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Shapiro JA. Implications of the Read-Write Genome view. Phys Life Rev 2013; 10:347-50. [PMID: 23988879 DOI: 10.1016/j.plrev.2013.07.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Accepted: 07/16/2013] [Indexed: 10/26/2022]
Affiliation(s)
- James A Shapiro
- Dept. of Biochemistry and Molecular Biology, University of Chicago, GCIS W123B, 979 E. 57th Street, Chicago, IL 60637, USA.
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Bizzarri M, Palombo A, Cucina A. Theoretical aspects of Systems Biology. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2013; 112:33-43. [PMID: 23562476 DOI: 10.1016/j.pbiomolbio.2013.03.019] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Revised: 03/20/2013] [Accepted: 03/25/2013] [Indexed: 12/20/2022]
Abstract
The natural world consists of hierarchical levels of complexity that range from subatomic particles and molecules to ecosystems and beyond. This implies that, in order to explain the features and behavior of a whole system, a theory might be required that would operate at the corresponding hierarchical level, i.e. where self-organization processes take place. In the past, biological research has focused on questions that could be answered by a reductionist program of genetics. The organism (and its development) was considered an epiphenomenona of its genes. However, a profound rethinking of the biological paradigm is now underway and it is likely that such a process will lead to a conceptual revolution emerging from the ashes of reductionism. This revolution implies the search for general principles on which a cogent theory of biology might rely. Because much of the logic of living systems is located at higher levels, it is imperative to focus on them. Indeed, both evolution and physiology work on these levels. Thus, by no means Systems Biology could be considered a 'simple' 'gradual' extension of Molecular Biology.
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Affiliation(s)
- Mariano Bizzarri
- Department of Experimental Medicine, Systems Biology Group Lab, Sapienza University of Rome, via Scarpa 14-16, 00161 Rome, Italy.
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Abstract
The central dogma of molecular biology has come under scrutiny in recent years. Here, we reviewed high-throughput mRNA and protein expression data of Escherichia coli, Saccharomyces cerevisiae, and several mammalian cells. At both single cell and population scales, the statistical comparisons between the entire transcriptomes and proteomes show clear correlation structures. In contrast, the pair-wise correlations of single transcripts to proteins show nullity. These data suggest that the organizing structure guiding cellular processes is observed at omics-wide scale, and not at single molecule level. The central dogma, thus, globally emerges as an average integrated flow of cellular information.
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Affiliation(s)
- Vincent Piras
- Institute for Advanced Biosciences, Keio University Tsuruoka, Yamagata, Japan ; Graduate School of Media and Governance, Keio University Fujisawa, Kanagawa, Japan
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Abstract
AbstractThe science of genetics is undergoing a paradigm shift. Recent discoveries, including the activity of retrotransposons, the extent of copy number variations, somatic and chromosomal mosaicism, and the nature of the epigenome as a regulator of DNA expressivity, are challenging a series of dogmas concerning the nature of the genome and the relationship between genotype and phenotype. According to three widely held dogmas, DNA is the unchanging template of heredity, is identical in all the cells and tissues of the body, and is the sole agent of inheritance. Rather than being an unchanging template, DNA appears subject to a good deal of environmentally induced change. Instead of identical DNA in all the cells of the body, somatic mosaicism appears to be the normal human condition. And DNA can no longer be considered the sole agent of inheritance. We now know that the epigenome, which regulates gene expressivity, can be inherited via the germline. These developments are particularly significant for behavior genetics for at least three reasons: First, epigenetic regulation, DNA variability, and somatic mosaicism appear to be particularly prevalent in the human brain and probably are involved in much of human behavior; second, they have important implications for the validity of heritability and gene association studies, the methodologies that largely define the discipline of behavior genetics; and third, they appear to play a critical role in development during the perinatal period and, in particular, in enabling phenotypic plasticity in offspring. I examine one of the central claims to emerge from the use of heritability studies in the behavioral sciences, the principle of minimal shared maternal effects, in light of the growing awareness that the maternal perinatal environment is a critical venue for the exercise of adaptive phenotypic plasticity. This consideration has important implications for both developmental and evolutionary biology.
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James A. Shapiro: Evolution: a view from the twenty-first century. EVOLUTIONARY INTELLIGENCE 2012. [PMCID: PMC3425741 DOI: 10.1007/s12065-012-0069-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
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Van Regenmortel MHV. Basic research in HIV vaccinology is hampered by reductionist thinking. Front Immunol 2012; 3:194. [PMID: 22787464 PMCID: PMC3391733 DOI: 10.3389/fimmu.2012.00194] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Accepted: 06/21/2012] [Indexed: 01/05/2023] Open
Abstract
This review describes the structure-based reverse vaccinology approach aimed at developing vaccine immunogens capable of inducing antibodies that broadly neutralize HIV-1. Some basic principles of protein immunochemistry are reviewed and the implications of the extensive polyspecificity of antibodies for vaccine development are underlined. Although it is natural for investigators to want to know the cause of an effective immunological intervention, the classic notion of causality is shown to have little explanatory value for a system as complex as the immune system, where any observed effect always results from many interactions between a large number of components. Causal explanations are reductive because a single factor is singled out for attention and given undue explanatory weight on its own. Other examples of the negative impact of reductionist thinking on HIV vaccine development are discussed. These include (1) the failure to distinguish between the chemical nature of antigenicity and the biological nature of immunogenicity, (2) the belief that when an HIV-1 epitope is reconstructed by rational design to better fit a neutralizing monoclonal antibody (nMab), this will produce an immunogen able to elicit Abs with the same neutralizing capacity as the Ab used as template for designing the antigen, and (3) the belief that protection against infection can be analyzed at the level of individual molecular interactions although it has meaning only at the level of an entire organism. The numerous unsuccessful strategies that have been used to design HIV-1 vaccine immunogens are described and it is suggested that the convergence of so many negative experimental results justifies the conclusion that reverse vaccinology is unlikely to lead to the development of a preventive HIV-1 vaccine. Immune correlates of protection in vaccines have not yet been identified because this will become feasible only retrospectively once an effective vaccine exists. The finding that extensive antibody affinity maturation is needed to obtain mature anti-HIV-1 Abs endowed with a broad neutralizing capacity explains why antigens designed to fit matured Mabs are not effective vaccine immunogens since these are administered to naive recipients who possess only B-cell receptors corresponding to the germline version of the matured Abs.
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Affiliation(s)
- Marc H. V. Van Regenmortel
- Stellenbosch Institute of Advanced Study, Wallenberg Research Center at Stellenbosch University,Stellenbosch, South Africa
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58
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He R, Eggert JA. The finger of an angel: memory return with epigenetic manipulation. Epigenomics 2012; 4:295-302. [DOI: 10.2217/epi.12.19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Scientists have been trying to crack the memory code for hundreds of years; however, centuries later, even the simplest elements of memory formation are still not fully understood. Recent studies in epigenetics indicate neuronal activity can induce transient reprogramming of epigenetic codes required for long-term memory consolidation. This suggests epigenetics as a basic mechanism in the regulation of long-term memory; and highlights the possibility that epigenetic modifications, as well as environmental factors, can change certain gene expression of brain neurons to restore the ability to remember, even with an aging brain or innate mental deficits. This article is an overview of basic knowledge and current research on epigenetic regulation of long-term memory, and prospects for future research.
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Affiliation(s)
- Ran He
- Healthcare Genetics Program, College of Health, Education & Human Development, Clemson University, Clemson, SC 29634, USA
| | - Julia A Eggert
- Healthcare Genetics Program, College of Health, Education & Human Development, Clemson University, Clemson, SC 29634, USA
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59
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Noble D. A theory of biological relativity: no privileged level of causation. Interface Focus 2012; 2:55-64. [PMID: 23386960 PMCID: PMC3262309 DOI: 10.1098/rsfs.2011.0067] [Citation(s) in RCA: 172] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2011] [Accepted: 10/17/2011] [Indexed: 12/29/2022] Open
Abstract
Must higher level biological processes always be derivable from lower level data and mechanisms, as assumed by the idea that an organism is completely defined by its genome? Or are higher level properties necessarily also causes of lower level behaviour, involving actions and interactions both ways? This article uses modelling of the heart, and its experimental basis, to show that downward causation is necessary and that this form of causation can be represented as the influences of initial and boundary conditions on the solutions of the differential equations used to represent the lower level processes. These insights are then generalized. A priori, there is no privileged level of causation. The relations between this form of 'biological relativity' and forms of relativity in physics are discussed. Biological relativity can be seen as an extension of the relativity principle by avoiding the assumption that there is a privileged scale at which biological functions are determined.
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Affiliation(s)
- Denis Noble
- Department of Physiology, Anatomy and Genetics, University of Oxford, Parks Road, Oxford OX1 3PT, UK
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Rosenfeld S. Mathematical descriptions of biochemical networks: stability, stochasticity, evolution. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2011; 106:400-9. [PMID: 21419158 PMCID: PMC3154973 DOI: 10.1016/j.pbiomolbio.2011.03.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
In this paper, we review some fundamental aspects, as well as some new developments, in the emerging field of network biology. The focus of attention is placed on mathematical approaches to conceptual modeling of biomolecular networks with special emphasis on dynamic stability, stochasticity and evolution.
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Affiliation(s)
- Simon Rosenfeld
- National Cancer Institute, 6130 Executive Blvd., EPN, Rm 3108, Rockville, MD 20852, USA.
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Plankar M, Jerman I, Krašovec R. On the origin of cancer: Can we ignore coherence? PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2011; 106:380-90. [DOI: 10.1016/j.pbiomolbio.2011.04.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2011] [Accepted: 04/09/2011] [Indexed: 01/06/2023]
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Noble D. Neo-Darwinism, the modern synthesis and selfish genes: are they of use in physiology? J Physiol 2011; 589:1007-15. [PMID: 21135048 PMCID: PMC3060581 DOI: 10.1113/jphysiol.2010.201384] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2010] [Accepted: 11/29/2010] [Indexed: 12/22/2022] Open
Abstract
This article argues that the gene-centric interpretations of evolution, and more particularly the selfish gene expression of those interpretations, form barriers to the integration of physiological science with evolutionary theory. A gene-centred approach analyses the relationships between genotypes and phenotypes in terms of differences (change the genotype and observe changes in phenotype). We now know that, most frequently, this does not correctly reveal the relationships because of extensive buffering by robust networks of interactions. By contrast, understanding biological function through physiological analysis requires an integrative approach in which the activity of the proteins and RNAs formed from each DNA template is analysed in networks of interactions. These networks also include components that are not specified by nuclear DNA. Inheritance is not through DNA sequences alone. The selfish gene idea is not useful in the physiological sciences, since selfishness cannot be defined as an intrinsic property of nucleotide sequences independently of gene frequency, i.e. the 'success' in the gene pool that is supposed to be attributable to the 'selfish' property. It is not a physiologically testable hypothesis.
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Affiliation(s)
- Denis Noble
- Department of Physiology, Anatomy and Genetics, Parks Road, Oxford OX1 3PT, UK.
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63
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Dinicola S, D'Anselmi F, Pasqualato A, Proietti S, Lisi E, Cucina A, Bizzarri M. A systems biology approach to cancer: fractals, attractors, and nonlinear dynamics. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2011; 15:93-104. [PMID: 21319994 DOI: 10.1089/omi.2010.0091] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Cancer begins to be recognized as a highly complex disease, and advanced knowledge of the carcinogenic process claims to be acquired by means of supragenomic strategies. Experimental data evidence that tumor emerges from disruption of tissue architecture, and it is therefore consequential that the tissue level should be considered the proper level of observation for carcinogenic studies. This paradigm shift imposes to move from a reductionistic to a systems biology approach. Indeed, cell phenotypes are emergent modes arising through collective nonlinear interactions among different cellular and microenvironmental components, generally described by a phase space diagram, where stable states (attractors) are embedded into a landscape model. Within this framework cell states and cell transitions are generally conceived as mainly specified by the gene-regulatory network. However, the system's dynamics cannot be reduced to only the integrated functioning of the genome-proteome network, and the cell-stroma interacting system must be taken into consideration in order to give a more reliable picture. As cell form represents the spatial geometric configuration shaped by an integrated set of cellular and environmental cues participating in biological functions control, it is conceivable that fractal-shape parameters could be considered as "omics" descriptors of the cell-stroma system. Within this framework it seems that function follows form, and not the other way around.
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Affiliation(s)
- Simona Dinicola
- Department of Experimental Medicine, Sapienza University, Roma, Italy
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Astolfi P, Salamini F, Sgaramella V. Are we Genomic Mosaics? Variations of the Genome of Somatic Cells can Contribute to Diversify our Phenotypes. Curr Genomics 2010; 11:379-86. [PMID: 21358981 PMCID: PMC3018717 DOI: 10.2174/138920210793175949] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2010] [Revised: 05/01/2010] [Accepted: 05/07/2010] [Indexed: 12/11/2022] Open
Abstract
Theoretical and experimental evidences support the hypothesis that the genomes and the epigenomes may be different in the somatic cells of complex organisms. In the genome, the differences range from single base substitutions to chromosome number; in the epigenome, they entail multiple postsynthetic modifications of the chromatin. Somatic genome variations (SGV) may accumulate during development in response both to genetic programs, which may differ from tissue to tissue, and to environmental stimuli, which are often undetected and generally irreproducible. SGV may jeopardize physiological cellular functions, but also create novel coding and regulatory sequences, to be exposed to intraorganismal Darwinian selection. Genomes acknowledged as comparatively poor in genes, such as humans', could thus increase their pristine informational endowment. A better understanding of SGV will contribute to basic issues such as the "nature vs nurture" dualism and the inheritance of acquired characters. On the applied side, they may explain the low yield of cloning via somatic cell nuclear transfer, provide clues to some of the problems associated with transdifferentiation, and interfere with individual DNA analysis. SGV may be unique in the different cells types and in the different developmental stages, and thus explain the several hundred gaps persisting in the human genomes "completed" so far. They may compound the variations associated to our epigenomes and make of each of us an "(epi)genomic" mosaic. An ensuing paradigm is the possibility that a single genome (the ephemeral one assembled at fertilization) has the capacity to generate several different brains in response to different environments.
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Affiliation(s)
- P.A. Astolfi
- Department of Genetics and Microbiology, University of Pavia, Italy
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Noble D. Biophysics and systems biology. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2010; 368:1125-39. [PMID: 20123750 PMCID: PMC3263808 DOI: 10.1098/rsta.2009.0245] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Biophysics at the systems level, as distinct from molecular biophysics, acquired its most famous paradigm in the work of Hodgkin and Huxley, who integrated their equations for the nerve impulse in 1952. Their approach has since been extended to other organs of the body, notably including the heart. The modern field of computational biology has expanded rapidly during the first decade of the twenty-first century and, through its contribution to what is now called systems biology, it is set to revise many of the fundamental principles of biology, including the relations between genotypes and phenotypes. Evolutionary theory, in particular, will require re-assessment. To succeed in this, computational and systems biology will need to develop the theoretical framework required to deal with multilevel interactions. While computational power is necessary, and is forthcoming, it is not sufficient. We will also require mathematical insight, perhaps of a nature we have not yet identified. This article is therefore also a challenge to mathematicians to develop such insights.
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Affiliation(s)
- Denis Noble
- Department of Physiology, Anatomy and Genetics, University of Oxford, , Parks Road, Oxford OX1 3PT, UK.
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Abstract
A career of following unplanned observations has serendipitously led to a deep appreciation of the capacity that bacterial cells have for restructuring their genomes in a biologically responsive manner. Routine characterization of spontaneous mutations in the gal operon guided the discovery that bacteria transpose DNA segments into new genome sites. A failed project to fuse lambda sequences to a lacZ reporter ultimately made it possible to demonstrate how readily Escherichia coli generated rearrangements necessary for in vivo cloning of chromosomal fragments into phage genomes. Thinking about the molecular mechanism of IS1 and phage Mu transposition unexpectedly clarified how transposable elements mediate large-scale rearrangements of the bacterial genome. Following up on lab lore about long delays needed to obtain Mu-mediated lacZ protein fusions revealed a striking connection between physiological stress and activation of DNA rearrangement functions. Examining the fate of Mudlac DNA in sectored colonies showed that these same functions are subject to developmental control, like controlling elements in maize. All these experiences confirmed Barbara McClintock's view that cells frequently respond to stimuli by restructuring their genomes and provided novel insights into the natural genetic engineering processes involved in evolution.
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67
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Sgaramella V, Astolfi PA. Somatic genome variations interact with environment, genome and epigenome in the determination of the phenotype: A paradigm shift in genomics? DNA Repair (Amst) 2010; 9:470-3. [PMID: 20153268 DOI: 10.1016/j.dnarep.2009.11.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2009] [Accepted: 11/03/2009] [Indexed: 01/18/2023]
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Shapiro JA. Mobile DNA and evolution in the 21st century. Mob DNA 2010; 1:4. [PMID: 20226073 PMCID: PMC2836002 DOI: 10.1186/1759-8753-1-4] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2009] [Accepted: 01/25/2010] [Indexed: 01/05/2023] Open
Abstract
Scientific history has had a profound effect on the theories of evolution. At the beginning of the 21st century, molecular cell biology has revealed a dense structure of information-processing networks that use the genome as an interactive read-write (RW) memory system rather than an organism blueprint. Genome sequencing has documented the importance of mobile DNA activities and major genome restructuring events at key junctures in evolution: exon shuffling, changes in cis-regulatory sites, horizontal transfer, cell fusions and whole genome doublings (WGDs). The natural genetic engineering functions that mediate genome restructuring are activated by multiple stimuli, in particular by events similar to those found in the DNA record: microbial infection and interspecific hybridization leading to the formation of allotetraploids. These molecular genetic discoveries, plus a consideration of how mobile DNA rearrangements increase the efficiency of generating functional genomic novelties, make it possible to formulate a 21st century view of interactive evolutionary processes. This view integrates contemporary knowledge of the molecular basis of genetic change, major genome events in evolution, and stimuli that activate DNA restructuring with classical cytogenetic understanding about the role of hybridization in species diversification.
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Affiliation(s)
- James A Shapiro
- Department of Biochemistry and Molecular Biology, University of Chicago, Gordon Center for Integrative Science W123B, 929 E 57th Street, Chicago, IL 60637, USA.
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69
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Olovnikov AM. Biological evolution based on nonrandom variability regulated by the organism. BIOCHEMISTRY (MOSCOW) 2009; 74:1404-8. [PMID: 19961425 DOI: 10.1134/s0006297909120177] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
A hypothetical mechanism for rapid and nonrandom emergence of evolutionary adaptations is proposed. It is supposed that some transcription factors and transcription regulators that are able to cross membranes can leave the cells of their origin and move within the organism using a specialized transport system when individual development occurs under conditions extreme for the given species. This system, in particular, connects soma with germline. The supply of germline cells with unusual transcription regulators changes the balance of their nuclear regulatory RNAs, thus initiating RNA-dependent epigenetic modifications of the germline genome and therefore changes in phenotypes of the progeny. It is highly probable that some of these phenotypes are adaptive and lay the basis for the origin of the next biological species. The proposed mechanism can serve as a basis for a new theory of the origin of species.
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Affiliation(s)
- A M Olovnikov
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, 119334, Russia.
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