Why did the primitive form of life not permit the evolution of other trunks of higher life to shoot up from time to time? Why did similar branches not evolve out of the main “trunk” from time to time, again and again?

Why is the proper presentation of the evolution of life not a forest or bush? The standard response is that life was quickly crowded on Earth and all niches were rapidly occupied, which did not allow any new “trunks” or “branches” to appear, but only further development at the tips of the trunk and branches. This is not totally believable. Geological instability on Earth repeatedly formed new islands (as Australia, Iceland, the Hawaiian or the Galapagos islands) or remote valleys (as in the Himalayas). Steep climate changes (ice ages and new warm periods) or catastrophes repeatedly opened immense areas for new niches of life.

The rate of mutation of DNA in various cells is rather constant over long periods of time. Most such mutations lead to failure and, consequently, no evolutionary progress. Evolutionary progress depends upon the arrival of more suitable characteristics for propagation or survival in a constantly changing environment that is also subject to catastrophes. This results in the fact that the rate of evolution of the tree of life is not uniform, neither along the “trunk” of the tree toward higher levels, nor along any of the branches or twigs in the evolution of families or species of beings. Some species are wiped out, others remain unchanged for millions, if not hundreds of millions, of years (for example, the horseshoe crab). At other times, one can observe rather swift evolution of certain characteristics in some species – if not the appearance of new species. The evolution by punctual swift phases of evolution seems to be the rule rather than the exception. This may specifically be the case when new opportunities for evolution appear, as in the form of new niches not occupied by other species, or when nature “discovers” new niches by randomly providing some species with some new characteristics – for example, a very large brain.

There is an often repeated discussion whether there can be genetic adaptation to learned and successful habits. In detail, there are two effects. Environmental factors, including learned behavior, can have an influence on gene expression. Certain biochemical intake by pregnant mothers lead to different fetus development. Certain biochemical intake or environmental factors lead to different growth and aging processes, possibly by influencing gene expression. But these effects are restricted to individuals and do not become hereditary, unless damage to the genes occurred. All else is based on genetic changes, not necessarily in code changes, but also in variation of gene expression on gene multiplicity with those events having a much higher probability than genetic code changes and being responsible for some of the spurts in species development. These questions are being investigated by the field of epigenetics as discussed above.

Interesting evolutionary “progress” occurred in our time through the interference with nature by means of domestic animal or plant breeding by humans. Not only were new domesticated species created, but lately their genetic variation has been artificially accelerated, as in cattle, dairy cows, and horses. Equally rapid is the human genetic engineering in plants. A large effort is under way for the genetic engineering of cures for human diseases – possibly resulting in the evolutionary change of the human species. Complex questions of bioethics and practicality are involved.

In other words, human science takes control of the evolution of the tree of life in accelerating some evolution, bringing unforeseen changes, as well as cutting many branches by extinguishing many species – the latter being welcome when it is a matter of extinguishing certain diseases (for example, polio) or pests (for example, malaria-carrying mosquitoes). In general, mankind moves along an unknown path in pursuing genetic manipulation – not clearly knowing or agreeing what the goals are, not clearly seeing the consequences, not really knowing what we truly want, how an ideal world would look and still be functional, and what we should avoid.

In every instance that science has been able to analyze, the evolution of life was led by the “basic principle of natural evolution”, whereby each evolutionary step was conditioned by the starting conditions and by the boundary conditions and was driven by statistical or random variation of some genetic characteristics – with subsequent propagation beyond available resources and selection of the survivors or progenitors by the prevailing of the fittest.

3.2. Oxygen, Life Feeding on Life, Mobility, New Functions, the Brain, Complex “Systems”, Ecological Communities

As indicated, the availability of an increasing amount of oxygen in the atmosphere and oceans led to the appearance of a new energy cycle for the growth and reproductive needs of early forms of life utilizing the oxidation of already existing organic material – leading to more complex, larger beings and the evolution of the “tree of life” [33]. There were still other significant evolutionary consequences of this development:

- Not only bio-detritus was used for oxidation – but life began to feed on other life in a predatory mode of behavior.

- Feeding of life became not only predatory by hunt-and-kill, but also by smaller organisms attacking larger ones (for example, such pests as lice, ticks, and mosquitoes) or by invading larger ones (viruses, bacteria, worms, and snails) – the beginning of diseases and other afflictions.

- Occasionally, predatory behavior turned into important symbiotic arrangements – for example, the inclusion of mitochondria in animal cells, bacteria in the digestive tract, or the fungus cultures of some ants – in modern time, the care for fruit trees or the keeping of domesticated animals.

- Mobility was needed (and the fittest were selected) in order to prevail in the search for more biomaterial after the immediate surroundings were harvested. The mobility increased competition and led to fighting, leading to evolution for the prevailing in that situation, too.

- Sexuality was facilitated – the initiation of multiplication upon combination of DNA from two different generating organisms – later leading to gender differentiation. This had two benefits for evolution. “Inbreeding” resulting from the accentuation and repetition of genetic errors was avoided. Evolution was accelerated where different favorable traits form the parental organisms where combined in the one new organism.

New Functions:

The important innovations supporting this development toward a dynamic mode of life were the appearance of new functions:

- Sex organs – for the production of multiple seeds or eggs and pollen or semen

- The muscles for motion – for the search of new food sources and food ingestion (biting, eating), for attack or for defense

- The circulatory system to bring large quantities of oxygen to concentrated muscle packages

- Sensory capability to recognize favorable directions for motion

- Nerves to process the signals from the new sensors, for (initially reflexive) control of the muscles

- Interconnection of nerves and networks of nerves for complex signal processing of sensory inputs, for complex motions, and for strategy formulation

- The last finally resulting in the formation of the brain

The propagation or multiplication by means of dedicated sex organs and seeds or eggs was a most important, miraculous and ingenious “invention” of evolving nature and became necessary as the cell-by-cell division of large, complex organisms “in toto” for multiplication became impractical or would have been impossible [34]. The multiplication through seeds or eggs and subsequent growth required the appearance of growth control – as by an internal “clock” – accomplished by rather complex protein processes – sometimes under external influences (the blooming of plants after, at first, a cold period followed by the warming in spring).

Early cell deformation for motion may have been simple, functioning under the influence of external or inter-cell signals (such as in anemones and jellyfish). But mammalian muscles became rather complex and operated under the influence of nerve signals that act on ATP and protein strings within the cells. How did limbs evolve? Where they some tentacles in more primitive organisms that added motion?

The circulatory system may have evolved out of a fold or borderline between tissues of primitive organisms.

Sensors for light, chemical compounds, touch, or sound evolved in many branches of the tree of life and in many different ways (from various forms of eyes to antennas or skin sensitivity). Sensors became meaningful only as nerves became available to control subsequent behavior.

It is a mystery of nature how nerves were originally developed. Why, and how, would a very long cell have developed in early organisms for the purpose of signaling between two points or between groups of dedicated cells within the organism (as for contraction after some input signal)? Could this also have occurred along some tissue folds or borders? [35] It too is a mystery that basically only one type of nerve (with minor variations) was ever developed and can be found on all branches of the tree of life. The nerve is rather complex and slow, using a fairly complex system of neurotransmitters for signaling. Why was no other type of nerve ever developed by nature (for example, with metallic conductivity)? [36]

The Brain:

Linear nerves permit reflexive behavior (if you burn your fingers, your arm twitches and retracts the hand with the fingers). A significant step in evolution occurred when a nerve began to act on another nerve. Two nerves with feedback to each other allow the formation of a “flip-flop” for “on-off” behavior with memory. More complex interconnections allow for complex memory and for complex responses, leading to networks of nerves.

Certain midbrain functions must have developed very early in the evolution of animals, thus allowing the fast and economic summary assessment of situations for basic reactions as “fight or flight”. Special nuclei developed in the early brains for these evaluations. Later developments led to the appearance of ever more refined “emotions” – and, ultimately, to ethics and our human system of values that give structure, direction, and meaning to our lives.

Nerves did develop a variety of neurotransmitters for the biochemical coupling of nerves. This variety of neurotransmitters, some of them specialized for different functions in the body and brain, allowed for differentiated influences on body and brain functions – as by biochemical substances in connection with emotions (for example, the formation and effect of adrenalin or dopamine).

The formation of ever more complex networks of nerves led to the appearance of large accumulations of interconnected nerves close to the output of the most important sensors – for fast and appropriated response based on memory. This, in turn, led to the formation of the complex brain of mammals. The expansion of the cortex, mainly in the frontal regions, led not only to greater memory. Of equal or even greater importance was the increase in interconnectivity and greater addressability of memory elements. Thereby, language skills appeared, but also higher intellectual capabilities for mental creativity and strategy formulation – including a higher degree of consciousness.

The cerebellum, almost a second brain, was developed to assume routine motor coordination and controls – including those of skillful athletes and musicians. It is quite a mystery how this second brain could have been developed and function so efficiently parallel to the main brain.

Complex “Systems”:

The many different and significant structural and functional developments of organisms are not all “linear”, e.g. the development of one element in a quantitative or qualitative way. Many evolutionary developments made sense only in a certain co-evolution or co-development of different functional elements at the same time in a “coordinated” way.

Examples reach from molecular biology to the complex “system” of a snake’s poison tooth consisting of a hollow tooth and a pressure-sensitive poison gland – or the “system” forming the eye, consisting of a protective lid, a muscle-controlled flexible lens, a retina, and a complex neural network feeding into the neural nerve to the brain. Another “system” is the combination of the feathered wing, muscle, and bone structure in birds to facilitate flight. The brain can be seen as a subsystem of neural nuclei within itself, embedded in the larger, complex system of the body, including sensory and motoric functions as well as functions derived from the biochemistry of the body. These “systems of functions” became the most important features of complex life. They are another example of the “Combinatorial Principle” of evolution explained previously.

Biology or physiology should be seen more in this view of “systems” than in the analysis of individual functional components.

Ecological Communities:

To adequately understand life and its evolution, one must look beyond systems of functions in single organisms. One has to see the next level of the "Combinatorial Principle”, the complex structure of life including interconnected organisms – where the life of one organism is coordinated with and depends upon the life of the other or a variety of other types of organisms. This does not, for example, concern only the symbiotic utilization of certain bacteria within the digestive system of mammals; it also concerns the complex interdependence of various forms of life within different ecological areas, biotopes, or systems – in certain wetlands, prairies, forests, or ocean areas – most famously in the Sargasso Sea in the Atlantic Ocean.

3.5. The Virus – the Sneaky, the Parasite, the Drop-Out

It would be an error to see life over time only as a rush forward in the course of evolution to higher complexity. Certain species demonstrated a negative aspect of evolution, as when cave-dwelling species lost eyesight or snakes their limbs.

Quantitatively seen, most of life stayed rather primitive, remaining on or close to the monocellular level (plankton, algae, and bacteria). There even is one form of life that developed downward toward the most simple – the virus. Some basic characteristics of the virus are

- Consisting mainly of floating, minimal bits of RNA or DNA

- Barely protected within a uniquely formed shell

- The shell provides just the right form to attach to or penetrate the lipid bubble protecting the cells of organisms

- The virus possesses just enough RNA or DNA to highjack the host’s DNA and make it work for the attacking virus’s multiplication

- The virus demonstrates a very high rate of mutation, thereby circumventing systematic defenses by organisms

2.1.8. Further Changes or Interruptions – the Extinctions and New Beginnings

There are five significant causes for substantial evolutionary changes in the past and equally so in the future – by destroying some ecological niches or species and by opening vast new niches:

- Geological changes

- Climate changes

- Major diseases, plagues, or species instability

- Catastrophes leading to extinctions

- Astronomical cycles

Geological changes:

Plate tectonics – terrestrial changes – can raise or lower terrain surfaces and move plates or plate segments from equatorial to polar regions or the reverse, thereby changing the climate on those plates significantly. Plate tectonics can also lead to changes in ocean elevation, thereby forming new oceans or deleting oceans by squeezing their area (see the formerly very large Tethys Ocean [37], now remaining only in such small pieces as Lake Aral, the Caspian Sea, the Black Sea, and the Mediterranean).

Plate tectonics can also lift the ground under existing oceans (see the remnants of coral reefs incorporated in some peaks of the Alps or the disappearance of the shallow ocean that once covered the central areas of North America).

Another important effect of plate tectonics can be the changes in ocean currents – with significant effects on marine life and terrestrial climate (see the importance of the Gulf Stream for Europe). Plate tectonics can lead to the formation of a large variety of isolated areas with ever-changing climates for diversified evolution in complex mountain ranges or coastlines. Geological changes include the formation of new islands from volcanism. New islands in locations separated from existing land masses can allow the formation of new branches of life (possibly also of a new “trunk”) from accidentally acquired forms of life (for instance, the separate developments in Australia and the Galapagos).

Geological changes are occurring slowly – most of them allowing for natural evolutionary adaptation. Continental drift is in the 4 cm/year range. The rising of mountain ranges is also in the cm/year range at most. But even slow geological changes can result in violent local events – earthquakes, tsunamis, land slides, floodings, and volcanic eruptions. These can bring regional or local temporary catastrophes. The often locally restricted findings of fossil remains are witness to that.

Climate changes:

Natural climate changes, ice ages, warm periods, wet and dry periods – often changing within a very short time – all contribute to accelerated evolution – by destroying the habitat for some species and binging their extinction while opening opportunities or niches for new ones as changes are reverted.

These climate changes cannot only occur very rapidly in geological time (within hundreds of years), but often do occur in a sequence of very short waves – sequences of just a few very dry years in some areas or excessive flooding in others. Examples of the catastrophic consequences of such short cycles are numerous – the accumulation of fossil bones around the “last” watering hole at Agate Fossil Beds in Nebraska, the disappearance of the Anasazi culture from New Mexico, the Dust Bowl events of the American Middle West, possibly beginning to be repeated now.

Major diseases, plagues, or species instability:

Such events, for example, in forests or among animals living in herds, can lead to the extinction of species (branches of life) and, thereby, opening of opportunities for the development of others. For example, the North American forests had a prevalence of chestnut trees. After an invasive blight, practically none of them were left. Then, hemlocks prevailed. These are now rapidly disappearing due to an affliction by mites. An analysis of tropical rainforest canopies shows a constant coming and going of tree species in specific areas.

The often exponential expansion of plagues does not allow for adaptation and can lead to extinctions. But often there are some few resistant individuals that survive and bring a subsequent adaptation, leaving the former plague as an irritant in the subsequent generations – for example, smallpox.

Catastrophes leading to extinctions:

Five major “extinctions” have occurred already since the beginning of the grandiose diversification of multicellular life on Earth about 600 million years ago – and some more before that time – as evidenced by fossils. The extinction that occurred about 450 million years ago must have wiped out 99% of all species and some interesting anatomical plans of organisms that never appeared again. The next extinction occurred about 350 million years ago. The double extinction 250 to 200 million years ago wiped out the then dominant Trilobites and with them 95% of all species. The most recent among the very large extinctions, 65 million years ago, wiped out the dinosaurs and with them about 80% of all species. The “population” loss (number of individual living beings) may be different, since one does not know the number of individuals that constituted each species.

At least two of those extinctions, the one 65 million years ago and one of the two 250 to 200 million years ago – can be seen in connection with “meteorite” impacts. A newer theory (by Jason Phipps Morgan, 1999 to 2004, at the University of Kiel, Germany, now at Cornell) indicates that those “meteorites” actually were enormous ejecta (called “Verneshots”, after a Jules Verne phantasy) occurring early, but not necessarily at the very beginning of gigantic basaltic eruptions that had actually started several hundred thousand years beforehand.

Every one of those great extinctions actually was connected to – and, most likely, caused by – enormous bubbles of highly liquefied basaltic magma that were rising up at random intervals from the D” or other layers deep within Earth (see McLean, VA Polytech, Jason Morgan (Sr.), Princeton, and Courtillot, Paris [38]). As these upsurges perforated the surface of the Earth, they caused enormous explosions and the delivery of very large quantities of poisonous gases (sulfur and carbon dioxide), some reaching high up into the Earth’s stratosphere, destroying the entire ozone layer and causing copious acid rain. Then followed the formation of large cracks on the surface of the Earth, many hundreds of miles long, some perpendicular to each other, leading to the fast distribution of the highly liquid basalts over very large areas and the delivery of more gases. This occurred in dozens of individual ejections over some time – each one possibly occurring within days and quickly running up to hundreds of miles in distance. In the course of those events, the above-mentioned “Verneshots” may have taken place and appeared as “meteorites” upon their reentry to Earth. Due to related geological events, the surface of the oceans dropped by up to 800 feet, destroying the most abundant, remaining aquatic life in the shallow waters that was not destroyed by the poisonous gases and consequent acid rains.

The most famous basaltic deposits resulting from those events are the “Deccan Traps” in India, about the size of France and more than 5,000 feet thick in some places, connected with the dinosaur extinction. Equally important were the very large “Siberian Traps”, connected with the earlier extinction of life of the Trilobite era. Areas in Ethiopia, seabeds in the Pacific, the Palisades along the Hudson River close to New York, and an area along the Columbia River are minor basaltic deposits.

It appears certain that more catastrophes of this sort will occur at random time intervals (or in astrophysical connection) in the future. Would mankind and its civilizations survive? What direction could evolution take after mankind’s demise? Future deep scanning of the Earth – as already somewhat used at less depth for oil exploration – may permit us to detect and “see” any future basaltic bubble as it rises – over thousands of years from its depth but only within hundreds of years in going through the surface layers. How would society react when staring into the face of another major extinction? Will future technology permit controlled slow release of the bubbles pressure and channeling of basaltic masses? Will there be controlled survival of a selected few – to be left with what on a devastated Earth?

Astronomical and Geophysical Cycles and Risks

Some of the above described changes or interruptions of natural evolution were found to be more or less cyclical. This led to the search for underlying reasons. The following phenomena were recognized as having special significance:

- The wobbling of the Earth’s axis of rotation

- Cyclic changes of orientation of Earth’s axis of rotation under the influence of Jupiter

- Reversals of the polarity of the Earth’s magnetic field

- The traversing of the spiral arms of our Milky Way galaxy by Earth

It is easy to see that the changes in the orientation of Earth’s axis of rotation would lead to climate changes. If those are extreme, they lead to secondary changes of ocean currents, glaciations or melting, and changes of ocean elevation – with consequences, as discussed above.

The reversal of the polarity of the Earth’s magnetic field leads to intermediate phases of the absence of any magnetic field – suppressing the very important protective, radiation-shielding effect of that field. This can lead to great genetic damage – or to an acceleration of genetically controlled evolution.

As indicated earlier, it is assumed that Earth rotates around the center of our galaxy once every 200 million years and, in the process of doing so, that it crosses one of the spiraling arms of our galaxy once every 200 million years, requiring about 50 million years to do so. Those 50 million years are a time of increased risk for passing areas of high radiation from nascent or exploding stars.

They are also a time of higher risk of encountering large comets or meteorites resulting from ejected chunks of material from star formations or explosions. Consequently, those times should indicate a higher probability of extinctions on Earth, either from radiation, meteorite impact, or other perturbations leading to the detachment of basaltic bubbles deep within Earth and consequent volcanic “trap” eruptions described above. There actually were major extinctions 450, 250, and 65 million years ago. [39]

In addition to the cyclical risks for natural evolution, there is the risk of catastrophic events in outer space close enough to Earth to cause extinctions, for example supernova explosions or the origin of new black holes (implosions combined with the ejection of enormous amounts of radiation), dangerous to Earth when within the distance of a few thousand light-years.

Resilience and new beginnings:

In view of all these catastrophes, the resilience of life on Earth is remarkable. Not only did life survive in certain niches, but it mostly began to reestablish itself on a higher level of evolution or complexity. The trilobites were followed by the dinosaurs and those by the mammals as leading species.

A special “invention” of nature was the body’s temperature control at a rather elevated level in mammals. Higher body temperature allows intensive use of all bodily functions – for feeding, fighting, and mating. Cellular temperature is controlled by means of the mitochondrial metabolic function in the cells. It may have appeared as an aberration or anomaly – to do the opposite of what would be expected, not to slow down as temperature sinks and to accelerate when temperature rises. The benefits were manifold – extended activity into cool period of the day or year and into remote geographic areas of altitude or latitude. Specifically, after glaciations – often subsequent to other catastrophes – new niches and areas could be conquered. With the multitude of glaciations and their oscillations, this became important.

Nature’s resilience after the last ice age was accomplished by the evolution of the mental capabilities of mankind – fire-making and, later, husbandry and agriculture.

Will there be any more innovations of nature – after the next catastrophe – a germ-related or nuclear one?

2.2. Biological and Human Evolution, the Human Brain

2.2.1 Advances in Animal Development, Mammals, Homo Sapiens

The natural evolution of animals is understood to occur by the selection of the fittest. In further analysis, the determination of the fittest for survival or propagation may be determined by a variety of factors:

- Competition for food, shelter, or mates: This is the most commonly accepted selection process, as in fighting between competitors.

- Memory of and adherence to resource sources: For example, the finding of hidden food by squirrels, the return of migratory birds to prior successful nesting areas – and also the exotic return of salmons to their river location of origin. Those rivers may have been pleasant, once in geological times, with swamps as food supplies for smaller fish and easy transfer to the ocean for the larger fish requiring more and larger prey. But, with the slow lifting of coastal mountain ranges, co-evolution of fish began as the rivers became increasingly difficult to navigate, some being cut off from fish migration by bad rapids and waterfalls.. Struggling in vain across those would lead to failure. Those fish, however, that remembered navigable rivers with suitable spawning areas, survived or became more successful in propagation. Similarly, spreading of oceans let only those migratory birds survive that remembered manageable passages – a capability not found where ocean distances contracted and could have opened new transmigration opportunities – see the “Wallace Line” separating the once converging Indonesian islands in naturalist’s terms.

- Danger avoidance: Examples are the nocturnal or shy animals, living in crevasses or remote areas.

- High propagation rate, as among many rodents.

- Selection of mates by the females: This the selection process may have resulted from selection of expressions of health and strength in mates, but often leading to some of the most surprising results – excessive coloration, extreme feather décor, exotic mating behavior, song and the artistic arrangements of the Bower Birds – many times appearing to be a hindrance in non-mating survival.

- Exploratory behavior (curiosity), leading to the discovery of new niches or new territories with resources [40] or new usage of resources, as to find better food, as also resulting in lower mortality, especially among children, the main component of mortality in primitive species or societies.

In the course of evolution, certain characteristics were developed in a great variety of forms, colors, or sounds, as if not critical to survival – the shapes of shells, the colorations of tropical fish or flowers, the sounds of languages – at best, serving for self-recognition of species. Other capabilities were developed several times (the art of flying: insects, fish, birds, bats, and some squirrels – also the poisonous sting: some mollusks, insects, fish, and snakes), but some only once (for example, permanent erect posture and erect bipedal walking [41]). The most important development in the evolution of organisms is the large and complex brain of mammals; so far, it has appeared only once – in humans.[42]

It is not quite clear why a larger brain and consequent higher mental capabilities did not develop among the dinosaurs. Could higher strategic skills not have been an evolutionary advantage for some of them, too? Could some not have used more articulate arms and hands – first for climbing, then for tool usage – or have benefited from more memory and language skills? [43]

In any event, it was the mammals that developed higher mental skills in the branch leading up to humans. Did this have anything to do with living in the fruit-bearing trees of rainforests (the dinosaurs did not) and then facing climate changes that were leading to foraging on the ground, bipedalism, and the diverse usage of their hands? [44] In other words, did they go through changes in their environment that some of the dinosaurs had also gone through, but humans then found solutions leading to greater opportunities, new ways of risk avoidance, and new niches in evolution? Some scholars indicate the capability of speech as a motor for the development of larger brain size – but why did the dinosaurs not accomplish this evolution? Why did none of the other apes? [45]

It appears as if incremental brain growth has happened in various instances [46], but the ultimate human brain appeared only once, about 400,000 years ago in homo sapiens. Competition (mutual extermination) is always at the fiercest between adjacent species on the tree of life. But large brain size could have developed at geographically separated points – even on different continents – and it did not.

Considering the enormous growth in intellectual activities and density of information processing from the historic times of the earliest humans to our time, it appears that the large brain was oversized for early humans. What did they do with all that neural potential? If it was not used, its development and support was a luxury. Nature does not normally permit luxuries. Why did nature create an oversized brain – or what did our earliest ancestors use it for? Did they just look out of their caves, as so many of us watch television – and not much else? Or was hunting and fighting with each other the main utilization of their large and complex brains?

2.2.2 The Human Brain

The brain evolved as sensors required more complex signal processing for the formulation of motion strategies. After the simple “reaction” mode of sensor signals leading to a simple movement, more complex neural networks offered distinctive advantages in complex situations. It could well be that it was the mid-brain with the limbic system that evolved next. [47] This system, now known as the source of emotions, allowed for summary assessment of situations, possibly leading only to fight-or-flight decisions. Complex interactions of brain nuclei, biochemical effects involving some specific glands, environmental factors, or food intake, and genetically given behavior actuation resulted in what we call emotions and consequent behavior (some described in more detail in the essay on “Personality” on the website www.schwab-writings.com, in the “Brain-Mind” section).

Some memory provided further advantages and, more so, its interconnectivity. Animals with very large brains may not have more than that – complex sensor signal analysis, some mid-brain functions, and some memory with complex interconnections.

The human brain may merely have added an enormous amount of memory and an equally enormous amount of memory interconnectivity – plus such special features as speech recognition and, separately, speech formulation. Additionally, there was great progress in functional differentiation and evolution – for example, in the multitude of hypothalamus sub-nuclei. The embryonic development of the human brain may reflect and, thereby, explain the actual evolutionary development. [48]

There are different approaches to studying the complexity of the brain and its functioning:

- The study of the function of local brain areas

- The study of the brain’s structure and interconnectivity (brain physiology)

- The study of neural activity related to the brain’s topography (mapping)

- The study of signaling in the brain – by type and pathways

- The study of biochemistry within the brain

An especially effective, practical approach in studying the brain results from the investigation of secondary consequences of accidents and diseases that result in disruptions or changes in restricted local areas of the brain – for example, analysis of stroke consequences, brain surgery for the mitigation of epilepsy, or accidents such as the famous one Phineas P. Gage suffered, who shot a rod through his forebrain.

The study of brain structure and interconnectivity is well advanced, especially through the recent improvement of micro-probes. But there is a limit to the number of probes one can apply at any one time. Therefore, the majority of human brain processes, whether in thought or strategy formulation, remain difficult to analyze by this process.

Brain mapping by means of electronic scanners has been the approach of preference to the study of the brain in recent years. Some significant insights resulted in the allocation of brain activities to certain areas. But brain mapping remains an inadequate, or insufficient, approach for the understanding of mental functions. One does not understand the workings of a computer by mapping its layout and activation changes. What is additionally needed is an understanding of the type and flow of signals within the brain – see the essays on the website www.schwab-writings.com.

This gets closer to the question of brain “software”, as in computers that accomplish its function using a certain amount of “hardware”. Without the knowledge of the software, one cannot understand how a computer accomplishes what it does.

In the analysis of signaling in the brain, one finds some drastic differences between the signaling in computers and signaling in the brain. In computers, signaling occurs through linear sequences of “0” and “1” signals along the same transmission line, with at most a few lines in parallel to transfer “bytes” or “words”, whether by wire or wireless, all in form of digital codes (except in the few strictly analog computers for special applications). In the brain, signaling is different:

- There is a basic duality of signaling in the brain – the synaptic “on-off” signaling (comparable to digital or discrete signaling) and signaling by firing rate (a form of analog or continuously variable signaling). This simultaneous duality of signaling within the brain leads to the very complex information-processing capabilities of the brain beyond the capabilities of merely digital or only analog computers

- Complex messages are transmitted in “parallel” mode in the brain, through a multitude of synaptic connections to a multitude of other neurons – as in the coupling between sequential “visualizations” discussed later, each coupling possibly comprising many thousands of neurons.

- Messages can also be transmitted through several inputs arriving in parallel at a single neuron (or very few of them). This is accomplished by the fact that most neurons accept a number of input connections from other neurons – whereby some inputs signal “activation”, while others are neuron activity inhibiting. This allows either for alternative or logic-“or” functions, or it allows for the parallel inhibition of competing sites leading to dominance situations of certain signals and groups of neurons. This is necessary to eliminate confusion in the brain when multiple inputs arrive – as is quite normal in daily life.

- The brain does not have a “clock” for synchronization of signals, as computers possess. Consequently, minor differences in the arrival time of enabling or inhibiting signals at a receptor neuron may lead to vastly different consequences (see Chaos Theory).

- One must assume that the brain has a large amount of “bus”-connections, with a signal being generated by one neuron leading to a multitude of receiving neurons. Certain brain functions cannot be explained differently, and the economy of natural evolution demands such a solution – for example, to bring the effect of amygdala-based valuations to many receiving places, while there actually is only a rather limited neural connection from the amygdala to the other parts of the brain. Another example is the establishment of dominance situations, as in foreground activation of subsequent alternative thought sequences (“visualizations”), as discussed later.

It is important to note that some of the most important brain functions – mental creativity, strategy formulation, language, and consciousness – may be seen as resulting solely from memory and its interconnectivity (see the essays on the website www.schwab-writings.com in the “Brain/Mind” section relating to these issues).

The study of biochemistry within the brain, related mainly to neurotransmitters, concerns the “mood” setting within the brain and the influencing of neural networks in a summary manner. This led to the discovery that different neurotransmitters are prevalent in different parts of the brain, permitting some selective influencing of brain functions.

Biochemical analysis of the brain allowed understanding of the action of certain biochemical substances (for example, alcohol, coffee, drugs – even merely the availability of food when needed or the lack thereof).

2.3. Singularities in Natural Evolution and Anomalies in Nature

What are “singularities” in evolution?

- Extremely unlikely developments (very low probability) that provided for substantial progress toward natural or human evolution

- Developments that did occur, but only once, and never occurred again

- The lack of beneficial evolutionary steps that one should have expected but did not happen

The most significant, and surprising, singularity in natural evolution is the singularity of the “tree of life”, the pictorial presentation of natural evolution, as discussed above. Why do not new types of multi-cell organisms arise all the time out of the level of single-cell beings such as bacteria or algae? Why did all branches of evolution occur only once – as, for example, insects, marsupials, or mammals? Why is there no “forest of life” or “brush of life”?

One reason could be that competition and mutual elimination are always fiercest between related species in adjacent niches of existence. In any evolutionary step, this leads to “burning the bridges” behind their evolutionary advance. But the evolution that actually occurs indicates that there always are new niches or opportunities for evolution. Therefore, the above question remains.

The following singularities of natural evolution could be listed and were mostly discussed above. The list is not comprehensive:

- The regularity of electron shells around atomic nuclei as the key factor for the combinatorial appearance of molecules and for the significance of carbon in all organic structures

- The appearance of RNA and DNA as the foundation of life

- The lack of an enzyme in large animals to break up cellulose (as in brush or woods) for use as food (sheep do it by way of bacteria that produce “cellulase”)

- The phenomenon of aging, based on internal sequences in time and molecular degeneration, ultimately leading to death

- The appearance of bisexual propagation

- multiplication by seeds or eggs

- The appearance of temperature regulation in the body

- The appearance of the nerve

- The appearance of the coupling of nerves, ultimately leading to the brain

- The appearance of emotions, ultimately leading to values as guides of human existence

- The appearance of “visualizations” in the brain (visual, verbal, acoustic, taste-related, scent-related, or tactile), ultimately leading to thought, creativity, consciousness, and religion – as discussed in the next chapters.

- The absence of metallic conductivity and electronic communication

- The absence of wheels

Obviously, a more thorough analysis should reveal important singularities in early evolution among plants or lower animals. One should consider not only the fact that these “singularities” occurred in evolution at all, but also, at the time scale of evolution, how fast some singularities occurred.

Anomalies in the biological world, as the anomaly of water in the physical world, are more difficult to define, mostly being consequences of evolution. A list could be established and investigated. Could mate selection by factors that appear to be counterproductive for survival be considered an anomaly? Could unlimited propagation of bacteria in hosts, thereby destroying their sustenance or excessive foraging by some insects or prairie dogs and thereby destroying their sustenance, be considered an anomaly regarding the law of the survival of the fittest? Was increased mitochondria activity at lower temperatures, thereby stabilizing body temperature, an anomaly of nature?

Both of these and other “contradictory” effects occur too often in nature to be called “anomalies”.

10-03-05

[1] An excellent presentation of cosmic and planetary evolution – also covering the origin of life on Earth, going into detail and a depth considerably beyond this essay – is presented in Peter Ulmschneider’s book, “Intelligent Life in the Universe”, published by Springer in 2003/4, ISBN 3-540-43988-9, 250 pages. Additionally, the swift progress of astrophysics and astronomy requires ongoing awareness of the newest leading publications in that field.

[2] The consideration of extremophile microbes – existing in very hot or very cold environments – would largely extend the habitable zones. But extremophile microbes at hot vents deep under oceans, deep under rock, or under ice and snow are not seen as candidates for higher forms of life.

[3] The “Search for Extra-Terrestrial Intelligence” project, supported by NASA, utilizes large antennas or arrays of multiple antennas to discover radio signals from outer space.

[4] See the excellent book, Rare Earth, by Ward and Brownlee, Copernicus Books, 2000, ISBN 0-387-95289-6.

[5] Amino acids were found in the Murchison meteorite that came down in Australia in 1969.

[6] It is assumed that some 10,000 comets hit Earth during the 50 million years between the appearance of liquid water (oceans) on Earth and the appearance of first life (see the fossils in rocks on Greenland and Iceland).

[7] The high deuterium content of comets indicates interstellar origin. Water on Earth indicates origin within the solar system.

[8] The quinine derivative hemoglobin “heme” contains an iron atom, while chlorophyll replaced the iron atom by magnesium, thereby allowing the absorption of the specific light frequencies of the solar spectrum.

[9] Some very primitive (and, possibly, the oldest) bacteria do not use solar energy as their energy supply, but the transformation of FeS + H₂S into FeS₂ (Pyrite) + H + energy. The energy can be used to break down the ubiquitous carbon dioxide to provide carbon for the building of organic substances.

[10] De Duve, in 1991 and 1998, offers a more comprehensive, and somewhat complicated, theory of the origin of the first pre-biotic steps leading up to RNA replication, the origin of life – later, the DNA world.

[11] Thoughts about different forms of original life will be discussed in a later chapter on extraterrestrial life, for example, Chapter 3.4.1.

[12] By one estimate, 50 million meteorites of about 1 meter diameter or more had reached early Earth within 8 million years. About half a dozen meteors of 1 pound of weight or more still reach Earth from Mars every year.

[13] By one estimate, about 40,000 tons of dust and debris from outer space is still falling on Earth every year, and much more arrived during the early history of Earth. Up to 10% may be proto-organic material (see the ER2 project). Large comets or meteors, with more than 1 km diameter, rarely from outer space beyond the solar system, still hit Earth in the average of one every 300,000 years, but mainly contain rocky or metallic material besides water.

[14] See Richard Lathe, Fast Tidal Cycling and the Origin of Life, University of Edinburgh, 2003.

[15] The first traces of former life were found in the 3.8 billion-year-old Isua rocks of southwestern Greenland.

[16] As a comparison: There are only ten numerals (from 0 to 9) in our number system, but this allows the formation of all the numbers one can think of, in the trillions and beyond, through the “splicing” of these numerals into chains.

[17] Just recently (in 1986 and 2002) two more amino acids, Selenocystein and Pyrrolysin, were found to exist, but only in some exotic bacteria.

[18] Beyond these 20 amino acids contributing to the formation of proteins, 150 others have been found to exist.

[19] A quote from Cell and Molecular Biology, by Gerald Karp, ISBN 0-471-19279-1, Chap. 2.5, concerning the array of functions proteins have in a cell: “As enzymes, proteins vastly accelerate the rate of metabolic reactions; as structural cables, proteins provide structural support …. as hormones, growth factors, and gene activators, proteins perform .. regulatory functions; as membrane receptors and transporters, proteins determine what a cell reacts to and what types of substances enter or leave the cell; as contractile elements, proteins constitute the machinery for biological movements; … in other functions, proteins act as antibodies, serve as toxins, form blood clots, absorb or reflect light, and transport substances”. “The explanation (for their varied functions) resides in the virtually unlimited shapes that proteins, as a group, can assume”.

[20] Sheep and some other animals use certain bacteria in their guts to provide an enzyme that can break down cellulose.

[21] See Joseph Kirschvink, California Institute of Technology, 1992 and 1998, explaining the appearance of eukaryotic cells about 2.1 billion years ago at the end of a severe glaciation period

[22] An excellent overview is provided by the textbook, Cell and Molecular Biology by Gerald Karp, published by John Wiley & Sons, ISBN 0-471-19279-1.

[23] A bacterium that would have entered that cell would be about 2 feet long in this comparison, a virus only 0.1 inch.

[24] The linear progress of an individual molecule in Brownian movement is a random event. Consequently, diffusion rates are seen as statistical averages. In other words, some ATP molecules emanating from the mitochondria may arrive at the opposite side of the cell in a small fraction of a second, while others may linger for minutes. The need for ATP at a specific site may be satisfied by the first molecules arriving there – if there were not enough already from prior distribution densities.

[25] A major computational effort was announced on November 16, 2004, by IBM in collaboration with the National Institutes of Health and the United Nations to use a vast grid of possibly millions of private computers by way of the Internet (as the SETI project already does) to accelerate proteome research, attempting to identify all proteins and their folding into specific shapes in the human body and their function.

[26] Some additional nucleotides may have been derived from variations in the original DNA between a multitude of such possible formations and subsequent attachment of dissimilar DNA variants to each other. Even later in evolution, primitive bacteria were still able to transfer whole sections of their small genomes into the genome of another cell, thereby generating a new form of life.

[27] Another explanation indicates that the remnants of virus infections could have left a large portion of those extra nucleotides in the human genome.

[28] The term “epigenetics” appeared some hundred years ago. The above indicated research within molecular biology, however, gained focus and momentum after about 2000.

[29] Best known these days is the action of “oxidants”, radical variants of molecules leading to unfavorable cell metabolism, countered by certain anti-oxidant food supplements.

[30] An exotic scientist once calculated that, of a horse that was killed in one of Caesar’s battles, now each European may have over a hundred atoms in his or her own body.

[31] Imagine a wide boulevard in a very populous city. Imagine millions of people walking along this boulevard in a constant stream. In one area of the boulevard, certain obstructions cause the stream of people to form a complex pattern, resulting in smaller whirls on the side and to the confrontation of many people, some then forming temporary groups as they move along, before they leave the perturbation within a short time. The people move on and on. The perturbation stays at the obstruction. Does that perturbation form an “individual” – a living being?

[32] Discovered by the geologist Edson Bastin, University of Chicago, and microbiologist Frank Greer in the 1920s and confirmed only in 1987 through deep boreholes by the U.S. Department of Energy, expanded in South Africa in 1997 to a 3.5 km depth. Those microbes are understood to live on hydrogen and carbon dioxide dissolved in those rocks and are the base of a subsequent microbial food chain.

[33] A very good overview of the evolution of the genome and the diversity of life is presented in Peter Ulmschneider’s book, Intelligent Life in the Universe, published by Springer in 2003/4, ISBN 3-540-43988-9.

[34] Copies of two-dimensional sheets of paper are made by lifting-off of the copy in the third dimension. A copy of a three-dimensional organism would require the extraction in a fourth dimension – hence the ingenuity of doing a copy by having the blueprint for the whole organism in specially produced seed or egg cells and developing copies from there.

[35] The early spinal cord develops in the embryo in a fold of skin. Nerves develop out of the same group of cells in the fetus as the skin.

[36] The consequences for the structure of the human body would have been significant. Smaller dimensions for neurons would have led to smaller heads. This, combined with better neuron conductivity, would have allowed the placement of the brain securely within the chest.

[37] Tethys was a Greek Titan goddess, daughter of Uranos and Gaia, who became the wife of Okeanos.

[38] See “Evolutionary Catastrophes”, Cambridge University Press, 1999, 0-521-89118-3.

[39] It was indicated that Earth is now close to entering a spiral arm, again.

[40] These characteristics led many Europeans in past centuries to settle in America, thereby avoiding wars and political persecutions. It now leads many migrants to the Western nations.

[41] Erect posture and erect walk possibly are of benefit only if the capability to fight with weapons and the need to carry personal possessions exist, and the need to climb trees no longer exists.

[42] The brain of some whales and elephants is larger than the human brain but is used either for complex sonar signal processing only; or it may be large, but much less complex in structure and interconnectivity.

[43] The specialized development or deterioration of the dinosaurs’ arms may have been useful in their specific niche of existence, but it led them into a dead end concerning later development of tool usage or fire-making and the consequent development of intelligence.

[44] Temperatures on Earth during the early Tertiary (that was beginning 66.4 million years ago) were somewhat elevated, having led to an expansion of tropical rain forests – but began cooling as of the Eocene (beginning about 50 million years ago), leading to substantial reductions of the tropical rain forests.

[45] Other tree-dwelling animals may also have gone to bipedal posture on the ground. However, that left them in competition with proto-humans. Only one species, the proto-humans, became the dominant one, suppressing all others, as the dinosaurs had suppressed early mammals, which remained small and insignificant.

[46] Somewhat larger brain sizes occurred in at least eight different sprigs on the evolutionary branch of “apes” – namely, those in Eastern and Western Chimpanzees, Bonobos, Eastern and Western Gorillas, and early hominids from the Australopiths to Homo Sapiens and, finally, Modern Humans – beginning some 20 million years ago.

[47] See the embryonic development of the brain.

[48] Several textbooks present this embryonic development of the brain, for example, “Neuroanatomy” by John H. Martin, Elsevier Science Publishing Co., ISBN 0-444-01331-8.