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Journal of Cosmology, 2009, Vol 2. 235-255. Cosmology, October 15, 2009 Extinction, Metamorphosis, Evolutionary Apoptosis, and Genetically Programmed Species Mass Death Rhawn Joseph, Ph.D. Cosmology.com Genes, cells, and entire species undergo evolutionary apoptosis and are continually pruned from the tree of life. Programmed death is essential to life and evolution, and genetically programmed evolutionary apoptosis is one of the many causes of species death and extinction. Evolution and extinction can be likened to embryogenesis and metamorphosis as all involve the selectively turning on and off of specific genes and nucleotide sequences, the shedding of cells and tissues which are replaced, and dramatic alterations in the organs and skeletal muscular system. "Evolution" is under genetic regulatory control, in coordination with the biological activity of viruses and single celled prokaryotes (archae, bacteria, Cyanobactera), their donated and horizontally transferred genes (including those which gave rise to mitochondria), and the genetically engineered environment. The interaction between the environment and genetic activity, the secretion of chemicals, enzymes and gasses such as oxygen and calcium, regulates the emergence of new species, and the elimination of yet others--a form of evolutionary-apoptosis. Genes act on the environment, and the changing environment acts on gene selection, activating specific genes, silencing others, and giving rise to new species which emerge from the old, with entire populations of genes, cells, tissues, and species proliferating and others dying out. Like programmed cell death, extinction is often intrinsic to and necessary for the development, evolution, and metamorphosis of increasingly complex species.
1. Introduction
Birth, death, evolution and extinction, are part of the cycle of life. Like programmed cell death, extinction may be intrinsic to and necessary for the development, evolution, and metamorphosis of increasingly complex species (Joseph 2009a). Extinction, in some instances, may be considered a form of evolutionary sculpting and "apoptosis"--from a Greek word referring to leaves “falling off” a tree--and promotes the spread and diversification of new life.
Broadly considered, extinction may be due to a number of factors (Bradshaw and Brook 2009; Elewa 2009; Raup 1991), including: (1) "accidental causes" such as gamma rays, bolide impact and volcanic activity, whereby numerous species are wiped out by random uncontrolled catastrophic forces (Arens and West 2008; Elewa 2009; Jablonski 1994; Melott et al. 2004; Thompson and Crutzen 1988), or (2) "biological causes" (Casadaveli 2005; Jones 2009; Poinar and Poinar 2008; Miller et al. 2004), including interactive biological (Ward 2009) environmental feedback mechanisms (Lovelock 2006) and genetic preprogramming leading to species death and eradication (Joseph 2009a). In the latter instances, extinction is linked to metamorphosis and evolutionary-apoptosis, with new species emerging from the old.
Although extinction is often considered a byproduct of Darwinian natural selection, Darwin's hypothesis (Darwin 1859, 1871) can be best summed up as "survivors survive because they are fit, and they are fit because they survive" --a view which is little more than circular reasoning (Joseph 2000a). Darwin's tautology cannot be used to make predictions, cannot be scientifically tested, and can only be applied after-the-fact. Darwin's central dogma emphasizing "small steps" (Darwin 1859,1871) is in fact completely refuted by the fossil record, as eukaryotic evolution generally proceeds in quantum leaps in the absence of intermediary forms (Eldredge and Gould 1972; Gould 2002). Variation is not evolution.
Contrary to Darwinism, there is no convincing fossil evidence of gradual change from one species to another or any fossil record of transitional forms acting as an evolutionary bridge between species (Eldredge and Gould 1972; Gould 2002; Hoyle and Wickramasinghe 1984, 2000). Eukaryotic evolution generally occurs in bursts of explosive speciation followed by long periods of stasis and equilibrium with little or no change (Eldredge and Gould 1972; Gould 2002). Evolution is not random, or due to mutations, and does not take place in small steps, but is a function of a highly regulated interactions between genes and the internal and external environment (Joseph 2000a, 2009a).
As a form of evolutionary apoptosis, extinction is tightly regulated at the genetic and cellular level, and specific environmental (Lovelock 2006) and biological triggers (Ward 2009), will initiate the mass death and elimination of specific species. Multicellular organisms which served as a genetic bridge to subsequent species, and which have fulfilled their biological purpose and provide no additional biological/environmental function, are destroyed by biologically/genetically regulated processes (Joseph 2009a).
Over the course of the history of this planet billions of species may have been genetically programmed to commit biological suicide (Ward 2009); a consequence of the fact that genes act on the environment and the changing environment acts on gene selection and induces gene gain and gene loss and the evolution vs the extinction of species (Joseph 2000a, 2009a). The interaction between the environment and genetic activity, regulates the emergence of new species and the elimination of yet others--a form of evolutionary-apoptosis.
It is this genetically preprogrammed apoptosis, and the biological activity of viruses and prokaryotes, which may help explain why numerous distinct species evolved or became extinct during and after the first two global ice ages (Joseph 2009a) and during the Ediacaran age, only to die out (Amthor et al. 2003; Narbonne 2005), and then again during the Cambrian explosion only to become extinct (Palmer 1998; Westrop and Ludvigsen 1987; Zhuravlev and Wood 1996).
Likewise, if we accept the view of gradualists (e.g., MacLeod et al. 1997) vs the catastrophists (e.g., Alvarez 2008), preprogrammed apoptosis could explain why dinosaurs were progressively and selectively wiped out, such that by 65 million years ago, after a rein of over 200 million years, these species disappeared (Alvarez 2008; Arens and West 2008; Elewa 2009; Poinar and Poinar 2008) whereas others, such as mammals, recovered, continued to thrive, diversified, and became increasingly intelligent and cognitively complex.
2. Apoptosis, Mitochondria, and Species Mass Death
Species may become extinct due to a variety of causes (Bradshaw and Brook 2009; Firestone 2009; MacLeod et al. 1997; Miller et al. 2004; Poinar and Poinar 2008) many of which are only tangentially related to the forces associated with natural selection. For example, species-destroying-diseases induced by bacteria, fungi, and viruses (Casadevall 2005; Devaraj 2000; Emiliani 1993; Gong et al. 2008; Poinar and Poinar 2008), may have little to do with natural selection, and everything to do with evolutionary apoptosis, and alterations in the host-genome or the genome of the pathogen, which enable pathogens to selectively target and kill off a specific host long after it has evolved (Flint et al. 2009; Norkin 2009). Not uncommonly, diseases which have extinction-potential, are transmitted vertically, from genome to genome via mitochondria (Engelstädter and Hurst 2007), or, as is the case of retroviruses within the nuclear genome, and will selectively sicken or kill specific species in response to as yet unknown biological and environmental triggers (Joseph in press). Male-killing bacteria, for example, can hitchhike over thousands of generations, from mother to offspring, embedded within the mitochondrial genome (Jiggins 2003) and may begin destroying a species only after a related species has evolved. Genes which encode for retroviruses can be passed down for millions of years, embedded in the eukaryotic nuclear genome, and when expressed not only promote speciation and the evolution of new species but simultaneously eradicate others (Joseph in press).
Interactions between the genome of mitochondria and the eukaryotic nucleus, which are derived from microbes, and the biological activity of microbes and their effects on the environment (Joseph 2009a), play a central role in apoptosis and the genetically programmed extinction of species. In fact, stasis vs alterations within the mitochondrial genome have been directly linked to species extinction (Ballard and Rand, 2005; Gilbert 2008; Hofreiter et al. 2007), and mitochondria are directly implicated in apoptosis and cell death (Yin and Dong 2009).
As a form of evolutionary apoptosis, extinction is in part a direct consequence of the same cellular mechanisms which lead to cell death; albeit at the level of an entire species.
3. Apoptosis: Competition for Survival and Programmed Death
Consider, for example, the developing brain where millions of neurons proliferate and compete for functional representation with the losers dying out (Casagrande & Joseph, 1978, 1980; Joseph, 1999, 2000b; Joseph & Casagrande, 1978, 1980). This competition leading to the death of billions of healthy neurons, is due, in part, to the effects of the environment on gene activity, and enables the brain to differentiate, to become "fine tuned," and to function at optimal capacity.
Likewise, during human fetal development, billions of healthy cells compete, and losers continually die (Joseph 2000b), such as those linking the fingers and the toes (Alberts et al. 2007); otherwise, these appendages would be fused and webbed together leading to disability and reduced functional capacity. The individual digits separate only as the tissues between them undergo programmed cell death such that a webbed appendage becomes a hand.
Tissue and organ development are typically preceded by cellular proliferation, differentation, and competition, with excess or uncessary cells "pruned" away by apoptosis (Alberts et al. 2007; Yin and Dong 2009). It has been estimated that 50 billion cells die each day due to apoptosis in the average human adult (Alberts et al. 2007; Yin and Dong 2009). The same can be said of extinction events and those processes which lead to the emergence of new species.
According to Prothero (1998) up to 50 billion species have become extinct over the life time of this planet, leaving less than fifty million alive today. This means over 99.9% of all species have become extinct! However, mass extinctions may account for less than 5% of all species who have disappeared from the face of the Earth (Erwin 2001). In fact, in instances where many species are driven to near extinction, some recover whereas others die out (Erwin 1998). Thus, it appears that certain species are selectively targeted for eradication as if they are being "pruned" from the tree of life, thereby making way for the development and evolution of new species which take their place.
4. Embryogenesis and Evolution
What has been called "evolution" in some respects parallels metamorphosis and embryonic development (Joseph 2000a,b, 2009a). For example, the common ancestors of humans and chimpanzees likely had a tail, as is the case with monkeys and many other species of primate-mammal. Human and chimpanzee embryos develop a tail which atrophies and recedes to form the coccyx (Keith 2009; Laubichler and Maienschein 2007; Robert 2008). Whales evolved from land mammals, but upon returning to the sea lost their hair and legs. Yet during embryonic development, whales become hairy and develop leg extremities which then atrophy and recede (Laubichler and Maienschein 2007).
Be it fish, reptile, or human primate, the embryos of each of these species forms an internal skeleton consisting of a vertebral column, ribs, limb girdles, and limb cartilages which are initially remarkably similar and then progressively differentiate as competing cells live or die (Laubichler and Maienschein 2007). These embryos also develop "gill slits" which in humans becomes the pharyngeal arches and clefts of the throat, and pouches that become modified and form the middle ear canals (Laubichler and Maienschein 2007; Robert 2008). Yet a third pouch arising from the embryonic "gill slits" becomes the parathyroid and thymus glands (Keith 2009; Robert 2008) which are involved in the metabolism of calcium. Calcium plays a significant role in apoptosis (Mattson and Chan 2003) and the evolution of animals (Joseph 2009a).
Ontogeny does not replicate phylogeny. Nevertheless, many aspects of embryology and metamorphosis parallel physical events associated with extinction and evolution, and involve apoptosis and the death of billions of cells.
5. Metamorphosis
Embryological development can be likened to metamorphosis, as both involve the proliferation and death of healthy cells, and the selectively turning on and off of specific genes and nucleotide sequences; and the same can be said of evolution (Joseph 2000a, 2009a). A wide variety of species, including barnacles, bivalves, bryozoans, crabs, echinoderms, gastropods, mollusks, sea squirts, flat fish, flounder, eels, insects, amphibians, and reptiles, undergo profound physical alterations after birth and infancy which are often accompanied by significant changes in behavior and habitat (Barss, et al. 1995; Duellman and Trueb 1994; Evans and Fernald 1990; Evans and Claborne 2005; Heifman et al. 2009; Tackett and Tacket 2002).
Flounder and other flatfish, for example, are born as a symmetrical fish larva, but then become decidedly asymmetrical and both eyes are displaced to the dorsal surface as they reach adulthood (Barss, et al. 1995; Evans and Claborne 2005; Gilbert 2009; Heifman et al. 2009; Tackett and Tacket 2002; Wells 2007). Eels undergo a tail to head metamorphosis with a complete shift of the digestive and urinary tracts from posterior to anterior. Many species of insect first enter a larval followed by a pupal stage and then undergo transformations in morphology and physiology, growing wings, legs, reproductive organs and complex compound eyes which sprout from discrete infolded pockets of tissue (Gilbert 2009). Depending on species, insect metamorphosis often involves holometabolism and complex gene-environmental interactions resulting in the death of most of the cells of the body. Holometabolism can be considered a form of cell-suicide. The insect's body will "digest" itself, leaving only a few cells intact which then feed upon the dead cells and then rapidly grow, undergoing a radical transformation into a seemingly completely different species.
Amphibian metamorphosis is also dramatic and involves a series of major physical transformations as these animals grow from egg to a larva/tadpole to an adult (Duellman and Trueb 1994; Wells 2007). After emerging from the egg the tadpole possess gills and a tail and swims, fish-like, in the water. As the tadpole grows it sprouts hind legs and front legs, its tail disintegrates and is absorbed by the body. The eyes also migrate rostrally and dorsally, and like its skin and blood supply, undergoes a chemical transformation. Further, its mouth, intestines, and digestive tract become transformed, and these animals subsequently change their diet, mode of digestion, and excretions from nitrogen and ammonia to urea. Also they cease to breath through the gills which disintegrate, and instead develop lungs and breathe through the mouth. Moreover, they grow an additional brain structure, the cerebellum, which sits atop the brainstem. Thus, the skin, eyes, mouth, internal organs, skeletal-muscular system, and the brain, undergo dramatic and major transformations, and the fish-like tadpole becomes a frog who no longer lives in the water, but near the water on land (Duellman and Trueb 1994; Wells 2007).
Metamorphosis, therefore, results in profound and rapid alterations in gene expression and body structure as cells differentially die and are replaced, such that a completely different and more complex and advanced life form emerges from a body which essentially dies. The same can be said of embryogenesis and evolution. However, if metamorphosis took a million years, instead of a single season, the Darwinians would claim this as evidence of random mutation and natural selection, when in fact the entire process is due to genetic-environmental interactions and is under precise, genetic regulatory control. 6. Genetic Apoptosis When a new species emerges, it is not completely unique but shares genetic, skeletal, neurological, and other physical similarities with other species, including ancestral species who have been eradicated. These commonalities include the skeletal system, the eye, heart, body and brain, and the genes which code for these organs and structures (Callaerts et al. 1997; Gehring and Ikeo 1999; Hadrys et al. 2005; Quiring et al. 1994; Salvini-Plawen & Mayr 1977; Sodergren et al. 2007). There are genetic commonalities and the presence of hundreds and thousands of highly conserved genes which in modern species, including humans, are shared with the genomes of even distantly related species (Snel et al. 2002; Mirkin et al. 2003; Kunin and Ouzounis 2003; Koonin 2003; Mushegian 2008; Bejerano et al. 2004), and which can be traced to common ancestors which died out over a billion years ago (e.g., Hedges & Kumar, 1999; Joseph 2009a; Wang et al. 1999). Many of these highly conserved genes were were acquired from archae and bacteria (Yutin et al. 2008; Esser et al. 2004, 2007; Rivera and Lake 2004) via horizontal gene transfer, possibly over 4 billion years ago (Joseph 2009a). Individual genes also undergo apoptosis often following an episode of gene proliferation and the duplication of the entire genome (Aravind et al. 2000; Dehal and Boore 2005; Durand 2003; Katinka et al. 2001; Moran 2002; Scannell et al. 2007; Wolfe and Shields 1997). Genes proliferate and compete for expression, with losers dying out and undergoing genetically programmed apoptosis (Joseph 2009a). The entire genome has been duplicated repeatedly over the course of evolution, growing in size with genes proliferating and others dying out. Whole gene and whole genome duplication, coupled with gene loss and gene deletion, date back to the emergence of the first eukaryotic cells or their ancestors (Makarova et al. 2005). Gene proliferation coupled with gene loss is a major feature of evolutionary processes which have given rise to distinct species and lineages (Aravind et al. 2000; Moran 2002). Genome analysis has revealed the extensive loss of genes after whole genome duplication in chordates (Dehal and Boore 2005; Durand 2003; McLysaght et al. 2002), plants (Soltis et al. 2008; Tuskan et al. 2006), and yeasts (Katinka et al. 2001; Scannell et al. 2007; Wolfe and Shields 1997).
Gene loss is a common phenomenon and appears to play an important role in shaping genome content (Snel et al. 2002) and the evolution of new species (Joseph 2009a). The extent of gene loss can be dramatic, and it can occur relatively rapidly under a strong selective pressure (Baumann et al. 1995) such that, not only do new species acquire additional genes, but they lose yet others which had belonged to the genomes of ancestral species which became extinct. Substantial gene loss has occurred in all phylogenetic lineages (Snel et al. 2002; Mirkin et al. 2003); indicating that gene eradication plays a significant role not just in evolution, but extinction.
The eradication of the original gene may also play a role in the expression of the duplicate which may jump to a new position within the genome, thereby altering the genetic code (Joseph 2009a). Some of these duplicate genes appeared to have been freed from inhibitory restraint and were able to undergo an accelerated rate of sequence change thereby inducing the rapid evolution of new characteristics and abilities (Seoighe et al. 2003). After genome duplication followed by gene deletion, the duplicate or original genes, now freed of suppressive constraints, can express an already encoded function (“neofunctionalization”) which had been repressed (Conant and Wolf 2008).
What this means is that new species do not evolve new genes. Genes are inherited, and these genes may be duplicated, change their position in the genome, exons and introns may be shuffled, and nucleotide sequences may be lengthened or shortened, such that genes inherited from ancestral species may come to be silenced or remain repressed (Nichoh et al. 2008) until activated by changes in the environment or the genome (Joseph 2000a, 2009a). Likewise, following gene deletion, genes are freed of competitive restraint, and come to be expressed, whereas others may be lost or inhibited; thus new species emerge and others become extinct.
It is not uncommon for the new gene paralogs to retain or express distinct subsets of the original functions of the ancestral gene whereas the rest of the functions differentially deteriorate (Lynch and Force 2000; Lynch and Katju 2004). However, when ancestral genes are pruned from the genome, the cells, tissues, organs, and structures they code for also become modified, or are lost and undergo apoptosis, paralleling the genetic mechanisms regulating embrogenesis and metamorphosis.
Therefore, the shaping of a new species involves not just the emergence of new traits, but the activation or suppression of specific genes that code for specific physical features, coupled with gene gain and gene loss (Joseph 2009a). The result is the modification or elimination of certain physical characteristics associated with an ancestral species which may become extinct. Therefore, cells and genes that can give rise to specific physical characteristics in a progenitor species may be lost in a subsequent species, and this is due, in part, to apoptosis and selective cell and gene death. Due to the selective preservation or loss of specific genes and cells, new species can be rapidly built from the genome of a progenitor species which ceases to exist. Hence, there is no need for an intermediary species to link the old with the new. Evolutionary change, like metamorphosis, can be rapid and dramatic. New species, therefore, emerge from ancestral species in genetically preprogrammed quantum leaps, whereas ancestral species are pruned from the tree of life.
Apoptosis and alterations within species-specific genetic codes, are an integral aspect of extinction and evolution.
The extinction of species, like programmed cell death and the events associated with metamorphosis and embryological development serve a genetically programmed biological purpose. If this were not so, a tadpole could not become a frog, a butterfly would remain a caterpillar, and an embryo could not become an infant, a child could not become an adult, and the ability of new and increasingly intelligent species to emerge, separate, diversify, and invade empty niches, would be significantly hindered.
7. Genetic Seeds of Life: Evolution & Extinction
Life gives birth to life, and stars give birth to stars in an endless cycle of death and rebirth. It is a cosmic dance which may have been ongoing for all eternity. It is the death of a star, and the mass extinction of the species which populated its planets, which gave birth to our world and life on Earth (Joseph 2009b). Life on Earth came from other planets (Joseph 2000a, 2009a,b), delivered via comets (Hoyle and Wickramasinghe 2000), asteroids, meteors, and planetary debris.
Every creature alive today, and their DNA, can be traced backward in time to the first viruses and prokaryotic life forms to take root on Earth (Joseph 2009a,b; Woese 1994, 2002); i.e. archae, bacteria and blue-green algae--also known as Cyanobacteria. Hence, these first life forms, these "genetic seeds" contained the genetic potential for the evolution of all subsequent species, leading to woman and man (Joseph 2000a; 2009a); and not just their evolution, but their extinction. All cells and all multi-cellular species contain the "genetic seeds" of their own destruction.
These first Earthlings (archae, bacteria, and Cyanobacteria) contained the genes and genetic information for altering the environment, the "evolution" of multicellular eukaryotes, and the metamorphosis of all subsequent species and their extinction (Joseph 2000a, 2009a). These "genetic seeds" which were transferred to the eukaryotic genome by prokaryotes, 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 (Charlebois and Doolittle 2004; Dehal and Boore 2005; Harris et al. 2003; Koonin et al. 2004; Koonin and Wolf 2008; Lynch and Conery 2000; Lynch et al. 2001; McLysaght et al. 2002). Prokaryotes (archae and bacteria) provided eukaryotes with the regulatory elements which control gene expression and which have repeatedly duplicated individual genes and the entire genome thereby enabling the eukaryote gene pool to grow in size. However, among these genetic mechanisms, were the tools for eliminating genes and entire species (Joseph 2009a).
And where did these first prokaryotic Earthlings obtain these genes? On other planets via the same mechanism employed on Earth, through horizontal gene exchange (Joseph 2000a, 2009a).
Although there is evidence indicating that microbial eukaryotes (as well as prokaryotes and viruses) survived the cataclysm which brought life to Earth (Joseph, 2009b), there is also considerable evidence supporting the theory that viral and prokaryotic genes may have been combined to fashion the first Earthly eukaryotes within the first billion years after the Earth was formed (Feng et al. 1997; Hedges, 2002; Martin and Koonin 2006; Rivera and Lake 2004). Regardless of their origin, after eukaryotes began to evolve, prokaryotic genes continued to be transferred to eukaryotes, and these donated genes were subsequently expressed in response to biologically engineered environmental influences, often in busts of explosive evolutionary change, as typified by the Cambrian Explosion (Joseph 2009a).
DNA-equipped cells biologically alter the environment and secrete and manufacture waste products, e.g. methane, oxygen, calcium carbonate, sulphate, ferrous iron, etc., which act on gene expression, generating eyes, bones, bodies, and brains (Joseph 2009a). These genes did not evolve. They were inherited and then activated or suppressed by the changing environment. However, some of these same substances, such as calcium (Mattson and Chan 2003) and oxygen (Yin and Dong 2009) not only promoted the metamorphosis of new life forms, but trigger cell death and possibly the biological suicide of entire species.
Over the course of this planet's history, innumerable microbes and millions of species have genetically engineered the climate, triggering episodes of global freezing and global warming and flooding the oceans and atmosphere with a variety of gasses and secretions, thereby selectively destroying billions of life forms in favor of their more advanced cousins who were perfectly adapted for a genetically altered world which had been biologically prepared for them (Joseph 2009a). Genes act on the environment which acts on gene selection, giving rise to increasingly complex species, while simultaneously driving others to biological extinction.
All cells and all multi-cellular species contain the "genetic seeds" for their evolution and their extinction. And among these "genetic seeds" are mitochondria.
8. Genetic Seeds: Archae and Bacteria Fusion, Eukaryotic Evolution, Mitochondria
There is no evidence to support the belief that life on Earth was generated via abiogenesis in an organic soup. Life has never been created from non-life, at least not on Earth. Therefore, life on Earth must have come from life, and thus life on Earth must have come from other planets (Joseph 2000a, 2009b). Moreover, the preponderance of evidence suggests that the first creatures to arrive on this planet, i.e. bacteria, archae, and blue-green algae (Joseph 2009b), likely contained, within their genomes, the necessary genetic material and genetic instructions for the evolution and metamorphosis of all subsequent life which has evolved on this planet (Joseph 2000a, 2009a).
At the level of DNA, all species are linked and can be traced backward in time to common ancestors (Bejerano et al. 2004; Gu 1998; Koonin 2003; Koonin et al. 2004; Koonin and Wolf, 2008; Mirkin et al. 2003; Mushegian 2008; Nei et al. 2001; Peterson et al. 2004; Snel et al. 2002; Wang et al. 1999). Therefore, all species, and their DNA, can ultimately be traced to the first creatures to arrive on Earth (Joseph 2000a, 2009a,b). However, what this implies is that the DNA of the first Earthlings also leads backwards in time, to DNA-based life forms which lived on other planets (Joseph 2000a, 20009a,b).
Therefore, based on a genomic analysis, and from the perspective of metamorphosis and embryology, rather than a random evolution, evolution may be a form of metamorphosis, the replication of creatures that long ago lived on other worlds (Joseph 2000a, 2009a). That is, just as an apple seeds contains the genetic machinery for growing an apple tree if planted in the right environment, the first (and subsequent) microbes to arrive on Earth contained the genetic machinery for growing the tree of life and for altering the womb of the planet so this "tree" could grow branches and bear fruit in the form of increasingly complex species. And just as most trees lose branches and leaves, species also fall from the tree of life and become extinct. However, life on Earth is just a sample of life's possibilities and completely different life forms may evolve in other planetary environments.
Hence, "evolution," like embrogenesis and metamorphosis, is under genetic control, and these genetic mechanism were encoded into the genomes of the first creatures to arrive on this planet; microbial life forms which began biologically engineering the environment, and sharing genes.
Based on genomic analysis, 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 (Embley 2006; van der Giezen and Tovar 2005), such that their genomes combined. The result of this genetic fusion may have been the first Earthly proto-eukaryote (Hedges et al. 2001; Martin and Koonin 2006; Martin and Muller 1998).
Specifically, it is believed that a few hundred million to a billion years after the Earth was formed, the combination and activation of genes from photosynthetic and methane-eating microbes, via interactions with the environment, triggered eukaryogenesis. Photosynthesizing Cyanobacteria and methane eating/secreting archae, not only donated genes, but the biological activity of these specific prokaryotes over the course of the following three billion years would significantly impact and change the environment (Joseph, 2009a). Genes act on the environment and the interactions between environment and DNA led to the selective activation of specific genes originally donated by viruses and single celled prokaryotes to the eukaryotic genome, thus triggering the metamorphosis of mitochondria and the evolution and extinction of numerous eukaryotic multi-cellular species (Joseph 2009a). Multicellular life forms began to proliferate; made possible via the genetic/environmental activation or deletion/inhibition of genes transferred from the viral and prokaryotic to eukaryotic genome, and the metamorphosis of mitochondria (Joseph 2009a).
Some scientists believe that mitochondria are stripped down bacteria which had invaded or were engulfed by a eukaryote or a methanogenic archae (Margulis et al. 1997). Mitochondria may represent the genetic remnants of a photosynthesizing Cyanobacteria, a methane-eating or methane-secreting archae, and/or a α-proteobacterium.
Be it genetic fusion, DNA donation, or engulfment, the α-proteobacterium/Cyanobacteria, once incorporated, became part of the proto-eurkaryote, and appears to have 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 Koonin 2006; Martin and Muller 1998; Rivera and Lake 2004). In fact, the genomes of all extant multi-cellular eukaryotes contain genes which can be traced to α-proteobacterial ancestors that gave rise to the mitochondria (Embley 2006; van der Giezen and Tovar 2005). Mitochondria and related organelles now reside in all multi-cellular eurkaryotic cells.
Mitochondria serve as the powerhouse of the eukaryote cell and are located outside the nucleus--which may also be the remnants of a genetically-stripped down bacteria/archae which had invaded or were engulfed by a eukaryote (Dyall et al. 2004; Embley and Martin, 2006; Horiike et al. 2004; Lake and Rivera 1994; Margulis et al. 1997; Martin and Koonin, 2006). Mitochondria are enclosed in their own inner and outer membrane and 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; 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; Herrmann and Neupert 2000). Mitochondria also play a significant role in cell signaling, the control of the cell cycle and cell growth, as well as cellular differentiation, apoptosis, and cell death (Anderson et al. 1981; Chipuk et al. 2006; Mannella 2006; Rappaport et al. 1998). Mitochondria are essential to the functioning of the eukaryote cell and enabled eurkayotes to proliferate, diversify, evolve and become extinct.
Mitochondria not only promoted and made possible the evolution of increasingly diverse and complex species, but also their eradication. Mitochondria play a major role in apoptosis and programmed cell death, and possibly the extinction of entire species.
9. Oxygenation and Mitochondria
The genomes of all extant eukaryotes contain genes which can be traced to ancestors that possessed the α-proteobacterial endosymbiont that gave rise to the mitochondria (Embley 2006; van der Giezen and Tovar 2005) . Prior to the metamorphosis of mitochondria, the progenitor bacterium which would give rise to mitochondria, 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 which began building up in the atmosphere. Hundreds of millions of years would pass before eukarayotes began breathing oxygen (Schafer et al. 1996).
Initially, those α-proteobacterium genes which contained the DNA instructions for the metamorphosis of mitochondria (Embley and Martin, 2006; Gray et al. 1999; Martin and Koonin, 2006; Martin and Muller 1998; Rivera and Lake 2004), remained suppressed as the environment and atmosphere of the Earth lacked the necessary oxygen and chemicals such as NADH and other oxidases necessary to trigger their expression (Joseph 2009a). In the absence of an oxygen rich atmosphere, eurkaryotes had no need for mitochondria, and instead employed alternate energy sources. Once the environment became sufficiently oxygenated and enriched with biologically-produced sulphides and ferrous iron which could served as oxygen acceptors (Sleep and Bird 2008) these donated prokaryotic genes were activated and the genome of the α-proteobacterium underwent metamorphosis to become a mitochondria (Joseph 2009a), around 2.3 billion years ago (Mentel and Martin 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). The activation of these genes, and the metamorphosis of mitochondria enabled eukaryotes to grow in size and to become more efficient at extracting and using energy. Eukaryotes began to colonize emerging aerobic environments.
10. Prokaryotic Genes and the Eukaryotic Genome
At the level of DNA, all Earthly-life forms are linked (Joseph 2000a). Further, genes are continually horizontally transferred between prokaryotes, between prokaryotes and eukaryotes, and between eukaryotes and from viruses to viruses and from viruses to prokaryotes and eukaryotes (Aravind et al, 1998; Forterre 2006; Hotopp et al. 2007; Iyer et al. 2006; Koonin 2009; Martin et., al. 2002; Nelson et al. 1999; Nikoh et al. 2008; Zambryski et al 1989). Therefore, not only are modern day genes linked to ancestral species including the first life forms to arrive on Earth, but intra- and interspecies DNA transfer, exchange, and interaction, raises the possibility that genetically all of Earthly life are components of a single, planet-wide, supra-DNA organism whose growth, evolution, and extinction, is coordinated and guided by genetic mechanisms in interaction with the environment (Joseph 2000a).
For the first 4 billion years most organisms were microscopic and prokayotes outnumbered all other forms of life, just as they do today (Staley et al. 1997). These prokaryotes also donated essential genes to the eukaryotic genome; and this exchange was under genetic regulatory control and served a biological purpose: evolution and metamorphosis. Subsequently, the activity of these prokaryotes, and their genes, had a profound effect upon the growth and evolution of the tree of life and on those genes donated to the eukaryotic genome. These genetic mechanisms led to the growth and evolution of a supra-DNA-organism, and the metamorphosis of increasingly complex creatures that long ago lived on other worlds. However, just as a tree sheds leaves and branches as it grows, species would also be shed in favor of continued evolutionary growth. Therefore, we see that photosynthesizing prokaryotes secreted massive amounts of oxygen and other chemicals into the environment, the result of which was the metamorphosis of mitochondria, the evolution of increasingly complex life forms, and the extinction of other species.
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 (Joseph 2009a).
Archae provided the eukaryote genome with genes for information processing and expression (translation, transcription, replication, and repair). 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). In fact, an analysis of ribosomal structure and ribosomal protein sequences indicates a specific affinity between eukaryotic genes and their orthologs from archae (Lake 1988; 1998; Lake et al. 1984; Rivera and Lake 1992; Rivera and Lake 2004; Vishwanath et al. 2004). Thus, archae were also a major source of introns and transposable elements.
By contrast, bacteria provided operational genes responsible for the eukaryotic membrane system, the inner cytoskeleton, complex metabolic activity, metabolic enzymes, and the production of the principal enzymes of membrane biogenesis (Esser et al. 2004, 2007; Pereto et al. 2004; Rivera and Lake 2004; Yutin et al. 2008). These include genes and proteins which directly influence metabolism and the ingestion and excretion of various waste products. Operational genes have been repeatedly and continuously horizontally transferred over the course of evolution (Jain et al. 1999).
The combination of these two sets of genes, informational and operational, which were donated by prokaryotes to the eurkaryotic genome, contributed significantly to the evolution of eukarayotic complexity.
Likewise, many of the proteins that regulate eukaryotic signal transduction networks, including those involved in apoptosis and programmed cell death, are derived from the prokaryotic genome (Aravind et al. 1999; Bidle and Falkowski 2004; Koonin and Aravind 2002). These signaling molecules are common in bacteria, Cyanobacteria, and archae and include proteases from the AP-ATPase family. These proteases perform catalytic functions, and are found in the plant and animal genome (Bidle and Falkowski 2004; Koonin and Aravind 2002) and are utilized by mitochondria. Therefore, the genes coding for these products were also transferred from prokaryotes to eukaryotes.
11. Mitochondria, Oxygenation, Glaciation
Mitochondria, as a distinct entity within eukaryotic cells, did not arise until between 2.3 to 1.8 bya (Mentel and Martin 2008) when oxygen had begun to enrich the atmosphere (Barleya et al. 2005). It was during this time that the Earth became glaciated, fueled by oxygenic photosynthesis by prokaryotes (Evans et al. 1997; Kirschvink, et al. 2000). This rise in oxygen has been referred to as the Paleoproterozoic "Great Oxidation Event" (~2.3 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) and which coincides with the onset of the Proterozoic, and the first "snow ball Earth." Thus not just the metamorphosis of mitochondria but the Earth's earliest ice age are linked to the rise of oxygen in Earth's atmosphere; a time period when many species became extinct and others evolved (Joseph 2009a; Raup 1991).
Prior to the first global ice age, triggered by prokaryotic biological activity, the Earth had been experiencing a period of global warming from a greenhouse effect and an organic haze created by increasing levels of H2 and CH4 secreted by methane-producing microbes as a waste product (Brocks et al. 1999, 2005). The high levels of methane also acted on gene selection, and archae, known as methanotrophs and methylotrophs, began to proliferate. These were methane eaters, and in ever growing numbers they metabolized and broke down methane, as demonstrated by the presence of hopanes and high relative concentrations of 2α-methylhopanes in Archean rocks (Brocks et al. 2005). These methane eaters had also contributed genes to eukaryotes which were also utilizing alternative energy sources.
As methanotrophs proliferated, methane levels were reduced, thus dissipating the organic haze and allowing more sunlight to strike the Earth, which enabled increased photosynthesis by Cyanobacteria and other microbes (Joseph 2009a). By 2.45 bya, oxygenic photosynthesis had become widespread (Brock et al. 2005; Buick 2008) and atmospheric oxygen levels continued to rise (Bau et al. 1999; Kirschvink et al. 2000, 2008) to values between 0.02 and 0.04 atm (Holland 2006).
Oxygen also breaks down methane. The presence of even small amounts of O2 in the atmosphere would have been associated with decrease in CH4 and this decrease would have caused the planet to rapidly cool (Kasting and Ono 2006; Young et al. 1998).
Increased oxygen levels beginning around 2.4 bya, eventually shut down sulphur MIF production and caused a rapid and drastic decrease in atmospheric CH4, thus triggering glaciation. That is, increased levels of O2 which were secreted as a waste product by prokaryotes and eukaryotes, acted to oxidize sulphide, such that dissolved sulphate levels increased just as O2 levels increased. Both began to build up in shallow marine sediments which resulted in decreases in methagenesis and reductions in the CH4 and caused significant reductions in atmospheric methane (Kharecha et al. 2005; Pavlov et al. 2000, 2001, 2003). Temperatures began to drop. The increased levels of sulphate in turn triggered a proliferation of sulfur-eating bacteria, which caused a drawdown in H2 and CH4, a consequence of bacterial sulphate reduction (Kasting and Ono 2006).
Photosynthetic bacteria were also employing H2, H2S and/or Fe2+ to reduce CO2 to organic matter (Pierson 1994). Reductions in methane coupled with reductions in CO2 and increases in oxygen secondary to photosynthesis, eliminated the greenhouse effect and accelerated the cooling of the planet which began to freeze (Roscoe 1969, 1973), creating the first "snowball Earth" referred to as the "Makganyene" glaciation. However, Photosynthetic bacteria which were employing H2, began to die as did those organisms which were not adapted to freezing temperatures.
Thus, biological activity of methane-eating and photosynthesizing microbes and the release of oxygen into the atmosphere triggered the first global ice age, such that by 2.2 bya much of the Earth and its oceans were frozen or covered with ice and snow (Evans et al. 1997; Kasting and Howard, 2006; Kirschvink, et al. 2000; Roscoe 1969, 1973), creating the first "snowball Earth" and the first mass extinction.
As the Earth continued to freeze, these blankets of snow and layers of ice also provided protection against UV rays, but allowed light penetration (McKay 2000). This enabled photosynthesizing creatures and Cyanobacteria to proliferate near the surface (Cockell et al. 2002; Cockell and Cordoba-Jabonero 2004). Cyanobacteria secreted even more oxygen into the atmosphere, thus maintaining the low temperatures.
The changing environment acts on gene activation and inhibition, and increased oxygen levels triggered the metamorphosis of mitochondria (Joseph 2009a). The genomes of all extant eukaryotes contain genes which can be traced to ancestors that possessed the α-proteobacterial endosymbiont that gave rise to the mitochondria (Embley 2006; van der Giezen and Tovar 2005). Presumably, the genes of this α-proteobacterium symbiont, and those genes donated by archae and cynobacteria, underwent metamorphosis in response to the increasing levels of oxygen in the atmosphere, becoming a mitochondria.
Therefore, we see that species of prokaryotes which transferred genes to eukaryotes, acted on the environment, which acted on the genes donated by prokaryotes, thereby triggering the metamorphosis of mitochondria and multicellular eukaryotes due to the oxygenation of the planet. However, innumerable microscopic species, both eukaryotic and prokaryotic, were also driven to extinction. In fact, environmental stresses, including extremes in temperature and fluctuations in oxygen (Alberts et al. 2007; Ballard and Rand 2005; Yin and Dong 2009; Zhuravlev and Wood 1996), directly act on mitochondria (as well as the eukaryotic genome) and can promote or inhibit gene expression (Nagata 2000; Rutherford & Lindquist 1998; Waterland and Jirtle, 2003; Wolff et al. 1998) and thus induce evolutionary change (Rutherford & Lindquist, 1998), as well as cellular proliferation, or apoptosis and cell death (Alberts et al. 2007; Yin and Dong 2009).
Death can also serve life. The first microbial mass extinction resulted in the formation of thick layers of carbohydrate enriched organic matter, thereby providing nutrients for yet other species who were yet to evolve. Dead microbes also provided fodder for surviving microbes who would significantly impact the environment via methanogenesis and the degradation of organic matter (Holland 2006; Joseph 2009a).
Methanogens and multicellular eukaryotes equipped with mitochondria, began to flourish and 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 and which could now invade and colonize new environments. Oxygen breathing species proliferated, and others were shed from the tree of life.
12. Mitochondria and Evolutionary-Apoptosis
The mitochondria which changed the world and enabled eukaryotes to evolve from simple cell to woman and man, would also play a significant role in evolutionary-apoptosis and programmed species death. The genome of the mitochondria, in fact, contains the instructions for the manufacture of molecules which trigger cell suicide (Chiarugi and Moskowitz 2002; Yin and Dong 2009) thereby initiating the death of the organism, and possibly the eradication of an entire species.
For example, just as mitochondria reacted to increased oxygen levels, and the changing environment, by enabling new species to emerge and conquer the oxygenated environments which had been fashioned for them, mitochondria also react to environmental stresses, including temperature extremes, by manufacturing and releasing a cascade of chemicals, including caspase activators, which regulate and trigger the massive die off of cells (Brüne 2003; Chiarugi and Moskowitz 2002; Popov et al. 2002).
The death of an organism may be due injury, disease, profound environmental change, and the incapacity of cells to function; and central to cell death is the mitochondria and the chemicals manufactured by its genome which induce cell suicide. The biochemical cascade released by mitochondrial activity, can exert profound morphological changes impacting the cell membrane, causing cells to atrophy, fragmenting the cellular nucleus, and attacking, fracturing, and destroying DNA (Brüne 2003; Chiarugi and Moskowitz 2002; Nagata 2000; Kumar et al. 2009; Popov et al. 2002).
Consider the events leading up to and following the first snow ball Earth which involved not just temperature extremes but alterations in UV and other radiation. Changes in heat, oxygen, and radiation exposure also induce apoptosis (Kumar et al. 2009; Yin and Dong 2009). Hence, innumerable species were eliminated, others prevailed, and yet others emerged: a consequence of the enviroment acting on gene selection and cell function.
These events were triggered and regulated biologically and led to the emergence of new species and the extinction of others, who were removed from the tree of life.
Cells in fact have "death receptors" along their surface which trigger procaspase activation which can kill cells (Kumar et al. 2009; Yin and Dong 2009). Killer lymphocytes produce Fas ligand proteins which bind to death receptor proteins thereby activating procaspases and inducing apoptosis. In this way cells can kill themselves by triggering procaspase aggregation and activation from within the cell.
Stress, disease, or injury can also trigger the creation of procaspases which induce caspase cascades which cleave together and become activated, triggering and even amplifying a cell's death signal and spreading death throughout the cell and the organism (Kumar et al. 2009; Yin and Dong 2009).
However, these pathways also involve the mitochondria which releases cytochrome c into the cytosol, where it binds with and activates an adaptor protein called Apaf-1 which also triggers procaspase activation thereby accelerating and amplifing the caspase cascade and ushering in the mass suicide of cells (Kumar et al. 2009; Yin and Dong 2009).
Disease and viral organisms also trigger apoptopic cell death (Everett and McFadden 1999; Hay and Kannourakis 2002; Polster et al. 2004; Teodoro and Branton 1997) and thus the death of the organism or an entire species. In fact, viruses can also act on genetic regulatory mechanisms, such as p53, by inhibiting its ability to bind with protiens or engage in transcriptional activity (Wang et al. 1995). If the immune system, or master regulatatory genes, such as p53, are targeted (Wang et al. 1995), not just an individual organism, but an entire species may be wiped out.
However, viruses are selective and only attack the genomes of specific tissues or specific hosts (Flint et al. 2009; Norkin 2009), thereby selectively wiping out the members of specific species while leaving others unscathed. If fact, viruses can also prevent apotosis (Teodoro and Branton 1997), such that, whereas one species is impacted, another may be protected by the same pathogen (Flint et al. 2009; Norkin 2009). What this means is that viruses are selective and may act only when appropriate species have evolved.
13. Cyanobacteria, Calcium, and Oxygen Secreting Plants
While the planet was in the midst of the first world-wide deep freeze, Cyanobacteria (such as black cyanobacterium Scytosiphon) probably colonized much of the icy snowy surface, forming thick black bacterial mats (Cavalier-Smith 2006) which in turn prevented light and heat from being reflected back into space. In the arctic these creatures can reduce albedo and warm soil by 4 to 5 °C and increase the temperature of icy surfaces by 8 to 12 °C (Gold 1998).
Moreover, oxygen, which had contributed to methane reduction and the cooling of the Earth, was now being reduced and removed from the atmosphere via mitochondrial activity. Methane levels were also rising. In consequence, the planet began to warm, and there ensued yet another world-wide mass extinction of prokaryotes and eukaryotes, followed by the evolution of increasingly complex eukaryotes whose intra-cellular mitochondria were now breathing oxygen (Joseph 2009a).
It was during or following glaciation, between 2.2 to 1.6 billion years ago, that Cyanobacteria may have been engulfed by or invaded a multicellular eukaryote, donating over a thousand of its genes, and forming a symbiotic relations with the common ancestors for plants (Delwiche et al. 1997; Doolittle 1999; Martin et al. 2002; Nosenko and Bhattacharya 2007). This stripped down Cyanobacteria (Martin et al. 2002), became a chloroplast. Chloroplast and Cyanobacteria clearly resemble one another and share many identical genes (Joyard et al. 1991; Martin et al. 2002). The chloroplast are surrounded by two lipid-bilayer membranes (which correspond to the Cyanobacteria membrane) and has its own DNA which codes for redox proteins (the plastome) involved in electron transport in photosynthesis (Joyard et al. 1991; Krause 2008; Keeling 2004).
Therefore, just as genes donated by archae, bacteria, and Cyanobacteria contributed to the fashioning of the eukaryotic genome and the metamorphosis of mitochondria, a Cyanobacteria, following engulfment, became an organelle, i.e. the chloroplasts inside the body of the first proto-plant. As part of the plant cell genetic machinery, it began conducting photosynthesis. Hence, the first ocean dwelling planets appeared, i.e. seaweeds, dated to between 1.6 to 1.7 bya (Zhu & Chen 1995).
Due to biologically engineered changes in the gas composition of the atmosphere, the planet began to warm and the first global ice age came to an end. Climate change, oxygenation, oxidation, and numerous other factors all acted on gene selection, such that, beginning around 1.8 to 1.6 bya there was an exponential explosion of diverse DNA-based eukaryotic life across the planet and within its seas (Dyall and Johnson 2000; Hedges et al. 2001, 2004; Hedges & Kumar, 1999; Wang et al. 1999). Some eukaryotes soon consisted of approximately 10 different cell types (Hedges et al. 2004) and included unornamented organic-walled acritarchs (Li et al. 1995, 1998; Wan et al. 2003; Yan & Liu 1993).
This increase in size and complexity was made possible by the energy provided by mitochondria which used oxygen as an energy source; the ample supply of biologically produced nitrates and carbohydrates which could be converted to amino acids and which were utilized to expand the genome; and the abundance of food consisting of organic residue and layers of dead and living bacteria which had formed thick bacterial mats (Joseph 2009a).
As genes act on the environment which acts on gene selection, additional genes were activated, genomes were duplicated, genes were discarded, and new functions, characteristics, and species began to appear whereas others became extinct. 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."
By 1.6 bya the genome of photosynthesizing eukaryotes again duplicated in size (Alvarez-Buylla et al. 2000) and plants and animals diverged from all possible common ancestors (Wang et al. 1999). In plants, this whole genome duplicative event created multiple copies of MADS-box genes (Alvarez-Buylla et al. 2000) which over a billion years later would regulate the expression of flower, fruit, leaf, and root development (Ng and Yanofsky 2001; Pelaz et al. 2000). Whole genome duplication in the plant lineage would be followed by a number of recombination events creating new plant-gene sequences from old genes coupled with gene loss and deletion (Alvarez-Buylla et al. 2000).
Over the course of the next billion years these common ancestors for plants would continue to diverge, undergo evolutionary metamorphosis, and eventually give rise to lichens, corals, and angiosperms. All would employ the Cyanobacteria-derived genome, the chloroplast and the plastomes, to engage in photosynthesis, and secrete oxygen into the atmosphere.
However, of equal importance, corals and Cyanobacteria were also secreting and pumping calcium into the seas. Calcium would act on gene selection to trigger brain, body, bone and skeletal metamorphosis thereby inducing metazoan metamorphosis and the evolution of increasingly intelligent species (Joseph 2009a). The buildup of calacium, however, was associated with yet additional extinction events. Indeed, calcium directly impacts the functional integrity of mitochondria and can trigger cell death (Mattson and Chan 2003).
14. Cyanobacteria and Calcium
Photosynthesizing Cyanobacteria were among the first to take root on this world, and there is evidence they were deposited on this planet encased in meteors and other debris, remnants of the parent star which gave birth to our own (Joseph 2009a). Cyanobacteria contributed to the eurkaryotic gene pool, formed thick Cyanobacteria reefs and mats, established symbiotic relations with eukaryotes (some of which became plants), and secreted not just oxygen, but calcium carbonate into the oceans and the seas (Alois 2008; Kremer et al. 2007).
This feedback system has been in effect since Cyanobacteria took root on this planet and began using photosynthesis to obtain energy, with calcium continually leaching or flooding into oceans and streams. For example, the warming spell that ensued at the end of the first "snow ball Earth" would have induced the degradation and evaporation of Cyanobacteria mats, releasing large quantities of calcium into the ocean (Joseph 2009a). Moreover, Cyanobacteria photosynthetic activity and calcium carbonate bio-mat production followed by evaporation also occurred during the warming spells that developed after the second, and third world-wide glacial periods (Grey et al. 2003); the last of which, the Marinoan/Gaskiers, came to an end around 580 mya during the Ediacaran era. Therefore, calcium concentrations have increased by 100,000 times in the last 3 billion years (Kempe and Degens, 1985) and the calcium secretions of Cyanobacteria were supplemented by corals and other photosynthesizing organisms who possessed Cyanobacteria genes within their genomes. Calcium is the most ubiquitioius metal ion in the cellular system and plays a universal role as messenger and regulator of protein activities (Williams 2007). Ca2+ ions acts on gene selection, increasing the permeabilization of the inner mitochondrial membrane (Castilho et al. 1995), facilitating photophobic responses, and significantly increasing photosynthetic activity (Colombetti et al. 2008). Ca2+ ions therefore, can increase energy efficiency and the amount of oxygen pumped into the environment. Increased energy could also support increases in body size and complexity made possible by a calcium-collagen skeletal system. The buildup of calcium also coincided with increased levels of silica and iron, and the synthesis of collagen, all of which would act on gene selection, triggering metazoan metamorphosis and brain and skeletal formation after the end of the Marinoan/Gaskiers glacial period, 580 mya (Joseph 2009a). 15. Calcium, Cerebrums, & Metazoan Multicellularity Calcium plays a central role in cellular proliferation and differentation, cell to cell adhesion and fusion, apoptosis, and programmed cell death (Brown and MacLeod 2001; Cheng et al. 2007). In the absence of Ca, cells stop aggregating, embryos fail to adhere, cell aggregates disintegrate, and bones become soft and easily break. Following the end of the Marinoan/Gaskiers glaciation, calcium flooded the oceans due to coral reef and stromatolite evaporation. The rapid and massive increase in calicium levels triggered a whole spectrum of calcium binding, and calcium-collagen proteins activities, including the creation of the skeletal system (Joseph 2009a). Cells absorb and secrete Ca2+ and calcium receptors and sensors are located throughout the body and the muscular-skeletal system, including cartilage and bone cells (Brown and MacLeod 2001; Chang et al. 1999; Cheng et al. 2007). Calcium binding proteins also regulate many important cellular processes such as smooth muscle contraction and motion in skeletal muscle. Hence, calcium plays a key role in skeletal muscle movement and contraction, and the regulation of cell, muscle, and skeletal functioning in metazoans. The buildup of calcium was central to the metamorphosis of macro-multicellular eukaryotes which diversified and increased in size following the end of the Marinoan/Gaskiers glaciation. As the planet began to warm following the Marinoan glaciation, and by 600 mya ago, before the onset of the Gaskiers ice age, the oceans were becoming increasingly saturated with calcium, creating "calcite seas" (Hardie 2003). Even as early as 635 mya, a number of taxa were already displaying calcium carbonate mineralization. These included sponges who had first evolved a silica-collagen skeleton, which included calcium, thereby forming soft, lacelike silica skeletons, spicules, and spines which enabled them to enlarge their cell walls and grow in size (Gehling and Rigby 1996; Li, et al. 1998; Tiwari et al. 2000; Xiao et al. 2000). Following the end of the Marinoan/Gaskiers glaciation, as calacium-enriched mats and reefs created by Cyanobacteria and corals began to evaporate flooding the oceans with calcium, a complex variety of bilaterian forms began to appear (Bowring et al. 2003; Grotzinger et al. 1995; Martin et al. 2000). For example, fossils of a well-developed animal, Kimberella have been discovered in rocks located in northern Russia and dated to around 555 mya (Martin et al. 2000).
There is no evidence suggestive of eyes, hearts, brains, or a nervous system in any species prior to 575 mya. Further there is no evidence for sensory-guided coordinated behaviors that might be mediated by a nervous system or visual-chemosensory system. However, Ca2+ ions not only promote skeletal development, but brain development, and interact with genes which code for functions mediated by the central nervous system (Glezer et al. 1999; Hong et al. 2000; Llinás et al. 2007; Köhler et al. 1996; Mori et al. 1991; Perez-Reyes 2003; Weisenhorn 1999). Hence, following the end of the Marinoan/Gaskiers glaciation and the flooding of the oceans with calcium, evidence of horizontal and vertical burrowing appears (Erwin and Davidson 2002), and by by 545 mya metazoans began displaying evidence of behavior guided by a brain. Once calcium levels and other substances built up sufficiently the changing environments acted on gene selection and triggered explosive bursts of evolutionary innovation, giving rise to animals sporting shells, exoskeletons, bilateral bodies, bones and complex brains--a function of the massive amounts of oxygen, carbon, calcium, zinc, copper, and other liberated minerals and gasses acting on gene selection. By the onset of the Cambrian Explosion, 540 mya, an incredible variety of complex creatures began to appear. However, increased intracellular CA can also trigger apoptosis (Mattson and Chan 2003). Thus, as metazoans began to proliferate, yet other species suffered a progressive and massive die off, including the Ediacaran fauna which became extinct, bringing the Ediacaran era to a close. 16. Calcium and the Cambrian Explosion "If it could be demonstrated that any complex organ existed which could not possibly have been formed by numerous successive, slight modifications, my theory would absolutely break down" (Darwin, 1857).
Until around 580 million years ago, the vast majority of life forms sojourning on Earth and beneath the seas, were single celled organisms and simple, microscopic multi-celled creatures composed of less than 11 different cell types (Bottjer et al. 2006; Narbonne 2005; Narbonne and Gehling 2003; Shen et al. 2008). Until sufficient oxygen, silica, and calcium had been released and the oceans had become oxygenated, body and cell size were restricted and unable to expand or engage in strenuous physical activity. Larger bodies require skeletal support. Internal organs require skeletal protection. Moreover, in the absence of ozone, larger sized bodies would be burnt by UV rays and would pop and explode. Therefore, once silica, calcium, and oxygen levels had increased and a protective ozone layer was established, there was a sudden explosion of complex life, creatures expanded significantly in size, diversified, and grew spines, silica skeletal compartments, silica-collagen skeletons, collagen-calcium skeletons, armor plates (sclerites) and small shells like those of brachiopods and snail-like molluscs (Butterfield 2003; Conway Morris 2003; Lin et al. 2006; Mooi and Bruno,1999).
By the onset of the Cambrian Explosion, 540 mya, 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, and equipped with shells or skeletal systems which could support their internal organs and bodies, innumerable complex creatures began to swim the surface waters and 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. Those who breathed oxygen were at a signficiant advantage, increasing the number of environments they could invade and conquer.
Thus the biologically engineered environment acted on gene selection, activating genes contributed by bacteria, Cyanobacteria, and archae to the eukaryotic genome, triggering mitochondria and multicellular metamorphosis, producing the first plants, then bilateral bodies, bones, and brains, and giving rise to new traits and new species perfectly adapted for a world that had been biologically prepared for them.
Beginning around 540 mya, there was a vast and sudden explosion of bilaterian/metazoan diversity and complexity that appeared multi-regionally throughout the oceans of the Earth within 5 million to 10 millions years. Without any evidence of intermediary forms, over 32 phyla suddenly evolved, many with the complex eyes, nervous system structures, and body plans seen in modern animals (Budd and Jensen 2000; Conway Morris 2000; Fortey et al. 1997).
Over the following 500 million years, billions of new species would evolve, alter the environment, and then disappear from the face of the Earth. Extinction and death is the nature of life, and evolution. 17. Conclusion Life on Earth came from other planets, delivered by comets, asteroids, meteors, and planetary debris (Hoyle and Wickramasinghe 1984, 2000; Joseph 2000a, 2009b). And these "genetic seeds" of life contained the DNA/genetic instructions for the tree of life, and for fashioning and evolving every multi-cellular creature which has walked, crawled, swam, or slithered upon the Earth (Joseph 2000a, 2009a). Life on Earth, however, is just a sample of life's evolutionary possibilities. Given different environments on different planets, wholly different DNA-based life forms would likely evolve and undergo metamorphosis, or they might never evolve and quickly become extinct. Evolution on Earth could be likened to metamorphosis and embryology. However, rather than 9 months, it takes billions of years to grow a human from a single cell; and an integral aspect of that evolutionary growth is apoptosis. Of course, if embryogenesis or invertebrate/vertebrate metamorphosis took a billion years instead of 9 months or a single season, the Darwinians would claim these developments are due to natural selection, mutation, and random variation, when in fact the entire process is under strict genetic regulatory control. Embryogenesis is under genetic control. Metamorphosis is genetically regulated. All aspects of development are guided and controlled by genetic-environmental interactions. Why should evolution be any different? "Evolution" is also under genetic regulatory control, in coordination with the biological activity of single celled prokaryotes, their donated and horizontally transferred genes, and the genetically engineered environment. Genes act on the environment, and the changing environment acts on gene selection, activating specific genes, silencing others, and giving rise to new species, with entire populations of genes, cells, tissues, and species proliferating and others dying out.
Genes, cells, and entire species undergo evolutionary apoptosis and are continually pruned from the tree of life. Programmed death is essential to life and evolution, and evolutionary apoptosis is one of the many causes of species death and extinction.
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Reviewer's Comments Chandra Wickramasinghe, Ph.D., Executive Editor, Astrobiology, Journal of Cosmology, Director of Astrobiology, Cardiff University, UK and Genetically Programmed Species Mass Death Rhawn Joseph, Ph.D. Emeritus, Brain Research Laboratory, Northern California Reviewer's Comments by Chandra Wickramasinghe, Ph.D.,
"For a generation or more astronomers have been accustomed to thinking of star-forming episodes accompanied by the production of vast clouds of interstellar grains. The episodes are sometimes local but they are often galaxy-wide. They are thought to be triggered by some large-scale event, the after effects of which linger on for some considerable time, several hundred million years. The condensation of the exceptionally bright stars which delineate the spiral structures of galaxies has often been associated with these episodes. From our argument it seems then that even the origin of the spiral structures of galaxies may well be biological in nature." "The potential of bacteria to increase vastly in their number is enormous. It should occasion no surprise, therefore, that bacteria are widespread throughout astronomy. Rather would it be astonishing if biological evolution had been achieved on the Earth alone, without the explosive consequences of such a miracle ever being permitted to emerge into the Universe at large. How could the Universe ever be protected from such a devastating development? This indeed would be a double miracle, first of origin, and second of terrestrial containment." "Some biologists have probably found themselves in opposition to our arguments for the proprietary reason that it would seem as if an attempt were being made to swallow up biology into astronomy. Their ranks may now be joined by those astronomers who see from these last developments that a more realistic threat is swallow astronomy into biology." -"Space Travellers - the Bringers of Life" - F. Hoyle and C. Wickramasinghe (University College, Cardiff Press, 1981) Coming back to Dr. Joseph's paper, "Extinction, Metamorphosis, Evolutionary Apoptosis," I find the analogy between embryogenesis and metamorphosis to be particularly brilliant. I particularly liked the concluding sentence of section 2: "As a form of evolutionary apoptosis, extinction is in part a direct consequence of the same cellular mechanisms which lead to cell death; albeit at the level of an entire species." Great stuff. I'm impressed.
Chandra Wickramasinghe, Ph.D., |
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