On Arduinos and Homebrew Genetics

For a while preceding buying my own Arduino, I spent my time looking at all the cool projects people have used them for on the Make blog, Fashioning Technology and the Arduino wiki itself. Although I love all the projects that showcase the artistic use of electronics, and I’m impressed with the more utilitarian uses also, I see great untapped potential in the Arduino as a replacement technology for certain niches where equipment is prohibitively expensive.

One such niche I am intimately aware of is Biotechnology, particularly molecular biotechnology. For example, I work daily with a machine called a thermal cycler. These machines perform a seemingly simple duty; they accurately vary the temperature of a metal casing in which you place little plastic tubes containing your reaction mixes for molecular biology. You set them up to cycle through a variety of temperatures so as to help enzymes work at optimal efficiency, break the double-helix of DNA with heat, permit only certain molecules to adhere to one another during a reaction, or to inactivate enzymes through heat-treating. They are most often used for the Polymerase Chain Reaction, a cornerstone of modern genetics, and so they are often called PCR machines.

The odd thing about these machines is the cost. A thermal cycler can cost over €2,000 for a used robotic version, or as low as €200 for an ancient, damaged one. These machines almost universally have a poor interface, too; few can connect easily to a computer, and none are open-source.

What’s going on here? Am I missing some deep secret of thermal cyclers that should make them so expensive and limited? So far as I know, a modern thermal cycler technically only uses one basic technology; a Peltier thermoelectric device. These little semiconductor/ceramic plates get hot on one side and cool on the other when supplied with electricity, with the orientation depending on the polarity of the voltage. In short, the work like an electric heat pump, heating or cooling one side on demand. And, they cost less than €10 on ebay with free postage.

In principal all that’s needed to make one, then, is a Peltier unit, a temperature sensor (60c in Maplin), a little breadboarding ( < €20) and an Arduino (€20). Connect it to a PC, optimise your code, and you have a highly flexible Thermal cycler for less than €50.

This ties into something of a broader interest for me, that of someday having my own lab wherein to do my research. I think it’s just part of my personality that I feel compelled to do stuff for myself, and tend to lose interest in projects not my own. I look forward to working on nutty genetics projects that I fancy might, just might, have the potential to help improve the world..or at least look nice growing in a pot by the window.

Setting up a Genetics lab is the big obstacle here; because you need such specialised equipment and reagents, it’s not a simple matter of building a shed and ordering from a catalog. (Update: I started a shop on Shapeways where I am already selling some cheap lab equipment: LabsFromFabs) Although a growing community of people are taking an interest in homebrew biology, their ability to do so will be constrained by the price of setting up and maintaining a working lab.

Thankfully, this is slowly changing. Much as electronic technology used to be a very exclusive field until prices plummeted and homebrew electronics became an affordable hobby, certain powers that be are working to bring Biology labs into the home for enthusiasts and clubs. Update: See the LavaAmp for one such project that is already near the market!

One such effort is OpenWetWare, a wiki project that aims to build a directory of Protocols, Tutorials and Essays to teach the knowledge and practices of Biology online, for free. Most homebrew clubs I’ve encountered maintain a page on OpenWetWare to showcase their work or share their experiences.

Another, potentially even more revolutionary example is the Biobricks Foundation, which aims to standardise genetic material to enable swift, easy construction of complex genetic tools and systems. Although they suffer from a terrible website design and a general lack of beginner-friendly information or support, the system they are using is seemingly reliable and robust. It should require no more specialised equipment than four enzymes and a special breed of e.coli to start making things that glow, smell like bananas or release special enzymes in response to something. Technically.

Best of all, existing genetic “parts” (read; the bits of whole genes such as the coding sequence, promoter, terminator, etc) can be modified so that they are themselves new “Biobrick” parts, and can be added to the Biobricks Registry of Standard Parts. If someone wants your part, they can ask you to mail some over to them!

Finally, and perhaps most importantly, those interested in genetics at home will be excited to hear that I **firmly **believe a service will be available within this decade where you can simply order a gene from scratch and have it delivered already transformed into e.coli (at least!). Mail order GMOs.

I say this because you can go right now over to Mr. Gene and order up to 3kb worth of DNA to be synthesised from scratch at a competitive price (€0.32 per nucleotide), which is enough to contain a whole functioning bacterial gene. Not only that, but their web-tools will help you easily add in all the special sequences you want, while excluding those you don’t, while maintaining the coding sequence and optimising it by species. That’s pretty much all the hard work.

The price is still expensive; although €960 should cover 3kb at 35c/n, it can cost a bit more for a useful gene to be made due to the relative difficulties in synthesising odd or difficult sequences. However, I have learned (through my own travails working in a genetics lab) that producing and stably assembling a gene by yourself is sometimes so time consuming (months!) and expensive that you’d be better off just paying the extra money and getting a guaranteed sequence in 15 days.

It is a small step from being able to order a complete gene and the e.coli separately, and transforming them on your benchtop, to having a company do all of this for you in advance and delivering the finished, genetically modified product by courier.

It would also be a small thing to order a modified strain of another bacterium, known as Agrobacterium tumefaciens. The significant difference here is, Agrobacterium is known for its ability to transfer DNA into plants, and is routinely used as the most simplistic means of creating GMO plants. So, mail order transformed Agrobacterium = Mail order modified plants.

I eagerly look forward to this day. For the moment though, and coming back to the beginning of this post, I aim to create an open, free and publicly available design for at least one piece of specialised equipment. With this and other similar projects, I’m hoping lab equipment stops being so damned exclusive and comes quickly to the Maplin Catalog. Update: See LabsFromFabs, my Shapeways shop where I’m already selling some lab equipment!

And if someone else reading this has the tech savvy to help (I’m an electronics n00b), please do!

Edit: The price of gene synthesis wasn’t €0.35, it was $0.35. Much cheaper than I quoted.