[2017-11-30]
protein folding [[complexity]][2017-05-15]
Fermentation [2020-12-26]
Reverse Engineering the Source Code of the BioNTech/Pfizer SARS-CoV-2 Vaccine | Hacker News
[2020-04-08]
Watch the Life Cycle of HIV in Colorful New Detail - Scientific American Blog Network [[biology]][2020-04-26]
Ask HN: What scientific phenomenon do you wish someone would explain better? | Hacker News [[biology]]
[2020-08-15]
OpenWorm - Wikipedia [[sim]][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]]
[2019-08-05]
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 [2019-08-25]
How are molecular structures determined with such precision? How were they determined in the past? /r/askscience [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]][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]][2019-12-06]
"How Quantum Biology Might Explain Life’s Biggest Questions | Jim Al-Khalili | TED Talks" [2019-02-10]
(6) Simplicial Complexes - Your Brain as Math Part 2 | Infinite Series - YouTube [[brain]] [[topology]][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 [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 [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]][2019-03-29]
The World in UV - YouTube [[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 [2020-12-26]
Reverse Engineering the source code of the BioNTech/Pfizer SARS-CoV-2 Vaccine - Articles [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 [2020-01-09]
AFEW - Flora & Fauna [2021-03-11]
penicillin [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 [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 [[tostudy]][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]
Fermentationyeast 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 >
@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/...
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/askscienceMy 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?
[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 мозгhttps://nplus1.ru/material/2019/03/28/head-transplantation
[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 вакциныСитуация 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 - ArticlesHowever, 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 SeaMeals 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 & FaunaThe 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]
penicillinPenicillin 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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