Weird words of science: scientist

Woman teaching geometry to men
illus. 14th century copy of Euclid's Elements

Scientist may not sound like a weird word, but when it was first coined, it was thought "unpalatable," along with (understandably) "nature-poker." Recently my sister tagged me in a Facebook post linking to a series of articles on women in science. She thought it interesting that the word had been coined to honor the work of a woman in science.

"Not only did Scottish mathematician, science writer, and polymath Mary Fairfax Somerville (December 26, 1780–November 28, 1872) defy the era’s deep-seated bias against women in science, she was the very reason the word “scientist” was coined: When reviewing her seminal second book, On the Connexion of the Physical Sciences, which Somerville wrote at the age of 54, English polymath and Trinity College master William Whewell was so impressed that he thought it rendered the term “men of science” obsolete and warranted a new, more inclusive descriptor to honor Somerville’s contribution to the field." — from Maria Popova and Lisa Congdon's 2013 project The Resurrectionists

Oddly enough, I'd read William Whewell's review of Somerville's On the Connexion of the Physical Sciences while writing an essay about the public conception of scientists, and my recollection was that the coining of scientist, while reported in this review, was not in fact spurred by Somerville's work.  So I went back and read it again.

Whewell was certainly impressed with Somerville and her book, but his tale of the creation of the word 'scientist' makes no mention of honoring Somerville or her contribution.  About the only person Whewell seems impressed with in this context is the "ingenious gentlemen," thought to be himself!

A curious illustration of this result maybe observed in the want of any name by which we can designate the students of the knowledge of the material world collectively. We are informed that this difficulty was felt very oppressively by the members of the British Association for the Advancement of Science, at their meetings at York, Oxford, and Cambridge, in the last three summers. There was no general term by which these gentlemen could describe themselves with reference to their pursuits. Philosophers was felt to be too wide and too lofty a term, and was very properly forbidden them by Mr. Coleridge, both in his capacity of philologer and metaphysician ; savans was rather assuming, besides being French instead of English; some ingenious gentleman proposed that, by analogy with artist, they might form scientist, and added that there could be no scruple in making free with this termination when we have such words as sciolist, economist, and atheist—but this was not generally palatable; others attempted to translate the term by which the members of similar associations in Germany have described themselves, but it was not found easy to discover an English equivalent for natur-forscher. The process of examination which it implies might suggest such undignified compounds as nature-poker, ornature-peeper, for these naturae curiosi; but these were indignantly rejected." [from the Quarterly Review, 1834, emphasis mine]

Interestingly, Wherwell does tackle the issue of women in philosophy/science:  "Our readers cannot have accompanied us so far without repeatedly feeling some admiration rising in their minds, that the work of which we have thus to speak is that of a woman."  It's a fascinating read, in which you can see the threads of imagery that is still current (and still unsupported by data) about the innate differences between the minds of men and women.

And in the end, scientist would catch on, by the early 20th century it was far eclipsed "natural philosopher" as the preferred general term.

Science at Play

The Chemical Heritage Foundation in Philadelphia's latest exhibit is called "Science at Play" — and even if you can't get to Philadelphia, you can browse some of the materials on Tumblr, including animated videos of experiences — good and bad — with chemistry kits.

When my kids were young, I encouraged them to play with science stuff.  I wanted them to be willing to get messy, to make mistakes, to think about stuff where it wasn't perfectly clear what was going on and to begin to understand that protective gear wasn't a ritual or a costume, but part of thinking through how to reduce risk.  That you could make your own equipment.

Though kits have gotten far more tame over the years — no more uranium ore or instructions for making ammonia in your hand — there are still commercial kits that let kids play not only responsibly, but productively, with chemistry.  The new MEL kits that Todd Bookman's piece on chemistry kits for The Pulse (listen here - full disclosure, I was interviewed for this segment) highlights are particularly cool in that they plug into another important skill for budding scientists:  how to share your work.  The kit comes with a lense that you can snap over a cell phone camera, giving you an up close look at what you are doing, and enabling you to share it via social media.

But as important as kits are, I think the ad hoc experiences of doing science are equally critical.  They hone the ability to read instructions (and reveal how much is not revealed in the methods sections of any science communique), encourage a sense of scale and quantitation (how much is 1 gram of something, as opposed to pour in this packet) and help novice scientists get comfortable with tinkering to build apparatus when they don't have exactly what they need. And when tackling a new research problem, do you ever have precisely what you need?

While you can make do with measuring cups and kitchen scales, I'm with the Chemical Heritage Foundation's Erin McLeary, who notes the appeal of having the real stuff in your hands.  These days you can easily and inexpensively acquire a few real beakers, graduated cylinders and other lab equipment -- along with gloves and other protective gear.

So if you're looking for an interesting and unique gift for a kid interested in science, try assembling a small kit and including the instructions and materials for a couple of experiments.  For starters, extracting DNA from dried peas or copper electroplating (yes, it uses something you shouldn't eat - don't and wash your hands) or even the infamous water electrolysis (sans smoldering splint and thereby less risk of singed eyebrows).  Offer to help supervise or be the videographer.

---

To read more of what I've written about chemistry kits and doing chemistry outside the laboratory see:

"Homemade Chemists" in Nature Chemistry
"Felony Science" at Slate
"Handheld Chemistry" on the blog, about the making of ammonia in your hand

Polysemy and Polyphony: Listening to Messiah

Last spring I wrote a piece for Nature Chemistry on polysemy — the phenomenon where words take on quite different meanings in different contexts. The iconic chemistry example might be mole (the quantity versus the animal versus the verb¹), but there's a long list.

So you might think that when I ran into a homograph² on Twitter the other day, I'd be alert to the possibility. My first thought when the conversation between two chemists about the insights they find in Messiah showed up in my feed they were talking about the classic quantum mechanics text by French physicist Albert Messiah.  Actually, not.  Handel's Messiah was the text under discussion.  Polyphony crashes into polysemy.  And evidence I really am a science geek first and foremost.

The text is still in print, though Albert Messiah died in 2013 at aged 92.   I used Messiah's text when I took a year long course in quantum physics as a graduate student (from the physics department, have exhausted the chemistry offerings as an undergrad). We pronounced his name "mess-ee-uh" rather than "mess-eye-uh," making this technically a homograph (though not a capitonym³).  I wondered today how he might have pronounced his name, is it really a homograph, or did my professor simply choose to pronounce it this way to avoid sounding like an evangelical preacher when he assigned reading?  I dove into the interwebs to see if I could uncover any clues.  I discovered Messiah had been part of the French Resistance in World War II (joining at age 19, the age my youngest son is now), worked at the Institute for Advanced Study in Princeton with Niels Bohr and eventually returned to France to teach and write this text.

I also listened to a few minutes of a presentation Messiah gave in 2009 at Le Ecole Polytechnique.  It was oddly moving to hear the voice of someone whose written words I had spent so much time wrestling with almost forty years ago.  And at the end of the questions, I learned how he pronounced his name.

And, on the Sceptical Chymist, Reuben Hudson has a post responding to my column on a different kind of doubling-up in chemical language.

---

1.  Yes, mole is a verb, to mole a garden is to remove the moles.
2.  Homographs are words that have the same spelling, but different pronunciation (lead and lead).
3.  Capitonyms are homographs with different capitalization.  DEFT and deft.

Shedding some light on chemistry: Mole Day and the Year of Light

[If you want to participate in some science about science blogs, see the bottom of this post!]

It's October and there is lots of science to celebrate.  Chemists in the US and elsewhere are celebrating Mole Day on Friday (October 23 at 6:02 pm) to honor Avogadro's number (6.02 x 10²³ items are in a mole -- it's the chemist's version of a dozen).  It's also the International Year of Light, and while you might think that light is the purview of physicists, it's an element of chemistry as well.  I suggested in a recent essay that one might want to celebrate the year of light on the 10th October at 3 in the afternoon (3 x 10¹⁰  is the speed of light in cm/sec)

I've written two pieces on the relationship between chemistry and light for the celebration.  The first for Nature Chemistry, The Enlightenment of Chemistry, looks at the two-way relationship between chemistry and light.  Light is  not just an energy source for doing chemistry, but the production of light in various ways has pushed chemistry forward.  The full text is here.

The second, for the UN's Year of Light blog celebrates the October 27th anniversary of Bunsen's and Kirchhoff's publication on the spectroscope and atomic emission spectra — and the role the spectroscope played in not only filling out the periodic table, but in confirming the periodicity of the table.

"Hunting for new elements spectroscopically meant you didn’t actually need to have any of it in your lab or even on your planet, as long as you could observe the light from a burning sample. In 1868 several chemists and astronomers independently observed a faint line in the spectrum of the sun, and assigned it to a new element, helium, which as far as they knew did not exist on earth. It would take nearly 30 years for two Swedish chemists to confirm that it was present on earth — by matching the spectrum with that of a gas found in a uranium ore. (The helium to be found on earth comes from radioactive decay.)" — read the rest here.

Want to participate in some science to celebrate?

Help us do science! I’ve teamed up with researcher Paige Brown Jarreau to create a survey of the Culture of Chemistry's readers. By participating, you’ll be helping me improve the blog and contributing to SCIENCE on blog readership. You will also get science art from Paige's Photography for participating, as well as a chance to win a t-shirt, a $50 Amazon gift card and other perks!   It should only take 10-15 minutes to complete. You can find the survey here: http://bit.ly/mysciblogreaders. 

Building scientists #istandwithahmed #kierawilmot

So what's this kid doing in the high school auditorium after school?  He's drilled holes and put pipes into a cooler, there's some kind of heating device or trigger. Wires.  And it looks like a boat load of some sort of chemical in that bowl that he's dumping in there.  And then...and it shoots out some kind of gas.  Kids scream. The gas begins to cover the stage.

"What's happening?" wants to know the teacher who hears the commotion from the hallway.  "I'm testing a fog machine I built for the class play."

Yes, at first glance the situation looks potentially perilous.  But a quick question, followed by a bit of common sense and the teacher is reassured that all is well.

Now that everyone is sure that there is no bomb, what should happen to the kid?

A.  Pull the child into the principal's office and demand that he sign a statement admitting his guilt.

B.  Call the police, who will arrest him and charge him with building an explosive device.

C. Call the police, who will arrest him and charge him with building a "hoax bomb"

D. Nominate him for a theater award for special effects, for having designed and built an inexpensive fog machine to use for the school's upcoming production of Grease.

The kid is my kid and the school's response was D.  But imagine if my kid wasn't white and male.  If his name were Ahmed Mohamed or Kiera Wilmot?  There might have been handcuffs, felony charges, letters home to parents about "the incident".  If someone had called the police, would they have arrested him because he couldn't explain why he'd built one, when they could have rented a fog machine?  (The police thought it suspicious when Ahmed Mohamed couldn't tell them anything more than his device was a clock.) Why would you build a fog machine, or a clock?  He must have built it for a purpose, nefarious almost certainly.

Perhaps the purpose was to understand how these machines work?  There is an amazing amount of joy in showing that you understand something well enough to build a working apparatus. To tweak and fix.

As a parent, I want the school to exercise an abundance of caution.  But once you're sure it's just a clock — or a fog machine — perhaps it's time to slow down, and engage some common sense.  Is there anything else that suggests this kid would build anything danger?  Besides his name, or the color of her skin, or his religion.

Scientists and engineers are not hatched full grown from eggs in labs.  As kids, they tinker and think and build and design, with Legos and parts from Radio Shack and Home Depot.  They are in theater and on robotics and Science Olympiad teams.  We need to get as excited about what they do as we are about how the football team is doing.

From the portals of hell to built-in fire protection: intumescents

A friend posted the link to this demonstration, wondering if it was safe. (Do listen to the children in the background - their cries of "kraken" at 1:02 are worth it.  Science is great fun!)

The caption that came with it noted that it was a mixture of ammonium dichromate ((NH₄)₂Cr₂O₇ )and HgSCN (mercurous thiocyanate).¹ Mercury and chromium, probably not something you want to eat I told my friend. The whole thing made me curious, just what were those tentacles come out of the burning pile? And what chemical reactions were driving it?

It's a coupled set of decomposition reactions. The volcano comes from the decomposition of ammonium dichromate

(NH₄)₂Cr₂O₇(s) → Cr₂O₃(s)+ N₂(g)+ 4H₂O(g)

The reaction produces a lot of heat, which makes the particles being thrown off by the rapid expansion of the two gases (nitrogen and water vapor) glow.

The heat then triggers the decomposition of the mercury compound:

2 Hg(SCN)₂(s) → 2HgS + 4CS₂ + carbon nitrides

The erupting tentacles are an example of intumescence², a property of mercury thiocyanates noted long ago by the venerable Friedrich Wöhler³. It's a well known demonstration, often called Pharaoh's Serpents. Many material intumesce when heated, and thus produce their own insulation.  Some passive fire protection systems rely on this property of polymers, by which they essentially rapidly produce their own insulating layer upon heating, or by swelling up to block air ducts to prevent smoke and other gases from spreading too quickly through a ventilation system.

It works with mercuric thiocynate as well (Hg(SCN)₂) — by some accounts even better — and better yet if you toss a bit of potassium nitrate and a bit of fuel in the form of sugars. In other bits of historical trivia, the mercuric thiocyanate was originally made by the aptly named Otto Hermes. The sale of mercuric Pharaoh's Eggs ceased after some kids ate them with deleterious (fatal) effects.

If you just want to see the snakes minus chromium salts or mercury - try this demonstration based on calcium gluconate instead or check out pyrotechnic expert Tenney Davis suggestions in the Journal of Chemical Education.

---

1.  From the Latin verb "to swell" — related to thumb and tuber (as in root vegetables like potatoes)

2.  The chemist who showed in 1828 that compounds made by nature do not have some "vital essence" that distinguishes them from the same structure crafted by a chemist from inorganic (never living) materials.  Something the Food Babe and hawkers of 'bioidentical' hormones do not get.

Read more:

Brian Clegg at Chemistry World.  A paper on the demonstration from Journal of Chemical Education in 1940, by Tenney Davis of MIT who taught courses in explosives way back when ($).

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 a_n = 2 x a_n-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 (a_n = 2 x a_n-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
dec-10
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?

Chemists' Magic Decoder Ring

What if we gave out chemical name
decoders instead of periodic tables?
Vintage magic decoder ring.
Used under CC license. Source.

Earlier this week the Royal Society of Chemistry released a report on the public perceptions of chemistry.  It's a great set of data for those of us who write and talk about chemistry outside of the classroom environment. This infographic sums up the key findings, one of which is that people lack confidence in talking about chemistry.

Stuart Cantrill, chief editor of the journal Nature Chemistry (full disclosure, I contribute regularly to the editorial content of the journal), noted in the discussion which followed the presentation that chemistry uses a very "specific technical language...if you're not talking the same language as someone you are talking to, they can't engage with you...it's almost like a secret language that only chemists know." (Listen here starting at 25:45)

It made me wonder if we should hand out a cheat sheet on how to decode chemical names and functionality instead of the traditional and iconic periodic tables at events. It might make for less splashy t-shirts or shower curtains, but then again, Andy Brunning of Compound Interest makes amazing graphics on all sorts of chemical themes.

Next post:  the secret language of chemists and why butter makes me think of four!

Say that again? Why chemical names tangle on the tongue

Michael Pollan's Food Rules famously advises not eating anything with an ingredient a 3rd grader can't pronounce.  The rule is more about eating closer to the production point, about consuming things that are familiar to 3rd graders (like broccoli and eggs), than it is that chemicals that are hard to pronounce are inherently hazardous, though in some corners it's taken on just that sort of magical thinking.

Why are chemical names so weird looking? Take 2-Methyl-5-(6-methylhept-5-en-2-yl)cyclohexa-1,3-diene for example.  It certainly doesn't sound like anything you would want to eat, but it is just the formal name for the compound that is the main component of ginger oil, and responsible for much of ginger's characteristic bite.  Like crystallized ginger, ginger tea, or a good stir fry?  You've eat this compound in significant quantities.

Chemical names can look like alphabet soup, but they are a way for chemists to paint a compact picture of the structure, or at least to point out key structural features.  Why is it so important to know what a molecule looks like?  The structure of a chemical is what determines its behavior, how it will react, in the body and in the environment.  It's key to understanding how things work on the molecular level:  structure determines function.  Period.

Formal chemical names, called IUPAC names (for the International Union of Pure and Applied Chemists, the body that decides on everything from what new elements will be called to the standards for drawing molecules), are in fact a code from which the full structure of the molecule can be unraveled.  Most of the time chemists call chemicals by a common name, which also gives clues to the structure, though not so many that the molecule could be unambiguously drawn.

So back to 2-Methyl-5-(6-methylhept-5-en-2-yl)cyclohexa-1,3-diene, which looks like

The "methyl"s (METH-ill) in the name refer to a CH₃ group. What, you don't see any CH₃'s here?  This is a chemical line structure, where each intersection point (or end of a line) is a carbon atom, and the hydrogen atoms have almost all been left off.  A chemist sees this structure as 

with the methyls at either end.  The little red dots count off a seven membered chain, the "hept" in the name. The "cyclohexa" (sigh-clo-HEX-uh) points to a six membered ring, while "diene" (DIE-een) means it has two double bonds in it. The numbers tell you where to attach methyls and draw the double bonds.  The little "2-yl" (too-ill) means the seven membered chain is linked to the six membered ring at the second carbon in line.

So these tangled names to a chemist are codes, and once you can read the code, even a bit, you can begin to see a molecule taking shape in your mind when you read its name.

This pronounces as 2-METH-ill / 5, 6-METH-ill-hept 5 een 2 ill cyclo HEX uh 1 3 DIE-een.

There's probably a reason this is better known as zingiberene, which suggests its common origin (ginger or zingiber), but not much about its structure.

Formaldehyde: not just for dead things

Next spring I'm teaching a course on the physical chemistry of food while a colleague is teaching a course on the analytical chemistry of foodstuffs.  Among other science texts we'll be using John Coupland's Introduction to the Physical Chemistry of Food, but I'm also collecting short pieces to put some of the work into a historical and social context.

These aren't actual biological specimens preserved
in formaldehyde, but Halloween decorations.  

Though these days we tend to think of chemists as the untrustworthy creators of toxic, artificial everything, the systematic training of chemists was driven in part by the desire for the public to know what was in their food and water.  In 19th century Britain, hundreds of chemists made their living testing the purity of everything from butter to well water.  So when the Food Babe tells you there is something "yucky" in your food, the reason we know it is there is some chemist developed a careful protocol for its analysis, and other chemists tested the material.

Molecular structure
of formaldehyde

I've been thinking about formaldehyde, one of the simplest organic molecules (to a chemist, organic means made up mostly of carbon and hydrogen atoms, and has nothing to do with whether the molecule is synthetic or natural or...). Last year, formaldehyde, which is a preservative, was in the news because Johnson & Johnson had agreed to remove it from baby shampoo, though as Matt Hartings and Tara Haelle clearly pointed out in a piece at Slate, it was in such low concentrations that it posed no risk to babies (who, they point out, themselves contain substantial amounts of formaldehyde.)

Pepsi is reformulating Diet Pepsi to take out the artificial sweetener aspartame. The Food Babe is crowing that she and her army have forced Kraft to remove the so-called coal tar dyes (e.g. tartrazine/FD&C Yellow 5), to be replaced by natural colorings from spices.  What does all this have do do with formaldehyde?

From the Food Babe's 'campaign' literature.

To start with those natural colorings - at least one of them used in the UK version of mac and cheese, beta-carotene, isn't extracted from natural sources but synthesized from petroleum feedstocks (just like those coal-tar dyes).  One of the starting materials:  formaldehyde. The other natural colorings on the table — annatto, turmeric and paprika — are not quite what you might think either.  While you might imagine shaking in some spices from a quaint bottle, the spices themselves are not used as colorants, the colorants are extracted using organic (not that kind of organic, the chemist's kind of organic) solvents, such as ethyl acetate.  It's unclear to me why these colorants, particularly beta-carotene pass muster with the Food Babe.


Aspartame is sometimes vilified because it is metabolized into methanol and formaldehyde in the body.  Which it is.  You already contain a lot of formaldehyde, about 12 milligrams per liter of fluid in your cells.  One source is metabolism of the amino acids, particularly, serine and glycine (in naturally occurring proteins), from which your body scavenges methyl groups (CH₃) to pop on to various structures.  Aspartame is a very tiny protein, so the same pathways that produce methanol and formaldehyde from natural sources, dismantle aspartame to yield methanol and formaldehyde, though the amounts produced are tens of times lower than what comes from eating apples and fish.

Because formaldehyde occurs naturally in foods (about 5 mg per serving in some fruits, fish is also high, pectin containing fruits such as apples add significantly to the amount of formaldehyde ingested), our bodies have a mechanism for dealing with it, we process about 60 to 100 grams of formaldehyde a day and do so quickly.  Formaldehyde has a half-life of about 1 to 2 minutes in the body.

---

Why are those spices colored?  What does it have to do with quantum mechanics, flamingos and canaries?  Read this post, the very first one written for the blog,  to find out.

References
EFSA report on endogenous versus exogenous sources of formaldehyde.
EFSA review of curcurmin, a component of turmeric, which had been suspected of being genotoxic.

Feeding the pseudoscience rumor mill

Source.

LA Times columnist Michael Hiltzik has a piece this week considering how (or whether) journalists should address pseudoscience and its purveyors.  He, along with others — Keith Kloor/Discover and Julia Belluz/Vox most recently —  have worried whether reporting on pseudoscience gives it more credibility and visibility than it deserves, particularly when the people involved are not otherwise newsworthy. And since most of the information about new science reaches people through the mass media, journalists play an enormous role in the ecosystem by which the public, that is to say all of us, scientists included, learn about and then use, information about science.

There is a growing body of social science research suggesting that effective science communication needs to be more than just filling in facts.  The notion that simply pushing out correct facts is unhelfpful isn't new.  Andrew Noymer modeled the spread of misinformation using epidemiological methods, and in 2001 showed that the persistence of information in the public sphere is improved if you have people trying to debunk the myths.  (Op-ed here, full paper here.)

Emotion potentially plays a bigger role than fact.  Katherine Milkman and Jonah Berger have explored what makes online content go viral (full paper here ($), summary here), suggesting that information that tugs at our emotions, particularly ones that run deep — anger or anxiety or awe — is more likely to spread.  Vani Hari, known as The Food Babe, plays off both the anger (can you believe that they put yoga mat in your bread?) and the anxiety (you don't know what you are eating?).

The who, where and how of the presentation matter as much or more (see the Yale Cultural Cognition Project for some well designed work on this), not just about what people conclude about the science, but about what they think scientists believe to be true.  It matters not just what an expert says, but who we think the expert is - in the sense of what are their core values.

What should journalists do?  What should scientists do?  Should both groups ignore pseudoscience entirely?

It has me thinking about how and when I might tackle pseudoscience, either on the blog, or perhaps even more importantly, in my classroom.   Given the knowledge that it may in fact reinforce the circulate myth, doing so is not necessarily benign.  So what are my personal guidelines?

1.  What is the risk of a lack of understanding?  Can it kill you not to know?  (Don't mix bleach with pesticides - it will not only kill more bugs, but more people.)
2.  Is there reliable and understandable information readily available online?
3.  Do I have the expertise to address the issue?
4.  Can I back up any assertion I make from the peer-reviewed literature?  (It's not personal opinion, but careful reading.)
5.  Can I help people develop a stronger conceptual framework, so that they can be usefully skeptical on their own?  In other words, I should not only assert, but communicate basic principles of science.  

Additional questions I might ask myself before approach something about pseudoscience in the classroom:

1.  Does it illustrate a concept this course addresses?
2.  Do my students have the knowledge base and conceptual framework to debunk something themselves, if prompted?  

Food Babe versus the Science Babe: Of Beaver Butts and Bullshit

A few weeks ago I wrote a piece for Slate about the Food Babe's tactics, prompted by the flurry of publicity for her new book, The Food Babe Way.  I pointed out the Food Babe's strategy of "malicious metonymy" whereby she deliberately confuses the source or use of something with the molecules.  So instead of reason you get "because beaver butts," her favorite example being that vanilla ice cream might contain castoreum, a  purportedly vanilla scented natural flavoring extracted from sacs found in beavers (yes, near their butts): "Readers of my blog know that the next time you lick vanilla ice cream from a cone, there’s a good chance you’ll be swirling secretions from a beaver’s anal glands around in your mouth." There is not, and here is why.

"While in low concentrations castoreum reputedly tastes of vanilla with a hint of raspberry, I’ll admit I’ve never tasted it. Not because I’m particularly disgusted by the source—I eat animal products and am inordinately fond of the fermented genitalia of Theobroma cacao—but because of its scarcity and cost. Enough castoreum extract to replace the vanilla in a half-gallon of ice cream would cost $120. Worldwide, less than 500 pounds of castoreum is harvested annually from beaver pelts, compared with the more than 20 million pounds of vanilla extracted from the ovaries of Vanilla planifolia orchids each year. Perfumers, not ice cream manufacturers, are the real market for castoreum. So while beaver secretions just might be in the expensive perfume you dabbed on your pulse points or in the aftershave you splashed on your face—did you just touch that with your hands, yuck—rest easy, there is no chance that the pint of ice cream you picked up at the store contains it. Not at the price you paid for it." -- read the rest at Slate.

The Science Babe took on the Food Babe yesterday in Gawker - neatly taking apart each of her standard tropes, with references to others who have done the same. The Food Babe wasn't happy and shot back.  Her response to the Science Babe, who has a long history of debunking her claims, begins with a nasty ad hominem attack.  But none of Food Babe's rant changes the science, or the history.

No Food Babe, nitrogen is not an additive to air in airplanes mixed in by evil airlines (up to 50% oh dear!), we breathe 80% nitrogen all the time.

No Food Babe, the microwave was not used by the German army in WW II, even Wikipedia knows it was invented after WW II.

Yes, Food Babe, that "MSG free tomato soup" you tout on your blog contains 400 mg of glutamate per serving and a lot of sodium, which makes?  Monosodium glutamate.  MSG.  It exceeds the limits for added MSG in the UK.

And did you know that Food Babe recommends high daily doses of oxidane, laced with 2-methyl-5-(6-methylhept-5-en-2-yl)cyclohexa-1,3-diene?  Write her now and demand that she confess to drinking chemicals with gross and hard to pronounce names.

Eat naturally, but eat knowledgeably.