Field of Science

A chemistry decoder

A basic guide to decoding organic compound names
© Andy Brunning/Compound Interest
The August 17th edition of C&EN — Chemical and Engineering News, the American Chemical Society's weekly newsmagazine — was devoted to the intersection of chemistry and the internet.  I have a piece in there on the ways in which the internet allows pseudoscience to spread and what chemists might do to counteract the spread.  I point to Andrew Noymer's work on the mathematical modeling of rumor spread, which suggests that rumors and autocatalytic reactions such as the classic Lotke-Volterra systems are not dissimilar.

Noymer's results suggest that damping down the spread of rumor requires both persistent debunking and increased resistance among the susceptible population.  Though at first glance it seems counterintuitive, just periodically debunking rumors leads to a steady state situation, where there is always a (not so small) part of the population who believe.  Debunking needs to be strong and regular, and even then, if you don't have a resistant population, you land in a steady state regime.  The best you can do is to reduce a rumor to something that periodically breaks out.  Like the "Mars will be as big as the Moon in the sky!" meme which you see circulating on social media every summer like clockwork.  (Spoiler alert: It wasn't. It won't be.  Ever.)

What does it take to make a population resistant to pseudoscience?  Some tactics are not unique to the pseudoscience issue:  teaching critical thinking (as Phil Plait points out and Joel Achenbach implies here). Slower fingers when it comes to hitting "share." But it also means giving the population some basic tools for reading science.  After the Royal Society of Chemistry released a large study of the public awareness of chemistry, I wrote that it might be helpful if instead of periodic tables, chemists handed out a cheat sheet for decoding chemical names.  I wished and voilà, the brilliant Andy Brunning of Compound Interest created this graphic.  Print it out and post it in your kitchen.  Link to it on Facebook.  Browse the rest of his collection.  Buy his forthcoming collection about the chemistry of food and give it to the family member who keeps sending you links to the Food Babe.

Most all, talk about what you do as chemist, debunk garbage science when you hear it, swiftly and without mocking, and grab as many opportunities as you can to help people learn to decode chemistry on their own.

Eating periodically: is there thallium in your wasabi?

Wasabi, Iwasaki Kanen 1828
via Wikimedia Commons 

Could your wasabi peas be poisoning you?  Short answer. Maybe.

Delish recently posted an article on thallium — a highly toxic metal — in kale, the quintessential healthy green.  The Internet relished the irony of finding toxic metals in the highly touted greens. The piece points to an article in Craftsmanship magazine, which attempts to make a link between consumption of kale and thallium levels.  This is not new news.  There are dozens of reports, going back two decades, in the scientific literature of thallium in cruciferous vegetables, such as kale and brussell sprouts — and wasabi.

Thallium is definitely a nasty element, and has an infamous history of use as a poison in fact and fiction, starting with Ngaio Marsh's Final Curtain.  Read Deborah Blum's hair-raisingly fascinating Poisoner's Handbook (or her short article at Wired about a recent murder case in Princeton).  But as with everything, dose makes the poison, and the amounts of thallium in plants vary widely depending on the concentrations in the soil.  In highly contaminated soils, plants can contain enough thallium to be hazardous.  But if such highly contaminated soils were widespread, we'd have seen the effects already. (See this paper for some background.) (Also, you can leverage this ability and use it to clear out the thallium from a contaminated area.)

So how does thallium get into the plants? There is some evidence that thallium ions travel the same pathways as potassium ions (which play key roles in plant metabolism), and so might find their way into plants (and animals) though similar processes.

Thallium is also in the same column as boron, and elements in the same column of the periodic table often have similar behaviors, because their electrons are arranged in similar patterns.  For example, strontium, which is underneath calcium, sneaks into the body by way of the same processes calcium does. Boron is found in plants (coffee is a good source, and plants in the same family as kale are also heavy absorbers of boron); it is believed to be critical to cell wall formation.

And if there is boron and thallium, indium - in the same column is another likely companion. And yes, indium has been detected in plants in the cabbage family.  

As always, eating a wide variety of things is good advice, and it's key to remember that "natural" is not the same as "safe."

First woman in 'space'

I keep checking to see how far away New Horizons is from Pluto (459,770 km at 0235 GMT) even though I know there's nothing to see at the moment, but I am a space junkie.

The first space launch I can remember seeing is the last of the Mercury missions, launched in May of 1963.  I was 5 and I was hooked on space.  In retrospect, I suspect my hours watching rockets erect on their launch pads, the vapor streaming off the only sign this was live TV,  fed my desire to do science as much as the biography of Marie Curie I chewed through while ill one summer or my parents' careers.

I'd be glued to the TV for every launch I could for the next decade, and I confess I can still be found streaming a launch in the corner of my screen while grading.  I'm still hooked on space.

S o I was delighted to discover the first woman to leave the atmosphere — at least the breathable part of it — was both a chemist and an alum of the college where I teach.  In October of 1934, Jeannette Ridlon Piccard, a licensed balloon pilot, flew a balloon with her husband on board to an altitude of 17.5 km, well into the stratosphere.  Her altitude record (for women) would not be broken until Russian astronaut Valentina Tereshkova's flight in June 1963.  You can watch the Piccards take off in this video and see the wreckage of the gondola after they crash landed.  Her first person account of the trip was published in the New York Times the next day, including her chagrin at such an inelegant landing.

Ridlon's entry in Bryn Mawr's Undergraduate Catalog of 1916, she
would concentrate on chemistry and physics over the next 2 years. 
Piccard was a Bryn Mawr College graduate, class of 1918, taking course work in chemistry and physics, as well as psychology and philosophy.  She went on to get her master's degree in chemistry from the University of Chicago and later a Ph.D. in education from the University of Minnesota.  All wonderful preparation for being an...executive secretary (those were not the days), pilot and stratospheric explorer.  Piccard's papers are the Library of Congress and I'd love to go read the experimental notes from that epic flight.

Piccard's grand-nephew Bertrand Piccard is one of the pilots on the Solar Impulse, a solar powered plane attempting to circumnavigate the globe.

My thanks to Bryn Mawr College's registrar, Kirsten O'Beirne, for figuring out how "majors" worked in the early 20th century.

Sequencing data

The New York Times recently posted a piece on problem solving which asked readers to first solve a problem:

"We’ve chosen a rule that some sequences of three numbers obey — and some do not. Your job is to guess what the rule is. We’ll start by telling you that the sequence 2, 4, 8 obeys the rule."

You can test your hypotheses by typing sequences into three boxes to see if they follow the unstated rule.  Once you think you know, you type in a description.  Most people it turns out, suggest an answer without ever trying a sequence that returns a firm "NO."  Psychologists interpret this as being evidence of confirmation bias: once we get a "yes" for our theory - we don't poke around trying to find a "no."

When I teach chemical kinetics, I point out to students that few experiments can prove a reaction goes in a particular sequence, only that the data is consistent with a proposed mechanism.  No answers can be as or more critical to problem solving as yes.

I failed to 'correctly' solve the puzzle, [SPOILER ALERT] though I did get several no answers.  One rule I tried was an: 21, 22, 23 = 2, 4, 8.  The sequence 1, 1, 1 follows that rule (11, 12, 13 are all one), but yielded a no.  The rule an = 2 x an-1: 2, 2x2=4, 2x4 worked for every sequence I tried, but is not 'the 'answer.  The answer is that correct sequences have each number larger than the last.

The study suggests I failed not only because of confirmation bias, but because I complicated the problem, assuming that there was some sort of trick to the rule. Actually, I assumed the technical mathematical meaning of sequence held, in that there was a rule that uniquely specified each number in the sequence given the starting value(s). An ordered list of numbers, each of which is larger than the previous value is not a sequence in the mathematical sense.

In retrospect, I should have tried the sequence 0, 0, 0. It follows the rule I proposed (an = 2 x an-1) as the correct one, but returns a "no." It would have ruled out my proposed rule, a useful "no".  (I might also have tried non-integer numbers.)  I failed in part because I didn't understand the question they were asking, we didn't have the same definition of "sequence."  In some sense I fell prey to the "when all you have is a hammer, everything looks like a nail" scheme.

There are more than 2500 rules that would give you the mathematical sequence 2, 4, 8.  See Sloane's encyclopedia of integer sequences.  My first proposed sequence is A000079 in the collection.

For more about sequences and Sloane's encyclopedia, read this article at AT&T.

Eating periodically (not a quantum diet)

What elements are in chocolate?

Answer #1

Carbon (Chocolate)
Hydrogen (CHocolate)
Oxygen (ChOcolate)
Holmium (CHocolate)
Cobalt (ChoColate)
Lanthanum (ChocoLate)
Astatine (Chocol(ChocolAte)
Tellurium (ChocolaTe)

So you could have: CHoCoLaTe or CHOCOLate or....

Answer #2

(Presuming the letters are not required to be used in order - and yes, I wrote a piece of code to give me this for any word)
All of the above and
aluminum (Al), chlorine (Cl), calcium (Ca), cerium (Ce), helium (He), actinium (Ac), Technetium (Tc), thorium (Th), thallium (Tl) and tantalum (Ta)

Answer #3

Elements that have been detected in chocolate (in this case dark chocolate, rough percent of my recommended dietary allowance in parentheses assuming I eat only a 100 gram bar).

Carbon, hydrogen, nitrogen, oxygen, potassium (why cocoa is detectably radioactive), calcium (about 5% of my RDA), iron (125%), magnesium (70%), phosphorous, potassium (almost a gram, 20%), sodium, zinc (40%), nickel, sulfur, silicon, cadmium, lead (yep, lead, mostly from dust contamination during transport), mercury, arsenic, uranium (trace amounts, but yes, more radioactivity), aluminum, copper (from pesticides, but on the plus side gives you your RDA for this element), and manganese

Nearly one fifth of the known elements have been detected in chocolate, which clearly should be the backbone of any periodic diet.

What other elements are you eating?

Just in case your chocolate doesn't have enough radioactivity for you:

Chemists are wildly polysemous

STO-3G//STO-3G calculated Raman spectrum of arsole
A few months ago this BBC news report - about the evacuation of a building because of a volatile compound got chemists on Twitter talking about language, particularly those words that mean one thing to chemists and something quite different to the rest of the world.  (Thanks @NatalieFey_NLS, ‏@stephengdavey and @stuartcantrill!) Like volatile (high vapor pressure vs. explosive) or to my mind the most overexposed chemical example and the inspiration for far too many t-shirts: mole.  One thing led to another, or at least, one comment by @stuartcantrill led to my Thesis column in  this month's Nature Chemistry.
Is RT retweet or 2.5 kJ/mol?

This piece was pure fun to write.  I enjoyed crowdsourcing examples of chemical double meanings. (List of 200 examples is here.) By far the favorite mechanism of formation for chemists is polysemy, where words share a common ancestor, but the meanings have drifted apart.  Take flush, as in flush a column, or flush a toilet or  flush game or even a straight flush.  All these senses derive from the Latin fluxus for flow.  (Don't see the connection to poker? The OED suggests you think of a flush as a "run" or flow of cards.)

Sometimes the two meanings sit close to the surface for chemists, other times we are pretty blind to the lexical ambiguity.  My youngest son is toying with the idea of a chemistry major, and when I read him examples from the list, he was quick to note both senses for many words: cell, salt, aromatic.  But when I got to molar, he wanted to know what else it meant beyond the concentration of a solution.  "Teeth?" I suggested.  He face palmed.  Whether he majors in chemistry or not, we've already messed with his mind.

Polysemy is productive — as the linguists would say — not just in terms of the language, but of new chemistry.  We ought not to discourage lexical play in chemists (not that one has much control over language in any case, IUPAC's gold book notwithstanding) it gives us a rich set of images to draw on and as I said in the essay, "we can't look for what our language doesn't let us imagine."

Read the essay here. ($)

What is the half-life of a tweet?

My tweets apparently have a half-life of about two hours, but I have no idea if that's unique to me.  My spouse is new to Twitter and as I was showing him how he could see some data about his tweets, I noticed that the graph of the data looked familiar.  Probably because I taught chemical kinetics twice last year (in pchem and general chemistry).

Over lunch today, while waiting for my car to be serviced, I decided to explore the kinetics of my tweets.  I used data from the first 10 hours after I posted a tweet, and used tweets that had several hundred total impressions and few retweets.  Using five data sets from the past month, I fit the tweets to linear models for 0th, 1st and 2nd order kinetics.  R2 values suggest that a 1st order model is most appropriate, with a rate constant of 0.35/hour, which translates to a half-life of 2.0 ± 0.4 hours.  I'm curious if that's relatively constant for me, or whether it's characteristic of other parameters, but time is up.

Perhaps because I'm writing this outside in a park, I'm reminded of an infamous problem about the temperature dependence of the chirp rate of male snowy tree crickets in many general and physical chemistry texts.  A discussion of the phenomenon (first recorded in the late 19th century, and not true of cricket everywhere) can be found in Thomas Walker and Nancy Collins. “New World Thermometer Crickets: The Oecanthus Rileyi Species Group and a New Species from North America.” Journal of Orthoptera Research 19 (2010): 371–376. 

Molecular Jek-yls and -hydes

Like Jekyll and Hyde, changing a functional group changes 
a molecule's behavior. Image from Library of Congress.
Chains of pure carbon and hydrogen, called hydrocarbons by chemists, are notoriously hard to get a chemical handle on.  One of the major driving forces in chemical reactions is "opposites attract" — in this case opposite charges.  Since carbon and hydrogen have essentially the same desire for electrons (negative charges), there is not much difference in charge around to drive a reaction. Swap out a hydrogen for something else that does have a relative charge —  chlorine, fluorine, oxygen, nitrogen — and suddenly you have something to react with.  Chemists call these riffs on a basic carbon framework "functional groups" - they are often the parts of a molecule's structure that drive its function.

Change up the functional group, and you change the molecule's behavior. Like Jekyl and Hyde.  Ethanol is something to drink on a Friday night, ethanal is found in the coffee you drink for the hangover the next morning (in an ironic twist, it's also produced as your body metabolized the ethanol.)

The first part of a chemical name tells the size of the carbon framework, the ending tells you about its function — or lack thereof.  Names that end in -yl or -ane mean a hydrocarbon chain without any fancy functionality.  Propane, a popular fuel, is a three carbon hydrocarbon chain.  Methyl mercaptan (added to odorless natural gas to make it smell, and make leaks quickly noticeable), has a one carbon long "chain" in it. Change -yl to -ol and you have made an alcohol, a chain with an -OH group on it (Ethanol is CH3CH2OH, sometimes written EtOH, a 2 carbon chain with an OH group on it.)

Knowing the functional groups means knowing something about the kinds of things a molecule can do.  Esters smell floral, carboxylic acids can remove a layer of skin, and are found in many lotions.

So to decode:
-ol means an alcohol (functional group = -OH) but not necessarily the kind of alcohol you drink 
-al means an aldehyde (-COH); these often smell sweetish 
-oxy means an ether (an oxygen sandwiched between two carbon chains) 
-oic acid or -ic acid means a carboxylic acid (pronounced "car-box-sill-ick") salicylic acid, often found in face washes 
-oate means an ester (a COO group sandwich between two chains); ethyl nonanoate smells like grape, the functional group is between a 2 carbon chain (ethyl) and nine carbon chain (nona) 
-one means a ketone, a CO group sandwiched in between two chains

Check out Andy Brunning's of Compound Interest's great graphic on functional groups and their names and Practically Science's map of molecules in food and their smells.

Getting at the truth: gender in the lab

Nobel prize winning biochemist Tim Hunt made an unfortunate series of remarks at a luncheon for women science writers and journalists at the World Conference of Science Journalists in Seoul, South Korea: “Let me tell you about my trouble with girls … three things happen when they are in the lab … You fall in love with them, they fall in love with you and when you criticise them, they cry.”

Today he's said he's sorry for having made those remarks to that particular audience, suggesting first that it was a misunderstood attempt at irony, but he stands by his comments: "I just meant to be honest, actually."

He went on to say that, "It's terribly important that you can criticise people's ideas without criticising them and if they burst into tears, it means that you tend to hold back from getting at the absolute truth....Science is about nothing but getting at the truth and anything that gets in the way of that diminishes, in my experience, the science."

What I'm thinking about is how the documented tendency of men (or should I say boys?) to be overconfident in their self-assessment of ability in science and math might diminish the effective functioning of a research group? Shelley Correll's work showing that "males assess their mathematical competence higher than females who perform at the same ability level and who receive the same feedback about their mathematical competence."makes me wonder if when Tim Hunt criticizes a boy's ideas, the boy discounts the criticism because he is overconfident.  [Amer. J. Soc. 106 (2001): 1691–1730.] #justbeinghonest

Hunt's remarks should come as no surprise, given what he said in this interview:
Labtimes: In your opinion, why are women still under-represented in senior positions in academia and funding bodies? 
Hunt: I'm not sure there is really a problem, actually. People just look at the statistics. I dare, myself, think there is any discrimination, either for or against men or women. I think people are really good at selecting good scientists but I must admit the inequalities in the outcomes, especially at the higher end, are quite staggering. And I have no idea what the reasons are. One should start asking why women being under-represented in senior positions is such a big problem. Is this actually a bad thing? It is not immediately obvious for me... is this bad for women? Or bad for science? Or bad for society? I don't know, it clearly upsets people a lot.
If he wants a hint, it's bad for science.  Restricting the pool means you get fewer breakthroughs. Last fall I built a simple Monte Carlo simulation of "science" to find:

"I wonder if framing the issue of women in science as one of equity to individuals — it's not fair to deny women the opportunity to play the game — blinds us to the costs to science as a whole of unwittingly perhaps, but systematically regardless, hampering the participation of women in science. We see science as a meritocracy, where the best people and the best ideas bubble up and we fear efforts to play fair could undermine the overall quality of science. But are 'fair' and 'best' necessarily at odds with each other in the arena of scientific discovery? Stated another way, at any given time do discoveries go unmade because the person who might make them is not in the scientific workforce?

In an attempt to roughly quantify the answer to this question, I built a simplistic computational model of scientific discovery. The model used a Monte Carlo approach to create a scientific community from a larger population of one million. Inherent scientific ability was assumed to correspond to a single integer variable, with values ranging from a low of zero to a maximum of 200 and to follow a normal distribution (σ = 30); potential scientists were assumed to have a score above 140 on this measure. The parameters were set such that one discovery was expected per thousand potential scientists. Discoveries were not uniformly distributed throughout, but weighted such that higher ability scores were more likely to have the potential to make a breakthrough.

A model scientific community was selected from the full population using a weighted random selection procedure, which again favoured the 'best' end of the pool, and the number of 'discoveries' made by this select group were added up. The simulation was run for a total of one thousand trials. Models that limited the selection of women to 10% of the pool incurred a 10 to 15% average penalty on the number of discoveries made, compared with pools with roughly equal numbers of men and women.

Having 10% of potential scientific breakthroughs go undiscovered may sound insignificant, not worth the bother of figuring out how to bring more women into a field. That is, until you are asked to take a 10% pay cut, or if I ask which of the top-ten organic reactions you would prefer to do without. Heck? Diels–Alder? Within the limits of my model, choosing fairly with respect to gender does not compromise the quality of the scientific community, in fact, the opposite is true." [Nature Chemistry 6 (2014): 842–844.]

Correll, Shelley J. “Gender and the Career Choice Process: The Role of Biased Self‐Assessments.” American Journal of Sociology 106 (2001): 1691–1730.  See also the discussion in Cordelia Fine's Delusions of Gender pp 48-50.

Francl, Michelle. “Seeding Crystallography.” Nature Chemistry 6 (2014): 842–844.  ($)

The Secret Language of Chemists: Why does butter make us think of four?

Butter and why it means "four" to chemists.
c. Michelle Shrank CC license
Every time I take a stick of butter out of the 'fridge I think of the number four.  No, it's not some odd form of synethesia, but a side effect of being a chemist.

Names of molecules and their structures are (sometimes) related to each other.  You can think of organic molecules (molecules that are principally built from carbon, hydrogen, oxygen and nitrogen) are constructed like Lego buildings.  There are blocks, each block has a name and you click them into place (that last isn't so simple in practice) to build a molecule. So knowing the secret language of chemistry gives you a window into the structure, which in turn is a clue how the molecule works and what it might be good for.

So why does butter make a chemist think of four?  The stem but — pronounced like "butte" the land formation  —  is used to indicate a four carbon building block.  It is a back-formation from butyric acid, responsible for the smell of rancid butter, which has four carbons in it.  (Butane, a flammable liquid used in lighters, is a four carbon chain.)

The rest of the secret code:

meth- 1 carbon
another back-formation, this time from methanol (wood alcohol) from the Greek root for wine (μέθυ ≡ methy)

eth- 2 carbons
from the Greek, ether, the uppermost reaches of the atmosphere; as seen in ethylene (the sweet smelling flammable gas produced by ripening fruit, particularly bananas.  It's technically a hormone!)

prop- 3 carbons
This one also comes from the Greek (surprise!) for proto and fat, as propionic acid was the first "fatty acid" (acid molecules that also behave like fats or oils); propane gas used in stoves and grills has three carbon atoms and 8 hydrogen atoms per molecule.

but- 4 carbons
From the rancid butter!

after four the prefixes are derived directly from the numbers in the chain
pent- 5
hex- 6
hept- 7
oct- 8
non-  9
undec- 11
dodec- 12

So when you see references to the food additive BHA, which stands for butylated hydroxyanisole, one thing you can say about it is that it has a four-carbon unit in it somewhere.  Though, I admit, that's not much help in answering the important questions: What does it do, and how will affect me?