Synthetic Biology Creates Living Computers

Most people have at least a fuzzy idea of what DNA is. Ask about RNA, though, and unless you are talking to a biologist, you are likely to get even more handwaving. We hackers might have to reread our biology text books, though, since researchers have built logic gates using RNA.

Sometimes we read these university press releases and realize that the result isn’t very practical. But in this case, the Arizona State University study shows how AND, OR, and NOT gates are possible and shows practical applications with four-input AND gates and six-input OR gates using living cells. The key is a construct known as an RNA toehold switch (see video below). Although this was worked out in 2012, this recent study shows how to apply it practically.

In the cellular world (that’s biological cells, not mobile phone cells), the DNA is almost like a disk drive–it contains information about what to do. RNA has a similar chemical structure, but–unlike DNA–is usually single-stranded. It can copy segments of the DNA using a transcription process. This messenger RNA can then fold into a complex three-dimensional shape since it isn’t bound to a second strand. Ribosomes can read this RNA and stitch together amino acids to form proteins that actually do the work in the cell.

We aren’t pros on biology, but you could make the case that DNA is like mass storage for a program, RNA is the RAM memory, and the ribosomes are the CPU and 3D printer of the whole setup. RNA is also used to move raw material to the ribosomes, much as RAM memory can hold instructions and data. And just as  CPU itself usually contains memory in the form of registers, the components that make up a ribosome are proteins and RNA. We aren’t biologists, so take that analogy with a grain of salt.

Because of the tiny size of cells and the way RNA-based computing works, it offers the opportunity for major parallelism, similar to quantum computing. In addition, because this can affect living cells, researchers think it will lead to new types of smart drugs and better medical diagnostic tools. A similar technique from the same team has already demonstrated it can detect the Zika virus.

The next step is to create neural networks inside cells and the formation of a cell network (again, not the telephone kind) allowing processing elements in one cell to talk to another. We have the Internet of things. Perhaps one day we’ll have the Internet of cells.

If you are into the biology hacking, we’ve talked about using RNA transcription as a means of stopping infections. If you want to know a lot more about how to synthesize oligonucleotides (fancy talk for DNA and RNA), we looked at how to make them in space.

24 thoughts on “Synthetic Biology Creates Living Computers

  1. I’d be interested to see if this means we will soon be able to quickly sequence DNA. I’m not looking forward to the actual viruses that people could make with this knowledge. :/

    1. Don’t be. We are already capable of sequencing DNA in a really fast way, it is mostly a matter of costs, and that increases with the length you want to sequence. That knowledge is long gone by now. This is more of a “how can we apply the structure of one of the most complex and fine tuned network we know of, to perform work for us, like we did with electrons and silicon”. Think more in a “cells doing math” than in a “bioweapon killing machine”. This doesn’t really bring much new to the second, we already know plenty on how to kill eachother by modifying organisms

  2. I can’t help but wonder if using biocomputers as carbon capture devices to scrub atmospheric CO2, whilst performing useful computation would be good eco-engineering Futuretech

        1. Yep, its like all the hype about electric cars. Although they will likely reduce toxic pollusion in urban areas, which is a good thing, some people actually believe that going electric will definitely reduce carbon emissions, not realising that electricity is mainly produced by burning fossil fuels to make steam to make a wheel go round.

          1. Oh, this grid is dirty argument is never gonna get old. Yes, some proportion of the grid is still fossil fuels but it is continuously getting cleaner making the electric cars total emissions go lower. Internal combustion engine in your car is never gonna get any cleaner.

          2. there are countries that produce more than they need from renewables on a good day, even by rather huge margins, Denmark has over 160% capacity in pure renewables, when the wind is blowing.

          3. Soman and oodain make good points, and I agree that renewables are getting stronger (and will hopefully one day eclipse fossil fuel burning), my point is that, for now, about 85% of electricity is from fossil fuels but many people don’t realise it. You also have to take into account the energy loss through transmission of electricity (about 8-15%). At the moment, in many countries, electric cars probably cause more CO2 to be released than combustion engines.

  3. Quote:
    “Perhaps one day we’ll have the Internet of cells.”

    Oh no…. Does that mean we, the future modified humans ARE the real Skynet???

    Interesting to see Moors law taking alternative routes to miniaturization.

    1. Even more interesting .. take a look at the Carlson Curve,and compare it to Moore’s law. The rate at which our ability to read and write DNA is improving vastly outpaces the rate of improvement in our ability to manipulate electronic components.

      DNA based data storage is actually a thing, and it may well become the predominant storage format for lomg-term mass storage.

  4. Oligosynthesis is massively expensive from the computation point of view and tightly controlled–for obvious reasons. DNA computing won’t be a thing for the average person until someone comes up with a way better than supergluing nucleotides to massive–from their point of view–precious metal spheres and using special nucleotides that are designed to only add one base pair, both very expensive unless you’re dealing with economy of scale.

  5. Thinking vinyl-figuratively, the DNA is the original master, kept in a secure place. The RNA is a printing master, copied off the original master and delivered to and used in the presses (ribosomes) to make lots of duplicate vinyl LPs (proteins) until it is worn out. then the LPs, left out in the car in the sun, take their natural shape and so do proteins in their environment. :-) Of course the final shape of the protein is a bit more useful than a melted LPs shape. :-)

Leave a Reply

Fill in your details below or click an icon to log in: Logo

You are commenting using your account. Log Out / Change )

Twitter picture

You are commenting using your Twitter account. Log Out / Change )

Facebook photo

You are commenting using your Facebook account. Log Out / Change )

Google+ photo

You are commenting using your Google+ account. Log Out / Change )

Connecting to %s