Archive for the 'philosophy' category

Repost: Culture gap: synthetic chemists and learning biology

Apologies for more reposting... I'm still trying to get out from the vacation backlog of life. New thoughts to come soon!

I started responding to this comment:

Now that you have invested so long to transform in to a ‘chemicalbiologist’, would you mind suggesting some quick tips from your journey for the people ho want to take the same path? Are there any books or some crash courses etc?

And got so in depth that I decided to make it a post of its own. So here are my thoughts about where to start to develop better flexibility as a synthetic chemist who wants to work on bilogical problems.

The best crash course I got was weekly lab meetings in a lively, rigorous yeast genetics/molecular biology/kinase signaling lab (one of my postdoc labs). I started out so clueless that I felt like I was on Mars for the first year and a half or so. But because the people in that lab were so open and helpful, and the PI is an engaged, active teacher, they helped me learn the “language” of biology-type ways of thinking and data/information representation.

It’s that language that you really need as a chemist moving into biology. And by “language,” I mean more than just terminology (although that is a big part of it). It’s also a change in visualization of information and getting better at logic puzzles. Imagine a multi-step synthesis with a blank at step 2, where 4-5 possibilities (which you have assumed based on either mechanism or other times people have done similar things) could fit in there to result in the product (or mixture thereof). In biology, you have to come up with ways to test *which* of those possibilities comes from the retrosynthetic direction (for which you are only postulating a route) and will result in the product(s).

In all of this you also have to accept that: a) your only measurement techniques are indirect, i.e. you usually can’t just analyze the structures with some direct spectroscopic technique and figure out what they are; and b) your assumptions might be wrong. So you have to do lots of control experiments where you also assume some certain set of reagents should DEFINITELY give the products, and some other set should DEFINITELY NOT. That gives you yet another indirect way to make you feel more comfortable with your assumptions. The hardest part for many chemists is having to be okay with indirect information. The second hardest part is having to remember that if your “result” gives you something analogous to “75% yield of the product,” you still have to think a lot about WHAT molecules/interactions are represented in that other 25%. You can’t just purify it away and pretend it didn’t exist.

Getting used to reading gel electrophoresis/Western blot (antibody detection) data, as well as biological “cartoon” format (where you mostly worry about conceptual connections, and not so much molecular mechanism and byproducts etc.), are some great ways to start. But you’ll probably need a coach to guide you through it and translate how the experiments work and what the results mean. Finding friendly, sharp biologists (whether faculty, postdoc or grad student–it doesn’t pay to be snobby about this, sometimes the trainees are gonna be WAY better at teaching you! Just make sure to credit them or repay them somehow!) can be the difference between this working vs. not working.

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My Big Picture (tongue only partly in cheek)

Aug 09 2008 Published by under crazy talk, philosophy, the big picture

So, I don't currently have a working drawing program on my computer so I have to make a Google Image collage to illustrate my most mostest pulled-back biggest picture, my philosophy of my world on days when I am not OCDing about something stupid that bothers me, my Zen of path through science-human-space.

We each have our little place in it, our little walk through all the possible avenues, and just like vision (and macro lenses) we can only focus on the part right in front of us. Probably it's only practical to expect to clearly see about the next year or two of plan in any great detail. I point myself in the direction I want to go, starting at the "chemistry" paradigm point and going towards the "biology" paradigm cluster. A zoom in on the detail of how I get there would probably look like this:

Except that most of the other nodes around me, and most of the path I had taken and will take would be a lot fuzzier to the eye. A good strategist will learn how to zoom their lens back just enough to see the next set of decisions to make, while keeping active on the current processes until they reach some degree of maturity. Not saying I am a good strategist yet, but I hope to learn how to be one by paying attention to what's going on around me.

So what is everyone's personal goal? Usually to make both their paths and destinations "important." But of course, importance itself has a lot of stochastic elements and the ultimate measure would be to be 'right' about it, right about how this crazy universe/space/world/us REALLY work. But what is "right?" To go really philosophical about it: how do we know it DOES work any particular way and that we're not affecting it just by trying to look? Just because I find some spit on the cat's hair I managed to tweeze out of the box with my incredible intellectual power, I still don't know if the cat is alive or dead or even if it's a cat or maybe a RASCAL that ate a cat...

SO to get back to things that don't wake me up in the night impressing the weight of the vastness of existence on my soul, what I really want to be able to do is maximize my experience at and travel between focus nodes, and not get bogged down with either the nodes themselves, nor the paths the lab ends up taking to them.

For the purposes of communicating as a human with humans, I'm calling this "STUDYING SIGNALING BIOLOGY USING CHEMICAL TOOLS" and we will work towards doing a very good job of making whatever we need to get information about cell signaling that allows us to make more emergent observations about how that stuff is REALLY interacting in there. If I can mature in my strategic abilities, we'll be able to be both thorough and flexible, and not get stuck in the mud of either our tools or our questions while still being able to make both of those things valuable to the overall enterprise of understanding how stuff works, to gradually add elements of information to the drawing until we get a picture of what the whole thing looks like.

To put it an even sillier way, I plan on rolling my chemical biology katamari through the paradigm world and picking up stuff as I go, and hopefully by the time I retire it will be so big I can even stick things like WHOLE PEOPLE and cars and stuff. Right now it is real tiny, so we can only pick up little additional methods and small observations and such, but with some luck and luck I make myself by being sufficiently strategic, it will grow fast enough.


(**you can find the sources for all my images by looking at their links with right click, thanks to the people who gave them homes on the internets for me to find**)

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