📚 node [[biology misc]]
📓 garden/karlicoss/biology/biology-misc.md by @karlicoss

Table of Contents

related [[study]]

B vs T immunity [[tostudy]] [[biology]]

[2017-11-30] protein folding [[complexity]]

given a chain of amino acids, can you predict how is it going to fold?
ideally, folding should end up in the minimal energy state. if it doesn't you end up with prions?
in general, folding is an NP complete problem, are our body cells actually solving them somehow?
conjecture: evolution wouldn't actually use hard instances of protein folding, only computationally easy ones.

[2017-05-15] Fermentation

yeast anaerobic -> alcohol
muscle anaerobic -> lactic acid 

Fermentation is a metabolic process that converts sugar to acids, gases, and/or alcohol.
Fermentation takes place in the lack of oxygen (when the electron transport chain is unusable) and becomes the cell’s primary means of ATP (energy) production.[1] It turns NADHand pyruvate produced in the glycolysis step into NAD+ and various small molecules depending on the type of fermentation (see examples below). In the presence of O2, NADH and pyruvate are used to generate ATP in respiration. This is called oxidative phosphorylation, and it generates much more ATP than glycolysis alone. For that reason, cells generally benefit from avoiding fermentation when oxygen is available. Exceptions include obligate anaerobes, which cannot tolerate oxygen.

https://ru.wikipedia.org/wiki/%D0%91%D1%80%D0%BE%D0%B6%D0%B5%D0%BD%D0%B8%D0%B5 

Пируваты (соли пировиноградной кислоты) — важные химические соединения в биохимии. Они являются конечным продуктом метаболизма глюкозы в процессегликолиза. Одна молекула глюкозы превращается при этом в две молекулы пировиноградной кислоты. Дальнейший метаболизм пировиноградной кислоты возможен двумя путями — аэробным и анаэробным.

[2020-12-26] Reverse Engineering the Source Code of the BioNTech/Pfizer SARS-CoV-2 Vaccine | Hacker News

Synthetic Biology: A Primer
Wetware: A Computer in Every Living Cell

[2021-02-22] https://news.ycombinator.com/item?id=24345320 [[toread]]

There's a good book, Wetware: A Computer in Every Living Cell, by Dennis Bray going into detail on how much functionality and physical processes are at work even in the most simplest cells that is routinely ignored by these analogies of the brain to a digital computer.

there have only been maybe {~1040} organisms in earth’s history [[drill]] [[biology]]

from ip Shtetl-Optimized » Blog Archive » On two blog posts of Jerry Coyne

[2020-04-08] Watch the Life Cycle of HIV in Colorful New Detail - Scientific American Blog Network [[biology]]

https://blogs.scientificamerican.com/observations/watch-the-life-cycle-of-hiv-in-colorful-new-detail/

[2020-04-26] Ask HN: What scientific phenomenon do you wish someone would explain better? | Hacker News [[biology]]

The issue with these animations is that they're getting rid of all the thermal noise.
In reality, single proteins are flying around the whole length of the cell many times a second, just from their thermal motion.
And when processes like DNA transcription happen, they're not like a regular conveyor belt -- a fraction of the time the machine will even accidentally run steps in reverse!
However, if any of this were shown, the animations would become impossible to understand.

[2020-05-09] https://news.ycombinator.com/item?id=22993812

It's not so much "magic" as it is the sheer rate of molecular collisions in the cytosol. There are so many collisions happening that at least one of them will do what you want. Here's a back-of-the-napkin example, admittedly with many simplifications:
A tRNA molecule at body temperature travels at roughly 10 m/s. Assuming a point-sized tRNA and stationary ribosome of radius 125 * 10^-10 m, the ray casted by the moving tRNA will collide with the ribosome when their centers are within 125 * 10^-10 m of each other. The path of the tRNA sweeps a "collidable" circle of the radius of 125 * 10^-10 m, for a cross-sectional area of 5 * 10^-16 m^2. Multiplied by the tRNA velocity, the tRNA sweeps a volume of 5 * 10^-15 m^3 per second. Constrained inside an ordinary animal cell of volume 10^-15 m^3, the tRNA would have swept the entire volume of the cell five times over in a single second. Obviously the collision path would have significant self-overlap, but at this rate it's quite likely for the two to collide at least once any given second.
Now, consider that this analysis was only for a single ribosome/tRNA pair. A single ribosome will experience this collision rate multiplied by the total number of tRNA in the cell, on the order of thousands to millions. If a ribosome is bombarded by tens of thousands of tRNA in a single second, it's very likely one of those tRNA will (1) be charged with an amino acid, (2) be the correct tRNA for the current 3-nucleotide sequence, and (3) collide specifically with the binding site on the ribosome in the correct orientation. In actuality, a ribosome synthesizes a protein at a rate of ~10 amino acid residues per second.
Any given molecule in the cell will experience millions to billions of collisions per second. The fact that molecules move so fast relative to their size is what allows these reactions to happen on reasonable timescales.

[2020-08-15] OpenWorm - Wikipedia [[sim]]

OpenWorm is an international open science project to simulate the roundworm Caenorhabditis elegans at the cellular level as a simulation.[1][2][3] Although the long-term goal is to model all 959 cells of the C. elegans, the first stage is to model the worm's locomotion by simulating the 302 neurons and 95 muscle cells.

how cell compute [[towatch]]

<https://twitter.com/karpathy/status/1261457314713792512 > 

@karpathy: This was actually really good. I've spent some time translating biology to CS/EE terms/abstractions, this makes a lot of those analogies explicit. +"Genetic circuit design automation" Science paper [2016] link science.sciencemag.org/content... twitter.com/Reza_Zadeh/status/...

sympathetic nervous system {“accelerator”} and your parasympathetic nervous system {“brake”} [[drill]]

from Come as You Are

[2019-01-29] 5 Minute DNA Extraction in a Shot Glass: 7 Steps (with Pictures) https://www.instructables.com/id/5-minute-DNA-Extraction-in-a-Shot-Glass/ [[dna]]

[2019-01-29]

The detergents in the dish soap (like the sodium laurel sulfate, aka sodium dodecyl sulfate) destabilize the membranes of the cells, spilling their contents into the rest of the solution of saliva.

can you do this with muscle cells? E.g. shred meat, add some water and salt and see what happens

[2019-08-05] Eli Shlizerman on Twitter: "1/ THREAD: Excited to share our work on whole nervous system and body model for celegans. The model simulates how connectome + neural interactions + body interact together to generate locomotion. Preprint: https://t.co/vgwGbIeuGc Samples of videos: https://t.co/0afVJ7MBuo https://t.co/0Tb9Z6LSBX" / Twitter

<https://twitter.com/shlizee/status/1158486688307400705 >

[2019-08-25] How are molecular structures determined with such precision? How were they determined in the past? /r/askscience

My question was inspired by learning that [lutein](https://en.wikipedia.org/wiki/Lutein#/media/File:Lutein_molecule_spacefill.png) and [zeaxanthin](https://en.wikipedia.org/wiki/Zeaxanthin#/media/File:Zeaxanthin_molecule_spacefill.png) are nearly identical molecules (C40H56O2), with the only difference between the two being that a single double bond is found in neighboring positions along a hexagon at one end of the molecule. These molecules are rather large. How are molecular structures determined so exactly? When did chemists acquire this capability? And what were the major milestones in our ability to determine molecular structure?

I don't just mean how many of each kind of element and where they are, but also things as subtle as the position of a single double bond. A lot of molecules are smaller than a wavelength of visible light, so it's not as if we could just look at them under a microscope, yet we know their structures exactly. So how do chemists figure these things out?

[2020-04-05] How does “even if this flu shot isn’t an exact match, if you do get the flu it won’t be as bad” work? /r/askscience [[vaccine]]

There's actually a very cool effect where either getting infected with flu or getting vaccinated boosts your antibody response to all previous strains of flu you've encountered (by getting flu or by being vaccinated). In recent years WHO have begun to shift towards using antigenically advanced vaccines, whereby they predict how currently circulating strains of flu will evolve and artificially create vaccines for the flu strain they think will be circulating in 6 months time, as even if the virus doesn't mutate to a new strain, the antibody backboost means you still get protection against most circulating strains. Check out this paper (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4246172/) if you want a more detailed explanation, but basically the vaccine can boost your antibody response to a fairly wide range of influenza virus strains  (this is at least true for type A H3N2 influenza, there are 4 different types of influenza in the annual vaccine)

[2019-03-28] Cellular Visions: The Inner Life of a Cell - Studio Daily http://www.studiodaily.com/2006/07/cellular-visions-the-inner-life-of-a-cell/ [[biology]] [[viz]]

[2019-10-27] How Trees Bend the Laws of Physics - YouTube [[physics]] [[biology]]

wonder what if you hack into the tubes and push the water? would it make trees grow higher?

[2019-12-06] "How Quantum Biology Might Explain Life’s Biggest Questions | Jim Al-Khalili | TED Talks"

Photon Coherense inside photosynthesic bacteria?
Protons/electrons tunnel? (enzymes)
Birds might sense magnet field via entangled electrons?

http://vmh.uni.lu/#reconmap metabolism interactive map [[biology]] [[metabolism]] [[viz]]

[2019-02-10] (6) Simplicial Complexes - Your Brain as Math Part 2 | Infinite Series - YouTube [[brain]] [[topology]]

https://www.youtube.com/watch?v=rlI1KOo1gp4

hmm. pretty interesting – betty numbers are counting numbers of holes of different dimensions
can we use it for figuring out the fundaemntal group after that?
0th betty number – connected components
e.g. torus – second betty number is 1 since the hole are the insides of torus

neuron connections are a higher dimension simplicial complex

[2021-01-10] keller-mark/awesome-biological-visualizations: A list of web-based interactive biological data visualizations. [[biology]] [[viz]]

[2021-01-16] [(1) Olga V. Pettersson on Twitter: "Балтимор, в 70х, открыл вирусный механизм, который этим занимается. Чтобы вирусу встроиться в геном, у него должно быть два гена: 1) обратная транскриптаза для перевода РНК в ДНК и 2) интеграза, кодирующая белок который встраивает свежесделанную вирусную ДНК в геном." / Twitter](https://twitter.com/OlgaVPettersson/status/1350337989134659584 )

Чтобы вирусу встроиться в геном, у него должно быть два гена: 1) обратная транскриптаза для перевода РНК в ДНК и 2) интеграза, кодирующая белок который встраивает свежесделанную вирусную ДНК в геном.

[2020-06-09] prathyvsh/formal-systems-in-biology: Application of formal systems to model biological systems

[2019-03-31] Пациент без головы: Научились ли хирурги восстанавливать перерезанный спинной мозг

https://nplus1.ru/material/2019/03/28/head-transplantation

  • Благодаря его разработкам в 1967 году стала возможна успешная пересадка сердца от человека к человеку. Сделавший ее хирург Кристиан Барнард неоднократно приезжал в лабораторию Демихова и впоследствии называл его своим учителем.
  • С этой проблемой Канаверо тоже предполагал справиться хирургическим путем — разрушив участок мозга, отвечающий за передачу эмоционального компонента боли, который и вызывает связанное с ней страдание

[2021-01-04] podcast: [Sean Carroll's Mindscape: Science, Society, Philosophy, Culture, Arts, and Ideas] 112 | Fyodor Urnov on Gene Editing, CRISPR, and Human Engineering https://podcastaddict.com/episode/111823121 via @PodcastAddict [[biology]]

very cool podcast, the guy is super enthusiastic, pleasure to hear such people

[2019-03-29] The World in UV - YouTube [[dna]]

huh, apparently UV protective pigments are also inside the cells, around nucleus to protect DNA

[2021-01-11] DNA seen through the eyes of a coder (or, If you are a hammer, everything looks like a nail) - Articles

[2021-01-06] Без вакцины

Ситуация осложняется тем, что после первого же промаха ружье можно выкидывать. Поскольку ВИЧ — ретровирус, он встраивает свои гены в ядерную ДНК. И вычеркнуть их оттуда мы уже не можем — по крайней мере, до сих пор не научились

[2020-12-26] Reverse Engineering the source code of the BioNTech/Pfizer SARS-CoV-2 Vaccine - Articles

However, it turns out that RNA with a higher amount
of Gs and Cs is also converted more efficiently into proteins,
And this has been achieved in the vaccine RNA by replacing many characters with Gs and Cs wherever this was possible.

[2020-12-26] Dna the Code of Life - Articles

[2019-02-14] Gene Engineering Kits - The ODIN

[2019-02-14] Biohacker 101 Class - The ODIN

[2019-12-07] The Deep Sea

Meals are rare in the deep sea. Deep sea creatures have adapted to this - one Giant Isopod in captivity went five years without eating.

[2020-01-09] AFEW - Flora & Fauna

The guide presents a catalogue of curious creatures and life-forms that have evolved in often unexpected ways to cope with the stresses and pressures of a changed world.

[2021-03-11] penicillin

Penicillin kills bacteria by inhibiting the completion of the synthesis of peptidoglycans, the structural component of bacterial cell wall.

[2021-03-31] [(1) The Thought Emporium on Twitter: "@PowerDNSBert Modern biology isn't usually done yourself. You outsource 95% of it. So the distinction is irrelevant. If you know the right companies you can get anything done, including this. And it's neither hard nor expensive. The last 5% can in fact be done at home." / Twitter](https://twitter.com/EmporiumThought/status/1376936685062086660 )

Modern biology isn't usually done yourself. You outsource 95% of it. So the distinction is irrelevant. If you know the right companies you can get anything done, including this. And it's neither hard nor expensive. The last 5% can in fact be done at home.

[2021-04-05] [Bert Hubert on Twitter: "Some people asked if I knew of a quick intro to molecular biology. While you have to realize this is a somewhat bold question, this https://t.co/QgucmCctHt by Alexander Zien looks pretty useful. https://t.co/gTvWHjOQZM" / Twitter](https://twitter.com/PowerDNS_Bert/status/1379073534211817474 ) [[tostudy]]

Some people asked if I knew of a quick intro to molecular biology. While you have to realize this is a somewhat bold question, this  https://bioinformatics.nl/courses/BioSB-AfBN/prep/Molecular%20biology%20primer.pdf by Alexander Zien looks pretty useful.
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