WWWTP? Math Non-profit Edition

Saw this "promoted Tweet" go by on the Twitterz earlier this evening.
But something just didn't add up.

Can you spot the problem?

WWWTP? Slate "slate" Edition

A slate on Slate, a frustrated man next to a frustrated organic structure. The title?
"Teaching the Teachers."

Judging by his chemical acumen - yes, this man needs teaching. Desperately.

 How did he manage to make the western 1,4 diene without it slipping into conjugation?
Inquiring minds want to know.

WWWTP? BBC's Sherlock Edition

Chemical degradation by microscope? Incorrectly-scrawled structures? Wikipedia analyses?
Looks like Scotland Yard should send their consulting detective back to University.

I'm referring, of course, to Sherlock, the BBC reboot that re-imagines Detective Sherlock Holmes and his partner Dr. John H. Watson as modern* Londoners, with text messages and nicotine patches in place of telegrams and pipes. Quick reminder: the Sherlock of Sir Arthur Conan Doyle's original books represents the first fictional character ever recognized by the Royal Society of Chemistry for contributions to science.

Sherlock Holmes hacks into a secret British government database and finds...pyridine and phenol!
Credit: Benedict Cumberbatch and BBC-One

In "The Hounds of Baskerville," Holmes and Watson investigate claims of a giant, red-eyed monster lurking outside - wait for it - a secret military research laboratory called Baskerville. Naturally, the dynamic duo break into the lab under false pretenses, questioning a scientist accused of genetically re-engineering a pet bunny to glow green.**

They later return to Baskerville with a hypothesis: a psychoactive drug, perhaps hidden in an innocuous foodstuff. Holmes sets to work using the analytical instrument of choice for modern chemists - the light microscope. Using nothing more than a pipette and glass window that would have made Bob Woodward proud, Sherlock performs some crude chemical degradation studies:

Who needs NMR, kinetic studies, or a mass spectrometer? I have a mallet and a watch-glass.
Credit: BBC-One

(I'm guessing Sherlock wrote "D-Deuterium?" at the top left to remind himself that the evil research agency might have tried improving their mind-control drug's physicochemical properties : )

The silly Hollywood chemistry builds to a peak when Dr. Watson timidly investigates a scary chemical structure on the lab wall. Don't blink; it's only on-screen for about a second:

"Vancomycin" - Close enough for television?
Source: BBC-One

Well, at least the creators got something right - vancomycin certainly ranks as a "chemical weapon," but it's for killing marauding bacteria, not innocent townsfolk. That chlorocyclohexane on the right *should* be fully aromatic, and I'm sure if I had a higher-res image, I'd start to spot some more structural snafus.

I won't spoil any more of the show, but there's a few other chemical flights of fancy, such as Sherlock analyzing multiple components of floor wax using nothing more than some colored test tubes and his nose. Readers, cue up your online streaming service of choice, and have a look at episode 2.2 - let me know if I've missed more molecular mishaps.

--

* Spoiler - the goofy hat remains. Not a bad look, if you ask me.

**The show does mention that the green fluorescent protein was isolated from a jellyfish, which might be the most accurate science in the entire episode.

WWWTP? Cover Art Conformations

Like everyone else in the chemblogosphere, I spent a fair amount of time mulling over what the new Burke Science paper holds in store for synthetic chemistry. Did anyone check out the cover art?

Images, from top R, clockwise: Heathcock et.al., JACS 1995;
Burke et.al., Science Supporting Information; Chris Brown Photography

I've stared at that picture a looong time. Funny - the Lego blocks seem intended to symbolize how Burke's new system renders synthesis highly modular...perhaps that it's even child's play. 

The asterisk in each line drawing (at right) represents where the artist holds the secodaphnane core. The entire structure, as pictured, is "flipped" such that it the two syn methyl groups (red and green in Burke's representation) should be touching the table. That conformation gives me twitches; nothing's quite where it should be in 3D space! I almost wonder if it's not hooked up quite right...

Sometimes, molecules make for capricious photo subjects. But I can't grok the way that one looks. Anyone else agree?

Friday Fun: WWWTP? Linkin Park Edition

Through the wonders of the Internet, I've found this still image from the 2003 Linkin Park video for "Numb":

In the video, a young, disaffected student dreams of traveling to far-flung cities to practice her true talent - sculptural drawing. However, it seems an evil chemistry professor stands in her way.

But look behind the (hilariously stereotyped) man with the chalkboard pointer. NaK...as an alloy, perhaps? And how come there's a subscript number before the nitrous acid?

If that were my science teacher, I'd feel "numbed" by his complete lack of chemistry education.

Happy Friday,
See Arr Oh

WWWTP - Lab Signs Edition

From the Sept 2014 issue of Wired magazine:

I understand that magazines require flashy, highly-posed photographs to move copy.
That said, did no one in the Editor's office notice all the warnings on that hood sash?
They read:

"Wear proper PPE (Goggles, Gloves, Protective Clothing)"

"Always properly label your chemicals, including your initials. Any unknowns will be disposed of as Hazardous Waste"

"NO STORAGE"

As far as I can tell, the researcher pictured is in violation of all three signs. Ye Gods.

WWWTP? SciAm Epigenetics Edition

From the August 2014 issue of Scientific American:

This illustration hurts on a few levels. "Methyl" and "Acetyl" are functional groups - common clusters of atoms that appear in larger molecules - not themselves chemicals, per se. If the methyl were actually represented by this red ball, it wouldn't be quite so large (it's only four atoms), nor would it be attached at the outside of the sugar backbone (it's on the nucleobases themselves).

Did no one see last year's Discover infographic? At least SciAm's gets the helix right!

Readers - Anyone know who fact-checks scientific illustrations?

Friday Fun - WWWTP? NASA Secret Food Edition

Pretty sure this counts as an epic Google Ads failure...

Happy Friday,
See Arr Oh

WWWTP? Travel Edition

JLC hit the road a few weeks back, and collected a bit of chemical mayhem along the way!

First, a follow-on to a strange beauty products ad used by Kiehl's. First noticed by ChemBark and Stu Cantrill, I've now managed to find the full structure in (photonegative?) a completely different airport:

I'm willing to take bets on what readers think Kiehl's might be trying to draw; I don't have access to SciFinder until tomorrow morning. First blush? Looks like a strange, mangled version of digoxigenin, which I certainly wouldn't want in my face creams!

Second, a comparison of two toothpastes: one manufactured in the ol' US of A, and the other in Thailand. Same brand. Notice anything different?

Different fluoride sources! I hadn't realized that the FDA allows MFP, or even stannous fluoride, in place of sodium fluoride in toothpaste. Huh.

WWWTP? Dallas ACS Edition

Update: 3/17 - More photos from the #ACSDallas informant clearly show the mangled chemistry on both the Exposition banner and some promotional backings from the Chemglass booth. Though I understand what my commenters have remarked upon as "artistic license," I cannot believe that ACS supports glaringly wrong structures adorning their conference walls. 

Standards matter.

Exposition Hall Arch

Chemglass booth

From a contact inside the 2014 ACS Spring Meeting comes this picture, purportedly from the archway leading into the Exposition Hall.

Now, before I start jumping into lectures about Texas* Carbons, non-planar aromatics, and the like, could someone out there corroborate?

Once a few comments confirm or deny, I'll commence gently scolding.

*Get it? 

WWWTP? C'mon, TIME Magazine!

Update, 18:00 GMT - TIME has removed the stock photo,  fixed the strange "Period Table" language, and appended a correction. Kudos to the editorial staff for fast turnaround.

You can't go anywhere on the Internet today without hearing the clamor surrounding newly-confirmed element 115. Fantastic achievement, and another stepping stone towards the long-predicted "island of stability" - super-heavy atoms rumored to have longer lifetimes and higher stability (somewhere north of 118).

But the reporting surrounding the feat? A little less excellent.

Take, for example, this snippet from TIME's Science & Space desk. It hits all the high points, culling quotes from Lund's press release and explaining in plain English how the element came to be. But there's two glaring errors in the first inch of column!

Source: Time.com

1. Where on Earth did that stock photo come from? And who vetted it? First, no one uses the term "Joliotium" for Element 105 anymore; that's been Dubnium since 1997. Even when Joliotium was in play, no one abbreviated it as "Ji" (they used Jl). And Rutherfordium (Rf) isn't 106, but 104. 106 honors Glenn Seaborg, and shortens to Sg.

2. I've never heard the Periodic Table called the "Period Table" before. Are we describing atoms and elements, or 18th-century furniture?

C'mon, TIME, you can do better than this!

WWWTP? "Tristillation?" Not So Fast, Zarco

A goofy, over-the-top marketing campaign for Zarco* tequila made its Twitter rounds yesterday (thanks, David Perry, ChemBark, and Chemjobber!).

Here's the company's video, titled "Tristillation (TM) Explained." I can't succinctly explain all the goofy pseudo-science in one fell swoop, so I'll just go second by second.

0:01 - Welcome to Zarco! Why, oh why, does everyone believe labs need a blinding hospital-white color scheme?
0:03 - Do you usually use a light microscope to examine molecules? I certainly don't.
0:04 - That retort in the background is boiling away, but there's NO FLAME underneath it (?!?)
0:06 - When's the last time you used a separatory funnel to isolate your distillate?

0:11 - Laymen's terms - Dear Zarco: Distillation doesn't work like that! The crude fermentation isn't sitting there in some sort of "pre-alcohol" waiting for you to add heat. When you distill, you're purifying the ethyl alcohol (their 'C-two-H-five-Oh-H') away from the water.

Ye Gods.

0:17 - A third undiscovered 'element' - this part is so inane I forgot to laugh. Short answer: no.
0:22 - Chemetron Medical products collection jar in the background. That's a plastic autoclave bottle; I'd never use it for this.

There's a few other videos save on their YouTube portal, Highlights include near-complete lack of gloves, goggles, or other safety equipment, and (chuckle) a background reflux condenser, which you'd actually use to distill something, sitting abandoned on a clamp.

I get the kitschy, comedic sci-fi vibe Zarco was going for, but they'd better hope their target audience isn't science literate. I can't get past the stupid long enough to buy a bottle.

*Does it bother anyone else that "Zarco" sounds like Darco, the fine activated carbon powder we actually DO use in lab? (to remove colors from solutions)

Hydrogen: A Metal?

Had a bit of fun this morning playing with Scientific American's new interactive Periodic Table.

Most of the entries were spot-on, and the link-backs to Nature Chemistry's IYE series (now free!) certainly help a lot. Just one small quibble:

Doesn't that say "alkali metal?" Although I appreciate that might be true at incredibly high pressures (thanks, Dr. Eisen, for link), what about everyday, ordinary hydrogen gas?

Protons? Sure, they're sort of the classic metal-though-not-a-metal. But, to be fair, you can make lots of things behave like metals (see: O, Br, I, C, Si...) that normally wouldn't.

I'd love to hear some spirited debate in the comments, and appreciate any Sci Am editorial responses.

Update: Stu Cantrill sends over this Nature News article covering Eremets' and Troyan's work.

Neil Withers jumps in with a contradictory example, also from Nature.

WWWTP? Epigenetics Edition

Dan Hurley's piece in Discover's May 2013 issue really fascinated me. Covering the mouse research of Profs. Meany and Szyf, Hurley explained how tragic events in ancestral lifetimes are passed down to offspring via DNA methylation, altering gene expression for generations.

As my chemist's eyes flitted across the page, I smiled at some familiar friends on p. 51 - line structures of nucleotide base cytosine. Just one* a few small problem(s)...did you catch them???

Source: Discover 5.2013

****


See that nitrogen at the bottom? In the language of my sophomore organic professor, it's "very unhappy" that way. Nitrogen usually gets three bonds and a lone pair of electrons; I won't over-critique the missing dots, but there needs to be one of three things on that structure:

1. A generic R-group (meaning a new carbon chain)

2. A proton (indicating the free cytosine base)

3. A "minus" sign (indicating an anion)

Kudos to the graphic artist, though, who actually used standard chemical notation here. Many general science mags would have just used a colored-in hexagon.

*Update, 6/17/13 - As commenters have piled on, we note the empty valences on the two aromatic carbons (carbanions?), as well as questions over whether a methyl group counts as a "compound."

WWWTP? Operatic Chemistry in the Boston Globe

Has anyone seen the fantastic writeup by Carolyn Johnson in the Boston Globe today?

Johnson covers the J. Chem. Ed. recently penned by Prof. João Paulo André, of the Universidade de Minho to celebrate the storied use of poisons in opera. I hadn't realized, honestly, that this rich history involved poisons from such a wide variety of plants, minerals, and animals, or that specific references to each substance can be found in the libretti. Fascinating!

Unfortunately, the graphic that accompanies the story takes a few chemical liberties, which I've circled:

(Update 4/7/13 - I should point out that more structures are right than wrong here, which a commenter points out is more than you usually see in mainstream media. Kudos to the BG for covering the article the way they have)

I've written a short note to the author, reprinted below, and I will post any response I receive.

Dear Carolyn:

Good afternoon! My name is See Arr Oh (a pseudonym), and I blog at Just Like Cooking, a chemistry blog aimed at general-interest audiences.

http://justlikecooking.blogspot.com

I noticed your article in today's Globe, and I want to applaud you for your outreach. The article is well-written, and the science seems solid.

http://www.bostonglobe.com/ideas/2013/04/06/treasury-opera-poisonings/gKPw3zoiVNx7mZeRK1p0KL/story.html

However, the image that accompanies your article includes several inaccurate structures for the discussed poisons. For example, the structures of mannitol don't show explicit stereochemistry (3D structure); these might well be glucose drawn this way. 

Scheele's Green is actually a copper complex; trimethylarsine is the poisonous gas that evolves from the dye. Arsenic trioxide and mercuric sulfide aren't actually monomeric, as drawn, but adopt several different crystal forms involving multiple As and Hg atoms, respectively.

Finally, the neurotoxin shown in the "snake venom" box is not actually venom, rather, it's anatoxin-a, from blue-green algae. 

Please consider changes to the illustration. If you need anything further, don't hesitate to contact me at seearroh_AT_gmail.com

Sincerely,

See Arr Oh

WWWTP? "Third-Party" Edition

Source: Kishida Chemical

A blog buddy sent along this puckish reminder of customer perception in the crowded chemical sourcing market. Seems Oakwood Chemical, a U.S.-based supplier, recently partnered with Kishida, a Japanese fine chemicals company.

Kishida specializes in med-chem building blocks, but seems to have a problem with their structure-drawing program (right)...where did all the hydrogens go? Don't think it's just on the website - the catalog goes 50/50 for abnormal heteroatom saturation.*

Readers, am I missing something (other than those "H" atoms)? Is this part of some common fragment representation, or is it just lazy drawing?

Comments welcome.

*For a good time, check cyclobutylhydrazine dihydrochloride (PK0-13441), which seems to be missing a record five (5) hydrogens! Can anyone top that?

WWWTP? MedChemComm Edition

E tu, Pfizer? Sheesh.
Modified from MedChemComm, 2013

Blogosphere buds Chemjobber and Organometallica took turns finding "eccentricities" in a recent MedChemComm cartoon abstract (right). OK, I get it, a hilarious cartoon of the liver as a ravenous monster, chewing up your precious drug leads...

But look closer: What on Earth is up with that structure? As CJ / OM pointed out, we've got chain breaks, Texas carbons, neutral four-coordinate amines, floating atoms, the works!

Now, this review looks to have been scribed by some heavy hitters - two Pfizer PK folks, and two medicinal chemists. Worse still? Both med chemists are from top-flight groups (Nicolaou and Corey), and I've profiled one of 'em over at my place.

So, caveat auctor - If you're listed as part of a multi-author review, always check it over* before someone else submits it! "Only YOU Can Prevent Unwanted Blogosphere Satire."

*And chemists, don't let non-chemists draw molecules for you, especially if they end up in scientific papers!

Friday Fun: WWWTP? CAS Stock Photo

OK, Chemical Abstracts Service, here's where I get stabby...

c. 2012, Chemical Abstracts Service

I clipped this well-meaning low-res stock photo out of a SciFinder help page. First off, what's with the incomplete PPE? Don't you suppose this enthusiastic young lady analyzes (urine?) whilst wearing gloves? She looks like she's selling glassware, BTW...I've never shown off my products quite like that.

And who are the MBA-types posing on the periphery? If they're admiring the benchwork, they should have goggles at the least! Methinks this may have been photoshopped from a med school recruiting website, perhaps?

CAS, you're part of the largest scientific society on the planet. How's about an accurate picture?

Thanks,
SAO

WWWTP? "Unjunked" Candy

While shopping in Target (Tar-ZHAY) earlier tonight, some food in eye-popping purple & black wrappers caught my eye. UNREAL markets so-called "unjunked" candy, which contains "no corn syrup, GMOs, or artificial flavors." Naturally, I bought one ($0.89, not too shabby) and I can report that it tasted just like the intended Snickers bar facsimile.

But here's the rub: a list on the back (see picture) proudly displays corporate commitment to "chemical-free" - by transforming a bunch of scientific adjectives into pseudo-plural nouns. What, may I ask, is a single "hydrogenated?" Would you say "No Crafts" if your fridge were devoid of craft beer?

The 'organic' ingredients they've constructed the candy from include:

Milk chocolate (cane sugar, chocolate, cocoa butter, milk powder, organic blue agave inulin, skim milk, soy lecithin, vanilla extract), caramel (tapioca syrup, cane sugar, fructan (prebiotic fiber), organic palm kernel oil, whey, milk protein concentrate, organic cream, vanilla extract, salt, soy lecithin), peanuts, tapioca syrup, cane sugar, organic palm kernel oil, skim milk, peanut flour, salt, hydrolyzed milk protein, evaporated cane syrup, soy lecithin

Inulin? Fructan? New to me. Turns out both are fructose-based dietary fibers, which in this context replace some of the fats and sugars found in similar candy bars. However, these soluble fibers often aren't well-tolerated intestinally, similar to known gut troublemakers sorbitol, maltitol, or lactose. My current stomach ache indicates I might be susceptible; please think on my sacrifice when the Pulitzers go out next year...

P.S. I'm no marketing whiz, but "Unreal?" If unable = not able, and unclear = not clear, doesn't 'unreal' = not real? For a candy bar made without "artificial" ingredients? I think the intended sarcasm might be lost on the way to the checkout.

Holiday Chemophobia: Can't We All Just Get Along?

Know what this is?
Me neither.
Source: LWON

First: A belated 'Happy Holidays' to all those chemists already returned to work.

Second: From the Twitter-verse comes a post from the (normally) fine writers over at Last Word on Nothing. 

Titled "Secret Satans: Chem101" (get it?!), the post fits in with a holiday series at LWoN. I'll let the editors explain:

"We are choosing our most daunting subjects and writing about why they scare us."

As a reader, I expected to hear some gripes and groans about the unfairness of chem grading, those interminable labs, perhaps pronunciation of long IUPAC-mandated noms-du-chem. But instead, right in the introduction, I spot this: "cold sweats," "freaked out," "deep dread," "chemophobia."

Yes, readers, this is a science blog.

I can hear the commentary now: "Calm down, SAO, this is a snarky, fun, satirical holiday piece. Right?" Well, no. "Hate" and "hatred" both appear, as does "loathe," "disaster," "evil plot," and "screwed up." Cue up the sardonic comparisons, like "cryptic as Arabic" or "esoteric knowledge, secret formulas kept by early metallurgists and alchemists." One of the authors speaks of a safety mishap involving [sic] "bromide gas," which recounts how her inadvertent calculation error caused a building evacuation. Fun stuff!

And then there's the graphics. How many times must we plead - Don't let art directors draw your molecules! I don't know exactly what these "animal tracks in the snow" represent, but if the piece aims to vilify simple chemical knowledge, it certainly does that (P.S. I know they're from Shutterstock, but that doesn't excuse their inclusion).

So why am I so critical? Shouldn't we just give LWoN a pass, have a chuckle at a favorite scientific punching-bag, and move on? 

No. Blogs, and especially science blogs, should try to take the high road. We're the voice of reason, the nagging suspicion, the social conscience of the wild, woolly online world. We should aim to advise, not attack, and question where others condemn. That cute anecdote at the end? Doesn't make up for the 709 words you just used to drag chemistry through the muck.

You can do better.