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

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The Origin of Life

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Molecular Biology

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Natural Evolution,Human Evolution

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This essay is onlyPart 2 of a larger essay. 

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

That essay is nowavailable in the following separate sections:

1.  Cosmogony, CosmicEvolution, Evolution of Earth

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

3.  The Evolution andFunction of the Human Mind

4.  Evolution andFunctions of Societies and Cultures

5.  “IntelligentDesign Theory” as opposed to Natural Evolution

6.  ExtraterrestrialIntelligence?  What could it Mean to Us?

7.  The Future andExpected End of Mankind and the Universe

8.  Closing Commentsand Conclusions

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

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Introduction                                                   

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1.  The Origin of Life                                    

1.1.  Habitable Zones                                    

1.2.  The Origin of Life                                 

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2.  Molecular Biology

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

2.2.  Cell Evolution:  Genomics,Proteomics,

ComputationalBiology, Epigenetics, Death                        

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3.  Natural and Human Evolution                                                     

3.1.  The Changing of the Oceansand Atmosphere.  Organisms.  The Tree of Life

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

the Brain,Complex “Systems”, Ecological Communities               

3.3.  Advances in AnimalDevelopment, Mammals, Homo Sapiens                       

3.4.  The Human Brain                                                                                  

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

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4.  Further Changes andInterruptions – the Extinctions and New Beginnings

5.  Singularities in NaturalEvolution and Anomalies in Nature                 

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Introduction:

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When we pause for a moment in ourbusy life – at lunch, during a holiday, on vacation – we can perceive thewonderful and sometimes cruel existence we live in – the universe, nature onthis planet Earth, our surroundings, our body, our mind.  In trying tounderstand 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 understandour existence, we should attempt to understand this evolution.

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Not too many years ago, one ofthe early NASA space projects provided the very first and rather beautifulpictures of Earth as seen from outer space.  Astronomic telescopes had alreadyprovided excellent pictures of distant galaxies.  Now we could visualize howour own “Milky Way” galaxy would look with the tiny spot of our Sun as one of abillion others somewhere in its outer reaches – and a still smaller, blueplanet, "Earth”, whirling around that tiny sun – about four billion timesalready since its appearance.  That small Earth is our only home, butour brains that evolved only a few ten thousand years ago allow our mindsto span the universe in time and space.  What were the startingconditions, principles, laws, and forces of nature that let this evolutionoccur?

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

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

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Comealong on a mental voyage – to explore the existence which we live in – from thevastness of the universe to submicroscopic molecular life, the virtualphenomena of the mind, and unfolding civilizations – from an origin in thedistant past to an expected end in the distant future!

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This essay is only on part (Part2) 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 “Scienceand Evolution”.

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1.  The Origin of Lifeand Natural Evolution

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1.1.  Habitable Zones

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

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This indicates that suchhabitable zones can be found only within galaxies, since gas clouds outsidegalaxies are too cold and lack energy sources.  Within galaxies, their centralareas, with their higher density, are thought to have too much radiation,possibly in connection with central black holes, as well as too many supernovaeresulting 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 heavymaterials from past supernovae.  This leaves a certain band of certaingalaxies as a habitable zone where solar systems could harbor life.

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Within individual solarsystems, great proximity of planets to their central sun would resultin excessive surface heating – with life basically restricted to the verynarrow band between 0 and 50oC surface temperature on planets – forthe availability of liquid water and a heat level below destructiveness forlarge organic molecules (except for extremophile bacteria).  A large distanceof planets from the central sun would not provide enough heat from this energysource.  Depending on the size and age of a star – and its consequentheat-radiating intensity – the habitable zone for its planetswould be closer to or farther away from the central star, possibly shiftingwith the age and radiation of the star.  The early Earth demonstratesthat atmospheric greenhouse effects allow for the extension of thehabitable zone to an area of lower heat reception.  This allowed Earthto become habitable at an early time when the Sun had only 70% of its presentluminosity.  The habitable zone of our solar system, including atmosphericinfluences, begins beyond Mercury and includes the region from Venus byway of Earth to Mars.  Beyond that area, there are not enough heavyelements and an excess of water content (beyond the Asteroid Belt).  The outerplanets are too cold (distance from Sun), largely gaseous, and, therefore, notconsidered habitable for life as we know it – except possibly some of theirmoons that may be kept warm through extreme tidal deformation.  In sum, ourEarth is in a very habitable zone of the universe, being about 60% of ourgalaxy’s radius away from its center and, within our solar system, about onehundred times the diameter of our specific sun away from it. 

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The assessment whether “habitablezones” are fairly plentiful in the universe and, consequently, whether wehumans are a highly unusual phenomenon in the universe, or whether muchother intelligent life can be expected in the universe, is a subjective one. Depending upon the individual scientist and the general trend in the sciencesat any one time, the glass is either half full or half empty.  In timespast, plenty of other intelligent life had been expected in the universe.  TheSETI project [3]was started to discover and communicate with that supposed life.  Then, a morecritical 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 possibilityfor extensive bacterial life).  Lately, the discovery of “extremophile”bacteria deep under ice, at very hot deep-sea vents, or deep within rocks, hasopened a view allowing for larger “habitable zones” and, therefore, greaterprobabilities.  But the expected, randomly repetitive large catastrophesremained as the limiting factor, possibly not allowing enough time for the slowdevelopment of higher forms of life.  But do we really know whetherhigher evolution must always be slow? 

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

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The assumption that higher formsof life have required billions of years to develop on Earth should be put inperspective with the arrival of large quantities of oxygen only some 600million years ago.  This oxygen, consequently, led to the oxidizing ofbiomaterials as a source of energy and, therefore, required mobility, thenleading to nerves and, finally, the brain as the main characteristic of what wecall “higher” form of life. 

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Life’s development in the last600 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 theuniverse not have shown even faster mammal development?  It could haveoccurred, for example, in lieu of dinosaur development after an earliercatastrophe, hundreds of millions of years earlier in evolution than on Earth.

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In sum, this author assumes asomewhat more temperate position, seeing the very special character ofEarth as a harbinger of life in the vastness of the universe, but also seeingthe probability for other Earth-like planets in other solar systems and inother galaxies to harbor higher forms of life – with enough shielding againstradiation and impacts and with atmospheres with enough resilience, like ourown, to overcome catastrophes.  This would allow for considerably moreintelligent life in the universe than has recently been assumed – specificallyin consideration of the very large number of existing galaxies (severalbillions) and the very large number of solar systems within them (severalbillions in each of them). 

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After all, the product of anexceptionally large number and a small probability still allows for the resultto be anything, but possibly also a large number.

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1.2.  The Origin of Life

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Living beings are composed ofmolecules.  Certain molecules are called “organic” by scientists, because theywere found to appear mainly in combination with, or as products of, processesof living organisms.  Later, it was found that some of these organic molecules– they should be called “proto-organic” – existed before life arose on Earthand 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” hexagonalring of six carbon atoms – did not originate in the universe in connection withany organic life.  Later, however, as life arose, these molecules actually didoccur in life processes and became the dominant form of molecules in livingbeings – hence their group designation as “organic” molecules. 

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The question arises why carbonbecame the key atom in all organic molecules and, consequently, all livingorganisms – though combined with hydrogen, nitrogen, oxygen, phosphorus, andmany spurious materials.  Atoms consist of a nucleus composed of positivelycharged protons and neutrons.  They attract negatively charged electrons in anumber equal to the protons.  The electrons can be visualized as circling theatomic nucleus on a sphere or “shell”.  But when more than two electrons areneeded for the nucleus, the first shell is full and the extra electrons circle onan additional shell.  More electrons are added for heavier nuclei, until, ateight electrons, that second shell is full and another one has to be started –and so on.  Electrons can be shared with other atoms, thereby establishingbonds with those other atoms.  Two hydrogen atoms, with only one electron each,can establish bonds with an oxygen nucleus requiring two electrons to completeits second shell – thereby forming H2O, water.  Carbon has fourelectrons in its second shell that could hold eight and, thereby, can establishfour bonds in all directions with all kinds of other atoms (nitrogen, the nextmost important atom in organic chemistry, can have only three bonds and oxygenonly two).  Those electrons, being of an inner shell, are very stable.  This makescarbon a versatile and strong building block for complex structures or chains. In other words, it is the regularity of the electron shellstructure of atoms that led to the combinatorial bonding of atoms and that letcarbon become the key element of organic composition and consequent naturalevolution.

As described above, simple“organic” but not “living” molecules – such as methane and some aminoacids [5]– had already been constructed in cosmic space from the ejecta of collapsedstars by means of ultraviolet light and radioactivity in the universe and werefloating around in space before Earth was formed.  Consequently, whenthe origin of Earth took place as it “accreted” (coagulated) in its band of gasand dust around the Sun, such proto-organic molecules became part of Earth andmay have survived this forming process, at least at high altitudes of theatmosphere and, less likely so, in some niches of the surface crust, possiblyat some depth.  On the other hand, Earth reached extremely high temperaturesupon accretion, early formation, and under early comet impact and may havebecome sterilized thereby. 

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A different theory concerning theorigin of life on Earth appears more promising.  During the violent time ofEarth’s formation and thereafter, asteroids and comets consisting of iceimpacted 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 inspace, and ultraviolet light.  The dust particles that accreted to formthe comets consisted of mineral or metallic material.  “Cosmic” ice [7]had formed in outer space on these dust particles (or dust particles hadaccumulated on the ice) and contained already complex organic molecules asavailable in space – as one knows from the recent investigation of comets.  Thecombination of a catalytic effect of the mineral or metallic surfaces of thedust particles – with the energy provided by ultraviolet radiation as availablein space and the effect of the ice to hold the proto-organic material, to giveit yet some limited mobility – facilitated the formation of more complexmolecules, especially since cosmic ice goes through transformations into differentstates (amorphous, cubic, hexagonal, and liquid). 

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

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-       Nitriles (for example, Propionitrile CH3CH2CN)consists of carbon, hydrogen, and nitrogen atoms.  When immersed in water, aswhen cosmic ice temporarily melts under the influence of radiation or when ithits an ocean on Earth, it is transformed into a lipid acid.  Certainlipids (for example, phospholipids and other amphipathetic lipids) canspontaneously form “micelles”.  Micelles are hollow spheres or bubblesorganized 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 thealready existent methane, ammoniac, and carbon dioxide.  Quinone has certain chemicalsimilarities to chlorophyll [8]. On the one hand, it can transform absorbed radiation into chemicallystored energy.  On the other hand, it protects otherproto-organic molecules from the destructive radiation that exists inspace and existed on early Earth even before Earth’s final atmosphere wasformed. 

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

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

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Some icy comets, as also somerocky comets, do not fully vaporize upon entry into Earth’s atmosphere.  Icycomets that do not fully vaporize have the additional advantage ofkeeping their inner temperatures moderate, thereby allowing the complexproto-organic substances to survive.

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

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Calculations indicate that anycomet that hit Earth may have deposited 1024 dust particles into theearly oceans!

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

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In sum, the icy comets mayhave been the source not only of water for Earth but also of the organicevolution on Earth and the origin of life.  This may explain why lifeoriginated so quickly, within only 50 million years after Earth had cooled andstabilized. 

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

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A famous experiment by scientistsshows that additional quantities and types of “organic” material could appearnaturally in this environment when lightning hit waters rich in basicproto-organic molecules.  More likely, such formations occurred when earlyorganic molecules accumulated on clay or pyrite surfaces or at underwatervolcanic vents (“hot-spots”) rich in iron and sulfur efflux [9]. Clay and pyrite surfaces are electrostatically attractive to such proto-organicmolecules.  In environments rich in such molecules, these can form a denselayer on the surfaces of those clays in shallow ponds or pyrites at deep-seavolcanic wells, keeping the individual basic molecules somewhat immobile inclose proximity to each other. 

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

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

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

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

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

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The present status of scienceindicates that RNA was the first molecule that was self-replicating,utilized resources from its environment and was leading to evolution, thereforecalled a “living” molecule.  But, while all precursor organic moleculescould be synthetically produced by now, it was not yet possible to simulate thenatural starting conditions sufficiently to produce RNA synthetically and proveany of the theories of its origin. 

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RNA is a verycomplex molecule – with a complex composition and structure, not flat as shownin 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 theearly Earth or were transported there at a later time.  Most, if not all,chemical processes can work in both directions.  Consequently, couldnatural, aboriginal amino acids, some early nucleo-base, and cosmicformaldehyde have led to the formation of the first pieces of RNA?  Aspointed out in a later chapter, the translation of RNA into amino acids is notsimple and commonly utilizes some facilitating proteins.  Did some primitiveproteins and nucleotides facilitate the back-translation of amino acids intoRNA pieces?  This may be the bottleneck for synthetic replication of RNAgeneration and may be providing for the uniqueness of its appearance in thefirst place. 

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

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

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For these reasons, DNA mayhave prevailed at that early time over any other possible self-replicatingmolecules – 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 ofchemical compounds, as well as sufficiently undisturbed to allow nature toexperiment with the formation of those molecules over some period of time. Some scientists believe that it may have taken 10 million years to produceDNA.  But, as said, it has not been possible so farto synthetically reproduce any such “living” molecules. 

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It is equally difficult tounderstand why no other self-replicating and evolving molecule,different from RNA or DNA and their derivatives, has ever appeared subsequentlyin the course of the last 3.9 billion years.  Theoretically, otherforms of life along the lines of DNA should have become viable, even thoughpropagating less efficiently than the one that prevailed.  So many latermicrobes, 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 starta different, surviving strain of life from that which we know and are made of. This must be counted among the mysterious singularities inevolution, as will be pointed out in a later chapter of this essay [11].

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

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There is a new conjectureindicating that the formation and multiplication of DNA were specifically favoredon 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 areasand then leaving them to dry out again.  This left more salt in the tidalareas.  It is known that the double-stranded DNA helix tends to break up in onecondition, only to form a new double helix in the other condition thereafter. Consequently, under the most favorable circumstances, there could have been adoubling of DNA with each tidal cycle, quickly leading to dominance.  Theproblem consists in the fact that this assumes the existence of the Moon closeto Earth at the time of the origin of DNA, some almost 4 billion years ago.  Asindicated above, in the chapter on the origin of the Moon, there are someserious problems with this assumption. 

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

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

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

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2.  Molecular Biology

 

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

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

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

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DNA is formed bytwo almost identical, twisted strings constituting the famous “doublehelix”.  The individual segments of the DNA strands, theso-called nucleotides described below, consist of sugar molecules withattached “nitrogenous bases”.  Each nucleotide along the nucleic acid string islinked to the next one by a “phosphate group”, a single oxidized phosphorusatom.  The phosphorus links may allow – with all the necessary stability ofthose DNA molecules – the introduction of minor variations in the DNAstrands under special external influences (chemical- or radiation-related). Such variations can lead to the mutations necessary for evolution, which inturn lead to different or higher forms of life at an acceptable rate.  The variationsmust be slow enough to allow for the development of large colonies ofviable living beings.  On the other hand, the variations must be fastenough to allow for evolution to use opportunities and avoid risks connectedwith climatic changes, ecological changes, and the limited lifetime of our Sunand Earth – ultimately to reach the development of higher civilizationsin the time between major catastrophes, as described in a laterchapter. 

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The length of DNA maybe only a few hundreds or thousands of nucleotides in simple organisms, but it reachesalmost 3 billion of such nucleotide segments in humans.  Such a longstrand (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 histoneproteins) produced in the cell, with just 1.8 windings or 140 base pairs of DNAper core (this DNA section then being called a nucleosome).  The nucleosomesare separated by 20 to 100 base pairs of DNA and the whole spiral is then oncemore formed into a super-spiral.  It is intriguing to notice that the spiralingis done in such a fashion as to leave important “addresses” (regulatoryelements of the genetic helix) for later transcription accessible on theoutside.  The still very long spiral of a spiral can then be coiled andformed, upon fertilization or cell division, into some larger species-specificpatterns, the so-called chromosomes, including the famousX-shaped and Y-shaped chromosomes of humans. 

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

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An individual subunit ofDNA, the combination of a sugar molecule with its nitrogenous base, iscalled a “nucleotide”.  There are only four different kinds ofnucleotides, according to the only four types of attached nitrogenousbases 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 ofbases (or letters, as indicated) from one strand to the other are possible dueto the very different configurations of the ends of those bases that have tomeet and link between the two strands of DNA – and also to complement eachother in their different sizes, thereby keeping the double DNA helix atrelatively constant width.   

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Subgroups of three adjacentnucleotides along a DNA string are called a “codon”,because it always takes one such codon group of three nucleotides to letthe subsequent messenger-RNA produce one specific amino acid as abuilding block of proteins.  The type of amino acid that results is determinedby the types and sequence of bases in the codon being expressed.  The sequenceof 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 thoseamino acids, which is then called a protein.

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A significant string ofmany codons, resulting in the expression of a protein, is calleda “gene”.  So far, about 20,000 human genes have been identified and5,000 more are expected to be identified in the future, for a total of possiblyeven less than 25,000 human genes.  This is just about the number ofgenes some fishes have and just 25% more than the number of genes for someworms.  The difference comes from the capability of the human genome forgene splicing and control.  Thereby, the same number of genes canexpress 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 withlarger number of genes but which are not capable of splicing.  Additionaldifferences may come from variations in gene coiling (or condensations,compressions) in the chromosomes, providing or inhibiting gene expression (seethe new field of epigenetics discussed below).

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RNA is similar toDNA, but consists of only one strand of somewhat different nucleotides.  Thenucleotide designated by the letter “T” in DNA is replaced by the nucleotidedesignated by the letter “U” in RNA.  Three types of RNA are produced throughtranscription of DNA.  Messenger RNA, the mRNA, is the agent in thecreation of amino acids and their chain-like assembly intoprotein molecules, the main actors of life in the cells.  Some aminoacids do appear naturally in cosmic space out of the material available fromearlier star explosions, transformed by the radiation permeating space.  Butmost of the specific amino acids needed in organisms must be produced by thoseorganisms themselves, beginning with the material that is available in theirseed or egg cell.  This is accomplished by mRNA based on the code found onDNA. 

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Another kind of RNA transcribedfrom DNA is called “rRNA”.  Its transcription from DNA isfacilitated 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 mRNAinto amino acid sequences, the new proteins.

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

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

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Amino acids:  Thecore cluster of an amino acid consists of a nitrogen atom with two or threeattached hydrogen atoms (an “amino group”) that is connected to a carbon atomwith two attached oxygen atoms (a “carboxyl group”) by way of an intermediatecarbon atom.  Attached to this core cluster is one of 20 possible chains thatdefine 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, orS, 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 bythe 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 carbonand hydrogen atoms (in Tryptophan, designated by the letter W), and more [18].                                                                                                          

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

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

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Most proteins, specifically thelarger ones, do not stay in an extended state but, after being formed, quicklyfold into complex shapes.  Each type of protein assumes a specificshape.  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 nicheswhere actually most of the protein’s action on, or sensitivity to, itsenvironment takes place. 

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There may be 10,000different 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 inthe human body at different times.   

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Lipids are adiverse group of molecules including fats used by the body for energystorage 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. 

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The first lipid bubbles may havebecome 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 amatter of time until this capability led to ongoing production of protectivebubbles around the DNA and its associated protein factory – an arrangement wenow call “cells”. 

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Lipid acids, morecommonly now called fatty acids, are chains of, typically, 14 to20 carbon atoms, each with two attached hydrogen atoms.  Their high carboncontent explains their energy content when used in the form of fats asnourishment.  Fats are three lipid acid chains connected at theirend by a combination of a few carbon, hydrogen, and oxygen atoms.  Lipidbilayers are double sheets of small interconnected molecules, eachhaving two lipid acid chains attached, but all directed toward the intermediatespace between two sheets forming the bilayer. 

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Carbohydrates: Carbohydrates include the various forms of sugars and larger molecules composedof sugars.  The simple sugars (fructose and glucose) containshort chains of carbon atoms, with attached hydrogen atoms to one side andoxygen-hydrogen atom combinations, on the other, as well as more complexconfigurations of atoms at the end of the chain.  These end-configurationsdetermine the difference between the various sugars.  Some sugars can formthree-dimensional hexagonal rings out of their chains.  Carbohydrates providean easily accessible energy supply to the body – by way of oxidation inthe mitochondria – providing heat and forming ATP – the latter transferringenergy to wherever it attaches itself to.

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

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

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ATP:  The small molecule adenosinetriphosphate (ATP) plays a key role in the cell wherever energy isneeded – for example, in the formation of proteins through transcriptionand in the deformation of proteins as in working muscles.  ATP consistsof a complex head formed by a couple of hexagonal or pentagonal rings of carbonand nitrogen atoms with an attached tail of three phosphorus atoms,coupled by oxygen atoms and with oxygen atoms to their sides.  The lastof these phosphorus atoms can be shed with an explosive effect, drivingthe 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 alarger one by overcoming the mutual repulsion provided by their electronorbits.  It may also help molecules to move forward against fields of electricpotential as when moving through openings (“channels”) in a cell wall. Finally, it may serve to bring a protein molecule to a different foldingpattern, with different geometric aspects resulting, for example, in themovement of muscle fibers relative to each other.  That can result in a “shortening”of a packet of muscles on the body. 

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ATP is produced orreconstituted in the mitochondria of a cell with the assistance of anelectron-donor molecule (NAD, resulting from the vitamin niacin) and thecomponents and energy from sunlight in plants or, in animals, from oxidizingcarbohydrates (glucose, a hexagonal ring of carbon atoms with attached hydrogenatoms, then becoming carbon dioxide and water) and fats (fatty acids,ultimately also becoming carbon dioxide and water).  There may be amillion ATP molecules in a single cell at any one time, beingreplenished by the mitochondria as needed. 

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One cannot leave this section without marveling how the few basicatoms – carbon, oxygen, hydrogen, and phosphorus (why phosphorus, andno other?) – arranged in a few interconnected simple patterns – in simplehexagonal and pentagonal rings or just in more or less extended strings – canresult in so many different molecules with such widely different and importantfunctions in the human body (or in any other organism), thereby providingthe phenomenon of life. 

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All of these phenomena oforigin of organic molecules, their interaction, and life can be seen as anotherdemonstration of the Combinatorial Principle that was presented inconnection with cosmic evolution as facilitating and driving the amazingevolution in the universe – whereby individual particles are capable ofcombination in such a way that the resulting larger components present totallydifferent types of characteristics from their constituent parts.  Carbondioxide, water, and some other small molecules were able to form proteins,lipids, and carbohydrates – that were able to form living cells – that wereable to form organisms – that ultimately had brains – and formedcivilizations. 

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

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

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Upon the origin of life, the formationof “cells” was the most important innovation after the appearance of RNA andDNA, possibly occurring simultaneously out of self-forming lipidbubbles protecting their interior space where undisturbed proto-organicevolution could have taken place.  The original living and multiplying cellsmay have contained little else but DNA, RNA, some proteins, and a nutrientsolution of water. 

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It was the most importantaccomplishment of the following three billion years of slow evolution, prior tothe appearance of complex organisms, to develop some advanced cells, the“eukaryotic” cells [21],with a number or important internal structures and functions – settingthe stage for the subsequent explosive evolution of higher forms of life. These internal structures of cells, also called “organelles” – somepossibly 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 intochromosomes, 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 thenucleus providing surfaces for directed molecular transport

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

o  Lysosomes:  Membrane enclosed spaces for transport and digestionof imported materials

-       Structures serving the energy household of the cell

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

o  Mitochondria: Membrane-enclosed sub-units, now believed to besymbiotically incorporated basic bacteria with their own DNA, providingoxidation of organic materials resulting in either heat or production of ATPfor subsequent processes requiring energy (muscle movement, formation ofproteins, and more)

-       Structures for the physical stabilization of the cell and materialtransport within

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

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

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The essence of life and the coreof a living cell is the DNA double helix.  It has a surprisingly simplestructure – but the dynamic world of all the many thousands, if not manymillions, of molecules within a cell is astonishingly complex.  Allmolecules are in constant movement, in either a slight wiggle at a given placeor in a zigzag movement under the influence of perpetual collisions withneighboring particles.  Some of those movements follow certain surfaces ofstructures within the cell; others occur in the three-dimensional space of thecell liquid, the cytoplasm.  This movement is the energetic expressionof heat and is called “Brownian” movement, sensed by us astemperature.  Equally important are movements of certain molecules thatare guided by electric potentials along the outside of largermolecules, as when providing the translation of DNA and RNA or when passingthrough “gates” in the cell membranes.  Between these erratic Brownianmovements and the guided progressions, the choreography of moleculesin a cell is a strange combination of random events and strictly regulated progressions– a dichotomy that was already described in cosmic evolution andappears as a basic principle of all natural evolution – and that canstill be found in human thought and human societies in their progression.

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To understand the dynamics of theworld 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 twopositive or two negative charges repel each other.  As discussed before, atomicnuclei are composed of protons that are being held together by neutrons.  Eachproton has one positive charge, consequently capturing one electron with itsnegative charge.  The electrons “circle” the nucleus at a certain distance, notunlike planets.  The all negative electron spheres, also called “shells”, ofadjacent atoms repel each other, keeping the atoms or molecules apart.  Butwhen an electron is missing in the outer shell of an atom, the forcing togetherof adjacent atoms, as in collisions, can lead to the sharing of an electron. This provides a permanent bond between those two atoms.  Consequently, theBrownian zigzag movement of all the molecules within a cell result from thoseparticles being bounced off the electron shells of other molecules, but thismovement can also lead to new bonds, resulting in “chemical reactions” of themolecules among each other. 

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

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If one were able to shrinkoneself – to the size of a molecule within a cell, – one would be in alarge room comparable to, say, 20 feet length, width, and height (if oneequates one foot to 1 micrometer, which is one-millionth of a meter). The organelles described above would appear as bulky furnituredistributed within it and, in the case of the lysosomes, movingthree-dimensionally through the cell.  There would be plenty of water moleculesfloating around, constituting as much as 70% of the cell content(“cytoplasm”), each about one-thousandth of an inch wide (correspondingto a few Angstroms or to 10-10 meters).  The very numerous ATPmolecules (up to a million within a cell) are about ten times larger than thewater molecules, in our presentation about one-hundredth of an inch wide (lessthan 100 Angstroms).  The thousands of proteins in a cell (constituting up to40% of the cytoplasm in some cells) are about one-tenth of an inch wide (lessthan 100 nanometers, 10-9 m), but would be up to several inches longif they were not coiled up in little balls a few tenths of an inch indiameter.  The chromosomes that appear only upon cell division would be shortof a foot tall (less than a micron), but if the human DNA string were everextended, it would be about 1.3 miles long in this visualized miniature world [23].   

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The above indicates that thelarger molecules and organelles are imbedded in a very fine quicksand ofwater and ATP molecules, which constantly wiggle and move around. This lets even the largest molecules move erratically, as they themselves moveand are being pushed by surrounding molecules in Brownian movement.  Diffusionfigures 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 ameter) per minute to 400 microns per second.  This indicates that proteinmolecules may need several minutes or only small fractions of a second to movefrom one end of a cell to the other (possibly as little as one-thousandth of asecond, especially the smaller molecules when they move along the surfaces ofthe flat cell structures, the organelles, described above) [24]. This lets the innards of a cell appear not just like a boiling stew, butlike a most dramatic convulsion of the thousands of types of molecules that areon the loose in the cytoplasm, with the flat surfaces of internalcell structures exhibiting swiftly moving molecular layers like oilslicks on pavement. 

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The need for this dynamicbehavior becomes apparent when one looks at the process of generating newproteins through translation of RNA, specifically during rapid cell division. Some bacteria cells can multiply in less than 20 minutes under favorablecircumstances. 

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Compared to this randomconvulsion, the motions of directed molecules following prescribed pathsappear calm and determined.  Take, for example, the duplication of DNAupon cell division or the transcription of DNA into RNA or the translation ofRNA into proteins.  A special protein (the “initiator” protein in the case ofDNA duplication, a specific “transcription factor” in the case of selective DNAtranscription, 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.  Thesespecial molecules are created by the cell upon the need for certainproteins or under the influence of neighboring cells, thereby controlling thedestiny or role of a cell in the body in the formation of whole tissuesor patterns (including surface colorations of flowers and butterflies).  Thereare other proteins that continue the process of transcription. In the case ofDNA being transcribed to RNA, it is RNA polymerase; in RNA translation intoproteins, it is ribosome.  There are at least 30 different types ofprotein involved in the complete transcription and translation. 

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

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The transcription ortranslation proteins slide along the respective DNA or RNA string like asequence of pearls, guided by their shape and driven by fieldpotentials at the point of their action and by energy supplied by ATP whenshedding one of its phosphorus atoms. 

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The progress of translationcan be in the order of hundreds of nucleotide steps per second.  Thisis even more impressive if one considers that, at this rate, matching the typeof nucleotides of the string to be translated with the proper nucleotidematerial from the cytoplasm has to be accomplished in the propercombinations(!).  This explains, to some extent, the need for the greatquantity and great mobility of the molecules in the cytoplasm that have tobecome 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 translationtakes place in the cell at a time; multiple DNA genes can be transcribed at thesame time.  The same gene (or part or combinations thereof) can be transcribedseveral times.  A piece of mRNA can be translated simultaneously by asubstantial number of ribosomes into a stream of identical output proteins. 

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

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Transcribing DNA or RNA andproducing proteins is not all that a cell does.  Once the proteins are formedand properly folded, assisted by a group of many other proteins, they enter avery complex network of interactions of molecules.  At any one time,there may be thousands of types of proteins in some cells and some hundreds ofthousands 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 genesor their splicing and combinations in transcription.  Others are provided byprotein interactions in post-translational modifications, thereby contributingto protein diversity.  Some special ones are provided by food intake (forexample, vitamins and medications).    

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Modern science has been able totrace the network of protein interactions for some important cellfunctions.  On paper, they look like strange line patterns with manyintersections and back-and-forth progressions across the picture, somerepetitive or circular.  Considering the fact that the human genome can producetens of thousands of proteins, there are many such network patterns ofprotein interactions that are active at any one time in the cell.  Allthis must be visualized not only in chemical, but also in physical terms as thewild motion of molecules in erratic diffusion or guided paths, therebyperpetually combining, unfolding, refolding, and separating – with the additionof the large number of explosive ATP hydrolizations providing the requiredenergy.  The discovery and understanding of all the possible networksof protein interactions may well be the main task of molecular biology and“proteomics” in the foreseeable future.

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One may want to look at ATP(adenosine triphosphate) in greater detail.  The human energy source isfood, digested and distributed throughout the body to each cell.  Within eachcell, there are domains called “mitochondria” – possibly the remnants ofonce-independent organisms that were symbiotically incorporated into moreadvanced cells when the cycle of energy from the Sun through chlorophyll wasreplaced by energy gained through the oxidizing of organic material throughevolutionary steps some 600 million years ago (possibly beginning already some1.5 billion years ago). 

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Mitochondria’s mainfunction within a cell is the production of ATP from glucose andfats.  The amount of mitochondria in a cell or tissue varies with the functionand need of the cell or tissue.  Depending upon demand in the cell, a more orless copious stream of ATPs emanates from the mitochondria into the cytoplasmthat obviously can store only a limited amount of these molecules.

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

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Another dynamic effect resultsfrom openings in the cell membranes.  There are either “gates”for the transfer of materials or merely some protruding proteins poking partwaythrough the membranes for signaling between cells and theirsurroundings, as for controlled cell growth or behavior.  Suchmolecular signals let the cell realize its specific function within thetexture of the body.  This leads not to total DNA replication but tothe transcription of only those parts of DNA into RNA and translation intoproteins that are required for the cell’s function at its specific place andtime.  The gates transfer not only signals and nutrients into thecell and waste product out of the cell, but also transfer substances for cellmetabolism or, in the case of glands, transfer necessary substances from thecell into the organism’s body.

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The enormous complexity ofsimultaneous and alternative molecular activities in the cell can nolonger be analyzed or influenced by conventional laboratory processes.  Increasingly,computer analyses and models are utilized.  Potential processesare computer-modeled, even the folding of large proteins.  The models areincreasingly refined and have now reached a high degree of accuracy. Interdisciplinary molecular biology supported by computer scientistsutilizing large computers (“computational biology”) is the most advanced formof research at this time, concentrated mainly on “proteomics”, thefield of science related to proteins, their composition (their amino acid sequences),their folding into specific shapes, and their great variety of interactions [25].  

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The large variety ofproteins in the cell and the very complex molecular interactions must haveevolved 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 weknow.  Subsequent DNA and chance enlargements of its molecular chain throughattached nucleotides [26]may have given origin to new proteins, some useful and retained in superiorcells, others not, leading to cellular “birth defects” and the disappearance ofthose cells.  Could the large number of unusable nucleotides (introns) on thehuman genome partially be witness to that? [27]Life existed for more than 3 billion years on the monocellular level beforecomplex organisms arose.  If one counts possibly two cell divisions per day inthe most prolific areas on Earth, there were about a trillion generations forthe evolution of cellular complexity – and many trillions of cells were evolvingin parallel – resulting in trillions time trillions of nature’s experiments.

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It is interesting to note that itwas the complexity of the above described molecular dynamics thatpermitted an increasing diversification of cells and, later, of the swiftlyevolving organisms.  Diversification and evolution required at leastsome changes in the DNA-RNA-Protein sequences.  More often, it required theaddition of new steps on the genome, genome splicing and control of expression,and, thereby, the production of additional types of proteins, specifically asthe rise of complex organisms required a great variety of different cells todevelop out of the same seed or egg cell. 

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To explain the swiftness of someimportant hereditary adaptations to the environment in biological evolutiononly by the theory of random changes in the genome has left some scientistsdissatisfied.  While religious people look for divine interference in geneticevolution (see the Intelligent Design Theory, discussed later), these scientistsrecently began to look for another scientifically provable mechanism of geneticchange.  The field of Epigenetics [28]investigates the occurrence of heritable changes in gene expression withoutchanges in the DNA sequence.  Specifically, DNA methylation, histoneacetylation, and RNA interferences are being investigated.  This leads to theconsideration that the very complex multiple gene coiling in chromosomesmay possibly become influenced by environmental factors.  This can leadto the covering of expression addresses on the genome and, hence, expressioninhibition – and possibly other factors

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

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It is a mysterious fact of naturethat cells do not live eternally.  The limited life and ultimate death ofall complex organisms, including humans, is based on molecular circumstances onthe level of cells.  For one, there can be pathological events in consequenceof invasions by bacteria or viruses.  There also can be errors on the genomeleading to the production of erroneous, “toxic”, or non-functional key proteinsthat result in the cell not being able to continue its function.  The wholeorganism may not be able to survive, as when excessive cancerous growth occursin the brain. 

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On the other hand, there arevarious molecular circumstances that lead only to aging and age-related deathof 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’sdysfunction.  At that time, the cell initiates its own termination, aform of cellular suicide.  The debris of a single or a few cells is quicklyremoved from the body.  A dead body, returned to earth, quickly returns to thecycle of materials and energy in nature and may be taken up again by otherorganisms [30]. While this leads to the conclusion that all cells are mortal, the eggcell of an organism, forming a new organism in the next generation, actuallysurvived.  Consequently, there is a form of “permanent” lifefor one strand of cells through all generations.  This is even moreapparent in monocellular organisms propagating by simple cell division.  

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From the human point of view, onemust marvel at the dynamic world of the molecules in the cell – not only as thecarriers of our lives and minds – but also leading us to ask an existentialquestion of our existence:  what, or who, are we if our component partsare constantly changing, new ones arriving in our bodies, old ones disappearingfrom us such that, at the end, possibly none of the original parts we were bornwith is still within us – yet, we are still the same individual.  Is theessence of living beings not in their physical substance, but only in theirconfiguration (“Gestalt”)?  [31]

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In sum, it is the dynamicworld of the proteins and other molecules in the cells that provides for theevolution and functioning of all life, even in the largest and mostsophisticated organisms.  Of course, a protein does not “know” what it does; itjust appears to follow the given circumstances in adherence to thenatural laws of physics and chemistry.  When a nerve impulse reaches acertain cell, the fibers within it are moved by the action of released calciumthat activates ATP (by hydrolysis), and a muscle contracts – with whateverconsequences for the organism.  But when a certain pattern of neurons inthe brain are activated in connection with a “thought visualization”,some cells in the body may produce large amounts of adrenalin, activatingthe whole organism, leading to whatever beneficial or catastrophicconsequences for the whole organism.  In other words, the molecules in the celldo not merely follow blind laws of physics and chemistry.  There can be acontrolling – or, at least, somewhat influencing – mind far beyond thecells.  We will see more of this in the discussion of the brainand mind in later chapters.

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In the course of evolution, itwas first the cosmic evolution that produced its great variety of phenomena andstructures and is now moving on for many more billions of years toward itsultimate exhaustion and dissolution.  But subsequent to this physical evolution,the origin of life on Earth – and most likely on other planets in theuniverse well before – produced another evolution of new phenomena inexistence, namely, in the cells.  This new natural, biologicalevolution may appear less powerful but it became at least equally if notmore 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.

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3. Natural and Human Evolution

 

3.1.  The Changing of the Oceansand Atmosphere.  Organisms.  The Tree of Life

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Life requires the input of energyto 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 organicprocesses was presented at the fissures where continental plates slowly separatedover 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 andmaterial for organic processes were in shallow waters or directly under thesurface of the oceans.  Consequently, nascent life split rather earlyinto those two directions.  The undersea life of Archaea bacteriaand a resulting deep sea food chain as well as the variety of primitivemicrobes living deep within rocks [32]will not be further discussed in this essay, even though they may wellconstitute a large portion of the mass of all living organisms on our planet. It was the other direction, of Sun-based life, that ultimatelyevolved into human life and that will be the object of further discussion.  

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

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The original oceans on Earthcontained large amounts of dissolved iron, augmented mainly bysubmarine volcanic activity and the influx of sediments.  The dissolved oxygenfrom the original atmosphere and any other oxygen subsequently formed by algaephotosynthesis, as just mentioned, were quickly depleted in forming insolubleiron oxides that resulted in deposits of banded iron formations and red claysat the bottom of the oceans.  Only after all iron had been deposited outof the oceans could oxygen accumulate in any significant quantity in the oceansand atmosphere.  This began about 2.5 billion years ago.  Oxygenavailability has increased steeply since that time as a product of increasingbiological activity.

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Beginning about 800 million yearsago – and more rapidly about 550 million years ago – the abundance of oxygen inthe atmosphere and oceans facilitated the appearance of a new energycycle for the growth and reproductive needs of early forms of life byutilizing the oxidation of already existing organic material as thesource of energy.  This had a number of significant evolutionaryconsequences:

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

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

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

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

-       Differentiation allowed the utilization of ecological niches in anincreasingly crowded world – ultimately leading to the population of the dryland of the continents.  Speed of differentiation or of evolutionaryadaptation allowed early occupation of niches.

-       Larger size and the accumulation of specialized cells increasinglyrequired coordination and control within the organisms – at leastin balanced growth and balanced function – as known to be largely accomplishedby inter-cell and intra-cell control mechanisms on the level ofproteomics, facilitated by an increase in the number of types ofproteins and their interaction.  In other words, the increasing complexity oforganisms went hand in hand with the increasing complexity of proteinfunctions.

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

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

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

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Subsequently, a very early splitinto two branches of cells – the undersea cells living atsubmarine hot-spot vents and the earliest cells living in shallow surfacewaters – allow the assumption that either one of the two was the earlier formof life with the other being a derivative.

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Even later, as life branched intovarious forms and higher forms of life appeared, it is often not possible toindicate precisely the sequence of evolutionary development.  There isdiscussion 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 willbe exterminated in the next global catastrophe and even higher life wouldevolve from a different branch than mammals, leaving humans as an abandonedside branch?

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There is one valid comparisonwith a tree – the lower branches of life’s development are wider spread, arequantitatively larger, and arrived at greater diversification than the topbranches – possibly on account of more time having been available, but also onaccount of the shorter reach of smaller organisms and their fastermultiplication.

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

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Why is the properpresentation of the evolution of life not a forest or bush?  Thestandard response is that life was quickly crowded on Earth and all niches wererapidly 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 isnot totally believable.  Geological instability on Earth repeatedly formed newislands (as Australia, Iceland, the Hawaiian or the Galapagos islands) orremote valleys (as in the Himalayas).  Steep climate changes (ice ages and newwarm periods) or catastrophes repeatedly opened immense areas for new niches oflife. 

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The rate of mutation of DNA invarious cells is rather constant over long periods of time.  Most suchmutations lead to failure and, consequently, no evolutionary progress. Evolutionary progress depends upon the arrival of more suitable characteristicsfor propagation or survival in a constantly changing environment that is alsosubject to catastrophes.  This results in the fact that the rate ofevolution 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 theevolution of families or species of beings.  Some species are wiped out,others remain unchanged for millions, if not hundreds of millions, ofyears (for example, the horseshoe crab).  At other times, one can observerather swift evolution of certain characteristics in some species – ifnot the appearance of new species.  The evolution by punctual swiftphases 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 newcharacteristics – for example, a very large brain. 

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There is an often repeateddiscussion whether there can be genetic adaptation to learned andsuccessful habits.  In detail, there are two effects.  Environmentalfactors, including learned behavior, can have an influence on gene expression.  Certainbiochemical intake by pregnant mothers lead to different fetus development. Certain biochemical intake or environmental factors lead to different growthand 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 geneticchanges, not necessarily in code changes, but also in variationof gene expression on gene multiplicity with those events having a muchhigher probability than genetic code changes and being responsible for some ofthe spurts in species development.  These questions are being investigated by thefield of epigenetics as discussed above.

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

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In other words, humanscience takes control of the evolution of the tree of life inaccelerating some evolution, bringing unforeseen changes, as well as cuttingmany branches by extinguishing many species – the latter being welcomewhen 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 geneticmanipulationnot clearly knowing or agreeing what the goalsare, not clearly seeing the consequences, not really knowing what wetruly want, how an ideal world would look and still be functional, and what weshould avoid. 

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In every instance that sciencehas been able to analyze, the evolution of life was led by the “basicprinciple of natural evolution”, whereby each evolutionary step was conditionedby the starting conditions and by the boundary conditions and was driven bystatistical or random variation of some genetic characteristics – withsubsequent propagation beyond available resources and selection of thesurvivors or progenitors by the prevailing of the fittest.

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3.2.  Oxygen, Life Feeding onLife, Mobility, New Functions, the Brain, Complex “Systems”, EcologicalCommunities

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As indicated, the availability ofan increasing amount of oxygen in the atmosphere and oceans led to theappearance of a new energy cycle for the growth and reproductive needs ofearly forms of life utilizing the oxidation of already existing organicmaterial – leading to more complex, larger beings and the evolution ofthe “tree of life” [33]. There were still other significant evolutionary consequences of thisdevelopment:

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

-       Feeding of life became not only predatory by hunt-and-kill, butalso by smaller organisms attacking larger ones (for example, such pests aslice, 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 symbioticarrangements – for example, the inclusion of mitochondria in animalcells, bacteria in the digestive tract, or the fungus cultures of some ants –in modern time, the care for fruit trees or the keeping of domesticatedanimals.     

-       Mobility was needed (and the fittest were selected) inorder to prevail in the search for more biomaterial after theimmediate surroundings were harvested.  The mobility increasedcompetition and led to fighting, leading to evolution for theprevailing in that situation, too.

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

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NewFunctions:

The important innovationssupporting this development toward a dynamic mode of life were the appearanceof new functions:

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

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

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

-       Sensory capability to recognize favorable directions for motion

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

-       Interconnection of nerves and networks of nerves for complexsignal processing of sensory inputs, for complex motions, and for strategyformulation

-       The last finally resulting in the formation of the brain

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

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Early cell deformationfor motion may have been simple, functioning under the influence of external orinter-cell signals (such as in anemones and jellyfish).  But mammalian musclesbecame rather complex and operated under the influence of nerve signals thatact on ATP and protein strings within the cells.  How did limbs evolve?  Wherethey some tentacles in more primitive organisms that added motion? 

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The circulatory systemmay have evolved out of a fold or borderline between tissues of primitiveorganisms.

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

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

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TheBrain:

Linear nerves permitreflexive behavior (if you burn your fingers, your arm twitches andretracts the hand with the fingers).  A significant step in evolution occurredwhen a nerve began to act on another nerve.  Two nerves with feedback toeach other allow the formation of a “flip-flop” for “on-off” behavior withmemory.  More complex interconnections allow for complex memoryand for complex responses, leading to networks of nerves. 

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

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

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

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The cerebellum, almost asecond brain, was developed to assume routine motor coordinationand controls – including those of skillful athletes and musicians.  Itis quite a mystery how this second brain could have been developed and functionso efficiently parallel to the main brain.

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Complex “Systems”:

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

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Examples reach from molecularbiology to the complex “system” of a snake’s poison tooth consisting of ahollow tooth and a pressure-sensitive poison gland – or the “system” formingthe eye, consisting of a protective lid, a muscle-controlled flexible lens, aretina, and a complex neural network feeding into the neural nerve to thebrain.  Another “system” is the combination of the feathered wing, muscle, andbone structure in birds to facilitate flight.  The brain can be seen as asubsystem of neural nuclei within itself, embedded in the larger, complexsystem of the body, including sensory and motoric functions as well asfunctions derived from the biochemistry of the body.  These “systems offunctions” became the most important features of complex life.  Theyare another example of the “Combinatorial Principle” of evolution explainedpreviously. 

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Biology or physiologyshould be seen more in this view of “systems” than in the analysis ofindividual functional components.

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EcologicalCommunities:

To adequately understand life andits evolution, one must look beyond systems of functions insingle organisms.  One has to see the next level of the "CombinatorialPrinciple”, the complex structure of life including interconnectedorganisms – where the life of one organism is coordinated with and depends uponthe life of the other or a variety of other types of organisms.  Thisdoes not, for example, concern only the symbiotic utilization of certainbacteria within the digestive system of mammals; it also concerns the complexinterdependence of various forms of life within different ecologicalareas, biotopes, or systems – in certain wetlands, prairies, forests,or ocean areas – most famously in the Sargasso Sea in the Atlantic Ocean. 

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

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

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

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-       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 thelipid bubble protecting the cells of organisms

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

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

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2.1.8.  Further Changes orInterruptions – the Extinctions and New Beginnings

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There are five significant causesfor 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:

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-       Geological changes

-       Climate changes

-       Major diseases, plagues, or species instability

-       Catastrophes leading to extinctions

-       Astronomical cycles

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Geologicalchanges:

Plate tectonics – terrestrialchanges – can raise or lower terrain surfaces and move plates or plate segmentsfrom equatorial to polar regions or the reverse, thereby changing the climateon those plates significantly.  Plate tectonics can also lead to changes inocean elevation, thereby forming new oceans or deleting oceans by squeezingtheir 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). 

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Plate tectonics can also lift theground under existing oceans (see the remnants of coral reefs incorporated insome peaks of the Alps or the disappearance of the shallow ocean that oncecovered the central areas of North America).

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

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

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Climatechanges:

Natural climate changes, iceages, warm periods, wet and dry periods – often changing within a very shorttime – all contribute to accelerated evolution – by destroying the habitat forsome species and binging their extinction while opening opportunities or nichesfor new ones as changes are reverted.

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

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Majordiseases, plagues, or species instability:

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

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

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Catastrophesleading to extinctions:

Five major “extinctions” have occurred already since thebeginning of the grandiose diversification of multicellular life on Earth about600 million years ago – and some more before that time – as evidenced byfossils.  The extinction that occurred about 450 million years ago must have wipedout 99% of all species and some interesting anatomical plans of organismsthat never appeared again.  The next extinction occurred about 350 millionyears ago.  The double extinction 250 to 200 million years ago wiped out thethen dominant Trilobites and with them 95% of all species.  Themost recent among the very large extinctions, 65 million years ago, wiped outthe dinosaurs and with them about 80% of all species.  The“population” loss (number of individual living beings) may be different, sinceone does not know the number of individuals that constituted each species.

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At least two of those extinctions, the one 65 million years ago and oneof 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 theUniversity of Kiel, Germany, now at Cornell) indicates that those “meteorites”actually were enormous ejecta (called “Verneshots”, after a Jules Vernephantasy) occurring early, but not necessarily at the very beginning ofgigantic basaltic eruptions that had actually started severalhundred thousand years beforehand.  

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

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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 insome places, connected with the dinosaur extinction.  Equally important werethe very large “Siberian Traps”, connected with the earlierextinction of life of the Trilobite era.  Areas in Ethiopia, seabeds in thePacific, the Palisades along the Hudson River close to New York, and an areaalong the Columbia River are minor basaltic deposits.

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It appears certain that more catastrophes of this sort will occur atrandom time intervals (or in astrophysical connection) in the future.  Wouldmankind and its civilizations survive?  What direction could evolution takeafter mankind’s demise?  Future deep scanning of the Earth – as alreadysomewhat 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 itsdepth but only within hundreds of years in going through the surface layers. How would society react when staring into the face of another majorextinction?  Will future technology permit controlled slow release of thebubbles pressure and channeling of basaltic masses?  Will there be controlledsurvival of a selected few – to be left with what on a devastated Earth?

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Astronomicaland Geophysical Cycles and Risks

Some of the above describedchanges or interruptions of natural evolution were found to be more or lesscyclical.  This led to the search for underlying reasons.  The followingphenomena were recognized as having special significance:

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-       The wobbling of the Earth’s axis of rotation

-       Cyclic changes of orientation of Earth’s axis of rotation under theinfluence 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

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

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The reversal of the polarity ofthe Earth’s magnetic field leads to intermediate phases of the absence of anymagnetic field – suppressing the very important protective, radiation-shieldingeffect of that field.  This can lead to great genetic damage – or to anacceleration of genetically controlled evolution.

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

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

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

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Resilienceand new beginnings:

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

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

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

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Will there be any moreinnovations of nature – after the next catastrophe – a germ-related or nuclearone?

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2.2. Biological and Human Evolution, the Human Brain

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2.2.1  Advances in AnimalDevelopment, Mammals, Homo Sapiens

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

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

-       Memory of and adherence to resource sources:  For example, the findingof hidden food by squirrels, the return of migratory birds to prior successfulnesting areas – and also the exotic return of salmons to their river locationof origin.  Those rivers may have been pleasant, once in geological times, withswamps as food supplies for smaller fish and easy transfer to the ocean for thelarger fish requiring more and larger prey.  But, with the slow lifting ofcoastal mountain ranges, co-evolution of fish began as the rivers becameincreasingly difficult to navigate, some being cut off from fish migration bybad rapids and waterfalls..  Struggling in vain across those would lead tofailure.  Those fish, however, that remembered navigable rivers with suitablespawning areas, survived or became more successful in propagation.  Similarly,spreading of oceans let only those migratory birds survive that rememberedmanageable passages – a capability not found where ocean distances contractedand 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 increvasses or remote areas.

-       High propagation rate, as among many rodents.

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

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

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In the course of evolution,certain characteristics were developed in a great variety of forms, colors, orsounds, as if not critical to survival – the shapes of shells, the colorationsof tropical fish or flowers, the sounds of languages – at best, serving forself-recognition of species.  Other capabilities were developed several times(the art of flying: insects, fish, birds, bats, and some squirrels – also thepoisonous 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 largeand complex brain of mammals; so far, it has appeared only once – inhumans.[42]

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It is not quite clear why alarger brain and consequent higher mental capabilities did not develop amongthe dinosaurs.  Could higher strategic skills not have been an evolutionaryadvantage for some of them, too?  Could some not have used more articulate armsand hands – first for climbing, then for tool usage – or have benefited frommore memory and language skills? [43]

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In any event, it was the mammalsthat developed higher mental skills in the branch leading up to humans.  Didthis 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 toforaging on the ground, bipedalism, and the diverse usage of their hands? [44] In other words, did they go through changes in their environment thatsome of the dinosaurs had also gone through, but humans then found solutionsleading to greater opportunities, new ways of risk avoidance, and new niches inevolution?  Some scholars indicate the capability of speech as a motorfor the development of larger brain size – but why did the dinosaursnot accomplish this evolution?  Why did none of the other apes? [45]

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

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Considering the enormous growthin intellectual activities and density of information processing from thehistoric times of the earliest humans to our time, it appears that thelarge brain was oversized for early humans.  What did they do with allthat neural potential?  If it was not used, its development and support was aluxury.  Nature does not normally permit luxuries.  Why did nature create anoversized 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 – andnot much else?  Or was hunting and fighting with each other the mainutilization of their large and complex brains? 

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2.2.2  The Human Brain

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The brain evolved as sensorsrequired more complex signal processing for the formulation of motionstrategies.  After the simple “reaction” mode of sensor signals leading to asimple movement, more complex neural networks offered distinctiveadvantages in complex situations.  It could well be that it was the mid-brainwith the limbic system that evolved next. [47] This system, now known as the source of emotions, allowed for summaryassessment of situations, possibly leading only to fight-or-flightdecisions.  Complex interactions of brain nuclei, biochemical effects involvingsome specific glands, environmental factors, or food intake, and geneticallygiven behavior actuation resulted in what we call emotions and consequentbehavior (some described in more detail in the essay on “Personality” on thewebsite www.schwab-writings.com, in the“Brain-Mind” section).  

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

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The human brain may merelyhave added an enormous amount of memory and an equally enormous amount ofmemory interconnectivity – plus such special features as speechrecognition and, separately, speech formulation.  Additionally, there was greatprogress in functional differentiation and evolution – for example, in themultitude of hypothalamus sub-nuclei.  The embryonic development of thehuman brain may reflect and, thereby, explain the actual evolutionarydevelopment. [48]

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There are differentapproaches 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 (brainphysiology)

-       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

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

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

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

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This gets closer to the questionof brain “software”, as in computers that accomplish its function usinga certain amount of “hardware”.  Without the knowledge of the software, onecannot understand how a computer accomplishes what it does.

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In the analysis of signalingin the brain, one finds some drastic differences between the signalingin computers and signaling in the brain.  In computers, signaling occursthrough linear sequences of “0” and “1” signals along the same transmissionline, 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 fewstrictly analog computers for special applications).  In the brain, signalingis different:

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-       There is a basic duality of signaling in the brain – thesynaptic “on-off” signaling (comparable to digital or discrete signaling) andsignaling by firing rate (a form of analog or continuously variablesignaling).  This simultaneous duality of signaling within the brain leadsto the very complex information-processing capabilities of the brainbeyond 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 ofother 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 arrivingin parallel at a single neuron (or very few of them).  This isaccomplished by the fact that most neurons accept a number of input connectionsfrom other neurons – whereby some inputs signal “activation”, while others areneuron activity inhibiting.  This allows either for alternative or logic-“or”functions, or it allows for the parallel inhibition of competing sites leadingto dominance situations of certain signals and groups of neurons. This is necessary to eliminate confusion in the brain when multiple inputsarrive – as is quite normal in daily life.

-       The brain does not have a “clock” for synchronization of signals, ascomputers possess.  Consequently, minor differences in the arrival time ofenabling or inhibiting signals at a receptor neuron may lead to vastlydifferent 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 receivingneurons.  Certain brain functions cannot be explained differently, and theeconomy of natural evolution demands such a solution – for example, to bringthe effect of amygdala-based valuations to many receiving places, while thereactually is only a rather limited neural connection from the amygdala to theother parts of the brain.  Another example is the establishment of dominancesituations, as in foreground activation of subsequent alternative thoughtsequences (“visualizations”), as discussed later. 

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

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The study of biochemistrywithin the brain, related mainly to neurotransmitters, concerns the“mood” setting within the brain and the influencing of neural networks in asummary manner.  This led to the discovery that different neurotransmitters areprevalent in different parts of the brain, permitting some selectiveinfluencing of brain functions. 

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Biochemical analysis of the brainallowed understanding of the action of certain biochemical substances (forexample, alcohol, coffee, drugs – even merely the availability of food whenneeded or the lack thereof).

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2.3. Singularities in Natural Evolution and Anomalies in Nature

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What are “singularities” in evolution?

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-       Extremely unlikely developments (very low probability) that provided forsubstantial 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 expectedbut did not happen

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

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One reason could be that competitionand mutual elimination are always fiercest between related species inadjacent niches of existence.  In any evolutionary step, this leads to “burningthe bridges” behind their evolutionary advance.  But the evolution thatactually occurs indicates that there always are new niches or opportunities forevolution.  Therefore, the above question remains.

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The following singularities ofnatural evolution could be listed and were mostly discussed above.  The list isnot comprehensive:

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-       The regularity of electron shells around atomic nuclei as the key factorfor the combinatorial appearance of molecules and for the significance ofcarbon  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 inbrush 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 andmolecular 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 thebrain

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

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

-       The absence of metallic conductivity and electronic communication

-       The absence of wheels

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Obviously, a more thoroughanalysis should reveal important singularities in early evolution among plantsor lower animals.  One should consider not only the fact that these“singularities” occurred in evolution at all, but also, at the time scaleof evolution, how fast some singularities occurred.

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Anomalies in thebiological world, as the anomaly of water in the physical world, are moredifficult to define, mostly being consequences of evolution.  Alist could be established and investigated.  Could mate selection by factorsthat appear to be counterproductive for survival be considered an anomaly? Could unlimited propagation of bacteria in hosts, thereby destroying theirsustenance or excessive foraging by some insects or prairie dogs and therebydestroying their sustenance, be considered an anomaly regarding the law of thesurvival of the fittest?  Was increased mitochondria activity at lowertemperatures, thereby stabilizing body temperature, an anomaly of nature?

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

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10-03-05



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

[2]The consideration of extremophile microbes – existing in very hot or very coldenvironments – would largely extend the habitable zones.  But extremophilemicrobes at hot vents deep under oceans, deep under rock, or under ice and snoware 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 multipleantennas to discover radio signals from outer space.

[4] See the excellent book, Rare Earth, by Ward and Brownlee, CopernicusBooks, 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 yearsbetween the appearance of liquid water (oceans) on Earth and the appearance offirst life (see the fossils in rocks on Greenland and Iceland).

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

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

[9]Some very primitive (and, possibly, the oldest) bacteria do not use solarenergy as their energy supply, but the transformation of FeS + H2Sinto FeS2 (Pyrite) + H + energy.  The energy can be used to breakdown the ubiquitous carbon dioxide to provide carbon for the building oforganic substances.

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

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

[12]By one estimate, 50 million meteorites of about 1 meter diameter or morehad reached early Earth within 8 million years.  About half a dozen meteors of1 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 isstill falling on Earth every year, and much more arrived during the earlyhistory of Earth.  Up to 10% may be proto-organic material (see the ER2project).  Large comets or meteors, with more than 1 km diameter, rarely fromouter space beyond the solar system, still hit Earth in the average of oneevery 300,000 years, but mainly contain rocky or metallic material besideswater.  

[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 Isuarocks of southwestern Greenland.

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

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

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

[19]A quote from Cell and Molecular Biology, by Gerald Karp, ISBN0-471-19279-1, Chap. 2.5, concerning the array of functions proteins have in acell:  “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 reactsto and what types of substances enter or leave the cell; as contractileelements, proteins constitute the machinery for biological movements; … inother functions, proteins act as antibodies, serve as toxins, form blood clots,absorb or reflect light, and transport substances”.  “The explanation (fortheir varied functions) resides in the virtually unlimited shapes thatproteins, as a group, can assume”.     

[20]Sheep and some other animals use certain bacteria in their guts to provide anenzyme 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 atthe end of a severe glaciation period

[22]An excellent overview is provided by the textbook, Cell and MolecularBiology by Gerald Karp, published by John Wiley & Sons, ISBN0-471-19279-1.

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

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

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

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

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

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

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

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

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

[32]Discovered by the geologist Edson Bastin, University of Chicago, andmicrobiologist Frank Greer in the 1920s and confirmed only in 1987 through deepboreholes 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 hydrogenand carbon dioxide dissolved in those rocks and are the base of a subsequentmicrobial food chain.

[33]A very good overview of the evolution of the genome and the diversity of lifeis 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 copyin the third dimension.  A copy of a three-dimensional organism would requirethe extraction in a fourth dimension – hence the ingenuity of doing a copy byhaving the blueprint for the whole organism in specially produced seed or eggcells and developing copies from there. 

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

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

[37]Tethys was a Greek Titan goddess, daughter of Uranos and Gaia, who became thewife 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 tothe Western nations.

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

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

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

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

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

[46] Somewhat larger brain sizes occurred in at least eight different sprigs on theevolutionary branch of “apes” – namely, those in Eastern and WesternChimpanzees, Bonobos, Eastern and Western Gorillas, and early hominids from theAustralopiths to Homo Sapiens and, finally, Modern Humans – beginning some 20million 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., ISBN0-444-01331-8.