# gst: multiple Pareto-optimal solutions of the dissipation-adaptation trade-off

<< Adaptation refers to the ability to recover and maintain “normal” function on perturbations of internal or external conditions and is essential for sustaining life. Biological adaptation mechanisms are dissipative, i.e., they require a supply of energy such as the coupling to the hydrolysis of ATP. Via evolution the underlying biochemical machinery of living organisms evolved into highly optimized states. However, in the case of adaptation processes two quantities are optimized simultaneously, the adaptation speed or accuracy and the thermodynamic cost. In such cases one typically faces a trade-off, where improving one quantity implies worsening the other. The solution is no longer unique but rather a Pareto set—the set of all physically attainable protocols along which no quantity can be improved without worsening another. >> 

AA << investigate Pareto fronts in adaptation-dissipation trade-offs for a cellular thermostat and a minimal ATP-driven receptor-ligand reaction network. (They) find convex sections of Pareto fronts to be interrupted by concave regions, implying the coexistence of distinct optimization mechanisms. (They) discuss the implications of such “compromise-optimal” solutions and argue that they may endow biological systems with a superior flexibility to evolve, resist, and adapt to different environments. >>️

Jorge Tabanera-Bravo, Aljaz Godec. Multiple Pareto-optimal solutions of the dissipation-adaptation trade-off. 

Phys. Rev. Research 7, 013020. Jan 7, 2025.

https://journals.aps.org/prresearch/abstract/10.1103/PhysRevResearch.7.013020

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

Also: 'adaptation' in FonT  https://flashontrack.blogspot.com/search?q=adaptation   in Notes (quasi-stochastic poetry) (a) https://inkpi.blogspot.com/search?q=adaptation   

(b) https://inkpi.blogspot.com/search?q=adattamento

Keywords: gst, adaptation, dissipation

# game: in a iterated prisoner's dilemma scenario forgiveness turns out to be an adaptation

<< Prisoner’s dilemma is used to represent a range of real life phenomena such as economics, commerce, nature and wildlife. >>

<< Researchers working on iterated prisoner's dilemma (IPD) with limited memory inspected the outcome of different forgetting strategies in homogeneous environment, within which all agents adopt the same forgetting strategy at a time. In this work, with the intention to represent real life more realistically, (AA) improve existing forgetting strategies, offer new ones, and conduct experiments in heterogeneous environment that contains mixed agents and compare the results with previous research as well as homogeneous environment >>

<< in a more realistic environment consisting of all types of agents, in terms of both cooperation probabilities and forgetting strategies, agents who forget defectors consistently outperform other forgetting strategies for all memory ratio values. Moreover, the best performing defectors are also the ones that forget other defectors. In other words, agents who “forgive” defectors are the best performers. Hence, forgiveness is an adaptation. >>

FMC : Forget most cooperator first 

FMP : Forget most played first 

FMU : Forget most unpredictable first 

FR :  Forget randomly 

FLP : Forget least played first 

FMD : Forget most defector first 

Meliksah Turker, Haluk O. Bingol. Forgiveness is an Adaptation in Iterated Prisoner's Dilemma with Memory. arXiv:2112.07894v1 [cs.GT]. Dec 15, 2021

https://arxiv.org/abs/2112.07894

Also

keyword 'game' | 'tit-for-tat' in FonT

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

https://flashontrack.blogspot.com/search?q=tit-for-tat

keyword 'game' | 'tit-for-tat' in Notes

(quasi-stochastic poetry)

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

https://inkpi.blogspot.com/search?q=tit-for-tat

Keywords: game, iterated prisoner's dilemma, forgiveness, adaptation

# gst: stochastic adaptation, stochastic resonance.

<< Stochastic resonance is a phenomenon possessed by some nonlinear oscillators, in which a weak signal is boosted by noise. Both the monostable and bistable Duffing oscillators can exhibit this property. However, stochastic resonance has a strong frequency-dependence, as only a band of frequencies may be boosted by noise. >>️

<< Adaptive oscillators are a subset of nonlinear oscillators that can learn the features of an external force. (In this AA work), an adaptive state is added to a Duffing oscillator. This adaptive state enables the Duffing adaptive oscillator to outperform stochastic resonance over a wide range of frequencies by learning a resonance condition. >>️

Edmon Perkins. Comparison of stochastic adaptation and stochastic resonance. Phys. Rev. E 110, 064225. Dec 27, 2024.

https://journals.aps.org/pre/abstract/10.1103/PhysRevE.110.064225 

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

Keywords: gst, fluctuations, noise, transition, stochasticity, stochastic adaptation, stochastic resonance

# 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

# behav: persistent neuronal firing during flight in flies, like a pulsating gambler who has to decide quickly

<< A general principle of sensory systems is that they adapt to prolonged stimulation by reducing their response over time. >>

<< as opposed to most sensory and visual neurons, and in particular to the motion vision sensitive neurons in the brains of both flies and mammals, the descending neurons show little adaption during stimulus motion. (..) the optic-flow-sensitive descending neurons display persistent firing, or an after-effect, following the cessation of visual stimulation, consistent with the lingering calcium signal hypothesis. >>

AA results << show a combination of adaptation and persistent firing in the neurons that project to the thoracic ganglia and thereby control behavioral output. >>

Sarah Nicholas, Karin Nordstrom. Persistent Firing and Adaptation in Optic-Flow-Sensitive Descending Neurons. Curr Biol. doi: 10.1016/ j.cub.2020.05.019. May 28, 2020.

https://www.cell.com/current-biology/fulltext/S0960-9822(20)30658-8

Revealing how flies make decisions on the fly to survive. Flinders University. May 28, 2020

https://phys.org/news/2020-05-revealing-flies-decisions-survive.html

Also

the flexible mental maps of flies. FonT. Nov 21, 2019. 

https://flashontrack.blogspot.com/2019/11/brain-flexible-mental-maps-of-flies.html

<< Considerando invece l' immagine classica della "mosca nella bottiglia", >>  in: 2066 - voli a casaccio. Notes. (quasi-stochastic poetry). Oct 01, 2006.

https://inkpi.blogspot.com/2006/10/2066-voli-casaccio.html

# pnei: brain motor and fear circuits regulate leukocytes during acute stress

<< The nervous and immune systems are intricately linked. Although psychological stress is known to modulate immune function, mechanistic pathways linking stress networks in the brain to peripheral leukocytes remain poorly understood. Here, (AA) show that distinct brain regions shape leukocyte distribution and function throughout the body during acute stress in mice. >>️

Poller, W.C., Downey, J., et al. Brain motor and fear circuits regulate leukocytes during acute stress. Nature. doi: 10.1038/ s41586-022-04890-z. May 30, 2022. 

https://www.nature.com/articles/s41586-022-04890-z

PNEI: Psycho-Neuro-Endocrine-Immunology  

https://pubmed.ncbi.nlm.nih.gov/?term=pnei

Also

Inchingolo G. Percezione dello stato di salute e leucociti in anziani ultraottantenni.   Atti 36 Congresso Nazionale Società Italiana di Gerontologia e Geriatria, Palermo, 7-10 Novembre 1991.   Giornale di Gerontologia 1991; XXXIX(11): 753.

https://sites.google.com/site/inkgmr2/papers

keyword 'pnei' | in FonT

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

keyword 'pnei' | in Notes 

 (quasi-stochastic poetry)

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

Keywords: pnei, neuroimmunology, leukocytes, fear, stress, virus, viral infection, adaptation, adaptive immunity 

# life: Sea Nomads freediving skills (they free dive up to 70 meters deep)

<< Understanding the physiology and genetics of human hypoxia tolerance  has important medical implications, but this phenomenon has thus far only been investigated in high-altitude human populations. Another system, yet to be explored, is humans who engage in breath-hold diving. The indigenous Bajau people (“Sea Nomads”) of Southeast Asia live a subsistence lifestyle based on breath-hold diving and are renowned for their extraordinary breath-holding abilities >>

<< the Bajau, and possibly other diving populations, provide a new opportunity to study human adaptation to hypoxia tolerance >>

Melissa A. Ilardo, Ida Moltke, et al. Physiological and Genetic Adaptations to Diving in Sea Nomads.
Cell. 2018; 173 (3): 569 - 80.e15. doi: 10.1016/j.cell.2018.03.054. Apr 19, 2018.

http://www.cell.com/cell/abstract/S0092-8674(18)30386-6

<< Members of the Bajau can dive up to 70 meters with nothing more than a set of weights and a pair of wooden goggles >>

<< As they never dive competitively it is uncertain exactly how long the Bajau can remain underwater, but one of them told researcher Melissa Ilardo that he had once dived for 13 minutes consecutively >>

University of Cambridge. Genetic adaptations to diving discovered in humans for the first time. Apr 19, 2018.

https://m.phys.org/news/2018-04-genetic-humans.html

# brain: a new learning theory; the role of weak synapses

AA << demonstrate a new type of abundant cooperative nonlinear dynamics where learning is attributed solely to the nodes, instead of the network links which their number is significantly larger >>

<< The network dynamics is now counterintuitively governed by the weak links, which previously were assumed to be insignificant >>

Shira Sardi, Roni Vardi, et al. Adaptive nodes enrich nonlinear cooperative learning beyond traditional adaptation by links. Scientific Reports. 2018; 8 (5100). doi: 10.1038/s41598-018-23471-7. March 23, 2018.

https://www.nature.com/articles/s41598-018-23471-7

The brain learns completely differently than we’ve assumed, new learning theory says. New post-Hebb brain-learning model may lead to new brain treatments and breakthroughs in faster deep learning.  Mar 28, 2018.

http://www.kurzweilai.net/the-brain-learns-completely-differently-than-weve-assumed-new-learning-theory-says

# 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 

# behav: social isolation vs. evolutionary dynamics

<< For some animals—such as beetles, ants, toads, and primates—short-term social isolation can be just as vital as social interaction to development and long-term evolution. In a review published July 17 in the journal Trends in Ecology & Evolution, two evolutionary biologists describe approaches for testing how an animal's isolation might impact natural selection and evolution. >>

Social isolation: Animals that break away from the pack can influence evolution. Cell Press. Jul 17, 2018.

https://m.phys.org/news/2018-07-social-isolation-animals-evolution.html

AA << suggest that the 'index of social isolation', the mismatch between actual and optimal social interaction experienced by individuals within a population, may play a key role in releasing cryptic genetic variation, adaptation rates, diversification patterns, and ecosystem-level processes. Evolutionary dynamics arising from social isolation could have significant impacts in applied settings such as conservation, animal breeding, control of biological invasions, and evolutionary resilience to anthropogenic change. >>

Nathan W. Bailey, Allen J. Moore.  Evolutionary Consequences of Social Isolation. Trends in Ecology & Evolution. doi: 10.1016/j.tree.2018.05.008. Jul 17, 2018.

https://www.cell.com/trends/ecology-evolution/abstract/S0169-5347(18)30120-4

# life: apropos of transitional blennies

<< Research on blennies, a family of fish that have repeatedly left the sea for land, suggests that being a 'jack of all trades' allows species to make the dramatic transition onto land but adapting into a 'master of one' allows them to stay there. >>

<< a flexible diet and behavior were likely to be instrumental in the transition to land. However, once out of the water, restrictions on the type of food available triggered major evolutionary changes, particularly to their teeth, as land dwelling blennies have become specialists in scraping algae and detritus from rocks. >>

<< having a broad diet or being behaviorally flexible can help you move into a new habitat. But once there, this flexibility becomes eroded by natural selection. This presumably means those highly specialized species are less likely to be able to make further transitions, or cope with abrupt environment changes in their existing habitat. >> Terry Ord.

How fish got onto land, and stayed there. British Ecological Society. Jun 17, 2020.  

https://phys.org/news/2020-06-fish.html

Terry J. Ord, Peter J. Hundt. Crossing extreme habitat boundaries: Jack‐of‐all‐trades facilitates invasion but is eroded by adaptation to a master‐of‐one. Funct Ecol. doi: 10.1111/ 1365-2435.13600. Jun 16, 2020.

https://besjournals.onlinelibrary.wiley.com/doi/10.1111/1365-2435.13600

Also

The multifactorial relationship system evolved in Blenny. FonT. Jun 2, 2017.

https://flashontrack.blogspot.com/2017/06/s-behav-multifactorial-relationship.html

# gst: apropos to try numerically to discover states with desired response properties in chaotic (i.e. normal - ab.normal) systems, by Hridesh, Deng, Jean-Jacques, Jeremy.

  <<
Systems with many stable configurations abound in nature, both in living and inanimate matter. Their inherent nonlinearity and sensitivity to small perturbations make them challenging to study, particularly in the presence of external driving, which can alter the relative stability of different attractors. Under such circumstances, one may ask whether any clear relationship holds between the specific pattern of external driving and the particular attractor states selected by a driven multistable system. To gain insight into this question, (AA)  numerically study driven disordered mechanical networks of bistable springs which possess a vast number of stable configurations arising from the two stable rest lengths of each spring, thereby capturing the essential physical properties of a broad class of multistable systems.  (AA) find that the attractor states of driven disordered multistable mechanical networks are fine-tuned with respect to the pattern of external forcing to have low work absorption from it. Furthermore,  (AA)  find that these drive-specific attractor states are even more stable than expected for a given level of work absorption.  (AA)  results suggest that the driven exploration of the vast configuration space of these systems is biased towards states with exceptional relationship to the driving environment, and could therefore be used to 'discover' states with desired response properties in systems with a vast landscape of diverse configurations.
  >>

Hridesh Kedia, Deng Pan, et al. Drive-specific adaptation in disordered mechanical networks of bistable springs. arXiv:1908.09332v1 [nlin.AO] Aug 25, 2019.    https://arxiv.org/abs/1908.09332 

Also

keyword "three" in: FonT    https://flashontrack.blogspot.com/search?q=three

keyword "three" in: Notes      https://inkpi.blogspot.com/search?q=three

# behav: make yourself an ethoscope, by Quentin, Luis et al

<< Exploded drawing of an archetypal ethoscope. The machine is composed of ... >>

<< The ethoscope could be customised for a range of different scenarios >>

<< Another possible use of ethoscopes is the adaptation of the platform to detect behavior of other animals >>

Studying insect behavior? Make yourself an ethoscope. Oct 19, 2017.

https://m.phys.org/news/2017-10-insect-behavior-ethoscope.html

Quentin Geissmann, Luis Garcia Rodriguez, et al. Ethoscopes: An open platform for high-throughput ethomics. PLOS Biol 15 (10): e2003026. doi: 10.1371/journal.pbio.2003026

http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.2003026

# brain: perception of musical rhythms in mammals

AA << confirmed that beat perception, far from being a unique human trait, is likely strongly conserved in mammals >>

Andrew Masterson. Beat perception more primitive than thought. New research shows gerbils react differently to varying musical rhythms. Nov 9, 2017.

https://cosmosmagazine.com/biology/beat-perception-more-primitive-than-thought

Vani G. Rajendran, Nicol S. Harper, et al. Midbrain adaptation may set the stage for the perception of musical beat. Proc. R. Soc. B 2017 284 20171455; DOI: 10.1098/rspb.2017.1455. Nov 8, 2017.

http://rspb.royalsocietypublishing.org/content/284/1866/20171455

# behav: Calanoid copepods swim freely and jump in turbulence

AA << provide evidence for an active adaptation that allows these small organisms [Calanoid copepods] to adjust their motility in response to background flow >>

Francois-Gael Michalec, Itzhak Fouxon, et al. Zooplankton can actively adjust their motility to turbulent flow. PNAS. doi:10.1073/pnas.1708888114

http://m.pnas.org/content/early/2017/12/05/1708888114

<< These jumps enable the plankton to hunt their prey and the males to catch a female >> Markus Holzner.

Plankton swim against the current.
Dec 12, 2017.

https://m.phys.org/news/2017-12-plankton-current.html

# gst: self‐assembly of porous, chiral nano-patterns from simple building blocks.

<< Using a simple rod-like building block with hydroxamic acids at both ends scientists (..) created self- assembling porous, chiral nano structures.  >>

<< Like our left and right hands, the shape of two mirrored cage structures cannot be superimposed. Since the 19th century, academics have characterized this type of object symmetry as 'chiral,' from the ancient Greek meaning 'hand.' These kinds of molecules are frequently found in natural compounds. Chirality influences interactions of polarized light and magnetic properties and plays a vital role in life.  For example, our olfactory receptors react very differently to the two mirror images of the limonene molecule: one smells like lemon, the other like pine. This so-called chiral recognition is a process that can determine whether a molecule acts as medicine or poison. >>

Complex, porous, chiral nano-patterns arise from a simple linear building blocks. Technical University Munich. Jan 16, 2020.

https://m.phys.org/news/2020-01-complex-porous-chiral-nano-patterns-simple.html

<< Regrettably (in this specific experimental context), the end groups proved to be elusive >>

Chao Jing,  Bodong Zhang, et al. Snapshots of Dynamic Adaptation: Two‐Dimensional Molecular Architectonics with Linear Bis‐Hydroxamic Acid Modules. Angewandte Chemie International Edition. Volume 58, Issue 52. doi: 10.1002/anie.201912247. Oct 31, 2019. 

https://onlinelibrary.wiley.com/doi/full/10.1002/anie.201912247

Also

keyword 'chiral' in FonT

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