Fortuitous Screw-Ups, Acceptable Risk, and Heartless Machines

When life hands you lemons….trade them in for oranges, buy some vodka, and make yourself a screwdriver.

See what I did there?

Sometimes when life hands you a sucky situation, you take what you get and try to make something refreshing out of it (making lemonade out of lemons). The problem I have with that is even with the refreshing product you still get some of the residual suckiness of the primary constituent. For instance, when you take the sour lemons and squeeze the juice out of them, it’s still sour! I don’t care how much sugar you add to it, you’ll always taste some sourness.

But if life hands you something sucky and you figure out how to get rid of the suck factor and create a much more ideal situation – now that is pure genius! Lemon not your flavor? Get some oranges! Not in the mood for plain orange juice? Spice it up with some vodka! Then kick back and enjoy how your life just turned out until it drops another bomb on you.

Back in grad school, I was given a project on modeling organic materials. Let me give you some background information. Molecular modeling is the combination of chemistry and computers to study how a system behaves at the atomic level. In short, it’s a royal pain in the neck. But a very interesting pain in the neck. The hard part with modeling is that you have to provide every minor detail to the computer.

Let’s say I want to study butane (which is four carbon atoms “chained” together; the two end carbons each have three hydrogens attached to them and the two middle carbons each have two hydrogens). There are 3 carbon-carbon bonds (each one of which is single); 10 carbon-hydrogen bonds (also single); 2 carbon-carbon-carbon angles; 13 carbon-carbon-hydrogen angles; and 10 hydrogen-carbon-hydrogen angles. Then there are dihedrals, and I only have one thing to say about those:


It’s an angle with four atoms instead of three. (It’s actually more complicated than that, but I don’t like them and therefore don’t feel like talking about them because they have only caused me pain and misery in the past. Insert Taylor Swift’s song “Bad Blood.”)

All bond lengths and angles and their respective force constants need to be declared. Additionally, each atom type, its weight, and its partial charge need to be defined along with the order of bonding.

And that’s just setting up the system. For one molecule. That doesn’t include building a bigger system or running the calculation or analyzing the data from that calculation.

Like I said: royal pain in the neck.

In spite of all that, this field is extremely fascinating because you can actually watch the atoms from your model move and how they interact with each other. And you can also see how that affects the system as a whole. When I was given my project, I couldn’t wait to see what it would look like. It was a 100-atom molecule with mostly hydrogens and carbons but with two silicon atoms as well. There was a small glitch: there were two branches off the molecule’s backbone that contained a triple bond between two carbon atoms (which we call sp-carbon) and one of those carbons was bonded to silicon. The problem: no parameters existed in the force field we were using that described that interaction between sp-carbon and silicon.

Okay. No problem. Maybe another force field had those parameters.


Okay. Maybe someone else studied this same system computationally and they were able to parameterize the system.

Wrong again!

Alright. Don’t panic. Let’s see if we can put the unit cell (a square with a molecule at each corner) into this software that does a bunch of complicated quantum mechanical calculations and will automatically parameterize the system.

The software can’t handle a system that size. Too bad!

Oy vey.

The only available option was to parameterize the system myself. Ok. Maybe that won’t be so bad.

Definitely wrong again! I was on a roll.

Long story short (though it may be too late for that) I was able to calculate my own parameters which involved stretching and compressing bonds and angles and finding the energy at each configuration. Because that’s the first thing that comes to every scientist’s mind when they need to model a 400-atom system. 😦

But that wasn’t even the project. That was just the first step to setting up the project! All that work wasn’t even worth a pamphlet much less a journal article.

Finally, after a few thousand calculations of varied unit cell configurations and mapping an energy profile and inserting a solvent, I had enough data for a thesis and two articles. (I’m not the first author but I have my name on papers in Nature Communications and the Journal of the American Chemical Society! To me, that’s huge!) In the end, I took the lemons I was given and made my screwdriver! (Please do not read anything dirty into that. Let’s keep this G-rated.)

Why am I telling you this mostly depressing tale of unfortunate events that culminated in a semi-important ending?

Because my story is not unique. This is the way of research. Complicated, discouraging, and full of setbacks with the occasional pick-me-up that yields something usable. Finally, you get enough usable work to gain some recognition within your community.


I like to think of research as a series of fortunate screw-ups. Someone did something of value but it wasn’t perfect. But it was SOMETHING. It was a step in a direction (maybe not even the right one) that someone else can build on. And really, it doesn’t even matter how close that person was to the right answer. Maybe they were in the ballpark. Or maybe they weren’t even in the parking lot! (Let us not forget the practice of bloodletting that was the method of choice for curing diseases. Again, insert Taylor Swift’s “Bad Blood.”) Still, someone else with some insight will come along and help set the scientific compass pointing that much closer to true north.

The scientific community has come under a lot of criticism, especially in the medical field, because we haven’t been able to find the perfect solution for every possible disease. One of the big controversies today is getting kids vaccinated. Yes, parents have a choice, and yes, there are POTENTIAL negative side effects, and yes, there are many who have suffered those side effects. And I do feel for them.

However, those side effects are not the majority, and vaccinations have done much more good than harm. It’s because of vaccinations that many diseases that were either life-threatening or severely life-altering either disappeared or were reduced in severity. And it’s the lack of vaccinations that has led to those same diseases making a comeback.

Let me let you in on a little secret: Science itself is infallible. Scientists, however, are not. We make mistakes. We can’t possibly account for every possible scenario, and things will go wrong. The useful products of scientific research are really the results of a series of fortunate screw-ups. And the only way to know if it will work is to try it out and see what happens. Sometimes, the results aren’t what we hoped for. And when that happens, we take what we have and try to get even closer to the right answer. It takes a lot of iterations, but each time we get closer, the results improve the quality of life even more.

I’m going to say something that is going to sound very heartless:

There is such a thing as acceptable risk.

Scientific advances are determined fit for public consumption after rigorous statistical analysis. And when it comes to statistics, majority rules. If the likelihood of introducing a new technology, therapy, drug, or procedure yields more pros than cons and it can make a profit, then you can bet it’s going on the market.

I know my comment of “it can make a profit” will spark some backlash. But here’s another secret: scientists need to eat too. We spend at least four years in undergraduate programs and at least five years in graduate programs, which are the only places in America that slavery is actually legal. Again, probably more backlash, but let me explain before you start screaming at your computer.

Graduate students exist at the pleasure of their advisers. They work in their adviser’s lab on a project funded by said adviser and are paid from that adviser’s funds. If the results aren’t up to snuff, you don’t graduate. There is no union to protect grad students. If you have to work 70-80 hours a week to get results for a project that may not even work, then that’s what you do if you want your degree. You’ll have health insurance and your tuition will be covered. You’ll make enough money to survive, but that’s about it.

And even once we get that coveted Ph.D., it’s still a long road before arriving at our dream jobs with the comfortable paycheck and amazing benefits that allow us to have homes and support families and send our children to college. We devoted at least a decade of our lives solely to intense education and research before moving above the poverty line. We earned that profit.

But going back to acceptable risk. As scientists, we have to be realistic. We have to acknowledge that each new invention, drug, etc. will have both risks and benefits. This is true for anything, even in life. Every choice made has pros and cons. There is no way to determine where the outcome will take you, but you adjust as necessary. The same with science. We try to find a safer way to drive cars, a better way to kill a cancerous tumor without destroying healthy cells, a more efficient way to store energy. For now, we can’t do it perfectly so we will just have to do the best we can and hope someone else will move us even farther forward.

One of my favorite movies is Extraordinary Measures with Brendan Fraser and Harrison Ford. Brendan Fraser plays John Crowley, a business executive with a wife and three kids; two of those kids have Pompeii disease, a degenerative muscular disorder with a life expectancy of less than 10 years. He works with a scientist played by Harrison Ford to find a drug to help treat the disease. They are both upfront at the outset: the disease, right now, is incurable. However, it can be treated if a drug can be found.

Eventually, the two end up at a biotech company and Brendan Fraser and one of the head scientists get into an argument over procedure and protocol. Fraser accuses the scientist of being a “heartless machine” and the scientist tells Fraser that lack of emotion is necessary to finding a drug; otherwise, judgment is clouded, mistakes are made, and the results could do more harm than good. While I feel for Fraser’s character trying to save his kids’ lives, I have to side with the scientist on this one.

The point of science is to move society forward one step at a time. Sometimes it occurs in leaps and bounds as we’ve seen with the technological boom over the last twenty years. We analyze; we come to logical conclusions. We do consider the consumer and try to create a product that they would want; but many times that has to be secondary. We have to find the best solution, even if that solution has the possibility of negative consequences. From there, we can build even more.

It’s one thing to be passionate and excited about your work; it’s another to be driven completely by some emotional tie to your work. I worry about people who pursue careers because it’s what a relative did, or they want to find a cure for cancer because they were close to someone who died from it. It’s admirable to want to do something to honor a loved one. But more often than not, those people aren’t so much chasing answers as they are chasing ghosts.

Every bit of progress made is celebrated by scientists, in spite of the drawbacks. To us, we are reducing the setbacks from the previous attempt and moving asymptotically closer toward that screwdriver.

Peace, Prosperity, and Organic Photovoltaics,

Chic Geek and Chemistry Freak

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