Origins of life: a problem for physics, a key issues review

“There are some hints toward a potentially deep connection between information and thermodynamics due to the math­ ematical relationship between Shannon [186] and Boltzmann entropies [187].”

“This is significant as many biological systems, including meta­ bolic chemical reaction networks display similar topological properties [35].”

“Discovering ‘shadow life’ is not without precedent: archaea were once entirely unknown, until finally discovered as the third domain of life by 16S RNA sequencing (almost 300 years after the discovery of bacteria) [29].”

“In 1953 Miller demonstrated that organic molecules, including amino acids, could be synthesized in a simple spark­discharge experiment under reducing conditions [41].”

“The hypothesis that ancestral genetic systems were based on solely on RNA is called the “RNA world” [49].”

“taken into account. A commonly cited constraint is the error-threshold (see e.g. [72]), which places limits on the error-rate permitted for the information content of genetic systems to be heritable [73]. However, the concept of an error-threshold as proposed by Eigen and Schuster assumes that all molecules in a popul…”

“12 Here I follow the example of England in his rough sketch of the entropy production for a self­replicator coupled to a heat bath [124] to illustrate the approach, which leverages recent advances in non­equilibrium thermodynamics through the development of fluctuation theorems [127, 128].”

“Belief that progress in biology will come from shifting the conceptual basis from matter and energy flows to the abstract realm of information is becoming increasingly recognized [9, 46, 161, 166, 180, 181].”

“Popular among this set of hypotheses is that life first emerged in a hydrothermal vent system [116], perhaps not too unlike the black smokers found in Lost City [115].”

“ty of living matter, where living systems are often argued to be poised at the critical point between order and disorder (colloquially this is sometimes phrased as \poised at the edge of chaos") [133, 135, 134, 136, 137]. It is an open question how criticality in biological systems maps to our understanding of si…”

“Recent progress however has been made in synthesizing both purine and pyridine ribonucleotides in so­called ‘one­shot’, or multi­ component, experiments by the Sutherland lab [51, 52].”

“uld is chemical synthesis of organic molecules be thermodynamically favored? Much research in this direction has focused on the \iron-sulfur" world hypothesis as rst proposed by Wachtershauser [117], wherein life is proposed to have rst emerged in a hydrothermal vent at high pressure and high temperature. Under t…”

“Major transitions in evolution include the origin of eukaryotes, multicellularity, and eusocial and linguistic societies [184].”

“LUCA in reality should be thought of as community of organisms undergoing rapid horizontal exchange of genetic information, rather than an individual cell or species as the name might imply [20].”

“Such enantiomeric cross-inhibition is an essential aspect of producing homochirality in the original Frank model [141], from”

“This surface based, carbon-fixation metabolism could become network autocatalytic through the formation of a metabolic cycle in the form of an ancestral sulfur-dependent version of the reductive citric acid cycle (reverse TCA) [118].”

“For example, synthetic biology has already demonstrated that components of the chemistry of life can be expanded to molecules that are not biological in origin, such as unnatural base pairs [44] or alternative nucleic acids [45].”

“There have also been experimental demonstrations of autocatalytic sets of nucleotide­based polymers, including two­member sets [92, 93].”

“Many elementary steps in the iron-sulfur world hypothesis have been experimentally confirmed [121, 122].”

“The RNA­first view has thus far primarily held sway because of its simplicity, as well as the relative ease of studying RNA systems in the labo­ ratory as empirical models for exploring molecular evolution [56, 57], however new approaches are broadening this view.”

“A more formal definition of RAF sets is provided in [11,10], where we also introduced a polynomial-time (in the size of the reaction set R) algorithm for finding RAF sets in a general CRS Q = {X, R, C}.”

“There have also been experimental demonstrations of autocatalytic sets of nucleotide­based polymers, including two­member sets [92, 93].”

“[125]) and has been applied to origin of life models [129].”

“This perspective defines life as a direct outcome of planetary geochemistry [113, 114].”

“Even in the context of the RNA­world, the first role of RNA may not have been templated polymerization, RNA is known to undergo recombination and can spontaneously form networks [77]– perhaps the earliest roles for RNA were not strictly confined to a ‘DNA­like’ role.”

“as sub-networks that form units of heredity (as analogs of “genes”) in the evolution of autocatalytic sets [97].”

“Historically, the origin of life has been viewed as a problem for chemistry [1, 2, 3].”

“emerge from theories, not the converse [37].”

“This surface based, carbon-fixation metabolism could become network autocatalytic through the formation of a metabolic cycle in the form of an ancestral sulfur-dependent version of the reductive citric acid cycle (reverse TCA) [118].”

“2 It should be noted that while it is clear that the tree of life has a common root, it is not as clear where to place the root [22]).”

“Reproduction of the physical system occurs when those instructions specify how to construct the UC itself (this provides a physical mechanism for self­referential dynam­ ics [4, 5, 170], one of the hallmarks in table 2).”

“Six XNAs have recently been shown to be viable functioning polymers, capable of Darwinian evolution, aptamer activity [45] and even catalysis [69].”

“Additional support for this view comes from the fact that alternative nucleic acids or XNAs, such as peptide nucleic acid (PNA) [67] or threose nucleic acid (TNA) [68], are easier to synthesize under prebiotic conditions than RNA.”

“With the discov­ eries of Kepler [30] and other searches, hundreds of worlds have been discovered.”

“This argument, combined with increasingly frequent discov­ eries of ‘Earth­like’ worlds [15, 16], has lead many astrobi­ ologists to be optimistic that life should be common in the universe.”

“Farmer et al estimated the critical probability for this phase transition to occur to be [84]:”

“This argument, combined with increasingly frequent discov­ eries of ‘Earth­like’ worlds [15, 16], has lead many astrobi­ ologists to be optimistic that life should be common in the universe.”

“Physical sys­ tems encoding the information necessary to replicate fast will do so at an exponential rate [130], whereas sequences of sim­ ilar length that contain no fitness­relevant information will die.”

“As far as we know, life requires chemistry, but the properties of the living state emerge from the dynamical properties of that chemistry, including the temporal and spatial organization of chemical networks and the resultant information flows [181].”

“Salam first suggested that there should be a critical temper­ ature, Tc, above which any net chirality is destroyed in a prebi­ otic system [154].”

“Evidence for this common ancestry derives from phylogenetic reconstruction of the history of life on Earth, as inferred from modern organ­ isms [21]2.”

“the same abstract chemical space in a computational experiment, which is more likely to arise spontaneously - and under what assumptions? Could this then be tested in the lab? It may likely turn out that these hypotheses are not wholly independent – for example, catalytic sets and replicators both rely on the concept…”

“[23]), we do not have direct evidence for this and it does not change the nature of the anthropic selection arguments presented here in any case—for that, all that matters is there is a universal ancestry for extant life.”

“The original model of Kauffman considered the self-organization autocatalytic sets of proteins, and indeed a autocatalytic network of small peptides has now been confirmed in the laboratory [92].”

“An analogy to ‘my grand­ father’s axe’ has been made for the process of chemical evo­ lution of other genetic polymers that could have preceded even RNA [59].”

“Many of the most common definitions for life may be found compiled by Trifonov [38].”

“[71]), which places limits on the error­rate permitted for the information content of genetic systems to be heritable [72].”

“Reproduction of the physical system occurs when those instructions specify how to construct the UC itself (this provides a physical mechanism for self­referential dynam­ ics [4, 5, 170], one of the hallmarks in table 2).”

“Thus, the environment and selective pressures must be included in any discussion of the origins of life that aims to account for how simple chemical systems could increase in complexity over time [78].”

“A now classic example in the molecular evolution literature is Spiegelman’s monster, a 4500 nucleotides RNA virus evolved in vitro, which through competitive selection on replication evolved to be as short as 218 bases (the ‘monster’) [79].”

“constituents, or even other elements [27].”

“In this picture, the biosphere emerged as a direct outgrowth of the geosphere [7], driven by energy flows that generated structure at multiple hierarchical scales [111].”

“Approximations are known to exist – for example, the logical architecture of the cell has been equated to that of a UC on numerous occasions (see for example [172]).”

“it is proposed that chemical synthesis reactions could then produce more complex organic compounds, bifurcating down energy-releasing pathways to produce molecules of increasing complexity (see e.g. [120]). Genetic systems would have emerged later, as a CONTENTS 22 product of these kinds of synthesis reactions. Many e…”

“If true, life could be detected in the atmosphere of an exoplanet with the next generation of telescopes, such as the James Webb Space Telescope [17].”

“This is the key idea behind the philosophical concept of top-down causation [5, 170, 193].”

“Studies of real ribozymes demonstrate selectively neutral landscapes, leading to a relaxed error threshold when one accounts for selection on the phenotype of the molecule [74].”

“Additional support for this view comes from the fact that alternative nucleic acids or XNAs, such as peptide nucleic acid (PNA) [67] or threose nucleic acid (TNA) [68], are easier to synthesize under prebiotic conditions than RNA.”

“However, this model turns out over-estimate the likelihood of forming an autocatalytic set, and as pointed out by Lifson, would require an exponentially increasing level of catalysis with system size [86].”

“Here, we consider an explicit example where chiral symmetry breaking is con­ trolled by reaction fidelity to illustrate general mechanisms, utilizing the set of heterochiral polymerization reactions as proposed by Sandars [146]: + + L L L n k”

“ere favorable) is equally consistent with life being very common and also with it being exceptionally rare [24]. Spiegel and Turner later did a more formal analysis and arrived at the same conclusion [25]. Here I follow the reasoning of Carter’s original logic, which relies on Bayes theorem, and relays the essential p…”

“It was later shown within the context of RAF theory that only a quadratic [86] or even a linear [83, 87] Figure 2.”

“This suggests potential evolutionary pathways whereby one RAF set could transition to another [89].”

“Belief that progress in biology will come from shifting the conceptual basis from matter and energy flows to the abstract realm of information is becoming increasingly recognized [9, 46, 161, 166, 180, 181].”

“Nowak and collaborators, for example, have quantified an abrupt ‘phase transition’ from ‘pre­life’ to ‘life’ associated with the emergence of replicators with high fidelity [157].”

“Due to the ambiguity associated with many putative biosignatures REF and the very real potential for detecting false positives for life [31], the state of the art in exoplanet life detection is currently focused on identifying a suite of biosignature gases, combined with deep knowledge of planetary context.”

“The prob­ lem of continued growth in complexity via open­ended pro­ cesses is therefore dubbed a ‘millenial prize problem’ in the artificial life community [89].”

“sequence of nucleobases), or simple physical systems such at that proposed by Penrose and Penrose that can reproduce their own state [168].”

“During the emergence of life, a process driving increasing complexity with time was necessary [175].”

“In particular, a key challenge in identifying mech anisms of heredity is to better understand how dynamic networks store and process information [101, 102].”

“Programmable constructors do not necessarily operate on a universality class of objects, but through interaction with other physical systems can be “programmed” to perform specific physical transformations [169].”

“[151, 152] for two recent examples that do not need to include inhibitory feedback and instead rely on noise).”

“For example, autocatalytic sets have been found within the metabolic network of Escherichia coli [109].”

“the same abstract chemical space in a computational experiment, which is more likely to arise spontaneously - and under what assumptions? Could this then be tested in the lab? It may likely turn out that these hypotheses are not wholly independent – for example, catalytic sets and replicators both rely on the concept…”

“For one, understanding the origin and nature of life may not be separable problems as often thought [8]: windows into one will likely provide important insights into the other.”

“There are a number of models in recent years that begin to blur the boundary between ‘genetics’ and ‘metabolism’, for example in metabolic­replicator models as in [55, 107, 108].”

“For example, it has been shown that RNA can exchange information (template) with glycerol nucleic acid (GNA) or TNA, but TNA and GNA cannot directly exchange information with one­another [68].”

“e structure of living systems that remains to be fully explicated. We next discuss a few of these hallmarks, focusing on the concept of non-trivial replication (for more extensive discussion see e.g. [5, 170]). 6.2. Life as (programmable) constructors von Neumann was one of the rst to consider the active role informat…”

“Other planetary atmospheres, such as those of Mars, Venus and Titan, are more homogenous in their network organization, with global topology more consistent with ran­ dom networks [33].”

“relevant equation for the fraction of a replicating population that dies each generation due to deleterious mutations (the mutational load) is [76]:”

“The Sandars model can be truncated to N = 2 and still maintain all essential features of the dynamics leading to homochiralization [144], allowing one to model the reaction network utilizing tools of mean-field theory to characterize spontaneous chiral symmetry breaking [145].”

“The distinction between copying and programmable construction forms the core of distinguishing between trivial and non­ trivial replication [5, 174]—that is between copying and con­ struction, respectively.”

“to spontaneously self-organize [78], and was been formally demonstrated to be network autocatalytic [95].”

“That is, life should have emerged on Earth where there were opportunities for catalysis to expedite the release of chemical energy, for example in water–rock–organic systems [113].”

“A related question is whether homochirality preceded life or is a byproduct of it [156], in other words did this kind of symmetry breaking occur”

“In fitness landscapes where there exist lethal mutations, no error threshold is observed [74].”

“An example, attempting to unify the concept of catalytic networks with the emergence of genetic systems is provided by Kaneko and collaborators [103, 104].”

“also found the spontaneous formation of autocatalytic sets in a stochastic kinetic model to be a rare occurrence [98].”

“A very simple kinetic example was demonstrated in [95], showing that irreducible RAF sets (irrRAFS), defined as a RAF that cannot be reduced without loosing the RAF property (contains no subRAFs), can spontaneously form, and be outcompeted by subsequent irrRAFs that emerge later (thus suggesting evolutionary pro­ gres…”

“Due to these limitations, there has been increased interest in studying the origin of life not strictly as a problem for chemistry (or biology), but as a problem for physics [4, 5, 6, 7], with potentially deep implications for our most fundamental understanding of the natural world.”

“Feedback between the composition of replicators and their environment could also act to regulate selection dynamics to maintain heritability [77, 54].”

“between scales of organization [177] that do not generally permit this layer-by-layer decomposition of causation (information flows from ’higher’ to ’lower’ levels).”

“He recognized that copying information (even with mutation and selection) is not sufficient to generate the complexity of of living systems (which he hoped to emulate in artificial systems), but instead the concept of constructability must additionally be introduced [160, 166].”

“It has been hypothesized that re­organization of information, including new modes of storage and processing, drive these transitions [183] where the boundary of ‘individual’ too may change during the transition [184].”

“The unifying conceptual basis across these transitions is information, and it may in fact be that transitions in information flows (perhaps with the emer­ gence of new constructors or programs, see below) are pre­ cisely what drives such jumps in complexity [185].”

“Panspermia potentially increases the window of time within which the origin of life might have occurred [19], but adds its own complications in that it places the origin of life in an unknown environment that is even less constrained than what little we know about the environments on the early Earth.”

“An example, attempting to unify the concept of catalytic networks with the emergence of genetic systems is provided by Kaneko and collaborators [103, 104].”

“Life not only copies information but also uses it to construct itself [176] and can utilize information to construct other objects.”

“More work remains to be done to understand the dynamic emergence of separation of information storage and processing and its role in the evolvability of networks and the role of controllability [101].”

“We reported a similarly abrupt, but spontaneous transition in Mathis et al where the relevant order parameter is associated with the tuning of replicators to their environ ment [54].”

“The spatiotemporal dynamics of a chiral reaction network can be equated to a two­phase system undergoing a symmetry­breaking phase transition, where the order param­ eter is the net chiral asymmetry (A) [144, 145].”

“There are a number of models in recent years that begin to blur the boundary between ’genetics’ and ’metabolism’, for example in metabolic-replicator models as in [55, 107, 108].”

“[151, 152] for two recent examples that do not need to include inhibitory feedback and instead rely on noise).”

“Feedback between the exoplanet and origins of life communities need not go in one direction either: understanding planetary atmospheres of inhabited and uninhabited worlds could also help inform our understanding of chemical organization within living systems by providing null chemical models for their large scale org…”

“Parameters relevant to generating chiral asymmetry include fidelity of enzymatic reactions [146, 148], ratios of reaction rates [147], stereoselectivity [149], total system mass [150] and even stochastic noise [151, 152].”

“Defining heredity, for example, remains a challenge [98].”

“While there exist many models describing how homochirality may have emerged in prebiotic systems, the qualitative features of the majority of these models are similar: chiral symmetry breaking occurs due to the introduction of instabilities to the symmetric state (containing both chiral forms) that lead to spontaneous…”

“Nonetheless, given the present stage of understanding and lack of data, the possibilities for P(life jEarth-like) range from life being very common to very rare, as has been much discussed in the literature (e.g., Carter, 1983; Spiegel and Turner, 2012; Scharf and Cronin, 2016; Walker, 2017).”

“Physics Motion of mass and electromagnetic energy, quantum behavior, organization, dissipative structures, collective behavior, emergence, information, networks, molecular machines (Schrodinger, 1943; Goldenfeld and Woese, 2011; Walker, 2017) Conservation laws to constrain abiotic context.”

“Information-theoretical concepts have also been considered relevant in this context [477– 480].”

“to physics are adequate to solve this problem, or if new physics is necessary [11].”

“Despite these inherent uncertainties, the availability of free energy (Schrödinger, 1944; Deamer, 1997; Dyson, 1999; Pascal et al., 2013; Walker, 2017) is widely regarded as a necessary requirement for abiogenesis to take place.”

“Energy source for prebiotic chemistry The origin of life required suitable energy sources for the synthesis of prebiotic compounds (Ehrenfreund et al. 2002; Morowitz & Smith 2007; Luisi 2016; Walker 2017).”

“While life’s information storage and processing systems are often based on different material compositions (material level), each of these achieves greater efficiency or robustness through principles that are very general, such as error correction, sparse coding, and fractal architectures (Flack 2017; Davies and Walke…”

“Proposed mechanisms for the emergence of homochirality were reviewed from a physics perspective by Walker (2017) and Goldenfeld et al. (2017).”

“The issue of whether abiogenesis is an ‘easy’ or a ‘hard’ phenomenon remains currently unresolved (Walker 2017), but resolving this question will have important implications for gauging the likelihood of extraterrestrial life (Lineweaver and Davis 2002; Davies 2003; Spiegel and Turner 2012; Chen…”

“Indeed, energetic processes bear natural relevance to the origin of homochirality, as intense chemical and energetic environments with steep non-equilibrium gradients are thought to have conditioned the rise of self-adaptive chemical processes conjectured to predate modern living systems [19].”

“To understand this transition, one must study the dynamics in sequence space, which emerges when mononucleotides and short oligonucleotides inside a reaction volume collectively self-assemble into longer strands [28,29].”

“, 2016), theoretical and experimental breakthroughs in resolving the question of how life originated on our planet (Walker, 2017; Lingam and Loeb, 2021), advances in comprehending how Earth’s biogeochemical cycles have coevolved over time and the ensuing implications for our biosphere (Knoll and Nowak, 2017), among ma…”

“During the last decade, there has been some increased interest in the role of fluctuations; see a recent review by Walker (2017).”

“In astrobiology, Bayesian techniques are being increasingly employed in a diverse array of settings ranging from Earth to exoplanets ( e.g., Waltham 2011; Spiegel & Turner 2012; Walker 2017; Chen & Kipping 2018; Balbi & Grimaldi 2020; Kipping 2020; Truitt et al. 2020 ) .”

“…are so special that they have led some physicists to claim that new laws of physics are needed to explain them (e.g. Walker and Davies, 2013; Walker, 2017), prompting a response that showed how recasting the process of living as information processing enabled these properties to be…”

“Considering life as an emergent process taking place through the combination of different parts of a system, as normally taken in a reductionist approach [4], leads to difficulties in identifying the pathway by which the main features of life could have emerged.”

“In contrast, the origin of life remains an arguably bigger mystery and a number of competing hypotheses exist based on geochemical, physiological, and genomic considerations to name a few (Luisi 2016; Smith & Morowitz 2016; Walker 2017).”

“Specifically, our proposal is that what most distinguishes living systems is their causal and informational architecture (see, e.g., Walker (2017)) and that modern information measures, such as transfer entropy (Schreiber 2000), causal information flow (Ay and Polani 2008), effective information…”

“Whilethere is no universally valid definition of life that cannot be further questioned (Cleland and Chyba, 2002; Walker, 2017), now is the time to take the broadest look possible.”

“Phys . review [41]): nevertheless, it seems that we are now finding that Aristotle is not as wrong as we thought he was.”

“ion Numerous articles deal with the environmental and physicochemical conditions for -, and with the chemical reactions at the establishment of life on planet Earth, or somewhere else in the universe [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11]. Many of the suggestions are inspired by Darwin, and link these conditions and reac…”

“Modulating system complexity may allow us to improve the performance and scope of evolutionary processes (Mitchell et al., 1993; Walker, 2017).”

“This probability is therefore currently unconstrained and will continue to be unconstrained until we make a detection of alien life, rule out the possibility of life on some habitable worlds, or the mechanism for the origin of life on a planetary body is solved ( S. I. Walker 2017 ) .”

“…1983; Foote et al., 2023; Lineweaver, 2022; Lingam et al., 2023b; Lingam and Loeb, 2021; Spiegel and Turner, 2012; Verendel and Häggström, 2017; Walker, 2017), although they were not geared towards casting such statements into an explicit mathematical form insofar as p Lc speci fi cally is…”

“ena [10, 16, 106, 107], while the concept of catalytic closure in autocatalytic sets [11, 42] is rooted in that of critical transitions observed in random graph theory [108].”

“Walker and Davies have recently argued that the problem is more rooted in basic physics or mathematics than in biochemistry [2, 3].”

“In that context, some argue that physics is due to resolve the standing problems about life and its origin by explaining this phenomenon under a universal theory of life (Walker 2017).”

“Modulating system complexity may allow us to improve the performance and scope of evolutionary processes (Mitchell et al., 1993; Walker, 2017).”

“One fairly recent and unifying idea is that life is driven by information [1,2].”

“Various physics-based analyses have been conducted, such as in light of Bayesian probability, thermodynamics, and critical phenomena [41].”

“Physicists had been eager to find some fundamental concepts in this charmingly complex world [3–12].”

“It is hence desirable to develop a novel evolutionary theory which can integrate with research advances in multiple disciplines and explain some evolutionary conundrums in a comprehensive and comprehensible way [1-13].”

“Charles Darwin's theory, the Modern Synthesis, and some other evolutionary theories were largely extrapolated from microevolution (evolution within species) [1-16].”

“Moreover, these theories cannot integrate with multiple challenges identified in recent decades: evolution of many species showed the punctuated equilibrium tempo with little change in long geological periods and significant changes in short geological periods; many genetical mutations are neutral or even harmful in n…”

“The nature of this original accessible energy source and the initial equilibrium conditions remain unknown, though several hypotheses have been proposed (Walker, 2017).”

“Various physics-based analyses have been conducted, such as in light of Bayesian probability, thermodynamics, and critical phenomenon (Walker, 2017).”

“Instead, it represents a gradational evolution, what some describe as a continuum of increasing persistence, organization, and adaptability (Walker 2017 ; Shapiro 2006).”