Mathematic principles underlying genetic structures

In this review paper, we delve into the nascent field of molecular data storage, focusing on system implementations and code constructions. We start by providing an overview of basic concepts in synthetic and computational biology. Afterwards, we proceed with a review of the diverse approaches followed to implement such systems. In the process, we identify new problems in communication and coding theory, and discuss some relevant results pertaining to DNA sequence profiles, c...

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 inform...

We introduce a method to estimate the complexity function of symbolic dynamical systems from a finite sequence of symbols. We test such complexity estimator on several symbolic dynamical systems whose complexity functions are known exactly. We use this technique to estimate the complexity function for genomes of several organisms under the assumption that a genome is a sequence produced by a (unknown) dynamical system. We show that the genome of several organisms share the pr...

Life depends as much on the flow of information as on the flow of energy. Here we review the many efforts to make this intuition precise. Starting with the building blocks of information theory, we explore examples where it has been possible to measure, directly, the flow of information in biological networks, or more generally where information theoretic ideas have been used to guide the analysis of experiments. Systems of interest range from single molecules (the sequence d...

The post-genomic era has brought opportunities to bridge traditionally separate fields of early history of life and brought new insight into origin and evolution of biodiversity. According to distributions of codons in genome sequences, I found a relationship between the genetic code and the tree of life. This remote and profound relationship involves the origin and evolution of the genetic code and the diversification and expansion of genomes. Here, a prebiotic picture of th...

It has been repeatedly proposed to expand the scope for SETI, and one of the suggested alternatives to radio is the biological media. Genomic DNA is already used on Earth to store non-biological information. Though smaller in capacity, but stronger in noise immunity is the genetic code. The code is a flexible mapping between codons and amino acids, and this flexibility allows modifying the code artificially. But once fixed, the code might stay unchanged over cosmological time...

This paper introduces several fundamental concepts in information theory from the perspective of their origins in engineering. Understanding such concepts is important in neuroscience for two reasons. Simply applying formulae from information theory without understanding the assumptions behind their definitions can lead to erroneous results and conclusions. Furthermore, this century will see a convergence of information theory and neuroscience; information theory will expand ...

These are notes for a set of 7 two-hour lectures given at the 2010 Summer School on Quantitative Evolutionary and Comparative Genomics at OIST, Okinawa, Japan. The emphasis is on understanding how biological systems process information. We take a physicist's approach of looking for simple phenomenological descriptions that can address the questions of biological function without necessarily modeling all (mostly unknown) microscopic details; the example that is developed throu...

The yearly global production of data is growing exponentially, outpacing the capacity of existing storage media, such as tape and disk, and surpassing our ability to store it. DNA storage - the representation of arbitrary information as sequences of nucleotides - offers a promising storage medium. DNA is nature's information-storage molecule of choice and has a number of key properties: it is extremely dense, offering the theoretical possibility of storing 455 EB/g; it is dur...

Convolutional codes are error-correcting linear codes that utilize shift registers to encode. These codes have an arbitrary block size and they can incorporate both past and current information bits. DNA codes represent DNA sequences and are defined as sets of words comprised of the alphabet A, C, T, G satisfying certain mathematical bounds and constraints. The application of convolutional code models to DNA codes is a growing field of biocomputation. As opposed to block code...