Elements of revenge

I seriously can’t write fiction. I suspect it's not lack of imagination, but some odd form of writer’s block. Or perhaps it is too many years devoted to sifting defensible reality from experimental and computational data. Or is it that I’m unwilling to ask a reader to be confused about the real, the possibly real and the entirely imagined? Or maybe it is because the one and only piece of published fiction I wrote, came (almost) true within the year?  Would any other fiction I wrote become real? That’s clearly a flight of fancy, but even with one data point, do I want to take the risk?

I was invited to write a commentary on the elements that scientists thought they'd discovered (but hadn't) for Nature Chemistry's issue celebrating the International Year of the Periodic Table.  The IUPAC guideline for element names says that you can't re-use names already in circulation in the literature, even if they were ultimately discarded. Which got me thinking if that could be a way for an unscrupulous scientist to crush the dreams of a competitor of having an element named for them. Despite my demonstrated inability to write good fiction, I drafted an introduction to the essay that played out this idea.

In the end, I wrote a non-fictional introduction to the essay (which you can read here if you are of the mind to do so). But if I were to write a piece of fiction about the elements, it might begin like this:
_______________________________

Prof. Exuvgen leaned back in her desk chair and wondered for the thousandth time why she’d ever signed that retirement agreement. Time was slipping through her fingers.  In a month, she’d have to hand over the key codes and walk out the door.  No access to her data and worse yet, no access to the tools she would need to analyze it, that idiot of a director had made it clear her account would be wiped — wiped — at midnight on the 30th, and anything left in her office trucked out to the dumpster.  Tang Woh Kow, they maintained, was right. There were 243 elements in the universe and no more. When Tam Besper saw the traces of zuzenium in 2069, right in this building, that was the end of the era of the element hunters. The last chance to have your name remembered in every chemistry book in the solar system, if not the galaxy. Though if the Vulcans had their way, everyone would be using the systematic names.

Running her hands through her short grey hair, she turned again to the data on the screen.  She’d spent thirty years working toward puncturing Kow's ceiling on the elements, the last ten racing Sabaxoar’s extravagantly funded group on the moon. What was it Maxine had said at that last meeting? Oh, right. Time. That she wasn't in a hurry, she had years to work on this, given lunar life expectancies. And with that Maxine shook her blonde curls and floated off.  Would the director take her more seriously if she looked less weary, grey and face it, old?

Time. It's running out, was there enough to say, now, without a doubt, that they’d turned up an atom or two of 244 Sym in that last run? Maybe, though maybe that oxide of muscovium was rearing its ugly head, this wouldn't be the first umbral element sunk by 115. Certainly there was strong evidence of a new isotope of 243.  Time, there just wasn't enough time.

She tapped the bud in her ear, and started composing the manuscript of one last paper.  “We present here evidence for the creation of the 616 isotope of 243 Zz, half-life 82 msecs, along with traces of element 244, Uuq.” She glanced up at the list of proposed names for 244 her group had kept on the whiteboard, derived from the names of birthplaces and long dead mentors and far-flung galaxies and grinned wickedly. “…for which we propose the name sabaxorium, symbol Sx, in honor of our respected and long time competitor in this hunt, Maxine Sabaxoar.”

Four months later, Maxine wakes up to a tweetstorm of congratulations for having the first trans-zuzenium element named for her. She pulls up the paper and seeing the unmistakable traces of MvO in the accompanying supplementary data dump, shrieks, "I've been robbed.”
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Notes:  
In the 1970s, Tang Wah Kow of New Method College in Hong Kong suggested (based on an odd theory about triads and octaves) that the upper level for an element was Z=243. Further, he proposed that when that element was ultimately discovered, it should be called zuzenium (Zz). The suggested name he said was, "...deduced from a Chinese idiom 'The name stands behind Zun Zen, who (Zun Zen) came last on the list of successful candidates in a royal examination." [In "An Octagonal Prismatic Periodic Table" J. Chem. Ed. 49, 59 (1972)]

Hidden figures: 2.303, slide rules and classrooms mired in the last century

A five -place table of logarithms from my dad's CRC Handbook of 

Mathematics (why is that set of values circled?) and a circa 

1958 Hemmi 257 slide rule designed for chemical calculations.  

 Wonder why random values of 2.303 are "hidden" in formulae? To make them easier to use with a slide rule.¹ 

A slide rule?  The last slide rule slid out the door of Keuffel & Esser in 1975 (they sent their engraving equipment to the Smithsonian).  You can still find them, used and even new - still packaged up to sell to engineers and scientists.  The Oughtred Society has a online museum, as well.

We still have my mother-in-law's K&E, in it's leather case with her name impressed into it.  Family history says she bought it with the money she earned tutoring Jackie Robinson in chemistry at UCLA.

I have an essay out in this month's Nature Chemistry, "It figures", about how the computational tools we use shapes what we teach and not necessarily in good ways. Given that slide rules were obsolete by the time many of my student's parents were born, why does their use still linger in general chemistry book?  (The 2.303's in texts are lowly going away. I checked texts running back about a decade.)

More critically to my mind why, several decades after  digital computing tools became ubiquitous on college campuses do many physical chemistry texts eschew any discussion of numerical techniques for solving the rate equations for a chemical reaction?  I suspect the chasm between the computational tools used in the field and those used in the classroom is a result of apathy. We teach what we learned as we learned it.  As I note in the article, I don't think it is defensible on intellectual grounds.

Don't know how to use a slide rule?  It's fun, it's geeky. No need to buy one to play, check out this simulator and the instructions at Nature Chemistry!

You can read the article here:  http://rdcu.be/sY5Q

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1.  2.303 is the natural log of 10. To change the base of logs recognize that
x = b^log_bx
so
ln(x) = ln(10^log₁₀x)
ln(x) = log₁₀x ln(10)
ln(x) =(log₁₀x)(2.303)
ln(x) = 2.303(log₁₀x)

Chemists: Strangers to fiction

That Mars habitat?

"The basement corridor is dim, I can hear pumps chugging, hoods noisily venting, and the solid-state physicist down the hall swearing. 'Welcome to Mars!' says the cheery sign outside my colleague’s door. Perhaps it is the pile of grading on my desk or the endless round of meetings on my calendar that is fuelling my escapist fantasy, but every time I pass Selby’s office, I imagine the door is a portal and if I were to walk through, I’d  find myself in a habitat on Mars, its pumps working hard to compress the thin atmosphere." from "Strangers to Fiction" in Nature Chemistry, 8, 636-637 (2016).

I've been a sci-fi fan for going on five decades, imagining myself in labs on Mars, mining comets, and exploring strange new worlds. I don't read it for the chemistry, which is a good thing, because there isn't much fiction in which chemistry plays a key role.

My latest Nature Chemistry Thesis column looks at chemistry and fiction, suggesting that there are good reasons to both read SF, particularly for young chemists, and for chemists to encourage the writing of chemistry-inflected science fiction.  And if you have the talent for it (which I do not!) perhaps even give the writing of it a fly.

You can read the whole thing here.  My list of fictional chemistry is here.

Chemical fiction

Topi Barr's Antithiotimoline is in this vintage Analog

Seven years ago, Andy Mitchinson, an editor at Nature, wrote at The Sceptical Chymist (Episodes II and III) about the dearth of science fiction that involved the science of chemistry in a substantive way.  Why isn't there more of it?

He pointed to a list put together by Connie Willis, an award winning SF author, and an article by Philip Ball in Chemistry World.

I'm working on a column for Nature Chemistry about the ways in which chemistry and science fiction play off each other.  Is science fiction more than escapist entertainment?  Should chemists care that there's not more chemistry inflected fiction out there?  Should we deliberately expose students to science fiction? Should we encourage them to write it?

To go alone with the piece, I'm trying to create a periodic table of chemical fiction (not including articles called out by Retraction Watch).  Are there pieces on my list you particularly love?  Something I'm missing?  I'd love to hear in the comments!

For a full set of periodic science fiction short stories, I encourage you to browse Michael Swanwick's Periodic Table of Science Fiction.  What really happened to the Hindenburg?

	Author	Work
As	Asimov, Isaac	Whiff of Death, The Endochronic Properties of Resublimated Thiotimoline, Thiotimoline to the Stars, Pate de Fois Gras
Pb	Ball, Philip	The Sun and Moon Corrupted
Ba	Barr, Topi	“Antithiotimoline”
B	Bujold, Lois McMaster	Vorkosigan series
Ac	Christie, Agatha	"The Blue Geranium” in The Thirteen Problems
Cl	Clements, Hal	Phases in Chaos
Co	Conan Doyle, Arthur	Holmes
Md	Dewar, Michael	“Temporal Chirality:  The Burgenstock Communication”
F	Foster Wallace, David	Infinite Jest
Ag	Goodman, Allegra	Intuition
He	Heinlein, Robert	Glory Road, Have Spacesuit will Travel
Hf	Hoffman, Roald	Oxygen
Li	King, Laurie	Russell & Holmes series
U	Le Guin, Ursula	“Schrödinger’s Cat”
Sn	Lem, Stanislaw	“Uranium Earpieces” in Mortal Engines
P	Levi, Primo	The Monkey’s Wrench
Am	McCaffrey, Anne	Pern series
H	Piper, H Beam	Omnilingual
Kr	Robinson, Kim Stanley	Mars series
O	Sachs, Oliver	Uncle Tungsten
Dy	Sayer, Dorothy	The Documents in the Case
Sm	Smith, Edward Elmer “Doc”	“Tedric,” “Lord Tedric" in The Best of E. E. “Doc” Smith
Ne	Stephenson, Neal	Anathem
Br	Stoker, Bram	Dracula
Fr	Vance, Jack	“Potters of Firsk”
K	Vonnegut, Kurt	Cat’s Cradle
V	Vourvoulias, Sabrina	INK
Hg	Well, H.G.	“The Diamond Maker” in The Stolen Bacillus and Other Incidents
C	Willis, Connie	The Sidon in the Mirror

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.

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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.

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!

The most Zen of molecules

Chemists are the Zen masters of science. Chemistry is a minimalist art. Its structures and mechanisms resemble the spare ink characters which trickle down scrolls. We seek elegant syntheses in which a few, carefully chosen pieces collapse into a whole. There is particular pleasure chemists take in crafting a molecule that strains the bounds of possibility — such as cubane — which evokes the aesthetic of Noh, where nearly impossible movements are made to look effortless. And despite our abilities to peer into the depths of a molecule with lasers or beams of neutrons, we haven't lost our connection our history. We are still distilling and crucibles are not merely historical artifacts. Zen sees a beauty in the old and well-used, a touch of wabi.

I've a piece in this month's Nature Chemistry on what makes a molecule beautiful (here, $), through the lens of the ten molecules that I consider to be most beautiful. I've already had a couple of emails suggesting gorgeous molecules that didn't make my list. What's on your list of elegant molecules?

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My list of the ten most beautful molecules

azulene
carvone
ferrocene
ethanol
vanillin
penicillin
insulin
snoutane
cubane

Recording science

Bruce Gibb mused in a Thesis column in Nature Chemistry a few months back about taking small chunks of time to tune up your research apparatus. I'm on sabbatical leave this semester, and in addition to the research projects I've got going, I'm trying to devote some time on a regular basis to just this. I'm playing with an simple animation app, that would let me quickly put together animations for research talks or classes — and test driving apps for electronic research notebooks.

As a computational chemist, I've been balanced on the knife edge of digital record keeping my whole career. What goes into paper archives (hand kept, or printed), what stays electronic? Who backs stuff up, how often? Long term storage? I've encourage my students to think about how they want to track their data and, at least as importantly, their thinking about their data. Through it all (from punch cards to mag tape to memory sticks) I've always kept at least some of my work on real paper, in a traditional hardbound notebook. In ink. Dated. You know the drill.

I've been reluctant to let go of pen and paper. Just as I still outline just about any piece of writing, including this one, on real paper, I find I think differently off the keyboard. Keyboards tend to enforce a certain linearity of thinking, while a sheet of paper (or several and lots of stickies) lets me move into multiple dimensions, with fewer restrictions on insertions and more flexibility in formatting.

The work I'm doing now in the archives is facilitated by having photos of what I'm reading, many of the bound copies are too fragile to routinely scan or photocopy. Ironically, reading 19th century journals has catapulted me into the 21st century as far as my own record keeping is concerned. I'm using an integrated notebook app on my iPad which allows me to scribble and sketch by hand, take and incorporate photos (and mark them up if I wish), and input text from the keyboard. Finally, I can tag pages, and filter the notebook by tags (more consistent than my own hand written indexing procedures). The only thing I don't care for is that I can't write as small as I wish, making it harder to get an overall view of where I'm going. It's an experiment still,

Today's Nature [Nature 481, 410(2012)] has an editorial and an analysis piece on digital record keeping in science. One scientist notes that paper has nothing to offer her - she's gone entirely to her iPad. I may be right behind.

What makes a molecule beautiful?

I just finished a piece for the March issue of Nature Chemistry on what (in my mind) make a molecule beautiful. I will admit a preference for sparer, less baroque structures. (If you want to know more about my molecular aesthetic, you'll have to wait for the piece to appear!). In the meantime there is an article in this month's Nature Chemistry with the intriguing title "Quantifying the Chemical Beauty of Drugs" [Bickerton et al. Nature Chem. 4, 93-97 (2012), full text is free]. It's not so much beauty in the abstract these chemists are trying to quantitatively capture, but desirability. How attractive is this molecule as a target for drug development? Would a chemist be willing to surrender time and bench space to the synthesis of this molecule?

The model takes as its inspiration Lipinski's rule of 5. If most or all of Lipinski's five characteristics are present, a molecule has a good chance of being a viable candidate for an oral drug [Lipinkski et al. Adv. Drug Dev. Rev. 23 3-25 (1997)]. The goal is to develop an expert model system, one that mimics (or improves on) a chemist's intuition about what makes for a good drug.

Earlier work had suggested that chemical fashion sense is drifting toward more baroque structures for their drugs, despite various rule sets that suggest that bloated molecules are less likely to survive to clinical trials. Chemists apparently like their molecules "tractable" (which would seem to mitigate against molecular overelaboration?), synthetically and otherwise! Molecular docility is desirable.

For a somewhat darker take on chemical intuition and seat of the pants drug design read "Chemists in the Shadows" by Adam Piore in March's Discover Magazine. The article focuses on underground chemists who are developing new recreational pharmaceuticals that skirt current drug laws (steroids for athletes, and rave drugs). The conceptual framework used by some of these chemists would be familiar to any medicinal chemist (particularly in the early days, before QSAR).

Can gender gaps impede scientific progress?

My commentary on Marie Curie and the paucity of women chemistry Nobel laureates ends wondering

"...if what underlies the inability to fully acknowledge the social biases that obscure and downplay women’s scientific achievements, and the ways in which our spaces silently speak to us about who belongs and who doesn’t, who appears capable and who does not, is the assumption that if a Marie doesn’t make a critical breakthrough, of course, a Pierre somewhere will. Will chemistry make all the critical leaps it could, without the contribution of half of its finest minds?"

Last week, the president of Bryn Mawr College (where I teach) had an opinion piece in Inside Higher Ed about closing the gap for women in science and engineering. She, too, worries that progress in science and technology is impeded by lack of participation by women (and I would add the lack of recognition for women's work in these fields) President McAuliffe writes "As long as there is a gender gap in these fields, there will be an innovation gap."

Some readers of McAuliffe's essay had a hard time imagining that scientific progress could be impeded when women are underrepresented or sidelined in science and said so in the comments. Sam Kean's delightful Disappearing Spoon includes a clear counterexample: In 1934, Ida Noddak suggested the possibility of atomic fission. Her work was dismissed as "ill conceived and unfounded" by Emilio Segre (who won the Nobel prize in physics for the discovery of the anti-proton); Irene Joliet-Curie similarly thought it possible; Lise Meitner definitely discovered fission in 1939 (and Otto Hahn won the Nobel for the discovery).

Another example on the same theme: Lise Meitner also discovered the Auger effect, in 1922, a year before it was discovered by Pierre Auger (for whom it is named).

I realize these are historical examples, but they do prove the point. A blanket disregard (for whatever reason, be it gender, country of origin, venue for publication) for the contributions of a subset of scientists can impede the progress of science. As Matt

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Read about how the cover was made.

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Sex in the citadel of science

"The problem was to give birth to a boy
and not a girl," said the fathers of the atom bomb.
Marie Curie did not give birth to any joy.
Tenderly she leans toward jars of glowing radium,
as she had earlier at the bed
of her sleeping daughter Irene. (And then she bore Eve!)
Four years clothed in bitter smoke, in a shed,
stirring a mass in ebullition, nothing secretive,

an iron cauldron, iron rod nearly as big as herself,
a shed no one wanted, not fit for cadavers.
Science is the primordial interest of my life,
nor do I know whether I could live
without the laboratory. Her problem—to give breath,
to let there be light, out of slag, abandoned earth.

— from "Her Crucible: A Poem of Marie Curie" by Margaret Almon

In the latest issue of Nature Chemistry, I have a commentary speculating on why women, despite their increasing presence in the field, win the Nobel in chemistry less frequently than 100 years ago. The essay is framed around Marie Curie, the first woman to win the Nobel prize in chemistry. This year marks the 100th anniversary of Prof. Curie's Nobel (her second).

It's not about mathematical ability (sorry Larry Summers, there's hard data that punctures your theory) or lack of inherent interest. Instead, I wonder if it has to do with the built environment: the size, color, shape of the laboratory and its equipment:

Built space is not neutral, as Winston Churchill noted, “we shape our buildings, and afterwards our buildings shape us.” As much as scientists use labs to create science, labs themselves create scientists. (Read the rest here....)