Computing Inside a Living Cell

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Computing Inside a Living Cell

Posted by samzenpus on Thursday October 31, 2013 @02:07PM from the you're-going-to-need-a-smaller-chair dept.

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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Re:My feeling by OhANameWhatName · 2013-10-31 14:38 · Score: 3, Funny

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"
Endy is no longer the leader in this field by Anonymous Coward · 2013-10-31 14:49 · Score: 2, Insightful

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.
1. Re:Endy is no longer the leader in this field by Gravis+Zero · 2013-10-31 17:33 · Score: 4, Insightful
  
  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.
  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. :)
  
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2. Re:Endy is no longer the leader in this field by Daniel+Dvorkin · 2013-10-31 17:45 · Score: 4, Interesting
  
  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.
  
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3. Re:Endy is no longer the leader in this field by ath1901 · 2013-10-31 23:00 · Score: 1
  
  I would love to. Care to share some interesting links?
4. Re:Endy is no longer the leader in this field by mcgrew · 2013-11-01 05:03 · Score: 1
  
  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 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.
  
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Mutation by DigiShaman · 2013-10-31 15:05 · Score: 2

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?

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1. Re:Mutation by sqrt(2) · 2013-10-31 15:15 · Score: 4, Informative
  
  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.
  
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Re:My feeling by anubi · 2013-10-31 15:07 · Score: 4, Informative

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

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

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Gambling! by antifoidulus · 2013-10-31 15:10 · Score: 2

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".

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Yes, yes, very nice... by tutufan · 2013-10-31 15:27 · Score: 3, Funny

but can it mine bitcoins?!
1. Re:Yes, yes, very nice... by Gravis+Zero · 2013-10-31 16:47 · Score: 1
  
  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.”
  
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2. Re:Yes, yes, very nice... by gl4ss · 2013-10-31 23:15 · Score: 1
  
  what he is saying is that practicality doesn't matter and you could build fluid based computers that act faster in the same size...
  
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This gives a whole new meaning... by Alejux · 2013-10-31 16:07 · Score: 1

...to Cell processors.
Rinse, Repeat by Anonymous Coward · 2013-10-31 16:16 · Score: 1

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. by Gravis+Zero · 2013-10-31 16:38 · Score: 1

where do you plug in the keyboard? :)

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1. Re:just one question. by Chrontius · 2013-10-31 21:21 · Score: 2
  
  Bend over...
the most important part: it's free for everyone by Gravis+Zero · 2013-10-31 17:14 · Score: 3, Insightful

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! :)

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1. Re:the most important part: it's free for everyone by gl4ss · 2013-11-01 03:11 · Score: 1
  
  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..
  
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2. Re:the most important part: it's free for everyone by Gravis+Zero · 2013-11-01 06:59 · Score: 1
  
  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.
  
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An elegant "proof". by TapeCutter · 2013-10-31 19:08 · Score: 1

the fact that you can mentally process digital logic means that you are digital computer
Wish I had mod points...

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Blood Music by BarryHaworth · 2013-10-31 23:28 · Score: 1

This sounds like the scenario to the novel Blood Music by Greg Bear.

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1. Re:Blood Music by ihgreenman · 2013-11-01 02:59 · Score: 1
  
  Exactly what I thought. Now we need to be careful not to let the researchers inject the modified cells back into themselves.
  
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