Screw you VPN, you suck a big fat behind. So damn slow from home that there is no point in even using you. Taking five minutes to save a Word file. Not saving when saved to, so that updates get lost. Interrupting the flow of thought that is so hard to finally get into when we're writing these godforsaken things.


Uh oh!

I just got back home to find our Roomba had shut itself in the bathroom and run its battery down by frantically bumping in circles for who knows how long.

Poor old Roomba! It probably played the saddest little song to call out that it was confused and getting tired!

Getting somewhere

My cousin Nora had some scans for her metastases the other day, and many of them are stable! I am super excited about this. She has been trying a lot of different things: "Sir Spheres" nanoparticles to target leaky tumor blood vessels, Abraxane (a version of taxol that comes pre-packaged in a little albumin delivery system), cyber-knife (gold-nanoparticle-guided targeted radiation therapy), Sutent (an RTK inhibitor) and good old-fashioned clean living with lots of extra vegetables and nutritional supplements. All of these things together seem to be making some progress, something we had not seen much of in the past few years of her experience.

Things aren't all smooth sailing though. There are other things going on in there that still need to be dealt with.

Even so, it is fascinating, exciting and beautiful to see all the hot topics in my research area come together to actually directly affect the life of someone I love very much.

You go Nora!! Someday we will make the Nora mouse with some of your tumor tissue that they froze down from before, to find out WHY all these things worked for you, and WHY it isn't doing as much on others but for now, let's just celebrate that they seem to be making some difference! Keep me up on what else gets figured out.

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.

Faculty assessment

My institution is going through a big push to structur-ize and formalize many bits of language surrounding an overall "strategic plan." Since this is going on in layers at all levels of the organization, part of that means our department needs to participate. This is coming from the Dean, who got the directive from the President. So in other words, we gotta do it. We (with me coming in at the end of the process here) have been working to satisfy their requirements for a "Faculty Assessment System," which needs to include a portfolio-based reporting system for each individual's progress as well as a rating system of some kind to quantify whether people are meeting the "minimum" requirements. It makes for some long, contentious debates in faculty meetings. It also eventually comes down to a discussion around part of the fundamental philosophy of academia: how do you quantify the multidimensional achievements of someone who contributes to a huge range of essential activities in any meaningful way? What makes someone in a faculty position "a success" or at least "satisfying the minumum requirements" in a way that you can have in a spreadsheet when it comes to assess everyone at the end of the year?

Clearly it is nearly impossible to quantify. It's nearly impossible to even categorize thoroughly. There is a natural, instinctive resistance to the idea of quantifying or dissecting it from the more experienced faculty who know full well how differently each person brings their contributions to the table in a good department. On the other hand, those of us at the beginning (especially us supernoobs) kind of like, at some level, the idea of having a framework within which we are explicitly expected to operate. Rather than all the vague handwaving about having "enough" papers or "enough" grant money or "enough" teaching contribution that usually makes the tenure process so hard to navigate, we liked the concept of having some formalization to the assessment process... everybody's main problem (ours too) was with how to QUANTIFY that as a set of metrics.

So how could the professorial animal be metric-ified? We have a few computer science/biomodeling types in our department, maybe somebody could devise an extremely complex algorithm that could appropriately score and assign weight to all the various components of a successful faculty career, in some kind of Venn diagram shape so that if you contributed particularly strongly in one category you would balance your deficiencies in others... create the mathematical representation of ACADEMIC SUCCESS, the Plato "Idea Professor" that could be born in each of us as either a functional or dysfunctional Dr. Horse. That we could dutifully use to plug in all of our parameters, it could chug away on a Linux box somewhere for a few weeks, and spit back out to us a quantification of our own personal FIT to the model.

But it would still be just that: a model. Models never fully represent their living instances. They never take all the parameters into account. They sometimes show false positives, false negatives, and always come down to a bottom line that cannot fully describe the thing they are trying to assess because of emergent behaviors that no one was expecting when they created the model. So we would have to get to the point where we incorporate some kind of machine learning into the model, so it can adjust and change its mind and take into consideration other factors that were not known at the beginning and so on and so on...

And by then, we might as well just be a group of people with expertise in the matter thinking deeply, talking thoroughly and deciding upon it.

Which is great as long as you are in a department with people you trust, who you know have everyone's best interests in mind, and who have a track record of helping each other hold down the fort. That's the way my department is now. I just can't guarantee it will stay that way over the years, and so I still like the idea of having something formalized in a document (even if the complicated algorithm part would never take off).