Handbook for Pure Science

Audio version sloppily read by yours truly.

When I started working in a lab, I thought being clever was enough. “Each variable in an experiment is a Chess piece,” I told myself, “and the successful experiment is nothing more than moving the correct piece, in the correct way, ”

And so I tried to play science like one plays Chess. But what I didn’t realize is that in Chess your worst enemy is not the person sitting across the board from you, but actually your own blindness. Under the illusion of competition with another, your vision becomes tunneled on capturing his Queen, or putting him in check, and in so doing your mind becomes restricted. You blunder- you find yourself in checkmate.

In exactly the same way, the most dangerous enemy of scientific investigation is not any particular experimental detail but the 200 pound gorilla in the lab coat.

If you strive to cleverly checkmate your experiment you will eventually encounter big problems. The difficulty will appear to be external- in the fine details of what you endeavor to do, in the arrangement of the “Chess pieces”- but if you continue to investigate long enough you will find the source of the confusion is actually some wrong idea that you’ve stuck yourself to.

“This part of the assay works, the problem must be in this other part.” Sometimes this is troubleshooting, sometimes it is blindness.

You have some experimental result that indicates a method is working as intended, but you may expand that confidence to all of your assumptions about the “working” step. You’re liable to confuse your idealization of the experiment with reality. This is what causes problems down the road, but because the problem manifests in a later part of the experiment the connection is not obvious.

So the “problem” is not a misbehaving protocol; the “problem” is that you have a wrong idea that’s causing you confusion. You can’t see it or fix it because the cause and effect occur too far apart in time.

When I investigated the source of such misperceptions for myself, I found that ultimately my mistake was my answer to the question, “What is the job of the scientist?” I thought the job of the scientist was to be clever- to solve problems creatively in ways that other people couldn’t. While this may be how outsiders see a scientist, it turns out there is a big mismatch between what a scientist looks to be doing and what they’re actually doing.

The scientist is someone who observes some phenomena under some experimental circumstances in an effort to answer a question. From an external perspective they appear to be solving problems, but the baseline activity of a scientist is nothing more than unadulterated observation.

In the realm of pure science there isn’t even a single problem to solve– only dispassionate observation of some phenomena in some circumstances. The “problem” arises when you fail to maintain an open mind.

In other words, when you think you have a problem, the problem is actually that you’re not accepting your observations. If you observe your experiments with an open mind you will never be deluded and you will be able to think clearly.

“Oh this gel turned out poorly because I added too much template to my PCR reaction”, this statement is literally not even science. This is an assumption, not an observation, because you’re not seeing the data but only your surface level interpretation of it. You have instantly spun a story and added yourself to the situation, to the facts. This is not science.

“This PCR reaction appeared as a smear on this agarose gel, I should experiment further and replicate to understand why”, this is pure science. This is approaching your observations like an undergrad on their first day in lab.

When you find yourself in trouble with an experiment, you should first make sure that your science is pure. It takes effort and constant vigilance to keep your science pure and uncontaminated from the mind’s rationalizations and storytelling, but when you do you will never face a problem in your work. Your advisor will say that you have some problem to solve, but if you investigate whatever it is with a pure scientific mind then you will see it clearly, and your creative faculty will work more effectively with the extra information. You will not blind yourself to any possibility and will eventually find out why your observations differed from the expected.

What is the job of the scientist? To be an undergraduate on his first day of lab, every day.

What is the nature of the scientist? Just to watch a Chess match.

Thanks for reading.


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