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What's a virus, anyway? The bare-bones basics
- dimtion 7y agoIs there a a good read on how RNA and DNA work for a Computer Scientist? And more generally how biology, genetics, epigenetics, virus, etc work? Many vulgarization sources say that DNA is like the source code of life. But they mostly skim across the issue and go to conclusions like "this gene or set of genes are responsible for that outcome". But coming from a CS background that sounds a bit like non-sense. I feel like it is like saying that "this processor instruction is responsible for that outcome". But in the end what is important is not the individual instruction but the interaction between them and the environment (Input / Ouput).
- lordnacho 7y agoI listened to the Great Courses audiobook about Biology. There's a lot about how the machinery of the cell works, how it evolved, and so on. He goes through everything else as well, including the immune system, ecology, and so on. It all ties together. Regarding the genes and central dogma, he gives a LOT of detail about how for instance it was discovered that codons work in threes (not twos or fours). Also how it was discovered that DNA is the thing with the code, how the transcription process works, how the different kinds of RNA are involved, all the way to how the protein comes out. The audiobook also comes with a downloadable book in case you'd rather read it.
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- ethbro 7y agoIMHO, biology is most easily looked at as a recipe for order, from whatever ingredients happen to be laying around. Essentially, everything is in the service of increasing order. And maintaining it. Polymerase creates more genetic code out of raw ingredients. Genetic code creates proteins. Proteins perform all kinds of functions by leveraging physics and chemistry. Membranes prevent all of this from being blown away and scattered in the chemical equivalent of a slight breeze. ... so, as you ask, 'Why genetic material in the first place?' And to that, something of a tautology: because reproducing order reproduces. Randomly assembled self-assembling assemblages constitute the major components of our environment, because everything else... didn't. A rock is still one rock. Water is still water. A blade of grass is now a meadow. A tree, a forest. A slightly intelligent primate, civilization as we know it. And a single mutated coronavirus, a pandemic in every country on the globe.
- neuronic 7y agoTo me, what blows most comparisons and analogies out of the water, is the insane complexity to it all. That genes can influence and interact with each other. So gene expression (= gene -> protein) can change gene expression, e.g. based on environmental factors or folding of DNA etc... Gene A is responsible for property A is way way way too simplified.
- kaibee 7y agoThe sense I get is that its more like some unholy combination of brainfuck, vhdl, and game of life.
- ethbro 7y agoTrue, but in the same way that all engineering can be complex. Which is to say, you can use quantum mechanics to augment Newtonian physics, but the latter dominates results in most usages. Biology does have the quirk that sometimes (I guess because exponential growth / propagation?) nuances dominate observed result. But usually things proceed as expected. Otherwise, we'd be killing people left and right with pharmaceutical side effects!
- BitwiseFool 7y agoI recommend Crash Course's youtube series on biology. Specifically this video about DNA and replication. https://www.youtube.com/watch?v=8kK2zwjRV0M https://www.youtube.com/watch?v=8kK2zwjRV0M In very broad terms, the segments of code in DNA/RNA acutally provide a template for specific molecules and enzymes.
- tcgv 7y agoSo, from a CS point of view, I guess instead of comparing DNA to procedurally executed machine code we should be comparing it to the source code of a set of classes, which once instantiated produces specific proteins that perform all sorts of biological tasks in our bodies.
- vikramkr 7y agoI wouldn't recommend trying to understand it through analogy to CS - I'm a biologist and know enough CS to feel uncomfortable really using any of the usual analogies. The problem is that they work ok for a layperson understanding, but are fundamentally wrong enough that if you want to understand it at the level of something like virology you'll be lead constantly astray. I dont know of a better recommendation than "watch some recorder bio 101 lectures or pick up a textbook, and learn it like a bio major instead of a CS major." It's a lot of time commitment, but I think you have to put in the time to actually learn it from first principles. For context, imagine if I as a biologist asked you, what's a good read on CS for a biologist? And generally how algorithms, data science, AI, and operating systems work? You can understand why it would be difficult to recommend any readings on it. For me to learn to code at any level, I had to spend the time learning it from the fundamentals, and it was worth spending the time for me as it was far more rewarding than trying to wrap my mind around something like "so imagine source code is this thing that's like DNA + epigenetics + dna topology that codes for the information you want, but instead of a complex set of chemical and physical interactions, it's math, and you can change it at will and nothing is leaky on purpose, and the code you write doesnt evolve unless you tell it to which you might want to do sometimes for AI stuff, but usually not."
- Retric 7y agoIt’s hard to disagree with what your saying, but analogies are fun. I think the best analogy is DNA is a series of automated assembly lines. The workers, raw materials, and signals to turn sections on or off are separate. Each nucleotide station is called A, T, C, or G and adds a single element at a time to long chains which then get folded up into useful tools. DNA can also be used to manufacture either more stands of DNA or to do very simple repairs. Alternatively, a stack of computer punch cards with a program on them. In that it’s a standard format for information transfer that is physically altered by the message it carries. Further, on it’s own nothing happens but connected to the right machinery it’s useful.
- vikramkr 7y agoEdit - I'll concede that analogies are absolutely fun haha. They might be useful to come up with when you yourself are trying to better understand something by drawing connections to other things you know and all. But I don't think they're ideal for being taught the subject. And again, for a layperson, analogies are totally fine if you just want a surface level understanding of "oh, mitochondrias are powerhouses of the cell." But if you want to do anything with that, beware the dangers. The second analogy is ok, but again not really great if you want to understand what's actually going on. If you just want to get an intuition that DNA has something to do with storing information, as long as that comes with an understanding that information evolves (biology is really the study of evolution in many ways), that's probably more than enough for a layperson. But it's a dangerous understanding if you plan on using it as a foundation to try and explore more complicated topics in biology. There's no need to do so, but if you are going to, it's far far better to spend the time getting the correct first-principles understanding and get rid of this idea of "DNA as source code" so you can better grapple with the subject. I don't think the first analogy makes much sense since it makes nucleotides the sort of active agents here and needlessly focuses on individual nucleotides when codon triplets are what are involved in coding for proteins (probably better to, if you have to use an analogy, treat nucleotides as letters instead of words). And, especially in the context of this thread, neither analogy build the understanding needed to really dive into what RNA is, which is important for understanding what RNA viruses are, and what the coronavirus is.
- twomoretime 7y agoIt's like writing ultimate spaghetti code in a dynamic language. The nature of biology is much like classes and data floating around and all seemingly randomly interacting with each other, because ultimately this is just chemistry with thousands of unique compounds, which makes things messy. But through natural selection it seems to work. Like a totally incomprehensible compression algorithm learned by neural nets or evolved by genetic code. There should be a source somewhere around here...
- Viliam1234 7y agoThis. Spaghetti code beyond human imagination. Once I tried to learn this stuff by asking a biochemist, but I soon became frustrated because it seems there are no 100% rules, only "it is usually like this" all the way down. Like, did they teach you at school that eukaryotes have two sets of chromozomes, one from each parent? Yeah, "usually". But then also: https://en.wikipedia.org/wiki/Polyploidy https://en.wikipedia.org/wiki/Polyploidy And similarly with everything.
- jyounker 7y agoBut the code and products are also pieces of spaghetti :)
- Barrin92 7y ago>It's like writing ultimate spaghetti code in a dynamic language. The nature of biology is much like classes and data floating around and all seemingly randomly interacting with each other, because ultimately this is just chemistry with thousands of unique compounds, which makes things messy. It should be noted that biological systems were one of the exlicit inspirations for extremely dynamic and object oriented languages like smalltalk. Far from being a negative aspect the 'centerless' design and high degree of decentralization is messy, but also extremely robust.The internet as a whole is another example of a human technology that utilizes that sort of design.
- guscost 7y agoAnd not only is it far worse than the most spaghettified and surprising program/meta-program you've ever seen, it's also a quine.
- codekilla 7y agoThis is a good book along those lines: https://www.amazon.com/Touchstone-Life-Information-Communication-Foundations/dp/0195140575 https://www.amazon.com/Touchstone-Life-Information-Communica...
- learnstats2 7y agoDNA is literally only instructions for building proteins (each 'gene' commonly encodes one protein). It's a very low level code, then. The various proteins that are built are actually interacting with the environment. So, your desire to look at interaction with the environment might be better captured by a field other than genetics: maybe proteomics or molecular biochemistry.
- tomerico 7y agoMaybe you can help me understand a simple example - if there is a gene that controls the eye color, how does it express itself as eye color (vs something completely different)
- koeng 7y agoBasically, the variance in melanin is what causes different eye colors. So, if you have a gene that produces melanin, and then turn it's expression down, then you might get bluer eyes. The complicated part is that a lot of genes actually control for eye color - that is where the complications come. Each gene interacts with every other gene in a unique way.
- xigency 7y agoA gene is like a DLL. Asking how it works would require a lot of know-how that’s specific to the usage. When talking about how DNA is an instruction for making a protein, that protein is your data structure or a function. The next level of fundamental building block. Genes can contain a lot of information or non-information for proteins. Just like a program might have a lot of functions or data. The way they work together and interact is what creates a larger effect. I think maybe the best starting point for understanding biology is learning about enzymes up close. They are proteins that act as “machines”. It gets down to physics and chemistry to determine how they work, so that’s probably when to drop the analogies.
- learnstats2 7y agoIt's important that there isn't a gene that controls the eye colour. Eye colour is modulated by several genes which haven't necessarily been identified - I understand this to be an open question. I can give an example, though: Eye colour is a function of what pigments are present in the iris, the most relevant pigment (in humans) being melanin, which also contributes to dark skin and tanning. So, melanin is produced via the biochemical pathway 'melanogenesis'. Among other things, the process of melanogenesis requires the enzyme tyrosinase, a protein which has a decent length wikipedia page. If you are missing the TYR gene which codes for the protein tyrosinase, then you will likely be albino. This won't only affect your eyes, then. I say you will 'likely' be albino only because it's hypothetically possible that a lack of tyrosinase could be compensated for with another biochemical pathway. And, of course, albinism could come about by some other break in melanin production.
- RivieraKid 7y agoPart I of Molecular Biology of the Cell is the best read in my opinion, regardless whether you have a CS background.
- FPGAhacker 7y agohttps://archive.org/details/MolecularBiologyOfTheCell5th/mode/2up https://archive.org/details/MolecularBiologyOfTheCell5th/mod...
- rwmj 7y agoCan second this - a superb book that really helped me understand a little about what is going on.
- biophysboy 7y agoBiophys grad student here. If I'm understanding your frustration correctly, you're basically saying: "yes for the 1000th time, I KNOW DNA is the recipe book, but who is the chef?" Well, I'm sorry to report that there are a lot of chefs. And to make things worse, every cell is different, so there are also a lot of restaurants. For this reason, it is not possible to make a book on any of the topics you listed above without skimming. The solution to this is narrow your scope: is there a particular subtopic that interests you?
- ggm 7y agoYes: how can we make an omelette without breaking chefs?
- jarvist 7y agoI read this as a kid: https://www.amazon.co.uk/Cartoon-Guide-Genetics/dp/0062730991 https://www.amazon.co.uk/Cartoon-Guide-Genetics/dp/006273099... It provides a very useful bridge from a mechanistic / physic-y / computer point of view, to the more messy biochemistry. Still, whenever I think of a biochemical process, it's a cartoon from here that comes to my mind's eye.
- jacobwilliamroy 7y agoGO TO A UNIVERSITY AND TAKE SOME CLASSES YOU RUBE
- ufo 7y agoThe cliff notes version of it is that DNA encodes the information on how to build proteins. https://en.wikipedia.org/wiki/Central_dogma_of_molecular_biology https://en.wikipedia.org/wiki/Central_dogma_of_molecular_bio... Proteins are built out of a chain of aminoacids. There are 20 different kinds of aminoacid, and the particular sequence of aminoacids determines the shape of the protein, and therefore its biological function. https://en.wikipedia.org/wiki/Amino_acid https://en.wikipedia.org/wiki/Amino_acid To build a protein, the cell uses a strand of RNA as template. The RNA consists of a sequence of 4 kinds of bases (A=Adenine, C=Cytosine, G=Guanine, U=Uracyl) and there is a genetic code that maps each group of 3 RNA bases into one aminoacid. For example, "AGC" corresponds to serine, "AAG" means lysine, and "AGCAAG" means serine followed by lysine. https://en.wikipedia.org/wiki/Genetic_code https://en.wikipedia.org/wiki/Genetic_code DNA is built of similar pieces as RNA. The main difference is that RNA is single stranded, while DNA is double stranded with that famous double helix structure. Additionally, DNA uses T=Thymine in place of U=Uracyl. DNA acts a store of information. Each gene contains the genetic sequence that describes how to build one protein. When a gene is active, the cell copies that part of the DNA into a messenger RNA, and then uses that RNA as a template to build the protein in question. Every cell in the body has the exact same set of genes, but they differ in what genes are active at each time. ------------------------------------ Now on to viruses... The Coronavidus is an RNA virus. Each individual virius is a little ball made of proteins and lipids, encasing a genome made of RNA. By itself the virus is inert, but once that RNA finds its way to inside a human cell, it behaves like a fork bomb. The cell translates the viral RNA into proteins, just like it would with our own RNA. One of the proteins is a polimerase enzyme, which then makes even more copies of the viral genome. Soon, there are thousands of copies of the virus. Additionally, the viral genome also encodes the structural proteins for the capsule of the virus, including the "spike" protein that gives coronaviruses their signature look.
- vadimpilyugin 7y agoI have a CS background and for me the best explanation of how life fundamentally works was the MIT 7.00x "Introduction to Biology - The Secret of Life" course. It is absolutely amazing, requires only high school level knowledge and covers so many incredible stuff that I cannot possibly list all of it here. And not only is this course teaching you how stuff works but also the history behind it, how we, humans, figured it out. And, it's free and available online! If you ever wanted to get deeper into biology than reading news articles, I cannot recommend this course enough.
- surfmike 7y agoKhan Academy is probably a good resource: https://www.khanacademy.org/science/high-school-biology/hs-molecular-genetics#hs-discovery-and-structure-of-dna https://www.khanacademy.org/science/high-school-biology/hs-m... Also here, the three sections starting with “DNA as the genetic material”: https://www.khanacademy.org/science/biology https://www.khanacademy.org/science/biology An introductory biology textbook would be good too. Any AP biology textbook should cover it all.
- DantesKite 7y agoI like your perspective. I feel like information is the mother of all sciences and computer science has developed powerful tools for dealing with certain aspects of it. I don’t see why it can’t address certain fundamental issues in biology either.
- gravelc 7y agoThe reason why CS analogies don't work very well is that molecular biology is very context driven, and we often don't know what the context is. For example, in eukaryotes, the same piece of DNA can can produce different amounts of different proteins (i.e. with different amino acid sequences and different post-translational modifications), depending on things like DNA methylation (there's a number of different types), genomic location, accessibility, transcript methylation, multiple mRNA isoforms - the list goes on. A combination of these and other still unknown factors produces the final product, which may vary within a cell, between cells in a tissue, and between tissues. Things behave consistently and predictability, except when they don't. Makes the field interesting and frustrating.
- wesleywt 7y agoAnalogies obviously don't hold for many cases. But it's a good entry point to explain some basic concepts such as the Central Dogma. I am a biologist who has to teach molecular biology to computer scientists in our Bioinformatics department. It was the only way to bridge the gap. Once we got it we could start on the more detailed stuff.
- variaga 7y agoIf you must have analogies... - DNA: code in your repo - RNA: code in your working directory - transcriptase: 'git fetch' - ribosome: compiler - proteins: executable object code (ribosomes are also proteins, mostly) - epigenetics: build config options - promoter site: `ifdef First, imagine a system where every time you compile something, the object code is immediately launched in its own thread executing truly in parallel with all the others. The overall behavior of the cell is the interaction of all these threads. A gene is a single block of code. They can do lots of things, including changing build options and enabling/disabling the generation of other blocks of code. We say a particular gene causes a particular effect, but really it's the aggregate interaction that does things. Most traits require the cooperation of many genes to express. If we associate a gene with a particular trait, it's usually because it is a critical component of that trait; necessary so if you break the gene the normal aggregate behavior goes away, but not sufficient - it still needs a lot of other working genes to have the right effect. Now imagine that some of those threads run a constant cleanup process that kills running threads, delete your object code and delete files in your working directory (largely at random) while another set of threads are constantly fetching (transcriptase) and recompiling (ribosomes) code to launch new threads to keep the system working and your services up. During this process the relative number and type of running threads will change according to a combination of code and the environment. Viruses are a tiny executable (protien coat) that copies some rogue code (RNA) into your working directory, so that constant recompilation will generate new instances that copy more code, etc. Too many running virus instances will crash the system (kill the cell) by starving/corrupting normal processes. The random deletion and constant fetching from the repo slows the virus replication down however, and may stop it entirely. _Retro_viruses have an additional piece: - reverse transcriptase: 'git commit; git push' which will copy the virus code back into your repo. Now the regular 'fetch' will copy the virus code back into your working directory. Your immune system has processes which run around checking object hashes for threads. There's a whitelist for expected hashes (normal threads). If the same unexpected hash shows up too many times, it goes on a blacklist and you start generating antibodies- special threads that go around searching for a specific object hash and tagging that thread for deletion. If too many bad hashes are found in the same place, a white blood cell nukes the whole site from orbit. Once you generate enough antibodies, the virus threads start getting killed before they can replicate and you're immune. If the virus mutates, the hash may not match anymore and you'll be vulnerable to the new strain. Things like the common cold and influenza mutate all the time, so you can very them over and over while chicken pox rarely mutates and youth can usually only get it once. Vaccines are a bunch of copies of (usually inactive) threads with a particular hash, to encourage your immune system to put that hash on the blacklist. Autoimmune diseases happen when valid code accidentally gets on the blacklist. Cancer (a fork bomb) tends to evade the immune system because its code was already on the whitelist. But... this is a super simplified version of how things work, and really only applies to mammals. Do not take these analogies too far. Biology is fascinating, and definitely worth deeper study.
- monocasa 7y agoOne of the best intros I've seen: an intro to how DNA works for hackers wanting to get started with genetic engineering https://www.youtube.com/watch?v=xJFqqxxtbRY https://www.youtube.com/watch?v=xJFqqxxtbRY Gives you enough pointers to be able to start googling from there.
- forgotmypw16 7y agoImagine a machine learning algorithm to write Perl. This algorithm is allowed to run for 4.5 billion years, and it has produced, through random iteration, a very good CMS. The CMS works great most of the time, but there's a bug which rarely happens, which crashes the whole system. This bug has been correlated with lines 4632486 and 434876365 in module132413.pl being executed, but it is not exactly clear how. Your job is to figure out what these lines of code do, and how they cause the bug. Here they are, and you can download the whole source on github: module132413.pl:4632486: $a4918732 = $b13rqw9 && chomp $dfadfaadf4r; module132413.pl:434876365: print; Good luck with the debugging!
- akamoonknight 7y agoNot necessarily specifically RNA/DNA but a super accessible description of biology is The Machinery of Life (https://www.goodreads.com/book/show/6601267-the-machinery-of-life https://www.goodreads.com/book/show/6601267-the-machinery-of...). I can't get over much it makes me want to learn more, and as a lay-person, I think it gave me a much better idea of what's going on at pretty much an atomic level.
- achenatx 7y agoI have a microbiology degree and an EE degree (but more like comp E). DNA truly is a blue print. (almost) Every cell in your body has the source code for your entire body. "this gene or set of genes are responsible for that outcome" is generally going to be a true statement. The equivalent wouldnt necessarily be a processor instruction. If you wanted an analogy, a cell is like an entire minimal computer. Power supply, processor, memory, and I/O. Each computer can run different parts of the code, but every computer has the entire code base. Within the computer are specialized "organelles" for storage, graphics, network, etc. These are comparable to organelles such as mitochondria, nucleus, endoplasmic reticulum etc. DNA acts like code in that it produces outputs (messages) and receives inputs. Proteins are also like code in that they produce outputs and receive inputs. It might be that DNA is like the executable source code that is stored as files and proteins are more like in memory processes such as services and actively running programs that get spawned from the files to perform various tasks. Viruses are like hostile code in bound in an email or coming through as tainted packets. They cant actually do anything on their own - they are inert, but once the processor starts executing the code, they hijack the processor. Sometimes to spawn more malicious code to other computers in a trusted network To carry the analogy further, departments in a company are a bit like organs. The computers in that department all roughly do the same thing. Imagine if IT imaged every computer in the company the exact same way, but what software was actually used would be based on your department.
- ramraj07 7y agoI have discussed this exact analogy with a couple colleagues from a CS background. If someone said the genome is the source code that's very wrong. The more accurate analogy is that your genome is a compiled, highly compressed executable file (more or less 200 MB in size?) Where the optimizer blindly reuses variables and memory locations for multiple routines that may or may not be related. It probably is quite similar to oracle's DB2 codebase, where all this shit is in C, and you change some variable here and hell breaks loose somewhere else. For the most part though, if you don't tinker with it, it runs like a well oiled machine because a blind watchmaker programmer (with great intuition but no CS organization fundamentals) has debugged and patched it for billions of years, patch on top of patch millions of times over.
- twangist 7y ago"Oracle's DB2" - Do you mean Oracle's DBMS? DB2 is an IBM product.
- ses1984 7y agoThis doesn't exactly answer the question but if you haven't read the selfish gene, you should.
- mjfl 7y agoThe cell is an analog computer, but one who's computational state we are still working out describing (it consists of the concentrations of transcription factors as well as epigenetic modifications of DNA and chromatin), and who's evolution in time is governed by simple binding and enzyme kinetics, but that are integrated into networks that can be very complicated. One really simplified model (inaccurate, but useful) of the computational state and evolution of the cell involves DNA methylation. DNA is methylated to shut it off, demethylation turns it on. To turn some DNA off or on, either DNA methyltransferase (DNMT3a/b) for methylation or one of the Tet proteins for demethylation needs to be guided to that region of DNA, usually through the assembly of some transcription factor complexes. The assembly of these complexes is combinatorial and performs logical addressing depending on the cell state. For example the cell may be expressing TF's A, B, and C, and these guide DNMT3a/b to DNA locus 3xq3945 (made up, whatever) if beta catenin translocates to the nucleus as a response to Wnt signaling, to turn something off. If TF's A, B, and D are expressed, it may bring it to a different location, and may bring Tet there instead, for demethylation. Anyways, that's an example of "computery" description of cell biology. I don't really like how other responders shot your question down, I think the computer science mindset is really relevant to biology.
- matheusmoreira 7y ago> Is there a a good read on how RNA and DNA work for a Computer Scientist? DNA is source code. RNA is an intermediate representation. Enzymes compile DNA into mRNA. Ribosomes compile mRNA into proteins which can actually execute a wide variety of functions. Proteins may require post-processing before they're usable. The output of a ribosome is a primary protein: a linear, one-dimensional structure. By interacting with itself and other cell machinery, the protein could be folded into three-dimensional secondary and tertiary structures. Several of them might be assembled into a quaternary protein. https://en.wikipedia.org/wiki/Protein_structure https://en.wikipedia.org/wiki/Protein_structure The final result could be a simple peptide or some huge machine like this thing: https://en.wikipedia.org/wiki/Type_three_secretion_system https://en.wikipedia.org/wiki/Type_three_secretion_system The mitochondrion and the ATP synthase are like a hydroelectric power plant. The electrochemical gradient is the gravity, the hydrogen is the water and the enzyme is the turbine. https://en.wikipedia.org/wiki/ATP_synthase https://en.wikipedia.org/wiki/ATP_synthase Enzymes transform substrate into product. They're like functions. When one enzyme's product is another's substrate, a pipeline is formed. Metabolism is a parallel process. I've written about metabolism as a programming metaphor before: https://news.ycombinator.com/item?id=21562716 https://news.ycombinator.com/item?id=21562716 Sometimes bacteria save useful snippets of their own source code into gene cassettes. This allows the code to be exported to other bacteria via horizontal gene transfer. https://en.wikipedia.org/wiki/Gene_cassette https://en.wikipedia.org/wiki/Gene_cassette Developed an awesome antibiotic-destroying enzyme? Make copies and send them to friends through a pipe. Didn't manage to survive? Said friends might be able to absorb the DNA from the environment anyway. They can obtain the fallen's powers just like Mega Man.
- hoseja 7y agoAlso the "source code" is an unaligned quaternary tape of hyper-optimized inter-dependent assembly monolith.
- mseepgood 7y ago> Many vulgarization sources say that DNA is like the source code of life. DNA is a tape archive of files (genes). They are not binary (base-2) encoded, but base-4 encoded. A reading head (polymerase) reads sections of the tape and copies them into working memory. A 3D printer (ribosome) receives these sections from the working memory and prints nano machines (proteins) based on these tape snippets. DNA is not source code, it does not contain conditions or jumps (loops), it's data for the 3D printer. (Actually it's just a 1D printer, but the result folds into a 3D shape).
- supr_strudl 7y agoDNA seen through the eyes of a coder: https://berthub.eu/amazing-dna/ https://berthub.eu/amazing-dna/ Molecular Biology Made Simple and Fun https://www.amazon.com/dp/1889899070 https://www.amazon.com/dp/1889899070
- deleted 7y ago[deleted]
- lawrenceyan 7y agoIn the case of the coronavirus, we see a significant binding affinity to the ACE2 membrane protein, which explains why the infection targets the lungs and guts so readily.
- koheripbal 7y agoAnd also why common blood pressure medications which block that same receptor are (probably) and good anti-viral for them. Losartan is currently in clinical trials for this new usage.
- hpoe 7y agoMy Dr. said that preliminary results indicate that blood pressure medications, generally increase your risk with the COVID-19, as well as Ibuprofen.
- jschwartzi 7y agoIs this based on basic research or demographic analysis? Has the research ruled out the possibility that people who are being treated for high blood pressure are more likely to be older and in poorer shape? Because that's a pretty strong confounding effect unless the research in question is a randomized controlled trial. I've also heard conflicting reports about Ibuprofen. I don't think anyone knows for sure.
- vladus2000 7y agoMy initial thought on Ibuprofen is just correlation not causation. How many people who get a fever will try Ibuprofen to try to lower the fever? Probably quite a few. When these people die its easy to say "well they all had Ibuprofen". That doesn't mean it had any effect. On the flip side, NSAIDs do reduce inflammation and inflammation is part of the body's response to various stressors; I could see that lowering our response leads to worse outcomes when sick. I have always thought that cold medication increases the duration of a cold just from my own observations, so I do find it at least plausible. I agree on the high blood pressure, if you are on it that means you have hypertension and are likely in poorer shape than someone who does not take it. I can somewhat see diuretics having an impact though as those can flush needed minerals out of your body when your body is in need. They also dehydrate you, so if you are on one and don't get properly hydrated and have a proper mineral balance, I can see that being a big negative.
- tcgv 7y ago> Is a virus a living thing? Maybe. I remember 20 year ago, at school, when the biology teacher was presenting this dilemma. Ever since, when I hear someone saying "doing this will kill the virus", it triggers my brain into this subject, since you can't kill something if it's not alive ;) Somewhat related, I also like the concept of the "Viruses of the Mind" [1], which makes an analogy between the spreading of a biological virus and the spreading of an ideology. [1] https://en.wikipedia.org/wiki/Viruses_of_the_Mind https://en.wikipedia.org/wiki/Viruses_of_the_Mind
- Ericson2314 7y agoIt's easy if we say viruses and crystals are both alive.
- boring_twenties 7y agoIf you can kill a process, or a proposal I don't see why you shouldn't be able to kill a virus -- alive or not!
- whatshisface 7y agoProcess reproduce (through forking) metabolize (stdin->stdout) and maintain homeostasis (garbage collection). How could they not be alive?
- ethbro 7y ago(Morally) Because reproduction without purpose is not life. Necessary but insufficient.
- taylorlunt 7y agoThen you must know the purpose of our lives. Enlighten me.
- daseiner1 7y agowhat’s the purpose of an amoeba? or a mosquito? or a duck? or a chimpanzee?
- maxerickson 7y agoViruses don't have bones.
- lihaciudaniel 7y agoYou don't say
- deleted 7y ago[deleted]
- redindian75 7y ago> Is a virus a living thing? Maybe. Maybe Virus is akin to a SEED. Seeds are inert/dead by themselves, but it carries as all the code/DNA/instructions needed to spring to life, flourish & even reproduce infinitely when put in an friendly environment (nourished soil with water, O2 etc)
- heurifk 7y agoA seed is way more alive than a virus. It only needs very simple things.
- taylorlunt 7y agoBut a virus doesn't "spring to life." A virus is like a seed that just generates more seeds without ever making a plant.
- ajna91 7y agoThe seed analogy may be onto something. Some viruses don't directly cause the host to create new viruses. Instead they direct the creation of virus creating factories, which create the virus. Then you get virophages which are even tinier than normal viruses, which infect the virus factories of other viruses.
- djmips 7y agoWhen it takes over the cell, the cell is now the plant.
- jacquesm 7y agoSeeds are not dead. Seeds are alive because their cells are alive. If too many of the seeds cells die then the seed can no longer germinate. That's why seeds can survive long periods of frost and stay active over very long periods, it is their cells that ensure they will be able to react to changes in the environment that suggest that the seed could germinate.
- holler 7y agoRead this recently and found it fascinating! https://en.wikipedia.org/wiki/Viral_evolution https://en.wikipedia.org/wiki/Viral_evolution
- boneitis 7y agoTo add on to sources of fascinating information... At least for me, I had tons of pedestrian questions, as I haven't taken a biology/chemistry course since high school. A search for virology on the youtoobs led me here: https://www.youtube.com/watch?v=8_bOhZd6ieM https://www.youtube.com/watch?v=8_bOhZd6ieM I found it to be a homerun in all but addressing my 20-30 questions in these times just in the first ten minutes. To the point. Without the current yt culture of gratuitous cuts and FX.
- trehalose 7y ago> Try multiplying a billion billion billion billion by a trillion trillion trillion trillion, then multiply that by a thousand, and that (10 to the 31st power) is the mind-numbing estimate of how many individual viral particles are estimated to populate the planet. What definitions of "billion" and "trillion" are they using? 10 to the 31st would be only ten million trillion trillion, going by the common definition of million as 10 to the 6th and trillion as 10 to the 12th.
- im3w1l 7y agoYeah, if you multiply "a billion billion billion billion by a trillion trillion trillion trillion, then multiply that by a thousand" you get a larger number than the atoms in the observable universe.
- civil_engineer 7y agoThat’s a lot of viruses! I’m staying inside.
- FabHK 7y ago4 x 9 + 4 x 12 + 3 = 87 4 x 3 + 4 x 4 + 3 = 31. That’s the only genesis of this error I could come up with - somehow they associated billion with 3 and trillion with 4 (conceivably because “N-illion” = 1000^(N+1) [1], and then forgot about the factor of three embedded in the base of 1000). [1] in the US system. In Germany and historically the UK, apparently, it’s 1000,000^N = 1000^(2N), which I personally prefer.
- zaarn 7y agoIn germany the step size is twice as large; million, milliard, billion, billiard, etc. Makes things neater IMO.
- FabHK 7y agoFWIW, the article has been corrected now to read: > Try multiplying a billion by a billion, then multiply that by ten trillion, and that (10 to the 31st power) is the mind-numbing estimate of how many individual viral particles are estimated to populate the planet. (I can't find a "correction" notice... It's Stanford Medicine, not a proper newspaper.)
- luxuryballs 7y agoSomewhat funny to think how different I would expect an article with this headline to be if it was posted on HN this time last year.
- adam_fallon_ 7y agoGeohot has been doing a pretty unscientific but interesting look at the molecular & computational biology side of the coronavirus. Interesting for coders/hackers First in the series here: https://youtu.be/8vWaawiUteM https://youtu.be/8vWaawiUteM
- refurb 7y agoI always thought the "flightosome" picture was a great way that biologists can demonstrate just how complex biology is.[1] When you see a biologist draw a system in biology, say, how a protein interacts with a cell membrane and then causes a change in expression within the nucleus, it can look relatively simple. Well, it's about as simple as drawing how an airplane works. In this example, you have the "flightosome", which is made up of fuselage, wings, cockpit and landing gear. That's what transports passengers from one airport to another. Simple right? Well even the landing gear component is complex and with biology, we have very little understanding of it at all. [1]https://blogs.sciencemag.org/pipeline/archives/2017/02/01/the-flightosome https://blogs.sciencemag.org/pipeline/archives/2017/02/01/th...
- mindfulplay 7y agoI find this incredibly fascinating. I wasn't aware of how complex these things were. A few videos that blows my mind on what really happens inside your cells - https://youtu.be/bee6PWUgPo8 https://youtu.be/bee6PWUgPo8 https://youtu.be/Ofd_lgEymto https://youtu.be/Ofd_lgEymto
- ggm 7y agoWise words a former cell biology aware PhD said to me once: a cell is at a scale where van der Waals forces means 'water' isn't behaving like you think and the 'liquid' of a cell is possibly more like a matrix than a fluid. Those high school cell models are very misleading. He basically said macro scale intuition was useless for what it means to pierce the cell wall, as an example. What does "pierce" even mean?
- JshWright 7y agoI'd highly recommend the YouTube channel "Journey to the Microcosmos" for videos that do a great job of improving that intuition.
- nojvek 7y agohttps://m.youtube.com/channel/UCBbnbBWJtwsf0jLGUwX5Q3g https://m.youtube.com/channel/UCBbnbBWJtwsf0jLGUwX5Q3g ^ here is the link. Pretty great animation. Thanks for the recommendation.
- deleted 7y ago[deleted]
- computerphage 7y agoTo be clear, it's not an animation, it's video captured from a microscope.
- chadcmulligan 7y agoI picked up a microscope last year - they were on sale, and one of those things I'd always wanted to have a play with. I remember having a look with them in school and never seeing much and it seemed very hard. All you have to do is go to a pond or creek scoop out some weeds, dirt and water and stick it in a jar and there is hours of exploration in front of you. Once you start looking its like seeing an evolutionary world in front of you, everythings eating each other and trying to not be eaten. If you're thinking of getting a telescope (I had one), think of a microscope they open up a new world, its incredibly easy to see things - I thought it would be a lot more work. Probably there's so many on line resources now to - this guy is a great start - microbe hunter https://www.youtube.com/channel/UCDpKY8-oz5PWlBPNzNsbLug https://www.youtube.com/channel/UCDpKY8-oz5PWlBPNzNsbLug
- nojvek 7y agoThey say there is a part 2. Where is the said part 2, I couldn’t find the link.
- jmckib 7y agoLooks like it hasn't been posted yet. This article came out today, this is the most recent article from that author, and google didn't turn up anything. It's strange how the end implies that part 2 already exists though.
- titzer 7y agoAn insanely detailed molecular simulation of HIV infection is extremely illustrative: https://blogs.scientificamerican.com/observations/watch-the-life-cycle-of-hiv-in-colorful-new-detail/ https://blogs.scientificamerican.com/observations/watch-the-...
- nojvek 7y agoSomeone who is a molecular biologist, please correct my understanding. DNA is a molecule, made out of 4 amino acids. ACTG. There are 18 different kinds of amino acids. Amino acids are made out of carbon, nitrogen, hydrogen, oxygen. Amino acids make proteins. Proteins are the structural bricks (like LEGO) that are combined in various sequences by enzymes to build more complex machinery. The proteins make up cell organelles, which make up cells. How much of how DNA turns into proteins and different proteins build different structures is understood? Do we have a DNA simulator where I can write ACTG code and it tells me what kind of proteins will be made, how those proteins will interact to build complex structures? How close are we for computer science folks to actually start writing compilers, debuggers, frameworks and simulation tools for DNA and man made cell machinery ? How far away are we from making custom DNA + cells that act like 3D printers taking collagen and building nanometer precision complex structures? It seems our cells already do nano manufacturing and computation, how do I tap into that ?
- achenatx 7y agoDNA is made out of nucleic acids. Each sequence of 3 DNA nucleotides codes for an amino acid. There are 21 amino acids. How DNA -> proteins is well understood. Protein folding though is incredibly complex to model. It is easy to know the amino acid sequence, but hard to know how the protein will end up folding.
- timy2shoes 7y agoDNA is made of nucleic acids (deoxyribonucleic acids), not amino acids. DNA is translated to amino acids, except when it encodes long-noncoding RNAs, or miRNAs, or piRNAs, or untranslated regions, or intergenic regions, or transposons, or psuedogenes. And the protein coding sequences are coded into proteins, except when there are alternative splicing sites, or anti-sense RNAs. And then the protein sequence folds into their minimum free energy state, except when they are assisted by other proteins, or when they exist as disordered proteins. And it's not always DNA -> protein. Sometimes proteins make other proteins, for example circular proteins can only be made from other proteins. Then there are post-translational modifications, which change the RNA sequence between DNA to RNA and RNA to protein. And then there's RNA interference, where miRNAs interfere with RNA to protein translation. And then there's epigenetics such as DNA methlyation or histone modifications (histones are protein which compress DNA) which change what genes can be expressed when. Really, for every rule that you've been taught, there is an exception. Biology is so much more complicated than we understand. And understanding how to make a biological computer (different from the biological computing of Adelman, yes the same Adelman as RSA) would involve understanding how all the pieces fit together.
- js8 7y agoWhat always fascinates me is that biologists talk about how these large molecules bind and self-assemble, and how enzymes control the reactions and so forth, but what are the odds? It's almost like putting the parts in the mixer, and getting your little machine in the output. I have very hard time imagining it, especially in the cell which has thousands different molecules going on inside it, how everything gets in the proper place in the end.
- antman 7y agoYou seem to be trying to get yourself into a certain rabbit hole, if that's the case let me assist you by introducing you to the Watchmaker analogy: https://en.m.wikipedia.org/wiki/Watchmaker_analogy https://en.m.wikipedia.org/wiki/Watchmaker_analogy
- rwmj 7y agoFirstly, evolution over billions of years makes it possible. But in more direct answer to your question about how these things self assemble - at this level atomic forces are like little magnets (I mean, literally they are the electromagnetic force) and those cause the atoms to arrange themselves in particular ways. There are lots of videos online showing this, eg. one I picked at random: https://www.youtube.com/watch?v=muNNSAYZDS8 https://www.youtube.com/watch?v=muNNSAYZDS8
- acqq 7y agoExactly, molecular self-assembly is completely obvious once one can see the equivalent with his own eyes. I hope nobody complains "but he shakes the flask" -- because that is exactly what the temperature is -- how fast the particles "jiggle" as Richard Feynman would that describe: https://www.youtube.com/watch?v=K_y5iKcDdOQ https://www.youtube.com/watch?v=K_y5iKcDdOQ
- olejorgenb 7y agoFor a deeper dive I'll recommend this lecture series: https://www.youtube.com/playlist?list=PLGhmZX2NKiNldpyRUBBEzNoWL0Cso1jip&fbclid=IwAR0dV7y_dk0St28xOmqWLkW1GC4o1YrrZy8RCLWro0q0oTraRq3g7h0fn-g https://www.youtube.com/playlist?list=PLGhmZX2NKiNldpyRUBBEz...
- MichaelMoser123 7y agoit's sort of the low level live form is hacking the high level one. am i missing something?
- jacquesm 7y agoNatures pentest, red team edition.
- unexaminedlife 7y agoQuestion: How is the production of a cell wall encoded (or not) in DNA in a cell's replication process?