Nathaniel Virgo

Motility at the origin of life: Its characterization and a model

Due to recent advances in synthetic biology and artificial life, the origin of life is currently a hot topic of research. We review the literature and argue that the two traditionally competing replicator-first and metabolism-first approaches are merging into one integrated theory of individuation and evolution. We contribute to the maturation of this more inclusive approach by highlighting some problematic assumptions that still lead to an ximpoverished conception of the phenomenon of life. In particular, we argue that the new consensus has so far failed to consider the relevance of intermediate time scales. We propose that an adequate theory of life must account for the fact that all living beings are situated in at least four distinct time scales, which are typically associated with metabolism, motility, development, and evolution. In this view, self-movement, adaptive behavior, and morphological changes could have already been present at the origin of life. In order to illustrate this possibility, we analyze a minimal model of lifelike phenomena, namely, of precarious, individuated, dissipative structures that can be found in simple reaction-diffusion systems. Based on our analysis, we suggest that processes on intermediate time scales could have already been operative in prebiotic systems. They may have facilitated and constrained changes occurring in the faster- and slower-paced time scales of chemical self-individuation and evolution by natural selection, respectively.

Open-ended evolution: Perspectives from the oee workshop in york

We describe the content and outcomes of the First Workshop on Open-Ended Evolution: Recent Progress and Future Milestones (OEE1), held during the ECAL 2015 conference at the University of York, UK, in July 2015. We briefly summarize the content of the workshops talks, and identify the main themes that emerged from the open discussions. Two important conclusions from the discussions are: (1) the idea of pluralism about OEE—it seems clear that there is more than one interesting and important kind of OEE; and (2) the importance of distinguishing observable behavioral hallmarks of systems undergoing OEE from hypothesized underlying mechanisms that explain why a system exhibits those hallmarks. We summarize the different hallmarks and mechanisms discussed during the workshop, and list the specific systems that were highlighted with respect to particular hallmarks and mechanisms. We conclude by identifying some of the most important open research questions about OEE that are apparent in light of the discussions. The York workshop provides a foundation for a follow-up OEE2 workshop taking place at the ALIFE XV conference in Cancún, Mexico, in July 2016. Additional materials from the York workshop, including talk abstracts, presentation slides, and videos of each talk, are available at http://alife.org/ws/oee1.

A Strategy for Origins of Life Research

Contents 1. Introduction 1.1. A workshop and this document 1.2. Framing origins of life science 1.2.1. What do we mean by the origins of life (OoL)? 1.2.2. Defining life 1.2.3. How should we characterize approaches to OoL science? 1.2.4. One path to life or many? 2. A Strategy for Origins of Life Research 2.1. Outcomes—key questions and investigations 2.1.1. Domain 1: Theory 2.1.2. Domain 2: Practice 2.1.3. Domain 3: Process 2.1.4. Domain 4: Future studies 2.2. EON Roadmap 2.3. Relationship to NASA Astrobiology Roadmap and Strategy documents and the European AstRoMap  Appendix I  Appendix II  Supplementary Materials  References

Evolvable physical self-replicators

Building an evolvable physical self-replicating machine is a grand challenge. The main problem is that the device must be capable of hereditary variation, that is, replicating in many configurations—configurations into which it enters unpredictably by mutation. Template replication is the solution found by nature. A scalable device must also be capable of miniaturization, and so have few or no moving and electronic parts. Here a significant step toward this goal is presented in the form of a physical template replicator made from small plastic pieces containing embedded magnets that float on an air-hockey-type table and undergo stochastic motion. Our units replicate by a process analogous to the replication of DNA, except without the involvement of enzymes. Building a physical rather than a computational model forces us to confront several problems that have analogues on the nano scale. In particular, replication must be maintained by preventing side reactions such as spontaneous ligation, cyclization, product inhibition, and elongation at staggered ends. The last of these results in ever-lengthening sequences in a process known as the elongation catastrophe. The extreme specificity of structure required by the monomers is indirect evidence that some kind of natural selection took place prior to the existence of nucleotide analogues during the origin of life.

Autocatalysis Before Enzymes: The Emergence of Prebiotic Chain Reactions

How could complex, enzyme- or ribozyme-like molecules first have arisen on planet Earth? Several authors have suggested autocatalytic cycles as a partial answer to this question, since such reactions exhibit the life-like property of exponential growth while being composed of relatively simple molecules. However, a question remains as to the likelihood of an autocatalytic cycle forming spontaneously in the absence of highly specific catalysts. Here we show that such cycles form readily in a very simple model that includes no direct catalysis reactions. Catalytic effects nevertheless emerge as properties of the reaction network. This suggests that the conditions for the formation of such cycles are not difficult to achieve. The resulting cycles solve the problem of specificity not by being small and simple but by being large and complicated, suggesting that early prebiotic metabolisms could have been extremely complex. We predict that this phenomenon can be reproduced in wet chemistry. We discuss the challenges involved in this, as well as the implications for how we view the origins of life.

The Behavior-Based Hypercycle: From Parasitic Reaction to Symbiotic Behavior

Most researchers in the science of the origin of life assume that the process of living is nothing but computation in the chemical domain, i.e. information processing of a genetic code. This has had the effect of restricting research to the problem of stability, as epitomized by the concept of the hypercycle and its potential vulnerability against parasites. Stability is typically assumed to be ensured by a rigid compartment, but spatial self-structuring is a viable alternative. We further develop this alternative by proposing that some instability can actually be beneficial under certain conditions. We show that instability can lead to adaptive behavior even in the case of simple prebiotic reaction-diffusion systems. We demonstrate for the first time that a parasitic sidereaction on the metabolic level can lead to self-motility on the behavioral level of the chemical system as a whole. Moreover, self-motility entails advantages on an evolutionary level, thus constituting a symbiotic, behavior-based hypercycle. We relate this novel finding to several issues in the science of the origin of life, and conclude that more attention should be given to the possibility of a movement-first scenario.

The positive role of parasites in the origins of life

One problem in the origins of life is how parasitic side-reactions can be mitigated. It is known that spatial self-organisation can help with this, making autocatalytic chemical systems more robust to invasion by parasitic species. In previous work we have shown that in such scenarios parasitic reactions can actually be beneficial. Here we demonstrate for the first time a system in which the presence of a parasitic autocatalytic cycle is not only beneficial but actually necessary for the persistence of its host. This occurs due to the effect the parasite has on the spatial organisation of the system; the host-parasite system is more stable than the host alone, despite the fact that the parasites direct effect on its host is purely negative. We briefly discuss the implications for the origins of life.

Complex autocatalysis in simple chemistries

Life on Earth must originally have arisen from abiotic chemistry. Since the details of this chemistry are unknown, we wish to understand, in general, which types of chemistry can lead to complex, lifelike behavior. Here we show that even very simple chemistries in the thermodynamically reversible regime can self-organize to form complex autocatalytic cycles, with the catalytic effects emerging from the network structure. We demonstrate this with a very simple but thermodynamically reasonable artificial chemistry model. By suppressing the direct reaction from reactants to products, we obtain the simplest kind of autocatalytic cycle, resulting in exponential growth. When these simple first-order cycles are prevented from forming, the system achieves superexponential growth through more complex, higher-order autocatalytic cycles. This leads to nonlinear phenomena such as oscillations and bistability, the latter of which is of particular interest regarding the origins of life.

Many hands make light work: Further studies in group evolution

When niching or speciation is required to perform a task that has several different component parts, standard genetic algorithms (GAs) struggle. They tend to evaluate and select all individuals on the same part of the task, which leads to genetic convergence within the population. The goal of evolutionary niching methods is to enforce diversity in the population so that this genetic convergence is avoided. One drawback with some of these niching methods is that they require a priori knowledge or assumptions about the specific fitness landscape in order to work; another is that many such methods are not set up to work on cooperative tasks where fitness is only relevant at the group level. Here we address these problems by presenting the group GA, described earlier by the authors, which is a group-based evolutionary algorithm that can lead to emergent niching. After demonstrating the group GA on an immune system matching task, we extend the previous work and present two modified versions where the number of niches does not need to be specified ahead of time. In the random-group-size GA, the number of niches is varied randomly during evolution, and in the evolved-group-size GA the number of niches is optimized by evolution. This provides a framework in which we can evolve groups of individuals to collectively perform tasks with minimal a priori knowledge of how many subtasks there are or how they should be shared out.

Bulk measurements of messy chemistries are needed for a theory of the origins of life

A feature of many of the chemical systems plausibly involved in the origins of terrestrial life is that they are complex and messy—producing a wide range of compounds via a wide range of mechanisms. However, the fundamental behaviour of such systems is currently not well understood; we do not have the tools to make statistical predictions about such complex chemical networks. This is, in part, due to a lack of quantitative data from which such a theory could be built; specifically, functional measurements of messy chemical systems. Here, we propose that the pantheon of experimental approaches to the origins of life should be expanded to include the study of ‘functional measurements’—the direct study of bulk properties of chemical systems and their interactions with other compounds, the formation of structures and other behaviours, even in cases where the precise composition and mechanisms are unknown. This article is part of the themed issue ‘Reconceptualizing the origins of life’.