Biological Sciences
Genetic Information
Genetic information refers to the heritable material that determines the traits and characteristics of an organism. It is encoded in the DNA and RNA molecules and is passed from one generation to the next. This information contains the instructions for the development, functioning, and reproduction of living organisms.
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12 Key excerpts on "Genetic Information"
- David L. Hull, Michael Ruse(Authors)
- 2007(Publication Date)
- Cambridge University Press(Publisher)
6 Information in Biology 1. introduction The concept of information has acquired a strikingly prominent role in contemporary biology. This trend is especially marked within genetics, but it has also become important in other areas, such as evolutionary theory and developmental biology, especially where these fields border on genetics. The most distinctive biological role for informational concepts, and the one that has generated the most discussion, is in the description of the relations between genes and the various structures and processes that genes play a role in caus- ing. For many biologists, the causal role of genes should be under- stood in terms of their carrying information about their various products. That information might require the cooperation of various environmental factors before it can be ‘‘expressed,’’ but the same can be said of other kinds of message. An initial response might be to think that this mode of description is entirely anchored in a set of well-established facts about the role of DNA and RNA within protein synthesis, summarized in the familiar chart representing the ‘‘genetic code,’’ mapping DNA base triplets to amino acids. However, informational enthusiasm in biology predates even a rudimentary understanding of these mechanisms (Schrodinger 1944). And more importantly, current applications of informational concepts extend far beyond anything that can receive an obvious justification in terms of the familiar facts about the specification of protein molecules by DNA. This includes (i) The description of whole-organism phenotypic traits (including complex behavioral traits) as specified or coded for by information contained in the genes; 103 peter godfrey-smith
eBook - ePubHuman Population Genetic Research in Developing Countries
The Issue of Group Protection
- Yue Wang(Author)
- 2013(Publication Date)
- Taylor & Francis(Publisher)
(a) It is a relatively independent unit of heredity. As an information unit, a gene can refresh combinations of the genetic make-up of both parents by transferring them to offspring. What is more, a gene can instruct, influence and even decide creatures’ traits, such as body structure and living habits.(b) At a molecular level, a gene is a segment of a DNA molecule, the sequences of nucleotides (or bases) in genes represent the heredity of human beings and other creatures. The information in a gene is encoded in the sequence of base groups of DNA.(c) Genes are specific sequences of bases that encode instructions on how to make proteins.8 Gene sequences of DNA, when transferred into strands of messenger RNA, could be used as the basis for building their related protein piece by piece. The gene could not only transmit all of this information through replication, but also could dominate the organism’s character by controlling the process of synthesizing protein, which is called ‘gene expression’. In other words, a gene exerts its physical function through directing the production of proteins and RNA molecules.Genetic Information What is Genetic InformationAccording to Article 2(i) of the UNESCO International Declaration on Human Genetic Data, human genetic data is ‘the information about heritable characteristics of individuals obtained by analysis of nucleic acids or by other scientific analysis’.9 Although the intention of this definition is merely to set out the relationship between human Genetic Information and scientific research, it suggests that the real value of the gene is not its physical substance but the information carried in it.In general, Genetic Information is the information for making all of the proteins required by all organisms. These proteins determine, among other things, how the organism looks, how well its body metabolises food or fights infection, and sometimes even how it behaves.10
- Jason Rosenhouse(Author)
- 2022(Publication Date)
- Cambridge University Press(Publisher)
Is there anything playing those roles in the biological context? Moreover, information in human affairs seems intimately related to communication, but what is the analog of this 168 6 information and combinatorial search in biology? After all, DNA does not know it contains information. At the cellular level, everything just plays out according to the principles of physics and chemistry. Scientists have a pretty good understanding of the physical processes that transform a genotype into a phenotype, and you can understand these processes perfectly well without making any reference to information. We might then wonder whether information is genuinely a fundamental concept in molecular biology or is instead just a useful source of metaphors. This question has been the cause of considerable controversy among scientists and philosophers for many years. In a 1995 article, biologists Eörs Szathmáry and John Maynard Smith took the former view: A central idea in contemporary biology is that of information. Developmental biology can be see as the study of how information in the genome is translated into adult structure, and evolutionary biology of how the information came to be there in the first place. Our excuse for writing an article concerning topics as diverse as the origins of genes, of cells and of language is that all are concerned with the storage and transmission of information. (Szathmáry and Maynard Smith 1995, 231) Representative of the latter view is philosopher Paul Griffiths: It is conventional wisdom that insofar as the traits of an organism are subject to biological explanation, those traits express information coded in the organisms’ genes. … I will argue, however, that the only truth reflected in the conventional view is that there is a genetic code by which the sequence of DNA bases in the coding regions of a gene corresponds to the sequence of amino acids in the primary structure of one or more proteins.
eBook - ePub- Cédric Gaucherel, Pierre-Henri Gouyon, Jean-Louis Dessalles, Pierre-Henri Gouyon, Jean-Louis Dessalles(Authors)
- 2018(Publication Date)
- Wiley-ISTE(Publisher)
2 Genetic Information We started out with a view of information in the form that is most intuitive and most familiar to us, that is information in human communication. This notion of information involves a sender and a receiver, as well as a supporting code or language. We saw that this notion could easily be extended to animal communication. Can we go further, and speak of information, language and code in connection with biology in general? Of course we can. A domain of biology in which information plays a leading role, and which deserves a close study in its own right, is genetics. How this field is related to information, language, code and the specific features of that relationship are issues that we will consider in the following. 2.1. A central concept in biology Molecular biology devotes particular attention to information that is transmitted from generation to generation. The message of heredity is generally carried by an element of DNA. DNA is a linear chain consisting of pairs of nucleotides. The four nucleotides that constitute DNA are designated by the letters A, T, G and C, which stand for the corresponding molecules that are the chemical bases: adenine, thymine, guanine and cytosine. However, DNA does not resemble a string of pearls, in which each base would be one of four possible bases. Instead, it is more like a ladder (see Figure 1.1), in which each rung is a pair of nucleotides. This happens because of the affinities that exist between A and T, and between C and G. These affinities arise from hydrogen bonds that are strong enough to preserve their association, but not strong enough to make that association irreversible. The sequence of nucleotides is made complete by its complement, thus producing the well-known double helix that James Watson and Francis Crick discovered in 1953. The ladder was seen to be twisted so as to appear shaped like a helix. Each nucleotide faces its complement on this ladder – A with T, T with A, C with G, G with C
eBook - PDFBioinformatics Basics
Applications in Biological Science and Medicine
- Lukas K. Buehler, Hooman H. Rashidi, Lukas K. Buehler, Hooman H. Rashidi(Authors)
- 2005(Publication Date)
- CRC Press(Publisher)
For some the meaning extends to the concept of information flow within biological systems alluding to the transmission of genetically encoded information transmitted from genes to proteins, from the blueprint to the machinery of life. Bioinformaticians attempt to understand what it means to say that genes code for physiological traits such as enzyme activity, curly hair, or the susceptibility for disease. Through the creation, annotation, and mining of biological databases they help elu-cidate the mechanism of genetic complexity and evolutionary relationships among organisms. Bioinformatics depends on the assumption that quantifi-able relationships exist not only between the sequence of genes and the structure and function of proteins, but also between the activity of genes and their placement within the genome. Commencing from a single gene, single protein approach to a global view of gene activity and protein networks, bioinformaticians make use of database mining techniques to study protein complexes, metabolic pathways, and gene networks. The bread-and-butter of bioinformatics are gene sequences and protein struc-tures . So, how can bioinformatics contribute to answering questions in biol-ogy and medicine? Genes are the hereditary units of life, and genomes of contemporary organisms are the only molecular source of information of its history (with exceptions of well-preserved paleontological samples of soft tissue). While the accurate copying of Genetic Information from generation to generation is crucial for the viability of organisms and thus the continu-ation of life, randomly occurring mutations, i.e., the alterations of gene sequences, are equally central for biological evolution, e.g., the ability of organisms to adapt to environmental changes.
eBook - PDFInformation and the Nature of Reality
From Physics to Metaphysics
- Paul Davies, Niels Henrik Gregersen(Authors)
- 2014(Publication Date)
- Cambridge University Press(Publisher)
PART III BIOLOGY 7 The concept of information in biology john maynard smith The use of informational terms is widespread in molecular and developmental biology. The usage dates back to Weis- mann. In both protein synthesis and in later development, genes are symbols, in that there is no necessary connec- tion between their form (sequence) and their effects. The sequence of a gene has been determined by past natural selection, because of the effects it produces. In biology, the use of informational terms implies intentionality, in that both the form of the signal, and the response to it, have evolved by selection. Where an engineer sees design, a biologist sees natural selection. A central idea in contemporary biology is that of information. Developmental biology can be seen as the study of how infor- mation in the genome is translated into adult structure, and evolutionary biology of how the information came to be there in the first place. Our excuse for writing a chapter concerning topics as diverse as the origins of genes, of cells, and of language is that all are concerned with the storage and transmission of information. (Szathm´ ary and Maynard Smith, 1995) Let us begin with the notions involved in classical information theory . . . These concepts do not apply to DNA because they Information and the Nature of Reality: From Physics to Metaphysics, eds. Paul Davies and Niels Henrik Gregersen. Published by Cambridge University Press C P. Davies and N. Gregersen 2010, 2014. 157 Information and the Nature of Reality presuppose a genuine information system, which is composed of a coder, a transmitter, a receiver, a decoder, and an infor- mation channel in between. No such components are apparent in a chemical system (Apter and Wolpert, 1965). To describe chemical processes with the help of linguistic metaphors such as “transcription” and “translation” does not alter the chemical nature of these processes.
eBook - PDFBioinformatics for Geneticists
A Bioinformatics Primer for the Analysis of Genetic Data
- Michael R. Barnes(Author)
- 2007(Publication Date)
- Wiley(Publisher)
Altogether, we hope these new contributions will address the lion’s share of the newer and long-standing challenges that face the human geneticist. 1.2 The role of bioinformatics in genetics research The function of bioinformatics is now essential to the effective interrogation of genetic and genomic data as well as most other biological data. This makes expertise in bioinformatics a prerequisite for effectiveness in genetics. Expertise in bioinformatics is no mystery; the right bioinformatics tools, coupled with an enquiring mind and willingness to experiment (key requirements for any scientist, bioinformatician or not), can yield confidence and competence in handling bioinformatics data in a very short space of time. The objective of this book is not to provide an exhaustive guide to bioinformatics; other texts fulfil this role. Instead, it is intended as a specialist guide to help the human geneticist navigate the Internet to some of the best tools and databases for the job; that is, linking and associating genes with diseases and genetic traits. In this chapter, we give a flavour of the many processes in human genetics where bioinformatics can have a major impact, and refer to subsequent chapters for greater detail. 1.2.1 Gaining understanding of genetic traits The process of understanding a genetic trait typically proceeds through three stages: first, recognition of the disease state or syndrome, including assessment of its 1.3 GENETICS IN THE POST-GENOME ERA 5 hereditary character; second, discovery and mapping of the related polymorphism(s) or mutation(s); and third, elucidation of the biochemical/biophysical mechanism leading to the disease phenotype. Each of these stages proceeds with a variable de-gree of laboratory investigation and data analysis, often by bioinformatics methods. Both activities are complementary, bioinformatics without laboratory work is a sterile activity just as laboratory work without bioinformatics can be futile and inefficient.
eBook - PDFDarwinian Reductionism
Or, How to Stop Worrying and Love Molecular Biology
- Alexander Rosenberg(Author)
- 2008(Publication Date)
- University of Chicago Press(Publisher)
And they will hold that it is this program that explains development, that breakdowns in this program explain abnormalities in development, that mutations in it explain differences in development; and it is this program that provides the basis for converting the how-possible explana-tions of non-molecular evolutionary biology to the why-necessary explanations of molecular evolutionary biology. Opponents of genocentrism will grant that there is an attenuated sense of information in which many other things besides the genome carry information about development and hereditary traits. This is the sense of information as it figures in mathematical information theory. It is true that the mathematical theory of information due to Shannon and Weaver (1963) applies to any causal chain, including ones in the environment transmitting epigenetic “hereditary” information, just as well as it does to genetic transmission of hereditary infor-mation. This is simply because the Shannon-Weaver formalism is a way of mea-suring the quantity of information and the reliability of transmission which any causal chain can be employed to transmit. But the transmission of information requires more than a causal chain. Otherwise, the causal chain that transmits a scrambled TV signal would count as transmitting information (beyond the “information” that the signal was scrambled). 1 Unlike the other causes of development, genes are claimed to be information- bearing causes because the nucleotide sequence of adenine, thymine, guanine, and cytosine (hereafter A,T,G,C) constitutes a code in which the structure of proteins is expressed, and from which that structure can be read off. That it is literally code is reflected in several facts about it; for one, the genetic code is redundant. Though with four units one can send 2 6 (that is, 64) different bits 1.
eBook - PDF- Gerard Battail(Author)
- 2022(Publication Date)
- Springer(Publisher)
Part II Facts of Genetics and Information Theory 39 C H A P T E R 4 More on Molecular Genetics As with biology in general, molecular genetics is a complex topic. We shall deal very roughly with it: almost all statements in this survey, besides being simplified, actually have exceptions which are not mentioned for the sake of brevity and readability; similarly, only few references to the texts used for compiling this survey are given besides those of historical significance. We shall mention only the details of chemical structure which are relevant to our purpose. 4.1 MOLECULAR MEMORIES: DNA AND RNA 4.1.1 UNIDIMENSIONAL POLYMERS AS HEREDITARY MEMORIES Since the works of Avery et al. [2] and Chargaff [26], it is known that the hereditary information is borne by DeoxyriboNucleic Acid (DNA) molecules in all living beings (except for certain viruses where ribonucleic acid, RNA, performs this role). DNA has been shown by Franklin and Gosling [38] and Watson and Crick [76] to assume the famous double-helix shape. To convey information, a molecule must be a unidimensional polymer, i.e., a chain of an arbitrary number of links, each bearing a small molecule from a given finite repertoire, or alphabet. These information-bearing molecules succeed to each other in an arbitrary order; their sequence constitutes the genetic message. Similarly, a written text is a unidimensional sequence of letters, digits, separating spaces, and punctuation marks, i.e., symbols from a given alphabet, in the order that the author of the text chose. Unidimensionality is necessary in both a genetic message and a written text, since an order must exist between its symbols (information-bearing molecules or letters): given any two symbols, one of them should either precede or follow the other one. This is necessary for establishing syntactic rules, which are themselves necessary for the written message to convey a semantic content.
eBook - PDFThe Evolution of Biological Information
How Evolution Creates Complexity, from Viruses to Brains
- Christoph Adami(Author)
- 2024(Publication Date)
- Princeton University Press(Publisher)
10 The Many Roles of Information in Biology Nothing in biology makes sense except in the light of information. We have come to the last chapter of this book, so it is time to step back a little bit from the details—the mathematics and the experiments—and con- template the role of information in biology from a more general perspective. According to the quote above, which I confess I unashamedly modified from Dobzhansky’s original, information is everything in biology: nothing makes sense without it. In this age of bioinformatics and genomics, it may seem that the role of information—in the sense described by Shannon—was always accepted in biology, but this is far from the truth. As late as twenty years ago, the theoretical biologist John Maynard Smith was pleading to take the concept of informa- tion beyond the metaphorical, arguing for a more quantitative application of Shannon’s ideas not just to the storage of information, but to signaling and communication as well (Maynard Smith 2000). The unambiguous success of applying Shannon’s concepts to transcriptional regulation (Tkačik et al. 2008b) and biochemical signaling (Cheong et al. 2011) has certainly changed the landscape, but the idea that Shannon information quantitatively describes how much information is stored within genomes (and how to measure it) is still not widely accepted. Of course, there are aspects of biology that are not directly or indirectly due to information, but rather exist due to chance. After all, the evolutionary process itself (as pointed out in the very first chapter) fundamentally relies on three components: inheritance, selection, and . . . chance (in the form of random mutations). And while characters that exist due to chance can be inherited and therefore persist, they are by definition not relevant in our quest to understand how an organism relates to its environment. Many times we can 499 500 chapter 10 recognize nonadaptive traits as such.
eBook - PDF- B. Dowling(Author)
- 2005(Publication Date)
- Palgrave Macmillan(Publisher)
This occurs in much the same fashion that DNA is made up of genes which in turn are made up of the chemical bases (C, A, G, T). Themes drive market sentiment which is then reflected in asset pricing and overall index performance. Like- wise, a gene representation determines chromosome behavior which in turn determines cell structure and the organism’s phenotype. In fact, we would go as far as to argue that just as there is a Genetic Information genotype under- lying each and every organism’s phenotype, there is an analogous financial information genotype underlying each and every market price phenotype. It is our objective to ascertain this sequenced genetic coding of financial inform- ation – as information bytes come to comprise subgroup memes which in turn, form larger theme strings. In short, what we are effectively searching for is the “informational genome” of both individual asset prices and for the market as a whole. We feel such an identification of the actual biological- like component structure of the sequenced information underlying each and every asset price phenotype is a powerful result that has many implications for finance – not only from a theoretical modeling perspective but also from an applied perspective as well. But to take our analogy further we need to formalize our “informational genome” framework in much greater detail – this is the charter of the following section. 4.3 The building blocks of our evolutionary approach toward information in finance How to encompass the aspects of Table 4.1 into a comprehensive model of information evolution? At first we need to formalize the actual building blocks of financial information itself – how bytes form memes, how memes 12 A key distinction in Table 4.1 is that between genotype and phenotype (see vertical axis). In biology, the genotype is a complex set of Genetic Information (genes) encoded in the DNA of an organism. The phenotype is the physical appearance of the organism itself.
eBook - PDFOogenesis
The Storage of Developmental Information
- Chr. P. Raven, G. A. Kerkut(Authors)
- 2013(Publication Date)
- Pergamon(Publisher)
The epigenetic theory claims that this tremendous and, as it appears, unobservable additional information is not stored in the gamete in form of material modifications ,, (Elsasser, 1958, pp. 12-13). The second argument starts from the principle that a machine cannot generate information. Information once lost cannot be retrieved. Hence, the hereditary information in the germ cell, in the form of chemical complexity of the macromolecules, must be carefully preserved against degradation by noise, such as the random effects of chemical processes acting upon the molecular structures in which information is stored. The mechanist must assume that the information can be protected against all those unpredictable deleterious influences which we have summarized in the term noise, in spite of the reduction to extremely small size (Elsasser, 1958, p. 125). It is questioned whether such a device can be compressed into the volume of a few microns in diameter and still function reliably. Elsasser suggests that the information content of an organism does actually increase tremendously in the process of development. This cannot be explained by the laws of physics. Embryonic development is characterized by a preponderance of biotonic causality'' (p. 19). The term biotonic is suggested for those pheno-mena which cannot be fully interpreted in terms of pure mech- 206 INFORMATION THEORY AND BIOLOGY anisms. Biotonic laws express the conditions for the stability or reproduction of information in the organism in the absence of mechanistic storage. Biotonic laws cannot be derived deductively from physics (p. 146). They are empirical regularities pertaining to classes of organisms, well beyond the range where physical prediction could yield significant results (p. 157). Though biotonic laws are not deducible from physics, they are compatible with physical laws. The laws of physics invariably hold whenever they are being operationally verified in the organism.
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