Genes and knowledge: Response to Baverstock, K. the gene an appraisal. https://doi.org/10.1016/j.pbiomolbio.2021.04.005

Responses to commentaries on "The gene: An appraisal"

The central conclusions of "The Gene: An Appraisal" are that genetic variance does not underpin biological evolution, and, therefore, that genes are not Mendel's units of inheritance. In this response, I will address the criticisms I have received via commentaries on that paper by defending the following statements: 1. Epistasis does not explain the power-law fitness profile of the Long-Term Evolution Experiment (LTEE). The data from the evolution of natural systems displays the power-law form ubiquitously. Epistasis plays no role in evolution. 2. The common characteristics of living things (natural systems) are described by the principle of least action in de Maupertuis's original form, which is synonymous with the 2nd law of thermodynamics and Newton's 2nd law of motion in its complete form, i.e., F = dp/dt. Organisms strive to achieve free energy balance with their environments. 3. Based on an appraisal of the scientific environment between 1880 and 1911, I conclude that Johannsen's genotype conception was perhaps, the only option available to him. 4. The power-law fitness profile of the LTEE falsifies Fisher's Genetical Theory of Natural Selection, Johannsen's genotype conception, and the idea that 'Darwinian evolution' is an exception to the generic thermodynamic process of evolution in natural systems. 5. The use of the technique of genome-wide association to identify the causes and the likelihoods of inherited common diseases and behavioural traits is a 'wild goose chase' because genes are not the units of inheritance.

Misguided model of human behavior: Comment on C. H. Burt: "Challenging the utility of polygenic scores for social science…"

This commentary emphasizes two problem areas mentioned by Burt. First, that within-family designs do not eradicate stratification confounds. Second, that the linear/additive model of genetic causes of form and variation is not supported by recent progress in molecular biology. It concludes with an appeal for a (biologically and psychologically) more realistic model of such causes.

A Variational Synthesis of Evolutionary and Developmental Dynamics

This paper introduces a variational formulation of natural selection, paying special attention to the nature of 'things' and the way that different 'kinds' of 'things' are individuated from-and influence-each other. We use the Bayesian mechanics of particular partitions to understand how slow phylogenetic processes constrain-and are constrained by-fast, phenotypic processes. The main result is a formulation of adaptive fitness as a path integral of phenotypic fitness. Paths of least action, at the phenotypic and phylogenetic scales, can then be read as inference and learning processes, respectively. In this view, a phenotype actively infers the state of its econiche under a generative model, whose parameters are learned via natural (Bayesian model) selection. The ensuing variational synthesis features some unexpected aspects. Perhaps the most notable is that it is not possible to describe or model a population of conspecifics per se. Rather, it is necessary to consider populations of distinct natural kinds that influence each other. This paper is limited to a description of the mathematical apparatus and accompanying ideas. Subsequent work will use these methods for simulations and numerical analyses-and identify points of contact with related mathematical formulations of evolution.

Nasal Microbiome in COVID-19: A Potential Role of Corynebacterium in Anosmia

The evolution and the development of the symptoms of Coronavirus disease 19 (COVID-19) are due to different factors, where the microbiome plays a relevant role. The possible relationships between the gut, lung, nasopharyngeal, and oral microbiome with COVID-19 have been investigated. We analyzed the nasal microbiome of both positive and negative SARS-CoV-2 individuals, showing differences in terms of bacterial composition in this niche of respiratory tract. The microbiota solution A (Arrow Diagnostics) was used to cover the hypervariable V1-V3 regions of the bacterial 16S rRNA gene. MicrobAT Suite and MicrobiomeAnalyst program were used to identify the operational taxonomic units (OTUs) and to perform the statistical analysis, respectively. The main taxa identified in nasal microbiome of COVID-19 patients and in Healthy Control subjects belonged to three distinct phyla: Proteobacteria (HC = 14%, Cov19 = 35.8%), Firmicutes (HC = 28.8%, Cov19 = 30.6%), and Actinobacteria (HC = 56.7%, Cov19 = 14.4%) with a relative abundance > 1% in all groups. A significant reduction of Actinobacteria in Cov19 group compared to controls (P < 0.001, FDR = 0.01) was found. The significant reduction of Actinobacteria was identified in all taxonomic levels down to the genus (P < 0.01) using the ANOVA test. Indeed, a significantly reduced relative abundance of Corynebacterium was found in the patients compared to healthy controls (P = 0.001). Reduced abundance of Corynebacterium has been widely associated with anosmia, a common symptom of COVID-19 as suffered from our patients. Contrastingly, the Corynebacterium genus was highly represented in the nasal mucosa of healthy subjects. Further investigations on larger cohorts are necessary to establish functional relationships between nasal microbiota content and clinical features of COVID-19.