
Hacking DNA: CRISPR, Ken Thompson, and the Gene Drive - craigcannon
https://blog.ycombinator.com/hacking-dna-the-story-of-crispr-ken-thompson-and-the-gene-drive/
======
jfarlow
Here is our software you can use to start building your own tools that use
Cas9 [1]. Build new Cas9s with new functions, peer into and mix and match
functions that already exist, and build payloads to be delivered by Cas9. We
help you program biological 'function' into DNA at an abstraction above the
DNA sequence itself, and get you the DNA that encodes your functional designs
delivered to your door.

[1] [https://serotiny.bio](https://serotiny.bio)

Some protein designs that undergird entire companies:

Cure hemophilia:
[https://serotiny.bio/notes/proteins/hbb/](https://serotiny.bio/notes/proteins/hbb/)

Vaccinate against HIV:
[https://serotiny.bio/notes/proteins/ecd4ig/](https://serotiny.bio/notes/proteins/ecd4ig/)

Cure the American Chestnut of its blight:
[https://serotiny.bio/notes/proteins/oxo/](https://serotiny.bio/notes/proteins/oxo/)

Make spider silk clothing:
[https://serotiny.bio/notes/proteins/adf3/](https://serotiny.bio/notes/proteins/adf3/)

~~~
zitterbewegung
Your website looks interesting enough to warrant its own post like a Show: HN.

~~~
jfarlow
I have tried a few times. But the community is small enough that it gets no
upvotes :) We just released it. It's built with Ember & Go. I'd be happy to
answer any questions about our technologies (biological or technical).

~~~
theptip
Passed this on to some biochem buddies and got the following response:

"There are plenty of constructs I'd love to have but don't have the time or
expertise to make them. However, could this tool make them? There's so much
expertise that goes into "if i hang this tag here, will the protein still
traffic to where it needs to go/will it interfere with other domains/will it
hang on the right side of the membrane/if I change literally one other amino
acid the new tag will work but not if I leave it normal." The experts can
already design proteins, but if this tool democratizes that, who's going to do
QC?

AFAIK the real way people make substantive changes to proteins is to make 10
variants, test them all, and iterate the designs that worked best. Feels like
we're miles away from being able to drag and drop functions."

And "In principle proteins are modular but I can give you ten examples where
that principle ruined someone's life. The QC is hard and is case-by-case."

What is your editor aiming to help with? Is QC still the rate-limiting factor
to innovating new protein designs with your tool? Does your tool help with QC
in any way?

Thanks for sharing, I'm always interested to see new tech in this area.

~~~
jfarlow
That is _exactly_ what we aim to do:

\- We keep track of how domains have been used before (so as to mitigate if
not entirely predict that QC). We are trying to encode that expertise in a way
that is intuitive and frictionlessly sharable. The more people use it the more
helpful it becomes. We help encode biological institutional knowledge.

\- We collaborate with DNA synthesizers so that you just do the designing, and
we help get you the designed DNA to your bench at a reasonable cost. You get
_exactly_ the sequence that you want, not what someone gave your neighboring
lab's buddy sometime ago, or what some restriction enzyme/quick-change let you
that's probably good enough. We alleviate the pain of cloning.

\- We help you build entire sets by dragging and dropping: "I want these three
fluorophores upstream, these 4 linkers on these proteins of interest" \- Boom!
Buy! Done! (in literally as much time). We make efficient high-throughput
design.

\- It is true, there are many proteins that are note entirely modular. But
there are many more than 10 examples of proteins designed _exactly_ that way
(see Addgene's database). Biology is hard. We help you prevent failure buy
being able to see how other successes have been achieved, prevent stupid
mistakes, and get you your material to you as quickly and cheaply as possible.
If your design does fail, it has failed faster and with less sunk cost than if
you had to do all the construction yourself.

\- Finally, because combinatorial design and purchasing is reasonably priced
(and you don't have to do the construction work), you can order an entire
logical set of proteins to actually figure out which would work and which
would not. When I cloned I made some tiny fraction of what I expected to work
purely because cloning was so painful - and if that small fraction failed I
didn't even bother to figure out why or what would have worked.

I'd appreciate any feedback you might have.

~~~
theptip
My friends didn't seem to be convinced by this response for their own areas of
inquiry, but I'm not really qualified to hold a discussion here; happy to try
to arrange a conversation if you're interested in going to the source. (PhDs
and postdocs FWIW).

~~~
jfarlow
Hard to hold a conversation on HN. If you ever see this comment - I'd love to
hear their skepticism :)

Email is my first name at my company's domain.

-justin

------
entee
Re. Gene drives, the article points out (and links to [1]) a major issue, but
doesn't quite give the full story on that issue. Resistance to gene drives
will arise, and isn't even that difficult to have happen.

Key point:

 _One source of this resistance is the CRISPR system itself, which uses an
enzyme to cut a specific DNA sequence and insert whatever genetic code a
researcher wants. Occasionally, however, cells sew the incision back together
after adding or deleting random DNA letters. This can result in a sequence
that the CRISPR gene-drive system no longer recognizes, halting the spread of
the modified code._

CRISPR/Cas9 is a nuclease, it cuts DNA. It does not stitch it back together,
the cell does that afterwards. Sometimes that goes smoothly, other times it
doesn't, but one thing that happens frequently when you cut DNA is mutation.
It's why radiation exposure is bad, DNA breaks cause mutations. If mutations
yield immunity, then something that depends on mutations NOT happening to keep
operating, but itself CAUSES mutation, is unlikely to function for very long.

[1] [http://www.nature.com/news/gene-drives-thwarted-by-
emergence...](http://www.nature.com/news/gene-drives-thwarted-by-emergence-of-
resistant-organisms-1.21397)

~~~
dnautics
As someone who has done lots of molecular biology (and also is a reasonably
good programmer) I took issue with the comparison of CRISPR to ken thompson's
Unix hack for this very reason (among others).

------
salimmadjd
CRISPR is a biological weapon!

Yes, this is something that is mostly not talked about. CRISPR is a virus
engineered to attack and penetrate human cells and modify its DNA. It can be
used for good. But at the same time the technology is becoming so easy
accessible that it can be used to create a virus capable of whipping out the
people. Or put a dormant gene in there that gradually kills people.

Up to 80% of people have Oral Herpes by some estimates. Imagine a virus like
that could be engineered and spread quietly that in 10-20 years cause a
worldwide cancer.

My point is, CRISPR can be used for nefarious activities. It's inevitable! So
we need to create an antidote for it to prevent unwanted viruses that might
one day be created by CRISPR.

~~~
Turing_Machine
What would be the advantage of killing people in 10-20 years versus killing
them right now?

I mean, smallpox has been synthesized, and it spreads _fast_ , has pretty high
mortality rate, and hardly anyone is vaccinated against it any more.

I can't think of any military (or even terrorist) reason why you'd want that
kind of delayed mortality, but maybe I'm overlooking something.

~~~
spitfire
For genocide.

~~~
Turing_Machine
Okay, still not seeing why you would rather they be dead 20 years from now
instead of right now.

~~~
mherdeg
What I learned from the video game "Pandemic 2" is that the longer your
disease remains undetected, the more widely it can spread; if you're
asymptomatic and apparently harmless, you may be able to infect every human
before you activate the bad side effects. (Which is the goal of that game.)

~~~
drivebyops
In other words, any sign of symptoms would cause Madagascar to remain the last
place inhibited by humans since they would close their ports/airports real
quick

~~~
tscs37
It's always Madagascar. Always.

------
reasonattlm
There are a small number of known advantageous mutations already present in a
small number of humans that could be introduced to larger numbers via CRISPR,
brought to the clinic as a somatic gene therapy for adults. This is an
enormous market in comparison to "merely" curing all genetic disease, as near
every adult human would be able to benefit.

Not much movement in getting that into the clinic yet, however, for reasons
that are entirely cultural. The first company to get one of these working via
medical tourism will make a lot of money. CRISPR makes that goal pretty easy
in comparison to the past.

These changes include things like extra follistatin or knocking out myostatin
to gain greater muscle growth and less fat tissue, or removing or disabling
ANGPTL4 to reduce heart attack risk by 50%. There are others along the same
lines and more are being discovered as sequencing becomes ever cheaper.

The comparative lack of effort to make enhancement gene therapies a reality is
nothing short of crazy, given the observed benefits in the few humans lucky
enough to already have these variants or loss of function mutations.

------
feelix
For anybody interested in performing CRISPR in their kitchen with $150 worth
of pre-packaged materials, I would encourage them to take a look at The ODIN.
It is a kit to get you started, and it comes with tutorials to take you all
the way from knowing nothing to being able perform CRISPR and understand what
you are doing.

(I have no affiliation with the product, I just like it): [http://www.the-
odin.com/diy-crispr-kit/](http://www.the-odin.com/diy-crispr-kit/)

------
dv_dt
Listening to the description of applying Gene Drive in the radiolab episode
sounds worrying as a layman. First order manipulation with CRISPR sounds
reasonable, but then contemplation of Gene Drive, the adding of the editing
mechanism itself into the genetic material of a mosquito in the wild seems
wildly irresponsible. Now you're running an experiment x millions (billions?)
of variations where if or when a virus breaches a given mosquitos cell
defenses, they could potentially pick up the crispr gene themselves and then
one could be a cross-species jump away from re-introducing that same cross-
editing gene into other species (including humans).

~~~
socmag
DARPA are doing a heck of a lot with CRISPR, and as you can imagine for both
defense and offence angles.

[https://www.scientificamerican.com/article/u-s-military-
prep...](https://www.scientificamerican.com/article/u-s-military-preps-for-
gene-drives-run-amok/)

This whole video is great btw, where Arati Prabhakar spins through CRISPR,
Gene Drive and a heck of a lot more in a presentation at UW.

[https://youtu.be/ZHipS0-1ykE?t=2812](https://youtu.be/ZHipS0-1ykE?t=2812)

~~~
dv_dt
We can barely evaluate the effects of genetic changes within a single living
organism - probably pretty well with focused pinpointed areas, but with the
overall single living organism we can probably evaluate very little. It seems
sheer folly to claim that any such system would be 'safe' exposed to a wide
range of external parameters of virus, bacteria, immune systems, regular
replication errors, irradiance or chemical mutagens, etc.. that we can barely
enumerate thoroughly, let alone assess the interactions.

~~~
socmag
Quite.

This road seems a much bigger existential risk than any AI holocaust scenario
I can imagine. It's very scary stuff and everyone in the field seems to be
brimming with glee at how easy it all is.

Just consider that the very mundane HeLa cell line alone managed to jump
continents and invade the most stringent safety precautions at dozens of labs.
At least they are pretty benign.

Now imagine a nice mosquito delivery vehicle with payload strapped on that
nobody has a real clue what it is capable of. I shudder to think.

A lot of people talking about how to re-establish the baseline and that it's
not a big deal and nobody should worry.

I get that there are very many wonderful things that can come from this as
well, but on the other hand the research is going very fast and this is one
area we _should_ be exercising _extreme_ caution.

------
jfarlow
I think a better analogy is that CRISPR (Cas9) is the cursor package within
the text editor. The (nearly completed) genomic text editor is the the entire
suite of biological technologies we have at our disposal. Copy/Cut/Paste have
been around a long time and made these discoveries possible. Rendering has
been around for quite a while. Keyboards have permitted larger buffers to be
written. But until recently a non-random, arbitrarily positionable cursor has
been missing. Cas9 is importantly, and just, that piece of the suite.

~~~
dnautics
this analogy breaks down: A non-random, arbitrarily positionable cursor is
available in pretty much all lower organisms. CRISPR, for example, is totally
useless for yeast (because the effort to get it to work far outweighs "just
add addressed DNA" which is basically "how it works" for yeast). CRISPR is
really only spectacularly useful for higher organisms and higher organism
derived cell lines. There may be a limit to that for genes where there's high
copy number (often a problem in plants).

Als; CRISPR can specifically induce a strand break (which is the FIRST step),
but it is not quantitative, nor does it do selection. Generally as a part of a
CRISPR protocol you have to counterselect for cells which have the DNA
integration in them.

There is quite literally no computer science analogy to this. This would be
like having editing a database that is sharded and replicated over multiple
servers, randomly integrating the change you want on some (probably small)
fraction of the servers, and then going through, scanning all database
replicates for the existence of the change, and physically destroying with a
hammer the servers that had shards that were unchanged, as the mechanism to
insure eventual consistency across your database.

------
abetusk
One of the successes of Unix was because of free and open source software. One
part of that in a biological setting is free/libre data. Efforts like the
Harvard Personal Genome Project [1], Open Humans [2] and OpenSNP [3] are
trying to provide researchers and the community as a whole with free/libre
data so that research isn't done in silos or walled gardens.

CRISPR is pretty exciting but we also need to make sure there's a rich commons
to build on. I encourage everyone to look into and support projects that make
free/libre genomic data more available.

[1]
[http://www.personalgenomes.org/harvard/about](http://www.personalgenomes.org/harvard/about)

[2] [https://www.openhumans.org/](https://www.openhumans.org/)

[3] [https://opensnp.org/](https://opensnp.org/)

------
rm445
For those wondering, the article makes an analogy between Thompson's 'Trusting
Trust' paper and gene editing.

It wouldn't have surprised me to hear that Thompson had moved into gene
hacking (at the age of 74) but I think he still works for Google.

~~~
mauricioc
The analogy helped me understand things a bit, but I have a question coming
from what I think is an oversimplification in the explanation of Thompson's
Trusting Trust concept.

In the Trusting Trust attack, not only you change the compiler to miscompile
the "login" program, but you change the compiler to miscompile the compiler
itself so the "login" miscompilation persists even if you later revert all
changes to the compiler source (as long as you use the new binary once, of
course). Does this part of the attack have a gene drive analogy?

~~~
jfarlow
That part of the analogy does persist. It is the feature. The gene drive
doesn't just insert the change you want - it inserts the change, and the code
to make the change:

Wild type mosquito DNA: =================

Desired change to DNA: =============XX==

DNA encoding Cas9 and XX-Payload: =C9(XX)=

Gene Drivered Mosquito (before activation) (change to compiler):
====C9(XX)=============

Gene Drivered Mosquito (after activation) (change to login code):
====C9(XX)========XX===

\------------------------------

A normal mosquito mating with a XX mutant mosquito:

Mother Gamete: -----------------

Father Gamete: -------------XX--

Mendelian fraction of children (and grandchildren) are either --, --/XX,, or
XX/XX (if two chromosomal copies)

A normal mosquito mating with a Gene Drivered mosquito:

Mother Gamete: -----------------

Father Gamete: ---C9(XX)----XX--

All children: ====C9(XX)========XX=== (for all 'N' chromosomal copies)

------
nickelman90
It's important to consider that genome editing tools existed prior to CRISPR
and a novel technology is only as valuable as what preceded it. Tools such as
zinc-finger nucleases, and TALENs were used and millions of dollars have been
invested in developing those technologies to address the same problems for
which CRISPR could be applied to. The author also posits that CRISPR could be
used to edit any organism, which sounds impressive until you start to break
down what that means. Take for instance that >99% of all micro-organisms
haven't been cultured, which means that it's a really hard to make them
genetically tractable. It's not like you just filter seawater, get some
microbes and mix some CRISPR-encoded DNA with them. You would have to know
their sequences a priori. And to sequence them, you would have to lyse the
cells, generate large amounts of it, sequence it, thus leading to a classic
chicken-egg problem.

I'd also like to mention that this technology can be imprecise/precise and due
to the combinatorics of the systems you have to design in order to create
edits, the ability to reliably edit different parts of the genome can be
difficult to predict. It's not perfect. Furthermore, DNA self-replicates,
mutates, and has external forces which dictate whether those changes actually
should persist in the environment. What if a gene-drive mutates thus rendering
it non-functional? The number of mutations that could render such a system to
be non-functional vastly outnumbers the number of gene drives you would need
to deal with said mutations. Although these types of mutations are unlikely,
I'd just like to emphasize that DNA is constantly evolving, unlike say, a
series of UNIX commands.

Also, spider-silk producing goats existed before CRISPR was used to create
spider-silk producing goats. [https://phys.org/news/2010-05-scientists-goats-
spider-silk.h...](https://phys.org/news/2010-05-scientists-goats-spider-
silk.html). And so did glow-in-the-dark cats:
[http://www.bbc.com/news/science-
environment-14882008](http://www.bbc.com/news/science-environment-14882008).
The only difference is that they didn't have to pay millions of dollars in
licensing fees to the Broad Institute.

I get that this sounds like I'm saying CRISPR sucks. It doesn't. It's a very
valuable technology, which has much to offer. I just want to readily identify
the ceiling of the hype.

------
mtalantikite
I recently went to see George Church and Siddhartha Mukherjee talk about
genetic manipulation at Pioneer Works here in Brooklyn. Of course CRISPR/cas-9
came up for part of the discussion, but one question I wanted to ask and
didn't get a chance to is: what is the error rate on the technique? I can't
imagine that it is zero, and every article I read about CRISPR/cas-9 seems to
leave that part out. Can anyone speak to that?

~~~
jfarlow
I don't think the 'technique' is settled enough to have an answer to your
question yet. There are a lot of different 'errors' that can happen, each of
which has entire sections of researchers working to ameliorate them.

The floor to error is that a wild-type Cas9 protein with a naively generated
guide RNA, and a payload DNA along with it, just dropped into a petri-dish of
cells correctly edits some single-digit percent of cells. That's the crudest
of experiments a grad student might do on their first try. And that it is that
robust (in a biological laboratory) is precisely why it is so powerful.
Single-digit percent activity on an unoptimized first try is actually pretty
amazing in the context of biology.

~~~
mtalantikite
Thanks, that's helpful to know. I'm actually thinking about within the context
of that edit of the cells. Is it a binary thing where either the cell is
edited or it isn't, or can we have an edit with some error rate in regards to
what actually was pasted in? The cutting seems highly specific, you need some
sort of homology between your guide RNA and the target sequence, right? It's
the pasting I'm mainly curious about.

All the pop science articles seem to make it out to be a flawless system, and
the engineer in me is highly skeptical of that narrative.

~~~
jfarlow
The cutting is _mostly_ specific (given you have a reasonable target sequence
- a pure 'GGGGGGGGGGGGGG' sequence is just chemically problematic anyway).

The cutting splits the DNA in half completely. It has to rejoin itself (by a
not-well understood mechanism termed 'NHEJ'). This rejoining of the DNA is the
kind of 'well it works (mostly, sometimes!)' part that is actively being
better understood. Cas9 really has no relevance to this part of the process -
unless it is used as a platform to attach DNA-repair machinery onto.

Like in all things biology, concentration and time matter. So if you leave
Cas9 on 24/7 at very high concentrations with nothing to do, it will go ahead
and cut all over the place. The goal is now to bring to bear everything else
we know about biological expression to put the Cas9 homing system in its
place, only when it should be in place. We already know pretty good mechanisms
to make sure Cas9 only turns on under certain conditions, at certain times, is
inhibited under other conditions, is otherwise made even more specific. Those
are engineering 'details' at this point. And by 'details' I mean you have a
huge academic and corporate effort underway currently figuring out how most
efficiently and most accurately control Cas9's function.

Common results with a naive wild-type Cas9 (which we have moved on from in a
lot of ways):

(no change): ====== --> ======

(unhealed breakage): ====== --> === & ===

(forwards insert): ====== --> ===(insert)===

(backwards insert): ====== --> ===(tresni)===

(tandem insert): ====== --> ===(insert)(insert)(...)===

(off-target insert): ====== --> =(insert)=====

(intermediate failure: ====== --> ===(insert) & === || ....

There are also very powerful uses for Cas9 that do not cleave DNA at all.
Sticking a gigantic 'BREAK()' command onto Cas9 (that cannot cut DNA) can be
very useful where the natural break command has been lost.

------
aerovistae
Here's something I don't understand about this, maybe someone can help explain
it. To implement a change in a person, you would have to modify the DNA in
every cell in their body, would you not? I understand how the change is made
to DNA with CRISPR, that's clear, but how can that change be propagated to
affect an entire individual? Even an embryo is multicellular, is it not?

~~~
sxv
If you were to modify the genome of a sperm cell and fertilize an egg cell
with it, then the resulting individual will have the modifications in all of
its cells.

------
joshma
Relatedly, if you're an engineer looking to build the software that powers
CRISPR[0], Benchling (YC S12) is hiring!

Most of the major research organizations working with CRISPR leverage
Benchling -- the Broad Institute, various labs at Berkeley, companies like
Editas, etc.

Shoot me an email: josh at benchling dot com

[0] [https://benchling.com/crispr](https://benchling.com/crispr)

------
splike
If anyone wants to play around with designing CRISPR guides, check out the
Desktop Genetics website[1]

I work in the R&D side of the company, but our front end team has built a
really nice website to design CRISPR gene knock-out/knock-in experiments from
start to finish. Its all free to use until the final checkout where you order
your CRISPR guides.

[1][https://www.deskgen.com/](https://www.deskgen.com/)

------
vertis
Slightly off topic, but where does a layman start learning the fundamentals of
DNA and proteins, etc?

It seems to be such a huge body of knowledge and the field seems to be moving
so quickly.

------
joshbaptiste
_sigh_ for the life of me I never remember the expanded acronym of CRISPR off
the top of my head.

------
tridint
Listening to CS people talk about biology is maddening.

"CRISPR... is to genomics what vi (Unix’s visual text editor) is to software.
"

This terrible comparison between DNA and code has been happening for years. In
2012, Thiel did the same thing in CS 183. We get to look back and see that he
was wrong, but we'll have to wait a while before the 'DNA is code' group will
admit this essay is bad. At least its not a TED talk and at least its better
than Aubrey De Grey.

"Each VC on the panel made 2 predictions about technology in the next 5 years.
The audience voted on whether they agreed with each prediction. One of my
predictions was that biology would become an information science." -PT

~~~
jfarlow
So help educate. There is clearly an interest. If you know the bio then you
know it gets a fraction of the funding and attention of standard tech stuff.
Help smooth the analogies out, correct timelines, and otherwise inform outside
industries about the powerful things biology _is_ doing.

------
rasengan0
My microbiome is laughing its ass off. Stupid humans.

------
aetherspawn
This is how bio-bloat ware starts.

