World, Hello!

As this is my first post to the blogger world, I'd like to introduce myself:

My name is Tommy. I am Ph.D graduate student studying protein interactomes (networks) at Cornell.

                                             

What does that mean? 

Well, starting from the core basics - all living organisms have DNA which sometimes encode for RNA which sometimes encode for proteins. Proteins are these molecules with all sorts of strange shapes and sizes which float around in the cell and often interacts physically with everything around them, including with other proteins! These physical interactions between proteins can lead to other interactions to happen, which can then lead to other ones, and so on so forth. The point is, eventually and somehow, "protein-protein" interactions lead to very confusing and complex cascades of events that lead to the plethora of phenotypes there are. Brave souls out there have worked for decades trying to map out these cascades (or pathways) but scientists have only begun to scratch the surface. For an example of some pretty well worked out cascades, try googling "p53 cascade" or "ras cascade". Scientists like myself believe that if we can accurately draw out ALL of these interaction pathways in a cell at any given time under any given condition, we will be able to unlock exactly the mystery of how and why a cell does what it does.

It's a small-world out there.

One of the weird things about these protein networks is that, in many ways, they are quite similar to social networks. This point was first illustrated by the Watts and Strogatz in their 1998 Nature paper "Collective dynamics of 'small-world' networks". Basically, many interaction networks seem to "organize" itself by having a few things interacting with a ton of other things, whereas most things will have their own small niche. The first time I learned about this concept, I thought about the social dynamics of high school - you have the few popular kids who seem to know everyone and everyone knows them, but most of the student body will know much less people. Furthermore, many of us have probably heard the "six-degrees of separation" theory where every person in the world is separated from each other by at most 6 steps (or 6 linearly related people). In this high school example, it is pretty easy to understand the small-world idea. But the fact that networks of inanimate objects (proteins) follow very similar patterns is just bizarre. This is how I initially got intrigued by the idea of biological networks - how and why are inanimate objects, with no canonical thinking capability, able to organize their relationships the same way that humans do?

Google map it.

Today, what would you do if you wanted to find directions to some location? Use apple maps? Of course not! You would google map it. Back to the original idea of harnessing the power of interactomes, what if we could generate "Google maps" of biological entities? I think that is one of the major goals of systems biology today, one in which I am actively involved in as a graduate student.

The experiment.

Now that you know my interest lies in how things relate to each other at a network level, I will impart one of my reasons for this blog. This is an experiment (probably a poor one but it will suffice to amuse me) where I want to discover the network of my own scientific interests. I plan on blogging about anything I find amusing/interesting related to science and my science career progress. As I am in a malleable state in my scientific development, I would imagine it difficult to force myself to be interested in and post only a very narrow range of topics. If the small-world theory holds up, the long-term of this blog should do well at capturing the size of my interest network and the "architecture" of it.

I suppose I will now begin the journey that I was already on, though this would be the first time I would be documenting it. Enjoy blogger-sphere.