Friday, December 14, 2007

The future (and present) of science

Science, chemistry in particular, is a very interesting world to be involved in, academically and professionally. Actually, I hate the word interesting, too vague. Allow me to start over...

Chemistry is pretty bad ass for the most part. The classes are fascinating if you pay attention and you understand the implications, the implications are important because chemistry, plainly put, is involved in every single thing you experience every second of your life, and practically every experience you have in a research environment has the potential to be novel.

When I started my undergrad research project at SDSU in metal-organic frameworks, I was immediately struck by the open-source nature of the chemistry community. This was something I experienced in my position at Johnson & Johnson but had never seen first hand. For those of you outside of this world that I am just now getting acclimated to, here's exactly how chemistry works:

The skeleton (in this case meaning underlaying framework) is one or a group of very smart people. These are the PhDs and the post docs (those who have continued their formal research after a doctorate degree has been achieved) and they are the heart of any lab environment. They are the brain and kidneys too and, while we're at it, probably the lungs and DNA and hemoglobin as well. I'm really getting out of hand with these anatomical metaphors and probably losing a little focus as well. Keep in mind I'm just now trying to recover from an intense two weeks preparing for final exams. I'm recovering by working a 10 hour day if that makes any sense.

What I'm trying to say is that chemistry is nothing without some serious brain power hanging around. What is interesting about PhDs and professors and so on is that they are not the main workers (most work damn hard, don't get me wrong), they are the directors, the conductors if you will. I would venture a guess that if you're not involved in chemistry that you might think it's all about mixing colorful liquids to get colorful solids that save the world. The real work is done researching and problem solving OUTside of the lab. Let me be clear: the mixing and heating and solvating and freezing and separating and roto-vapping and analyzing are what all of the research is for but, without a plan, the scientific foot-work is useless.

You might be surprised if you knew how much time people spent in front of a computer or notebook doing any number of (somewhat) tedious tasks: recording results, calculating molarity and yield, summarizing information, setting up presentations, and, the major time sink, researching the NEXT STEP. Doing this research can be massively frustrating and, for the time being, is a very medieval (almost spelled that right first time around) system. I guess it might seem a bit ridiculous to call building molecules in a software program and searching through countless records accessed through this crazy thing called the interweb 'medieval' but, to someone who deals with "optimizing web experiences," it's a PITA.

What we do in chemistry is start with a problem, gather as much information as we can, and then just poke at solutions until we find an answer. The first time you start doing this, you're struck by how inefficient the whole process is. Just to start working might take an hour or more of baking glassware and pumping equipment into the "airbox:"

The point I'm meaning to address through this long, ridiculous ramble is that the scientific process for chemistry has come a LONG, LONG way and is almost incomprehensible in terms of its complexity and capacity but there is A LOT of room for improvement. The biggest/best change I could suggest (from my very novice POV) is a vast improvement in the sharing and exchange of information. Right now, we search through existing successful chemical procedures in the form of academic papers which may or may not be clear, free, safe, in English, capable of producing a usable yield, or incredibly expensive. The person who wrote the report may of may not be alive, still reachable, or even willing to answer any questions. They also might be wary of competition for grant money or fame and fortune (and groupies, of course). Here's an example of, basically, what we use to direct our research...
Click here and select "Full Screen" to view it better...

It is, of course, amazing that so much information is available on-line to academic institutions but using it is a drawn-out, frustrating hunt-and-peck activity that can go on for hours or days. The question is, how do you take work that people have, potentially, spent their whole lives accumulating, work that exists in many different forms, published or not?

Science, in a lot of ways, is a very open environment that wants, more than anything, the simple pleasure of accomplishment. Scientific advancements are also the source of a fantastic amount of money and will be as long as sentient beings are mucking about. So what is the middle ground? How can I retain sovereignty over work I've done while giving back to the system that made this work possible? I certainly don't have the answer to that question and I think that no one truly does.

Personally, I'm a fan of things being as open as possible. That's why I blog, plain and simple. That's also why I help people around me with anything I'm good at. I would be much happier in a world with more incorporation, more community, more open-source everything and less chances to be fantastically rich, less copyright laws , and less restriction altogether. "What about the work you do?!!" If everything I did needed to have a clear, upfront monetary value, I would be A LOT LESS BUSY. I certainly wouldn't blog, I wouldn't read, and I would be hard-pressed to stay as diligent in school as I have been. I am truly a fan of open information and will always contribute with that sentiment in mind.

Which brings me to the article that I stumbled upon (yes, that was definitely one hell of an introduction). From the Chronicle of Higher Education:

Microsoft is partnering with several universities to create open-access Web sites where chemists, freely and easily, can find details about molecules and atoms. That’s the report today from Peter Murray-Rust of the chemistry department at the University of Cambridge, in his blog.

Murray-Rust notes that Microsoft has financed and developed a software design called Object Re-Use and Exchange “which sees the future as composed of a large number of interoperating repositories rather than monolithic databases.” Using it, he continues, will allow bench chemists and undergraduates to browse libraries of molecular structures to get information they need for research and publications, rather than being restricted to whatever database to which they happen to have a password.

“We shall also be ‘scraping’ (ugly word) any material we can legally access,” Murray-Rust writes.

Partners in the program, besides Cambridge and Microsoft, include Penn State University, Cornell, Los Alamos National Laboratory, and the PubChem project, a free database of molecular structures hosted by the National Institutes of Health

We will, hopefully, see this more and more as time goes on. As Google keeps making uncopyrighted work available for free and science opens up further and further, people will see the benefits that don't have an intrinsic dollar value.

The best part about this is that the ones who create the information (students, professors, etc) are FAR more likely to be the ones who want the information shared (compared to executives, deans, etc.). Though the universities where the work was done have some kind of claim over the knowledge, it is ultimately up to the scientist whether that information goes anywhere. They can share it clandestinely, talk about it whenever they want, and help 'competing' researchers take that next step. The information always belongs to the holder, no matter how many copyright laws there are.

Here's another example of a push for professors to share their research (also from the Chronicle):
Dan Cohen, director of the Center for History and New Media at George Mason University, wants scholars to stop keeping their research materials to themselves. Just about every academic has notes, photographs, digital scans of research documents, and plenty of other data on their hard drives, he says, but they rarely share anything beyond what makes it into their final books or journal articles. Why not upload such material to a shared online database for other scholars to draw from?

The center announced yesterday that it will work with the nonprofit Internet Archive to create just such a database — and to build tools to make it easy for professors to add their personal research files. The Andrew W. Mellon Foundation awarded $514,000 to the center to support the effort, and gave more than $700,000 more to the Internet Archive for the project as well.

Mr. Cohen said that the key to his plan was ease of use. Many professors are using the Zotero software already, he said, and the upload will take place with just a few clicks. Plus, adding materials might enhance a scholar’s reputation, since his or her name will remain attached to the contribution. Materials in the archive should be easy enough to find, since the Internet Archive, where the materials will be posted, is already popular online.

Open it up, folks, let your information out. Your value, monetary or otherwise, is based largely on your future potential, not your past body of work. Your past body of work serves as a possible indicator of your future potential. Get out there and share what you have, no matter what it is. Everyone will benefit, yourself the most.


ChemSpiderMan said...

We're right in the middle of this with ChemSpider. We're doing a number of things to facilitate access to molecules...18 million of them to be precise. Take a look at , an overview of the system is here:

We've linked it to US, European and WO patents by CHEMICAL STRUCTURE, have linked up to 50,000 Open Access articles and are presentyl going through the articles with robots, extracting chemical names, converting to structures and adding to the database. We let people deposit in real time to the database and curate what's on there. Check out and for info about what we're doing. I think you'll like it ....

Josh C said...

Thank you for the comment. I will check out ChemSpider in more detail when I have the time to do so. I think it's fantastic that you're taking your own time to put this together. I'll show it off to my research adviser as well and see if we can find a little more information on our current project.