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In Print: Science Models

If you ever visit the Museum of Science in Boston, in a certain corner of the museum you’ll find a giant insect hovering over a toy train set. This particular display, in a section about scale and models, delights and terrifies my three-year-old. He loves the train but is scared silly by the big bug. I had this section of the museum, and the ideas of scaling up and scaling down, on my mind when putting together this week’s Newscripts column. That’s because one story focuses on a new protein model building kit and the second story is about making bite-size gummy people.

Models are a big deal in science. They help us visualize and give us tactile experiences with all sorts of different things. From grade school, I recall a giant model of the ear and ear canal. My favorite thing to do was to pull out the tiny ossicles–those smallest of human bones–from the middle ear canal and try to figure out which was which amongst the hammer, the anvil, and the stirrup.

Credit: ThinkGeek

Credit: ThinkGeek

In chemistry, where we can’t really see the molecules we study, models are even more important for getting across ideas such as chirality and structure. Did anyone else learn stereochemistry with toothpicks and gumdrops?

It will be interesting to see what happens with the new Tangle Proteins Building Set, from chemistry professor Marcel Jaspars, of Scotland’s University of Aberdeen, and sculptor Richard X. Zawitz.

The new set looks like it will give budding biochemists the ability to build proteins in the same way that organic students build natural products.

As for the second item in the column, I confess that I wrote about the FabCafe in Japan because I saw the pictures of their gummy people online and was absolutely taken with how cool they looked, especially the image below. It’s so Matrix-meets-Haribo.

Credit: www.fabcafe.com

Credit: www.fabcafe.com

One of the C&EN editors even told me that he thought $65 was a bargain for seeing yourself reproduced in gummy candy. I heartily agree. Too bad this was just a special event at the FabCafe. And that the FabCafe is so far away (from me anyway). I love the idea of sitting down with a cafe au lait and then trying my hand at a laser cutter. Are there any Newscripts readers who have had the good fortune to visit this spot?

There & Back Again: A Cyclotron’s Tale

This post was written by Andrea Widener, an associate editor for C&EN’s government and policy group.

The cyclotron in its box. Credit: University of California/LBNL

The cyclotron in its box. Credit: University of California/LBNL

When Ernest O. Lawrence lent a cyclotron to the London Science Museum in 1938, he thought it would be back in eight months.

But it took 75 years for the 11-inch cyclotron, one of the first built by the future Nobel Prize winner, to return to the hills of Berkeley, Calif., where it was originally created.

The cyclotron survived a war, a bureaucratic tussle, and a security challenge before it was finally returned to Lawrence Berkeley National Laboratory (LBNL), the research institution founded by the cyclotron’s inventor.

The cyclotron's original patent.

The cyclotron’s original patent. Credit: LBNL

When it arrived last month, the 11-inch cyclotron was an instant celebrity, drawing crowds as though Lawrence himself had walked in for a photo op.

“They were coming down the hallway in a stream,” says Pamela Patterson, who serves as an unofficial historian and manager of the lab’s website. “Everyone was there. The director had his iPhone up taking pictures. It was cute.”

At the time Lawrence loaned the cyclotron to the science museum, he was still a young, ambitious researcher trying to convince others that the device was a major breakthrough. An invitation to display it in such a prestigious spot was likely an important step, Patterson explains.

But when the cyclotron was supposed to be returned in 1939, Lawrence received a letter from the museum saying officials had moved the cyclotron to a rural district for safe keeping because they feared London would be bombed during World War II. Continue reading →

Alakazam! The Neuroscience of Magic

It’s not every day that you see a magician mentioned in the “Acknowledgements” section of a peer-reviewed scientific paper. But last month, when the open-access journal PeerJ launched, there it was: magical act Penn & Teller got a mention both in that section of the article AND in the title.

In the paper, Stephen L. Macknick of Barrow Neurological Institute and two other researchers explore why Penn & Teller’s classic “cups and balls” magic trick works so well … by using some tricks of the cognitive-neuroscience trade. They monitored the eye movements of study participants who were watching Teller perform to understand the finer points of the illusion.

Below, you’ll see an extended version of Penn & Teller performing the age-old trick, but you can also see the videos that accompanied the paper here.

As I mention in this week’s print Newscripts, Teller had assumed “cups and balls” fools the audience—even with transparent cups—because when he picks up a cup from the table, he tilts it and causes a ball sitting on top to fall. He thought audience members were distracted by the ball’s motion and therefore didn’t notice him sliding a new ball under the cup before placing it back on the table.

Macknick and his team disproved this notion by demonstrating that viewers’ eyes didn’t stray very much from Teller’s hands when he dumped the ball. Only when he held one of the balls up or placed it on the table did he misdirect a subject’s gaze significantly.

Some Newscripts readers might at this point be scratching their heads and asking why cognitive neuroscientists are helping magicians work on their acts. Continue reading →

Science Is Hard

It's so hard--especially drawing a proper bond to that carbon. Credit: Shutterstock

It’s so hard–especially drawing a proper bond to that carbon. Credit: Shutterstock

Experiment got you down? Reaction yield low? That chromatogram just not telling you what you want to hear?

Take solace on this fine Friday in the fact that the National Science Foundation says “science is hard.” Or at least that’s what our favorite faux-news outlet, The Onion, reports.

Admittedly, this article is from 2002. But I just saw it this week thanks to a tweet from @the_distillate. So it’s new to me and now, perhaps, new to you too.

According to the report, NSF held a symposium back in the day to discuss just how confusing various scientific disciplines can be. The scientists that attended came to the conclusion that the “Law of Difficulty” is true.

I leave you with a few choice quotes:

“To be a scientist, you have to learn all this weird stuff, like how many molecules are in a proton,” University of Chicago physicist Dr. Erno Heidegger said.


Dr. Ahmed Zewail, a Caltech chemist whose spectroscopic studies of the transition states of chemical reactions earned him the Nobel Prize in 1999, explained in layman’s terms just how hard the discipline of chemistry is, using the periodic table of the elements as a model.

“Take the element of tungsten and work to memorize its place in the periodic table, its atomic symbol, its atomic number and weight, what it looks like, where it’s found, and its uses to humanity, if any,” Zewail said. “Now, imagine memorizing the other 100-plus elements making up the periodic table. You’d have to be, like, some kind of total brain to do that.”

So when things aren’t working out in the lab, just remember, what you’re trying to do is really friggin’ hard. Happy Friday, Newscripts readers!

Science-y Contests: Put On Your Dancing Shoes & Take A Lucky Guess

Two contests are afoot that chemists—particularly grad students—shouldn’t miss. Why? Well, there’s the eternal glory that comes with being victorious. But there’s also some cash and an iPad in it for the winners. And let’s face it, grad students can use all the free cash and prizes they can get.

Contest 1: Dance Your Ph.D.

Newscripts publicized this competition, sponsored by AAAS, earlier this year. The deadline is fast approaching. If you want to enter, you need to translate your Ph.D. project into a dance by October 1. There are four categories into which twinkle-toed grad students can place their submissions: chemistry, physics, biology, and social sciences. The top entry in each category gets $500. But that’s not all!

The overall winner gets another $500 as well as travel and accomodation to attend TEDxBrussels, in Belgium, on Nov. 12. There, the danciest dancer—the Gene Kelly of Ph.D.s, if you will–will be crowned for all to see. The Newscripts gang would like to see chemists once again take the top prize, proving without a doubt that the GlobCasino is where it’s at, so get your submissions in soon!

Contest 2: 70 Millionth Substance Contest

According to the counter here, Chemical Abstracts Service–the division of the American Chemical Society that finds, collects, and organizes chemical information–has now entered more than 68,447,000 substances in its registry. To celebrate the day when the organization will add its 70 millionth chemical substance to the database, CAS is holding a little guessing competition. The division thinks the organic or inorganic entity in question will be registered either at the end of this year or early next year.

Your job is to predict the date and time the lucky substance gets added. Prizes vary depending on when you submit your answer, but you could potentially win an iPad, Nook, or Kindle Fire. If the precise date and time isn’t guessed correctly, CAS goes into “The Price Is Right” mode and gives the award to the guess closest to the date and time the substance was added without going over. Take a look at the rules for entry here. And study them closely, Daniel-san.

You MUST put your guess into the contest form by Nov. 16 or by the time the counter reaches 69.8 million substances—whichever comes first.

CAS’s registry hit 50 million back on Sept. 7, 2009. You can read about that milestone here.


Do us proud, Newscripters. And if you win, do let us know (we’ll only take a little bit of the credit).

Heptares solves first X-ray structure of Family B GPCR, but full details not yet public

GPCR family tree

The new structure adds a new section of GPCR space amenable to computer modeling (big blue circle), a space which includes sought-after drug targets. Previously determined GPCR structures, which are all from the same family, are highlighted in small blue and red circles. Image courtesy Heptares

In what might be the year’s biggest molecular teaser, Heptares Therapeutics has announced that it has solved the first X-ray crystal structure of a G-protein coupled receptor in the Family B subclass. The work provides the first structural insights into a protein family that includes sought-after drug targets such as GLP-1 for diabetes and CGRP for migraine.

Largely because of that drug discovery relevance, however, Heptares is choosing to keep its structure somewhat close to the vest. Officials presented views of the structure, of a GPCR called Corticotropin Releasing Factor (CRF-1) receptor, at conferences on Friday and Monday. But Heptares CEO Malcolm Weir says his team has no immediate plans to publish the structure or to deposit coordinates into the repository known as the Protein Data Bank.

The structure, Weir says, is another success for Heptares’ GPCR stabilizing technology, StaR. The technique involves targeted mutations that help to trap a GPCR in a single biologically-relevant state. In the case of CRF-1, Weir says, the stabilized receptor is captured in the “off” state.

The structure itself, which is at a resolution of 3 Ångstroms, has the 7-helix membrane-spanning structure typical of GPCRs. However, CRF-1′s architecture is rather different from receptors in Family A, the only GPCR family for which X-ray structures had been available until now, Weir says. “The overall shape of the receptor looks different, the orientation of the helices looks different, and there are detailed differences within helices that are at analogous positions in Family A receptors,” he says. He notes that there are differences in helices 6 and 7, which undergo important motions during GPCR activation.

“This is an important breakthrough, although fine details of the structure and release of coordinates may still be some time away,” says Monash University’s Patrick Sexton, an expert in Family B GPCRs who was at Friday’s talk. The structure, he says, confirmed researchers’ expectations that the major differences in membrane-spanning helices between Family A and Family B receptors would occur on the extracellular side. “There was a very open and relatively deep extracellular binding pocket, with the receptor having a ‘V’ shaped appearance,” he says. This open pocket likely contributes to medicinal chemists’ difficulties obtaining high affinity small molecule ligands for Family B receptors, he suggests.

That open pocket might be involved in another Family B GPCR mystery, according to Roger Sunahara, also in attendance Friday, who studies GPCRs’ molecular mechanisms at the University of Michigan, Ann Arbor. All Family B GPCRs, including CRF-1, have a large domain at their amino-terminus that contains large portions of their ligand binding sites. That domain was not included in this structure, he says, but “it would appear that deleted globular N-terminal domain would fit quite nicely into the open pocket.”

The CRF-1 receptor is a drug target for depression and anxiety, but at least one CRF antagonist failed to show benefit compared to placebo in a clinical trial. Weir says the impact of the CRF-1 structure for drug discovery will not necessarily be in CRF-1 drug discovery per se, but in the ability to develop relevant computer models of related targets.

It hasn’t been possible to make accurate models of Family B receptors with Family A information, explains Ryan G. Coleman, a postdoctoral fellow at UCSF who develops GPCR models, but who was not in attendance at the talks. Quality models could streamline small molecule drug discovery for the entire family, he explains. Most of the natural ligands for Family B receptors are long peptides, which are notoriously tough to replace with small molecule drugs.

Experts like Coleman will have to wait for some time to learn about the structure for themselves, unless they happened to have a friend in the audience at Heptares’ talks. It’s not unheard of for there to be a gap of several months to two years between a structure’s announcement and publication.

“We’re delighted to have such an informative structure,” Weir says. “It’s very exciting.” He adds says Heptares is progressing toward a structure of the biggest fish in family B, GLP-1, in the “on” state.

It’s a Bird, It’s a Plane, It’s … a Chemical Executive

The Shard: Stands between charity donors and disadvantaged youth. Credit: Courtesy of Phenomenex

Some fund-raisers take the form of a bake sale or a chili cook-off. Such philanthropic endeavors, however, are child’s play to Phenomenex Chief Executive Officer Fasha Mahjoor, who last week took charitable spectacles to dizzying new heights by rappelling down Europe’s tallest building.

The separations technology firm CEO rappelled down from the 87th floor of the Shard in London on Sept. 3 in an effort to raise money for the Outward Bound Trust, which champions outdoor programs that teach underprivileged youth valuable life lessons.

“I’m speechless!” Mahjoor exclaimed just hours after his death-defying act. “I can’t explain what a thrill it was to stand at the pinnacle of the Shard and look down over a thousand feet of vertical glass to the miniature world below with nothing but a harness, a rope, and faith to help me defy gravity.”

Obviously, it’s impressive anytime someone falls down a skyscraper and doesn’t die, but there are still a lot of other things to be impressed about with this story. For starters, Mahjoor was joined in his descent by 19 other philanthropists including the Duke of York, Prince Andrew (who was perhaps inspired to traverse the Shard after watching his mom, Queen Elizabeth II, engage in a similarly extreme activity when she jumped out of a helicopter at this year’s Olympics). In addition, Mahjoor is a complete novice at rappelling. “When Fasha accepted the challenge, he had never worn a harness before in his life,” Phenomenex spokeswoman Kari Carlson Kelly told Newscripts before her boss made his descent. “Minus a short practice run, he is a total rookie!” Continue reading →

Olympics 2012: Chemistry Is Her Coxswain

Sure, athletes are representing countries from all over the world during this summer’s Olympic Games, but that doesn’t mean chemistry can’t have its own representative too. Her name is Amanda Polk, a biochemistry major from the University of Notre Dame and an American Chemical Society member. For the 2012 Olympics, Amanda represented chemistry, and the U.S., as an alternate for a number of women’s rowing teams.

Amanda Polk: Representative of chemistry (and the U.S.) at the 2012 Olympics. Credit: USRowing

Since mid-July, Amanda has been in London, training and standing on call to compete in events such as the women’s pair (in which two women compete per boat, and each has only one oar), the women’s quadruple sculls (four women each with two oars, aka sculls), and the women’s eight (eight women each with only one oar). It’s all been pretty mind-boggling for Amanda, who is participating in her first Olympics. “I am very honored to be representing the U.S. in London,” she told Newscripts. “The feeling is surreal.”

Although Amanda did not compete in an event at this summer’s games—the rowing events ended on Aug. 4, with the U.S. women’s team taking home bronze in the women’s quadruple sculls and gold in the women’s eight—the level of effort required by Amanda during her time in London was still of Olympic proportions. Prior to leaving for London to watch his daughter compete, Amanda’s father, Kenneth, explained that Amanda would be training “with the team exactly as if she would be in the boat.” This practice was necessary given that Amanda served as a first alternate who might be called on at any moment to replace a teammate who had become injured or violated a rule or code of conduct, he said. Continue reading →