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      Sequences and consequences

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          Abstract

          The conversion of data into knowledge constitutes a great challenge for future biological research. The new science of Systems Biology claims to be able to solve the problem but I contend that this approach will fail because deducing models of function from the behaviour of a complex system is an inverse problem that is impossible to solve. In addition, one cannot easily escape into high-level holistic approaches, since the essence of all biological systems is that they are encoded as molecular descriptions in their genes and since genes are molecules and exert their functions through other molecules, the molecular explanation must constitute the core of understanding biological systems. We then solve the forward problem of computing the behaviour of the system from its components and their interactions. I propose that the correct level of abstraction is the cell and provide an outline of C ellmap, a design for a system to organize biological information.

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          Most cited references 3

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          Life, logic and information.

           Paul Nurse (2008)
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            Genomics. The end of the beginning.

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              Theoretical biology in the third millennium.

              During the 20th century our understanding of genetics and the processes of gene expression have undergone revolutionary change. Improved technology has identified the components of the living cell, and knowledge of the genetic code allows us to visualize the pathway from genotype to phenotype. We can now sequence entire genes, and improved cloning techniques enable us to transfer genes between organisms, giving a better understanding of their function. Due to the improved power of analytical tools databases of sequence information are growing at an exponential rate. Soon complete sequences of genomes and the three-dimensional structure of all proteins may be known. The question we face in the new millennium is how to apply this data in a meaningful way. Since the genes carry the specification of an organism, and because they also record evolutionary changes, we need to design a theoretical framework that can take account of the flow of information through biological systems.
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                Author and article information

                Journal
                Philos Trans R Soc Lond B Biol Sci
                RSTB
                royptb
                Philosophical Transactions of the Royal Society B: Biological Sciences
                The Royal Society
                0962-8436
                1471-2970
                12 January 2010
                12 January 2010
                : 365
                : 1537 , Theme Issue 'Personal perspectives in the life sciences for the Royal Society's 350th anniversary' compiled and edited by Georgina Mace
                : 207-212
                Affiliations
                [1 ]King's College, Cambridge CB2 1ST, UK
                [2 ]Crick-Jacobs Center, simpleSalk Institute of Biological Studies , 10010 North Torrey Pines Road, La Jolla, 92037 CA, USA
                Author notes
                Article
                rstb20090221
                10.1098/rstb.2009.0221
                2842711
                20008397
                © 2010 The Royal Society

                This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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                Philosophy of science

                cellmap, biological information system, systems biology

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