The theory of facilitated variation

Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA.
Proceedings of the National Academy of Sciences (Impact Factor: 9.67). 06/2007; 104 Suppl 1(Suppl 1):8582-9. DOI: 10.1073/pnas.0701035104
Source: PubMed


This theory concerns the means by which animals generate phenotypic variation from genetic change. Most anatomical and physiological traits that have evolved since the Cambrian are, we propose, the result of regulatory changes in the usage of various members of a large set of conserved core components that function in development and physiology. Genetic change of the DNA sequences for regulatory elements of DNA, RNAs, and proteins leads to heritable regulatory change, which specifies new combinations of core components, operating in new amounts and states at new times and places in the animal. These new configurations of components comprise new traits. The number and kinds of regulatory changes needed for viable phenotypic variation are determined by the properties of the developmental and physiological processes in which core components serve, in particular by the processes' modularity, robustness, adaptability, capacity to engage in weak regulatory linkage, and exploratory behavior. These properties reduce the number of regulatory changes needed to generate viable selectable phenotypic variation, increase the variety of regulatory targets, reduce the lethality of genetic change, and increase the amount of genetic variation retained by a population. By such reductions and increases, the conserved core processes facilitate the generation of phenotypic variation, which selection thereafter converts to evolutionary and genetic change in the population. Thus, we call it a theory of facilitated phenotypic variation.

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    • "Key developmental genes arose more than 1.1 billion years ago, before the emergence of complex animal body plans during the Cambrian period [1]. An evolutionarily refined set of these transcriptional/developmental genes, termed the " basic genetic toolbox, " allowed the emergence of the immense variation in animal forms observed in this and later geological periods [2] [3]. In this context, two fundamental types of homologous genetic relationships are found: paralogous and orthologous genes, which evolve through duplication/deletion and speciation, respectively [4] [5] [6]. "
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    ABSTRACT: The paired box (PAX) family of transcription/developmental genes plays a key role in numerous stages of embryonic development, as well as in adult organogenesis. There is evidence linking the acquisition of a paired-like DNA binding domain (PD) to domestication of a Tc1/mariner transposon. Further duplication/deletion processes led to at least five paralogous metazoan protein groups, which can be classified into two supergroups, PAXB-like or PAXD-like, using ancestral defining structures; the PD plus an octapeptide motif (OP) and a paired-type homeobox DNA binding domain (PTHD), producing the PD-OP-PTHD structure characteristic of the PAXB-like group, whereas an additional domain, the paired-type homeodomain tail (PHT), is present in the PAXD-like group, producing a PD-OP-PTHD-PHT structure. We examined their patterns of distribution in various species, using both available data and new bioinformatic analyses, including vertebrate PAX genes and their shared and specific functions, as well as inter- and intraspecific variability of PAX in primates. These analyses revealed a relatively conserved PAX network, accompanied by specific changes that led to adaptive novelties. Therefore, both stability and evolvability shaped the molecular evolution of this key transcriptional network. Copyright © 2015. Published by Elsevier Ltd.
    Seminars in Cell and Developmental Biology 08/2015; DOI:10.1016/j.semcdb.2015.08.014 · 6.27 Impact Factor
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    • "What are the mechanisms of such exaptation? For example, Gerhart (2007) believes that evolution is not only selection but also using existing genetic material. However, the term " use " does not really clarify the situation. "
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    ABSTRACT: Non-trivial quantum effects in biological systems are analyzed. Some unresolved issues and paradoxes related to quantum effects (Levinthal's paradox, the paradox of speed, and mechanisms of evolution) are addressed. It is concluded that the existence of non-trivial quantum effects is necessary for the functioning of living systems. In particular, it is demonstrated that classical mechanics cannot explain the stable work of the cell and any over-cell structures. The need for quantum effects is generated also by combinatorial problems of evolution. Their solution requires a priori information about the states of the evolving system, but within the framework of the classical theory it is not possible to explain mechanisms of its storage consistently. We also present essentials of so called quantum-like paradigm: sufficiently complex bio-systems process information by violating the laws of classical probability and information theory. Therefore the mathematical apparatus of quantum theory may have fruitful applications to describe behavior of bio-systems: from cells to brains, ecosystems and social systems. In quantum-like information biology it is not presumed that quantum information bio-processing is resulted from quantum physical processes in living organisms. Special experiments to test the role of quantum mechanics in living systems are suggested. This requires a detailed study of living systems on the level of individual atoms and molecules. Such monitoring of living systems in vivo can allow the identification of the real potentials of interaction between biologically important molecules. Copyright © 2015. Published by Elsevier Ltd.
    Progress in Biophysics and Molecular Biology 07/2015; 119(2):137-161. DOI:10.1016/j.pbiomolbio.2015.07.001 · 2.27 Impact Factor
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    • "(Hindré et al., 2012), evolvable genotype–phenotype mappings, e.g. (Gerhart and Kirschner, 2007; Wagner and Altenberg, 1996; Wills, 2014), and major transitions, e.g. (Maynard Smith and Szathmáry, 1995). "
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    ABSTRACT: Open-ended evolutionary dynamics remains an elusive goal for artificial evolutionary systems. Many ideas exist in the biological literature beyond the basic Darwinian requirements of variation, differential reproduction and inheritance. I argue that these ideas can be seen as aspects of five fundamental requirements for open-ended evolution: (1) robustly reproductive individuals, (2) a medium allowing the possible existence of a practically unlimited diversity of individuals and interactions, (3) individuals capable of producing more complex offspring, (4) mutational pathways to other viable individuals, and (5) drive for continued evolution. I briefly discuss implications of this view for the design of artificial systems with greater evolutionary potential.
    Presented at the EvoEvo Workshop at the European Conference on Artificial Life 2015 (ECAL 2015), University of York, UK; 07/2015
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