106,952 research outputs found
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.Comment: 13 pages, 1 tabl
Erwin Schroedinger, Francis Crick and epigenetic stability
Schroedinger's book 'What is Life?' is widely credited for having played a
crucial role in development of molecular and cellular biology. My essay
revisits the issues raised by this book from the modern perspective of
epigenetics and systems biology. I contrast two classes of potential mechanisms
of epigenetic stability: 'epigenetic templating' and 'systems biology'
approaches, and consider them from the point of view expressed by Schroedinger.
I also discuss how quantum entanglement, a nonclassical feature of quantum
mechanics, can help to address the 'problem of small numbers' that lead
Schroedinger to promote the idea of molecular code-script for explanation of
stability of biological order.Comment: New and improved version of the essay, now published in the online
journal 'Biology Direct'. Contains more expanded discussion on entanglement.
18 pages, 2 figures. The file includes open reviews by E.Koonin, V.Vedral and
E.Karsent
Wide-Field Multi-Parameter FLIM: Long-Term Minimal Invasive Observation of Proteins in Living Cells.
Time-domain Fluorescence Lifetime Imaging Microscopy (FLIM) is a remarkable tool to monitor the dynamics of fluorophore-tagged protein domains inside living cells. We propose a Wide-Field Multi-Parameter FLIM method (WFMP-FLIM) aimed to monitor continuously living cells under minimum light intensity at a given illumination energy dose. A powerful data analysis technique applied to the WFMP-FLIM data sets allows to optimize the estimation accuracy of physical parameters at very low fluorescence signal levels approaching the lower bound theoretical limit. We demonstrate the efficiency of WFMP-FLIM by presenting two independent and relevant long-term experiments in cell biology: 1) FRET analysis of simultaneously recorded donor and acceptor fluorescence in living HeLa cells and 2) tracking of mitochondrial transport combined with fluorescence lifetime analysis in neuronal processes
The Biosemiotic Approach in Biology : Theoretical Bases and Applied Models
Biosemiotics is a growing fi eld that investigates semiotic processes in the living realm in an attempt to combine the fi ndings of the biological sciences and semiotics. Semiotic processes are more or less what biologists have typically referred to as “ signals, ” “ codes, ”and “ information processing ”in biosystems, but these processes are here understood under the more general notion of semiosis, that is, the production, action, and interpretation of signs. Thus, biosemiotics can be seen as biology interpreted as a study of living sign systems — which also means that semiosis or sign process can be seen as the very nature of life itself. In other words, biosemiotics is a field of research investigating semiotic processes (meaning, signification, communication, and habit formation in living systems) and the physicochemical preconditions for sign action and interpretation.
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Open problems in artificial life
This article lists fourteen open problems in artificial life, each of which is a grand challenge requiring a major advance on a fundamental issue for its solution. Each problem is briefly explained, and, where deemed helpful, some promising paths to its solution are indicated
Computing Substrates and Life
Alive matter distinguishes itself from inanimate matter by actively maintaining a high degree of inhomogenous organisation. Information processing is quintessential to this capability. The present paper inquires into the degree to which the information processing aspect of living systems can be abstracted from the physical medium of its implementation. Information processing serving to sustain the complex organisation of a living system faces both the harsh reality of real-time requirements and severe constraints on energy and material that can be expended on the task. This issue is of interest for the potential scope of Artificial Life and its interaction with Synthetic Biology. It is pertinent also for information technology. With regard to the latter aspect, the use of a living cell in a robot control architecture is considered
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