While I was working away at WashU, preparing for graduate school, I imagined myself as a grad student. In that imagination land I was working my ass off, learning all kinds of things, and sharing every bit of that with others via this platform. My work would be totally open. In reality, I am doing only those first two things.

Every couple of days I have an awesome research experience or an interesting new idea and come home planning to write about it. Then I start thinking about how I can present the experience while maintaining the proper level of censorship. Perhaps unsurprisingly, my motivation always quickly evaporates. You may be wondering: why is there any censorship required at all?

Well, it turns out that biological research must remain shrouded in secrecy for at least two major reasons: [1] Just like in any other profession, there are charlatans, thieves, and liars to avoid; and [2] biological research results are potentially worth huge mountains of cash. I’m still hoping that most biological scientists really do fit my ideal image of a Scientist, but the problem is that it only takes a few jerks to make life difficult for everyone else.

There is a lot at stake for researchers, as a lot of money and time is sunk into any project. So if some other group manages to do the same or similar work, and get published first, then much can be lost. Fear of outright idea-theft is one of the huge problems, but the more surprising one is that competing researches don’t want to give each other a leg up by sharing information because sharing leads to reduction or even loss of credit. If you share, your cool idea might end up becoming a novel tool used in someone else’s Nature paper instead of your own. And then you have more trouble getting funding, and students, and tenure…

So the funding system necessarily leads to closed science, which would be true even without the explicit jerks. And then money gets involved on the other side of discovery. Universities, companies, and researchers are patenting the crap out of new biological discoveries. Mutant proteins, dead viruses, synthetic compounds, techniques to synthesize or purify natural compounds, plasmids, and so on and so on. Most of these things aren’t worth much (except for knowledge-value) and so their defenses just end up making life a little more difficult. Others are hugely useful, but are better left to companies anyway (pharmaceuticals or complicated and expensive processes, for instance). Others still are hugely useful, but only for research purposes, and have no business being tied to business. For example: plasmids (circular DNA containing a handful of genes).

I have been building a plasmid for the past few weeks (for my secret research project) and ran into a totally unexpected problem. I wanted a certain fluorescent protein in my plasmid, and we have several in the lab on different plasmids that we have gotten from other labs or companies. For those unfamiliar with cloning (the molecular kind, not the sheep kind), it’s actually a rather routine process to stick a bunch of genes together into a plasmid. In order to get enough copies of a gene to efficiently construct one of these things, a researcher will use PCR. This awesome technology lets you go from a few copies of a gene to billions (literally) in a few hours. You can PCR any gene you want, so long as you know its sequence.

So my plan was to find the fluorescent protein gene from one of our plasmids, make a bunch of copies of it by PCR, then stick it into another one of our plasmids. Simple. But then it turns out that many of our plasmids  have Material Transfer Agreements (MTAs) attached to them, and that each MTA has different requirements for what I can and cannot do with the plasmid’s components. One plasmid has three genes, each “licensed” by a different university! One of the things the MTA prevents me from doing, for example, is to make any changes to the fluorescent protein gene from one of these plasmids. This actually sucks a lot, because that was something that I needed to do. And this requirement was by a university. I understand and expect that kind of behavior from a company, as companies exist to make money in whatever way possible. Companies aren’t supposed to have ethics, or have a primary goal of advancing human knowlege. But universities are supposed to have both of those things.

In the end, I just went with a probably-slightly-crappier fluorescent protein that, I hope, is not under an MTA. And it looks like it is doing what I designed it to do. So there’s that.

In conclusion, it looks like my relationship with biological research will become the same as my relationship with software: I’ll make my work as open as I can, hope that others do the same, and generally use free-and-open slightly-crappier versions of expensive-and-closed things (whether those things are plasmids or office software).

Hopefully the likely-more-complex reality turns around again so that I will find myself back at idealism. I expect that the process of publishing my first paper (whenever that happens) will reveal a lot…

A CSS file is just a text file, at MOST a few kilobytes.

In other news, you can get 20 gigabytes of extra space from Google for $5/year…

While a total ripoff, I was tired of WordPress’ themes never being quite right, and wanted to have the standard theme I use in presentations: maroon and shades of grey.

Still a better deal than text messaging…

I’m working on a post on the awesomeness of Regular Expressions, specifically in Notepad++ and for use on FASTA sequence data. Check back soon (if you care…)!

Terrororists sometimes try to get onto airplanes;

Therefore, you might be a terrorist.

An upper limit to the value of comview may not exist, but that would depend entirely on how views are tallied. If every refresh of a blog page is considered a view, and leaving a comment requires a refresh, then the upper limit would be 1. If access by a specific IP address in a certain window of time is considered a view, then the upper limit is much higher than 1 and would depend on how many comments a person was physically capable of leaving in that time frame. In either definition, it is clear that a higher comview would indicate a higher social value (the site is not read-only). Of course, this metric could be refined to include actual numbers of visitors as well as proportion of unique visitors, though additions such as those would require arbitrary judgments on what is considered more socially valuable (i.e. is a blog with 10 regular viewers who each comment 100 times/day more socially valuable than one with a million viewers that post .1 times/day?).

I was hoping to find some comview stats for a few blogs to see what kind of values are around but, unfortunately, I can’t find a source for either necessary statistic. I could data mine for for average number of comments/post, but I see no way of locating a number-of-views statistic. Perhaps comments/post (“compost”) would be a similar metric, and that is one which I could mine for. Thoughts?