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The complete sequence of a human Y chromosome

nature.com

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Re: The complete sequence of a human Y chromosome

#41

Post by dekhn »

cvoss wrote: post #33
khazhoux wrote: post #20

Earlier quoted context omitted.

It's just about 3 gigabytes (each byte a letter). Pretty mind-blowing, if you ask me.

It's a slight exaggeration of the information content to report the data size using an ASCII encoding. Since there are 4 bases, each can be encoded using 2 bits, rather than 8. So we're really talking 750 megabytes. But still mind-blowing.

And since the data is highly redundant the 750MB can be compressed down even further using standard approaches (DEFLATE works well, it uses both huffman coding and dictionary backreferences).

Or, you could build an embedding with far fewer parameters that could explain the vast majority of phenotypic differences. the genome is a hierarchical palimpsest of low entropy.

My standard interview question- because I hate leetcode- walks the interviewee through compressing DNA using bit encoding, then using that to implement a rolling hash to do fast frequency counting. Some folks get stuck at "how many bits in a byte", others at "if you have 4 symbols, how many bits are required to encode a symbol?", and other candidates jump straight to bloom filters and other probabilistic approaches (https://github.com/bcgsc/ntHash and https://github.com/dib-lab/khmer are good places to start if you are interested).

Re: The complete sequence of a human Y chromosome

#42

Post by dekhn »

UI_at_80x24 wrote: post #8

For a very entertaining and educational book that tangentially related; I can highly recommend: Y - The Descent of Man by Steve Jones [0] I am thrilled to see more chromosomes being mapped/sequenced. Please excuse my high-school level of biology knowledge here, but have we definitively progressed beyond correlation when it comes to genes, gene expression, and how they all interact? Take "Blue eyes" as an example, we…

Eye color is subtle. How do you define blue eyes? It's not just one phenotype; there are a range of blue eyes, whose differences correspond to fairly subtle variations between people. The article you linked [1], is quite good but requires quite some time to absorb completely.

Re: The complete sequence of a human Y chromosome

#43

Post by alexchantavy »

dekhn wrote: post #38
chihuahua wrote: post #9

Earlier quoted context omitted.

I've never understood this either. I assume the genome is many megabytes of [ATCG]+. If we have that sequence, what does it tell us? Do we look at it and say "Ah, yes, ...ATGCTACGACTACGACTAGCG... very interesting?"

If you think like an ML engineer, the genome is a feature vector 3B bases (or 6B binary bits) long that is highly redundant (many sections contain repeats and other regions that are correlated to other regions), and the mapping between that feature vector and an individual's specific properties (their "phenotype", which could be their height at full maturity, or their eye color, or hair properties, or propensity to d…

Fascinating, are there lots of people looking at genetics with this ML kind of lens?

Re: The complete sequence of a human Y chromosome

#44

Post by khazhoux »

cvoss wrote: post #33
khazhoux wrote: post #20

Earlier quoted context omitted.

It's just about 3 gigabytes (each byte a letter). Pretty mind-blowing, if you ask me.

It's a slight exaggeration of the information content to report the data size using an ASCII encoding. Since there are 4 bases, each can be encoded using 2 bits, rather than 8. So we're really talking 750 megabytes. But still mind-blowing.

Yes, and if you gzip it it's even smaller. But the big takeaway is that the amount of info that fully defines a human, is what we consider "not much data," even in its plainest encoding.

Re: The complete sequence of a human Y chromosome

#45

Post by senkora »

borissk wrote: post #37
cvoss wrote: post #33

Earlier quoted context omitted.

It's a slight exaggeration of the information content to report the data size using an ASCII encoding. Since there are 4 bases, each can be encoded using 2 bits, rather than 8. So we're really talking 750 megabytes. But still mind-blowing.

I'm curious if these 750MB + the DNA of mitochondria + the protein metagenomics contain all the information needed to build a human, or if there's extra info stored in the machinery of the first cell. That is if we transfer the DNA to an advanced alien civilization - would they be able to make a human.

I can’t wait until we can bootstrap a human from a stage 3 tarball.

Re: The complete sequence of a human Y chromosome

#46

Post by johnnyanmac »

kaliqt wrote: post #29
tomrod wrote: post #27

Earlier quoted context omitted.

I'm sorry, are you saying the media, whose job it is to report and not serve as experts, are useless ignorants, or Celera, which lied to the public, are useless idiots? If the first, time to let that dead dog lie. It's a tired trope.

Not a tired trope because that dog isn't dead. Until the media either 1. has no influence or 2. stops being dishonest then it needs to constantly be called out and berated.

I think Hanlon's razor applies here. ignorance is not dishonesty.

Re: The complete sequence of a human Y chromosome

#47

Post by dekhn »

borissk wrote: post #37
cvoss wrote: post #33

Earlier quoted context omitted.

It's a slight exaggeration of the information content to report the data size using an ASCII encoding. Since there are 4 bases, each can be encoded using 2 bits, rather than 8. So we're really talking 750 megabytes. But still mind-blowing.

I'm curious if these 750MB + the DNA of mitochondria + the protein metagenomics contain all the information needed to build a human, or if there's extra info stored in the machinery of the first cell. That is if we transfer the DNA to an advanced alien civilization - would they be able to make a human.

This is a complex question. The cocktail soup in a gamete (sperm or egg) and the resulting zygote contains an awful lot of stuff that would be extremely hard to replace. I could imagine that if the receiving civilization was sufficiently advanced and had a model of what those cells contained (beyond the genomic information) they could build some sort of artificial cell that could bootstrap the genome to the point of being able to start the development process. it would be quite an accomplishment.

If they just received the DNA without some information about the zygote, I don't think it would be practical for even advanced alien civilization (LR5 or LR6) but probably an LR7 and definitely an LR8 could.

Re: The complete sequence of a human Y chromosome

#48

Post by [deleted] »

khazhoux wrote: post #20
chihuahua wrote: post #9

Earlier quoted context omitted.

I've never understood this either. I assume the genome is many megabytes of [ATCG]+. If we have that sequence, what does it tell us? Do we look at it and say "Ah, yes, ...ATGCTACGACTACGACTAGCG... very interesting?"

It's just about 3 gigabytes (each byte a letter). Pretty mind-blowing, if you ask me.

[deleted]

Re: The complete sequence of a human Y chromosome

#49

Post by AnthonyMouse »

lemmsjid wrote: post #39
kaliqt wrote: post #29

Earlier quoted context omitted.

Not a tired trope because that dog isn't dead. Until the media either 1. has no influence or 2. stops being dishonest then it needs to constantly be called out and berated.

What if it is apparent that there are other groups pushing the narrative that the media is untrustworthy so that they themselves can own the narrative? Any given group of humans will have a mixture of deceptive and trustworthy participants. Singling one group out for constant castigation, held against an impossible standard, makes it easier for dishonest members of other groups to avoid the spotlight.

"The media" isn't a uniform entity, but when people refer to it in this context they typically mean the large consolidated media corporations that own major print and television outlets. And those entities have essentially eroded their own credibility to the point that trusting anything they say is foolish. If they say the sky is blue, go out and check.

They could do better, but until they do, it makes sense to castigate them when they err, because avoiding that reputational harm is their incentive to do better. Or, if they fail to do better, the thing that should ultimately kill them so they can be replaced with something that can do better.

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