# evol: emergence of single vs. multi-state allostery

      FIG. 1. The elastic network model

<< Allostery, the change of activity of a  macromolecule in response to a perturbation at a distance from its active site, is thought to be a ubiquitous feature of proteins. Initially described in the context of multimeric proteins, it is now understood to underlie the regulation of proteins with diverse structural architectures, from receptors to signaling proteins and metabolic enzymes. >>️

<< Here, (AA) analyze a simplified model of protein allostery under a range of physical and evolutionary constraints. (They) find that a continuum of mechanisms between two archetypes emerges through evolution. In one limit, a single-state mechanism exists where ligand binding induces a displacement along a single normal mode, and in the other limit, a multi-state mechanism exists where ligand binding induces a switch across an energy barrier to a different stable state. Importantly, whenever the two mechanisms are possible, the multi-state mechanism confers a stronger allosteric effect and thus a selective advantage. >>

️

Eric Rouviere, Rama Ranganathan, Olivier Rivoire. Emergence of Single- versus Multi-State Allostery. PRX Life 1, 023004. Nov 9, 2023.

https://journals.aps.org/prxlife/abstract/10.1103/PRXLife.1.023004

Also: allostery in FonT https://flashontrack.blogspot.com/search?q=allostery

Also: allosterico in Notes 

(quasi-stochastic poetry)

https://inkpi.blogspot.com/search?q=allosterico

Keywords: gst, allostery, elastic, evolution

# gst: self-trapped nonlinear waves with multiple phase singularities.

AA << investigate the existence of self-trapped nonlinear waves with multiple phase singularities. >>️

They << focus on configurations with an antivortex surrounded by a triangular arrangement of vortices within a hosting soliton. (AA) find stationary patterns that can be interpreted as stable self-trapped vortex crystals, constituting the first example of a configuration of this sort with space-independent potentials. Their stability is linked to their norm, transitioning from unstable to stable as their size increases, with an intermediate region where the structure is marginally unstable, undergoing a remarkable and puzzling self-reconstruction during its evolution. >>️

Angel Paredes and Humberto Michinel. Self-trapping of vortex crystals via competing nonlinearities.  Phys. Rev. E 109, 024216. Feb 22, 2024. 

https://journals.aps.org/pre/abstract/10.1103/PhysRevE.109.024216

Also: waves, soliton, vortex, in https://www.inkgmr.net/kwrds.html

Keywords: gst, waves, soliton, self-trapping, vortex 

# gst: the hypothesis of a new type of rogue waves.

<< Much attention of researchers has been paid in the recent decades to the study of rogue waves. Various mechanisms of formation of these waves were suggested. The occurrence of rogue waves is most often investigated on the basis of the mechanisms of modulation instability and superposition of waves. In both cases, an evolution of rogue waves takes place against the background of a wave field, which is reflected in the definitions of such waves. In this report, the localized waves developed in the absence of the background wave fields are considered. At the same time, their dynamics corresponds to the dynamics of rogue waves that ”appear from nowhere and disappear without a trace”. >>️

<< The waves of this type are distinguished by the fact that their dynamics occur on the zero background. This implies that rogue waves presented here are formed solely due to the nonlinear focusing. >>️

N.V. Ustinov. New type of rogue waves. arXiv:2310.17254v1 [nlin.SI]. Oct 26, 2023.  

https://arxiv.org/abs/2310.17254

Chaos, Solitons & Fractals V. 179, Feb 2024, 114467. https://www.sciencedirect.com/science/article/abs/pii/S0960077924000183

Also: waves, in https://www.inkgmr.net/kwrds.html

Keywords: gst, waves, rogue waves 

# art: nature as a bizarre artist, the self-sculpted Sphinx.

<< There is evidence that the Great Sphinx was a natural landform before its surface features were chiseled by the ancient Egyptians. Is this controversial theory plausible? >>

AA << carried out experiments on the fluid mechanical erosion of clay. Based on accounts of the nonuniform composition of the Sphinx, we tested the effect of hard inclusions within hillocks of softer clay. The flow of a water tunnel mimics the prevailing winds of Giza, and three-dimensional optical scanning records the history and evolution of the shape as it erodes. >>

<< These results show what ancient peoples may have encountered in the deserts of Egypt and why they envisioned a fantastic creature. >>️

️

Samuel Boury, Scott Weady, Leif Ristroph. Sculpting the Sphinx. Phys. Rev. Fluids 8, 110503. Nov 16, 2023.

https://journals.aps.org/prfluids/abstract/10.1103/PhysRevFluids.8.110503

https://gfm.aps.org/meetings/dfd-2022/6323dcaf199e4c2c0873fad7

Also: brain, perception, in https://www.inkgmr.net/kwrds.html 

Keywords: art, sculpt, Sphinx, erosion, fluid mechanical erosion, brain, mind, perceptions.

# gst: evolution of survivors compared to discrete vs continuous noise

<< Environmental variations can significantly influence how populations compete for resources, and hence shape their evolution. Here, (AA) study population dynamics subject to a fluctuating environment modeled by a varying carrying capacity changing continuously in time according to either binary random switches, or by being driven by a noise of continuous range. >>

<< the slow strain fixation probability can be greatly enhanced for a continuously varying environment compared to binary switches, even when the first two moments of the carrying capacity coincide. >>️

Ami Taitelbaum, Robert West, et al. Evolutionary dynamics in a varying environment: Continuous versus discrete noise. Phys. Rev. Research 5, L022004. April 4, 2023. 

https://journals.aps.org/prresearch/abstract/10.1103/PhysRevResearch.5.L022004

Also: noise, in https://www.inkgmr.net/kwrds.html

Keywords: gst, evolution, noise, discrete vs continuous noise

# gst: pattern generation through turbulent cascades

<< Fully developed turbulence is a universal and scale-invariant chaotic state characterized by an energy cascade from large to small scales where the cascade is eventually arrested by dissipation. In this Letter, (AA) show how to harness these seemingly structureless turbulent cascades to generate patterns. Conceptually, pattern or structure formation entails a process of wavelength selection: patterns typically arise from the linear instability of a homogeneous state. By contrast, the mechanism (they) propose here is fully non-linear and triggered by a non-dissipative arrest of turbulent cascades. Instead of being dissipated, energy piles up at intermediate scales. Using a combination of theory and large-scale simulations, (AA) show that the tunable wavelength of these cascade-induced patterns is set by a non-dissipative transport coefficient called odd or gyro viscosity. This non-dissipative viscosity is ubiquitous in chiral systems (..). Beyond chiral fluids, cascade-induced pattern formation could occur in natural systems (..) as well as in industrial processes (..). >>

Xander M. de Wit, Michel Fruchart, et al. Pattern formation by non-dissipative arrest of turbulent cascades. arXiv: 2304.10444v1 [cond-mat.soft]. Apr 20, 2023.

https://arxiv.org/abs/2304.10444

Also: 'turbulence', 'vortex', 'game', 'evolution', 'ai' in https://www.inkgmr.net/kwrds.html

Keywords: gst, vortex, vorticity,  turbulence, turbulent cascade, pattern formation, game, evolution, ai (artificial intelligence)

# evol: gentle bonobos vs. aggressive chimps ...

<< Among the great apes, the chimpanzees and the bonobos are the most genetically related to us as we share about 98.7% of our DNA with them. >>️

<< So where exactly do humans stand? We seem to have incorporated the traits of both species, resulting in a tension between our aggressive and harmonious proclivities. Our tendency for conflict mirrors the competitiveness of chimpanzees, and yet the bonobos teach us that we have it in us to be altruistic and that society can be organised in more peaceful ways. This selflessness underlies the large-scale cooperation that has helped Homo sapiens share ideas, form nations, explore the universe and outlast other early humans such as Homo erectus. >>️

Jose Yong. Bonobos and chimps: what our closest relatives tell us about humans. theconversation.com. April 4, 2023. 

https://theconversation.com/bonobos-and-chimps-what-our-closest-relatives-tell-us-about-humans-202265

Img: https://images.theconversation.com/files/519318/original/file-20230404-897-1b84fi.png

Also: 'evolution', 'chimps', 'behav' in https://www.inkgmr.net/kwrds.html

Keywords: evolution, chimps, bonobos,  chimpanzees, behavior

# gst: the physiological emergence and evolution of cell-spanning vortices (inside Drosophila oocytes).

<< Life in complex systems, such as cities and organisms, comes to a standstill when global coordination of mass, energy, and information flows is disrupted. Global coordination is no less important in single cells, especially in large oocytes and newly formed embryos, which commonly use fast fluid flows for dynamic reorganization of their cytoplasm. Here, (AA) combine theory, computing, and imaging to investigate such flows in the Drosophila oocyte, where streaming has been proposed to spontaneously arise from hydrodynamic interactions among cortically anchored microtubules loaded with cargo-carrying molecular motors. >>️

Sayantan Dutta, Reza Farhadifar, et al. Self-organized intracellular twisters. arXiv: 2304.02112v2 [physics.bio-ph].  Apr 6, 2023. 

https://arxiv.org/abs/2304.02112

Also

keyword 'vortex' in FonT

https://flashontrack.blogspot.com/search?q=vortex

keyword 'vortice' in Notes

(quasi-stochastic poetry)

https://inkpi.blogspot.com/search?q=vortice

Keywords: gst, fluid dynamics, vortex, vortices, vortexes, vorticity,

# behav: even the first asynchronous decisions might tend to be correct and exhibit information cascades.

<< It is usually assumed that information cascades are most likely to occur when an early but incorrect opinion spreads through the group. Here (AA) analyse models of confidence-sharing in groups and reveal the opposite result: simple but plausible models of naïve Bayesian decision-making exhibit information cascades when group decisions are synchronous; however, when group decisions are asynchronous, the early decisions reached by Bayesian decision makers tend to be correct, and dominate the group consensus dynamics. Thus early decisions actually rescue the group from making errors, rather than contribute to it. (AA) explore the likely realism of our assumed decision-making rule with reference to the evolution of mechanisms for aggregating social information, and known psychological and neuroscientific mechanisms. >>️

Andreagiovanni Reina, Thomas Bose, et al.  Asynchrony rescues statistically-optimal group decisions from information cascades through emergent leaders.  bioRxiv. doi: 10.1101/ 2022.04.05.487127. Feb16, 2023.

https://www.biorxiv.org/content/10.1101/2022.04.05.487127v3

Also

'asynchronous' in FonT

https://flashontrack.blogspot.com/search?q=asynchronous

'game' in FonT

https://flashontrack.blogspot.com/search?q=game

'behav' in FonT

https://flashontrack.blogspot.com/search?q=behav

Keywords: behavior, behaviour, game, decision-making, synchronous- asynchronous group decisions, social interactions, information cascade, life, jazz

# gst: towards (insights into) intermittency and inhomogeneity of turbulent mixing

<< Fluid elements deform in turbulence by stretching and folding. In this work, by projecting the material deformation tensor onto the largest stretching direction, the dynamics of folding is depicted through the evolution of the material curvature. Results from direct numerical simulation (DNS) show that the curvature growth exhibits two regimes, first a linear stage dominated by folding fluid elements through a persistent velocity Hessian which then transitions to an exponential growth driven by the stretching of already strongly bent fluid elements. This transition leads to strong curvature intermittency at later stages, which can be explained by a proposed curvature-evolution model. The link between velocity Hessian to folding provides a new way to understand the crucial steps in energy cascade and mixing in turbulence beyond the classical linear description. >>

Yinghe Qi, Charles Meneveau, Greg Voth, Rui Ni. Folding dynamics and its intermittency in turbulence. arXiv: 2301.10341v1 [physics.flu-dyn]. Jan 24, 2023. 

https://arxiv.org/abs/2301.10341

Also

keyword 'intermittency' in FonT

https://flashontrack.blogspot.com/search?q=intermittency

keyword 'turbulence' in FonT

https://flashontrack.blogspot.com/search?q=turbulence

keyword 'turbolento' | 'turbolenza' in Notes (quasi-stochastic poetry)

https://inkpi.blogspot.com/search?q=turbolento

https://inkpi.blogspot.com/search?q=turbolenza

keyword 'transition' | 'transitional' in FonT

https://flashontrack.blogspot.com/search?q=transition

https://flashontrack.blogspot.com/search?q=transitional

keyword 'transition' | 'transizion*' in Notes (quasi-stochastic poetry)

https://inkpi.blogspot.com/search?q=transition

https://inkpi.blogspot.com/search?q=transizione

https://inkpi.blogspot.com/search?q=transizioni

Keywords: gst, intermittency, turbulence, transition

# gst: apropos of transitions, disordered systems mimic genetic evolution.

<< A bacterial genome’s evolution under changing drug concentrations displays effects of memory formation and mimics how disordered solids respond to external forces. >>️

AA << simulate the effect on adaptation of an environment that is constantly changing. Using a model that describes how slow-moving disordered systems respond to external forces, (they) find that microbe evolution in changing drug concentrations exhibits hysteresis and memory formation. They use analytical methods and numerical simulations to connect these statistical physics concepts to bacterial drug resistance. >>️

AA << find that this behavior mimics that of disordered systems driven by external forces, such as ferromagnetic materials subjected to magnetic fields or amorphous materials subjected to a shearing force. They say that while their approach focuses on the evolution of drug resistance, the framework can be adapted to other problems in evolutionary biology that involve changing environmental parameters. >>

️

Rachel Berkowitz. Disordered Systems Mimic Genetic Evolution. Physics 15, s118. Sep 20, 2022. 

https://physics.aps.org/articles/v15/s118

Suman G. Das, Joachim Krug, Muhittin Mungan. Driven Disordered Systems Approach to Biological Evolution in Changing Environments. Phys. Rev. X 12, 031040. Sep 20, 2022.

https://journals.aps.org/prx/abstract/10.1103/PhysRevX.12.031040

Also

keyword 'disorder' in FonT

https://flashontrack.blogspot.com/search?q=disorder

keyword 'disordine' in Notes

(quasi-stochastic poetry)

https://inkpi.blogspot.com/search?q=disordine

Keywords: gst, disorder, disordered systems, evolution, genetic evolution 

# gst: apropos of transitions, evaporating binary microdroplets with phase segregation

<< Phase segregation triggered by selective evaporation can emerge in multicomponent systems, leading to complex physiochemical hydrodynamics. Recently, Li et al. (2018) and Kim & Stone (2018) reported a segregative behavior (i.e., demixing) in an evaporating binary droplet. In this work, by means of experiments and theoretical analysis, (AA) investigate the flow dynamics after the occurrence of the phase segregation. >>

<< First, (AA) experimentally reveal the overall physiochemical hydrodynamics of the evaporation process, including the segregative behavior and the resulting flow structure close to the substrate. By quantifying the evolution of the radial flow, (they) identify three successive life stages of the evaporation process. >>

<< At Stage I, a radially outward flow is observed. It is driven by the Marangoni effect. At the transition to Stage II, the radial flow partially reverses, starting from the contact line. This flow breaks the axial symmetry and remarkably is driven by the segregation itself. Finally at Stage III, the flow decays as the evaporation gradually ceases. At this stage the segregation has grown to the entire droplet, and the flow is again controlled by the Marangoni effect. The resulting Marangoni flow homogenizes the distribution of the entrapped volatile water over the whole droplet. >>️

Yaxing Li, Pengyu Lv, et al. Physiochemical hydrodynamics of the phase segregation in an evaporating binary microdroplet.arXiv:2208.07861v1 [physics.flu-dyn]  Aug 16, 2022.

https://arxiv.org/abs/2208.07861

Marangoni effect. 

https://en.m.wikipedia.org/wiki/Marangoni_effect   

https://youtu.be/vGb6t5Gfq6s   

Also

keyword 'drop' | 'droplet' in FonT

https://flashontrack.blogspot.com/search?q=drop

https://flashontrack.blogspot.com/search?q=droplet

Keywords: gst, droplet, transition, evaporation, phase transition, phase segregation, Marangoni flow

# life: a proposito di transizioni ...

a proposito di transizioni ... 

<< se si considera la limitatezza del numero degli standards da essi tante volte 'rigenerati'. >> 

<< Il problema qui - in una prospettiva sperimentale - non sembra la generazione (quasistocastica?) delle forme inattese, bensi' inerente la struttura logico- funzionale dei "filtri", dei setacci cioe', capaci di trattenere (e conservare) le soluzioni funzionali al codice, "metastabili" in senso evolutivo, con l'eliminazione di tutto cio' che puo' contribuire alla rigidita' strutturale dell' insieme.  >>

2134 - bizzarrie bop sugli standard. Notes. Apr 29, 2007. 

https://inkpi.blogspot.com/2007/04/2134-bizzarrie-bop-sugli-standard.html

https://twitter.com/flashontrack/status/1547867345502158853

Also

keyword 'transition' | 'transitional' in FonT

https://flashontrack.blogspot.com/search?q=transition

https://flashontrack.blogspot.com/search?q=transitional

keyword 'transition' | 'transizion*' in Notes (quasi-stochastic poetry)

https://inkpi.blogspot.com/search?q=transition

https://inkpi.blogspot.com/search?q=transizione

https://inkpi.blogspot.com/search?q=transizioni

Keywords: life, transition, evolution, quasi-stochastic,  poetry, quasi-stochastic poetry,  fuzzypoe, droploids.

# evol: spontaneous, immediate asymmetry, the chiral twist

<< When holding a right hand in front of a mirror, one can see a reflected image of a left hand and vice versa. In 1848, Louis Pasteur discovered that organic molecules are much like our hands: they come in mirror-image pairs of left- and right-handed variants. Nowadays, we know that this handedness or chirality (from the Greek word for "hand") is a hallmark of organic molecules. >>

<< Organic molecules are rich in carbon atoms, which form bonds to create either a right or a left "nano-hand." Yet, puzzlingly, life almost always selects to exclusively use one of the two mirror-image twins—a phenomenon called homochirality. For example, terrestrial life is based on left-handed amino acids and right-handed sugars. >>️️

<< A model now proposes a novel explanation for the emergence of homochirality in life—a longstanding puzzle about the origin of life on Earth. >>️

<< Homochirality emerges spontaneously in prebiotic chemical networks that adapt to optimize energy harvesting from the environment. Previously, it was believed that chiral symmetry breaking requires multiple loops of auto-catalysis, which increasingly produces one enantiomer of a molecule while inhibiting the formation of the other. However, the IBS team's results showed that the underlying mechanism of symmetry breaking is very general, as it can occur in large reaction systems with many random molecules and does not require sophisticated network architectures. It was found that this sharp transition to homochirality stems from the self-configuration of the reaction network in order to achieve more efficient harvesting of energy from the environment. >>️

Learning chemical networks give life a chiral twist. Institute for Basic Science. Apr 26, 2022. 

https://phys.org/news/2022-04-chemical-networks-life-chiral.html

William D. Pineros, Tsvi Tlusty. Spontaneous chiral symmetry breaking in a random driven chemical system. Nat Commun 13, 2244. doi: 10.1038/ s41467-022-29952-8. Apr 26, 2022.

https://www.nature.com/articles/s41467-022-29952-8

Also

keyword 'chiral' in FonT

https://flashontrack.blogspot.com/search?q=chiral

keyword 'self-assembly' in FonT

https://flashontrack.blogspot.com/search?q=self-assembly

Keywords: evolution, gst, randomness, self-assembly, self-configuration, break symmetry, asymmetry, chiral, chirality  

# phyto: weird, jazzy Nature, the 'transference of sexuality', 'some sexual consequences of being a plant'.

<< Plants have characteristic features that affect the expression of sexual function, notably the existence of a haploid organism in the life cycle, and in their development, which is modular, iterative and environmentally reactive. For instance, primary selection (the first filtering of the products of meiosis) is via gametes in diplontic animals, but via gametophyte organisms in plants. Intragametophytic selfing produces double haploid sporophytes which is in effect a form of clonal reproduction mediated by sexual mechanisms. In homosporous plants, the diploid sporophyte is sexless, sex being only expressed in the haploid gametophyte. However, in seed plants, the timing and location of gamete production is determined by the sporophyte, which therefore has a sexual role, and in dioecious plants has genetic sex, while the seed plant gametophyte has lost genetic sex. This evolutionary transition is one that E.J.H. Corner called ‘the transference of sexuality’. The iterative development characteristic of plants can lead to a wide variety of patterns in the distribution of sexual function, and in dioecious plants poor canalization of reproductive development can lead to intrasexual mating and the production of YY supermales or WW superfemales. Finally, plant modes of asexual reproduction (agamospermy/apogamy) are also distinctive by subverting gametophytic processes. >>

Quentin Cronk. Some sexual consequences of being a plant. Philos Trans R Soc Lond B Biol Sci. doi: 10.1098/ rstb.2021.0213. Mar 21, 2022. 

https://royalsocietypublishing.org/doi/10.1098/rstb.2021.0213

Also

keyword 'phyto' | 'plant' in FonT

https://flashontrack.blogspot.com/search?q=phyto

https://flashontrack.blogspot.com/search?q=plant

keywords: evol, evolution, phyto, plant, sex, sexuality

# life; a hypothetical externalization of knowledge effects; humans are thought to have decreased in brain volume since the end of the last ice age (3,000 y.ago)

<< Human brain size nearly quadrupled in the six million years since Homo last shared a common ancestor with chimpanzees, but human brains are thought to have decreased in volume since the end of the last Ice Age. The timing and reason for this decrease is enigmatic. Here (AA) use change-point analysis to estimate the timing of changes in the rate of hominin brain evolution. (They) find that hominin brains experienced positive rate changes at 2.1 and 1.5 million years ago, coincident with the early evolution of Homo and technological innovations evident in the archeological record. But (AA) also find that human brain size reduction was surprisingly recent, occurring in the last 3,000 years. >>

Jeremy M. DeSilva, James F. A. Traniello, et al. When and Why Did Human Brains Decrease in Size? A New Change-Point Analysis and Insights From Brain Evolution in Ants. Front. Ecol. Evol.,  doi: 10.3389/ fevo.2021.742639. Oct 22, 2021. 

https://www.frontiersin.org/articles/10.3389/fevo.2021.742639/full

When and why did human brains decrease in size 3,000 years ago? Ants may hold clues. Frontiers. Oct 22, 2021.

https://phys.org/news/2021-10-human-brains-decrease-size-years.html

Also

keyword 'nomade' | 'nomad' | 'nomads' | 'nomadic' | 'hunter-gatherers' in FonT

https://flashontrack.blogspot.com/search?q=nomade

https://flashontrack.blogspot.com/search?q=nomad

https://flashontrack.blogspot.com/search?q=nomads

https://flashontrack.blogspot.com/search?q=nomadic

https://flashontrack.blogspot.com/search?q=hunter-gatherers

keyword 'nomade' | 'nomadi' in Notes (quasi-stochastic poetry)

https://inkpi.blogspot.com/search?q=nomade

https://inkpi.blogspot.com/search?q=nomadi

keyword 'ctz' entities in FonT

https://flashontrack.blogspot.com/search?q=ctz

keywords: evolution, brain, brain size, nomads, post-nomads, sociocultural effects

# 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.

https://phys.org/news/2022-01-evolutionary-theory-dna-mutations-random.html

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.

https://www.nature.com/articles/s41586-021-04269-6

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.

https://flashontrack.blogspot.com/2017/05/s-phyto-three-ways-of-plastoquinone.html

Also

keyword 'evolution'  in FonT

https://flashontrack.blogspot.com/search?q=evolution

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

https://inkpi.blogspot.com/search?q=evolution

https://inkpi.blogspot.com/search?q=evoluzione

keyword 'jazz' in FonT

https://flashontrack.blogspot.com/search?q=jazz

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

https://inkpi.blogspot.com/search?q=jazz

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

# 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. 

https://www.nature.com/articles/s41564-021-01026-3

<< 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.

https://phys.org/news/2022-01-gene-exchange-viruses-hosts-evolution.html

Also

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

https://flashontrack.blogspot.com/2019/01/evol-nonlinear-effects-in-shaping-human.html

keyword 'evolution'  in FonT

https://flashontrack.blogspot.com/search?q=evolution

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

https://inkpi.blogspot.com/search?q=evolution

https://inkpi.blogspot.com/search?q=evoluzione

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

# gst: small-scale random perturbations, Arnold's cat spontaneously stochastic

<< Multi-scale systems (..) may possess a fascinating property of spontaneous stochasticity: a small-scale initial uncertainty develops into a randomly chosen largescale state in a finite time, and this behavior is not sensitive to the nature and magnitude of uncertainty (..). >>

A << intriguing form is the Eulerian spontaneous stochasticity (ESS) of the velocity field itself: an infinitesimal small-scale noise triggers stochastic evolution of velocity field at finite scales and times. >>

AA << prove that a formally deterministic system with scaling symmetry yields a stochastic process with Markovian properties if it is regularized with a vanishing small-scale random perturbation. Besides its significance for understanding turbulence, (their) model extends the phenomenon of ESS beyond the scope of fluid dynamics: (AA) discuss a prototype of a feasible experiment for observing ESS in optics or electronics, as well as potential applications in other physical systems.>>

Alexei A. Mailybaev, Artem Raibekas. Spontaneously stochastic Arnold's cat. arXiv:2111.03666v1 [nlin.CD]. Nov 5,  2021.

https://arxiv.org/abs/2111.03666

keywords: gst, Arnold's cat, randomness, stochasticity, spontaneous stochasticity, small-scale random perturbations, noise, turbulence, chaos 

# gst: intermittent large-intensity pulses (LIE) due to instabilities in quasiperiodic motion (in Zeeman laser)

AA << report intermittent large-intensity pulses that originate in Zeeman laser due to instabilities in quasiperiodic motion, >>

<< one route follows torus-doubling to chaos and another goes via quasiperiodic intermittency in response to variation in system parameters. >>

<< During quasiperiodic intermittency, the temporal evolution of the laser shows intermittent chaotic bursting episodes intermediate to the quasiperiodic motion instead of periodic motion >>

<< The intermittent bursting appears as occasional large-intensity events (LIE). In particular, this quasiperiodic intermittency has not been given much attention so far from the dynamical system perspective, in general. >>

S. Leo Kingston, Arindam Mishra, Marek Balcerzak, Tomasz Kapitaniak, Syamal K. Dana. Instabilities in quasiperiodic motion lead to intermittent large-intensity events in Zeeman laser. arXiv: 2109.11847v1 [nlin.CD]. Sep 24, 2021. 

https://arxiv.org/abs/2109.11847

keywords: gst, quasiperiodic motion, intermittency, quasiperiodic intermittency, instability, chaos.