# gst: apropos of 'normal' (jazzy?) codes, bacteria encode hidden, free-floating genes outside their genome.

AA << show that bacteria break that rule and can create free-floating and ephemeral genes, raising the possibility that similar genes exist outside of our own genome. >>️

<< What this discovery upends is the notion that the chromosome has the complete set of instructions that cells use to produce proteins, (..) We now know that, at least in bacteria, there can be other instructions not preserved in the genome that are nonetheless essential for cell survival. (..) The DNA molecule is a fully functioning, free-floating, transient gene. >> Samuel Sternberg. 

Bacteria Encode Hidden Genes Outside Their Genome—Do We? Columbia University Irving Medical Center. Aug 8, 2024. 

https://www.cuimc.columbia.edu/news/bacteria-encode-hidden-genes-outside-their-genome-do-we   

Stephen Tang, Valentin Conte, et al. De novo gene synthesis by an antiviral reverse transcriptase. Science. doi: 10.1126/ science.adq0876. Aug 8, 2024. 

https://www.science.org/doi/10.1126/science.adq0876

Also: 

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

DNA  https://flashontrack.blogspot.com/search?q=dna

RNA  https://flashontrack.blogspot.com/search?q=rna

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

normal, jazz, in https://www.inkgmr.net/kwrds.html 

Keywords: gst, codes, dna, rna, crispr, normal, jazz

# evol: flip of the script when an entity invert code sequences

<< Jekyll and Hyde flip of the script when bacteria invert gene sequences. If a cell can diversify its own genome, this can be advantageous in the face of changing environmental conditions. Bacteria have been found that can alter encoded proteins by using the trick of sequence inversion inside genes. >>️

Chia-Chi Chang, Robert R. Jenq. Jekyll and Hyde flip of the script when bacteria invert gene sequences. Nature 634, 42-43. Sep 25, 2024. 

https://www.nature.com/articles/d41586-024-02807-6

Chia-Chi Chang, Robert R. Jenq. Bacteria invert gene sequences to flip the script. Nature. Vol 634. Oct 3, 2024 (pdf)  https://media.nature.com/original/magazine-assets/d41586-024-02807-6/d41586-024-02807-6.pdf

Chanin RB, West PT, et al. Intragenic DNA inversions expand bacterial coding capacity. Nature. 2024 Oct; 634 (8032): 234-242. doi: 10.1038/s41586-024-07970-4. Sep 25, 2024. 

https://pubmed.ncbi.nlm.nih.gov/39322669/

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

Also: 

DNA https://flashontrack.blogspot.com/search?q=dna 

RNA https://flashontrack.blogspot.com/search?q=rna 

CODES https://flashontrack.blogspot.com/search?q=codes

Also (quasi-stochastic poetry): 

DNA  https://inkpi.blogspot.com/search?q=dna 

RNA https://inkpi.blogspot.com/search?q=rna 

CODICE https://inkpi.blogspot.com/search?q=codice

Keywords: evolution, codes, DNA, RNA

# soc: pulsatile self-destructive choices, by Oliver and Julia

<< Let’s all be thankful that FiveThirtyEight readers don’t control America’s nuclear arsenal >>

Last week AA << published an article on the game theory of nuclear standoffs. That article included an interactive game ... >>

Oliver Roeder, Julia Wolfe. Thank God You People Don’t Have The Nuclear Codes. Sep. 14, 2017.

https://fivethirtyeight.com/features/thank-god-you-people-dont-have-the-nuclear-codes/

<< Shall we play a game? >>

Oliver Roeder. How To Win A Nuclear Standoff. President Trump and Kim Jong Un’s saber-rattling is dangerous, but not irrational. Sep. 6, 2017

https://fivethirtyeight.com/features/how-to-win-a-nuclear-standoff/

# gst: apropos of the structure of natural codes, a RNA folding knot (origami-style) dance

 << Every second, a myriad of shapeless strands of RNA fold, origami-style, into intricate structures inside living cells. Now, for the first time, researchers can watch a data-driven video of this folding as RNA molecules are made by the cellular machinery. >> 

<< as the RNA strand grows, it twists, forming knot-like structures. But as more RNA building blocks are added to the strand, the knots unravel, allowing the molecule’s structure to emerge. >> 

Ground-breaking films show RNA’s complex curves take shape. Experimental data and predictive algorithms combine to reveal the essential biomolecule’s shape-shifting.

Nature. Jan 19, 2021. 

https://www.nature.com/articles/d41586-021-00126-8

AA << model the folding of an RNA called SRP, an ancient RNA found in all kingdoms of life. The molecule is well-known for its signature hairpin shape. When watching the videos, the researchers discovered that the molecule ties itself into a knot and unties itself very quickly. Then it suddenly flips into the correct hairpin-like structure using an elegant folding pathway called toehold mediated strand displacement. >>

<< To the best of our knowledge, this has never been seen in nature, (..) We think the RNA has evolved to untie itself from knots because if knots persist, it can render the RNA nonfunctional. The structure is so essential to life that it had to evolve to find a way to get out of a knot. >> Julius Lucks. 

Amanda Morris. New Videos Show RNA as it's Never Been Seen. First-ever data-driven movies illuminate RNA's mysterious folding process.  McCormick School of Engineering. Jan 15, 2021.

https://www.mccormick.northwestern.edu/news/articles/2021/01/new-videos-show-rna-as-its-never-been-seen.html 

https://youtu.be/2XTi9LG9NnU

Angela M Yu, Paul M. Gasper, et al. Computationally reconstructing cotranscriptional RNA folding from experimental data reveals rearrangement of non-native folding intermediates. Molecular Cell. doi: 10.1016/ j.molcel.2020.12.017

Jan 15, 2021. 

https://www.cell.com/molecular-cell/fulltext/S1097-2765(20)30936-9

# s-phys-tech-bot: crackin' as a snap

<< If quantum computers existed, they would revolutionize computing as we know it. Based on fundamental properties of matter, the potential power of these theoretical workhorses would solve problems in a new way, cracking extremely complex spy codes and precisely modeling chemical systems in a snap. >>

http://www.eurekalert.org/pub_releases/2015-12/acs-aqs112415.php

Joseph M. Zadrozny, Jens Niklas, et al  Millisecond Coherence Time in a Tunable Molecular Electronic Spin Qubit. ACS Central Science, 2015; DOI: 10.1021/acscentsci.5b00338

http://pubs.acs.org/doi/full/10.1021/acscentsci.5b00338

# s-brain: to distinguish between reality and imagination

<< neurons in the part of the brain found to be abnormal in psychosis are also important in helping people distinguish between reality and imagination >>

AA << investigated how the brain codes visual information in reality versus abstract information in our working memory and how those differences are distributed across neurons in the lateral prefrontal cortex region of the brain >>

Crystal Mackay. Researchers identify specific neurons that distinguish between reality and imagination. June 1, 2017

http://mediarelations.uwo.ca/2017/06/01/researchers-identify-specific-neurons-distinguish-reality-imagination/

AA << results indicate that a functionally diverse population of LPFC (lateral prefrontal cortex) neurons provides a substrate for discriminating between perceptual and mnemonic representations of visual features >>

Diego Mendoza-Halliday & Julio C. Martinez-Trujillo. Neuronal population coding of perceived and memorized visual features in the lateral prefrontal cortex. Nature Comm. 8, Article no: 15471 (2017) doi: 10.1038/ncomms15471 Publ. Jun 01,  2017

https://www.nature.com/articles/ncomms15471

# evol: iterative hacking mechanics; a large group of viruses can assemble human-virus codes to produce novel chimeric (UFO) proteins

<< Like a scene out of "Invasion of the Body Snatchers," a virus infects a host and converts it into a factory for making more copies of itself. Now researchers have shown that a large group of viruses, including the influenza viruses and other serious pathogens, steal genetic signals from their hosts to expand their own genomes. >>

AA << looked at a large group of viruses known as segmented negative-strand RNA viruses (sNSVs), which include widespread and serious pathogens of humans, domesticated animals and plants, including the influenza viruses and Lassa virus (..) by stealing genetic signals from their hosts, viruses can produce a wealth of previously undetected proteins. The researchers labeled them as UFO (Upstream Frankenstein Open reading frame) proteins, as they are encoded by stitching together the host and viral sequences. There was no knowledge of the existence of these kinds of proteins prior to this study. >>

Viruses can steal our genetic code to create new human-virus genes. The Mount Sinai Hospital. Jun 18, 2020.

https://phys.org/news/2020-06-viruses-genetic-code-human-virus-genes.html

Jessica Sook Yuin Ho, Matthew Angel, et al. Hybrid Gene Origination Creates Human-Virus Chimeric Proteins during Infection. Cell. Vol 181, Issue 7, P1502-1517.e23. doi: 10.1016/ j.cell.2020.05.035. June 25, 2020. 

https://www.cell.com/cell/fulltext/S0092-8674(20)30630-9

# gene: stuttering, syncopated (but not junk) codes

<< All organisms have DNA, the genetic material that provides a blueprint for life. The long double-helix-shaped DNA molecules in the body's cells are first translated into RNA molecules and then translated into proteins that ensure the functioning of the cell and the entire organism. But there are large parts of the DNA that are not used for making proteins. This is called 'junk DNA', because its function remained unclear for a long time. However, a certain type of junk DNA that is found in mosquitoes and which repeats itself dozens of times, known as 'satellite DNA', has now been shown to play an essential role in the early development of mosquito embryos. >>

Stuttering DNA orchestrates the start of the mosquito's life. Radboud University Medical Center. Apr 9, 2020.

https://www.sciencedaily.com/releases/2020/04/200409100332.htm 

AA << results reveal a mechanism by which satellite repeats regulate global gene expression in trans via piRNA-mediated gene silencing that is essential for embryonic development. >>

Rebecca Halbach, Pascal Miesen, et al. A satellite repeat-derived piRNA controls embryonic development of Aedes. Nature 580, 274–277. doi: 10.1038/s41586-020-2159-2. 

Apr 1, 2020.

https://www.nature.com/articles/s41586-020-2159-2

Also

keyword 'piRNA' in ncbi pubmed

"piRNA"[all] AND (Review[ptyp]) AND ("last 3 years"[PDat])

http://www.ncbi.nlm.nih.gov/pubmed

# gst: apropos of transitions, erratic, bursty growth processes in cellular sprawl

<< A new “bursty growth” model for organelles—internal components of biological cells—helps explain observed size fluctuations. >>

<< Biologists have identified within cells many specialized structures called organelles that carry out crucial tasks, but how cells regulate the size and the number of organelles has remained a puzzle. Now, using simulations backed by experiments, biophysicists have demonstrated that cells appear to produce organelles through a seemingly erratic, or “bursty,” growth process, which enables them to control average organelle sizes and numbers while also constraining organelle size variations within any cell. The work helps to build up a more fundamental understanding of the mechanisms of cellular function. >>️

<< We wondered if organelle growth, far from being an orderly ‘brick-by-brick’ assembly, might occur in more random bursts,  (..) The burst model can thus explain how cells balance organelle sizes and numbers while also keeping size fluctuations within a narrow window, >> Shankar Mukherji.

<< This “universal” behavior suggests that the burst mechanism underlies all organelle growth, despite the fact that each organelle has a unique building process. >>️

️

Mark Buchanan. Organelle Building Codes. Physics 16, 3. Jan 6, 2023. 

https://physics.aps.org/articles/v16/3

Kiandokht Panjtan Amiri, Asa Kalish, Shankar Mukherji. Robustness and Universality in Organelle Size Control. Phys. Rev. Lett. 130, 018401. Jan 6,  2023. 

https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.130.018401

Also

keyword 'growth' in FonT

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

keyword 'erratico' | 'erratica' in Notes

(quasi-stochastic poetry)

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

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

keyword 'erratic' in FonT

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

Keywords: gst, cell, cell assembly, growth, erratic growth, transition

# s-gst: Shakespeare and Wordsworth' sound patterns of texts

<< Alexander Clark and Thao Tran evaluated sound patterns of texts, with the goal of comparing the sonnets of Shakespeare and Wordsworth. Clark and Tran used the soundex algorithm, a method of converting words into 5 digit "codes." >>

http://www.math.union.edu/~framem/AprilWorkshop/DataIFS/Texts/Clark/Clark.html

<< however close you look, the complexity stays >>

Dilip D'Souza.  Fri, Jan 15 2016. 12 40 AM IST

http://www.livemint.com/Opinion/78slqi9jU44QuvhxPAsJNL/All-your-lifes-a-fractal.html

# s-ai: MICrONS is working in reverse

<<  MICrONS  (Machine Intelligence  from  Cortical  Networks)  project  seeks  to  revolutionize  machine learning  by  reverse  engineering  algorithms  of  the  mammalian  cortex. >>

<< MICrONS  is  fundamentally  different,  both  technically  and  logistically. Rather  than  building  a  simulation  of  the  human  brain,  which  the  HBP  [Human  Brain  Project] set  out to  do,  MICrONS  is  working  in  reverse.  By  mapping  out  the  intricate connections  that  neurons  form  during  visual  learning  and  observing  how  they change  with  time,  the  project  hopes  to  distill  sensory  computation  into mathematical  “neural  codes”  that  can  be  fed  into  machines,  giving  them  the power  to  identify,  discriminate,  and  generalize  visual  stimulation. The  end  goal:  smarter  machines  that  can  process  images  and  video  at human-level  proficiency. >>

Shelly  Fan. US  Bets  $100  Million  on  Machines That  Think  More  Like  Humans. Mar 13,  2016.

http://singularityhub.com/2016/03/13/us-bets-100-million-on-machines-that-think-more-like-humans/