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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

#141

Post by hk__2 »

lopis wrote: post #120
jshorty wrote: post #6

Could someone explain exactly what it means to be "completely sequence" the human genome when all humans have distinct genetic makeup (ie, different sequences of nucleobases in their DNA/RNA)?

While you are correct, the differences between different people's DNA is tiny, less 1% at best. So this information is still very valuable. This article is talking about the first time in finishing sequencing one person's Y chromosome's DNA.

> While you are correct, the differences between different people's DNA is tiny, less 1% at best

How do we know this, if we have only sequenced the chromosome of one individual?

Re: The complete sequence of a human Y chromosome

#142

Post by scandum »

yellowcake0 wrote: post #24
bonestamp2 wrote: post #10

Earlier quoted context omitted.

As others have asked in this thread, what does "fully sequenced" mean to the layman?

It looks like from the preprint that they sequenced the Y chromosome of HG002, which was one of the original 1000 genomes samples from way back in the day, still held in deep freeze at a number of biobanks. Short-read sequencing data is a notoriously bad datatype for reconstructing the low-complexity / repetitive regions of genomes, so up until recently the most commonly used reference genomes have left many of these…

Isn't the problem the absence of random DNA?

I wouldn't call random data 'complex', but it is easy to sequence when assembling short reads.

Re: The complete sequence of a human Y chromosome

#143

Post by astrange »

hotnfresh wrote: post #87
astrange wrote: post #60

Earlier quoted context omitted.

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.

Some of the research about being able to make simple animals grow structures from other animals in their evolutionary “tree” by changing chemical signaling—among other wild things like finding that memories may be stored outside the brain, at least in some animals—makes me think you need more than just the “code” to get the animal that would have been produced if that “code” were in its full context (of a reproductiv…

My favorite trivia here is that flamingos aren't actually "genetically" pink but "environmentally" pink because they pick up the color from eating algae.

Except of course "genetics" and "environment" aren't actually separate things; sure, people's skin color isn't usually affected by their food, but only because most people don't eat colloidal silver.

https://en.wikipedia.org/wiki/Paul_Karason

Re: The complete sequence of a human Y chromosome

#144

Post by dotancohen »

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
No conflict of interest there!

Re: The complete sequence of a human Y chromosome

#145

Post by spookie »

Earw0rm wrote: post #111
dclowd9901 wrote: post #85

Earlier quoted context omitted.

But you can only know that by having a large sample of very “stable” (have few genetic irregularities) gene samples compared to a large pool of samples from people with very narrow and pronounced gene irregularities, right? Is this why it’s so hard? This feels more like a healthcare records keeping people and less like an “actually reading the data problem”. I can’t help but feel like some form of single payer health…

Single payer healthcare here (UK) is still subject to privacy controls in a way which would make it very difficult to do that. (Also our health system's IT is a hellscape, but one reason for that is that people would literally rather not have a working system at all, than one with less than impeccable privacy controls. Personally I'd gladly sacrifice a fair bit of medical privacy in return for giving scientists great…

I trust the scientists, the problem isn't them. Look at the whole abortion data scandal in the U.S.

Re: The complete sequence of a human Y chromosome

#146

Post by lopis »

hk__2 wrote: post #141
lopis wrote: post #120

Earlier quoted context omitted.

While you are correct, the differences between different people's DNA is tiny, less 1% at best. So this information is still very valuable. This article is talking about the first time in finishing sequencing one person's Y chromosome's DNA.

> While you are correct, the differences between different people's DNA is tiny, less 1% at best How do we know this, if we have only sequenced the chromosome of one individual?

We have sequenced the genome using different sampling and statistical models for a long time.

Re: The complete sequence of a human Y chromosome

#148

Post by kovacs_x »

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.

it's bit like- if i have source code of Linux (think DNA), can I build a machine running Linux? (think cell). no- you cant, you need to have machine that can run the code.

ie. "software" without "machine" to run it on, is kind of a useless.

Re: The complete sequence of a human Y chromosome

#149

Post by wizofaus »

borissk wrote: post #131
pmoriarty wrote: post #122

Earlier quoted context omitted.

"if we transfer the DNA to an advanced alien civilization - would they be able to make a human." I'm really surprised that in all these responses to your question no one's mentioned the womb or the mother, who (at least with current technology) is still necessary for making a human. That's not to mention the necessity of the egg. We're not just DNA.

Instructions on how to make a womb and an "egg" are contained within the human DNA.

But maybe you needed a pre-human womb to bootstrap the first human, and we no longer have the blueprint for that...

Re: The complete sequence of a human Y chromosome

#150

Post by ekianjo »

lemmsjid wrote: post #90
AnthonyMouse wrote: post #49

Earlier quoted context omitted.

"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 cast…

The larger news outlets are some of the few remaining places that actually hold their news rooms to some kind of factual standard and facsimile of objective reality. If NYT or the Economist or the BBC tells me the sky is blue, I'm pretty sure it is. If they report on some scientific topic the reporter is not an expert on, I understand that there's probably some signal lost. If they publish something on a contested po…

> If NYT or the Economist or the BBC tells me the sky is blue

Since these journalists are spending their time on Twitter and never put a foot outside on the real world, no, I dont trust anything they say.

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