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lunedì 31 gennaio 2022

# evol: the hypothesis of quasi-stochastic 'jazzy' metamechanics of biological evolution (in Arabidopsis thaliana)


<< Mutations occur when DNA is damaged and left unrepaired, creating a new variation. The scientists wanted to know if mutation was purely random or something deeper. What they found was unexpected. >>️

<< We always thought of mutation as basically random across the genome, (..) It turns out that mutation is very non-random and it's non-random in a way that benefits the plant. It's a totally new way of thinking about mutation. >> Grey Monroe. ️

Study challenges evolutionary theory that DNA mutations are random. UC Davis. Jan 12, 2022.


Monroe JG, Srikant T, et al. Mutation bias reflects natural selection in Arabidopsis thaliana. Nature. doi: 10.1038/ s41586-021-04269-6. Jan 12, 2022.


FonT 

for a long time I have developed the suspicion that the small plant cared for by grandmother on the windowsill could be a not trivial image of (r)evolution ... 

The three ways of the plastoquinone inside the photosystem II complex. May 23, 2017.


Also

keyword 'evolution'  in FonT


keyword 'evolution' | 'evoluzione'  in Notes (quasi-stochastic poetry)



keyword 'jazz' in FonT


keyword 'jazz' in Notes (quasi-stochastic poetry):


keywords: evol, dna, mutations, randomness, quasi-stochasticity, jazz



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sabato 29 gennaio 2022

# life: "Simmetrico, purtuttavia caotico", la rivisitazione






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martedì 11 gennaio 2022

# gst: apropos of discomfort tolerances, maximize a sweet spot (of a sound zone)


AA << considered the sweet spot as the region where the a sound scene is psycho-acoustically close to a desired auditory scene. >>

They << developed a method (SWEET-ReLU algorithm) that generates a sound scene that maximizes this sweet spot while guaranteeing no discomfort over a spatial region of interest. (..) the sweet spot and the discomfort tolerance can be modeled within a flexible monaural psycho-acoustic framework. >>

Pedro Izquierdo Lehmann, Rodrigo F. Cadiz, Carlos A. Sing Long. Maximizing the Psycho-Acoustic Sweet Spot. arXiv: 2201.01461v1 [eess.AS]. Jan 5, 2022.


Keywords: sound, psycho-acoustics, discomfort tolerance


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domenica 9 gennaio 2022

# ecol: mycological jazz

<< "Mycological" draws conceptually from fungal networks in forests and their interactions. Inspired by the work of ecologist Suzanne Simard, author Michael Pollan, and mycologist Paul Stamets; Krolak saw many parallels between biological networks and the social network known as jazz, as well as, the acoustic networks created when musicians interact through their instruments. Aesthetically, the work is of the free and avant-garde traditions of jazz. Drawing inspiration from John Coltrane to Sonny Sharrock to Makaya McCraven, Krolak seeks to create a space for various elements to play out and find their own connections. >>

Mycological By Nicholas Krolak. All About Jazz. Jan 8, 2022. 


Also

Apropos of 'mycological jazz', a old  perplexity of mine, who knows why substantial funds were no longer allocated to sci research on viruses, bacteria, fungi (..) and their ecological 'jazzy interactions' ... ? 😏

keyword 'virus' | 'bacteria' | 'fungi' in FonT




Also

Much of intelligence (quasi-stochastic poetry). Notes. Dec 16, 2005.


keyword 'jazz' in FonT


keyword 'jazz' in Notes (quasi-stochastic poetry):


Keywords: jazz, viruses, bacteria, fungi, interactions, acad, scires, funds


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venerdì 7 gennaio 2022

# evol: viruses as a facilitator / driver of horizontal gene transfer among eukaryotes


<< Gene exchange between viruses and their hosts acts as a key facilitator of horizontal gene transfer and is hypothesized to be a major driver of evolutionary change. Our understanding of this process comes primarily from bacteria and phage co-evolution, but the mode and functional importance of gene transfers between eukaryotes and their viruses remain anecdotal. >>

AA << systematically characterized viral–eukaryotic gene exchange across eukaryotic and viral diversity, identifying thousands of transfers and revealing their frequency, taxonomic distribution and projected functions. Eukaryote-derived viral genes, abundant in the Nucleocytoviricota, highlighted common strategies for viral host-manipulation, including metabolic reprogramming, proteolytic degradation and extracellular modification. Furthermore, viral-derived eukaryotic genes implicate genetic exchange in the early evolution and diversification of eukaryotes, particularly through viral-derived glycosyltransferases, which have impacted structures as diverse as algal cell walls, trypanosome mitochondria and animal tissues. These findings illuminate the nature of viral–eukaryotic gene exchange and its impact on the evolution of viruses and their eukaryotic hosts. >>️

Irwin, N.A.T., Pittis, A.A., Richards, T.A. et al. Systematic evaluation of horizontal gene transfer between eukaryotes and viruses. Nat Microbiol. doi: 10.1038/ s41564-021-01026-3. Dec 31, 2021. 


<< We knew from individual examples that viral genes have played a role in the evolution of eukaryotes. Even humans have viral genes, which are important for our development and brain function, (..)  We wanted to understand more broadly how HGT (horizontal gene transfer) has affected viruses and eukaryotes from across the tree of life. >> Nicholas Irwin. ️

<< We were interested to find that certain groups of viruses, especially those that infect single-celled eukaryotes, acquire a lot of genes from their hosts, (..)  By studying the function of these genes we were able to make predictions about how these viruses affect their hosts during infection. >> Patrick Keeling.

<< Many of these viral-derived genes appear to have repeatedly affected the structure and form of different organisms, from the cell walls of algae to the tissues of animals, (..) This suggests that host-virus interactions may have played an important role in driving the diversity of life we see today. >> Nicholas Irwin. ️

<< These transfers not only have evolutionary consequences for both virus and host, but could have important health implications, >> Patrick Keeling.️

<< we think that this work serves as an interesting reminder that viruses have also contributed to the evolution of life on Earth, >>️ Nicholas Irwin. 
️
New research shows gene exchange between viruses and hosts drives evolution. University of British Columbia. Jan 5, 2022.


Also

Nonlinear effects in shaping human evolution, the role of viruses. Jan 15, 2019. 


keyword 'evolution'  in FonT


keyword 'evolution' | 'evoluzione'  in Notes (quasi-stochastic poetry)



Keywords: evolution, virus, gene exchange, horizontal gene transfer, HGT


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martedì 4 gennaio 2022

# behav: learning walks related to home burrow navigation (among desert grassland scorpions Paruroctonus utahensis)


<< The Navigation by Chemotextural Familiarity Hypothesis (NCFH) suggests that scorpions use their midventral pectines to gather chemical and textural information near their burrows and use this information as they subsequently return home. For NCFH to be viable, animals must somehow acquire home-directed “tastes” of the substrate, such as through path integration (PI) and/or learning walks. >>️

AA << found that once animals established their home burrows, they immediately made one to several short, looping excursions away from and back to their burrows before walking greater distances. We also observed similar excursions when animals made burrows in level sand in the middle of the arena (i.e., no mound provided). These putative learning walks, together with recently reported PI in scorpions, may provide the crucial home-directed information requisite for NCFH. >>️

Douglas D. Gaffin, Maria G. Munoz, Marielle Hoefnagels. Evidence of learning walks related to scorpion home burrow navigation. bioRxiv 2021.12.28.474378; Dec 30, 2021. 


Also

keyword 'walk' | 'walking' in FonT



keyword 'passo lieve' | 'walk' | 'walking' in Notes (quasi-stochastic poetry)




Keywords: behav, walk, walking, learning walk, NCFH



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lunedì 3 gennaio 2022

# gst: weird but not so weird dynamics, basins with tentacles could be common in high-dimensional systems.


<< Basins of attraction are fundamental to the analysis of dynamical systems (..). Over the years, many remarkable properties of basins have been discovered (..), most notably that their geometry can be wild, as exemplified by Wada basins (..), fractal basin boundaries (..), and riddled or intermingled basins (..). Yet despite these foundational studies, much remains to be learned about basins, especially in systems with many degrees of freedom. >>

AA show that for locally-coupled Kuramoto oscillators << high-dimensional basins tend to have convoluted geometries and cannot be approximated by simple shapes such as hypercubes. Although they are impossible to visualize precisely (because of their high dimensionality), (they) present evidence that these basins have long tentacles that reach far and wide and become tangled with each other. Yet sufficiently close to its own attractor, each basin becomes rounder and more simply structured, somewhat like the head of an octopus. >>

<< In terms of (AA) metaphor, almost all of a basin’s volume is in its tentacles, not its head. This finding is not limited to Kuramoto oscillators. (AA) provide a simple geometrical argument showing that, as long as the number of attractors in a system grows subexponentially with system size, the basins are expected to be octopus-like. As further evidence of their genericity, basins of this type were previously found in simulations of jammed sphere packings (..) where they were described as “branched” and “threadlike” away from a central core (..) and accurate methods were developed for computing their volumes (.,). There is also enticing evidence of octopus-like basins in neuronal networks (..), power grids (..), and photonic couplers (..). >>

<< Figure 4 is a further attempt to visualize the structure of high-dimensional basins, now by examining randomly oriented two-dimensional (2D) slices of state space, either far from a twisted state or close to one. (..) Despite the fact that each basin is connected (..)  the basins look fragmented in this 2D slice. >>

 Fig. 4(a): << Perhaps another metaphor than tentacles—a ball of tangled yarn—better captures the essence of the basin structure in this regime, far from any attractor, in which differently colored threads (representing different basins) are interwoven together in an irregular fashion. >>

Fig. 4(b): << The basin structure near an attractor is strikingly different. (..) the basins near an attractor are organized like an onion. >>

Yuanzhao Zhang, Steven H. Strogatz. Basins with tentacles. arXiv: 2106.05709v3 [nlin.AO]. Nov 2, 2021. 



Also

Reshaping Kuramoto model, when a collective dynamics becomes chaotic, with a surprisingly weak coupling. Dec 27, 2021.


Keywords: gst, dynamical systems, high-dimensional systems, Kuramoto oscillator, attractors, basin of attraction 



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