
A programming language for living cells - ctoth
http://phys.org/news/2016-03-language-cells.html
======
justsaysmthng
> "You could be a student in high school and go onto the Web-based server and
> type out the program you want, and it spits back the DNA sequence."

Woah, hold your horses right there.

One of the first things I did when I learned to program in high school was to
write a virus.

So I'd think twice before making a "Web-based server" which spits out DNA and
letting everyone use it.

It's not just about high schoolers or terrorists.

"The only way to solve the issues that the world is facing is for the
population to drop by 60%".

These were the words of a successful tech entrepreneur, who's lived in a dozen
countries, fairly young, open minded and intelligent who I had dinner with a
couple of days ago.

And I see his point - the overpopulation issue is real - but I'm scared that
this idea is taking roots in our minds, even in the minds of people who should
know better.

This was spoken in the context of a discussion about war, but why do war, when
one person can design an organism that wipes out 60% of humans ?

Our consciousness is not evolved enough to handle the ability of designing
random organisms and viruses.

I've voiced this opinion before, but the community seemed to not agree with it
much. But I'm still standing by it - be very careful with this tech.

In fact, I think this shouldn't be allowed to get out of the lab. Not yet.

~~~
jamessb
Design tool like Cello produces a string of characters representing the
sequence of a DNA molecule, not a physical molecule of DNA. To actually do
something with this in the real world, you would need to place an order with a
DNA Synthesis company (assuming you don't own a DNA synthesizer yourself).
Fortunately, these companies screen sequences for things like genes encoding
toxins, and work with law enforcement agencies. See for example Marcus Graf's
talk at SB6.0: [http://sb6.biobricks.org/session/day-2/assessing-risk-
managi...](http://sb6.biobricks.org/session/day-2/assessing-risk-managing-
biocontainment/)

Also, the capabilities of this tool are rather limited. It is not clear to me
how being able to design a small combinatorial logic circuit would directly
help a potential bioterrorist.

~~~
adrianN
I'd guess this type of screening only works because we're currently very bad
at programming cells. Checking whether a DNA sequence is malicious can't be
simpler than checking that a computer program is malicious. And we all know
how well that works.

~~~
dnautics
It's arguably easier to check for malicious DNA than malicious computer
programs. The motifs for pathogens are pretty common. It's also highly
unlikely that someone will create something totally novel, and the experiments
required to test malicious properties of a bioagent would be somewhat
detectable.

------
Terr_
> "The damn program should just work."

> "Cytoplasm isn't exactly a eutactic environment. Certain operations just
> fail."

\-- Deus Ex (2000)

~~~
justifier
but the organic molecules that make up the organic compounds that make up that
cytoplasm sure are

i would suppose one could extrapolate then that the cytoplasm must be too

just significantly more multidimensional

i'd also add it is my intended inference that you can also go the other
direction, and say the elements and atoms and on that make up those organic
molecules are as well

------
100ideas
Sci-hub: [https://sci-hub.io/download/c7c5/nielsen2016.pdf](https://sci-
hub.io/download/c7c5/nielsen2016.pdf)

~~~
dnautics
The drift from predicted in three component systems is telling.

------
fapjacks
Here's a Github repo apparently:
[https://github.com/CIDARLAB/cello](https://github.com/CIDARLAB/cello)

------
kmonad
Does this look a bit like a flux simulator? I haven't got access right now.
But from the abstract and the pictures it makes a sound a bit as if. Basically
model and simulate the flux of metabolites via connected functions, linear-,
step-, etc. It looks a bit like Matlab's SimuLink? Will read tomorrow and
amend if necessary.

------
bendbro
What exactly does it mean when one of these "circuits" "responds to
conditions"?

~~~
jamessb
The circuits are combinatorial logical circuits implemented as transcriptional
circuits: they produce a particular protein (in this case YFP - yellow
flourescent protein) when they receive an appropriate combination of inputs
(presence of absence of the small molecules IPTG, aTC, L-arabinose,
respectively).

~~~
bendbro
Ah so these circuits are useful because if you're trying to construct cell
organelles you need to be able to trigger release different proteins at
different stages of development?

Is any of that protein folding stuff useful for this?

------
evanpw
Seems to be real, despite the date:
[http://www.cellocad.org/about.html](http://www.cellocad.org/about.html).

------
foota
For anyone trying to access the site, you annoyingly have to register before
going to anything other than the index.

------
rvikmanis
Is this a joke?

~~~
88e282102ae2e5b
No, but it's not as interesting as it sounds.

~~~
theideasmith
Why not?

~~~
88e282102ae2e5b
It just automates what was previously something done manually. But it only
works 75% of the time. It's a nice tool to have if this is your domain but
it's not like you get any guarantees about success. Biology is still
stubbornly complex.

~~~
frevd
Given that you can run the same program on a billion bacteria should quite
improve the odds of getting the job done.

Surely, also one has to account for possible other "jobs" that get done due to
interference.

However, if your goal is to automate processes rather than develop cures to
"run" in the human body then this is a very interesting alternative to using
silicon, the parallel pipeline potential is enormous.

EDIT: Would it be possible to develop a biological CPU this way? I.e. having
"instruction sensors" and a touring-machine-like DNA-robot that can execute
externally supplied instructions? Putting that into a bacteria that can clone
itself would surely cut down on costs of computing.

~~~
dnautics
>Would it be possible to develop a biological CPU this way? I.e. having
"instruction sensors" and a touring-machine-like DNA-robot that can execute
externally supplied instructions?

No, it is not possible (not this way). Tl;Dr how do you plan on storing
information on the Turing machine tape? If you're happy doing computation with
a relatively high stochastic failure rate things look better, but I wouldn't
count on it.

------
dluan
Yeah, but we're actually not too far from this.

------
100ideas
why verilog?

~~~
jjoonathan
EDIT: I am assuming you meant "Why verilog as opposed to go/ruby/c/etc?"
rather than "Why verilog as opposed to system verilog / VHDL / etc." If not,
hopefully someone else finds the explanation useful anyway.

Because at the physical layer everything "executes" simultaneously, all the
time, in parallel, and verilog/vhdl/etc embrace that type/level of abstraction
while sequential languages don't. Sequential execution of "instructions" is
one level higher than the "everything is parallel" layer -- you put it in
place if it makes sense to impose strict reliability requirements and
sacrifice raw parallel computational power for the simplicity and versatility
of your favorite Turing machine. Unfortunately, biology isn't nearly as
reliable or as fast as silicon, even "early" silicon, so the tradeoff won't
make sense for some time to come if ever.

~~~
100ideas
I DID mean why verilog as opposed to system verilog, VHDL, “etc.,” or whatever
the verilog of 2020 is.

~~~
jamessb
It's currently only feasible to produce very small circuits (the paper goes up
to 8 gates and 3 inputs), and Cello is currently focused on a narrow class of
circuits ("asynchronous combinatorial logic without feedback"). The first step
of their algorithm is to convert the Verilog code into a truth table.

When your circuits are so simple, I suppose it doesn't really matter what
language you use to specify them, and the authors just went for whatever they
thought was most convenient to parse.

~~~
100ideas
The authors want to create Electronic Design Automation (EDA) tools to
facilitate engineering genetic systems at scale. Is verilog a reasonably
modern foundation from which to draw inspiration, or are there "better" EDA
tools nowadays? Maybe one of the resident HN semiconductor experts can weigh
in on this.

------
Myrth
"Anything can go wrong?"

"Don't be a buzzkill, man!"

