# gst: a bizarre extension of the Jelly Roll approach, the morphogenesis of the leaves (plant Utricularia gibba)

AA << discovered that simple shifts in gene activity in the leaf bud provide a flexible mechanism for how leaves of all shapes and sizes are made. >>

<< We've discovered a general principle by which leaves from flat sheets to needle-like and curved shapes are formed,  (..) We found that the complex leaf shapes of carnivorous plants evolved from species with flat leaves through simple shifts in gene activity in the leaf bud. What surprised us is that how such a simple mechanism could underlie such a wide diversity of leaf shapes.  (..) If you want to understand why water boils at 100°C, look for situations in which it doesn't, like the top of Mount Everest where it boils at 70°C. From that we learn the general principle that boiling point depends on air pressure. Similarly, if you want to understand why most leaves are flat, you might study exceptions, like the leaves of some carnivorous plants which form pitchers to trap prey, >> Enrico Coen.

Nature's secret recipe for making leaves. John Innes Centre. Nov 21, 2019. 

https://m.phys.org/news/2019-11-nature-secret-recipe.html

Christopher D. Whitewoods, Beatriz Goncalves, et al. Evolution of carnivorous traps from planar leaves through simple shifts in gene expression. Science. eaay5433 doi: 10.1126/science.aay5433. Nov 21, 2019

https://science.sciencemag.org/content/early/2019/11/20/science.aay5433

Also

keyword "Jelly Roll" in Notes:

https://inkpi.blogspot.com/search?q=jelly+roll

keyword "Jazz" in Notes:

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

keyword "Jelly Roll" in FonT

https://flashontrack.blogspot.com/search?q=jelly+roll

# phys: the qu-wave of the natural antibiotic gramicidin

<< One of the great counterintuitive puzzles of quantum mechanics is wave-particle duality. This is the phenomenon in which objects behave both like particles and like waves. >>

AA << for the first time, have demonstrated quantum interference in molecules of gramicidin, a natural antibiotic made up of 15 amino acids. Their work paves the way for the study of the quantum properties of  biomolecules and sets the scene for experiments that exploit the quantum nature of enzymes, DNA, and perhaps one day simple life forms such as viruses. >>

A natural biomolecule has been measured acting like a quantum wave for the first time. Mit Tech Rew - Emerging Technology from the arXiv. Nov 9, 2019. 

https://www.technologyreview.com/s/614688/a-natural-biomolecule-has-been-measured-acting-in-a-quantum-wave-for-the-first-time/

Armin Shayeghi, Philipp Rieser, et al. Matter-wave interference of a native polypeptide. arXiv:1910.14538v1 [quant-ph]. Oct 31, 2019.

https://arxiv.org/abs/1910.14538

Also

keyword "quantum" in FonT

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

# gst: apropos of elusive interference effects (at the nanoscale)

AA << investigate and characterize a subspace of the weak coupling regime between quasidiscrete and quasicontinuum localized surface plasmon resonances where infrared plasmonic Fano antiresonances appear.  >>

Kevin C. Smith, Agust Olafsson, et al.  Direct Observation of Infrared Plasmonic Fano Antiresonances by a Nanoscale Electron Probe. Phys. Rev. Lett. 123, 177401. 21 Oct 21,  2019. 

https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.123.177401

<< In 1961, atomic physicist Ugo Fano theorized that electrons harbor another and unexpected talent: They can interfere with themselves as they simultaneously take two different quantum-mechanical paths. On one path, they jump within the atom between discrete energy states. On the other path, they jump off the atom into the continuum of free space. >>

<< Fano described a complicated-and even counterintuitive-type of energy transfer that can occur in these systems, (..) It's like having two children on neighboring swings that are weakly coupled to each other: You push one child, but that swing isn't the one that moves. Instead, the other child's swing moves due to this interference. It's a one-way energy transfer. >> David Masiello.

Team uses golden 'lollipop' to observe elusive interference effect at the nanoscale. University of Washington. 

 Nov 8, 2019.

https://m.phys.org/news/2019-11-team-golden-lollipop-elusive-effect.html

# life: an anti-flood approach, techno- humans ask beavers for help

<< The National Trust has announced plans to release Eurasian beavers at two sites in the south of England next spring to help with flood management and to improve biodiversity. >>

National Trust announces first beaver reintroductions. Press Release. Nov 20, 2019. 

https://www.nationaltrust.org.uk/press-release/national-trust-announces-first-beaver-reintroductions

Beavers brought in to beat flooding in Britain. Nov 20, 2019.

https://m.phys.org/news/2019-11-beavers-brought-britain.html

Also

Facing a cross-border crimes. FonT.   May 9, 2017. 

https://flashontrack.blogspot.com/2017/05/n-soc-facing-cross-border-crimes.html

# brain: the flexible mental maps of flies

<< In the Drosophila brain, 'compass'  neurons track the orientation of the body and head (the fly’s heading) during navigation >>

<<  a visual cue can evoke synaptic inhibition in compass neurons and that R (ring) neurons mediate this inhibition. Each compass neuron is inhibited only by specific visual cue positions, indicating that many potential connections from R neurons onto compass neurons are actually weak or silent. (..) the pattern of visually evoked inhibition can reorganize over minutes as the fly explores an altered virtual-reality environment. >>

Yvette E. Fisher, Jenny Lu, et al. Sensorimotor experience remaps visual input to a heading-direction network.  Nature. doi: 10.1038/s41586-019-1772-4. Nov 20, 2019. 

https://www.nature.com/articles/s41586-019-1772-4

To navigate, flies make flexible mental maps of the world. Howard Hughes Medical Institute. Nov 20, 2019.

https://m.phys.org/news/2019-11-flies-flexible-mental-world.html

Also

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

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

# gst: measuring biological noise of gene expression

<< Essential genes are often expressed with high variability during the development of cells. Scientists call this phenomenon "biological noise" and suspect that it is also decisive for the fate of cells, i.e. the developmental pathway a cell takes. Max Planck researcher Dominic Grun now presents a method based on single-cell data to quantify this variability in gene expression.  >>

Dominic Grun << hopes to gain a better understanding of the extent to which noise regulates development or is even necessary for the differentiation of cells. >>

How gene expression noise shapes cell fate. Max Planck Society. Nov 18, 2019. 

https://m.phys.org/news/2019-11-gene-noise-cell-fate.html   

Grun D. Revealing dynamics of gene expression variability in cell state space. Nat Methods (2019) doi:10.1038/s41592-019-0632-3. Nov 18, 2019.

https://www.nature.com/articles/s41592-019-0632-3

Also

keyword 'noise' in Notes:

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

keyword 'noise' in FonT:

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

# gst: interface mobility enhances the bounce effect of bubbles

<< Theoretically, when a bubble reaches the surface of a pure liquid, the thin film of liquid between the bubble and the air above should quickly drain away, allowing the bubble to coalesce with the air. The same would be expected when two bubbles meet within the liquid or when two droplets of oil come together in water.  >>

<< Counterintuitively, bubbles or droplets reaching the highly mobile fluorocarbon liquid-air interface bounced off of the interface much more strongly than from the immobilized interface. The reason is that there is less friction on the mobile interface and thus less energy is lost during the bounce. "To our knowledge, our studies and simulations are the first to demonstrate an enhanced bounce effect due to interface mobility," >> Ivan U. Vakarelski.

When bubbles bounce back.  King Abdullah University of Science and Technology. Nov 13, 2019.

https://m.phys.org/news/2019-11-when-bubbles-bounce-back.html

Ivan U. Vakarelski, Fan Yang, et al. 

Mobile-surface bubbles and droplets coalesce faster but bounce stronger. Science Advances  25 Oct 2019:

Vol. 5, no. 10, eaaw4292 DOI: 10.1126/sciadv.aaw4292 

https://advances.sciencemag.org/content/5/10/eaaw4292

# gst: marginally outer trapped surfaces (during a binary Black Hole merger)

<< do MOTSs (marginally outer trapped surfaces, or marginal surfaces) merge in a BBH (binary black hole ) coalescence, and if so, how, exactly? >>

<< It is an underappreciated fact that event horizons are not really very useful for studying astrophysical properties of black hole mergers, (..) What is much more useful are surfaces which go under the boring name of marginally outer trapped surfaces (..). This uninteresting name hides their importance in understanding black holes. >>

Ingrid Fadelli. Numerical evidence for the merger of MOTSs inside a binary black hole. Nov 1, 2019

https://m.phys.org/news/2019-11-numerical-evidence-merger-motss-binary.html

Daniel Pook-Kolb, Ofek Birnholtz, et al. 

Interior of a Binary Black Hole Merger. Phys. Rev. Lett. 123, 171102 Oct 21, 2019. 

https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.123.171102

# gst: apropos of turbulences close to a wall, the repetitive structure of a vortex

<< At the boundary where a fluid flows over a fixed structure, a turbulent boundary layer is created where the fluid interacts with the wall, creating eddies in the current. These eddies may seem to be random on first glance, but they actually create distinct patterns, with countless tiny eddies close to the wall; fewer but larger eddies located a little farther out; and even fewer, but still larger, eddies beyond those. >>

<< "We knew that, underlying these very complicated structures, there had to be a very simple pattern. We just didn't know what that pattern was until now," says McKeon, who next plans to dig deeper into the model to quantify just how many eddies should be included to create an accurate representation of the whole. >>

Engineers exploit the repeating structure of turbulence to create a more complete model of the phenomenon. California Institute of Technology. Nov 6, 2019.

https://m.phys.org/news/2019-11-exploit-turbulence-phenomenon.html

Beverley J. McKeon. Self-similar hierarchies and attached eddies. Phys. Rev. Fluids 4, 082601(R). Aug 26, 2019.

https://journals.aps.org/prfluids/abstract/10.1103/PhysRevFluids.4.082601

# gst: multiple singularities by optical vortices (a 30y review)

<< Vortices are common phenomena that widely exist in nature, from quantum vortices in liquid nitrogen to ocean circulation and typhoon vortices and even spiral galaxies in the Milky Way. Vortices also exist in optics, the concept of which was first proposed by theoretical physicist Pierre Coullet and colleagues [Opt. Commun. 73, 403 (1989)] thirty years ago. Hitherto, owing to their amazing structures, optical vortices have engendered tremendous advanced applications such as optical tweezers, quantum entanglement, and nonlinear optics, throughout every branch of modern optics. >>

Commemorating 30 years of optical vortices: A comprehensive review. 

Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences. Nov 4, 2019.

https://m.phys.org/news/2019-11-commemorating-years-optical-vortices-comprehensive.html

Yijie Shen, Xuejiao Wang, et al. Optical vortices 30 years on: OAM manipulation from topological charge to multiple singularities. Light: Science & Applications volume 8, Article number: 90. Oct 2, 2019.

https://www.nature.com/articles/s41377-019-0194-2

# behav: 'run and tumble' behavior (among bacteria)

<< Bacteria in groundwater move in surprising ways. They can passively ride flowing groundwater, or they can actively move on their own in what scientists call "run and tumble" behavior.  >>

AA << noted a distinct run (movement in one direction) followed by a tumble (a sudden, random change in direction). By calculating the length and timing of these movements, they could develop a simple Continuous Time Random Walk (CTRW) model to predict how the bacteria would move. When compared to current models for bacterial remediation, the CTRW model was better at predicting bacterial transport in many circumstances. The CTRW model is the first step in developing and testing new reactive transport models that incorporate bacterial transport behavior.  >>

Rishi Parashar. Calculating 'run and tumble' behavior of bacteria in groundwater. Environmental Molecular Sciences Laboratory. Oct 31, 2019. 

https://m.phys.org/news/2019-10-behavior-bacteria-groundwater.html  

Xueke Yang, Rishi Parashar, et al. On Modeling Ensemble Transport of Metal Reducing Motile Bacteria. Scientific Reports volume 9, Article number: 14638. Oct 10, 2019. 

https://www.nature.com/articles/s41598-019-51271-0

# behav: adaptive synchronizations; the tendency to anticipate during auditory rhythms

<< Dancing and playing music require people to coordinate actions with auditory rhythms. In laboratory perception-action coordination tasks, people are asked to synchronize taps with a metronome. When synchronizing with a metronome, people tend to anticipate stimulus onsets, tapping slightly before the stimulus. The anticipation tendency increases with longer stimulus periods of up to 3500ms, but is less pronounced in trained individuals like musicians compared to non-musicians.  >>

Iran R. Roman, Auriel Washburn, et al.  Delayed feedback embedded in perception-action coordination cycles results in anticipation behavior during synchronized rhythmic action: A dynamical systems approach. PLoS Comput Biol 15(10): e1007371. doi: 10.1371/journal.pcbi.1007371. Oct 31, 2019.

https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007371

Delayed neural communication may underlie anticipatory behaviors. Public Library of Science. Oct 31, 2019.

https://m.phys.org/news/2019-10-neural-underlie-anticipatory-behaviors.html

# evol: apropos of our origin, the KhoeSan trunk of the human tree

<< Where was the evolutionary birthplace of modern humans? The East African Great Rift Valley has long been the favoured contender – until today. (AA) new research has used DNA to trace humanity’s earliest footsteps to a prehistoric wetland called Makgadikgadi-Okavango, south of the Great Zambezi River. >>

<< KhoeSan have the most diverse mitogenomes of anyone on Earth, which suggests their DNA most closely resembles that of our shared common ancestors. If we all sit on branches of the human family tree, then KhoeSan are the tree's trunk. >>

Vanessa Hayes. Humanity’s birthplace: why everyone alive today can call northern Botswana home. University of Sydney. Oct 28, 2019.

https://theconversation.com/humanitys-birthplace-why-everyone-alive-today-can-call-northern-botswana-home-125814

Eva K. F. Chan, Axel Timmermann, et al.  Human origins in a southern African palaeo-wetland and first migrations. Nature (2019) doi:10.1038/s41586-019-1714-1. Oct 28, 2019.

https://www.nature.com/articles/s41586-019-1714-1