Probing complexity: thermodynamics and computational mechanics approaches to origins studies

A self-sustaining serpentinization mega-engine feeds the fougerite nanoengines implicated in the emergence of guided metabolism

The demonstration by Ivan Barnes et al. that the serpentinization of fresh Alpine-type ultramafic rocks results in the exhalation of hot alkaline fluids is foundational to the submarine alkaline vent theory (AVT) for life's emergence to its 'improbable' thermodynamic state. In AVT, such alkaline fluids ≤ 150°C, bearing H2 > CH4 > HS--generated and driven convectively by a serpentinizing exothermic mega-engine operating in the ultramafic crust-exhale into the iron-rich, CO2> > > NO3--bearing Hadean ocean to result in hydrothermal precipitate mounds comprising macromolecular ferroferric-carbonate oxyhydroxide and minor sulfide. As the nanocrystalline minerals fougerite/green rust and mackinawite (FeS), they compose the spontaneously precipitated inorganic membranes that keep the highly contrasting solutions apart, thereby maintaining redox and pH disequilibria. They do so in the form of fine chimneys and chemical gardens. The same disequilibria drive the reduction of CO2 to HCOO- or CO, and the oxidation of CH4 to a methyl group-the two products reacting to form acetate in a sequence antedating the 'energy-producing' acetyl coenzyme-A pathway. Fougerite is a 2D-layered mineral in which the hydrous interlayers themselves harbor 2D solutions, in effect constricted to ~ 1D by preferentially directed electron hopping/tunneling, and proton Gröthuss 'bucket-brigading' when subject to charge. As a redox-driven nanoengine or peristaltic pump, fougerite forces the ordered reduction of nitrate to ammonium, the amination of pyruvate and oxalate to alanine and glycine, and their condensation to short peptides. In turn, these peptides have the flexibility to sequester the founding inorganic iron oxyhydroxide, sulfide, and pyrophosphate clusters, to produce metal- and phosphate-dosed organic films and cells. As the feed to the hydrothermal mound fails, the only equivalent sustenance on offer to the first autotrophs is the still mildly serpentinizing upper crust beneath. While the conditions here are very much less bountiful, they do offer the similar feed and disequilibria the survivors are accustomed to. Sometime during this transition, a replicating non-ribosomal guidance system is discovered to provide the rules to take on the incrementally changing surroundings. The details of how these replicating apparatuses emerged are the hard problem, but by doing so the progenote archaea and bacteria could begin to colonize what would become the deep biosphere. Indeed, that the anaerobic nitrate-respiring methanotrophic archaea and the deep-branching Acetothermia presently comprise a portion of that microbiome occupying serpentinizing rocks offers circumstantial support for this notion. However, the inescapable, if jarring conclusion is drawn that, absent fougerite/green rust, there would be no structured channelway to life.

Provenance of life: Chemical autonomous agents surviving through associative learning

We present a benchmark study of autonomous, chemical agents exhibiting associative learning of an environmental feature. Associative learning systems have been widely studied in cognitive science and artificial intelligence but are most commonly implemented in highly complex or carefully engineered systems, such as animal brains, artificial neural networks, DNA computing systems, and gene regulatory networks, among others. The ability to encode environmental information and use it to make simple predictions is a benchmark of biological resilience and underpins a plethora of adaptive responses in the living hierarchy, spanning prey animal species anticipating the arrival of predators to epigenetic systems in microorganisms learning environmental correlations. Given the ubiquitous and essential presence of learning behaviors in the biosphere, we aimed to explore whether simple, nonliving dissipative structures could also exhibit associative learning. Inspired by previous modeling of associative learning in chemical networks, we simulated simple systems composed of long- and short-term memory chemical species that could encode the presence or absence of temporal correlations between two external species. The ability to learn this association was implemented in Gray-Scott reaction-diffusion spots, emergent chemical patterns that exhibit self-replication and homeostasis. With the novel ability of associative learning, we demonstrate that simple chemical patterns can exhibit a broad repertoire of lifelike behavior, paving the way for in vitro studies of autonomous chemical learning systems, with potential relevance to artificial life, origins of life, and systems chemistry. The experimental realization of these learning behaviors in protocell or coacervate systems could advance a new research direction in astrobiology, since our system significantly reduces the lower bound on the required complexity for autonomous chemical learning.

Searching for Life, Mindful of Lyfe’s Possibilities

We are embarking on a new age of astrobiology, one in which numerous interplanetary missions and telescopes will be designed, built, and launched with the explicit goal of finding evidence for life beyond Earth. Such a profound aim warrants caution and responsibility when interpreting and disseminating results. Scientists must take care not to overstate (or over-imply) confidence in life detection when evidence is lacking, or only incremental advances have been made. Recently, there has been a call for the community to create standards of evidence for the detection and reporting of biosignatures. In this perspective, we wish to highlight a critical but often understated element to the discussion of biosignatures: Life detection studies are deeply entwined with and rely upon our (often preconceived) notions of what life is, the origins of life, and habitability. Where biosignatures are concerned, these three highly related questions are frequently relegated to a low priority, assumed to be already solved or irrelevant to the question of life detection. Therefore, our aim is to bring to the fore how these other major astrobiological frontiers are central to searching for life elsewhere and encourage astrobiologists to embrace the reality that all of these science questions are interrelated and must be furthered together rather than separately. Finally, in an effort to be more inclusive of life as we do not know it, we propose tentative criteria for a more general and expansive characterization of habitability that we call genesity.

Does Stochasticity Favour Complexity in a Prebiotic Peptide-Micelle System?

A primordial environment that hosted complex pre- or proto-biochemical activity would have been subject to random fluctuations. A relevant question is then: What might be the optimum variance of such fluctuations, such that net progress could be made towards a living system? Since lipid-based membrane encapsulation was undoubtedly a key step in chemical evolution, we used a peptide-micelle system in simulated experiments where simple micelles and peptide-stabilized micelles compete for the same amphiphilic lipid substrate. As cyclic thermal driver and energy source we used a thermochemical redox oscillator, to which the micelle reactions are coupled thermally through the activation energies. The long-time series averages taken for increasing values of the fluctuation variance show two distinct minima for simple micelles, but are smoothly increasing for complex micelles. This result suggests that the fluctuation variance is an important parameter in developing and perpetuating complexity. We hypothesize that such an environment may be self-selecting for a complex, evolving chemical system to outcompete simple or parasitic molecular structures.

The "Water Problem"(sic), the Illusory Pond and Life's Submarine Emergence-A Review

The assumption that there was a "water problem" at the emergence of life-that the Hadean Ocean was simply too wet and salty for life to have emerged in it-is here subjected to geological and experimental reality checks. The "warm little pond" that would take the place of the submarine alkaline vent theory (AVT), as recently extolled in the journal Nature, flies in the face of decades of geological, microbiological and evolutionary research and reasoning. To the present author, the evidence refuting the warm little pond scheme is overwhelming given the facts that (i) the early Earth was a water world, (ii) its all-enveloping ocean was never less than 4 km deep, (iii) there were no figurative "Icelands" or "Hawaiis", nor even an "Ontong Java" then because (iv) the solidifying magma ocean beneath was still too mushy to support such salient loadings on the oceanic crust. In place of the supposed warm little pond, we offer a well-protected mineral mound precipitated at a submarine alkaline vent as life's womb: in place of lipid membranes, we suggest peptides; we replace poisonous cyanide with ammonium and hydrazine; instead of deleterious radiation we have the appropriate life-giving redox and pH disequilibria; and in place of messy chemistry we offer the potential for life's emergence from the simplest of geochemically available molecules and ions focused at a submarine alkaline vent in the Hadean-specifically within the nano-confined flexible and redox active interlayer walls of the mixed-valent double layer oxyhydroxide mineral, fougerite/green rust comprising much of that mound.

Defining Lyfe in the Universe: From Three Privileged Functions to Four Pillars

Motivated by the need to paint a more general picture of what life is—and could be—with respect to the rest of the phenomena of the universe, we propose a new vocabulary for astrobiological research. Lyfe is defined as any system that fulfills all four processes of the living state, namely: dissipation, autocatalysis, homeostasis, and learning. Life is defined as the instance of lyfe that we are familiar with on Earth, one that uses a specific organometallic molecular toolbox to record information about its environment and achieve dynamical order by dissipating certain planetary disequilibria. This new classification system allows the astrobiological community to more clearly define the questions that propel their research—e.g., whether they are developing a historical narrative to explain the origin of life (on Earth), or a universal narrative for the emergence of lyfe, or whether they are seeking signs of life specifically, or lyfe at large across the universe. While the concept of “life as we don’t know it” is not new, the four pillars of lyfe offer a novel perspective on the living state that is indifferent to the particular components that might produce it.