Open Source Sequencing and Colossal Squid

The Polonator has a really cheesy name (Arnie dressed as a giant bee?) , but it's a really important step in molecular biology. It's a DNA sequencing machine, there are lots of these around at the moment as people have managed to make systems that beat the traditional dideoxy Sanger-sequencing method (which was used to sequence the human genome) in speed and in the bulk cost of sequencing. Examples include 454's pyrosequencer and the dubiously capitalised SOLiD system. Both produce substantially shorter reads, single sequences of DNA, than the ABI 3700's used to sequence the human genome (though I've heard rumours that a new 454 machine that can do 500 bp reads is on the cards), but do millions at a time.

If you want to run one of these systems, you purchase them for hundreds of thousands from the manufacturer, get trained how to run them by the manufacturer and buy the consumables from the system from the manufacturer. You don't necessarily know what the reagents are in these consumables and therefore all the trouble-shooting you do involves the manufacturer too. This is because these machines are expensive to make, not many people buy them and they become defunct very quickly. It ties labs to the machine, probably long past the time when they're cutting edge.

In some ways it's silly to keep these reagents secret. I worked for AstraZeneca for a year as an undergraduate (which was great experience - companies are much stricter about lab protocol than universities and you pick up good habits!) and they purchased a machine for typing bacteria that I was involved with validating for use - the RiboPrinter Microbial Characterisation system. We bought their kits and never knew what was in them, but myself and another student, frustrated by the fact that we had to write a report for university that would contain no science at all as we didn't know what was in these kits, sat down and attempted to work out what they contained. Judging by the comments from the sales reps from Dupont who make the system, we were pretty close in our estimation. If two undergraduates can work out what's in the various solutions (which is a long way from making a working machine, but at least would mean we weren't reliant on buying inevitably more expensive proprietary reagents) what's the point in the secrecy anyway?

The Polonator is different in that the system is open source. They give you full specs of the machine, they give you full details of the reagents required: what's in them and the concentrations. You can get the machine and make your own protocols for it and share them with other users. According to the article in Technology Review (via Digg) users are already collaborating to improve the chemistry.

Surely this is how science should be done? The philosophy is that scientists share their work and it's peer-reviewed before grants are rewarded, after papers are written and discussed by the community at conferences and after publication. This should allow everyone to build on each others' work and mean that resources aren't wasted - molecular biological research is not cheap to do. This isn't in reality what happens. Labs have their own protocols for performing experiments that might be shared amongst collaborators, but more rarely with the whole scientific community unless it's a more ground-breaking achievement. Minor improvements to protocols that could save time and money are shared perhaps by word-of-mouth. Negative results are generally not reported, meaning that identical experiments could be performed again, perhaps many times, in another lab, wasting resources again.

There are good reasons why some information shouldn't be shared, perhaps to allow a patent to be taken out on the intellectual property to prevent someone nicking the idea for their own gain. But I believe that there are more benefits in the majority of cases for sharing results. There's not a lot of truly open source science going on out there currently. Another example would be the OpenWetWare project, which aims to make sharing of information and protocols amongst bioscientists easier - to the extent that they encourage lab notebooks to be kept online on their wiki. It takes brave souls to get involved initially, posting up their failed and frustrating experiments along with the successes, but then once more people are involved I reckon the benefits will speak for themselves.

Hopefully more projects like this will be initiated and we can have a truly open, more productive scientific community.

On a completely different topic, a group of scientists at the Museum of New Zealand Te Papa Tongarewa have been investigating three Giant Squid (Architeuthis dux) and one Colossal Squid (Mesonychoteuthis hamiltoni, it's bigger, I reckon they're reserving the name Ginormous Squid for the next bigger one they find) that they've had on ice. The blog is fascinating, with pictures of the biggest eye in nature and some clips of them during the dissection. I like squid, and own a T-shirt to prove it - linky.