Cosmology, 2009, Vol 1, 100-150
Peer Reviewed
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 began in an "organic soup" following the buildup of organic sludge which through a serious of fortuitous accidents, achieved life (Menor-Salván, 2009; Sidharth, 2009). Therefore, life on Earth came from non-life. Central to the belief in 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 (Hoyle and Wickramasinghe 2000; Joseph 2000a, 2009a; 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 (Arrhenius 2009; Hoyle and Wickramasinghe 2000; Joseph 2000a, 2009a).
"Seeds" do not randomly germinate into a variety of forms as dictated by chance, Darwinian principles, or "natural selection." Seeds contain precise genetic instructions and what will grow is under genetic regulatory control. In response to the changing environment specific genes are activated and seeds will produce a variety of growing plants that may change as they develop. 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 abiogenesis.
Darwinism and the abiogenesis hypothesis are intrinsically linked. The Darwinian-abiogenesis consensus is that an accident of chance 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. Through unknown mechanisms, this first single living cell was blessed with DNA and the ability to replicate and create variable copies of itself and its genome. 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.
Joseph (2000a, 2009b) has detailed numerous flaws in the Darwinian conception of evolution, pointing out that Darwinism 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).
Joseph (2000a, 2009a) has also ridiculed the "life-began-on-Earth" theory of abiogenesis, calling it "religion masquerading as science" and points out there is absolutely no evidence to support the abiogenesis hypothesis. Life has never been created from non-life despite repeated attempts by creation scientists to intelligently design life in a laboratory.
Proponents have defended abiogenesis and the embarrassing lack of supportive evidence by claiming that "absence of evidence is not evidence of absence." However, "the absence of evidence" means there is no evidence. Without evidence there are no facts. Belief in abiogenesis, in the absence of evidence and in the absence of facts, is not science. Its magical thinking. Belief in abiogenesis is based on "faith," which is the domain of religion.
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 organic soup, but was inherited from life forms whose ancestors lived on other planets (Joseph 2000a, 2009a,b).
2. EXTREME ENVIRONMENTS AND SPACE JOURNEYING MICROBES
As first theorized and proposed by Joseph (2000), long before Earth or our solar system were formed, extraterrestrial microbes and other forms of life continually exchanged DNA with species living on other planets. This was accomplished through plasmids, viruses, and lateral and 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, these extraterrestrial microbes and their descendants 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. The descendants of these microbes, with their vast genetic libraries, 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 (Vreeland et al. 2000).
Spores
Moreover, 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 prior exposure and adaption, 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, thus producing a variety of species which also acted on and changed the environment (Joseph 2000a, 2009b).
However, 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 on 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.
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. 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 which code for these traits to subsequent species. It is only when the environment has been sufficiently altered, including 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.
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. 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 genome consists of bacteriophages, plasmids, and transposable elements which include 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 (bacteria and archae) 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 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 who then possess 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, this frees up considerable genomic space. Not all microbes 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 microbes and vast numbers of species, maintaining different genetic volumes (acquired from different extraterrestrial sources) which can be shared 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). 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). Up to 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), and HGT likely also took place when extraterrestrial microbes encountered complex eukaryotes on other planets.
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). 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. 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, and 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 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 not only provide prokaryotes with genes but eukaryotes and this genetic endowment had directly impacted evolution leading to the metamorphosis of humans.
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 exchanged and genes may be 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 they can then insert 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.
It is possible that some viral elements are in fact plasmids, or are created by free-DNA, or packets of RNA, which are expelled from one cell or from one organism, only to invade and take up residence in the genome of another host. In this way, the DNA of one species can be inserted into the genome of another. Likewise, it is in this manner 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). 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 message, 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 the 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). As noted, bacteria can also influences the genetic functioning of plants so that they too produce enzymes and amino acids, i.e. opines, which serve as nutrients for agrobacteria.
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. However, of equal importance, it has been determined that the human gut is a ‘hot spot’ for horizontal gene transfer (Kurokawa, et al. 2007). In fact, 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.
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 other 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 formed (Schoenberg et al. 2002), and it is during this time period, between 4.5 to 3.8 BYA that life took root on Earth (Joseph 2009a). 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), (Joseph 2000, 2009a,b) 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 revealed 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),
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. This enabled 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).
However, 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 a α-proteobacterium, thereby producing a combined genome and thus the first eukaryote (Hedges et al. 2001).
Based on a genomic analysis, this α-proteobacterium, triggered eukaryogenesis (Martin and Koonin 2006; Martin and Muller, 1998), and the genetic fashioning of the first proto-eukaryotes around 4 billion years ago (Hedges et al., 2001). This genetic fusion, and subsequent environmental and genetic events, eventually led to the first Earthly eukaryotes within a few hundred million to a billion years later (Feng et al., 1997; Hedges, 2002) and could account for the simplified eukaryotic microfossils dated to 3.8 BYA (Pflug 1984).
Presumably this α-proteobacterium 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 may have been fashioned from this genetic union, or 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).
These genes donated by prokaryotes (and possibly 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 became multicellular and then increasingly complex and intelligent.
Further, this α-proteobacterium, and/or its genes, once incorporated as part of the proto-eurkaryote, may have also served as 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 (and possibly a virus) may have joined together, combining their genomes, and in so doing, created the first Earthly eukaryotes, and/or via HGT donated essential genes to those eukaryotes which also arrived encased in comets, meteors and cosmic debris. Nearly 4 billion years later, the ancestors of the first Earthly eukaryotes would give rise to humans.
10. OPERATIONAL AND INFORMATIONAL GENES
The ancestral prokaryotic genes which were donated to eukaryotes included regulatory genes, introns, transposable elements, and all the genetic machinery necessary for fashioning unicellular and multicellular eukaryotes and their genomes. Further, prokaryotes and viral agents provided eukaryotes with the regulatory elements which control 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 that convey the instructions 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 include genes and proteins which directly influence metabolism and the ingestion and excretion of various waste products.
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. 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 influences.
Although initially massive numbers of genes were transferred to the eukaryotic genome, 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 infrequent yet massive horizontal transfers, such as at the initial stages of eukaryotic evolution. Subsequently, informational genes appear to have undergone horizontal transfer only periodically and much less frequently as compared to operational genes (Jain et al., 1999; Rivera et al., 1998). This suggests that information genes may be transferred only when specific hosts evolve or in response to specific environmental events thereby triggering the next stage of metamorphosis during critical windows of opportunity.
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.
The functional maintenance and eventual expression of a gene, therefore, requires a successful integration in the recipient chromosome. The success of this 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); again suggesting that genes may be transferred only when specific hosts evolve and during critical windows of evolutionary opportunity, and that the transfer of genes is under precise genetic regulatory control.
Thus, the frequent and continued horizontal transfer of informational genes would likely completely disrupt the functional integrity of the host genome (due to increased complexity) and thus must be resisted, whereas the continous insertion of operational genes would not. Therefore, the transfer of informational genes occurs 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.
Other factors also play a significant role in gene transfer, such as those involving the types of 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).
Most genes, informational genes in particular, were probably transferred during the initial stages of eukaryogenesis, billions of years ago. Subsequently, these genes and the whole genome were repeatedly duplicated, and the eukaryotic genome grew in size.
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. Thus transferred genes 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.
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 of bacteria and archae genes to create the first Earthly eukaryote, or the merging of the genes from these 3 domains to fashion the first multi-cellular eukaryotes, 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. Thus after these genes were combined, eukaryotes began to increase in size and complexity.
Again, in these instances, HGT was from prokaryote to eukaryote and not between prokaryotes indicating precise genetic purpose and control thus ensuring that progressive evolutionary development would be restricted to eukaryotes with their combined prokaryote genes. 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. Because of their now larger, more complex cell size, some prokaryotes could form symbiotic relations with eukaryotes after phagocytosis (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 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).
However, to perform these functions 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). Yet other, such as Na+, Cl− and Ca2+, had been rejected by the prokaryotic genome, but came to be employed by eukaryotes for messaging, signaling, and even metabolism, thus increasing energy uptake and the ability to quickly acquire and respond to information in the environment (Williams & Fraústo da Silva 2006). Thanks to HGT from prokaryotes, including those forming symbiotic relations, 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).
In contrast to prokaryotes, the eukaryotic genome became more sensitive to environmental changes which acted on gene selection. Therefor, eukaryotes and not prokaryotes, began to evolve and became increasingly complex in response to genetically engineered alterations in the environment.
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).
The DNA of multicellular eukaryotes is contained within the nucleus of every cell and mitochondria sit adjacent to the nucleus. The nucleus which protects the eukaryotic genome, and the establishment of compartments, may have originally consisted of stripped down bacteria/archae.
Thus, the nucleus may be a derived endosymbiont, a descendant of an archaeon that invaded a bacterial host, or a bacteria and archae which invaded or was engulfed and phagotocyzed by the first eukaryotes (Lake and Rivera 1994; Horiike et al. 2004; Hartman and Fedorov 2002). Others believe that the 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).
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 hundreds of millions of years after phogotrophy and hundreds of millions of years before the metamorphosis of mitochondria (Margulis et al., 1997).
Therefore, phagotrophy and symbiosis appeared in advance of the nucleus and mitochondria. Phagotrophy, and the digestion of nutrients would have resulted in increased cell size. Increased size in the initial absence of a nucleus, would have enabled simple eukaryotes to ingest and incorporate bacterial and archael genes which were then easily combined with the eukaryotic genome (Dyall et al., 2004; Margulis et al., 1997). 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), and enabled eukaryotes to become more complex and conquer new environments which then acted on gene selection.
12. ANCESTRAL GENE EXPRESSION & THE ENVIRONMENT
As detailed in this paper (and in Parts 2, 3, and 4), there is considerable evidence that genes donated by prokaryotes to eukaryotes and which were inherited from ancient ancestors contributed significantly to the evolutionary-metamorphosis of increasingly complex creatures in response to biologically engineered changes in the environment (Joseph 2000a, 2009b). 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 possibly genes inserted into the eukaryotic genome by retroviruses. These genes (as well as prokaryotic organisms) also 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). Genes act on the environment 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.
13. CONSERVED GENES & GENE EXPRESSION
Genes which code for advanced functions have as their sources, ancestral genes. Further over the course of evolutionary history genes were repeatedly inserted, via HGT, into the eukaryotic genome. Through inherited genetic regulatory mechanisms, 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 turned genes on or off, and entire networks of genes were inhibited or expressed.
Despite this 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), it has been established that 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; 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, (Koonin 2002) and gene sequences (Koonin 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. Given that there is nothing random about the organization and expression of DNA, coupled with the highly regulated fashion in which these genes have been exchanged and expressed, it clear that the genes originally donated by prokaryotes have performed crucial functions that have guided what has been termed evolution.
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, 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 or acquire them via HGT from neighboring species already equipped with brains, eyes, or hearts, as these organs had not evolved until around 540 mya. These genes within the genome of this living fossil, were inherited from ancestral species who also lacked these organs.
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 the changing 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, both of 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 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. 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 the 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 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 had 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 lacking flowers began to flower (Mandel and Yanofsky 1995; Pelaz et al., 2000, 2001).
The ancient pedigree of these inherited genes is demonstrated by the fact that plants contain genes donated by cyanobacteria (blue-green algae) and arachae billions of years ago (Doolittle 1999; Nosenko and Bhattacharya 2007). Cyanobacteria and arachae were also among the first to colonize Earth, and their own ancestry leads to extraterrestrial sources.
These genes crucial to the development of flowering plants did not randomly evolve but were inherited from ancestral species. They underwent at least one whole genome duplicative event, possibly at the divergence between animals and plants (Alvarez-Buylla et al., 2000), but remained suppressed for at least a billion years until activated 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.
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 environmental change.
These genetic-environmental interactions on gene expression are mediated through 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 regulatory proteins, changing the configuration of these proteins and 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 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). 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).
Therefore, 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. 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. For example, 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, perhaps 4 billion years ago. As there is no evidence supporting 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.
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 with a photosynthetic cyanobacteria (Rivera and Lake 2004), or a α-proteobacterium, and then diverged to create a proto-eukaryote (Hedges et al. 2001). The other possibility is that bacteria, archae, viruses, and blue-green algae donated genes to whatever eukaryotes had also been deposited on the new Earth contained within the cosmic debris that had been pounding the planet. Eukaryotes, equipped with these genes, and in response to the biological engineering of the environment, diversified 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 was formed. However, this genetic transition from single celled to multicellular eukaryote may have been 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 began to seep into the environment (Buick 2008; Eigenbrode and Freeman 2006). The altered environment acted on gene selection, thus triggering multicellular eukaryosis.
The action of prokaryotes and their genes also contributed to the alteration of 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, and 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).
Viruses contributed photosynthesizing genes to cynaobacteria (e.g., (Lindell et al., 2004; Sullivan et al., 2005, 2006; Williamson et al., 2008), and photosynthesizing cyanobacteria contributed genes to the eukaryotic genome (Howe et al., 2008), possibly at the initial stages of eukaryotic evolution. Gene transfer may have taken place secondary to endosymbiont engulfment by non-photosynthetic eukaryotic hosts (Howe et al., 2008). The genes donated by these cyanobacteria enabled some eukaryotes to develop 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 eurkayotes began to engage in photosynthesis in an oxygen free environment, 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 donated genes and possibly the horizontal transfer of these activated genes from 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, and 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 reductant as early as 3.0 bya (Olson 2006). However, 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 no longer or not as useful (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). Thus, newly 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.
The liberation and incorporation of these chemical substances led to increasing cellular complexity, a function of cells acting on the environment which acts on gene selection which acts on the environment, creating a complex feedback system which promotes the evolution of increasingly complex creatures.
For example, and 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
In addition to photosynthesis, some prokaryotes including cynaobacteria and aerobic photoautrophic marine plankton were producing oxygen via 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 acted on gene expression.
Some researchers believe that 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). Some believe the nucleus may be a derived endosymbiont, a descendant of an archaeon that invaded a bacterial host, or a bacteria and archae which invaded or was engulfed and phagotocyzed by the first eukaryotes (Lake and Rivera 1994; Horiike et al. 2004; Hartman and Fedorov 2002).
It is believed that a proteobacterium became incorporated within these initial proto-eurkarytoes, and may have also served as 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 α-proteobacterial endosymbiont that gave rise to the mitochondria (van der Giezen and Tovar 2005; Embley 2006). Presumably, the genes of this α-proteobacterium symbiont underwent transformation in response to the increasing levels of oxygen in the atmosphere, becoming a mitochondria.
Thus, many researchers also believe that the mitochondria are directly linked to the engulfment of an anaerobic symbiont α-proteobacterium (reviewed by Gray et al., 1999) or a free-living photo-synthesizing bacteria by a methanogenic archaeon. Presumably this bacterium 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. Hundreds of millions of years would pass before eukarayotes began breathing oxygen (Schafer et al., 1996) via mitochondria (and related organelles) which now reside in all subsequent multicellular eukaryotic cells.
 
Once the environment became sufficiently oxygenated, the α-proteobacterium 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). The activation of these genes, and the metamorphosis of mitochondria enabled eukaryotes to colonize emerging aerobic environments.
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 emerging 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, had begun to enrich the atmosphere (Barleya et al., 2005; Eigenbrode and Freeman 2006). Because of this biological activity, 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-proteobacterium 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.
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
There is also evidence supporting the possibility that mitochondria arose when the first multi-cellular eukaryotes internalized and formed a symbiogenetic relationship with a free-living proto-mitochondria or an α-proteobacterium symbiont (Cavalier-Smith, 2009). 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.
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 proteobacterial descent (Gray et al., 1999).
Mitosomes therefore, may also be related to to a proteobacteria 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). Thus mitosomes appear to be mini-mitochondria albeit stripped of its 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 an proteobacteria 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 and enzymes including oxygen (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.
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 that the metamorphosis of mitochondria ensued via the transformation and activation of genes provided by α-proteobacterium. The alternative is symbiosis following the metamorphosis of multicellular eukaryotes. Either scenario would have been triggered by the changed environment and the signfiicant increases in oxygen levels (Hedges et al., 2004) and other essential elements necessary for the functioning of mitchondria such as NADH.
However, the rise of oxygen was also 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).
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). 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); a process Andersson (2005) refers to as “endosymbiotic gene transfer."
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). 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. These changes were due to the effects of the biologically altered environment and thus were genetically regulated and not some chance event.
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.
During this same time period, when oxygen levels increased, 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. 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 their ancestors. 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.
23. THE EVOLUTION OF LIFE FROM OTHER PLANETS
Despite the claims of those who believe it possible to intelligently design and create life in a laboratory, the belief in abiogenesis does not have a scientific or factual foundation but is based on faith which is the domain of religion. 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.
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.
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 only to be hurled upon the newly forming Earth hundreds of millions of years later. This would account for the presence of microfossils resembling yeast cells and fungi, discovered in 3.8 BY old quartz (Pflug 1978) and the abundance of evidence 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)
However, it was probably not necessary for most microbes and microbial eukaryotes to form spores. Many could have continued to thrive, flourish, and reproduce, deep beneath the surface of giant asteroids or moon-sized objects which eventually slammed into the newly forming Earth. Consider for example, the bacterium, Desulforudis audaxviator, discovered 2.8-kilometers (1.74 miles) beneath the surface of this planet. Genomic analysis of its 2,157 protein-coding genes indicates this species "is capable of an independent life-style well suited to long-term isolation from the photosphere deep within Earth's crust and offers an example of a natural ecosystem that appears to have its biological component entirely encoded within a single genome" (Chivian et al., 2008). The genome of D. audaxviator indicates it has never been exposed to sunlight, obtains its nourishment from non-biological sources, and can form spores. Numerous species of microbe have been discovered flourishing over a mile deep within this planet, including below the subfloor of the ocean (Biddle et al., 2008; Chivian et al., 2008; Doerfert et al., 2009; Moser et al., 2005; Gohn et al., 2008; Hinrichs et al., 2006; Sahl et al., 2008), and there is no reason to believe that similar creatures would not be able to survive miles beneath the surface of extraterrestrial debris.
If eukaryotes also arrived encased within debris, then once on Earth, they 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. A second possbility is that the first Earthly eukaryotic cells were created by the genetic fusion of bacteria and archae, and possibly the injection of viral genes.
Both scenarios lead to the same result: genes donated by archae, bacteria (and possibly viruses), in combination with biologically engineered environmental influences, fashioned the first multicellular eukaryotes, which, nearly 4 billion years later, would give rise to humans. The step-wise, sometimes leaping progression leading from simple to complex species and 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.
This does not mean that evolution and metamorphosis leading to modern humans was genetically pre-determined. Rather, the life forms that have evolved on Earth are just a sample of life's manifold evolutionary possibilities. Different environments can act on different genes which may produce innumerable life forms, only some of which have evolved on this planet. Hence, rather than pre-determined, all possible traits, functions, organs, tissues, and characteristics have been pre-coded, which is why the genes coding for advanced characteristics, such as for the eyes and the brain, appear in ancestral species prior to their expression.
In fact, many genes including those of the human genome, can be traced backward in time to the "last common ancestors" of eukaryotes and to prokayotes; i.e. to archae and bacteria, microbial species whose ancestors arrived in debris jettisoned from other planets. Thus all life on Earth has a cosmic genetic ancestry.
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 creatures. Horizontal gene transfer has likely taken place on innumerable planets, wherever life comes in contact. When microbes are jettisoned into space, they carry with them vast genetic libraries, with different microbes maintaining different genetic luggage. In their role as intergalactic genetic messengers, this is the equivalent of sending out trillions of genes via innumerable microbes, thus insuring that at least some of this genetic cargo and these genetic libraries are delivered to other worlds. Therefore, once these microbes took root on Earth, they began exchanging genes, many of which became part of the genomes of the first eukaryotes on Earth.
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. These elements and genetic mechanisms, including RNA polymerase, and replicative DNA polymerase, 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). Because individual genes as well as the entire genome can be duplicated and then transmitted to subsequent species, this gave rise to preprogrammed diversity and allowed the same trait or characteristic to evolve, seemingly independently, in numerous divergent species in response to changes in the internal or external environment.
Via these mechanisms, the genes, gene sequence, and related elements that encode for advanced characteristic, such as the heart, eyes, and brain, could be duplicated and passed down to subsequent species which would maintain these genes even without expressing them and without losing information. However, in response to major alterations in the environment, and after undergoing repeated duplications, and in reaction to environmental, regulatory, and other genetic signals, the traits coded by these genes were expressed. Ultimately this led to increasing multicellular, then vertebrate complexity and the rapid evolution of new species (Seoighe et al., 2003).
The genetic and fossil record does not support Darwin's theory. The metamorphosis of new species does not take place in small transitional steps, but in quantum leaps, following the activation of ancestral genes in response to environmental-biological interactions. Some of the more dramatic environmental changes, such as the flooding of the oceans with oxygen, and then later (cyanobacteria-produced) calcium and the creation of a protective ozone, led to the most dramatic explosion of life in the history of Earth, 540 mya. Indeed, 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.
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. These genes did not randomly evolve, they were inherited from the first Earthlings whose ancestors hailed form other more ancient worlds.
What has been called a random evolution, has been under precise genetic regulatory control. Genes do not randomly evolve, they are inherited. Evolution is metamorphosis, the replication of life forms that long ago lived on other planets.
The Evolution and Genetics of Life From Other Planets. Part 2. Part 2
Bactria, 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
The Evolution and Metamorphosis of Life From Other Planets. Part 3. Genes, Microbes. Metazoan Metamorphosis: Brains, Bodies & the Cambrian Explosion
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