7 ms·
The life cycle of HIV in 3D [video]
- colordrops 8y agoI know it's just my own biased anthropomorphizing but the virus almost looks sinister and intentional in its actions.
- untangle 8y agoAgreed. These Harryhausen-like creatures are every bit as menacing as the Kraken. I naively failed to realize the deadly complexity (genius) of the HIV virus. Well done piece.
- baobrien 8y agoThe music really helps with that. The video gave me a spooky feeling.
- colordrops 8y agoHa, I didn't even watch it with sound. Will have to do that when I get home.
- iandanforth 8y agoMindblowing. To think that chance+time produced something like that is staggering.
- colordrops 8y agoChance+time also created a network of trillions of similar things that are now comprehending this sentence right now. It's absurd.
- Liron 8y ago+reproduction +selection
- Cogito 8y agoI haven't yet seen a good explanation as to why this focus on randomness is so prevalent, but chance really is almost irrelevant when it comes to evolution. The main mechanisms of reproduction and selection that you point out have almost no randomness at a population level. Selection of individuals has some randomness associated with it, as death can come unexpectedly to anyone, but at population levels it is the genes that make it more likely for an individual to survive/pass on their genes that are the ones that get passed on. It's possible that an entire population gets wiped out, or a particular gene gets wiped out due to chance, but as long as the population is reproducing then on average the genes that are passed on are the ones that help the population survive. Similarly reproduction isn't random at population levels either. Sexually reproducing populations mix their surviving genes evenly within geographical locations over evolutionary timescales (such as trees), or selectively if individuals choose their mates (like humans!). Neither of those things are random. Mutations that happen during reproduction are somewhat random but, as for asexual populations, the amount of mutation at the population level is not random. It's reasonable to expect the reproductive mechanisms to be selected for in such a way to maintain coding errors and the like (at an appropriate level) so that mutations continue to develop and strengthen the gene pool. While there are lots of single events where randomness and chance come into play, as soon as you have a collection of things that reproduce those things must either get better at reproducing or cease to exist. Chance has nothing to do with it.
- lawrenceyan 8y agoENTROPY BABY.
- baobrien 8y agoI think articles like Ken Shirriff's "Cells are very fast and crowded places"[1] are good companions for visualizations like this. It helps to keep in mind that the things moving around in cells are flying around at break-neck speeds if you scale them up linearly. 1 - http://www.righto.com/2011/07/cells-are-very-fast-and-crowded-places.html http://www.righto.com/2011/07/cells-are-very-fast-and-crowde...
- jdtang13 8y agoThis is a really great share! Truly mindblowing.
- TeMPOraL 8y agoWhere "flying around" means "constantly bumping into everything else". This means small stuff doesn't just fly around the cell, it has to diffuse through it. A nice side effect is that eventually, everything gets into contact with everything else. That, as I understand, is how small molecules get to their right place. Also, this means that it's too tight for large stuff to move around at all. Hence the specialized machinery within the cell that transports large molecules. Source for both: I'm 1/3d of th way through The Machinery of Life[0]. Incidentally, I learned about this book from HN. It's absolutely amazing. The biggest selling point are the drawings - David S. Goodsell created a lot of illustrations (like these[1]) that give you a good perspective on how stuff is packed within cells. EDIT: that blog post you linked covers the diffusion aspect well, I second the recommendation to read it. -- [0] - https://www.goodreads.com/book/show/6601267-the-machinery-of-life https://www.goodreads.com/book/show/6601267-the-machinery-of... [1] - http://mgl.scripps.edu/people/goodsell/illustration/public http://mgl.scripps.edu/people/goodsell/illustration/public
- terminado 8y agoYeah, thinking about incidental chemistry occurring due to many collisions at or near the speed of sound while packed into a fluid solution or compressed gas, definitely puts things in perspective, in terms of how specifically matched and optimized everything needs to be, in order to be fortuitous as an otherwise unplanned event. It's like stumbling into elevator after elevator, while running the hundred yard dash at top speed, everywhere you go, only to encounter the perfect dance partner to fall in love with at first sight.
- stanislavb 8y agoThat looks scary. VERY scary!
- imranq 8y agoAbsolutely insane how this is actual reality. That millions of people have died from such a small object that seems to have more creativity and complexity than I’ve ever seen.
- DINKDINK 8y agoYou might enjoy: Influenza A (H1N1) – How many bits does it take to kill a human? https://www.bunniestudios.com/blog/?p=353 https://www.bunniestudios.com/blog/?p=353
- ryanmarsh 8y agoThanks for sharing. That’s terrifying. I feel like this should be read by more people.
- rqs 8y agoAlso, video: https://www.youtube.com/watch?v=NPr-i-IbA7s https://www.youtube.com/watch?v=NPr-i-IbA7s This one is about Influenza: https://www.youtube.com/watch?v=7Omi0IPkNpY https://www.youtube.com/watch?v=7Omi0IPkNpY (not H1N1, but quality is better) I learned a lot today (At least that's what I felt) LOL
- phaefele 8y agoMy favourite cell documentary is this. Has more information about the various transport mechanisms in the cell itself. Simply awesome - have watched several times to understand better. See https://www.youtube.com/watch?v=FzcTgrxMzZk https://www.youtube.com/watch?v=FzcTgrxMzZk
- juancampa 8y agoI would love to know how this animation was made. Is there any sort of simulation happening?
- colordrops 8y agoYes, that was my first thought as well. I'm curious what parts are accurate and what parts are simplifications for ease of visualization and comprehension. Colors are clearly not representative. What about movements? Relative speed of movements? Shapes? Density? If we could see these processes in some magical microscope would this look close to what is happening or not?
- discrisknbisque 8y agoDrew Berry creates similar animations and refers to them (in this talk) as "accurate representations", but doesn't go into much detail. Interesting history in the beginning as well. https://www.youtube.com/watch?v=WFCvkkDSfIU https://www.youtube.com/watch?v=WFCvkkDSfIU
- fizixer 8y agoIt's two separate things, both mentioned in your question: simulation then animation. Both steps are computationally expensive enough that they can't be done in one run. For simulation, typically a molecular dynamics code is used along with features specific to biological analysis (since MD by itself is a physics simulator). NAMD is one of the well-known MD tools used for bio work. Depending on the complexity and features/accuracy sought, a whole host of other tools might be involved. The timeframe of simulation is of the order of weeks to months given massive computational power (e.g., a large allocation on one of the national supercomputing grids). Once tons of simulation data is generated (as the output of simulation), then 3D visualization tools can be used. NAMD has a sister vis tool called VMD. Blender is another option. Incidentally, Janet Iwasa (the narrator and researcher behind this work) is a visualization expert, so it's likely she only worked on the second step (animation) by using existing simulation data, or collaborating with a simulation group. (Again the computation required for rendering is very high, on the order of days to weeks using a large allocation on a supercomputer).
- kevin2r 8y agoQuestion. How is that even knowing the lifecycle of HIV at this level of detail, there is not a cure for it?
- rqs 8y agoI Googled it for you: https://www.ted.com/talks/janet_iwasa_why_it_s_so_hard_to_cure_hiv_aids https://www.ted.com/talks/janet_iwasa_why_it_s_so_hard_to_cu... https://www.seeker.com/will-we-ever-cure-hiv-1792546668.html https://www.seeker.com/will-we-ever-cure-hiv-1792546668.html https://en.wikipedia.org/wiki/Management_of_HIV/AIDS https://en.wikipedia.org/wiki/Management_of_HIV/AIDS Also you may interested: https://en.wikipedia.org/wiki/The_Berlin_Patient https://en.wikipedia.org/wiki/The_Berlin_Patient
- jacobwilliamroy 8y ago>in the U.S. HIV kills 10,000 people per year I remember an early passage from Buckminster Fuller's Grunch of Giants where he tells the reader to visualize fully packed stadium and explains that's what 10,000 people looks like.
- piker 8y agoI'm not sure 10,000 packs a stadium in the US. Maybe the bleachers of a high school football stadium.
- stenl 8y agoOne major issue is the fact that reverse transcriptase, which copies the HIV genome inside the cell, is sloppy and makes lots of mistakes. As a consequence, every viral particle produced is a little different. A drug that targets any given HIV protein to disrupt it, will work on most particles, but there’s always some that carry mutations that allow them to escape. The solution is to treat with multiple orthogonal drugs. However,a second major issue is what’s mentioned in the movie, that the viral genome integrates into the host genome and can lie dormant for years. So even if you kill off every single viral particle, years later new particles can be produced from the dormant genome. A third major issue is that HIV specifically infects T cells, which are the very immune cells that are supposed to combat infection. This weakens the natural defenses, and also makes it difficult to create a successful vaccine.
- sytelus 8y agoThe amazing part for me was that virus "code" automatically finds the unrelated host "code" in what is effectively an equivalent of space travel inside a host body, does copy and paste to insert itself somewhere in host code and everything just works! I can't think of any of our computing models that is capable of doing this and so robust at errors.
- smallhands 8y agoWait, it is really interesting may HIV can solve N=NP problem
- JackFr 8y agoLisp
- betolink 8y agoRelated to this type of animation, there is a great book called "The Machinery of Life" that talks abut molecular level biology with amazing illustrations. https://www.amazon.com/Machinery-Life-David-S-Goodsell/dp/0387849246 https://www.amazon.com/Machinery-Life-David-S-Goodsell/dp/03...
- Liron 8y agoLiving in 2018 is quite a privilege. Most microbiologists who spent their lives trying to puzzle this out won't get to sit back and watch the answer.
- ubershmekel 8y agoHere's the video on vimeo https://vimeo.com/260291607 https://vimeo.com/260291607
- czardoz 8y agoHard to believe that no one has programmed this. Evolution is insane.
- nkozyra 8y agoIf you look at a "program" in a more abstract way and recognize that evolution is declarative it's a bit easier to reconcile.
- danielmain 8y agoSeems that you are not a programmer. Even with Intelligence people can write code (much much simpler and buggy) how can chaos build such a complex thing? Can you answer what was first? information (RNA/DNA) or the first cell?
- czardoz 8y agoWhat makes you think I'm not a programmer? I was marveling at how evolution can lead so something so systematic. > Can you answer what was first? information (RNA/DNA) or the first cell? No I can't. What are you getting at?
- yread 8y agoAmazing! So there is self-replicating, self-modifying code (HIV quickly mutates to avoid detection) code, that sometimes jumps into middle of an instruction (GAG proteins being cut into the enveloping proteins).
- 8iterations 8y agoA better animation is the winner of the AutoPACK challenge few years back: https://vimeo.com/62635232 https://vimeo.com/62635232 Those guys did an awesome job because: a) use of brownian motion b) sick af music.
- Retric 8y agoThat's a poor visual of Brownian motion. Things don't giggle they randomly fly around at ~250 miles an hour. It's still a great video just IMO misleading in its own way.
- kartan 8y agoWhen I see the animations I can't stop thinking about a Turing machine. How it works in a similar fashion, copying symbols to keep track of the program while generating the result in the process. It will be nice to know if you can build a Turing complete machine using DNA and the cellular mechanisms. https://www.quora.com/Is-DNA-a-Turing-machine https://www.quora.com/Is-DNA-a-Turing-machine
- cornholio 8y agoAs a technologist, I have mixed feelings when I see the fascinating details of life. On one hand, mastering this molecular machine would give us literally God-like powers: we could fabricate, grow or heal anything. We could solve all current problems, we could terraform planets using a few milligrams of DNA and literally redefine what it means to be human. On the other, I see the human body as a completely unsecured cybernetic system, that can be so easily tricked to pick up any random bit of programming and insert it into it's own code. There is no forethought or design, no rational defense, just good enough systems that have evolved randomly against non-rational adversaries that happened to emerge out of the protein soup surrounding us. The troubling fact is that mastering the wondrous biomolecular machine necessarily comes with the power to kill every human on the planet. Truly God-like powers.
- nabla9 8y agoInterestingly the Gene Regulatory Network (GRN) - the interaction of genes and proteins that control the prosess inside the cell is computationally very similar to recurrent neural network. Gene expression levels is controlled by proteins that are produced by active genes. https://en.wikipedia.org/wiki/Gene_regulatory_network https://en.wikipedia.org/wiki/Gene_regulatory_network Harnessing this mechanism directly for neural computation would be grand project.
- daveguy 8y agoI think it's a bit of a stretch to say GRN is "computationally similar" to neural networks. That seems to be a shoehorn of the most popular technology of one field into another field. Just because the GRN contains feedback loops with multiple influences doesn't mean it's suited to NN computation. The GRN is orders of magnitude more complex than computational NNs and it is orders of magnitude slower than signal transduction of axons. I agree it will be awesome to be able to harness molecular machinery to "do stuff" for us. The "nanotechnology" in our bodies is way beyond any current manufactured nanotechnology. We currently have only crude control of the cellular functionality -- think point a wind up toy in the direction we want or modify it by taping a flashlight to the top. We are pretty far from being able to use the manufacturing equipment to make cars instead of windup toys. (Not to mention the manufacturer is already making rockets)
- titzer 8y agoMakes one really wonder just what, exactly, is out there mindlessly gobbling and reproducing itself in an endless quest to just keep going. Puts human life in perspective too. We're all just mindless gobblers when zoomed out enough.
- deleted 8y ago[deleted]
- callesgg 8y agoWow that gives me shivers, creepy.
- sizzle 8y agoThis is why I'll never go on tinder or screw around, frightened about getting stds. My friends act like STDs are no big deal and joke around about the times they've contracted chlamydia and gonorrhea etc like it's a cost of doing business (getting laid). I'll stick to long term relationship.