11 ms·
Why does the SARS-Cov2 genome end in aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa? (2020)
- nashashmi 4y agoSo upon multiple sequential infections, the polytail A will reduce?
- matt_daemon 4y ago[flagged]
- ugjka 4y ago[flagged]
- einpoklum 4y ago[flagged]
- brookst 4y ago[flagged]
- fuckyah 4y ago[dead]
- rmbyrro 4y ago[flagged]
- luckylion 4y agoHad it started with aaaaaaaaaaaaa, I would've put my money on someone optimizing for the virus yellow pages.
- xwdv 4y agoIt’s a good thing people aren’t more intelligent, otherwise they would be able to construct and propagate deeper and more advanced conspiracies like this. Most people thankfully don’t even know what a genome is.
- aatd86 4y ago[flagged]
- jtchang 4y agoIt's like a NOP slide for viruses: https://en.wikipedia.org/wiki/NOP_slide https://en.wikipedia.org/wiki/NOP_slide Just kidding...sort of!
- _3u10 4y ago[flagged]
- uxp100 4y agoUser Zoe Sparks on that page covers why they don’t really feel it’s like a nop slide. I think that answer is a good supplement to the accepted one.
- akira2501 4y agoI think they miss the point entirely. The environment in the cell is mostly mechanical, but it's also dominated by random forces. If you are unable to guarantee where you are going to "enter the sled" or when the "tail hits the ribozyme" then the nop sled seems to be an equivalent feature. So.. to me, it's odd they invoke "legitimate code." The comparison I'd consider would be "combative code." For example, the old game "core wars." Thinking in that mindset, I can see several uses for a "nop sled" in "legitimate code."
- zxcvbn4038 4y agoMaybe the scientist who made it died before he finished? ATTACGAAAAAAAAAAAAAAAAAAAAAAAA……
- jMyles 4y agoLook, if he died while engineering a virus, he wouldn't bother to code "AAAAAAA" he'd just say it!
- mynameisash 4y agoWell that's what it says.
- DonHopkins 4y agoPerhaps he was dictating? https://www.youtube.com/watch?v=ZlIz0q8aWpA https://www.youtube.com/watch?v=ZlIz0q8aWpA
- akiselev 4y agoDictated, not transcribed.
- dilznoofus 4y agoDictated, but not read
- notfed 4y agoWhy the downvotes? Video is hilariously relevant.
- brassattax 4y ago[flagged]
- naasking 4y agoClearly he died at his computer and his face landed on the keyboard.
- HL33tibCe7 4y agoRead https://berthub.eu/articles/posts/reverse-engineering-source-code-of-the-biontech-pfizer-vaccine/ https://berthub.eu/articles/posts/reverse-engineering-source...
- gleenn 4y agoI don't think this is nearly as true for virii genomes, but larger species have lots of protetive sections of DNA to protect from mutations. If you lose a non-protein-coding section of DNA to mutation, no harm to the species occurs. In humans, only about 1.5% of our DNA codes for protein that is actually generated. Virii are physically extremely tiny in terms of cell size and must be very efficient in terms of storing the DNA within them so way more actually codes, but no doubt there are similar factors at play.
- flobosg 4y agoViral genomes are very compressed. In fact, viruses usually have overlapping genes, where one genomic region can codify for more than one product. See the following review for more information: https://www.nature.com/articles/s41576-021-00417-w https://www.nature.com/articles/s41576-021-00417-w
- hknmtt 4y ago[flagged]
- FormerBandmate 4y agoThe top answer at the link explains it best: Good observation! The 3' poly(A) tail is actually a very common feature of positive-strand RNA viruses, including coronaviruses and picornaviruses. For coronaviruses in particular, we know that the poly(A) tail is required for replication, functioning in conjunction with the 3' untranslated region (UTR) as a cis-acting signal for negative strand synthesis and attachment to the ribosome during translation. Mutants lacking the poly(A) tail are severely compromised in replication.
- subroutine 4y agoAdding a poly(A) tail when engineering rna plasmids is so common that it's part of the standard feature library of most plasmid editors. Here I have a screenshot of the ApE editor displaying one plasmid I made for a neurobio experiment involving the overexpression of two chimeric proteins (actin and profilin, respectively linked to green and red fluorophores; note the editor has autotagged the polyA tail feature): https://ibb.co/XSCSKC9 https://ibb.co/XSCSKC9
- x-shadowban 4y agoCan you add any number of A's, or just 1, or shorten it by 1, and it still is functional?
- subroutine 4y agoThe number of adenine repeats that confer functional properties is quite variable but it definitely needs to be more than "just 1". I've seen anywhere from 25-250 used in designed plasmids. The exact number people use in their engineered sequence is based on a number of factors, not all of them scientific in nature (e.g. companies charge per basepair synthesize a bespoke polypeptide; e.g. you copied the sequence from a previous clone into ApE and that sequence used 30 repeats and worked fine).
- deleted 4y ago[deleted]
- psanford 4y agoI can't see that and not think: base64 null byte padding.
- layer8 4y agoYeah, I’d be worried if it was AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA===. ;)
- personjerry 4y agoThe virus printer adds padding to make the genome a multiple of 64
- deleted 4y ago[deleted]
- roenxi 4y agoFile formats are really easy to figure out and are a big advantage for moving data around. Even without an academic theory, pretty much everyone in software starts to figure out the same tricks as soon as reliable transmission becomes a goal. I assume that at least one reason for this is that genomes are data, data likes to live in structured formats, and file terminators are more reliable for biology to process than encoding the length of the genome (although, biology being messy, I wouldn't be shocked if both were done). Evolution has a good grasp of engineering principles. Are there probably desirable chemical properties? Yes. Is nature overloading each part of a genome with uses? More than likely. Has it figured out how to terminate a sequence? Obviously.
- roughly 4y agoSo something to keep in mind when looking at biological systems, and especially when looking at genomics - evolution doesn't actually have a master plan or agency, it's just drift and reproduction. There's a lot of reuse and a lot of parsimony that can look elegant, but there's no 'design' process of evolution - it's a pile of things that looked enough like other stuff that over time with some tweaks they could take on dual roles. There's also no separation of concerns - DNA is a molecule, and it's acted upon by other molecules following the same rules of chemical and quantum interactions that affect everything else. Certain RNA sequences aren't transcoded but rather fold into functional molecules and enzymes, and protein folding and subsequent structure and function is affected by how fast the RNA is transcribed, which is affected by the population of available tRNA molecules. Genomics only looks like information - it's still chemistry.
- bailoon 4y ago[flagged]
- m0llusk 4y agoObligatory: https://uncyclopedia.com/wiki/AAAAAAAAA https://uncyclopedia.com/wiki/AAAAAAAAA!
- gryn 4y ago[flagged]
- awhow 4y ago[flagged]
- ipython 4y ago[flagged]
- brundolf 4y ago[flagged]
- jkingsman 4y agoIf this sort of question fascinates you, you might like "Reverse Engineering the source code of the BioNTech/Pfizer SARS-CoV-2 Vaccine"[0], an article written with a tone that I've found to resonate with engineers and like-minded folk. [0] https://berthub.eu/articles/posts/reverse-engineering-source-code-of-the-biontech-pfizer-vaccine/ https://berthub.eu/articles/posts/reverse-engineering-source...
- sirsinsalot 4y agoThat was exceptionally informative and accessible. Thank you
- doctor_eval 4y agoFantastic article!
- farkanoid 4y agoWhat a fascinating article! Thanks for sharing. I didn't realise there was so much crossover between embedded design and biology!
- a_w 4y agohttps://news.ycombinator.com/item?id=25598270 https://news.ycombinator.com/item?id=25598270
- Apocryphon 4y agoNominative determinism
- more_corn 4y ago[flagged]
- mlhpdx 4y agoI am entirely unqualified to answer, but I choose to believe it’s the equivalent of scratch (reserved stack) memory in an executable image. If I’m wrong, well at least I’m enjoying it.
- quickthrower2 4y ago[flagged]
- yazzku 4y ago[flagged]
- aceon48 4y ago[flagged]
- 1letterunixname 4y ago[flagged]
- kazinator 4y agoThis ending is the result of the Lisp closing parenthesis being important enough to be directly mapped to a dedicated nucleotide base.
- instagraham 4y ago[flagged]
- jboy55 4y agoIt amazes me that the genome is only 29k long. If you were to write a computer virus now, it probably wouldn't be that short, let alone something that can infect and kill millions of people.
- IshKebab 4y agoA computer virus that just replicates and causes damage can be a lot smaller than that.
- tduberne 4y agoVery interesting. I first wondered how nature can randomly generate such a pattern, and then realized we are just falling for our "built in" pattern recognition: it would feel much more "natural" for the stop sequence to be the encoding of some specific protein without any clearly recognizable pattern... But it would actually be more unlikely to appear/survive mutation than "any long-enough sequence of A". I also like how it is established that this has an effect on replication, but that as far as I understand we do not understand the underlying process. Humbling.
- deleted 4y ago[deleted]
- inDigiNeous 4y ago[flagged]
- sirsinsalot 4y ago"Maybe" isn't a good replacement for "I don't know". Other people do know and you can find this information out. The body uses it in RNA for denoting the life cycle of reuse to avoid degradation. The linked article tells you
- otherme123 4y agoOf all the possible signatures of SARS-CoV-2 being lab-made, the polyA isn't one or them. https://en.m.wikipedia.org/wiki/Polyadenylation https://en.m.wikipedia.org/wiki/Polyadenylation
- cykros 4y ago[flagged]
- fspacek 4y ago[dead]
- fspacek 4y ago[dead]
- pimpampum 4y agoTrying to Buffer overflow the cell.