Sep 12, 2012 information theory helps unravel dna s genetic code. The difference between life and matter is information the information is located in the onedimensional dnasequence of four letters a,t,c,g which is translated with the help of the genetic code to the onedimensional sequence of 20 different amino acids in proteins. Each unpaired nucleotide will attract a complementary nucleotide from the medium. This information theoretic view falls in the realm of dna sequencing theory 29. Werner gitt, robert compton and jorge fernandez a general theory of information cost incurred by successful search william a dembski, winston ewert and robert j marks ii pragmatic information john w oller, jr. Dna consists of two polynucleotide strands twisted around each other in a double helix. Apr 02, 2012 shannons mathematical theory of communication applied to dna sequencing nobody knows which sequencing technology is fastest because there has never been a fair way to compare the rate at which.
Note the difference in groove width and the relative displacements of the base pairs from the central axis. A gene is a specific sequence of bases which has the information for a particular protein. Each egg and sperm cell carries half of the dna complement 23 chromosomes. However, the team at dna worldwide decided to test this theory by combining forensic dna profiling and genomic sequencing. The secret of life molecular biologist james d watson gives the reader an in depth tour of genetics, its history, where it stands today and where its going tomorrow.
The same genetic information can be written in a book, stored in a compact disk or sent over the internet, and yet the quality or content of the message has not changed by changing the means of conveying it. The following module discusses the properties of dna, semen, and saliva so that we can better understand their use in forensic science. The intent was to develop the tools of ergodic theory of potential use to information theory and to demonstrate their use by proving shannon coding theorems for the most general known information sources, channels, and code structures. Information theory applications for biological sequence analysis. Indeed the diversity and directions of their perspectives and interests shaped the direction of information theory. The dna molecule carries the genetic language, but the language itself is independent of its carrier. This book provides a comprehensive overview of pcr theory, instrumentation and methods. Dna is the genetic material of all cells, containing coded information about cellular molecules and processes. The pattern in dna is not like a code, it is a code, by definition. Research into ancient dna began more than 25 years ago with the publication of short mitochondrial dna sequence fragments from the quagga, an extinct relati. Clearly, the structures of dna and rna are richer and more intricate than was at. The scientists applied ultradeep, next generation sequencing and combined this with bioinformatics, sequencing the dna from sperm samples of two twins and a blood sample of the child of one twin. As we shall see in this chapter, there are in fact vari.
It begins as a broad spectrum of fields, from management to biology, all believing information theory to be a magic key to multidisciplinary understanding. Now researchers at the indian institute of technology in delhi have used techniques from information theory to identify dna introns and exons an order of magnitude faster than previously developed. Nov 19, 2015 the amount of information you need for free is essentially zero. The subjects of stochastic processes, information theory, and lie groups are usually treated separately from each other. Information theory in genome analysis springerlink. Its a history book a narrative of the journey of our species through time. This information theoretic view falls in the realm of d na. The unique material properties of dna have made it an attractive molecule for material scientists and engineers interested in micro and nanofabrication.
Copying genetic information for transmission to the next generation. The notion of entropy, which is fundamental to the whole topic of this book, is. Information theory it addresses the analysis of communication. This unique twovolume set presents these topics in a unified setting, thereby building bridges between fields that are rarely studied by the same people.
Geoffrey wests book scale ponders the question of why we age. The genetic code is the sequence of bases on one of the strands. Logos are only the beginning, however, as the information theory measure used to compute them gives results in bits. Errorcorrecting codes, in particular, convolution code models, were also applied do dna with the goal of extracting features for sequence comparison and analysis 146. This information is stored in the form of long polymer chains. The pivotal role of the dna molecule stems from the fact that it and only it carries the whole information, and in all details, about the composition and properties of any living organism. Shannons mathematical theory of communication applied to. The tiny code thats toppling evolution united church. This onedimensional sequence of the protein determines the 3d structure of proteins. A recent book by chaitin provides an excellent and highly readable account of. Dec 21, 2019 david sinclairs information theory of aging is a convincing theory as to why we age. Historically, the federal bureau of investigation is often considered the goto resource for forensic science information and knowledge. Deep learning and an information theory of aging intuition. Although the information they carry is onedimensional, it is essential to understand the 3d structure of nucleic.
Chemists say, i still dont understand what youre saying, because they dont understand information theory, but theyre listening. Information theory is a framework for understanding the transmission of data and the effects of complexity and interference with these transmissions. Shannons mathematical theory of communication applied to dna. Information theory provides tools for such an investigation. Nov 04, 2015 the pivotal role of the dna molecule stems from the fact that it and only it carries the whole information, and in all details, about the composition and properties of any living organism.
But why would a binding site have some number of bits. Information theory an overview sciencedirect topics. The first step in cellular division is to replicate dna so that copies can be distributed to daughter cells. Its a shop manual, with an incredibly detailed blueprint for building every human cell. Some dna sequences encode important information for the cell. Its true that matter or energy can carry information, but they are not the same as information itself. The practical aspects revolve around designing and optimizing sequencing projects known as strategic genomics, predicting project performance, troubleshooting experimental. Mixing of genetic markers occurs across the dna molecule during the formation of sperm cells and egg cells. Begins with the unwinding of the double helix to expose the bases in each strand of dna. Information theory clearly indicates that the quantity of information carried by a sequence of amino acids is only sufficient to generate the earlystage es folding intermediate and that additional information must be provided in order to correctly model the remainder of the folding process. And its a transformative textbook of medicine, with. Biological information world scientific publishing company. Stochastic models, information theory, and lie groups.
Information theory, evolution and the origin of life presents a timely introduction to the use of information theory and coding theory in molecular biology. We shall often use the shorthand pdf for the probability density func. The unique material properties of dna have made it an attractive molecule for material scientists and engineers interested in micro. A small selection of the frequently asked questions about information theory are now listed and answered briefly. Birhanu worabo biotechnology is founded upon an ever increasing understanding of the mechanisms that maintain living organisms and allow them to reproduce from generation to generation. At the heart of every cell lies a collection of molecules that hold the key to biologys incredible diversity. Information theory and evolution discusses the phenomenon of life. A wellknown lower bound on the number of reads needed can be obtained by a coverage analysis, an approach pioneered by lander and waterman 12. Dna sequencing theory is the broad body of work that attempts to lay analytical foundations for determining the order of specific nucleotides in a sequence of dna, otherwise known as dna sequencing. David sinclairs information theory of aging is a convincing theory as to why we age. Watson and crick were bubbling at the fact that they had another chance to find out the structure of dna photograph of the double helix was shown to watson by wilkins. Because of this, the knowledge of all features of the dna structure is of a.
It is a recommended purchase for all microbiology and molecular biology laboratories and university libraries. Information theory and biological sequences erill lab. Information theory is one of the few scientific fields fortunate enough to have an identifiable beginning claude shannons 1948 paper. In fact, gatlins book is among the very few that does not incur some kind of. The theory is often applied to genetics to show how information held within a genome can actually increase, despite the apparent randomness of mutations. Dna dna deoxyribonucleic acid dna is the genetic material of all living cells and of many viruses. This unique twovolume set presents these topics in a unified setting, thereby building bridges between fields that are rarely studied by. Recombinant dna technology development and applications b. Model, theory and evidence in the discovery of the dna.
Model, theory and evidence in the discovery of the dna structure. Applying this equation to the joint distribution of the sample neuron gives a mutual information of 0. Recombinant dna refers to the creation of new combinations of dna segments that. Progress on the book was disappointingly slow, however, for a number of reasons. Dna replication california state university, northridge. Dec 30, 2015 classical concepts of information theory are quickly summarized and their application to the computational analysis of genomes is outlined. Biological information theory and the theory of molecular.
The sequence of bases letters can code for many properties of the bodys cells. The genetical information system, because it is linear and digital, resembles the algorithmic language of computers. The notion of entropy, which is fundamental to the whole topic of this book, is introduced here. According to a fundamental theorem of information theory, errorcorrecting. Now researchers at the indian institute of technology in delhi have used techniques from information theory to identify dna introns and exons an. The junk dna tends to accumulate near the ends and close to the centromeres of the chromosomes. The practical aspects revolve around designing and optimizing sequencing projects known as strategic genomics, predicting project performance. Because of this, the knowledge of all features of the dna structure is of a paramount significance. It has also been applied to highlevel correlations that combine dna, rna or protein features with sequenceindependent properties, such as gene mapping and phenotype analysis, and has also provided models based on communication systems theory to describe information transmission channels at the cell level and also during evolutionary processes. Recent studies in information theory have come up with some astounding conclusionsnamely, that information cannot be considered in the same category as matter and energy. Genomes are long strings, and this open the possibility of.
The book represents an excellent, detailed guide for anyone interested in the development and use of pcr technology. The use of information theory in evolutionary biology. Over three decades ago, in a seminal book 8, lila gatlin explored. Pdf dna sequencing is the basic workhorse of modern day biology and medicine. Stochastic models, information theory, and lie groups, volume. All human cells with a nucleus, except gamete cells egg and sperm cells. As per the dna structure, the dna consists of two chains of the polynucleotide, each in the form of a spherical spiral. We know that defense attorneys will want to be able to access this information in places where the internet may not be available. Tom schneider is best known for inventing sequence logos, a computer graphic depicting patterns in dna, rna or protein that is now widely used by molecular biologists. Research into ancient dna began more than 25 years ago with the publication of short mitochondrial dna sequence fragments from the.
Lecture notes intro to forensic science dna, semen, and saliva dna the following module discusses the properties of dna, semen, and saliva so that we can better understand their use in forensic science. Lila gatlins 1972 classic manuscript on applying information theory to living systems. Information theory helps unravel dnas genetic code. Dna is used by researchers as a molecular tool to explore physical laws and theories, such as the ergodic theorem and the theory of elasticity. Dna is a complex information system, so it must have come from an information sourcethe mind of the creator god. Classical concepts of information theory are quickly summarized and their application to the computational analysis of genomes is outlined. The difference between life and matter is information the information is located in the onedimensional dna sequence of four letters a,t,c,g which is translated with the help of the genetic code to the onedimensional sequence of 20 different amino acids in proteins. The story of the evolution of how it progressed from a single theoretical paper to a broad field that has redefined our world is a fascinating one. May 21, 2005 dna language not the same as dna molecule. Shannons mathematical theory of communication applied to dna sequencing nobody knows which sequencing technology is fastest because there has never been a fair way to compare the rate at which. Information theory applications for biological sequence. Importance of dna rna 3d structure nucleic acids are essential materials found in all living organisms. Application of information theory to dna sequence analysis. Indeed, there is no one generic structure for dna and rna.
Other techniques derived from signal theory, such as fourier transform, autocorrelation, spectral analysis, random walks or chaotic dynamics, have also been applied. Coding theory, the evolution of the genetic code and models for dna to protein information transfer 144, 145 were also object of several studies. So information theory applied to dna is not an analogy and actually has a possibility of making real progress in this debate. Pioneered for the study of binding sites in dna sequences, information. This is perhaps the first time the rigorous application of information theory is raining upon these chemists, but theyre willing to. It was the result of crucial contributions made by many distinct individuals, from a variety of backgrounds, who took his ideas and expanded upon them. The information theory argument is based on rigorous logical and mathematical definitions, and longstanding conventions in electrical engineering. Information theory was not just a product of the work of claude shannon. The book is provided in postscript, pdf, and djvu formats. Their main function is to maintain and transmit the genetic code.
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