Chemistry Photo-Op

Carrying high-resolution cameras in our collective pockets has spawned a new age of lab photography. Witness Chemistry in Pictures, the official American Chemical Society Tumblr site. There you’ll find mazelike porphyrin crystals (below), glowing TLC plates, and ultralight aerogels poised atop fragile flowers.

Credit: Anna Slater | Chemical & Engineering News Tumblr

Want to dive even deeper into the laboratory? Kristof Hegedus has you covered: his aptly-named site Photos from an Organic Chemistry Laboratory brings forth reaction gifs, failed black tars, and icy fractals of crystalline intermediates. Perhaps your interests lean towards chemical education – the picture blog for you is Picture It… Based out of the University of Bristol, and freely available for re-use through Creative Commons, the authors overlay well-posed plants, foods, and common substances alongside their constituent molecules. 

Finally, for the effete artiste, we present Beautiful Chemistry. A joint venture of Tsinghua University Press and the University of Science and Technology in China, this site has it all: Priestly’s apparatus, HD videos of crystal growth, and animated DNA nanostructures. A true treat for the chemically and artistically inclined.

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, Cartoons!

Anyone out there watch Adventure Time? The animated show, currently airing on Cartoon Network, follows the adventures of a boy and his talking dog in the magical Land of Ooo.

(Bear with me, I've only seen this episode)

Source: Cartoon Network

While flipping through the channels, I happened to land on a rather new episode, called "Goliad." It involves one of the main characters - a synthetic biologist? - spawning a giant pink Sphinx from a mixture of DNA, 'chemicals,' chalk dust, and an old tooth. But that's not what caught my eye: check out the prop chalkboards set up in the "lab" - those are resonance structures on there!

(Ironically, though the characters understand electron movement for the carbonate anion, and can apparently clone life forms, the resonance structure for benzene escapes them. But, hey, this adventure occurs in a castle shaped like a wedding cake, so...caveat lector)

Everything's bigger in Texas.

One tiny problem: this chemistry know-how seems to disappear between takes. Here's another clip from the same episode, where the previously-correct carbonate has mysteriously grown another bond.

Most kids watching this will just gloss over it, assuming some mad-scientist gobbledygook. But, those of us in the WWWTP camp just can't help ourselves.

Happy Friday! Go watch some (scientifically accurate) cartoons!

Arsenic Life Wrap-Up: The Good, the 'Not-So-Good'

"Arsenic Life," a hot-button issue for much of the past year, reemerged this week with two new papers, one propitious, and one, well...not so much.

GFAJ-1 bacteria
Source: nasa.gov

As covered by Curious Wavef(n), the first paper related Prof. Rosie Redfield's well-documented efforts coaxing the GFAJ-1 strain to flourish in arsenic-rich media, which, if successful, would imply arsenate linkages in the bacterial DNA. Redfield bursts the bubble nicely, utilizing multiple tools (LC-MS, cell growth assays, gels) to cast doubt on the earlier study, even mentioning that most of the detected arsenate could be washed away with distilled water.

Well, if timing is everything, then the second #arseniclife publication really missed the boat. Last week, a commentary appeared in the open-access online journal Biomolecules, bearing the epic title From Phosphorus to Arsenic: Changing the Classic Paradigm for the Structure of Biomolecules. Heavy stuff!

This summary takes the opposite tack, casting "Dr. Wolfe-Simon's discovery" as a fighting underdog - viewed skeptically today, but enshrined and glorified by future generations much like Copernicus or Darwin (both name-dropped inside). The prose shakes the reader with thrilling, emphatic statements, lines you might find in a rousing stump speech or an action movie. A few choice selections:

"...Some have died as a result
of these discussions..."
Image Credit: Silver Lining

"It is no surprise that this work has come under what some may consider a brutal attack in the past year; the proposed repercussions almost beg of it."

"...members outside of the scientific community may view the criticisms and other events that have transpired as superfluous, vindictive, and outright scathing." 

"...the implications of [arsenic life] have the potential to shake the foundation of biology as we have known it for centuries."

 "This discovery...would be absolutely groundbreaking to all of science."

You get the point. These excesses, coupled with a few cut-and-paste sources (N.B. Don't include "page-access" dates in references) and a passing remark to Wolfe-Simon's potential scientific martyrdom, complete the commentary. Yesterday, several Twitter denizens, led by the industrious Carmen Drahl, noted a very familiar vibe to this piece. To borrow a phrase from Derek and Leonid, it sounded suspiciously like a "term paper," final reports students submit to wrap up specific college courses.

My feelings, reading Paper #2
Source: Jobbing Scriptwriter

Was it? A very strong maybe. Check out this editorial, culled from the Colorado State University Journal of Undergraduate Research  (p. 16), scribed by the lead author. Bears a rather striking homology to the Biomolecules piece, sources* and all. The second author, currently an undergraduate at Boston University, may have interacted with the CSU authors at a conference, or perhaps on a summer REU.

As corresponding author, Prof. Mark Brown (CSU) would, I'd believe, have final say over the manuscript. Did he check it against the lead author's previous work? The journal's Author Information section mentions that five external reviewers must be named, although "...the Editor will not necessarily approach them."

So, to round up this bizarre publishing escapade, we have undergraduate authors submitting previous work in an open-access, loosely-reviewed, and barely-edited online journal, all with the benediction of a faculty member? Sounds dubious...much like arsenate linkages in DNA.

*Can someone please tell me where to find Ed "Young" at Discover Blogs? : )


Update, 6.8.12 - Commenter Stuart Cantrill (Editor, Nature Chemistry) points out on Twitter that the original piece also misspelled "phosphorous" in the title. Sigh.

In Which You are What You Eat

I love food. Always have – both the process of making food (which may be why I’m a synthetic chemist) and the joy of consuming one’s labors (which lab work definitely doesn’t allow!). Recently, however, modern science blurs the line between the stomach and brain. “You are what you eat” no longer just refers to body weight or proper nutrient intake. We humans are superorganisms, meaning that our intestinal microbiology plays a huge role in our everyday lives. Turns out, where you were born, where you live, what you eat, and where you’ve travelled can all influence the metabolic phenotype (appearance) of the bacteria that inhabit your intestinal tract.

Hey baby, what's your gut microbiome?
Credit: Healthy Perceptions blog

Some microbiologists posit that humans can be grouped, not by race, creed, height, or sex, but by “gut profile.”  A recent multi-institution Nature paper, led by Bork and Ehrlich, disclosed three major enterotypes (gut profiles), based on DNA sequencing (of, well, poop) of 22 people from 4 different countries. The scientists try not to paint too broad a picture with this initial result, but note that gut bacteria influence key genes that regulate aging and body mass index, which may suggest microbial management of a wide variety of diseases.

Your gut bacteria also impact your emotions. WSJ’s Jonah Lehrer reports that yogurt – specifically the kind filled with “good” (probiotic) bacteria – can actually cause marked behavioral effects, at least in mice. Probiotic-fed mice showed fewer symptoms of stress and anxiety, even when placed in new situations. An ideal cure for modern social anxiety, right? Unfortunately, no: other scientists interviewed quickly point out neurological patients’ inability to feel fear or stress causes them to make even worse future decisions in similar situations, since they lack the negative feedback from the prior event.

Mmm, gene regulation!
Credit: eating-in.com

Yogurt aside, your salad may also be helping to regulate your genes. Earlier this week, researchers in China disclosed new methods that can detect short strands of plant-derived RNA present in human bodily fluids. The researchers were especially surprised to find certain microRNAs actually inhibited the removal of LDL (low-density lipoprotein, the so-called “bad cholesterol”) from the bloodstream. Overall, the team found about 40 different microRNAs, from at least five different crops, and expects to find many more. Just more news to chew on, while you ruminate over your afternoon snack.