# 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: 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)

# 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 

# 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

# evol: Megalopta genalis, the bee that flies in the dark with dorsal landmark navigation

<< People -- who get lost easily in the extraordinary darkness of a tropical forest -- have much to learn from a bee that can find its way home in conditions 10 times dimmer than starlight. >>

AA << reveal that sweat bees (Megalopta genalis), find their way home based on patterns in the canopy overhead using dorsal vision. >>️️

<< For a human observer, the most obvious visual cues in the forest at night are gaps in the canopy when we look straight up because the sky is much brighter than the forest below, (..) We see a quite complex pattern of criss-crossing branches, but the bees'-eye-view is much less complex. They see broad blobs of light that vary in shape and position. We knew that ants could use canopy patterns to navigate as they walk through the forest, and we wondered if maybe bees were doing the same thing. >> Eric Warrant.

Dorsal navigation found in a flying insect. Smithsonian Tropical Research Institute. Jun 17, 2021. 

https://www.sciencedaily.com/releases/2021/06/210617101221.htm

Sandra Chaib, Marie Dacke, et al. 

Dorsal Landmark Navigation in a Neotropical Nocturnal Bee.  doi: 10.2139/ ssrn.3805162. Mar 15, 2021.

https://papers.ssrn.com/sol3/papers.cfm?abstract_id=3805162

# evol: ancient photosynthesis could be as old as life itself

<< the earliest bacteria had the tools to perform a crucial step in photosynthesis,  (..) The finding also challenges expectations for how life might have evolved on other planets. >>️

<< Photosystem II show patterns of evolution that are usually only attributed to the oldest known enzymes, which were crucial for life itself to evolve >> Tanai Cardona.️

<< enzymes capable of performing the key process in oxygenic photosynthesis -- splitting water into hydrogen and oxygen -- could actually have been present in some of the earliest bacteria. The earliest evidence for life on Earth is over 3.4 billion years old and some studies have suggested that the earliest life could well be older than 4.0 billion years old.  Like the evolution of the eye, the first version of oxygenic photosynthesis may have been very simple and inefficient; as the earliest eyes sensed only light, the earliest photosynthesis may have been very inefficient and slow. (..) that oxygen production was present at all so early on means in other environments, such as on other planets, the transition to complex life could have taken much less time. >>️

Photosynthesis could be as old as life itself. Imperial College London. Mar 24, 2021. 

https://www.sciencedaily.com/releases/2021/03/210324142839.htm

Thomas Olivera, Patricia Sanchez-Baracaldo, et al. Time-resolved comparative molecular evolution of oxygenic photosynthesis.Biochimica et Biophysica Acta (BBA) - Bioenergetics, 2021; 1862 (6): 148400. doi: 10.1016/ j.bbabio.2021.148400. Jun 1,  2021.

https://www.sciencedirect.com/science/article/pii/S0005272821000335

Also

Lewis M. Ward, Patrick M. Shih. Granick revisited: Synthesizing evolutionary and ecological evidence for the late origin of bacteriochlorophyll via ghost  lineages and horizontal gene transfer. PLoS ONE 16(1): e0239248. doi:10.1371/journal.pone.0239248. 

Jan 28, 2021. 

https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0239248

# phys: trace the birth and evolution of a quasiparticle entity

<< The idea of quasiparticles was first introduced in the 1930s by physicist Lev Landau, who was trying to gain a better understanding of complex quantum systems. >>

<< Over the past decades, physicists worldwide have been trying to gain a better understanding of non-equilibrium dynamics in quantum many-body systems. Some studies investigated what are known as quasiparticles, disturbances or entities in physical systems that exhibit behavior similar to that of particles. >>

In this study AA << observed three distinct regimes of impurity evolution marked by dynamic transitions. These regimes then link initial few-body and later many-body physical dynamics. >>

Ingrid Fadelli. Observing the birth of a quasiparticle. Mar 11, 2021.

https://phys.org/news/2021-03-birth-quasiparticle.html

<<  These results offer a systematic picture of polaron formation from weak to strong impurity interactions. They reveal three distinct regimes of evolution with dynamical transitions that provide a link between few-body processes and many-body dynamics. Our measurements reveal universal dynamical behaviour in interacting many-body systems and demonstrate new pathways to study non-equilibrium quantum phenomena. >>

Magnus G. Skou, Thomas G. Skov, et al. Non-equilibrium quantum dynamics and formation of the Bose polaron. 

Nat. Phys. (2021). doi: 10.1038/ s41567-021-01184-5. Feb 25, 2021.

https://www.nature.com/articles/s41567-021-01184-5

"three distinct regimes"  

https://www.nature.com/articles/s41567-021-01184-5.epdf?no_publisher_access=1&r3_referer=nature

# zoo; apropos of extreme dwarf entities, the nano-chameleon (Brookesia nana)

<< An international team, (..) has discovered a minuscule new species of chameleon.  (..) They have named the new species Brookesia nana. >>

 << At a body length of just 13.5 mm and a total length of just 22 mm including the tail, the male nano-chameleon is the smallest known male of all 'higher vertebrates' >> Frank Glaw.

<< Unfortunately, the habitat of the Nano-Chameleon is under heavy pressure from deforestation, but the area has recently been designated as a protected area, and hopefully that will enable this tiny new chameleon to survive, >> Oliver Hawlitschek.

Meet the nano-chameleon, a new contender for the title of world's smallest reptile. Staatliche Naturwissenschaftliche Sammlungen Bayerns. Feb 01, 2021. 

https://phys.org/news/2021-02-nano-chameleon-contender-title-world-smallest.html    

Glaw, F., Kohler, J., Hawlitschek, O. et al. Extreme miniaturization of a new amniote vertebrate and insights into the evolution of genital size in chameleons. Sci Rep 11, 2522. doi: 10.1038/ s41598-020-80955-1. Jan 28,  2021.

https://www.nature.com/articles/s41598-020-80955-1 

# brain: flies, mice and humans, comparable behaviors for balance and motor control

<< Comparative developmental genetics indicate insect and mammalian forebrains form and function in comparable ways. However, these data are open to opposing interpretations that advocate either a single origin of the brain and its adaptive modification during animal evolution; or multiple, independent origins of the many different brains present in extant Bilateria. Here, (AA) describe conserved regulatory elements that mediate the spatiotemporal expression of developmental control genes directing the formation and function of midbrain circuits in flies, mice, and humans. These circuits develop from corresponding midbrain-hindbrain boundary regions and regulate comparable behaviors for balance and motor control. (They) findings suggest that conserved regulatory mechanisms specify cephalic circuits for sensory integration and coordinated behavior common to all animals that possess a brain. >>

Jessika C. Bridi, Zoe N. Ludlow, et al. Ancestral regulatory mechanisms specify conserved midbrain circuitry in arthropods and vertebrates. PNAS. doi: 10.1073/ pnas.1918797117. Aug 3, 2020.

https://www.pnas.org/content/early/2020/07/31/1918797117  

Humans and flies employ very similar mechanisms for brain development and function. King's College London.  Aug 3, 2020.

https://phys.org/news/2020-08-humans-flies-similar-mechanisms-brain.html

Also

'mosca in bottiglia' in: 2066 - voli a casaccio. Notes. Oct 01, 2006.   (quasi-stochastic poetry)

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

Also

keyword 'flies' in FonT

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

# life: a paradigm shift; extinction vs. evanescence, relict species, ...

<< The first "complete" paradigm of extinction was proposed as "the multigenerational, attritional loss of reproductive fitness," for which MALF is a suitable acronym. A "complete" paradigm must encompass cause, effect, and a mechanism. The primary goal of this study is to verify the new paradigm. (AA) cite four independent tests of the paradigm employing observational, experimental, and wholly theoretical techniques, >>

<< "extinction" presents certain problems with adjectival and gerund forms. (AA) do not refer to a process of "extinctioning" or "extincting" and there is no disciplinary field named "extinctionary" biology, ecology, or genetics. There are several possible verbs for extinction that treat the population or species as agent. These include "devolve," "senesce," "die off," "terminate," and "disappear," among others. However, all of these are in common use with connotations that would distract from (they) proposed meaning. "Devolve" is common in antievolutionist literature. "Senesce" is usually applied only to individuals. "Die off" does not have a single-word noun form. "Terminate" used intransitively comes close to our proposed meaning, but the popularity of the Arnold Schwarzenegger film Terminator will suggest the transitive form to most people. "Disappear" suggests something that is merely out of sight, not necessarily extinct. Instead of these common words, (they) propose using a verb with no distracting connotations. (AA) take our cue from Jefferson’s concern over extinction. Jefferson (1799:256) uses the term "evanish," or in its modern form, "vanish." The adjectival form "vanished" is usable but the noun form sounds a bit awkward: "vanishment." However, Jefferson’s "evanish" calls attention to the Latin root, e + vanescere = to pass away. "Evanesce" has an elegant noun form, "evanescence," and several adjectival forms covering a range of states: "evanesced" denoting the completed action, "evanescing" denoting an action in process, and "evanescent" denoting action in process or in potential. In physics, the adjective "evanescent" is used to designate an electromagnetic field that does not propagate waves beyond the vicinity of the source of the field. Physics and biology are sufficiently distinct that (AA) proposed usage would not create confusion. "Evanescence" does not imply an external agent performing the action and fits the understanding of extinction as a process without adding confusing connotations. This process may be a precursor or complement to evolution, but not necessarily so. >>

Delbert Wiens, Timothy Sweet, Thomas Worsley. Validating the New Paradigm for Extinction: Overcoming 200 Years of Historical Neglect, Philosophical Misconception, and Inadequate Language. The Quarterly Review of Biology. Vol. 95, Issue 2, Pages 109-124. doi: 10.1086/709086. Jun 2020.

https://www.journals.uchicago.edu/doi/10.1086/709086   

Goodbye 'extinction,' hello 'evanescence'? Validating a new paradigm. University of Chicago. Jun 18, 2020. 

https://phys.org/news/2020-06-goodbye-extinction-evanescence-validating-paradigm.html   

# evol: traces of weird evolution, ancient crocodiles walked on two legs, like dinosaurs

<< some species of ancient crocodiles walked on their two hind legs like dinosaurs and measured over three meters in length. >>

<< At one site, the footprints were initially thought to be made by a giant bipedal pterosaur walking on the mudflat, we now understand that these were bipedal crocodile prints, (..) "And while footprints were everywhere on the site, there were no handprints. (..) Dinosaurs and their bird descendants walk on their toes. Crocodiles walk on the flat of their feet leaving clear heel impressions, like humans do. >> Anthony Romilio.

Ancient crocodiles walked on two legs like dinosaurs. University of Queensland. Jun 11, 2020.

https://phys.org/news/2020-06-ancient-crocodiles-legs-dinosaurs.html 

Kim, K.S., Lockley, M.G., et al. Trackway evidence for large bipedal crocodylomorphs from the Cretaceous of Korea. Sci Rep 10, 8680. doi: 10.1038/ s41598-020-66008-7. 

https://www.nature.com/articles/s41598-020-66008-7

# evol: apropos of a big mystery; Neanderthal may have been surrounded and terminated (killed) by Sapiens competition (and/or probably by Sapiens multitudes, their viruses, their chatter, ...)

<< Climate scientists from the IBS Center for Climate Physics discover that, contrary to previously held beliefs, Neanderthal extinction was neither caused by abrupt glacial climate shifts, nor by interbreeding with Homo sapiens. According to new supercomputer model simulations, only competition between Neanderthals and Homo sapiens can explain the rapid demise of Neanderthals around 43 to 38 thousand years ago. >>

Supercomputer model simulations reveal cause of Neanderthal extinction. Institute for Basic Science. May 20, 2020.

https://phys.org/news/2020-05-supercomputer-simulations-reveal-neanderthal-extinction.html    

<< Anatomically Modern Humans are the sole survivor of a group of hominins that inhabited our planet during the last ice age and that included, among others, Homo neanderthalensis, Homo denisova, and Homo erectus. Whether previous hominin extinctions were triggered by external factors, such as abrupt climate change, volcanic eruptions or whether competition and interbreeding played major roles in their demise still remains unresolved. (..)  a realistic extinction of the Neanderthal population can only be simulated when Homo sapiens is chosen to be considerably more effective in exploiting scarce glacial food resources as compared to Neanderthals. >>

Axel Timmermann. Quantifying the potential causes of Neanderthal extinction: Abrupt climate change versus competition and interbreeding. Quaternary Science Reviews. 

Volume 238, 15 June 2020, 106331. May 15, 2020. 

https://www.sciencedirect.com/science/article/pii/S0277379120302936

Also

keyword 'Neanderthal' in FonT

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

# ecol: when a predator could help his prey to adapt to an uncertain future (among the fly Iteomyia salicisverruca) ...

<< The loss of biodiversity is rewiring the web of life; however, it is uncertain how this will affect the ability of remaining populations to evolve and adapt to future environments. >>

AA << conducted a field experiment that either maintained a natural community of predators or removed all but one of the predators that was able to impose selection on a common prey. (They) found that the loss of predators acted to constrain prey evolution toward a particular combination of traits. Moreover, (they) found that the loss of predators could make it more difficult for prey to adapt to uncertain future environments. Taken together, (these) results suggest that the simplification of the web of life may constrain the adaptive potential of remaining populations. >>

Matthew A. Barbour, Christopher J. Greyson‐Gaito, et al. Loss of consumers constrains phenotypic evolution in the resulting food web. Evolution Letters. doi: 10.1002/ evl3.170. Apr 20, 2020. 

https://onlinelibrary.wiley.com/doi/full/10.1002/evl3.170

<< Thinking about the big picture, our study hints at a potential insidious side effect of extinctions, (..) The extinction of natural enemies may compromise the ability of remaining species to adapt and persist in an uncertain and changing world. If this is true, this would put many ecosystems at even greater risk than we currently realize. >> Matthew A. Barbour.

Predators help prey adapt to an uncertain future. University of Zurich. 

 May 4, 2020

https://phys.org/news/2020-05-predators-prey-uncertain-future.html

# gst: shape-shifting dynamics; tiny evolutionary changes have turned a tongue into a fast elastic recoil mech (in salamanders)

<< relatively minor changes in the musculoskeletal morphology of the tongue apparatus and in the timing of muscle activation have, through evolutionary time, transformed a muscle-powered system with modest performance and high thermal sensitivity into a spring-powered system with extreme performance and thermal robustness, in parallel in both major groups of this largest family of salamanders. High performance and thermal robustness evolve together, indicating they are both properties of the same elastic-recoil, "bow-and-arrow" mechanism. Similar evolutionary patterns may be found in other ectothermic animals with extreme performance. >>

Stephen M. Deban, Jeffrey A. Scales, et al. Evolution of a high-performance and functionally robust musculoskeletal system in salamanders. PNAS. doi: 10.1073/pnas.1921807117. Apr 27, 2020.

https://www.pnas.org/content/early/2020/04/21/1921807117

Bob Yirka. Minor evolutionary changes helped transform the salamander tongue into a fast elastic recoil mechanism. Apr 28, 2020.

https://phys.org/news/2020-04-minor-evolutionary-salamander-tongue-fast.html

Also

keyword 'tiny' in FonT

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