streamspace

This post concerns a theme that has been threading through my various social circles and fields-of-activity, and it comes down to this question: What do you hear when someone says "Anything goes"? Many conflicts I've come across in several areas - such as privacy and civil rights activism, or the advent of citizen biotech and its biosafety issues - can be framed as a conflict between parties who perceive "Anything goes" as a threat, and those who perceive it as a promise. Note that neither of these answers is universally right or wrong - but which answer a person chooses will tell you something about how they see the world and which side they're likely to be on in the above mentioned conflicts. Example? The discussion between old-school privacy activists and their post-privacy counterparts. Let me give a polemic summarization of the rationale that underpins the arguments each side tends to put forward: Old-school privacy activists: "Oh my god, ...

Last weekend, some fifteen people gathered in London for a workshop on the ethics of DIYBio, and I thought that I should write about it. The goal was to work out some kind of code for people who kinda-sorta feel associated with the DIYBio movement. The workshop was organized by Jason Bobe from diybio.org , who deserves thanks and bunnies and rainbows for bringing all these people together. So. This is mainly a post about my personal impressions from the workshop, excluding any actual results, the reason being that there will be an analogous workshop in the States in June, and we agreed that we don't want to influence or bias it by publishing any of our results or discussions. First off: It was brilliant to meet everyone. We had participants from Le Paillasse in Paris, London Hackspace, DIYBio Manchester, BiologiGaragen in Copenhagen, and from Cork (Ireland), Freiburg and Berlin. Definitely expanded my "places to travel to in the near future" list. Truth be told,...

Andrew Ellington, Fraser Professor of Biochemistry at UT Austin, has recently published an opinion piece in The Scientist concerning garage biology, synthetic biology, hype and regulation. His main points seem to be: Synthetic biology is nonsense and nothing but a hype, a fantasy Garage biology is nonsense and nothing but a hype, a fantasy The analogy of early computer garage innovation and early biotech garage innovation is nonsense and nothing but a hype, a fantasy. Ellington and his fellow students considered it 30 years ago. They found it impractical then, therefore it's nonsense for all eternity. All this hype and nonsense is threatening the work of real scientists by making authorities go into a panicked regulation frenzy I do agree that there's a lot of hype and fantasizing going on, and I'm not sure I'm buying into the whole BioBricks-approach to biological engineering. And yes, BioBricks-style synthetic biology may turn out to be biology's Artificia...

A few days ago, I was reading a book on working with cell cultures , which includes an overview of the legal requirements for working with GMOs in a lab. This was a bit of a smack on the head for me - I had never thought of that before. With all that talk and all the recent articles hyping garage biology (often meaning garage genetic engineering), I had never come across a discussion of the legal situation. How could I have missed that? So I looked into the matter, talked to people on the DIYBio mailing list, and it turns out that opening up a biohacking space in Germany as an autodidact is somewhat tricky. The following is a summary of the legal situation in Germany (though bear in mind that I'm no legal expert). Genetic engineering is regulated through the Gentechnikgesetz (GenTG) and the Gentechniksicherheitsverordnung (GenTSV) . Any work that inserts synthetic DNA into an organism falls under this law. To do that kind of work, you have to register a lab. This lab has to...

The first tests gave me temperature readings that were off by 30 degrees C from what I'd expect from the thermocycler program I was running. Next up are some auxiliary tests to make sure my setup isn't producing errors. I strongly suspect it is. However, that'll have to wait until the current day job project thing is done, which is keeping me away from Vienna and thus my lab for five days a week. Lesigh.

Random thing I learned today: One of the many details one has to pay attention to when genetically modifying an organism revolves around a thing called codon bias . What led me to this bit of information is part of a writing assignment for the course " Laboratory Fundamentals of Biological Engineering" , taught at MIT. Here's part of the documentation for this course . The question was this: " Would you expect the phage to tolerate p8 modifications that encode all Leucines with the CTA codon instead of the CTG codon? Would you expect the phage to tolerate these same modifications to p3? " When the authors ask whether the phage would "tolerate" this or that modification, I assume they mean to ask whether the phage would still be active and reasonably effective after the modification. Leucine is an amino acid. p8 signifies the protein VIII of bacteriophage (a virus that infects bacteria) M13. Proteins, of course, are chains of amino acids. A codon is...

Way too long ago, I bought a used thermocycler on ebay. It's quite a monster, a Perkin Elmer Cetus, and I've been meaning to test it. I initially thought about testing it simply by running a PCR and seeing whether I get the expected results, but there are so many sources of error in this plan that I've discarded it. There are just so many things that can go wrong with a PCR, even if the thermocycler works perfectly - not least due to my very limited lab skills. So instead, I'm going to measure the temperature of the heating block over a few cycles. There are even sources on the internet that document the temperature profiles of other thermocyclers, so I can use those as a reference. All in all, this approach does not only yield quantifiable results, but seems more attainable to me. Plus, this will (ideally) produce a setup that allows me to test other thermocyclers, too. So. After some investigation of temperature sensors in general and in particular, I decided to use...