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Computing Inside a Living Cell

samzenpus posted about 9 months ago | from the you're-going-to-need-a-smaller-chair dept.

Biotech 41

First time accepted submitter Rozanne writes "The new issue of Stanford Medicine magazine has a story on Stanford professor Drew Endy's creation of microscopic computers out of biological components for use inside living cells. His work is a mash-up of molecular biology and computer engineering: Instead of a computer made of silicon, metal and plastic, it's a computer made of DNA, RNA and enzymes. Endy says biologists are typically confounded at first when he explains how the computers work and how they could be used."

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41 comments

My feeling (0)

Anonymous Coward | about 9 months ago | (#45296825)

Based on not reading the article, is that probably there is not really an analogy with computing figured out in detail. Yet.

Re: My feeling (-1)

Anonymous Coward | about 9 months ago | (#45296847)

Bitches be crazy

Re:My feeling (3, Funny)

OhANameWhatName (2688401) | about 9 months ago | (#45296955)

Based on not reading the article, is that probably there is not really an analogy with computing figured out in detail. Yet.

As a fellow uninformed member of the /. community, I'd like to second your notion and move for a vote.

All those in favor of calling Drew Endy nasty names, say "I"

Re:My feeling (4, Informative)

anubi (640541) | about 9 months ago | (#45297073)

If you want some more detailed explanation, I would suggest reading about what Craig Venter's take on it is. He is one of the principal researchers on the Human Genome Project, and has taken the time to write a book for the layman to grasp the magnificence of what he has found.

http://www.amazon.com/Life-Speed-Light-Double-Digital/dp/0670025402 [amazon.com]

This book was released October 17, just a few days ago...

Endy is no longer the leader in this field (2, Insightful)

Anonymous Coward | about 9 months ago | (#45297009)

For all his talk, Drew Endy hasn't actually pushed the synthetic biology field forward, and it was always questionable whether his vision of "standardized biological parts" would be the best way to engineer biology. His analogies to computer engineering are mostly false, as biology operates according to physical and chemical rules. Not Ohm's Law. Not digital logic. You can engineer biology to mimic digital logic, but it's truly analog governed by biomolecular interactions and stochastic dynamical processes.

There are other people in the Synthetic Biology field who are doing much more innovative and interesting work.
Go read stories about them.

Re:Endy is no longer the leader in this field (4, Insightful)

Gravis Zero (934156) | about 9 months ago | (#45297609)

His analogies to computer engineering are mostly false, as biology operates according to physical and chemical rules. Not Ohm's Law. Not digital logic. You can engineer biology to mimic digital logic, but it's truly analog governed by biomolecular interactions and stochastic dynamical processes.

(human) brains are both analog and digital simultaneously. [yale.edu]

even if you argue it's really all analog, the fact that you can mentally process digital logic means that you are digital computer... with lots of extra features. :)

An elegant "proof". (1)

TapeCutter (624760) | about 9 months ago | (#45297873)

the fact that you can mentally process digital logic means that you are digital computer

Wish I had mod points...

Re:Endy is no longer the leader in this field (1)

mcgrew (92797) | about 9 months ago | (#45301575)

even if you argue it's really all analog, the fact that you can mentally process digital logic means that you are digital computer

Any analog computer [wikipedia.org] can process digital logic. The difference between analog and digital is with analog you have noise, with digital you have rounding errors (and those rounding errors can be simulated in an analog computer).

You can make a simple analog computer (actually more like an electric slide rule) with a couple of batteries, a couple of potentiometers, a voltmeter and a little wire. More complex analogs were built, of course, with outputs to CRTs.

Re:Endy is no longer the leader in this field (0)

Anonymous Coward | about 9 months ago | (#45308465)

My education focused mainly on analog and rf, with basic digital fundamentals. When I started doing digital troubleshooting the best advice I got was that "digital is just a special case of analog". It's true, it's either full on, or full off (neglecting switching time, when it really is analog)!

Re:Endy is no longer the leader in this field (4, Interesting)

Daniel Dvorkin (106857) | about 9 months ago | (#45297675)

Yeah. I don't know enough about his work to comment, but when I read the part about how all this computational stuff is just too confusing for those poor biologists, my bullshit alarms went off. Speaking as a bioinformaticist, whose job it is to bridge the bio/CS gap all the time, I've observed that computer scientists often have at least as hard a time grasping biology as biologists have grasping computer science. Endy's kind of smugness does no one any good.

Re:Endy is no longer the leader in this field (1)

ath1901 (1570281) | about 9 months ago | (#45298585)

I would love to. Care to share some interesting links?

Re:Endy is no longer the leader in this field (0)

Anonymous Coward | about 9 months ago | (#45303115)

I would love to. Care to share some interesting links?

Engineering biology to mimic digital logic: http://www.nature.com/nature/journal/v491/n7423/abs/nature11516.html

Autonomous regulation of synthetic metabolic pathways: http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.2689.html

Rational design and optimization of genetic parts: http://www.nature.com/nbt/journal/v27/n10/abs/nbt.1568.html

Mutation (2)

DigiShaman (671371) | about 9 months ago | (#45297061)

Mutation is the result of DNA change. Often from external sources such as radiation or chemicals. The change could be good, bad, or nothing readily noticeable. So that said, how can you rely on the results of a biological computer that's prone to mutation and thus corrupting the results?

Re:Mutation (4, Informative)

sqrt(2) (786011) | about 9 months ago | (#45297099)

At its lowest level, the hardware we use today to store data is prone to errors. Your HDD functions perfectly well misreading data hundreds of times a second. You don't even notice until it becomes especially bad; when the errors overwhelm the ability to check and correct the data. A certain amount of errors are expected, and correctable. The simplest method is a simple checksum. Report the intended length of the message you're sending and the receipient then checks to make sure at least the length is correct. Then you can build in redundancy and error correction through more sophisticated means. These problems have largely been solved in the abstract, so they're not dependent on any particular media.

Re:Mutation (0)

Anonymous Coward | about 9 months ago | (#45297415)

MTBF of a person catching cancer at the "system" level is higher than that of a computer memory.

DNA code density is low, so chances of an "error" that messes important genes up is low., so hopefully the non-corrupted one survives.
There are lots of redundancies cells. You don't count on the result of a single cell when you can grow a whole petri dish worth of them.

Re:Mutation (0)

Anonymous Coward | about 9 months ago | (#45303791)

Checksums. DNA has had it for billions of years now in some form, just to greater or lesser efficiencies in different creatures.

I mean, look at tardigrades, they more-or-less told the suns radiation to suck his cock when they were pointed at the sun, IN SPACE at that. (not to mention other things too)
They are basically the hardiest creature on this planet. More like hardigrades. Tough little buggers and they are only 1mm.

Sure, there are extremes where data will fall apart, but even this system as-is would likely still outlive that hard drive, flash drive or solid-state drive you are using right now. Hell, likely outlive modern society if it was fed or given the ability to keep itself alive. Living Memories, in stores now!

Re:Mutation (0)

Anonymous Coward | about 9 months ago | (#45304505)

Instead of leaving artefacts for humans to find once they are sufficiently evolved, an advanced extraterrestrial civilizations might instead incorporate information into the human genome, allowing it to be copied and maintained over immense periods of time.

The downside with leaving behind alien artefacts is that they will not survive for millions of years. A coded message hidden in our DNA, on the other hand can be saved for a very long time.

The coded message would only be discovered once the human race had the technology to read and understand it. -

http://www.messagetoeagle.com/aliendnamessage.php [messagetoeagle.com]

Gambling! (2)

antifoidulus (807088) | about 9 months ago | (#45297077)

Now we can finally start betting on sperm races. All you need to do is the following:

1. Put a tiny bit of compute power in each sperm cell that identifies the sperm.

2. Proceed to give odds, take bets
3. Fuck

4. Profit! After the egg has been fertilised you can use the tracking chip in the sperm to see which one "won".

Re:Gambling! (0)

Anonymous Coward | about 9 months ago | (#45298155)

There's just one flaw in your plan: Step 3 is impossible.

Re:Gambling! (0)

Anonymous Coward | about 9 months ago | (#45298755)

That already exists. It's called a orgy followed by a paternity test.

Re:Gambling! (0)

Anonymous Coward | about 9 months ago | (#45301325)

You mean something like this: http://www.theguardian.com/media/2005/jan/30/realitytv.germany

don't get this (0)

humaniverse (838580) | about 9 months ago | (#45297143)

We, as human being built by tons of living cells, are more advanced computer. Now we want to evolve backward to dumb computer?

Yes, yes, very nice... (3, Funny)

tutufan (2857787) | about 9 months ago | (#45297169)

but can it mine bitcoins?!

Re:Yes, yes, very nice... (0)

Anonymous Coward | about 9 months ago | (#45297259)

I sense a new meme in the force.

Re:Yes, yes, very nice... (1)

Gravis Zero (934156) | about 9 months ago | (#45297453)

but can it mine bitcoins?!

yes... but very slooooowly. it takes about 15 minutes per cycle.

Speed-wise at least, IBM won’t feel threatened by the biocomputer. “The microbial processor operates in the millihertz time frame — about one cycle every 1,000 seconds, or about four times per hour,” Endy says, “But in biology it doesn’t always matter; slow can be beautiful.”

Re:Yes, yes, very nice... (1)

gl4ss (559668) | about 9 months ago | (#45298655)

what he is saying is that practicality doesn't matter and you could build fluid based computers that act faster in the same size...

Is the first Biological or AI? Does it matter? (0)

Anonymous Coward | about 9 months ago | (#45297255)

I'd like to see the first virus attack it. Will it be biological, AI, or as I suspect, both, with a good mix of probablistic retries of infection,
until when beats it? Will the attack vector be the result of generational learning? Hmm. Things are looking creepy, I tell ya...

Re:Is the first Biological or AI? Does it matter? (0)

Anonymous Coward | about 9 months ago | (#45298439)

I suspect the first will be an boot virus...

I can smell it coming....

This gives a whole new meaning... (1)

Alejux (2800513) | about 9 months ago | (#45297327)

...to Cell processors.

Rinse, Repeat (1)

Anonymous Coward | about 9 months ago | (#45297347)

About 15 or 20 years ago, there was a lot of biological computing going on where they would attempt to use bacteria to solve NP-hard problems and also crack encryption in n time (basically by replicating the bacteria and getting n^3 or o^n bacteria reproducing and breaking a code. They used large vats of bacteria instead of acres of cores. And now this. Its either 2013, or 1993, or 2033.

just one question. (1)

Gravis Zero (934156) | about 9 months ago | (#45297411)

where do you plug in the keyboard? :)

Re:just one question. (2)

Chrontius (654879) | about 9 months ago | (#45298227)

Bend over...

the most important part: it's free for everyone (3, Insightful)

Gravis Zero (934156) | about 9 months ago | (#45297553)

With electronic signal amplification, a very small change in electrical flow is sufficient to open and close gates that control massive rivers of electrons. “The biological transistor, what we call a ‘transcriptor,’ does the same thing.

He has formally donated the transcriptor and biological logic gates to the public domain via the BioBrick Public Agreement. That means anyone is free to use them. A similar declaration for the biological Internet is in process.
The only piece of biocomputer technology Stanford and Endy have patented is the biological digital memory.
“Some other groups have patented technologies claiming to accomplish a similar goal,” explains Endy. “If we have a patent, we can assure the technology is free and available to all simply by not pursuing our patent rights. But if we don’t have a patent, someone else could claim the technology and restrict its use.”

finally someone that invents a great technology and understands that patents stifle innovation!

bold tag! :)

Re:the most important part: it's free for everyone (1)

gl4ss (559668) | about 9 months ago | (#45300493)

actually patents don't work quite like that.
they could just have published it as prior art as well, thereby guaranteeing that any patent could have been fought in court easily.

(of course the trick to patents is that you don't really have to have invented how to do the actual thing nowadays to get one.. even when you should).

but now the patent exists, it can pass to some other hands. otoh, it's unlikely it wont expire before any practical application..

Re:the most important part: it's free for everyone (0)

Anonymous Coward | about 9 months ago | (#45302031)

Which method is "better" comes down to how much you trust the current patent holder to keep his word. However over all I think this method is still best with the current patent system.

Publishing prior art as you suggest will still guarantee an expensive court battle against the first patent troll to claim to have invented this.
This also makes it at least very likely that someone (if not quite a few someones) are successfully sued in court, since prior art must be proven while claiming invention does not.

A rough timeline of events will go like this:
1) Creator releases enough information to show prior art on the invention.
2) Patent troll files patent for invention - this is granted without question.
3) Patent troll sues small firms using invention, who can not afford to prove the prior art in court and settle.
4) Patent troll finally sues firm that can defend itself, prior art is shown, and the patent is invalidated after a couple years of appeals.

Using the current method of filing for a patent and not enforcing it, as long as the patent stays in his hands and he stays true to his word, literally anyone can use it.

If the patent is sold off or he goes back on his word, you still have an expensive court case similar to above, but you can present his claim that you are licensed for $0 to use the patent as evidence you owe no royalties or damages.
You still have to pay your own lawyers, but nothing above and beyond, and certainly nothing to whomever holds the patent at the time.

The only downside is the patent doesn't get invalidated automatically (or likely at all), so the new patent holder can start a few lawsuits before being smacked down for abuse of the courts.

Clearly neither is ideal, but the current method used will provide free use of the invention for a time, and worse case is slightly better than had it not been patented at all.

Re:the most important part: it's free for everyone (1)

Gravis Zero (934156) | about 9 months ago | (#45303013)

actually patents don't work quite like that.

incorrect. they shouldn't work like that but they do.

they could just have published it as prior art as well, thereby guaranteeing that any patent could have been fought in court easily.

it's extremely difficult to invalidate a patent and very expensive to fight, even if there is clear and blatant prior art. this is why a bunch of companies just pay for a license instead of fighting it. we have a legal system, not a justice system.

fai7zo8s (-1)

Anonymous Coward | about 9 months ago | (#45297671)

Itself. You can'%t be in a scene and

Intel Inside (0)

Anonymous Coward | about 9 months ago | (#45298567)

"Intel Inside" get's a whole new meaning!

Blood Music (1)

BarryHaworth (536145) | about 9 months ago | (#45298715)

This sounds like the scenario to the novel Blood Music [wikipedia.org] by Greg Bear.

Re:Blood Music (1)

ihgreenman (148607) | about 9 months ago | (#45300383)

Exactly what I thought. Now we need to be careful not to let the researchers inject the modified cells back into themselves.

Bio Message hash1877465 (0)

Anonymous Coward | about 9 months ago | (#45300271)

record format:
queue num | sender id | receiver id | msg type | msg text | action req

msg #4389303:
388 | H. Pylori sub mod 3 | E. Coli sub mod 6 | food sense | chili dog consumption detected | produce explosive diarrhea

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