Cosmology
Astronomy - Astrobiology - Earth Sciences
Origins, Evolution, Metamorphosis, Extinction

THE EVOLUTION OF LIFE FROM OTHER PLANETS GENES, MICROBES, METAZOAN & METAMORPHOSIS
Rhawn Joseph, Ph.D.
A comprehensive review of published scientific evidence is presented, detailing how life from other planets evolved on Earth. These first Earthlings (archae, bacteria, and cyanobacteria) contained the genes and genetic information for altering the environment, the "evolution" of multicellular eukaryotes, and the metamorphosis of all subsequent species. These included exons, introns, transposable elements, informational and operational genes, RNA, ribozomes, mitochondria, and the core genetic machinery for translating, expressing, and repeatedly duplicating genes and the entire genome. Prokaryotic genes were initially combined to fashion the first eukaryotes and/or were donated and transferred to unicellular eukaryotes and subsequently expressed in response to biologically engineered environmental influences, often in busts of explosive evolutionary change, as typified by the Cambrian Explosion. Genes biologically alter the environment and secrete waste products, e.g. methane, oxygen, calcium carbonate, sulphate, ferrous iron, etc., which act on gene expression, generating eyes, bones, bodies, and brains. However, these genes and life on Earth did not randomly evolve. Evolution is metamorphosis. These genes were inherited from ancestral species who acquired these genes and these genetic instructions from life forms that long ago lived on other planets.

Parts 1 & 2
Part 3 Genes & Metazoan Metamorphosis:
Brains, Bodies & the Cambrian Explosion.

THE EVOLUTION OF LIFE FROM OTHER PLANETS GENES, MICROBES, & METAZOA METAMORPHOSIS
Rhawn Joseph, Ph.D.

PART 3
Genes Acts on the Environment Which Acts on Genes,
Evolution, Metazoan Metamorphosis
Brains, Bodies, Eyes,
Cambrian Explosion

BIOCHEMICAL LIBERATION OF MINERALS AND GASSES
Following the accretion, differentiation, layering, and establishment of the Earth, the crustal outer surface was impacted by a variety of biological, geological, solar, stellar, and geochemical forces, including strikes by moon-sized debris, volcanism and degassing, plate tectonics which produced the first continents, water-atmospheric surface weathering, and the breakdown and liberation of chemicals, minerals and gasses by prokaryotes (Falkowski and Godfrey 2008; Hazen et al., 2008; Nisbet and Nisbet 2008; Sleep and Bird 2008).

Geochemical and biological influences, especially the activity of archae and bacteria, triggered repeated episodes of global warming and global freezing, the creation of banded iron formations, the establishment of hydrothermal ore and large-scale surface mineral deposits, the excretion or breakdown of various gasses, and the differentiation and liberation of over 4000 different mineral species (Hazen et al., 2008; Nisbet and Nisbet 2008; Schwartzman et al., 2008; Sleep and Bird 2008).
The liberation, oxidation, or irradiation of these minerals, gasses, elements, and ions, including those in the atmosphere, the planetary surface (H (H2, H2O, H2S), C (CO, CO2, CH4), N (NH3, N2), S (H2S)) and ions in the sea (Na+; K+; Mg2+; Ca2+; Mn2+; Fe2+; Co2+; Ni2+; Cu+; Zn2+; Mo or W; Se (H2Se); P; V(VO2+); contributed to changing atmospheric and ocean chemistry (Falkowski and Godfrey 2008; Nisbet and Nisbet 2008; Richardson 2000; Williams 2007) and ultimately made possible skeletal biomineralization and the progressive evolution of multicellular life (Hazen et al., 2008; Mentel and Martin 2008; Williams and Fraústo da Silva 2006).
However, most of the minerals, elements, and gasses were biochemically liberated or oxidized in a sequential, seemingly step-wise progression These were not random events, but under bio-chemical and genetic regulatory control, which, in conjunction with geochemical events, impacted and paralleled the evolution of increasingly complex species (Hazen et al., 2008; Williams 2007).
For example, unlike eukaryotes, most single cell anaerobes do not possess genes or proteins which respond to copper and dioxygen. Likewise, they possess few proteins which bind to calcium (Mitchell 1961; Williams 1961). In fact, initially Ca2+ levels were negligible (Williams 2007). Correspondingly, there were almost no intracellular Ca2+-binding proteins in early cells which instead employed proton gradients to drive many energized activities (Mitchell 1961; Williams 1961).
Following repeated episodes of single gene and whole genome duplication, exon-shuffling, and intron and transposon alterations in regulatory activity, eukaryotes came to possess numerous copper, dioxygen, and calcium-binding proteins and genes which reacted to and employed these susbstances for signaling (Williams & Fraústo da Silva 2006),
And the same is true of progressive increases in the availability of Zn2+, Mn2+, Fe2+, Co2+, Ni2+ and Cu+ (Cu2+), and various metal ions. All acted on gene selection, and this was accomplished via, for example, metalloproteins which were matched and bound to specific DNA sequences (Williams 2000). However, these proteins and genes existed prior to their expression or exposure to these molecules.
Proteins that respond to Ca2+, Zn2+, Mn2+, Fe2+ form a homeostatic link such that they bind together thereby inducing gene expression (Dupont et al. 2006; Morgan et al. 2004; Williams & Fraústo da Silva 2006). Indeed, changes of the metal elements (ions) and the isotopes of non-metals as detected in sedimentary mineral deposits (Holland 2006), are "directly related to the expression of DNA" (Williams 2007).
As Ca2+, Zn2+, Mn2+, Fe2+ levels increased, they acted on gene selection, possibly triggering several whole genome duplication events, which increased the number of genes that could produce a greater number of Ca2+, Zn2+, Mn2+, Fe2+ proteins. Thus the release and buildup of these environmental agents acted on gene selection thereby generating increasingly complex multicellular creatures which now possessed numerous compartments (i.e. cytoplasmic, periplasmic, vesicular, extracellular) each of which were specialized for processing these chemicals (Williams & Fraústo da Silva 2006).
Hence, eukaryotic cells evolved as these chemicals became available and this is because the cells contained genes, proteins, and enzymes that could respond to these elements. Consider the proteins used for intracellular transport within the Eukaryotes and the number of species known to contain genes coding for actin, myosin (Richards & Cavalier-Smith 2005), tubulin (Baldauf et al. 2000), kinesin (Lawrence et al. 2002) and dynein (Asai & Wilkes 2004). These genes did not randomly evolve. The genes coding for microtubule/kinesin/dynein and f-actin/myosin were inherited from a common ancestor and were activated once the necessary elements, minerals, metals, and gasses became available.
By contrast Prokaryotes, having donated the necessary genes to eukaryotes, did not respond to these chemicals and minerals, and thus required and maintained only one major compartment, enclosed by one major membrane, within which floats the cytoplasm (Williams & Fraústo da Silva 2006) and cytoskeletal elements(Møller-Jensen & Lowe 2005),
Hence, some organisms responded to and accumulated certain elements while selectively rejecting others that were useless to them or which would be poisonous to the cell. Yet later appearing organisms rejected the elements that had been accepted by previous species, and instead responded to and replaced them with yet other elements and gasses which had been subsequently liberated (Williams and Fraústo da Silva 1996, 2006).
Accumulation and rejection requires energy which results in the creation of waste products (Falkowski and Godfrey 2008; Richardson 2000; Sleep and Bird 2008). However, these oxidized wastes subsequently acted on gene selection and some of these wastes (e.g. carbohydrates, sulphates, ferrous iron) were also utilized as sources of energy by later emerging more complex life forms (Williams and Fraústo da Silva 1996, 2006; Sleep and Bird 2008) as well as by innumerable microbes as is the case with modern prokaryotes (Berks et al., 1995; Castresana and Saraste 1995; Lovley 1991, 1997; Schafer et al., 1996; Vargas et al., 1998). Some substances took billions of years to accumulate at which point they were biologically utilized; oxygen is a prime example.
CYANOBACTERIAL ENGINEERING OF THE ENVIRONMENT
Initially, the new Earth was lacking free oxygen, calcium, and other environmental agents necessary to induce significant genetic and evolutionary change. Instead, the initial atmosphere contained hydrogen, helium, neon, argon, ammonia, carbon dioxide and various lighter and inert gases (Kasting and Ackerman 1988; Sleep & Zahnle 2001; Walker 1985), some of which seeped into space (Tian et al. 2005) or were bound up in minerals which chemically reacted to their presence (Williams 2007).
In the absence of oxygen, some cyanobacteria use hydrogen sulfide, or sulphur, or reduced nitrogen for energy or engaged in H2-based anoxygenic photosynthesis (Herrero and Flores, 2008). As carbon dioxide levels increased, some species broke down CO2 to form carbohydrates which directly acted on gene expression, facilitating, for example, the creation of additional RNA and DNA macromolecules, and essential proteins and lipids (Matthews et al., 1999).
Simple carbohydrates (monosaccharides) such as ribose and deoxyribose form the backbone chains in nucleic acids which create DNA and RNA. Ribose is used in RNA and deoxyribose is used in DNA. Thus, the gene pool and genome increased in size once these chemicals, minerals, and metals were liberated, oxidized, or broken down.
Complex carbohydrates (polysaccharides) form the structural elements in the cell walls of bacteria and plants including the synthesis of cellulose which is one of the most abundant organic compounds in the biosphere (Matthews et al., 1999). Carbohydrates are also employed for energy. Thus, simple organisms and their genomes increased in size and complexity.
In addition to carbohydrates, cyanobacteria also secreted waste products such as ferrous iron and oxygen, which eventually acted on gene selection. The buildup of carbohydrates, iron and oxygen (Herrero and Flores, 2008), would play a major role in the diversification of prokaryotes, and the evolution of the genome and complex multi-cellular organisms.

Cyanobacteria Fossils - Orgueil Meteorite

Cyanobacteria Fossils - Murchison Meteorite

Microfossils of cyanobacteria have been found in a number of meteors which predate the origin of this solar system (Hoover 1997, 1998, 2006), including the Murchison and Orgueil.

Cyanobacteria

Cyanobacteria (also known as blue-green algae) form spores (Bryant 2007; Carr and Whitton, 1982; Herrero and Flores, 2008; Simon 1977) and are perfectly adapted for surviving the rigors of space. In the absence of oxygen or sunlight they, and other microbes can reduce nitrogen, iron, methane and carbon for energy; releasing nitrates, nitrogen dioxide, ammonia, and oxygen as waste products (Berks et al., 1995; Castresana and Saraste 1995; Chaudhuri et al., 2001;Kashefiand and Lovley 2000; Price 2000; Tor et al., 2001; Vargas et al., 1998), all of which act on gene selection.

Moreover, cyanobacteria can utilize and reduce CO2 and H2O. CO2 H, and N2 levels were already quite high even 4.5 bya (Kasting & Ackerman 1986) due to volcanic activity and outgassing (Kasting and Ono 2006; Kirschvink 1992; Hoffman et al. 1998) whereas by 4 bya much of the planet may have been covered by shallow seas (Valley et al. 2002).
Coupled with the reduction of atmospheric compounds CO, CO2 and N2, the resulting gasses, chemicals and polymers that were created as a result of cyanobacteria activity, also acted on gene selection and contributed to the major components of a cell and its DNA, i.e. lipids, proteins, saccharides and nucleic acids. Moreover, the resulting polymers and chemicals were easily reduced by CO2 and H2O. As these gasses were abundant in the early atmosphere of the Earth (Kasting & Ackerman 1986; Knauth & Lowe 2003), these interactions created a bio-environmental feedback cycle that continually acted on gene expression.
However, some of the gasses and minerals liberated or consumed by micro-organisms, in conjunction with geochemical forces, also impacted the climate and triggered repeated episodes of global warming and global freezing; cyclic events which also impacted gene expression and which paralleled the evolution of increasing complex species.
THE HOT HADEAN EARTH
For the first two billion years after the Earth was formed the sun may have been 80-90% of its current size, 70% to 75% as luminous, and did not generate as much heat as the modern sun (Gough 1981; Kasting and Ono 2006; Lang 2001). Nevertheless, despite insufficient sunlight the Earth did not freeze and remained warm if not hot, secondary to geothermal heat flow and internally generated temperatures (Davies 1990), and the presence and buildup of carbon dioxide which created a heat-trapping greenhouse effect (Kasting and Ackerman 1988; Sleep & Zahnle 2001; Walker 1985). Much of this CO2 (including H2) was pumped into the atmosphere by volcanism (Berner (2004; Kirschvink 1992; Hoffman et al. 1998).

According to Kasting and Ackerman (1986), if the early atmosphere contained 10 bars of CO2 this would have resulted in a dense greenhouse atmosphere. However, others have calculated that atmospheric CO2 levels were much lower (Sleep & Zahnle 2001) which suggests that the planet was hot, but not broiling.
Therefore, the early Earth was much warmer than it is today, with some estimates ranging as high as 80°C (176°F) at 4.5 Ga (Kasting & Ackerman 1986), and fluctuating from 45°C to 85 °C (113°F to 185°F) at 3.3 Ga (Knauth & Lowe 2003); even though solar luminosity at 3.3 Ga was only 77% of its present value (Gough 1981).

More recently Kasting (Kasting and Howard 2006) has revised his initial estimates and concludes "the early Earth was warm, not hot." This is also the conclusion of Condie et al. (2001) and others (Holland 1984; Sleep & Hessler (2006) as based on calculations of chemical alterations in Precambrian rocks dated from between 3.5 to 3.0 Ga.
The early Earth was first warmed by high levels of CO2 which cyanobacteria and other microbes utilized to manufacture carbohydrates (e.g. ribose and deoxyribose) which directly act on gene creation and expression and which serve as the building blocks of the backbone chains in those nucleic acids which form DNA and RNA. Moreover, carbohydrates serve as nutrients and energy sources which enabled other prokaryotes, such as methanogens, to diversify and flourish.

Methanogen

Methanogens secrete methane (CH4), as well as CO2. Thus around 3.5 to 3.0 bya, as methanogens began to proliferate, atmospheric CH4 levels began to rise forming an organic haze, thereby initially adding to the greenhouse warming effect (Schwartzman et al., 2008). Indeed, methane is a powerful greenhouse gas; per molecule its warming effect is 21 times that of CO2. Moreover, as based on detailed photochemical modelling (Pavlov et al. 2001) in an anoxic atmosphere the lifetime of CH4 is approximately 1000 times longer than today.
The combination of high levels of methane and CO2 which made up the Earth's early atmosphere, created a greenhouse effect which warmed the planet (Pavlov et al. 2000; Kasting & Siefert 2002; Kasting & Ono 2006). Indeed, Pavlov et al. (2000) calculated the effects of modest amounts of CH4 and CO2 in the atmosphere, and determined that around 3.0 bya, the Earth's surface temperature would have been about 50°C, even though the sun was approximately 80% as luminous as today.
Therefore, the planet was quite warm if not hot, for the first 1.5 billion years after its formation, and did not begin to cool until 2.9 bya (Young et al. 1998).

Cyanobacteria

Methanogens

Hence, the warmth of the planet was maintained by the activity of prokaryotes, such as cyanobacteria which utilized carbon dioxide to fashion carbohydrates, the result of which was the diversification and increased activity of other microbes, such as methanogens. Hence, methanogens and other prokaryotes began to flourish due to the activity and death of cyanobacteria. Thus the buildup of a methane greenhouse followed the buildup of CO2 (Schwartzman et al., 2008), a conclusion based an analysis of weathering feedbacks in the carbonate-silicate cycle.
CYANOBACTERIA, OXYGENATION & MULTI-CELLULAR EUKARYOTES
Microfossils of cyanobacteria have been found in a number of meteors which predate the origin of this solar system (Hoover 1997, 1998, 2006). Cyanobacteria were likely among the first to arrive on this planet. Despite the lack of a protective ozone layer, they were protected from UV rays by mineral grains (Cavalier-Smith, 2006) and thus could congregate near the surface and were able to engage in photosynthesis (Hoashi et al., 2009) immediately upon being deposited on this planet.
In the absence of oxygen or sunlight these initial cyanobacteria feasted on, and reduced nitrogen, iron, methane and carbon dioxide for energy (Berks et al., 1995; Castresana and Saraste 1995; Chaudhuri et al., 2001; Kashefiand and Lovley 2000; Price 2000; Tor et al., 2001; Vargas et al., 1998), releasing nitrates, nitrogen dioxide, ammonia, carbohydrates, and oxygen as waste products. As carbon dioxide levels were initially quite high (Kasting & Ackerman 1986; Knauth & Lowe 2003), due to volcanic out gassing (Berner 2004; Kirschvink 1992; Hoffman et al. 1998), cyanobacteria flourished and diversified, leaving their fossilized and geochemical footprints in the planet's oldest rocks, including those dated to 3.5 bya (Hoashi et al., 2009; Schopf 1993).

Cyanobacteria Cellular Structure

Cyanobacteria are the only known prokaryotes capable of oxygenic photosynthesis. Therefore, these prokarotes were largely responsible for releasing massive amounts of oxygen (DesMarais 2000) which resulted in increased atmospheric oxygen levels, which also acted on gene selection and which induced the metamorphosis of mitochondria and multicellular eukaryotes. Thus these microorganisms made a major impact on the biochemistry, geochemistry, and the evolution of life on Earth.

By 3.46 bya these photosynthesizing microbes were releasing significant amounts of oxygen into the atmosphere and oceans (Hoashi et al., 2009). Moreover, these or other oxygen secreting microbes may have been congregating near undersea volcanoes and thermal vents and reducing metals, minerals and carbon dioxide. As based on analysis of marine sedimentary rocks dated to 3.46 bya, Hoashi and colleagues (2009), found evidence of oxygenation in haematite crystals and associated minerals which were formed at temperatures greater than 60 °C in an oxygenated body of water rich in ferrous iron. "To have this amount of oxygen, the Earth must have had oxygen producing organisms like cyanobacteria actively producing it" (Hoashi et al., 2009).
However, although large quantities were being pumped into the environment, it took almost 2 billion years for the free oxygen concentration to rise to 1% of present levels (Kasting & Siefert 2002). This is because large quantities of oxygen were consumed in the process of oxidizing and reducing inorganic and organic compounds. Thus, the O2 pressure was buffered for a long time and this too played a key, sequential role in the targeted activation of genes giving rise to the metamorphosis of increasingly complex species culminating in the Cambrian Explosion.

Thus, initially, except for isolated pockets, the Earth's atmosphere and oceans were largely devoid of free oxygen (Holland 2006).
Around 3.2 bya, there was a spike in atmospheric oxygen, a consequence of increased oxygen photosynthesis (Ohmoto et al. 2005). This spike in oxygen levels may have also been the result of photochemical degradation and H2 drawdown by sulphate-reducing bacteria (Kasting & Ono 2006) thus liberating and releasing O2 into the atmosphere. Anoxygenic photosynthesizers employ H2 as a reductant. Moreover, autotrophic methanogens feed on H2 of which there are ample supplies in the ocean.
Therefore, around 3.2 bya oxygen levels increased (Ohmoto et al. 2005). Oxygen, however, also breaks down methane. Therefore by 2.9 bya, the planet began to cool, a function of increased oxygen reducing the methane greenhouse effect (Young et al. 1998; Kasting & Ono 2006).
By 2.8 bya, oxygen-producing cyanobacteria were creating thick cyanobacterial mats (Buick 1992) and leaving their fossilized signatures in shales and stromatolites (Brocks et al., 1999; Olson 2006). They also began to diversify into a range of species and clades (Tomitani et al., 2006) and were secreting oxygen and fixating and converting nitrogen into nitrates.

Cyanobacteria Mat

The environment acts on gene selection, and the buildup of nitrates would be utilized and incorporated by innumerable organisms to create addtional amino acids, proteins and DNA. This would have led to an increase in gene number, providing the raw materials for duplications of individual genes and the entire genome.
The combined buildup of nitrates, oxygen, carbohydrates, and other liberated elements, metals, and ions, coupled with temperature and climate change, acted on gene selection giving rise to the first multi-cellular eukaryotes by 2.7 BYA [Dyall and Johnson 2000; Hedges et al., 2001]. These creatures consisted of around 2-3 cell types (Hedges et al., 2004). It was following this oxygenated cold period that various species of eukaryote began to switch from anaerobic to oxygen dependent enzymes in order to breath oyxgen (Kirschvink and Kopp, 2008).
However, O2 levels began dropping after 2.8 bya. (Ohmoto et al. 2005); a possible consequence of solar flares and increased UV radiation on the viability of photosynthesizing organisms. Moreover, methanogens were flourishing and were slowly creating a thickening organic haze (Pavlov et al. 2001) that was interfering with photosynthesis (McKay et al. 1991; Pavlov et al. 2000) thus reducing O2.
After a cooling spell which may have lasted 100 million years, the Earth again began to warm. This warming spell may have been due to vulcanism releasing CO2 or sunlight-blocking ash into the atmosphere, and the activities of methanogens which were increasing atmospheric levels of methane and H2. H2 levels may have increased because the organic methane haze may have been acting as a blanket which was preventing H2 from escaping into space (Tian et al. 2005). The presence of increasing H2 and CH4 contributed to the thickness of this haze and the greenhouse effect which warmed the planet. However, photosynthesis and oxygen production continued, and a balance was achieved and temperate climates prevailed (Condie et al., 2001; Holland 1984; Kasting and Howard 2006; Sleep & Hessler 2006)
By 2.45 bya (and for the next 600 million years), atmospheric oxygen level had risen to values between 0.02 and 0.04 atm (Holland 2006). Although the deep oceans continued anoxic, surface layers and pockets of shallow ocean became mildly oxygenated (Holland 2006).
By 2.3 billion years ago the Earth's land masses and ocean floors were partly covered with thick bacterial mats and other organisms (Ohmoto, 1999) and by 2.1 bya eukaryotes were leaving their fossilized impressions embedded in rock and stone (Han and Runnegar 1992). Organic material began to build up in the oceans and soil, serving as nutrients and producing other substances which would act on gene selection and promote cell growth and diversification.
Many of these organisms feasted on minerals and organic residue, including iron from the upper layers of rock and soil, and secreted a variety of organic acids which in turn formed iron rich laterites (Ohmoto 1999). As pointed out by Ohmoto (1999), oxygen may have been sufficient 2.3 billion years ago, at least in some areas, to sustain the generation of land-based biota and to convert iron to iron oxides. These acids and the buildup of iron-related substances would later act on gene selection.
Even so, the atmosphere and seas remained largely anoxic, with the exception of isolated pools of oxygen in the surface ocean and pockets of shallow ocean where biological productivity was high (Holland 2006; Mentel and Martin 2008).
THE FIRST SNOW BALL EARTH
This warming of the Earth, following a spike in oxygen and cold weather 2.9 bya, and which lasted for at least 500 million years, was due to the buildup of high atmospheric levels of methane and H2. The presence of increasing H2 and CH4 had created a thick organic haze resulting in global warming from the greenhouse effect. However, this even thicker layer of organic haze may have blocked so much sunlight that it began to contribute to global cooling (McKay et al. 1991; Pavlov et al. 2000).

The high levels of methane also acted on gene selection and archae known as methanotrophs and methylotrophs began to proliferate. These were methane eaters, and in ever growing numbers they metabolized and broke down methane, as demonstrated by the presence of hopanes and high relative concentrations of 2α-methylhopanes in Archean rocks (Brocks et al., 2003). Reductions in methane began to cool the planet.
As methanotrophs proliferated, methane levels continued to be reduced, which allowed more sunlight to strike the Earth, which triggered increased photosynthesis. By 2.45 bya, oxygenic photosynthesis had become widespread (Brock et al., 2003; Buick 2008) and atmospheric oxygen levels rose (Bau et al. 1999; Kirschvink et al. 2000) to values between 0.02 and 0.04 atm (Holland 2006).
Oxygen also breaks down methane. Indeed, the presence of even small amounts of O2 in the atmosphere would have been associated with a large decrease in its CH4 content, and this decrease would have caused the planet to rapdily cool (Young et al. 1998; Kasting & Ono 2006).
This transient spike of O2 levels 3.2 bya, followed by increased oxygen levels beginning around 2.4 bya, eventually shut down sulphur MIF production and caused a rapid and drastic decrease in atmospheric CH4, thus triggering glaciation (Kasting and Howard, 2006). That is, increased levels of O2 acted to oxidize sulphide, such that dissolved sulphate levels increased just as O2 levels increased. Both began to build up in shallow marine sediments which resulted in decreases in methagenesis and reductions in the CH4 and thus caused significant reductions in atmospheric methane (Pavlov et al. 2003; Kharecha et al. 2005). The increased levels of sulphate in turn triggered a proliferation of sulfur-eating bacteria, which caused a drawdown in H2 and CH4, a consequence of bacterial sulphate reduction (Kasting and Ono, 2006).
Moreover, CO2 levels were being reduced by photosynthetic bacteria who were employing H2, H2S and/or Fe2+ to reduce CO2 to organic matter (Pierson 1994). The reductions in methane coupled with reductions in CO2 would have accelerated the cooling of the planet.
Thus, between 2.4 bya to 2.2 bya, as oxygen levels rose, the greenhouse effect was eliminated, and the planet grew cold and began to freeze (Roscoe 1969, 1973), creating the first "snowball Earth" referred to as the "Makganyene" glaciation. Indeed, by 2.2 much of the Earth and its oceans were frozen or covered with ice and snow (Evans et al., 1997; Kirschvink,, et al. 2000; Roscoe 1969, 1973), creating the first "snow ball Earth."

However, these blankets of snow and layers of ice also provided protection against UV rays, but allowed light penetration (McKay 2000). This enabled photosynthesizing creatures to proliferate near the surface (Cockell et al. 2002; Cockell & Cordoba-Jabonero 2004) who secreted even more oxygen into the atmosphere, thus maintaining the low temperatures.
And then temperatures began to rise.
THE BIO-MELTING OF SNOWBALL EARTH
Innumerable microbes may have died due to the glacial conditions, thus forming thick layers of carbohydrate enriched organic matter on land and sea. Oxygen rapidly degrades and destroys organic matter and under current conditions over 99% of organic matter is subsequently destroyed; a function of the redox state of the atmosphere–ocean system.
However, two billion years ago, the oxygen being released by photosynthesizing microbes was actively being reduced and removed from the atmosphere; consumed in the process of oxidizing and reducing inorganic and organic compounds. Other factors may have included submarine volcanoes (Krump 2008). As argued by Krump (2008) "the gasses emitted by submarine volcanoes, were binding atmospheric oxygen with a variety of minerals, thus stripping oxygen from the atmosphere."
Since oxygen levels were at such low levels, degradation of organic matter would have also taken place via methanogenesis (Holland 2006); thus methanogens would have again begun to prolifer. Therefore carbon dioxide and methane also began to be pumped back into the atmosphere by a variety methagenic microbes living within the ocean, deep beneath the Earth, within the snow, and feasting on dead microbes and decaying organic matter in shallow pools of melt water and muddy soil. Further, volcanoes were belching carbon dioxide. The increasing levels of carbon dioxide and methane again began to create a greenhouse effect.
Moreover, cyanobacteria (such as black cyanobacterium Scytosiphon) probably colonized much of the icy snowy surface, forming thick black bacterial mats (Cavalier-Smith 2006) which in turn prevented light and heat from being reflected back into space. In the arctic these creatures can reduce albedo and warm soil by 4–5 °C and icy surfaces by 8–12 °C (Gold 1998).
Over time, as the sun grew in mass it also began to increase its heat output (Gough 1981; Lang 2001). Thus, the Earth began to warm, the "Makganyene" glaciation came to an end, sea levels rose, and the climate and environment of the planet underwent significant change; all of which acted on gene expression thereby triggering a burst of eukaryotic cellular evolution.
GENETIC ENGINEERING OF THE WOMB OF THE PLANET
Oxygen breathing eukaryotes did not evolve earlier in the history of the Earth, simply because evolutionary development takes place in stages which coincide with the availability of chemicals, gasses, and other elements which are required at specific developmental stages. Evolution and metamorphosis can be likened to embryology and development (Joseph 1997, 2000). However, instead of 9 months, it takes billions of years to genetically alter the womb of the planet. And like embryological-neonatal development, various enzymes and chemicals must be released in timed sequences of targeted release with act on gene expression with one stage of development logically following and building upon the next. One targeted host serves as the foundation for the next.
For example, certain elements and gasses could only be employed at various stages of metamorphosis and only after they had been synthesized or excreted as a waste product over hundreds of millions of years of time (Williams & Fraústo da Silva 2006). Upon reaching certain levels, acted on specific genes and proteins which may have been freed up from regulatory restraint, following, for example, whole genome duplication, which in turn may have been triggered by a previous environmental event.
For example, CO2 had to be broken down to create carboydrates, which led to increased energy availability, increases in the size of the genome, species diversity, and the flourishing of methanogens which warmed the planet. To generate oxygen, CO2 and H2O had to be broken down or combined, which led to the formation of polymers and vital biopolymers (cellulose, starch, proteins, peptides) thereby creating complex multi-compartmented eukaryote cells (Williams 2007) and further expanding the size of the genome; possibly inducing whole genome duplicative events.
The cyclic buildup of methane/carbon dioxide followed by oxygen, followed by methane/carbon dioxide, directly impacted the climate and world temperatures, with alternative cycles of global warming and global freezing acting on regulatory genes and proteins, thus inducing increased speciation and possibly additional whole genome duplicative events.
The subsequent release of ferrous iron and sulphates also acted on gene selection, and served as oxygen receptors, and acted on gene selection. Oxygen breathing creatures began to proliferate.
However, prior to the oxygenation of the atmosphere and the seas, numerous elements had already been oxidized. These oxidized elements acted on gene selection which converted cellular machinery to efficiently metabolize and to handle the availability of this oxidative chemistry (Williams and Fraústo da Silva 1996, 2006).
Central to metamorphosis of increasing complex species were H, C, N, P, S, K, Mg and Fe. H, C, N and P, all of which make up a major component of the general chemistry of cells. By contrast, ions, Na, Cl, Ca and other heavy metals were largely rejected (Williams 2007) and this is because the receptors, proteins and genes did not exist.
H, C, N, S and P, can easily build water-soluble polymers and other chemicals. The continuously linked backbone of a polymer consists of chains of carbon atoms. Polymers give rise to biopolymers: polysaccharides, polypeptides, and polynucleotides and they may be synthesized by enzyme-mediated processes, such as the formation of DNA, which is catalyzed by DNA polymerase.
H, C, N, S and P, are also kinetically stable at 27 C (80.33 F, 300 K) which has been the average ambient temperature of this planet for much of the last two billion years of its history (Williams and Fraústo da Silva 2006). However, extremes in temperatures, such as global warming followed by global cooling, and then a repetition of this cycle, induced kinetic instability which acted on gene selection.
The initial hot Hadean era was followed by first global ice age, which was followed by another period of warming, and this cycle would repeat itself at least twice more before the onset of the Cambrian Explosion.
Extremes in temperature impact gene selection and induce gene expression by reducing the suppressive effects of protein products like Hsp90 (Rutherford & Lindquist, 1998). Hsp90 is part of a networks of regulatory proteins such as Hsp70, and p23 (Pratt and Toft 2003). These proteins act as "molecular switches" which control gene expression in unicellular and mutlti-cellular eukaryotes (Feder and Hofmann 1999; Rutherford 2003; Sangster et al.2004).
In addition, genes which are most responsive to external environmental stimuli, have transcripts enriched with TEs (van de Lagemaat et al., 2003) which in turn suppress gene activity via methylation. However, certain environmental triggers can induce or remove methylation thus enabling the expression of these genes (Waterland and Jirtle, 2003; Wolff et al., 1998).
These molecular switches, transposons, environmentally sensitive genes, and other protein products and regulatory mechanisms were likely repeatedly impacted by these temperature extremes and other ensuing environmental alterations, giving rise to repeated bursts of eukaryotic evolutionary innovation including single gene and whole genome duplications. These additional genes, in turn, could fashion additional protein products in response to the increasing levels of gasses, minerals, ions, and carbon compounds, thus giving rise to diversity, increasingly complex cells and multi-cellular creatures.
Therefore, in addition to cyclic changes in global temperatures, alterations in the bio-chemical environment also acted on gene selection. For example, the release of carbohydrates and oxygen as waste products led to the liberation and oxidation of additional elements and carbon compounds. These chemical compounds and gasses were utilized as energy or to create proteins and lipids, thus increasing the energy supply and making available oxides, polymers and biopolymers, thereby creating an increasingly complex cell.
Specifically, as oxygen levels increased the environment came to be oxidized, thus converting iron to iron oxide, sulfur to sulfur oxide, carbon to carbon oxide and hydrogen to hydrogen oxide; which cells utilized to create biopolymers. DNA and RNA, Proteins and peptides, and cellulose and starch, are all vital biopolymers. Therefore, cells and their genomes could expand in size.
In addition to oxygen cyanobacteria were fixating and converting nitrogen into nitrates. The buildup of nitrates would be utilized and incorporated by innumerable organisms to create additional amino acids, proteins and DNA.
Thus, global warming, global freezing, oxidation, increased levels of oxygen, sulphur, ferrous iron, and so on, acted on gene selection and gene duplication, thereby increasing the size of the genome and triggering the next stage of evolutionary metamorphosis.
A POST GLACIAL EXPLOSION OF LIFE
Within a 800 million year period extending from 2.3 to 1.5 BYA, oxygen levels had increased and stabilized in the atmosphere, reaching levels between 0.02 and 0.04 atm (Holland 2006). The metamorphosis of mitochondria ensued and oxygen breathing multi-cellular eukaryotes grew in complexity (e.g. Brocks et al., 1999).
Climate change, oxygenation, oxidation, and numerous other factors all acted on gene selection, such that, beginning around 1.8 to 1.6 bya there was an exponential explosion of diverse DNA-based eukaryotic life across the planet and within its seas (Dyall and Johnson 2000; Hedges et al., 2001, 2004; Hedges & Kumar, 1999; Wang et al., 1999). Some of the eukaryotes soon consisted of approximately 10 different cell types (Hedges et al., 2004) and included unornamented organic-walled acritarchs dated from 1.7 bya to 1.8 bya (Yan & Liu 1993; Li et al. 1995; Wan et al. 2003).
This increase in size and complexity was made possible by the energy provided by mitochondria which used oxygen as an energy source; the ample supply of nitrates and carbohydrates which could be converted to amino acids and utilized to expand the genome; and the abundance of food consisting of organic residue and layers of bacteria which had formed thick bacterial mats.

Cyanobacteria Blue Green Algae

It was during this period of following glaciation between 2.2 to 1.6 billion years ago, that cyanobacteria (also known as blue green algae) may have may have been engulfed by a multi-cellular eukaryote, donating over a thousand of its genes, and forming a symbiotic relations with the common ancestors for plants (Delwiche et al., 1997; Doolittle 1999; Martin et al., 2002; Nosenko and Bhattacharya 2007). This stripped down cyanobacteria (Martin et al., 2002), became a as both clearly resemble one another and share identical genes (Joyard et al., 1991; Martin et al., 2002). The chloroplast are are surrounded by two lipid-bilayer membranes (which correspond to the cyanobacteria membrane) and has its own DNA which codes for redox proteins (the plastome) involved in electron transport in photosynthesis (Joyard et al., 1991; Krause 2008; Keeling 2004).

Thus, a cyanobacteria, following engulfment, became an organelle, i.e. the chloroplasts and as part of the plant cell genetic machinery, and began conducting photosynthesis. Thus the first ocean dwelling planets appeared, i.e. seaweeds, dated to between 1.6 to 1.7 bya (Zhu & Chen 1995).

By 1.6 bya the genome of this photosynthesizing eukaryote duplicated in size (Alvarez-Buylla et al., 2000) and plants and animals diverged from all possible common ancestors (Wang et al., 1999). In plants, this duplicative event created multiple copies of MADS-box genes (Alvarez-Buylla et al., 2000) which over a billion years later would regulate the expression of regulate flower, fruit, leaf, and root development (Ng and Yanofsky 2001; Pelaz et al., 2000). Whole genome duplication in the plant lineage would be followed by a number of recombination events creating new plant-gene sequences from old genes ((Alvarez-Buylla et al., 2000).

Likewise, over the course of the next billion years these common ancestors for plants would continue to diverge, undergo evolutionary metamorphosis, and eventually give rise to lichens, corals, and angiosperms which uitlize chloroplast and the plastomes to engage in photosynthesis, and would secrete oxygen into the atmosphere and feed on nitrates released as waste products by a variety of microbes.

However, the plant genome would continue to maintain copies of animal SRF-like MADS domains (Alvarez-Buylla et al., 2000) indicating that MADS-box genes were inherited from common ancestors that lived over 1.6 bya and which may have been donated by cyanobacteria to its eukaryotic host.
THE SECOND EXPLOSION OF LIFE
By 1.5 BYA, oxygen levels had increased and stabilized in the atmosphere, reaching levels between 0.02 and 0.04 atm (Holland 2006). However, whereas the shallow oceans remained mildly oxygenated, the deep oceans continued to be mostly anoxic (Holland 2006)
In addition to cyanobacteria and the activity of methagens, organic matter was broken down by a variety of microbes which liberated oxygen, organic acids, nitrates, phosphates, and numerous other the minerals and nutrients (Richardson 2000) some of which transformed the geochemical cycles of Fe and of S (Holland 2006). These gasses, minerals, and ions acted on gene selection (Baker 2006).
The increased levels of sulphate triggered a proliferation of sulfur-eating bacteria, which produced sulfides, a consequence of bacterial sulphate reduction (Kasting and Ono, 2006). The increase in sulphides and ferrous iron acted on gene expression and provided additional sources of energy and nourishment (Williams and Fraústo da Silva 2006). Moreover, sulphide and ferrous iron serve as oxygen acceptors (Sleep and Bird 2008). Thus oxygen-dependent ATP-generating pathways in the ancestors for animals and plants, replaced the less efficient oxygen-independent pathways and eukaryotic cells underwent a second explosive burst of evolutionary development and divergent speciation.
For example, an analysis of molecular sequence divergence and calibrated rates of seven independent data sets by Wray et al. (1996), indicates that the common ancestors for fungi, plants, invertebrates, and vertebrates had diverged between 1.5 bya to 1.2 Billion years ago (Wang et al., 1999).

According to Javaux et al. (2001) "based on an examination of fossils found in shales in northern Australia "cytoskeletal and ecological prerequisites for eukaryotic diversification were already established in eukaryotic microorganisms nearly 1,500 Myr ago."
Between 1.6 to 1.2 bya a varied assemblage of complex multi-cellular eukaryotes diverged and proliferated (e.g., Hedges & Kumar, 1999; Wang et al., 1999). These include green and red algae, dinoflagellates, ciliates, amoebae, and a diverse array of acritarchs which came in a variety of shapes and sizes (Butterfield, 2000; Porter and Knoll, 2000; Knoll, 1996; Xiao and Knoll, 1999; Zhou et al., 2001). Many species of acritarch were surface dwellers and engaged in photosynthesis to obtain energy. These included concentrically ornamented and process-bearing acritarchs dated to 1650 Myr (Javaux et al. 2004).

Acritarch Fossil
Based on a genomic analysis, the basal animal phyla (Porifera, Cnidaria, Ctenophora) diverged between 1.5 to 1.2 bya (Wang et al., 1999); a conclusion supported by the fossil record. For example, there is evidence for bedding planes within microbial mats found in rocks of the Appekunny Formation dated to 1.4 BYA ago, (Fedonkin et al., 1994), and branching traces in rocks from India dated to 1.2 BYA Mya (Seilacher et al., 1998), suggestive of a very primitive metazoa of algae.
These primitive metazoan-like eukaryotes would lead to vertebrates and invetebrates. Algae would lead to plants.
As the common eukaryotic ancestors for plants, fungi, invertebrates, and vertebrates diverged between 1.5 bya to 1.2 Billion years ago (Wang et al., 1999) it thus appears that all the genes, proteins, and genomic elements that are common to and conserved between plants, fungi, invertebrates and vertebrates were also dispersed into the genomes of the common ancestors for these species between 1.6 to 1.2 BYA.
Hence, during this period creature with cell walls and those with complex ultrastructure, cylindrical processes, and regular ornamentation began to proliferate and diversify (Javaux et al. 2004; Knoll et al., 2006).
However, as the lineage leading to vertebrates and vertebrates contain genes and mitochondria which can be traced to an alpha-bacteria ancestors (Martin and Muller 1998; Rivera and Lake 2004; Martin and Koonin 2006; van der Giezen and Tovar 2005; Embley 2006), whereas the lineage leading to fungi and plants include genes and chloroplasts which can be linked to cyanobacteria (Delwiche et al., 1997; Doolittle 1999; Martin et al., 2002; Nosenko and Bhattacharya 2007), it thus appears that only the lineage leading to invertebrates and vertebrates may have included the genes for eyes, hearts, bilateral bodies and brains.
These genes would continue to be transferred vertically, and probably horizontally, through subsequent species, undergoing repeated duplications, until freed of regulatory restraint, and then activated by major environmental and climatic changes between 750 to 580 mya, thus giving rise to the Cambrian Explosion around 540 mya.
THE SECOND SNOW BALL EARTH
in addition to plate tectonics and weathering, innumerable microbes were impacting the earth, breaking down and leaching iron, and were transforming the land masses of the planet. Beginning around 850 to 820 MA, the pre-Pangean supercontinent named Rodinia, which occupied the tropical equatorial regions, began to slowly break apart; a consequence of plate tectonics, mantle subduction, and extensive volcanism coupled with magma super plumes (Druschke et al., 2006; Li et al. 2003; Sung et al., 2006; Wang and Li 2002; Zhou et al., 2002). This pattern of breakup would continue for the next 200 million years, with lakes, rivers, and seas filling in the newly formed basins and fractures (Lia et al., 1999; Torsvik 2003; Weila, et al., 1998) and inundating and flooding huge land masses with torrential rains and oceans of water (Johnson et al., 2005). Tropical wetlands thousands of miles in size formed creating an ideal habitat for methanogenic microbes which began excreting massive amounts of methane into the atmosphere (Cavalier-Smith 2006). On the modern earth, methane is broken down and removed by oxidation in combination with O2. However, as O2 levels were still low, the buildup of methane created yet another greenhouse which, in conjunction with CO2 emitted from volcanoes, warmed the planet.

As Rodinia continued to fracture and drift apart, greater masses of formerly very dry land were increasingly exposed to greater amounts of moisture and ocean water (Johnson et al., 2005). Microbial activity also increased. The chemical composition of the soil also began to undergo severe weathering. The combined effects of microbe and weathering resulted in the release of a variety of carbonate aerosols, including massive amounts of silicates that had been liberated from the soil (Cavalier-Smith 2006). The silicates bled into the atmosphere and drained into the seas.
Silica interacts with carbonate, and together the carbonate–silicate cycle directly impact climate, and can lower temperatures by affecting ocean water chemistry (Berner et al., 1983; Berner 2004; Walker et al. 1981). As the climate cooled, silicate weathering slowed down, and atmospheric CO2 levels increased due to continued volcanic activity, thereby causing temperatures to rise which triggered increase weathering and additional release of silicates. Therefore, the cycle repeated itself, creating stasis. So long as the waters of the earth remain liquid, this cycle ensures that the Earth's climate remains temperate (Kirschvink 1992; Hoffman et al. 1998).
The buildup of silica would eventually act on gene selection, triggering siliceous biomineralization and giving rise to lacelike silica spines and skeletons.
As early as 800 mya, Acritarchs, as well as plankton, coccoid and filamentous cyanobacteria, protozoa, fungi, amoebozoans, cercozoans, and eukaryotic and marine algae proliferated throughout the oceans and inland seas (Butterfield 2005a; Butterfield et al. 1994; Butterfield & Rainbird 1998),Butterfield 2005b; (Porter 2004). Many were engaging in photosynthesis, reducing the levels of CO2, and releasing so much oxygen it rose to present levels (e.g. Holland 2006). However, many were heterotrophic rather than photosynthetic (Butterfield (2005a,b).
Moreover, as acritarchs, amoeba, and other creatures died and then sank into the deep ocean, such that phosphorite levels and organic material began to significantly increase (e.g. Butterfield & Rainbird 1998; Cook & Shergold 1986; Porter & Knoll 2000; Porter et al. 2003). The increased downward transport of organic matter and the expenditure of oxygen breaking down this material returned anoxic conditions to the deep oceans (Holland, 2006; Mao et al. 2002).

Around 730 MYA, silicate weathering secondary to the continued breakup of Rodinia, coupled with increase levels of O2 began to significantly effect the climate. Methane and CO2 levels began to to drop as O2 levels rose (Cavalier-Smith 2006). Temperatures began to rapidly fall. As more of the Earth's surface and oceans became covered with ice, carbonate–silicate cycle became destablized and temperatures began to plummet.

Thus, around 725 mya the surface of the oceans and the planet, from the poles to the equatorial latitudes, froze and became glaciated, leaving perhaps only islands of open-water refuges on the surface, and of course, deep beneath the sea (e.g. Harland 2007; Hyde et al., 2000; Kaufman et al., 1997; Hoffmann et al., 1998). Innumerable species were doomed to extinction. Yet others diversified and thrived (e.g. Butterfield et al. 1994; Butterfield & Rainbird 1998). This period of world wide glaciation is known as the "Sturtian."
As more of the planet froze, the growing areas of ice and snow began to reflect more solar radiation back into the space. Therefore, the planet became even colder, creating a self-sustaining ever worsening feedback system (Cavalier-Smith 2006).
This second global ice age, referred to as "Sturtian" may have lasted until 670 mya (Fanning and Link 2004) However, given the numerous islands of open water, and as equatorial sea ice was probably thin, unicellular eukaryotic algae, protozoa, cyanobacteria, and other creatures would have been able to continue engaging in photosynthesis (McKay 2000).
Further, it is likely that these vast regions of ice and snow were soon colonized by psychrophiles (cold-loving organisms, e.g. Price 2000) and covered with thick black mats of cyanobacteria just as they are in the modern day arctic (Quesada et al., 1999; Vincent 2000) The growth of these darkening colonies would have greatly reduced albedo and trapping heat and UV rays just as they do in the Arctic (Quesada et al., 1999). Moreover, they may have liberated and excreted not just oxygen, but CO2. In fact, organic carbon and biomarkers indicate extensive bacterial photosynthesis during the Sturtian snowball glaciation (Olcott et al. 2005).
In consequence, temperature began to rise, the snows began to melt, and signficant amounts of methane and CO2 were again released into the atmosphere, bringing the Sturtian glaciation to an end around 700 mya.
THE ENVIRONMENT ACTS ON GENE SELECTION
Despite the melting ice, the oceans remain largely anxoic, with surface waters consisting of an acidic, sulfuric mixture (Canfield et al., 2007, 2008), with deeper waters overflowing with silicates and iron-rich ferritin proteins that may have been secreted by innumerable iron-eating microbes (e.g. Mikucki et al., 2009; Richardson 2000). Much of the oceans, therefore, had become an anoxic ferrous brine; a condition that would not significantly change until around 635 to 580 mya (Canfield et al., 2007; Shen et al., 2008). Indeed, throughout this period anoxic conditions remained widespread beneath the mixed layer of the oceans; and deeper water masses were permeated with silica and enriched with Fe2+ (Canfield et al., 2008).
However, these substances also acted on gene selection, combining their influences to generate skeletal elements. For example, the morphogenetic activity of silicate increases gene expression of silicatein and collagen (Krasko et al., 2001; Müller et al., 2003). The formation of spicules is mediated by the enzyme silicatein which is dependent on ferric iron and is directly related to silica. Thus around 650 to 600 mya, spicules then collagen began to appear in the cytoplasm and the extracellular space of multi-cellular eukaryotes including the sponge (Gehling and Rigby 1996; Li, et al., 1998; Tiwari et al., 2000). Spicules and collagen also began to form in the nucleus (as silicate crystals) forming rigid compartments.
The major skeletal elements in the (Porifera) sponges, are spicules formed from hydrated, amorphous silica and collagen. The expression of the gene encoding collagen is activated in the presence of silicate and the level of transcripts for collagen strongly increases (Krasko et al., 2001). Thus the presence of silicate influences the expression of the enzyme silicatein and also the expression of collagen,.
Thus siliceous biomineralization preceded calcareous biomineralization, and in the basal lineage leading to animals, these substances were employed to enlarge the cell wall, create silica reinforced compartments, and thus enables these creatures to diversify and grow in size.
The presence of both iron and silica also stimulated the activity of silicatein which generated a collagen matrix into which the spicules were embedded (e.g. Muller et al., 2003). The result was the creation of the first collagenous proto-skeletal system and the growth of externally protruding spiines, which made these creatures more formidable and enabling them to withstand predators and to significantly increase in size.
The great amounts of silicates and ferrous material which had been building up in the oceans since 2.3 bya, and which had been secreted by innumerable microbes, were finally acting on gene selection around 650 to 600 mya. Sponges and other Eurkaryotes began to incorporate silica to form soft, lacelike silica skeletons and spines which enabled them to enlarge their cell wall, and grow in size with spines acting to protect against predators (Gehling and Rigby 1996; Li, et al., 1998; Tiwari et al., 2000; Xiao et al., 2000).
Acritarchs (which are of unknown origin or phyla) may be related to planktic eukaryotic algae and dinoflagellates (Arouri et al., 2000), and others to lower metazoans such as the sponge (Zhang 1998). Sphaeromorph acritarchs have a single cell wall structure where Acanthomorph acritarchs have two or more cell walls (Arouri et al., 2000), it is this latter species which appears more closely related to algae (Arouri et al., 2000). Most dinoflagellates are unicellular About half of all dinoflagellates are photosynthetic. Some are predators, some form endosymbionts of marine animals and protozoa, and yet others eat protozoa. in most photosynthetic dinoflagellates contain chloroplasts--and thus this branch of acritarch/dinoflagellates contain cyanobacteria genes.
Like the sponge, some species of Acritarch also developed elaborate spinose ornamentation around this same time period (Peterson and Butterfield 2005; Vorob'eva et al., 2009). Indeed, profusely ornamented microfossils comprise a distinctive paleontological component of sedimentary rocks dated to 635 mya (Cohen et al., 2009).

Spines, spicules, and spinose ornamentation may have been an adaptation against predators (e.g. Harper and Skelton, 1993; Vermeij, 1993) such as benthic eumetazoans (Peterson and Butterfield 2005). Defensive spines also likely acted on gene selection in predators, leading to further morphological diversification and escalating evolutionary development (42, Butterfield 2004; Vermeij, 1993). The presence of defensive spines also suggests that predatory proto-eumetazoans may have evolved between 635 mya to 600 mya.
And then the climate again began to cool and many of these creatures became extinct.
THE 3RD SNOWBALL EARTH
Between 640 to 580 MYA, the planet underwent yet another global ice age, the "Marinoan" (Bowring et al., 2003; Condon et al., 2005; Kaufman et al., 1997; Hoffmann et al., 1998, 2004; Hyde et al., 2000) (29, 30) followed by a less extreme period of cooling referred to as Gaskiers [580 Ma (31)].(Eyles & Eyles 1989), These global ice ages were likely triggered by a combination of oxygen buildup and the spewing of volcanic ash into the atmosphere. For example, U-Pb zircon dates from volcanic ash beds within the Doushantuo Formation (China) indicate extensive volcanic activity beginning around 635 (Condon et al., 2005).

The Marinoan/Gaskiers (M/G) glaciation lasted until 580 mya. It was brought to an end in a manner similar to the "Sturtian."
Massive volcanic activity vented tons of CO2 into the air thereby generating greenhouse warming (Kirschvink 1992; Hoffman et al. 1998). Conversely because of glaciation, C02 consumption was limited. CO2 levels began to rise, thus contributing to global warming.
Likewise, due to the death, extinction, and decay of innumerable life forms from freezing, and the decomposing actions of various bacteria including methagens, massive amounts of methane were again spewed into the environment. The buildup of methane (Bao et al., 2008), which may have also been released from equatorial permafrost (Shields 2008), and the combined increase in levels of CO2, again generated a greenhouse effect. The planet began to warm and this was followed by a global meltdown and the end of the "Marinoan" glaciation.
However, as much of the melting ice contained high amounts of oxygen, oxygen levels in the ocean began to rise (Canfield et al., 2007).
Innumerable creatures died and many species became extinct during the Marinoan glaciation, thus freeing up niches which could be exploited by other organisms. Moreover, increased oxygenation acted on gene selection and metabolism, and provided oxygenated environments throughout the ocean which could be exploited and colonized by oxygen breathing creatures. Therefore, although life forms perished during this glacial period, a third explosion of life would ensue (Condon et al., 2005; Peterson and Butterfield 2005) including the evolution of megascopic Ediacarans (Narbonne 2005; Narbonne and Gehling 2003).
TRICHOPLAX & SILENT HEART & BRAIN GENES
It was during the earlier part of this period, around 640 to 635 milion years ago, that the Ediacaran period began ( Knoll et al., 2004) and a number of distinct species appeared, including the Ediacaran fauna (Narbonne and Gehling 2003), Echinodermata-Arkarua adami (Gehling 1987) and a "living fossil" known as Placozoa Trichoplax (Srivastava, et al., 2008). Some species of photosynthesizing Ediacarans and other photosynthesizing organisms active during the Ediacaran age would contribute to the evolution of future species via the secretion of calcium carbonate. Echinodermata and Trichoplax would contribute their genes.
Placozoans Trichoplax adhaerens is an amoeba-shaped, multi-cellular animal that belong to the Trichoplax family, and may represent a primitive metazoan. Trichoplax fossils, dated to 635 million years ago, have been found in an oil field on the Arabian Peninsula (Srivastava, et al., 2008).

Trichoplax Placozoan

Trichoplax is a "living fossil" and the body plan of Placozoans involves a mere four cell types and they have no muscle cells. Nor do not posses a heart, cardiac tissue, or blood. And yet, Placozoans possess the necessary genes and numerous transcription factors including multiple basic helix–loop–helix family genes and GATA-family zinc-finger transcription factors associated with the complex regulation of cell patterning and differentiation, and the specification of muscle, endodermal, cardiac and blood cell fates (Srivastava, et al., 2008), even though they have no heart, muscles, or blood.
Four putative opsin genes, which function in light reception, are present (Srivastava, et al., 2008). Their genome also contains PAX genes which code for the visual system (Srivastava, et al., 2008). And yet Trichoplax is blind, they have no eyes, and their genome does not encode the basic machinery required for photoreception.
The Trichoplax genome also encodes a rich array of transcription factors and signalling genes, including many subfamilies of the animal-specific Sox Sry-related HMG-box family involved in cell division, mitosis, and in the regulation of embryonic development (Srivastava, et al., 2008). They also possess genes for sexual reproduction and germ cells for embryological development, even though they do not have sex, and do not generate offspring or embryos. Trichoplax reproduces by fission, whereby two (sometimes three) parts of the animal move away from each other until their connection is ruptured.
In fact, the first evidence for cell division and embryonic cell lineage differentiation, and thus embryos does not appear in the fossil record until between 580 mya 550 mya (Condon et al., 2005; Hagadorn et al., 2006). Some of these include planula larvae and hydrozoan embryos and resemble gastrula stage embryos of bilaterian/metazoan forms (Chen et al., 2000).
Trichoplax contains a rich repertoire of transcription factors that regulate cell type specification and cell differentiation. These include multiple LIM-homeobox genes typically associated with the specification in neurons, and multiple basic helix–loop–helix family genes associated with neural cell fates, neural signalling, the establishment of the synapse and post-synaptic formation proteins (Srivastava, et al., 2008).
The synapse and these channels are essential in nerve cell communication and enable neurons to communicate and transmit message to one another and to the brain. Their genome also contains genes associated with neural migration and axon guidance, and thus the genes which guide the development of the brain.
However, Trichoplax is brainless. There is no evidence of nerves, sensory cells, neurons, synapses, or anything remotely suggestive of a brain or nervous system in this species which first appeared on the Earth around 635 million years ago; one hundred million years before the brain evolved. Further, they lack of any kind of symmetry, sexuality, organs, muscle cells, basal lamina, heart, visual system, and yet possess all the genes necessary for creating these specific organs, tissues, body parts, including eyes and brains.
CONSERVED GENES, GENE EXPRESSION & PUNCTUATED EQUILIBRIUM
Trichoplax and other ancient species did not randomly evolve complex genes which code for vision, sex, and the body and the brain, and then fail to activate them. Nor did Trichoplax gradually evolve vision, sex, a body and a brain.
Contrary to Darwin's theory (Darwin 1859,1871), species do not gradually evolve into other species but stay basically the same from the moment of their first appearance to their extinction. As is evident from the fossil record and as detailed by Eldredge and Gould (1972; Gould 2002), evolution proceeds in bursts of of explosive speciation followed by long periods of stasis and equilibrium with little or no change. Eldredge and Gould (1972; Gould 2002) called this "punctuated equilibrium" such that periods of stasis are interrupted with bursts of evolutionary development.
"Punctuated equilibrium" can also be applied to gene expression. The genes coding for hearts, eyes, bodies, brains and other core functions were inherited from ancestral specie who were also without hearts, eyes, bodies, and brains and who diverged anywhere from 900 mya to 1.2 bya. These genes were then passed down vertically to numerous diverging species.
Genome sequencing has revealed an extensive conservation of the same repertoire of genes coding for core cellular functions, in the genomes of Trichoplax and humans, primitive animals, the sea anemone, sea urchin, and as well as birds (Putnam et al., 2007; Miller and Ball, 2008; Srivastava et al., 2008), plants, fungi (Koonin and Wolf, 2008; Koonin et al., 2004) and prokaryotes (Koonin and Wolf, 2008; Koonin et al., 2004).
Given that modern and ancient archae and bacteria are believed to be of equal genetic complexity (Snell et al., 2002; Makarova et al., 2007), the presence of these core genes in prokaryotes indicates they may be over 4 billion years in age and were most likely inherited from single celled creatures who first arrived on this planet over 4 billion years ago. These genes were likely repeatedly duplicated as they were passed down to subsequent species including the last common ancestor for eukaryotes and the common ancestors for vertebrates and invertebrates (Snell et al., 2002; Mirkin et al., 2003; Koonin 2003, Kunin and Ouzounis 2003; Mushegian 2008).
In fact, 2150 orthologous sets can be traced to the first eukaryotic common ancestor and 4137 orthologous gene can be traced back to the last eukaryotic common ancestor (Bejerano et al., 2004) indicating they have been duplicated at least once during this transition, and are billions of years in age. Likewise, genes encoding core cellular functions, such as translation, transcription, replication and central metabolic pathways, can be traced to prokaryotes and may have been conserved, repeatedly duplicated, and passed down for over 4 billion years.
Over the following 4 billion years these genes and the entire genome were repeatedly duplicated and subjected to a variety of environmental agents, and were repeatedly dispersed among the common ancestors for numerous species, and then passed down vertically through subsequent species and numerous diverging common ancestors, and were then activated only after the environment had been significantly modified 100 million years after Trichoplax evolved. These major alterations in the environment included the buildup of silica, iron, calcium, and oxygen, all of which acted on gene selection thus giving rise to brains and hearts in multiple species whose common ancestors lived a billion years ago. This explains why the genomes of so many unrelated species including chordates contains the same genes which code for eyes, bodies and brains even though they did not descend from Trichoplax.
Trichoplax, Echinodermata, and the so called "higher" metazoans, diverged from a common ancestor that lived anywhere from 900 mya (Peterson et al., 2004) to over 1.2 bya (Wray et al., 1996). Trichoplax (placozoans) and other so-called "lower" metazoans (including Placozoa, corals, and jellyfish) evolved in parallel to "higher" animals (all other metazoans, from flatworms to chordates), and they and their relatives are in a separate lineage from all other metazoans (starfish, bivalves, anthropoids, crustaceans and chordates) including Echinodermata. And yet even humans and Trichoplax share many of the same genes (Srivastava et al., 2008).
As genes are not created from nothing, this means these common ancestors must have also inherited these genes. These genes were then dispersed to diverging species and remained in a state of stasis until activated by alterations in the environment giving rise to explosive evolutionary development of the same organs in numerous species beginning around 540 mya, during the Cambrian Explosion.
The Trichoplax genome, which is extremely compact, contains 11,514 protein coding genes and consists of 98 megabases, distributed over six chromosomes. The sequencing and analysis of the approximately 98 million base pair nuclear Placozoan genome has demonstrated conserved gene content and structure and synteny and linkage in relation to other ancient species, as well as the human genome with a significant concentration of orthologues on one or more human chromosome segments (Srivastava et al., 2008). These shared genes include those involved in the development of the nervous system, the heart, and a wide variety of cell types. Thus, the same genes inherited by Trichoplax were later inherited by and activated in the human genome, even though the ancestors of both diverged from a common ancestor between 900 mya to over 1.2 bya (e.g., Wray et al., 1996; Peterson et al.., 2004). Many of these linkages date back to the placozoan–vertebrate last common ancestor.
In conserved regions of the human genome, 82% of human introns have orthologous counterparts with the same position and phase in Trichoplax. Analysis of the exon–intron structure of orthologous genes also demonstrates a high degree of conservation in Trichoplax. Trichoplax genes have an intron density (7.6 per kb) comparable to that found in vertebrates (8.5 per kb). Introns play an important role in gene regulation, suppression, and expression.
In the human genome, these ultraconserved elements often overlap introns or nearby genes involved in the regulation of transcription and development. They also overlap or are adjacent to exons involved in RNA processing (Bejerano et al., 2004). Thus, these genes may have been inherited from prokaryotes and are also regulated by introns that may have been inherited from and donated by archae and alpha-proteobacteria (Martin and Koonin 2006).
This explains why so many diverse species possess the same genes which code for hearts, lungs, eyes, and brains. These genes did not evolve, they were inherited. However, whereas these genes came to be activated in humans and other vetebrates, they were silent and suppressed when Trichoplax evolved.

MULTICELLULAR METAZOAN METAMORPHOSIS
Metazoa ancestry stems from at least two ancient lineages, the Eumetazoa (cnidarians, placozoans, and bilaterian phyla) and phylum Porifera (sponges) (e.g., Cavalier-Smith et al., 1996; Borchiellini et al., 2001; Medina et al., 2001; Collins, 2002; Wallberg et al., 2004).
Based on phylogenetic studies of divergences among animal phyla, plants, animals and fungi, Wang et. al. (1999) concluded that the basal animal phyla, i.e., Porifera, Cnidaria, Ctenophora, diverged between about 1.5 to 1.2 bya. Thus the common ancestors for all major "higher" and "lower" metazoan phyla may have diverged over a billion years ago. Subsequently, their descendants continued to diversify and undergo speciation in response to biologically engineered alterations in the environment and increasing levels of silica and calcium carbonate.
By around 800 mya, this diversity included amoebae, protozoa, Choanoflagellates, and an array of acritarchs which came in a variety of shapes and sizes (Butterfield, 2000; Porter and Knoll, 2000; Knoll, 1996; Xiao and Knoll, 1999; Zhou et al., 2001). Some species of Acritarch are related to plants. It was after this period that the sponge began to evolve (Zhang 1998).
Following the "Sturtian" glaciation 725 mya to 670 mya), the planet grew warm, the seas were enriched with silica, and life in the seas quickly recovered. Photosynthesizing cyanobacteria continued to pump oxygen into the atmosphere and build mats and stromatolites (Grey et al., 2004). Microscopic eukaryotes diversified.
Between 640 to 580 MYA, the planet underwent yet another global ice age, the "Marinoan" However, even as the planet was beginning to freeze, and continuing into the Ediacaran era (i.e. 635 to 541 million years ago) multicellular animals continued to evolve and diversify (Harland and Rudwick; 1964; Gehling and Rigby 1996); Fedonkin andWaggoner 1997; Xiao et al., 1998; Knoll and Caroll 1999; Fedonkin 2003) . This marine fauna included Silicarea sponges dated to around 630 to 650 mya (Love et al., 2006; Tiwari et al., 2000; Xiao et al., 2000), and creatures whose embryos were forming in eggs--as based on fossils dated to 632 mya (Yin et al. 2007). Fossil evidence dated to 630 to 600 mya, includes embryos, eggs, sponges, and bilaterian forms (Chen et al. 2000; Xiao & Knoll 2000; Yin et al. 2001, 2004, 2007; Chen & Chi 2005; Dornbos et al. 2006; Li et al., 1998; Liu et al. 2006; Tang et al. 2006; Xiao et al. 2007).
Therefore, extreme changes in climate and the buildup of various metals, gasses, minerals, and ions, including silicate, were directly associated with explosive eukaryotic speciation and evolution.
As early as 650 mya, sponges began to incorporate silica to form soft, lacelike silica skeletons and spines which enabled them to enlarge their cell wall, and grow in size (Gehling and Rigby 1996; Li, et al., 1998; Tiwari et al., 2000; Xiao et al., 2000). In addition to Silicarea sponges some species of Acritarch also developed elaborate spinose ornamentation around this same time period (Peterson and Butterfield 2005; Vorob'eva et al., 2009). The spines were likely employed to protect against predators which may have been predatory eumetazoans (Peterson and Butterfield 2005) and giant protozoa which had begun to profilerate (Seilacher et al., 2003).
The evolution of these predators may explain why acanthomorph arcritarcs began to disappear from the fossil record by the end of the Edicaran era. Species interact and are a major component of the environment, and the changing environment acts on gene selection. Likewise, the development of spinose ornamentation would have served as a challenge to predators and may have also acted on gene expression. Predator-prey interactions could provide a partial explanation for the sudden expansion in the size of many species of eukaryotic organisms following the end of the last glaciation (Peterson & Butterfield 2005).
However, predators have hunted the oceans for billions of years. And yet, despite predatory pressures, eukaryotes remained microscopic for much of this planet's evolutionary history. Until 580 mya, the largest eukaryotes were macroscopic and consisted of less than 11 different cell types.
Size increase, therefore, and the evolution of large multcellular organisms were dependent on other factors. These included, most notably, increases in oxygen (Canfield et al., 2007), silica, and calcium, coupled with increased synthesis of collagen, which in turn triggered the evolution of the silica-collagen skeletal system. The silica skeleton was followed by the evolution of the calcium-collagen skeleton and then metazoans with a nervous system.
CHOANOFLAGELLATES, ADHESION GENES, MULTICELLULARITY
The evolution of the skeletal system was an epochal event in the metamorphosis of metazoans and the lineage known as animalia. The skeletal system provided protection for internal organs, allowing these tissues and the body to grow and diversify. It provided a mechanical support for an outer layer of cells that covered and enclosed the body, and protected interior cells and organs from environmental challenges and provided a stable enclosure which could support the evolution of large organs and internal structures.
This was made possibly not just by the buildup of silica and calcium, but by an array of genes and cell adhesion and extracellular matrix protein domains, which made possible multicellular fusion and three dimensional organization (King et al., 2007). These genes and proteins did not randomly evolve. They were inherited from ancestral species who inherited their genes from prokaryotes including cyanobacteria who altered the environment and secreted the oxygen and much of the calcium which would activate those genes that would give rise to 3-dimensional multicelluarity, the skeletal system, and then the brain.
Cyanobacteria, therefore, not only provided numerous genes to the eukaryotic gene pool, but substances, such as calcium, which promote adhesion and multicelluarlity; genes, including regulatory genes, such as introns, which were likely passed on not just to plants, but to other unicellular eukaryotes such as choanoflagellate, and then to multicellular creatures such as the sponge and animalia.
The descendants of the last common ancestors of Metazoa include the "sister groups" choanoflagellates and Porifera, the sponges- (Carr et al., 2008; Lang et al., 2002; Leadbeater 1983; Maldonado 2004 Ruiz-Trillo et al., 2008). There is evidence to support the belief that choanoflagellates may be simplified sponge-derived metazoans (reviewed by Maldonado, 2004). The divergence of sponges is followed by the Ctenophora, Cnidaria and placozoan Trichoplax adhaerens (Wainright et al., 1993).
However, species-rich phylogenetic analyses have demonstrated that choanoflagellates are not derived from metazoans, but are a distinct lineage that evolved before the origin of metazoans (Carr et al., 2008; Lavrov et al., 2005; Rokas et al., 2005). Thus, Choanoflagellates may have evolved before the sponge and before the origin and diversification of metazoans (Lavrov et al., 2005; Rokas et al., 2005). Hence, a proto-choanoflagellate may have been the last common ancestor for the sponge (Steenkamp et al., 2006; Wainwright et al., 2993); though recent evidence indicates otherwise (Carr et al., 2008).

Based on a genome analysis of ribosomal RNA and the heat-shock protein coding genes of fungi, animals and Choanoflagellate, it has been determined that metazoans may not have evolved from Choanoflagellates, but that Choanoflagellates are nevertheless the closest living relative to metazoans (Carr 2008; James-Clark, 1886; Saville 1889:
There is also considerable evidence suggesting that abundant domain shuffling followed the separation of the choanoflagellate and metazoan lineages (King et al., 2007) which may have taken place after divergence of fungi (Lang et al., 2002). Therefore, because of their ancient pedigree which may extend back over a billion years, many gene families in choanoflagellates have a single gene, whereas these same gene families have expanded in sponges and in more complex animals, due to single gene and whole genome duplicative events (King et al., 2007).

Choanoflagellates, therefore, share numerous genes and protein domains with the sponge and higher metazoans (King, N. & Carroll, 2001; King et al., 2001; Segawa, et al., 2006; Snell et al., 2006). These include 78 protein domains that are exclusive to choanoflagellates and metazoans and which are central to cell signalling and adhesion processes in metazoans (King et al., 2007).

Choanoflagellate

Adhesion proteins lock individual cells together, and play a key role in multicellular development and the evolution of the skeletal system. Without adhesion, cells would drift apart and multi-cellularity would be an impossibility. Adhesion makes it possible for unicellular organisms to live in colonies

Choanoflagellates Colony
Choanoflagellates are unicellular. These adhesion proteins and the genes which code for them must have also must have been inherited from a unicellular ancestor. Indeed, ancient cyanobacteria and their descendants, such as algae, must have also possessed the genes and the proteins enabling them to secrete substances which promote adhesion and a colonial life style.
Likewise, it is these genes and proteins which enabled some species of Choanoflagellate to form colonies (King et al., 2007). These genes then underwent repeated duplicative episodes, contributing to multicellularity (King et al., 2007) and the metamorphosis of multicellular metazoa and the skeletal system. These genes were inherited they did not randomly evolve.
For example, the Choanoflagellate genome of M. brevicollis, contains a diverse array of cell adhesion and extracellular matrix protein domains which are also present in the metazoan genome (King et al., 2007). The Choanoflagellate genome (M. brevicollis) also contains and shares 23 homologous genes with metazoa, which are responsible for cell sorting and adhesion during metazoan embryogenesis (King et al., 2007). However, choanoflagellates reproduce asexually through binary division. They do not generate embryos.

Choanoflagellates Colony

Likewise, the genome of Trichoplax, which evolved 635 mya (Schulze et al., 1883), contains many subfamilies of the animal-specific Sox Sry-related HMG-box family involved in cell division, mitosis, and in the regulation of embryonic development (Srivastava, et al., 2008). They also possess genes for sexual reproduction and germ cells for embryological development, even though they do not have sex, and do not generate offspring or embryos.
Therefore, the genes responsible for adhesion and embryological development did not randomly evolve. They were inherited from the common ancestors of Trichoplax and choanoflagellates which diverged over a billion years ago, and whose own ancestors include the first multicellular eukaryotes which evolved 2.7 bya (Feng et al., 1997; Hedges 2002). The common ancestors for these first multicellular eukaryotes obtained, in turn, obtained these genes, transposons, and introns, from prokaryotes.
These genes underwent repeated duplicative events, and were passed down vertically to subsequent species, including Choanoflagellate and Trichoplax and then activated in subsequent species in during a time period in which the environment was enriched with oxygen, silica, and calcium carbonate.

Trichoplax

The first evidence for cell division and embryonic cell lineage differentiation, and thus embryos does not appear in the fossil record until between 580 mya 550 mya (Condon et al., 2005; Hagadorn et al., 2006), long after the evolution of Choanoflagellates and Trichoplax. These include fossils which resemble planula larvae, hydrozoan embryos, and gastrula stage embryos of bilaterian/metazoan forms (Chen et al., 2000).
These evolutionary developments took place during and these genes were expressed following the onset of the Ediacaran age and during or after the ending of the Marinoan/Gaskiers glacial period 580 mya when the planet began to warm and calcium-rich cyanobacterial mats began to dissolve and decompose.
Calcium acts on gene selection, thereby activating those genes which contribute to sexual reproduction, the generation of embryos, and which would give rise not just to the skeletal system, but the brain.
COLLAGEN
Multicellular organisms, metazoans in particular, maintain their structural integrity via calcium and collagens. Collagen is the primary protein of the connective tissue of metazoans (Muller 2003), and is the most abundant protein in mammals making up to 35% of the whole-body protein content (Di Lullo et al., 2002 ). Collagen plays a major role in the determination of cell phenotype, cell adhesion, and the creation of tissue infrastructure and extracellular matrices including the skeletal system (Exposito et al., 2002).
Collagen is a key to the transition to multicellularity (Exposito et al., 2002) and the evolution of metazoans (Erwin 1993; King et al., 2007). The keys are also found in the genome of choanoflagellate and metazoa (King et al., 2007) and include the extracellular matrix (ECM) protein domains and collagen-domain-encoding genes.
In metazoa, collagen ECM polymerizing proteins form a major component of the epithelia membrane and the the extracellular matrix (Exposito et al., 2002; King et al., 2007). The extracellular matrix provides structural integrity to multicellular organisms, including plants, invertebrates and vertebrates.
The precuros proteins for collagen exists in choanoflagellates and the plant-like phytoflagellates (Lamport 2001; Willmer 1990). Phytoflagellates and choanoflagellates also tend to aggregate and form colonies (Willmer 1990), indicating that cell adhesion is taking place. It is the activation of these genes which eventually contributed to biocalicifcation and which would subsequently enable plants and some species of metazoa to leave the ocean and migrate to land.
The genome of choanoflagellates (M. brevicollis) contains five of the same collagen-domain-encoding genes which are found in and which are organized in a manner nearly identical to metazoan collagen genes (King et al., 2007; van der Rest, et al., 1991). These same genes are present in multicellular species ranging from sponges to humans (Exposito et al., 2002).
The presence of collagen within the internal or external environment activates these genes. Subsequently, these collagen-domain-encoding genes and the ECM protein complex appear to have undergone repeated duplicative events, thus creating additional genes which were then activated by increasing levels of silica and calcium thereby giving rise to skeletal bone comprised of collagen-calcium. As concluded by King and colleagues (2007) "ECM proteins in a free-living choanoflagellate suggests that elements of the metazoan ECM evolved in contact with the external environment."
COLLAGEN, CALCIUM & SKELETAL BONES
The activation of this collagen-calcium complex appears to have begun with the "Sturtian" glaciation, and the weathering and breakup of the Rodinia supercontinent, when large quantities of iron and silica bled into the oceans (Cavalier-Smith 2006). Silica acted on gene selection which resulted in siliceous biomineralization and the evolulution of the Silicarea sponge, creatures which have been dated to around 630 to 650 mya (Love et al., 2006; Tiwari et al., 2000; Xiao et al., 2000). The Silicarea sponge has a soft honey-comb skeleton comprised primarily of silica and collagen.
Silicate increases gene expression of silicatein and collagen (Krasko et al., 2001; Müller et al., 2003) creating silica spikes and a silica skeleton consisting of silica and collagen. However, bones, teeth, and the skeletal system require large quantities of calcium which is bound with collagen, creating a collagen-calcium-protien matrix. Massive amounts of calcium would later enrich the oceans following the M/G glaciation.
The biosynthetic pathway responsible for collagen production is exceedingly complex and are encoded and expressed by a variety of genes found on a number chromosomes. As the collagen molecule is synthesized, it undergoes many post-translational modifications which take place in the Golgi compartment of the endoplasmic reticulum, and is dependent upon peptides, calcium, and Vitamin C and Iron as cofactors. The endoplasmic reticular also has a high concentration of calcium and calcium promote protein folding and binding (Michalak et al., 2002) and collagen binding.
As summared by Michalak and colleagues (2002), The endoplasmic reticulum is a centrally located organelle which affects virtually every cellular function. Its unique luminal environment consists of Ca2+ binding chaperones, which are involved in protein folding, post-translational modification, Ca2+ storage and release, and lipid synthesis and metabolism. Moreover, calcium increases the synthesis of collagen (Chen et al., 1992).
Collagen proteins (procollagen) are transported to the extracellular spaces where they are acted upon by specialized enzymes called procollagen proteinases that remove these peptides which re-enter the cell and regulate the amount of collagen synthesis by feed-back. These same extracellular spaces also contain high concentrations of calcium (Michalak et al., 2002). The processed molecule thus becomes collagen.
Once collagen is secreted into the extracellular spaces it undergoes yet another modification via triple helical collagen molecules (THCM). The collagen triple helix module forms large multimodular proteins creating multivalent supramolecular networks which can give rise to skeletal elements and promote cell adhesion (Exposito et al., 2002). However, to create bone requires calcium.
THCMs and this protein complex appears to have undergone duplicative events, and to have first become activated following the S glaciation which flooded the oceans with silicate (Exposito et al., 2002). This may have been followed by additional duplicative events and gene activation during and after the onset of the Edicaran age, when massive amounts of calcium were released into the environment; thus leading the evolution of metazoans and the calcium-collagen skeletal system.
Collagen stimulates calcium binding (Chen et al., 1992) and exhibits a high affinity for calcium ions resulting in calcification and thus the creation of bones. Collagen-calcium binding also attracts phosphoproteins, and this resuls in the creation of bones consisting of a collagen-calcium-phosphoprotein matrix. Moreover, as calcium levels in bone increase, additional phosphoprotein bind to the collagen-calcium matrix, thus increasing the strength and elasticity of the bone.
Calreticulin, a major Ca2+ binding (storage) chaperone in the endoplasmic reticulum (ER), is a key component responsible for the folding of newly synthesized proteins and glycoproteins (Michalak et al., 2002). Collagen is also synthesized in the ER. The function of calreticulin and other proteins is affected by continuous fluctuations in the concentration of Ca2+ Calreticulin appears to be upstream regulators in the Ca2+-dependent pathways that control cellular differentiation and/or organ development. (Michalak et al., 2002).
Thus there is a complex interaction where calcium promotes collagen synthesis, then collagen stimulates calcium binding, and then increased concentrations of calcium stimulate additional proteins to bind with the collagen-calcium matrix (Chen et al., 1992). Phosphoprotiens in fact resist binding, and cannot attach to collagen or grow in the absence of calcium (Saito et al., 1998). Thus the protein matrix becomes positively charged by virtue of the bound calcium ions, which attracts neutralizing phosphate and carbonate ions, which then allow further calcium ion binding (Ury 1971) thereby creating shells, bones, and teeth.
Indeed, the activation of this complex and the creation of shells, bones, teeth, and the skeletal system, beginning with S sponges, and then calcareous sponges, required calcium. The resulting bone, therefore, consists of a matrix of calcium crystals of calcium carbonate and phosphate embedded among collagen fibres, providing strength and elasticity.
Although this entire process is collagen dependent (Chen et al., 1992), the result is due to the effect of calcium on bound collagen, for as calcium levels icnrease it induces comformational changes in phosphoproteins which also increasingly bind to the collagen-calcium matrix, thereby creating hard bones and the skeletal system.
With the evolution of the calcium-carbonate skeletal system, metazoans were able to dramatically increase in size and exploit new environments. Metazoan metamorphosis was triggered not just by oxygen, but calcium.
ACRAMAN ASTEROID, GONDWANA & CALCIUM
The buildup of calcium had several major sources, the most important of which includes cyanobacteria and other photosynthesizing organisms. However, increased temperatures and plate tectonic also played a role in the evolution of the calcium-collagen based skeletal system which began to replace the silica-collagen skeletal system beginning between 580 mya to 500 mya.
Due to weathering, plate tectonics, the action of microbes breaking down rock, iron, and soil, and the effects of freezing then thawing, the super continent Rodinia began splitting into 2 halves approximately 750-700 million years ago (Johnson et al., 2005). A third continent - the Congo craton was pushed up into the middle, and became north-central Africa (Johnson et al., 2005). And then the two halves of Rodinia slid down and around it, forming a new supercontinent called Gondwana around 580 mya.
The Earth was also struck by the "Acramen" asteroid 580 mya creating a collapsed crater ~90 km (55 miles) in diameter and 40 km deep, scattering ejecta across 300 km to 1000 km (620 miles) of land surface (in what is today Acraman, Australia), with an estimated impact energy exceeding 106 (10,000,000) Mega tons (Williams 1986, Williams and Wallace 2003). It appears to have impacted an area covered by a shallow sea.

Acraman Impact Crater - Acraman Lake

The impact of the Acraman asteroid most likely produced a massive dust cloud large that extended well beyond the northern and southern halves of the planet and which likely blocked out sunlight and caused a biotic crisis (Gostin et al., 1989; Grey et al., 2003, 2004; Williams and Wallace 2003).
However, it may have also delivered living bacteria and viral particles to the surface of the planet. The Acraman impact is associated with the emergence of between 37 to 50 new species, and the diversification of Ediacaran fauna (Grey et al., 2003, 2004).
The effect of the Acraman asteroid on plate tectonics and continental drift is unknown. However, its impact occurred at a time when the Gondwana supercontinent was fracturing, splitting, and sliding together. Massive vulcanic eruptions were also triggered which poured forth titanic amounts of basalt lava (Cavalier-Smith, 2006). Basalt lava weathers rapidly and is a rich source of Ca2+ ions (Cavalier-Smith, 2006). Calcium-rich bacteria mats also began to decompose, and calcium leached into the rivers and streams and poured into the oceans and was absorbed by innumerable species.
Cells absorb and secrete Ca2+ and calcium receptors are located throughout the body and the muscular-skeletal system of simple metazoans (Brown and MacLeod 2001; Cheng et al., 2007).
Ca2+ ions acts on gene selection, increasing the permeabilization of the inner mitochondrial membrane (Castilho et al., 1995), facilitating photophobic responses, and significantly increasing photosynthetic activity (Colombetti et al., 2008). Ca2+ ions therefore, can increase energy efficiency and the amount of oxygen pumped into the environment. Increased energy could also support increases in body size and complexity made possible by a calcium-collagen skeletal system.
CALCIUM & MULTICELLULARITY Calcium is the most ubiquitioius metal ion in the cellular system (Williams 2007) and plays a universal role as messenger and regulator of protein activities (Kazmierczak and Kempe 2004). Calcium acts directly on gene expression (Castilho et al., 1995), and the regulation of programmed cell death (apoptosis), cellular proliferation and differentation and cell to cell adhesion and fusion (Brown and MacLeod 2001; Cheng et al., 2007). Thus in the absence of CA cells stop aggregating, embroyos fail to adhere, cell aggregates and disintegrate, and bones become soft and easily break (Kazmierczak and Kempe 2004).

Calcium carbonate crystals

Over the last 3 billion years calcium concentrations have increased by 100,000 times (Kempe and Degens, 1985) with the greatest increases occurring during and following the Marinoan/Gaskiers glaciation.
The rapid increase in calicium levels triggered a whole spectrum of calcium binding and calcium-collagen proteins activities including the creation of the skeletal system. Moreover, calcium binding proteins also regulate many important cellular processes such as smooth muscle contraction and motion in skeletal muscle (Kazmierczak and Kempe 2004). In fact, Cao2+ sensors exist in cartilage and bone cells that mediate some or even all of the known effects of Cao2+ on these cells (Brown and MacLeod 2001; Chang et al., 1999).
Hence, calcium plays a key role in regulation of skeletal muscle movement and contraction, and thus the regulation of cell, muscle, and skeletal functioning in metazons (Kazmierczak and Kempe 2004). Hence, the buildup of calcium played a central role in the creation of macro-multicellular eukaryotes which diversified and increased in size following the end of the Marinoan/Gaskiers glaciation.
CYANOBACTERIA & CALCIUM
Although volcanoes and hydrothermal vents were contributing factors, most of the influx of CA during the precambrain was due to cyanobacteria and photosynthesizing eukarotes including corals and possibly Edacarans.
Photosynthesizing Cyanobacteria were among the first to take root on this planet. They contributed to the eurkaryotic gene pool, formed thick cyanobacteria mats, established symbiotic relations with eukaryotes (some of which became plants), and secreted not just oxygen, but calcium carbonate into the oceans and the seas (Alois 2008; Kazmierczak and Stal 2008).

Cyanobacteria Colony

Cyanobacteria secrete calcium carbonate within their mucous (Kazmierczak and Stal 2008). These secretions are used to glue and cement stramatolites together, and to create thick cyanobacterial mats, allowing vast colonies of cyanobacteria to adhere to one another (Alois 2008). The lithification of these marine cyanobacterial mats, to create rock-like sediments, is thought to be driven by metabolically-induced increases in calcium carbonate saturation (Alois 2008). Calcium carbonate also infilitrated carbonate rocks (Alois 2008) and accllerated the mineralogy of reef-building (Porter 2006). Thus, these mats, stromatolites, carbonate rocks and reefs served as vast ocean preserves of calcium carbonate which had been building up for over 3 billion years.

Proterozoic Stromatolites

Stromatolites
Increased levels of calcium carbonate potentiates photosynthesis (Colombetti et al., 2008). Increased photosynthesis increases the production and secretion of calcium carbonate (Alois 2008; Porter 2006). Thus, a feedback mechanism is maintained where calcium carbonate potentiates photosynthesis which results in the release of more calcium carbonate as well as more oxygen.
This feedback system has been in effect since cyanobacteria took root on this planet and began using photosynthesis to obtain energy. Moreover, cyanobacteria photosynthetic activity and calcium carbonate bio-mat production persisted during the first, second, and third world-wide glacial periods (Grey et al., 2003, 2005; Moczydłowska 2008). Thus calcium concentrations have increased by 100,000 times in the last 3 billion years (Kempe and Degens, 1985) as did cyanobacterial communities which can flourish even during glacial conditions.
According to Seilacher and collealgues (2003), Ediacaran biota were dominated by procaryote biomats and giant protozoa immediately following the Marinoan snowball earth (Seilacher 1984). The larger Ediacarans possibly employed photosynthetic symbionts, and thus engaged in photosynthesis. Likewise, giant protozoa which live a heterotrophic phagocytozing life style, may have also formed symbiotic relations with photosynthetic symbionts (Cavalier-Smith 1993). Thus these photosynthesizing organisms were easily able to survive and flourish despite the catastrophic consequences imposed by repeated global glaciations. Calcium carbonate is also produced as a byproduct of photosynthesis.
The survival of these and other species also suggests that despite these glacial conditions, the entire Earth may not frozen solid. Thus whereas parts may have resembled a snow ball, others resemble slush, with islands of ice free open marine water providing access to the sea floor as well as the ocean surface thus enabling this biota to survive and flourish (Moczydłowska 2008).
Indeed, there is a large fossilized assemblage of cyanobacteria and phytoplankton dated to around 580 mya indicating they survived the last glaciation (Moczydłowska 2008). These include benthic autotrophic and aerobic cyanobacteria which lived in functionally complex communities of mat-builders, as well as photosynthesizing planktic eukarotes (Moczydłowska 2008). . Some of these species survived by colonizing surface ice. Other dwelled in pockets of sunlit, well-oxygenated open marine waters (Moczydłowska 2008). However, yet others flourished in the absence of direct sunlight, and lived a Heterotrophic lifestyle (Kelly et al., 2007), praying upon other creatures, or living off organic matter.
For example, Kelly et al., (2007), determined that n-alkanes samples from before 550 mya were anomalously enriched in 13C signifying a high relative abundance of bacterial heterotrophs that extensively recycled organic matter (Corg) in the water column.
An increase in Heterotrophic activity is to be expected during prolonged glacial periods where sunlight would be prevented from penetrating deep beneath the ice and snow. Instead of engaging in photosynthesis, heterotrophs uses organic substrates to obain chemical energy. Although most Cyanobacteria engaged in photosynthesis, cyanobacteria often live in association with heterotrophic bacteria.
Some species of cyanobacteria, such as Synechocystis are capable of both autotrophic and heterotrophic growth. Under photoheterotrophic conditions, and diminished sunlight, Synechocystis can obtain energy from glucose which is used as a carbon source, and light as an energy source (Bullerjashn et al., 1985; Der-Vartanian et al., 1981).

Cyanobacteria Synechocystis

Therefore, even under global glacial conditions, cyanobacteria living upon the ice, those living beneath the surface of frozen seas, and those receiving only a limited amount of light, would be able to engage in photosynthesis. Yet other could engage in Heterotrophic activity, and produce oxygen or high levels of C resulting in large pools of C and then the oxidation of this C upon the release of molecular oxygen via enhanced Corg burial (Kelly et al., 2007). The ultimate result is the creation and buildup of calcium carbonate. However, these vast calcium preserves were then liberated into the environment when temperatures rose, as rising temperatures enhances evaporative events and accelerates the release of calcium into the environment.
Over the course of evolutionary history, and following the end of the Marinoan/ Gaskiers glaciation, and thus beginning around 580 mya, the earth began to significantly warm which accelerated bacterial mat evaporation and cyanobacterial mucous decomposition. The seas became saturated with calcium carbonate.
POST GLACIAL SKELETAL CALCIFICATION
This period of of post glacial warming was due to a significant buildup of atmospheric CO2 due to volcanogenic CO2 emissions (Cavalier-Smith, 2006), and an increase in methane levels due to to oxidation of methane released by methagenic archae, and from permafrost by deglaciation (Bao et al., 2008; Shields 2008). The atmosphere also became increasingly oxygenated which resulted in the oxidization of the large reservoir of organic carbon which had been building up in the oceans for nearly 4 billion years (Fike et al., 2006).
As the planet began to warm, and by 600 mya ago, the oceans were becoming increasingly saturated with calacium, creating "calcite seas" (Porter, 2006). However, even as early as 635 mya, a number of taxa were already displaying calcium carbonate mineralization. These included sponges who had first evolved a silica-collagen skeleton, which included calcium, thereby forming soft, lacelike silica skeletons, spicules, and spines which enabled them to enlarge their cell wall, and grow in size (Gehling and Rigby 1996; Li, et al., 1998; Tiwari et al., 2000; Xiao et al., 2000).

However, as the oceans became saturated with calcium carbonate, and as the Marinoan glacial period was coming to an end, sponges evolved a calcium based skeleton with the outerbody adorned with siliceous, monaxonal spicules (Li et al., 1998). Thus, the calcium-based skeleton evolved after the silica skeleton (Brasier et al., 1997).
Porter (2006) in his analysis of ocean chemistry and skeletal mineralization concludes that increases in "Ca2+ played a direct role in influencing the nature of skeletons that evolved at this time."
Skeletons are comprised of a calcium-collagen matrix. Exogenous calcium levels can increase 10-fold the synthesis collagen (Bonen and Schmid 1991). Calcium also interacts with collagen to induce cell adhesions. Thus the buildup and liberation of vast quantities of calcium resulted in skeletal metamorphosis.
CA buildup in the sea led to two main lineages, one with cell walls rich in polysaccharides (which led to plants), the other containing collagen (metazoans). Thus, multceullarity required calcium and the synthesis of collagen, leading to biocalicifcation, and then plants and anmials were able to leave the ocean and migrate to land.
The development of a calcium-based skeleton was thus the culmination of a step-wise series of envirinmental events, triggered initially by the massive amounts of silica released into the environment following the second world wide glaciation. The next stage was triggered when calcium carbonate secreted by photosynthesizing cyanobacteria flooded the oceans due largely to the degradation of thick cyanobacteria mats which evaporated when temperatures rose at the end of the Marinoan glacial period.
All this was set in motion by the increases in silica, which stimulated collagen synthesis, which bound calcium. The resulting calcium-collagen matrix resulted in the metamorphosis of shells, bones, teeth, and brains.
CNIDARIANS, SYNAPSES & THE BRAIN
Sponges, the oldest known living animal group, have no neurons, no synapses, no internal organs and consist of only a limited number of discrete cell types [2]. Sponges are regarded as animals without true tissues and therefore may represent the earliest stage in the evolution of animal multicellularity (Boero et al., 2007).
Silicarea sponges evolved following the Sturtian glaciation (Gehling and Rigby 1996; Li, et al., 1998; Tiwari et al., 2000; Xiao et al., 2000) when the seas were enriched with silica. The "Sturtian" may have lasted until 670 mya (Fanning and Link 2004)
Calcareous sponges evolved during and after the Marinoan glacial period, which ended 580 mya. These were purse, vase, pear or cylinder-shaped and had evolved a honey-combed skeletal system made up of of calcium carbonate, with the outerbody adorned with siliceous, monaxonal spicules (Li et al., 1998). Therefore, calcium-based skeleton evolved after the silica skeleton (Brasier et al., 1997).

PreCambrian and Cambrian calcareous Sponges

Likewise, Calcareous sponges evolved after the metamorphosis of Trichoplax (Placozoa) which evolved at around the same time as Silicarea sponges, i.e. 635 mya. However, like the sponge, Trichoplax do not have a brain or a nervous system. Nevertheless, Placozoa (Srivastava et al., 2008) and the sponge (Sakarya et al., 2007) contains the necessary genes for creating a nervous system.
Based on a whole-genome phylogenetic analysis, Srivastava et al., (2008), argue that placozoans belong to a 'eumetazoan' clade that includes cnidarians and bilaterians, with sponges as the earliest diverging animals. Other have presented evidence indicating that calcareous sponges are also more closely related to the Eumetazoa (cnidarians, ctenophores, triploblasts) than other sponges (Cavalier Smith et al. 1996; Borchiellini et al. 2001; Peterson & Butterfield 2005; Tiwari et al., 2000), including sponges with siliceous skeletons, i.e. silicisponges: demosponges, and hexactinellids (Peterson and Butterfield, 2005).
Calcareous sponge evolved after Placozoa, and Placozoa are far simpler than the sponge or cnidarian and are the simplest of living multicellular animals (Schierwater 2005). Placozoa posses only four somatic cell types, and lack any kind of extracellular matrix (Grell and Ruthmann 1991). Placozoans, therefore, are considered by many scientists to be "the earliest divergent metazoans in which the ancestral state of animal multicellularity is conserved;" though others believe that honor belongs to the sponge (reviewed by Boero et al., 2007).
Yet others proposed that cnidarians and ctenophores are the earliest diverging extant lineage (Collins et al. 2005).
What all three lineages have in common are the genes which code for brain tissue (Sakarya et al., 2007; Srivastava et al., 2008). However, unlike cnidarians and ctenophores (Grimmelikhuijzen and Westfall 1995) both the sponge (Sakarya et al., 2007) and Trichoplax Placozoa (Srivastava et al., 2008) lack nerves, neurons, synpses, or any tissue resembling a nervous system or ganglionic brain.

The sponge and Placozoa are brainless although the genomes of both species contains the genes which code for nervous system structures, including the synapse (Sakarya et al., 2007; Srivastava et al., 2008). In fact, in an examination of the phylogenies for 36 gene families involved in the post-synaptic complex in the genomes of the sponge and two basal metazoans, drosophilia, and Homo Sakarya et al. (2007) discovered a " large number of vertebrate post-synaptic gene homologs in the sponge." The genome of Placozoa also maintain many of the same genes which in mammals code for the brain including the generation of the synapse (Srivastava et al., 2008).

The synapse is a central feature of nerve cell conduction, signalling, and communication and enables neural cells to link with other neurons, so that information received in one area of the body can be transmitted to yet other areas. This enables the coordination of purposeful and reflexive body movement in response to the reception of sensory impressions. Increasing body size requires a network of nerves to coordinate body movement. The synapse is the basic building block for the nerve cells, the nerve net, the nervous system, and the brain.

More than 1000 proteins and hundreds of genes are required for building the synaptic complex including the pre and post synaptic membranes and their channels and receptors. Sakarya et al. (2007) concluded that the last common ancestor to all living animals likely possessed most of these genes and proteins which code for these basic, fundamental components of neural signaling and brain functioning.
However, neither the sponge or Trichoplax evolved a synapse or a neuron, although both possessed the necessary genes.
Cnidarians also possess ancestral genes and homologues (Technau et al. 2005) including those which code for the fundamental features of bilaterality (Hayward et al. 2002; Finnerty 2003; Finnerty et al. 2004; Matus et al. 2006), and the nervous system (Miljkovic-Licina et al. 2004).
CNIDARIANS, CORALS & THE SKELETAL NERVOUS SYSTEM
Although they lack a brain, cnidarians have a nervous system that consists of a network of nerve nets that include sensory and motor neurons, mechanoreceptors, photoreceptors and chemoreceptors all differentiating from a common stem cell line (Grimmelikhuijzen and Westfall 1995; Seipel and Schmid 2006; Willmer 1990), and controlled by regulatory genes homologous to metazoans (Miljkovic-Licina et al. 2004).

Evolution of the Nerve Net

Cnidarians may belong to a 'eumetazoan' clade that includes sponges and Trichoplax placozoans, with sponges as the earliest diverging animals (Srivastava et al., 2008). However, it also appears that cnidarians, (including cteno-phores, triploblasts) are more closely related to calcareous sponges than other sponges (Cavalier Smith et al. 1996; Borchiellini et al. 2001; Peterson & Butterfield 2005; Tiwari et al., 2000).
Peterson and Butterfield (2005) have calculated that the lineage leading to metazoans diverged from the sponge between 723 may to 867 Ma. They further estimate the common ancestors for calcareous sponges and other eumetazoans may have diverged between 634 and 826 Ma and the common ancestors for cnidarians diverged from other eumetazoa (triploblasts) between 604 and 748 Ma.
Hence, the convergence of opinion is that Cnidaria (subphylum Medusozoa of the Cnidaria), calcareous sponges and Trichoplax Placozoa, are Eumetazoa and are directly related, and that Cnidaria evolved after the metamorphosis of Placozoa and the sponge. This impression is also supported by the fossil record.
Cnidarians may represent stem-group eumetazoans (Xiao et al., 2000). Cnidarians include, corals, sea pens, sea anemones, jellyfish and Hydrozoa.
The first fossil evidence of Cnidaria appears during the latter part of the Edicaran age, after the seas had been enriched with calcium. This fossil assemblage includes Charnia which has been classified as a proto-cnidarian which resembles sea pens (Glaessner 1984; Gehling 1991); Cyclomedusa which is thought by some to resemble sea anemone and frond-like organisms which resemble or have affinities witch sea pens or colonial soft octocorals (Briggs et al., 1994); and coral-bearing reefs located in South Australia (Savarese et al., 1993).
The Australian coral reef assemblage is diverse and includes calcareous sponges and two species of coral-like skeletonized colonial cnidarians which resemble tabulate corals (Savarese et al., 1993).
Therefore, whereas all calcareous sponges and Trichoplax possess the genes which code for brain structures, only Cnidaria, which evolved after Placozoa and the sponge, evolved neurons, synapses, and a nervous system (Breidback O, Kutsch 1995; Grimmelikhuijzen and Westfall 1995). These Cnidarians were also the first to evolve calcium-carbonate skeletal structures that are common throughout all Metazoa (Boero et al., 2007).

Cnidarian Nervous Systems

CORALS, CALCIUM & THE SKELETAL-NERVOUS SYSTEM
Corals are Cnidarians and may be the first species to develop a skeleton and a nervous system. The coevolution of the skeletal system and the nervous system in this species may well be mutually linked to calcium produced by these Corals.
Corals are sessile long-living colonial organisms, typically found in tropical well-illuminated oceans, where they are the main contributors to reef formation. Coralline skeletal material is composed of aragonite (Barnes and Chalker 1990; Vago et al., 2002) which consists of naturally occurring polymorphs of calcium carbonate. Their skeletons are also communal such that colonial corals are often linked by shared skeletons. Thus corals trigger skeletal formation in other corals.

Corals (Cnidarians) also secrete calcium carbonate, and their calcium-carbonate skeletal system promotes the development of bones, nerve cells, neurons and astocytes in species other than corals, including humans(Devecioglu et al., 2004; Ohgushi 1997, Ohgushi et al., 1992; Peretz et al., 2007; Shany et al., 2003, 2005).
It has been repeatedly demonstrated (Ohgushi 1997, Ohgushi et al., 1992) that implanted disks of calcium carbonate derived from coral skeletons promoted de novo bone matrix formation, adhesion, proliferation, and differentiation (Abramovitch-Gottlib et al., 2006; Birk et al., 2006). Moreover, differentiation takes place without the addition of any bone-promoting factors to the growth medium.
Corals secrete external skeletons made of calcium carbonate. Calcium is not only a major component of the skeletal system (Nudler et al., 2003; Urbano et al., 2002), but acts on a number of genes to build and maintain the integrity of the excitable membranes of heart, glandular, and muscle cells. Calcium also plays a central role in neural generation, the functioning of the synapse, the activation of DNA which codes for neural functional organization and expression, and thus the development and functional integrity of the brain (Glezer et al., 1999; Hong et al., 2000; Llinás et al., 2007; Köhler et al., 1996; Mori et al., 1991; Perez-Reyes 2003; Weisenhorn, D. M. (1999).
Calcium secreted by corals also promote nerve cell development.
Biomatrix obtained from the exoskeleton of the coral P. lutea has been shown to promote the morphological development of neural tissue, including astrocytes, pyramidal and granule neurons, and tissues resembling hippocampal neurons (Peretz et al., 2007; Shany et al., 2003, 2005). These includes nerve cell axons and dendrites which rapidly grow, and the development of pre and post synaptic membranes and synaptic connections with presynaptic sites.

Corals

Retina Neuron

Hence, the skeletal system of the calcium secreting corals (Cnidarians) not only builds bones but the tissues of the brain including the synapse. Likewise, corals which lived during the Ediacaran age, may have also stimulated neural development, as well as skeletal and shell formation in other species.
Thus, one of the major keys to to the evolution of the first metazoans equipped with skeletons and brains appears to be the evolution of calcium secreting Cnidarians.
MULTICELLULAR METAZOAN METAMORPHOSIS
There is no evidence suggestive of eyes, hearts, brains, or a nervous system in any species prior to 575 mya. Further there is no evidence for sensory-guided coordinated behaviors that might be mediated by a nervous system or visual-chemosensory system. For example, evidence of horizontal burrowing does not appear until after 575 Mya, whereas vertical burrowing appears after 543 Mya (Erwin and Davidson 2002).
The first evidence of complex bilaterian forms began to appear around 555 MYA (Martin et al., 2000). Nevertheless, there is a complete absence of fossil evidence that can be related to a likely common ancestor for bilaterian in rocks older than 580mya--Nor is there any evidence of intermediate forms. This is because the silent genes coding for advanced sensory, neurological, and physical-skeletal traits although inherited from ancestral species, had not been activated until after 580 mya. It was only around this date that the environment had been significantly altered and enriched with silica, iron, oxygen and calcium all of which acted on gene selection, and activating genes coding for the calcium-collagen skeletal system, and the nervous system.
Genes act on the environment which acts on gene selection. Between 575 mya to 548 Myr ago the oceans was becoming relatively free of toxins, poisons and acids, and simultaneously oxygenated due melting glaciers, and the actions of Ediacaran fauna, cyanobacteria and other photosyntesizing organism (Fike et al., 2006; Towe 1970) An oxygenated ocean and the increase in calcium, zinc, copper, silica, and ferrous elements, coupled with the stepwise restructuring of the carbon. and sulphur cycles, (Fike et al., 2006) began to significantly impact gene selection and stimulated the subsequent metamorphosis of bilatera.
Initially prokaryotes and the early eukaryotes were exposed to a hostile environment due to increasing levels of Na+, Cl− and Ca2+ and transition metal ions, and the reduced levels of C, N, S, Se and Fe2+ due to oxidation (Williams & Fraústo da Silva 2006).
Thus changes in the increased availability and use of Ca2+, Zn2+, Mn2+, Fe2+, Co2+, Ni2+ and Cu+ (Cu2+) and the activation of their cellular binding-proteins corresponded to increases in the oxidation of these substances and their increased availability in the environment, all of which acted on gene expression and resulted in the metamorphosis of increasing complex life which could utilize these materials when they became available (Williams 2007).
This was accomplished, in part, via metalloproteins which were matched and bound to specific DNA sequences (Williams 2007). These cells have genes proteins, and enzymes that could respond to and interact with these materials when they become available. These proteins form a homeostatic link and thus bind to these metal ions thereby inducing gene expression (Dupont et al. 2006; Morgan et al. 2004; Williams & Fraústo da Silva 2006).
However, these genes and their protein products existed prior to their expression or their exposure to these metal ions. These genes do not evolve after exposure. Rather, if the genes did not exist prior to exposure, they would could not have been affected.
For example, most single cell anaerobes do not possess genes or proteins which respond to copper and dioxygen. Likewise, they possess few proteins which bind to calcium. In fact, initially Ca2+ levels were negligible (Williams 2007). Thus there were few or no intracellular Ca2+-binding proteins in early cells which instead employed proton gradients to drive many energized activities (Mitchell 1961; Williams 1961).
By contrast, single celled and simple multicellular eukaryotes posses genes and proteins which respond to calcium and possess calcium-binding proteins which employ calcium for signaling (Williams & Fraústo da Silva 2006). The presence of these substances and their impact on genes appear to have triggered gene expression, gene duplication, and the metamorphosis of increasingly complex and intelligent species.
As Ca (as well as Zn and Fe) levels increased, they acted on gene selection, possibly trigger several whole genome duplication events, which increased the number of genes that could produce a greater number of Ca, Zn, and Fe proteins. Thus the release and buildup of these environmental agents acted on gene selection thereby generating increasingly complex multicellular creatures which now possessed numerous compartments (i.e. cytoplasmic, periplasmic, vesicular, extracellular) each of which were specialized for processing these chemicals (Williams & Fraústo da Silva 2006).
By contrast Prokaryotes, having donated the necessary genes to eukaryotes, did not respond to these chemicals and minerals, and required and maintained only one major compartment. This compartment was enclosed by one major membrane, within which floats the cytoplasm. Prokaryotes in fact reject Na+, Cl− and Ca2+ (Williams & Fraústo da Silva 2006).
Many of these chemicals, compounds, and elements were released and liberated continuously, and with others being released sequentially, almost one after the other, in a temporal order over long periods of time, paralleling increasing cellular complexity (Williams & Fraústo da Silva 2006). For example, Cyanobacteria, continuously secreted oxygen and calcium carbonate, and their contributions were supplemented by other photosynthesizing organisms. The buildup of calcium was supplemented by the buildup of silica and iron, and the synthesis of collagen. Yet other creatures also began to secrete calcium during the Ediacaran period. Following the end of the M/G glaciation, calacium-enriched mats and reefs created by cyanobacteria and corals began to evaporate flooding the oceans with calcium, which acted on gene selection, triggering metazoan metamorphosis and the evolution of diverse species with brains, bilateral bodies, and skeletal systems.
Chave et al (1972) estimates that for each hectare of reef surface exposed on the sea floor, up to 2,000 tones of calcium carbonate are produced yearly, producing 700 billion kg of carbon each year.
Silica, collagen, calcium-carbonate all act on gene expression, including those coding for the body, brain, and skeletal system.
Thus, a complex variety of bilaterian forms began to appear (Bowring et al., 2003; Grotzinger et al., 1995; Martin et al., 2000). For example, fossils of a well-developed animal, Kimberella have been discovered in rocks located in northern Russia and dated to around 555 MYA (Martin et al., 2000).

Kimberella
It can be assumed from evidence of horizontal and vertical burrowing (Erwin and Davidson 2002), the fossil record, and genomic analysis, that by 540 mya, Kimberella and other bilateria probably possessed a ring of neurons creating a thin nerve network, as well as a visual-chemosensory system, and were capable of coordinated behaviors guided by the analysis of sensory and perceptual information.
It was also around this time that the large super continent Pannotia/Gondwana was breaking apart forming four fractured continents (Johnson et al., 2005l Meerta and Liebermanb 2008). This increased the area of continental shelf, produced shallow seas, and expanded diversity of environmental niches in which animals could specialize and speciate. Ecosystems became more complex because of the geochemical, ecological and tectonic changes and the changing environment acted on gene selection.

The joining together and fracturing of Pannotia/Gondwana during the waning stages of the Proterozoic, coupled with water-weathering, and the activity of innumerable microbes, resulted in the liberation of a variety of minerals, ions, enzymes, oxidized products, and metals including zinc and copper which were dumped into the oceans (Williams & Fraústo da Silva 1996, 2006).
As environmental levels of zinc, calcium and copper increased the number of zinc, calcium and copper transcription factors and receptor proteins significantly increased whereas nickel-binding proteins and transcription factors dropped out (Morgan et al. 2004; Williams & Fraústo da Silva 1996).
This increase in genes and proteins were most likely secondary to whole genome duplications, coupled with gene loss. Thus, with the increases in genes that code for specific proteins responsive to zinc, calcium, copper, ferrous iron , and other chemicals, minerals and enzymes, the use of these chemicals increased. By contrast, the necessity for others, such as nickel, decreased as reflected by gene loss (Williams & Fraústo da Silva 2006).
These changes were not due to random variation but were under regulatory control in the service of evolutionary metamorphosis. Specifically, zinc proteases break down collagen filaments and this allows for skeletal growth and development, such as from embyro to neonate to adult. Collagen played a significant role in the evolution of early metazoans (Towe 1970).
Zinc enzymes also act as receptors for sterols, and play a role in extracellular digestion thus increasing nutrient and energy extraction which are important for growth (Williams & Fraústo da Silva 2006).
Copper enzymes oxidize collagen allowing for collagen filaments to bind together with calcium, which also promotes skeletal and muscular growth.
Further, copper enzymes also oxidize organic molecules to synthesize adrenaline and amidated peptides which are employed as messengers, fast transmitters, and for signaling, which are also important in nerve cell communication. However, adrenaline and amidated peptides perform these functions by binding with receptors linked to Ca2+( Williams & Fraústo da Silva 1996), which recruited these substances in the service of nerve cell conduction.
Moreover, Ca2+ ions interact with genes which code for functions mediated by the central nervous system (Glezer et al., 1999; Hong et al., 2000; Llinás et al., 2007; Köhler et al., 1996; Mori et al., 1991; Perez-Reyes 2003; Weisenhorn 1999; Ubach et al., 1998). Because ancient species passed on the necessary genes coding for the brain and nervous system, once calcium levels and other substances built up sufficiently these genes were activated in subsequent species, giving rise to the first shelled animals and those equipped with exoskeletons (e.g., the trilobites) and thus the Cambrian Explosion.
However, the genes coding for and responding to these ions and compounds existed prior to their expression. They did not randomly evolve. As summed up by Williams (2007) "Given that the changes of all these functional uses of metal ions occur almost simultaneously in time in all the three branches of multicellular organisms, it could hardly be that random mutation led to simultaneous appearance of these similar novelties in all of them. The common factor is the environment change."
The changing environments acted on gene selection and can trigger explosive bursts evolutionary innovation. Thus, by the onset of the Cambrian Explosion, 540 mya, numerous creatures began sporting shells whereas others would develop bones, bilateral bodies, and complex brains--a function of the massive amounts of oxygen, carbon, calcium, zinc, copper, and other liberated minerals and gasses acting on gene selection.
THE CAMBRIAN EXPLOSION
"If it could be demonstrated that any complex organ existed which could not possibly have been formed by numerous successive. slight modifications, my theory would absolutely break down" (Darwin, 1857).
Until around 580 million years ago, the vast majority of life forms sojourning on Earth and beneath the seas, were single celled organisms and simple multi-celled creatures composed of less than 11 different cell types (Bottjer et al., 2006; Glaessner, et al. 1988; Narbonne 2005; Narbonne and Gehling 2003; Shen et al., 2008).
Until sufficient oxygen, silica, and calcium had been released and the oceans had become oxygenated, body and cell size were restricted and unable to expand or engage in strenuous physical activity. Larger bodies require skeletal support. Internal organs require skeletal protection.
Moreover, in the absence of ozone, larger sized bodies would be burnt by UV rays and would pop and explode. Therefore, once silica, calcium, and oxygen levels had increased and a protective ozone layers was established, creatures expanded in size, diversified, and grew spines, silica skeletal compartments, silica-collage skeletons, collagen-calcium skeletons, armor plates (sclerites) and small shells like those of brachiopods and snail-like molluscs (Matthews and Missarzhevsky, 1975; Mooi and Bruno,1999; Butterfield 2003; Conway Morris 2003; Lin et al., 2006).

Beginning around 540 mya, there was a vast explosion of bilaterian/metazoan diversity and complexity that appeared multi-regionally throughout the oceans of the Earth within 5 my to 10 millions (Levinton, 1992; Kerr, 1993, 1995). Over 32 phyla suddenly evolved, many with the body plans seen in modern animals (Fortey et al., 1997; Valentine et al., 1999; Conway and Morris 2000; Budd and Jensen 2000; Peterson et al. 2005)

Five-Eyed Opabin

Five-Eyed Opabin
Many of these creatures were very complex and bizarre in appearance (Cloud 1948; Whittington 1979) and immediately died out (Mooi and Bruno,1999). These included the five-eyed Opabinia Organisms were so unusual it has been assumed they must represent phyla that became extinct. However, other reserachers believe these bizarre forms are in fact among the stem groups of the extant phyla, (Smith 1984; Runnegar 1996; Budd & Jensen 2000).

EVOLUTION OF THE EYE
Many of the species which evolved during this period possessed the basic anatomy common to all subsequent forms of sea life, including completely modern eyes that quite suddenly evolved seemingly ex nihilo in the absence of intermediate forms. Trilobites, for example "could see in their immediate environment with amazingly sophisticated optical devices in the form of large composite eyes" (Levi-Setti, 1995).
However, t he genes coding for the eyes and visual perception, such as the PAX genes, did not randomly evolve but were inherited from ancestral species who in turn obtained their genes from prokaryotes. Pax genes involved in eye development, known as "Pax-6" and opsin in vertebrates and "eyeless" in fruit flies, have been isolated from numerous species. Over 1000 genes involved in visual functioning, including Pax 6, are homologous between phyla (Quiring et al., 1994; Gehring and Ikeo, 1999),(Tomarev et al. 1997). Between 70% to 80% of these visual genes are common and evolutionary conserved in the genomes of mammals, squid, octopus, flatworm, ribbonworm, ascidian, and nematode mosquitos, flies, tunicates, and vertebrate genomes including humans (Ogura et al., 2004). Moreover, of 1052 genes associated with the human eye, 1019 had already existed in the common ancestor of bilateria, (Ogura et al., 2004), which diverged anywhere from 1.3 bya to 830 mya (e.g., Wray et al., 1996; Peterson et al.., 2004, Nei et al., 2001; Gu 1998). In fact, the single most prerequisite for vision is the vitamin-A-related chromophores in the visual pigment, and this is also found in bacteria as well as algae (Seki and Vogt 1998; von Lintig, J., Vogt 2004).

These genes were passed down vertically and some were expressed in unicellular organisms, which developed "eyespots" and could therefore detect ambient brightness. With the evolution of multicellular metazoa eyespots became eyecups, which led to the "pinhole camera" eye which are found in creatures such as nautilus.
PAX genes were inherited by Trichoplex Placozoa (Srivastava et al., 2008)and the descendants of Arkarua adami which include Sea urchins (Sodergren et al., 2006, 2007) and which is of the phylum Echinodermata. The fossil of the earliest known echinoderm, Arkarua adami date to the Early preCambrian (Gehling 1987; Mooi, 2001). Arkarua had no mouth, there is no evidence for eyes, and its body had a five star radial symmetrical shape. Presumably they engaged in photosynthesis and nitrogen fixation. Thus, they evolved at the same time as Trichoplex.

Arkarua adami

In addition to sea urchins, other members of Echinodermata include sea stars, sea cucumbers, brittle stars, and crinoids many of which would appear during the Cambrian Explosion. They are of the clade of metazoans and thus of the kingdom Animalia which includes humans. They evolved in parallel to "lower metazoans" as represented by Trichoplex.
Sea urchins and humans belong to the kingdom Animalia and share genes directly related to the limbs, immune system, brain functioning and the visual, auditory, and olfactory system (Sodergren et al., 2006, 2007). Sea urchins and humans share more than 7,000 genes (Sodergren et al., 2006, 2007). Sea urchins share more genes with humans than fruit flies and worms (Sodergren et al., 2006, 2007). These include PAX genes directly involved in eye development.

Sea Urchin

However, sea urchins have no eyes, and lack an auditory and olfactory system (Sodergren et al., 2006, 2007). Instead, only a limited repertoire of photoreceptor genes are expressed in their tube feet (Burke et al., 2006). In fact, the sea urchin, humans, as well as Trichoplax share numerous genes involved in sensory functioning including the Pax eye genes ((Srivastava et al., 2008; Sodergren et al., 2006) even though neither Trichoplax nor the sea urchin have eyes. In addition, the genome of the sea urchin includes genes encoding transcription factors regulating the development of the retina (Burke et al., 2006).

The retina of the eye is basically and outgrowth of the brain. The evolution of the brain is linked to the buildup of calcium and the calcium-carbonate skeleton. Moreover, calcium plays a major role in retinal functioning including photoreceptor transduction, transmitter release by retinal neurons, and modulation of postsynaptic potentials in retinal ganglion cells (Akopian and Witkovsky 2002).
Thus with the evolution of calcareous skeleton, genes coding for nerve cells in the echinoderms (Burke et al., 2006; Cobb 1987) were also expressed creating neural tissue, and PAX genes coding for visual functioning were also expressed as they were in numerous metazoans at the outset of the Cambrian Explosion.
These novel, albeit complex eye-equipped metazoans also included brachiopods, molluscs, arthropods, annelid worms, crustaceans (Briggs et al., 1994; Chen and Zhou, 1997; Chen et al., 1995, 1999, 2003; Shu et al., 1999; Shu et al., 2001; Siveter et al., 2001), and the phylum Chordata; i.e. tunicates and the first jawless fish who possessed a notochord and simplified brain that consisted of a brainstem and limbic forebrain. The first chordates in fact appeared at the onset of the Cambrian Explosion, during the first 10 million years (Chen et al., 1995, 1999). This was followed by yet another explosion of life in the succeeding Ordovician Period which saw the emergence of modern body plans.
Hence, during the Cambrian epoch there was also a visual, cerebral and thus a cognitive perceptual explosion as the first true eyes and brains were established, eyes and brains which would continue to undergo a genetically preprogrammed metamorphosis until finally ending up in human heads.
GENES ARE INHERITED. THEY DO NOT EVOLVE
During the Cambrian Explosion, a complex array of life appeared throughout the world within 10 million years (Levinton, 1992; Kerr, 1993, 1995). With no history of derivative ancestral forms, all manner of complex life forms suddenly emerged with gills, intestines, joints, brains, and modern eyes equipped with retinas and fully modern optic lenses. These included organisms with a hard tube-like outer-skeleton consisting of calcium carbonate, and all manner of "small shelly fish" (Anabrites, Protohertzina), as well as jelly fish, mollusks, brachiopods, and the first chordates and arthropods (e.g. trilobites) which immediately sprouted legs and primitive brains.
These traits, and the genes that code for them did not randomly evolve. These species and these characteristics were precoded into genes which had been inherited from ancestral species, leading backward in time to the first creatures to appear on this planet.
However, this does not mean to imply pre-determination. In fact, a variety traits such as body colour, wing color, the visual system, the skeletal system, have repeatedly evolved in divergent species by alterations of the same genes (Prud'homme et al., 2006). Different environments can trigger the activation and silencing of a variety of genes and gene sequences. Gene networks are evolutionarily very flexible and are not hard wired. No species is genetically predetermined.
Rather, these genes, gene sequences, and gene networks can be employed as a platform for further evolutionary variation depending on the nature of the environment (Erwin and Davidson 2002), and the effects and interactions of other species whose genes may be transferred to one another. Many of these genes are highly conserved and were inherited from ancient common ancestors. A comparison of the numbers of ancestral gene clusters with those of extant animals such as the nematode, fly, mouse and human, established that extant bilaterian animals have retained more than 3500 gene clusters of the ancestral gene set (Ogura et al., 2004).
Genes linked to the heart, body, and the brain, and which are common in vertebrates and invetebrates, can also be traced to common ancestors for bilatera (Doe et al., 1991; Ogura et al., 2004; Vaessin et al., 1991; Matsuzaki et al., 1992) who may have lived anywhere from 600 mya (Ayala et al., 1998) to 1.6 bya (Wray et al., 1996; Gu, 1998; Cutler, 2000). These genes and their duplicates were then passed down vertically to numerous subsequent species which thus inherited the same genes and evolved the same functions, structures, and organs.
Consider, for example, the homeobox gene prospero which is essential for the development of CNS. Prospero can be linked to the common ancestor for invertebrates, insects (Doe et al., 1991; Vaessin et al., 1991; Matsuzaki et al., 1992) C. elegans (Burglin, 1994; Wilson ef al" 1994) and vertebrates (Oliver el al., 1993; Tomarev et al., 1996; Zinovieva et al" 1996) including humans (see Tomarev 1997 for review). Calibrated rates of seven independent data sets and an analysis molecular sequence divergence suggest that invertebrates diverged from chordates about a 1.2 Billion years ago (Wray et al. 1996).
Likewise, regulatory genes that control and guide the development of specialized differentiated cells are highly conserved, and can be traced to a common ancestor. These regulatory genes include tinman/nkx2.5 in heart, otx/orthodenticle in the CNS, dachshund in CNS and eyes, apterous/Lhx in limbs, caudal/cad in posterior gut, and the Pax genes which mediate vision.
However these protein coding genes and the genes and genetic mechanisms which regulate them, remained silent, or suppressed until the environment had been enriched with oxygen, silica, iron, calcium, and other minerals, enzymes, and gasses. The environment as well as the genomes of host species, had to be significantly altered and a variety of substances and minerals secreted into the air and the sea, before these silent genes could be activated.
Because numerous species inherited the same genes, introns, transposable elements, and the same master regulatory genes, once exposed to the same environmental triggers (Erwin, 1992; Erwin, 1999; Valentine et al., 1999; Knoll and Carroll, 1999), hundreds if not thousands of these genes were almost simultaneously expressed. This explains why hearts, eyes, complex bodies and brains were able to evolve quite suddenly, in numerous unrelated species, within a 10 million year time perior during the Cambrian Explosion.

CONCLUSION
Genes are transferred and expressed among all species, and these mechanisms have guaranteed a uniform genetic code across-species and the coordinated involvement of numerous genomes giving rise to the evolution of increasingly complex species.
The uniformity of the genetic code has allowed microorganisms to journey from planet to planet, acquiring and exchanging genetic information with innumerable species. This uniformity also enabled them to decipher and use genes transposed from foreign species, and to transfer, donate, and inject these genes into yet other species. Once transferred to a host genome, the new host was able to easily integrate these genes, and then activate or suppress them, and/or transmit them horizontally or vertically to yet other species until a time when environmental and other regulatory factors act on these genes so t hey can be utilized to express and affect complex morphological traits.
Yet another factor, explored in a later chapter, includes the presence of virus which inject their own genes into the genomes of the host, affecting gene expression and inducing significant evolutionary change (Forterre 2006; Iyer et al., 2006; Koonin et al., 2006; Samuelson et al., 1990; Weinbauer and Rassoulzadegan 2004).
Prokaryotes, and probably viruses, provided eukaryotes with genes, key enzymes, and numerous other critical components and regulatory elements and proteins important in replication and genetic continuity, including the genetic mechanisms that would enable the genome to accurately increase and repeatedly double in size without losing important information. This insured that specific genes and gene sequences coding for more advanced traits were duplicated and passed on to subsequent species for hundreds of millions or billions of years without any loss or degradation of genetic information.
Therefore, innumerable genomes of a vast array of species, came to posses numerous copies of the same genes through gene and whole genome duplication, thus insuring that this critical information would not be lost to future generations. This was made possible via horizontal and vertical gene transfer, and repeated episodes of "exon shuffling" and single gene and whole genome duplication and by the preservation of the original functions coded by the genes when they were first donated to or acquired by eukaryotes billions of years ago.
Gene duplication provides raw material for rapid functional innovation and major evolutionary transitions including the emergence of new species from old in the absence of obvious intermediaries. The genome appears to have been duplicated at least every 100 million years (Lynch et al., 2001; Lynch and Conery 2000), and at the outset of the Cambrian Explosion, and this duplicative event played a central role in the subsequent radiation of chordates (Dehal and Boore 2005). After the onset of the Cambrian Explosion, 540 mya, there followed additional duplications during chordate evolution, thereby forming many of the gene families of vertebrates (McLysaght et al., 2002).
Likewise, individual genes, regulatory genes, introns, and transposable elements have been repeatedly duplicated and shifted to new positions within the genome over the course of evolution thus exerting widespread influences on the expression and inhibition of wide networks of genes simultaneously, even duplicating themselves and inserting copies into different regions of the genome to coordinate gene expression.
When genes are duplicated and moved to a new location, the original gene, or its copy, may come to be freed of repressive restraints, become sensitive to environmental triggers, and express functions which have been suppressed. The duplicate or its parent gene can also selectively inhibit or express genes which had formerly been expressed or inhibited. For example, a duplicated gene, intron, or transposable element may leap to a different position adjacent to or overlapping an exon which is then expressed or silenced (Finnegan, 1989; Dibb & Newman, 1989; John & Miklos, 1988; Kuhsel, et al. 1990).
Thus, a wide array of genes can be switched on or off, new proteins with specific properties may be manufactured, and new cells can differentiate and develop increasingly specialized shapes and functions.
Moreover, the environment can act directly on gene expression such as by removing inhibitory and repressive influences. Thus we see that oxygen induced the metamorphosis of mitochondria. Silica triggered the formation of soft, lacelike silica skeletons and spines which enabled eukaryotes to enlarge their cell wall, and grow in size. Calcium carbonate was incorporated to create soft then hard shells and interacted with genes coding for the central nervous system. Contractile cells gave rise to the heart. Photoreceptors expanded into a variety of eyes. Digestive and secretory cells became organized into guts. The cytoskeletal system was replaced by a dense connective tissue consisting of collagen and elastin fibers that gave rise to cartilage, then bone, then the calcium-carbonate-collagen skeletal system which coincided with the generation of neurons, the nerve net and the creation of the brain.
However, these genes and proteins coding for these organs, tissues, and species, did not randomly evolve. They were inherited. They required biologically induced alterations in the environment to act on gene activation, perhaps in concert with regulatory genes that had also been donated by prokaryotes to the eukaryotic genome. In consequence, the cumulative effect of vast changes in the chemistry of the oceans and the atmosphere triggered genome duplicative events and the expression of a massive number of suppressed genes, thereby giving rise to multicellular eukaryotes, mitochondria, metazoan metamorphosis, the evolution of the skeleton and nervous system, and then the Cambrian Explosion.
Genes biologically engineer the environment, and it is the changed environment which in concert with introns, tranposons, and other regulatory elements, can act on and trigger gene expression, including the duplication of single genes or the whole genome.
Thus beginning over 4 bya, and over the ensuing hundreds of millions and then billions of years these genes and entire genomes were duplicated and yet other genes were deleted, freeing duplicate or the original genes from restraint and making them more susceptible to environmental triggers; introns, transposons and other genetic regulatory elements were transposed to new positions shuffling exons, creating new genes, inducing single gene and possibly whole genome duplications and inhibiting or acting on gene expression; the environment was biologically altered and genes and introns were donated by archae, bacteria, and cyanobacteria which were simultaneously altering the environment; and then around 540 mya, thousands of genes were expressed giving rise to an explosion of complex animal life.
The provision of these genes, proteins, enzymes, regulatory elements, and whole genome duplicative events, were not random accidents of chance, but under regulatory control and designed to guide the evolution and metamorphosis of multi-cellular eurkayotes and their genomes, the replication of creatures that long ago lives on other planets. Evolution is not random. Evolution is metamorphosis.
This explains why so many genes are highly conserved, why the same genes are found in divergent species, and why these same genes can be found in the genomes of ancient creatures who did not possess the traits these genes code for. This also accounts for the widespread evidence of parallelism in the fossil record where the same structures, organs, tissues, and body parts evolved, often nearly simultaneously, in a wide range of divergent species.
Further the ability of these genes to self-regulate, to duplicate, and to transposed themselves to other regions of the genome, including the genomes of other species, and the fact that these genes can be activated or silenced by changes in the environment, accounts for why evolution often occurs in explosive bursts, and why "higher" or more advanced or complex species, suddenly evolve without the benefit of intermediate or transitional forms. Further, and in conjunction with horizontal gene transfer, this explains why evolution is not isolated to a single member of a single species, but why many members of the same species evolve at the same time.
These genes did not randomly evolve. They are under precise genetic regulatory control and were inherited from creatures whose own ancestors, and their DNA, arrived on Earth from other planets.
The ultimate carrion eaters are bacteria. Innumerable bacteria reside within the guts, mouths, and other bodies parts of innumerable eukaryotes including humans (Baquero et al. 2008; Doolittle 1998). Bacteria can directly ingest large DNA molecules and incorporate genes from higher organisms (Doolittle 1998; Davies 1994; Martinez 2009). And they are continuously exposed to and incorporate genes from throughout the living world. Thus when flung upon the surface of a new world, some of these microbes contain vast genetic libraries which code for a wide range of traits and species, and these include regulatory genes and genes which can act on the environment, which in turn acts on gene selection. Thus we see that archae, bacteria, and photosynthesizing calcium-secreting cyanobacteria contributed numerous genes to the eukaryotic genome, and then biologically transformed the environment, releasing gasses, chemicals, and minerals which acted on and triggered the expression of genes which had been transferred from the prokaryotic genome.
Thus, prokaryotes can journey from world to world, exchange and acquire genes, and act with yet other microbes to induce environmental changes to activate these genes, thus guiding the metamorphosis and replication of creatures that long ago lived on other planets.
The genetic seeds of life flow throughout the cosmos, and identical genetic seeds have fallen upon innumerable worlds, including those much older than our own. The Earth was genetically seeded to grow complex life, and what has taken place on this planet, during the course of the last 4.6 billion years, is not a random evolution, but the replication, metamorphosis, and evolution of life from other planets.

The Evolution of Life From Other Planets
The Evolution of Life From Other Planets. Part 1 The First Earthlings. Interplanetary Genetic Messengers. ExtraTerrestrial Horizontal Gene Transfer. The Genetics of Eukaryogenesis and Metamorphosis Rhawn Joseph Ph.D., Journal of Cosmology, 2009, 1, 100-150.	The Evolution and Genetics of Life From Other Planets. Part 2. Prolaryotes, Viruses, ExtraTerrestrial Genes, Genetic Libraries, Gene Transfer, Introns, Transposons; Conserved - Silent & Regulatory Genes, Whole Genome Duplication, & the Big Brain, Big Breast Revolution. Rhawn Joseph Ph.D., Journal of Cosmology, 2009, 1, 150-200.	The Evolution and Metamorphosis of Life From Other Planets. Part 3. Genes, Microbes, Metazoan Metamorphosis & the Genetically Engineered Environment: Brains, Bodies & the Cambrian Explosion. Rhawn Joseph Ph.D., Journal of Cosmology, 2009, 1, 700-760.