1,188 research outputs found
On the Growth Rate of Non-Enzymatic Molecular Replicators
It is well known that non-enzymatic template directed molecular replicators X
+ nO ---> 2X exhibit parabolic growth d[X]/dt = k [X]^{1/2}. Here, we analyze
the dependence of the effective replication rate constant k on hybridization
energies, temperature, strand length, and sequence composition. First we derive
analytical criteria for the replication rate k based on simple thermodynamic
arguments. Second we present a Brownian dynamics model for oligonucleotides
that allows us to simulate their diffusion and hybridization behavior. The
simulation is used to generate and analyze the effect of strand length,
temperature, and to some extent sequence composition, on the hybridization
rates and the resulting optimal overall rate constant k. Combining the two
approaches allows us to semi-analytically depict a fitness landscape for
template directed replicators. The results indicate a clear replication
advantage for longer strands at low temperatures.Comment: Submitted to: Entrop
A biosemiotic conversation: Between physics and semiotics
In this dialogue, we discuss the contrast between inexorable physical laws and the semiotic freedom of life. We agree that material and symbolic structures require complementary descriptions, as do the many hierarchical levels of their organizations. We try to clarify our concepts of laws, constraints, rules, symbols, memory, interpreters, and semiotic control. We briefly describe our different personal backgrounds that led us to a biosemiotic approach, and we speculate on the future directions of biosemiotics
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
A model of protocell based on the introduction of a semi-permeable membrane in a stochastic model of catalytic reaction networks
In this work we introduce some preliminary analyses on the role of a
semi-permeable membrane in the dynamics of a stochastic model of catalytic
reaction sets (CRSs) of molecules. The results of the simulations performed on
ensembles of randomly generated reaction schemes highlight remarkable
differences between this very simple protocell description model and the
classical case of the continuous stirred-tank reactor (CSTR). In particular, in
the CSTR case, distinct simulations with the same reaction scheme reach the
same dynamical equilibrium, whereas, in the protocell case, simulations with
identical reaction schemes can reach very different dynamical states, despite
starting from the same initial conditions.Comment: In Proceedings Wivace 2013, arXiv:1309.712
Is defining life pointless? Operational definitions at the frontiers of Biology
Despite numerous and increasing attempts to define what life is, there is no consensus on necessary and sufficient conditions for life. Accordingly, some scholars have questioned the value of definitions of life and encouraged scientists and philosophers alike to discard the project. As an alternative to this pessimistic conclusion, we argue that critically rethinking the nature and uses of definitions can provide new insights into the epistemic roles of definitions of life for different research practices. This paper examines the possible contributions of definitions of life in scientific domains where such definitions are used most (e.g., Synthetic Biology, Origins of Life, Alife, and Astrobiology). Rather than as classificatory tools for demarcation of natural kinds, we highlight the pragmatic utility of what we call operational definitions that serve as theoretical and epistemic tools in scientific practice. In particular, we examine contexts where definitions integrate criteria for life into theoretical models that involve or enable observable operations. We show how these definitions of life play important roles in influencing research agendas and evaluating results, and we argue that to discard the project of defining life is neither sufficiently motivated, nor possible without dismissing important theoretical and practical research
Mind the Gap!
In his review of Protocells, Antonio Lazcano explores how the self-assemblage properties of lipids into bilayers, micelles, and liposomes can be used to model minimal cells, design biochemical microreactors, and provide insights into the predecessors of the first living beings
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