Reasons to be in Ireland this October: Synbio AXLR8R, Grow Your Own

As is often the case when I fail to post for months, I’ve been busy. In addition to my own work in the lab, which currently entails bypassing and leapfrogging existing affinity chromatography standards while making DIY protein purification trivial (!), I’ve been roped into organising an ambitious Synthetic Biology business accelerator programme in my home city, Cork, and I’m officially a co-curator for the upcoming Synthetic Biology exhibition in Science Gallery, “Grow Your Own”.

Both of these deserve individual attention here. And in both cases it’s worth saying that I’m not the only, or even primary, organiser. Left to my own devices, I’m not likely to instigate a business-focused program, despite my own aspirations to make a living out of biohacking. And were I to do so anyway, it would probably come with a series of stipulations against patents, and perhaps exhorting some manner of copyleft licensing for the outputs. Likewise, while I thoroughly enjoy the sort of exhibit Science Gallery generate, and I have done (and continue to) small work with designers and artists on Synbio projects for exhibits, I’m equally unlikely to personally declare an exhibit and carry it to execution and display.

The reason I’m saying this is simultaneously to avoid stealing undue credit, but also to avoid granting the false impression that, for example, there will be a bias towards “Free/Libre Biotech” in the accelerator, or an undue bias away from centralised-industry in the exhibit. I’ll have ongoing input in both though, so I think/hope both will appeal to those of like mind to myself.

Synbio AXLR8R

If you’re a maker or hacker type, you may have heard of HAXLR8R, a startup accelerator programme tailored towards hardware and electronics. As it happens, “AXLR8R” is a brand in itself, and several sub-accelerators have already taken place under this moniker.

The latest of these, then, is to be Synbio-AXLR8R. The format is planned similarly to HAXLR8R and friends; a rapid-iteration, batteries-included*, abundantly-mentored program with a generous investment and a strong social element. But this time, the “hardware” is “wetware”.

Of course, this raises unique challenges; SynBio is a young technology, and the prototyping iteration-times are, at present, far more punishing than hardware. Depending on strategy (order parts and splice/resplice, or re-order each prototype de-novo), either a great deal of error-prone benchwork or a long lead-time will be required between each iteration, and the costs of ordering DNA remain somewhat high.

To some extent, these problems can be mitigated through use of defined, reliable “primitives” such as the well-characterised, safely-licensed but very limited parts available in the Biobricks.org Contributions Database. No, not the MIT “Parts Registry” of iGEM fame; parts from there must be chosen with care to avoid a patent-bomb and to ensure sufficient testing, although it is often useful nevertheless. Whatever the source, understanding the part itself is critical, and open access scientific literature is the desired next-step; every part should be complemented with a set of papers and studies that detail exactly how it works under different conditions, and the would-be engineer must understand the part prior to re-engineering into a new context.

A basis in good primitives and research-driven selection of components can be complemented with good software. Indeed, the use of software to tailor a good primitive to a new context is one of the defining characteristics that separates Synthetic Biology from prior forms of genetic engineering, and even the transitional modular assembly methods (eg. the various ‘biobrick’ standards) used to tide us through the ongoing plateau of gene synthesis costs.

With good software and primitives, the remaining element is the right development cycle and mindset; this is often a problem for scientists accustomed to rigorous problem-solving, whereas in development one must forego the answer-seeking urge and often “go with gut feeling” to achieve results in good time. Likewise for inventive steps; the bioscientist will be used to changing one thing at a time to narrow down the point of failure, and this is the ideal path if time is abundant. However, to create and test a new product in a practicable time, sometimes you have to do more than one thing at once, and simply attempt to make your designs self-testing. For an engineer or computer scientist dipping toes into synthetic biology, the opposite problem arises; it is easy to imagine that the “code” of life is as predictable and linear in performance as computer code, but any biologist can laugh that misconception away in no time; biology is full of random, competing systems that can play havoc with a carefully designed, hair-trigger system, and success in this field, right now, requires a lot of tolerance for noise and unexpected combinatory behaviour.

Knitting all of this together can be hard for anyone to manage: whether a scientist being thrown into a business climate, or an engineer accustomed to things working-as-designed being given a biological part that fails despite fitting every theoretical parameter necessary, or a business-minded entrepreneur unaccustomed to long, unpredictable development cycles. This is where mentorship comes in. Not a single mentor suffering from her or his own set of prejudices, but by many mentors from all walks of the biotech life.

And that’s the final ingredient in a rapid accelerator, and one that Synbio AXLR8R aims to fill in. As things stand, I have the honour of being on the (short) list of confirmed mentors for the programme (pity the poor participants), but it is my understanding that the mentor list is set to expand and include as many fascinating names as we can harvest from the synbio, business and bioscience communities. I’d like to make it an even broader set, and include persons who might normally never be seen by Synbio afficionados on their home turf: perhaps members of oppositional groups who normally rail against bioscience, to provoke a dialogue and a discussion of practical measures that participants might consider to make their work more accessible, acceptable and trustworthy to the broader public.

Time will tell if good primitives, software, mindsets and mentorship will assist in making a 3-month Synthetic Biology accelerator work; it will be a learning experience for everyone concerned, at least!

Grow Your Own

And now, for the other major event of my Autumn. In tandem with the Startup Program (predating it in terms of planning), Science Gallery in Dublin will be launching their 2013 “flagship” exhibit, Grow Your Own (which lacks anything but a scheduling mention, for now), which will be digging into the subject of Synthetic Biology from as many angles as possible. Featured will be a look at the industrial, academic, political and domestic implications of this new form of biotechnology.

Without revealing anything prematurely, this is planned to include exhibits with an authentic GM element (what would be the point of a synbio exhibit without any synbio cells?), those with a bioinformatic focus, exhibits questioning the role of biopatents and “Intellectual Property” in the natural sciences, exhibits that explore the social and legal impacts, the new forms of activist, outlaw and criminal actions enabled or provoked by the new biotech, and exhibits that position themselves generously along the scale of domestic to distant-industrial biotech. Perhaps the biggest question for me surrounding this field (and one I’m personally engaged in answering) is whether biotech will finally escape the big-pharma fermentors and become part of our daily lives; that is emphatically part of the theme of Grow Your Own.

It’s especially interesting for me whenever I have occasion to work with designers and artists in this sphere. It makes it clearer to me in some ways what it means to be a scientist, an engineer, a designer, or an artist, when I take part in collaborations, brainstorms or just planning sessions of this nature.

A scientist may often feel she is trained to ask questions, but I think that while many do ask questions, our training is in fact towards finding the best way to answer questions. It appears to me that artists and designers (the border between which remains fuzzy and perhaps politicised to me) are the ones who specialise in framing, but not actually answering, questions. And that’s part of the enjoyment for me; seeing the process of a good question being made, and feeling the cogs tick in my head as the scientist in me seeks ways of answering it. But, for an exhibit, that’s not the point; the point is the question, and a good exhibit asks you a lot, and kicks you out the door with an unsatisfying sense of “where now?”. I think we’ll get that with Grow Your Own.

I’m happy to say, selfishly I suppose, that a good number of the exhibits feature people I’m personally familiar with, including members of our diverse biohacking (neĆ© DIYbio) community in Europe, Asia, and America. For me this October looks set to be the social event of the decade; if this is your interest too, then you have good reason to make it to Cork or Dublin this October!

Other

Now that I’ve broken my “I haven’t blogged in ages” mental taboo, I can resume some other updates. A strategic blogger might try to space these things out, but I’m a do-or-do-not kind of blogger when I deserve that descriptor at all, so I may as well post ASAP. Yet to be covered in upcoming posts:

  • PySplicer, my own based-on-research codon optimisation program works.
  • Some thoughts on existing “Open Source” biotech licenses, and where we need to go with licenses before we realise Free/Libre Biotech.