AlphaGenome: AI for better understanding the genome

Posted by i_love_limes 5 days ago

AlphaGenome: AI for better understanding the genome(deepmind.google)

526 points | 176 commentspage 3

kat529770 4 days ago|

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sahil_sharma0 4 days ago||

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Scaevolus 5 days ago||

Naturally, the (AI-generated?) hero image doesn't properly render the major and minor grooves. :-)

jeffhwang 4 days ago||

When I was restudying biology a few years ago, it was making me a little crazy trying to understand the structural geometry that gives rise to the major and minor grooves of DNA. I looked through several of the standard textbooks and relevant papers. I certainly didn't find any good diagrams or animations.

So out of my own frustration, I drew this. It's a cross-section of a single base pair, as if you are looking straight down the double helix.

Aka, picture a double-strand of DNA as an earthworm. If one of the earthworms segments is a base-pair, and you cut the earthworm in half, and turn it 90 degrees, and look into the body of the worm, you'd see this cross-sectional perspective.

Apologies for overly detailed explanation; it's for non-bio and non-chem people. :)

https://www.instagram.com/p/CWSH5qslm27/

Anyway, I think the way base pairs bond forces this major and minor grove structure observed in B-DNA.

dekhn 4 days ago||

It's not really just base pairs forcing groove structure. The repulsion of the highly charged phosphates, the specific chemical nature of the dihedral bonds making up the backbone and sugar/base bond, the propensity of the sugar to pucker, the pi-pi stacking of adjacent pairs, salt concentration, and water hydration all contribute.

My graduate thesis was basically simulating RNA and DNA duplexes in boxes of water for long periods of time (if you can call 10 nanoseconds "long") and RNA could get stuck for very long periods of time in the "wrong" (IE, not what we see in reality) conformation, due to phosphate/ 2' sugar hydroxyl interactions.

dnautics 4 days ago||

Jeffhwang is correct, and dekhn is thinking way too hard. If you have any asymmetric planar structure that stacks into a helix into the third dimension there will be a minor groove and a major groove.

solarwindy 4 days ago|||

For anyone wondering: https://www.mun.ca/biology/scarr/MGA2_02-07.html

AntiqueFig 4 days ago|||

Maybe they were depicting RNA? (probably not)

dekhn 4 days ago||

No; what they drew doesn't look like real DNA or (duplex double stranded) RNA. Both have differently sized/spaced grooves (see https://www.researchgate.net/profile/Matthew-Dunn-11/publica...).

At least they got the handedness right.

nh23423fefe 4 days ago|||

when a human does it, its style! when ai does it, you cry about your job.

jeffbee 5 days ago||

And yet still manages to be 4MB over the wire.

smokel 4 days ago||

That's only on high-resolution screens. On lower resolution screens it can go as low as 178,820 bytes. Amazing.

twothreeone 4 days ago||

Maybe "Release" requires a bit more context, as it clearly means different things to different people:

> AlphaGenome will be available for non-commercial use via an online API at http://deepmind.google.com/science/alphagenome

So, essentially the paper is a sales pitch for a new Google service.

i_am_not_groot 4 days ago||

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hyfgfh 4 days ago||

Cant await for people to use it for CRISPR an it hallucinate some weird mutation

mattigames 4 days ago|

I bet the internal pitch is that genome will help deliver better advertisement, like if you are at risk of colon cancer they sell you "colon supplements", its likely they will be able to infer a bit about your personality just with your genome, "these genes are correlated with liking dark humor, use them to promote our new movie"