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Hesson LB, Pritchard AL. Genetics and Epigenetics: A Historical Overview. Clin Epigenetics 2019. [DOI: 10.1007/978-981-13-8958-0_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Laubichler MD, Prohaska SJ, Stadler PF. Toward a mechanistic explanation of phenotypic evolution: The need for a theory of theory integration. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2018; 330:5-14. [DOI: 10.1002/jez.b.22785] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Revised: 11/03/2017] [Accepted: 11/15/2017] [Indexed: 01/01/2023]
Affiliation(s)
- Manfred D. Laubichler
- School of Life Sciences; Arizona State University; Tempe Arizona
- Marine Biological Laboratory; Woods Hole; Massachusetts
- Santa Fe Institute; Santa Fe New Mexico
| | - Sonja J. Prohaska
- Santa Fe Institute; Santa Fe New Mexico
- Computational EvoDevo Group; Department of Computer Science; Leipzig Germany
- Interdisciplinary Center of Bioinformatics; University of Leipzig; Leipzig Germany
| | - Peter F. Stadler
- Santa Fe Institute; Santa Fe New Mexico
- Interdisciplinary Center of Bioinformatics; University of Leipzig; Leipzig Germany
- Bioinformatics Group, Department of Computer Science; University of Leipzig; Leipzig Germany
- Max-Planck Institute for Mathematics in the Sciences; Leipzig Germany
- Fraunhofer Institut für Zelltherapie und Immunologie-IZI; Leipzig Germany. Department of Theoretical Chemistry; University of Vienna; Wien Austria. Center for Non-Coding RNA in Technology and Health; University of Copenhagen; Frederiksberg Denmark
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Kempes CP, Wolpert D, Cohen Z, Pérez-Mercader J. The thermodynamic efficiency of computations made in cells across the range of life. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2017; 375:20160343. [PMID: 29133443 PMCID: PMC5686401 DOI: 10.1098/rsta.2016.0343] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 07/31/2017] [Indexed: 06/01/2023]
Abstract
Biological organisms must perform computation as they grow, reproduce and evolve. Moreover, ever since Landauer's bound was proposed, it has been known that all computation has some thermodynamic cost-and that the same computation can be achieved with greater or smaller thermodynamic cost depending on how it is implemented. Accordingly an important issue concerning the evolution of life is assessing the thermodynamic efficiency of the computations performed by organisms. This issue is interesting both from the perspective of how close life has come to maximally efficient computation (presumably under the pressure of natural selection), and from the practical perspective of what efficiencies we might hope that engineered biological computers might achieve, especially in comparison with current computational systems. Here we show that the computational efficiency of translation, defined as free energy expended per amino acid operation, outperforms the best supercomputers by several orders of magnitude, and is only about an order of magnitude worse than the Landauer bound. However, this efficiency depends strongly on the size and architecture of the cell in question. In particular, we show that the useful efficiency of an amino acid operation, defined as the bulk energy per amino acid polymerization, decreases for increasing bacterial size and converges to the polymerization cost of the ribosome. This cost of the largest bacteria does not change in cells as we progress through the major evolutionary shifts to both single- and multicellular eukaryotes. However, the rates of total computation per unit mass are non-monotonic in bacteria with increasing cell size, and also change across different biological architectures, including the shift from unicellular to multicellular eukaryotes.This article is part of the themed issue 'Reconceptualizing the origins of life'.
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Affiliation(s)
| | - David Wolpert
- The Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Beyond Center, Arizona State University, Tempe, AZ 85287, USA
| | - Zachary Cohen
- Department of Biology, University of Illinois, Urbana Champagne, Urbana, IL 61801, USA
| | - Juan Pérez-Mercader
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA 02138, USA
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Abstract
This paper presents a history of the changing meanings of the term "gene," over more than a century, and a discussion of why this word, so crucial to genetics, needs redefinition today. In this account, the first two phases of 20th century genetics are designated the "classical" and the "neoclassical" periods, and the current molecular-genetic era the "modern period." While the first two stages generated increasing clarity about the nature of the gene, the present period features complexity and confusion. Initially, the term "gene" was coined to denote an abstract "unit of inheritance," to which no specific material attributes were assigned. As the classical and neoclassical periods unfolded, the term became more concrete, first as a dimensionless point on a chromosome, then as a linear segment within a chromosome, and finally as a linear segment in the DNA molecule that encodes a polypeptide chain. This last definition, from the early 1960s, remains the one employed today, but developments since the 1970s have undermined its generality. Indeed, they raise questions about both the utility of the concept of a basic "unit of inheritance" and the long implicit belief that genes are autonomous agents. Here, we review findings that have made the classic molecular definition obsolete and propose a new one based on contemporary knowledge.
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Affiliation(s)
- Petter Portin
- Laboratory of Genetics, Department of Biology, University of Turku, 20014, Finland
| | - Adam Wilkins
- Institute of Theoretical Biology, Humboldt Universität zu Berlin, 10115, Germany
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Boem F, Ratti E, Andreoletti M, Boniolo G. Why genes are like lemons. STUDIES IN HISTORY AND PHILOSOPHY OF BIOLOGICAL AND BIOMEDICAL SCIENCES 2016; 57:88-95. [PMID: 27155220 DOI: 10.1016/j.shpsc.2016.04.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Revised: 04/22/2016] [Accepted: 04/25/2016] [Indexed: 06/05/2023]
Abstract
In the last few years, the lack of a unitary notion of gene across biological sciences has troubled the philosophy of biology community. However, the debate on this concept has remained largely historical or focused on particular cases presented by the scientific empirical advancements. Moreover, in the literature there are no explicit and reasonable arguments about why a philosophical clarification of the concept of gene is needed. In our paper, we claim that a philosophical clarification of the concept of gene does not contribute to biology. Unlike the question, for example, "What is a biological function?", we argue that the question "What is a gene?" could be answered by means of empirical research, in the sense that biologists' labour is enough to shed light on it.
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Affiliation(s)
- F Boem
- Dipartimento di Oncologia ed Emato-oncologia, Università di Milano, Italy
| | - E Ratti
- Center for Theology, Science and Human Flourishing, University of Notre Dame, USA.
| | - M Andreoletti
- Dipartimento di Scienze della Salute, Universita' di Milano, Italy; Department of Experimental Oncology, European Institute of Oncology, Italy
| | - G Boniolo
- Dipartimento di Scienze Biomediche e Chirurgico Specialistiche, Università of Ferrara, Italy; Institute for Advanced Study, Technische Universität München, Germany
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The Cellular Chassis as the Basis for New Functionalities: Shortcomings and Requirements. Synth Biol (Oxf) 2015. [DOI: 10.1007/978-3-319-02783-8_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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Martínez-Gómez P, Sánchez-Pérez R, Rubio M. Clarifying omics concepts, challenges, and opportunities for Prunus breeding in the postgenomic era. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2012; 16:268-83. [PMID: 22394278 DOI: 10.1089/omi.2011.0133] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The recent sequencing of the complete genome of the peach, together with the availability of new high-throughput genome, transcriptome, proteome, and metabolome analysis technologies, offers new possibilities for Prunus breeders in what has been described as the postgenomic era. In this context, new biological challenges and opportunities for the application of these technologies in the development of efficient marker-assisted selection strategies in Prunus breeding include genome resequencing using DNA-Seq, the study of RNA regulation at transcriptional and posttranscriptional levels using tilling microarray and RNA-Seq, protein and metabolite identification and annotation, and standardization of phenotype evaluation. Additional biological opportunities include the high level of synteny among Prunus genomes. Finally, the existence of biases presents another important biological challenge in attaining knowledge from these new high-throughput omics disciplines. On the other hand, from the philosophical point of view, we are facing a revolution in the use of new high-throughput analysis techniques that may mean a scientific paradigm shift in Prunus genetics and genomics theories. The evaluation of scientific progress is another important question in this postgenomic context. Finally, the incommensurability of omics theories in the new high-throughput analysis context presents an additional philosophical challenge.
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Abstract
Genes are generally assumed to be primary biological causes of biological phenotypes and their evolution. In just over a century, a research agenda that has built on Mendel's experiments and on Darwin's theory of natural selection as a law of nature has had unprecedented scientific success in isolating and characterizing many aspects of genetic causation. We revel in these successes, and yet the story is not quite so simple. The complex cooperative nature of genetic architecture and its evolution include teasingly tractable components, but much remains elusive. The proliferation of data generated in our "omics" age raises the question of whether we even have (or need) a unified theory or "law" of life, or even clear standards of inference by which to answer the question. If not, this not only has implications for the widely promulgated belief that we will soon be able to predict phenotypes like disease risk from genes, but also speaks to the limitations in the underlying science itself. Much of life seems to be characterized by ad hoc, ephemeral, contextual probabilism without proper underlying distributions. To the extent that this is true, causal effects are not asymptotically predictable, and new ways of understanding life may be required.
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Affiliation(s)
- Kenneth M Weiss
- Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania 16802, USA.
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Abstract
The diverse fields of Omics research share a common logical structure combining a cataloging effort for a particular class of molecules or interactions, the underlying -ome, and a quantitative aspect attempting to record spatiotemporal patterns of concentration, expression, or variation. Consequently, these fields also share a common set of difficulties and limitations. In spite of the great success stories of Omics projects over the last decade, much remains to be understood not only at the technological, but also at the conceptual level. Here, we focus on the dark corners of Omics research, where the problems, limitations, conceptual difficulties, and lack of knowledge are hidden.
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Affiliation(s)
- Sonja J Prohaska
- Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany
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Falk R. What is a gene? - Revisited. STUDIES IN HISTORY AND PHILOSOPHY OF BIOLOGICAL AND BIOMEDICAL SCIENCES 2010; 41:396-406. [PMID: 21112014 DOI: 10.1016/j.shpsc.2010.10.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2010] [Revised: 09/04/2010] [Indexed: 05/30/2023]
Abstract
The dialectic discourse of the 'gene' as the unit of heredity deduced from the phenotype, whether an intervening variable or a hypothetical construct, appeared to be settled with the presentation of the molecular model of DNA: the gene was reduced to a sequence of DNA that is transcribed into RNA that is translated into a polypeptide; the polypeptides may fold into proteins that are involved in cellular metabolism and structure, and hence function. This path turned out to be more bewildering the more the regulation of products and functions were uncovered in the contexts of integrated cellular systems. Philosophers struggling to define a unified concept of the gene as the basic entity of (molecular) genetics confronted those who suggested several different 'genes' according to the conceptual frameworks of the experimentalists. Researchers increasingly regarded genes de facto as generic terms for describing their empiric data, and with improved DNA-sequencing capacities these entities were as a rule bottom-up nucleotide sequences that determine functions. Only recently did empiricists return to discuss conceptual considerations, including top-down definitions of units of function that through cellular mechanisms select the DNA sequences which comprise 'genomic-footprints' of functional entities.
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Affiliation(s)
- Raphael Falk
- Department of Genetics and The Program for the History and Philosophy of Science, The Hebrew University of Jerusalem, Jerusalem, Israel.
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Evolvability and Speed of Evolutionary Algorithms in Light of Recent Developments in Biology. ACTA ACUST UNITED AC 2010. [DOI: 10.1155/2010/568375] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Biological and artificial evolutionary systems exhibit varying degrees of evolvability and different rates of evolution. Such quantities can be affected by various factors. Here, we review some evolutionary mechanisms and discuss new developments in biology that can potentially improve evolvability or accelerate evolution in artificial systems. Biological notions are discussed to the degree they correspond to notions in Evolutionary Computation. We hope that the findings put forward here can be used to design computational models of evolution that produce significant gains in evolvability and evolutionary speed.
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Evolutionary epistemology as a scientific method: a new look upon the units and levels of evolution debate. Theory Biosci 2010; 129:167-82. [DOI: 10.1007/s12064-010-0085-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2009] [Accepted: 11/04/2009] [Indexed: 10/19/2022]
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