January 27, 2012


chemistry.org Newsletter

See You in Anaheim!

The 241st ACS National Meeting & Exposition kicks off this Sunday, March 27, in Anaheim. As always, the meeting features hundreds of technical presentations, workshops, special and social events, networking opportunities, and much more! To make the most of your time at the meeting, use the Itinerary Planner, a handy online tool for organizing your week in Anaheim. Using the Itinerary Planner, you can browse the technical program and mark technical sessions or other meeting events that you'd like to attend, then download your daily meeting schedule to your PDA or Outlook calendar.

January 27, 2012 04:03 PM

January 25, 2012


The Culture of Chemistry

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).

January 25, 2012 02:18 PM

January 14, 2012


The Culture of Chemistry

Being a philosophess


"...as a Philosophess she will not be discouraged by one or two Failures" Benjamin Franklin, in a letter to William Brownrigg dated 7 November 1773, where he wonders if Mrs. Brownrigg has succeeded in making Parmesan cheese (which I have to admit, I did not think was a cheese that colonial Americans knew of).

I appreciate Franklin's confidence that a woman could conduct rational experiments, particularly as at this moment I am virtually sitting on top of the site of Franklin's house in Philadelphia — I can see it from my window — working at being a Philosophess myself. I began a two month stay at the Chemical Heritage Foundation in Philadelphia today, as the Herdegen Fellow in the History of Scientific Information. My project is looking at how chemists, now and in the 19th century, deal with critical commentaries on the primary literature. Where are the commentaries located and does location change their tenor and/or content. I'm off to learn a bit about ways to computationally evalauate emotional tone, and to find some compelling narratives of critique in the 19th century and the 21st century.

I briefly wondered in my most recent Nature Chemistry Thesis column about what it meant for me to be working as both a historian of chemistry and a chemist, and how much of one field should we be exposing students of the other field to. Just how much history of chemistry does a chemist need to know to function well as a chemist? And if you do need to know something, what sorts of things? Dates? People? Materials? Methods? You can read my musings at Nature Chem, and those of Qian Wang and Chris Toumey on the same topic here. (Sorry...you or your institution need a subscription to see these, or if you would like a reprint of mine, drop me an email.)

January 14, 2012 08:17 PM

December 29, 2011


The Culture of Chemistry

Don't drink the water


"Don't drink the water from the sink!” read a sign taped to the mirror. As I was in rather desperate need of a glass of water before rehearsing the piece I would sing solo at Christmas, I was glad to find someone had left a gallon jug of distilled water and a stack of paper cups. Rehearsing the next day, as I went to grab a cup of water, a colleague pointed out that yesterday someone had mistakenly put out distilled water, which he had swapped for spring water. “Hopefully no one drank it!” he said.

“Why not?” I inquired.

“You’re not supposed to drink distilled water.”

Ah. Yes and no.

Distilled water is water that has been boiled, trapped as steam and condensed, leaving behind the non-volatile impurities (the stuff that doesn’t easily turn into a gas, like metal salts). Other components, like alcohols can still be carried along into the distillate.

Distilled water lacks most of the ions that tap water has, and thus, much of its flavor. Some of the ions (such as fluoride) in regular tap water may have health benefits, so a steady diet of distilled water may deprive you of certain useful trace elements. Conversely, drink water that is too hard (has a lot of ions in it) is correlated with kidney stones. It’s unlikely that the ionic content of your drinking water has a huge impact on your health (despite claims found here and there). All of the trace elements (including fluoride) can be found in other food sources. And distilled water’s osmotic pressure isn’t so different from that of plain water, therefore drinking it will not cause the cells in your body to suck up water until they burst and you begin to bleed internally (yes, this theory is out there, for both distilled water and deionized water). Bottom line, yes, you can drink distilled water.

That said, you probably shouldn’t drink the distilled water in most labs, as it is not tested to be free of bacterial contamination (which it can pick up in storage tanks) or volatile organic compounds. The same goes for bottled distilled water that hasn’t been tested to be certain it’s potable.

And while we're on urban myths about water, it's impossible to completely remove all the ions from water. Water is always in equilibrium with hydronium ions (H3O+) and hydroxide (OH-).


Image Copyright Filipe B. Varela, 2011. Used under license from Shutterstock.com

December 29, 2011 09:37 PM

September 02, 2011


The Culture of Chemistry

Changing exams


I just handed out a math assessment in my physical chemistry class, the same one I’ve used for the last several years. I generally don’t re-use exams (though I know colleagues who do), though I do re-use questions. By now I’ve been creating exams for more than a quarter of a century, and I wonder what the drift has been like over that time. How are the questions I ask now different (or not!) from what I asked 25 years ago? Or have the questions remained the same, and just the answers changed?

Fueling my introspection are the selections from the University of London’s 19th century bachelor’s degree exams. (H/T to a tweet from Nature Chemistry and the RSC). The chemistry question is one I could envision asking my students on an exam: “Explain the nature, from a chemical point of view, of the chief operations involved in the production of a photograph.”

The only catch, of course, is that the answer I’m expecting could be quite different than what the examiners in 1892 expected. In 1892, production of a photographic print necessarily involved silver, developers and fixing agents — and a darkroom. In 2011, production of a print could involve silicon and germanium, and a clean room. The theoretical underpinnings are less about pH and solution chemistry and more about semi-conductors and quantum mechanics.

What other reasonable exam questions might I ask, where the answers have changed so dramatically?

(And you have to love the example English question - just how important were werewolves in the 19th century?)

Photo of 39/365 Kodak Vigilant Six-20 Antique Camera, by M.Christian on Flickr.

September 02, 2011 04:15 PM

August 23, 2011


The Culture of Chemistry

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

August 23, 2011 12:06 PM


The Culture of Chemistry

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....)

August 23, 2011 10:56 AM

July 21, 2011


The Culture of Chemistry

Psychrometry - or how to tell when it's crazy hot out


The heat index is 107 oF (42oC) at the moment. It's hot, and I'm procrastinating going outside by blogging.

My youngest son is doing summer theater, and their rehearsal space is not all air conditioned. So I bought him a cooling towel to help him stay comfortable. When he asked how it worked, I said it was like having a portable swamp cooler — a familiar item as my dad used one for years to cool his house.

The basic principle at work is that it takes energy to make water evaporate. Unless the relative humidity is 100% (in other words, the air has all the water it can hold), water will evaporate. If you keep running air past a wet surface (think a fan blowing past a damp towel, or the breeze blowing over your sweaty face), water will continue to evaporate as drier air is constantly being replenished. The energy to turn the water from a liquid into a gas has to come from somewhere, in this case, the surrounding air and the water itself. The air gets cooler. Whew!

The towel works similarly, there is a very large damp surface area (why the fancy $15 towel really does works better than a damp cotton lawn handkerchief, a much higher surface area than the smooth cotton weave) and as you move around, air moves past. The water evaporates, pulling energy from the water in the towel and makes it colder.

To get a sense of how much energy that is, it takes about 34,000 J to evaporate 15 grams of water (about a tablespoon). 34,000 J is roughly 8 nutritional calories. If you pulled all that energy out of a cup of water, the cup of water would cool off to about 41o F. (In practice, you don't get things this cool!)

This whole endeavor depends on the air being able to soak up some water, so if the humidity is too high, you are going to be crazy hot towel or no. Swamp coolers work great in desert areas (where my dad lives, for example), and are pretty much useless in New Orleans.

So how cool can you get? To figure it out you need the dry bulb temperature and the wet bulb temperature of the air. The dry bulb temp is just the temperature of the air measured in the usual way (being careful to keep the thermometer out of the sun). The web bulb temperature is obtained by blowing air over a thermometer whose bulb is fitted with a tiny damp sock. For that you can use a sling psychrometer (see the video).

Too hot to be slinging thermometers around? Look up the dew point (your favorite weather app will likely have it) and you can estimate the wet bulb temp this way:

1. Subtract the dew point from the ambient temperature (what your regular thermometer reads)
2. Divide what you get in step 1 by 3.
3. Subtract the result in step 2 from the ambient temperature.

Right now the thermometer outside my window reads 100o F, the National Weather Service says the dew point is 70o F, so I take 100-70=30; 30/3 = 10; so the approximate wet bulb temperature is 100-10 or 90o F.

Once you've got the wet bulb temp you can figure out just how much cooling you can get with a fan and a damp towel!

1. Subtract the wet bulb temp from the ambient temp (the dry bulb temperature)
2. Multiply the difference by 0.8 (assuming the process is about 80% efficient, which is a pretty reasonable estimate)

My calculations suggest that the best I could do to produce cool air in my study this afternoon would be 80% of *100-90) or 8 degrees of cooling. 100o F or 92o F? Both are way too hot...I think it's time to stop writing for the day and head for the pool!!

There are more sophisticated ways to do this, talk to the meteorologists if you want to know more.

Psychrometry comes from the Greek for cold ("psuchron") and should not be confused with anything psychiatric (unless you are talking about mad dogs and Englishmen...)

July 21, 2011 06:21 PM

July 11, 2011


The Culture of Chemistry

Writing (in) blocks


I'm writing this summer on a wide range of projects, which means writing for a substantial period every day. That said, I recently took a bit more than a full week away from the keyboard, doing no writing at all (not even email) except for few (handwritten) sentences each day. In their delightful piece in Nature on turbocharging your writing (free), Maria Gardiner and Hugh Kearns point out that "binge writing" — writing on the rare occasions when you have huge blocks of time — is generally not as effective as "snack writing" writing often (nearly every day) for shorter periods. (In my life it can be a challenge in some weeks to find an uninterupted 45 minutes or hour each day.)

Gardiner and Kearns note the barrier to writing again when it's been a long time since you last sat down to write can be huge. I won't argue with that. As I sat down this weekend to work on a 500-600 word column due this morning (at the latest!) after my week off, I could feel the creaks and groans. Really, 500 publishable words? How about I warm up with a blog post or write a couple of emails? Fortunately, deadlines are great motivators, especially those that are hard and fast as this one is (the paper goes to bed on Tuesdays, with or without my column). The piece went off this morning, and I'm ready to really dig into a couple of project tomorrow morning.

I would add to Gardiner and Kearns good advice that interruptions — those that knock at your door and your own desktop temptations — are a real hazard. Silence the phone, close the email browser, barricade the door (necessary in my house, the cat opens it otherwise), tell students/colleagues/kids that you cannot be disturbed for anything short of (fill in your favorite catastrophe here). Some research suggests that each interruption costs 5 to 10 minutes of time to refocus on the task at hand (plus whatever time it took to deal with the situation that led to the interruption). If you only have 45 minutes to write, and are interrupted twice, you may have lost nearly half your writing time.

If you want more advice about writing for the professional science journal, join me on Thursday, July 14 for a one hour conversation I'm moderating for the American Chemical Soceity with Dr. Cynthia Burrows (senior editor at Journal of Organic Chemistry) and Dr. George Schatz (editor in chief of Journal of Physical Chemistry.) More details are here. They are taking questions live, so sign up (it's free, but you need to register) and ask away.


Photo is by Brandi Korte. Used under Creative Commons license.

July 11, 2011 10:06 PM

June 06, 2011


Net World Directory: Chemistry blog

Upping the anti

Science fiction is fast approaching science fact as scientists are progressing rapidly toward "bottling" antimatter. In a paper published online today by the journal Nature Physics, the ALPHA experiment at CERN, including key Canadian contributors, reports that it has succeeded in storing antimatter atoms for over 16 minutes. While carrying around bottled antimatter like in the movie Angels and Demons remains fundamentally far-fetched, storing antimatter for long periods of time opens up new vistas for researchers struggling to understand this elusive substance. ALPHA managed to store twice the antihydrogen (the antimatter partner to normal hydrogen) 5,000 times longer than the prior best, setting the stage, for example, to test whether antihydrogen and normal hydrogen fall the same way due to gravity........

June 06, 2011 02:54 AM


Net World Directory: Chemistry blog

Seeing hidden building blocks of life

Researchers from Finland and France have developed a new synchrotron X-ray technique that may revolutionize the chemical analysis of rare materials like meteoric rock samples or fossils. The results have been published on 29 May 2011 in Nature Materials as an advance online publication. Life, as we know it, is based on the chemistry of carbon and oxygen. The three-dimensional distribution of their abundance and chemical bonds has been difficult to study up to now in samples where these elements were embedded deep inside other materials. Examples are tiny inclusions of possible water or other chemicals inside martian rock samples, fossils buried inside a lava rock, or minerals and chemical compounds within meteorites........

June 06, 2011 02:54 AM

April 27, 2011


The Culture of Chemistry

Two thousand mockingbirds

I'm writing final exams for two intro chem courses. I try for a light touch brush of humor on at least a couple of the questions, it's stressful enough without every question probing deeply important things. (Stage notes: reverb last line)

Some useful (in this context) unit conversions:

2000 mockingbirds = 2 kilomockingbirds
10-6 fish = 1 microfiche
454 graham crackers = 1 pound cake
10 millipedes = 1 centipede
10 monologs = 5 dialogues
2 monograms = 1 diagram
8 nickels = 2 paradigms
10-2 mental = 1 centimental

Have more to suggest?

April 27, 2011 05:06 PM

March 31, 2011


The Culture of Chemistry

Bunsen and quantum mechanics



Today's Google doodle honors the 200th birthday of Robert Bunsen, the inventor (or not?)of the eponymous burner. The doodle is great, click on it and it bubbles and whirs.

"It is known that several substances have the property of producing certain bright lines when brought into the flame. A method of qualitative analysis can be based on these lines, whereby the field of chemical reactions is greatly widened and hitherto inaccessible problems are solved. We limit ourselves here to developing the method for alkali and earth-alkali metals and demonstrating its value by some examples.

The lines show up the more distinctly the higher the temperature and the lower the luminescence of the flame itself. The gas burner described by one of us (Bunsen, these Ann. 100, p. 85) has a flame of very high temperature and little luminescence and is, therefore, particularly suitable for experiments on the bright lines that are characteristic for these substances." Opening to Gustav Kirchhoff and Robert Bunsen, Annalen der Physik und der Chemie 110 (1860), 161-189.

Bunsen is not a name typically associated with the development of quantum mechanics, yet I might argue he is one of the key figures. The observation of line spectra and the realization that the lines are characteristic of particular elements is a significant step toward the development of quantum mechanics. It's one of the observations that Bohr was trying to explain in his model of the atom. General chemistry texts boast figures of line spectra to demonstrate the point - I showed several in my lecture last week. This apparatus developed by Kirchoff and Bunsen made possible the routine observation of such lines. I have a beautiful brass example in my office.

This paper goes on to note that sodium, even at very low concentrations produces quite bright lines. It reminds me of the many happy hours I spent playing with my mom's gas stove and making flame tests on anything I could scrounge up (most of which contained sodium). Is this the formative experience that impelled me toward quantum mechanics? Who knows! I do still think of sodium and line spectra every time the pasta boils over and the flame on my stove flares that characteristic sodium yellow-orange.

Happy birthday, Bunsen, I might not have a job without you!

There is more on Bunsen beyond the burner at The Sceptical Chymist.


March 31, 2011 08:42 PM

March 24, 2011


The Culture of Chemistry

Writing Science: The End






My quarter long science writing course came to a close last Friday. We test-drove one of the methods sections students wrote early on (how to make the perfect cup of hot chocolate, rather than coffee), ate pastries from the wonderful shop down the street and read from favorite works we'd written or read as part of the course. It was a lovely way to bring things to an end.

The final "writing" prompt
Bring a selection (roughly 200 to 300 words in length) from a piece you wrote that you'd like to read or a piece you read during the course that you'd like to share.

Thanks, too, to everyone who followed along, and especially those who shared, here (in the comments) and there.

Reading
I had more on my list of things to read than we could possibly get to -- if anyone would like the full reading list, send me a note and I'd be happy to share.

Final writing assignment
Write an 'In Your Element'-style essay for Nature Chemistry's science writing contest on any one of the following elements — helium, nitrogen, sodium, copper, bromine, indium or plutonium. 700-800 -words. All the details are here. Deadline is August 1, 2011.
Illustration is from Wikimedia commons.

March 24, 2011 09:43 AM

March 23, 2011


chemistry.org Newsletter

ACS On Campus Rides into Houston Next Month

ACS On Campus heads to Houston, TX, on April 15, for ACS on Campus: Rice University. Sessions will range from a discussion of what the "Journal of the Future" will look like to a SciFinder Solutions Session demo with our partners at Chemical Abstracts Service. For a complete list of events and speakers at Rice University, as well as an opportunity to RSVP, visit pubs.acs.org/page/4librarians/acsoc/rice.html. You can also find video, PowerPoint presentations, and other content from previous ACS On Campus events at pubs.acs.org/r/acsoc. We look forward to seeing you on campus!

March 23, 2011 06:20 PM

March 10, 2011


The Culture of Chemistry

Lab Notes: Walking the walk


Some days you have to be willing to walk the walk as well as talk the talk. My primary care physician keeps copious, real time notes on her encounters with her patients. She starts every visit with her pad in her lap - writing notes to herself (and best, yet, notes to me on what I need to follow-up on, complete with phone numbers and details) as the visit proceeds. So when she inquired about my immunization status during my physical yesterday, and she asked about tetanus, I thought I recalled getting a booster in 2008. Nothing in her notes on that.

Do we trust my memory or her notes? We'd chatted about my science writing, and given my expressed thoughts about (good) field notes - it was no contest. I have a sore arm, but no regrets.

The book I really want to read about field notes is not yet out (but I've ordered a copy) - Field Notes on Science and Nature edited by Michael Canfield of Notes from the field. The cover is beautiful and the contents look intriguing.

Image is from Wikimedia commons. A 1964 poster boosting boosters.

March 10, 2011 02:50 PM

March 03, 2011


The Culture of Chemistry

Writing Science: Punch Lines

"When a thing is funny, search it carefully for a hidden truth." George Bernard Shaw

How seriously should we take science? Is science inherently funny - are those odd spots where truth is hidden? Can science be humorous without being a caricature? Do you have to be a scientist to get the joke? What role might humor play in teaching science? And for that matter, why are words with a hard c sound (like cryogenic) funny?



Readings

Brian Malow - superb stand up science comedy
The Big Blog Theory - the science behind the humor on The Big Bang Theory

Periodic table humor.

XKCD a comic strip which carries the warning: "this comic occasionally contains strong language (which may be unsuitable for children), unusual humor (which may be unsuitable for adults), and advanced mathematics (which may be unsuitable for liberal-arts majors)." And apparently unsuitable for high school students, it's blocked as "adult content" where I'm on the web. I'm in the high school nominally supervising the theater tech crew as they construct a set. Don't ask about the decibel level!)

Men of Mystery (subscription only) Taking on the stereotypes of science: why are scientists drawn as guys in white coats with bad hair? M.M Francl, Nature Chemistry, 2, 68-70 (2010).

March 03, 2011 05:19 PM

February 25, 2011


The Culture of Chemistry

Writing Science: Poetic Movements

Paul Dirac (Nobel Prize in physics, 1933) once said: "In science one tries to tell people, in such a way as to be understood by everyone, something that no one ever knew before. But in poetry, it's the exact opposite."

Is it? Can or should poetry and science mix? Should we teach scientists how to write poetry as a matter of course?




Writing Prompt
Using 2 to 5 words from the list write a poem. Stuck for form? Try haiku.
(5 syllables, 7 syllables, 5 syllables)

protein, atom, diffuse, drosophila, phylum, differential, set, scalar, momentum, graphite, ionized, equilibrium, eutrophic, entropy, catalyst, precipitate

Reading
When Science and Poetry Were Friends, an essay by Freeman Dyson
The Future of Science is Art, Jonah Lehrer, Seed Magazine
Roald Hoffman (Bio here) Individual poems here.
Sabrina Vourvoulais Fata Morgana
Karl Kirchewey, Propofol
J.C. Todd, Instant of Turbulence and Endless Caverns, in What Space This Body
Photo is from surrealmuse, used under a Creative Commons license.

February 25, 2011 07:49 PM


The Culture of Chemistry

Writing Science: Fact in Fiction

Can you communicate science via fiction? What are the risks? the benefits? Are there signals in a fiction piece that mixes fact and fiction that help you sort? Should there be?

Writing Prompt
Write a (very) short story using the following three words: planet, curry, madman. Don't like these words? Generate a set using a random word generator.

Reading
  • "A Little Heart" Baruch, Jay. Fourteen Stories: Doctors, Patients, and Other Strangers. Kent State University Press, 2007.
  • "Dissections" Baruch, Jay. Fourteen Stories: Doctors, Patients, and Other Strangers. Kent State University Press, 2007.
  • Rothman, Claire Holden. The Heart Specialist. Cormorant Books, 2009. Ch. 13
  • "Carbon: Part One" by Justina Robson and Andrew Bleloch in Ryman, Geoff. When It Changed: 'Real Science' Science Fiction. Comma Press, 2010
  • "Moss Witch" by Sara Maitland and Jennifer Rowntree in Ryman, Geoff. When It Changed: 'Real Science' Science Fiction. Comma Press, 2010
  • "Without a Shell" by Adam Marek and Vinod Dhanak in Ryman, Geoff. When It Changed: 'Real Science' Science Fiction. Comma Press, 2010
  • “A History Lesson” Robert Scherrer, Nature, 469, 574 (2011).
  • “A Question of Breeding” Jeff Hecht, Nature, 453, 562 (2008).
  • “All of Me” Ed Rybicki, Nature, 454, 1028 (2008).
  • “The Last Laboratory” John Gilbey, Nature, 469, 126 (2011).
Photo is from Wikimedia.

February 25, 2011 03:38 PM

February 21, 2011


The Culture of Chemistry

Scientists should blog about their pets

My latest Thesis column is out in March's Nature Chemisty: Blogging on the sidelines (subscription needed). In part a response to Royce Murray's editorial in Analytical Chemistry last fall, the column considers what the role of blogging critically about the primary literature might be. Does blogging by scientists about science help researches? My short answer is yes, it's an effective post-publication filter, a niche that has been filled at other times in other ways.

But I also think that scientists writing about life in the lab or their pets or commute has a role to play in making better science. That wouldn't fit in the column, so the delightful editors at Nature Chem have posted it on their blog.

February 21, 2011 05:14 PM

February 16, 2011


The Culture of Chemistry

Writing Science: Gee-Whiz


How do great science writers engage their readers? How do they get into - and out of - a piece?

Writing Prompt
The article is titled "The Case of the Orange Flake". Start writing it. Five minutes.

Read
  • "Writing Well About Science" in Blum, Deborah, Mary Knudson, and Robin Marantz Henig. A Field Guide for Science Writers: The Official Guide of the National Association of Science Writers. Oxford University Press, USA, 2005. pp 26-33
Read at least one from A and at least one from B

A
  • "Narrative Writing" in Blum, Deborah, Mary Knudson, and Robin
    Marantz Henig. A Field Guide for Science Writers: The Official Guide of
    the National Association of Science Writers. Oxford University Press,
    USA, 2005. pp 138-144
  • "Gee Whiz Science Writing" in Blum, Deborah, Mary Knudson, and Robin
    Marantz Henig. A Field Guide for Science Writers: The Official Guide of
    the National Association of Science Writers. Oxford University Press,
    USA, 2005. pp 126-130
  • "The Science Essay" in Blum, Deborah, Mary Knudson, and Robin
    Marantz Henig. A Field Guide for Science Writers: The Official Guide of
    the National Association of Science Writers. Oxford University Press,
    USA, 2005. pp 145-150

B
  • "Withering Heights: Bailing out from Space," in Roach, Mary. Packing for Mars: The Curious Science of Life in the Void. W. W. Norton & Company, 2010. pp 247-264
  • "Of lice and men: An itchy history" Emily Willingham, SciAm blog
  • "The Case of the Wide-Eyed Boy," in Edlow, Jonathan A. The Deadly Dinner Party: and Other Medical Detective Stories. Yale University Press, 2009. pp 116-128
  • "Radium (Ra) 1928-29," in Blum, Deborah. The Poisoner's Handbook: Murder and the Birth of Forensic Medicine in Jazz Age New York. Penguin (Non-Classics), 2011. pp 176-195
  • "The Case of the Red Leg," in Gawande, Atul. Complications: A Surgeon's Notes on an Imperfect Science. Metropolitan Books, 2002. pp 228-252
Writing assignment
Write your own version of "The Itch" (but not about itching), a 300-400 piece on the science of some common experience, using a strong narrative.

February 16, 2011 03:36 PM

February 14, 2011


The Culture of Chemistry

Writing Science: Science-speak - jargon or dialect?


How good is your ear? How does scientific language play in a piece written for a broad popular audience?

Writing prompt
You are headed for Mars, you may take 2 kg (not quite 4 and a half pounds) of personal gear. What would you take and why? Bear in mind that you will have varying gravity conditions during the trip. What could you not bear to run out of?

Reading
  • "Avoid Fancy Words" in Strunk, William, and E.B. White. The Elements of Style Illustrated. Penguin (Non-Classics), 2007. pp 111-113
  • "Do not use dialect unless your ear is good" in Strunk, William, and E.B. White. The Elements of Style Illustrated. Penguin (Non-Classics), 2007. pp 113
  • "Avoid Foreign Languages" in Strunk, William, and E.B. White. The Elements of Style Illustrated. Penguin (Non-Classics), 2007. pp 115
  • Carl Zimmer's list of words that should be banned from science writing (H/T ejwillingham)

February 14, 2011 03:46 PM

February 09, 2011


The Culture of Chemistry

Writing Science: Itchy Writing


We're moving onto looking at science journalism.

Writing out of the lab - how well does translation work between the scholarly scientific literature and the newspaper or magazine? What is most likely to get lost? What gets added? Should popular science writers be/have been scientists? Should scientists have editorial control over articles written about their work? Should there be (are there) ethical rules for how science can be popularized?

Questions on the table How does the narrative work in that piece versus the shorter pieces? How is scientific language deployed? is it decorative or iconic or instructive? The titles? What did they promise versus deliver?

Several of my students began Atul Gawande's piece thinking it was fiction - what are the clues that suggest this is science reporting embedded in a riveting narrative? Several others had read it almost three years ago (when it appeared in June of 2008) and still remembered the article (as did I!) - what is so compelling about The Itch?


Read
Writing prompt
Write about a time you itched. The itch could be literal or metaphorical. Five minutes.

Up next? Do not use dialect unless your ear is good

"Clipping" was generated by fodey.com from this blog post: Sex and the scientist

February 09, 2011 05:50 PM

February 02, 2011


The Culture of Chemistry

Writing Science: The Short and Sweet of It, Titles and Tweets


We're thinking about writing short bits of science with style and precision: titles and tweets, abstracts and blog posts.

What makes a great title? One theory (here) suggests great book titles should be PINC ("pink"): make a promise, create intrigue, identify a need, and/or describe content.

Are there other things that titles should do in a science piece (be it blog post, tweet or scholarly article)? How would you prioritize these for different audiences, different genres?

Should an abstract tease? Is there a place for wit in the formal scientific literature? When? How? Who? Is it OK for someone of Paul Wender's stature to indulge?

Readings

Writing assignment #3
Write 5 tweets pointing colleagues to recent articles in the field (give me title/ref for the article); In 50-100 words comment on the construction of your tweet in light of the criteria you have developed for a good science tweet.

Writing Prompt for the day
Write a series of possible titles for the abstracts below. When you get stuck, move to the next abstract! Five minutes. (Click on the links to see the title the authors chose.)

A. Human infants face the formidable challenge of learning the structure of their social environment. Previous research indicates that infants have early-developing representations of intentional agents, and of cooperative social interactions, that help meet that challenge. Here we report five studies with 144 infant participants showing that 10- to 13-month-old, but not 8-month-old, infants recognize when two novel agents have conflicting goals, and that they use the agents’ relative size to predict the outcome of the very first dominance contests between them. These results suggest that preverbal infants mentally represent social dominance and use a cue that covaries with it phylogenetically, and marks it metaphorically across human cultures and languages, to predict which of two agents is likely to prevail in a conflict of goals. Science 331, 477-480 (2011)
B. The effect of environmental change on ecosystems is mediated by species interactions. Environmental change may remove or add species and shift life-history events, altering which species interact at a given time. However, environmental change may also reconfigure multispecies interactions when both species composition and phenology remain intact. In a Caribbean island system, a major manifestation of environmental change is seaweed deposition, which has been linked to eutrophication, overfishing, and hurricanes. Here, we show in a whole-island field experiment that without seaweed two predators—lizards and ants—had a substantially greater-than-additive effect on herbivory. When seaweed was added to mimic deposition by hurricanes, no interactive predator effect occurred. Thus environmental change can substantially restructure food-web interactions, complicating efforts to predict anthropogenic changes in ecosystem processes. Science 331, 461-463 (2011)

February 02, 2011 02:34 PM

January 30, 2011


The Culture of Chemistry

Cooling trends


In a previous piece about density and the insulating power of whipped cream, I mentioned that trapped "nothingness" was even better at insulating things than the trapped air in the whipped cream.

A hot object can transfer heat to its surroundings by conduction and convection, in other words by having molecules (or atoms) in the surroundings collide with the surface of the object, pick up some of its energy and move off. Imagine a little bucket brigade, stepping up to the object, grabbing a piece of heat (energy, really) and heading off to dump it elsewhere. Air doesn't conduct heat very well, and trapping it reduces convection (the bulk movement of the air - air currents), hence trapped air is an effective insulator.

If you halt the bucket brigade - prevent any molecules from walking off with a chunk of energy, all the energy stays in the object and voila my cocoa stays hot. So if I could envelop my cocoa in a bubble of nothingsness — a vacuum — I could keep it from cooling via conduction and convection. (Of course, I'd have to put a vacuum tight lid on the thing, lest it instantly boil off — but that's another post…) A convenient way to do this is to use a vacuum flask, where a 'layer' of vacuum is enclosed between two walls. Originally glass walls were used. If you're my age, you might remember dropping your lunch box, and then opening your thermos at lunch to find shard of glass inside. These days stainless steel or plastic walls make lugging your milk to school a less risky proposition.

Chemists still use the glass walled version of a thermos. We call it a Dewar (for James Dewar, who invented the contraption in 1892).

But an object untouched by other molecules can still lose heat by radiation, by emitting infrared photons - light at wavelengths longer than visible light. Reflective wrappings, like metalized Mylar, keep the light - and the warmth - inside.

A friend recently wondered why clear weather was cold weather. The earth radiates some of its heat back out into the universe as infrared radiation. Clouds act as insulating wraps for the earth, the water molecules grabbing the heat before it radiates out into space and re-emitting some of it back toward the planet's surface. (This is the greenhouse effect — it's not up for debate.) On a clear night, no clouds, so less heat is retained. Suddenly the temperatures are well below freezing.

(Other molecules besides water help trap infrared radiation within the atmosphere, including carbon dioxide and methane.)

Photo is from Wikimedia.

January 30, 2011 03:01 PM

January 28, 2011


The Culture of Chemistry

Writing Science: What do journal articles and romance novels have in common?


The anatomy of a scientific paper. What do scientists mean when we say "the literature" (in hushed reverent tones)? What role does it play? Is a journal article as formulaic as a romance novel? Is this a bad thing? Where is the drama packed into a scientific paper? The introduction? The conclusion? Or are articles (as one of my students put it) "stripped of all their drama"?

Writing prompt of the day

Pick one of the titles below and write an introduction to this paper. If you don't know the meaning of a particular term, create a meaning. Five minutes.

• Kinetic Isotope Effects for the Reactions of Muonic Helium and Muonium with H2
• Enhanced lithium depletion in Sun-like stars with orbiting planets
• One small step for a mouse
• Transient Hoogsteen base pairs in canonical duplex DNA

Next up?

What sets the tone in an article? Grab a journal article at random and start circling all the qualifiers - are they "needless words" (as William Strunk of Elements of Style fame would have it) or careful bounding on the part of the authors as to their claim?

And would a set of journal covers look as similar to an untutored eye as these romance novel covers?
Romance novel covers art from http://www.flickr.com/photos/wackystuff/2551278302/

January 28, 2011 01:57 PM

January 26, 2011


The Culture of Chemistry

Writing Science: The. Article.


Yes, the is an article, but "the article" is considered by many to be the best, the most important, the only way to communicate about science (at least to other scientists). Yes? No?

Who should be writing about science? What kinds of writing about science constitute scientific communication? Who should be writing them?

Writing prompt
"All I want is a proper cup of coffee, made in a proper copper coffee pot." —Trout Fishing in America

Describe how your perfect cup of coffee is made. Start where you wish - with the beans, or with pouring it from a pot, or buying it at a cafe. Be specific and detailed. Don't drink coffee? (I don't!) Do the same with tea or hot chocolate or a favorite sandwich. Five minutes.

Alternate:
Pick a routine prep you do in lab. Describe the perfect process. Be specific and detailed. Five minutes.

Next up
The anatomy of a scientific paper: what does one of those all important journal articles look like?

What we're reading
  • Anatomy of a Scientific Paper, Excerpted from Anatomy of a Scientific Paper
  • Abstract, Communicating Science: A practical guide, Pierre Laszlo, Springer, 2010.
  • How to write a scientific paper (book review), R.W. Guillery, J. Anat. (2008) 213, 629–630.
  • Whitesides' Group: writing a paper, George Whitesides, Adv. Mater. 2004, 16, 1375-1377.
  • Writing Summaries and Abstracts, Margot Northey & Judi Jewinski, Making Sense: A student's guide to research and writing, Oxford 2009. pp 31-38
  • Writing a scientific paper, From Research to Manuscript: a guide to scientific writing, Michael Jay Katz, Springer, 2006. pp 53-124
  • Instructions for authors, Journal of the American Chemical Society
ADDENDUM: A chemist muses about coffee here....

January 26, 2011 02:37 PM

January 25, 2011


The Culture of Chemistry

A fluff piece on density

We're covering density in my introductory chemistry this week - which prompted this post.


Density is the ratio of mass to volume and often (though not always) one of the easiest physical properties of a substance to measure. Introductory chemistry labs often feature an exercise where the mass of an object is determined using an analytical balance or somesuch and the volume is determined by displacement (often in a graduated cylinder).

In certain of my teen-aged sons' circles it's in fashion to write in public - to take your notebook (computer or spiral bound) and head to the local coffee shop. You can write the scene while being seen. Personally, I write in public as a last resort. Last week, while waiting to meet a friend for coffee I did haul out my iPad to see if I could inhale some of the fumes of caffeine and inspiration wafting around and some first thoughts for a column hammered out. No coffee for me, hot chocolate - with a serious mound of whipped cream on top.

While I'm all for decadence when it comes to chocolate, hot or otherwise, the whipped cream was a practical touch. My friend is notoriously late, and I wanted the chocolate to stay hot until he arrived.

The ability of a material to conduct thermal energy - heat - depends to some extent on its density. On a molecular level, heat transfer is mostly about collisions between molecules. If you are a molecule with lots of thermal energy, you are generally stuck with it all until you collide with another molecule!

Air at 20oC (68oF) feels warm (yes, I know it's about 3oC here right now, but a girl can dream, can't she?) while water at the same temperature feels refreshingly cool. Water is about a thousand times denser than air, so there are many more molecules in contact with your body surface. The more molecules boucing off a surface, the more opportunities there are for energy transfer. If you're hot, you'll get cooler faster by fully immersing yourself than by standing in a cool room. Conversely, if you want something to stay hot, surround it with air, not water. Air is a good thermal insulator, relative to water, because it is far less dense.

The whipped cream atop my hot chocolate is full of air, which lowers the density and so it floats on top of the cocoa. Heat transfer to the airy cream isn't very efficient due to the low density. Since the air trapped inside the cream isn't moving around (and thereby not presenting fresh molecules to take away the energy presently in the liquid in my cup), the system quickly equilibrates, with most of the heat in the system staying there.

Trapped air (or other gas) is a great insulator, but trapped nothingness works even better. Put my cocoa into a vacuum chamber and it should stay nice and toasty (though there would be other complications - but that is another post!).

January 25, 2011 04:47 PM

January 23, 2011


The Culture of Chemistry

Writing Science: Material Science

Writing prompt Day 3: Pen or pencil? What is your preferred tool for writing by hand? Why? Describe your ideal pen or pencil, weight, ink, color, thickness, material. Expound on your preferences - why is a blue ballpoint infinitely preferable to a black marker? Five minutes.

On the table today: reading field notes

Next class: What is science writing? Who does it?

Readings for next time:

Science Blogs and Caveat Emptor, Royce Murray
Table of Contents, Oxford Book of Modern Science Writing
What is the primary literature? from Oberlin College Library


Photo is from http://www.flickr.com/photos/angelocesare/304107607/ used under a Creative Commons license.

January 23, 2011 10:19 PM

December 03, 2009


EnvironmentalChemistry.com

Nitrogen Dioxide, Ozone & Lead Partner to Increase Pollution Dangers to Urban Children

Scientists from the University of California, Irvine have found that Nitrogen Dioxide (NO2) and Ozone (O3) react with surfaces painted with lead based paint to increase the release of lead from said paint posing an even greater risk for children. By Roberta Barbalace

December 03, 2009 08:30 PM

October 29, 2009


The Chem Blog

The final step in evolution is extinction


Dear Gentle Readers,

For a long time I have been an author and outlet for many in the chemistry community and the run was, to say the least, more than I could have ever expected.  It was through this blog that I found a cathartic release of frustration, anger and, most importantly, the insatiable curiosity I have always had for science.

Some time ago, a reader named Bethany Halford asked me a question about why I blog and I framed my answer in as quotable of a context as I could – because I wanted to see how far I could push this thing.  I think I have pushed it far enough and I have reached the end of my intellectual interest and now wish to divest myself from blogging so that I may completely free myself for the pursuit of other things.  No doubt you have noticed that the frequency of posting has diminished as my other projects have begun to take off and my fullest efforts are required there.

Now that blogging appears to be an activity which is regulated by the FTC, I think it’s safe to say that it has finally arrived.  I now know (or at least I think I know) what it takes for someone to develop a successful web presence and what sort of innovations are needed to build on that presence.  My programming skills are also none the worse for the endeavor.

In any regard, this is the end.  The lights will be shut off next month, the gmail account will no longer be answered and the chemblog store with its catchy EJ cup and functional group poster will be deleted.

Good bye, world.

Yours,

Kyle Finchsigmate

October 29, 2009 08:12 PM

October 23, 2009


The Chem Blog

I would like a fish in my hood


Today I constructed a brand new shelf in my hood.  I love hood shelves.  You can put chemicals on them, solvents, glassware… all kinds of things that would ordinarily go somewhere else more… public.   After I was done constructing my masterpiece I began to admire my handiwork and populate it with things (mostly chemicals) but, while I was standing there talking with my hood neighbor, the consensus was reached that the new shelf begged a novel hood design:  it needed hood Feng Shui.

While I have no idea what Feng Shui actually is, I’m 99% certain it has something to do with colorful fish or those lucky bamboo things they sell at Target and since 99% is basically 100% I figured my hood needs a fish inside of it.

Of course, I’m a realist.  I can’t put a whole aquarium in my hood – that would be chest slappingly short bus retarded.  Since I don’t want to run an air pump through my hood I need a labyrinth fish.  The king of such fish is the betta fish or the Siamese fighting fish.  And  because I’m 99% sure Feng Shi also means making sure your shit matches, it needs to be in a round bottom flask.  (That useless 29/42 ground glass is suddenly less useless!)

So, I’m thinking about something like this:

fishinaflask

I would put the fish in a flask on my shelf, where I would feed it and it could watch my reactions for me at night (and tell me who the fuck keeps turning my hood’s airflow alarm back on).

Alternatively, I could set up an ant farm and run the ant tubes all over my hood.  That would prolly kick ass, too.

October 23, 2009 03:15 AM

October 16, 2009


EnvironmentalChemistry.com

Initial Energy Audit for 70s House Eco Renovation

This energy audit was conducted on our house as part of our 70s house eco renovation project to help us prioritize weatherization and energy efficiency projects. This is one in a series of articles documenting the eco renovation of our house. By Erik North, Free Energy Maine LLC.

October 16, 2009 12:30 AM