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## Largest DNA-Based Computational Circuit Created57

Posted by timothy
from the artificial-one-that-is dept.
angry tapir writes "Researchers from the California Institute of Technology have built [abstract] what they claim is the world's largest computational circuit based on DNA (deoxyribonucleic acid), using a technology that they said could easily scale to even greater complexity."
Adds reader cwmike: "The researchers formed 130 different synthetic DNA strands that can be used to compose logic circuits. From this source material, they created one 74-molecule, four-bit circuit that can compute the square root of any number up to 15 and round down the resulting answer to the nearest integer. In their setup, the multi-layered strands of DNA are fashioned (see video) into biochemical logic gates that can perform the basic Boolean AND, OR and NOR operations executed by today's transistor-based computer processors."
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## Largest DNA-Based Computational Circuit Created

• #### In their dreams! (Score:4, Funny)

on Thursday June 02, 2011 @11:29PM (#36328296)
I've been running a MUCH larger DNA-based computational circuit for YEARS now! Course, sometimes it fails me completely.
• #### Re:In their dreams! (Score:5, Informative)

on Thursday June 02, 2011 @11:37PM (#36328326)

Well, yes, while DNA based computing may sound like something from Science fiction, it looks like this is a small step:

The researchers formed 130 different synthetic DNA strands that can be used to compose logic circuits. From this source material, they created one 74-molecule, four-bit circuit that can compute the square root of any number up to 15 and round down the resulting answer to the nearest integer.

then

Reif also pointed out a few downsides. One is the speed of calculation. The execution of a single gate can take anywhere from 30 to 60 minutes. Executing a four-bit square root could take up to 10 hours.

So don't be expecting any DNA based mass computing revolution anytime soon.

• #### Re: (Score:2)

On the other hand, imagine the parallelizing opportunities with thousands and thousands of such gates!

• #### Re: (Score:3)

I am not saying that this isn't cool, but even if you had thousands and thousands of these gates, their individual processing power seems miniscule, and given the very lengthy times required to derive a solution to a problem, parallel operations would be limited.

While I think it is very "nifty" for them to have done this, it doesn't appear (and I am happy to be corrected here) to have any direct applications, nor does it appear to be a stepping stone to anything in anything but the very distant future. Agai

• #### Re: (Score:1)

Interesting, but what if we see this as a storage device instead? Isn't the purpose of DNA to be robust, which is perfect for longtime storage, and a DNA-molecule should be very small thus enabling very high storage densities, exactly what our cells are using it for!
• #### Re:In their dreams! (Score:5, Interesting)

<ninja@slaphack.com> on Friday June 03, 2011 @12:12AM (#36328444) Journal

If you're talking about your brain, that's not what this is. This is using actual DNA to perform computations.

Oh, by the way, last I checked, it's slow, and this is no exception:

Reif also pointed out a few downsides. One is the speed of calculation. The execution of a single gate can take anywhere from 30 to 60 minutes. Executing a four-bit square root could take up to 10 hours.

This isn't like quantum computing -- maybe they can make it faster, but I really don't see this having any inherent advantages over old-school tech like CMOS anytime soon.

What makes this interesting is the potential to do calculations inside living systems, or to actually interface our code with otherwise strictly biological processes. These "circuits" are just solutions of custom-designed DNA, and each "gate" takes small single-strands of DNA as input, and produce them as output, whether as a "wire" to another gate, or as the final output to be measured to check if the circuit is working. Now imagine putting that in a cell. (Oh, and this is why formal methods matter -- if someone's going to be putting code in your body, it's not enough to debug it, you want that shit proven correct.)

Disclaimer: While I did take a class (COM S 433 at ISU [iastate.edu]) which attempted to examine this stuff, this was covered at the very end of the semester, and no one (including the instructors) really had a good idea how these things actually work. I know enough to be dangerous, but there's a good chance I'm wrong about pretty much anything I say here. Read the papers yourself -- it's fascinating stuff.

• #### Re: (Score:3)

... last I checked, it's slow, and this is no exception: ... This isn't like quantum computing

There shall be Quantum-DNA computing then! I hear DNA is prone to hybridisation.

• #### Re: (Score:2)

These "circuits" are just solutions of custom-designed DNA, and each "gate" takes small single-strands of DNA as input, and produce them as output, whether as a "wire" to another gate, or as the final output to be measured to check if the circuit is working. Now imagine putting that in a cell. (Oh, and this is why formal methods matter -- if someone's going to be putting code in your body, it's not enough to debug it, you want that shit proven correct.)

I can imagine putting this in a cell. I just can't imagine why - or how.

The problem with most bottom-up molecular design like this is trying to replicate in miniature the macro-level machines we make. Biological design is necessarily messy; it has to work under a huge range of noisy conditions, and with components of varying quality. It's not like the well-ordered, quiet, dry environment that you find in a computer.

For example : what would happen if the DNA computer starts to get transcribed? Or broken down

• #### Re: (Score:2)

Bound to be a decent horror movie in this plot, though. Imagine a cultured brain that didn't stop growing.

Hmm. "The Brain from Planet Arous". On the shelf...

• #### Re: (Score:2)

I can imagine putting this in a cell. I just can't imagine why - or how.

I can imagine a few 'why's. Right now, in the barely-related field of DNA Origami, people are building machines out of DNA which target cancer cells -- I've heard it described as a "box" filled with chemotherapy poison, opens when it detects a cancer cell. The results are pretty jaw-dropping, if maybe a bit preliminary -- something like a 98% kill rate on the cancer cells without touching the healthy cells.

I'm being deliberately vague, because I'm already out of my depth on the comp sci side, and the bio si

• #### Re: (Score:2)

I want a DNA computer that can decide I need new teeth regrown, then show my body how to do it.
• #### Towel? (Score:2)

I've been running a MUCH larger DNA-based computational circuit for YEARS now! Course, sometimes it fails me completely.

That's because you need to wipe it off with a towel when you are finished or the keyboard gets too sticky to operate. ;)

• #### Douglas Adams, prophet (Score:1)

The Hitch Hiker's Guide to the Galaxy immediately came to mind. Fact emulates fiction .... So who are the white mice? Has anyone seen a porpoise recently?
• #### A single logic gate operation takes 30-60 minutes (Score:4, Funny)

on Thursday June 02, 2011 @11:35PM (#36328316)
Thats exactly how my DNA-based computer works too :)
• #### Did you say 'de oxy ribo nucleic ACID'? (Score:2)

That sounds like dangerous stuff! Its an ACID! That could hurt people too!

I sure hope they are very safe about these circuits and have warnings all over them. Something about this sciency nerdy 'deoxy' whatever the hell you called it ACID is going to get us killed. God bless us all. ;)

• #### Re: (Score:3)

That sounds like dangerous stuff! Its an ACID!

I dropped some DNA last night and tripped some balls.

• #### Re: (Score:3)

My DNA tripped last night and my balls dropped.

• #### Re: (Score:2)

Chill. Take two tablets of acetylsalicylic acid with a glass of hydric acid and wait for the palpitations to pass.
• #### "I compile to gene" (Score:1)

by Anonymous Coward

While the speed presents an inherent limitation, the fact that they made a compiler for it is seriously cool.

• #### Re: (Score:2)

While the speed presents an inherent limitation, the fact that they made a compiler for it is seriously cool.

Suggestion: wait until they'll implement the -O3 flag in that compiler (10 hours for an execution is not so exciting).

• #### Once upon a time there was a magic book... (Score:2)

[What the hell are you talking about you liars! There is not now, nor has there ever been a magical book -- magical thinking perhaps...]

Blah blah piano too loud for me to hear you say: "In this book, 'the magic spirits', which are small ... DNA, can be represented as colored lines with arrow heads marking their" -- ffffFFFFFUUU! (I lost)

(See video link in TFS -- you rage, you loose.)

• #### Science: it's a tough life (Score:5, Funny)

on Friday June 03, 2011 @01:07AM (#36328636)
I keep telling girls at bars I'm a scientist who just wants to perform a complex calculation using DNA and then they throw a drink in my face for some reason.
• #### 4-bit square root? (Score:2)

Seems pretty trivial to me. They did say round down, so ...

0 --> 0
1 --> 1
2 --> 1
3 --> 1
4 --> 2 ...
8 --> 2
9 --> 3 ...
15 --> 3

For most inputs, the answer matches the highest 1 bit in the number (exceptions: 0, 1 and 9). Wouldn't be hard to make a circuit do that.

10 hours? As in, 20 operations? Seems excessive...

• #### Re: (Score:2)

Actually, if we name the input bits i0 (LSB) to i3 (HSB) and the output bits o0 (LSB) and o1(HSB) then the calculation to do is:

o1 = i4 OR i3
o0 = (i4 OR NOT i3) AND (i1 OR i2 OR i3)

Indeed, not very complicated.

• #### Re: (Score:2)

Which implies that the input is encoded in binary ... which it isn't.

Sometimes it is really interesting and helpfull to RTFA.

angel'o'sphere

• #### Re: (Score:1)

Which implies that the input is encoded in binary ... which it isn't.

From the Science abstract (emphasis by me):

we experimentally demonstrated several digital logic circuits, culminating in a four-bit square-root circuit

They were encoding numbers into bits and didn't use binary?

• #### Re: (Score:2)

Well, that is how articles are written I assume.

If you read further you see that they use "standard DNA" chemical reactions. DNA fragments (data) are docking on the DNA gates (circuits). The input is read/decoded and transformd into new DNA strands which are able to dock at the next circuit. There the same process continues. Over several steps the original input is decoded and reconstructed into a computational result which happens to be the square root of the input.

It is not 100% clear but for me that idic

• #### Re: (Score:2)

I think your logic gates are backwards. I used espresso and came up with (Inputs A-D, MSB to LSB and outputs X and Y, MSB to LSB, NOT has highest precedence):

X = A OR B
Y = (NOT B AND D) OR (NOT B AND C)

I wrote out the truth table, and my version seems right.

• #### Re: (Score:2)

Actually, if we name the input bits i0 (LSB) to i3 (HSB) and the output bits o0 (LSB) and o1(HSB) then the calculation to do is:

o1 = i4 OR i3
o0 = (i4 OR NOT i3) AND (i1 OR i2 OR i3)

I like what you did there! But... i0 is not used, and i4 is not defined. If we adjust the formula by shifting the indices down by one so that we have:

o1 = i3 OR i2
o0 = (i3 OR NOT i2) AND (i0 OR i1 OR i2)

Then it seems to work just fine! (Please forgive the appearance; workaround to overcome /.'s formatting and lameness filter limitations.)

_i i3_i2_i1_i0 o1 o0 s
_0 _0__0__0__0 _0__0 0
_1 _0__0__0__1 _0__1 1
_2 _0__0__1__0 _0__1 1
_3 _0__0__1__1 _0__1 1
_4 _0__1__0__0 _1__0 2
_5 _0__1__0__1 _1__0 2
_6 _0__1__1__0 _1__0 2
_7 _0__1__1__1 _1__0 2
_8 _1__0__0__0 _1__0 2
_9

• #### Re: (Score:1)

What I'd like to know: is that the MINIMAL set of logic operations required to compute this? How could one prove it?

Apply Karnaugh maps or the Quine-McCluskey method to find the minimal set. It might not be unique, but it'll be minimal.

• #### Thanks for the clarification (Score:1)

Researchers from the California Institute of Technology have built [abstract] what they claim is the world's largest computational circuit based on DNA (deoxyribonucleic acid)

Thanks for the clarification. I had no ideas what the acronym DNA means, but of course I'm familiar with the term deoxyribonucleic acid.

• #### Re: (Score:2)

But what is this "California Institute of Technology?" Is that anything like Caltech?
• #### Ooooo! (Score:1)

You are meddling with forces that you cannot possibly control or understand! And erm, can you do one in Mac? :0)
• #### Hmmmm (Score:2)

What is a blue whale?

• #### Not ground breaking (Score:2)

The mice have been doing this for ages.

• #### Synaptic MultiProcessing (Score:2)

I wonder if they can get multiple strands to work together for processing. I don't know how they would get around the body rejecting it but I could see it being useful as an implant. For one, it could send impulses at calculated times to initiate motor response. That would require a boat load of computation though.

• #### A computer based on this (Score:2)

would give 'computer virus' new meaning.

• #### *New* DNA-based computational ciruit discovered. (Score:2)

Called a brain. While little used by journalists or politicians, dolphins have found them quite useful.

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