Évolution, complexité et métahistoricisme

L’histoire cherche à combiner des descriptions particulières dans des cadres généraux dans le but d’expliquer des séquences d’événements. Dans cet esprit, l’histoire adopte une approche transdisciplinaire qui couvre une variété de champs allant de la biologie à la géologie, en passant par l’anthropologie et l’histoire humaine. Je cherche à caractériser ce cadre métahistorique général comme exemple d’une dynamique complexe, évolutionniste et généalogique. Cela suppose quelques travaux particuliers sur les modes de transmission d’information, les niveaux des fonctions de système, l’identification multiple, les variables causales et sur les moyens de démêler les événements contingents des processus réguliers qui filtrent ces événements.History seeks to combine particular descriptions within general frameworks in order to explain event sequences. In this respect, history is a transdisciplinary approach that encompasses a range of fields, from biology and geology, through to anthropology and human history. I seek to characterize this general metahistorical framework as an instance of a complex, evolutionary and genealogical dynamic. This involves a specification of the modes of information transmission, the levels of system function, the identification of multiple, causal variables, and a means of disentangling contingent events from regular processes through which these events are filtered

The stochastic behavior of a molecular switching circuit with feedback

Background: Using a statistical physics approach, we study the stochastic switching behavior of a model circuit of multisite phosphorylation and dephosphorylation with feedback. The circuit consists of a kinase and phosphatase acting on multiple sites of a substrate that, contingent on its modification state, catalyzes its own phosphorylation and, in a symmetric scenario, dephosphorylation. The symmetric case is viewed as a cartoon of conflicting feedback that could result from antagonistic pathways impinging on the state of a shared component. Results: Multisite phosphorylation is sufficient for bistable behavior under feedback even when catalysis is linear in substrate concentration, which is the case we consider. We compute the phase diagram, fluctuation spectrum and large-deviation properties related to switch memory within a statistical mechanics framework. Bistability occurs as either a first-order or second-order non-equilibrium phase transition, depending on the network symmetries and the ratio of phosphatase to kinase numbers. In the second-order case, the circuit never leaves the bistable regime upon increasing the number of substrate molecules at constant kinase to phosphatase ratio. Conclusions: The number of substrate molecules is a key parameter controlling both the onset of the bistable regime, fluctuation intensity, and the residence time in a switched state. The relevance of the concept of memory depends on the degree of switch symmetry, as memory presupposes information to be remembered, which is highest for equal residence times in the switched states. Reviewers: This article was reviewed by Artem Novozhilov (nominated by Eugene Koonin), Sergei Maslov, and Ned Wingreen.Comment: Version published in Biology Direct including reviewer comments and author responses, 28 pages, 7 figure

The Debate Over Understanding in AI's Large Language Models

We survey a current, heated debate in the AI research community on whether large pre-trained language models can be said to "understand" language -- and the physical and social situations language encodes -- in any important sense. We describe arguments that have been made for and against such understanding, and key questions for the broader sciences of intelligence that have arisen in light of these arguments. We contend that a new science of intelligence can be developed that will provide insight into distinct modes of understanding, their strengths and limitations, and the challenge of integrating diverse forms of cognition.Comment: Under submission as a Perspective articl

A statistical analysis of the three-fold evolution of genomic compression through frame overlaps in prokaryotes

<p>Abstract</p> <p>Background</p> <p>Among microbial genomes, genetic information is frequently compressed, exploiting redundancies in the genetic code in order to store information in overlapping genes. We investigate the length, phase and orientation properties of overlap in 58 prokaryotic species evaluating neutral and selective mechanisms of evolution.</p> <p>Results</p> <p>Using a variety of statistical null models we find patterns of compressive coding that can not be explained purely in terms of the selective processes favoring genome minimization or translational coupling. The distribution of overlap lengths follows a fat-tailed distribution, in which a significant proportion of overlaps are in excess of 100 base pairs in length. The phase of overlap – pairing of codon positions in complementary reading frames – is strongly predicted by the translation orientation of each gene. We find that as overlapping genes become longer, they have a tendency to alternate among alternative overlap phases. Some phases seem to reflect codon pairings reducing the probability of non-synonymous substitution. We analyze the lineage-dependent features of overlapping genes by tracing a number of different continuous characters through the prokaryotic phylogeny using squared-change parsimony and observe both clade-specific and species-specific patterns.</p> <p>Conclusion</p> <p>Overlapping reading frames preserve in their structure, features relating to mutational origination of new genes, but have undergone modification for both immediate benefits and for variational buffering and amplification. Genomes come under a variety of different mutational and selectional pressures, and the structure of redundancies in overlapping genes can be used to detect these pressures. No single mechanism is able to account for all the variability observed among the set of prokaryotic overlapping genes but a three-fold analysis of evolutionary events provides a more integrative framework.</p> <p>Reviewers</p> <p>This article was reviewed by Eugene Koonin, Marten Huynem, and Han Liang.</p

Abraham Inc. featuring David Krakauer, Fred Wesley, and Socalled: An Evening of Klezmer-Funk Music

Daniel Pearl World Music Days Concert.https://digitalcommons.fairfield.edu/bennettcenter-posters/1292/thumbnail.jp