Single Nucleotide Polymorphisms: A Window into the Informatics of the Living Genome.

Georgia M Dunston,Tshela E Mason,James Lindesay,William Hercules

doi:10.4236/abb.2014.57073

Abstract

Nested in the environment of the nucleus of the cell, the 23 sets of chromosomes that comprise the human genome function as one integrated whole system, orchestrating the expression of thousands of genes underlying the biological characteristics of the cell, individual and the species. The extraction of meaningful information from this complex data set depends crucially upon the lens through which the data are examined. We present a biophysical perspective on genomic information encoded in single nucleotide polymorphisms (SNPs), and introduce metrics for modeling information encoded in the genome. Information, like energy, is considered to be a conserved physical property of the universe. The information structured in SNPs describes the adaptation of a human population to a given environment. The maintained order measured by the information content is associated with entropies, energies, and other state variables for a dynamic system in homeostasis. “Genodynamics” characterizes the state variables for genomic populations that are stable under stochastic environmental stresses. The determination of allelic energies allows the parameterization of specific environmental influences upon individual alleles across populations. The environment drives population-based genome variation. From this vantage point, the genome is modeled as a complex, dynamic information system defined by patterns of SNP alleles and SNP haplotypes.

Highlights

IntroductionThe completion of the Human Genome Project (HGP) in 2003 introduced a new 21st century knowledge-base
The completion of the Human Genome Project (HGP) in 2003 introduced a new 21st century knowledge-baseHow to cite this paper: Dunston, G.M., Mason, T.E., Hercules, W. and Lindesay, J. (2014) Single Nucleotide Polymorphisms: A Window into the Informatics of the Living Genome
In this short report on single nucleotide polymorphisms (SNPs), we explore a biophysical perspective on the genome as the most sophisticated living “information and communication system” known to mankind

Summary

Introduction

The completion of the Human Genome Project (HGP) in 2003 introduced a new 21st century knowledge-base. In this short report on single nucleotide polymorphisms (SNPs), we explore a biophysical perspective on the genome as the most sophisticated living “information and communication system” known to mankind. As such, it is expressed in and through all levels of existence, from the invisible world of quantum physics through the visible biological hierarchy of molecules, cells, tissues, organs, and systems integrated in whole individuals, to the limitless, global diversity of all human populations that constitute humanity. Online public availability of SNP alleles and SNP haplotype data for global populations, defined geographically by continent of origin, have forged a new era in population genetics, offering unprecedented opportunities to investigate adaptive forces that have shaped patterns of common variation in natural populations

The Human Genome Model of Life

Dynamics of Genome-Environment Homeostasis

Human Genome Variation and Human Identity

Conclusion