Thursday, April 26, 2012

There's Always Next Year?

Just found out that I won't be hosting the upcoming PBS series "The Mystery of Matter - Search for the Elements." The project director, Stephen Lyons, kindly wrote this message to anyone who sent along an 'audition' video:

Although I'm a little disappointed, I realize the gig will go to someone truly awesome, and there's other chemical video contests to enter while I wait for my big break.

Maybe next time, I'll wear a nicer T-shirt...

Friday, April 20, 2012

Friday Fun - Lab Arts-n-Crafts

The Leaning Tower of Septa
It's been a long few weeks at the "real job," and I haven't had a lot of time for serious, analytical posts. I'll try to have a few up before month's end. 

Until then, here's a few pics from around the lab. Call it recycling, call it art, call it something to make you smile. It certainly helps me when I'm going past Hour 60 and starting to get punchy...
Watch the thorns on this bouquet...

I've Got the World on a Flask

Wednesday, April 18, 2012

Chem Logos - Mythical Defense Edition

Unlike most other disciplines, chemists still have one foot firmly stuck in the world of the supernatural and otherwordly (after allonly in the last few centuries did we realize that aether, vitalism, and phlostigon were all just philosophical fool's gold). Biologists don't reference the Yeti when discussing arctic adaptations, and physicists don't believe that the Earth rests on the back of a giant turtle. Chemists, meanwhile, have a periodic table brimming with legends: cobalt, vanadium, mercury, palladium, helium, and uranium all speak to our alchemical past. But, would you expect to find modern-day examples . . .on military stationery?!

"The Duck"
Credit: CNET | Dan Terdiman
Preparedness for biological, radioactive, or chemical threats falls to the JPEO-CBD, a division of the U.S. Department of Defense. Want to see all their cool scientific toys? I found this slideshow, compiled by CNET reporter Daniel Terdiman during a visit to Dugway Proving Grounds (UT) in 2009.

Due to some strongly-worded disclaimers, I won't link directly to the government pages that describe the various offices under the JPEO's umbrella. But, given the DoD's social media outreach efforts - they're on Twitter, Facebook, and YouTube - I'll assume it's OK to share two program logos with the chemblogosphere.

Credit: DoD
Two mythically-inspired logos caught my eye: the Critical Reagents Program, which develops validated assays and sampling kits, displays a menacing green gargoyle, arms akimbo, with flashing red eyes. Likewise, the Contamination Avoidance program, specializing in risk assessment and recon, shows a huge, perched green dragon, with wings cupped as if to shield its young.

Credit: DoD
Therein lies the effectiveness of these two images - although the characters are legendary, we associate both creatures with protection and defense. There's also that hint of menace, a spooky warning against potential attackers. 

Should the DoD require more defensive imagery, I'm sure Batman and the Golem are standing by...

Saturday, April 14, 2012

Posed Science - LC/MS Edition

When you buy a lab instrument, do you read the manual first? Or, do you just unpack the thing and try to figure out what connects to what? 

"I'm so good at this, I don't even need to look!"
Credit: Thermo
Many regular JLC readers have trekked with me down the road of sourcing, pricing, set-up, and installation of a new (used) LC/MS - liquid chromatography with mass spectrometry, a method to tell what's going on in a chemical reaction using molecular mass and retention times. Though the units aren't much bigger than a microwave oven, they're fairly complex and full of intricate, delicate (read: breakable), expensive parts.

The past few weeks have been whirlwinds: late nights with engineers, software downloads, cable swaps, and last-minute orders for critical components. We're finally installed now, so I look forward to 10-20 years of "problem-free" operation (Note: Insert audience laugh track / rim-shot here).

"Manual reads: Hold button for ten minutes."
Credit: Agilent
Trying to catch any last-minute issues, I looked over the User Manuals for both the HPLC and MS instruments...and that's when I saw the pictures. Equipment companies realize that, like car dealers or computer salesmen, "action shots" of people interacting with the product motivate customer purchasing. Theory goes that you'll vicariously insert yourself into the scene, so you can be the one driving that Toyota or typing on that iPad

Here's two pictures, one from a Thermo guidebook, the other courtesy of Agilent. Note the lack of goggles, or attention to what's actually going on - one scientist pipets without looking, while the other seems to be mashing the "." key on the LC Gameboy

Not that either 'researcher' really far as I can tell, their instruments aren't even on! The LEDs that show system activity aren't lit, and the solvent hoses don't seem to be hooked up. Perhaps too much scientific content ruins the photo shoot.

Friday, April 13, 2012

Egg Block Copolymer

Sifting through the detritus left behind after another Easter weekend, I came upon a few empty, abandoned plastic Easter eggs. Just for fun, I thought it might be fun to make an "oligomer" out of the polymeric ova.

This random block copolymer shows a low polydispersity index (PDI): exactly one, since there's just one strand! Manufacture should be trivial, since the component blocks literally snap together. Sadly, previous force testing (with my foot) indicates that we probably need to increase the shatter resistance.

Theoretically, to spiral one more "meta" layer downward, one could recycle eggshell-derived plastics into next year's Easter eggs!

What would a post about Easter eggs be without an Easter egg?

Wednesday, April 11, 2012

Space Dinos! Prebiotic Chemistry Meets Paleozoic Commentary

Source: Columbia Giving
When I open Google News, I usually expect to see trade agreements, protests, car shows, or sports quotes. But, when I read a title like Dinosaurs from Space! (Smithsonian), or Do Intelligent Dinosaurs Really Rule Alien Worlds? (Discovery) I'm admittedly drawn in.

Ready for the real shocker? It's a paper published in JACS! No joke - here's the ACS presser. Bonus: the paper's written by a well-respected research lion - Ron Breslow, long a veteran of Columbia's chemistry department (Aside: I couldn't recall if ChemBark had seen Breslow's professorial "portrait," (right), courtesy of Columbia's University Giving Office).

The paper, a Perspective, reads fairly well: Breslow muses about the origin of homochirality on the early Earth, a subject near and dear to researchers such as Robert Shapiro, Albert Eschenmoser, Jack Szostak - and #1 on Philip Ball's list of chemical "grand challenges." Breslow recalls that scientists measured small enantiomeric excesses in amino acids, from 2-15% of the S (also called "L-") form, found in several meteorites that fell to Earth in the last 50 years. He then demonstrates, using a clever mix of solvation energies and autocatalytic reactions, some possible prebiotic setups leading to enrichment of single-enantiomer sugars and amino acids. 

Sound good? Well, it's all fine up until the closing paragraph - again, no exaggeration on my part:
"An implication of this work is that elsewhere in the universe there could exist life forms based on D amino acids and L sugars...Such life forms could even be advanced versions of dinosaurs,  if mammals did not have the good fortune to have the dinosaurs wiped out by an asteroidal collision, as on Earth. We would be better off not meeting them."
Artist's Representation: Life Elsewhere
I'm actually both horribly amused, and somewhat embarrassed by that conclusion. It's playful and exciting, yes, but, as others have pointed out, it sounds suspiciously like bait to draw sensationalist reviews and lure more casual readers. 

Well, two can play at this game! Without further ado, I'd like to offer a few novel O.O.L. speculations of my own: 
- On "Earth 2," in a far-off galaxy, a preference for body hair, muscles, and heavy brows favored Neanderthals over modern humans. 

- Life on distant planets proven to be highly evolved amoebas, who had the good fortune never to form into any multi-cellular critters.

D-amino acids + L sugars = Luck Dragons?
Source: Kristen Lamb
- In the land of Fantasia, a young boy named Atreyu must find the Nothing killing his world (wait, no, that's the Never Ending Story...).

- On Planet 2G, slightly different rules of gravity and lack of water, combined with a preponderance of slightly chiral amino acids led to...really beautiful crystal gardens, but not much life. (sorry, everyone!)

Saturday, April 7, 2012

More 'Found Molecules'

This week, I've rounded up three examples of "molecules" - one real, two not-so-real - from the world outside the lab.

Source: Wellcome trust
Amino Acid - I watched a YouTube clip of Guardian Neurophilosophy blogger Mo Costandi explaining to the Wellcome trust about why he blogs (Fun Fact: Mo worked as a security guard prior to becoming a science writer). At the end of the video, Wellcome displays a splash card with a mission statement and a ball-and-stick model: hey, it's L-serine! It's always nice to see a correctly-drawn molecule in advertising, especially when they could have picked a neuron, a cell, or a goofy staged picture instead (Watch, as science blogger adds droplets to bright red solution!!!).

Of course, my science spider-sense needs to clarify two very minor points. First: at neutral pH, solitary amino acids usually like to exist as zwitterions, which would mean that the nitrogen (blue) picks up a proton, and the carboxylic acid (red) loses one (COO-). Two: since we're discussing neurology here, I can't help but feel that they might have meant to show neurotransmitter D-serine, the enantiomer (mirror image). Turns out, the body generates D-serine from L-serine in the brain using a specific enzyme, serine racemase.

Found: hanging on the Shell station door
Nitrogen Enhanced Gas - Last month, Shell Oil company released a new generation of its detergent-containing gasoline, designed to protect your engine from "performance-robbing gunk," or carbon deposit buildup on intake valves. Look at their new logo*, pasted all over the station's pumps, doors, and road signs: what the heck is that blue thing? Counting quickly, I'd assume that it's nonane, the 9-carbon cousin of octane, the main component of gasoline. Well, that can't be it, because that doesn't have any nitrogen! Writer Michael McCoy came up against the same such pseudo-scientific "ziggy-zaggy molecule"  in his C&EN article (Chem. Eng. News 2009, 87(14), 20-21).

Digging briefly through the patent lit, I came across US7,901,470B2 (2011), titled simply "Gasoline Additives," and co-written by six Shell Oil engineers. A sampling:
"a hydrocarbyl the range 155 to 255 as an additive in unleaded gasoline...for reducing injector nozzle fouling...
Looks like we're on the right track. Read a few more 'grafs down, and they mention...dodecylamine. In fact, they say "...found to be particularly effective," which in patent-speak means they should probably add a few more carbons and an amine group onto that sign! On a more serious note, there's a debate brewing over whether such detergents help engines while harming the atmosphere, by producing extra NOx emissions.

Credit:  ST:TNG | Paramount Pictures
Star Trek Set Design - Watching through old episodes of ST:TNG, a tiny detail caught my eye. In the 24th Century, young Wesley Crusher, the oft-misunderstood teen wunderkind, studies such subjects as nano-engineering, quantum physics, and...chemistry? Check out this screen shot from season 3, episode 1; it seems researchers in Stardate 43125.8 are still using the old HGS modeling kit (a personal favorite, btw).

And what structure do we have here? Judging by the color-code, normally, red = O, black = C, white = H, I'd guess a type of dual hyperoxygen**, an oxygen with four connected bonds (oxygen usually likes two bonds, or 3, tops). I've heard of Olah's hypercarbon, so maybe it's a take on that? Perhaps a form of matter we just haven't found yet? More likely, following the example from National Lampoon's Christmas Vacation, set designers simply aren't versed in synthesis.

Dear Hollywood - If you need to vet a structure or formula, do feel free to ask me. Operators with chalkboards and books are standing by!

*Editor's Note: Is that a registered trademark (R) symbol next to the word "nitrogen?" I wasn't aware that element names could be trademarked! Of course, I'll be immediately contacting the Just Like Cooking legal department to file for Argon(TM), Strontium(TM), Niobium(TM), and Roentgenium(TM). Y'all can fight over the rest.
**Bonus Round: Try putting "hyperoxygen" into Google. Mostly homeopathic cures, hyperbaric chambers, and folks who don't know what hydrogen peroxide really is.

Thursday, April 5, 2012

Chicken Chemophobia

A recent New York Times Op-Ed spot made the rounds late last night on Twitter. Full of inflammatory language, it seemed wholly bent on scaring the heck out of anyone reading it. The title - "Arsenic in Our Chicken?" - didn't exactly calm me down.

Is this in my chicken? Only very, very little
Well, I'm a scientist, so let's look at this rationally. First things first: here are links to the two papers referenced in the study, one from Environmental Science and Technology (ACS), and one from Science of the Total Environment (Elsevier). (Editor's Note - Whenever a columnist feels pressed to validate his opinion with the words 'published in a peer-reviewed scientific journal,' I turn on the skepticism). 

In both papers, analytical chemists take a peek at feather meal, a poultry industry byproduct, for compounds you might expect from factory farms: antibiotics, stimulants, and antihistamines. A surprise dark horse was encountered in arsenic, which apparently caught everyone so off guard that they required a full second paper to adequately discuss it. 

Glancing quickly at both journals' major tables, it's clear we're talking small amounts here: parts per billion (ppb), which for EST means ng / g, and for STE ug / kg. To put this in perspective, let's imagine we had a swimming pool, which we filled with 1000 L (~270 gallons) of water, which will weigh 1000 kg (density of water = 1 g / mL @ room temp). Now, what's a ppb for this scale? One milligram of material, or about what you'd add if a snowflake fell into your pool.

Better start eating....
Source: Home of Science Wonders
Overall, the article smacks of rampant chemophobia and fear-mongering. While the individual compounds, in acute (high) doses might be cause for concern, the detected values aren't near that much. The LD50 (oral, mouse) for arsenic, the value at which half of tested lab animals die, is 145 mg / kg; the maximum arsenic detected in feather meal = 4 mg / kg! This leap of logic contains an even more far-fetched premise: you'd have to eat two pounds of feathers just to take in that much!

Remember: infinitesimally tiny amounts of several "bad" substances float by you every day, but you don't often see people dropping dead.

Maybe that's the reason that this NYT reporter buries his lede - a quote from his source, Dr. K. Nachmann, an author on both papers: "We haven't found anything that is an immediate health concern." 

And look, now I've gone and buried it, too.

(Update, 12:09 4/5 - Commenters on Twitter point out that a topic I did not address - detection of banned antibiotics - could be cause for concern. I agree with that point)

Wednesday, April 4, 2012

Abstract Coloring Book: Take Two

The "colored abstract bug" spreads quickly. Since I began cataloguing appearances, they've cropped up in several other journals, including at least 3 examples in just the last 48 hours.

First, here's some ACIEE oroidin fun, courtesy of the Romo and Molinski groups (sea sponge in the background?):

Next, a sweet little palladacycle OM, thanks to the Gonzalez-Herrero and Vicente groups, in Spain (bright yellow, for Pd?):

Finally, submitted for your consideration, this chalcogen cluster assembly graphic from the Holm lab at Harvard, which recently graced JACS ('M' is tungsten, in case you missed it...):

Again, I'd like to point out that I'm not opposed to deft use of color, to draw the eye, differentiate, or point out an otherwise missed detail. But when the abstracts look more like abstract art? Too much.

Side Note: I couldn't resist showing one more, even though it's not from this past week. A 2011 KCN classic, nonetheless - behold, Epicoccin G (now in color!)

Monday, April 2, 2012

Chemist Wins Lotto, Pays Off Student Loans

Asking someone what they'd do after winning the lottery is a sort of personality test - anyone who says they'd still show up for work on Monday must really enjoy their job (right? right!?).

Cure for student loans?
When the largest jackpot in lottery history - Mega Millions, $640 million USD - finally ended this past Friday, a few lucky folks got to make just such a decision. As reported by the Boston Globe Metro Desk, a Boston-area chemist was among the winners, and he'll take his prize as a lump sum of $175,000. 

However, that's not the best part: what do you suppose he'll spend it on? Fast cars? Cruise ships? World Travels? No, he's going to " off his student loans and make a down payment on a house."

At first I was shocked, but slowly realized that I'd do the exact same thing. Cars depreciate, clothes go out of style, stocks fluctuate, but not having to pay loan agencies every month? That's a gift that keeps on giving.

Press Release Supplement

As part of my new editorial gig over at Nature Cooking, I've had sit-downs with all the major factions in the company, including the fine folks over at Nature Protocols. They were kind enough to suggest a theme for our first issue; apparently, that's chemistry cookies!
Credit: Nature Protocols, via "The Twitter"
In an attempt to please my new colleagues, I scoured the Electrical Highway for at least 5 minutes, until I found these critical lab instruments:
Scientific Cookie Cutters | Credit:
Oddly, the strychnine and maitotoxin shapes were on back order....c'est la vie.

Sunday, April 1, 2012

"And Let the Power of Chemistry Do the Work"

I love to listen to NPR on Sunday mornings. They usually recap all the great shows, from Wait, Wait, Don't Tell Me! to Says You. But, I reserve a special place in my heart for Car Talk, the hilarious auto advice show produced by two Boston natives, who dub themselves "Click and Clack."

If this were my car, I wouldn't pour acid on it!
1957 Ford Thunderbird
This morning, a caller wanted advice on a "body problem" with his car. He claimed to have driven by a construction site, and had had concrete inadvertently splashed on the door and window of the passenger's side. The show hosts cracked a few jokes, then mentioned that he could probably scrape the concrete off the window simply using a straight-edge razor blade.

But the door frame was another matter - how do you remove concrete from a painted plastic panel? One of the hosts suggested a simple rubber mallet, but the other mentioned muriatic acid (HCl, or hydrochloric acid). He posited that the acid would seep in and dissolve the concrete, while leaving the underlying paint relatively untouched. The title of this post (see above) summed up his final comments to the caller.

Of course, you might not want to pour HCl over your hood, or the undercarriage...I'm sure mufflers, battery terminals, and engine blocks don't hold up too well to this home remedy!

Press Release

(08:00, USA; 13:00, London GMT, For Immediate Release)*
 'Just Like Cooking' to Merge with Nature Publishing Group; New Journal 'Nature Cooking'

Just Like Cooking, a somewhat relevant chemistry blog based in the United States, has agreed in principal to merge with Nature Publishing Group (NPG), London. The union will result in a new publication - Nature Cooking - set to premiere in 2013 with blogger See Arr Oh as Editor.

Said Nature Chemistry Chief Editor, Stuart Cantrill: "We were thinking about ways to grow the brand beyond simple chemistry and biology, and hit upon this idea whilst eating LN2 ice cream at Chin Chin Laboratorists. See Arr Oh brings a wealth of kitchen-based knowledge, and we'll try for a real 'molecular gastronomy' flavour with this journal." Added Associate Editor Neil Withers: "Quite so."

Editorial staff will be selected from the finest food scientists and celebrity chefs (P├ępin, Lagasse, and Morimoto have already signed on), and each issue will feature a fold-out pictorial of the Editorial staff dining at fine Michelin restaurants. Initial issues will explore the finer intricacies of British cuisine, including GC headspace analysis of haggis, density checks for Cornish pasty manufacture, and isolation of potent anti-cancer molecules from Christmas puddings.

Potential Nature Cooking dress code
Reaction around the blogosphere has been decidedly mixed. C&EN Associate Editor Carmen Drahl fought back tears, saying "We were about to rename Newscripts to Foodscripts, just to get See Arr Oh to stay." Bloggers Paul Docherty and B.R.S.M. both applauded the move, while Chemjobber lamented the loss: "I'm not happy, as this reduces chemical employment stateside, but if he sends me back some jammie dodgers and a Doctor Who poster, we'll call it even."

*Please see here for more information.