# gene: bacteria and archaea CRISPR everywhere in nature

<< Single-celled bacteria and archaea use CRISPR systems to defend themselves against viruses known as bacteriophages. (..) Until now, researchers had identified six types of CRISPR system, designated I–VI. >>

AA << developed an algorithm called FLSHclust, which analyses genetic sequences in public databases. (..) By looking at the predicted function of the clusters, the researchers found around 130,000 genes associated in some way with CRISPR, 188 of which had never been seen before, >>️️

<< It’s a treasure trove for biochemists, >> Lennart Randau.

Sara Reardon. ‘Treasure trove’ of new CRISPR systems holds promise for genome editing. Nature. doi: 10.1038/ d41586-023-03697-w. Nov 23, 2023. 

https://www.nature.com/articles/d41586-023-03697-w

Han Altae-Tran, Soumya Kannan, Feng Zhang, et al. Uncovering the functional diversity of rare CRISPR-Cas systems with deep terascale clustering. 

Science, Vol 382, Issue 6673. doi: 10.1126/ science.adi1910. Nov 23, 2023. 

https://www.science.org/doi/10.1126/science.adi1910

Also: 'CRISPR' in https://flashontrack.blogspot.com/search?q=crispr  

Keywords: genome, gene, crispr, crispr system, ai, artificial intelligence

# gst: when a turbulence can be confined

<< Turbulence is hard to control. Its ephemeral nature prevents us from treating it as an ordinary state of matter. Here (AA) create a stationary and isolated blob of turbulence using only elemental building blocks: vortex rings.  The turbulence is confined in a spherical region, surrounded by a quiescent environment, initiated and sustained by vortex rings. Crucially, vortex rings can be endowed with conserved quantities such as energy and helicity, which can be transferred to the turbulent state. Using 2D particle image velocimetry and 3D particle tracking velocimetry, (AA) demonstrate how confinement of turbulence occurs when vortex rings repeatedly collide, in contrast to coherent vortex reconnections. The pathlines depict the difference between these states of flow. >>️

Takumi Matsuzawa, Noah P. Mitchell, Stéphane Perrard, William T. M. Irvine. Turbulence through sustained vortex ring collisions. Phys. Rev. Fluids 8, 110507. Nov 16, 2023.

https://journals.aps.org/prfluids/abstract/10.1103/PhysRevFluids.8.110507

75TH ANNUAL MEETING OF THE APS DIVISION OF FLUID DYNAMICS (NOVEMBER 20, 2022 — NOV 22, 2022). V0008: Turbulence through sustained vortex ring collisions. 

https://doi.org/10.1103/APS.DFD.2022.GFM.V0008

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

Keywords: gst, turbulence, vortex, vortex ring collisions

# gst: kirigami exposed to external flows.

<< Kirigami patterned materials have found several applications in recent years due to their ability to assume complicated shapes and exhibit emergent physical properties when exposed to external forces. >>️

<< Consisting of an array of cuts in a thin material, fabrication of these patterns can be quite simple. Here (AA) show that when they are placed in fluid flow, kirigami cut sheets with various patterns produce a verity of flow patterns in the wake. Through several sets of experiments, (AA) show that the kirigami sheets placed in flow can undergo static or dynamic flow-induced instabilities as a result of which they can buckle or undergo limit cycle oscillations, or they can remain stable while undergoing very large elongations. >>️

<< The ability to create controlled small-scale vortex shedding, induce desired flow-induced instabilities on structures, and form specifically-angled jets will enable several future applications in flow mixing (e.g., by producing small vortices in uniform flow at low Reynolds numbers), flow control (e.g., by controlling the direction and the number of jets that are produced downstream), and underwater soft robotics (e.g., by imposing desired flow-induced oscillations on structures). >>

️

Adrian G. Carleton, Yahya Modarres-Sadeghi. Kirigami Sheets in Fluid Flow.  arXiv: 2311.09381v1 [physics.flu-dyn]. Nov 15, 2023. 

https://arxiv.org/abs/2311.09381

Also: kirigami, origami, vortex, in https://www.inkgmr.net/kwrds.html 

Keywords: gst, kirigami, origami, fluid flows, vortex

# gst: collective patterns generated by capillary surfers.

<< Millimeter-sized “surfers” can self-propel across a vibrating liquid surface, interacting with other surfers to create collective patterns. >>

<< Self-propelled objects can move in mesmerizing patterns. The collective movements of groups of such objects typically occur in one of two flow regimes: the inertial regime—think swirling schools of fish in water—or the viscous regime—think swarming colonies of bacteria in mucus. Some self-propelled objects can travel in both flow regimes, a possibility that is less explored. >>️

AA << have studied the motion of a new system of self-propelled objects that move in this intermediate regime, finding that the objects organize into several distinct and tunable motion patterns. >>️️

<< Pairs of self-propelled surfers observed by the team move in one of seven different patterns (the video shows five). These include the “orbit,” where a pair of surfers rotate around a central point; the “tailgate,” where one surfer closely follows another, head to tail in a linear path; and the “jackknife,” where a pair of perpendicular surfers rotate stern to stern around their collision point. >>

<< When only one surfer was present, these mismatched amplitudes propelled the surfer in the direction of its bow. When there were two surfers close to each other, interactions among the waves caused the surfers to either repel each other so that they moved in opposite directions or to come together so that they collectively traced one of seven distinct patterns. >>️

️

Maggie Hudson. Synchronized Surfing of Self-Propelled Particles. Physics 16, s156. Nov 7, 2023. 

https://physics.aps.org/articles/v16/s156

Ian Ho, Giuseppe Pucci, Anand U. Oza, Daniel M. Harris. Capillary surfers: Wave-driven particles at a vibrating fluid interface. Phys. Rev. Fluids 8, L112001. Nov 7, 2023.

https://link.aps.org/doi/10.1103/PhysRevFluids.8.L112001

Anand U. Oza, Giuseppe Pucci, Ian Ho, Daniel M. Harris. Theoretical modeling of capillary surfer interactions on a vibrating fluid bath. Phys. Rev. Fluids 8, 114001. Nov 7, 2023.

https://link.aps.org/doi/10.1103/PhysRevFluids.8.114001

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

Keywords: gst, waves, wave-wave, capillary waves, particles, self-propelled particles, fluid-particle interactions, wave-particle interactions

# behav: the self-care hypothesis of the puteketeke bird (great crested grebe, Podiceps cristatus)

<< The Puteketeke bird has been elected as New Zealand's Bird of the Century after John Oliver promoted the bird not just on his show, but around the world. >>

<< It also exhibits some unusual antics, like eating feathers to help it vomit up parasites,  >> AILSA CHANG

️

<< They have a mating dance where they both grab a clump of wet grass and chest bump each other... >> JOHN OLIVER

Kat Lonsdorf, Christopher Intagliata. The Puteketeke bird has been elected as New Zealand's Bird of the Century. npr.org Nov 15, 2023. 

https://www.npr.org/2023/11/15/1213287236/the-puteketeke-bird-has-been-elected-as-new-zealands-bird-of-the-century

L’uccello del secolo della Nuova Zelanda l’ha deciso John Oliver. ilpost.it. Nov 15, 2023. 

https://www.ilpost.it/2023/11/15/john-oliver-uccello-secolo-nuova-zelanda/

the bird: https://youtu.be/98ceB5SPRXI

John Oliver, an interview: https://youtu.be/uVE1hBzHn3s

many thanks to Tammi ( https://www.inkgmr.net/tammi ) for this news. 

Also: Self-perception of health and survival. A 10-year follow-up among Italians aged over sixty. INRCA, Technical Report, Genova, 7 March 1995: 1-19. Minerva Med 1997 Jan-Feb 88:1-2 15-23. [abst] https://pubmed.ncbi.nlm.nih.gov/9093288/

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

Keywords: behaviour, self-care, perceptions

gst: actually and counterintuitively a coherent jump could generate disorder.

AA << consider a quantized version of a model for “random walk in random environment.” (..) For a ring geometry (a chain with periodic boundary condition) it features a delocalization-transition as the bias in increased beyond a critical value, indicating that the relaxation becomes underdamped. Counterintuitively, the effective disorder is enhanced due to coherent hopping. >>

Ben Avnit, Doron Cohen. Quantum walk in stochastic environment. Phys. Rev. E 108, 054111. Nov 7, 2023. 

https://journals.aps.org/pre/abstract/10.1103/PhysRevE.108.054111

Also:  Voli a casaccio. Notes (quasi-stochastic poetry). Oct 01, 2006.

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

Also: 'random', 'transition', 'disorder', 'chaos', in https://www.inkgmr.net/kwrds.html

Keywords: gst, walk, random walk, quantum walk, qu-walk, jump, transition, disorder, chaos

# life: a painted texture glimpsed through 25 words

<< If you want to understand the complicated nature of the United States in 2023, ask Americans to define their country themselves. In the past year, the American Communities Project did just that. It visited four different counties and asked passersby to define 25 words, including America, and the responses showed a range of opinions. >>️

<< The media tends to explain the divides in United States in binary terms — red/blue, left/right, urban/rural. News stories discuss war between two conflicting “cultures” in the country. Sometimes included is a third option for “independents” or “centrists.” But look closer and the picture is far more complicated, marked by fault lines that can be hard to see. >>️

Dante Chinni, Ari Pinkus. New Survey Breaks Down America’s Complicated Landscape. American Communities Project/Ipsos. Oct 26, 2023. 

https://www.americancommunities.org/new-survey-breaks-down-americas-complicated-landscape

Also: 

Immediate 'shot', the three second time window in art, music, poems and language processing. FonT. Apr 30, 2021.

https://flashontrack.blogspot.com/2021/04/gst-immediate-shot-three-second-time.html

Effetto Northridge. Notes. Sep 26, 2005.

(quasi-stochastic poetry)

https://inkpi.blogspot.com/2005/09/1887-effetto-northridge.html

Keywords: life, self-perception