The Role of Theory in Advancing 21st-Century Biology Catalyzing Transformative Research (2008) / Chapter Skim
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7 What Is the Information That Defines and Sustains Life?
7 What Is the Information That Defines and Sustains Life?
Pages 110-129
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From page 110... ...
For example, DNA sequence data on the genes of many organisms and satellite imagery of many ecosystems are now available. While this proliferation of data presents exciting new opportunities, making good use of it also presents significant challenges.
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From page 111... ...
From the sequence of a DNA molecule, to sounds, nerve impulses, signaling molecules, or chemical gradients, scientists find it useful to characterize biology in terms of information. From the critical discovery of the "genetic code" as the coupler between DNA sequence and protein synthesis, to the marvelous ability of bees to convey information about the location and quality of resources through dance, it is intuitively appealing to describe the processes and structures of biology in information terms.
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From page 112... ...
Cell biology seeks to understand how intracellular components encode and interpret the information necessary to organize cellular structure, maintain homeostasis, and carry out cellular functions. Development can be seen as the study of how these messages are used to extract and interpret the information in the genome in order to turn a single cell into a complex multicellular organism composed of thousands of cells with specialized functions.
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From page 113... ...
The storage and transmission of information are fundamental to living things, but they are not the exclusive properties of life. For inanimate matter, the power of information storage and transmission is decidedly limited, but not entirely absent -- for example, crystals, dendritic minerals, snowflakes, and other physical and chemical structures form, and thereby store, information in spontaneous order.
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From page 114... ...
that deals with information outside of the field of biology. One approach is provided by information theory as founded by Claude Shannon and Norbert Wiener to quantitatively understand communication channels (Shannon, 1948; Wiener, 1948; Shannon and Weaver, 1949)
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From page 115... ...
The question then is: What does that mean -- literally all possible amino acid sequences of that length, or all possible sequences represented in living organisms, or all possible sequences in the currently known database of protein sequences, or some other way of characterizing the possibilities? These different possible "sources" would all yield different measures for information.
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From page 116... ...
Then if we receive signal B, this example, a pheromone or vocal call of one species commonly conveys little information to another species (or at least a very different kind of information) ; a common human gene, rich in information for a human cell, is likely to carry no meaningful information in a bacterial cell; a segment of amino acid sequence that folds into a functional protein structure in the context of the sequence of its native protein may be useless and nonfunctional when set in the context of another protein sequence; the structure of an orchid's
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From page 117... ...
For biology, context is almost always essential, and consistent and useful theoretical tools are needed to describe, measure, and use contextual information in complex biological systems.
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From page 118... ...
STORING AND EXPRESSING INFORMATION IN THE GENES The discovery of how biological systems transduce genetic information was one of the most profound triumphs of 20th century science. Somehow, the cells of an organism contain the hereditary information that -- given appropriate interactions with the environment -- determines phenotype and behavior.
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From page 119... ...
These rules are now known as the "genetic code" even though it is now known that much more than the protein sequence information is contained in the DNA molecule of every organism. Much of the subsequent revolution in molecular biology that unfolded in the last half of the 20th century elaborated biologists' understanding of how each step of this process works: how DNA encodes protein structure, how the cellular machinery translates this code into proteins, and how the rest of the molecule provides information for the control of which proteins to synthesize and when.
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From page 120... ...
The inducer binds directly to the lactose repressor and causes the protein itself to change its conformation, rendering it incapable of binding tightly to the operator. This is the basic induction response of the lactose operon -- a disabling of a negative regulatory mechanism that allows transcription of the gene to proceed.
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From page 121... ...
If the regulatory response were binary, or Boolean -- on or off -- it can be considered as an "AND gate." While the lactose operon is complex in the sense that several proteins, specific DNA protein interactions, induced conformation changes in the repressor and the CAP protein, metabolic sensors, and enzymatic activities are involved, it behaves like a simple "AND gate" as depicted in Box 7-2c from the point of view of the cellular logic. The quantitative aspects of the behavior of the operon are important for some aspects of the cell's response, so that the Boolean model is insufficient in detail, but the basic response is really very simple.
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From page 122... ...
Because the critical factors that the cell is responding to are metabolic in nature -- the need to use lactose as a carbon source -- the genetic regulatory network is coupled to the metabolic network of the cell. The lactose system was a fortunate choice by Jacob and Monod because it turns out to be a very simple system indeed -- at least by the standards of genetic regulatory networks.
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From page 123... ...
sites for a number of proteins in the DNA and the DNA sequences that are actual protein-encoding segments of DNA. These proteins bind to sites in the DNA near genes, some of which encode other proteins that bind DNA sites and regulate their expression (transcription factors)
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From page 124... ...
There is also unseen complexity in the batteries of other genes, including the metabolic and structural genes that are expressed in each cell type driven by the presence of the specific set of transcription factors in the cells of each type. This example illustrates the nature of the information needed and the degree of complexity involved in early embryogenesis.
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From page 125... ...
Box 7-3 gives examples of a particular circuit used in several different developmental pathways. SHARING INFORMATION Much of the accumulation of biological complexity that has occurred over the history of life on Earth has arisen through major transitions in which previously unassociated entities either joined into a common reproductive fate or developed cooperative associations while maintaining reproductive independence (Maynard Smith and Szathmáry, 1995)
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From page 126... ...
The regulatory interactions of a small set of genes that drive the transition of the network to the next stage are a recurring theme. Despite the variety of organisms and cell differentiation pathways represented in the four examples shown here (two from the sea urchin (a and d)
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From page 127... ...
Drosophila tracheal placode trh dfr 0 0 1 1 trh dfr Downstream signaling genes Regulatory and downstream genes d. Sea urchin oral ectoderm gsc repr dri gsc repr 0 1 0 1 0 1 Arboral ectoderm genes dri Oral ectoderm regulatory genes SOURCE: Figure courtesy of David Galas, based on information contained in D avidson (2003)
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From page 128... ...
Clearly, there will be situations in which sharing information devalues that information -- for example, if a person shares the location of a limited food source with others, the information sharing is likely to reduce the amount of food that the person gets from that location. But devaluing information by sharing is not an inherent property of the information itself; rather, it is a consequence of the situation.
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From page 129... ...
further draw out the relation between theoretic measures of genomic information and the concept of Darwinian fitness. These analyses hint that the two different ways of measuring information -- the Shannon framework and the decision theory framework -- could be closely related under special circumstances.
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