streamspace

Biotinkering & DIYBio - 2011 in review

2012-01-20T00:25:00.001+01:00

I've been meaning to summarize what happened in 2011 in the DIYBio and biotinkering sphere, and I finally got around to it. So here's the review of my personal year 2011.

First off, the main thing that happened in 2011, I think, is that both the global and the European community started connecting on a personal level. Which was awesome, and I hope this trend will continue in the future.

The first months, working alone

For the first few months of 2011, I was mostly tinkering on my own in the non-space in the old location of the Space Agency, a Berlin-based hackerspace (https://trac.raumfahrtagentur.org/). I was just trying to get my hands dirty, trying to get the basics to work, such as gel electrophoresis and PCR. After getting frustrated with my semi-functional old thermocycler, I had decided to fork out a substantial amount of money and buy a new one in late 2010, a 24-well Piko thermal cycler. Part of the reasoning in this was that the OpenPCR was still unavailable, and the Piko was small and light enough for me to carry around and take to workshops.

Freiburg geekend

I eventually made contact with another Berlin-based biohacker, Sascha, and another one in Freiburg, Ruediger. We agreed that it might be fun to have a geekend together, and so, in April, Sascha and I drove down to spend a weekend tinkering around in Ruediger's home lab. I had previously ordered a subset of the primers that are part of a standard DNA forensics kit, and Ruediger had ordered another subset of that. I brought my thermocycler and we had a lot of fun drooling into test tubes, testing Ruediger's custom-made electrophoresis power supply, trying out different DNA extraction methods and kits, and running gels to determine our personal DNA forensic profiles.

DIYBio Continental Congress

Shortly after that, in May, there was the DIYBio Continental Congress in London, initiated by Jason Bobe. I daresay that most of the European community was represented there (see my brief summary post here). While the point of the meeting was to work on a code of conduct for DIYBio and we didn't really get around to do much biotinkering, it was fantastic to finally meet everyone in person.

Hackteria Lab Retreat

After that, at the end of July, a motley crew of artists, engineers, hackers and whatnots gathered in an old monastery in Romainmotier, Switzerland, for the Hackteria Lab Retreat - among them Brian Degger and Mackenzie Cowell, the founder of DIYBio.org. I've also been told that it was the first time that all three of the marvellous founders of Hackteria, Marc Dusseiller (Zurich), Andy Gracie (Barcelona), and Yashas Shetty (Bangalore) happened to be in the same place at the same time. The people in attendance at this meeting were quite a different crowd than the ones in London, and the spirit of the event was much more anarchic and artistic. Apart from wandering the Swiss mountains and talking to the other participants, I mostly did conceptual work on the idea of a portable molecular biology lab - the lab-in-a-backpack. Which I need to do more work (and a write-up) on.

CCCamp and the wider hacker community

I also had nice chats about biotinkering at the German CCCamp in August, among others with members of the Metalab, where a group of interested people have started to gather and initiated the establishment of a biolab.

Building the new Space Agency lab

Sometime in May, the Space Agency had moved to a new and bigger location, and so for most of the summer, I was busy converting a former restroom there to a small biolab. Which was a lot of work, but eventually yielded a small, but very useable little lab. Soon after I was done with that, I finally acquired an affordable spectrophotometer and spend a few weeks getting acquainted with it and reverse engineering its serial interface so I'd be able to do wavescans.

DIYBio UK Summit

Another memorable event was up in Octobre, the DIYBio UK Summit in Manchester. Once again, it brought together some of the European community, plus Sung and Oliver from Genspace, who had flown over from NYC for the occasion. There were several workshops - the one I joined centered around microbial fuel cells. It turned out that these are astonishingly easy to make, and I mentally filed MFCs as a good subject for future workshops to get people playing around with biotech at a low budget.

More interconnection - getting in touch with MIT's IIH

In Septembre, Jose Gomez-Marquez from MIT's Innovations in International Health Lab asked around on the DIYBio mailing list whether there where any biohackers in Berlin. We got in touch, and he generously gave a talk the the Space Agency about his work at the IIH, which was fascinating. I encourage everyone to have a look at their activities around collaborating with health professionals in third-world countries.

To be continued...

So, now 2011 is over, 2012 is upon us. What next? There are a few things I'd like to see/make happen in the next year:

1) Hold/organize more workshops and talks, DIYBio-wise. Genspace is my shining example here.
2) Work on my own projects - top on the list is the above-mentioned lab-in-a-backpack - ideally in cooperation with others.
3) Personal goal: Blog more :)
4) Collaborate more. One thing that's high on my list but is highly dependent on my always-tight time budget: Go visit Cathal Garvey of Indie Biotech. Not sure that's going to happen, as I have other things lined up for 2012 that look to be very time-intensive.
5) Possibly find more collaborators in Berlin, and build up a bigger space together - while the lab at the Space Agency is nice and cute, it can hardly accommodate two people working at the same time, and hence is spectacularly unsuitable for workshops or several people working together.
6) Explore the possibilities of biotinkering within the frame of German law if you don't have an S1 license - DNA analysis, metagenomics experiments, and RNA interference experiments come to mind here.
7) Visit some other biohacking spaces, if time permits it. High on my list are Genspace in NYC, Biocurious in the Bay Area, Nullspace in LA, Lapaillasse in Paris, and BiologiGaragen in Copenhagen.

So. Those were my thoughts on 2011 as far as I could scrape them together. I'd love to see others from the community post their summaries of the past year and their plans for the coming one.

Finde den Fehler

2011-12-26T20:24:00.001+01:00

Zwei der möglichen Arten, als Mann über Genderfoo zu schreiben:

1) Zu der Erkenntnis kommen, dass allgegenwärtige, normative Genderstereotype auch für männlich identifizierte Personen Nachteile, Probleme und Einschränkungen mit sich bringen, und dass ein Gegenhalten gegen diese Stereotype häufig zu Frust und schlechter Laune führt; darüber reflektieren und die Erkenntnisse aufschreiben.

2) Für Obiges den Feminismus verantwortlich machen, seinem Beissreflex gegenüber dem bösen F-Wort freien Lauf lassen, selbigen vorwiegend mit vagen und noch nicht reflektierten Eindrücken von "Feminismus" begründen ("Ich hab da vor 15 Jahren mal gelesen, dass eine Feministin Männer doof fand") und ansonsten sein "Argument" vor allem aus Anekdötchen konstruieren über all die Male, die man von Frauen schlecht behandelt wurde.

Hausaufgabe für die Leserschaft: Welche der beiden Varianten ist konstruktiv und lädt zu empathischer Auseinandersetzung ein, und welche ist destruktives, unreflektiertes Gejammere?

What do you hear when someone says "Anything goes"?

2011-11-09T14:36:00.000+01:00

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, there are so many possibilities with all this new technology! Our highest priority should be to guard and fight against its misuse by authorities, companies and other powerful entities!"

Post-privacy activists: "Oh my god, there are so many possibilities with all this new technology! Our highest priority should be to do amazing things with it that change the world for the better!"

This doesn't mean that the old-schoolers don't see the possible benefits, or that the post-privacy people are completely oblivious to the dangers of all our shiny technology toys; it's more of a difference in priorities.

Personally, I'm a bit on the fence. I've been surrounded by adherents to the threat-centered narrative of new technology for what feels like forever, and I've lately been asking myself whether they may not have gotten stuck in this mindset to the point of becoming irrational about it. Put differently, I'm wondering whether it's a mistake to put so much energy and time into reactively fighting threats (that may or may not turn out to be real) that there's hardly any left for proactively building awesome shit. On the other hand, I am very much aware that the proactive stance has its risk, and they're no small ones. This proactive, or (literally) constructive, approach requires a lot of trust in the way things will play out and our ability to cope with it - a bit of a happy-go-lucky attitude, if you will. This may also explain why the old-schoolers like to accuse the post-privacy people of being naive and starry-eyed.

Another example for the gap between "Anything goes" as threat or promise is the biosafety and bioethics debate around the fledgling DIYBio movement. There's the faction of people calling for tight regulation, control and oversight of any and all genetic manipulation, and for limiting this activity to thoroughly vetted and controlled institutions by all means possible. The more extreme cases even call for forbidding this kind of research altogether, invoking possible risks of bioterrorism, grey goo and just general atrocities. This is the faction that hears "Anything goes" and interprets it as a threat. And then there's another faction that basically says "Look, the solution, clearly, is to use the immense potential of this technology, and put a lot more weight behind understanding it and learning how to use it safely, to the point where we're capable enough to outrun any upcoming threats." For this particular issue, I'm firmly with the people who perceive "Anything goes" as a promise, but I've certainly met people who've called this position reckless.

Closing remark: These rambling ruminations have been sparked by the article "Cognitive Biases in Times of Uncertainty". It brings up the issue of threat-based narratives and their harmful side-effects:

"Threat based narratives take root – enemies are gathering force and intent on destroying or appropriating what we have. We need to be vigilant and band together to protect our interests. [...] Threat based narratives lead to polarization – if you're not with us, then you must be against us.

Threat based narratives again have a pernicious effect – they reinforce our tendency to focus on the short-term. They lead us to further magnify risk and discount potential rewards. The threat is imminent – we must focus on protecting ourselves now from the enemies gathering force. We can't afford to be diverted by longer-term issues – the battle is here and now. If we don’t win today, we will have no tomorrow."

In short, I've become somewhat wary of threat-based narratives - sure, they can alert us to potential danger, but they also tend to be self-reinforcing and endless, they're an excellent way of driving ourselves crazy, they leave us in a mindset where we have neither the time nor the energy to develop positive long-term visions for the future, and if we let them run away with us, they make us an easy target for manipulation.

Bonus points to any reader who noticed that the last paragraph - the one complaining about threat-based narratives - was itself outlining yet another threat-based narrative :)

DIYBio Continental Congress, London, May 8th 2011 - Personal Impressions

2011-05-11T00:34:00.005+02:00

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, getting to meet people in person was my main reason for attending. Having grown up in the comparatively old and well-established German hacker sphere, somewhere between the ultra-political Chaos Computer Club and the more free-spinning parts of the hacker community, I'm somewhat cynical when it comes to community codes.
Despite that, it was certainly interesting to learn the various viewpoints, motivations and aspirations of the attendees. And of course, the post-workshop pub session was at least as interesting as the workshop itself.

All in all, I think a significant outcome of the workshop may have been to bring the very scattered European DIYBio community closer together. Contacts and mutual invitations were exchanged, and there has been talk of organizing a more hands-on get-together in the near future, which would be just rad. Let's see whether we can make it happen.

Ramblings: "On Regulation" by Andrew Ellington

2011-03-05T15:19:00.003+01:00

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 Artificial Intelligence. And again, yes, careful with basing your regulatory work on a collective fantasy.
Generally, though, I see a couple of issues with Ellington's text.

First thing: He's jumbling together things that would better be treated separately, namely synthetic biology and the molecular biology/biotech garage culture. Yes, many of the garage biotech enthusiasts are fascinated by the idea of a biological equivalent to an Arduino. But that's not the only thing DIYBio is about. It's also a culture that's about taking part in the current developments that will probably transform society in one way or another, with a hands-on spirit. Another undercurrent seems to be a certain scepticism towards and disillusionment with today's system of academic research. Ellington's display of (self-identified) verified-old-person patronization is really not helping with that.

The article has the whiff of the idea that the future is essentially the same as the present, just a bit later. But it isn't. Example: Would a 70ies IBM representative have been able to predict the whole mess of web application security or the considerable black market for identities, credit cards, botnets and exploits that we're dealing with today? Probably not. William Gibson did, but he was a novelist, who is in the business of, well, you know, fantasizing and informed nonsense.

Ellington goes on to explain why the analogy between early computer garage innovation and today's garage biotech is a mirage:

The difference between DIY Bio and Michael Dell putting computers together in his garage is the difference between the availability of the raw materials. There is no 'Radio Shack' for DNA parts, and even if there were, the infrastructure required to manipulate those parts is non-trivial for all but the richest amateur scientist.

Try googling "DNA synthesis" and just pick one of the sponsored links. Then take into consideration that "non-trivial" does not usually deter someone overly enthusiastic, young, and unverified. And then imagine that a tight budget can be a motivator to come up with alternative routes, or that there are, in fact, moderately wealthy amateurs out there who have the means and motivation of pooling resources, and who'll be happy to share and let others use their infrastructure.
In short: I'm not convinced by that argument.

As a closing statement, Ellington imparts the following:

But can we at least leave out this part of the conversation, the notion that there could be a black market because folks who hook up platinum electrodes to car batteries and pour agarose gels in Play Doh molds might someday actually create a bacterium that converts glucose to gold?

Now, see, that's exactly the kind of condescension that drives overly enthusiastic, young, unverified people to antagonize academe, adopt a "Fuck you, I do what I want" stance and create the very underground that Ellington finds so cute and unrealistic.
It happened in IT, where it contributed to the genesis of today's black hat culture, parts of which now fuel the world of organized computer crime. So tread carefully.

DIYBio and biotinkering - Laws and regulations in Germany

2011-02-02T17:07:00.000+01:00

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 fulfill certain requirements, depending on the kind of work you want do. There are four categories (or levels) of work, from Level 1 (no risk to humanity or the environment) to Level 4 (high risk to humanity and the environment). This categorization is done based on a risk assessment and is closely associated with the kinds of organisms you want to work with.
There's a number of organisms that have already had an assessment done (see this document) - for example, E. Coli K12 is Level 1; Hepatitis C virus is Level 3.

Building and equipping a Level 1 lab seems doable, as the requirements are straightforward - it has to be a sufficiently spacious room, with a door that opens to the outside, a sink, workspace surfaces that are suitable for the chemicals that are used in the work and during disinfection, with an autoclave somewhere on the premise, and a number of other smallish things. Once you've registered such a Level 1 lab, you don't need to register every single project you're doing, but you have to keep detailed records for all of them.

The real hurdle is that you have to name two separate people in the registration, a project lead and a biosafety commissioner, both of whom need to have a degree in biology or medicine or closely related field, plus three years of work experience in an established genetic engineering lab and completion of a government-approved biosafety training.
Apparently, the agency responsible is a bit flexible on the qualifications of the project lead and biosafety commissioner, but very likely not to the point where they'd accept complete autodidacts.

This essentially means that any kind of biohacking space in Germany will have to rely on finding established professionals who are willing to cooperate and assume liability for anything that happens in this space.

Oh, and the penalty for doing any kind of genetic engineering work without going through this process is three years in jail or a fine of around 100,000 Euros.

All of this is currently a bit of a problem for me, as I have neither the formal proof of qualification, nor do I have two people with such proof of qualification who would be willing to act as project lead and biosafety commissioner, respectively.

I'm wondering how well suited this law is to the current development of a DIYBio movement in Germany, and whether it may provoke the creation of a biohacking "underground", which would be impossible to control or even monitor. Maybe a change to this law would be better able to police and integrate the current diffusion of genetic engineering technology amongst enthusiastic and capable autodidacts.

Meanwhile, in the US, the Obama administration seems prepared to take a more open-minded approach to garage biotechnology, as reflected in this article on Slate: "Faking Organisms: How can we govern the garage biologists who are tinkering with life?".

Brief update: Testing my PCR thermocycler

2010-08-29T23:30:00.001+02:00

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.

Genetic engineering bits and pieces: Codon bias

2010-08-29T22:58:00.003+02:00

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 a triplet of nucleotides that codes for an amino acid. Some amino acids have more than one codon associated with them, which is possible because triplets of A, C, G, T can encode 4^3 = 64 amino acids, but cells only use 20.
It turns out that not all codons are created equal - within an organism, there is usually a bias towards some codons over others - some codons occur more frequently than others. This is associated with the relative abundance of the corresponding tRNAs (transfer RNAs). tRNAs are molecules that "carry" an amino acid on one side and a triplet of ribonucleotides on the other. They are used in building the actual amino acid chains of proteins. Here's an illustration from the Wikipedia entry on tRNA:

The more tRNAs of a certain type there are, the more proteins incorporating the amino acid associated with this codon can be built in a fixed timeframe. Compare this to a factory setting: If you have ten workers that are assigned to mount a tire on a car, then you can mount at most ten tires simultaneously. If you have twenty workers assigned to this task, then you can mount at most twenty tires at a time and so on.
It turns out that E. coli, the host that M13 is supposed to infect in the course's experiments, has a codon bias towards CTG for Leucerine. As can be seen in Table 2, here, the frequency of the codon CTG for Leucerine is 0.49, while the frequency for CTA is only 0.04. In Table 3 of the same document, it becomes apparent that the tRNA concentration associated with CTA is "minor", compared to that associated with CTG. This means that there will be few CTA-tRNAs floating around an E. coli cell.
Now, a virus such as M13 "hijacks" the cellular machinery of its host to replicate and assemble itself. It has to make do with what it finds in its host cell. And if it finds very few of the resources it needs to replicate itself, then its chances of survival are diminished.
M13's p8 is its coat protein - the protein that builds its outer shell. A wild-type virus needs 2700 copies of those. p3 is the phage tail, of which there are only five per virus.
So one answer to the question is: The phage may still be active and effective if you change the CTA codons in p3 to CTG codons, because the low number of CTG-tRNAs floating around may still be enough to make the five required copies per phage, but it will probably take a hit if you change the CTA codons to CTG in the gene that codes for p8.
To summarize: while there are many other factors that play into this whole protein synthesis performance thing, codon bias is definitely something to keep in mind when reengineering organisms.

Testing my PCR thermocycler, Part I: Setup

2010-08-14T21:25:00.007+02:00

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 an IC. There are some that are accurate enough for this purpose in the required temperature range, and I wanted to spare myself the hassle of constructing a circuit for an NTC, calibrating it etc. I selected the Dallas Semiconductors DS1621S, which comes in an SOIC8 package. Have a look at the data sheet, if you're interested. The device gets stuffed into 0.5 ml PCR tube, with the wires protruding out the top, like this:

The Perkin Elmer Cetus doesn't have a heated lid, so just leaving the lid open for the wires shouldn't distort the temperature readings too much.
The DS1621S gets hooked up to an Arduino and the data collected on my computer.
After soldering, I realized that I won't be needing all eight pins, but alas. If the data from the initial run make any sense at all, I'll prepare more of these sensor tubes, so as to measure temperature across different positions on the heating block. But now, on to the actual measurements. Data will be made into pretty graphs and posted here once I'm done.

Ghetto Sanger Sequencing, Part I

2010-06-01T21:54:00.002+02:00

Here are some ruminations about the first steps I'm taking towards a kind of Ghetto Sanger sequencing contraption:

Basically, what I'm trying to build is a setup that will automate some of the steps in Sanger sequencing. One of these steps involves automatically starting a gel electrophoresis, which includes placing the gel into the buffer-filled gel box, firing up the power source, monitoring the gel's progress, shutting down the power source in time and removing the gel from the gel box.

One of the problems here is that gels are somewhat difficult to handle for something like a robotic arm. It's much like trying to transfer a slab of Jell-O into a water bath and then out again.

So my idea was to use plastic slides with gel-filled channels. Let's call them gel slides for short. The material should be non-conductive, transparent, and withstand a certain a mount of heat. Here's a sketch of one, with 8 channels, 6 of them are sketched as being gel-filled:

Initially, I thought I could just cut channels into a piece of acrylic using a laser cutter or CNC mill. Unfortunately, people who know their milling have explained to me that neither is trivial.

So for the first prototype, I used a sandwiched design, with a kind of laser-cut "comb" glued on top of a solid bottom slide. The comb turned out very irregular, which is not good:

It will be a bitch to glue this onto the bottom slide correctly, and since these gel slides will probably be a consumable, this kind of hassle is not really an option. So I'll have to do something differently next time.

I'm thinking about maybe using a design that is closed on both sides rather than just one, but I have no idea whether this would undesirably impact the electric field during electrophoresis.

Also, someone pointed out to me that it might be much better to cast the gel slides rather than cut them. Or, perhaps, there is a much better way to do this altogether. Needs more thinking.

The German Pirate Party Gender Debate: An outside view

2010-05-16T13:32:00.001+02:00

Intro: I am not a member of the Pirate Party, nor of any other party. I briefly considered joining the PP, but changed my mind. I have not actively participated in said debate, and I've been following it casually rather than obsessively. Still, here's the impression it left me with:

The gender debate was a classic example of political conflict, where the participants hold very different beliefs, values and perceptions of what the world is like. What I expect from a good politician is that they can relate to their opponent on some level, accepting that just because someone doesn't agree with them doesn't necessarily mean they're wrong, hostile or just plain stupid. I expect them to understand that in a complex world, there are many valid experiences and many valid viewpoints, and that politics is about reaching an understanding between this multitude of positions.

What the Pirate Party (through many of its members, sympathizers and leading voices) exhibited, was pretty much the exact opposite of this ideal I just described. People who held a view not in concordance with the majority's were shot down, insulted, threatened with violence and publicly ridiculed. An environment where political conflict is handled in such a way is quite simply not a place for me. It recreates a major part of what sucks about established parties. Same old, same old, and far from progressive.
Note that all I've said so far is largely independent of what the debate was actually about.

Concerning the actual subject of the debate, it reminded me a lot of something Neal Stephenson wrote in "Snow Crash":

"It was, of course, nothing more than sexism, the especially virulent type espoused by male techies who sincerely believe that they are too smart to be sexists."

Amen.

Term confusion: Synthetic biology, Biohacking, DIYbio

2010-03-10T13:01:00.000+01:00

There seems to be some confusion as to what these concepts mean and how they differ. I'll make an attempt at clarification and explain what these three terms - Synthetic biology, DIYbio, Biohacking - mean to me.

Synthetic biology (synbio): This is an academic field of study that moves the focus from biology as an activity of observation to one of manipulation. One motivation here is that of understanding by synthesis, much like a beginning electronics enthusiast would build a circuit from scratch to understand how the different components interact, what happens when you leave out one component, how the behaviour of the circuit changes when you use a different resistor etc.
Apart from this, one important idea in the synbio community seems to be that biotechnology should become a true engineering discipline, which requires standardization, abstraction, modularization, and componentization. This is the spirit behind BioBricks and the Registry of Standard Biological Parts.

DIYbio: Do-it-yourself biology. I think this is a bit of a misnomer. DIY biology has been around for a long time - think of hobbyists collecting and identifying bugs or plants, or bird-watching. The current excitement is more about DIY biotechnology - modifying biological organisms or analyzing their genomes in your garage, using the ever-growing tool box of DNA sequencing, DNA synthesis and genetic engineering. It's about appropriation and diffusion of an up-and-coming technology by amateur enthusiasts.

Biohacking: Possibly the fuzziest of the three terms. I consider biohacking a niche of DIYbio, one with a subversive edge, and it is more of a mindset than anything else. It's about figuring out how DNA forensics works and how it can be subverted, creating knowledge and methods for all to use outside the patent thicket of present-day biotech, designing and building tools that deliberately undercut the high-price market of lab equipment, developing and distributing home test kits for known genetic modifications in food, or reverse engineering the fiercely protected software at work in today's DNA sequencers.

So there. Comments welcome.

Gene Assembly in Ciliates - A glimpse into biological information processing

2010-02-16T02:06:00.003+01:00

When researching material for a term paper on biocomputing, I came across a fascinating group of critters called ciliates. Ciliates are unicellular organisms that process their genomic information in a peculiar and unique way, one that was fascinating to study for the computer scientist side of me. In ciliates, we find a very illustrative example of how biological systems use structure as information. Plus they use pointers and linked lists.

There they are. Some ciliates. [Image from http://www.liacs.nl/~rbrijder/views_gene_assembly/]

Ciliates, unlike other eukaryotes, have two different kinds of nuclei: macronuclei and micronuclei. A macronucleus is used in the everyday operation of the organism, for synthesizing the proteins it needs to survive. A micronucleus only comes into play during sexual reproduction (I'm stressing this because ciliates can also reproduce asexually). During sexual reproduction, two ciliates recombine their genetic material. The result is somewhat unusual: instead of yielding 2+n organisms - two parents, n children - this reproduction transforms the two original organisms which are then more like twins than anything else.
This is odd to begin with, but the way this works is even more interesting. Because after exchange of genetic material, each of the individuals discards its macronucleus and assembles a new one from the genetic material in the micronuclei.

Now, the genetic material as stored in the micronuclei is highly redundant and scrambled. Parts of genes are scattered all over the micronucleic genome, and during gene assembly, these scattered parts are cut and pasted back together. The mechanism of this, as last I heard, is not entirely understood. But we do know that fragments of genes contain pointers - short DNA sequences at the end of a fragment that match the start of the next fragment somewhere in the micronucleic genome. To me, this looked an awful lot like linked lists, with genes being the entire list and gene fragments being the list elements, chained together by pointers that link the one element to its successor. However, this can't be the whole picture, because the "pointers" in the micronucleic genome are not unique - some pointers are only three bases long and point to any number of locations in the genome. One hypothesis is that the macronucleic DNA is not entirely discarded at first, but serves as a "template" for the genome-in-making. However, this, too, leaves some questions open.

The other point I alluded to earlier - about structure being information - is an important concept in pretty much every type of biological information processing, and it also comes in during gene assembly. The assembly process relies on the three-dimensional structure of the DNA molecules to bring gene fragments together and align them in a way that lends itself to their cutting and pasting. Bazinga.

So much for a brief overview of gene assembly. If you're hooked: There is one book on the subject that gives a good overview, "Computation in Living Cells: Gene Assembly in Ciliates" by Ehrenfeucht et al. Maybe this is your starting point for going down the rabbit hole of biological information processing.

Follow-up on "To GM or not to GM?"

2010-02-04T13:51:00.001+01:00

In a previous post, I wrote about the controversy around a toxicity study of Monsanto crops. This post got a very valid comment, which I'd like to respond to here.

Paul wrote:

"de Vendomois' statistics are poor and not applicable to the Monsanto research data they used. The funding for their research was also funded in its entirity by Greenpeace. You have to ask yourself why Greenpeace/de Vendemois used the statistical approach they did knowing its flaws (as pointed out to them by the European Food Safety Authority in 2007). A cynic would suggest they conspired to use whatever method appeared to shed a negative light on GM crops. Would this collaboration have published truly independant research that showed no difference in toxicity between GM and Non-GM plants?
I'm no fan of multinational corporations profiting from our basic food needs, but the dodgy, deceitful and blindly prejudiced approaches used by NGOs such as Greenpeace as part of their scaremongering campaigns is far worse than the in-house research by companies like Monsanto as far as I can see."

This is a very good point.
One thing that made me rather uncomfortable when reading the Vendomois paper was my inability to follow the statistic acrobatics they performed. Which has prompted me to go and brush up on my statistics, but meanwhile, I can only pick up on the points that seem to be valid even without having to judge the validity of the statistics employed - the legal battle around data that was supposed to be public anyway, the fact that genetic manipulations as employed are more of a shotgun approach than anything else, and the failure of regulatory bodies to require elucidation of the (inadvertent) changes in the plants' genomes.

Generally, I'm in a bit of a troubling spot: I'm generally in favor of biotechnology, genetic manipulation, and whatnot, but also skeptical of how it is practiced today. I can stand neither the fear-mongering that Greenpeace and friends are spreading, nor the glorious promises and dubious practice of corporations like Monsanto. I'm trying to find my way in between these two extremes, which is rather difficult. Apparently, with the blog post in question, I haven't done a very good job at it.

Google Xistence - a new approach to identity

2010-01-26T16:56:00.002+01:00

It's a public secret: The world of social networks is about constructing identity. Let's be honest: Every one of us has probably tweeted about the cool club we've been to, or what airport we're currently stuck at, or that we're reading poems in some cool foreign language, to make our lives appear intriguing and cosmopolitan. Social networks are as much about constructing identities as anything else. They have enabled a construcivist approach to that elusive beast, identity, and Google Xistence is merely taking this a step further.

Inside rumours that shed a bit more light on how Google Xistence works have reported that there will be a host of preset identities to mix and match - start with a "Renaissance Man" baseline, then throw in some "World Citizen" and "Political Activist", and Xistence will generate status updates, photos, locations and more that fit this synthetic persona.

But who wants to be stuck with a static identity? This is why the folks over at Google Labs also provide the option of changing your persona whenever you feel that it's time for a change in your life. The algorithms they use for that will phase out the old persona and phase in the new one over a safe period of time, ensuring a smooth, believable transition.

Becoming who you want to be has never been so easy, and I sure as hell want an invite. Because, you know, being glamorous all by myself is just a little too tedious for me at times.

To GM or not to GM? Another look at the data...

2010-01-14T20:20:00.005+01:00

A recently circulated paper by Vendomois et al takes an independent look at data from food trials of genetically modified (GM) corn on rats. The data was originally obtained in studies conducted by Monsanto as part of the application for market approval of these GMOs. I'd like to highlight a few points here. But first, some introduction.

The original data stems from a trial where a population of rats was fed different kinds of GM corn over a period of 90 days. The GM crops in question were Monsanto's NK 603, MON 810 and MON 863.

NK 603 is one of the Roundup Ready crops. Roundup Ready crops are genetically engineered to withstand large doses of Monsanto's herbicide Roundup. The idea is that fields can be sprayed with Roundup, the genetically engineered Roundup Ready crops survive, and all the weeds around it die. Let it be mentioned here that this approach has drawbacks all its own, as weeds have started to develop a resistance to Roundup over the years, which led to ever increasing doses of the pesticide being necessary to kill weeds, as documented in another report.

MON 810 and MON 863 are Bt crops, which use a different approach. In these crops, a transgene derived from Bacillus thuringiensis was introduced into the genetic material: These plants were genetically engineered to synthesise the pesticide themselves.

So the suspicion, with all three crops, is that they may contain residual toxins: NK 603 from the exposure to large doses of pesticide, MON 810 and MON 863 because they actually synthesise the pesticide. The original study and analysis by Monsanto concludes that the crops are still suitable as food and feed. And this is what the authors of the independent study dispute.

To summarize, Vendomois et al have two main points of criticism. One is the methodoloy of Monsanto's study. They point out that several important physiological parameters were simply not recorded in the study, that the setup of the study had flaws, that the trial period of 90 days was much too short, and that the statistical power of the recorded data points is not sufficient to conclude that the GM corn is not toxic.

The other point of criticism is derived from a re-analysis of the available data. The authors find signs that point to a possible toxicity where the original Monsanto analysis glossed over certain things, for example claiming that a disturbance in kidney function was nothing to do with the GM corn, but stemmed from a susceptibility to kidney problems of the specific strain of rat used. Vendomois et al point out here that even with such a susceptibility, the rats in the study were too young to spontaneously develop kidney disease, and what's more, the disturbance of kidney function was specific to the MON 863 group - none of the other two GM groups or control groups exhibited this kind of problem.

Generally, Vendomois et al conclude that the study does not support the claim that the GM crops in question are safe. Instead, the data indicates a necessity for further studies and signs of possible toxicity. For a lack of enough data, the authors can only speculate whether the signs of toxicity stem from the residual pesticides in the crops or whether they are due to as yet unknown side effects of the genetic manipulation.

Let me elaborate here: Genetic manipulation is not as neat as one might imagine. It's not a matter of laying out the genomic material on a table, neatly cutting out the features one does not want and inserting others in a suitable place and be done. The way genetic manipulation currently works is messy and known to be mutagenic in ways that are almost impossible to predict. The process is rather disruptive and can cause rearrangements, insertions and deletions in parts of the genome that were never targeted. The mutagenic effects of genome manipulation are explained in more detail in the paper "The Mutagenic Consequences of Plant Transformation" by Latham et al. Consider the following passage from Latham et al:

"One [study] analysed the commercialised Roundup Ready soybean insertion event 40- 3-2. In addition to the intended EPSPS (enoylpyruvate shikimate synthase) transgene described in the original application for commercial approval, the authors found a 254 bp EPSPS gene fragment, a 540 bp segment of unidentified DNA, a segment of plant DNA, another 72 bp fragment of EPSPS, and evidence for additional alterations to flanking plant DNA, (USDA Application # 93-258-01p). These insertion-site mutations were reported only after commercialisation of Roundup Ready soybean insertion event 40-3-2. Interestingly, independent analysis of another commercialised event, Maize YieldGard (event Mon810), also found evidence for previously unreported insertion-site mutations."

So when you introduce new material into a plant's genome, you do not really know in which ways specifically you altered the plant. This is what Vendomois et al are talking about when they wonder whether the toxicity might not be due to some other, unknown change in the corn's genome. What with the ever-dropping prices of genome sequencing, I wonder whether it might not be feasible and insightful to sequence the parent strain of the GM corn, then sequence the GM corn and hunt for unexpected differences that might have arisen during the genetic manipulation.

The paper contains one more interesting point, in the section on Data Collection:

"The raw biochemical data, necessary to allow a statistical re-evaluation, should be made publically available according to European Union Directive CE/2001/18 but unfortunately this is not always the case in practice. On this occasion, the data we re- quired for this analysis were obtained either through court actions (lost by Monsanto) to obtain the MON 863 feeding study material (June 2005), or by courtesy of governments or Greenpeace lawyers. We thank the Swedish Board of Agriculture, May 30, 2006 for making public the NK 603 data upon request from Greenpeace Denmark and lawyers from Greenpeace Germany, November 8, 2006 for MON 810 material."

Well, isn't this just fascinating? Monsanto was obliged to publish the data, but had to be forced to fulfill their obligations through lawyers and court action.

One last word of caution against roundly condemning GM crops: In the case of Roundup Ready crops, we don't know yet whether the signs of toxicity are due to the pesticide residues or due to side effects of the genetic manipulation. If it proves to be the former, then let it be said that genetic engineering would not be the culprit here at all. A similar effect would have been observed had the crops been traditionally bred to withstand high doses of pesticide.

Now go and enjoy your food.

Readings: "Steps toward broad-spectrum therapeutics: discovering virulence-associated genes present in diverse human pathogens"

2009-11-28T19:03:00.007+01:00

Reading Stubben et al: "Steps toward broad-spectrum therapeutics: discovering virulence-associated genes present in diverse human pathogens"
BMC Genomics, Volume 10, Issue 501, 2009
http://www.ncbi.nlm.nih.gov/pubmed/19874620

I found this paper interesting for several reasons: first, it follows a metagenomics approach, second it involves data mining work, and third, it's a step towards making an abstraction from individual pathogenics organisms to a more general understanding of virulence at a biomolecular level.

In the abstract, the authors summarize the objective of their work:

"New and improved antimicrobial countermeasures are urgently needed to counteract increased resistance to existing antimicrobial treatments and to combat currently untreatable or new emerging infectious diseases. We demonstrate that computational comparative genomics, together with experimental screening, can identify potential generic (i.e., conserved across multiple pathogen species) and novel virulence-associated genes that may serve as targets for broad-spectrum countermeasures."

It is interesting that the authors investigate virulence as a possible target in combating pathogens. The rationale behind this is to avoid killing bacteria - which fosters the development of strains that are antibiotics resistant. Instead, the idea is to "disarm" the bacteria by targeting and eventually disabling their virulence factors.

Virulence: The damage a pathogen causes to the host during infection

The authors thus attempted to computationally identify virulence-associated proteins. The idea was to consider all proteins produced by a set of bacteria, both pathogenic and non-pathogenic, group the proteins by similarity across species, and then look for groups of proteins that are present in all pathogenic organisms, but in none of the non-pathogenic ones.
To this end, they obtained a collection of 617.000 proteins from all the 214 microbial genomes that have been completely sequenced to date. They then aligned each of these 617.000 proteins against all others, selected the 1000 best hits for each protein and grouped these hits using a clustering technique. They then recorded which of the clusters was represented in which organism.With this information, it was possible to search for clusters that were associated with many organisms that are known to be pathogenic, but only with few nonpathogenic organisms.
Neat.

In a closing word, the authors underline again the potential benefit of targeting virulence factors rather than deploying broad-spectrum antibiotics:

"An advantage of our approach is that commensal flora, which often play important roles in the well-being of humans, should be minimally affected. This is dramatically illustrated in the development of Clostridium difficile-associated colitis where the administration of broad- spectrum antibiotics significantly impacts the commensal gut flora producing an environment where the pathogenic C. difficile can proliferate [39]. Additional grounds for targeting virulence per se is furnished by recent metagenomic studies in humans, which suggest that the human metagenome contains several orders of magnitude more microbial genes than Homo sapiens genes and that our bodies themselves contain perhaps ten times as many microbial cells as “human” ones [40, 41]."

Resources:

For background reading on clustering, an unsupervised machine learning technique, try Chapter 11, "Unsupervised learning and Clustering" in the book "Pattern Classification" by Duda, Hart and Stork
Basic Local Alignment Search Tool (BLAST), online version available at http://blast.ncbi.nlm.nih.gov/
Database of Essential Genes (DEG), a database documenting genes that are known to be critical to the viability of an organism. Available at http://tubic.tju.edu.cn/deg

Paper-a-day

2009-11-21T18:04:00.001+01:00

A few words on the posts labeled with "paper-a-day": Every day, I'll try to write about one paper I read that day. I mainly do this because writing about a paper helps me understand and remember its contents better. And maybe someone out on the interwebs gets something out of these summaries, too.

P.S.: I renamed the category to "paper-a-week", for obvious reasons.

Readings: "Alternative trans-splicing: a novel mode of pre-mRNA processing" by Horiuchi et al

2009-11-21T17:58:00.007+01:00

Reading Horiuchi et al: Alternative trans-splicing: a novel mode of pre-mRNA processing
Biology of the Cell, Volume 98, Issue 2, 2006
http://www.ncbi.nlm.nih.gov/pubmed/16417469

Horiuchi's paper summarizes a number of findings concerning the subject of trans-splicing.
Trans-splicing is a mechanism that naturally occurs in cells. It has also been experimentally used to correct genetic defects in mice, so it is both an interesting natural phenomenon and a possible avenue of investigation for therapeutic applications.

Splicing, inside a cell, is one of the numerous steps from DNA to RNA to protein. Splicing operates on premature mRNA (pre-mRNA for short), from which it excises introns and joins the remaining exons back together. Splicing comes in two varieties: cis and trans. Cis-splicing joins exons within a single pre-mRNA molecule, while trans-splicing joins exons from different pre-mRNA molecules. Trans-splicing seems to be rare compared to cis-splicing, but it has been documented for a number of organisms, including unicellulars, the roundworm C. elegans, Drosophila, rat, and human. In unicellulars, all mRNAs are prepended with an SL (spliced leader) RNA through trans-splicing. This process of SL addition is well documented. Note that it does not expand the diversity of the proteome of the organism, since the SL sequence is non-coding.
Things may be different in the higher organisms in which trans-splicing has been documented, where the identified cases do not follow the pattern of SL addition. A functional signficance of trans-splicing has only been established for some of these cases - for others the question of functional significance remains open, as does the question of how frequent trans-splicing events are in different species or how exactly trans-splicing works. In the case of the lola gene in Drosophila, trans-splicing was studied by observing the effects of targeted interallelic mutation. A schematic of the experimens and their results is shown in the following figure:

Depicted are three experiments, each with one introduced mutation per allele. The viability of the bottom-most experiment can be explained by interallelic trans-splicing of the intact exons.
The authors also speculate on a possible conditional advantage of trans-splicing over cis-splicing:

In the cis-splicing mode, the proper expression of isoforms requires strict regulation of all potential polyadenylation sites in coordination with the alternative splicing. The regulatory mechanism would be enormously complex if the gene contains as many exons as mod(mdg4) or lola. Trans-splicing may overcome this problem, allowing for the joining of exons between two discontinuous transcripts without any mechanism that would select a particular polyadenylation site to produce a given isoform.

So far, no particular genomic "signal" sequences are known that would let us recognize trans-splicing sites from the genomic sequence alone - for all we know at the moment, the splice sites of trans-spliced exons look just like those of cis-spliced ones.
One hypothesis on the mechanism of trans-splicing hinges on the observation that in vitro trans-splicing between synthetic pre-mRNAs is enhanced when intronic regions of the pre-mRNA molecules contain complementary sequences. Watson-Crick base-pairing between the pre-mRNAs could indeed explain how trans-splicing is enabled or at least facilitated.