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Posts Tagged ‘Information Theory

Information Theory And The Origin of Life

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Christoph Adami
Research investigating the origins of life usually focuses on exploring possible life-bearing chemistries in the pre-biotic Earth, or else on synthetic approaches.
Little work has been done exploring fundamental issues concerning the spontaneous emergence of life using only concepts (such as information and evolution) that are divorced from any particular chemistry.
Here, I advocate studying the probability of spontaneous molecular self-replication as a function of the information contained in the replicator, and the environmental conditions that might enable this emergence.
I show that (under certain simplifying assumptions) the probability to discover a self-replicator by chance depends exponentially on the rate of formation of the monomers.
If the rate at which monomers are formed is somewhat similar to the rate at which they would occur in a self-replicating polymer, the likelihood to discover such a replicator by chance is increased by many orders of magnitude.
I document such an increase in searches for a self-replicator within the digital life system avida …
… Read more at arxiv.org/pdf/

Read also medium.com/the-physics-arxiv-blog

Written by physicsgg

September 10, 2014 at 2:16 pm

Posted in BIOLOGY, Chemistry, PHYSICS

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Information Theory of DNA Sequencing

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Schematic for shotgun sequencing

Abolfazl Motahari, Guy Bresler, David Tse
DNA sequencing is the basic workhorse of modern day biology and medicine. Shotgun sequencing is the dominant technique used: many randomly located short fragments called reads are extracted from the DNA sequence, and these reads are assembled to reconstruct the original sequence. A basic question is: given a sequencing technology and the statistics of the DNA sequence, what is the minimum number of reads required for reliable reconstruction? This number provides a fundamental limit to the performance of any assembly algorithm. By drawing an analogy between the DNA sequencing problem and the classic communication problem, we formulate this question in terms of an information theoretic notion of sequencing capacity. This is the asymptotic ratio of the length of the DNA sequence to the minimum number of reads required to reconstruct it reliably. We compute the sequencing capacity explicitly for a simple statistical model of the DNA sequence and the read process. Using this framework, we also study the impact of noise in the read process on the sequencing capacity….
Read more: arxiv.org/pdf/1203.6233v2.pdf

Written by physicsgg

April 2, 2012 at 2:14 pm

Posted in BIOLOGY

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