phenotype

From base editing to RNA editing (7)

Group Description Human ethology is the study of the biology of human behavior, including the behavior’s phylogeny (evolutionary history), ontogeny (development), proximate causes, and adaptiveness (survival value). Jay R. Feierman wrote: This has nothing to do with human ethology. So, I can’t publish it to the group. This is what he refused to publish to the group: ———— Two generations of serious scientists have already been taught to make claims like this (although some must be forced to do it):…

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Explorers who do not know what is known

Can genetic testing determine antimicrobial susceptibility? EUCAST experts say not yet… (link opens pdf) Reported as:  Whole genome sequencing cannot yet be used to determine antimicrobial susceptibility For most bacterial species there is currently insufficient evidence to support the use of WGS-inferred AST to guide clinical decision making. WGS-AST should be a funding priority if it is to become a rival to phenotypic AST. My comment: JVKohl said… Perhaps the focus should be on what can be done with WGS.…

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From precis to pre-mRNA and proof of concept in F1, F2, F3

The Gene Ontology Handbook, edited by Christophe Dessimoz & Nives Škunca Open Access, Download it here See also: New trends in evolutionary biology: biological, philosophical and social science perspectives November 7-9, 2016 See also: BioGenomics 2017 – Global Biodiversity Genomics Conference February 21-23, 2017 See also: Using fast-acting temperature-sensitive mutants to study cell division in Caenorhabditis elegans Conclusion: The current limiting factor in using this technology is the availability of fast-acting ts alleles. Previous forward genetic screens for ts alleles…

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Biological evolution as a philosophy, not a science

There is no indication in the abstracts that any of the presenters are going to address the facts that link quantised energy to polycombic ecological adaptation and virus-driven energy theft from hecatombic evolution to all pathology in all living genera. Virus-mediated archaeal hecatomb in the deep seafloor (2016) provides details on the hecatombin evolution of all patholgoy From Fertilization to Adult Sexual Behavior (1996) provides details on the polycombic ecological adaptation of all healthy longevity. For these experts to address…

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Pathology constrains X-linked evolution

Long-range evolutionary constraints reveal cis-regulatory interactions on the human X chromosome Excerpt: “Experimental methods are already able to indicate the interactions between enhancers and genes8, 13, 17, 18, 19 but they are strongly constrained by the tissue and time where and when the interaction takes place. In contrast, evolutionary linkage is independent of the tissue or time of expression of the gene, and is applicable to any sequenced vertebrate genome, as it was done here for human.” My comment: Experimental…

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MicroRNAs and invasive phenotypes

Variability helps mammals to become invasive Excerpt: The authors argue that species exposed to a novel environment will have higher chances of surviving if they are variable and can therefore adapt to many different environmental conditions. My comment: Nutrient-dependent pheromone-controlled morphological and behavioral phenotypes are linked by microRNAs to adaptive radiation and to all of extant biodiversity. For an example of the role of RNA-mediated events that link metabolic networks to genetic networks, see: “Large Numbers of Novel miRNAs Originate…

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Understanding cell type differentiation

The Wisdom of the Fly Crowds by Ed Yong Excerpt: “This is a landmark study of collective behaviour,” says Iain Couzin… “Never before has it been possible to unweave the intricate coding of social behaviour during collective decision-making.” When it comes to fruit flies, scientists…  can really start to understand the origins of collective behaviour—how genes in the fly’s neurons are activated, how those neurons process signals from the fly’s environment, and how they drive individual behaviours that, in turn,…

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Eliminating correlations from evolutionary ecology

De novo creation of olfactory receptor genes clearly links food odors via amino acid substitutions to cell type differentiation in mosquitoes, and in nematodes, flies, honeybees, etc. It would be surprising if cause and effect did not extend to vertebrates from invertebrates. Indeed, Elekonich and Robinson (2000) linked our 1996 model of RNA-mediated cell type differentiation to hormone-organized and hormone-activated behavior in insects more than a decade ago. Since then, Vosshall’s lab has established the role that amino acid substitutions…

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We need pattern recognition, not a prologue

Prolegomenon “a preliminary discussion…; a prologue.” “… we need a mapping from genotype to phenotype, from phenotype to what is selected, and from what is selected to the new genotype (Lewontin, 1961). — cited in Prolegomenon to patterns in evolution Excerpt:  “…we cannot derive what selection, acting at the level of the whole organism in its world, will “select” among the possible but unprestatable…” My comment: Organisms naturally select the nutrients that enable thermodynamic cycles of protein biosynthesis and degradation,…

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Epigenetically-effected metabolic shifts and ecological adaptations

Epigenetics of Trained Innate Immunity: Documenting the epigenetic landscape of human innate immune cells reveals pathways essential for training macrophages. By Ruth Williams | September 25, 2014 [open access] Excerpt: “…they then analyzed genome-wide distributions of four epigenetic indicators of gene activity: DNAse hypersensitivity and three different histone modifications—trimethylation of histone H3 at lysine 4, monomethylation of histone H3 at lysine 4, and acetylation of histone H3 at lysine 27. They also analyzed genome-wide transcription and transcription factor binding. Together…

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