Definitions of life as epistemic tools that reflect and foster the advance of biological knowledge

Martínez, Alba Amilburu; Moreno, Álvaro; Ruiz-Mirazo, Kepa

doi:10.1007/s11229-020-02736-7

Cited by 8 publications

(6 citation statements)

References 31 publications

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“…Infusing cell-free biology with system’s level evolution will provide testbeds for exploring the roots of evolutionary processes in living organisms, as well as a new perspective in our understanding of life’s fundamental properties. It would also significantly contribute to the ongoing fluid interrelationship between theoretical definition of life and empirical assessment thereof ( Amilburu et al, 2020 ).…”

Section: Discussionmentioning

confidence: 99%

Roadmap to Building a Cell: An Evolutionary Approach

Abil

Danelon

2020

Front. Bioeng. Biotechnol.

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Laboratory synthesis of an elementary biological cell from isolated components may aid in understanding of the fundamental principles of life and will provide a platform for a range of bioengineering and medical applications. In essence, building a cell consists in the integration of cellular modules into system's level functionalities satisfying a definition of life. To achieve this goal, we propose in this perspective to undertake a semirational, system's level evolutionary approach. The strategy would require iterative cycles of genetic integration of functional modules, diversification of hereditary information, compartmentalized gene expression, selection/screening, and possibly, assistance from open-ended evolution. We explore the underlying challenges to each of these steps and discuss possible solutions toward the bottom-up construction of an artificial living cell.

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Section: Discussionmentioning

confidence: 99%

Roadmap to Building a Cell: An Evolutionary Approach

Abil

Danelon

2020

Front. Bioeng. Biotechnol.

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“…Explanation of arrow relations: dotted arrows indicate influences, normal arrows indicate productions, dash‐dotted arrows indicate interpretations. This graph was originally inspired by [ 20 ] (in particular, Figure 1 and the contents of section 4, in there)…”

Section: Methodological Suggestions: a Case For “Rule‐based” Computat...mentioning

confidence: 99%

“…Explanation of arrow relations: dotted arrows indicate influences, normal arrows indicate productions, dash-dotted arrows indicate interpretations. This graph was originally inspired by [20] (in particular, Figure 1 and the contents of section 4, in there) effects on the underlying chemistry ought to be the main target of the experiments. But, in turn, this points toward the need to reformulate quite radically the way of carrying out empirical research on the origins of metabolism, as we will discuss next.…”

Section: Metabolic Viability Involves Autonomous Control Developmentmentioning

confidence: 99%

“…[ 16,17 ] This conception appears to be fairly congruent and secure, until one realizes that it is entirely dependent on how one answers the question of what life is, or what a living being is—which are tricky issues, still far from reaching consensus in the academic sphere. [ 18–20 ] An alternative approach would be to consider metabolism in its own terms: namely, as a chemistry that is strongly linked to biological phenomena, but not fully subordinate to them. From that standpoint, one could think about metabolic processes that are not necessarily part of a full‐fledged biological organism.…”

Section: Introductionmentioning

confidence: 99%

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“Minimal metabolism”: A key concept to investigate the origins and nature of biological systems

2021

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The systems view on life and its emergence from complex chemistry has remarkably increased the scientific attention on metabolism in the last two decades. However, during this time there has not been much theoretical discussion on what constitutes a metabolism and what role it actually played in biogenesis. A critical and updated review on the topic is here offered, including some references to classical models from last century, but focusing more on current and future research. Metabolism is considered as intrinsically related to the living but not necessarily equivalent to it. More precisely, the idea of “minimal metabolism”, in contrast to previous, top‐down conceptions, is formulated as a heuristic construct, halfway between chemistry and biology. Thus, rather than providing a complete or final characterization of metabolism, our aim is to encourage further investigations on it, particularly in the context of life's origin, for which some concrete methodological suggestions are provided. Also see the video abstract here: https://youtu.be/DP7VMKk2qpA

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“…Addressing the challenge of the de novo synthesis of life starts with defining the target. While a generally accepted definition of life does not exist, , a pragmatic approach to defining this target is to list the key (functional) characteristics that any form of life should encompass . These characteristics are summarized in Figure and include:…”

Section: Introductionmentioning

confidence: 99%

An Approach to the De Novo Synthesis of Life

Otto

2021

Acc. Chem. Res.

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Metrics & MoreArticle Recommendations CONSPECTUS: As the remit of chemistry expands beyond molecules to systems, new synthetic targets appear on the horizon. Among these, life represents perhaps the ultimate synthetic challenge. Building on an increasingly detailed understanding of the inner workings of living systems and advances in organic synthesis and supramolecular chemistry, the de novo synthesis of life (i.e., the construction of a new form of life based on completely synthetic components) is coming within reach. This Account presents our first steps in the journey toward this long-term goal.The synthesis of life requires the functional integration of different subsystems that harbor the different characteristics that are deemed essential to life. The most important of these are self-replication, metabolism, and compartmentalization. Integrating these features into a single system, maintaining this system out of equilibrium, and allowing it to undergo Darwinian evolution should ideally result in the emergence of life. Our journey toward de novo life started with the serendipitous discovery of a new mechanism of self-replication. We found that self-assembly in a mixture of interconverting oligomers is a general way of achieving self-replication, where the assembly process drives the synthesis of the very molecules that assemble. Mechanically induced breakage of the growing replicating assemblies resulted in their exponential growth, which is an important enabler for achieving Darwinian evolution. Through this mechanism, the self-replication of compounds containing peptides, nucleobases, and fully synthetic molecules was achieved. Several examples of evolutionary dynamics have been observed in these systems, including the spontaneous diversification of replicators allowing them to specialize on different food sets, history dependence of replicator composition, and the spontaneous emergence of parasitic behavior. Peptide-based replicator assemblies were found to organize their peptide units in space in a manner that, inadvertently, gives rise to microenvironments that are capable of catalysis of chemical reactions or bindinginduced activation of cofactors. Among the reactions that can be catalyzed by the replicators are ones that produce the precursors from which these replicators grow, amounting to the first examples of the assimilation of a proto-metabolism. Operating these replicators in a chemically fueled out-of-equilibrium replication-destruction regime was found to promote an increase in their molecular complexity. Fueling counteracts the inherent tendency of replicators to evolve toward lower complexity (caused by the fact that smaller replicators tend to replicate faster). Among the remaining steps on the road to de novo life are now to assimilate compartmentalization and achieve open-ended evolution of the resulting system. Success in the synthesis of de novo life, once obtained, will have far-reaching implications for our understanding of what life is, for the search for extraterrestrial life, for ...

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Definitions of life as epistemic tools that reflect and foster the advance of biological knowledge

Cited by 8 publications

References 31 publications

Roadmap to Building a Cell: An Evolutionary Approach

Roadmap to Building a Cell: An Evolutionary Approach

“Minimal metabolism”: A key concept to investigate the origins and nature of biological systems

An Approach to the De Novo Synthesis of Life

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