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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

#51

Post by borissk »

ejstronge wrote: post #40
borissk wrote: post #37

Earlier quoted context omitted.

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.

> That is if we transfer the DNA to an advanced alien civilization - would they be able to make a human. You'd need a cell to start the process, with the various nucleic acids distributed correctly and proteins/energy with which to create further proteins using the information encoded by the DNA. Thus the civilization would need information about cells and a set of building blocks before being able to use the DNA.

The DNA contains all the code that creates and regulates the proteins.

Re: The complete sequence of a human Y chromosome

#53

Post by borissk »

dekhn wrote: post #47
borissk wrote: post #37

Earlier quoted context omitted.

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…

The code how to build a sperm and an egg is inside the human DNA, isn't it?

Re: The complete sequence of a human Y chromosome

#54

Post by dekhn »

alexchantavy wrote: post #43
dekhn wrote: post #38

Earlier quoted context omitted.

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?

Sure, although I'm not aware of anybody who is contemplating quite the level I believe is necessary to really nail the problem into the ground. When I worked at Google, I proposed that Google build a datacenter-sized sequencing center in Iowa or Nebraska near its data centers, buy thousands of sequencers, and run industrial-scale sequencing, push the data straight to the cloud over fat fiber, followed by machine learning, for health research. I don't think Google wants to get involved in the physical sequencing part but they did listen to my ideas and they have several teams working on applying ML to genomics as well as other health research problems, and my part of my job today (working at a biotech) is to manage the flows of petabytes of genomic data into the cloud and make it accessible to our machine learning engineers.

The really interesting approaches these days, IMHO, combine genomics and microscopic imaging of organoids, and many folks are trying to set up a "lab in the loop", in which large-scale experiments run autonomously by sophisticated ML systems could accelerate discovery. It's a fractally complex and challenging problem.

Statistics has been key to understanding genetics from the beginning (see Mendel, Fisher) and so at a big pharma you will see everything from Bayesian bootstrappers using R to deep learners using pytorch.

Re: The complete sequence of a human Y chromosome

#55

Post by sublinear »

dekhn wrote: post #30
10g1k wrote: post #5

For those who don't recall: Back in the Dark Ages, there was a race to decode the human genome. The leading competitiors (wealthiest) were Celera Genomics and the Human Genome Project. After some time, Celera (headed by Craig Venter), announced they had done the deed. However, what Celera had actually done was used what they called a "shotgun method", which meant they took small samples here and there, then built a m…

Yes, but the HGP didn't make a full sequence either, using their scaffold-based contig assembly. Both groups declared a truce and announced they were "finished with the first draft" 35 years ago: https://www.nytimes.com/1987/12/13/magazine/the-genome-proje... 33 years ago: https://www.nytimes.com/1990/06/05/science/great-15-year-pro... 29 years ago: the competition gets fierce https://www.nytimes.com/1994/02/22/scien…

> The primary author of the shotgun assembly was Gene Myers, who previously had written BLAST...

So... um... BLAST processing?

Re: The complete sequence of a human Y chromosome

#56

Post by dekhn »

borissk wrote: post #53
dekhn wrote: post #47

Earlier quoted context omitted.

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…

The code how to build a sperm and an egg is inside the human DNA, isn't it?

Yes, but it currently requires developmentally mature individuals to build the gametes, and the "code" is so complex you couldn't really decipher it from first principles.

Re: The complete sequence of a human Y chromosome

#57

Post by jghn »

dekhn wrote: post #30
10g1k wrote: post #5

For those who don't recall: Back in the Dark Ages, there was a race to decode the human genome. The leading competitiors (wealthiest) were Celera Genomics and the Human Genome Project. After some time, Celera (headed by Craig Venter), announced they had done the deed. However, what Celera had actually done was used what they called a "shotgun method", which meant they took small samples here and there, then built a m…

Yes, but the HGP didn't make a full sequence either, using their scaffold-based contig assembly. Both groups declared a truce and announced they were "finished with the first draft" 35 years ago: https://www.nytimes.com/1987/12/13/magazine/the-genome-proje... 33 years ago: https://www.nytimes.com/1990/06/05/science/great-15-year-pro... 29 years ago: the competition gets fierce https://www.nytimes.com/1994/02/22/scien…

Lets not forget how Perl Saved The Human Genome Project [1], which I remember seeing in a print magazine at the time.

As someone who is in the genomics world now as a software person, I find it amusing that I've gotten more into perl over the last year or so. It has its place, in the way that grep/sed/awk/etc does.

[1] https://news.ycombinator.com/item?id=30327812

Re: The complete sequence of a human Y chromosome

#58

Post by kortilla »

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.

It doesn’t matter, because “the media” doesn’t work as a concept. It’s a bunch of amateurs trained on nothing more than hiding the fact that they are not an expert.

How much of the reporting from the media revealed that Theranos was a fraud? Anything that wasn’t was fucking useless because it’s just a megaphone for corporate PR, despite what they think.

The entire concept of a weekly news is risible, let alone daily news. A fully investigated story actually worthy of the term journalism requires probably 2 employee years worth of actual work.

Look at how many articles the NYTimes publishes daily, multiply it by 700, and then compare that number with the actual number of journalists they have. It’s a complete farce.

Re: The complete sequence of a human Y chromosome

#59

Post by dekhn »

mikepurvis wrote: post #15
gorjusborg wrote: post #7

Earlier quoted context omitted.

I had the same question. Perhaps this will help you. https://en.m.wikipedia.org/wiki/DNA_sequencing

That page describes the human genome as having been sequenced back in 2003. *confusion intensifies*

the project started around 1990, they announced a draft completed in 2000, "completion" in 2003 (this was more a token announcement based on a threshold than a true milestone). Even then the scientists knew that major parts of the centromere, telomere, and highly repetitive regions were not fully resolved, and that was fully admitted. The work by Karen Miga at UCSC and others is more of a mop-up now that genome sequencing is a mature technology and we have much better ways at getting at those tricky regions.

another "completion" happened 3 years ago, before this announcement. but this is the last one. I promise.

Re: The complete sequence of a human Y chromosome

#60

Post by astrange »

khazhoux wrote: post #44
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.

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.

We don't know that it fully defines a human until we can create one without the starting condition of being inside another human. It's prototype-based inheritance.
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