Prokaryotes

Part I

Prokaryotes are defined as cellular organisms who lack a nucleus.

Part II

Part III

Part III.a.

Because the eukarya share a more recent common ancestor with the archaea than the archaea with the bacteria,

Part III.b.

Part III.b-1.

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.

Part III.b-2.

Part III.c.

Part III.c-1.

Part III.c-2.

Part IV

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

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

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)

Brian J. Enquist, Professor, Ecology and Evolutionary Biology. Life on Earth: By Chance or By Law? The University of Arizona
Available online @ https://www.youtube.com/watch?v=YQZEmieP6zM

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.

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.

References