|
Journal of Cosmology, 2009, Vol 1, In press JournalofCosmology.com September 2009 Genes, Microbes, Metazoan Metamorphosis Cambrian Explosion and the Genetically Engineered Earth Rhawn Joseph, Ph.D., Emeritus, Brain Research Laboratory, Northern California, 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 biologically altering the environment via the liberation of oxygen, silica, calcium and other substances, which promoted the "evolution" of multicellular eukaryotes, and the metamorphosis of all subsequent species. 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. The climate and temperature of Earth have also been genetically modified, triggering repeated episodes of global warming and global freezing. These dramatic temperature fluctuations acted on regulatory genes and buffering proteins and led to the removal of inhibitory influences on gene expression. Precoded traits were then expressed and species evolved into a world which had been biologically prepared for them. Following the last glacial period, massive amounts of calcium were liberated into the oceans following the melting of cyanobacteria mats. This calcium acted on gene expression to induce the evolution of bones, eyes, and brains. Corals evolved and continued to secrete massive amounts of calcium, such that by 540 mya, there was an explosion of life in every ocean of Earth, with innumerable creatures having suddenly evolved, simultaneously, complex bones, shells, eyes, brains, and bilateral bodies; a consequence of the altered environment acting on gene expression. 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.
EARTH BEFORE IT BECAME EARTH Before Earth became Earth, it was most likely a super-Earth which orbited a main sequence star similar to or perhaps many times the size of our sun. When that star had consumed much of its hydrogen fuel and began to die it also began losing mass at an accelerated rate, blown off by powerful solar winds. Planets closest to that star were consumed as its corona mushroomed in size, whereas those at a greater orbital distance drew further away and were eventually expelled. One of those ejected rogue planets, included a world that eventually was captured by this solar system and became Earth. And before it became Earth and before it went rogue, it may have already supported life.The standard view of planet formation is based on the accretion model, where particles of dust and bits of debris crash into each other and stick together, growing in size. This concept is not supported, however, by observation or basic physics. Rocks which crash into each other fragment into smaller pieces and do not stick together. The only way a planet can form in this fashion is if debris sticks to a moon-sized extremely hot, molten-iron core which was first ejected from a star upon supernova (Joseph and Schild 2010). Planets which grow by accretion around a hot iron core form in nebular clouds and not within accretion discs (Joseph and Schild 2010). Moreover, as hydrogen predominates within nebular clouds, most of these planets initially accumulate a hydrogen atmosphere. Those which are hundreds of times the size of Jupiter may also ignite forming a proto-star. Thus, proto-stars also form in nebula, and smaller planets such as super-Jupiters and super-Earths may begin to orbit around them. However, initially not all of these planets will orbit or rotate or spin in the same direction and many if not all, will eventually slam into one another. Nebular clouds may be cradles of life, possibly generating life from chemicals, metals, ions and gasses which coalesce and begin replicating following billions of years of chance combinations (Joseph and Schild 2010a). Nebular clouds are also depositories of life which are cast into these clouds clinging to particles of dust, droplets of water, and planetary debris (Joseph and Schild 2010a,b). As stars become red giants, their increasingly powerful solar winds will strip and blow away planetary atmospheres, surface material, and oceans of water, along with microbial life, all of which will be deposited in the growing nebular cloud. Therefore, planets formed in nebular clouds, and rogue planets ejected into nebular clouds, may inevitably become contaminated with life. Planets which are expelled, and those which form in nebula, may collide, causing them to fragment and grow smaller in size. In fact, most planets may have begun as super-planets, and then grew smaller as they crashed into each other. The larger fragments may be moon-sized, Earth-sized, or Jupiter-sized, at which point they may grow larger by accretion as small fragments and debris crash into them and the broken pieces are captured by gravity of the much larger planet. However, if this stellar debris which begins to accumulate on the surface of a captured planet, also harbored life, perhaps as spores or living microbes buried several feet or more deep inside, then these growing planets may again be contaminated with life. Therefore, planets do not grow in size by accretion unless debris sticks to a hot molten core ejected by supernova, or they are already planet-sized to begin with, having been ejected prior to supernova. These super-Jupiters and super-Earths are then fragmented as other super planets slam into them. And, if these planets did not already harbor microbes deep beneath the surface, then it is likely that would have been contaminated with microbial life as life-bearing debris and other living planets slammed into them. Thus, before Earth became Earth it may have orbited a main sequence star, perhaps as a super-Earth. Once the star began to die, this super-Earth was ejected and then subsequently fragmented, and then began to grow again by accretion. If correct, the first Earth not only originated in another solar system, but it may have already harbored life.
BIOCHEMICAL LIBERATION OF MINERALS AND GASSES
There is evidence that life was present on this planet from the very beginning, as based on residue discovered in the oldest rocks of Earth (REF). These life forms were likely deposited on this planet, encased in the debris which continually pounded new Earth, for almost 800 million years after it became a member of this solar system (Joseph 2000, 2009a).
Around 500 million years after Earth was captured by this solar system, it was struck by a Mar-sized planet (REF), causing a moon-sized mass to be ejected, and which may have become the Moon (REF). The new Earth was also being struck by giant asteroids, comets, meteors, and began to grow by accretion as smaller debris continually slammed into it for the next 700 million years. These conditions may it impossible for life to form on this planet via abiogenesis (the so called organic soup). However, some of the life forms contained in that debris, or which dwelled deep beneath the surface, likely survived. In fact, only one microbe had to survive and could rapidly cover the entire planet with bacterial offspring within a few months.
During the first several hundred millions years, layers were formed and began to differentiate as the outer surface of this planet was impacted by a variety of geological, solar, stellar, and geochemical forces. These included strikes by moon-sized debris, volcanism and degassing, water-atmospheric surface weathering, and plate tectonics which produced the first continents. Biological forces were also at work. The overall confluence of evidence, based on astrobiology, astrophysics, geophysics, and genetics indicates that at least two families of life were present from the beginning, i.e. archae and bacteria (Joseph 2009a,b,c; Joseph and Schild 2010a). They were most likely accompanied by viruses which essentially served as genetic storehouses and gene libraries. If single celled eukaryotes also were present on this planet from the beginning is unknown. However, based on a genomic analysis, it is clear that archae, bacteria, and viruses donated genes to what would become the multi-cellular eukaryotic genome. These prokaryotes also began genetically engineering the planet.
From the moment they took root on new Earth, Prokaryotes began digesting the planet and each other. Prokaryotes were and have been the primary agents responsible for the breakdown and liberation of a variety of chemicals, minerals and gasses (Falkowski and Godfrey 2008; Hazen et al., 2008; Nisbet and Nisbet 2008; Sleep and Bird 2008). And these biologically induced alterations in what would become the biosphere, acted on those genes donated to eukaryotes, and eukaryotes began to evolve.
Over the course of the next 4 billion years, 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). These activities were not random, but purposeful. The biologically altered environment created a biosphere which acted on gene section, thereby activating silent genes transferred from prokaryotes and viruses to eukaryotes and which coded for and expressed the necessary tissues and organs for building and replicating complex species which long ago lived on other planets.
The liberation, oxidation, or irradiation of these minerals, gasses, elements, and ions, included those on the planetary surface and gasses in the atmosphere, H (H2, H2O, H2S), C (CO, CO2, CH4), N (NH3, N2), and S (H2S), ions in the sea (Na+; K+; Mg2+; Ca2+; Mn2+; Fe2+; Co2+; Ni2+; Cu+; Zn2+; Mo or W; Se (H2Se); P; V(VO2+) and secretion of calcium which flooded into the oceans. Thus microbial activity contributed to changing atmospheric and ocean chemistry (Falkowski and Godfrey 2008; Nisbet and Nisbet 2008; Richardson 2000; Williams 2007) and ultimately made possible the metamorphosis of mitochondria and metazoans, skeletal biomineralization and the progressive evolution of multicellular life (Hazen et al., 2008; Mentel and Martin 2008; Williams and Fraústo da Silva 2006) leading to the Cambrian Explosion and beyond.
The creation of a changing biosphere, what could be likened to the "womb of the planet" was not hap hazard, but under strict genetic regulatory control. Most of the minerals, elements, and gasses were biochemically liberated or oxidized in a sequential, seemingly step-wise progression, which, in conjunction with geochemical events, impacted and paralleled the evolution of increasingly complex and intelligent species (Hazen et al., Joseph 2000; 2008; Williams 2007).
That these events were genetically programmed is also demonstrated by the genetic mechanisms controlling horizontal gene transfer and gene silencing vs gene activation. For example, archae, bacteria, and viruses transferred core genes to what would become the multicellular eukaryotic genome. This genetic inheritance included exons, introns, transposable elements, informational and operational genes, RNA, ribozomes, and the core genetic machinery for translating, expressing, and repeatedly duplicating genes and the entire genome. Once transferred most of these genes were deleted from the prokaryotic genome or transferred to viruses for genetic storage. Therefore, when archae and bacteria labored to create a biosphere which acted on gene selection, this insured that only eukaryotes would evolve.
For example, most single cell anaerobes do not possess genes or proteins which respond to copper, oxygen, or dioxygen. Likewise, they possess few proteins which bind to calcium (Mitchell 1961; Williams 1961). Instead, these genes were horizontally transferred to the eukaryotic genome. However, initially oxygen, copper, and Ca2+ levels were negligible (Williams 2007). Thus, during the early stages of eukaryotic evolution, these genes were not activated and Ca2+binding proteins were basically nonexistent. Early eukaryotes instead employed proton gradients to drive many energized activities (Mitchell 1961; Williams 1961).
Prokaryotes, upon digesting the planet, released oxygen into the atmosphere. Cyanobacteria also secreted calcium. The changing environment acted on gene selection, and as new species emerged, they were target by viruses which inserted regulatory genes. This coordinated activity triggered repeated episodes of single gene and whole genome duplication, exon-shuffling, and intron and transposon alterations in regulatory activity (Joseph 2009b,c). Silent genes were activated, proteins were fashioned, and 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). Increased oxygen also triggered the metamorphosis of mitochondria (Joseph 2009d).
Just as the uterus undergoes a series of progressive biochemical and biophysical changes which correspond to and promote embryological development, the biosphere of the planet was also biologically engineered. Thus there followed progressive increases in the availability of Zn2+, Mn2+, Fe2+, Co2+, Ni2+ and Cu+ (Cu2+), and various metal ions, which acted on gene selection thereby promoting evolutionary development; 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 which were liberated biologically. Genes biologically alter the environment which acts on gene selection, and these silent genes were inherited from prokaryotes whose ancestors obtained these genes through horizontal gene transfer (Joseph 2000, 2009b,c; Joseph and Schild 2010b).
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 specific genes, activating their expression and 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.
GENE EXPRESSION, HSP90 & MOLECULAR SWITCHES
Archae, bacteria, and viruses contributed most if not all the core genes and regulatory elements which became the multi-cellular eukaryote genome. However, not all these genes regulatory elements were active. Instead, they were silent, or silenced by other regulatory elements, or via protein coats which isolated them from triggering influences. These silent genes became part of the germline and were passed down, vertically, through subsequent generations and species until activated.
Proteins such as Hsp90, may prevent DNA expression by wrapping around the gene and acting as a buffer between silent genes and the environment. Therefore these genes are inhibited and are only expressed in reaction to changes in the environment which deactivate these protective proteins and their buffering products (Rutherford & Lindquist, 1998). Hsp90 is a highly conserved multifunctional protein that targets multiple signal transducers which act as "molecular switches" which directly control gene expression in eukaryotes ranging from yeast to humans (Feder and Hofmann 1999; Rutherford 2003; Sangster et al., 2004). Hsp90 "normally suppresses the expression of genetic variation affecting many developmental pathways" (Rutherford & Lindquist, 1998). Thus, when this protein coat is neutralized or removed, genes which had been buffered can be activated, and silent precoded traits are expressed giving rise to variation or even new species.
Hsp90 does not act alone in maintaining gene silence, but is part of a networks that includes other buffering protiens such as Hsp70, and p23 (Pratt and Toft 2003). As summarized by Cossins (1998, p. 309), these and related regulatory and signaling proteins, are sometimes referred to as "chaperones and have been discovered in all organisms studied so far. These signaling proteins form complex webs of molecular switches that allows signals both within and between cells to be transduced into responses." However, the coordination of these responses, can be influenced by the environment.
Moreover, genes are silenced by methylation. Change the environment, or even change diet, and the inhibitory suppressive effects of methylation are neutralized and these genes can be expressed (Waterland and Jirtle, 2003; Wolff et al., 1998).
Thus the release and buildup of specific environmental agents acts on gene selection and can activate silent genes, thereby releasing precoded traits and generating increasingly complex multicellular creatures which evolve as these chemicals became available. Silent gene activation is accomplished by removing inhibitory proteins, neutralizing suppressive mechanisms, or by directly activating specific genes, proteins, and enzymes that selectively respond to these elements. Consider the genes which code for myosin, actin, kinesin, and dynein and the proteins used for intracellular transport within the Eukaryotes, and the number of species who inherited the same genes coding for actin, myosin (Richards & Cavalier-Smith 2005), tubulin (Baldauf et al. 2000), kinesin (Lawrence et al. 2002) and dynein (Asai & Wilkes 2004). The genes responsible for these proteins did not randomly evolve. The genes coding for microtubule/kinesin/dynein and f-actin/myosin were inherited from a common ancestor but remained silent and suppressed until activated when the necessary elements, minerals, metals, and gasses became available.
Most scientists agree that the common ancestors for multi-cellular eukaryotes obtained their genes from archae and bacteria. It is also believed the once multi-cellular eukaryotes evolved and increased in size, bacteria and archae invaded or were engulfed by these eukaryotes. Symbiotic relationships were established and additional genes were horizontally transferred to the eukaryotic genome. These stripped down archae and bacteria were transformed in the process, forming numerous compartments and protective envelopes, including the nucleus. Each of these compartments provided a protective environment which contained the proteins and genetic machinery which were specialized for processing these chemicals (Williams & Fraústo da Silva 2006).
Hence, eukaryotic cells evolved as they acquired the necessary genes from prokaryotes which also formed specialized compartments which acted on the chemicals, minerals and gasses secreted or liberated by free-roaming prokaryotes. As the changing environment can activate silent genes, eukaryotes continued to evolve.
By contrast Prokaryotes, having donated the necessary genes to eukaryotes, did not respond to the chemicals and minerals they excreted or liberated. Further, whereas some prokaryotes formed a number of specialized compartments within eukaryotic cells, prokayotes as a species maintained a single compartment, enclosed by one major membrane, within which floats the cytoplasm. Thus, eukaryotes and not prokaryotes evolved into higher organisms.
Over the course of the last 4.5 billion years, Earth has been gradually genetically modified. When certain chemicals, gasses and elements were at trace levels, eukaryotes utilized others which were at higher levels. However, as oxygen and other waste products built up, specific genes were activated and others silenced, and eukaryotes rejected those chemicals and gasses which they formerly relied upon. 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). For example, oxygen-dependent ATP-generating pathways replaced the less efficient oxygen-independent pathways and eukaryotic cells underwent a significant alteration and began breathing oxygen via the metamorphosis of mitochondria (Schafer et al., 1996).
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) and these wastes also acted on gene selection. Some of these wastes also acted on prokaryotic genes, thereby enabling them to more efficiently extract and use energy to produce additional wasteproducts such as oyxgen and calcium (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 by eukaryotes and new species emerged. Oxygen and the metamorphosis of mitochondria is a prime example of how the changing environment triggered silent gene expression.
CYANOBACTERIAL ENGINEERING OF THE ENVIRONMENT
Cyanobacteria Fossils - Orgueil Meteorite
Cyanobacteria Fossils - Murchison Meteorite
Microfossils of cyanobacteria and others resembling fossilized algae have been found in a number of meteors which predate the origin of this solar system including the Murchison, Orgueil, Efremovka meteorite (Claus & Nagy 1961; Hoover 1984, 1997; Nagy et al. 1962; Nagy et al. 1963a,b,c; Zhmur and Gerasimenko 1999).
Cyanobacteria
The vast array of prokaryotes which took root on new Earth likely included Cyanobacteria, also know as blue-green algae.
Cyanobacteria 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 fact if buried deep enough beneath the surface of debris cast into space, Cyanobacteria (and other microbes), in the absence of oxygen or sunlight they can reduce nitrogen, iron and carbon 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). Hence, the could easily survive space travel and if cast upon the Earth, they could easily go forth and multiply.
Initially, the new Earth was lacking free oxygen, calcium, and other environmental agents necessary to induce significant genetic and evolutionary change, and the oceans were anoxic and possibly sulphidic (Barleya et al., 2005; Canfield 2005; Holland 2006; Mentel and Martin 2008). 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). Cyanobacteria, anerobic organisms, and those adapted to breathing hydrogen or methane, or feasting on iron and sulphites and other minerals and metals in the absence of oxygen, were able to thrive (Barleya et al., 2005; Olson 2006; Rosing and Frei 2004; Sleep and Bird 2008). In the absence of oxygen Cyanobacteria use hydrogen sulfide, or sulphur, or 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). Even in the absence of oxygen, Cyanobacteria, would have also been able to engage in H2-based anoxygenic photosynthesis (Herrero and Flores, 2008). These and other microbes, however, released oxygen, carbon dioxide, and calcium into the environment as waste products.
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).
As carbon dioxide levels increased, some species broke down CO2to 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 and made available.
Complex carbohydrates (polysaccharides) form the structural elements in the cell walls of bacteria and plants, and make possible 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 as vast amounts of carbohydrates were manufactured.
In addition to carbohydrates, cyanobacteria also secreted waste products such as ferrous iron and oxygen, which eventually acted on gene selection. They did not act alone. Chemolithotrophic microbes break down and convert ferric iron which is employed as an oxidant to decompose other minerals, thereby producing sulfate and ferrous iron as waste products (Fernandez-Remolar et al., 2008). Thus, in addition to oxygen soil weathering, innumerable bacteria and archae were also acting on rock and soils, such that ferrous iron and sulphates were being liberated and draining into the oceans. 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 complex multi-cellular organisms and their genome.
.
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 contributed to the major components of the eukaryotic 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), whereas by 4 bya much of the planet may have been covered by shallow seas (Valley et al. 2002), these interactions created a bio-environmental feedback cycle that continually acted on gene expression.
In addition, 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 triggered and 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). Photosynthesizing Cyanobacteria would not have not found these conditions deleterious as they are accompanied by viruses which can provide additional photosynthesizing genes under conditions of reduced sunlight (Lindell et al., 2004; Sullivan et al., 2005, 2006; Williamson et al., 2008). Thus, oxygen continued to be pumped into the atmosphere.
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), as well as from high temperatures generated by the continual pounding of debris at it slammed into the planet. In addition, carbon dioxide levels significantly increased creating a heat-trapping greenhouse effect (Kasting and Ackerman 1988; Sleep & Zahnle 2001; Walker 1985). Much of this CO
How hot was it? According to Kasting and Ackerman (1986), if the early atmosphere contained 10 bars of CO
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 and 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
In addition to Cyanobacteria, clusters of microfossils similar to methanogens have been identified in the Murchison meteor (Pflug 1984) which predates the origin of this solar system. Methanogens secrete methane (CH4), as well as CO2. Thus, although the Earth may have begun to cool by 4 bya, within another 500 million years there was another period of global warming. Around 3.5 to 3.0 bya, as methanogens continued to proliferate, atmospheric CH4 levels began forming an organic haze, thereby triggering another greenhouse warming of the planet (Schwartzman et al., 2008). 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) the lifetime of CH4 in an anoxic atmosphere is approximately 1000 times longer than today.
Thus the high levels of methane combined with CO2 created a powerful greenhouse effect which warmed the planet (Pavlov et al. 2000; Kasting & Siefert 2002; Kasting & Ono 2006) thereby producing profound climate change and global warming. 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 (122°F), even though the sun was approximately 80% as luminous as today.
Therefore, although there may have been a period of cooling beginning around 4 bya, the planet was quite warm if not hot, for the first 1.5 billion years after its formation, and did not begin to significantly cool until or grow cold until 2.9 bya (Young et al. 1998).
Cyanobacteria
Methanogens
Hence, the warmth of the planet was maintained predominantly by the activity of prokaryotes whose waste products enabled yet other microbes to flourish and contribute to the global climate and creation of the biosphere. For example, cyanobacteria wutilized carbon dioxide to fashion carbohydrates which served as a food source to other microbes which diversified, died, flourished, died, thus building up additional organic wastes. Thus, methanogens and other prokaryotes began to flourish.
CYANOBACTERIA, OXYGENATION & MULTI-CELLULAR EUKARYOTES
Microfossils of Cyanobacteria have been found in a number of meteors which predate the origin of this solar system, and Cyanobacteria were likely among the first to take root on the surface of this planet. Despite the lack of a protective ozone layer, they could have easily been protected from UV rays by mineral grains (Cavalier-Smith, 2006) and thus could congregate near the surface and engage in photosynthesis (Hoashi et al., 2009). Presumably, they began photosynthetic activity immediately upon reaching the surface of this planet.
In the absence of oxygen 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 had access to a powerful energy source, and they 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).
Cyanobacteria Cellular Structure
Cyanobacteria are the only known prokaryotes capable of oxygenic photosynthesis (DesMarais 2000). By 3.46 bya these photosynthesizing microbes had released significant amounts of oxygen into the atmosphere and oceans (Hoashi et al., 2009). In fact, they were performing the same functions from deep beneath the sea and were 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. These were formed 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). Thus these microorganisms made a major impact on the biochemistry, geochemistry, and the evolution of life on Earth.
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, O2 pressure was buffered for billions of years. However, reduced levels of oxygen allowed for other materials to accumulate including calcium. The controlled buildup of these materials played a key, sequential role in the targeted activation of specific genes in a specific order, the result of which was the metamorphosis of increasingly complex species culminating in the Cambrian Explosion.
Thus, initially, except for isolated pockets and during specific periods, the Earth's atmosphere and oceans were largely devoid of free oxygen (Holland 2006). However, during specific periods, oxygen levels did rise dramatically and then fall again; and these fluctuations were also under biological control.
Around 3.2 bya, there was a spike in atmospheric oxygen, a consequence of increased oxygen photosynthesis (Ohmoto et al. 2005). This sudden increase in oxygen levels may not have been due to increased photosynthesis, but 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 and methane levels increased (Ohmoto et al. 2005). Oxygen, however, also breaks down methane. In consequence, 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).
Increased atmospheric oxygen levels, coupled with temperature change, acted on gene selection and by 2.8 bya induced the metamorphosis of mitochondria and multicellular eukaryotes (Joseph 2009b).Oxygen-producing cyanobacteria were also proliferating and 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. Coupled with increases in oxygen, carbohydrates, and other liberated elements, metals, and ions, as well as significant changes in world temperature and climate, a host of silent genes were activated. Moreover, these liberated elements and gasses provided the raw materials for creating duplicates of individual genes and the entire genome. By 2.7 BYA, the genome significantly increased in size and singled celled eukaryotes were being supplanted by the first multi-cellular eukaryotes (Dyall and Johnson 2000; Hedges et al., 2001). These multi-cellular eukaryotes consisted of around 2-3 cell types (Hedges et al., 2004) and 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 again pumping methane into the atmosphere and creating a thickening organic haze (Pavlov et al. 2001) that was interfering with photosynthesis (McKay et al. 1991; Pavlov et al. 2000). Moreover, volcanoes were belching CO2 and sunlight-blocking ash into the atmosphere. H2 levels may have also increased because the organic methane haze was acting as a blanket thereby preventing H2 from escaping into space (Tian et al. 2005).
After a cooling spell which may have lasted 100 million years, the Earth again began to warm. 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 were anoxic, surface layers and pockets of shallow ocean became mildly oxygenated (Holland 2006).
By 2.3 bya 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 eukaryotic and prokaryotic 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 bya, 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: THE MAKGANYENE GLACIATION
Following a spike in oxygen and cold weather 2.9 bya, the Earth began to warm, and a period of global warming ensued which lasted for at least 500 million years due to high atmospheric levels of methane and H2 which created a greenhouse effect. However, as this layer of thick organic haze grew more dense it blocked so much sunlight that the planet began to cool (McKay et al. 1991; Pavlov et al. 2000), triggering the Makganyene glaciation.
Because of the high levels of methane 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). As methanotrophs proliferated, methane levels continued to be reduced, which contributed to the cooling of the planet, which also 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 significant decrease in its CH4 content, and this decrease would have caused the planet to rapdily cool (Young et al. 1998; Kasting & Ono 2006). In fact, O2 levels became so high around 2.4 bya that sulphur MIF production collapsed, and this 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 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 accelerated the cooling and glaciation 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." The first snow ball Earth was orchestrated biologically.
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. Under current conditions, over 99% of organic matter is destroyed; a function of the redox state of the atmosphere–ocean system.
However, two billion years ago, the oxygen 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 contributing to reductions in O2 levels 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 being reduced to low levels, methanogenesis was playing a greater role in the degradation of organic matter (Holland 2006). Methanogens again began to proliferate. 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 lying in shallow pools of melt water and muddy soil. Further, volcanoes were belching carbon dioxide. The increasing levels of methane coupled with carbon dioxide belched out by volcanoes and other microbial life forms, again began to create a greenhouse effect.
Temperatures also were also initially reduced by the proliferation of cyanobacteria (such as black cyanobacterium Scytosiphon) which colonized much of the icy snowy surface which was increasingly covering the planet. These ice-hugging Cyanobacteria likely formed 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 can warm the soil by 4–5 °C and icy surfaces by 8–12 °C (Gold 1998). However, as they proliferated they also died in greater numbers, provided nutrients for methane produced microorganisms, and thus methane levels increased further.
Over time, as the sun grew in mass it increased its heat output (Gough 1981; Lang 2001). Thus, due to increased heat generation from the sun, and the methane-carbon dioxoide green house effect, the global ice age and "Makganyene" glaciation came to an end, the Earth began to warm, sea levels rose from melt water, and the climate and environment of the planet underwent significant change; all of which acted on gene expression thereby triggering a burst of eukaryotic 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. Oxygen-breathers could not evolve until there was sufficient oxygen, coupled with extremes in temperature fluctuations, all of which acted on gene selection.
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, gasses, and chemicals must be released in timed sequences of targeted release which act on gene expression. Hence, one stage of development logically follows and builds upon the next. One species 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). These wastes upon reaching certain levels, acted on specific genes and proteins which were 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 carbohydrates. The increasing available of carbohydrates led to increased energy availability, increases in the size of the genome, species diversity, some of whom were releasing carbon dioxide as a waste product. 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). These substances, all of which were biologically produced, were incorporated to create complex multi-compartmented eukaryote cells (Williams 2007). They were also utilized to expand the size of the genome; possibly inducing whole genome duplicative events.
The cyclic nature of these events, be it fluctuations in temperature, or the time release of various gasses and other substances, were not random, but under genetic and biological control. Certainly, the nature of Earth played a role, such as volcanic eruptions, plate tectonics, and the location of Earth relative to the sun. If, for example, Earth was located outside the "habitable zone" and was of insufficient or excessive gravity and did not posses oceans of water, life could not have evolved and these biologically generated cyclic events would have been an impossibility. Further, alterations in the biosphere can also be caused by non-biological forces, and these too can impact evolution. However, given the right planet, the nature of life is to over come these uncontrolled catastrophic change, and to impose biological even if it takes hundreds of millions or billions of years.
Oxygen, DNA, and Evolution of the Geo-Chemical Environment
The biosphere of this planet is a biological construction, and so too were the cyclic changes which included the buildup of methane/carbon dioxide followed by oxygen, followed by methane/carbon dioxide, and then more oxygen, all of which directly impacted the climate and world temperatures. Specifically, alternative cycles of global warming and global freezing, coupled with the rise and fall of specific gasses, acted 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. Further, bot before and after the rise in oxygen, numerous elements had already been oxidized. These oxidized elements acted on gene selection which converted cellular machinery so as 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 eukaryotic 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. 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 transposable elements (van de Lagemaat et al., 2003), some of which 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 eukaryotic cell with an expanded genome.
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--all of 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 stage after stage of evolutionary metamorphosis.
A POST GLACIAL EXPLOSION OF LIFE
Within a 800 million year period extending from 2.3 to 1.5 BYA, atmospheric oxygen levels had increased and stabilized, 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 living and dead bacteria which had formed thick bacterial mats.
Cyanobacteria Blue Green Algae
It was during this period, between 2.2 to 1.6 billion years ago, that cyanobacteria (also known as blue green algae) may have may invaded or may have been engulfed by a multi-cellular eukaryote. That is, just as archae, bacteria, and viruses, had contributed the core genes and regulatory elements to the what would become the genome of multi-cellular eukaryotes over 4 billion years ago, Cyanobacteria began transferring and donating over a thousand of its genes to specific multi-cellular eukaryotes--the ancestors of what would become plants. Cyanobacteria not only donated genes, but formed symbiotic relations with the common ancestors for plants (Delwiche et al., 1997; Doolittle 1999; Martin et al., 2002; Nosenko and Bhattacharya 2007).
Some species of archae and bacteria donated genes and were incorporated into eukaryotic cells, and these stripped down microorganisms were transformed into compartmentalized envelopes, and helped form the nucleus and triggering the metamorphosis of mitochondria.
Likewise, this stripped down cyanobacteria (Martin et al., 2002), not only contributed genes to the ancestors of plants, but was transformed into a chloroplast as both clearly resemble one another and share identical genes (Joyard et al., 1991; Martin et al., 2002). For example, the chloroplast 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, cyanobacteria, following engulfment, became organelles, i.e. the chloroplasts and as part of the plant cell genetic machinery, and began conducting photosynthesis. This transformation may have begun in earnest 2.2 to 1.6 bya. This gave rise to the first ocean dwelling plants, 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). However, this engulfment was selective. Not all eukaryotes obtained Cyanobacteria genes or formed symbiotic relationships with this bacteria. The invasion was selective, and may have triggered the divergence between plants and animals and a duplication in the genome of the common ancestors for plants (Wang et al., 1999). Thus, animals also contain some Cyanobacteria genes.
In plants, this genomic duplicative event created multiple copies of MADS-box genes (Alvarez-Buylla et al., 2000) which over a billion years later would 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).
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. These species all uitlize chloroplast and the plastomes to engage in photosynthesis, and to secrete oxygen into the atmosphere. Further, they feed on nitrates released as waste products by a variety of microbes; interactions which did not take place by random, but which were and continue to be under genetic regulatory control.
The insertion of these genes may have taken place in successive waves, with the first occurring prior to the plant-animal split, i.e. between 1.5 bya to 1.2 bya (Wang et al., 1999). Thus, plants and animals share genes, and the plant genome, even after it evolved, continues to maintain copies of animal SRF-like MADS domains (Alvarez-Buylla et al., 2000). This also indicates 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 prior to the divergence between animal and plant.
THE SECOND EXPLOSION OF LIFE
By 1.5 BYA, atmospheric oxygen levels had increased to levels ranging from 0.02 and 0.04 atm (Holland 2006). By contrast, the shallow oceans remained mildly oxygenated and the deep oceans continued to be mostly anoxic (Holland 2006)
In addition to photosynthetic activity of cyanobacteria, 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.
These cascading series of alterations in the biosphere had profound effects on silent gene expression and numerous species families split off from one another. 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).
The divergence of these species families was not a random accident of chance. 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
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. However, this also means that these species inherited genes from common ancestors who also inherited these genes, leading back to the first Earthlings and then to their ancestors who came from other planets. Most of these genes were inherited in silent form, and were then activated by changes in the environment. Hence, during this period creatures 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, the not all species inherited the same silent genes
The lineage leading to vertebrates and vertebrates contain genes and mitochondria which can be traced to an 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). Thus whereas plants inherited genes making photosynthesis possible, the lineage leading to invertebrates and vertebrates instead included the genes for eyes, hearts, bilateral bodies, bones, and brains. These silent genes selectively inherited by the ancestors of animals would continue to be transferred vertically, and probably horizontally, through subsequent species and generations, undergoing repeated duplications, until freed of regulatory restraint. Indeed, many of these silent genes, were activated by major environmental and climatic changes between 750 to 580 mya, thus giving rise to the Cambrian Explosion around 540 mya.
SILICA, WEATHERING, RODINIA, AND SPECIATION.
From the very beginning innumerable microbes were impacting the earth, releasing oxygen, methane, carbon dioxide, and calcium, breaking down and leaching iron, altering the climate and atmosphere, and were transforming the land masses of the planet. The biosphere of Earth, although largely a biological construction, has also been impacted by naturally occurring phenomenon, such as volcanisms, plate tectonics and weathering. However, the history of this planet also shows signs of deliberate attempts to overcome these uncontrolled forces, and to continue genetically engineering the planet in ways that would benefit species which had yet to be born, and those already living.
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, 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), and the biological digestion of rock and Earth. 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 rivers of 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 and microbes, 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 and rapid 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 impacts 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 and microbial 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 ensured that the Earth's climate remained 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. Silica directly acted on gene selection and new species emerged.
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 of these new microbial species were heterotrophic rather than photosynthetic (Butterfield (2005a,b) and therefore ate each other.
A variety of life forms were flourishing, proliferating and dying. As acritarchs, amoeba, and other creatures died and then sank into the deep ocean, phosphorite levels and organic material began to significantly increase and accumulate (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).
THE SECOND SNOW BALL EARTH: THE STURTIAN GLACIATION
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 CO2levels dropPED as O2 levels rose (Cavalier-Smith 2006). Temperatures fell rapidly and snow and ice covered more and more of Earth. As more of Earth's surface and oceans became covered with ice, the carbonate–silicate cycle became destablized and temperatures began to plummet. The Earth froze.
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 deep beneath the ice covered seas (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). The icy surface of the planets was also probably 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 would have trapped heat just as they do in the Arctic (Quesada et al., 1999).
As has been emphasized, cyclic changes in weather and climate are biologically regulated. When natural, uncontrolled forces alter the biosphere, the living biomass labors to bring it back into balance, or to repeat the next cycle. Therefore, as Cyanobacteria covered the frozen Earth, the production of oxygen was decreased, even as photosynthetic activity increased. Instead, they liberated and excreted CO2. In fact, organic carbon and biomarkers indicate extensive bacterial photosynthesis during the Sturtian snowball glaciation (Olcott et al. 2005). Moreover, methenogens were again feasting on decaying organic matter and releasing methane. 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.
COLLAGEN AND THE SILICA SKELETON
Despite the melting ice, the oceans remain largely anxoic. Surface waters consisted of an acidic, sulfuric mixture (Canfield et al., 2007, 2008), while deeper waters overflowed 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). Throughout this period anoxic conditions remained widespread beneath the mixed layers 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), thereby producing silica spines and spicules. The formation of spicules is mediated by the enzyme silicatein which is dependent on ferric iron and is directly related to silica.
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 which grew larger in size (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 rudiments of a silica skeleton were being established.
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. Silica therefore increases the level of transcripts for collagen thereby producing collagen (Krasko et al., 2001). Thus the presence of silicate influences the expression of the enzyme silicatein and also the expression of collagen, both of which combined to form silica-collagen biomineralization and the creation of skeletal elements.
Thus siliceous biomineralization preceded calcareous biomineralization which would also employ collagen. In the basal lineage leading to animals, silica and collagen were employed to enlarge the cell wall, create silica reinforced compartments, all of which enabled 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 spines, which made these creatures more formidable and enabling them to withstand predators and to significantly increase in size.
Therefore, in summary, due to biological activity, great amounts of silicates and ferrous material had been building up in the oceans since 2.3 bya, and which had been secreted by innumerable microbes. These biologically manufactured materials reached such high levels around 650 to 600 mya that they triggered silent gene expression, and 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 which had also grown larger and more dangerous (Gehling and Rigby 1996; Li, et al., 1998; Tiwari et al., 2000; Xiao et al., 2000).
ACRITARCHS
Acritarchs which are of unknown origin or phyla, represent a broad range of species. Some are related to planktic eukaryotic algae and dinoflagellates (Arouri et al., 2000). Others to lower metazoans such as the sponge (Zhang 1998). Thus they are related to both animal and plant. 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) and cyanobacteria.
Most dinoflagellates are unicellular and have acquired genes from cyanobacteria. About half of all dinoflagellates are photosynthetic. Some are predators, some became endosymbionts of marine animals and protozoa, and yet others began to eat protozoa. Most photosynthetic dinoflagellates contain chloroplasts--and thus this branch of acritarch/dinoflagellates are closely related to Cyanobacteria and plants.
Some species of Acritarchs evolved into, or share a common ancestor with metazoans. They may in fact share many common ancestors, including the sponge. Like the sponge, some species of Acritarch developed elaborate spinose ornamentation over 630 mya (Peterson and Butterfield 2005; Vorob'eva et al., 2009). 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). Species are part of the environment. Since the environment can activate or silence networks of genes, predators and prey can trigger gene activation and promote evolutionary development in each other. For example, defensive spines were a consequence of predation, and also likely acted on gene selection in predators, leading to further morphological diversification and escalating evolutionary development (Butterfield 2004; Vermeij, 1993). The presence of defensive spines also suggests that predatory proto-eumetazoans may have evolved by 635 mya, a time period coinciding with the the cooling of the planet and what would become the 3rd snowball Earth. However, many species not only evolved, but many also became extinct.
3RD SNOWBALL EARTH: THE MARINOAN AND GASKIERS GLACIATION
Beginning around 640 mya, the planet experienced 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). Alterations in temperature act on gene selection, and it was during the onset of the Marinoan glaciation, that a number of distinct species appeared in an an evolutionary burst, including the Ediacaran fauna (Narbonne and Gehling 2003) who may have been as much plant as animal. They were accompanied by species collectively referred to as "Echinodermata-Arkarua adami" (Gehling 1987) and the heartless, brainless Placozoa Trichoplax whose genome possessed the silent genes necessary for fashioning a heart and brain (Srivastava, et al., 2008).
The "Marinoan" glaciation was followed by a very brief period of global warming, and then a less extreme period of cooling referred to as Gaskiers, which came to a close 580 Ma (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 which blocked out sunlight. For example, U-Pb zircon dates from volcanic ash beds within the Doushantuo Formation (China) indicate extensive volcanic activity beginning around 635 mya (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 not just ash but tons of CO2 into the air thereby generating greenhouse warming (Kirschvink 1992; Hoffman et al. 1998). Conversely because of glaciation, C02 consumption was limited. As microbes were also venting carbon dioxide, 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), coupled with volcanic ash and increases in CO2, again generated a greenhouse effect. The planet began to warm and this was followed by a global meltdown and brought the "Marinoan" glaciation to a close.
However, as much of the melting ice contained high amounts of oxygen, oxygen levels in the ocean began to rise (Canfield et al., 2007) at the same time the planet began to warm. These changes in global temperature, like those from previous cycles, again acted on gene selection. Innumerable creatures evolved and just as many died and became extinct during the Marinoan/Gaskiers glaciation and its global warming aftermath. A variety of niches were emptied of life and which were then exploited by other organisms. Moreover, increased oxygen provided oxygenated environments throughout the ocean which could be exploited and colonized by oxygen breathing creatures. Coupled with increased calcium, and silica, vast networks of silent genes were activated, and others silenced and an explosion of life ensued (Condon et al., 2005; Peterson and Butterfield 2005) and a new wave of speciation was unleashed, including the evolution of megascopic Ediacarans (Narbonne 2005; Narbonne and Gehling 2003). Eukaryotic life had made a giant leap from microscopic to megascopic.
TRICHOPLAX & SILENT HEART & BRAIN GENES
It was during the onset of the Marinoan glaciation, around 640 million years ago, that the Ediacaran period began (Knoll et al., 2004). During this same cold spell, the heartless, brainless Placozoa Trichoplax also evolved, and whose genome possessed the silent genes necessary for fashioning a heart and brain (Srivastava, et al., 2008). These genes did not randomly evolve through natural section, as they were silent and had been inherited. In fact, hearts and brains would not evolve until another 100 million years had passed.
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. They do not have muscle cells and 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, as well as those coding for endodermal, cardiac and blood cells (Srivastava, et al., 2008), even though they have no heart, muscles, or blood.
Their genome also contains four putative opsin genes, which code for light reception, as well as 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 contains genes which encode a rich array of transcription and signalling factors, 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) even though they do not produce embryos. 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. 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 the first embryos do not appear in the fossil record until between 580 mya 550 mya (Condon et al., 2005; Hagadorn et al., 2006), almost 60 million years after this species evolved. These first embryos include planula larvae and hydrozoan embryos and resemble gastrula stage embryos of bilaterian/metazoan forms (Chen et al., 2000).
Although the lack any semblance of nervous tissue, the Trichoplax genome 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 to transmit messages 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.
These genes did not randomly evolve. They were inherited, and were then transmitted through subsequent species until activated by yet other major changes in the environment, including the flooding of the oceans with calcium over 540 mya.
CONSERVED GENES, GENE EXPRESSION & PUNCTUATED EQUILIBRIUM
It is not reasonable to assume that Trichoplax and other ancient species randomly evolved complex genes which code for vision, sex, and the body and the brain, and then failed to activate them. Contrary to Darwin's theory (Darwin 1859,1871), Trichoplax did not gradually evolve vision, sex, a body and a brain even though they possessed all the genes necessary for the construction of these organs and tissues.
Contrary to Darwinism or "neo-Darwinism" species do not gradually evolve into other species but stay basically the same from the moment of their first appearance to their extinction, though admittedly they may become more variable. However, "variability" is not evolution.
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, humans, the sea anemone, sea urchin, 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). Thus the same genes can be traced to the representatives of the first species to appear on Earth: single celled Prokaryotes.
Given that modern and ancient archae and bacteria are of equal genetic complexity (Snell et al., 2002; Makarova et al., 2007), the presence of these core genes in prokaryotes indicates these genes were most likely inherited from single celled creatures who first arrived on this planet over 4.2 billion years ago. These genes were likely donated by archae and bacteria to single celled eurkaryotes and then 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. However, these genes did not randomly evolve 4 billion years ago. They were also inherited from prokarotes and viruses whose ancestry leads to other planets (Joseph 2009b,c; Joseph and Schild 2010a,b).
Once on Earth and following the transfer of these genes to single celled eukaryotes, 4 billion years ago, these genes and the entire genome were repeatedly duplicated and activated or silenced by a variety of environmental agents, and were repeatedly dispersed among the common ancestors for numerous species and passed down vertically through subsequent species and numerous diverging common ancestors. Many of these silent genes, such as those coding for the brain, body, visual system and heart, were finally activated only after the environment had been significantly modified 100 million years after Trichoplax evolved, i.e. 540 mya. These major alterations in the environment included the buildup of silica, iron, oxygen, and especially calcium, all of which acted on gene selection thus giving rise to brains, bones, and hearts in multiple species whose common ancestors diverged over 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. They inherited these genes from common ancestors who in turn inherited these genes from species whose own ancestry leads to other worlds; genes which were acquired by prokaryotes and viruses from extra-terrestrial eukaryotes through horizontal gene transfer, exactly as takes place on this planet.
The "lower metazons" Trichoplax (placozoans) and 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). The so-called "lower" metazoans (including Placozoa, corals, and jellyfish) also evolved in parallel to "higher" animals (all other metazoans, from flatworms to chordates to humans). However, Trichoplax (placozoans) are in a separate lineage from all other metazoans (starfish, bivalves, anthropoids, crustaceans and chordates) including Echinodermata. And yet despite all these diverging and parallel ancestries, 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 which were then passed down and inherited in parallel by these divergent species of metazoan. These genes were dispersed to diverging species and remained in a state of stasis until activated by alterations in the environment which triggered 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, structure, synteny and linkage in relation to other ancient species, as well as the human genome and in fact has a significant concentration of orthologues on one or more human chromosomes (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, and many were inserted into the eukaryotic genome by viruses.
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, bacteria (Martin and Koonin 2006) and viruses.
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 from species who were among the first to take root on the surface of this planet. However, whereas these genes silent and suppressed when Trichoplax evolved they subsequently came to be activated in humans and other vetebrates.
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 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" As the planet began to freeze, and continuing into the Ediacaran era (i.e. 635 to 541 million years ago) multicellular animals rapidly evolved and diversified in explosive bursts of speciation (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 (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 the evolution of metazoans with a nervous system which was encased in and protected by a hard inner shell of bony-structures.
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 a mechanical support for an outer layer of cells that covered and enclosed the body, and protected interior organs from environmental challenges and provided a stable enclosure which could support the evolution of large organs and internal structures, allowing these tissues and the body to grow and diversify.
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 provided numerous genes to the eukaryotic gene pool, as well as substances, such as calcium, which promote adhesion and multicelluarlity. Cyanobacteria also donated 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). The divergence of sponges from other metazoans is followed by the evolution of Ctenophora, Cnidaria and placozoan Trichoplax adhaerens (Wainright et al., 1993).
There is some evidence that Choanoflagellates may be simplified sponge-derived metazoan (reviewed by Maldonado, 2004). However, species-rich phylogenetic analyses have demonstrated that choanoflagellates are not derived from metazoans, but are a distinct lineage that evolved before the sponge and before the origin and diversification of metazoans (Lavrov et al., 2005; Rokas et al., 2005). Hence, a proto-choanoflagellate (which are related genetically to cyanobacteria) 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). Therefore, cyanobacteria may be related to metazoans.
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 the 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). This is significant as Cyanobacteria provided numerous genes to choanoflagellates (and the eukaryotic gene pool), including regulatory genes and those which promote adhesion and multicelluarlity. Cyanobacteria also secrete calcium, which promote adhesion and multicelluarlity and which act on those genes donated by cyanobacteria to eukaryotes.
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 and for organisms to become multi-cellular.
It is these adhesion 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 even though they possess the genes which contribute to embryo development.
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 including cyanobacteria.
These genes underwent repeated duplicative events, and were passed down vertically to subsequent species, including Choanoflagellate and Trichoplax and were then activated in subsequent species in during a time period in which the environment was enriched with oxygen, silica, and calcium carbonate.
These evolutionary developments took place during and these genes were expressed following the onset of the Ediacaran age and 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.
Hence, a complex genetic-environmental feedback system involving genes donated by prokaryotes and the activities of prokaryotes, resulted in the activation of these genes, thereby creating brains and bones.
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 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 precursor proteins for collagen can be found 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 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). It can be surmised that the link to choanoflagellates extends to Cyanobacteria.
Over the course of evolutionary history, 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." However, these external substances, i.e. calcium, were secreted by Cyanobacteria, which are also the likely original source of these genes.
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 when global warming melted the calcium-mats produced by Cyanobacteria.
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 Sturtian glaciation which flooded the oceans with silicate (Exposito et al., 2002). This may have been followed by additional genome duplicative events during and after the onset of the Edicaran age, when massive amounts of calcium were released into the environment; thus leading to gene activation and 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 results 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. Again, much of this calcium was produced by Cyanobacteria which donated many of the genes which high levels of calcium would later activate. As calcium levels increased it induces comformational changes in phosphoproteins which sould 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 which was produced by Cyanobacteria which donated many of the necessary genes for forming skeletal tissue.
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 two 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 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 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 and these extra-terrestrial microbes and viruses may have transferred a variety of genes into the denizens of this world thereby triggering speciation and the evolution of new species. In fact, 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 pouring 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 cyanobacteria 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 and plays a universal role as messenger and regulator of protein activities (Kazmierczak and Kempe 2004; Williams 2007). 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). 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). Therefore, until sufficient quantities of calcium had been biologically produced and then liberated, embryos and bones were an impossibility.
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, muscular, and nervous system. Calcium binding proteins in fact regulate smooth muscle contraction and motion in skeletal muscle (Kazmierczak and Kempe 2004), and Cao2+ sensors are located 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 the evolution and regulation of skeletal muscle movement and contraction, and thus the regulation of cell, muscle, and skeletal functioning in metazons (Kazmierczak and Kempe 2004). Once sufficient quantities had been produced, genes were activated and complex species with muscles, bones (and brains) evolved.
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 contributed, for the first 4 million years after this planet became Earth, most of the calcium on this planet was produced biologically by cyanobacteria, and then later by photosynthesizing eukaryotes including corals and possibly Ediacarans.
Photosynthesizing Cyanobacteria were among the first to take root on this planet. They contributed to the eukaryotic 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).
This feedback system has been in effect since cyanobacteria took root on this planet and began using photosynthesis to obtain energy. Moreover, this feedback system also likely involved viral gene exchange during episodes of green house global warming or global freezing, despite reduced sunlight. Viruses act as store-houses for genes which code for photosynthesis (Lindell et al., 2004; Sullivan et al., 2005, 2006) and they transfer these genes to cynobacteria during periods of reduced light, and which augment photosynthetic activity (Sullivan et al., 2006). Thus, 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).
However, by the onset of the third "snow ball Earth" photosynthetic activity was augmented by cyanobacteria which had formed symbiotic relations with eukaryotes (Cavalier-Smith 1993), and various members of the Ediacarans biota (Seilacher et al. 2003). Specifically, because many species of eukaryote had grown in size due to the evolution of a silica skeleton, made possible by prokaryotic silica production, cyanobacteria were able to invade and form a symbiotic relationship with these species, contributing additional genes to the eukaryotic genome in the process. Thus the larger Ediacarans possibly employed photosynthetic symbionts, and 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).
As calcium carbonate also produced as a byproduct of photosynthesis, calcium levels began to rapidly increase during the third "snow ball Earth."
Cyanobacteria also proliferated during and following the end of the Gaskiers glaciation. There is a large fossilized assemblage of cyanobacteria and phytoplankton dated to around 580 mya (Moczydłowska 2008). These include benthic autotrophic and aerobic cyanobacteria which lived in functionally complex communities of mat-builders, as well as photosynthesizing planktic eukaryotes (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). However, as noted, viruses will transfer photosynthesizing genes into cyanobacteria during times of stress, insufficient nutrients, and diminished sunlight (Lindell et al., 2004; Sullivan et al., 2005, 2006; Williams et al., 2008).
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, were able to engage in photosynthesis and calcium production. 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 was the creation and buildup of massive amounts of calcium carbonate which had been biologically produced for a specific purpose which paralleled significantly increased oxygenation of the ocean and atmosphere and dramatic alterations in temperature. 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) and following the global meltdown at the end of the Gaskiers glaciation.
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 eukaryotic 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.
ENVIRONMENTAL ACTIVATION OF SILENT GENES
Archae, bacteria, and viruses contributed to the eukaryotic genome, the core genes which made the evolution of increasingly complex species possible. However, many of these genes were inhibited or suppressed by proteins, hemachromatin, and via methylation and the actions of introns and regulatory genes which were inserted by viruses and prokaryotes. These included silent genes coding for eyes, bones, muscles, and brains.
Genes passed down from ancestral species can be expressed by varying the environment and through other stresses including fluctuations in temperature, oxygen levels, and diet (e.g., de Jong & Scharloo, 1976; Dykhuizen & Hart, 1980; Gibson & Hogness, 1996; Polaczyk et al., 1998; Rutherford & Lindquist, 1998; Wade et al., 1997).
Genes often interact in networks. Change the environment and gene expression patterns may be altered, giving rise to slight or major differences in the products produced and allowing for the expression of pre-determined traits (Rutherford & Lindquist, 1998). As demonstrated by experiments performed by Rutherford and Lindquist, (1998) when these suppressive protein-buffering actions are altered by environmental change, including temperature fluctuations, "variants are expressed and selection can lead to the continued expression of these traits, even when" the actions of these repressor proteins are restored.
This takes place when certain environmental stimuli act on buffering proteins, removing these proteins and the suppressive effects of hemachromatin, methylation, and specific regulatory genes including introns and transposons, thus enabling the expression of silent genes (Waterland and Jirtle, 2003; Wolff et al., 1998).
Hsp90 is part of a vast regulatory network which suppresses gene expression. "At normal temperatures it binds to a specific set of proteins, most of which regulate cellular proliferation and cell development" (Cossins, 1998). At significantly lower or higher temperatures Hsp90 ceases to bind to these proteins thus allowing for gene expression (Rutherford and Lindquist 1998). Thus they can also act for or against genetic variation and can trigger or prevent the expression of silent characteristics (Cossins, 1998; Rutherford and Lindquist 1998).
In response to signifcantly lowered or increased temperatures, Hsp90 levels are reduced and no longer act as effective buffers against the expression of signal-transduction proteins which leads to the expression of genes that had been inhibited (Rutherford and Lindquist 1998). This allows for the expression of hidden genetic variation leading to new developmental and evolutionary patterns. As demonstrated by, Rutherford and Lindquist (1998, p. 341) Hsp90 acts as an "explicit molecular mechanism that assists the process of evolutionary change in response to the environment" and it accomplishes this through the "conditional release of stores of hidden morphological variation.... perhaps allowing for the rapid morphological radiations that are found in the fossil record."
This has important implications for evolution as Earth has repeatedly undergone global ice ages followed or preceded by periods of high temperatures secondary to greenhouse warming. As lowered or raised temperatures can eliminate the suppressive influences of chaperones such as Hsp90, dramatic climate change, such as global glaciation or global warming, could affect a wide variety of signal-transduction proteins that are stabilized by Hsp90, thus inducing gene expression and the expression of precoded traits thus inducing the next stage of evolutionary metamorphosis; with animals and plants evolving into a world which has been biologically prepared for them.
The Hsp90 complex also regulate nuclear receptors (Arbeitman and Hogness 2000; Feder and Hofmann 1999; Mayer and Bukau 1999; Picard 2002; Rutherford 2003; Pratt and Toft 2003). These include receptors for retinoic acid, thyroid hormone, signal-transduction proteins, ligand-dependent transcription factors, tyrosine/serine/threonine kinases, and steroids. When steroid receptors were finally expressed, distinct sex differences and males vs females emerged.
Most nuclear receptors appear to be restricted to metazoans (Laudet 1997; Escriva et al. 2000; Thornton 2001; Baker 2005). However, the metamorphosis of the first metazoans did not take place until during or after the 3rd world wide glaciation.
Earth has undergone at least three major world-wide glaciations (Hoffman et al. 1998; Hyde et al., 2000; Runnegar 2000; Lubick 2002) including the Marinoan/Gaskiers. Each was preceded and followed by periods of global warming and the diversification and evolution of new species. However, the last glaciation which began around 635 mya is also associated with the evolution of the the first primitive metazoan, i.e. a "living fossil" known as Trichoplax, around 630 mya (Srivastava, et al., 2008). Trichoplax, however, was not a true bilateral animal and lacked muscle, heart, eyes or brain. Thus, although its genome likely possessed all the genes that code for these structures, including nuclear receptors (Srivastava, et al., 2008), the preponderance of evidence suggests they had not been expressed.
By the end of the Gaskiers glaciation, around 580 mya, what may be the first bilateral-symmetrical metazoan had evolved; an Echinodermata, Arkarua adami (Gehling 1987). In fact, a wide range of increasing complex species appeared following the Gaskiers glaciation and ensuing warming cycle, leading to an explosive burst of evolutionary change and diversification. By 540 mya complex animals and chordates equipped with bilateral bodies, eyes, and brains had evolved (Chen et al., 1995, 1999; 2003; Shu et al., 2001; Siveter et al., 2001). It was during this same time period, between 580 to 540 mya, that the genome duplicated in size (Holland 1994, 1999; Dehal and Boore 2005) and there was an explosive evolutionary burst of complex life forms, including the evolution of every phylum which is in existence today.
Yet another factor was the massive number of bacteria and eukaryotes who evolved and proliferated during the Marinoan/Gaskiers glaciations, and then died out when the climate and global temperature began to increase. The thick layers of dead provided food for the living, and alterations in diet and nutrition directly act on gene expression (Van den Veyver 2002; Waterland and Jirtle, 2003; Wolff et al., 1998).
Diet and foods consumed has played a significant role in evolutionary metamorphosis and gene expression by influencing inhibitory mechanisms such as methalation. For example, it has been demonstrated that nutritional supplementation to the mother can permanently alter gene expression in her offspring by activating or silencing Agouti genes via methylation (Waterland and Jirtle, 2003; Wolff et al., 1998). In one set of experiments pregnant mice that received dietary supplements of vitamin B12, folic acid, choline and betaine, gave birth to babies with brown coats whereas the control group gave birth predominantly to mice with yellow coats (Waterland and Jirtle, 2003). These four nutrients possessed chemicals that donated methyl groups which reduced the expression of a specific gene, Agouti via DNA methylation. Thus, diet altered the color of the coats by acting on gene selection. This effect is referred to as "epigenetic" because it occurs over and above the gene sequence without altering the four-unit genetic code.
Thus, silent and active genes passed down from ancestral species can be expressed or inhibited by varying the environment and through other stresses including fluctuations in temperature, oxygen levels, and diet and nutrition (e.g., de Jong & Scharloo, 1976; Dykhuizen & Hart, 1980; Gibson & Hogness, 1996; Polaczyk et al., 1998; Rutherford & Lindquist, 1998; Wade et al., 1997).
Change the environment, and gene expression patterns may also be altered, giving rise to slight or major differences in the products produced. Thus, the abundance of food resources, and increases in the levels of oxygen, calcium, and other elements and gasses significantly impacted gene selection beginning around 580 mya such by 540 mya male and female animals with bodies, bones, brains and eyes, had evolved.
THE TANGLED ANCESTRAL WEB: 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. 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, the calcium-based skeleton evolved after the silica skeleton (Brasier et al., 1997).
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 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 the later evolving 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). These genes were then passed down, in silent form, to later emerging species at which point they were expressed. In fact, Sakarya et al. (2007) upon examining the phylogenies for 36 gene families involved in the post-synaptic neural complex in the genomes of two basal metazoans, discovered a "large number of vertebrate post-synaptic gene homologs in the sponge" as well as in humans. 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 brain function and nerve cell conduction. The synapse serves as a link between two neurons, and makes possible signalling, and communication and enables neural cells to transmit information to other neurons. Therefore, information received in one area of the body can be transmitted to yet other areas. Synaptic communication is rapid and efficient, and enables the coordination of purposeful and reflexive body movement in response to the reception of sensory impressions. Animals can react instantly. With the evolution of the skeletal system, the body greatly increased in size. Increasing body size required a network of nerves to coordinate body movement. Calcium, which triggered the genes and became the substance that made bones possible, is also linked to the evolution and functioning of the brain, including the synapse.
The synapse is the basic building block for the nerve cells, the nerve net, the nervous system, and the brain. The evolution of these structures was triggered by the same substance which was biologically produced, and which is responsible for the skeletal system. These were not random acts of chance. They were under biological control, with genes acting on the environment, which acts on gene selection, thereby coordinating the evolution of myriad species perfectly adapted for a world which has been prepared for them.
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, CORALS & THE SKELETAL NERVOUS SYSTEM
Cnidarians inherited ancestral genes and homologues (Technau et al. 2005) 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). These genes were activated in the Cnidarian genome. 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 which controlled by regulatory genes homologous to metazoans (Miljkovic-Licina et al. 2004). Thus, they possess sensory and motor neurons, which enable them to immediately respond to sensory signals and these same genes were inherited by other animals.
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). 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). Therefore, one source for these genes includes those sponges who reacted to increased calcium levels by building a calcium skeletal network. These genes, however, were inherited from yet other ancestral species.
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. Thus, they may have inherited these genes from Trichoplax who in turn inherited these genes from ancestral species. 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 from the period after 580 mya, 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 the sea anemone; frond-like organisms which resemble or have affinities witch sea pens or colonial soft octocorals (Briggs et al., 1994); and corals which built coral-bearing reefs 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 possessed 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).
Corals are Cnidarians and may be the first species to have evolved a skeleton and nervous system. The coevolution of the skeletal system and the nervous system in this species is mutually linked to the calcium produced initially by cyanobacteria and liberated during the warming period following the Gaskiers glaciation. Corals, however, also secrete calcium.
Corals are sessile long-living colonial organisms, typically found in tropical well-illuminated oceans, where they are the main contributors to the creation of reefs. 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 to one another by shared skeletons. Thus corals trigger skeletal formation in other corals.
Corals (Cnidarians) secrete external skeletons made of 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, bone differentiation takes place without the addition of any bone-promoting factors to the growth medium.
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 secreted by corals also promote nerve cell development. 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).
Therefore, when cyanobacterial mats decomposed after temperatures rose following the Gaskiers glaciation, massive amounts of calcium were liberated triggering the evolution of the skeleton and nerve tissue, which may have first appeared in corals. Corals the began secreting massive amounts of calcium into the ocean, thereby triggering gene expression in innumerable species which quite suddenly evolved skeletons and brains.
For example, 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); the hippocampus being involved in memory. Rapid growth of nerve cell axons and dendrites are also triggered coupled with the development of pre and post synaptic membranes and synaptic connections with presynaptic sites.
Corals
Hence, the skeletal system of the calcium secreting corals (Cnidarians) not only builds bones but the tissues of the brain including the synapse. Therefore, corals which lived and evolved during the Ediacaran age, stimulated neural development, as well as skeletal and shell formation in later appearing species. Thus, one step leads to the next, and once calcium secreting corals evolved, complex and increasingly intelligent animals equipped with skeletons and brains followed.
MULTICELLULAR METAZOAN METAMORPHOSIS
There is no evidence suggestive of eyes, hearts, brains, or a nervous system in any species prior to 575 mya. Further prior to this period, there is no evidence for sensory-guided coordinated behaviors that might be mediated by a nervous system or visual-chemosensory system. The first evidence of complex bilaterian forms began to appear around 555 MYA (Martin et al., 2000), and it is only with bilaterality that a nervous system becomes a necessity so as to coordinate the movement of the bilateral body in response to sensory signals and environmental challenges. Since, evidence of horizontal burrowing does not appear until after 575 Mya, whereas vertical burrowing appears after 543 Mya (Erwin and Davidson 2002) and as there is no evidence of bilaterality from earlier time periods, it can be deduced that a simple nervous system did not evolve until after the end of the glacial period 580 mya. In fact, the first evidence of animals with a possible nervous system, Kimberella, does not appear in the fossil record until 555 MYA (Martin et al., 2000). Kimberella was bilateral and probably possessed as a visual-chemosensory system and a ring of neurons which were linked together into a thin nerve network, which would have made them capable of coordinated behaviors guided by the analysis of sensory and perceptual information.
Thus, it took 4 billion years to genetically alter the biosphere, such that between 580 and 540 mya a complex variety of bilaterian forms began to appear (Bowring et al., 2003; Grotzinger et al., 1995; Martin et al., 2000), one of the first of which was a well-developed animal, Kimberella, whose fossils have been discovered in rocks located in northern Russia dated to around 555 MYA (Martin et al., 2000). Kimberella possessed as a visual-chemosensory system, and were capable of coordinated behaviors guided by the analysis of sensory and perceptual information.
NATURE HAS A MIND OF HER OWN: PANNOTIA, GONDWANA, AND METAL LIBERATION.
It is obvious that factors other than biology have affected the biosphere. Natural "disasters" such as erupting volcanoes, increased solar activity, meteor strikes and other phenomenon also impact the environment, and these events can also affect gene expression. Around 580 mya 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 in the environment
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).
Moreover, 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, all of 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.
THE GENETIC ENGINEERING OF THE ENVIRONMENT
Between 575 mya to 548 Myr ago the oceans were becoming relatively free of toxins, poisons and acids, and simultaneously oxygenated due melting glaciers, and the actions of the 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 bilateral animals.
As repeatedly stressed, these events were not due to random chance. Nor could they take place on any planet. Certain conditions must be met, beginning with an Earth-like planet orbiting in the "habitable zone" of its sun. Just as embryogenesis begins with a single cell which grows into a fetus then neonate in parallel with biological changes in the womb and the turning on and off of genes, likewise, the evolution of complex creatures also required a step-wise sequence of environmental changes coupled with genes being turned on and off. For example initially Ca2+ and oxygen levels were negligible (Williams 2007). The biosphere had to be gradually altered, and as it changed, many species perished, and other evolved in bursts of speciation. For example, as Na+, Cl− and Ca2+ levels increased, this created a hostile environment for many species of prokaryotes and early eukaryotes. The buildup of transition metal ions, and the reduced levels of C, N, S, Se and Fe2+due to oxidation also posed hazards to these early Earthly life forms, but promoted the evolution of more complex life (Williams & Fraústo da Silva 2006).
Increased availability of Ca2+, Zn2+, Mn2+, Fe2+, Co2+, Ni2+ and Cu+ (Cu2+), and the oxidation of these substances led to the activation of cellular binding-proteins corresponded which acted on gene expression and resulted in the metamorphosis of increasing complex life which could utilize these materials as they became available (Williams 2007). Thus, the genes and their protein products existed first, and were then activated; and this was accomplished, in part, via metalloproteins which were matched and bound to specific DNA sequences (Williams 2007). Even before these metals and substances were released into the environment, eukaryotes already had inherited the genes proteins, and enzymes that could respond to and interact with these materials when they become available. These metal ions form a homeostatic link and thus bind to these proteins thereby inducing gene expression (Dupont et al. 2006; Morgan et al. 2004; Williams & Fraústo da Silva 2006). Again, these genes do not evolve after exposure. Rather, if the genes did not exist prior to exposure, they would could not have been affected. However, they did not exist in all species, but instead were donated from the genomes of viruses and prokaryotes (archae and bacteria) to the eukaryotic genome, thereby insuring that multi-cellular eukaryotes and not single celled species would evolve. Hence, most single cell anaerobes do not possess genes or proteins which respond to copper, dioxygen, or oxygen, which were also at low levels for the first few billion years. Likewise, they possess few proteins which bind to calcium as these genes had been donated to eukaryotes (in silent form) and as 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).
Viruses, archae and bacteria donated core genes to the eukaryotic genome, thus insuring that eukaryotes and not prokaryotes would evolve. Thus, 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). Over billions of years of time, increases in Ca, Zn, Fe, oxygen and other substances triggered gene expression, gene and whole genome duplication, which increased the number of genes that could produce a greater number of Ca, Zn, and Fe proteins, 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, including corals began to secrete calcium during the Ediacaran period. Following the end of the Gaskiers 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 bilateral species with brains, 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. Ca2+ ions have a special affinity for 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, beginning around 640 mya, once silica, calcium, and oxygen levels had increased and a protective (oxygen-initiated) ozone layer was established, creatures expanded in size, diversified, and grew spines, silica skeletal compartments, then silica-collagen 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 bilaterial 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 rapidly evolved, many with the "modern" 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)
EVOLUTION OF THE EYE
Many of the species which evolved during the Cambrian Explosion possessed the basic anatomy common to all subsequent forms of sea life. This included completely modern eyes that quite suddenly evolved seemingly ex nihilo in the absence of intermediate forms. Trilobites, for example, which evolved quite suddenly in the absence of intermediate forms, "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 evolutionary conserved and common 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 the development of vision, is the vitamin-A-related chromophores in the visual pigment, and this is also found in bacteria as well as algae and cyanobacteria (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 sea creatures such as nautilus.
PAX genes were inherited by Trichoplex Placozoa (Srivastava et al., 2008) and the descendants of Arkarua adami, such as Sea urchins (Sodergren et al., 2006, 2007) which are 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.
In addition to sea urchins, other members of Echinodermata include sea stars, sea cucumbers, brittle stars, and crinoids many of which evolved during the Cambrian Explosion. These are all 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). Like Tricoplax, they maintain an extensive repertoire of "silent" genes which code for functions which would not come to be expressed until the evolution of later species. 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. Moreover, PAX genes coding for visual functioning were also expressed in these and numerous other metazoans at the outset of the Cambrian Explosion.
These eye-equipped metazoans 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. The first Chordata (meaning: with a spinal cord) included 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). They also evolved in an explosive evolutionary burst in the absence of intermediate species.
Hence, during the Cambrian epoch there was a visual, skeletal, neural, 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 AFFECT THE ENVIRONMENT WHICH ACTS ON GENE EXPRESSION
Genes were transferred to the eukaryotic genome by archae, bacteria, and viruses, and were passed down, often without expression, through diverging and subsequent species. Prokaryotes also biologically modified the biosphere which triggered gene expression.
As different chemicals, gasses, minerals, and metals were sequentially released, various genes were activated and other silenced, giving rise to increasingly complex eukaryotic species. Climatic change, including and especially cyclic changes in global freezing and global warming also acted on gene expression; however, these climatic alterations were also a product of biological activity. With the onset of global warming and the ending of the Gaskiers glacial period 580 mya, the oceans were flooded with calcium, which triggered the expression of genes which regulate vision, the brain, and skeletal system.
By 540 mya, 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 and regulatory genes 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). 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 (Tomarev 1997). 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 common ancestors which include prokaryotes and viruses (Joseph 2009b,c). 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.
CONCLUSIONS
Life on Earth came from other planets. Earth may have harbored life before it became Earth and a member of this solar system. Earth may be a rogue planet, ejected from its parent solar system with it star began to lose mass and become a Red Giant (Joseph 2009a,b; Joseph and Schild 2010a,b).
The first life forms to take root on the surface of the new Earth, included a variety of archae and bacteria including Cyanobacteria. They were accompanied by viruses and their vast storehouses of genes. It is possible single celled eukaryotes may have also arrived from other planets, perhaps encased in giant asteroids, oceans of water, and planetary debris.
Prokaryotes and viruses, via horizontal gene transfer 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, and can duplicate single genes or the whole genome. Species then evolve.
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.
Living organisms effect the environment and the changing biosphere acts on gene selection, creating an interactive feedback loop which significantly impacts the speed and rate of evolutionary metamorphosis. These biologically engineered environmental influences directly influenced those genetic mechanisms involved in gene silencing, gene duplication, and gene expression, thereby giving rise to traits, functions, organs, and species, which had been precoded into silent genes inherited from ancestral species. 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.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Copyright 2009, 2010, All Rights Reserved