
Metagenomic Analysis of a Blood Stain from French Revolutionary Jean-Paul Marat - Hooke
https://www.biorxiv.org/content/10.1101/825034v1
======
mnemonicsloth
Metagenomics is the biological equivalent of suddenly being able to see dark
matter.

Normally, if you want to analyze a microbe, you do it by culturing the
organism in Petri dishes. By varying the growth medium you can find out a lot
about your organism: what it eats, if it breathes, how it metabolizes various
things. The problem is that only 5-10% of bacteria grow on plates.
Microbiologists call this the "plate count anomaly" and what it means is this:
your sample in a microscope could be teeming with life, but if you plate it
you'll probably get this homogeneous little sample of not very many organisms.
The rest are called "microbial dark matter."

With metagenomics, we could see them all. It made people a little funny in the
head. You might remember that "The Microbiome" was a big idea in the media for
a while. It got pretty flattering treatment, considering what it is: a mass of
mostly proto-shit floating around inside your colon. But the enthusiasm wasn't
too far misplaced, because a major area of biology is growing by leaps and
bounds now.

If you are a computer programmer considering a career change you should really
take a day off to look into the new genetic technologies on offer. Performance
is doubling every year [1]. The world is changing. And computing is at the
center of it, both practically (all that research generates a lot of data) and
conceptually (because gene expression is information processing). So give it a
look.

[1] Remember that?
[https://en.wikipedia.org/wiki/Moore%27s_law](https://en.wikipedia.org/wiki/Moore%27s_law)

~~~
rovyko
>If you are a computer programmer considering a career change you should
really take a day off to look into the new genetic technologies on offer.

What resources would you recommend, and do you have any advice for someone who
is just starting their career?

~~~
mnemonicsloth
It depends on how big a commitment you want to make. I quit my job to go study
biology and it worked out pretty well for me. Programming opens doors for you
because the majority of biology grad students can't do it. You get good work
and an accelerated path through classes, TAships, research and other
university business. If you want to work in IT, the experience you get is
perfect for applying for prestige places like Google, Facebook or Amazon.
Mostly I've spent the last year writing pattern matchers to extract subtle
patterns from huge data files.

If you're not ready for a big commitment (and even if you are), I'd recommend
taking some classes too get a feel for the subject. Khan Academy has two (or
you can google around for more) that look pretty good. The just-plain-Biology
one covers a surprising amount of useful information. The one on Genetics is
useful too, although you might want to skip past some of the stuff about
cross-breeding animals and whatnot.

Another thing you can look at is Synthetic Biology, which is biology plus
design, biology for hackers. Synbio says biology has been too interested in
describing and cataloguing, and not interested enough in building. So even
though what we can do is pathetically simple next to the evolutionary process
that designs new organisms, we can still do little things like making human
beings immune to all viruses and designing cyanobacteria that produce crude
oil from air, water and sunlight. If you're interested in Synbio you should
check out the iGEM competition, which is a major event and an organizing site
for useful information.

If you don't feel like crawling around the iGEM database of standardized
biological parts (it's like the library docs for Life) you could look at these
videos instead: [https://www.ibiology.org/playlists/synthetic-
biology/](https://www.ibiology.org/playlists/synthetic-biology/)

Email's in my profile. Don't be a stranger if you have questions.

~~~
hobofan
Though I'm still very early into it, I can highly recommend starting a
biochemistry degree, if you already have a programming/computer science
background. Bioinformatics would be the direct route to that field, but in a
bioinformatics degree, there is usually still not much of a focus on the low-
level biochemical mechanisms and biochemical methods that form the basis for
all the data you will be working with. Biggest downside though is a lot of
lab-time, which for me personally is hard as I'm still freelancing on the
side.

I'm only in the middle of my second semester and through taking a few
biochemistry classes in advance and reading though the papers of our
universities research groups it's already starting to come together a bit.
Things start to click and I'm getting pretty far in trying to understand and
reproducing some SOTA papers in weekend projects. For such a short amount of
time of studying the subject, I think that's a pretty good payoff.

------
kbenson
> The advent of second-generation sequencing technologies allows for the
> retrieval of ancient genomes from long-dead people and, using non-human
> sequencing reads, of the pathogens that infected them.

This is pretty cool. I'm not sure what state of the art is in DNA sequencing,
but it sounds like this is impressive. The abstract mentions that it's the
oldest DNA sequencing sourced the celluloid (a newspaper in this case), but I
don't know if there are successes from other sources that are older.

~~~
mnemonicsloth
Second generation sequencing is fast and in wide use. Third generation
sequencing is the new hotness

[https://en.wikipedia.org/wiki/Third-
generation_sequencing](https://en.wikipedia.org/wiki/Third-
generation_sequencing)

