
Breakthrough DNA Editor Borne of Bacteria - mr_tyzic
https://www.quantamagazine.org/20150206-crispr-dna-editor-bacteria
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ivanca
TL;DR: Some bacteria use their DNA as a database of bad viruses for
identification purposes. This way of editing DNA has been replicated
artificially and it's called CRISPR. Awesome.

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o_____________o
CRISPR is the type of DNA sequence.

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therzathegza
Nature is full of interesting goodies. My favorite is the discovery taq
polymerase from thermophile bacteria that lives on thermal vents at the bottom
of the ocean.

[http://en.m.wikipedia.org/wiki/Polymerase_chain_reaction](http://en.m.wikipedia.org/wiki/Polymerase_chain_reaction)

Another form of code reuse!

I also wonder what amazing things we could find in rare/niche ecosystems
giving that in such a short time we've seen things like this and rapamycin.

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ismail
Interestingly, someone else holds a patent for this.

[http://www.technologyreview.com/featuredstory/532796/who-
own...](http://www.technologyreview.com/featuredstory/532796/who-owns-the-
biggest-biotech-discovery-of-the-century/)

~~~
daughart
It's not yet clear who will ultimately own this IP, of Doudna, Zhang, Church
(in the US, the European patents have other contenders). Last I heard, Doudna
and Zhang were set to have dueling lab notebooks. I wouldn't underestimate
Church's position either given his record of visionary patents (e.g. Nanopore
sequencing). Disclaimer I work in the Church lab.

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etimberg
Maybe you can enlighten me, but how can any of this be patented in the first
place?

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o_____________o
Because the patent system is outdated. But the supreme court ruled that
"synthetic" or "complementary" DNA is eligible for patent protection.

Basically, it's not the discovery of mechanisms, but the unnatural
manipulation of them that is patentable.

But some of the rush to the patent office is because it places the onus on
challengers; the actual patent takes years to clear, even without
complications.

~~~
etimberg
I agree that the patent system is broken. I'm wondering what exactly about the
manipulation is patentable given that the manipulations could happen randomly
in nature. I was hoping daughart could provide his arguments as someone who
works in one of the labs.

~~~
refurb
I don't see why this is any different than the patenting of chemicals. Lots of
chemicals exist in nature, but if you make something "new" why shouldn't that
be protected?

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vanderZwan
This is going a bit off-topic, but the more I read about these new insights
into the workings of single-celled life, the more I get the feeling that on
the cellular level, we multicellular organisms are like nations. The more
sophisticated ones, like us, being like an ethnically homogeneous and very
xenophobic society in a totalitarian state with closed borders). Meanwhile,
the single-celled ecologies out there function like some kind of anarchic
jungle society were everyone is self-reliant.

It kind of makes me wonder what the future of human society holds.

~~~
gus_massa
We are not a "ethnically homogeneous" society, we are a "clone" society.

In an "ethnically homogeneous" society there are small differences, and it's a
good idea for the genes of the small differences to try to get more offspring.

In a "clone" society, there are no differences (or they are extremely small),
so it doesn't matter who has the offspring, because it's equivalent. So it's
easy to get cooperation.

An interesting cases are the hymenopter (ants, bees, ...) because they have a
different system to select sex. For a female is better to have a sister than
have a daughter, so the better strategy is to help your mother, then it's a
good idea to form a hive.

~~~
tomp
I'd say we're more alike to the Brave New World society - the cells might be
created identical, but because of different environmental influences, they
develop different functions.

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toufka
And the cells are commanded to do their birth-given duty. Any cells that
choose to act otherwise, or take part in any activity they were not given
access to, including unlawfully reproduce, shall be sentenced to suicide. And
if not committed in a timely manner, shall be killed.

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davidw
> Barrangou and his colleagues found that the bacteria had stuffed DNA
> fragments from the two viruses into their spacer

Sounds almost Lamarckian, doesn't it?

~~~
klmr
In a way, _all_ mutations in single-celled organisms that are inherited by
daughter cells are acquired during the mother’s life-time, so they’d all meet
some definition of Lamarckism. CRISPR isn’t that special in this regard.

Many evolutionary biologists also prefer not to call this Lamarckism – not
because it would be entirely wrong, but because it is misleading to many lay
people, who imagine that this would somehow be in conflict with Darwinian
evolutionary theory of evolution by natural selection (it’s a hobby of many
creationists to search for press releases mentioning Lamarckism to crow “ha!
Darwin is refuted again!”). This choice isn’t a problem in practice because
Lamarckism – unlike neo-Darwinism – doesn’t offer explanatory models which are
essential to understand and reason about these processes.

~~~
davidw
> Many evolutionary biologists also prefer not to call this Lamarckism

Maybe that's why I got downvoted for - as it turns out - writing the exact
thing the scientist said.

It was just something that popped into my head.

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klmr
Yeah, don’t understand the downvotes. It’s an interesting question, and the
whole subject of Lamarckism is far from trivially obsolete. Richard Dawkins’
_The Blind Watchmaker_ contains a coherent and convincing argument why
Lamarckism is actually _wrong_ as an evolutionary explanation (in a nutshell,
Lamarckism fundamentally cannot explain increase in complexity, as Darwinian
evolution can, and it additionally doesn’t explain _how_ adaptations of
complex traits could possibly be acquired from scratch) – and this is a
fundamental, epistemological objection which no amount of evidence could
overturn. But few people refer to this reasoning when claiming that Lamarckism
is “wrong”.

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im2w1l
What about this: sequence a tumour, find a distinguishing part of its genome.
Make a virus that search and replaces that with self destructing genes. Inject
into tumour.

~~~
refurb
A big challenge is that cancer cell genomes are not well conserved. A study
was done a while back to look at 1000 breast cancer patients. Mutations were
rampant with only a few percentage actually sharing common mutations.

~~~
tankerdude
Perhaps the point really isn't about having an effective cure for all cancer
patients, but just this one.

One of these days, we can detect the cancer cell, and the specific mutation
for that person. The detection would take a day or less, and then prime your
immune system to recognize and attack it.

So therapies and cures and not like a flu shot, like a jigsaw puzzle, where
the last piece for the cure is different for every person (or a few people).

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Htsthbjig
This is something that some people has suspected in the field for a long time.
I had terrible discussions as we made some software in the field and met
people there.

The pure Darwinism evolution dogma has extended a lot because it was an easy
answer, like the world being created in 6 days. But it was incomplete in lots
of ways.

For example, considering all DNA we did not understand as "junk" DNA was
incredible arrogant, when it seems like it is in fact software or other kinds
of data.

You have comments on me on hacker news talking about that like 5 years ago or
something.

Great job what those researchers have done.

~~~
jjoonathan
> considering all DNA we did not understand as "junk" DNA was incredible
> arrogant

I never heard an actual biologist take that view, only popsci talking heads.

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hga
I seem to remember getting the impression that many "actual biologists" did
refer to it and often think of it as "junk" DNA in the '80s. But that's just
an impression since I never bought into the concept it was "junk" and to the
extent I paid attention, it was to those trying to find why it was there and
what it did.

~~~
refurb
I agree. Back in the '80s scientists claimed that a large proportion of DNA
didn't encode for anything (introns) and therefore was "junk".

Now our understanding is that although DNA might not encode for anything, it
still plays a role in DNA expression.

