Status report, part I: Bubble, bubble, toil and trouble...

Howdy, and welcome to another installation of the BioBoard project! While the guys wind down tonight's meeting in the background, I've gone straight to the box to tell you all about our latest progress, because I am really, really excited about this! Although yesterday was originally meant to be our final deadline for the sensor build, we've decided to extend that by another 10 days (until April 27th), leaving ourselves only a single week to make sure that all components communicate and do what they're supposed to. That might seem a little rash - and admittedly, we'll probably be feeling the pressure at the end - but after having seen a home-built pH probe made from Christmas baubles, a ruthenium catalyst glowing beautifully bright orange under pure blue light, and an near-infrared probe for less than $15, we all agreed that there was no way we could stop building now. Hopefully this means that by the end of the challenge, we'll be able to provide designs and tutorials for DIY temperature, NIR, pH and dissolved oxygen sensors, as well as schematics and Ardunio sketches for two different microcontroller set-ups, with and without wi-fi shield, respectively.

Last week, I showed you pictures of the circuitry and read-out from the digital thermo sensor, which has been encased in acrylic tube and hot glue (probably not food safe, so don't try this at home just yet), wired up, and is now a fully functional, perfectly waterproof digital thermometer. This is a really important accomplishment for os, as temperature is a key parameter in most of the microbial processes we expect to be monitoring. Additonally, both pH and oxygen concentation are temperature dependent, so to celebrate our first real victory, here's a shot of the finished thing, and the Boarduino it's running off:

Last week's edition also included a picture of Rolf's initial NIR circuit mock-up incl. an obviously lit infrared LED, and a rather rough hand-drawn sketch of my probe design. One of the interesting challenges of this project is the fact that we intend to measure in liquids, so all our probes have to be 100% watertight, as they need to be able to stand being fully submerged for weeks at a time. This, I assure you, is a non-trivial task. First of all, welding acrylic with acetone is not as easy as it sounds when your personal pet chemist says piece of cake. Not nearly. In fact, to weld acrylic using acetone (or other water thin solvent or glue), both surfaces have to be perfectly planed, and perfectly smooth, which is in practice impossible to achieve with a hacksaw, a file and sandpaper. A Dreml and finer file works better, but acrylic cement of the syrupy variety is really what you need for this sort of rough-job. Hot glue also works fairly well, and in the end, a combination of the two turned out to be our best bet against the wet.

So, having solved that problem, we wired the IR LED and phototransistors (nowly safely encased in acrylic and hot glue - not a worry in this case, since it's enclosed in food safe acrylic) up to a voltmeter, and started measuring the output from the phototransistor and started testing it under different conditions. We got nice, steady readings of about 3.8V (almost theoretical max.) in open air and 3.7V in tap water - much encouraged by the fact that the readings seemed much less sensitive to distance, angle and background light than we had feared - and then dumped the probe in a cup of kombucha - only to see the strangest thing: starting at around 1.5V, the readings kept drifting steadily (and quite rapidly) to as high as 2.8V! We talked it over, brought in  the oscilloscope, mused at the possibility of microbial locomotion as a cause of the phenomenon, light absorbance vs. light scattering, all without coming to any useful conclusion - until it suddenly occured to one of us to actually look at the thing. So we moved kombucha and probe to a clear glass, let it sit for a while, and sure enough: tiny bubbles of CO2 were forming all over glass, probe, and - hence our troubles - LED and phototransistor. A problem we'll only have in carbonated liquids, but since we're fairly fond of both beer and kombucha around here, that's bad enough, and something that would have to be fixed. It turned out to be a relatively simple hack: since shaking the sensor dislodges the bubbles, we merely attached an old cell-phone motor (safely encased) to the assembly with rubber bands. Next step will be to make a daylight shade and outer case for the whole thing from a piece of 1-inch opaque PVC tube. Thankfully, we've still got time to improve upon the design, and will be sure to keep you posted. We'll also be making a thorough How-To wiki for all parts of this project on the Noisebridge website, but for now, pictures will speak more than...well, several hundred words, at least:

Tomorrow, I'll tell you all about what the crazy chemists have been up to - stay tuned for part 2, and don't forget: be excellent to each other, dudes!