Original

Dustin Jon Scott
Donald Morisato
The Gene: History of an Idea
[In Progress]


Contents

Introduction
I. Origin of The Mitochondrion
I.a. Bacterial Origins
I.a-1.) Endosymbiotic Theory
I.a-1A.) Attempted Predation / “Phagocytosis First”
I.a-2.) Origins of the Bacteria
I.a-2A.) Relation to The Archaea & The Eukarya
I.a-2B.) The Terrestrial Origin of Life
I.a-2Bα.) Replicator-First Approaches
I.a-2Bβ.) Metabolism-First Approaches
I.a-2C.) The Possibility of Panspermia
I.a-2D.) Independent Origins & Cross-Contamination
I.a-2Dα.) Problems with Independent Origins
I.a-2Dβ.) To Mars & Back: Alternative to Independent Origins
I.a-2E.) The Protoplanetary Origin of Life
I.a-2F.) Synthesis: Molecular Panspermia & Subsequent Mars-Earth Interplanetary Lithopanspermia
I.b. Other Hypotheses
II. Importance of The Mitochondrion
II.a. The Role of The Mitochondrion in Eukaryogenesis
II.c. The Role of The Mitochondrion in Eukaryotic Multicellularity
II.c-1.) Eukaryotic versus Prokaryotic Multicellularity
II.c-1A.) Bacterial Multicellularity
II.c-1B.) Archaeal Multicellularity
II.c-1C.) Eukaryotic Multicellularity
II.c-2.) The Role of The Mitochondrion in Eukaryotic Gene Regulation & Cellular Differentiation
III. Conclusions
III.a. Implications & Predictions
III.a-1.) Biogeochemical Roles of the Prokaryotic Domains
III.a-2.) Trends in Specializations of Extremophiles
III.a-2A.) Terrestrial Biostratification
III.a-3.) The Search for Extraterrestrial Life
III.a-3A.) Extraterrestrial Multicellularity
III.a-3Aα.) The Drake Equation
III.a-3Aβ.) The Fermi Paradox
III.a-3B.) Possible Tests
III.a-3Bα.) Martian Observations
III.a-3Bβ.) Venerean Observations
III.a-3Bγ.) Europan Observations
III.a-3Bδ.) Extrasolar Observations
III.e. Summary
Works Cited

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D. J. Scott

“Mitochondrigeny”

The Origin & The Evolution of The Mitochondrion
-and-
Possible Implications for Astrobiology
Copyright © 2017-2018 by Dustin Jon Scott
[Last Update: December 1st, 2017]


Introduction

Almost all known eukaryotes have mitochondria, and those few who lack them are widely regarded as having descended from earlier eukaryotes who still possessed them.



I. Importance of The Mitochondrion

Adenosine triphosphate (ATP) is the primary

"It is understood that functional mitochondria are required for all cell processes due to common energetic requirements. Recent data expand on this requirement, however, and place the emphasis on this organelle as a relevant signaling platform for cell-cycle progression."

(McBride et al., 2006)

The heterotrimeric 5' adenosine monophosphate-activated protein kinase (AMPK), which is known to act as a cellular energy sensor by activating in response to rising AMP (i.e., when ATP:AMP ratios favor AMP over ATP, indicating fewer energy-carrying phosphate groups attached to adenosine), initiates upon activation a phosphorylation cascade that alters ATP consumption and production (McBride et al., 2006), and "switches on catabolic pathways that generate ATP, such as the uptake and oxidation by cells of glucose and fatty acids, while switching off ATP-requiring processes that are not essential to the short-term survival of the cell, including most biosynthetic pathways," (Hardie, 2005). The kinase AMPK carefully maintains an ATP:ADP ratio of about 10:1, far above the minimum ATP requirements for cell function (Hardie et al., 2003), thus acting as a sort of "alternator" continually re-charging our cells with ATP.



I.a. The Role of The Mitochondrion in Eukaryotic Multicellularity

(Hardie, 2005)

(McBride et al., 2006)

A study involving a series of experiments on Drosophila melanogaster have shown that reduced ATP production in and of itself is insufficient to hault cell-cycle progression (McBride et al., 2006)

(Niklas & Newman, 2013)



I.a-1.) Eukaryotic versus Prokaryotic Multicellularity

(Ereskovsky et al., 2013)


I.a-1A.) Bacterial Multicellularity

Bacterial multicellularity can be grouped into three general categories (Lyons & Kolter, 2015):

☣ Filaments —
☣ Aggregates —
☣ Biofilms —
☣ Swarms —
☣ MMPs (multicellular magnetotactic prokaryotes) —



I.a-1B.) Archaeal Multicellularity

(Fröls, 2013)

(Orell et al., 2013)



I.a-1C.) Eukaryotic Multicellularity

Eukaryotic multicellularity can be grouped into these general categories:

  1. Aggregates — Slime molds.
  2. “Complex” multicellulary organisms — like the majority of familiar, macroscopic plants, animals, and fungi, experience “complex” multicellularity or “true” multicellularity, a form of obligate multicellularity that has only evolved a handful of times and is found only in eukaryotes.
    1. Weismannists — in which there exists a distinction between the soma and the germline (the so-called “Weismann barrier”) and the former is begat by the latter (Weismannist development). This includes the majority of familiar vertebrates, arthropods, and mollusks.
      1. “Super-Weismannists” — might be a good way to think of eusocial insects, whose colonies are made up of distinct “somatic” multicellular organisms (workers, soldiers) and “germline” organisms (queens, drones). Eusociality can be thought of as “next level” multicellularity or “trans-multicellularity”.
    2. “Para-Weismannists”? — such as land plants, which have gametes but can produce them from vegitative tissue, and some sea-dwelling animals that are often perceived as “plant-like” (corals, sponges, &c.), which reproduce mitotically, seem to exprience Weismannist-like development, but the “Weismann barrier” is absent for these creatures.

(Schirrmeister & al. 2013)



I.a-2.) The Role of The Mitochondrion in Eukaryotic Gene Regulation & Cellular Differentiation

(Hardie, 2005)

(Varga-Weisz, 2001)

(Vignali et al., 2000)



I.b. The Role of The Mitochondrion in Eukaryogenesis

Mitochondria are nigh-ubiquitous among the eukarya. Even microbial eukaryotes who were once believed to have diverged from the other eukarya before the acquisition of mitochondria have their own equivalent ATP- and ADP-synthesizing organelles that now appear to be derived from a mitochondrial ancestor, making it probable that the common ancestor of all known eukaryotes possessed a mitochondrion (Embley et al., 2003). Furthermore, the ATP-sensing kinase AMPK is found in all eukaryotic cells (Hardie et al. 2003).

"Along the lineage leading to LECA, what we might choose to designate as the first eukaryotic common ancestor (FECA) (11) depends (barring that miraculous cataclysm) on which eukaryote-defining feature we take as necessary and sufficient for eukaryoteness. Nowadays, many theorists would nominate the mitochondrion as that feature.

(Booth & Doolittle, 2015)

(Lopez-Garcia & Moreira, 2015)

(Forterre, 2013)

(Hardie, 2005)

(McBride et al., 2006)

(Gross & Bhattacharya, 2010)



I.b-1.) Symbiogenesis: Endosymbiotic Theory



I.b-1A.) Arkaryan Hypothesis


I.b-1B.) TACK & The Eocyte Tree Fusion Scenario

Places the ancestor of the Eukaryotes within the Archaea rather than merely defining them as sister-groups.

TACK (Thaumarchaeota-Aigarchaeota-Crenarchaeota-Korarchaeota) superphylum (Guy & Ettema, 2011)

It is tempting to speculate that the archaeal ancestor may have been a multicellular archaeon, such as an archaeal biofilm, and that the acquisition of the mitochondrion permitted eukaryotic gene regulation and therefore complex multicellularity. However, since there are a large number of unicellular and facultatively multicellular eukaryotes, it's just as likely that facultative multicellularity in eukaryotes, bacteria, and archaea, is an example of convergent evolution.



I.b-2.) Other Theories



I.c. The Timing of Mitochondrial Acquisition in Eukaryogenesis

(Martin & Koonin, 2006)

"The evolutionary origins of the oldest components of the AMPK pathway, however, extend into the pre-eukaryotic era, and descendants of these ancient proteins can still be found in contemporary prokaryotes. The TOR complex in turn appears as a eukaryotic invention, possibly to aid in retrograde signaling between the mitochondria and the remainder of the cell," (Roustan et al., 2016)"

Because the AMPK pathway has not been conserved among the prokaryotes, it may be inferred that in general it is highly variable and that such a dramatic anatomical restructuring as nucleus-cytosol compartmentilization would not likely have kept this system intact were it not constrained by the presence of mitochondria in the eukaryotic cell. This may be interpreted as indicating that the acquisition of the mitochondria either antedates or coincided with nucleus-cytosol compartmentalization.

"The central finding is that a subset of archaea encode actins that are not only monophyletic with eukaryotic actins but also share unique structural features with actin-related proteins (Arp) 2 and 3. All phagocytic processes are strictly dependent on remodeling of the actin cytoskeleton and the formation of branched filaments for which Arp2/3 are responsible. The presence of common structural features in Arp2/3 and the archaeal actins suggests that the common ancestors of the archaeal and eukaryotic actins were capable of forming branched filaments, like modern Arp2/3. The Rho family GTPases that are ubiquitous regulators of phagocytosis in eukaryotes appear to be of bacterial origin, so assuming that the host of the mitochondrial endosymbiont was an archaeon, the genes for these GTPases come via horizontal gene transfer from the endosymbiont or in an earlier event," (Yutin et al., 2009).


II.c-1.) “Phagocytosis First" Hypothesis

"Phagocytosis, that is, engulfment of large particles by eukaryotic cells, is found in diverse organisms and is often thought to be central to the very origin of the eukaryotic cell, in particular, for the acquisition of bacterial endosymbionts including the ancestor of the mitochondrion," (Yutin et al., 2009).



I.c-1A.) Archezoan Hypothesis
"Under the so-called archezoan hypothesis, the organism that acquired the endosymbiont was a proto-eukaryote (dubbed the archezoan) that already possessed the nucleus, the endomembrane system, the cytoskeleton, and other hallmark structures of the eukaryotic cell [5,7,8]. In other words, the hypothetical archezoan is envisaged as an amitochondrial, unicellular eukaryotic organism. The major difficulty faced by the archezoan hypothesis is that so far all candidate archezoa, such as Diplomonada, Parabasalia, and Microsporidia, have been shown to possess organelles derived from or, at least, related to mitochondria (hydrogenosomes, mitosomes, and others) as well as some nuclear genes of apparent mitochondrial (alpha-proteobacterial) origin [1,6]. Thus, the proponents of the archezoan hypothesis are forced to postulate that the archezoa represent an extinct lineage of primitive eukaryotes [8]," (Yutin et al., 2009).



I.c-1B.) Phagocytosing Archaeon Theory (phAT)



II.c-1C.) NuCom & Primal Eukaryogenesis

(Egel, 2011)

(Staley, 2013)



I.c-2.) “Symbiogenesis First" Hypothesis

States that the original host cell which acquired the mitochondrion was an archaeon.

“The hypotheses that oppose the archezoan concept are symbiotic scenarios in which the mitochondrial endosymbiosis is seen as the event that triggered eukaryogenesis in the first place. This idea traces back to the classic 1967 paper of Sagan (Margulis) [4] but received a major boost from the discovery of mitochondria-related organelles and genes of apparent mitochondrial origin in all thoroughly characterized eukaryotic cells [1,9,10]. Under the symbiotic scenarios that differ in details, the host that engulfed the alpha-proteobacterial ancestor of the mitochondria is posited to have been not a proto-eukaryote but rather an archaeon that closely resembled the currently known archaea, at least, in terms of the cell organization [1,11-13]. The advantage of the symbiotic scenarios is that they provide plausible, even if rather general explanations for the origin of the remarkable organizational and functional complexity of the eukaryotic cell as a result of diverse interactions between the host and the endosymbiont. However, the potentially serious difficulty faced by these scenarios is that prokaryotes have no known mechanisms for engulfing other prokaryotic cells (although at least one case of endosymbiosis among bacteria has been reported [14]). Thus, under these scenarios, the symbiosis between two prokaryotic cells would depend on an extremely rare, if not unique, spurious event – the "fateful encounter" hypothesis using the memorable phrase of De Duve [15]." (Yutin et al., 2009)



I.c-3.) Ectosymbiotic Precursor?



II. Origin of The Mitochondrion

The origin of mitochondria is of vital importance to understanding eukaryotic evolution.

(Emalyanov, 2001)

(Martin & Koonin, 2006)

(Kuntzel & Heinrich, 1981)



II.a. Bacterial Origin



II.b. Evolutionary Context



II.c. Origin & Evolution of The Prokarya

The Archaea were likely the first domain of diversified life (Caetano-Anollés &al., 2014).

Prokaryan evolution might not be describable according to the standard “tree” model (Bapteste et al.).



II.c-1.) The Last Universal Common Ancestor (LUCA)

While the progenitor of the eukarya is now traditionally nested within the archaea, Carl Woese (1998) suggests that the Last Universal Common Ancestor (LUCA) of the three domains may antedate individuation into discrete lifeforms separated by cell membranes, and that the LUCA may have actually been a community of proto-cells with extremely primitive, porous membranes — called "progenotes" (Woese, 1998) — through which, due to pervasive lateral gene transfer (LGT) (Woese, 2002), genetic material was exchanged and propogated itself more-or-less freely. The picture this evokes is one in which, prior to the “Darwininian threshold" (Woese, 2002), the primary, smallest, most irreducible unit of life was less like a modern cell than like a modern chromosome.

Woese came to this conclusion after using rRNA phylogeny to trace the Tree of Life (TOL)

This situation to

Other authors (e.g. Martin & Russell, 2003; Koonin & Martin, 2005) have taken up modifications of Woese's theory which agree that the common ancestor of the Archaea and the Bacteria was a pre-organismal, pre-Darwinian community, but which take this further in hypothesizing that the last common ancestral state (LUCAS) was "not a typical, membrane-bounded cell but rather a consortium of replicating genetic elements" (Mulkidjanian et al., 2009), and which reassert the importance of Endosymbiotic Theory in understanding eukaryogenesis. If true, this would mean that the bacteria, whence the mitochondria evolved, and the archaea, a lineage of which went on to become the eukarya, represent two separate evolutions of "true" (discrete, cellular) life. The consequences of this are that (1) the divergence of the two prokaryotic domains from a common ancestor is inextricably interwoven with the origins of life, and (2) that eukaryogenesis represents both a novel convergence of two independently evolved forms of life and a genetic reconvergence of hereditary material that had been separated since before the origin of "true" life.

This view is not universally accepted (Jékely, 2006; Koonin, 2014), with some authors simply preferring a more "Woesean" model involving a LUCA possessing only primitive, porous membranes (e.g., Mulkidjanian et al., 2009) but not going so far as to outright reject the notion of amembranous replicons as the LUCAS, and some going so far as to adopt literary bravados which (wrongfully) assert that this idea has been abandoned altogether due to common membrane-encoding genes shared by all three domains (e.g., Forterre, 2014), alternate explanations for these shared genes, such as lateral gene transfer (LGT), or even (plausibly, considering the small size and streamlined organization of prokaryotic genomes) convergenet evolution, have not been ruled out.



II.c-1A.) The Terrestrial Origin of Life

Currently there are two primary approaches to the scientific investigation into the origins of life: the replicator-first approach and metabolism-first approach (Anet, 2004). These approaches differ conceptually in hypothesizing either an autocatalytic string of covalently bonded informational molecules at least functionally akin to DNA, or a sequence of chemical reactions a among set of noncovalently bonded molecules that was autocatalytic as whole and thus functionally akin to metabolism (von Meijenfeldt, 2013), as the essential origin of life.

Here it should be noted that the designations "replicator-first" or "metabolism-first" may apply either literally or figuratively. An approach which places primary emphasis on replication over metabolism, for example, may be regarded as a "replicator-first" approach even if it is not literally suggesting that replicators antedate metabolic systems, and vice versa. These are designations of emphasis, not necessarily descriptors of sequence.

(Delaye & Lazcano, 2005)



II.c-1Aα.) Replicator-First Approach

The most crucial entity in and most basal unit of evolution is the replicator (Zachar, 2010).

Since the 1982 discovery of ribozymes (Kruger et al.) proved that RNA had catalytic properties, and could therefore “act both as information carrier and as catalyst” (Alberts et al., 2002), resolved the DNA-protein “chicken & egg” paradox by demonstrating that RNA could act as both “chicken” and “egg” (Bernhardt, 2012; Sankaran, 2013), the replicator-first approach has quite naturally come to be dominated by the “RNA World” hypothesis (von Meijenfeldt, 2013) and this has only been reinforced by the now much-expanded catalytic repertoire of RNA and the import thereof with regard to key cellular reactions (Doudna & Cech, 2002) “which can be viewed as molecular fossils of an earlier world,” meaning we never fully transitioned out of the RNA World (Alberts et al., 2002). Evidence indicating that the common ancestor of the Archaea and the Bacteria possessed an RNA-based genome (Leipe & al., 1999) and only after divergence each separately acquired DNA from DNA viruses, in which DNA first arose (Leipe & al., 1999; Forterre, 2002), has further reinforced this hypothesis.

(Achbergerová & Nahálka, 2011)

(Fegley & Lewis, 1980)

"messy RNA" (Szostak, 2017)



II.a-1Aβ.) Metabolism-First Approaches

Emphasizing ecosystems over discrete organisms and metabolism over reproduction, Eric Smith et al. have characterized the emergence of Earth's biosphere as a sort of geochemical "discharge" resulting from a build-up of energy between the hydrosphere and the lithosphere (Smith, 2007; 2015).

(Smith et al., 2004)

(Copley et al., 2007)

(Morowitz et al., 2008)

Water is necessary to fold proteins (McLain, 2017)

first cells (Szostak, 2017)

(Hazen, 2005)

(Hazen, 2006)

(Hazen & Sverjensky, 2010)

(Hazen & Deamer, 2006)

(Hazen, 2006)

(Deamer et al., 2002)

(Deamer & Monnard, 2006)



II.c-1Aγ.) Problems with a Terrestrial Origin

While the "plausibility" criterion for a given chemical pathway suggested as being involved in prebiotic synthesis generally requires that the chemical environment has to be one which could have plausibly been present on the early Earth, such a criterion ignores that the early Earth isn't the only place that life could have formed. Such is an a priori assumption completely unsupported, and one might go so far as to say contradicted, by all experimental and observational data thus far gathered. The Earth is but one planet among hundreds known and among billions thought to exist in our galaxy alone. Furthermore, there is no particular reason to hypothesize that the generation of life is something which must occur on a planet at all! Especially when one considers how early in the geological record life first began to appear on Earth, other environments such as other Solar planets, exoplanets, planetesimals, asteroids, comets, moons, protoplanetary disks, protostellar nebulae and the stelliferous nebulae (star-forming regions of giant molecular clouds) to which they belong, as well as any interactions between such systems, must all be considered as potential environments for the various stages of prebiotic synthesis, and "plausibility" determined only when a particular chemical pathway has been demonstrated to be likely (or not) in one of such environments. An early-Earth-based "plausibility" criterion is, frankly, an unnatural constraint which ignores the fact that in our universe, no planet is an island.

Many stages of prebiotic synthesis wouldn't have worked out in hydrothermal vent scanrios or on a hot early Earth.

1.

The half-lives of the nucleobases guanine, adenine, cytosine, and uracil are far too short (t½ for adenine and guanine ≈ 1 year; uracil = 12 years; cytosine = 19 days) at the 80-110°C temperatures hypothesized in hydrothermal vent scenarios for the origin of life (based on the preferred temperature ranges of hyperthermophiles, assumed by hydrothermal vent scenarios to be among the oldest extant lineages of living things), and indeed are too unstable at temperatures much above 0°C, to allow for the formation of the first replicators in a reasonably long timespan, indicating a low-temperature origin of life (Levy & Miller, 1998).

2.

RNA hydrolyzes rapidly (Szostak, 2012; part 3), and is especially prone to doing so in hot environments, much to the chagrin of those who favor hydrothermal vent models for the origin of life.

3.

While hydrothermal vent hypotheses imply a hyperthermophilic progenote with an optimal growth temperature (OGT) ≥80°C, which is consistent with thermophilia (OGT=65±15°C) in the last bacterial ancestor as well as the last archaeal ancestor as part of a more-or-less linear progression to the overwhelmingly mesophilic (OGT≤50°C) modern prokaryotic domains, dual phylogenic rRNA and protein analyses show that while both the bacterial ancestor and the archaeal ancestor were thermophilic (OGT=65°C±15°C), the LUCA was mesophilic with an OGT≤50°C (Boussau et al., 2008).

4.

The very first protocells were likely obligate cryophiles with an OGT≈1°C (Szostak, 2012; part 1)

The hydrothermal vent model, though seemingly ruled out, would give us a mathematically elegant and thermodynamically sensible sequence of OGT≥80°C, OGT=65±15°C, OGT≤50°C and a cellular LUCA model gives us a progressive OGT≈0°C, OGT≤50°C, OGT=65±15°C thermotolerance sequence before a general decline to OGT≤50°C with a few modern lineages OGT=65±15°C or even OGT≥80°C, while a precellular LUCA model merely gives us an OGT≤50°C; OGT≥50°C threshold separating the cryophilic-to-mesophilic nucleobases, RNA, LUCA, and protocells, and the thermophilic-to-hyperthermophilic first true lifeforms, followed eventually by diversification into various levels of thermotolerance.

(Szostak, 2012; part 2)

(Sleep, 2010)

Cool Early Earth model.

Here, however, we run into another problem. Water is highly corrosive, and would've been deadly to the first RNA-based replicators (Barras, 2014)

(Ricardo et al., 2004)

Hydrolysis (Benner et al., 2012)



II.c-1B.) The Possibility of Panspermia

The hardiness of bacteria features in many lithopanspermia models, the most conservative of which are interplanetary lithopanspermia models, most relavent to we Earthlings in the hypothetical case of Mars-Earth interplanetary lithopanspermia, in which life found its way to Earth from our neighbor, Mars.

We know that bacteria could have been ejected into space by planetary impacts (Stoffler et al. 2006), survive the subsequent rapid acceleration (Mastrapaa et al. 2001), survive exposure to vacuum and high radiation (Saffary et al., 2002; Bucker & Horneck, 1970; Horneck, 1971; Nicholson, et al. 2005), thrive and grow in asteroidal and meteoritic interiors (Mautner 2002), survive re-entry into a planetary atmosphere (blah) and subsequent impact (blah),

Deinococcus radiodurans, first isolated in Corvallis, Oregon, in 1956 (Anderson, et al.)



I.a-1Bα.) Interplanetary Lithopanspermia

Radioresistance in bacteria. Mars fertile for life before Earth.

(Hoch & Losick, 1997)

(Fajardo-Cavazos et al., 1997)

(Matti et al., 2009)

(Clark, 2001)

(Loupkin, 2006)

“So, back to the period of heavy bombardment and with computer simulations you can, you can model what happens when an impact hits a planetary surface. And it's not much different from if you sprinkle Cheerios on a bed [...] and then you smack the surface of the bed, there's a— a sort of a recoil in effect and Cheerios pop upwards. It turns out Mars may have been wet — we've known at some point it had water — and fertile for life before Earth, and at this period of heavy bombardment if it had started life — surely it would've been simple life, as we've no reason to think otherwise — we've learned bacteria can be quite hardy, as I'm sure you know, so we imagine a bacterial stowaway in the nooks and crannies in one of these rocks that are cast back into space. In fact if you do the calculation, there's hundreds of tons of Mars rocks that should that should have fallen to Earth by now, over the history of the Solar system. Maybe one of those rocks carried life from Mars to Earth, seeding life on Earth. My great disappointment would be going to Mars and finding Mars life based on DNA. That it would not've been a separate experiment in life.” — Neil Degrasse Tyson to Richard Dawkins (Dawkins & Tyson, 2016, 6:05-7:24 minutes in)


I.a-1Bβ.) Interstellar Lithopanspermia

Microbe-containing impact ejecta from Earth may be subsequently pulverized by collisions into micron-sized particles that, though large enough to contain colonies of microbial life and shield them from UV radiation, would be small enough to be carried out to the Kuiper Belt via Solar winds eventually to be deposited in the protoplanetary discs of future planetary systems as the Solar system moves through interstellar dust clouds in its course through the Milky Way (Wallis, 2003; Napier, 2003), seeding the Milky Way in just a few billion years, which, considering any Earth-like planet could hypothetically have done the same, makes it highly unlikely that Earth Herself was not a benefactor of such a process (Napier, 2003).



II.c-2.) Independent Origins & Cross-Contamination

It's entirely possible that the reason why so much of the “biological evidence" for panspermia is related to the hardiness of bacteria isn't because all of life on Earth ultimately descends from a Martian ancestor, but because bacterial life specifically evolved on Mars.



II.c-2C.) Problems with Independent Origins


II.c-2Cα.) Alternative Explanations for Apparent Evidence of Independent Origins

The apparent "biological" evidence for independent origins, which mainly has to do with various bacteria having adaptations which confer upon them survivability when exposed to spacial conditions as opposed to the archaea, may be explainable by known conditions in Earth's past.

To space and back during the LHB (Wells, et al., 2003).

Natural fission reactors (Davis et al., 2014) representing a “critical event” (Gauthier-Lafaye et al., 1996) possible formation of the Moon by a nuclear explosion at Earth's core-mantle boundary (CMB) (de Meijer et al., 2010).

Another possibility is that Earth and Mars were both seeded by a common source of biological life.



II.c-2Cγ.) Genetic Relationships
"What we need is a second sample of life. We have only one at present. It would be- it would a disappointment, as you say, to find life based on DNA, or at least life on Mars based on the same DNA code. [You can] just about imagine DNA evolving twice, but you couldn't imagine the same, uh, four-letter code, um, uh, evolving twice." (Richard Dawkins to Neil Tyson, Dawkins & Tyson, 2016, 7:30-7:57 minutes in)

Since modern RNA can be used as a template to synthesize DNA, with the uracil in RNA matching the thymine in DNA, it is entirely possible that what Dawkins refers to as “the same four-letter code" in DNA could have evolved twice, so long as the two DNA codes were derived from a common RNA code. This could be said to be dodging the issue of how DNA evolved twice in the same way that (most) panspermia hypotheses dodge the issue of how life began. This therefore begs the question: How could the same four-letter RNA code have evolved twice? The most obvious solution is that the same four-letter RNA code couldn’t have evolved twice, but must have come from a common RNA-based ancestor. The independently-derived DNA codes could thus be compatible with one another so long as the RNA codes on Earth and Mars had not yet greatly diverged since their common ancestor. That is to say, if in the early Solar system there was RNA-based life on both Mars and Earth, and these lifeforms (or quasi-lifeforms) were still very closely related and compatible with one another, and DNA originated roughly in this time period, independently on both worlds, then the DNA on either planet very well may have been compatible with the other simply by virtue of having been synthesized by nearly identical RNA codes.

Furthermore, there is, as noted earlier evidence indicating that the common ancestor of the Archaea and the Bacteria possessed an RNA-based genome (Leipe & al., 1999) and only after divergence was DNA acquired separately in the two lineages, possibly from DNA viruses in which DNA first arose (Leipe & al., 1999; Forterre, 2002).

Regardless, whether DNA evolved once, on either Earth or Mars, or twice, separately in the ancestors of the Archaea and the Bacteria, the fact that Archaea and Bacteria can experience LGT with one another and presumably would have been able to do so far more easily in the distant past, leaves us with the inescapable reality that there must have been a common origin for both of these groups. The Archaea and the Bacteria simply could not have evolved entirely independently ex nihilo.



II.c-2D.) Analysis of Independent Origins

In spite of the limitations of doing general and special counts, there remain a number of reasons to suspect independent origins. Not only were the Archaea likely the first domain of diversified life (Caetano-Anollés &al., 2014) on this planet, but the Archaea appear much more involved in the "baseline" biogeochemistry of the Earth. Additionally, while "[m]ost extremophiles are microorganisms (and a high proportion of these are archaea) [...]" and "Archaea is the main group to thrive in extreme environments," (Rampelotto, 2013), the Bacteria seem far more often tolerant (exapted?) to spacial extremes. The overall theme here is unmistakable: The apparent nativity of the Archaea is greater than that of the Bacteria, while the apparent foreignness of the Bacteria provides the most compelling reason to suspect panspermia.

The main problem for independent origins remains that the Archaea and Bacteria seem to share a common ancestor. There are a number of potential resolutions of this apparent paradox: (1) Life on Earth may have originated on Mars, but the Archaea got here first, followed by a "second wave" made up of Bacterial late-comers. (2) Both the Archaea and the Bacteria first appeared on Earth, but Bacteria spent part of their evolution (a) closer to Earth's surface prior to the establishment of a permanent atmosphere, or (b) off-world, either (i) in space, or (ii) on Mars, and in space during Mars-Earth transit. (3) Archaea were shaped mainly by evolving on Earth while Bacteria were shaped by evolving on Mars, but both ultimately descend from a common "third-party" source, which might be (a) another planet, or (b) no planet at all, but some other prebiotic environment, such as (i) a comet, (ii) an asteroid, (iii) a moon, (iv) a proto-planet, (v) a planetesimal, (vi) the dust cloud of a young proto-planetary disc such as that which our own Solar System accreted from, (vii) a proto-stellar nebula such as the Proto-Solar Nebula, (viii) a molecular cloud, (ix) an interraction between two or more of one of these sources, (x) an interraction or interractions between, or sequence of interractions between, some combination of two or more of these sources, or (xi) any combination of these.



II.c-3.) The Protoplanetary Origin of Life

The earliest stages of life on Earth very likely antedate the Earth Herself. This idea has been variously referred to as “molecular panspermia", “quasi-panspermia", or “pseudo-panspermia".

"Essential to the spontaneous origin of life was the availability of organic molecules as building blocks. The famous ‘prebiotic soup’ experiment by Stanley Miller (Miller 1953, Miller-Urey experiment) had shown that amino acids, the building blocks of proteins, arose among other small organic molecules spontaneously by reacting a mixture of methane, hydrogen, ammonia and water in a spark discharge apparatus. These conditions were assumed to simulate those on the primitive Earth. Already in 1922 Oparin had proposed that the early Earth had such a reducing atmosphere (in his classic ‘The Origin of Life’ from 1936 he expanded on these ideas). Observations of Jupiter and Saturn had shown that they contained ammonia and methane, and large amounts of hydrogen were inferred to be present there as well (it is now known that hydrogen is the main atmospheric component of these planets). These reducing atmospheres of the giant planets were regarded as captured remnants of the solar nebula and the atmosphere of the early Earth was assumed by analogy to have been similar." -- The Origin of Life by Albrecht Moritz

(Moritz, 2010)

The conditions of the Miller-Urey experiments more closely resemble the conditions of the Solar nebular than the conditions of the primordial Earth (Hill & Nuth, 2003).

"Indigenous purines and pyrimidines have been detected in several carbonaceous chondrites. The pyrimidine uracil and the purines adenine, guanine, xanthine, and hypoxanthine (Stoks & Schwartz 1979, 1981) were detected in the CM carbonaceous chondrites Murchison and Murray, as well as in the CI meteorite Orgueil, in total concentrations of about 1.3 parts per million (ppm). Upper limits exist (detection limit of 0.01 ppm) for the concentrations of thymine and cytosine, as well as other heterocyclic compounds, in the Murchison meteorite (van der Velden & Schwartz 1977)."

(Peeters et al., 2003)

(Martins et al., 2008)

(Ehrenfreund & Cami, 2010)

(Ziurys, 2008)

(Coggins & Powner, 2017)

The purine bases adenine and guanine have been detected in meteorites, although the only pyrimidine-base compound formally reported in meteorites is uracil (Stoks & Schwartz, 1979), however cytosine cannot be ruled out (Shapiro, 1998; Peeters et al., 2003; Martins et al., 2006) and ultraviolet irradiation of low-temperature ices (the dominant phase of H2O in cold astrophysical environments is ice, and most ices in such environments are H2O-rich) has been shown to produce not only amino acids, quinones, and amphiphiles, but have also, with the introduction of pyrimidine, been shown to produce uracil (Nuevo et al., 2009), cytosine, and even thymine, though the abiotic synthesis of thymine is less straightforward compared to other pyrimidine-base compounds (Sandford et al., 2014). (That this would logically make the prebiotic synthesis of RNA easier than that of DNA could explain why RNA has a larger repertoire of functions than does DNA in modern cells.) Additionally, ribose and related sugars have been produced experimentally in interstellar ice analogues (Meinert et al., 2016).

Cytosine can be synthesized from cyano-acetylene and cayanate, this is unlikely to have occured in acqueous media as cayanate is rapidly hydrolized into CO2 and NH3.

Cyano-acetylene is an abundant interstellar molecule and can by produced by a spark discharge in a CH4/N2 environment.

hydrolysis of cyanoacetylene leads to cyanoacetaldehyde

reaction of cyanoacetaldehyde with urea produces cytosine in 30-50% yields

Hydrolysis of cytosine leads to uracil

(Robertson & Miller, 1995)

(Pudritz, 2016)

(Sandford, Bera et al., 2014)

(Kuga et al., 2015)

Organic methyl cyanide in comet-forming region of MWC 480.

What all of this means is that hypothetical geochemical pathways for the production of key organic compounds here on Earth, though interesting, are completely superfluous, since the biochemical building blocks of life were already being produced astrochemically before the formation of the Earth. Occam's razor therefore dictates that such geochemical hypotheses for the prebiotic synthesis of organic compounds should be regarded as irrelevant to the origin of life problem.

Clear liquid turns brown as amino acids form peptides. Jennifer Blank. Experiment.

Amino acids + impact = peptides (Blank & al. 2001)

Being that ribonucleotides can form sugar-phosphate backbones in clays when frozen (cite) we should consider whether it be possible that the first RNA molecules were produced by the sublimation/condensation cycles of clayey, H2O-rich spinning grains along the snowline of the protoplanetary disc.

Figure out minimum grain size for clay sheet formation.



II.c-4.) Synthesis: Molecular Panspermia & Subsequent Mars-Earth Interplanetary Lithopanspermia

Rather than an “RNA world" on either Earth or Mars, the Last Universal Common Ancestor (LUCA) may have lain in the “RNA cloud" of the protoplanetary Solar nebula. The early RNA-based replicons wouldn't necessarily have been “life" in the modern sense of the word, and might have lacked lipid cell membranes as some researches (cite) have suggested for the LUCA even in purely terrestrial models, with the development of cell membranes being an example of parallel evolution. If the development of more modern features of life (or rather, the features we associate with “true life") such as cell-membranes, and possibly even thymine-using nucleic acid, occured separately on Earth and Mars, the result would be two independent evolutions of “true life" that would appear to be very closely related to one another by having shared a relatively recent amembranous RNA-based ancestor. DNA and cell membranes may have evolved separately in parallel simply because this was the most sensible way for the LUCA to respond to the two nearly identical new environments of early Earth and early Mars as the Solar nebula accreted into the terrestrial planets. (This also means it may not be a futile endeavor to search for past-life on Venus, as the environment of early Venus was very much like the environment of early Earth and early Mars, and a sort of “Bacteria from Mars, Archaea from Venus" scenario, with the eukarya developing on Earth, being most closely related to Venereal/Archaeal life but having incorporated Martian/Bacterial life in the form of mitochondria, isn't difficult to envision, either).

(Belbruno, 2012)

So while the first and most obvious objection to the idea of independent origins should be that all life on Earth appears to have descended from a common ancestor, it does not necessarily follow that all life on Earth must have originated on a single planetary body — this objection could only seem reasonable to researchers who wrongly assume that the environments of the planets have always been as isolated from one another as they presently appear to be, which is simply not the case. The early Solar system was a chaotic place; organic molecules were likely already present when the material that would later accrete into the planets were but a diffuse and relatively (compared to today) homogenous gas cloud, which “curdled" gradually into something like a vast asteroid field, the rocky, protoplanetary bodies growing larger and fewer in number as the material accreted until the planets we are now familiar with arose out of the chaos. When the planets were smaller and surrounded by yet-to-be-accreted debris, impacts would have logically been far more frequent, and the smaller sizes of the proto-planetary bodies relative to the modern planets would've meant that lower-speed impacts — and therefore a larger proportion of the impacts which occured — were kicking impact debris back into space.



III. Implications & Predictions



III.a. Terrestrial Tests & Observations



III.a-1.) Terrestrial Simulations of Protoplanetary Conditions

Protoplanetary particle analgoues (PPPAs)



III.a-1A.) Snowline Simulation

Protoplanetary particle analgoues (PPPAs)

Ice-coated grains.

Phosphorus



III.a-1Aα.) Grain Composition

Grain composition — clays/silicates, adenine, guanine, pyrimidine, uracil.



III.a-1Aβ.) Ice Composition

Ice composition — H2O, pyrimidine, cytosine, thymine.



III.a-2.) Trends in Specializations of Prokaryotic Extremophiles

If the Archaea evolved on Earth as the Bacteria were evolving on Mars, and there was occasional cross-contamination which intensified during the LHB, then we should expect extremophiles which specialize in tolerating spacial extremes, like cold, drouth, low pressure, radioactivity, hyperacceleration and hypergravity, to be found mostly among the Bacteria, while extremophiles among the Archaea should be expected more often to specialize in tolerating decidedly planetary extremes such as heat, high pressure, acidity, salinity, and alkalinity.



II.a-2A.) Adaptations to Terrestrial Extremes


III.a-2Aα.) Acidophiles & Hyperacidotolerant, Near-Acidophilic Neutriphiles

This group includes organisms capable of thriving in hyperacidic conditions, most of which have an optimal growth pH of 5 or lower (OGpH<5), although a few have an OGpH slightly above this (e.g., Nanoarchaeum equitans, OGpH=6) but can nonetheless be found flourishing in hyperacidic environments (pH=0.5-1.5).

Described Genera
Domain Genus Source Ratio σ (–ρ) ρ %>H0
Archaea Acidianus Johnson, 1998 27:16 16/43
(37%)
27/43
(63%)
26%
Acidiplasma ()
Aenigmarchaeum Golyshina et al., 2017
Cuniculiplasma Golyshina et al. 2016
Ferroplasma (Dopson et al.2003)
Halarchaeum ()
Candidatus Haloredivivus Golyshina et al., 2017
Candidatus Lainarchaeum Golyshina et al., 2017
Candidatus Mancarchaeum ()
Metallosphaera Johnson, 1998
Candidatus Micrarchaeum Baker et al., 2010
Nanoarchaeum Golyshina et al., 2017
Nanobsidianus
Nanopusillus
Candidatus Nanosalina Golyshina et al., 2017
Candidatus Nanosalinarum Golyshina et al., 2017
Nitrosopumilus Lehtovirta-Morley et al., 2014
Nitrosotalea Lehtovirta-Morley et al., 2011 2014)
Candidatus Parvarchaeum Baker et al., 2010
Picrophilus Rampelotto, 2013, Johnson, 1998
Stygiolobus Johnson, 1998
Sulfolobus Johnson, 1998
Sulfurisphaera ()
Sulfurococcus Johnson, 1998
Thermogymnomonas ()
Thermoplasma Johnson, 1998
Bacteria Acetobacter Johnson, 1998
Acidiphilium Johnson, 1998; Fashola et al., 2015
Acidithiobacillus Johnson, 1998
Acidobacterium Johnson, 1998
Acidimicrobium Johnson, 1998
Acidocella Johnson, 1998; Fashola et al., 2015
Acidomonas Johnson, 1998
Alicyclobacillus Johnson, 1998; Fashola et al., 2015
Bryocella ()
Ferrimicrobium Johnson, 1998
Helicobacter
Leptospirillum Johnson, 1998; Lehtovirta-Morley et al., 2014
Sulfobacillus Johnson, 1998; Fashola et al., 2015
Telmatobacter ()
Thiobacillus Johnson, 1998
Thiomonas Johnson, 1998

Described Species
Domain Genus & Species OGpH Source Ratio σ (–ρ) ρ %>H0
Archaea Acidianus ambivalens <3 Johnson, 1998 78:29 29/107
(27%)
78/107
(73%)
46%
Acidianus brierleyi <3 Johnson, 1998; Fashola et al., 2015
Acidianus convivator <4 ()
Acidianus infernus <3 Johnson, 1998
Acidianus manzaensis 1.5-2.5 (Ding et al. 2011)
Acidianus pozzuoliensis
Acidianus sulfidivorans Plumb et al. 2007
Acidianus tengchongensis 2.5 He et al. 2004
Acidiplasma aeolicum <4 ()
Acidiplasma cupricumulans <4 ()
Candidatus Aenigmarchaeum subterraneum 0.5-1.5 Baker et al., 2006; Golyshina et al., 2017
Candidatus Cenarchaeum symbiosum A <4 Herbold et al., 2017
Cuniculiplasma divulgatum 1-1.2 Golyshina et al. 2016
Ferroplasma acidarmanus <3 (Dopson et al.2003)
Ferroplasma acidiphilum (Fashola et al., 2015)
Ferroplasma cyprexacervatum <4 ()
Halarchaeum acidiphilum <4 ()
Candidatus Haloredivivus sp. 0.5-1.5 Baker et al., 2006; Golyshina et al., 2017
Candidatus Lainarchaeum andersonii 0.5-1.5 Baker et al., 2006; Golyshina et al., 2017
Candidatus Mancarchaeum acidiphilum 0.5-1.5 Baker et al., 2006; Golyshina et al., 2017
Metallosphaera hakonensis <4 ()
Metallosphaera prunae <3 Johnson, 1998
Metallosphaera sedula <3 Johnson, 1998; Fashola et al., 2015
Metallosphaera yellowstonensis <4 ()
Candidatus Micrarchaeum acidiphilum 0.5-1.5 Baker et al., 2006; Baker et al., 2010; Golyshina et al., 2017
Candidatus Nanoarchaeum equitans 6*; 0.5-1.5 Baker et al., 2006; Baker et al., 2010; Golyshina et al., 2017
Nanobsidianus stetteri
Nanopusillus acidilobi sp.
Candidatus Nanosalina sp. 0.5-1.5 Baker et al., 2006; Baker et al., 2010; Golyshina et al., 2017
Candidatus Nanosalinarum sp. 0.5-1.5 Baker et al., 2006; Baker et al., 2010; Golyshina et al., 2017
Candidatus Nitrosoarchaeum koreensis <4 Herbold et al., 2017
Candidatus Nitrosoarchaeum limnia <4 Herbold et al., 2017
Candidatus Nitrosoarchaeum limnia <4 Herbold et al., 2017
Candidatus Nitrosocosmicus oleophilus <4 Herbold et al., 2017
Candidatus Nitrosopelagicus brevis <4 Herbold et al., 2017
Candidatus Nitrosopumilus maritimus <4 Lehtovirta-Morley et al., 2014; Herbold et al., 2017
Candidatus Nitrosopumilus viennensis <4 Lehtovirta-Morley et al., 2014
Candidatus Nitrosopumilus sp. SJ <4 Herbold et al., 2017
Candidatus Nitrosopumilus sp. NF5 <4 Herbold et al., 2017
Candidatus Nitrosopumilus sp. AR1 <4 Herbold et al., 2017
Candidatus Nitrosopumilus sp. AR2 <4 Herbold et al., 2017
Candidatus Nitrosopumilus salaria <4 Herbold et al., 2017
Candidatus Nitrosopumilus sp. D3C <4 Herbold et al., 2017
Candidatus Nitrososphaera evergladensis <4 Herbold et al., 2017
Candidatus Nitrososphaera viennensis <4 Herbold et al., 2017
Candidatus Nitrososphaera gargensis <4 Herbold et al., 2017
Candidatus Nitrosotalea okcheonensis <4 Herbold et al., 2017
Candidatus Nitrosotalea sinensis <4 Herbold et al., 2017
Candidatus Nitrosotalea devanaterra 4-5 Lehtovirta-Morley et al., 2011 & 2014; Herbold et al., 2017
Candidatus Nitrosotalea bavarica <4 Herbold et al., 2017
Candidatus Nitrosotenuis uzonensis <4 Herbold et al., 2017
Candidatus Nitrosotenuis chungbukensis <4 Herbold et al., 2017
Candidatus Nitrosotenuis cloacae <4 Herbold et al., 2017
Candidatus Parvarchaeum acidiphilum 0.5-1.5 Baker et al., 2006; Baker et al., 2010; Golyshina et al., 2017
Candidatus Parvarchaeum acidophilus 0.5-1.5 Baker et al., 2006; Baker et al., 2010; Golyshina et al., 2017
Picrophilus sp. 1 (Baker-Austin & Dopson, 2007)
Picrophilus oshimae 2.2 Rampelotto, 2013, Johnson, 1998
Picrophilus torridus ≥0; 0.06-0.07 Rampelotto, 2013, Johnson, 1998
Stygiolobus azoricus <3 Johnson, 1998
Sulfolobus acidocaldarius <3 Johnson, 1998
Sulfolobus hakonensis <3 Johnson, 1998
Sulfolobus islandicus <4 ()
Sulfolobus metallicus <3 Johnson, 1998; Fashola et al., 2015
Sulfolobus mirabilis <3 Johnson, 1998
Sulfolobus neozealandicus <4 ()
Sulfolobus shibatae <3 Johnson, 1998
Sulfolobus solfataricus 2-4 Johnson, 1998, Dopson (2003)
Sulfolobus tengchongensis <4 ()
Sulfolobus thuringiensis <4 ()
Sulfolobus tokodaii <3 Dopson 2003
Sulfolobus yangmingensis <4 ()
Sulfurisphaera ohwakuensis <4 ()
Sulfurococcus mirabilis <4 ()
Sulfurococcus yellowstonensis <4 ()
Sulfurococcus yellowstonii <3 Johnson, 1998
Thermogymnomonas acidocola <4 ()
Thermoplasma acidophilum 1.8 Johnson, 1998
Thermoplasma volcanium <3 Johnson, 1998
Bacteria Acetobacter aceti Johnson, 1998
Acidiphilium acidophilum
(Thiobacillus acidophilus)
<3 Johnson, 1998
Acidiphilium multivorum <3 (Dopson 2003)
Acidithiobacillus albertensis
(Thiobacillus albertis)
<3 Johnson, 1998; Fashola et al., 2015
Acidithiobacillus caldus
(Thiobacillus caldus)
<3 Johnson, 1998;
Fashola et al., 2015
Acidithiobacillus ferridurans <4 ()
Acidithiobacillus ferriphilus <4 ()
Acidithiobacillus ferrivorans <4 (Fashola et al., 2015)
Acidithiobacillus ferroxidans
(Thiobacillus ferrooxidans)
<3 Johnson, 1998; Fashola et al., 2015
Acidithiobacillus thioxidans
(Thiobacillus thioxidans)
<3 Johnson, 1998; Fashola et al., 2015
Acidobacterium capsulatum <3 Johnson, 1998; Fashola et al., 2015
Acidimicrobium ferroxidans <3 Johnson, 1998; Fashola et al., 2015
Acidocella spp. <3 Johnson, 1998
Acidomonas methanolica <3 Johnson, 1998
Alicyclobacillus thermosulfidooxidans <3 Johnson, 1998
Alicyclobacillus thermosulfidooxidans
(Sulfobacillus thermosulfidooxidans)
<3 Johnson, 1998; Fashola et al., 2015
Bryocella elongata <4 ()
Ferrimicrobium acidiphilum <3 Johnson, 1998
Ferrimicrobium acidiphilus <3 Fashola et al., 2015
Gallionella ferruginea (Fashola et al., 2015)
Helicobacter pylori
Hydrogenobacter acidophilus (Fashola et al., 2015)
Leptospirillum ferriphilum <3 Lehtovirta-Morley et al., 2014
Leptospirillum ferroxidans <3 Johnson, 1998; Fashola et al., 2015
Leptospirillum thermoferrooxidans <3 Johnson, 1998
Sulfobacillus acidophilus <3 Johnson, 1998; Fashola et al., 2015
Telmatobacter bradus <4 ()
Thiobacillus acidophilus <4 ()
Thiobacillus dentrificans (Fashola et al., 2015)
Thiobacillus organovorus <4 ()
Thiobacillus prosperus <3 Johnson, 1998
Thiomonas cuprina
(Thiobacillus cuprinus)
<3 Johnson, 1998

Zhang et al., 2015
Edwards et al., 2000
Ding et al., 2011
Dopson et al., 2003
Baker et al., 2010
Plumb et al., 2007
Whitman et al., 1999
"Nitrosotalea is an abundant, globally distributed genus of AOA found in acidic soils (Gubry-Rangin et al., 2011). Thirty per cent of the world's soils are considered acidic (pH < 5.5; von Uexküll & Mutert, 1995), and ammonia oxidation in low pH soils is dominated by AOA, rather than AOB (Gubry-Rangin et al., 2010; Lehtovirta-Morley et al., 2011)."

Craig W. Herbold, Laura E. Lehtovirta-Morley, Man-Young Jung, Nico Jehmlich, Bela Hausmann, Ping Han, Alexander Loy, Michael Pester, Luis A. Sayavedra-Soto, Sung-Keun Rhee, James I. Prosser, Graeme W. Nicol, Michael Wagner and Cecile Gubry-Rangin. Ammonia-oxidising archaea living at low pH: Insights from comparative genomics. Environmental Microbiology (2017) 19(12), 4939–4952



III.a-2Aβ.) Alkaliphiles
Domain Genus & Species Ratio σ(%)<(ρ=100%) ≈ ρ ≈ %>H0
Archaea Halalkalicoccus 16:1 1/16 (6.25%) 15/16 (93.75%) 87.5%
Haloarcula
Halobaculum
Halobiforma
Haloferax
Halorubrum gandharaense
Nanobacterium gregoryi
Natronococcus amylolyticus
Natronococcus jeotgali
Natronococcus occultus
Natronolimnobius
Natronomonas pharaonis
Natronorubrum
Thermococcus alkaliphilus
Thermococcus acidaminovorans
Methanohalophilus
Bacteria (Coming Soon)
Domain Genus & Species Ratio σ(%)<(ρ=100%) ≈ ρ ≈ %>H0
Archaea Halalkalicoccus 16:1 1/16 (6.25%) 15/16 (93.75%) 87.5%
Haloarcula
Halobaculum
Halobiforma
Haloferax
Halorubrum gandharaense
Nanobacterium gregoryi
Natronococcus amylolyticus
Natronococcus jeotgali
Natronococcus occultus
Natronolimnobius
Natronomonas pharaonis
Natronorubrum
Thermococcus alkaliphilus
Thermococcus acidaminovorans
Methanohalophilus
Bacteria (Coming Soon)

Elis Watanable Nogueira, Elize Ayumi Hayash, Enne Alves, Claudio Antônio de Andrade Lima, Maria Talarico Adorno, Gunther Brucha. Characterization of Alkaliphilic Bacteria Isolated from Bauxite Residue in the Southern Region of Minas Gerais, Brazil. Brazilian Archives of Biology and Technology vol.60 Curitiba 2017 Epub May 11, 2017
http://dx.doi.org/10.1590/1678-4324-2017160215



III.a-2Aγ.) Barophiles
Domain Genus & Species Ratio σ(%)<(ρ=100%) ≈ ρ ≈ %>H0
Archaea Pyrococcus abyssi 6:1 1/7 (14%) 6/7 (86%) 72%
Pyrococcus endeavori
Pyrococcus furiosis
Pyrococcus glycovorans
Pyrococcus horikoshii
Pyrococcus woesei
Bacteria Salinicola salarius

(Gareeb & Setati, 2009)
(Pikuta et al., 2017)

III.a-2Aδ.) Halophiles


II.c-2Aε.) Haloalkaliphiles


III.a-2Aζ.) Hyperthermophiles
Domain Genus & Species Ratio σ(%)<(ρ=100%) ≈ ρ ≈ %>H0
Archaea Aeropyrum pernix 6:1 1/7 (14%) 6/7 (86%) 72%
Pyrolobus fumaril
Pyrococcus furiosus
Archaeoglobus fulgidis
Methanococcus jannaschii
Stygiolobus azoricus
Sulfolobus acidocaldarius
Sulfolobus islandicus
Sulfolobus neozealandicus
Sulfolobus shibatae
Sulfolobus solfataricus
Sulfolobus tengchongensis
Sulfolobus thuringiensis
Sulfolobus tokodaii
Sulfolobus yangmingensis
Methanopyrus kandleri
"Strain 121"
Bacteria Aquifex aeolicus
Geothermobacterium ferrireducens
Theromotoga maritima


III.a-2Aη.) Thermoacidophiles


III.a-2Aθ.) Thermobarophiles


III.a-2Aι.) Totals for Planetary Extremes
Extreme Domain Number Ratio σ(%)<(ρ=100%) ≈ ρ ≈ %>H0
Acidity Archaea 18 18:7 7/25 (28%) 18/25 (72%) 44%
Bacteria 7
Alkalinity Archaea 6 16:1 1/16 (6.25%) 15/16 (93.75%) 87.5%
Bacteria 1
Salinity Archaea
Bacteria
High Pressure Archaea 6 6:1 1/7 (14%) 6/7 (86%) 72%
Bacteria 1
Heat Archaea 18 6:1 1/7 (14%) 6/7 (86%) 72%
Bacteria 3
Total Archaea
Bacteria

Archaeal goodness-of-fit
Extremophile typeObservedExpectedO-E(O-E)2(O-E)2/E
Acidophilic1812.55.530.252.42
Alkaliphilic1688648
Barophilic63.52.56.251.79
Halophilic
Haloalkaliphilic
Hyperthermophilic1810.57.556.255.36
Thermoacidophilic
Thermobarophilic
X2=


III.a-2B.) Adaptations to Spacial Extremes


III.a-2Bα.) Radioresistant Prokaryotes
Domain Genus & Species Ratio σ(%)<(ρ=100%) ≈ ρ ≈ %>H0
Archaea Pyrococcus furiosis 1:4 1/5 (20% 4/5 (80%) 60%
Haloferax volcanii
Natrialba magadii
Thermococcus gammatolerans
BacteriaBacillus subtilis
Bacillus atropheus
Bacillus thuringiensis
Bacillus cereus
Bacillus megaterium
Deinococcus radiodurans
Escherichia coli
Rubrobacter sp.
Achromobacter sp.
Acinetobacter sp.
Alcaligenes sp.
Enterococcus sp.
Micrococcus sp.
Pseudomonas sp.
Staphylococcus sp.
Streptococcus sp.

(Abrevaya et al., 2011)
(Bucker & Horneck, 1970)
(Horneck, 1971)
(Nicholson, et al. 2005)

III.a-2Bβ.) Xerophilic Prokaryotes
Domain Genus & Species Ratio σ(%)<(ρ=100%) ≈ ρ ≈ %>H0
Bacteria Bacillus subtilis 2:0 0/2 (0%) 1/1 (100%) 100%
Escherichia coli


III.a-2Bγ.) Cryophilic Prokaryotes
Domain Genus & Species Ratio σ(%)<(ρ=100%) ≈ ρ ≈ %>H0
Bacteria Bacillus subtilis 2:0 0/2 (0%) 1/1 (100%) 100%
Escherichia coli


III.a-2Bδ.) Hypobarotolerant Prokaryotes


III.a-2Bε.) Totals for Spacial Extremes
Extreme Domain Number Ratio σ(%)<(ρ=100%) ≈ ρ ≈ %>H0
Radioactivity Archaea 4 4:1 1/5 (20%) 4/5 (80%) 60%
Bacteria 20
Hyperacceleration / Hypergravity Archaea
Bacteria 2
Low Pressure Archaea
Bacteria
Cold Archaea
Bacteria
Drouth Archaea 0 2:0 0/2 (0%) 1/1 (100%) 100%
Bacteria 2
Total Archaea
Bacteria


III.a-2C.) Totals for Prokaryotic Extremophiles
Extreme Type Ratio σ(%)<(ρ=100%) ≈ ρ ≈ %>H0
Acidity Planetary 18:7 7/25 (28%) 18/25 (72%) 44%
Alkalinity 16:1 1/16 (6.25%) 15/16 (93.75%) 87.5%
Salinity
High Pressure 6:1 1/7 (14%) 6/7 (86%) 72%
Heat 6:1 1/7 (14%) 6/7 (86%) 72%
Radioactivity Spacial 1:4 1/5 (20%) 4/5 (80%) 60%
Hyperacceleration / Hypergravity
Low Pressure
Cold
Drouth 2:0 0/2 (0%) 1/1 (100%) 100%

Archaeal goodness-of-fit
Extremophile typeObservedExpectedO-E(O-E)2(O-E)2/E
Planetary75%50%25%125%75%
Spacial25%50%-25%125%75%
Df=1
X2=0.075

Bacterial goodness-of-fit
Extremophile typeObserved %Expected %O-E(O-E)2(O-E)2/E
Planetary2550-251252.5
Spacial7550251252.5
Df=1
X2=5

Extremophile typeρH0ρ-H0(ρ-H0)2(ρ-H0)2/H0
Acidophile
X2=


III.a-2D.) Limitations on Methodology

General and special counts performed with described genera and species are necessarily problematic, for several reasons:

1.

Species and genera are largely arbitrary, especially in prokaryotes.

2.

The number of genera and species can change.

3.

Performing the count is difficult. Even under ideal circumstances (i.e., a perfect, non-arbitrary, universally applicable criterion for determining taxonomic rank, complete genomic knowledge of every living organism on the planet, phylogenies already well-determined and described in the published literature, and every species' tolerances and optimal growth conditions studied in painstaking detail and accurately described) it would be a monumental task to sift through and pore over the seemingly infinite number of papers, journal articles, and books published on the subject in order to count every genus and species ever described.

4.

General and special counts might not mean much. Even under ideal circumstances and with a complete count performed, it's questionable how useful this information would truly be. Bacteria seem to have inhabited the planet for at least 3.5 GA. There has been ample opportunity for Archaea and Bacteria to adapt to every conceivable condition on this planet, so these tendencies could be mere coincidence. While some groups of Archaea and Bacteria certainly appear to contain preponderances of certain varieties of extremophile, many of these adaptations co-evolved in diverse lineages, and are not always indicative of common ancestry. Additionally, genes involved in "planetary" extremophily seem in some cases related to genes involved in "spacial" extremophily. Furthermore, many of these genes were acquired via LGT (Fuchsman, &al. 2017; Herbold et al., 2017).

The conceit here is that the "overal theme" regarding which domain seems to be better at adapting to certain sorts of extremes is indicative, in a very general way, of evolutionary history.



III.a-3.) Biogeochemical Roles of the Prokaryotic Domains

(Offre et al. 2013)

(Dubey et al., 2015)

(Gubry-Rangin et al., 2010; Lehtovirta-Morley et al., 2011)

Archaea in Biogeochemical Cycles Annual Review of Microbiology Vol. 67:437-457 (Volume publication date September 2013) First published online as a Review in Advance on June 26, 2013 https://doi.org/10.1146/annurev-micro-092412-155614

Hang-Wei Hu, Zhi-Hong Xu, Ji-Zheng He. Ammonia-Oxidizing Archaea Play a Predominant Role in Acid Soil Nitrification — Chapter Six. Advances in agronomy vol. 125, 2014, p. 261-302



III.b. Extraterrestrial Multicellularity

If the acquisition of The Mitochondrion was the definitive event in the evolution of the eukaryotic cell, and The Mitochondrion is ultimately derived from the Bacteria though the Eukaryotes otherwise descend from Archaeal ancestors, and the Bacteria and the Archaea evolved mostly independently on Mars and Earth respectively, but ultimately share a LUCA in the protoplanetary disc of the Solar nebula prior to its accretion into the planets, when the Sun was relatively young, then, being that multicellularity, though having appeared many times independently, has thus far been nigh-exclusively and doubtless most impressively observed among the Eukaryotes, this implies that while we might expect to find microbial extraterrestrial life almost ubiquitously in the “Goldilocks" (habitable) zones of stars throughout the universe, presumably ranging in sophistication and/or individuation into discrete lifeforms along a continuum from “simple" organic molecules in stelliferous nebulae ("star hatcheries") through amembranous replicons in protoplanetary discs, to protocells with simple spherical lipid structures to prevent hydrolysis-induced degradation in the transition from a relatively dry protoplanetary environment to the more watery environments of recently-coalesced planets, to the full-fledged biospheres of some terrestrial planets and natural satellites (perhapse this apparent “progression" is an evolutionary response to the selective pressure of stellar evolution and planetary formation, and/or represents changes in the integral organic chemistry necessary for the thermodynamic maintenance of these systems), we may expect to find multicellular life predominantly in planetary systems that, in addition to hosting a planet that appears as though it could support life at the time we view it, have at least one other planet that, if it does not also appear as though it might support life at the time of viewing, at least looks as if it could have hosted life at some point early on in the history of said planetary system, and perhaps “complex" multicellular life to the degree found among eukaryotes exclusively in such planetary systems. In other words: If we want to find the most promising planetary systems for hosting our sort of “complex" multicellular life, we ought to focus on locating and examining planetary systems that contain analogues of the Mars-Earth relationship. (The potential importance of the Moon's stabalizing effect on Earth's axial tilt mustn't be ignored with regard to the evolution of complex multicellular lifeforms, however, so any extrasolar Mars-Earth-relationship analogues might require the Earth-analogue to be a near-perfect Earth-Moon analogue in order for there to be a significant chance it would generate anything remotely like what we think of as complex multicellular life. Furthermore, the presence of a Jupiter-analogue might also be necessary to protect the Mars-Earth-relationship-analogue from devastating impacts. This would make the Rare Earth hypothesis essentially correct with regard to the development of obligate complex multicellular life.)

Alternately, if we search for “complex" multicellular life in all conceivable environments yet find it exclusively — or at least predominantly — in planetary systems with Mars-Earth-relationship-analogues, that would constitute very strong evidence in favor of this hypothesis.



III.b-1.) The Drake Equation

N = R* · fp · ne · fl · fi · fc · L

TermDefinition
NThe number of communicative civilizations in the Milky Way.
R*The average rate of star formation in the Milky Way galaxy.
fpThe fraction of formed stars with planetary systems.
neAmong the stars which have planets, the average number of planets capable of supporting life.
flThe number of those planets which actually develop life.
fiThe fraction of life-bearing planets which produce civilizations.
fcThe fraction of civilized planets that develop communications technologies capable of being detected across interstellar space.
LThe average length of time over which such civilizations broadcast or leak their communications into space.


III.b-1A.) The Fermi Paradox


III.b-1B.) The Great Filter


III.b-1C.) The Rare Earth

Should be changed to:

N = N* · ne · fg · fp · fpm · fi · fc · fl · fm · fj · fme

TermDefinition
NThe number of communicative civilizations in the Milky Way.
N*The number of stars in the Milky Way.
neThe average number of planets in a star's habitable zone.
fgThe fraction of stars in the Milky Way's galactic habitable zone.
fpThe fractions of stars in the Milky Way that have planets.
fpmThe fraction of planets that are tellurian or "rocky" rather than gaseous.
fi
fc
fl
fm
fj
fme



III.b-1D.) The Mother Earth — Father Mars Scenario

Should be changed to:

N = N* · fp · fd · ne · fl · fr · ff · fm · fa · fi · fc · L

TermDefinition
NThe number of communicative civilizations in the Milky Way.
N*The number of stars in the Milky Way.
fpThe fraction of formed stars with planetary systems.
fdThe fraction of planetary systems with at least two planets capable of supporting life.
neAmong the planetary systems with at least two two planets capable of supporting life, the average number of such planets.
flThe fraction of those planets which actually develop life.
frThe fraction of those planets which are also recipients of lifeforms from neighboring planets.
ffThe fraction of recipient planets in which the donated lifeforms are incorporate into some of the native lifeforms, yielding something like a eukaryotic cell.
fmThe fraction of planets with eukaryoid lifeforms which produce complex multicellular lifeforms.
faThe fraction of planets with complex multicellular lifeforms which produce animal life.
fiThe fraction of planets with animal life which produce civilizations.
fcThe fraction of civilized planets that develop communications technologies capable of being detected across interstellar space.
LThe average length of time over which such civilizations broadcast or leak their communications into space.



III.b-1E.) Synthesis: The Rare Mother Earth & Father Mars Scenario


III.b-2.) Extraterrestrial Observations

It would be highly beneficial to perform tests in Earth orbit to determine whether a low pressure, microgravity environment replete with chemical compounds and minerals thought to be present in the protoplanetary disk could provide a stable environment for phosphodiester bonds to form between ribose molecules, for hydrogen bonds to link nucleobases,

If at first such tests prove fruitless, additional tests should be performed using equipment which can simulate free-fall, such as slow centrifuge-like mechanisms, to see if gravitational energy may have played a roll in the formation of RNA.

Other possible tests might include



III.b-2A.) Intrasolar Observations


III.b-2Aα.) Martian Observations

If life had managed to persist on Mars, as does not currently appear to be the case, then we might expect to find the opposite arrangement, with the native Martian bacterial extremophiles better suited to planetary extremes, and non-native Martian archaeal extremophiles more tolerant to spacial extremes. (Perhaps there could even have evolved “anti-eukaryotes": Bacteria-descended cells with archaea-descended mitochondria-analogues housed in a cytoskeletal structure.)



III.b-2Aβ.) Venerean Observations


III.b-2Aγ.) Asteroidal Observations


III.b-2Aδ.) Europan Observations

If there appears to be only a single domain of life in Europa's ocean, and is absent any form of multicellularity more complex than aggregates like biofilms or perhaps algaes and maybe structures like kelp forests, but nothing analogous to the many-structured and diverse forms of the animals, plants, and fungi here on Earth, and if the cells of the Europan lifeforms show no internal organelles analogous to mitochondria, chloroplasts, or any other traces of creatures whose ancestors came from another domain of life, then that could be taken as very strong circumstantial evidence for the Mother Earth — Father Mars scenario.

If the LUCA was the “prebiotic cloud" of the Solar nebula, we can reasonably expect to find life related to us in Europa's ocean. Being that Europa has been isolated from us for so long and is so much further away from Earth than Mars is, we might not necessarily expect Earth-specific life to have greatly influenced its evolution.

The discovery of Europan life which appears to be somewhat more closely related to our Bacteria than to our Archaea could be interpreted as indicating that our Bacterial life is “something inbetween" our native Archaea and that which we (in this hypothetical scenario) find in Europa's ocean. This would speak strongly in favor of the possibility that Bacteria are from someplace slightly further out in the Solar system; from a planet between us and Jupiter.

If the reverse should be true, and the Europan life seems somewhat more closely related to our Archaea than to our Bacteria, this might imply that Bacteria must be from somewhere much further away, and taken as evidence of Interstellar Panspermia.

If we find a multiple-domain system of life in Europa's ocean with many different varieties of unicellular, pluricellular, and “complex" multicellular forms, complete with animal-analogues swimming around, but they have no structures in their cells analogous to the organelles of eukaryotes, then that would indicate that there's nothing particularly special about the eukaryotic cell and no particular need for something like mitochondria in order to get “complex" multicellular life.

If we find a multiple-domain system of life in Europa's ocean and there do appear to be eukaryoid organisms organizing into “complex" multiceullar forms with mitochondria-like organelles, but neither the host cells nor the mitochondrites appear to be any more or any less closely related either to our Archaea or to our Bacteria, then this could be interpreted as indicating that “complex" mutlicellular life is somewhat inevitable and would not necessarily have depended on Earth-Mars interaction. Although, interaction between Europa and one or more of Jupiter's many other natural satellites resulting in a sort of “miniature" Earth-Mars-relationship-analogue would have to be ruled out for this interpretation to carry any real weight.

(Lunine, 2016,1:06:19 minutes in)

(Grunsfelf, 2015)

(Hand, 2014)



III.b-2Aε.) Titanian Observations


III.b-2Aζ.) Enceladan Observations


III.b-2Aη.) Cometary Observations


III.b-2Aθ.) Plutonian Observations


III.b-2B.) Extrasolar Observations


V. Conclusions



V.a. Summary



V.a-1.) Timeline of Events

— formation of the Milky Way

— formation of the Giant Molecular Cloud (GMC), 106-108 M (Montmerle, 2006), containing complex organic molecules (Ehrenfreund & Charnley, 2000)

— formation of a star-forming region similar to the Orion Nebula
"in a large star-forming region that produced massive stars, possibly similar to the Orion Nebula.[16][17] Studies of the structure of the Kuiper belt and of anomalous materials within it suggest that the Sun formed within a cluster of between 1,000 and 10,000 stars with a diameter of between 6.5 and 19.5 light years and a collective mass of 3,000 M. This cluster began to break apart between 135 million and 535 million years after formation.[18][19]"

— fragmentation of the GMC, first into fragments 1 parsec in diameter and then into "cloudlets" 0.01-0.1 parsecs or 2k-20k AU in diameter and around 1 M (Montmerle, 2006).

— formation of the Pre-Solar Nebula, a fragment of the GMC about 1 M (Montmerle, 2006).

4.6 GYA — beginning of the Stellar era (first million years of Solar evolution), the Disk era (first 10 million years of Solar evolution), and the Telluric era (first 100 million years of Solar evolution): formation of the Sun in a stellar cluster via accretion of a circumstellar disk fed by a progressively diminishing circumstellar envelope (Montmerle, 2006), possibly incited by a nearby supernova (Montmerle, 2006; Williams, 2009).

4.599 GYA — Stellar era ends, 99 million years prior to the end of the Telluric era and 90 million years prior to the end of the Disk era (Montmerle, 2006).

4.59 GYA — Disk era ends, 90 million years prior to the end of the Telluric era (Montmerle, 2006).

4.5682 GYA — oldest solid material in the Solar system.

4.55 GYA — formation of the Earth

4.53 GYA — formation of the Moon

4.5 GYA — Telluric era ends. Noachian period begins on Mars.

"Several simulations of our young Sun interacting with close-passing stars over the first 100 million years of its life produce anomalous orbits observed in the outer Solar System, such as detached objects.[20]"

(Brasser et al. 2013)

(Brasser et al. 2017)

(Lykawka & Ito, 2013)

Journal of Asian Earth Sciences journal homepage: www.elsevier.com/locate/jseaes Full length article Earth’s thermal evolution, mantle convection, and Hadean onset of plate tectonics W.G. Ernst Journal of Asian Earth Sciences 145 (2017) 334–348

4.4 GYA — "Cool Early Earth" begins

(Valley et al., 2002)

4.3 billion years ago — earliest evidence of liquid water

Asteroid, Comets, Meteors Proceedings IAU Symposium No. 229, 2005 D. Lazzaro, S. Ferraz-Mello & J.A. Fern´ andez, eds. c  2006 International Astronomical Union doi:10.1017/S1743921305006861 Origin of water on the terrestial planets Michael J. Drake 1 and Humberto Campins

Planet migration. Nice model. Quaker belt? Kuiper belt? Ice falls inward, planets move outward. Jupiter orbits twice for every one Saturn orbit (2:1 resonance).

(Walsh & Morbidelli, 2010)

(Gomes et al., 2010)

4.1 billion years ago — onset of The Late Heavy Bombardment (LHB), or lunar cataclysm; earliest evidence of biogenic carbon (Bell et al. 2015)..

4 billion years ago — "Cool Early Earth" ends, plate tectonics

3.8 billion years ago — end of The Late Heavy Bombardment (LHB), or lunar cataclysm.

3.5 billion years ago — Noachian period ends on Mars; establishment of the geomagnetic field on Earth, protecting the atmosphere from being swept away by Solar winds.

2.45 billion years ago — the Great Oxygenation Event.



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