Archive for the ‘Scientific’ Category

Science As An Article of Faith

Monday, May 24th, 2010

Being a scientist living in the land of religious lunacy, I’m often asked what I believe in. My stock answer to this is “Gravity.” After all, you just can’t escape it. Don’t believe me? Try to make the egg you just dropped levitate before it hits the floor or stop yourself when you’re half way to the ground from an uncomfortable height. Gravity’s a bitch, and it will get you every time. This is truly something you can believe in.

That had to hurt, and believe me, those people would have become instant atheists if it would negate the effects of gravity. See? I’m thinking of a clever advertising slogan here: Gravity: Finally there’s something to believe in.

I’m a chemist. Well, let me clarify. I’m an American chemist, which means I can design and make the drugs, I just can’t sell them. It goes without saying that I don’t have much use for theories you can’t prove and phenomena you can’t replicate. I also don’t have much use for people harassing me about how I “just have to believe” something, “have faith in things unseen”, or “need the _______ (Fill in deity of your choice, except Cthulhu. That guy’s just a bastard.) in my life.” I don’t buy any of this, and I make no apologies for it.

This is not to say my life is entirely devoid of faith. See, I have tons of faith in things unseen. When I do an enzyme assay, I have to take it on faith the enzyme is in there, because I can’t actually see it. I have to have faith that a color change indicates a chemical reaction took place. A lot of science takes place on paper, white boards and in the heads of individuals. You have to have faith in the math. No easy task.

Hmmm. I think it may be missing an exponent.

At the risk of boring the vast majority of you who all too readily recognize the above equation, let me do a little explaining to the new initiates. What you see above you is a portion (only a portion) of the equation that explains the existence of alternate realities. It helps explain the universe’s response to paradox. It tells us a little bit about how an object is not really there until we turn around and observe it.

Particles and cats can be sneaky things. You never know if they’re going to be there.

The above elementary musing is a portion of the String Theory equation. String Theory and quantum theory are intimate and incestuous. It makes me feel dirty just thinking about it. You can barely separate them, but they are, technically, different disciplines. One other thing: both take approximately one assload of faith to accept. The door to the universe one atom away from you is always open; you just have to have faith in the math. But think about this for a minute and tell me it doesn’t take your mind to wondrous places. You can see the past, the future, the world where the glass repairs itself after being broken or the world after the Allies lost World War II. Don’t worry if you’re a failure in this life, because in another string you’re actually the King of Sweden. Neato.

Of course, maybe we’re just pulling this out of our asses.

That just about sums it up.

Well, no matter. You don’t need to be a physicist to appreciate the sense of wonder the universe can instill. Here, take a look at this:

Antenna Galaxy

That’s a galaxy, and it’s a real object. If you have a mighty radio telescope, you can see it for yourself. Right now, we just have to leave it up to Hubble and the Internet. Look at it and tell me you don’t have faith in something grander than yourself. The thing is, unlike rule books written by perfectly fallible human beings or supposed miracles barely witnessed by anyone, this thing is hardcore reality. There it is; hanging around the cosmos, minding its own business, completely oblivious to your presence. It does not give a shit about you. Giving a shit about you is what we would consider “Well BENEATH Its Pay Grade.” It’s larger than your mind can comprehend. Nobody has to “believe” it’s there, we can see it’s there. Faith made simple.

Okay, now that the religious zealots have called me all sorts of names, bragged loudly about how they’re all praying for me and left the building, let’s take a minute to calm down, clear our heads, and think this thing through one last time.

Nam-myo-renge-kyo. See, I feel better already.

I believe my enzyme is in there. I believe in LeChatlier’s Principle. I believe there are 6.02 x 10^23 particles in a mole. I believe in that nebula. I believe the cat will be there when I open the box. Science is faith. Religion is rules and semantics. Don’t ever tell a scientist that s/he lives a godless life devoid of faith and hope. Far from it. We all believe in something larger than ourselves, otherwise, why go to work every day?

A religious icon for the ages.

I love you and want the best for you, so I’m leaving you that very special religious ceremony. It’s been passed down among our people for about a century. Now you can believe in LeChatlier’s Principle too. Safety tip: you’re not going to want to drink those when you’re finished with them. It’s one thing to believe in the practical and wonder-inspiring. It’s another thing to drink the magic Kool-Aid.

Chemistry Student and the Thesis of Doom

Tuesday, May 11th, 2010

So, I’m a biochemistry student, and I’m currently working on my master’s thesis. Now, I’m not the typical student, so I don’t appreciate that type casting. I’m old, I’m miserable, and I’m not trying to get into heaven anymore. I don’t spend weekends plastered off my ass and I have never seen an episode of Jersey Shore, The O.C. or whatever the hell else kids are watching these days. What I have seen, sort of, is this:

Mammalian Epoxide Hydrolase. That miserable little bastard.

Thank you Protein Data Bank. You can visit the Protein Data Bank too; I left you a link in the margins of the page. I’ll wait; I know it could take a while. If you’re not scientifically minded, start by typing in a common protein name. I’d go with albumin or lipase or something simple. Go ahead try it; then come back. I’ll be here.

Back so soon? I think I put too much faith in you people. I didn’t put that link there for my health, you know. Just try it once, that’s all I ask. Anyhoo, I’m writing my thesis on how to make epoxide hydrolase in the lab and how to tell if it’s working or not. Here’s the problem: I don’t know if it’s working. So far I have not been able to develop a single test to see if it’s working. Now, I have nothing to write about. No successful thesis began with the words, “After working in the lab for two years, I can say with a fair amount of accuracy that I am an abject failure in figuring out if the damn thing works.”

Although, to be fair, there’s ways to say that without actually admitting what an abject failure I actually am. However, I’d really rather not go into that. Now, I know what you’re thinking, because it only makes sense at this point. You’re thinking, “Well, how do you even know it’s in that test tube? I mean, it’s not like you can actually see it in there, and if it’s not doing anything, it just stands to reason…”

You’re right. No, no, you’re absolutely right. So I did some SDS-PAGE gels. The pretty blue line appears if your protein is in there. Here’s my gel. I’ve had better. Yeah, all that crap you see on forensics files is the scientists telling the interns and undergrads to run that shit until they see something absolutely perfect. I’m not so lucky. I don’t have any undergrads.

It’s there, but the damn thing won’t work.
I tried an alphabet soup of tests to see if I could get it to work – it won’t work.
I tried re-folding dialysis – it won’t work.
I tried changing pH, temperature, buffer and co-factors – it won’t work.
I tried begging it – it won’t work.
I tried crying about it – it won’t work.
I tried bribing it – it won’t work.

Remember that big scene where Indiana Jones runs from the big rolling ball in the temple? It looked like this, only it didn’t involve a giant LEGO ball and wasn’t totally fake.

The whole time I watched the original I kept thinking, “Why doesn’t he just lay flat and let the ball pass over him on those ramps?” Seriously. Why didn’t he just do that? Was it the panic of the moment? The rush of adrenaline? Or maybe it was Spielberg telling him that if he didn’t play along he wouldn’t work in that town again. I don’t know. All I know is that the giant ball is coming, but unlike the movies, I don’t have anywhere to duck.

I also don’t have much to say. Maybe I could just try to bullshit my way through this, or write something like, “I like ponies,” and I could squeak by on mental disability. I fear I may not be so lucky. (Although those that know me also know that there’s some merit to the mental disability argument.) There’s a cruel irony to all of this. Here, you want to have nightmares tonight? Look at this:

Schrodinger Wave Equation for Hydrogen. Be afraid, be very afraid.

I’ve had to solve this for at least two dimensions on a one-electron molecule. Yes, it’s just as confusing and diabolical as it sounds. However, once you see the actual proof, the results are not hard to replicate. You see, that nasty piece of business there is actually a road map to success.

The damn enzyme is not. It still doesn’t work. There’s no road map, and those that have published are annoyingly silent on how exactly they managed to get their assays to work. I’m open for suggestions. If not, I think I may have to resort to haiku:

Enzyme does not work
Beating head against a wall
Thesis still eludes

Cut me some slack, it’s a work in progress.