# 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: life as a product of molecular self-assembly

<< There are currently two main schools of thought regarding the origins of RNA. In one school, RNA is considered to be a product of nonenzymatic, prebiotic reactions. In the other, RNA is considered to be a product of chemical and/or biological evolution. >>

AA << report progress toward finding a proto-RNA that is the product of molecular self-assembly. >>

Cafferty B.J., Fialho D.M., Hud N.V. (2018) Searching for Possible Ancestors of RNA: The Self-Assembly Hypothesis for the Origin of Proto-RNA. In: Menor-Salvan C. (eds) Prebiotic Chemistry and Chemical Evolution of Nucleic Acids. Nucleic Acids and Molecular Biology, vol 35. Springer, Cham. doi: 10.1007/978-3-319-93584-3_5

https://link.springer.com/chapter/10.1007%2F978-3-319-93584-3_5

Joelle Renstrom. New study identifies possible ancestors of RNA. Astrobiol  Mag. Sep 17, 2018.

https://m.phys.org/news/2018-09-ancestors-rna.html 

# gst: quantum chaos to approach the evolution of a dynamic system

<< A study on the evolution of dynamic systems [..] has unexpectedly led to a better understanding of the chaos in the quantum world >>

<< The tools needed to explore the rigidity of dynamic systems [..] far exceeded those currently available, forcing the team to learn from neighboring disciplines >>

<< As a by-product of this process, researchers have identified the applicability of this project to quantum mechanics, which has led them to formulate a new theorem of thermodynamic quantum chaos combining ideas from large networks. Large networks — such as Big Data, social networks, convolutional neural networks of Artificial Intelligence models — which, although commonly used today, do not yet have adequate theories to explain their operation >>

Shakes Gilles. Study of dynamical systems leads to better understanding of quantum chaos. March 27, 2018.

https://www.thetalkingdemocrat.com/2018/03/study-of-dynamical-systems-leads-to-better-understanding-of-quantum-chaos/

# s-behav: the multifactorial relationship system evolved in Blenny

AA << investigate the evolution of fangs, venom, and mimetic relationships in reef fishes from the tribe Nemophini (fangblennies) >>

Nicholas R. Casewell, Jeroen C. Visser, et al. The Evolution of Fangs, Venom, and Mimicry Systems in Blenny Fishes. Current Biology. Vol 27, Issue 8, p1184–1191, 24 Apr 2017

http://www.cell.com/current-biology/fulltext/S0960-9822(17)30269-5

<<  It’s a good venom story >> Rich Pyle.

Christie Wilcox. Beware the blenny’s bite: scientists uncover the toxins in fang blenny venom.  Mar 30, 2017

http://blogs.discovermagazine.com/science-sushi/2017/03/30/fang-blenny-venom-toxins/

<< Si tratta del fang blenny, o blennide dalle zanne (..) noto anche come "senza paura", perche' non sembra temere troppo i predatori >>

Gli oppioidi del blennide. Le Scienze vol 586 p 24 Giu 2017

http://www.lescienze.it/

# 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

# s-brain-evol: lizard, an ancient dreamer

<< Lizards  might  snooze  like  humans  do. Sleeping  lizards  appear  to share  distinctive  brain  activity  patterns  with  sleeping  birds  and mammals (..)  If  true,  the  results  suggest  that  human  sleep patterns  evolved  by  around  300  million  years  ago  in  a  common  ancestor  of  birds,  mammals  and reptiles. >>

Sarah  Schwartz. Dragons  sleep  like  mammals  and  birds. Proof  of  reptiles’  slow-wave  and  REM  cycle  could  alter  understanding  of  slumber’s evolution. 2:19pm,  April  28, 2016

https://www.sciencenews.org/article/dragons-sleep-mammals-and-birds

<< Sleep  has  been  described  in  animals  ranging  from  worms  to  humans.  Yet  the electrophysiological  characteristics  of  brain  sleep,  such  as  slow-wave  (SW)  and  rapid  eye movement  (REM)  activities,  are  thought  to  be  restricted  to  mammals  and  birds.  Recording from  the  brain  of  a  lizard,  the  Australian  dragon  Pogona  vitticeps,  we  identified  SW  and REM sleep  patterns,  thus  pushing  back  the  probable  evolution  of  these  dynamics  at  least  to the  emergence  of  amniotes.  The  SW  and  REM  sleep  patterns  that  we  observed  in  lizards oscillated  continuously  for  6  to  10  hours  with  a  period  of  ~80  seconds.  >>

Mark  Shein-Idelson ,  Janie  M.  Ondracek, et al. Slow  waves,  sharp  waves,  ripples,  and  REM  in  sleeping dragons. Science 29  Apr  2016: Vol.  352,  Issue  6285,  pp.  590-595 DOI:  10.1126/science.aaf3621

http://science.sciencemag.org/content/352/6285/590

# s-evol: just three traits to explain, by Tereza & John

AA << found that just three traits explained most variation in diversification and species numbers among phyla: the most successful phyla have a skeleton (either internal or external), live on land (instead of in the ocean), and parasitize other organisms. >>

<< Other traits, including those that might seem more dramatic, had surprisingly little impact on diversification and species numbers: evolutionary accomplishments such as having a head, limbs, and complex organ systems for circulation and digestion don't seem to be primary accessories in the evolutionary "dress for success."  >>

<< "Parasitism isn't correlated with any of the other traits, so it seems to have a strong effect on its own," said Wiens [John Wiens]. >>

How to be winner in the game of evolution. Jan. 13, 2017

https://m.phys.org/news/2017-01-winner-game-evolution.html

Tereza Jezkova, John J. Wiens. What Explains Patterns of Diversification and Richness among Animal Phyla? The American Naturalist (2017). DOI: 10.1086/690194

http://www.journals.uchicago.edu/doi/10.1086/690194

# s-ecol: asymmetric cooperation during symbiosis (among Polynucleobacteria)

<< Relationships where two organisms depend on each other, known as symbiosis, evoke images of partnership and cooperation. But a new study in Nature Ecology and Evolution shows that, when it comes to certain microorganisms, symbiotic partners are actually being held "hostage" >>

Hostage situation or harmony? Researchers rethink symbiosis. July 27, 2017

https://m.phys.org/news/2017-07-hostage-situation-harmony-rethink-symbiosis.html

Vittorio Boscaro, Martin Kolisko, et al.  Parallel genome reduction in symbionts descended from closely related free-living bacteria. Nature Ecology & Evolution 1, 1160–1167 (2017) doi: 10.1038/s41559-017-0237-0 Publ. July 21,  2017

https://www.nature.com/articles/s41559-017-0237-0

# s-evol: more grey on their backs to camouflage (Meliphagidae and Acanthizidae songbirds)

<< Tropical birds are well known for their colorful appearance: vibrantly colored macaws, parakeets and parrots are widely considered to be the quintessential birds of this region. >>

<< But do birds evolve to become more colorful when they move to the tropics? >>

<<  "The pattern is really clear" Friedman [Nicholas Friedman]  reports, "birds living in the desert tend to be more grey on their backs, while birds living in the forest have evolved to be more of a dark green - we think they are evolving these colors to match their background." >>

<< This would be an example of natural selection, in this case more camouflaged organisms can survive and pass on their genes.
"These results help to explain the origins of the diversity of life, how species end up evolving different characteristics over time" >>

Okinawa Institute of Science and Technology. New research provides insight into plumage evolution. Nov. 4, 2016.

http://m.phys.org/news/2016-11-insight-plumage-evolution.html

Friedman NR, Remes V. Ecogeographical gradients in plumage coloration among Australasian songbird clades. Global Ecol. Biogeogr. 2016  doi:10.1111/geb.12522 Publ.  Sept. 25, 2016.

http://onlinelibrary.wiley.com/doi/10.1111/geb.12522/abstract

# 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

# 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

# s-evol: smoking, mutation and evolution

<< A genetic mutation may have helped modern humans adapt to smoke exposure from fires and perhaps sparked an evolutionary advantage over their archaic competitors >>

Matt Swayne. Where there's smoke and a mutation there may be an evolutionary edge for humans. August 2, 2016

http://news.psu.edu/story/419626/2016/08/02/research/where-theres-smoke-and-mutation-there-may-be-evolutionary-edge

<< (..) a functionally significant change in the AHR (aryl hydrocarbon receptor) occurred uniquely in humans, relative to other primates, that would attenuate the response to many environmental pollutants, including chemicals present in smoke from fire use during cooking. >>

Troy D. Hubbard, Iain A. Murray, et al. Divergent Ah receptor ligand selectivity during hominin evolution. Mol Biol Evol (2016) doi: 10.1093/molbev/msw143 First published online: August 2, 2016

http://m.mbe.oxfordjournals.org/content/early/2016/07/17/molbev.msw143

# brain: negative emotional contagion and cognitive bias (in ravens, Corvus corax).

<< after witnessing a conspecific in a negative state, ravens perform in a negatively biased manner on a judgment task. >>

AA << findings thus suggest negative emotional contagion in ravens, and in turn advance our understanding of the evolution of empathy. >>

Jessie E. C. Adriaense, Jordan S. Martin, et al. Negative emotional contagion and cognitive bias in common ravens (Corvus corax). PNAS. first published  doi: 10.1073/pnas.1817066116 May 20, 2019.

https://www.pnas.org/content/early/2019/05/14/1817066116  

Bob Yirka. Researchers find evidence of negative emotional contagion in lab ravens. Phys.org. May 21, 2019.

https://phys.org/news/2019-05-evidence-negative-emotional-contagion-lab.amp

# 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

# gst: a chaos-inducing approach against superbugs evolution

<< The CHAOS [Controlled Hindrance of Adaptation of OrganismS] method takes advantage of this effect, pulling multiple genetic levers in order to build up stress on the bacterial cell and eventually trigger a cascading failure, leaving the bug more vulnerable to current treatments. The technique does not alter the bug's DNA itself, only the expression of individual genes, similar to the way a coded message is rendered useless without the proper decryption. >>

<< We now have a way to cut off the evolutionary pathways of some of the nastiest bugs and potentially prevent future bugs from emerging at all, >> Peter Otoupal

Chaos-inducing genetic approach stymies antibiotic-resistant superbugs. University of Colorado at Boulder. Sept 3, 2018.

https://m.phys.org/news/2018-09-chaos-inducing-genetic-approach-stymies-antibiotic-resistant.html 

<< While individual perturbations improved fitness during antibiotic exposure, multiplexed perturbations caused large fitness loss in a significant epistatic fashion. >>

Peter B. Otoupal, William T. Cordell, et al. Multiplexed deactivated CRISPR-Cas9 gene expression perturbations deter bacterial adaptation by inducing negative epistasis. Comm  Biol 1 (129) Sept 3, 2018

https://www.nature.com/articles/s42003-018-0135-2

# 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 

# phys: the strange world of quantum mechanics

<< In the normal world, an object such as a baseball can only be in one place at one time. But in the quantum world, a particle such as an electron can occupy an infinite number of places at the same time, existing in what physicists call a superposition of multiple states. >>

<< in the quantum world, two individual particles, such as photons can be entangled, such that the mere act of sensing one photon with a detector instantaneously forces the other photon, no matter how far away, to assume a particular state. >>

<< evidence is mounting from the world of plant physiology that some biological processes that rely on quantum superposition occur at normal temperatures, raising the possibility that unimaginably strange world of quantum mechanics may indeed intrude into the every day workings of other biological systems, such as our nervous systems. >>

<< Evolution, in its relentless quest to engineer the most energy-efficient life forms, appears to have ignored physicists’ belief that useful quantum effects can’t happen in the warm, wet environments of biology. >>

Eric Haseltine. Why You Should Care About Quantum Neuroscience.
Hints of an incredibly exciting future. Dec 31, 2018

https://www.psychologytoday.com/us/blog/long-fuse-big-bang/201812/why-you-should-care-about-quantum-neuroscience

FonT

davanti a una immagine di "enzima allosterico" qualsiasi bravo scientist sa immediatamente con cosa avra' a che fare: avra' a che fare con il caos, vale a dire con oggetti che possono generare dinamiche senz'altro confinate purtuttavia bizzarre, jazz, funky, fuzzy; invece davanti a concetti quali i due citati sopra (superposition, entanglement), e gli ipotetici effetti immaginabili all'interno di strutture biologiche, neurobiologiche, informatiche, ho idea che chiunque potrebbe sentirsi vagamente disorientato (qui si sottolinea "vagamente") ...

# 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

# 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.

# chem: mimic a stable photosynthesis (inside a porous 'scaffold' to avoid deactivation / decomposition)

<< When molecules of cobalt oxide cubane, so named for its eight atoms forming a cube, are in solution, the catalytic units eventually collide into one another and react, and thus deactivate. To hold the catalysts in place, and prevent these collisions, the researchers used a metal-organic framework as a scaffold.  >>

<< Our study provides a clear, conceptual blueprint for engineering the next generation of energy-converting catalysts, >> T. Don Tilley

Theresa Duque. Here comes the sun: a new framework for artificial photosynthesis. Lawrence Berkeley National Laboratory. Jun 18, 2019

https://m.phys.org/news/2019-06-sun-framework-artificial-photosynthesis.html

Andy I. Nguyen, Kurt M. Van Allsburg, et al. Stabilization of reactive Co4O4 cubane oxygen-evolution catalysts within porous frameworks. PNAS 116 (24) 11630-11639. doi: 10.1073/pnas.1815013116. Jun 11, 2019.

https://www.pnas.org/content/116/24/11630