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Biology
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Biology in the Early 21st Century: Evolution Beyond Selection
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Biology in the Early 21st Century: Evolution Beyond Selection

A special issue of Biology (ISSN 2079-7737).

Deadline for manuscript submissions: closed (15 September 2017) | Viewed by 31188

Special Issue Editors

Dr. William B. Miller, Jr

E-Mail Website
Guest Editor
Independent Researcher, 6526 N. 59th St., Paradise Valley, AZ 85253, USA
Interests: cognition; information fields; hologenomics; epigenetics; niche construction; cell–cell communication
Prof. Dr. John S. Torday

E-Mail Website
Guest Editor
Emeritus Professor, Department of Pediatrics, Harbor-UCLA Medical Center, 1124 W.Carson Street, Torrance, CA 90502, USA
Interests: First Principles of Physiology; ambiguity; unicellular state; endothermy; qualitative:quantitative evolution; free will/determinism

Special Issue Information

Dear Colleagues,

The conventional NeoDarwinian appraisal of evolution is based on corresponding pillars of random genetic variation and selection via differential fitness. In the 21st century, a salient question arises. Is this a sufficient evolutionary narrative? This Special Issue will offer several differing perspectives on evolutionary development and phylogeny that extend beyond Darwinian selection. The role of cellular cooperativity, cellular cognition, self-reference, niche construction, stigmergy, self-organization, epigenetic modifications, genetic transfer and mobility, endosymbiosis, hologenomics, and non-stochastic genetic mechanisms will be addressed. In particular, cell–cell communication and aspects of cellular/genetic self-engineering will be considered. Over many years, movement towards a substantial revision of the NeoDarwinian synthesis has gained slow momentum through many diverging approaches. This Special Issue will explore a variety of contemporary alternative views that may provide a pathway towards a dominant, cohering, and predictive non-Darwinian narrative for evolutionary development.

Dr. William B. Miller, Jr.
Prof. John S. Torday
Guest Editors

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Keywords

  • evolutionary biology
  • cognition
  • niche construction
  • cellular engineering
  • cell–cell communication
  • hologenome
  • epigenetics
  • self-organization
  • ambiguity/uncertainty
  • self-Reference
  • entropy/negentropy
  • First Principles of Physiology
  • determinism/free will

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Published Papers (3 papers)

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Review

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961 KiB  
Review
Was the Watchmaker Blind? Or Was She One-Eyed?
by Raymond Noble and Denis Noble
Biology 2017, 6(4), 47; https://doi.org/10.3390/biology6040047 - 20 Dec 2017
Cited by 41 | Viewed by 11635
Abstract
The question whether evolution is blind is usually presented as a choice between no goals at all (‘the blind watchmaker’) and long-term goals which would be external to the organism, for example in the form of special creation or intelligent design. The arguments [...] Read more.
The question whether evolution is blind is usually presented as a choice between no goals at all (‘the blind watchmaker’) and long-term goals which would be external to the organism, for example in the form of special creation or intelligent design. The arguments either way do not address the question whether there are short-term goals within rather than external to organisms. Organisms and their interacting populations have evolved mechanisms by which they can harness blind stochasticity and so generate rapid functional responses to environmental challenges. They can achieve this by re-organising their genomes and/or their regulatory networks. Epigenetic as well as DNA changes are involved. Evolution may have no foresight, but it is at least partially directed by organisms themselves and by the populations of which they form part. Similar arguments support partial direction in the evolution of behavior. Full article
(This article belongs to the Special Issue Biology in the Early 21st Century: Evolution Beyond Selection)
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664 KiB  
Review
Living Organisms Author Their Read-Write Genomes in Evolution
by James A. Shapiro
Biology 2017, 6(4), 42; https://doi.org/10.3390/biology6040042 - 6 Dec 2017
Cited by 53 | Viewed by 13648
Abstract
Evolutionary variations generating phenotypic adaptations and novel taxa resulted from complex cellular activities altering genome content and expression: (i) Symbiogenetic cell mergers producing the mitochondrion-bearing ancestor of eukaryotes and chloroplast-bearing ancestors of photosynthetic eukaryotes; (ii) interspecific hybridizations and genome doublings generating new species [...] Read more.
Evolutionary variations generating phenotypic adaptations and novel taxa resulted from complex cellular activities altering genome content and expression: (i) Symbiogenetic cell mergers producing the mitochondrion-bearing ancestor of eukaryotes and chloroplast-bearing ancestors of photosynthetic eukaryotes; (ii) interspecific hybridizations and genome doublings generating new species and adaptive radiations of higher plants and animals; and, (iii) interspecific horizontal DNA transfer encoding virtually all of the cellular functions between organisms and their viruses in all domains of life. Consequently, assuming that evolutionary processes occur in isolated genomes of individual species has become an unrealistic abstraction. Adaptive variations also involved natural genetic engineering of mobile DNA elements to rewire regulatory networks. In the most highly evolved organisms, biological complexity scales with “non-coding” DNA content more closely than with protein-coding capacity. Coincidentally, we have learned how so-called “non-coding” RNAs that are rich in repetitive mobile DNA sequences are key regulators of complex phenotypes. Both biotic and abiotic ecological challenges serve as triggers for episodes of elevated genome change. The intersections of cell activities, biosphere interactions, horizontal DNA transfers, and non-random Read-Write genome modifications by natural genetic engineering provide a rich molecular and biological foundation for understanding how ecological disruptions can stimulate productive, often abrupt, evolutionary transformations. Full article
(This article belongs to the Special Issue Biology in the Early 21st Century: Evolution Beyond Selection)

Other

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194 KiB  
Opinion
Natural Knockouts: Natural Selection Knocked Out
by Peter Borger
Biology 2017, 6(4), 43; https://doi.org/10.3390/biology6040043 - 12 Dec 2017
Cited by 3 | Viewed by 4905
Abstract
In functional genomics studies, research is dedicated to unveiling the function of genes using gene-knockouts, model organisms in which a gene is artificially inactivated. The idea is that, by knocking out the gene, the provoked phenotype would inform us about the function of [...] Read more.
In functional genomics studies, research is dedicated to unveiling the function of genes using gene-knockouts, model organisms in which a gene is artificially inactivated. The idea is that, by knocking out the gene, the provoked phenotype would inform us about the function of the gene. Still, the function of many genes cannot be elucidated, because disruption of conserved sequences, including protein-coding genes, often does not directly affect the phenotype. Since the phenomenon was first observed in the early nineties of the last century, these so-called ‘no-phenotype knockouts’ have met with great skepticism and resistance by died-in-the-wool selectionists. Still, functional genomics of the late 20th and early 21st centuries has taught us two important lessons. First, two or more unrelated genes can often substitute for each other; and second, some genes are only present in the genome in a silent state. In the laboratory, the disruption of such genes does not negatively influence reproductive success, and does not show measurable fitness effects of the species. The genes are redundant. Genetic redundancy, one of the big surprises of modern biology, can thus be defined as the condition in which the inactivation of a gene is selectively neutral. The no-phenotype knockout is not just a freak of the laboratory. Genetic variants known as homozygous loss-of-function (HLOF) variants are of considerable scientific and clinical interest, as they represent experiments of nature qualifying as “natural knockouts”. Such natural knockouts challenge the conventional NeoDarwinian appraisal that genetic information is the result of natural selection acting on random genetic variation. Full article
(This article belongs to the Special Issue Biology in the Early 21st Century: Evolution Beyond Selection)
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