I ran across an interesting Wired article discussing the merits of a new initiative: Open Notebook Science. This touches directly on the issue I brought up in a previous post.

So what happens to all the research that doesn’t yield a dramatic outcome — or, worse, the opposite of what researchers had hoped? It ends up stuffed in some lab drawer. The result is a vast body of squandered knowledge that represents a waste of resources and a drag on scientific progress. This information — call it dark data — must be set free.

It is a well written article, if a bit short, expressing why all research data should be open for public viewing. The “dark data”, results that didn’t see the limelight because they failed, were inconclusive or even contrary to the project, may be important to other research labs. Your trash may be my treasure.

In a similar vein, there is a movement called Open Notebook Science, championed by chemist Jean-Claude Bradley. This movement wants to make science completely open and transparent by having scientists post their notebooks. Complete access to notebooks, including the good, bad and ugly, would move science forward at a striking pace. I happen to agree with them. It is the next revolution in science. That said, it might take years to happen. There are a lot of politics and money tied up in the current system. Old habits die hard.

More links:

Jean-Claude Bradley’s blog
UsefulChem on Open Notebook Science
Science in the Open - blog on Open Science
Jeremiah Faith’s Open Notebook - Graduate student at Boston University
Jeremiah’s thoughts on Open Science

I like art. I almost went to an art school to become an artist instead of an engineering school. I was at first intrigued by what my school was doing, a “BioArt” exhibit. Sounds interesting, doesn’t it?

From Lab Work to Artwork: New Initiative Melds Biotechnology, Electronic Art
“Through ongoing art and research exhibitions open to the public, the BioArt program at Rensselaer will bridge the arts and sciences in a very real, very tangible way,” said Kathy High, head of the Arts Department and one of three faculty members leading the initiative. “I see the discipline as a way to allow all people to feel involved and participate in the advances made in biotechnology.”

I was walking through the Biotech building on my way to lab when a large poster caught my eye (it was new). Stopping to take a look, I saw a poster of artist Caitlin Berrigan inserting a butterfly needle into a vein in her arm. Another section of the poster showed her dripping the freshly removed blood over a terrarium of dandelions. The caption detailed how she ate dandelion root as a medicine for Hepatitis C, so she was “giving back” to the dandelions by giving them some of her own blood.

That’s something that makes you stop and go “hmm”. Not a good “this is enlightening me”-hmm. More like a “how did they convince the administration this was a good idea”-hmm.

More details after the jump.

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I’ve been attending a Neuroscience Journal Club here at RPI since last year. I find they are very informative and enjoyable For those of you that don’t know what a journal club is, I’ll let you in on a disappointing secret: they aren’t held in treehouses

More thoughts and my experience with presenting after the jump.
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After a busy week and a weekend of violent sickness (food poisoning), you’d think I would take it easy for a while. Nope, you guessed wrong. I’m trying to learn BLAST.

Dramatic sigh goes here.

BLAST stands for Basic Local Alignment Search Tool. It is a set of programs that can either be downloaded or run through a web interface at NCBI. BLAST allows researchers to compare sequences of both nucleotides and amino acids. It can be used to deduce the function of novel proteins, determine what novel genes encode, find similar proteins, etc. Essentially, BLAST is an algorithm (actually, a set of algorithms) that can troll genome databases looking for similarities and return heaps of data.

Unfortunately, BLAST is by no means user friendly. Even after reading a few tutorials and playing around for a few hours I only have superficial knowledge of what I’m doing. I can run basic searches but any advanced queries (ie. the kinds I need right now) give me nonsense data or data I can’t understand.

I swore I would never get involved in Bioinformatics. It seems like a likely choice since I switched from Computer Science to Biology but I hate statistics, databases and everything Bioinformatics stands for. Unfortunately, it appears to be a powerful tool and it would be foolish to neglect it just because of personal opinion. And it might make me a more valuable asset in lab, which is good considering I am a lowly undergraduate trying to learn basic protocols.

My current plan is to purchase a copy of BLAST by Ian Korf and start pounding my head against the wall. I might get motivated and set up a dedicated Linux BLAST machine. My inner computer nerd is giggling with happiness.

Wish me luck. If you have any tips or are familiar with BLAST, please feel free to leave me comments. I’d love to hear from others!

Advisor: Is this going to give us good news today Zach?
Zach: I hope so, or else it would have been a waste of a day.
Advisor: *laugh* Welcome to science, you waste lots of days.

Made me laugh =)

A few posts ago I mentioned the new Zeiss scope my advisor aquired. Today I got to play with this sexy, $120,000 scope. And it was awesome.

I felt very at home working with this machine today, especially compared to my first lab day. Old computer-science habits die hard and I picked up the software pretty quickly. The software package that comes with the beautiful machine is pretty shoddy, especially considering the price tag. It is unintuitive, frustrating and a bit buggy, occasionally crashing. The auto save function only works sometimes, meaning you could lose some interesting images if you aren’t careful. Despite that, it works well and gets the job done. Its like any other professional program (like a CAD package or a programming IDE), once you learn all the widgets and doodads imaging is pretty easy.

While the software may be less than optimal, the machine itself is glorious. Completely motorized stage (which is very nice for fine tuning), multiple objectives, including an awesome 60x oil objective, multiple fluorescent bulbs and regular transmitted light. Everything is automated and can be controlled via a touchpad on the machine itself or through the software on the computer. There is live capture, video, multi-fluorescent overlays, you name it. I think there is even a microwave and coffee maker attached to the back.

My favorite feature to play with was the Z-Stack. With this baby you define the top and bottom of the specimen being imaged. The software then automatically captures slices of the specimen at specific intervals from top to bottom, which is then reconstructed into a three-dimensional image. This is also, mind you, used in conjunction with fluorescence. At the end of the imaging, you have a fully 3D model of the cells showing the antibodies you fluoresced. Very, very cool.

It was a very fun day and I’m looking forward to using the scope a lot more this year. Now if only I could buy one for myself…

What a day. Wow. Imagine your first kiss. Remember the odd mix of terror and excitement? Fast pulse and racing thoughts? That was me today, except I wasn’t kissing anyone.

Today was my first day working in the lab on real-world research. I can assure you it was nothing like the labs we had for my cell biology class. I don’t think I have ever felt so utterly overwhelmed and yet so completely excited before. Today was a day of simultaneous terror and ecstasy.

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Between taking 19 credit hours and being a member of a fraternity, free time is rare. Whats the obvious solution to this problem? Join a lab and do research on the side, obviously!

While my free time will now be nonexistent, I’m quite excited to finally be doing some real research. I was going to do research with this particular professor over the summer but chemistry courses got in the way. We met a few days ago to hammer out the details to my Undergraduate Research Proposal (which forces RPI to pay me, always a plus). He also showed me the new scope they just bought from Zeiss. It one very sexy, very expensive machine. =)

All in all, I’m excited to start working. After I slog through a few hundred pages of literature to write this proposal I’ll start doing benchwork. Who needs free time anyway?!