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 impoverished conception of the phenomenon of life. In particular, we argue that the new consensus has so far failed to consider the relevance of intermediate timescales. We propose that an adequate theory of life must account for the fact that all living beings are situated in at least four distinct timescales, which are typically associated with metabolism, motility, development, and evolution. On 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 life-like phenomena, namely of precarious, individuated, dissipative structures that can be found in simple reaction-diffusion systems. Based on our analysis we suggest that processes in intermediate timescales could have already been operative in prebiotic systems. They may have facilitated and constrained changes occurring in the faster- and slower-paced timescales of chemical self-individuation and evolution by natural selection, respectively.Comment: 29 pages, 5 figures, Artificial Lif

recent theoretical approaches to minimal artificial cells

Minimal artificial cells (MACs) are self-assembled chemical systems able to mimic the behavior of living cells at a minimal level, i.e. to exhibit self-maintenance, self-reproduction and the capability of evolution. The bottom-up approach to the construction of MACs is mainly based on the encapsulation of chemical reacting systems inside lipid vesicles, i.e. chemical systems enclosed (compartmentalized) by a double-layered lipid membrane. Several researchers are currently interested in synthesizing such simple cellular models for biotechnological purposes or for investigating origin of life scenarios. Within this context, the properties of lipid vesicles (e.g., their stability, permeability, growth dynamics, potential to host reactions or undergo division processes…) play a central role, in combination with the dynamics of the encapsulated chemical or biochemical networks. Thus, from a theoretical standpoint, it is very important to develop kinetic equations in order to explore first—and specify later—the conditions that allow the robust implementation of these complex chemically reacting systems, as well as their controlled reproduction. Due to being compartmentalized in small volumes, the population of reacting molecules can be very low in terms of the number of molecules and therefore their behavior becomes highly affected by stochastic effects both in the time course of reactions and in occupancy distribution among the vesicle population. In this short review we report our mathematical approaches to model artificial cell systems in this complex scenario by giving a summary of three recent simulations studies on the topic of primitive cell (protocell) systems

La biología sintética como desafío para comprender la autonomía de lo vivo

We here offer an alternative view of synthetic biology, quite distant from the engineering approaches that currently set the main research agenda of the field. Our analysis centres on those lines of work, both theoretical and experimental, whose primary objective is understanding the living phenomenon per se. A detailed review of several cases of artificial in vitro implementation of 'self-productive' chemical systems will help us reflect on the enormous challenge of transforming a descriptive scientific discipline, like biology, into an enterprise that comprises and fosters investigations articulated around the notion of synthesis or fabrication. The challenge is huge because of the intrinsic metabolic nature of biological systems, what makes our efforts to control or build them de novo much harder, forcing us to develop intervention/implementation platforms at the molecular level that do not threaten that inherent autonomous dimension of the living.En este artículo se ofrece una visión de la biología sintética alternativa a los planteamientos ingenieriles que marcan gran parte de la agenda de investigación del campo. Nuestro análisis se centra en enfoques, teóricos y experimentales, cuyo objetivo fundamental es la comprensión del fenómeno de la vida per se. Una revisión detallada de varios casos de implementación artificial, in vitro, de sistemas químicos ‘auto-productivos’ nos ayudará a reflexionar sobre el enorme reto que supone transformar una disciplina científica eminentemente descriptiva, como la biología, en un proyecto que incluya y potencie líneas de investigación basadas en la idea de síntesis o fabricación. El reto es mayúsculo debido al carácter intrínsecamente metabólico de los sistemas biológicos, lo cual hace que nuestro empeño en controlarlos o en construirlos de novo sea mucho más dificultoso, forzándonos a desarrollar plataformas de intervención/implementación a nivel molecular que no pongan en compromiso esa inherente dimensión autónoma de lo vivo

Behavioral metabolution: the adaptive and evolutionary potential of metabolism-based chemotaxis

We use a minimal model of metabolism-based chemotaxis to show how a coupling between metabolism and behavior can affect evolutionary dynamics in a process we refer to as behavioral metabolution. This mutual influence can function as an in-the-moment, intrinsic evaluation of the adaptive value of a novel situation, such as an encounter with a compound that activates new metabolic pathways. Our model demonstrates how changes to metabolic pathways can lead to improvement of behavioral strategies, and conversely, how behavior can contribute to the exploration and fixation of new metabolic pathways. These examples indicate the potentially important role that the interplay between behavior and metabolism could have played in shaping adaptive evolution in early life and protolife. We argue that the processes illustrated by these models can be interpreted as an unorthodox instantiation of the principles of evolution by random variation and selective retention. We then discuss how the interaction between metabolism and behavior can facilitate evolution through (i) increasing exposure to environmental variation, (ii) making more likely the fixation of some beneficial metabolic pathways, (iii) providing a mechanism for in-the-moment adaptation to changes in the environment and to changes in the organization of the organism itself, and (iv) generating conditions that are conducive to speciatio

La circularité biologique : concepts et modèles

National audienceThis chapter offers an overview of the theoretical and philosophical tradition that, during the last two centuries, has emphasised the central role of circularities in biological phenomena. In this tradition, organisms realise a circular causal regime insofar as their existence depends on the effects of their own activity: they determine themselves. In turn, self-determination is the grounding of several biological properties and dimensions, as individuation, teleology, normativity and functionality. We show how this general idea has been theorised sometimes through concepts, sometimes through models, and sometimes through both. We analyse the main differences between the various contributions, by emphasising their strengths and weaknesses. Lastly, we conclude by mentioning some contemporary developments, as well ass some future research directions.Ce chapitre propose un aperçu de la tradition théorique et philosophique qui, au cours des deux derniers siècles, a mis la circularité au centre de l'analyse des phénomènes biologiques. Selon cette tradition, les organismes réalisent un régime causal circulaire dans la mesure où leur existence dépend des effets de leur propre activité : les organismes biologiques s'autodéterminent. A son tour, l'autodétermination est le fondement d'un certain nombre de propriétés et dimensions biologiques, telles que l'individuation, la téléologie, la normativité ou encore la fonctionnalité. Nous montrons comment cette idée générale a fait l'objet d'une théorisation qui a pris, selon les cas, la forme d'une conceptualisation, d'une modélisation ou les deux à fois. Nous analysons les différences principales entre les différentes contributions, en soulignant leurs qualités et faiblesses. Enfin, nous concluons en évoquant certains développements contemporains de cette tradition, ainsi que quelques pistes de recherche futures

Between pebbles and organisms: Weaving autonomy into the Markov blanket

The free energy principle (FEP) purports to provide a single principle for the organizational dynamics of living systems, including their cognitive profiles. It states that for a system to maintain non-equilibrium steady-state with its environment it must minimise its free energy. It is said to be entirely scale-free, applying to anything from particles to organisms, and interactive machines, spanning from the abiotic to the biotic. Because the FEP is so general in its application, it is for this reason that one might wonder in what sense this framework captures anything specific to biological characteristics, if details at all. We take steps to correct for this here. We do so by taking up a distinct challenge that the FEP must overcome if it is to be of interest to those working in the biological sciences. We call this the pebble challenge: it states that the FEP cannot capture the organisational principles specific to biology, for its formalisms apply equally well to pebbles. We progress in solving the pebble challenge by articulating how the notion of ‘autonomy as precarious operational closure’ from the enactive literature can be unpacked within the FEP. This enables the FEP to delineate between the abiotic and the biotic; avoiding the pebble challenge that keeps it out of touch with the living systems we encounter in the world and is of interest to the sciences of life and mind

Organization needs organization: Understanding integrated control in living organisms.

Organization figures centrally in the understanding of biological systems advanced by both new mechanists and proponents of the autonomy framework. The new mechanists focus on how components of mechanisms are organized to produce a phenomenon and emphasize productive continuity between these components. The autonomy framework focuses on how the components of a biological system are organized in such a way that they contribute to the maintenance of the organisms that produce them. In this paper we analyze and compare these two accounts of organization and argue that understanding biological organisms as cohesively integrated systems benefits from insights from both. To bring together the two accounts, we focus on the notions of control and regulation as bridge concepts. We start from a characterization of biological mechanisms in terms of constraints and focus on a specific type of mechanism, control mechanisms, that operate on other mechanisms on the basis of measurements of variables in the system and its environment. Control mechanisms are characterized by their own set of constraints that enable them to sense conditions, convey signals, and effect changes on constraints in the controlled mechanism. They thereby allow living organisms to adapt to internal and external variations and to coordinate their parts in such a manner as to maintain viability. Because living organisms contain a vast number of control mechanisms, a central challenge is to understand how they are themselves organized. With the support of examples from both unicellular and multicellular systems we argue that control mechanisms are organized heterarchically, and we discuss how this type of control architecture can, without invoking top-down and centralized forms of organizations, succeed in coordinating internal activities of organisms

Organization needs organization: Understanding integrated control in living organisms

Organization figures centrally in the understanding of biological systems advanced by both new mechanists and proponents of the autonomy framework. The new mechanists focus on how components of mechanisms are organized to produce a phenomenon and emphasize productive continuity between these components. The autonomy framework focuses on how the components of a biological system are organized in such a way that they contribute to the maintenance of the organisms that produce them. In this paper we analyze and compare these two accounts of organization and argue that understanding biological organisms as cohesively integrated systems benefits from insights from both. To bring together the two accounts, we focus on the notions of control and regulation as bridge concepts. We start from a characterization of biological mechanisms in terms of constraints and focus on a specific type of mechanism, control mechanisms, that operate on other mechanisms on the basis of measurements of variables in the system and its environment. Control mechanisms are characterized by their own set of constraints that enable them to sense conditions, convey signals, and effect changes on constraints in the controlled mechanism. They thereby allow living organisms to adapt to internal and external variations and to coordinate their parts in such a manner as to maintain viability. Because living organisms contain a vast number of control mechanisms, a central challenge is to understand how they are themselves organized. With the support of examples from both unicellular and multicellular systems we argue that control mechanisms are organized heterarchically, and we discuss how this type of control architecture can, without invoking top-down and centralized forms of organizations, succeed in coordinating internal activities of organisms

Motility at the Origin of Life: Its Characterization and a Model

Abstract 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 impoverished 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