2010, an Excellent Year In Review

Well, everyone is doing it so I may as well jump on board. As it happens, 2010 has been a really, really exciting year for me, so writing this will be an indulgent remembrance. In fact, looking back this morning, I was surprised at how much of the things I’ve lately been happy with took place in 2010; some of them seemed like so long ago. Like any year, it’s been full of good, bad and ugly, but for the most part good. If you have any remote interest in my self-indulgence, read on, but this one’s all about me, me, me, me, me. Also, it’s really long. This happens when I don’t blog in ages. Don’t worry, after this things go back to medium-long-normal, with me discussing less self-absorbed stuff.

Things I Did Well

In roughly chronological order, here are some things I did this year of which I am proud.

Dremelfuge

My last creative act of 2009 was to print out several iterations of a centrifuge rotor for my Dremel. I was hoping but not expecting to have a working centrifuge rotor that could be used with common household tools, and early designs were pretty dumb in hindsight.

Dremelfuge 1.0 was prone to ejecting tubes at high speed when used at the medium-to-higher settings on a Dremel, which meant it was effectively unsafe and impractical for routine use. However, early in 2010 I revised, tested and finished the design and put it up for sale on Shapeways. It got lots of positive attention and constructive criticism, which I found really encouraging. And nobody has yet put their eye out, so my fears were thankfully unfounded.

It was initially Creative Commons by-sa-nc, but I later decided to remove the “Non-Commercial” requirement so it could be real Open-Source-Hardware according to the earliest drafts of the OSH license. I’ve since seen a fair few being bought on Shapeways, but alas I don’t know by who, or to where they have gone! I hear tell that quite a few have been printed, also, and there are some nice print pictures on the Thingiverse page for Dremelfuge. I hope someday to meet one in the wild, even in use. Certainly I’ll be using mine a lot more in 2011.

Homebrew Microbiology and Bioluminescence

I was inspired by Mackenzie Cowell’s glowing squid success, and decided to give it a go: how cool would it be to tell people they could culture glowing stuff straight out of a Pandoran puddle if they wanted to give DIYbio a try? So I rubbed my microbiology-fu and the internet together and came up with a protocol, and gave it a whirl.

As it turns out, I was pretty lucky first-go. For reasons that were entirely unintentional, my own unwashed, unfrozen squid carcass ended up always in the dark. This would later turn out to be a requirement for the bacteria to glow! I had also gambled on using a homebrew form of “tryptone”, the peptic-enzyme-digested milk protein commonly used in microbiology. I substituted instead Soy Protein digested with bromelain, a pineapple enzyme. Mostly I did this because it was also more convenient to find soy protein than lactose-free milk protein. As it turned out, the gamble worked, and the bacteria grew excellently.

The gritty details: I was looking for a psychrophilic (cold-loving) bacteria that is alternately called “Photobacterium phosphoreum” or “Vibrio phosphoreum”, depending on who you ask. It likes to grow at 4C-18C, and it only grows in briny conditions. It’s found pretty abundantly on squids, with whom it often has a friendly relationship.

I was more excited the more I learned: this bacteria seemed too good to be true for DIYbio. Not too distantly related to E.coli, it could serve as a nice surrogate model organism, and according to the biosafety classification it was safer than E.coli to boot. It was easy to culture at home without contamination, because no common pathogens grew at 4C on saltwater. Unfortunately for me and several other excited DIYbioers, it turns out that the bacteria also produces a potentially nasty toxin, so I decided not to endorse its use by beginners. Nevertheless, it was great fun to do, and I left the bioluminescence experiment up on my blog for people to try, provided they heeded the safety notice and didn’t eat the bacteria or keep them in the kitchen.

Maker Faire

Following my success with Dremelfuge and Homebrew Microbiology, I was pretty confident that Brian Degger (of Transitlab.org) and I could put on a good show at Newcastle Makerfaire. I wasn’t disappointed, but I was really stunned at how brilliant everything else there was. Our table was really just that, a table with pamphlets and information on DIYbio and some neat projects. It attracted lots of attention because the concepts were cool, but the table itself was probably as bare as they came.

Other attractions at Maker Faire included a musical tesla coil hooked up to a piano, a rubix-cube solving robot, and some robotic spiders with cameras for heads. It was crazy, and inspiring. We’re booked in again for Makerfaire Newcastle 2011, and we’re hoping to get something more advanced together this time round.

For all that we had a quiet table with no hard projects to show off (I couldn’t very well fly with bacteria in my pocket, could I?), we got lots of attention, and even an interview with the BBC (1:42 on the video) where I misrepresented Brian Degger’s DNA extraction protocol by omitting the Salt. Whoops! So, Makerfaire was one of the real highlights of 2010.

Dublin Ignite 4

Ignite Dublin, April 14th in the Science Gallery saw me presenting a dense review of the Makerbot, Reprap and Thingiverse world . I forgot my lines halfway through and missed a slide or two, but who doesn’t on their first Ignite? The bit I didn’t mention in the talk: My Makerbot was actually broken that day, and remained so for some time. Marathon printing at slightly excessive temperatures had worn out the original plastruder, and I would only get it working again with the help of a brand new Makergear plastruder.

The reception was great, people were excited to see this thing and talk to an owner, and I got lots of people pledging that they were gonna go buy one too. In fact, the organiser of Ignite Dublin, Conor Houghton, now officially has a better Makerbot than me, their new Thing-O-Matic. Jealousy abounds.

Getting Hitched

Most significantly of all, May 15th 2010 saw me getting married to Niamh Dunne, a girl I have loved long and deeply. The wedding day was fantastic, and unforgettable. We were married at Gougane Barra, a really magical place with special significance for Niamh, and had our party in the Macroom Castle Hotel. Both extended families and friends joined us for a resounding evening of spontaneous trad song and dance, and our DJ gave us an AudioVisual swing-dancing show to get people out on the floor. It’s been six months, and it just keeps getting better.

It’s between me and my new Wife, so it’s not a long entry in the 2010 review, but this is the most important thing I’ve ever done, let alone this year. Suffice to say, if I seem proud of the rest you can imagine how great I feel about Marriage!

Nexus Cork

Helping to found a Hackerspace in Cork was something I’m both proud and bothered by, because although we now have a room full of fun equipment and a membership sufficient to sustain our activities, there hasn’t been enough activity that I could participate in during my postgrad-induced hermitage. This will change soon, but 2010 was the year Cork earned a Hackerspace at last. Thanks to the Camden Palace Hotel for hosting Nexus Cork, we’ll be sure to help things get more awesome in the coming year!

Building a Lab

I’ve spent much of the year slowly building a collection of equipment, glassware and consumables (including chemicals and reagents) for a home biotechnology lab. Far-fetched as it sounds, I’m nearly finished; pretty much all I need now are DNA (which I’ll get from a synthesis company to-order when I have designed something worthy), Enzymes for DNA work (available from supply companies everywhere, but I won’d buy til I need them), and a working thermal cycler and gel electrophoresis rig (both on order from OpenPCR.org and PearlBiotech.com). I might even get away without the Thermal Cycler if I use the Gibson assembly method and a hot cup of coffee to run my reactions. It’s gonna be a fun year!

In the lab I have tested methods of producing, sterilising and inoculating bacterial agar and broth, and I’ve had great results. The broth for my favourite microbe of the moment, Bacillus subtilis, can be made with leftover water from boiled potatoes and some glucose. I’ve also grown and stored those same bacteria, and I have a lazy experiment in sporulation underway. Eventually I’ll dip one of the many slips of paper I coated in spores in some sterile broth and see if bacteria emerge (they almost certainly will).

It’s been a quiet success, because for now I’m ony doing routine tasks and haven’t had time to write up on them. But pretty soon I’ll be making a big fuss about lab work on this blog and on my new site, indiebiotech.com.

Barcamp Cork

I made it my intention to visit more unconference things after a great experience in Newcastle pre-makerfaire and at Ignite Dublin. So when I learned there was to be a Barcamp in Cork, I decided to offer a talk on Synthetic Biology and Ireland. There were hiccups, like my talk starting 10 minutes late due to a timetabling hangup and IT problems stemming from my long-term lack of a good laptop and the need to bring-your-own-hardware for the projectors. But it was well-received and I got a small posse of people interested in doing DIYbio as a hobby in Cork, possibly as part of Nexus Cork.

Things I Failed At

Every Year has its Fail Whales. This year saw a few things I tried and failed at, which I’m not so proud of. Since it’s good to temper pride with humility, here’s some lame stuff.

Mousetrap Contest

I have much guilt here. There was a time, after my invention of Dremelfuge and Microlathe, when I felt my Makerbot could do no wrong, and that I could print anything in short order and to great accuracy. So I decided to do something fun with the community, and start a little 2010 3D printing-technology inspired design contest.

I had some plastic on order from RepRapSource, so I didn’t worry about my diminishing stocks of ABS. I announced a rough-and-ready contest without including many terms or conditions that I really should have. I said I’d print any entries for Live Mousetraps that were submitted within X timeframe, and the first one to catch a mouse would win $25. The entries poured in faster than expected. It ended up at 8 pretty quickly and I closed submissions. First fail was in underestimating the enthusiasm of the Makerbot community (never again). I started printing some traps, and ran out of plastic. No problem, I’d wait for the new shipment.

New shipment arrived, and it didn’t work in the Makerbot. The bore of the plastruder was too thin for this subtly-too-large plastic, and it was a different breed of ABS, intended for use in RepRaps, not Makerbots. The only way to get it working would be to permanently alter my plastruder, which would screw my chances of using Makerbot plastic thereafter. So I dumped the RRS plastic in a corner, bit the bullet, and ordered lots of Makerbot branded plastic despite the shipping burden.

That plastic arrived, and I started printing again. Then my plastruder hot-end (heater barrel) broke, permanently. A replacement from Makergear would bail me out, but only after a nice long wait for the next batch, plus some time for the in-house testing by Makergear (I wanted something plug-and-play, and that’s exactly what I was given! Awesome folks, those Makergearers).

Of course, by the time I was up-and-running again, I had scant time to test a few traps before I was getting married, and then honeymooning. Some traps were assuredly tested outdoors, and at least one was visited but no catch made. Printing of several traps was problematic due to their having not been tested or printed by their designers. Printing of others was pure IT issue, such as weird archive formatting leading to files that couldn’t be used upon unarchiving. One of the most promising traps, the Tilt’n’trap, which was actually shown to catch a mouse in a captive experiment, seemed to be missing the file for the swinging door when I downloaded it though this may have been fixed since.

My ability to calibrate or use my Makerbot has suffered for the last two seasons from a grudging dedication to my Masters, which deserves its own discussion as a matter of fail. Since I simply cannot focus on something I dislike while there are more interesting options at hand, I had to lock away my Cupcake up in the attic to get any work done on the Masters, which is now looking like it mightn’t come to anything anyway. Live and learn.

At present, I’m resigned to the fact that the Mousetrap contest is long dead. I could print out and test each trap and award something to the first winner, but the fire and spark is long gone from the contest, much to my shame. If I can get my Makerbot printing accurately again soon, I may resume, though I think I’ll have lots of problems with damp plastic and too much flow, so the outlook isn’t good. For all my great luck in getting the Cupcake working nicely, I’ve never gotten the hang yet of calibrating Skeinforge, opting instead for altering the parameters of printed files to make them emerge from a badly calibrated printer well enough for use. It’s reached a point where that won’t really work anymore, and I have to bite the bullet sometime in 2011 and learn Skeinforge before I proceed any further.

Masters and Thesis

I’ve learned an incredible amount from doing my Masters. Not all of what I have learned can or should be shared online, because a Masters or PhD is a project consisting of more than just the student. Suffice to say I learned a lot about why I don’t really want to pursue the academic career anymore, at least not for now. I’ve also learned that sometimes a project is irredeemable, and there’s very little you can do to fix that once it’s happened. You can spend a whole year hacking at DNA with outdated enzymes to make a plasmid system that ultimately mightn’t work at all.

In my case, I have a terrible antibiotic system called Zeocin to thank for most of the fail: even resistant cells continue to take DNA damage, and with the cells I’m using that DNA damage induces death-by-autophagy by the look of things. In other words, for the cells I’m targeting the system can’t be selected for by antibiotic, a prerequisite for ease of use. I have at least one positively transformed cell line with the plasmid, which works great for those cells, but they aren’t human cells so they are irrelevant to the final outcome.

To make matters worse, the future use of the plasmid system involved whole body imaging, so it seemed sensible to use a bioluminescent system from fireflies called Luc-2. When you add luciferin, an expensive reagent, the enzyme makes a glow that can be detected by a machine called a luminometer, or by a sensitive CCD camera. But you can’t use it to test for cells in-vitro. The glow isn’t bright enough to be seen by eye, and maximum glow is obtained by killing cells, so it’s a poor way to select for positive cells. Green Fluorescent Protein would have been great, in hindsight, but then Hindsight is always 2020.

Bottom line: I made something which works on paper but not in practise, and I had to do it the old fashioned way. I’ve come to hate the old-fashioned way, and I’ve learned how to do it better next time, when I’m depending on my own money and time. But it’s too late to fix this project, and it qualifies as the big fail of 2010. Not that I’m upset. What I’ve learned is far more valuable than a successful result ever would have been. Expect all of this to inform my work in Indie Biotech! Rapid prototyping of carefully designed systems, designed with ease-of-use in mind, and a willingness to ditch failures early, will hopefully bear fruit quickly.

What’s Coming In 2011

I am unreasonably excited about the year to come. I have a lab in the attic, a wealth of experience in DNA work and microbiology, and hundreds of ideas jotted on paper, napkin and phone. I’ve already got two events lined up: Ignite 6 on February 10th, and Makerfaire Newcastle in March. DIYbio is proceeding at a great pace and I’m diving in full-time to help kick-start DIY synthetic biology in earnest.

On top of that, I’m looking forward to being finished with my postgrad. That will give me more time for a more holistic geek lifestyle, including more time spent working in Nexus Cork (our lovely Hackerspace), and more time spent playing games with friends. Hopefully I’ll have more to share here in the near future.