this post was submitted on 25 Oct 2024
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Curated Tumblr

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For preserving the least toxic and most culturally relevant Tumblr heritage posts.

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# This has been reposted here to Lemmy as part of the "Curated Tumblr Project."

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[–] fartsparkles 99 points 1 month ago (2 children)

What is up with the bird at the end?

[–] [email protected] 110 points 1 month ago* (last edited 1 month ago) (4 children)

A bot strips away all spaces and letters that aren't A, T, C or G, then treats the rest like a genetic sequence and checks it against some database.

Presumably, it runs through many terabytes of data for each comment, as the Gallinula chloropus alone has about 51 billion base pairs, or some 15 GiB. The Genome Ark DB, which has sequences of two common moorhens, contains over 1 PiB. I wonder if a bored sequencing lab employee just wrote it to give their database and computing servers something to do when there is no task running.

No, I won't download the genome and check how close the "closest match" is but statistically, 93 base pairs are expected to recur every 2^186^ bits or once per 10^40^ PiB. By evaluating the function (4-1)^m^ × mℂ93 ≥ 4^93^ ÷ (pebi × 8), one can expect the 93-base sequence to appear at least once in a 1 PiB database if m ≥ 32 mismatches or over ⅓ are allowed. Not great.

This assumes true randomness, which is not true of naturally occuring DNA nor letters in English text, but should be in the right ballpark. Maybe fewer if you account for insertions/deletions.

[–] [email protected] 70 points 1 month ago* (last edited 1 month ago) (2 children)

The FAQ on the user's page says:

  1. They are not a bot, just neurodivergent

  2. They're using BLAST

ie, this

https://blast.ncbi.nlm.nih.gov/Blast.cgi

They did not code anything beyond a very simple regex function that strips down posts to a t c g, and then they copy paste it into the above website, then copy paste the output.

Hell, you can see they aren't even removing apostrophes and quotes, not even forcing it to all lower case or all upper case, removing spaces and line breaks...

... as a former database admin/dev/analyst, I was losing my fucking mind at the notion that someone with direct access to a genomics DB, would just hook it up to tumblr, via an automated bot, and spam the db with non work related requests, all on their own, when they can barely modify a string correctly.

Thank fucking god this is just using a publicly available, no doubt extremely low fidelity, watered down search via an API.

... You need literal, state of the art, absurdly expensive, power hungry, and secure supercomputers to be able to do genomic comparisons.

Probably one of the dumbest things you could do, quickest way to get fired, and then never be able to work in the field again, would be for a random genomics lab worker who does not know how to code to open up a whole bunch of security holes and cost god knows how much money (and damage if you write bad code) running frivolous bs searches in their state of the art genomics db... for a tumblr bot.

[–] [email protected] 30 points 1 month ago (1 children)

Not a bot, just neuro

Hilarious every time.

[–] [email protected] 7 points 1 month ago (1 children)

Wow. Just wow. Someone is still using CGI.

[–] [email protected] 5 points 1 month ago

Wayback Machine's earliest capture is from 2008.

It's a cutesy, public facing, extremely limited and low fidelity 'demo version' of a genomic search, basically made as a PR / Science Education promotion gimmick... by government contracted web/backend devs, in 2008.

Honestly its a miracle its still functional at all.

[–] [email protected] 30 points 1 month ago

That's hilarious, but I needed the explanation too. Thanks!

[–] [email protected] 6 points 1 month ago (1 children)

The genomes have likely been indexed to make finding results faster. Google doesn't search the entire internet when you make a query :P

[–] [email protected] 3 points 1 month ago* (last edited 1 month ago) (2 children)

I know that similar computational problems use indexing and vector-space representation but how would you build an index of TiBs of almost-random data that makes it faster to find the strictly closest match of an arbitrarily long sequence? I can think of some heuristics, such as bitmapping every occurrence of any 8-pair sequence across each kibibit in the list. A query search would then add the bitmaps of all 8-pair sequences within the query including ones with up to 2 errors, and using the resulting map to find "hotspots" to be checked with brute force. This will decrease the computation and storage access per query but drastically increase the storage size, which is already hard to manage.

However, efficient fuzzy string matching in giant datasets is an interesting problem that computer scientists must have encountered before. Can you find a good paper that works well with random, non-delimited data instead of just using the approach of word-based indices for human languages like Lucene and OpenFTS?

[–] [email protected] 5 points 1 month ago* (last edited 1 month ago)

As per my other post, this person isn't doing any of that.

But, since you asked for papers on generic matching algorithms, I found this during the silent conniption fit you sent me into after suggesting that some random tumblr user plugged a tumblr bot directly into a state of the art genomics db.

https://link.springer.com/article/10.1007/s11227-022-04673-3

Please note that while, yes, they ran this test on a standard office computer, they were only searching against 12 million characters.

A single tebibyte of characters would be more like 1 trillion characters. A pebibyte would be more like 1 ~~quintillion~~ quadrillion.

... much, much, much longer processing times.

Edit: Used the wrong word for stupendously large numbers that start with q.

[–] [email protected] 1 points 1 month ago

Yeah good point, not a trivial undertaking. I'm not an expert in that area but maybe elasticsearch or similar technology is able to find matches. Although I have no idea how that works under the hood

[–] breakfastburrito 3 points 1 month ago

It’s probably just ncbi

[–] [email protected] 18 points 1 month ago

hellsitegenetics is a gimmick blog on tumblr that looks through popular posts on the website and tries to identify genetic sequences with in them and then post the creature that the genetic sequence corresponds to.

They're a bit like haiku bot, which scans posts to see if they're haikus and then formats the haiku and posts it, but i think hellsitegenetics is an actual person cuz they have talked about it in the past