Scientific credibility: is it who you are, or how you do it?

Part of the appeal of science is that it’s a methodical quest for a reliable picture of how our world works. Creativity and insight is crucial at various junctures in this quest, but careful work and clear reasoning does much of the heavy lifting. Among other things, this means that the grade-schooler’s ambition to be a scientist someday is significantly more attainable than the ambition to be a Grammy-winning recording artist, a pro-athlete, an astronaut, or the President of the United States.

Scientific methodology, rather than being a closely guarded trade secret, is a freely available resource.

Because of this, there is a sense that it doesn’t matter too much who is using that scientific methodology. Rather, what matters is what scientists discover by way of the methodology.
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What about Dalibor Sames? The Bengü Sezen fraud and the responsibilities of the PI in the training of new scientists.

Unless you are a chemist or a habitual follower of scientific misconduct stories, it’s possible that you missed the saga of Bengü Sezen.

From 2000 to 2005, Sezen was a graduate student in chemistry at Columbia University, working in the laboratory of then-Assistant Professor Dalibor Sames. She appeared to be a talented scientist in training, and during her graduate studies was lead author on three papers published in the Journal of the American Chemical Society. Columbia University conferred upon her a Ph.D. in chemistry (with distinction).

But, as it turns out, her published results were not reproducible, an issue raised by chemists at Columbia and elsewhere as early as 2002. Further, the results were irreproducible for very good reason: as reported by Chemical & Engineering News, investigations by Columbia University and by the U.S. Department of Health & Human Services (which is home to the Office of Research Integrity) revealed

a massive and sustained effort by Sezen over the course of more than a decade to dope experiments, manipulate and falsify NMR and elemental analysis research data, and create fictitious people and organizations to vouch for the reproducibility of her results.

In the wake of the investigations, Sames has retracted the papers coauthored with Sezen (Sezen refused to retract them on the grounds that she stood by the work), and Columbia has revoked the Ph.D. it granted Sezen.

The evidence from the investigations supports the hypothesis that Bengü Sezen was a liar masquerading as a chemist, that she claimed to have done experiments that she hadn’t, to have obtained NMR spectra that she created (in part) with correction fluid, to have built molecules that she didn’t build. She committed fraud that introduced not just mistakes but lies into the scientific literature.

But she didn’t — she couldn’t — do this alone. She didn’t commit her fraud as a principal investigator (PI). Rather she did it as a scientific trainee, a graduate student working under the supervision of Dalibor Sames (who is currently an Associate Professor at Columbia). It’s worth examining what responsibility Sames bears for what happened here.
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Every diet has a body-count: in the garden with the vegetarian killing snails.

When the demand of my job and my family life allow, I try to take advantage of the fact that I live in California by maintaining a vegetable garden. One of the less pleasant aspects of vegetable gardening is that, every winter and spring, it requires me to embark on a program of snail and slug eradication — which is to say, I hunt for snails and slugs in my garden and I kill them.

As it happens, I’m a vegetarian and an ethicist. I’m not sure I’d describe myself as an “ethical vegetarian” — that suggests that one’s primary reason for eating a vegetarian diet is a concern with animal suffering, and while I do care about animal suffering, my diet has as much to do with broader environmental concerns (and not wanting to use more resources than needed to be fed, especially when others are going hungry) and aesthetics (I never liked the taste of meat). Still, given my diet and my profession, one might well ask, how ethical is it for me to be killing the slugs and snails in my garden?

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Environmental impacts of what we eat: the difficulty of apples-to-apples comparisons.

When we think about food, how often do we think about what it’s going to do for us (in terms of nutrition, taste, satiety), and how often do we focus on what was required to get it to our tables?

Back when I was a wee chemistry student learning how to solve problems in thermodynamics, my teachers described the importance for any given problem of identifying the system and the surroundings. The system was the piece of the world that was the focus of the the problem to be solved — on the page or the chalkboard (I’m old), it was everything inside the dotted line you drew to enclose it. The surroundings were outside that dotted line — everything else.

Those dotted lines we drew were very effective in separating the components that would get our attention from everything else — exactly what we needed to do in order to get our homework problems done on a deadline. But it strikes me that sometimes we can forget that what we’ve relegated to surroundings still exists out there in the world, and indeed might be really important for other questions that matter, too.

In recent years, there seems to be growing public awareness of food as something that doesn’t magically pop into existence at the supermarket or the restaurant kitchen. People now seem to recall that there are agricultural processes that produce food — and to have some understanding that these processes have impacts on other pieces of the world. The environmental impacts, especially, are on our minds. However, figuring out just what the impacts are is challenging, and this makes it hard for us to evaluate our choices with comparisons that are really apples-to-apples.
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Doing fun chemistry.

You may have noticed by now that the Scientific American Blog Network is having something of a Chemistry Day.

Reading about chemistry is fun, but I reckon it’s even more fun to do some chemistry. So, if you find yourself with a few moments and the need to fill them with chemical fun, here are a few ideas:

Make your own acid-base indicator:

With red cabbage and hot water, you can make a solution that will let you tell acids, bases, and neutral-pH substances apart.

Spend the afternoon classifying the substances in your refrigerator or pantry! Audition alternatives to vinegar and baking soda for your papier mache volcano!

Dye some eggs:

Gather up some plant matter and see what colors you can develop on eggshells.

One interesting thing you might observe is that empty eggshells and eggshells with eggs in them interact differently with the plant pigments. Ponder the chemistry behind this difference … perhaps with the aid of some cabbage-water indicator.

Play around with paper chromatography:

Grab some markers (black and brown markers work especially well), lay down some filter paper (or a paper towel or a piece of a coffee filter), and just add water to observe the pretty effects created when some components of ink preferentially interact with water while others preferentially interact with the paper.

If you like, play around with other solvents (like alcohol, or oil) and see what happens.

Make some mayonnaise:

Even just making canonical mayonnaise is a matter of getting oil and water to play well together, making use of an emulsifier.

But things get interesting when you change up the components, substituting non-traditional sources of oil or of emulsifier. What happens, for example, when an avocado gets in on the action?

Try your hand at spherifying a potable:

Molecular gastronomy isn’t just for TV chefs anymore. If you have a decent kitchen scale and food-grade chemicals (which you can find from a number of online sources), you can turn potables into edibles by way of reactions that create a “shell” of a membrane.

Sometimes you can control the mixture well enough to create little spherical coffee caviar or berry-juice beads. Sometimes you end up with V-8 vermicelli. Either way, it’s chemistry that you can eat.

Building knowledge (and stuff) ethically: the principles of “Green Chemistry”.

Like other scientific disciplines, chemistry is in the business of building knowledge. In addition to knowledge, chemistry sometimes also builds stuff — molecules which didn’t exist until people figured out ways to make them.

Scientists (among others) tend to assume that knowledge is a good thing. There are instances where you might question this assumption — maybe when the knowledge is being used for some evil purpose, or when the knowledge has been built on your dime without giving you much practical benefit, or when the knowledge could give you practical benefit except that it’s priced out of your reach.

Even setting these worries aside, we should recognize that there are real costs involved in building knowledge. These costs mean that it’s not a sure thing that more knowledge is always better. Rather, we may want to evaluate whether building a particular piece of knowledge (or a particular new compound) is worth the cost.

In chemistry, these costs aren’t just a matter of the chemist’s time, or of the costs of the lab facilities and equipment. Some of these costs are directly connected to the chemical reagents being brought together in reactions that transform the starting materials into something new. These chemical reagents (in solid, liquid, or gas phase, pure or in mixtures or in solutions) all come from somewhere. The “somewhere” could be a source in nature, or a reaction conducted in the laboratory, or a reaction process conducted on a large scale in a factory.

Getting a reasonably pure chemical substance in the jar means sorting out the other stuff hanging around with that substance — impurities, leftover reactants from the reaction that makes the desired substance, “side-products” of the reaction that makes the desired substance. (A side-product is a lot like a side-effect, in that it’s produced by the reaction but it’s not the thing you’re actually trying to produce.) When you’re isolating the substance you’re after, that other stuff has to go somewhere. If there’s not a particular way to collect the other stuff and put it to some other use, that other stuff becomes chemical waste.

There’s a sense in which all waste is chemical waste, since everything in our world is made up of chemicals. The thing to watch with waste products from chemical reactions is whether these waste products will engage in further chemical reactions wherever you end up storing them. Or, if you’re not careful about how you store them, they might get into our air or water, or into plants and animals, where they might have undesired or unforeseen effects.

In recent years, chemists have been working harder to recognize that the chemicals they work with come from someplace, that the ones they generate in the course of their experiments need to end up someplace, and to think about more sustainable ways to build chemical compounds and chemical knowledge. A good place to see this thinking is in The Twelve Principles of Green Chemistry (here as set out by Anastas, P. T.; Warner, J. C. Green Chemistry: Theory and Practice, Oxford University Press: New York, 1998, p.30.):

  1. Prevention
    It is better to prevent waste than to treat or clean up waste after it has been created.
  2. Atom Economy Synthetic methods should be designed to maximize the incorporation of all materials used in the process into the final product.
  3. Less Hazardous Chemical Syntheses Wherever practicable, synthetic methods should be designed to use and generate substances that possess little or no toxicity to human health and the environment.
  4. Designing Safer Chemicals Chemical products should be designed to effect their desired function while minimizing their toxicity.
  5. Safer Solvents and Auxiliaries The use of auxiliary substances (e.g., solvents, separation agents, etc.) should be made unnecessary wherever possible and innocuous when used.
  6. Design for Energy Efficiency Energy requirements of chemical processes should be recognized for their environmental and economic impacts and should be minimized. If possible, synthetic methods should be conducted at ambient temperature and pressure.
  7. Use of Renewable Feedstocks A raw material or feedstock should be renewable rather than depleting whenever technically and economically practicable.
  8. Reduce Derivatives Unnecessary derivatization (use of blocking groups, protection/ deprotection, temporary modification of physical/chemical processes) should be minimized or avoided if possible, because such steps require additional reagents and can generate waste.
  9. Catalysis Catalytic reagents (as selective as possible) are superior to stoichiometric reagents.
  10. Design for Degradation Chemical products should be designed so that at the end of their function they break down into innocuous degradation products and do not persist in the environment.
  11. Real-time analysis for Pollution Prevention Analytical methodologies need to be further developed to allow for real-time, in-process monitoring and control prior to the formation of hazardous substances.
  12. Inherently Safer Chemistry for Accident Prevention Substances and the form of a substance used in a chemical process should be chosen to minimize the potential for chemical accidents, including releases, explosions, and fires.

At first blush, these might look like principles developed by a group of chemists who just returned from an Earth Day celebration, what with their focus on avoiding hazardous waste and toxicity, favoring renewable resources over non-renewable ones, and striving for energy efficiency. Certainly, thoroughgoing embrace of “Green Chemistry” principles might result in less environmental impact due to extraction of starting materials, storage (or escape) of wastes, and so forth.

But these principles can also do a lot to serve the interests of chemists themselves.

For example, a reaction that can be conducted at ambient temperature and pressure requires less fancy equipment (i.e., equipment to maintain temperature and/or pressure at non-ambient conditions). It’s not just more energy efficient, it’s less of a hassle for the experimenter. Safer solvents are better for the environment and the public at large, but it’s usually the chemists working with the solvents who are at immediate risk when solvents are extremely flammable or corrosive or carcinogenic. And generating less hazardous waste means paying for the disposal of less hazardous waste — which means that there’s also an economic benefit to being more environmentally friendly.

What I find really striking about these principles of “Green Chemistry” is the optimism they convey that chemists are smart enough to figure out new and better ways to produce the compounds they want to produce. The challenge is to rethink the old strategies for making the compound of interest, strategies that might have relied on large amounts of non-renewable starting materials and generated lots of waste products at each intermediate step. Chemistry is a science that focuses on transformations, but part of its beauty is that there are multiple paths that might get us from staring materials to a particular product. “Green Chemistry” challenges its practitioners to use the existing knowledge base to find out what is possible, and to build new knowledge about these possibilities as chemists build new molecules.

And, to the extent that chemistry is in the business of finding new knowledge (rather than relying on established chemical knowledge as a master cook book), these twelve principles seem almost obvious. Given the choice, would you ever want to make a new compound for an application that had the desired function but maximized toxicity? Would you choose a synthetic strategy that generated more waste rather than less (and whose waste was less likely to break down into innocuous compounds rather than more)? Would you opt to perform the separation with a solvent that was more likely to explode if a less explosive solvent would do the trick? Probably not. Of course, you’d be on the lookout for a better way to solve the chemical problem — where “better” takes into account things like cost, experimental tractability, risks to the experimenter, and risks to the broader public (including our shared environment).

This is not to say that adhering to the principles of “Green Chemistry” would be sufficient to be an ethical chemist. Conceivable, one could follow all these principles and still fabricate, falsify, or plagiarize, for example. But in explicitly recognizing some of the costs associated with building chemical knowledge, and pushing chemists to minimize those costs, the principles of “Green Chemistry” do seem to honor chemists’ obligations to the welfare of the people with whom they are sharing a world.