Sunday, October 5, 2008

Chemical BiLOLogy

The funnest part of my journey from being a purely synthetic chemist into a chemical biLOLogist has been coming around to the point where I actually start understanding the biLOLogy part of things. I've been thinking about this as I work on writing an R21 proposal on a type of biological system I know practically nothing about. Chemical biLOLogy is fairly loosely defined as it is, that's why my tagline is "nobody knows what it really means."

It essentially means MAKING and using chemical tools that you then apply to biological systems in order to understand their function--rather than the traditional understanding of medicinal chemistry, which is more about making chemical tools you use to try to kill bad cells and/or protect good cells, or biochemistry, which is more about studying the chemical behaviors and properties of biological systems. So really it's just a classification along the gradient between those two things, and they are already just classifications along the gradient between hardcore chemistry (using the molecule as your basic unit of study) and biology (using the organism as your basic unit of study). It's all about FRACTALS, people, fractals whose philosophy of structure just keep repeating in expanding/microscoping versions as we go up or down the magnification of the basic unit.

Defining oneself as a 'chemical biologist' just means that you have to think more about the biological system than whether or not you can kill it. You have to start understanding biological systems organization and connectivities, and see places that you could manipulate them by knowing how their molecules work. Most chemical biologists get started by not really understanding the biology--I know I did. I was able to translate molecular principles into a few baby step biological systems (enzymes, their mechanisms, their products, e.g. biochemistry--they were all molecules so their processes made sense to me) in my head, and eventually get to the point where I could make something to go after an activity that was more mechanistic than the "death" level. The more I read and tried things, and the more systems I started to think about, the better I came to understand this fundamental underlying common thread that: really, if you can find, define and categorize the basic units of a system, any system, and how they interact according to the principles of whatever scale you're looking at (which always comes down to molecular physical properties if you zoom in close enough), YOU CAN UNDERSTAND ANYTHING.

That's where the fearlessness comes from. I know full well I won't get everything about a new idea right away, and I'll have to take the time to apply those translations so I can define and categorize the parts, but I know HOW to learn it. I know I won't remember the jargon, the terminology, and will have trouble calling things the right process and the cool kids might laugh at how I didn't even know what a Tak Mak was (true story). BUT I just don't care, and am not afraid to ask for that kind of information, because I know that when it comes down to it I can figure out how it is really working and see it for all its beauty, and sometimes find parts of it everyone had taken for granted and poke at them until they do something different, interesting and cool.

That's why I love this so much, and it has only been recently that I have felt my own personal evolution occur, from being someone trying to kludge around with basic biology to starting to see the finer details. It is such a good feeling to take a totally new kind of biology, start reading about it, and start seeing how all its parts fit together and get the gist of the workings so you can start going deeper into the particulars all within just a few days of starting to think about it. That's what chemical bilology training should be all about: teaching people to find the systems organization in things, characterize their molecular principles in your head, and think of them as nodes to explore, perturb and manipulate--no matter what degree of complexity the system comes at you with.

10 comments:

Comrade PhysioProf said...

The more I read and tried things, and the more systems I started to think about, the better I came to understand this fundamental underlying common thread that: really, if you can find, define and categorize the basic units of a system, any system, and how they interact according to the principles of whatever scale you're looking at (which always comes down to molecular physical properties if you zoom in close enough), YOU CAN UNDERSTAND ANYTHING.

That's what chemical bilology training should be all about: teaching people to find the systems organization in things, characterize their molecular principles in your head, and think of them as nodes to explore, perturb and manipulate--no matter what degree of complexity the system comes at you with.

Damn straight! And you know what it is that you are referring to? MOTHERFUCKING PHYSIOLOGY!!!!! w00t!!

Arlenna said...

Well then, I guess I am a chemical biphysiLOLogist! Go science!

kigarwoods said...

This was exactly what I needed to read (as a morale booster). I can't wait to go to grad school!


thanks for the post.

Anonymous said...

Chemical Biology = Getting funded for generating and studying new compounds that have no chance to be therapeutically useful.

Chemical Biology = What, a Michael acceptor/alkylating agent/ADMET-nightmare? So what, it's a "tool"...

Chemical Biology = Lowering the bar for the special people...

Arlenna said...

You're a tool, Anonymous!

Arlenna said...

And by the way Anonymous: not all compounds need to be "therapeutically useful" as drugs. In fact, figuring out how to not need the drugs in the first place through early diagnostics/better prevention would be WAY more valuable to humankind.

Vikas said...

Brilliant brilliant post. You captured the spirit of Chem Bio perfectly. Starting at the molecular level really is key when trying to understand physiology or pharmacology or just about any biology.

Its also fun to see how reality differs from our predictions based on molecular-level studies. One of my favorite quotes by Phil Anderson from an old Science perspective, 'More is Different' is - "The [reductionist] hypothesis breaks down when confronted with the twin difficulties of complexity and scale ... at each level of complexity, entirely new properties appear."

Thanks for a great post. I plan to share it with my students.

Arlenna said...

Thanks Vikas!! :)

Cath@VWXYNot? said...

"the cool kids might laugh at how I didn't even know what a Tak Mak was (true story)."

LOL! How did I miss this the first time I read this post?! That's awesome.

Anonymous said...

It was rather interesting for me to read the post. Thanks for it. I like such topics and anything that is connected to them. I definitely want to read more on that blog soon.