Black Gunk

I started out in science as a chemistry major in College. I liked chemistry much more than biology, because chemistry had rules, equations, and laws, and it made a lot of sense to me compared to the strange, messy, and incomprehensible world of biology (I have written about this before here). In chemistry, you could balance equations so that you could tell exactly what would happen if you reacted chemicals together.

Or so I thought. My education into the reality of chemistry began with the first advanced organic lab course I took. We were to perform a simple organic synthesis experiment: mix two reactant chemicals along with some reagents, add heat, then distill the product. I was careful to follow all the steps, measured precisely, made no mistakes, and everything seemed to be proceeding nicely. As predicted, the solution turned brown upon heating, and I started the distillation. Sure enough, I began seeing a nice clear liquid dropping from the end of the condenser, and as it collected I performed a test on this liquid to make sure it was the right chemical compound. It was. YAY. Success.

Well, sort of. One of the things we were supposed to determine was called the “yield” of the reaction. Now this thing called yield is not something that is discussed in basic chemistry, or in any part of theoretical chemistry. (It is a big deal in chemical engineering, but we won’t go there.) The yield of a reaction is the amount of the product of a reaction that we actually get compared to the amount you are supposed to get. The amount you are supposed to get is easily calculated from those equations I so loved to balance and solve. The amount you actually get is… well, totally mysterious. It has to do with your own skill, how pure are the starting reactants and reagents, the time of year, the phase of the moon, and so on.

Back to my synthesis. The condenser kept dripping precious drops of the pure product chemical, and the flask kept boiling away, but I noticed that the stuff in the flask was no longer that nice clear yellowish brown that it had once been. It was getting darker by the minute. As it darkened it also got opaque and viscous. Finally, no more vapor was coming out and the drops stopped dripping. I measured the amount of product I had synthesized, did the calculation, and found I had achieved a yield of 20%. I was mortified. After all that, I had succeeded in producing only one fifth of the amount of the product that I was supposed to. I allowed the flask to cool and examined it. It was full of a deep black gooey gunk; it took me an hour to clean the flask.

When the instructor came by, I was ashamed to show him the results. But when I did, he said “Great job! 20% yield is terrific”. I was shocked. It turned out I had the highest yield in the class, and two students hadn’t gotten anything. But what we all had was a flask of black gunk.

What is that black, tarry, gunky stuff – which, as it turns out, is the main product of practically every synthetic chemical reaction? Nobody knows. It is a mixture of hundreds of chemical compounds produced by hundreds of other reactions between the two reactant chemicals, as well as various degradation products of the two starting chemicals, reactions between these chemicals and the other reagents, and breakdown products of all of these, which also react with each other, and also break down and react, and so on. In other words, an unholy mess.

Disillusionment. My beloved chemistry, it turned out, was not the pure, pristine science of logical, rigorously predictable reactions between chemicals, but was in fact just about as much of “black” box (sometimes literally, as the box is often filled with black gunk) as biology. This is also true for physics, geology, and in fact all science, as I later found out. So when I went to graduate school, I thought I might as well plunge into biology, since in reality it wasn’t much worse than chemistry. But I ended up compromising. I wasn’t quite ready to part company completely from my dream of a chemical approach to finding a grounding in the natural world, so I got my PhD in Biochemistry.  It was a good decision.




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11 Responses to Black Gunk

  1. NoahWhite says:

    I loved this, Sy; and it reminded me of the sheer awe (to paraphrase Einstein for the umpteenth time) that anything makes sense at all. I distinctly remember moping around my high school AP Biology class one morning after I’d broken up with the girl I had been dating, and my teacher (half-jokingly) telling me to just move on because they were “just chemical reactions”. I know you nor I go for all that nothing-buttery, but after reading this, I can help but find that the word “just” in that explanation is woefully inaccurate–when I take a step back, the very nature of chemicals is mind-boggling to me. Thanks for the great piece!

    • Thanks Noah for the kind words. And I will tell you as a very experienced guy (married three times, lots of girl friends, etc) that chemical reactions are a very minor part of love, which you already know. Compared to that subject, science is a cinch.

  2. Ethan Ortega says:

    You can never paraphrase Einstein too many times Noah 😉 You’re correct; there is such a striking amazement that one can feel when they step back and consider the coherence of the natural world and all of its workings (though I wholeheartedly agree that it is a terribly inaccurate mindset to ever venture into nothing-buttery, and we’d all do well to stay out of that myopia). The very idea that the natural world has some rationality built into it is ever-fascinating to me, but I also like the endless mysteries that keep coming up. I like to think that God has us on a quest, a continuing search for truth, and that maybe even beyond this life, we’ll still have so much more to discover 🙂
    Thanks for writing this, Sy.
    Hope you all had a wonderful Thanksgiving.
    Peace of Christ

    • Thanks Ethan. Thanksgiving was good. I went to NY to be with my son, his mother (my ex), my current wife, and her two boys. We had a great time. I agree with you about the quest thing, I only wish I had started mine sooner. Peace to you.

  3. SheilaDeeth says:

    I stuck to physics through junior high and high school I was scared of fire, therefore wasn’t allowed to progress to those nice chemical equations; and I didn’t like cataloging smelly remains, which was almost all they let us do in first year bio, though looking at fertilized chicken eggs was seriously cool. Now I wish I’d done more of all three sciences. I read about them avidly though, oddly enough, I hadn’t read about black gunk before. I ended up studying math because it really does obey its own rules, out there in its own universe, just slightly separate from ours.

    • Ha ha. I know, Sheila that black gunk is not well covered in most textbooks. Yet it remains a fact of chemistry. As for me, I am in converse situation, I now wish I had paid more attention to math. As for following its own rules, I suppose that is true, but are there any exceptions? I was thinking of fractals, and Cantor sets and some aspects of chaos theory. I think I read that Mandelbrot was considered a bit mad when he first started in on fractals.

  4. Brings back a lot of memories of science classes (and life) not quite going to plan.

  5. Paul Bruggink says:

    You just needed a good chemical engineer to figure out what happened and how to improve the process to obtain a higher yield.

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