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Journal of Cosmology, 2009, Vol 1, 100-150

THE EVOLUTION OF LIFE FROM OTHER PLANETS
Part 1
The First Earthlings,
ExtraTerrestrial Horizontal Gene Transfer,
Interplanetary Genetic Messengers
and the Genetics of Eukaryogenesis and Mitochondria Metamorphosis

Rhawn Joseph, Ph.D.
Emeritus, Brain Research Laboratory, Northern California


ABSTRACT

What has been described as "evolution" is under genetic regulatory control and is a form of metamorphosis (Evolutionary Metamorphosis), the replication of life forms which long ago evolved on other planets. The genetic endowment of all living creatures can be traced to common ancestors, and these genes were obtained and inherited from creatures which lived on other worlds. These genes were transferred to Earth contained in the genomes of archae, bacteria, algae (cyanobacteria) and viruses. These first Earthlings (archae, bacteria, cyanobacteria, viruses) contained the genes and genetic information for altering the environment, the "evolution" of multicellular eukaryotes, and the metamorphosis of all subsequent species. This genetic inheritance included exons, introns, transposable elements, informational and operational genes, RNA, ribozomes, mitochondria, and the core genetic machinery for translating, expressing, and repeatedly duplicating genes and the entire genome. Once on Earth, 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 and in reaction to viral genes, often in busts of explosive evolutionary change. 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 bilateral bodies, eyes, and brains--features which were encoded into genes inherited from ancestors whose genetic ancestry leads to other worlds. This inherited extraterrestrial genetic machinery coordinates gene duplication and expression, speciation, and evolutionary innovation, thereby giving rise to a genetically regulated progression leading from simple to complex creatures including woman and man.



1. EARTH IS NOT THE CENTER OF THE BIOLOGICAL UNIVERSE

Panspermia and abiogenesis are two opposing, but not mutually exclusive scientific views about the origin of life. Where they differ is in the explanation of how life first appeared and then evolved on Earth.

The abiogenesis hypothesis posits that life on Earth came from non-life, and was created perhaps in a deep sea thermal vent where various chemicals were mixed together and heated (REF), or in an "organic soup" following the buildup of organic sludge which through a serious of fortuitous accidents, achieved life (Menor-Salván, 2009; Sidharth, 2009). Central to the belief in an Earthly abiogenesis is the religious, preCopernican notion that Earth is the center of the biological universe and is somehow special and unique in its ability to generate life from non-life.

"Let the earth bring forth all kinds of living creatures: cattle, creeping things, and wild animals of all kinds. And so it happened: And the earth brought forth grass, and herb... and the tree yielding fruit..." Genesis 1.

Panspermia is based on the fact that only life produces life. Therefore life on Earth also came from life which was deposited on this planet encased in meteors, asteroids, and cometary debris (Arrhenius 2009; Hoyle and Wickramasinghe 2000; Joseph 2000a, 2009a; Joseph and Schild 2010a,b; Wickramasinghe et al., 2009). Panspermia is based on the premise that life may be pervasive throughout the cosmos and that different planets, including Earth were seeded with life.

"Seeds" contain precise genetic instructions and do not randomly germinate into a variety of forms as dictated by chance, Darwinian principles, or "natural selection." What will grow is under genetic regulatory control. Likewise, the "seeds of life" which fell upon Earth, also contained the genetic instructions for the life forms which would eventually take root on this planet (Joseph 2000a, 2009b).

Just as an apple seed contains the genetic instructions for growing an apple tree, the "genetic seeds of life" which rained down upon Earth, contained the genetic instructions for the tree of life, and for every life form which has evolved on this planet; a view completely contrary to Darwinism and an Earth-based abiogenesis.

Darwinism and the belief in an Earthly-abiogenesis are intrinsically linked. The Darwinian-abiogenesis consensus is that an accident of chance on this planet resulted in the creation of a single life form and this is how life on Earth began and evolved: "all life on Earth, from bacteria to sequoia trees to humans, evolved from a single ancestral cell" (Eighth Conference on the Origins of Life, Berkeley, California, 1984).

The Darwinian-abiogenic hypothesis is that all the branches and twigs of the tree of life trace their roots to a single organism that emerged by a miracle of chance from the mixing of this organic soup which formed only on Earth. Through Darwinian mechanisms of natural selection, this chance event, where life emerged from non-life, gave rise to every creature on this planet including humans; a story reminiscent of the Biblical story of Genesis, where life emerges from Earth and becomes progressively complex culminating in woman and man.

The Darwinian conception of evolution, however, is not supported by genetics or the fossil record. Darwin (1859, 1871), for example, claimed evolution took place by tiny steps, whereas the fossil record indicates long periods of stasis followed by quantum evolutionary leaps (Gould, 2002; Hoyle and Wickramasinghe 1984, 2000). As detailed in this report and elsewhere (Joseph 2009b,c,d), evolution on this planet was not the result of random variations, but could be likened to metamorphosis and embryogenesis which are under precise genetic regulatory control, and where specific genes are activated giving rise to advanced traits and characteristics without need for intermediary forms; and this accounts for the periodic leaps in evolutionary development, coupled with mass extinctions over the course of the history of this planet.

Darwinism is a failed theory and requires that life began on Earth via a random mixture of chemicals--even though all the necessary ingredients were missing (Joseph and Schild 2010a). Thus, the Darwinist vehemently oppose panspermia as it renders Darwinism completely irrelevant. Even so, there is absolutely no evidence to support the Earthly abiogenesis hypothesis, and there is considerable evidence which demonstrates that life could never have begun on Earth (Joseph and Schild 2010a).

Life comes from life is a fact. This means the first living creatures to take root on Earth were produced by other life forms. Therefore, the DNA of these first Earthlings was not randomly created in an Earthly organic soup, but was inherited from life forms whose ancestors lived on other planets (Joseph 2000a, 2009a,b; Joseph and Schild 2010b).

However, as stated, abiogenesis and panspermia are not mutually exclusive. The universe may be infinite and eternal (Joseph 2010a,b), and given infinite time and infinite chance combinations, it can be predicted that life may have achieved life, infinite time and in infinite locations. However, life need have begun only once, perhaps in a nebular cloud (Joseph and Schild 2010ab), and then, via mechanisms of panspermia, could have spread throughout the cosmos and this galaxy, and eventually arrived on Earth.

2. EXTREME ENVIRONMENTS AND SPACE JOURNEYING MICROBES

Billions of years before Earth or our solar system were formed, space-journeying viruses and extraterrestrial microbes were deposited on planet after planet and continually exchanged DNA with species living on other worlds (Joseph and Schild 2010b). The sharing and acquisition of DNA was accomplished through horizontal gene exchange, exactly as takes place on Earth (Aravind et al, 1998; de Koning et al., 2000; Gogarten and Townsend 2005; Gogarten et al., 2002; Hotopp et al., 2007; Koonin 2009; Martin et., al., 2002; Nelson et al., 1999; Nikoh et al., 2008; Zambryski et al 1989). Thus, viruses and extraterrestrial microbes obtained copies of essential genes from the genomes of whatever simple and advanced life forms they encountered. Therefore, innumerable extraterrestrial microbial species developed vast genetic libraries, comprised of DNA from innumerable species from innumerable planets. And these genetic libraries came to be stored in viral packets of RNA and DNA (Joseph and Schild 2010b). The descendants of these microbes, accompanied by viruses and their vast depositories of genes, eventually fell to Earth.

Microbes are perfectly adapted for journeying through space (Burchell et al. 2001, 2004; Horneck et al. 1994, 2001a,b, 2002; Mastrapaa et al. 2001; Nicholson et al. 2000); abilities they inherited and did not randomly evolve. They can easily survive a violent hypervelocity impact and extreme acceleration and ejection from the planetary surface into space including extreme shock pressures of 100 GPa; the frigid temperatures and vacuum of an interstellar environment; the UV rays, cosmic rays, gamma rays, and ionizing radiation they would encounter; and the landing onto the surface of a planet (Burchell et al. 2001, 2004; Horneck et al. 2001a.b, 1994; Mastrapaa et al. 2001; Mitchell and Ellis 1971; Nicholson et al. 2000). Moreover, they can form spores and awaken after hundred of millions of years have passed (Dombrowski 1963; Vreeland et al. 2000).

Spores

The bacterial genome contains genes which enable microbes to immediately adapt to toxic environments (Jaffe et al. 1985; Gerdes et al. 1986; Hiraga et al. 1986; Hayes 2003), enabling them to survive in otherwise deadly habitats (Delgado-Iribarren et al. 1987; Herrero et al. 2008; Martinez & Perez-Diaz 1990). Therefore, these prokaryotes can quickly adapt almost regardless of planet, and which explains why these extremeophiles are able to proliferate and flourish in almost every conceivable environment, be it pools of radioactive waste, subzero temperatures, boiling hot springs, miles beneath Earth or at the bottom of the sea (Boone et al. 1995; Gilinchinsky 2002a,b; Nicholson et al. 2000; Setter 2002).

Archae hyperthermophiles.

Likewise, simple eukaryotes including lichens, fungi and algae can survive exposure to massive UV and cosmic radiation and the vacuum of space (Sancho et al. 2005). Many of these species, including bacteria can rebuild their genomes even if shattered by radiation (Lovett 2006; Scheifele and Boeke 2008).

As is evident in our own solar system, and the study of extrasolar worlds, most planets and moons have environments so completely different and unlike Earth that most Earthly-eukaryotes would be unable to survive. However, the same is not true of microbes, archae and extremophiles in particular, which are able to thrive almost regardless of conditions, including those never before encountered on Earth. It is the extraterrestrial genetic inheritance of these microbes which makes survival within extreme enivironments possible and this is because the ancestors of these microbes obtained the necessary genes from creatures which had thrived under the harsh, toxic, adverse and poisonous conditions of other planets and those of nebular clouds and cosmic debris.

For example, prior to the 1930s, poisonous pools of radioactive waste did not exist on Earth, and yet, in 1958, physicists discovered clouds of bacteria, ranging from two million bacteria per cm3 and over 1 billion per quart, thriving with pools of radioactive waste, directly exposed to radiation levels millions of times greater than could have ever before been experienced on this planet (Nasim and James, 1978).

Many species of microbe can withstand X-rays and atomic radiation, and are radiation resistant. These include Deinococcus radiodurans, D. proteolyticus, D. radiopugnans, D. radiophilus, D. grandis, D. indicus, D. frigens, D. saxicola, D. marmola, D. geothermalis, D. murrayi.

The genes providing this resistance and which make it possible to thrive in toxic environments did not randomly evolve. These genes were inherited and made it possible for these and other microbes to survive if they are exposed to poisonous, and radioactive environments similar to those experienced on other planets or while journeying through space.

Consider the relatively recent invention of antibiotics. Atibiotic resistance genes are maintained within the genomes of various bacteria (Moritz & Hergenrother 2007; Perichon et al. 2008; Sletvold et al. 2008), and these genes enable them to survive exposure even before they are exposed to these substances (Jaffe et al. 1985; Gerdes et al. 1986; Hiraga et al. 1986; Hayes 2003). Bacteria recovered from remote, isolated regions of the world, and which have never been exposed to antibiotics carry antibiotic resistant genes (Grenet et al. 2004; Bartoloni et al. 2009; (Gilliver et al. 1999; Livermore et al. 2001). These genes did not suddenly mutate after exposure, they were inherited and existed prior to the invention of antibiotics, drugs, and other toxins.

Various species of bacteria have large genomes which enables them to maintain an extensive genetic library of inherited genes, and these genes, when activated in response to specific environmental triggers, allows them to colonize different environments (Cases et al. 2003), including those which are radioactive, poisonous, or toxic. In fact, these genes allow microbes not just to flourish, but to secrete specific biodegradative enzymes which target toxins and poisons, and even newly invented antibiotics, and use them as a food resource (Dantas et al. 2008). It is this genetic library, obtained from ancestral extraterrestrial species, which provides these microbes with the ability to live in almost any environment, and to colonize toxic habitats (Cases et al. 2003; Matilla et al. 2007).

If we accept the basic premise of "natural selection" then the existence, inheritance, and preservation of these genes indicates exposure and adaption prior to exposure on Earth.

Since these genes existed prior to exposure on Earth, then this means the ancestors of these species were exposed to these substances and environments prior to arriving on Earth, i.e. an extraterrestrial source. Thus due to the inheritance of these genes (Stokes & Hall 1989; Mazel 2006) a wide range of microbes are able to flourish in almost any toxic habitat (Delgado-Iribarren et al. 1987; Martinez & Perez-Diaz 1990; Herrero et al. 2008) such as might be encountered on other worlds.

Therefore, microbial creatures, and their DNA, are perfectly adapted for traveling from planet to planet and from solar system to solar system, and have evolved the ability to survive in almost any environment, and this is how life on Earth began.

3. GENES ARE INHERITED

As detailed in the present article and elsewhere (Joseph 2000a, 2009b), the genetic "seeds of life" which fell upon Earth, began digesting the planet and released various gasses and substances as waste products such as oxygen, which changed the atmosphere and environment. The changing environment, in concert with other inherited genetic mechanisms, acted on gene selection, silencing, activating, duplicating, and altering the genome, thereby releasing inherited genetic instructions which coded for specific functions, features, appendages, organs, and body parts, including bilateral bodies, bones and brains. Over hundreds of millions then billions of years, a variety of species evolved into a world which had been genetically prepared for them, and then these species also acted on and changed the environment, which acted on gene selection (Joseph 2000a, 2009b).

The preponderance of evidence demonstrates conclusively that the genes responsible for these evolutionary innovations did not randomly evolve, they were inherited. For example, ancient species including the sponge and "placozoa" (Trichoplax) which first appeared around 635 million years ago, have no brain, no neurons, and no nervous system, yet their genomes contain the silent genes necessary for creating neurons, neurotransmitters, and brains (Srivastava et al., 2008). These brain-producing genes existed in unrelated brainless species and were then passed down for a hundred million years through subsequent generations and species and then became activated giving rise to the nervous system and brain at the onset of the Cambrian explosion 540 mya.

How did different brainless species who diverged from a common ancestor anywhere from 650 million years ago to over 1 billion years ago, somehow "evolve" in parallel, the same genes responsible for the nervous system? Darwinian apologists claim this is just nature arriving, by chance, at the same solution. A solution to what? These genes were inherited from ancestral species which never evolved a nervous system. This can only mean that these genes were acquired from extra-terrestrial species, with brains, which long ago lived on other planets, and which were then stored (in silent form) in the genomes of microbes, viruses, and eukaryotes until activated by changing environmental conditions on this planet.

Then there is the SEP gene which is responsible for producing petals in flowering plants. The SEP gene was inherited from ancient, leafless, nonflowering plants, and may likely be derived from genes contributed by cyanobacteria. However, this silent gene can be activated and will produce flowers in non-flowering plants (Mandel and Yanofsky 1995; Pelaz et al., 2000, 2001).

These are numerous examples of identical genes coding for advanced traits appearing in diverse, unrelated ancestral species who lack these characteristics and never develop these physical features, and who instead pass on these "silent" genes to subsequent species. It is only when the environment has been sufficiently altered, and following fluctuations in temperature, oxygen levels, and diet that these "silent genes" come to be activated (e.g., de Jong & Scharloo, 1976; Dykhuizen & Hart, 1980; Gibson & Hogness, 1996; Polaczyk et al., 1998; Rutherford & Lindquist, 1998; Wade et al., 1997). It has in fact been experimentally demonstrated "that populations contain a surprising amount of unexpressed genetic variation that is capable of affecting certain typically invariant traits" and that changes in environmental conditions "can uncover this previously silent variation" (Rutherford & Lindquist, 1998 p. 341). That is, these traits and these genes exist prior to their expression and they are activated by environmental change. However, the changes in the environment are not random, but are under genetic control. That is, the environment is altered biologically, and the changed environment which acts on gene selection (Joseph 2009d).

It is precisely because genes coding for advanced traits are inherited, that once the environment has been sufficiently biologically engineered (through the secretion of oxygen, calcium and other gasses and substances), and in response to the activity of regulatory genes, that new traits, and new species suddenly emerge, whereas others become extinct. Therefore, after long periods of stasis there have been periods of explosive evolutionary innovation, in the absence of intermediary forms, with many species becoming extinct, and yet others emerging in their place into a world which had been genetically prepared for them (Joseph 2009b).

Almost all scientists agree that the genetic ancestry of every creature on this planet can be traced backwards in time to the first creatures on Earth. Further, it is recognized that biological activity has greatly altered this planet, its climates, atmosphere, and oceans, making Earth hospitable to and contributing to the evolution of complex life forms. This means that the genetic information contained in the genomes of the first Earthlings and their descendants, possessed the genetic instructions for genetically engineering and altering the environment, and for the creation of every living thing which has walked, crawled, swam, or slithered upon Earth (Joseph 2000a, 2009b).

Although life on Earth is probably just a small sample of life's evolutionary possibilities, the preponderance of evidence indicates that evolution is under genetic regulatory control, a function of genes acting on the environment and the environment acting on gene selection (Joseph 2000a, 2009b). These complex gene-environmental interactions, including genes acting on genes, results in the release and expression of genetic information which had been inherited or obtained from creatures whose ancestry leads to other, more ancient worlds.

Evolution is not random. Evolution is metamorphosis; the replication of creatures which long ago lived on other planets.

4. HORIZONTAL GENE TRANSFER

As first proposed by Joseph (2000), long before Earth was formed, extraterrestrial viruses and microbes had obtained copies of genes from simple and complex creatures living on other worlds. Over billions of years of time, as their descendants were cast from planet to planet and solar system to solar system, microbes and viruses increased their store of genetic information which was shared with or obtained from yet other extraterrestrial creatures living on a variety of planets and under all manner of environmental conditions. Eventually these genetic libraries came to include the instructions for manufacturing a variety of proteins, tissues, and organs, and for biologically engineering and altering newly formed planets thus making possible the metamorphosis of innumerable species and increasingly complex life forms.

Bacteria, archae, and viruses serve as intergalactic genetic messengers and are ideally suited for acquiring and making copies of genes, transferring these genes to other species, as well as accepting foreign genes, and then later donating and transferring these genes, including their own genes, to yet other organisms (Forterre 2006; Hotopp et al., 2007; Iyer et al., 2006; Koonin 2009; Martin et., al., 2002; Nikoh et al., 2008) --for example, via plasmid exchange (Brock et al., 1994; Strachan & Read, 1996; Syvanen et al., 2002).

Genomic analysis has also demonstrated that genes are commonly shared between bacteria and archaea (Aravind et al, 1998; Nelson et al., 1999; Koonin 2009) and between prokaryotes and eukaryotes (Hotopp et al., 2007; Nikoh et al., 2008; Martin et., al., 2002; Zambryski et al 1989). This is accomplished via horizontal gene transfer (HGT). A substantial portion of the prokaryotic (bacteria and archae) genome consists of viral bacteriophages, plasmids, transposable elements, and numerous genes and even large segments of entire chromosomes which have been transferred from species to species via HGT (Frost et., al., 2005; Wollman et al., 1956). Among prokaryotes there are very few orthologous gene which were not obtained via HGT (Gogarten and Townsend 2005; Gogarten et al., 2002). Even introns, ribosomal proteins and RNA polymerase subunits are subject to HGT (Brochier et al., 2000; Iyer et al., 2004).

As summed up by Koonin (2009) "in prokaryotes, the interaction between bacterial and archaeal chromosomes and selfish replicons is so intensive, and the distinction between chromosomes and megaplasmids is blurred to such an extent that chromosomes are, probably, best viewed as ‘islands’ of relative stability in the turbulent ‘sea’ of mobile elements."

HTG also plays a significant role in the acquisition of antibiotic resistance which can be conveyed to a new bacterial host (Davies 1994; Ferrara 2006; Breidenstein et al. 2008). This is made possible via the exchange of plasmids (mini-chromosomes), and DNA which has been expelled into the cytoplasm of the bacterial cell only to exit and then invade another cell belonging to a different host which immediately develops resistance to antibiotics or various toxins and poisons (Bais et al. 2005, 2006; D'Acosta et al. 2006; Hiraga et al. 1986; Hayes 2003; Jaffe et al. 1985; Gerdes et al. 1986; Martinez et al. 2007; Wright 2007). That is, once these genes are activated by direct exposure, copies are generated which exit the genome and which are transferred to the genomes of yet other microbes which then acquire the genes necessary to combat these toxic agents (D'Acosta et al. 2006; Martinez et al. 2007; Wright 2007) even prior to exposure (Pallecchi et al. 2008). Further, these genes interact with yet other genes to provide resistance even to newly invented antibiotics (Breidenstein et al. 2008; Fajardo et al. 2008; Tamae et al. 2008).

Because prokaryotes are able to exchange genes, and as these genes may also be stored in viral genomes, this frees up considerable space within the bacterial and viral genome. Not all microbes and viruses contain the same genetic libraries, due to limitations in genomic capacity. However, what they lack in genomic space they can make up in numbers; innumerable viruses and microbes maintaining different genetic volumes which were acquired and inherited from different extraterrestrial sources, which can continue to be shared with yet other species via HGT.

Prokaryotes such as endosymbiotic bacteria also commonly acquire and transfer genes to and from eukaryotes (Hotopp et al., 2007; Martin et., al., 2002; Nikoh et al., 2008; Zambryski et al 1989). Given that the human body, human orifices, and the human gut is infested with bacteria, it should be no surprise that the human genome contains thousands of genes which can be traced to prokaryotes and viruses. In fact the human gut is a ‘hot spot’ for horizontal gene transfer (Kurokawa, et al. 2007). Given that over 100 trillion microorganisms live in the human gut, and 100s of trillions more flourish throughout the body and within every orifice (Dethlefsen et al., 2007), it could be said that microbes provided eukaryotes with the necessary genes to evolve humans (as well as plants and other animals), so as to provide microbes with additional environments in which to thrive and flourish. Because bacteria have colonized humans, and due to their close association, this had led to the notion that humans and microbes form one supraorganism consisting of trillions of genes.

Gene transfer takes place not only between the living, but the recently departed. Bacteria decompose, breakdown, incorporate and digest dead and dying plants and animals and their DNA (Beare et al., 1992; Naeem, et al., 2000; Swift et al., 1979). Bacteria are the ultimate eaters of carrion and can directly ingest and incorporate large DNA molecules (Baquero et al. 2008; Doolittle 1998).

Bacteria are in fact continuously exposed to and incorporate genes from throughout the living world (Davies 1994; Martinez 2009). For example, bacterial parasites share their niche with microbial eukaryotes such as parasitic protozoa. Parasitic creatures are the most likely to acquire and transfer genes between species (Hacker and Kaper, 2000; Hotopp et al., 2007; Koonan 2009; Ochman and Moran, 2001; Perna et al., 2001). Thus parasitic eukaryotes will acquire genes from bacterial parasites via horizontal gene transfer. However, those bacteria may have acquired these genes from other bacteria or arachae (de Koning et al., 2000).

Over 30% of the genome in many pathogenic and symbiotic bacteria were obtained via HGT (Hacker and Kaper, 2000, Ochman and Moran, 2001; Perna et al., 2001). However, given that genes are continually exchanged, the exact percentage is probably several times that.

Using Earth as an example, and as there is no reason to believe life is confined to or originated on Earth, it can predicted that horizontal gene exchange was also a common practice on other planets. Hence, when prokarotes arrived on Earth, it can be assumed they arrived with a full compliment of genes acquired from life forms living on other worlds. And accompanying these prokayotes as they and their descendants journeyed from planet to planet: Viruses. 5. VIRUSES

Viruses maintain a large reservoir of excess genes, and viral bacteriophages commonly invade bacteria and transfer genes which improve the functioning of the host (Sullivan et al., 2006; Williamson et al., 2008). Yet others provide genes to eukaryotes (López-Sánchez et al., 2005; Romano et al., 2007), and these genes also confer advantages to the host species and appear to have played a major role in evolutionary transitions. Thus, the eukaryotic genome, including that of humans, not only contains DNA inserted by prokaryotes, but genes inserted by viruses (Conley et al., 1998; López-Sánchez et al., 2005; Romano et al., 2007).

Viruses, like prokaryotes, may serve as intergalactic genetic messengers as they maintain large stores of beneficial genes which they provide to specific hosts (Sullivan et al., 2006; Zeidner et al. 2005). Viral particles and microbial fossils have in fact been discovered in ancient meteors (Pflug 1984), which are older than this solar system, and which may have originated on different planets (Joseph 2009a).

Viruses have been shown to survive simulated extraterrestrial conditions (Fekete et al., 2004; Walker, 1070). For example, in one set of experiments bacteriophage T7 and isolated bacteriophage T7 DNA were exposed to space conditions in the international space station including vacuum and UV radiation and temperatures of 0 °C (Fekete et al., 2005). It was determined that DNA lesions will accumulate but the amount of damage is inversely proportional to the thickness of shielding and layers (Fekete et al., 2005). Further, following simulated space conditions, including prolonged radiation, up to 60% of T7 phages remained active and were able to infect bacterial host cells, and those phages suffering damage were able to fully recover (Fekete et al., 2004). Likewise, wild type filamentous phage M13 retained their nucleic acid integrity and protein structure despite high pressure and even simulated silicification (Hall et al., 2003).

Viruses, including those with double-stranded DNA genomes have also been shown to survive in the most extreme of environments (Romancer et al., 2007; Walker,1970). Viruses have been discovered in extremely acidic hot springs with temperatures up to 93°C, and pH 4.5 (Häring et al., 2005; Rice et al., 2001), within hypersaline water at saturation where they outnumber bacteria 10–100-fold (Porter et al., 2007), and in deserts, soda lakes, deep sea thermal vents, and survive incredible hydrostatic pressures (Romancer et al., 2007).

Viruses are preadapted to surviving in extremely hostile environments, such as those which may be encountered in space or on other planets. Viruses, therefore, are capable of being transferred from world to world. As viruses can transfer genes to a host and receive genes back from the host it can therefore be predicted that viruses likely obtained genes from extraterrestrial life forms via the same genetic mechanisms they employ on Earth. Viruses are the ideal interplanetary genetic messenger.

Giant double-stranded DNA viruses (such as Acanthamoeba polyphaga, Mimivirus), with particle sizes of 0.2 to 0.6 microm, genomes of 300 kbp to 1,200 kbp, and commensurate complex gene pools (Claverie 2005) contain incredible genomic capacity and an extensive gene library which was likely obtained via horizontal gene transfer from a host to the virus. These giant double-stranded DNA viruses, such as Poxviridaem also have double-stranded linear DNA genomes which are larger than most bacteria.

Viruses out-number bacteria by 100 to 1, and serve as vast genetic libraries and sources of genes and DNA, which they can provide to specific hosts and which benefit or improve the functioning of the recipient (Sullivan et al., 2006; Williamson et al., 2008). Viruses serve as genetic storehouses of trillions of genes, which they can transfer to prokarotic and eukaryotic hosts, or to other viruses, thus directly impacting evolution (Sullivan et al., 2006; Zeidner et al. 2005). Moreover, once these viral genes are incorporated into the host genome, they can be transmitted, in "silent" non-acted form, to daughter cells, only to be expressed in response to specific environmental signals (Ackermann et al., 1987; Brussow et al., 2004) .

Thousands of viral genes have been discovered which encode host-specific environmentally significant functions (Williams et al., 2008) such as carbon metabolism during the dark cycle of host cells (Sherman and Pauw, 1976; Sullivan et al., 2005), and a variety of cellular processes such as vitamin B12 biosynthesis (cobS), host stress response (small heat shock proteins), antibiotic resistance (prnA) nitrogen fixation (nifU) and carbon metabolism (Williams et al., 2008). Therefore, viruses may directly participate in nitrogen fixation and the carbon cycle (Evans et al., 2009).

Moreover, viruses have acted as a store-house for genes which code for photosynthesis (Lindell et al., 2004; Sullivan et al., 2005, 2006) including photoadaptation and the conversion of light to energy (Williams et al., 2008). Some of these viruses (e.g., cyanophages) provide cynobacteria with genes which augment the host photosynthetic machinery during periods of stress, insufficient nutrients, or reduced sunlight (Sullivan et al., 2006). When the excess genes are no longer necessary, they are transferred from the bacteria genome back to the virus genome for storage (Lindell et al., 2004; Sullivan et al., 2005, 2006).

Viruses also inject their RNA and DNA into eukaryotic genomes (Conley et al., 1998; López-Sánchez et al., 2005; Romano et al., 2007). In fact 8% of the human genome consists of around 200,000 endogenous retroviruses (IHGSC 2001; Medstrand et al., 2002), and 3 million retro elements (Medstrand et al., 2002), and some of these retroviruses are still active (Conley et al., 1998; Medstrand and Mager, 1998). Further, the genomes of specific endogenous retroviruses were inserted into the primate genome millions of years ago, and then activated or silenced at key points of evolutionary divergence, such as the split between new world and old world monkeys, and hominids and chimpanzees (López-Sánchez et al., 2005; Romano et al., 2007). Therefore, viruses provide prokaryotes and eukaryotes with a variety of genes and this genetic endowment had directly impacted evolution leading to the metamorphosis of humans.

It is not reasonable to assume that these mechanisms randomly evolved. Viruses are not even alive. Further, there is a perfect genetic match between viruses and specific hosts. It is begs the imagination to believe that specific viruses and specific hosts randomly evolved genomes which became a perfect match for gene transfer and insertion. Rather, the evidence demonstrates that these viral agents must have obtained the genes they subsequently insert, from an identical genetic host. Further, as specific viruses only insert their genes after a specific host evolves, this indicates they must have obtained these genes from a host which long ago evolved on another world.

Thus, be it on Earth, within comets, asteroids, or beneath the surface of distant moons and planets, when viruses come in contact with microbes or eukaryotes, and microbes come in contact with other prokaryotes and eukaryotes, genes are and have been exchanged and genes have been stored in the viral and bacterial genome. Therefore, when the first prokaryotes and viruses took root on Earth, they arrived with vast genetic libraries acquired from life forms on other planets.

6. PLASMIDS & FREE DNA

All living cells are believed to contain free-DNA (plasmids) which circulates in the cytoplasm, but which may also be found in the nucleus. Plasmids are also referred to as mini-chromosomes and essentially consists of two ropes of nucleotides which may contain hundreds or even thousands of nucleotide sequences and base pairs (Kado 1998; Sundin 2007; Watson et al. 1992). These packets of free-DNA can also duplicate themselves and multiply, forming hundreds of identical copies which can be inserted into the main chromosome, including the DNA of alien species (Kado 1998).

Plasmids can exit the cell of one species, invade a second species and its genome, attach itself to a row of nucleotides, make or exchange copies, and then jump to yet another position within the helix, and/or exit this cell and transfer these DNA-copies to other hosts (Horsch et al. 1985; Strachan & Read, 1996; Zambryski, et al. 1989).

Plasmids, in many respects, act like viruses, and viruses may in fact be plasmids; i.e. a storage vehicle for genes which is ejected from the prokaryote or eukaryote genome. That is, packets of RNA or DNA, are purposefully expelled, thus freeing up genome space and insuring that copies of these genes are stored in a protective viral package. These viral storage vehicles, in turn contains the mechanisms which would allow for an unlimited number of copies to be made and injected, on an as-needed-basis, back into the genomes of specific prokaryotes or eukaryotes, or into identical hosts when they evolve on other planets.

Although viruses target specific species and specific hosts, it is possible for genes to be transferred from a virus to bacteria and from a bacteria to another bacteria or to a eukaryote, such that genes can journey between different hosts.

Thus, be it through viruses, prokaryotes, or free packets of plasmid DNA, the DNA of one species can be inserted into the genome of another. Likewise, it is through these genetic mechanisms that genes can be exchanged when extraterrestrial microbes come in contact with each other or with more complex eukaryotic extraterrestrials.

Hence, plasmids serve as genetic couriers which are able to travel from chromosome to chromosome, from cell to cell, and from species to species (and thus from planet to planet and from solar system to solar system) carrying copies of specific genetic instructions (Berkner, 1988; Moss et al. 1990; Slater et al., 2008; Sundin 2007; Wigler, et al. 1979). And viruses serve in the same capacity. Once transferred and incorporated into the genome of a host, plasmids can coordinate the acquisition of new traits or characteristics so that members of innumerable species may come to possess the same genes and can acquire traits and genetic information that had been acquired by a wholly different species (Berkner, 1988; Moss et al. 1990; Sundin 2007; Wigler, et al. 1979).

Therefore, in response to specific genetic messages, or changes in the environment, these transferred genes may be expressed, and yet others silenced, giving rise to new traits and even new species.

7. GENE TRANSFER AND PHYSICAL CHANGE IN EUKARYOTES

Bacteria have colonized not only Earth, but even complex eukaryotic species, including woman and man (Ley et al., 2008).

Further, these prokaryotes can induce significant genetic change in complex multi-cellular eukaryotes. For example, agrobacteria inject plasmids into the genomes of trees and plants forcing them to produce various bacterial nutrients. The plasmids (mini-chromsomes) floating in the cytoplasm of agrobacterium carry the genetic instructions for unregulated plant cell growth, coupled with the instructions for synthesizing a particular group of enzymes and amino acids called opines.

Opines serve as nutrients for these bacteria. Hence, once the agrobacterial plasmid has been injected and then integrated into the host cell's DNA, this results in the formation of crown gall tumors due to unregulated cell growth (Zambryski et al 1989). Crown gall tumors produce opines. Opines are of no use to the plant, but are a delicacy for these bacteria. In this manner the Agrobacterium can subvert the plant's genetic machinery for its own ends.

According to Watson and colleagues (1992). "The process of transfer from the bacterial cell to the plant cell is analogous to the process of biological conjugation; it is as though the Agrobacterium is mating with a plant cell."

Food and diet have played a major role in the evolution of Homo Sapiens, contributing to increases in the size of the brain and reductions in the size of the jaw (Joseph 2000b). However, the genes responsible for the evolution of the brain, existed prior to their expression in species which were without brains, bodies, or jaws. As will be detailed, some of these genes can be traced to the first common ancestors for eukaryotes.

Moreover, it is microbes which have enabled complex eukaryotes to digest the food which provided the enzymes which acted on these genes which are responsible for the development of the body and the brain (Ley et al., 2008). For example, during digestion it is the activity of microbes that reside within the gut, and which produce glycoside hydrolases and polysaccharide lyases (which humans lack), and which are also responsible for fermentation, which make it possible to breakdown complex plant polysaccharides and to liberate sugars from plants. Microbes, mammals (and humans) are the beneficiaries as all consume the breakdown products. Animal life would be impossible if not for bacteria. If these microbes were to die mammals would starve to death.

These microbes can also influence human behavior and body size (e.g., obesity); i.e. instead of crown gall tumors, they make the host fat. These microbes also influence numerous host pathways, including the production of aminos and blood metabolites and the metabolism of amino and glycan acids (Flier and Mekalanos 2009; Gill et al., 2006; Li et al., 2008; Turnbaugh et al., 2009). Therefore, not only can bacteria influence the genetic functioning of plants but humans, so that both produce enzymes and amino acids which serve as nutrients for bacteria. Therefore, just as various trees and plants can be genetically altered to create food for microbes, humans and other animals perform the same function for microbes.

8. THE FIRST EARTHLINGS

An assortment of microfossils have been discovered within meteorites which predate the origin of this solar system and which may have originated on different extrasolar planets (Joseph 2009a). These include fossilized colonies resembling cyanobacteria (blue-green algae) discovered in the Orgeuil, Murchison (Hoover 1984, 1997) and Efremovka meteorite (Zhmur and Gerasimenko 1999); cyanobacteria (Zhmur et al. (1997), virus particles and clusters of an extensive array of microfossils similar to methanogens and archae in the Murchison (Pflug 1984); and organized elements and cell structures that resemble fossilized algae and microscopic fungi within the Orgeuil (Claus & Nagy 1961; Nagy et al. 1962; Nagy et al. 1963a,b,c).

Meteors, asteroids, comets and moon sized debris continually slammed into Earth for the first 700 million years after this planet was captured by this solar system (Schoenberg et al. 2002), and it is during this time period, between 4.5 to 3.8 BYA that life took root on Earth. There is in fact evidence of biological activity in the oldest rocks on this planet, located in banded iron formations dated to 4.28 billion years ago (O'Neil et al. 2008), and within metasediments in Western Australia formed 4.2 billion years ago (Nemchin et al. 2008).

In addition, microfossils resembling yeast cells and fungi were discovered in 3.8 million year old quartz, recovered from Isua, S. W. Greenland (Pflug 1978). Evidence of biological activity including photosynthesis was also discovered in this area dated from the same time period (Rosing 1999, Rosing and Frei 2004) and in the nearby Akilia island dated to almost 3.9 BYA (Manning et al. 2006; Mojzsis et al. 1996).

Thus, based on data from meteors, the oldest rock formation, and genomic analysis, it can be deduced that the first creatures to take root on Earth likely included archae, bacteria, and blue-green algae (cyanobacteria), and possibly simple eukaryotes such as yeast and fungi. Since there is no evidence that life can be produced from non-life, this first forms of life must have arrived encased in the debris which was pummeling the early Earth (Joseph 2000a, 2009a).

Yeast and fungi are eukaryotes. These eukaryotes are also unique in that they can rebuild their genomes after radiation exposure (Scheifele and Boeke 2008). Fungi (as well as algae, lichens and spores), can also survive exposure to massive UV and cosmic radiation and the vacuum of space (Sancho et al. 2005). Fungi, algae and lichens show nearly the same photosynthetic activity before and after space flight, and multimicroscopy investigation reveales no detectable ultrastructural changes (Sancho et al. 2005). Therefore, it is conceivable that not just prokaryotes and viruses, but simple eukaryotes may have also been deposited on this planet early in its history (Joseph 2009a); which would explain why microfossils resembling yeast cells and fungi were discovered in 3.8 BY old quartz (Pflug 1978). The other possibility is eukaryotes along with microbes, survived the expulsion of this planet from the solar system which gave birth to our own.

9. ARCHAE, BACTERIA, EUKARYOGENESIS

There is thus evidence that life had taken root on this planet between 4.2 to 3.8 BYA, and these first life forms included bacteria, archae, blue-green algae, and yeast and fungi--as based on the analysis of ancient meteors, microfossils, and the residue of photosynthesis, oxygen secretion, carbon isotopes, the structure of banded iron formations and high concentrations of carbon 12, or “light carbon” found in ancient rock formations and which are typically associated with microbial life (Manning et al. 2006; Mojzsis et al. 1996; Nemchin et al. 2008; O'Neil et al. 2008; Pflug 1978; Rosing, 1999, Rosing and Frei, 2004; Schoenberg et al. 2002).

Once on Earth, these simplified eukaryotes may have phagatocized archae and bacteria (Kurland et al., 2006; Poole and Penny, 2007) and incorporated their genes, or were infiltrated by parasitic prokaryotes which donated genes to the eukaryotic genome. If complex eukaryotes were not already present, then the donation of these genes enabled single celled eukaryotes to become multicellular and to evolve.

Woese, (2004) has proposed that these initial bacteria, archaea and eukaryotes may have lived together and repeatedly swapped and shared genes via HGT. "Eventually this collection of eclectic and changeable cells coalesced into the three basic domains known today" (Woese, 2004).

It is generally assumed based on genomic analysis, that the first Earthly unicellular eukaryotes were fashioned when genes from archae and bacteria combined thereby inducing eukaryogenesis and giving rise to the eukaryote genome (Feng et al., 1997; Hedges, 2002; Hedges et al. 2001; Martin and Koonin 2006; Martin and Muller, 1998; Rivera and Lake 2004). These genes subsequently underwent repeated single gene and whole genome duplications, perhaps in response to regulatory signals or environmental triggers, and unicellular eukaryotes became multicellular and then increasingly complex and intelligent.

More specifically, there is genetic evidence supporting the possibility that an ancient photosynthetic archaeal prokaryote, or possibly a methanogenic archae that feasted on methane, may have fused with a photosynthetic Cyanobacteria (Rivera and Lake 2004), or some other species of bacteria, thereby producing a combined genome and thus triggered eukaryogenesis (Hedges et al., 2001; Martin and Koonin 2006; Martin and Muller, 1998), and the first single celled eukaryotes around 4 billion years ago (Feng et al., 1997; Hedges, 2002). If correct, this could account for the simplified eukaryotic microfossils dated to 3.8 BYA (Pflug 1984).

Presumably this bacterial ancestors extracted hydrogen from water, released oxygen as a waste product (Davidson 2000), and supplied hydrogen to a methane-eating archae (Martin and Muller, 1998; Rivera and Lake 2004). As noted, fossils of methanogens and other archae were discovered in the Murchison meteor (Pflug 1984) whose origins predated the origin of Earth.

These first Earthly Methanogens reacted H2 with CO2 to obtain energy and make organic matter. As oxygen levels were negligible at best, these creatures may have engaged in anoxygenic photosynthesis, using H2 in lieu of an oxygen ‘acceptor’ (Olson 2006; Sleep and Bird 2008). Yet other microbes may have produced, incorporated and then employed sulphides and ferrous as oxygen acceptors (Olson 2006; Sleep and Bird 2008); hence, the presence of iron banded formations dated to to 4.28 billion years ago, and which appear to be associated with biological activity (O'Neil et al. (2008).

Thus the first Earthly eukaryotes which acquired these prokaryotic genes via HGT, were able to survive on hydrogen and methane, or iron and sulphides, despite the initial lack of free oxygen. Hence, the first Earthly eukaryotic cells may have emerged as a result of HGT and a symbiosis between the genomes of methane or sulphide eating archaeon and a hydrogen or iron eating bacterium (Embley and Martin, 2006; Martin and Muller 1998; Martin and Koonin 2006).

Therefore, if single celled or multi-cellular Earthly eukaryotes did not arrive on this planet embedded within stellar debris, and did not survive the ejection of this planet from the parent solar system, it can be assumed that they were fashioned through precise, highly regulated genetic mechanisms. Moreover, it can be deduced that the genes donated to induce eukaryogenesis, were originally obtained from eukaryotes living on other worlds, via HGT. In other word, eukaryotic genes were combined or transferred into a single celled eukaryote to induce eukaryogenesis and the evolution of multi-cellular eukaryotes.

These eukaryotic genes donated by prokaryotes (and probably viruses) subsequently underwent repeated single gene and whole genome duplications, perhaps in response to regulatory signals and environmental triggers or the activity of viral agents. Unicellular eukaryotes therefore became multicellular and then increasingly complex and intelligent.

Further, an α-bacterium, and/or its genes, became incorporated within these initial Earthly proto-multi-cellular eurkaryotes, and may have become a direct ancestor to mitochondria which now live inside every single cell of every multi-cellular eukaryotic organism, adjacent to the nucleus (Martin and Muller 1998; Rivera and Lake 2004; Martin and Koonin 2006). The genomes of all extant multi-cellular eukaryotes, in fact, contain genes which can be traced to ancestors that possessed the bacterial endosymbiont that contributed genes which gave rise to the mitochondria (van der Giezen and Tovar 2005; Embley 2006). Mitochondria and related organelles now reside in all subsequent multi-cellular eukaryotic cells and enabled eukaryotes to breath oxygen, to become energy efficient, and to grow in size.

Thus, hundreds of millions of years after arriving on Earth, archae, bacteria, cyanobacteria, may have injected genes into a single celled eukaryote, or combined their genes in some other fashion, and with the assistance of viruses, created the first Earthly multi-cellular eukaryotes. Nearly 4 billion years later, the descendants of the first Earthly eukaryotes would give rise to humans.

10. OPERATIONAL AND INFORMATIONAL GENES

Viruses are found in association with archae and bacteria, in ratios of 10 to 1 and 100 to 1. Viruses also serve as interplanetary genetic luggage, such that innumerable genes or RNA/DNA-templates, are packaged into trillions upon trillions of viruses. These genes can be transferred to prokaryotes and to eukaryotes. When the first prokaryotes arrived on this planet, or emerged from dormancy, they were accompanied by viruses and their vast genetic libraries which likely included eukaryotic genes. Perhaps single celled eukaryotes were also among the survivors. Subsequently, genes were transferred, combined, and single celled eukaryotes became multi-cellular. Then they began to evolve.

The ancestral viral and prokaryotic genes and genetic elements which were donated to eukaryotes included regulatory genes, introns, transposable elements, and all the genetic machinery necessary for fashioning multicellular eukaryotes and their genomes and to enable their evolution. Further, prokaryotes and viral agents provided eukaryotes with the regulatory elements controlling gene expression and which duplicate individual genes and the entire genome thereby enabling the eukaryote gene pool to grow in size.

Broadly considered, the eukaryote genome contains two sets of functionally distinct prokaryotic genes, operational vs informational; one set derived from archaea and the other from bacteria (Esser et al. 2004; Rivera and Lake 2004).

It is now well established that archae provided the eukaryote genome with genes for information processing and expression (translation, transcription, replication, and repair) whereas bacteria provided operational genes responsible for the membrane system, the cytoskeletal system, and metabolic activity. The combination of these two sets of genes, informational vs operational, contributed significantly to the evolution of eukaryotic complexity.

Specifically, highly conserved eukaryotic protein-coding genes, particularly those involved in translation, transcription, replication, repair, and thus information-processing systems, are derived from archaea. In fact, over 350 eukaryotic genes have been identified that are of apparent archaeal origin and which were acquired via early horizontal gene transfer (Yutin et al., 2008).

Studies have shown that operational genes have been repeatedly and continuously horizontally transferred over the course of evolution (Jain et al., 1999). However, these same eukaryotic/archae genes are not found in the bacteria genome.

Likewise, the key proteins involved in DNA replication are homologous in archaea and eukaryotes but are not related to the proteins employed by bacteria (Leipe et al. 1999). In fact, an analysis of introns, transposable elements, and especially ribosomal structure and ribosomal protein sequences indicates a specific affinity between eukaryotic genes and their orthologs from archae (Lake et al. 1984; Lake 1988; 1998; Rivera and Lake 1992; Rivera and Lake 2004; Vishwanath et al. 2004). Thus, archae (along with viruses) provided numerous genes to the eukaryotic gene pool.

Conversely, hundreds of genes are homologous in eukaryotes and bacteria but are not found in archaea. These includes genes involved in the production of the principal enzymes of membrane biogenesis (Pereto et al. 2004). Bacteria also provided genes for the creation of the eukaryotic membrane system, the inner cytoskeleton, complex metabolic activity, metabolic enzymes, and which serve operational functions (Yutin et al., 2008; Esser et al. 2004, 2007; Rivera and Lake 2004). These donated genes and proteins directly influence metabolism and the ingestion and excretion of various waste products. Some of these waste products would eventually build up in the environment and act on gene selection, activating silent genes and promoting evolutionary metamorphosis.

Given the fact that archae and bacteria can share genes, the fact that these specific genes were selectively transferred from prokaryotes to eukaryotes (and not between archae and bacteria) indicates that HGT was purposeful and under precise genetic regulatory control. Further, the transfer of these genes may have been made possible with the aid of viruses which selectively transferred regulatory genes into the eukaryotic genome. In this way, these genes, in combination, could selectively affect the evolutionary development of eukaryotes whereas in contrast, prokaryotes would not be subjected to the same genetic influences.

Viruses selectively target specific hosts. If the host has not yet evolved viruses will inject genes which become part of the host genome and these genes will be passed down from generation to generation until that host evolves at which point these viral genes may be activated. Viral genes also play a significant role in speciation, and the evolution of new species. And, when new host species evolve they may also be targeted by viruses, archae, and bacteria, which inject additional genes into the new host genome. Thus, horizontal gene transfer is an ongoing process and which has played a major role in evolution leading to modern humans.

Initially massive numbers of genes were transferred to the eukaryotic genome. However, over the course of evolutionary history, not all genes have continued to be transferred at the same rates or frequency (Smith et al., 1993; Henze et al., 1995; Feng et al., 1997; Brown and Doolittle 1997; Ribeiro and Golding 1998; Rivera et al., 1998). For example, informational genes involved in transcription, translation, and related processes, appear to have undergone massive horizontal transfers during the initial stages of eukaryotic evolution. Subsequently, informational genes appear to have been transferred only periodically and much less frequently as compared to operational genes (Jain et al., 1999; Rivera et al., 1998). The periodic nature of information gene transfer may be associated to speciation events, taking place only when specific hosts evolve or perhaps triggering the next stage of metamorphosis during critical periods of environmental change.


The differences in the rate and frequency of transfer also appears to be related to the size and complexity of the genome (Jain et al., 1999) and the gene networks subserved by operational vs information genes. Operational genes belong to small assemblies that produce and interact with only a few gene products. Informational genes tend to be members of large networks of complex systems. Initially these networks within the eukaryotic genome were quite small, allowing for the transfer of large numbers of informational genes at the initial stages of eukaryogenesis.

Informational genes interact with nongene products such as ions, small molecules (GTP, GDP, etc.), and numerous proteins. For example, during assembly a single informational subunit protein interacts with four to five other ribosomal gene products (Jain et al., 1999). An operational gene protein may interact with just one. Therefore, as complexity increases informational gene transfers decrease due to added constraints on the ease of genomic integration.

The functional maintenance and eventual expression of a gene requires a successful integration into the recipient chromosome. A mismatch may induce disease and death due to introduction of errors into the system.

The success of every recombination event varies depending on the host and the homology between the incoming DNA and the chromosome of the recipient cell (Lovett et al. 2002; Thomas & Nielsen 2005).

Other factors also play a significant role including the types nuclei acids (single-stranded, double-stranded, linear, circular) and those related to transformation, transfection, and conjugation (Day, 1998; Syvanen and Kado, 1998).

The capacity of a gene product to function depends on its ability to make the necessary bonding interactions and to coordinate its activity with its neighbors (Jain et al., 1999). As complexity and the number of genes within the genome increases, the likelihood that the inserted gene will fail and disrupt the system also increases, unless the transferred gene remains silent and is not activated until the host's genome has been reorganized or duplicated.

Therefore, the probability of a successful horizontal transfer will be determined by the number of interactions a gene and its protein products must make with its neighbors, if other members of the gene network are able to coordinate their activities with the transferred gene (Jain et al., 1999), and if the transferred gene is transcriptionally active or silent and the nature of and the ability to recombine within the genome of the host (Lovett et al. 2002; Thomas & Nielsen 2005). Because integration is ruled by "lock and key" genetic mechanisms, this suggest that genes may be transferred only when specific hosts evolve and during critical windows of evolutionary opportunity, and that gene transfer is under precise genetic regulatory control, otherwise their insertion would completely disrupt the functional integrity of the host genome (due to increased complexity). By contrast, the continous insertion of operational genes is ruled by different mechanisms. Therefore, the transfer of informational genes has occurred more rarely such as when eukaryogenesis was initiated, and during critical stages of evolutionary divergence, and at the onset of the evolution of new species.

Often these transferred genes are immediately transcribed and activated (Hotopp et al., 2007). Some of these genetic elements may also be recruited (adapted) by eukaryotic host genes as regulatory elements, which then regulate the expression of yet other genes donated by prokaryotes. Regulatory genes have also been transferred from viruses into the eukaryotic genome. The insertion of regulatory elements can prevent the transfer of additional genes, as well as turn gene sequences on or off giving rise to evolutionary change and the emergence of new species. Again, when new species emerge, this is either triggered by previously inserted silent genes, or triggers the next wave of gene transfer. In fact, the transfer of massive numbers of genes to the eukaryotic genome appear to be directly related to evolutionary transitions (Lynch, 2007). Yet others may not be transferred and inserted until an appropriate host evolves or after the genome has been repeatedly duplicated.

Not all transferred genes are activated once they are acquired by a host. These inserted genes may not be expressed until passed on to later generations and later appearing species and only when exposed to specific environmental agents (Joseph 2009b). Thus many transferred genes, including those which are highly conserved, remain transcriptionally inactive, dormant and silent (Nicho et al., 2008). These silent genes are passed down vertically from generation to generation, and transferred horizontally from species to species, perhaps for hundreds of millions, even billions of years waiting for an activating signal from the environment, or the HGT of a regulatory gene which will induce transcription and evolutionary change.

11. EUKARYOTIC ARCHAE/BACTERIA SYMBIOSIS, PHAGOTROPHY, NUCLEATION, COMPARTMENTALIZATION

Donation or combination of bacteria, archae, and viral genes to create the first Earthly multi-cellular eukaryote, resulted in approximately 60 major innovations (Cavalier-Smith, 2009). These included the eukaryotic cytoskeleton and a complex internal endomembrane system where lipids and proteins are synthesized and which allow eukaryotes to engage in phagotrophy and digestion which provided additional energy and nutrition to the host. Thus after these genes were combined, eukaryotes began to increase complexity whereas the expansion in size enable them to form endosymbiotic relationships with smaller microbes.

Because the donation of these genes were from 3 separate sources which were combined in the eukaryotic genome, this ensured that the interactions of these genes, and subsequent evolutionary development would be restricted to eukaryotes. Initially, these eukaryotes, like prokaryotes, likely lacked a protective nucleus. In consequence, when archae and bacteria were ingested, or following HGT, eukaryotes were able to easily incorporate bacterial and archael genes with the eukaryotic genome (Dyall et al., 2004; Margulis et al., 1997). Eukaryotes and their genome, grew in size.

Increased size and phagocytosis also enabled microbes to easily form symbiotic relations with eukaryotes, and in so doing, donate their genes, the result was the formation of microbe-like compartments within the eukaryotic cell (Dyall et al., 2004). This symbiosis created a division of labor and freed eukaryotes of the necessity of synthesizing complex molecules, chemicals, and coenzymes that could be provided by prokaryotes and their genes (Dyall et al., 2004).

The same type of symbiotic relationship is maintained by modern humans and the microbes which live in their bodies. For example, after the first multi-cellular eukaryotes were fashioned, prokaryotes living inside eukaryotic cells provided these eukaryotes with nitrogen and engaged in denitrification from nitrate. Conversely, eukaryotes supplied various nutrients required by its prokaryotic symbiont (Margulis et al., 1997).

The phagocytosis of archae and bacteria and the subsequent donation of their genes to the eukaryotic host, resulted in the creation of subcompartments consisting of the ingested microbial body that had been stripped of most of its genes (Dyall et al., 2004). This led to the creation of organelles, each enclosed in their own lipid membranes, and which served a variety of functions including photosynthesis, oxidative phosphorylation, and the generation of energy in the form of ATP (Margulis 1998; Andersson et al. 2003). Yet other compartments were specialized for the digestion of large molecules, the synthesis of minerals and large glycosylated and sulphated molecules, the expression of lipids and proteins, oxidation, energy storage, and waste removal (Margulis et al., 1997; Williams & Fraústo da Silva 1996, 2006).

Therefore, in contrast to single celled prokaryotes, the cells of eukaryotes contain several internal compartments, vesicles, organelles, internal filaments, including a separate nuclear compartment containing the cell's DNA. Eukaryotic cells are also protected by a flexible membrane consisting of lipids, steroids and cholesterol (Summons et al. 2006).

Membrane flexibility made eukaryotes more sensitive to the environment, enabling the changing environment to more easily act on gene expression. It also enabled them expand in size and to easily digest and incorporate prokaryotes and their genes.

The establishment of compartments should not be viewed as random events related to chance encounters between microbes and eukaryotes. Just as embyrogenesis is under genetic regulatory control and proceeds from a single cell to complex multi-cellular organisms, the steps leading to multi-cellular eukaryogenesis are also highly regulated and purposeful. For example, the establishment of compartments serves a variety of purposes including protection. The DNA of multicellular eukaryotes is contained within the nucleus of every cell and the nucleus protects the eukaryotic genome. However, the nucleus, and the other compartments, may have originally consisted of symbiotic archae and bacteria which were subsequently stripped of their genes.

Thus, the nucleus may be a derived endosymbiont, a descendant of an archaeon that invaded and was engulfed and phagotocyzed by eukaryotes (Lake and Rivera 1994; Horiike et al. 2004; Hartman and Fedorov 2002). Likewise, organelles, as well as mitochondria may have been created following engulfment and the donation of bacterial and archae genes to the eukaryotic host (Embley and Martin, 2006; Margulis et al., 1997; Martin and Koonin, 2006; Martin and Muller 1998; Pace 2006; Woese 1994). Thus, the incorporation of these genes and the symbiotic relations developed between eukaryotes and genetically-stripped down bacteria and archae, led to the creation of the nucleus and compartmentalization (Dyall et al., 2004; Margulis et al., 1997).

The nucleus and compartmentalization made it possible for predatory eukaryotes to ingest and phagotocize other creatures while minimizing the risk of random gene mixing and the unregulated incorporation of foreign DNA. Therefore, it appear that the eukaryotic nucleus was fashioned first, thereby providing genomic protection, and this allowed other microbes to be safely ingested thereby giving rise to additional compartments including the metamorphosis of mitochondria. These developments enabled eukaryotes to become more complex and conquer new environments which then acted on gene selection.

However, the eukaryotic cytoskeleton and endomembrane system was no longer compatible with the normal processes of bacterial division and reproduction. This led to the evolution of the nucleus and mitotic cycle and then the metamorphosis of mitochondria (Margulis et al., 1997) which originally may have been an endosymbiotic bacteria.

Genes Act on the Environment

Genes act on the environment through the excretion of wastes such as oxygen, and the biologically engineered environment acts on gene selection. Therefore, species-environmental interactions also became increasingly complex, as did the biological needs of the eukaryotic cell. For example, eukaryotes developed a complex internal signaling system involving calcium ions, calmodulin, inositol phosphates, ubiquitin, cyclin, and GTP-binding proteins (Williams & Fraústo da Silva 2002, 2006).

Hence, for the eukaryotic cell to properly function also required the liberation, uptake, and utilization of Mg2+, Mn2+, Fe, Fe2+, Fe3, Cu, Mn2+, Sr2+, Na+, Cl−, and Ca2+, and all of which had to interact or bind with specific proteins (Davidson 2000; Williams & Fraústo da Silva 1996, 2006). Some of these chemicals, such as Fe2+ and Mg2+ had been employed by prokaryotes (Davidson 2000; Williams & Fraústo da Silva 1996, 2006) whereas other had not. Therefore, the necessary genes had to be inserted into the eukaryotic genome to make it possible to utilize substances such as Na+, Cl− and Ca2+; which in turn were employed for messaging, signaling, and metabolism, thus increasing energy uptake and the ability to quickly acquire and respond to information in the environment (Williams & Fraústo da Silva 2006). Therefore, eukaryotes and not prokaryotes, began to evolve and became increasingly complex in response to genetically engineered alterations in the environment. Eukaryotes, therefore, also began to increasingly modify the environment.

12. ANCESTRAL GENE EXPRESSION & THE ENVIRONMENT

As detailed here and elsewhere (Joseph REF), there is considerable evidence that genes donated by virsus and prokaryotes to eukaryotes and which were passed down and subsequent inherited from ancient ancestors contributed significantly to the evolutionary-metamorphosis of increasingly complex creatures in response to biologically engineered changes in the environment. What we call "evolution" has been under precise genetic, regulatory control.

However, the advanced characteristics and species encoded within the genomes of the first Earthlings and which were transferred to eukaryotes did not begin to "evolve" until after hundreds of millions and then billions of years had passed. This is because these genes had to be repeatedly duplicated and freed of inhibitory restraint and the environment had to be significantly altered and genetically engineered before these genes could be activated.

Therefore, initially many of these donated genes were repressed and the functions and traits they coded for were not expressed. Instead, these genes, along with those contributed by viruses, were passed down vertically, from generation to generation, and from species to species, until an activating signal triggered their expression (Joseph 2000, 2009b). These activating signals were provided, in part, by regulatory genes, introns, transposable elements, and by genetically engineered environmental change. Genes acted on the environment, changing the climate, atmosphere, and liberating various gasses, metals and ions, and other substances such as calcium, all of which acted on gene selection, triggering bursts of evolutionary change and the emergence of new species after long periods of stasis (Joseph 2009b). The environment is biologically altered which acts on gene selection, and new traits, organs, tissues, and species emerge. However, these genes and the functions they code for did not randomly evolve, they were inherited, and ultimately, their ancestry leads to extraterrestrial sources.

PART II

13. CONSERVED GENES & GENE EXPRESSION

Genes which code for advanced functions have as their sources, ancestral genes which in turn were inherited or obtained from creatures that long ago lived on other planets. Further over the course of evolutionary history genes were repeatedly inserted, via HGT, from viruses and prokaryotes into the eukaryotic genome. Through genetic regulatory mechanisms which have been transferred and inserted, genes and nucleotides have been shuffled or recombined, copies of genes have been manufactured and shifted to a different region of the genome, shorter or longer sequences of nucleotides were activated or silenced, regulatory genes were inserted and turned genes on or off, and entire networks of genes were inhibited or expressed. However, there is nothing random about these processes, as they are under precise genetic control and have performed highly regulated functions that have guided what has been termed evolution.

Despite the shuffling of genes and nucleotides and the repeated duplication of the ancestral genome, coupled with insertions, deletions and relocation of individual genes thereby erasing evidence of their ancestry, thousands of orthologous genes and hundreds of conserved genes can still be traced back to the last common ancestor for eukaryotes (Snel et al., 2002; Mirkin et al., 2003; Kunin and Ouzounis 2003; Koonin 2003; Makarova et al., 2005; Mushegian 2008; Bejerano et al., 2004). And often these orthologs express or perform the same function regardless of species. These conserved genes, proteins, and gene sequences (Koonin 2002, 2009b), include those coding for core cellular functions and are found in the genomes of prokaryotes and eukaryotes (Koonin et al., 2004; Koonin and Wolf 2008). These conserved genes govern translation, the core transcription systems, and several central metabolic pathways, such as those for purine and pyrimidine nucleotide biosynthesis (Koonin 2003).

Although the genome has been repeatedly duplicated and rearranged, thereby obscuring the ancestral history of most genes, protein sequence conservation extends from mammals to bacteria thus demonstrating their great antiquity (Dayhoff et al., 1974; Eck and Dayhoff 1966; Dayhoff et al., 1983). Therefore, the genomes of modern creatures including humans can be traced backwards in time to microbes including those who were among the first to call Earth, home.

Most genes are passed down from generation to generation and from species to species without benefit of expression. In yet other instances, these conserved genes were activated only after hundreds of millions of years had passed; expressed in response to changing environmental or regulatory conditions. These silent genes inherited from ancestral species, whose own ancestry leads to other planets, include those which code for the bilateral body, eyes, bones and brains.

14. GENETICALLY PRE-CODED EYES, BLOSSOMS, AND BRAINS

Consider, for example, a simple globular organism, Placozoa (Trichoplax) which first appeared around 635 million years ago. Placozoa have no heart, no brain, no neurons, and no nervous system. Yet their genomes contain the genes necessary for creating hearts, neurons, and brains (Srivastava et al., 2008). Obviously they did not randomly evolve these genes which then remained silent. They were inherited from ancestral species who also lacked these organs. Moreover, the organs and tissues coded by the genes did not evolve until around 540 mya.


Placozoa

Following the evolution of Placozoa (Trichoplax), the genes coding for the nervous and cariovascular system were then passed on for a hundred million years through subsequent generations and species and then became activated in response to biologically induced changes in the environment, giving rise to the heart, nervous system, and brain.

The genes coding for vision and the eye in humans and other mammals, such as Pax genes ("Pax-6") have been found in the genomes of numerous ancient species (including the sea urchin and trichoplax) which have no eyes and cannot see (Sodergren et al., 2007; Callaerts et al., 1997; Hadrys et al., 2005). In fact, sea urchins, Tricholplax, and humans, share genes directly related to the limbs, brain, and the visual, auditory, olfactory, and immune system (Sodergren et al., 2007; Hadrys et al., 2005) although they diverged from common ancestors who may have lived from 600 million years ago (mya) to 1.2 billion years ago (Nei et al., 2001; Peterson et al., 2004; Gu 1998; Wang et al., 1999). These genetic commonalities include the same genes necessary for core cellular functions, and which are also found in plants, fungi, and prokaryotes (Koonin et al., 2004; Koonin and Wolf, 2008). Their presence in the prokaryotic genomes indicates these genes have a history that may extend over 4 billion years in time, and thus to other planets. Therefore, these genes, even in the Sea urchins and trichoplax genome were inherited from even more ancient ancestors and were then passed down from genome to genome and from species to species albeit in silent form, only to become activated, almost simultaneously, in numerous species as witnessed by the Cambrian Explosion 540 mya.

Genes may be silenced or repressed through a variety of genetic mechanisms. However, the fact that silent genes code for functions that have been suppressed has been demonstrated experimentally.

Functionally suppressed and silent Pax-6 eye genes which code for eye structures, can be experimentally activated, creating eyes in tissues where eyes should never be located, including on different body parts that normally would never contain eyes. Activation of these genes has induced the creation of eye-specific structures including cornea, pigment cells, cone cells and photoreceptors on wings, legs, and attennae, thus creating eyes on body parts that have no connection to the brain (Gehring 1996; Halder el al., 1995a,b; Tomarev et al., 1997).

There are numerous examples of identical genes coding for advanced characteristics and functions appearing in diverse, unrelated species who lack these traits and who instead pass on these "silent" genes to subsequent, later emerging species, which then become activated, including, for example, the flowers of flowering plants. These genes genes did not randomly evolve, they were inherited from ancestral species.


First flowering plants.

Flowers evolved from non-flowering plants around 130 million years ago (Friedman 2006; Friedman et al., 2004) and the genes responsible for producing petals, stamens and carpells, and thus the flowers of flowering plants, i.e. MADS-box genes, APETALA1, and SEP genes, were inherited from ancient ancestral species which did not produce flowers (Theissen et al., 2000; Ng and Yanofsky, 2001; Pelaz et al., 2000). However, the leaves of non-flowering plants also contain the SEP, MADS-box, and APETALA1 genes, but in a non-activated form. Yanofsky and colleagues were able to activate these silent genes to produce flower petals from leaves such that the leaves of flowerless plants were converted into flowers; plants which normally never produce flowers began to flower (Mandel and Yanofsky 1995; Pelaz et al., 2000, 2001).

These genes have a very ancient pedigree. Plants contain genes donated billions of years ago by cyanobacteria (blue-green algae) and arachae (Doolittle 1999; Nosenko and Bhattacharya 2007). Cyanobacteria and arachae were also among the first to colonize Earth, their fossilized impressions have been discovered in the Murchison and Orgueil meteors (Hoover 1997, 2004; Nagy et al. 1961,1963a,b; Pflug 1984), and thus their own ancestry leads to extraterrestrial sources. IN fact, not just the ancestors of plants (cyanobacteria, algae) but fossils of Pedomicrobium, a flowering bacteria, have been recovered from the Murchison (Pflug 1984).

These genes crucial to the development of flowering plants did not randomly evolve but were inherited from ancestral species. They underwent several whole genome duplicative events, including possibly at the divergence between animals and plants (Alvarez-Buylla et al., 2000), but most of these genes remained suppressed for at least a billion years until activated by biologically induced environmental change to generate flowering plants.

15. GENE EXPRESSION, HSP90 & MOLECULAR SWITCHES

Silent genes inherited from the genomes of more ancient creatures, code for functions and characteristics which may remain suppressed for hundreds of millions and even billions of years. These genes are transmitted from generation to generation and from species to species, until activated by signals from within the external and internal environment, including, for example, periods of extreme climate change, i.e. global warming followed by global freezing, and then warming (Joseph 2009d).

In 1998, Rutherford and Lindquist demonstrated "that populations contain a surprising amount of unexpressed genetic variation that is capable of affecting certain typically invariant traits" and that changes in environmental conditions such as temperature "can uncover this previously silent variation" (Rutherford & Lindquist, 1998 p. 341). That is, these traits and these genes exist prior to their expression and are activated by changes in the temperature of the environment.

These genetic-environmental interactions on gene expression are mediated through regulatory protein products like Hsp90 (Rutherford & Lindquist, 1998). These proteins prevent DNA expression by acting as a buffer between silent genes and their nucleotides and the environment. However, changes in the environment can directly impact regulatory genes and change the configuration of these proteins thereby removing their buffering influences, such that silent genes are then activated.

Hsp90, for example, is a highly conserved multifunctional protein which targets multiple signal transducers which act as "molecular switches" which 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).

Hsp90 does not act alone but is part of a networks that includes other proteins such as Hsp70, and p23 (Pratt and Toft 2003). As summarized by Cossins (1998, p. 309), these and other regulatory and signaling proteins have been referred to as "chaperones and have been discovered in all organisms studied so far. These signaling proteins form complex webs of molecular switches that allow signals both within and between cells to be transduced into responses." However, the coordination of these responses can be influenced by the changes in the environment.

"Hsp90 is one of the more abundant chaperones. 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). 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).

The history of early Earth clearly demonstrates how changes in temperature induce significant evolutionary changes, coupled with species extinctions. The hot Hadean era was followed by the Archaean era and a 600 my episode of global warming associated with high levels of biologically produced methane and carbon dioxide and then a biologically induced rise in oxygen, a reduction in methane, all of which led to global freezing (2.3 bya) and then a rise in methane and a global meltdown (1.8 bya). At the outset of these cliimatic changes all life was microscopic, and eukaryotes may have consisted of less than 2 cell types (Hedges et al. 2004). However, it was during these episodes of temperature extremes that eukaryotes evolved and came to acquire mitochondria. Further with the next period of global warming, and by 1.5 BYA, eukaryotes underwent significant evolutionary change (Joseph 2009d). and had expanded to 10 cell types (Hedges et al. 2004). Continued changes in climate and the environment were in turn associated with the evolution of a varied assemblage of complex multi-cellular eukaryotes which by 1.2 bya, diverged into a variety of species such as green and red algae, dinoflagellates, ciliates, amoebae, and a diverse array of unornamented organic-walled acritarchs (Butterfield 2000; Porter and Knoll 2000; Wang et al. 1999; Xiao and Knoll, 1999; Zhou et al. 2001).

These two earlier periods of global warming and "snow ball Earth" were followed by additional episodes of extreme climatic and temperature change including two successive global ice ages, e.g. the "Marinoan" and the "Gaskiers," which came to a close around 580 Ma. These biologically induced temperature extreme were associated with the evolution and extinction of a variety of complex species, including the megascopic Ediacarans, and appear to have played a central role in the onset of the Cambrian Era and a virtual explosion of complex life (Elewa and Joseph 2009; Joseph 2009d).

Darwinism is not based on genetics, emphasizes "small steps" and is at odds with the fossil record, cannot account for biologically induced environmental change, and explains away progressive evolutionary development and related alterations in gene expression as due to "random" variations. Evolution is not random, but is under precise genetic regulatory control. Genes act on the environment and the biologically altered environment acts on gene expression. The climatic and temperature extremes briefly mention above were all due primarily to biological activity (Joseph 2009d). Specifically, in response to alterations in the environment, the inhibitory influences on gene expression are removed allowing for the expression of hidden genetic variation leading to new developmental and evolutionary patterns and thus the emergence of precoded - inherited traits, physical characteristics and species.

Hsp90 and other "chaperones" are directly impacted by alterations in the environment and temperature. 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."

Earth has undergone profound environmental, climatic, and atmospheric changes over the course of the last 4.5 billion years. Changes in the environment directly impact regulatory genes and regulatory proteins, making genes more susceptible to environmental activating influences. Further, genes inherited from ancestral species may biologically act on the environment, which triggers the activation of formerly silent genes. Thus we see that the first three global ice ages and the extinction of progenitor species and emergence of new, larger, more complex species can be directly linked to biological activity involving the release and breakdown of oxygen, methane, and carbon dioxide (Joseph 2009b). Increases in oxygen levels also directly impacted the metamorphosis of mitochondria (Joseph 2009b), and is responsible for the development of the ozone layer which blocked life-neutralizing radiation, allowing eukaryotes to emerge from the sea and from beneath the earth. The secretion of calcium by cyanobacteria, and biologically induced episodes of global freezing followed by global warming, also acted on gene selection, generating bones and nerve tissue, thereby allowing eukaryotes to grow in size and become increasingly intelligent.

Thus a complex feedback system, involving genes and the environment, control gene expression, including the activation of formerly silent genes and the expression of the traits, characteristics, and functions they code for. Genes contain and code for emergent traits and functions which had been precoded into those genes. The genetic heritage of all eukaryotes on this planet were inherited from ancestral species and include genes donated by archae, bacteria and viruses to the eukaryotic genome.

As there is no evidence supporting an Earth-based abiogenesis, and as the only evidence favors "life from life" then the first Earthly life forms, and their DNA, had to be inherited from other living creatures whose own ancestry leads to other planets. This means, these genes were inherited from creatures which long ago lived on other worlds.

16. PHOTOSYNTHESIS & OXYGENATION. THE ENVIRONMENT ACTS ON GENE SELECTION: EUKARYOTES

Around 4 BYA it appears that an ancient photosynthetic archaeal prokaryote, or possibly an archae that feasted on methane, may have fused or combined genes with a photosynthetic cyanobacteria (Rivera and Lake 2004), and then diverged to create a eukaryote (Hedges et al. 2001). It is also likely that bacteria, archae, viruses, and blue-green algae donated genes to whatever eukaryotes had survived the ejection of Earth from the parent solar system, or which had been deposited on the new Earth contained within the cosmic debris that pounded the planet for 700 million years after it became part of this solar system. Eukaryotes, equipped with these genes, and in response to the biological engineering of the environment, diversified, became multi-cellular, and evolved.

Based on comparative genomic analyses, the metamorphosis of the first Earthly multicellular eukaryote, had taken place by 2.7 BYA (Feng et al., 1997; Hedges 2002), almost 2 billion years after Earth became part of this solar system. Therefore, it took almost 2 billion years on a changing Earth for single cells to become multi-cellular.

The genetic transition from single celled to multicellular eukaryote was initiated by the changing environment (Joseph 2009b), for it was also around this time that Earth began to cool (Evans et al., 1997; Kirschvink, et al. 2000), and nitrates and oxygen levels began to significantly increase (Buick 2008; Eigenbrode and Freeman 2006). The environment was altered biologically, which acted on gene selection, thus triggering multicellular eukaryosis.

Prokaryotes and their genes directly impacted the environment, such as via the secretion of methane which contributed to global warming (Kasting and Siefert 2002; Nisbet and Nisbet 2008; Pavlov et al., 2000; Schwartzman et al., 2008), and the liberation of oxygen which contributed to global freezing (Nisbet and Nisbet 2008; Pavlov et al., 2000). According to Eigenbrode and Freeman (2006), "The data suggest that a global-scale expansion of oxygenated habitats accompanied the progression away from anaerobic ecosystems toward respiring microbial communities fueled by oxygenic photosynthesis," and this is what led to first global ice age 2.2 bya (Evans et al., 1997; Kirschvink,, et al. 2000; Roscoe 1969, 1973).

17. CYANOBACTERIA, PLASTIDS, AND OXYGENATION

Initially Earth was devoid of a significant atmosphere, lacked free oxygen, and the oceans were anoxic and possibly sulphidic (Barleya et al., 2005; Canfield 2005; Holland 2006; Mentel and Martin 2008). Only 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)--as is the case with many modern day species of bacteria and archae (Richardson 2000).

Archae and bacteria are accompanied by viruses, which served as genetic depositories. That is, excess genes are stored in the viral genome and are extracted and inserted into the archae, bacteria, or eukaryotic genome, on an "as needed basis." Therefore, when prokaryotes began to proliferate on new Earth, they were accompanied by vast viral libraries. And these viruses contained many of the genes necessary for genetically engineering new Earth and forming a complex-life-promoting atmosphere rich is oxygen. The included genes promoting photosynthesis

With the metamorphosis of eukaryotes, viruses, archae and bacteria continued to donate genes to the eukaryotic genome, as eukaryotes evolved and triggering bursts of evolutionary innovation. Viruses which accompany cyanobacteria possess photosynthesizing genes which they can transfer to cynaobacteria on an as needed basis (e.g., (Lindell et al., 2004; Sullivan et al., 2005, 2006; Williamson et al., 2008). Likewise, photosynthesizing cyanobacteria contributed genes to the eukaryotic genome (Howe et al., 2008), possibly at the initial stages of eukaryotic evolution and periodically thereafter. Further, some photosynthesizing cyanobacteria appear to have colonized and donated genes to a variety of non-photosynthetic eukaryotic hosts thereby conferring upon them the capacity to engage in photosynthesis (Howe et al., 2008). Some of the genes transferred by cyanobacteria triggered the development of pigmented plastids which engaged in photosynthesis. Plastid formed the major organelles which are now found in plants and algae and are responsible for the synthesis of fatty acids and the storage of starch.

Plastid DNA exists as large protein-DNA complexes, each containing at least 10 copies of the plastid DNA. Plastids also possess numerous internal membrane layers which raises the possibility that plastids are stripped down photosynthetic prokaryotic endosymbionts (Howe et al., 2008). Thus some eukaryotes, equipped with cynaobacteria genes or "stripped down cyanobacteria" began to engage in photosynthesis and to secrete oxygen as a waste product (Buick 1992; Holland 2006).

The excretion of "waste" products, such as oxygen, over hundreds of millions of years, directly altered the environment (Barleya et al., 2005; Buick 1992; Canfield 2005; Holland 2006; Rosing and Frei 2004), and the altered environment acted on gene selection, activating genes that had been donated to the eukaryotic genome by prokaryotes and viruses.

The buildup of free molecular oxygen resulted in nitrate being oxidized from ammonium and subsequently denitrified. Increased production of oxygen led to decreased fixed inorganic nitrogen in the oceans--as is evident from isotopic analyses of fixed nitrogen in sedimentary rocks from the Late Archaean (Falkowski and Godfrey 2008). The interaction between the oxygen and nitrogen cycles and the continued buildup of oxygen in Earth's atmosphere allowed nitrification to become dominant over denitrification (Falkowski and Godfrey 2008). In consequence, oxygenic photosynthesis and aerobic respiration became the preferred mode of energy acquisition within eukaryotic host cells-- a function of the activation of specific genes horizontal transferred from viruses and prokaryotes to eukaryotes (Falkowski and Godfrey 2008).

18. BIOLOGICALLY ENGINEERED ENVIRONMENT ACTS ON GENE SELECTION

As certain elements, gasses, and minerals built up as waste, they acted on gene selection (Joseph 2009b; Williams and Fraústo da Silva 1996, 2006), giving rise to metabolic processes that enabled these creatures to biologically catalyse electron transfer (redox) reactions, beginning with H, C, N, and then O and S (Falkowski and Godfrey 2008). This sequence of changing environments acting on gene selection, led to the production of oxygen via the photobiologically catalysed oxidation of water and photosynthesis. As atmospheric oxygen levels continued to build up, this resulted in the surface weathering of soil-bound sulphides which were reduced to sulphates which drained into the oceans as sulphate (Mentel and Martin 2008).

Under anaerobic conditions, 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 soils, such that ferrous iron and sulphates were being liberated and draining into the oceans.

In consequence, sulphate reducers and anaerobic, hydrogen sulphide-producing prokaryotes, as well as ferrous iron producing bacteria, began to proliferate on a global scale (Mentel and Martin 2008; Sleep and Bird 2008). The continued production and buildup of sulphide and ferrous iron were eventually incorporated within eukaryotic cells and were bound to proteins and became oxygen acceptors (Sleep and Bird 2008). Thus what had been oxygen-independent ATP-generating pathways, became oxygen-dependent.

In fact, cyanobacteria may have begun to use ferrous iron as a reductant as early as 3.0 bya (Olson 2006). As based on an analysis of microfossils, stromatolites, and chemical biomarkers in Australia and South Africa, chlorophyll containing cyanobacteria had switched to oxygenic photosynthesis by 2.8 Ga (Olson 2006).

Thus, a complex genetic-environmental feedback system was established, with genes acting on the environment and the biologically altered environment acting on gene selection which gave rise to species which utilized these "wastes" and rejected those which were not as useful or efficient (Richardson 2000; Williams 2007).

As summarized by Williams (2007), "in essence, organisms at all times had to accumulate certain elements while rejecting others. Central to accumulation were C, N, H, P, S, K, Mg and Fe while, as ions, Na, Cl, Ca and other heavy metals were largely rejected." One step leads to the next, beginning with the use of hydrogen, methane, Fe, sulphur, and nitrates by bacteria and archae (Berks et al., 1995; Bult et al., 1996; Gold, 1992; Lonergan et al., 1996; Lovley, 1991; Richardson 2000; Vargas et al., 1998), followed by oxygenic photosynthesis (Castresana & Saraste, 1995; Castresana & Moreira, 1999; Falkowski and Godfrey 2008; Schafer et al., 1996; Schwartzman et al., 2008; Sleep and Bird 2008).

One steps leads to the next in an orderly progression, with successive environments being prepared for species who had not yet evolved, and who upon evolving continue to biologically digest the planet, making it habitable for those yet to be born. Thus, successively emerging species utilized biological byproducts, such as sulphides, ferrous iron, glucose, pyruvate, and NADH, which provided new and additional sources of energy and nourishment, and which acted on gene selection (Williams and Fraústo da Silva 2006), thereby triggering the next phase of evolutionary-metamorphosis and the emergence of species who also began genetically engineering the planet.

As detailed by Williams (2007), "in order to form the vital biopolymers, C and H, from CO2 and H2O, had to be combined generating oxygen. As oxygen continued to be excreted, the environment came to be oxidized. These environmental changes took place in a step-wise fashion, one step leading to the next, and imposed a necessary sequential adaptation by organisms while increasing the use of energy. This means that "evolution" is under biological-chemical control, and has a specific direction as shaped by thge combined organism/environment ecosystem. In addition, the joint organization of the initial reductive chemistry of cells and the later need to handle oxidative chemistry forced organisms to form compartments where each could perform specialized functions when reacting to the environment. Complexity increased from bacteria to humans to take full advantage of these changes in a logical, physical, compartmental and chemical sequence that was coordinated and controlled by the genetically engineered biologically altered chemical environment (Williams 2007).

19. OXYGENATION & MITOCHONDRIA METAMORPHOSIS

Evolution can be likened to embryogenesis where the biologically engineered Earth becomes the womb of the planet, providing a progressively changing environment which becomes rich in the elements, gasses, proteins and nutrients necessary to promote each stage of evolutionary growth. For example, once the single cell becomes a multi-cell and then begins to differentiate and become increasingly multi-cellular, the uterus undergoes massive physical and chemical alterations, growing 20 times its initial weight and increasing its volume a thousand-fold. The blood supply therefore also dramatically increases, as does the delivery of oxygen. The uterus also fills with amniotic fluid which creates a protective environment and which is continually being "inhaled", swallowed and digested. This watery-atmosphere contains proteins, carbohydrates, lipids and phospholipids, urea and electrolytes, as well as stem cells which are also absorbed and whose unique silent DNA can differentiate into various tissues and cell-types, including brain and bone (De Coppi P., et al., (2007) Isolation of amniotic stem cell lines with potential for therapy. Nature Biotechnology 25, 100 - 106).

Likewise, the womb of the planet and its gaseous-watery environment was also progressively altered, and DNA was continually inserted into the genomes of species, thereby promoting evolutionary development. Thus, in the early history of new Earth, in addition to horizontal gene transfer, some prokaryotes including cynaobacteria and aerobic photoautrophic marine plankton were producing oxygen via photosynthesis and the photobiologically catalysed oxidation of water (Buick 2008; Falkowski and Godfrey 2008). They were also engaging in oxygen metabolism as demonstrated by U–Pb data from metasediments, and the creation of thick kerogenous shales dated to 3.8  bya to 3.2 bya respectively (Buick 2008).

When the environment had become sufficiently oxygenated and enriched with sulphide and ferrous iron which served as oxygen acceptors (Sleep and Bird 2008) 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). Therefore, the increased presence of oxygen and the liberation of other essential elements, gasses and proteins, acted on gene expression. Silent genes were expressed and the next stage of development unfolded.

Some researchers believe the eukaryotic nucleus, the organelles, as well as mitochondria may have been created from bacterial and archae genes (Pace 2006; Woese 1994; Embley and Martin, 2006; Martin and Koonin, 2006; Martin and Muller 1998), which in some respect could be likened to stem cells whose DNA becomes activated by the changing environment. As multi-cellular eukaryotes grew in size these genes may have been donated after bacteria and archae were "inhaled" and formed endosymbiont relationships with the eukaryotic host (Lake and Rivera 1994; Horiike et al. 2004; Hartman and Fedorov 2002). Thus bacteria and archae not only contributed genes via endosymbiotic gene transfer, which then came to be expressed, but upon being stripped of these genes, they became incorporated into and part of the eukaryote, forming, for example, the mitochondria which now live inside every single cell of every multi-cellular eukaryotic organism, adjacent to the nucleus (Martin and Muller 1998; Rivera and Lake 2004; Martin and Koonin 2006). The genomes of all extant multi-cellular eukaryotes, in fact, contain genes which can be traced to ancestors that possessed an α-bacterial endosymbiont that gave rise to the mitochondria (van der Giezen and Tovar 2005; Embley 2006). Presumably, the genes of this α-bacterium symbiont underwent transformation in response to the increasing levels of oxygen in the atmosphere, becoming a mitochondria.

Therefore, just as the amniotic atmosphere provides a changing environment which promotes development as well as stem cells whose DNA, once incorporated, can differentiate into specific tissues and organs, anaerobic hydrogen-breathing bacteria, photo-synthesizing bacteria and probably a methanogenic archaeon were incorporated into the eukaryotic host. Presumably, initially the bacteria supplied hydrogen to the host (Martin and Muller, 1998) which then engaged in anaerobic respiration to metabolize glycolytic products and turn them into energy; releasing oxygen as waste. The archaen enabled the eukaryote to breath extreme methane which warmed the planet. However, as oxygen was released, the planet began to cool and yet other silent genes were activated, such after hundreds of millions of years of oxygen accumulation eukarayotes began breathing oxygen (Schafer et al., 1996) via the metamorphosis of mitochondria (and related organelles) which now reside in all subsequent multicellular eukaryotic cells. Thus, instead of 9 months, it takes billions of years to alter the environment and to grow complex multi-cellular organisms.

Once the environment became sufficiently oxygenated, the α-bacterium either underwent metamorphosis to become a mitochondria, and/or the genes it contributed were activated and gave rise to aerobic mitochondria (Embley and Martin, 2006; Gray et al., 1999; Martin and Koonin, 2006; Martin and Muller 1998; Rivera and Lake 2004; Martin and Koonin 2006) via "endosymbiotic gene transfer." The activation of these genes, and the metamorphosis of mitochondria enabled eukaryotes to colonize emerging oxygenated environments; with the oxygen being produced biologically.

Mitochondria serves as the powerhouse of the eukaryote cell and are located outside the nucleus. Mitochondria generate most of the cell's supply of adenosine triphosphate (ATP) which is used as a source of chemical energy (Akao et al., 2001; Dahout-Gonzalez et al., 2006; Garlid et al., 2003; Margulis et al., 1997). The production of ATP is accomplished by oxidizing the major products of glucose, pyruvate, and NADH, which are produced in the cytosol (Akao et al., 2001; Dahout-Gonzalez et al., 2006; Garlid et al., 2003; Herrmann and Neupert 2000) and by bacteria and archae (Richardson 2000).

Many cells have only a single mitochondrion, whereas others contain several thousand. Mitochondria have their own independent genomes and their DNA shows substantial similarity to bacterial genomes (Pace 2006; Woese 1994). Mitochondria are enclosed in their own inner and outer membrane, play a significant role in signaling, cellular differentiation, cell death, as well as the control of the cell cycle and cell growth (Anderson et al., 1981; Chipuk et al., 2006; Mannella 2006; Rappaport et al., 1998). Thus, mitochondria are essential to the functioning of the eukaryote cell (Margulis et al., 1997) and enabled eukaryotes to grow larger in size and exploit the changing biologically engineered environments, which in turn acted on gene selection.

Mitochondria, as a distinct entity within eukaryotic cells, did not arise until between 2.3 to 1.8 BYA (Mentel and Martin 2008). It was during this time that oxygen, produced by photosynthetic bacteria and blue-green algae (Cyanobacteria), had begun to enrich the atmosphere (Barleya et al., 2005; Eigenbrode and Freeman 2006). Because of this biological activity, oxygen levels increased, methane levels decreased, and the Earth became glaciated, fueled by oxygenic photosynthesis (Eigenbrode and Freeman 2006; Evans et al., 1997; Kirschvink, et al. 2000). This rise in oxygen has been referred to as the Paleoproterozoic "Great Oxidation Event" (~2.2 to 2.0 Ga), when atmospheric oxygen may have risen to >1% of modern levels, a byproduct of oxygenic photosynthesis (Buick 2008; Canfield 2005; Holland 2006; Nisbett and Nisbett 2008; Olson 2006).

Initially, those α-bacterium genes which contained the DNA instructions for the metamorphosis of mitochondria, remained suppressed and were not activated, as the environment and atmosphere of Earth lacked oxygen and other chemicals such as NADH and other oxidases. In the absence of an oxygen rich atmsophere, eurkaryotes had no need for a mitochondria, and instead use alternate energy sources such as hydrogen and methane.

Therefore, the first eurkaytoes probably did not posses mitochondria but mitosomes, as is also exemplified by many unicellular eukaryotes (Bakatselou et al., 2003; Tovar et al., 1999; Williams et al., 2002).

20. MITOCHONDRIA, MITOSOMES AND SYMBIOSIS

It could be said that bacteria evolved humans (and other organisms) so to provide themselves with nutrient-rich environments within which they could comfortably dwell. The human body, its orifices, and gut, are crawling with billions of bacteria which have formed symbiotic relationships with their human hosts.

Likewise, as eukaryotes evolved and became multi-cellular they too provided an environment in which bacteria and archae could dwell. Thus, there is considerable evidence that mitochondria are stripped down bacteria which formed a symbiogenetic relationship with multi-cellular eukaryotes. This could explain why a few groups of unicellular eukaryotes lack mitochondria: the microsporidians, metamonads, and archamoebae. As based on phylogenetic trees constructed using rRNA information, these unicellular eukaryotes appeared before the origin of mitochondria. Thus, the endosymbiont may have been incorporated only after larger, more complex multicellular eukaryotes evolved in response to the biologically engineered changes taking place on Earth.

However, unicellular eukaryotes who are without mitochondria nevertheless, possess organelles of bacterial descent (Gray et al., 1999). This has led to the possibility that the genes giving rise to mitochondria, organelles, and the nuclear compartment originated at the same time in the common ancestor of all extant eukaryotes rather than in separate, subsequent events (Gray et al., 1999).

The mitosome, for example, is an organelle found in some unicellular eukaryotic organisms and is related to mitochondria (Bakatselou et al., 2003; Tovar et al., 1999; Williams et al., 2002). Like mitochondria, they have a double membrane. The mitosome, however, has been detected only in anaerobic or microaerophilic parasitic organisms that do not have mitochondria (Bakatselou et al., 2003; Mentel and Martin 2008; Tovar et al., 1999; Williams et al., 2002). Nevertheless, the organelles of most unicellular eukaryotes have also been shown to be of bacterial descent (Gray et al., 1999).

Mitosomes therefore, may also be related to to a bacteria which gave rise to mitochondria, or they may be derived from mitochondrial genes (Mentel and Martin 2008). However, unlike mitochondria, mitosome genes are contained in the nuclear genome of the eukaryotic host (Bakatselou et al., 2003; Tovar et al., 1999) whereas mitochondria are located outside the nucleus. Mitosomes may be mini-mitochondria albeit stripped of their genes ( Williams et al., 2002).

The existence of the mitosome does not appear to be compatible with endosymbiotic theory that postulates that mitochondria arose following the phagocytosis of a mitocondria-like organisms by a multi-cellular eukaryote (Mentel and Martin 2008). Unlike mitochondria mitosomes do not have the capability of gaining energy from oxidative phosphorylation (Mentel and Martin 2008) and this may be due anaerobic environments in which they dwell (Tovar et al., 1999).

The existence of the mitosome in anaerobic unicellular eukaryotes, and the link to bacteria and mitochondria, suggests that mitosomes and mitochondria are derived from the genes that were eiter donated to or which gave rise to the first eukaryotes, and that the metamorphosis of mitochondria was in response to increased levels of oxygen, sulphur and ferrous iron, and other gasses, ions and minerals; a consequence of the genetically engineered environment acting on gene selection.

21. MITOCHONDRIA & ENDOSYMBIOTIC GENE TRANSFER

The activity of photosynthesizing organisms and prokaryotic genes altered the environment via the liberation, secretion, and synthesis of a variety of chemicals, enzymes, and gasses including oxygen and NADH (Buick 1992, 2008; Falkowski and Godfrey 2008; Holland 2006; Olson 2006; Williams and Fraústo da Silva 2006). The changed environment acted on gene selection, activating genes contributed by bacteria and archae, giving rise to new traits and new species perfectly adapted for a world that had been prepared for them.

The rise of oxygen was a function of biological activity ( (Buick 1992, 2008; Castresana and Moreira 1999; Castresana and Saraste 1995; Falkowski and Godfrey 2008; Holland 2006; Olson 2006; Schafer, et al., 1996). Thus once altered by photosynthetic organisms the environment acted on gene selection, and the rise in oxygen resulted in the diversification and increased complexity of the photosynthetic life that produced the oxygen that changed the atmosphere (Guo et al., 2009).

Although the genes necessary for creating a mitochondria may have been present when Earthly eukaryotes were first fashioned, it was not until the planet became sufficiently oxygenated other elements were released such as NADH that the metamorphosis of mitochondria ensued.

As genes act on the environment which acts on gene selection, additional genes were activated, and new functions, characteristics, and species began to appear. However, not just the eukaryotic genome was impacted, but the mitochondria genome. Mitchondria subsequently donated numerous genes which were integrated into the eukaryotic genome (Rogers et al., 2007) via a process Andersson (2005) refers to as “endosymbiotic gene transfer." These included genes coding for organelles and the endoplasmic reticulum, as well as genes contributing to the nucleus, and the bacterial-type plasma membrane that displaced the original archaeal membrane (Esser et al., 2004; Rivera andLake 2004).

Endosymbiotic gene transfers are a common and ongoing process in diverse eukaryotes (Bensasson et al. 2001; Leister 2003; Timmis et al. 2004). Further endosymbiotic gene transfer from mitochondria may have facilitated the invasion of group II introns into host genes (Martin and Koon, 2006) which served as the precursors of spliceosomal introns (Cavalier-Smith, 2009). These introns were most likely transferred into the eukaryotic genome through viral invasion. This implies a coordinated interaction between viruses, and genes contributed by bacteria and archae, such that once these genes were activated they triggered the metamorphosis of hosts which could then be invaded by viruses which inserted introns and other regulatory genes. This invasion of introns exerted a profound effect on the regulation of gene expression (e.g. Brietbart et al., 1985; Leff et al., 1986; Yoshihama et al., 2007), the expansion and duplication of the eurkayotic genome, and the evolution and metamorphosis of increasingly complex creatures.

22. OXYGEN AND EUKARYOTIC METAMORPHOSIS

Thus, mitochondria were either engulfed and formed a symbiotic relationship and donated its genes or they evolved from prokaryotic genes, around 2.3 - 1.8 bya, when increasing levels of oxygen acted on gene selection. Using sulfur isotopes to determine the oxygen content of ~2.3 billion year-old rocks, Guo and colleagues (2009) found that "the Archean-Proterozoic transition is characterized by the widespread deposition of organic-rich shale, sedimentary iron formation, glacial diamictite, and marine carbonates recording profound carbon isotope anomalies." This includes the first known anomaly in the carbon cycle indicative of a sudden increase in atmospheric oxygen. "All deposits reflect environmental changes in oceanic and atmospheric redox states, in part associated with Earth's earliest ice ages...a rise in atmospheric oxygen... and the Great Oxidation Event (ca. 2.3 Ga)."

Thus not just the metamorphosis of mitochondria but Earth's earliest ice age are linked to the rise of oxygen in Earth's atmosphere which was engineered biologically. As noted, changes in temperature can directly impact regulatory genes and proteins, thereby promoting the expression of traits which had been suppressed and contributing to evolutionary change. Therefore, during this same time period, when oxygen levels increased and temperature dropped, eukaryotic organisms with more than 2-3 cell types appeared (Hedges et al., 2004). This increase in energy availability (oxygen) and the ability to extract it (mitochondria) conferred major advantages for the eukaryotic host which became increasingly complex and expanded in size, made possible, in part, by the energy provided by mitochondria which used oxygen as an energy source. By 1.5 BYA, eukaryotes expanded to approximately 10 cell types (Hedges et al., 2004).

A billion years later, and by the onset of the Cambrian Explosion, so much oxygen had been released into the atmosphere that ozone was established which blocked out life-neutralizing UV rays. Those who breathed oxygen were at a signficiant advantage, increasing the number of environments they could invade and conquer. And then, all manner of complex life quite suddenly exploded upon the world stage. With the establishment of ozone, innumerable creatures could emerge from the sea or from beneath the soil and exploit new environments; environments which acted on gene selection giving rise to new capabilities and new species that had been precoded into genes inherited from ancestors which long ago lived on other planets.

In fact, many of these inherited genes, although in divergent species, were expressed within a 10 million year period during the onset of the Cambrian Explosion (Levinton, 1992; Kerr, 1993, 1995) following a period of extreme environmental change, i.e. global warming, followed by global freezing, another warming episode, and the flooding of the oceans with (cyanobacteria-produced) calcium; all of which coupled with increased oxygen levels, led to the most dramatic explosion of life in the history of Earth, 540 mya.

The "Cambrian Explosion" and the genetic and fossil record does not support Darwin's theory of "small steps. The metamorphosis of new species takes place in quantum leaps, following the activation of ancestral genes in response to environmental-biological interactions. These genetic mechanisms and environmental factors, explains why primitive animals without eyes, brains, hearts, or a muscular-skeletal system, inherited and came to posses the silent genes which code for these traits and organs, and why these genes and functions come to be selected, activated, and expressed in later emerging species almost simultaneously 540 mya, following biologically engineered alterations in the biosphere of planet Earth. These genes did not randomly evolve, they were inherited from the first Earthlings whose ancestors hailed form other more ancient worlds.

As will be detailed and explained in the following article and chapter (Joseph 2009c) what has been called a random evolution has been under precise genetic regulatory control. Genes are not randomly expressed, nor do they randomly evolve. They are inherited and their expression is highly regulated. Further, these genes were acquired through horizontal gene transfer from extra-terrestrial sources when space-journeying viruses, bacteria, and archae were cast from planet to planet, from solar system to solar system, and from galaxy to galaxy (Joseph and Schild 2010b). The first Earthlings, and their viral genetic luggage, already possessed all the necessary genes for genetically engineering the biosphere and for generating every life form which evolved on Earth. What has been called evolution can be likened to embryological development and is a form of metamorphosis: the replication of complex creatures that long ago lived on other planets.



Cosmology, 2009, Vol 1, 150-200
Peer Reviewed
THE EVOLUTION AND GENETICS OF
LIFE FROM OTHER PLANETS
Part 3
Bacteria, Viruses and ExtraTerrestrial Genes,
Genetic Libraries and Gene Transfer,
Introns, Exons, Transposons, Conserved Genes, Silent Genes,
Regulatory Genes, Whole Genome Duplication,
and the Big Brain, Big Breast Revolution

Rhawn Joseph, Ph.D.
Emeritus, Brain Research Laboratory, Northern California


ABSTRACT

What has been described as "evolution" is under genetic regulatory control and is a form of metamorphosis (Evolutionary Metamorphosis), the replication of life forms which lived on other planets. The genetic endowment of all Earthly life can be traced to common ancestors, and these genes were obtained and inherited from creatures which lived on other worlds. This genetic inheritance included exons, introns, transposable elements, RNA, ribozomes, and the core genetic machinery for translating, expressing, and repeatedly duplicating genes and the entire genome. The first creatures to arrive on Earth acted as interplanetary genetic messengers, and were accompanied by viruses which served as intergalactic genetic libraries and depositories for genes which are held in storage. Once on Earth, prokaryotic and viral 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 demonstrated by the evolution of primates and leading to the sexual revolution and the physical-sexual attributes of woman and man. Viral genes interact with prokaryote genes which have been transferred to the eukaryote genome in a highly regulated, choreographed, coordinated manner, and which is often of direct benefit to the host. Viruses also insert RNA templates of DNA which are easily integrated with the genome of the host, selectively targeting specific hosts before or after they evolve. These templates match the host genome and existed prior to the evolution of the host, and this indicates the original source must have been an extraterrestrial host. Throughout the course of history these highly regulated interactions between viruses and prokaryote and eukaryote genes have guided the pace and trajectory of evolution, such as by turning genes on and off and releasing precoded genetic instructions. Human evolution has been shaped by repeated episodes of viral invasions and the injections of viral genes which interact with prokaryote genes in a purposeful manner. This inherited extraterrestrial genetic machinery has acted purposefully to coordinate gene duplication and expression, speciation, and evolutionary innovation, thereby giving rise to a genetically regulated progression leading from simple to complex creatures including woman and man.



1. THE EVOLUTION OF LIFE FROM OTHER PLANETS

As detailed by Joseph and Schild (2010), life could not have begun on this planet for the following reasons: A) All the essential ingredients for creating life were missing on the new Earth, including, and especially oxygen, sugar, and phosphorus B) DNA and complex organic molecules would have been destroyed by the environment of the early Earth and even proto-organisms would not have been able to surive . C) Given the complexity of a single protein and a single macromolecule of DNA, statistically, there was not enough time to create a complex self-replicating organism on this planet. D) No one has ever created life from non-life, and E) Life was present on this planet from the very beginning.

There is only one logical, scientific explanation for the origin of Earthly life: Life on Earth came from life whose ancestry leads to other, more ancient worlds (Joseph 2000, 2009a,b,c, 2010; Joseph and Schild 2010a,b).

The first Earthlings likely included archae, blue-green algae (cyanobacteria), bacteria, viruses, and possibly single celled eukaryotes. Some of these creatures may have journeyed through space as spores, yet others may have dwelled and reproduced within planetary debris, and some may have lived beneath the surface of this planet before it was captured by this solar system (Joseph and Schild 2010b).

Many species of bacteria form spores (Marquis and Shin 2006) and some survive in a state of suspended animation for hundreds of millions of years (Satterfield et al. 2005; Vreeland et al. 2000). Single celled eukaryotic organisms, including yeast and fungi (Botts et al., 2009), also produce spores, often for reproductive purposes, but also in response to adverse, life threatening conditions. Therefore, it is possible that some simple eukaryotic organisms, and their descendants, along with trillions of other microbes, may have survived the destruction of the parent star system and the ejection of this planet during that sun's red giant phase and prior to supernova. If so, this would explain the presence of microfossils resembling yeast cells and fungi, discovered in 3.8 BY old quartz (Pflug 1978) and for the evidence of biological activity in this planet's oldest rocks (Nemchin et al. 2008; O'Neil et al. 2008).

This proposition is in fact supported by the discovery of microfossils recovered from the Orgeuil, Ivuna, Murchison, Efremovka and other meteorites (Claus & Nagy 1961; Hoover 1984, 1997; Nagy et al. 1962; Nagy et al. 1963a,b,c; Zhmur and Gerasimenko 1999; Zhmur et al. 1997), each of which may have originated on ancient planets which predate the origin of this solar system. Therefore, it appears that simple eukaryotic and prokaryotic organisms may have been deposited on this planet soon after it became a member of this solar system.

If single celled eukaryotes also arrived on this planet encased within debris, or if they emerged from deep beneath the surface of this planet, they may have phagatocized surface dwelling archae and bacteria and incorporated their genes. Or they may have been infiltrated by parasitic prokaryotes which donated genes to the eukaryotic genome, thereby triggering multi-cellularity and compartmentalization. A third possbility is that the first Earthly eukaryotic cells were created by the genetic fusion of bacteria and archae coupled with the injection of viral genes. Each of these scenarios leads to the same result: genes donated by archae, bacteria and viruses, in combination with biologically engineered environmental influences, gave rise to the first multicellular eukaryotes, which 4 billion years later, would eventually evolve into humans.

Evolution is not random. The step-wise, sometimes leaping progression leading from simple to complex species to the metamorphosis of humans was genetically regulated by complex genetic-environmental interactions resulting in the expression of precoded genetic traits encoded into genes acquired on other, more ancient worlds (Joseph 2000). In fact, many genes including those of the human genome, can be traced to viruses and backward in time to the "last common ancestors" of eukaryotes as well as to archae and bacteria. However, these genes did not originate in an Earthly-organic soup or deep sea thermal vent. These genes were inherited and obtained from microbial species whose ancestors arrived in debris jettisoned from other planets, and from species which already dwelled deep beneath this world before it became Earth. As most scientists agree that modern life can trace its origins to the first Earthlings, then we can conclude that all life on Earth has a genetic ancestry which leads to more ancient worlds.

Microbes continually exchange genes, including genes they have acquired from other species, such that trillions of copies are collectively maintained in the genetic libraries of innumerable single-celled creatures and their viral associates. Horizontal gene transfer has likely taken place on innumerable planets and wherever life comes in contact with life or with viruses. Therefore, when microbes are jettisoned into space, they carry with them vast genetic libraries, with different microbes and innumerable viruses maintaining different genetic luggage (Joseph 2000, 2009b; Joseph and Schild 2010b). In their role as intergalactic genetic messengers, and via mechanisms of panspermia, this is the equivalent of dispersing trillions of genes via innumerable microbes and viruses, thus insuring that at least some of this genetic cargo and these genetic libraries are delivered to other worlds. Therefore, once these microbes and viruses took root on Earth, they began exchanging the genes acquired form other worlds, and which became part of the genomes of Earthly multi-cellular eukaryotes.

Eukaryotes received from prokaryotes a variety of genes, proteins and transcription enzymes which have played a major role in genetic continuity, gene duplication, and synthesis and transcription of long DNA molecules, thus shaping and guiding what has been called evolution. These elements and genetic mechanisms, including RNA polymerase, replicative DNA polymerase, introns and transposable elements, enabled genes and entire genomes to be duplicated, increased genetic linkage, insured accurate replication, and helped guarantee the ability to accurately transmit genetic information following gene or whole genome duplication (Harris et al., 2003) over billions of years of time. Because individual genes as well as the entire genome can be duplicated and then transmitted to subsequent species, once these genes were activated by biologically induced changes in the biosphere, this gave rise to preprogrammed diversity and allowed the same trait or characteristic to evolve, seemingly independently, in numerous divergent species, almost simultaneously, as took place during the Cambrian Explosion 540 bya.

Via these genetic mechanisms, silent genes, gene sequence, and related elements that encode for advanced characteristic, such as the heart, eyes, and brain, could be duplicated and passed down for billions of years to subsequent species which would maintain these genes even without expressing them and without losing genetic information. However, over billions of years of time, in response to major alterations in the environment, after undergoing repeated duplications, and in reaction to environmental, regulatory, and other genetic signals, the traits coded by these silent genes were expressed. Ultimately this led to increasing multicellularity, then vertebrate complexity and the rapid evolution of new species including humans.

2. THE ORIGIN OF EARTHLY LIFE

Life had taken root on the surface of this planet by 4.2 BYA, a time when Earth was undergoing continual pummeling from rogue planets and the remnants and planetary debris produced by the exploding parent star and its planetary system (Joseph 2009a). The nature of the first and earliest surface-dwelling Earthlings can only be inferred indirectly based on the residue of photosynthesis, oxygen secretion, carbon isotopes, the structure of banded iron formations and high concentrations of carbon 12, or “light carbon;” all of which are typically associated with microbial life (Manning et al. 2006; Mojzsis et al. 1996; Nemchin et al. 2008; O'Neil et al. 2008; Rosing, 1999, Rosing and Frei, 2004; Schoenberg et al. 2002). Some of those microbes may have included single celled eukaryotes, as microfossils resembling yeast cells and fungi were discovered in 3.8 BY old quartz (Pflug 1978). Thus eukaryotes such as fungi and yeast cells were already proliferating upon the surface by 3.8 BYA, and they were no doubt accompanied by bacteria and archae--and this has been demonstrated by geo-physical and biochemical analysis indicating evidence of biological activity from 4.2 to 3.8 bya (Manning et al. 2006; Mojzsis et al. 1996; Nemchin et al. 2008; O'Neil et al. 2008; Rosing, 1999, Rosing and Frei, 2004; Schoenberg et al. 2002).

3. THE FIRST EUKARYOTES

As detailed in Part 1 and elsewhere (Joseph 2009a; Joseph and Schild 2010b), archae, bacteria, and viruses can survive in almost any extreme environment, and bacteria and viruses are also preadapted to surviving the harsh conditions of space. Further, microfossils resembling archae, bacteria, and viruses have been discovered in meteors which predate the origin of this solar system and which may have originated on other planets. As there is no evidence that Earthly life can be produced from non-life, then the only scientific explanation for the origin of Earthly life is panspermia, i.e. life was deposited on this planet contained in comets, asteroids and planetary debris (Hoyle and Wickramasinghe, 1984, 2000; Joseph 2000, 2009a,b; Wickramasinghe et al., 2009).

As detailed by Joseph and Schild (2010a), life could never have begun on this planet, but was most likely first fashioned in a nebular cloud, long before Earth or this solar system were formed. Life may had more than one origin (Joseph 2010).

Once life became life then through mechanisms of panspermia, its descendants were cast from planet to planet, from solar system to solar system, and from galaxy to galaxy, and over eons of time, life evolved, diversified, became increasingly complex, then sentient and intelligent. And just as takes place on this planet, genes were exchanged through horizontal gene transfer. Thus, bacteria, archae, and viruses began acquiring vast genetic libraries, and eventually the descendants of these creatures, accompanied by their viral luggage, arrived on Earth (Joseph and Schild 2010b).

Woese (2004) has proposed that these initial bacteria, archaea and eukaryotes may have lived together and repeatedly swapped and shared genes. "Eventually this collection of eclectic and changeable cells coalesced into the three basic domains known today. These domains become recognisable because much (though by no means all) of the gene transfer that occurs these days goes on within domains" (Woese, 2004).

However, another important factor effecting eukaryotic evolution was the injection of viral genes. On the modern Earth bacteria are everywhere and are generally surrounded and outnumbered by viruses at a 1 to 10 and 1 to 100 ratio. Viruses often serve as genetic libraries, containing vast number of genes (Claverie 2005) which are often selectively provided to bacteria such as in times of stress, and which enhance bacteria functioning and even promote bacterial evolution (Lindell et al., 2004; Sullivan et al., 2005, 2006; Williamson et al., 2008; Zeidner et al., 2005). Viruses also provide genes to the eukaryotic genome (Conley et al., 1998; Medstrand et al., 2002) and some of these genes appear to have been involved in triggering evolutionary transitions such as between monkeys and apes and apes and hominids (López-Sánchez et al., 2005; Romano et al., 2007).

Evolution has been likened to metamorphosis and embryogenesis (Joseph 2000, 2009a,b). And just as embryological development and metamorphosis are under genetic-environmental control, what has been called a random "evolution" is also regulated by genes and the changing environment. And just as life comes from life, these genes were also inherited from other life forms, copies of which were obtained from creatures which long ago lived on other planets and which were deposited on Earth, like so many seeds, contained within the genomes of prokaryotes and viruses. And just as apple seeds contain the genetic instructions for the generation of apple trees, these extraterrestrial genetic seeds contained the genetic instructions for the tree of life, the replication of creatures which dwelled on other planets. However, rather than a single season, or a few years, it may take billions of years to genetically engineer a suitable planet and to grow complex species such as humans. Thus, in this regard, viruses, prokarotes and eukaryotes can be viewed as a genetic superorganism which interacts to promote evolution and metmorphosis.

Therefore, it is suspected that hundreds of millions of years after arriving on Earth, archae, bacteria, and virus may have joined together, combining their genomes, and in so doing, created the first multi-cellular eukaryotes, and/or they donated genes to the single celled eukaryotic genome, triggering multicellularity and increasingly complex eukaryotes which, nearly 4 billion years later, would give rise to humans.

4. ARCHAE VS BACTERIA: GENE TRANSFER

Numerous species of bacteria act as endosymbionts or endoparasites (Dyall et al., 2004; Poole and Penny 2007). Viruses are parasitic by nature. Archaea do not generally serve in this capacity--though there are exceptions as archae and associated viruses have been found in the human gut. Bacteria and viruses are completely distinct and even within species there are significant differences (Nakabachi et al., 2006; Ranea et al., 2005; Schulz and Jorgensen 2001; Schneiker et al., 2007) .

Considered in the broadest terms, archaea are highly distinct from bacteria, particularly in regard to the size of their genomes and cell membranes. For example, archaean membranes are made of ether lipids where as bacterial cell membranes are created from phosphoglycerides with ester bonds (De Rosa et al., 1986). Like bacteria, archae can live in the most extreme environments (Kimura et al, 2006, 2007; Leininger et al., 2006; Robertson et al., 2005). However, whereas bacteria are usually (but not always, e.g. Leininger et al., 2006) the most common form of life in the soil, archaeota are the most common form of life in the ocean, dominating ecosystems below 150 m in depth (Karner et al., 2001; Robertson et al., 2005).

The genomes of archae are rather uniform and compact in size ranging from 0.5 Mb in the parasite Nanoarchaeum equitans (Waters et al., 2003) to 5.5 Mb in Methanosarcina barkeri (Maeder et al., 2006).

Bacterial genomes can vary by two orders of magnitudes, from 180 kb in an intracellular symbiont, Carsonella rudii (Nakabachi et al., 2006), to 13 Mb in Sorangium cellulosum which dwells in soil (Schneiker et al., 2007). Although there are bacterial genomes of intermediate size, the vast majority of bacteria so far sequenced show a clear-cut bimodal distribution of genomes; i.e. large vs small, suggesting the existence of two distinct classes of bacteria: those with ‘small’ genomes (Ranea et al., 2005) with the highest peak at 2 Mb and those with "large" genomes at about 5 Mb (Schulz and Jorgensen 2001).

By contrast, eukaryotic genomes range wildly in size and are generally several magnitudes larger than those of prokaryotes. However, the genomes of some eukaryotic species, such as microsporidian Encephalitozoon cuniculi (Katinka et al., 2001) are substantially smaller than many bacteria and archaeal genomes. Encephalitozoon cuniculi is also a parasite and may serve as a genetic messenger.

Likewise, those bacteria and archae with the smallest genomes share a significant behavioral feature with Encephalitozoon cuniculi: they too are parasites and they prey upon other prokaryotes as well as eukaryotes (Waters et al., 2003; Huber et al., 2002). It is these parasitic behaviors which may explain their small genomes, and the presence of prokaryotic genes in the eukaryotic genome. These prokaryotes likely donate their genes after invasion or they form parasitic relations with those eukaryotes who already maintain these genes in their genomes. Moreover, many species of parasitic bacteria/archae have taken up residence inside a eukaryotic host after which they continued to transfer and donate genes (Dyall et al., 2004; Margulis et al., 1997).

Once donated many of these genes were not replaced due to genetic mechanisms which ensure that they will only become activated in targeted eukaryotic species

For example, prokaryotes with the smallest genomes, i.e. parasitic and symbiotic bacteria and archaeal parasites (e.g., N. equitans) no longer encode or express a variety of protein regulators, indicating the responsible genes have been transferred to the genome of the eukaryotic host. With the donation of these regulatory genes, the genomes of these parasitic and symbiotic prokaryotes decreased in size.

Hundreds of specialized prokaryotic genes have been donated to the genomes of their hosts, possibly by horizontal gene transfer (Yutin et al., 2008) and were then preserved, unchanged, often in the same position even after hundreds of millions and, perhaps, even after billions of years of evolution. Some of these donated genes appear to to be responsible for the metamorphosis of mitochondria which also donated genes to the eukarayote genome (Margulis et al., 1997).

These prokaryotic genes and bacteria/archae symbionts, enabled eukaryotes to become increasingly complex and to colonize and conquer new environments which were being genetically engineered by prokaryotic genes. For example, genes which are responsible for photosynthesis altered the environment via the liberation, secretion, and synthesis of a variety of chemicals and enzymes including oxygen (Buick 1992, 2008; Falkowski and Godfrey 2008; Holland 2006; Olson 2006; Williams and Fraústo da Silva 2006). Much of this photosynthesizing activity was carried out by cyanobacteria (blue green algae). However, as has been demonstrated (Lindell et al., 2004; Sullivan et al., 2005, 2006; Williams et al., 2008), viruses provided cyanobacteria with genes which enhanced their ability to engage in photosynthesis, thus releasing oxygen which acted on gene selection, activating genes contributed by bacteria, archae, and viruses, giving rise to new traits and new species perfectly adapted for a world that had been prepared for them.

5. VIRUSES AND GENE DONATION

Viruses serve as vast storehouses of genetic information and they remain viable even after these genes are transmitted to other species. Viruses act as gene conservatories and can increase the gene pool within the genome of a host (Sullivan et al., 2006; Zeidner et al., 2005). Some of these genes are transferred to other hosts only during times of environmental stress which threaten potential hosts. After these genes are transferred and when activated they benefit not only the host but innumerable life forms. For example, viruses store genes which code for photosynthesis (Lindell et al., 2004; Sullivan et al., 2005, 2006) and the conversion of light to energy (Williams et al., 2008). However, these genes provide no direct benefit to the virus and are transferred to the genomes of photosynthesizing organisms, such as cyanobacteria, during periods of reduced sunlight and when there are insufficient nutrients to maintain energy output (Sullivan et al., 2006). When cynobacteria receive these genes they are able to maintain or even increase photosynthetic activity during these periods of environmental stress, which means oxygen continues to be excreted into the atmosphere even after prolonged periods of decreased sunlight or nutritional depletion. The beneficiaries are all oxygen breathing creatures, and their genes. When sunlight or energy supplies increase, these genes are no longer necessary and are transferred back to the virus genome for storage (Lindell et al., 2004; Sullivan et al., 2005, 2006). Viruses maintain vast genetic libraries and the function and purpose of most of these genes are unknown.

When a virus invades a single celled organism, it may donate its genes which become incorporated into the genome of the host. When viruses invade eukaryotes, they may sicken the host and eventually die. However, virus induced illness appears to be a genetic programming error, due to a mis match between virus and host.

Often viral genes may be inserted into the genome of the host germline and are then passed on to offspring and subsequent species. These later type of viruses are called endogenous retrovirus (ERV) and they have had a direct impact on evolution leading to humans. In fact, human evolution has been shaped by successive waves of viral invasion (Sverdlov, 2000).

Endogenous retroviruses can alter host gene function and genome structure and the evolution of eukaryotic hosts. For example, in mammals, including humans, ERVs play an active role in placental, embryonic, and brain development (Anderson et al., 2002; Patzke et al., 2002 ; Wang-Johanning et al., 2001, 2003). Although viruses are often associated with disease, ERVs often provide substantial benefits to the host and are often subverted by the host for its benefit (Parseval and Heidmann 2005; Lorenc and Makalowski. 2003; Miller et al., 1999). For example, ERVs are responsible for the generation of proteins involved in the formation of placenta (Mi et al., 2000; Blond et al., 2000). ERVs promote cell fusion (Mi et al. 2000, Blaise et al. 2003) and provide a protective function, allowing for nutrients to pass from mother to fetus while simultaneously protecting the fetus against infection or rejection by the mother's immune system  (Ponferrada et al., 2003; Prudhomme et al., 2005). ERVs are also highly expressed in many human fetal tissues including heart, liver, adrenal cortex, kidney and the central nervous system (Anderson et al., 1996, 2002).

ERVs are very active in the human genome (Lower et al., 1993; Medstrand P, Mager DL. 1998). They regulate human gene expression (Jordan et al., 2003; van de Lagemaat et al., 2003) and contribute promoter sequences that can initiate transcription of adjacent human genes (Conley et al., 2008). ERV-derived promoters have been found in roughly a quarter of all the human promoter regions so far examined.

There is nothing random about these viral-host interactions. Nor can they be explained by Darwin's theory of evolution or Darwinian notions of natural selection. Rather, these collaborative interactions are purposeful, highly coordinated, and under precise genetic, regulatory control.

Eukaryotic evolution, in general, has been impacted by repeated episodes of viral invasion and the insertion of viral genes into the host genome and which have conferred functional advantages to the host. Tens of thousands of viral genes exert regulatory control over gene duplication, and mediate gene and genome rearrangement, transduction and the silencing vs activation of genes (Crombach and Hogeweg 2007; John and Miklos 1988). Further once inserted, these viral genes can rapidly replicate and increase in number (Doolittle and Sapienza 1980; Tsitrone et al., 1999). They can also insert themselves into a variety of locations within the genome where they may promote gene expression or duplication; and this has been shown to be true even in the human genome. These ERV sequences, such as promoters, enhancers, and silencers determine when and which genes should be turned on or off and play important roles in the evolution of new species and in fetal and brain development.

ERVs have invaded the germ cell lines of all species of vertebrate. Once incorporated into the genome, they replicate in Mendelian fashion, and are transmitted via the germline as an integral part of the sexual reproduction of the host. However, genomes and germlines of subsequent species may also be invaded. It is because of repeated viral invasion and viral gene duplication, and the role these viral genes play in host gene replication, that the so many eukaryotic genomes have become enormous in size.

Retroelements encompass 42.2% of the human genome and almost half of the mammalian genome (Deininger and Batzer 2002; van de Lagemaat et al. 2003). The human genome contains 200 000 copies of endogenous retroviruses grouped in three classes (Lander et al. 2001), which have been introduced through at least 31 infection events (Belshaw et al. 2005). Coupled with the 158,000 mammalian retrotransposons inherited from common ancestors, ERVs make up 8% of the human genome (IHGSC 2001). Retroviral sequences encode tens-of-thousands of active promoters and regulate human transcription on a large scale (Conley et al., 2008). However, these percentages are only gross underestimates.

Endogenous retroviruses show a significant tendency to recombine thereby creating a variety of different recombination products. When a retrovirus reproduces, identical copies of viral gene sequences are created on either side of the retroviral element. When two different proviruses combine this can lead to substantial deletions or rearrangements of cellular DNA (Sun, et al. 2000) resulting in a high frequency of gene conversion events (Johnson and Coffin 1999). However, because these retrogenes can rapidly reproduce, recombine, and then spread to new positions, the oldest insertions are impossible to recognize as viral genes (Eickbush and Jamburuthugoda 2008), even in the human genome, and may be misidentified as bona fide human genes (Parseval and Heidmann 2005).

Human endogenous retroviruses, therefore, have induced large-scale deletions, duplications and chromosome reshuffling over the course of human genomic evolution (Hughes and Coffin 2001). This has been accomplished by enhancing transcription levels, altering tissue specificity of gene expression, or creating new gene products with modified functions. Hence, viral elements have played a major role in mammalian-primate-human evolution and they have interacted with genes donated to the eukaryotic genome by prokaryotes.

5. CONSERVED GENES & GENE EXPRESSION

The number of eukaryotic genes which were donated by prokaryotes or viruses is unknown, though ultimately it may be that all eukaryote genes are derived from prokaryotes. Thousands of orthologous genes and hundreds of conserved genes can be traced back to the last common ancestor for eukaryotes (Snel et al., 2002; Mirkin et al., 2003; Kunin and Ouzounis 2003; Koonin 2003; Mushegian 2008; Bejerano et al., 2004). Almost all underwent duplication at the onset of eukaryotic evolution (Makarova et al., 2005), which, when coupled with gene deletions, exon shuffling, and the transposing of genes to other regions of the genome, obscured and erased considerable evidence of their prokaryotic origins.

These genes then continued to undergo repeated episodes of single gene and whole genome duplication such that the eukaryotic genome increased in size. However, these duplications were continued to be coupled with gene deletions and transpositions further obscuring their original relationship with prokaryotes and viruses.

Almost all of the genes donated by prokaryotes, including many inserted by viruses, have performed crucial functions that have guided the trajectory of evolution. These donated genetic elements included regulatory genes and genes controlling core cellular activities and the capacity to make duplicates of individual genes and the entire genome.

Genome sequencing has revealed an extensive conservation of the same repertoire of genes coding for core cellular functions in the genomes of prokaryotes and eukaryotes (Koonin et al., 2004; Koonin and Wolf 2008). A core set of approximately 70 genes contributed by archae and bacteria have been identified. These have been conserved and passed down, without deletion, for billions of years, and make up around between 1% to 10% of the genes in the genomes of all multicellular life (Koonin 2003; Koonin and Wolf, 2008; Harris et al., 2003; Charlebois and Doolittle 2004).

These conserved genes, proteins, (Koonin 2002) and gene sequences (Koonin 2009b), include those governing translation, the core transcription systems, and several central metabolic pathways, such as those for purine and pyrimidine nucleotide biosynthesis (Koonin 2003). Moreover, protein sequence conservation extends from mammals to bacteria thus demonstrating their great antiquity (Dayhoff et al., 1974; Eck and Dayhoff 1966; Dayhoff et al., 1983).

Between 2150 to 4137 orthologous gene sets are highly conserved and can be traced back to the last common ancestor for eukaryotes (Makarova et al., 2005). And often these orthologs express or perform the same function regardless of species. In the human genome, these ultraconserved elements often overlap introns or genes involved in the regulation of gene transcription and expression.

6. CONSERVATION OF VIRAL INTRONS

DNA includes stretches of nucleotides, called exons, that are encoded and expressed to produce various proteins (De Souza et al., 1996). These strings of nucleotides are punctuated, bracketed, framed, and interspersed with long stretches of non-encoding DNA, called introns (Belfort, 1991, 1993; Breathnach et al., 1978; Buchman and Berg 1988; Witkowski, 1988) which regulate and signal which lengths of exons are to be expressed (Belfort, 1991, 1993; Breathnach et al., 1978; Witkowski, 1988).

Introns are directly relevant to the regulation of gene function and expression and RNA processing and have also been highly conserved across lengthy periods of evolutionary history. Introns have been preserved often in the same places in the genome, over the course of evolution, be it the genes of Drosophila melanogaster (the fruit fly), Caenorhabditis elegans (nematode), mice, or humans (De Souza et al., 1996; Federov et al., 2002). Thus the positions of a large number of introns are conserved between plants and vertebrates (Fedorov, et al., 2002; Rogozin et al., 2003; Roy and Gilbert 2006) and between mammals and "living fossils" such as as Trichoplax and the sea anemone (Putnam et al., 2007; Srivastava et al., 2008); species which diverged over a billion years ago. This includes the positions of a large fraction of introns with 25–30% conservation in orthologs from plants and chordates (Fedorov et al., 2002; Rogozin et al., 2003; Roy and Gilbert 2006). This extreme conservation and preservation of their positions within genes and the genome, attests to their importance in regulating and coordinating the evolution and metamorphosis of numerous species.

Introns are of particular importance in regulating gene expression (Brinster et al., 1988; Buchman and Berg, 1988; Collis et al., 1990; Lai, et al., 1998; Noe et al., 2003) and play a major role in the regulation of gene transcription and the creation of new genes from old genes. If different "starter" or "stop" introns are activated this results in different segments or sequence lengths becoming expressed, thereby producing a different protein product (Belfort, 1991, 1993; Breathnach et al., 1978; Breibart et al., 1985; Leff et al., 1986) which can give rise to different tissues and organs. Hence, variation and diversity can be differentially induced if different "starter" or promoter introns are activated.

Some introns are found within or in association with ribosomes (Dürrenberger and Rochaix 1991; Jackson et al., 2002; Toro et al., 2007; Yoshihama et al., 2007). The functional part of the ribosome is fundamentally a ribozyme, the molecular machine that translates the RNA copies of exons into proteins (Cech 2000). Thus introns, in association with ribosomes play a major role in translation, transcription and protein synthesis. Ribozymes are also able to splice themselves and other introns out of the original transcript created by these RNA molecules (Jackson et al., 2002). Ribozymes can also be found in the intron of RNA transcripts, which had been removed from the gene sequence being processed and expressed.

Mitochondrial ribosomes and introns are considered to be of bacterial origin (Kenmochi et al., 2001); a product of endosymbiosis (Dyall et al., 2004; O'Brien 2002). Ribosomal introns and protein sequences which circulate in the cytoplasm appear to have originated in the archae genome, and were later donated to eukaryotes, as there is a specific affinity between eukaryotic genes and their orthologs from archae (Lake et al. 1984; Lake 1988; 1998; Rivera and Lake 1992 Rivera and Lake 2004 Vishwanath et al. 2004). Archae and bacteria, therefore, were a major source of introns and ribosomes.

However, viruses can also donate regulatory elements to prokaryotes who in turn may horizontally transfer these genetic elements to eukaryotes. Viruses can also directly insert regulatory elements into the eukaryotic genome, including the genome of humans. For example, group II introns and ribozymes which are derived from viruses are found in the genomes of archae, bacteria, and eukaryotes (Dai and Zimmerly 2003; Dai et al., 2003). This suggests that viruses may have served as a genetic storehouse for introns and ribozymes which were subsequently transferred to prokaryotes and eukaryotes. In bacteria, approximately 35% of group II introns are linked to plasmids and are thus highly mobile (Dai et al., 2003; Klein and Dunny 2002) and can exit the bacteria genome and insert themselves into the genomes of eukaryotes, prokaryotes, and possibly back into the viral genome.

Group II introns are highly mobile retroelements (Belfort et al., 2002. Lambowitz et al., 1999; Lambowitz and Zimmerly 2004) and include retrotransposons (Beauregard, et al., 2008) and are progenitors of nuclear spliceosomal introns (Cavalier-Smith 1991; Jacquier 1990; Sharp 1991). They can splice together exons (Bonen and Vogel 2001; Michel and Ferat 1995), thereby creating genes from genes. Spliceosomes and spliceosomal introns are responsible for splicing out introns and transposable elements, and insuring that the genetic sequences in introns are not translated into proteins. Thus, they regulate gene expression and help guarantee that only designated exons are translated and transcribed (Roy and Gilbert, 2006).


Spiceosomal introns and are found in the nuclear genes of higher eukaryotes including humans (Doolittle 1978; Gilbert 1978; Mattick 1994; Deutsch and Long 1999). However, they appear to have originated in viruses and prokaryotes and may have been first transferred to the eukaryotic genome billions of years ago. Indeed, group II introns are also self-silencing, and can thus be passed down vertically for hundreds of millions of year and then become activated in response to changing environmental or regulatory conditions. In fact, many viral genes and regulatory elements are activated by specific environmental triggers (Ackermann et al., 1987. Brussow et al., 2004) and may be transferred to other species where they are then expressed.

Thus, genes involved in transcription regulation and which were donated by viruses and prokaryotes to eukaryotes interact with and overlap genes and introns also contributed by viruses and prokarayotes to eukaryotes. Moreover, these same genes were repeatedly duplicated and dispersed to a wide range of divergent species, and when activated gave rise to identical or similar evolutionarily advanced characteristics such as the photoreceptors of the eye and the nerves and neurotransmitters of the brain. In fact, Presumably, viral genes which have become part of the eukaryotic genome are involved in the generation and metabolism of nerve tissues and the brain (Andersson et al., 2002; Conley et al., 2008; Seifarth et al., 2005) whereas yet others code for photoadaptation and the conversion of light to energy (Williams et al., 2008). Thus, viruses, these intergalactic genetic messengers, have also provided eukaryotes with the genes necessary to evolve highly complex perceptual and intellectual organs such as the eye and brain.

7. GENE CONSERVATION: THE EYE OF THE BEHOLDER

It has been claimed that the chief components of the eye, such as photoreceptors must have evolved essentially de novo 40–65 times independently according to Darwinian principles (Salvini-Plawen & Mayr 1977). However, genes do not evolve de novo or ex nihilo; they are transferred from another species, inherited from an ancestral species, or they are produced by exon shuffling, whole gene duplication, and numerous other replicative mechanisms.

Genes involved in eye development, known as Pax, "Pax-6" and opsin in vertebrates and "eyeless" in fruit flies, are homologous between diverse phyla (Quiring et al., 1994; Gehring & Ikeo 1999). Pax genes ("Pax-6") have also been found in the genomes of ancient species such as the sea urchin and trichoplax, both of which have no eyes and cannot see (Sodergren et al., 2007; Callaerts et al. 1997; Hadrys et al., 2005).

Pax-6 serves as a master regulator of a network of genes that can give rise to a variety of different types of eyes that utilize the same visual pigment genes. That is, Pax-6 appears to act on different genes to produce the different structures on which the pigment cells are mounted in different creatures giving rise to a variety of eyes (Sheng et al., 1997; Gehring and Ikeo, 1999; Davidson, 2001).

Moreover, Pax 6 proteins show an 90-90% identity between vertebrate and invetebrates (e.g. squid) as well as insects (Drosophila) and marine worms (Tomarev, 1997). These genes also utilize identical homologous Pax-6 proteins during eye development (Gehring & Ikeo 1999). As the common ancestors for vertebrates and invetebrates diverged between 600 mya to 1.6 bya (Ayala et al., 1998; Wray et al., 1996; Gu, 1998; Cutler, 2000), this is an indication of the great antiquity of Pax genes--many of which can be traced to ancestral species who had no eyes and were unable to see. Those ancestors could include prokaryotes and possibly viruses.

Consider, for example, vitamin-A-related chromophores in the visual pigment and which is the single most prerequisite for vision in the vertebrate or invertebrate genome. Vitamin-A-related chromophores are also found in bacteria as well as algae (Seki and Vogt 1998; von Lintig, J., Vogt 2004).

These highly conserved genes were then passed down through numerous diverging ancestral species until activated in the period leading up to and including the Cambrian Explosion. Over 1000 genes involved in visual functioning, including ancestral Pax-6 genes, were inherited and are homologous between phyla (Gehring and Ikeo, 1999; Quiring et al., 1994; Tomarev et al. 1997), and have been isolated from invertebrate and vertebrate species, including squid, flatworm, ribbonworm, ascidian, sea urchin, nematode, and fruit flies (Callaerts et. al., 1997; Tomarev, 1997).

Be it vertebrate, flatworm or insect, and in spite of the large differences in eye morphology and mode of development (Gehring 1996), the same genes and same gene products related to the visual system are under the same genetic control (Quiring et al., 1994). Thus, regardless of species some parts of the eyes are homologous because they are coded by the same genes and the same proteins.

Between 70% to 80% of these genes are common and evolutionary conserved in the genomes of mammals, squid, octopus, flatworm, ribbonworm, ascidian, and nematode mosquitos, flies, tunicates, and vertebrate genomes including humans (Ogura et al., 2004). The common ancestors for these species diverged anywhere from 1.2 bya to 830 million years ago (e.g., Wray et al., 1996; Peterson et al., 2004, Nei et al., 2001; Gu 1998). As there is no evidence for visual functioning in any creature before 550 mya, these genes were therefore inherited, in silent form, from ancestral species which could not see.

8. CONSERVED GENES AND VIABILITY

Regardless of their activity, genes that are highly conserved over the course of eukaryotic evolution not only remain in the same location but accumulate fewer substitutions in their protein sequences. Therefore the conservation of a gene and regulatory elements including introns, and the fact they are passed down vertically to subsequent species and are maintained unchanged in the same position, indicates biological importance. Further, many of these genes are passed down in silent form, and thus could not have been naturally selected according to Darinwian dogma. Then there is the fact that many of these conserved genes, once expressed by introns, play identical roles, almost regardless of species, and contribute to the progression known as "evolution." Darwinians are forced to engage in embarrassing mental gymnastics to make these findings compatible with Darwin's theory, and thus either ignore the evidence, or claim its just "nature's way of arriving at the same solution." All we need do is substitute the world "god" for "nature" to be confronted with the realization that these Darwinian explanations are little more than religion masquerading as science.

The importance of these conserved genes may also have more to do with the future of evolution rather than the survival of the species possessing that gene. Darwinian concepts of "Survival of the fit" or "natural selection" explain nothing. In fact, some highly conserved genes can be removed (knocked out) of various genomes without having any noticeable impact on the viability of the organism or its ability to function (Koonin 2000). Hundreds of genes have been knocked out, or stripped from the genomes of various species which remained viable (Glass et al., 2006; Koonin 2000).

Mycoplasma genitalium, for example, has one of the smallest genome of any organism but remained viable even after 100 of its 482 genes were removed (Glass et al., 2006). Further, 28% of the minimal set of genes coded for unknown functions (Glass et al., 2006). Moreover, 80 genes of the original minimal gene set were represented by orthologs in all forms of life and many of these coded for unknown functions (Koonin 2000).

Mycoplasma genitalium

Therefore, not all highly conserved genes are related to the viability or "fitness" of the organism. Nor were they conserved because of "natural selection." Many were passed on in silent form, and may serve to facilitate the evolution of new characteristics and thus species when they are activated in response to specific biologically environmental conditions. Therefore, highly conserved genes whose functions are unknown, may be held in reserve, in storage, and transmitted vertically and thus are inherited by yet other species where they may then be activated. And viruses may well be aiding in the transfer or storage of these genes.

9. VIRUSES AND GENOME DUPLICATION

Broadly considered from the genomic perspective, there are two types of viruses, those with an RNA genome and those whose genome consists of DNA. DNA viruses are completely dependent on the host cell's DNA and RNA synthesising and processing machinery. By contrast, RNA viruses manufacture their own RNA replicase enzymes and can therefore replicate themselves by hijacking the host cell's RNA machinery within the cytoplasm.

Retroviruses, however, take yet another step to become intwined with and part of the host genome. These viruses manufacture enzymes, reverse transcriptase, to reverse transcribe the host's RNA to create a complementary viral DNA.

Autonomous retrotransposable elements, for example, make copies of themselves by releasing reverse transcriptase, which is an RNA-dependent DNA polymerase, and this substance catalyzes reverse transcription of RNA transcripts into DNA, thus producing new copies of the retroelement and increasing their number by duplication. Retrotransposition is largely responsible for the very high copy number reached by retroelements in many vertebrate genomes.

Therefore, viruses contain the genetic instructions necessary for duplicating not just individual genes, but an entire genome.

After the RNA genome of an extracellular retrovirus is copied into DNA by virus-encoded reverse transcriptase it is then integrated into the nuclear DNA and thus the chromosome of the host cell via a viral enzyme integrase (Vogt 1997). Yet other retroviruses transpose via DNA excision and reintegration into the host genome (transposons). Integration is highly stable and, consequently, infection of germ line cells can lead to vertical transmission of retroviruses from parent to offspring as Mendelian alleles (Boeke and Stoye 1997).

Thus there are two classes of retroviruses based on their mechanism of mobilization: those that transpose via DNA excision and which are associated with transposons, and those involving an RNA intermediate and which are represented by retrotransposons and endogenous retroviruses (ERVs). These employ reverse transcriptase that copies the viral RNA template to its complementary DNA, which is then integrated into the chromosomes. The integrated DNA of a retrovirus is called a provirus.

10. VIRUSES TARGET SPECIFIC HOSTS TO PROMOTE HOST EVOLUTION

ERVs are relics of ancient viral infection events in the germ line, followed by long-term vertical transmission. They can increase in copy number by means of active replication or by chromosomal duplication (Boeke and Stoye 1997). The latter property provides a means for retroviruses to colonize the germ line. Therefore, the progeny of the infected germ cell will inherit the provirus formed as an endogenous retrovirus (Boeke and Stoye 1997).

A considerable proportion (~45%) of the primate genome consists of copies of mobile genetic elements (Landers et al., 2001). Retroelements constitute 90% of the ≈3 million transposable elements present in the human genome (Deininger and Batzer 2002) Analysis of human genes reveals that mobile elements, including retroelements, are overrepresented in the mRNAs of rapidly evolving mammalian genes. These findings point toward an active role for transposable elements in the diversification and expansion of gene families, increasing the speed of evolution in humans and other mammals.

Thus, be it RNA or DNA viruses, all are able to use the host's genetic endowment to create multiple copies of the virus genome. Likewise, it appears that viruses have donated some of their own replicative machinery into the genomes of prokaryotes and eukaryotes, as well as a variety of other genes. For example, the human genome contain over 3 million viral genetic elements and around 200,000 viral genes (IHGSC 2001; Medstrand et al., 2002), many of which are still active (Conley et al., 1998; Medstrand and Mager, 1998).

These donated viral genes, in turn,would have increased the size of the genome, and have played a major role in single gene and whole genome duplication. That is, just as viruses use the host genome to replicate the viral genome, this same genetic machinery may, in response to specific biologically engineered environmental signals, replicate and duplicate the genome of the host within which are embedded viral genes and other viral elements. In consequence, the host may evolve or at least acquire new or increased capacities enabling it to diversify and expand its host range and conquer additional niches and environments (Sullivan et al., 2005; Williams et al., 2008).

Therefore, if viruses provided these genes during the early stages of eukaryogenesis, this would explain why the eukaryotic genome duplicated in size soon after it was fashioned, and why these particular genes, so important to gene duplication, may have been preserved and conserved; that is, for the purpose of additional genome duplications.

Most viruses target bacteria. However, in this capacity they could be acting as gene banks, transferring, receiving, and storing genes on behalf of trillions of species of bacteria; genes which could also be inserted into the eukaryote genome as specific eukarotic species evolve. Viruses acting as genetic storehouses, therefore, could have inserted the necessary or additional whole-genome-duplicating genes, periodically, over the course evolutionary history. However, if viruses first provided some of these genes to prokaryotes which transferred these genes to eukaryotes, or if they transferred these genes to eukaryotes, although highly conserved, all traces of their original ancestral viral origin would be obscured or erased.

It must be emphasized that the defining feature of the viruses including retroviruses, is that they are host-specific. Further, the viral RNA genome is actually a template for DNA which must have been copied from another source. Further, the virus acts purposefully, targeting and inserting this DNA into specific hosts including the genetic instructions necessary for duplicating not just individual genes, but an entire genome. The ease at insertion and integration, the fact that they viral gene-host genome are a perfect match, indicates that the original viral source for this RNA template of DNA was the DNA copies from an identical host. However, as they are "relics" of ancient infections, this indicates that prior to infection these hosts did not possess the DNA which was inserted into their genome. Further, as these viral agents must have existed prior to the evolution of these hosts, then they must have obtained these RNA DNA-templates from identical hosts which must have existed on other planets. This would explain not just the perfect virus-host match and the ease of viral DNA insertion, but the fact that these inserted genes often interact smoothly with a network of host genes, often to benefit the host, and act to purposefully increase the size of the genome and to promote and speed up speciation and evolution.

11. GENE REPLICATION, FUNCTIONAL PRESERVATION, & WHOLE GENOME DUPLICATION

Genes donated by prokaryotes and viruses to the eukaryotic genome, engage in coordinated, highly choreographed interactions to regulate gene expression, suppression, duplication, and preservation. Throughout the course of history these interactions have provided direct benefits to the host and have guided the pace and trajectory of evolution.

Some highly conserved regulatory genes and proteins act as a genetic mechanism through which prokaryote genes, gene sequences, and proteins, can be inhibited and suppressed even as they are repeatedly duplicated within the eukaryotic genome. Thus, via these inhibitory mechanisms, conserved genes and the functions they code for can be preserved even as they grew in number and are passed down to subsequent species over hundreds of millions and even billions of years; at which point they may be expressed in response to biologically engineered changes in the environment.

For example, archae and bacteria contributed three subunits of the core DNA-dependent RNA polymerase (Iwabe et al. 1991; Klenk et al. 1993) and two enzymes of DNA metabolism, RecA and Pol1A to the eukaryotic genome (Eisen and Hanawalt 1999; Harris et al., 2003) . These enzymes and the core RNA polymerase subunits serve many regulatory and replicative functions. Both RecA and Pol1A contribute to genetic continuity by gene conversion after recombination. They also insure the integrity and maintenance of genetic information as the lengths of DNA strands increase and the genome grows larger in size (Eisen and Hanawalt 1999).

The replicative DNA polymerase, DnaN (COG0592), and the gene for the “sliding clamp” were also donated. This gene and proteins are necessary for the high degree of processivity of DNA polymerase during replication (Kuriyan and O'Donnell 1993; Hingorani and O'Donnell 2000). This enables the accurate replication of linked genes and the preservation of the information they encode.

Many of the proteins that regulate eukaryotic signal transduction networks, including those involved in programmed cell death, are also derived from the prokaryotic genome (Aravind et al., 1999; Koonin and Aravind 2002; Bidle and Falkowski 2004). These signaling molecules are common in bacteria, cyanobacteria, and archae and include proteases from the AP-ATPase family. These proteases perform catalytic functions, and are found in the plant and animal genome (Koonin and Aravind 2002; Bidle and Falkowski 2004) and are utilized by mitochondria.

Again, however, some of these genes may have originated in viruses. For example, numerous homologous relationships have been identified among the proteins of crenarchaeal viruses and those from cellular life forms, including enzymes of DNA precursor metabolism, RNA modification enzymes, glycosylases transcription regulators, and ATPases implicated in viral DNA replication and packaging (Prangishvili et al., 2006). Perhaps these proteins were obtained from crenarchaeal hosts or bacteria and were then stored in the viral genome; perhaps for the purpose of transfer from virus to eukaryote, or merely to be held in reserve until required.

If these genes were transferred back and forth between prokaryotes and viruses does not answer the question of their origin. Instead it indicates the highly regulated interactions and various complex routes these genes may take (Prangishvili et al., 2006), i.e. from prokaryote to eukaryote, or from prokaryote to virus to yet other viruses, and then to eukaryote. Nevertheless, the defining feature of a virus is its ability to force the host genome to engage in replication while preserving the genes undergoing replication, i.e. those belonging to the viral genome and those donated by prokaryotes; genes which were likely obtained from an extraterrestrial host (Joseph 2000, 2009a).

Replication is a universal feature of cellular organisms, and eukaryotes and prokaryotes share many genes and characteristics involved in replication, including the production of RNA primers, replication bidirectionality, strand synthesis, and the utilization of the same principal proteins involved in transcription and translation. That these genes were transferred from prokaryotes to eukaryotes is demonstrated by their commonality.

Prokaryotic genes which guide replication and duplication contributed to the expanding size of the eukaryotic genome. Indeed, the number of signal transduction and regulatory proteins that are encoded parallel the increasing size of the genome. Thus, the larger the genome, the greater the number of genes dedicated to signal transduction (van Nimwegen 2003; Konstantinidis Tiedje 2004; Galperin 2005).

Some of these genes that can be traced to a common ancestor also perform functions that involve the transfer of genetic information (Harris et al., 2003). Some interact with ribosomes and those ribosomal RNA genes which play fundamenal roles in cellular functioning and DNA translation and transcription (Harris et al., 2003). Ribosome and ribosomal RNA genes were also likely transferred from prokaryotes to eukaryotes (Lake et al. 1984; Lake 1988; 1998; Rivera and Lake 1992; Rivera and Lake 2004; Vishwanath et al. 2004). However, as noted, ribozomes also have viruses as their source.

Thus, the ability to replicate and duplicate genes, and to transfer genes and to express these genes can be traced backwards in time to prokaryotes (and viruses) and thus to the direct descendants of the first creatures to arrive on Earth. Nor are these replicative actions somehow random processes. Instead, they are under regulatory control, performing essential functions related to the metamorphosis and evolution of future eukaryotic species; the metamorphosis and replication of life forms which lived on other planets.

12. GENE DUPLICATION AND EXPRESSION

Gene and whole genome duplications (Dehal and Boore 2005; Lynch and Conery 2000; Lynch et al., 2001; McLysaght et al., 2002) does not necessarily result in gene expression. Instead, the original and the copy may be suppressed. Thus pre-coded genetic instructions can be duplicated while repressed, and then passed down through subsequent species. Then in response to activating signals from the environment, or within the genome, undergo yet another duplicative event and these conserved genes can be expressed giving rise to advanced traits which had been suppressed. Gene duplication is a major evolutionary mechanism (Ohno 1970).

However, with each duplication, duplicated genes may be freed from regulatory restraint. Genes are also deleted, and often the original prokaryotic insert may be removed or expelled from the genome; and this too may free up the copy from regulatory constraint thus giving rise to new functions, tissues and species. However, the deletion of an active gene may serve the same course, and reflect not just evolutionary leaps but extinction. Deletions and duplications can also obscure the prokarotic or viral origins of the original gene.

For example, a comparison of the numbers of ancestral gene clusters with those of extant animals such as the nematode, fly, mouse and human, has established that extant bilaterian animals have retained more than 3500 gene clusters of the ancestral gene set, and have lost more than 1600 gene clusters (Ogura et al., 2004). Following duplication the originals or the copies were moved to new locations within the eukaryotic genome and/or they exited the genome, like a virus or a plasmid, perhaps to be stored in the genome of yet another species or virus. Therefore, because of gene deletion, coupled with the movement of genes to new locations in the genome, most of the genes which originated in the prokaryote genome can no longer be traced back to their prokaryotic source.

Just as viruses can transfer genes to a host, and when no longer necessary these donated genes can be transferred back to the viral genome (Lindell et al., 2004; Sullivan et al., 2005, 2006), thus resulting in gene loss (virus) and gene gain (prokaryote) followed by gene loss (prokaryote) and gene gain (virus), genes donated and transferred to the eukaryotic genome have been simultaneously deleted from the prokaryotic gene pool. In fact, the same mechanisms of transfer may result in gene loss within the eukaryotic as well as the prokaryotic genome.

Unlike the back-and-forth gene exchanges between prokaryotes and viruses, many of the genes donated by prokaryotes to eukaryotes have not been transferred back to prokaryotes (though they may have been transferred to viruses for storage). In prokaryotes, gene loss is one of the two major evolutionary processes, along with horizontal gene transfer, that contribute to the intensive “gene flux” that seems to have shaped the genomes of these organisms.

The one-way transfer of genes from prokaryote to eukaryote has served a specific, highly regulated purpose. It ensures that these genes, when expressed in response to specific environmental or regulatory signals, effect only eukaryotes. Thus, eukaryotes evolve and become more intelligent and complex, not prokaryotes.

Those donated genes have included those regulating whole genome duplication. Thus, only the genomes of eukaryotes and not prokaryotes have undergone repeated duplication. There is little evidence of WGD in prokaryotes.

13. EVOLUTION AND GENOME DUPLICATION

There have been several whole gene duplications during the early evolution of eukaryotes and which date back to the emergence of the first eukaryotic cells or their ancestors (Makarova et al., 2005) and thus to the time period when genes were transferred to single celled eukaryotes by prokaryotes. Reconstruction of ancestral gene repertoires has identified 4137 orthologous gene sets in the last multicellular eukaryotic common ancestor, and 2150 orthologous sets in the hypothetical first unicellular eukaryotic common ancestor, which is indicative of WGD coupled with deletions following gene donation (Makarova et al., 2005).

There is evidence to suggest that the genome may be duplicated at least every 100 million years (Lynch et al., 2001; Lynch and Conery 2000). Therefore majority of the genes in most genomes of cellular life have undergone at least one duplication at some point during evolution (Lynch 2007; Koonin et al., 1996) and many genes belong to large families of paralogs.

Whole genome duplications have occurred in almost all lineages, including yeast (Wong et al., 2002; Vision et al., 2000; Kellis et al., 2004; Dietrich et al., 2004), fish (Van de Peer et al., 2003; Jaillon et al., 2004; Taylor et al., 2001), frogs (Tymowska et al., 1977; Jeffreys et al., 1980) and plants (Blanc and Wolfe 2004). The relatively large and complex vertebrate genome appears to have been duplicated at least twice (McLysaght et al., 2002; Dehal and Boore 2005).

Whole genome duplications coupled with massive deletions are related to the divergence of species and evolutionary transitions. For example, the number of ancestral gene sets at the time of the split of plant–animal–fungi and the divergence of bilaterian animals, is estimated to be 2469 and 6577, respectively (Ogura et al., 2004). There is a 2.7-fold increase in the number of gene clusters during the period from the evolutionary split of plant–animal–fungi to the divergence of bilaterian animals (Ogura et al., 2004).

Whole genome duplication played a central role in the primary radiation of chordates (Dehal and Boore 2005) during the Cambrian explosion over 500 million years ago. There followed additional duplications during chordate evolution, thereby forming many of the gene families of vertebrates (McLysaght et al., 2002).

Dehal and Boore (2005) reconstructed the evolutionary relationships of all gene families from the complete gene sets of a tunicate, fish, mouse, and human, and then determined when each gene underwent duplication relative to the evolutionary tree of each species. An analysis of the global physical organization and genomic map positions of paralogous genes indicates these specific genes were duplicated prior to the fish–tetrapod split, some 400 million years ago. This was followed by two distinct genome duplication events early in vertebrate evolution as indicated by clear patterns of four-way paralogous regions covering a large part of the human genome (Dehal and Boore 2005).

Large-scale genomic events marked the transition and divergence between yeast and fungi (Liti and Louis, 2005) chordates and non-chordates (McLysaght et al., 2002), fish and tetrapods (Dehal and Boore 2005), and then once or twice more after vertebrates began to colonize the surface of Earth (Dehal and Boore 2005).

In fact, the genome may have been duplicated dozens of times over the course of evolutionary history (Lynch and Conery 2000; Lynch et al., 2001) thereby triggering the transition and divergence between numerous species, ranging from yeast and fungi (Liti and Louis, 2005) to chordates and non-chordates (Dehal and Boore 2005; McLysaght et al., 2002).

Gene and whole genome duplication are crucial mechanisms of evolutionary innovation and when coupled with regulatory genes contributed by prokaryotes, enabled the genomes of eukaryotes to become increasingly complex as well as larger in size. This also allowed for multiple copies of the same genes to appear in divergent species and to be passed down until a regulatory or environmental signal triggered their activation.

Gene duplication appears to provide the raw material for major evolutionary transitions and triggered the emergence of new species in the absence of obvious intermediaries or transitional species. The duplication of all genes at the same time induced rapid and extensive evolutionary change; i.e. the emergence of new species from old. Whole genome duplication also enabled the entire expanded gene repertoire to evolve together and reach a greater level of interaction and complexity as compared to single gene duplications.

Duplication is often followed by accelerated sequence evolution as well as rearrangement of a gene, an evolutionary mode that obliterates detectable connections to the original gene source. Moreover, although numerous genes might be retained, other duplicated genes or the original might be quickly eradicated (Wolfe 2001) thus erasing the genetic footprints that would lead back to the prokaryotic source. This would make it appear that a new gene has emerged, when it is instead a duplicate, because its origins are no longer apparent. In fact, the vast majority of duplicated genes are subsequently deleted (Dehal and Boore 2005); an event which may also lead to freeing the original, or the duplicate, from inhibitory restraint, and which can erase all evidence of genome duplication (Dehal and Boore 2005).

14. GENE LOSS & GENE EXPRESSION

Gene loss and gene gain appear to be hallmarks of evolutionary transitions and metamorphosis; just as genes are turned on and off during embryogenesis and development. However, instead of genes being turned off thus resulting in the absorption of tissues or cellular apoptosis, genes are pruned from the genome just as species are pruned from the tress of life whose characteristics were shaped by those genes.

Lineage-specific gene loss is one of the major evolutionary processes that have been brought to light by comparative analyses of gene sets from completely sequenced genomes (Aravind et al. 2000; Moran 2002). Genome analysis has revealed the extensive loss of genes after WGD, in yeasts (Katinka et al. 2001; Scannell et al., 2007; Wolfe and Shields 1997), plants (Soltis et al., 2008; Tuskan et al., 2006), and chordates (Dehal and Boore 2005; Durand 2003; McLysaght et al., 2002).

Gene loss without replacement is a common phenomenon in many genomes and appears to play an important role in shaping genome content (Snel et al. 2002). The extent of gene loss can be dramatic, and it can occur relatively rapidly under a strong selective pressure (Baumann et al. 1995).

Although genomes of parasites expose the most striking cases of massive gene loss, a possible function of deletion following transfer, the fact is: substantial gene loss has occurred in all phylogenetic lineages (Snel et al. 2002; Mirkin et al. 2003).

The eradication of the original gene may also play a role in the expression of the duplicate. Some of these duplicate genes appeared to have been freed from inhibitory restraint and were able to undergo an accelerated rate of sequence change thereby inducing the rapid evolution of new characteristics and abilities (Seoighe et al., 2003). Thus after duplication followed by deletion, the duplicate or original genes, now freed of the constraints imposed on the original, could express an already encoded function (“neofunctionalization”) which had been repressed (Conant and Wolf 2008).

In many cases the 'new' function of one gene copy is a secondary property, or subfunction, that was always present, but which may have been suppressed, or which only came to be expressed when other more dominant functional capabilities were inhibited, suppressed or deleted. Therefore, old functions might be fractionated giving rise to new subfunctions (“subfunctionalization”). That is, the new function was not really "new" but had always been a property of a specific gene that could only be expressed following duplication, or duplication coupled with deletion.

Thus, it is not uncommon for the new paralogs to retain or express distinct subsets of the original functions of the ancestral gene whereas the rest of the functions differentially deteriorate (Lynch and Force 2000; Lynch and Katju 2004)

Duplication and the lessening of regulatory restraints might also make the gene more susceptible to environmental triggers.

15. INTRONS AND GENE EXPRESSION

DNA includes stretches of nucleotides, called exons, that are encoded and expressed to produce various proteins (De Souza et al., 1996). These strings of nucleotides are punctuated, bracketed, framed, and interspersed with long stretches of non-encoding DNA, called introns (Belfort, 1991, 1993; Breathnach et al., 1978; Buchman and Berg 1988; Witkowski, 1988). In complex multicellular organisms introns are often 10-fold longer than exons (De Souza et al., 1996). They also signal which lengths of exons are to be expressed (Belfort, 1991, 1993; Breathnach et al., 1978; Witkowski, 1988). Introns are typically snipped out as strings of exons are transcribed via RNA intermediaries, into proteins (Breibart et al., 1985; Leff et al., 1986).

Introns are of particular importance in regulating gene expression (Brinster et al., 1988; Buchman and Berg, 1988; Collis et al., 1990; Lai, et al., 1998; Noe et al., 2003). If different "starter" or "stop" introns are activated this results in different segments or sequence lengths becoming expressed, thereby producing a different product (Belfort, 1991, 1993; Breathnach et al., 1978; Breibart et al., 1985; Leff et al., 1986). Hence, variation and diversity can be differentially induced if different "starter" exons or promoter introns are activated.

Introns have been preserved often in the same places in the genome, over the course of evolution, be it the genes of Drosophila melanogaster (the fruit fly), Caenorhabditis elegans (nematode), mice, or humans ((De Souza et al., 1996; Federov et al., 2002). This extreme conservation and preservation of their positions within genes, attests to their importance in regulating and coordinating evolution and metamorphosis among numerous species. Many are catalytically active and facilitate chemical reactions, even catalyzing their own synthesis (De Souza et al., 1996).

Via the joining of exons after splicing, introns also trigger the synthesis of novel proteins with new properties (Brietbart et al., 1985; De Souza et al., 1996; Leff et al., 1986). They may also promote the creation of multiple copies of the proteins coded by single genes (Brietbart et al., 1985; Leff et al., 1986). In fact, the presence of an intron can increase transcriptional efficiency 100-fold whereas in the absence of the intron these genes may not be expressed at all (Brinster et al., 1988; Lai et al., 1998).

Hence, introns are involved in transcription, translation, signaling, protein synthesis, and regulating which gene sequences or portions of the gene should be expressed or inhibited (Brinster et al., 1988; Brietbart et al., 1985; Buchman and Berg 1988; Collis et al., 1990; Leff et al., 1986; Lai, et al., 1998; Noe et al., 2003). They also create new genes.

Introns guide or participate in the genetic recombinations between exons, a process called “exon shuffling" (Gilbert, 1978, 1987; Doolittle,1978; Blake, 1978). Exon shuffling is the process where new full-length genes are created from exon “pieces” by recombination within the introns (De Souza et al., 1996, 1998, 2003; Fedorov 2001, 2003; Long et al., 1995; Roy 2003; Roy et al., 1999, 2001, 2003). Exon shuffling is associated with the formation of new genes from old genes.

Introns also are implicated in the production of additional genes and even gene clusters which are located deep within the intron (Henikoff et al. 1986; De Souza et al., 1996; Strachan & Read, 1996). Thus, introns may be responsible for producing duplicate genes as well as new genes and clusters of genes, including numerous copies of highly repetitive sequences of nucleotide base pairs (Finnegan, 1989; Henikoff et al. 1986; Peters & Fink, 1982). Indeed, introns, and intronic gene clusters are considered a "hot spot" for homologous recombination (Wahls et al. 1990).

Introns also play a major role in the origin and diversity of proteins by facilitating recombination of sequence coding for small protein/peptide modules (Brietbart et al., 1985; Leff et al., 1986; Koonin 2006). If the length of the code is altered and reframed, or if introns change their positions within the genes, the products produced by the altered code may also undergo subtle or profound changes (Brietbart et al., 1985; Leff et al., 1986). Therefore a variety of tissues and organs can be fashioned.

Introns also contain copies of gene sections that have been silenced and suppressed (De Souza et al., 1996). They maintain the "old code" for genes that were once translated into a protein, as well as the codes for genes that have not yet been expressed. Introns are thus implicated in the release of genetically genetically pre-coded traits (de Jong & Scharloo, 1976; Dykhuizen & Hart, 1980; Gibson & Hogness, 1996; Polaczyk et al., 1998; Rutherford & Lindquist, 1998; Wade et al., 1997).

Hence, introns create genes from old genes, recombine pieces of genes, and thus can combine, fractionate, or reconfigure the structure of a gene, thereby creating new functions from the parsing or assimilation of old functions coded by single or multiple genes. Moreover, they can silence or activate the expression of the genes they create or those they regulate.

Introns, therefore, play a major role in evolution acting to regulate gene expression, maintaining copies of genes, and promoting the assembly of new genes and new gene sequences from old genes, and multiple copies of the same or a new protein product.

Thus, following the donation of introns to eukaryotes, new genes were assembled from old genes (De Souza et al., 1996, 1998, 2003; Fedorov 2001, 2003; Long et al., 1995; Roy 2003; Roy et al., 1999, 2001, 2003). The genome began to increase in size and complexity and genes expressed new, albeit precoded functions; which gave rise to new tissues, organs, and the evolution of new species (Duret 2001; Comeron and Krietman 2000). In fact, the number of introns per gene varies by more than two orders of magnitude between species (Roy 2004).

Therefore, introns, which may have originally been donated by prokaryotes (Cavalier-Smith 1991; Martin and Koonin 2006; Sharp 1991; Stoltzfus 1999), as well as viruses, may play a significant role in regulating, copying, and duplicating genes which had also been transferred to the eukaryotic genome by prokaryotes and viruses. Moreover, they appear able to regulate the manufacture of new proteins and thus guide the evolution of new tissues, organs, and species. These are not random events, but are under precise regulatory control.

16. PROKARYOTIC AND VIRAL ORIGINS OF INTRONS

Numerous introns invaded eukaryotic genes at the outset of eukaryogenesis as the first eurkayotes were being fashioned (Martin and Koonin 2006; Rogozin et al., 2005), and thus at the earliest stages of eukaryote evolution (Rogozin et al., 2005). All eukaryotes whose genomes have been sequenced, including parasitic protists, have been shown to possess introns (Doolittle 1978; Gilbert 1978; Mattick 1994; Deutsch and Long 1999; Nixon et al. 2002; Simpson et al. 2002; Vanacova et al. 2005). Even the simplest of eurkaryotes contain introns as well as spliceosomal proteins within their genomes (Collins and Penny 2005); with the presence of splicesomes indicating a viral heritage.

Hence, introns were present when simple eukarayotes took root on this planet, or they originated in the prokaryote (and viral) genome and were transferred to the first proto-eukaryotic organism (Cavalier-Smith 1991; Martin and Koonin 2006; Sharp 1991; Stoltzfus 1999). Introns then continued to be donated or duplicated as eukaryotes evolved.

Both archae and bacteria appear to have supplied eurkaryotes with numerous introns (Martin and Koonin 2006), perhaps flooding the eukaryotic genome with introns and transposable elements at the earliest stages of eukaryosis (Cavalier-Smith 1991; Martin and Koonin 2006; Sharp 1991; Stoltzfus 1999). Viruses have also been a major source of introns to eukaryotes. Perhaps viruses and prokaryotes supplied introns at the time the archae and bacteria genomes were either unified to create the first eukaryotes (Martin and Koonin 2006) or were horizontally transferred to unicellular eukaryotes thus triggering multicellularity. A massive influx of introns would also explain why ancient eukaryotes (Roy 2006) including the last common ancestors for eukaryotes, possessed high intron densities comparable even to modern vertebrates who posses intron-rich modern (Carmel et al., 2007; Csuros et al., 2008; Roy 2006).

Group II introns (retrotransposons) which may have originated in or were donated by retroviruses, are found in all three domains of life (Dai and Zimmerly 2003; Dai et al., 2003). Group II introns are thus highly mobile retroelements (Belfort et al., 2002; Lambowitz et al., 1999; Lambowitz and Zimmerly 2004) and they also became part of the mitochondrial and chloroplast genomes (Bonen and Vogel 2001; Copertino and Hallick 1993). Group II introns may also be progenitors of nuclear spliceosomal introns (Cavalier-Smith 1991; Jacquier 1990; Sharp 1991). Thus, it appears that viruses may have donated introns to the bacteria genome including that proto-bacteria which either invaded or donated its own genes to the eukaryotic genome, giving rise to mitochondria. Thus, in addition to viruses, mitochondria may also be a direct and indirect source for introns including group II self-splicing introns and spliceosomal introns (Dyall et al., 2004; O'Brien 2002; Roy and Gilbert 2006).

Thus, spliceosomal introns may have evolved from group II self-splicing introns which originated in the genome of the alpha-proteobacterial progenitor of the mitochondria (Koonin 2006), or from a retrovirus or both. Group II self-splicing introns are present in the genomes of many bacteria (Cavalier-Smith 1991; Koonin 2006; Roy 2006; Stoltzfus 1999). Thus, at least some eukaryotic introns may be linked to the same alpha-proteobacteria genome which gave rise to mitochondria which also donated numerous genes to the eukaryotic genome (Koonin 2006), along with the genes supplied by viruses.

Moreover, archae may have contributed introns, including ribosomal introns and protein sequences (Watanabe et al., 2002). Some archael genomes contain genes that are dotted with micro-introns and some archae proteins are also bracketed by introns (Watanabe et al., 2002) as is common in eukaryotes.

However, group II introns include ribozymes, and they are linked to highly mobile retroelements (Belfort et al., 2002; Lambowitz et al., 1999; Lambowitz and Zimmerly 2004). These ribozymes, derived from viruses, act to catalyze the splicing of their flanking exons (Bonen and Vogel 2001; Michel and Ferat 1995). As they are found in all three domains of life (Dai and Zimmerly 2003; Dai et al., 2003) this suggests that one major source may have been viruses which donated these elements to archae and eukaryotes, and/or that archae used these viruses to transfer these elements to eukaryotes.

Be it archae, bacteria, viruses, or a combination of influences, once these introns were donated to the eukaryotic genome, they then punctuated and framed numerous protein-coding genes and played crucial roles in recombination, gene creation, coordination of transcription and translation, the emergence of the spliceosome, as well as the nucleus, linear chromosomes, telomerase, the ubiquitin signaling system, inhibition and expression, gene duplication and creation, and the expansion of the genome (Comeron and Kreitman 2000; De Souza et al., 2003; Duret 2001; Fedorov 2003; Koonin 2006; Gilbert 1978, 1987; Long et al., 1995; Mattick 1994; Prachumwat et al., 2004; Roy and Gilbert 2006; Tonegawa et al., 1978).

Thus, introns which were donated by prokaryotes (and viruses), acted on genes which had been transferred by prokaryote to the eukaryotic genome (possibly via a viral intermediary), thereby creating new genes from old genes, expressing pre-coded traits, and giving rise to new species. Introns play a major role in the regulation of evolutionary metamorphosis.

The donation of introns by prokaryotes following the metamorphosis of the first eukaryotes, also explains the relative absence of introns in the genomes of most modern prokaryotes (Koonin 2006). Of course, this could also be a case of prokaryotes using viruses to store these elements, until needed. In either instance, introns were donated and were not replaced thus insuring that eukaryotes and not prokaryotes would evolve into new species.

That these prokaryotes at one time may have contained an abundance of introns may also account for why the genomes of archae and bacteria contain split genes (Dassa et al., 2007). Therefore, having contributed their introns to the eukaryotic genome, most archae and most bacterial genes lack or have only a few introns, and their genes are encoded as uninterrupted open reading frames. This indicates that the donation of introns was not random, but under precise genetic control, such that their transfer to eukaryotes played a highly regulated role in eukaryotic evolution whereas their deletion from the prokaryotic genome insured that only eukaryotes would continue to evolve.

17. SELF-SPLICING INTRONS

Introns have been implicated in the creation of new genes, new traits, new species, and thus evolutionary metamorphosis. They have played crucial roles in gene creation, coordination of transcription and translation, the expansion and possibly even the duplication of the genome, the emergence of the spliceosome, the nucleus, linear chromosomes, telomerase, the ubiquitin signaling system, and eukaryotic evolutionary innovation (Koonin 2006; Mattick 1994; Roy and Gilbert 2006).

Introns exert a significant regulatory influence over gene expression and may have played a role in the seperation between transcription and translation (Roy and Gilbert 2006). For example, they appear to have provided two types of RNA genes to the eukaryotic genome--mRNA and iRNA. These highly structured Eukaryotic RNAs are also linked with group II introns and might have originated from introns in the alphaproteobacterial progenitor of the mitochondria (Blumenthal, 2005; Toro et al., 2007) and which are directly linked to retroviruses.

Spliceosomal introns snip out introns and interrupt sequences of protein-coding genes and are among the defining features of eukaryotes (Doolittle 1978; Gilbert 1978; Mattick 1994; Deutsch and Long 1999). Numerous spliceosomal introns invaded genes of the emerging eukaryote during eukaryogenesis and thus must have originated in viruses or prokaryotes or both.

Splicing mechanisms are directly linked to viral group II introns, bacterial group II introns (Toro et al., 2007), to archae and bacteria (Lake et al. 1984; Lake 1988; 1998; Rivera and Lake 1992; Rivera and Lake 2004; Vishwanath et al. 2004) (Martin and Koonin 2006), to mitochondria (Blumenthal, 2005; Dyall et al., 2004; O'Brien 2002), and to bacterial operons (Garrett et al., 1994).

Self-splicing introns can be traced back to the earliest stages of eukaryotic evolution, and are linked to RNA and the basic machinery of gene expression: transcription, splicing, and translation (Blumenthal, 2005).

Likewise, spliceosomal proteins are part of the core cellular machinery that is conserved across eukaryotes, and are sometimes located within operons (Blumenthal and Gleason, 2003; Blumenthal et al., 2002; Garrett et al., 1994; Hill et al., 2000). Operons are sequences of nucleotides which include several structural genes and a promoter, and which produce messenger RNA (mRNA), via transcription by an RNA polymerase (Salgado et al., 2000). Operons are believed to have originated in the prokaryote genome (Che et al., 2006; Ermolaeva et al., 2001) and regulate the expression of various genes, depending on environmental conditions (Salgado, et al., 2000). This is accomplished by the binding of a repressor to the operator to prevent transcription, or by inserting an inducer molecule which binds to the repressor thereby allowing expression (Blumenthal et al., 2002; Salgado, et al., 2000). Introns have retained the operon capacity to repress or selectively express genes sequences.

Group II self-splicing introns also evolved in partnership with the spliceosome, both of which may have originated in organelles which transfered type II introns into the nucleus (Cavalier-Smith, 1985; Rogers, 1989). Organelles are linked to the alpha-bacterial symbiont whose genes combined with archae to fashion the eukaryotic genome and which gave rise to mitochondria.

Self-splicing Group II introns serve as catalytic RNAs (ribozymes) and mobile retroelements, which reinsert themselves into the genome after they are snipped out (Finnegan, 1989; Moran et al., 1999; Roy and Gilbert 2006). They can change their position within the genome and can influence the expression of different sequences of genes in a step-wise temporal-sequential fashion (Dibb & Newman, 1989; John & Miklos, 1988; Kuhsel, et al. 1990).

Group II introns therefore, have the mobile characteristics of transposons and retrotransposons and also serve as transposable genetic elements (Crick, 1979; Coghlan and Wolfe, 2004; Finnegan, 1989; Hickey 1992; Moran et al., 1999). Likewise, some novel introns appear to arise by transposon insertions (Crick, 1979; Dibb & Newman, 1989; John & Miklos, 1988; Kuhsel, et al. 1990). Conversely, some retrotransposons, which have the ability to reinsert themselves, appear to have evolved from mobile group II introns.

Introns and transposable elements (TEs) are intimately linked and in some instances are indistinguishable. Eukaryotic genomes contain numerous TEs, many of which are found in introns (Nekrutenko and Li 2001). Most eukaryotic genomes are littered with introns and transposable elements, and many TEs are located within introns or have been inserted into exons during evolution (Nekrutenko and Li 2001). Hallick et al., 1993).

Coghlan and Wolfe (2004) have examined intron matches and found that around 70% have a nucleotide identity identical to transposable elements. In many cases the new intron is homologous to a transposon and to another intron, indicating the intron acted as a transposon and made a copy of itself which was inserted into another region of the genome. In this manner introns duplicate themselves, jump to different regions of the genome, and can coordinate gene expression in a wide range of gene networks. In some cases what appears to be a new intron is in fact an intron reinsertion, transcript retroposition, intron duplication, or gene conversion. If due to duplication then deletion of the original intron following transposition, then intron gains and losses may be one and the same. However, intron loss may also be a function of transfer to another organism.

The original introns were likely highly mobile, retrotransposable genetic elements which actively invaded the eukaryotic genome at the outset of eukaryotic evolution, relying in part on internally encoded enzyme activities for mobility. Eukayotes, therefore, obtained their introns from viruses and prokaryotes, which in turn inherited this genetic architecture from organisms which lived on other planets, and where they performed functions identical to those performed on Earth.

18. INTRONS ARE CONSERVED

The positions of introns and numerous spliceosomal and spliceosome-associated proteins, have been highly conserved in the same locations and positions within the genes of numerous species (Anantharaman et al., 2002; Collins and Penny 2005; Federov et al., 2002). Thousands of introns are located in the exact same regions of the genome, even when comparing the genes of fungi and humans (Federov et al., 2002). This conservation of position and location indicates they exert extremely important influences on the coordination of gene regulation and expression even among different species, possibly even acting to coordinate the evolution of various species in relation to one another.

Studies have shown that highly conserved, shared intron positions are common in animal, plant and fungal genes (Federov et al., 2002). In one study it was found that 14% of animal introns match plant positions, and that ≈17–18% of fungal introns match animal or plant positions (Fedorov et al., 2002), even though animals and plants diverged from any common ancestors over a billion years ago (Wang et al., 1999).

Indeed, the three-way split between plants, animals and fungi has been estimated to have occurred around 1.6 bya, whereas the the basal animal phyla (Porifera, Cnidaria, Ctenophora) diverged between 1.2 to 1.5 bya (Wang et al., 1999). Introns have an ancient pedigree.

Federov et al., (2002) examined 30 nonrelated genes with the highest numbers of common animal–plant introns and found that "60% of the fungal introns have positions common to animal and/or plant introns, and 39% of fungal introns are common simultaneously to both plant and animal introns. This exceptionally high abundance of introns with positions common to all three taxa of animals, plants, and fungi strongly supports the antiquity of these common intron positions."

In yet another genomic study (Rogozin et al., 2003), intron positions were compared in 684 orthologous gene sets from 8 complete genomes of animals, plants, fungi, and protists/parasite. Approximately one-third of the introns in the protist parasite were shared with at least one crown group of eukaryote; indicating that these introns have been conserved for over 1.2 billion years of evolution.

Between 10% to 20% of intron positions and other genomic features without obvious functions are conserved throughout the evolution of eukaryotes leading up to an including in humans (Bejerano et al., 2004; Fedorov et al., 2002). However, the fact that these functions are not obvious is not an indication of a lack of importance. These unknown functions may not be expressed except in future species. "What is conserved is functionally relevant" should be considered a central tenant of biology, even if the functions are not yet obvious.

19. INTRON GAINS & LOSSES

Introns have been donated to the eukaryotic genome by archae, bacteria, and viruses. They have acted in a precise, highly choreographed, genetically regulated fashion, to activate, silence, and duplicate genes which had also been transferred to the eukaryotic genome by viruses, archae, and bacteria. Further, once their genetic mission has been accomplished, these introns may be deleted, or duplicated and transferred to yet another region of the genome. Introns, therefore, have play a major role in the evolution of all species, leading up to and including humans.

The donation or duplication and deletion of introns may have occurred throughout eukaryotic evolution, with introns coming and going (Roy and Gilbert 2006). Eukaryotes harbor multiple introns per gene (Logsdon 1998; Mourier and Jeffares 2003; Jeffares et al. 2006), requiring hundreds of thousands, if not millions of individual introns to have been donated or duplicated throughout eukaryotic evolution and even during recent evolutionary history (Cavalier-Smith, 1985; Logsdon 1998; Palmer and Logsdon, 1991). However, gains are often accompanied or followed by losses.

It is inferred that a relatively high intron density was reached early in the metamorphosis of eukaryotes (Carmel et al., 2007; Cavalier-Smith 1991; Csuros et al., 2008; Martin and Koonin 2006; Roy 2006; Sharp 1991; Stoltzfus 1999). It has been estimated that the last common ancestor of eukaryotes contained >2.15 introns/kilobase. The last common ancestor of multicellular life acquired even more, harboring ∼3.4 introns/kilobase, a greater intron density than in modern insects, most extant fungi and some animals (Carmel et al., 2007); indicating a massive intron duplicative event coupled with deletions. Among the top six intron-rich species, five are ancestral forms, indicating that some species have subsequently lost introns, whereas initially the number of introns actually increased during the evolutionary leap from uni-cellular ancestor to the first multi-cellular ancestor.

Just as prokaryotes may have lost introns upon donating them in massive amounts to ancestral eukarotes, the higher density of introns in ancient vs more recent species, also suggests that introns play a major role in evolution and then drop out in those species which will no longer evolve.

The evolution of eukaryotic genes is characterized by numerous gains and losses of introns (Carmel et al., 2007) and different species vary dramatically in their intron density, ranging from a few introns per genome to over eight per gene (Logsdon 1998; Mourier and Jeffares 2003; Jeffares et al. 2006). Introns are prevalent in complex eukaryotes but rare in the simple ones (Cavalier-Smith, 1985; Logsdon 1998; Palmer and Logsdon, 1991), indicating that the acquisition or duplication of introns is associated with species which have evolved. By contrast some introns have been eliminated from the genomes of those in a state of prolonged stasis and evolutionary equilibrium.

Therefore, intron gains and losses may be an indication of the evolutionary status of any particular species, if they are in a state of stasis, going extinct, or if their genome is primed to undergo additional evolutionary leaps. Thus intron gain, retention, or loss, may indicate if a species may continue to evolve or go extinct.

Gene gain may also represent new viral invasions and the insertions of viral elements. By contrast, genes which are lost may be transferred back to viruses by those species who evolution has come to an end.

For example, we see an elevated rate of intron loss in several lineages, such as fungi and insects, nematodes, and arthropods (Carmel et al., 2007; Rogozin et al., 2003); species which no longer appear to be evolving, and which may have diverged from vertebrates around 1.2 bya (Wang et al., 1999). Thus, in non-vertebrates the rate of intron loss and gain have decreased in the last 1.3 billion yr. (Carmel et al., 2007). Further, in these lineages and in the last 100 to 300 million years, there has been a dramatic decrease in intron duplicative events, such that gains decreased faster than the decrease in losses, resulting in many lineages with very limited intron gains (Carmel et al., 2007; Rogozin et al., 2003).

Nematodes are characterized by a high number of events, with losses being more plentiful than gains (Cho et al. 2004; Coghlan and Wolfe 2004). Fungi also show more losses than gains (Nielsen et al. 2004). Recent intron losses are also seen in plant genes (Charlesworth et al., 1998).

Whereas many ancestral introns have been lost in fungi and other lower forms, they are retained in the genomes of higher vertebrates (Rogozin et al., 2003) many of which evolved in the last 40 million years. Many "higher" vertebrate species have continued to gain introns, albeit at a rather slowed pace, whereas "lower vertebrates" appear to be losing introns and to be experiencing a rapid reduction in gains (Fedorov et al. 2003; Babenko et al. 2004; Coulombe-Huntington and Majewski 2007). A survey of mammalian genes found six cases of intron losses in rodents relative to human (Roy et al., 2003). In fact, for most extant species, the total number of losses outnumbers the number of gains (Carmel et al., 2007).

The accelerated rate of loss in many species may indicate that these introns have been donated to the genomes of yet other species where they are exerting regulatory and evolutionary influences on gene selection and expression. As introns are quite mobile, they can also jump from location to location like a plasmid, coordinating the expression or suppression of a wide range of genes simultaneously and thus making it appear that introns have been lost, or gained, when they have merely moved to a new location; or, perhaps, like a virus, jumped to the genome of a different species.

20. INTRONS & PUNCTUATED EVOLUTIONARY EQUILIBRIUM

Sequences within introns have changed considerably over the course of evolution, sometimes by orders of magnitude, and at a faster pace than those of the exons (Federov et al., 2002). Thus, these highly conserved introns are obviously active and are exerting a variety of influences on the genome and gene expression, as well as the evolution of new species. In fact, bursts of introns appear to have invaded the eukaryotic genome initially and possibly at key points in eukaryotic evolution, such as the origin of animals and prior to the divergence of extant eukaryotic lineages (Carmel et al., 2007). For example, lineages leading to animals seem to have experienced a phase of massive intron invasion early in their evolution (Carmel et al., 2007).

After billions, or hundreds of millions or tens of millions of years of stasis, armies of introns either invade or rapidly duplicate within the eukaryotic genome, and are directly associated with, or may have directly triggered bursts of branching speciation and explosions of evolutionary change in the absence of transitional forms; a phenomenon that Eldredge and Gould (1972; Gould 2002) described as "punctuated equilibrium." Indeed, there is no fossil evidence of gradual change from one species to another or any fossil record of transitional forms acting as an evolutionary bridge between species (Eldredge and Gould 1972; Gould 2002). Evolution occurs in leaps. Thus, the regulation and coordination of these great evolutionary leaps may well be yet another function of introns.

Although the position of an intron in a gene's coding sequence is well conserved, introns can make copies of themselves which can be snipped out and transposed to another region of the genome (Finnegan, 1989; Moran et al., 1999). Introns change position within the genome, acting as a viral retrosposons and transposable elements. Moreover, they can hitch a ride on a plasmid, and invade and transpose themselves into the genomes of cospecies (Dujon, 1989; Dujon et al., 1989; McDonald 1993). In this manner, they can coordinate gene expression among most members of the same species, such that all make the same evolutionary leaps simultaneously.

Also many drop out of the genome after serving their function, which in turn would effect gene selection and exon transcription. When introns drop out, their deletion may halt any further evolutionary advance, thus leading to another long period of stasis. Intron deletion would also obscure and erase evidence of any genetic footprints leading to prokaryotes, viruses, or a common ancestor.

21. RETROVIRUSES, SPECIATION, AND EVOLUTION

Group II introns, which are derived from retroviruses, are highly mobile retroelements (Belfort et al., 2002; Lambowitz et al., 1999; Lambowitz and Zimmerly 2004) and include retrotransposons (Beauregard, et al., 2008). These viral elements, therefore, act as introns, and can regulate gene expression. Group II introns are also progenitors of nuclear spliceosomal introns (Cavalier-Smith 1991; Jacquier 1990; Sharp 1991), and can splice together exons (Bonen and Vogel 2001; Michel and Ferat 1995) thereby creating new gene products, and contributing to speciation (Volff et al. 2000, 2001c) and evolutionary metamorphosis. Further, they can leap to different locations in the genome, transcribing genes which had been silent, or suppressing genes which had been active, thereby coordinating gene expression involving a variety of tissues and organs (Seifarth et al., 2005).

In the human genome, these retroviral sequences encode tens-of-thousands of active promoters and can initiate transcription of adjacent human genes and regulate human transcription on a large scale (Conley et al., 2008; Jordan et al., 2003; van de Lagemaat et al., 2003). Thus, these viral elements have exerted a major influences on the evolution of the human-non-human genome. There is nothing random about these viral-genomic interactions, as they are under precise genetic regulatory control and are regulated in a complex, precise manner comparable to cellular genes (de Parseval et al., 1999; Knossl et al., 1999; La Mantia et al., 1992; Lee et al., 2003; Nelson et al. 1996; Sjottem et al., 1996).

Group II introns and retrotransposons are also self-silencing, and can thus be transferred horizontally (Gentles et al. 2007; Kordis & Gubensek 1998; Piskurek & Okada 2007) and passed down vertically from species to species until activated by genetically engineered environmental triggers (Lesage and Todeschini 2005) including alterations in oxygen levels (Sehgal et all. 2007; Todd et al., 2006) UV radiation (Hohenadl et al., 1999) or food sources (Dai et al., 2007) at which point they may change position and activate a network of genes which release a variety of protein products (Sehgal et al., 2007) thereby creating diversity and inducing speciation (Volff et al. 2000, 2001c). Thus, new tissues, organs, or species may be appear, perfectly adapted for a world which has been biologically engineered and which triggered their expression.

In response to environmental stresses, these retroelements may rapidly proliferate, causing genome rearrangements that lead to changes in gene expression (Beauregard, et al., 2008) and the emergence of new species (Volff et al. 2000, 2001c) which had in fact, already been coded into the genome (Joseph 2000, 2009b).

Viruses, including retroviruses target specific hosts and often specific cells and tissues. Thus, until specific hosts evolve, the targeting virus may remain inactive. Endogenous retroviruses, however, by incorporating into the germ line, can be past down to subsequent generations and species, and then, in response to specific genetic-environmental changes, become highly active and proliferate and transposing throughout the genome, effecting gene regulation and expression, and in so doing, they may trigger the metamorphosis of host species which yet other viruses may then invade.

Flurries of ERV activity, invasions, proliferation, deletions, and extinctions have corresponded to the divergence and metamorphosis of numerous species, and are associated with the Cambrian Explosion over 500 million years ago, including the evolution of jawed vertebrates (Agrawal et al. 1998, Kapitonov & Jurka 2005), the split between fish and tetrapods 450 mya (Volff et al. 2003), the giant leap from teleost fish to amphibians 350 mya (Volff et al. 2001c), then reptiles (Hude et al., 2002) and leading up to birds, mammals (Herniou et al., 1998) then primates and humans (Hughes and Coffin 2001; Sverdlov 2000)

Genes have been turned on and off, genes have been split, different sequences of exons have been activated or silenced, and genes have been combined and then expressed giving rise to quantum leaps in evolutionary metamorphosis. For example, retroelements were transferred from reptiles to mammals using poxviruses (Piskurek & Okada 2007) and then many mammalian genes were formed by the activity of retrotranspons, creating families of genes which in turn were repeatedly duplicated from at least five independent molecular events (Campillos et al. 2006). From mammals there followed the metamorphosis of primates which were targeted by additional viral invasions and gene insertions coupled with flurries of retro-activity proceeded by ERV extinctions.

For example, with the evolution of monkeys, 55 mya, ERVs formed numerous proviruses which became highly active and increased their activity until the divergence of Old World and New World primates (Lavie et al., 2004). However, there is no trace of their activity in prosimians. In addition, following the split between New and Old World monkeys 30 to 35 mya, new classes of ERVs flourished (Mayer and Meese 2002; Mayer et al., 1998; Medstrand and Mager 1998; Medstrand et al., 1997; Seifarth et al., 1998; Sverdlov 2000). During a period of ape-primate proliferation from 15 mya to 6 mya ERVs were again repeatedly mobilized (López-Sánchez et al., 2005), with extensive traces being retained even in the human genome. There followed yet another period of ERV proliferation 8 to 6 MYA (Barbulescu et al., 1999; Johnson and Coffin 1999; López-Sánchez et al., 2005) corresponding with the divergence between the common ancestors for chimps and humans, and then many of the ERV families became inactive and went extinct (López-Sánchez et al., 2005).

Yet other ERV families have been very long lived, continuing in the primate lineage leading to humans and displaying periodic bursts of activity which continued after the human-chimpanzee split (Costas 2001; Mayer et al., 1998; Medstrand and Mager 1998; Reus et al., 2001). However, hundreds of retrogenes were also formed in both the chimpanzee and human lineages after they split from a common ancestor (Chimpanzee Sequencing and Analysis Consortium 2005). Yet others are unique to humans and continue to show activity (Barbulescu et al., 1999; Buzdin et al., 2003; Medstrand and Mager 1998), and have contributed to human genetic diversity (Seleme et al. 2006) and the evolution of numerous species Homo.

Thus we see a progressive pattern of speciation and primate-human evolution where viral elements exert major influences on the genome, leading to new primate-human species which are invaded by yet other viral elements, including waves of group II introns and retrosponsons. These events are accompanied by deletions and duplications which are also species specific. For example, comparisons of gene content between macaque, human and chimpanzee genomes (Hahn et al., 2007) support an overall increase in duplication activity in the common ancestor of chimpanzees and humans compared with other mammals. In addition, human duplications are genetically more diverse when compared with chimpanzee duplications (Cheng et al., 2005).

Further, once a new species has been genetically manufactured, many of these viral elements become inactive or they are deleted from the genome of subsequent species. For example, hundreds of deletions also took place independently in chimpanzee and human lineages after divergence from their last common ancestor (Sen et al. 2006, Han et al. 2007). There is evidence for an almost twofold increase in gene loss in humans and chimpanzees when compared with macaques, and an almost fourfold increase in contrast to other mammals including dogs, mice and rats (Hahn et al., 2007; Rhesus Macaque Genome Sequencing and Analysis Consortium, et al., 2007; Wang et al., 2006).

22. VIRUSES AND HUMAN EVOLUTION: THE BIG BRAIN BIG BREAST REVOLUTION

There is no general agreement as to the various phylogentic relationships shared by the wide variety of Plio-pleistocene hominids so far discovered, and it is not yet established if present-day humans descended from Australopithecus, Homo habilis, or both. Nevertheless, following H. habilis and Australopithecus were a wide range of quite different individuals collectively referred to as Homo erectus.

With the evolutionary transition from H. habilis to H. erectus, 2 million years ago, there was yet another burst of retroviral germline integrations (Hughes and Coffin 2004) creating lineage-specific phenotypic differences over a short period (Yohn et al., 2005). However, these flurries of retroviral activity were again accompanied by gene loss around 800,000 years ago (Stedman et al., 2004) followed by another burst of proliferation and activity around 580,000 years ago (Hughes and Coffin 2004).

These alterations in viral activity and the proliferation of new viral invasions corresponded to a major change in the human physique, human sexuality, and increases in the size of the human brain (Joseph 2000b). For example, the sarcomeric myosin gene, expressed primarily within muscles of the hominid mandible, underwent a 2 bp frameshift alteration (Stedman et al., 2004). The loss of this gene is believed to have caused an eightfold reduction in the size of type II muscle fibres in humans, thus effecting the massive muscles that attached the jaw to the skull.

Homo erectus were big and robust, with thick browridges, large teeth, and bulging shoulder muscles, and ranged throughout Africa, Europe, Russia, Indonesia and China from approximately 1.9 million until about 300,000 years ago, with a few isolated populations possibly hanging on in the island of Java, until 27,000 years ago (Joseph 2000b). Presumably, H. erectus is the common ancestor for Neanderthals and modern humans.

About 1.5 million years ago H. erectus learned to harness fire and by 500,000 B.P., the first hearths began to appear in China, France, Hungary and elsewhere, and this species of Homo was regularly constructing crude shelters and home bases; achievements that coincided with a major change in female sexuality and a dramatic increase in the size of the brain coupled with decreases in the size of the jaw (Joseph 2000b).

For example, the vaginal canal underwent a reorientation which enabled males and females to face one another during sexual intercourse, thus promoting interpersonal intimacy (Joseph 2000b). With the exception of the Bonobo who are more variable, all other primates and non-human animals generally assume a dorsal ventral posture when mating. Further the breasts of the human female may have become permanently enlarged during this evolutionary time period (Joseph 2000b). Other primate females develop "breasts" only when they are nursing and lactating. Likewise, humans but not other primates have been invaded by Class II ERVs which selectively target the mammary gland (Seifarth et al., 2005) and these viral elements are female-steroid hormone-responsive (Knossl et al., 1999; Ono et al., 1987). The development of breasts signaled a change in the human female's sexual status.

Between 800,000 to 500,000 years ago, human females became sexually receptive at all times, whereas other female primates are receptive when they enter estrus (Joseph 2000b). These great changes in sexual status and the development of secondary sexual attributes likely contributed to the development of long term male-female mating relationships as is suggested by the creation of the home base, semi-permanent shelters, and the hearth for cooking food. That is, once the female became sexually receptive at all times, and this was signaled by the enlarged breasts (and buttocks), male sought to form long-term attachments to these females, the "family" was born, and long-term dwellings equipped with hearths for cooking appeared (Joseph 2000b).

Food that is cooked releases more nutrients and is easier to chew and digest. This made it possible for the jaw and the jaw muscles to decrease in size, and for the skull to increase in size, thus increasing cranial capacity(Joseph 2000b). Changes in diet also effect gene selection including the activity of embedded retroelements (Dai et al., 2007).

With the loss of the sarcomeric myosin gene (between 800,000 to 580,000 years ago), and which is expressed primarily within muscles of the hominid mandible (Stedman et al., 2004) there resulted an eightfold reduction in the massive size of type II muscles in humans, which are attached to jaw and the apex of the skull. Jaw size was reduced and the face became less threatening and more human; and this change also contributed to "female choice" and the willingness to form long-term relations (Joseph 2000b). Also of importance: A skull freed of massive muscles, can increase in size and house a bigger brain.

Due to limitations in the size of the birth canal, the size of the human head is also constrained. Thus, with the reduction in the massive muscles attacked to the skull and jaw, the skull could increase in size and human cranial capacity increased, making it possible to give birth to big brained babies (Joseph 2000b). As the environment, including nutrition, acts on gene selection, including those provided by viruses, the brain also increased in size; and all these changes corresponded with changes in human female sexuality, the increase in the size of the breasts, and the development of perhaps long-term human relations between males and females (Joseph 2000b). In fact, Class II HERV activity is conspicuous not only in the mammary glands, but in the human brain (Seifarth et al., 2005).

The burst in viral gene activity around 580,000 years ago (Hughes and Coffin 2004) was followed by yet another endogenous viral invasion around 200,000 years (Turner et al., 2001) which coincides with the appearance of Neanderthal and the first archaic Homo sapiens.

Endogenous retroviruses, therefore, have profoundly affected the genomes of numerous species in the evolutionary lineage leading to Homo sapiens (Mayer and Meese 2005) and several ERV families are still active in present-day humans (Belshaw et al., 2005; Löwer et al., 1993; Medstrand and Mager 1998). Genome sequencing reveals that 8% of the human genome consists of human endogenous retroviruses (HERVs), and, if we extend this to HERV fragments and derivatives, the retroviral legacy amounts to roughly half our DNA (Bannert and Kurth 2005; Medstrand et al., 2002).

Human evolution, therefore, has been shaped by successive waves of viral invasion (Sverdlov 2000) which have induced large-scale deletions, duplications and chromosome reshuffling in the human genomic and have been a major source of genetic diversity (Hughes and Coffin 2004). In fact, about one quarter of all analyzed human promoter regions harbor sequences derived from viral elements (Jordan et al. 2003)

These viral invasions and contributions to human evolution should not be viewed as agents of chance. Rather, viruses, prokaryotes, and eukaryotes, constitute a genetic super-organism and the transfer of viral elements and the activation vs silencing of genes has been under precise genetic control. Further, there has been a progressive, step-wise sequential order to these viral invasions and gene deletions, and different host organisms have been manufactured and "evolved" accordingly.

Viruses are host specific and thus in order to invade, or to become activated, requires the manufacture of specific hosts species--and this too has taken place in a progressive highly regulated manner.

For example, most of the ERV sequences in the human genome are primate-specific (Sverdlov, 2000). By contrast, most human genes are far more ancient, have been highly conserved, and share orthologs with distantly related species. Hence, there is a specific interaction between ancient genes, many of which had been passed down for hundreds of millions if not billions of years, albeit in silent form, becoming activated by viral genes, introns, transposons, and promoters which selectively target these ancient genes within specific hosts species, thereby triggering episodes of speciation; each viral key had to await the evolution of a specific genetic lock and once that lock evolved, the key was inserted opening the door to the next stage in evolutionary metamorphosis.

Many of these genes, including those inserted by viruses, are held in abeyance until specific hosts evolve; at which point viruses may invade and insert genes which interact with ancient genes which had been donated by prokaryotes hundreds of millions if not billions of years before. These speciation events are often preceded or proceeded by additional invasions such that species diverge from common ancestors only to be invaded by yet another wave of viral elements when new hosts evolve.

23. TRANSPOSONS, INTRONS & GENE ACTIVATION VS GENE EXPRESSION

Introns also insert themselves into introns. The genomes of numerous species contain introns-within-introns (twintrons), indicating that introns are also targets of intron insertions (Copertino and Hallick 1991; Doetsch et al., 2001) . Thus introns may also regulate introns.

TEs inserted into introns also affect RNA processing, and intronic TEs can render its host gene susceptible to siRNA-mediated transcriptional gene silencing (Doetsch et al., 2001). Therefore, they can turn genes on, or off.

The majority of all introns in the eukaryotic and human genome have Alu insertions (Grover et al. 2004) which were derived from retroviruses. These Alu enzymes cut up foreign DNA in a process called "restriction" and are also found in bacteria and archaea (Arber and Linn 1969; Krüger and Bickle 1983). Possibly they were donated to the eukaryotic genome by viruses, perhaps as a protection against other viruses. "Restriction" is yet another means by which introns can silence genes, including nearby genes, as well as engage in cutting and splicing.

Moreover, transposons/introns, in association with RNA, can serve as regulators of gene expression and chromosome segregation by inserting and introducing heterochromatin which prevents gene expression by wrapping the gene in a protective protein coat (Hall et al., 2002; Grewal and Moazed 2003; Grewal and Martienssen, 2002; McClintock 1950; Volpe et al., 2002). Indeed, heterochromatin is characterized by a high density of transposons (Volpe et al., 2002). TE insertion therefore, can disrupt the coding sequences of a gene and inhibit the production of viable gene products.

These mechanisms mediating gene silencing and activation have also been adopted to evolve new traits (Liu et al., 2004). TE insertion within promoters, introns, and untranslated regions, can directly trigger incredible genetic variation and the full gambit of phenotypes, ranging from subtle epigenetic regulatory perturbations to the complete loss of gene function (Kidwell and Lisch, 1997; Wessler, 1988). That is, by turning genes on and off, different regions of a gene network may be activated and different products can be produced.

TEs that insert into introns are sometimes spliced out during mRNA processing. Even when spliced, however, these TE inserted introns can effect regulatory sequences and gene regulation in numerous ways including triggering or suppressing gene expression in certain tissues (Greene et al., 1994). Moreover, intronic transposable elements and transposons can significantly affect the expression of nearby genes (Finnegan, 1989; Dibb & Newman, 1989; John & Miklos, 1988; Kuhsel, et al. 1990; Lippman et al. 2004). Gene silencing is accomplished in a step-wise process involving RNA and the methylation of histones (Grewal and Martienssen, 2002; Hall et al., 2002).

Group II and III intronic retroelements often insert themselves into exons. Once inserted they are quickly integrated within these exonic sequence (Hallick et al., 1993) and can easily suppress these genes. Group III intron are sometimes formed from the domains of two individual group II introns (Hong and Hallick, 1994). The group III introns and group II introns also share a common evolutionary ancestor, which is linked to the alpha bacteria progenitator as well as archae.

These introns possess the genetic mechanisms which allow them to be efficiently spliced out of transcripts, and to reinsert themselves in another part of the genome. They are able to demarcate coding sequences and to regulate gene expression in different regions of the genome, perhaps simultaneously as well as sequentially. Thus they can guide the activity of a number of gene networks to coordinate gene expression.

Therfore, introns, which may have originated in prokaryotes, can duplicate and give birth to themselves, and possess the genetic machinery which enables them to propagate throughout the genome and to regulate gene expression via silencing and restriction. As is also demonstrated by their highly conserved nature, these are not chance, or random events.

24. INTRONS & RNA

Some introns may also propagate at the RNA level including within messenger RNA. Messenger RNA (mRNA) is transcribed from a DNA template and contains the codes for creating specific protein products which it transports to ribosomes for protein synthesis. These introns indicate which portions of the code are to be translated and transcribed and are then snipped out and are reinserted (spliced) into another region of the genome which is without an intron.

Presumably, the new intron-containing RNA is reverse-transcribed and undergoes gene conversion leading to a new intron. Therefore, via reverse-splicing an excised intron sometimes reintegrates back into a different site in the same mRNA (Coghlan & Wolfe 2004; Tarrío et al., 1998) thereby exerting multiple coordinated influences on gene expression and protein synthesis.

Introns may have been the original information source for the creation of genes which code for mRNA. Likewise, genes involved in mRNA processing and splicing, and germline-expressed genes, preferentially gain introns (Roy 2004). By contrast, introns/TEs are generally excluded from mRNAs of highly conserved genes (van de Lagemaat et al., 2003).

A gene ontology analysis has demonstrated that novel introns are unusually frequent in genes with mRNA processing functions, relative to germ-line-expressed genes. This suggests that it is the function of these genes, rather than their mode of transcription, that makes them amenable to gaining introns (Coghlan & Wolfe 2004). Thus, introns regulate functional expression. Thus introns regulate gene expression or suppression and control the transposition of these introns to different regions of the genome. These properties enabled introns to coordinate the expression or suppression of a wide network of genes.

For example, RNA not only serves as a messenger but can interfere with and inhibit and silence gene expression (Hall et al., 2002). This is accomplished, in association with transposons/introns via heterochromatin formation whose repressive capacity is mediated by components of RNA interference machinery (RNAi). This RNAi machinery acts to nucleate heterochromatin assembly and can initiate and propagates regional heterochromatic inhibition and gene silencing (Hall et al., 2002; Volpe 2002). RNAi in association with introns/transposons can even control chromosome segregation and the expression of large chromosome domains (Grewal and Moazed 2003).

Thus, introns and transposons can exert regulatory control of individual genes, chromosomes, and thus the entire genome.

TE-induced genetic alterations and changes in regulatory sequences, are of extreme evolutionary significance to their hosts and to the metamorphosis and evolution of future species (Britten 1996). TEs, especially when inserted into introns, can alter the size and arrangement of whole genomes, induce changes in single nucleotides, and generate new genetic variation on a scale, and with a degree of sophistication, ranging from subtle to dramatic alterations in the development and organization of tissues and organs (de Jong & Scharloo, 1976; Dykhuizen & Hart, 1980; Finnegan, 1989; Dibb & Newman, 1989; Gibson & Hogness, 1996; John & Miklos, 1988; Kuhsel, et al. 1990; Moran et al., 1999 Polaczyk et al., 1998; Rutherford & Lindquist, 1998; Strachan & Read, 1996; Wade et al., 1997). Such changes appear most likely if these insertions occur in coding regions and often confer useful traits on the host, as well as guide, coordinate, and regulate evolution and metamorphosis.

25. INTRONS INFECT OTHER SPECIES

Between 35% to 50% of the human genome is ultimately derived from transposable elements (International Human Genome Sequencing Consortium 2001; Lander et al., 2001; Smith 1996; Yoder et al., 1997), and there are many examples of human genes derived from single transposon insertions (Nekrutenko and Li, 2001; Sakai et al. 2007). Moreover, large numbers are found in human protein coding genes (Nekrutenko and Li, 2001).

In a study of genome-wide impact of transposable elements on evolution, Nekrutenko and Li (2001) found that almost 89% of these TEs reside within 'introns' and were recruited into coding regions as novel exons, such that it appears that TE insertion might create new genes (Nekrutenko and Li, 2001) and recruit new exons (Sakai et al. 2007), which would in turn, affect and accelerate species divergence. Numerous studies have in fact found that TEs in the mammalian genome promote the variation and diversification of genes, and affect the expression of many genes through the donation of transcriptional regulatory signals (Thornburg et al., 2006; van de Lagemaat et al., 2003; Jordan et al., 2003).

TEs therefore, contribute to pre-transcriptional gene regulation, especially by moving transcriptional signals within the genome which in turn leads to new gene expression patterns (Thornburg et al., 2006) and the creation of new genes from old genes (Nekrutenko and Li, 2001; Sakai et al. 2007). Further TEs are involved in gene duplication and the creation of large numbers of interspersed repetitive sequences (Smit 1996). By contrast, mRNAs of highly conserved genes are generally devoid of TEs (van de Lagemaat et al., 2003).

TEs are more frequent in duplicate than single copy protein coding genes (Sakai et al. 2007) indicating they are involved in gene duplication and diversity (van de Lagemaat et al., 2003) and not gene conservation. Thus TEs serve as recombination hot spots and may express or create specific cellular functions, through the control of protein translation and gene transcription (Thornburg et al., 2006). In fact because many TEs are taxon-specific, their integration into coding regions could accelerate species divergence and contribute to sudden bursts of evolutionary development (Jordan et al., 2003; Morgan 1993; Nekrutenko and Li, 2001; Sakai et al. 2007; van de Lagemaat et al., 2003).

Moreover, gene classes which react to external environmental stimuli, have transcripts enriched with TEs (van de Lagemaat et al., 2003). In addition, TEs are intimately involved in the simultaneous regulation of multiple genes (Jordan et al., 2003). Thus TEs can trigger gene expression in numerous genes simultaneously in response to changing environmental conditions; and this may include whole genome duplication and/or explosive evolutionary leaps after long periods of evolutionary equilibrium.

The life cycle of TEs in any single phylogenetic lineage can apparently last for many thousands or millions of years and can be considered as a succession of six phases: dynamic replication, movement to another region of the genome, transfer to another species, activation, inactivation, degradation (Kidwell, 1993; Miller et al., 1996).

TE are intrinsically parasitic (Doolittle and Sapienza, 1980; Dujon, 1989; Orgel and Crick, 1980; Hickey 1982; Kiyasu and Kidwell 1984; McDonald 1993; Yoder et al., 1997), and can easily duplicate themselves (Plasterk and Sherratt, 1995) and invade new species (Dujon, 1989; Dujon et al., 1989; McDonald 1993). A proclivity for horizontal transfer is consistent with the role of TEs as genomic parasites. TEs, therefore, also act as plasmids.

Horizontal transfer to another host lineage provides the opportunity for active TEs to begin the cycle over again in yet another species (Dujon, 1989; Dujon et al., 1989; Hurst et al., 1992; Kidwell, 1993; 1994; McDonald 1993) or to insure that all members of the same species undergo the same genetic and evolutionary changes at the same time (McDonald 1993).

Moreover, this enables these intronic TEs to coordinate gene expression among multiple members of the same or divergent species, such that different species may evolve in tandem or develop complimentary traits at the same time.

These TEs can survive over long periods of evolutionary time by spreading throughout numerous genomes belonging to numerous divergent and subsequent species. However, once transferred, transposed, and inserted, these TEs may serve only to inhibit gene expression (Waterland and Jirtle, 2003; Yoder et al., 1997). It may take hundreds of millions or even billions of years, before these genes become active and begin expressing new functions, new characteristics, and even new species; and this may require major changes in the environment and the elimination of suppressive influences.

26. GENE ACTIVATION & SUPPRESSION

Genes expression can be restricted and inhibited by a variety of mechanisms and proteins, such by "restriction" via Alu enzymes (Arber and Linn 1969; Krüger and Bickle 1983) which are linked to retroviruses, or the binding of a repressor molecule or protein to the operator to prevent transcription (Blumenthal et al., 2002; Salgado, et al., 2000). Inhibition can also be accomplished via methylation and/or the generation of heterochromatin (Waterland, 2006, Waterland and Jirtle, 2003; Yoder et al., 1997).

Further, TEs inserted into introns can inhibit mRNA processing, and can render numerous genes susceptible to siRNA-mediated transcriptional gene silencing (Doetsch et al., 2001). Heterochromatin formation and its repressive capacity are also mediated by RNA interference (RNAi) machinery (Grewal and Moazed 2003; Hall et al., 2002; Volpe et al., 2002). Therefore, they can turn genes on, or off.

Transposons which use the gene replication machinery to reproduce themselves, also utilize methylation to prevent their own replication and to prevent the expression of nearby genes (Yoder et al., 1997; Rakyan et al., 2002). Most transposable elements in the mammalian genome, along with the genes positioned near them, are silenced by methylation (Yoder et al., 1997; Rakyan et al., 2002). DNA methylation involves four atoms, the methyl group, which attaches to and coats the gene thus silencing the gene by preventing its expression. Methylation is commonly employed to inactivate a variety of genes (Wolff et al., 1998; Yoder et al., 1997; Van den Veyver 2002). However, by inactivating a TE, methylation may instead induce gene expression.

Transposable elements, therefore, in conjunction with methylation, "restriction" siRNA-mediated transcriptional gene silencing, and the generation of heterochromatin commonly silence or activate various genes, and can cause considerable phenotypic variability, making each individual mammal a "compound epigenetic mosaic" (Whitelaw and Martin, 2001).

27. ENVIRONMENT & GENE EXPRESSION: METHYLATION

Not just transposons and introns, but the environment also activates or silences genes, and can effect methylation. In fact, those genes which are most responsive to external environmental stimuli, have transcripts enriched with TEs (van de Lagemaat et al., 2003). However, certain environmental triggers can induce or remove methylation thus enabling the expression of these genes (Waterland and Jirtle, 2003; Wolff et al., 1998).


Red and green boxes represent silenced and active transposons

Those environmental influences can include diet and nutrition (Van den Veyver 2002; Waterland and Jirtle, 2003; Wolff et al., 1998). Diet plays a significant role in evolutionary metamorphosis and gene expression via 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.

Likewise, 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). Change the environment, and gene expression patterns may also be altered, giving rise to slight or major differences in the products produced. For example, increases in the levels of oxygen, calcium, and other elements and gasses significantly impacted gene selection around 540 mya, triggering what became the Cambrian Explosion.

28. GENE EXPRESSION, HSP90 & MOLECULAR SWITCHES

These genetic-environmental interactions on gene expression are mediated through protein products like Hsp90 (Rutherford & Lindquist, 1998). Hsp90 is a highly conserved multifunctional protein which targets multiple signal transducers which act as "molecular switches" which 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).

Hsp90 does not act alone but is part of a networks that includes other 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.

"Hsp90 is one of the more abundant chaperones. 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).

For example, these proteins may prevent DNA expression by acting as a buffer between silent genes and their nucleotides and the environment. Therefore these genes are inhibited and are only expressed in reaction to changes in the environment including temperature change.

29. HSP90, GENE EXPRESSION, NUCLEAR RECEPTORS & SNOW BALL EARTH

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.

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.

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.

As will be detailed in part 3 and elsewhere (Joseph 2009b), Earth has undergone at least three major world-wide glaciations (Hoffman et al. 1998; Hyde et al., 2000; Runnegar 2000; Lubick 2002). Each was 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 3rd 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 3rd glaciation and ensuing warming cycle, leading to an explosive burst of evolutionary change and diversification (beginning 540 mya), including the appearance of complex animals and chordates equipped with bilateral bodies, eyes, and brains (Chen et al., 1995, 1999; 2003; Shu et al., 2001; Siveter et al., 2001). It was during this same time period, known as the Cambrian Explosion, that the genome duplicated in size (Holland 1994, 1999; Dehal and Boore 2005) and which is associated with the evolution of every phylum which is in existence today.

It can be assumed that the metamorphosis of the first true metazoans and chordates, was paralleled by the functional expression of those nuclear receptors regulated by the Hsp90 protein complex, and which are associated with metazoans. Thus, the explosion of complex life at the onset of the Cambrian, could be related to the effects of world wide glacial freezing followed by global warming on the Hsp90 protein complex. This may have led to activation of genes that had been suppressed, and even the duplication of individual genes and the entire genome thus enabling their expression.

In fact, the genome underwent duplication at this time (Holland 1994, 1999; Dehal and Boore 2005) and nuclear receptors appear to have evolved by series of gene duplications, followed by functional expression of the duplicated gene (Laudet 1997; Baker 1997, 2003; Thornton 2001). Therefore, it appears that the genes coding for sex steroids, adrenal and other nuclear receptors, and which have an important role in development and sexual differentation, underwent duplications in chordates possibly during the Cambrian Explosion (Baker 1997, 2003; Laudet 1997; Escriva et al. 2000; Thornton 2001) and were expressed once freed of inhibitory restraints.

Therefore, Hsp90, which can prevent the expression of a variety of genes or enable these genes to express functions which had been suppressed, may have been impacted by the extremes climatic changes in global temperatures. These global temperature changes, which may have been induced by biological activity, in turn effected a wide variety of signal-transduction proteins that are stabilized by Hsp90, thereby allowing for their expression and thus the metamorphosis of complex species including those which appeared during the Cambrian Explosion.

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.

However, it as also the actions of genes, that is, biological organisms, which were largely responsible for these dramatic changes in the climate and global temperatures. Genes effect the environment and the environment acts on gene selection, creating an interactive feedback loop which significantly impacts the speed and rate of evolutionary metamorphosis. In order for these repressor proteins and other regulating genetic mechanisms to be switched off or on, requires contact and exposure to specific environmental agents.

Presumably, these environmental influences directly impacted 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, and which were donated to the eukaryotic genome by viruses and prokaryotes--the ancestors of which, arrived on Earth from other planets.

Part 3. Genes, Microbes & Metazoan Metamorphosis:
Brains, Bodies & the Cambrian Explosion


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