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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

#91

Post by asielen »

panosfilianos wrote: post #72
dekhn wrote: post #54

Earlier quoted context omitted.

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 lear…

I have spent the better part of the past year looking obsessively over genomics papers for cancer and I've grown very fond of the field. Are there any positions at Google/ companies you wold suggest me to look into? I'm coming from algortrading/ ML research with ML MSc.

You could try Calico. They are an Alphabet company that specifically studies aging. There how a good amount of machine learning roles. However biotech typically pays less than finance or software.

https://calicolabs.com/careers/

Re: The complete sequence of a human Y chromosome

#93

Post by ryandv »

dekhn wrote: post #63
jghn wrote: post #57

Earlier quoted context omitted.

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

Lincoln Stein is great, and perl was certainly critical to many processes, but it was and remains fairly niche in genomics, which used much more C++, Java, and later Python. IMHO the person who "saved the genome project" was WJ Kent, who developed the assembler, BLAT, that the public project needed. I strive to point out that he wasn't a sole hero, nor was Lincoln. What I really like about BLAT is that while Celera w…

I had the privilege of working a co-op term at Stein's lab at the OICR. I encountered quite a bit of Perl during my short time there, and have yet to see it elsewhere in the modern enterprise tech world. BioPerl in particular stands out as a fairly substantial project in the bioinformatics space.

Re: The complete sequence of a human Y chromosome

#94

Post by lemmsjid »

kortilla wrote: post #58
lemmsjid wrote: post #39

Earlier quoted context omitted.

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…

Aren't we all a bunch of amateurs hiding our lack of true expertise? Each passing decade I feel that all the more. I think you've described the human condition.

Re: The complete sequence of a human Y chromosome

#95

Post by dramebaaz »

mrazomor wrote: post #35

This is exciting! BTW. if you want to know the applications of this work, have a look at this ACM SIGPLAN Keynote: https://youtu.be/JTU3JYp3JYc?si=jOZz611ATQar3Gec (helped me understand DNA more than all biology classes at my high school)

Thanks for that ACM SIGPLAN talk link, it was very fascinating and engaging.

Re: The complete sequence of a human Y chromosome

#96

Post by singularity2001 »

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.

Our DNA does not contain the mitochondria nor the gut bacteria so the raw data would most certainly not be enough to build a working copy

Re: The complete sequence of a human Y chromosome

#97

Post by klyrs »

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?

Given code written for unknown hardware... can you execute it?

Re: The complete sequence of a human Y chromosome

#98

Post by quickthrower2 »

gandalfgreybeer wrote: post #78
coldtea wrote: post #77

Is this like: "we have a working keyboard driver" or more like "we identified all 104 keys on a standard 104-key US QWERTY layout"?

Not answering your question, but I have to say, this is one of the best analogies I've encountered in a while.

The keyboard driver means knowing what effect every key has?

Re: The complete sequence of a human Y chromosome

#99

Post by kibibyte »

penteract wrote: post #65
borissk wrote: post #51

Earlier quoted context omitted.

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

Including code for the proteins that read DNA to produce proteins. You might hit similar problems trying to understand C given the source code for a C compiler - a non-standard environment could reproduce itself given the source code, meaning the code alone doesn't strictly determine the output.

I'll torture this DNA and C source code analogy a bit.

Epigenetics is missing in this discussion about reproducing a human from just the DNA. These are superficial modifications (e.g. methylation, histone modification, repressor factors) to a strand of DNA that can drastically alter how specific regions get expressed into proteins. These mechanisms essentially work by either hiding or unhiding DNA from RNA polymerases and other parts of the transcription complex. These mechanisms can change throughout your lifetime because of environmental factors and can be inherited.

So it's like reading C source code, except there so many of these inscrutable C preprocessor directives strewn all throughout. You won't get a successful compilation by turning on or off all the directives. Instead, you need to get this similarly inscrutable configuration blob that tells you how to set each directive.

I guess in a way, it's like the weights for an ML model. It just works, you can't explain why it works, and changing this weight here produces a program that crashes prematurely, and changing a weight there produces a program with allergic reactions to everything.

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