arXiv subjects

Sara Imari Walker

Publications and source records attributed to Sara Imari Walker.

At least 19 recordsLinked to original sources

arXiv2026

Metrology of Complexity and Implications for the Study of the Emergence of Life

One of the longest standing open problems in science is how life arises from non-living matter. If it is possible to measure this transition in the lab, then it might be possible to understand the physical mechanisms by which the emergence of life occurs, which so far have evaded scientific understanding. A significant hurdle is the lack of standards or a framework for cross comparison across different experimental contexts and planetary environments. In this essay, I review current challenges in experimental approaches to origin of life chemistry, focusing on those associated with quantifying experimental selectivity versus de novo generation of molecular complexity, and I highlight new methods using molecular assembly theory to measure molecular complexity. This metrology-centered approach can enable rigorous testing of hypotheses about the cascade of major transitions in molecular order marking the emergence of life, while potentially bridging traditional divides between metabolism-first and genetics-first scenarios. Grounding the study of life's origins in measurable complexity has significant implications for the search for life beyond Earth, suggesting paths toward theory-driven detection of biological complexity in diverse planetary contexts. As the field moves forward, standardized measurements of molecular complexity may help unify currently disparate approaches to understanding how matter transforms to life. Much remains to be done in this exciting frontier.

q-bio.BM↗

arXiv2025

A Firefly-inspired Model for Deciphering the Alien

The Search for Extraterrestrial Intelligence (ETI) is, historically, a search for aliens like us, inspired by human centric ideas of intelligence and technology. However, humans are not the only instance of an intelligent, communicating species on Earth, and thus not guide to how we might think about ETI. Here, we explore the potential for the study of non-human species to inform new approaches in SETI research, using firefly communication patterns as an illustrative example. Fireflies communicate their presence through evolved flash patterns distinct from complex visual backgrounds. Extraterrestrial signals may also be identifiable not by their complexity or decodable content, but by the structural properties of the signal, as currently being explored in efforts to decode communication in non-human species across our biosphere. We present a firefly-inspired model for detecting potential technosignatures within environments dominated by ordered astronomical phenomena, such as pulsars. Using pulsar data from the Australia Telescope National Facility, we generate simulated signals that exhibit evolved dissimilarity from the surrounding pulsar population. This approach shifts focus from anthropocentric assumptions about intelligence toward recognizing communication through its fundamental structural properties, specifically, evolutionarily optimized contrast with natural backgrounds. Our model demonstrates that alien signals need not be inherently complicated nor need we decipher their meaning to identify them; rather, signals might be distinguishable as products of selection. We discuss implications for broadening SETI methodologies, leveraging the diverse forms of intelligence found on Earth.

astro-ph.IM↗

arXiv2025

The Emergence of Chirality from Metabolism

Molecular chirality is critical to biochemical function, but it is unknown when chiral selectivity first became important in the evolutionary transition from geochemistry to biochemistry during the emergence of life. Here, we identify key transitions in the selection of chiral molecules in metabolic evolution, showing how achiral molecules (lacking chiral centers) may have given rise to specific and abundant chiral molecules in the elaboration of metabolic networks from geochemically available precursor molecules. Simulated expansions of biosphere-scale metabolism suggest new hypotheses about the evolution of chiral molecules within biochemistry, including a prominent role for both achiral and chiral compounds as nucleation sites of early metabolic network growth, an increasing enrichment of molecules with more chiral centers as these networks expand, and conservation of broken chiral symmetries along reaction pathways as a general organizing principle. We also find an unexpected enrichment in large, non-polymeric achiral molecules. Leveraging metabolic data of 40,023 genomes and metagenomes, we analyzed the statistics of chiral and achiral molecules in the large-scale organization of metabolism, revealing a chiral-enriched phase of network organization evidenced by system-size dependent chiral scaling laws that differ for individuals and ecosystems. By uncovering how metabolic networks could lead to chiral selection, our findings open new avenues for bridging metabolism and genetics-first approaches to the origin of chirality, allowing tools for better timing of major transitions in molecular organization during the emergence of life, understanding the role of chirality in extant and synthetic metabolisms, and informing targets for chirality-based biosignatures.

q-bio.MN↗

arXiv2025

A Complex Systems Approach to Exoplanet Atmospheric Chemistry: New Prospects for Ruling Out the Possibility of Alien Life-As-We-Know-It

The near-term capability to characterize terrestrial exoplanet atmospheres may bring us closer to discovering alien life through atmospheric data. However, remotely detectable candidate biosignature gases are subject to false positive signals because they can also be produced abiotically, raising a critical need to develop methods to determine whether a gas is produced abiotically or not. To distinguish biological, abiotic and anomalous sources (unidentified as abiotic or biotic) of biosignature gases, we take a complex systems approach implementing chemical reaction network analysis of planetary atmospheres. We simulated 30,000 terrestrial atmospheres, organized in two datasets: Archean Earth-like worlds and modern Earth-like worlds. For Archean Earth-like worlds we study cases where CH4 is produced abiotically via serpentinization, biologically via methanogenesis, or from anomalous sources. We also simulate modern Earth-like atmospheres with and without industrial CFC-12. We show how network properties can effectively distinguish scenarios where CH4 is produced from methanogenesis and serpentinization. Network analysis also distinguishes modern Earth-like atmospheres with CFC-12 from those without it. Using Bayesian analysis, we demonstrate how atmospheric network statistics can provide stronger confidence for ruling out biological explanations compared to gas abundance statistics alone. Our results confirm how a network theoretic approach allows distinguishing hypotheses about biological, abiotic and anomalous atmospheric drivers, and importantly, allows ruling out life-as-we-know-it as a possible explanation. We conclude with a discussion of how further developing statistical inference methods for spectral data that incorporate network properties could significantly strengthen future biosignature detection efforts.

astro-ph.EP↗

arXiv2022

A Relational Macrostate Theory Guides Artificial Intelligence to Learn Macro and Design Micro

The high-dimesionality, non-linearity and emergent properties of complex systems pose a challenge to identifying general laws in the same manner that has been so successful in simpler physical systems. In Anderson's seminal work on why "more is different" he pointed to how emergent, macroscale patterns break symmetries of the underlying microscale laws. Yet, less recognized is that these large-scale, emergent patterns must also retain some symmetries of the microscale rules. Here we introduce a new, relational macrostate theory (RMT) that defines macrostates in terms of symmetries between two mutually predictive observations, and develop a machine learning architecture, MacroNet, that identifies macrostates. Using this framework, we show how macrostates can be identifed across systems ranging in complexity from the simplicity of the simple harmonic oscillator to the much more complex spatial patterning characteristic of Turing instabilities. Furthermore, we show how our framework can be used for the inverse design of microstates consistent with a given macroscopic property -- in Turing patterns this allows us to design underlying rule with a given specification of spatial patterning, and to identify which rule parameters most control these patterns. By demonstrating a general theory for how macroscopic properties emerge from conservation of symmetries in the mapping between observations, we provide a machine learning framework that allows a unified approach to identifying macrostates in systems from the simple to complex, and allows the design of new examples consistent with a given macroscopic property.

cs.AI↗

arXiv2022

False positives and the challenge of testing the alien hypothesis

The origin of life and the detection of alien life have historically been treated as separate scientific research problems. However, they are not strictly independent. Here, we discuss the need for a better integration of the sciences of life detection and origins of life. Framing these dual problems within the formalism of Bayesian hypothesis testing, we show via simple examples how high confidence in life detection claims require either (1) a strong prior hypothesis about the existence of life in a particular alien environment, or conversely, (2) signatures of life that are not susceptible to false positives. As a case study, we discuss the role of priors and hypothesis testing in recent results reporting potential detection of life in the Venusian atmosphere and in the icy plumes of Enceladus. While many current leading biosignature candidates are subject to false positives because they are not definitive of life, our analyses demonstrate why it is necessary to shift focus to candidate signatures that are definitive. This indicates a necessity to develop methods that lack false positives, by using observables for life that rely on prior hypotheses with strong theoretical and empirical support in identifying defining features of life. Abstract theories developed in pursuit of understanding universal features of life are more likely to be definitive and to apply to life-as-we-don't-know-it. In the absence of alien examples these are best validated in origin of life experiments, substantiating the need for better integration between origins of life and biosignature science research communities.

astro-ph.EP↗

arXiv2021

Inferring Exoplanet Disequilibria with Multivariate Information in Atmospheric Reaction Networks

Inferring the properties of exoplanets from their atmospheres, while confronting low resolution and low signal-to-noise in the context of the quantities we want to derive, poses rigorous demands upon the data collected from observation. Further compounding this challenge is that inferences of exoplanet properties are built from forward models, which can include errors due to incomplete or inaccurate assumptions in atmospheric physics and chemistry. The confluence of observational noise and model error makes developing techniques to identify predictive features that are robust to both low s/n and model error increasingly important for exoplanet science. We demonstrate how both issues can be addressed simultaneously by taking advantage of underutilized multivariate information already present in current atmospheric models, including thermodynamic statistics and reaction network structure. To do so, we provide a case study of the prediction of vertical mixing (parameterized as eddy diffusion) in hot Jupiter atmospheres and show how prediction efficacy depends on what model information is used - e.g. chemical species abundances, network statistics, and/or thermodynamic statistics. We also show how the variables with the most predictive power vary with planetary properties such as temperature and metallicity. Our results demonstrate how inferences built on single metrics do not have utility across all possible use cases. We also show how statistical measures derived from network analyses tend to be better predictors when accounting for the possibility of missing data or observational uncertainty. We discuss future directions applying multivariate and network model information as a framework for increasing confidence in inferences aimed at extracting features relevant to exoplanet atmospheres and future applications to the detection of life on terrestrial worlds.

astro-ph.EP↗

arXiv2020

Detectability of Life Using Oxygen on Pelagic Planets and Water Worlds

The search for life on exoplanets is one of the grand scientific challenges of our time. The strategy to date has been to find (e.g., through transit surveys like Kepler) Earth-like exoplanets in their stars habitable zone, then use transmission spectroscopy to measure biosignature gases, especially oxygen, in the planets atmospheres (e.g., using JWST, the James Webb Space Telescope). Already there are more such planets than can be observed by JWST, and missions like the Transiting Exoplanet Survey Satellite and others will find more. A better understanding of the geochemical cycles relevant to biosignature gases is needed, to prioritize targets for costly follow-up observations and to help design future missions. We define a Detectability Index to quantify the likelihood that a biosignature gas could be assigned a biological vs. non-biological origin. We apply this index to the case of oxygen gas, O2, on Earth-like planets with varying water contents. We demonstrate that on Earth-like exoplanets with 0.2 weight percent (wt%) water (i.e., no exposed continents) a reduced flux of bioessential phosphorus limits the export of photosynthetically produced atmospheric O2 to levels indistinguishable from geophysical production by photolysis of water plus hydrogen escape. Higher water contents >1wt% that lead to high-pressure ice mantles further slow phosphorus cycling. Paradoxically, the maximum water content allowing use of O2 as a biosignature, 0.2wt%, is consistent with no water based on mass and radius. Thus, the utility of an O2 biosignature likely requires the direct detection of both water and land on a planet.

astro-ph.EP↗

arXiv2017

The Emergence of Life as a First Order Phase Transition

It is well known that life on Earth alters its environment over evolutionary and geological timescales. An important open question is whether this is a result of evolutionary optimization or a universal feature of life. In the latter case, the origin of life would be coincident with a shift in environmental conditions. Here we present a model for the emergence of life in which replicators are explicitly coupled to their environment through the recycling of a finite supply of resources. The model exhibits a dynamic, first-order phase transition from non-life to "life," where the life phase is distinguished by selection on replicators. We show that environmental coupling plays an important role in the dynamics of the transition. The transition corresponds to a redistribution of matter in replicators and their environment, driven by selection on replicators, exhibiting an explosive growth in diversity as replicators are selected. The transition is accurately tracked by the mutual information shared between replicators and their environment. In the absence of successfully repartitioning system resources, the transition fails to complete, leading to the possibility of many frustrated trials before life first emerges. Often, the replicators that initiate the transition are not those that are ultimately selected. The results are consistent with the view that life's propensity to shape its environment is indeed a universal feature of replicators, characteristic of the transition from non-life to life. We discuss the implications of these results for understanding life's emergence and evolutionary transitions more broadly.

nlin.AO↗

arXiv2017

An information-based classification of Elementary Cellular Automata

A novel, information-based classification of elementary cellular automata is proposed that circumvents the problems associated with isolating whether complexity is in fact intrinsic to a dynamical rule, or if it arises merely as a product of a complex initial state. Transfer entropy variations processed by the system split the 256 elementary rules into three information classes, based on sensitivity to initial conditions. These classes form a hierarchy such that coarse-graining transitions observed among elementary cellular automata rules predominately occur within each information- based class, or much more rarely, down the hierarchy.

cs.CC↗

arXiv2016

The "Hard Problem" of Life

Chalmer's famously identified pinpointing an explanation for our subjective experience as the "hard problem of consciousness". He argued that subjective experience constitutes a "hard problem" in the sense that its explanation will ultimately require new physical laws or principles. Here, we propose a corresponding "hard problem of life" as the problem of how `information' can affect the world. In this essay we motivate both why the problem of information as a causal agent is central to explaining life, and why it is hard - that is, why we suspect that a full resolution of the hard problem of life will, similar to as has been proposed for the hard problem of consciousness, ultimately not be reducible to known physical principles.

q-bio.OT↗

arXiv2015

The Descent of Math

A perplexing problem in understanding physical reality is why the universe seems comprehensible, and correspondingly why there should exist physical systems capable of comprehending it. In this essay I explore the possibility that rather than being an odd coincidence arising due to our strange position as passive (and even more strangely, conscious) observers in the cosmos, these two problems might be related and could be explainable in terms of fundamental physics. The perspective presented suggests a potential unified framework where, when taken together, comprehenders and comprehensibility are part of causal structure of physical reality, which is considered as a causal graph (network) connecting states that are physically possible. I argue that in some local regions, the most probable states are those that include physical systems which contain information encodings - such as mathematics, language and art - because these are the most highly connected to other possible states in this causal graph. Such physical systems include life and - of particular interest for the discussion of the place of math in physical reality - comprehenders capable of making mathematical sense of the world. Within this framework, the descent of math is an undirected outcome of the evolution of the universe, which will tend toward states that are increasingly connected to other possible states of the universe, a process greatly facilitated if some physical systems know the rules of the game. I therefore conclude that our ability to use mathematics to describe, and more importantly manipulate, the natural world may not be an anomaly or trick, but instead could provide clues to the underlying causal structure of physical reality.

physics.hist-ph↗

arXiv2015

The Informational Architecture Of The Cell

We compare the informational architecture of biological and random networks to identify informational features that may distinguish biological networks from random. The study presented here focuses on the Boolean network model for regulation of the cell cycle of the fission yeast Schizosaccharomyces Pombe. We compare calculated values of local and global information measures for the fission yeast cell cycle to the same measures as applied to two different classes of random networks: random and scale-free. We report patterns in local information processing and storage that do indeed distinguish biological from random, associated with control nodes that regulate the function of the fission yeast cell cycle network. Conversely, we find that integrated information, which serves as a global measure of "emergent" information processing, does not differ from random for the case presented. We discuss implications for our understanding of the informational architecture of the fission yeast cell cycle network in particular, and more generally for illuminating any distinctive physics that may be operative in life.

q-bio.MN↗

arXiv2015

New Scaling Relation for Information Transfer in Biological Networks

Living systems are often described utilizing informational analogies. An important open question is whether information is merely a useful conceptual metaphor, or intrinsic to the operation of biological systems. To address this question, we provide a rigorous case study of the informational architecture of two representative biological networks: the Boolean network model for the cell-cycle regulatory network of the fission yeast S. pombe and that of the budding yeast S. cerevisiae. We compare our results for these biological networks to the same analysis performed on ensembles of two different types of random networks. We show that both biological networks share features in common that are not shared by either ensemble. In particular, the biological networks in our study, on average, process more information than the random networks. They also exhibit a scaling relation in information transferred between nodes that distinguishes them from either ensemble: even when compared to the ensemble of random networks that shares important topological properties, such as a scale-free structure. We show that the most biologically distinct regime of this scaling relation is associated with the dynamics and function of the biological networks. Information processing in biological networks is therefore interpreted as an emergent property of topology (causal structure) and dynamics (function). These results demonstrate quantitatively how the informational architecture of biologically evolved networks can distinguish them from other classes of network architecture that do not share the same informational properties.

q-bio.MN↗

arXiv2014

Self-referencing cellular automata: A model of the evolution of information control in biological systems

Cellular automata have been useful artificial models for exploring how relatively simple rules combined with spatial memory can give rise to complex emergent patterns. Moreover, studying the dynamics of how rules emerge under artificial selection for function has recently become a powerful tool for understanding how evolution can innovate within its genetic rule space. However, conventional cellular automata lack the kind of state feedback that is surely present in natural evolving systems. Each new generation of a population leaves an indelible mark on its environment and thus affects the selective pressures that shape future generations of that population. To model this phenomenon, we have augmented traditional cellular automata with state-dependent feedback. Rather than generating automata executions from an initial condition and a static rule, we introduce mappings which generate iteration rules from the cellular automaton itself. We show that these new automata contain disconnected regions which locally act like conventional automata, thus encapsulating multiple functions into one structure. Consequently, we have provided a new model for processes like cell differentiation. Finally, by studying the size of these regions, we provide additional evidence that the dynamics of self-reference may be critical to understanding the evolution of natural language. In particular, the rules of elementary cellular automata appear to be distributed in the same way as words in the corpus of a natural language.

nlin.CG↗

arXiv2013

Quantum Non-Barking Dogs

Quantum weak measurements with states both pre- and postselected offer a window into a hitherto neglected sector of quantum mechanics. A class of such systems involves time dependent evolution with transitions possible. In this paper we explore two very simple systems in this class. The first is a toy model representing the decay of an excited atom. The second is the tunneling of a particle through a barrier. The postselection criteria are chosen as follows: at the final time, the "atom" remains in its initial excited state for the first example and the particle remains behind the barrier for the second. We then ask what weak values are predicted in the physical environment of the "atom" (to which no net energy has been transferred) and in the region beyond the barrier (to which the particle has not tunneled). Previous work suggests that very large weak values might arise in these regions for long durations between pre- and postselection times. Our calculations reveal some distinct differences between the two model systems.

quant-ph↗

arXiv2012

The Algorithmic Origins of Life

Although it has been notoriously difficult to pin down precisely what it is that makes life so distinctive and remarkable, there is general agreement that its informational aspect is one key property, perhaps the key property. The unique informational narrative of living systems suggests that life may be characterized by context-dependent causal influences, and in particular, that top-down (or downward) causation -- where higher-levels influence and constrain the dynamics of lower-levels in organizational hierarchies -- may be a major contributor to the hierarchal structure of living systems. Here we propose that the origin of life may correspond to a physical transition associated with a shift in causal structure, where information gains direct, and context-dependent causal efficacy over the matter it is instantiated in. Such a transition may be akin to more traditional physical transitions (e.g. thermodynamic phase transitions), with the crucial distinction that determining which phase (non-life or life) a given system is in requires dynamical information and therefore can only be inferred by identifying causal architecture. We discuss some potential novel research directions based on this hypothesis, including potential measures of such a transition that may be amenable to laboratory study, and how the proposed mechanism corresponds to the onset of the unique mode of (algorithmic) information processing characteristic of living systems.

nlin.AO↗

arXiv2012

Evolutionary Transitions and Top-Down Causation

Top-down causation has been suggested to occur at all scales of biological organization as a mechanism for explaining the hierarchy of structure and causation in living systems. Here we propose that a transition from bottom-up to top-down causation -- mediated by a reversal in the flow of information from lower to higher levels of organization, to that from higher to lower levels of organization -- is a driving force for most major evolutionary transitions. We suggest that many major evolutionary transitions might therefore be marked by a transition in causal structure. We use logistic growth as a toy model for demonstrating how such a transition can drive the emergence of collective behavior in replicative systems. We then outline how this scenario may have played out in those major evolutionary transitions in which new, higher levels of organization emerged, and propose possible methods via which our hypothesis might be tested.

nlin.AO↗