#ChemMovieCarnival: Chocolate and chemical academia

It's time for the #ChemMovieCarnival, as organized by See Arr Oh (who posted this first day round-up). So far we've seen chemistry featured in Fight Club, Iron Man 2, The Great Escape, The Absent Minded Professor, G.I. Joe, Real Genius, and MacGyver, among others.

Some of the above examples highlight some pretty bad movie science. I thought I'd share a movie clip that was on the other end of the spectrum!

Everyone's familiar with Willy Wonka and the Chocolate Factory--the 1971 musical film starring the immortal Gene Wilder. The film's protagonist is Charlie Bucket, a child from a poor family whose genuine heart leads him to success where several other spoiled/privileged children fail. Early on, we're shown Charlie's education, including the following chemistry demonstration. The clip is a little modified from the original at the end (it was the only one I could find!).



It's a remarkably accurate portrayal of life in chemical academia. After all, all the hallmarks are there:

• Disregard for proper PPE/lab safety.
• Intellectual snobbery/faculty egotism.
• Over-eager undergrads who don't know what they're doing.
• Secrecy and irreproducibility.

Just like life in the lab! (Of course, Pure Imagination is perhaps more apt to describe the pragmatism of many projects).

Carrots, chlorine, and chemophobia

On a recent lunchtime "survey of the literature" (i.e. Facebook break) I noticed that an old classmate posted the following paragraph (it's not new--but I hadn't seen it before):

“DANGER TO YOUR FAMILY!!

From the Department of Life Education:

Baby Carrots:

The following is information from a farmer who grows and packages carrots for IGA, METRO, LOBLAWS, etc.

The small cocktail (baby) carrots you buy in small plastic bags are made using the larger crooked or deformed carrots which are put through a machine which cuts and shapes them into cocktail carrots – most people probably know this already.

What you may not know and should know is the following:

Once the carrots are cut and shaped into cocktail carrots they are dipped in a solution of water and chlorine in order to preserve them (this is the same chlorine used in your pool).

Since they do not have their skin or natural protective covering, they give them a higher dose of chlorine.

You will notice that once you keep these carrots in your refrigerator for a few days, a white covering will form on the carrots. This is the chlorine which resurfaces. At what cost do we put our health at risk to have esthetically pleasing vegetables?

Chlorine is a very well-known carcinogen, which causes Cancer. I thought this was worth passing on. Pass it on to as many people as possible in hopes of informing them where these carrots come from and how they are processed.

I used to buy those baby carrots for vegetable dips. I know that I will never buy them again!!!!”

First, it should be noted that the person who shared the post works in a biomedical profession and probably should know better. Second, this looks like a classic chemophobic recipe: (1) take familiar concept; (2) point out chemical; (3) extol nastiness of chemical, real or imaginary; (4) panic.

It should be pointed out, of course, that the "warning" is alarmist and exaggerated. Most fruits/veggies are rinsed in water containing low-ppm chlorine -- levels comparable to drinking water -- not in a highly-chlorinated solution as implied. Chlorine is an antimicrobial protectant in thse cases. Moreover, the white residue is, obviously to chemists, not chlorine 'resurfacing' (???) but simply dehydrated carrot. And something that needs mention: there's no evidence that chlorine is a carcinogen (see here and here for instance) (You wouldn't want to go on a date with pure chlorine, of course, but not because of a cancer danger).

The chemophobia doesn't surprise me, though, since "chlorine" sounds nasty.

I am surprised, however, by some of the responses on the internet. They're unusually fact-based! In fact, in the first two pages of Google search results for "baby carrots chlorine", only a few support the myth. But let's look at the chemophobic minority first:

The chemophobes

Angela Garrison, a writer at alternative health site The Alternative Daily, gave this warning about the carrots (also posted at RiseEarth) in 2012. She largely parrots the viral bite above, adding some nonsense about baby carrots being ground-up regular carrots (they're sliced, but certainly not ground, and it would be pretty impressive if manufacturers could reconstitute the texture like that from carrot paste). Additionally, the title ("Why Baby Carrots are Killing You") is perhaps more dramatic than warranted. She alleges that the chlorine bath gives them their orange color (and has never apparently heard of carotene). It's worth reading the article (which is characteristically factless); but I have to include this excerpt which does a smashing good job of confusing chlorine with chloroform and delightfully ignores both citation and any discussion of dosage:

As defined by the EPA, Chlorine is a pesticide. Its purpose is to kill living organisms. So it would make sense that when you ingest chlorine, it kills some parts of our body like the healthy bacteria in your gut and intestinal flora for instance. Chlorine is a highly toxic, yellow-green gas most heavily used in chemical agents like household cleaners and can be found in the air near industrial areas especially around paper processing plants. Exposure to Chlorine has been linked to health problems such as sore throat, coughing, eye and skin irritation, rapid breathing, narrowing of the bronchi, wheezing, blue coloring of the skin, accumulation of fluid in the lungs, pain in the lung region, severe eye and skin burns, lung collapse, a type of asthma known as Reactive Airways Dysfunction Syndrome (RADS).

Chlorine is also added to the public water supply. So not only are you drinking it, but you are absorbing it through the largest organ in your body, your skin. In fact, 2/3 of human absorption of chlorine is from inhaling the steam in the form of chloroform and fast absorption through your open pores in the warm shower or bath. The inhalation of chloroform is a suspected cause of asthma and bronchitis, especially in children… which has increased 300% in the last two decades. Other health risks associated with chloroform is cancer, potential reproductive damage, birth defects, dizziness, fatigue, headache, liver and kidney damage. Chloroform is also found in the air and in food, like baby carrots.

While no one is encouraging anyone to go breathe the stuff, that's a bit much.

Another unsuprisingly chemophobic source is Mercola.com (website for prominent snake-oil salesman Joseph Mercola). Mercola starts (in 2009) by insisting that chlorine is a carcinogen (spoiler: it's not), delves into a litany of other nasty roles chlorine and chlorinated byproducts can play, and ends by recommending chlorine-free carrots. Total Health magazine seems to largely echo (almost plagiarize) these claims.

The chemophobia has to have been taken fairly seriously by many--indeed, Bolthouse Farms created an entire website (truthaboutbabycarrots.com) to respond to the claims. But surprisingly, the above three examples were the only two immediate negative results in my two-page Google foray.

The non-chemophobes

Interesting, the majority of responses to the chlorine-carrot allegations are non-chemophobic (and largely come from non-scientists!). Journalist Bart Van Bockstaele at Digital Journal (2008) posts a  response that includes a discussion of the confusion around the 'chlorine' nomenclature whilst dismissing all health concerns and properly pointing out that science hasn't shown chlorine to be carcinogenic anyway. (Note that some of the text is pretty similar to that found on the somewhat odd website World Carrot Museum).

At FarmProgress (2013), editor Jennifer Vincent admonishes those spreading misinformation, pointing out the public health efficacy of chlorinated water and describing how she corrected someone else who was spreading the carrot scare.

Joel Mackey of Z6Mag (2013) gives a somewhat disorganized response, but two items stand out: (1) he contacted the companies and investigated the matter himself; and (2) there's some neat Google trends graphs that show that searches for 'baby carrots chlorine' increased going into 2013.

Lisa Leake of the whole-foods effort 100 Days of Real Food (which sounds like it should be brimming with chemophobia) has a nice, accessible response in which she (1) made a point of looking up the relevant information and not just trusting 3rd party information; and (2) explained some of the layperson chemical misconceptions in the carrot-chlorine scare.

Other, shorter responses include those by Dr. Andrew Weill, Linda Golodner of the Water Quality & Health Council (she points out the health-protective benefits of low levels of chlorine in water!), Megan Loberg of Eat, Pray, Farm (who points out that even 'organic' producers use chemicals to wash carrots), and Consumer Reports, Moms Against Cooties.

And of course, anti-hoax websites such as Snopes and wafflesatnoon dismiss the claims (Snopes is itself a little chemically misleading, implying that neat chlorine is used to treat the carrots).

Overall, the responses are encouragingly NOT chemophobic in general. That's a relief to see, I think: engagement by the non-chemical community is probably more convincing to the general public than engagement by chemists (whether we like it or not).

Analytical chemistry and the dinner table

I saw this headline recently on NPR: "Food Fraud Database Lets Us All Play Detective." From the description, I expected some degree of chemophobia (habit):

Spices colored with carcinogens? Milk that "never saw a cow"? A free global database opens the door on the many ways that people adulterate [food]

Though I expected the carcinogen to be simply "chemicals" or something, it turned out to be the (indeed carcinogenic) Sudan dyes. In fact, NPR avoided chemophobia on this one!

The article is worth checking out -- it's a brief read, and it points to a really interesting resource: the USP Food Fraud Database. I'm not going to delve much into what the database is, since the NPR highlight already did that. But it's worth pointing out a feature I found interesting (and perhaps contrary to my experience with the food world, where anecdotal claims are usually key)--the database lists food items (ingredients), what the adulterant was, and the method of detection (PCR, Raman, NMR, etc.). Moreover, the scholarly or other reference in question is listed, for those interested in further clickthroughs. Makes for a nice highlight of how analytical chemistry techniques are used in real-world applications--and how particularly techniques are uniquely suited for different classes of analytes.

But now I'm going to be burning some time searching all the ingredients in my kitchen.

Total synthesis funding declared top national priority

WASHINGTON -- Among recent changes to the federal budget was a joint announcement by the White House and the Congressional Budget Office (CBO) that along with postmodernist literature critique and intermediate basketweaving, natural product total synthesis has been declared a "top funding priority" for the nation.

The news of the funding priority shift Monday morning came as welcome news to thousands of synthetic chemists in academia, who had worried in recent years that federal belt-tightening might divert funds away from their activities.

Although the funding measures have been laid out in detail in a 6000-page document readily accessible on the CBO website, several government officials gave public statements early on Monday to clarify the scope and magnitude of the announcement.

From the White House's press room, President Barack Obama spoke to reporters. "I consider this my most important contribution to the nation's interest so far," he said, stepping away from his prepared script and wiping a hint of a tear from his eye as he addressed the cameras earnestly. "For too long, our federal government has prioritized translational and applied research. And while contributions to medicine and energy are somewhat important, or something, I guess, we've too long neglected the biggest questions in science that will keep our country great. For example, there are so many alkaloid and polyketides that have been isolated from sea sponges that we just don't know the absolute stereochemical configuration of. And a few of these have some sort of cytotoxic activity or something at millimolar concentrations," the President added.

Cries of "USA! USA!" could be heard from several reporters in the audience who were briefly overtaken with emotion.

NIH director Francis S. Collins issued a statement later in the day on behalf of the National Institute of Health. "We are allied with the President on this strategic historic decision," the report reads. "While some might object to the fact that the NIH has completely defunded cancer research, antibiotic research, and genetics projects, we caution the public that the money invested in total synthesis will reap much richer rewards for the scientific community and the public. For instance, one of the total syntheses might contribute a valuable synthetic method that can be used in a different total synthesis from the same lab group."

The NSF did not issue a statement but a source within the organization pointed out that all NSF predoctoral fellowships this year were awarded to students studying total synthesis.

Despite the billions of dollars of refocused funding, not everyone is happy with the move. The American Physics Society issued a formal letter of protest against the measures, which are estimated to result in the closure of 99.5% of physics labs across the country. Said the report: "What's a carbon?"

Surprising to many was an announcement by the Pentagon that drastic military funding cuts would be made to support the total synthesis effort. US Defense Secretary Chuck Hagel addressed troops worldwide via a televised message. "Um, yeah, so, guys, we appreciate your hard work and whatnot, but you can all go home. We're cancelling all this 'war' business, honestly. It's a money sink." In one video of an Army base in Afghanistan, soldiers were seen reacting to the news with elation. Hagel continued: "And let's be honest. Enlarging the postdoc pool is the true route to national security."

In other news, job prospects for chemists look to be increasingly encouraging. In 2013 alone, twelve of the fifteen largest pharmaceutical companies have launched massive hiring campaigns, resulting in nearly complete employment among recent PhD graduates.

Stipends: A waste of funding?

A little while ago the subject of teaching assignments came up among some colleagues (as it is wont to do).  Specifically, we were discussing which PIs had habits of sticking their students on repeated teaching assignments and which PIs didn't have their students teach unless they really wanted to.

I was a little surprised that one of the very well-funded synthesis groups here had an abundance of TAs. One of the students (him/herself a TA) explained it thus: "We don't like to waste money on paying people." The point was that they viewed grant money as primarily for supplies and fancy instrumentation. For instance, they'd shelled out quite a bit of cash recently for some fancy chromatography and microscopy equipment.

It was an interesting perspective, and I'm not sure what to think of the philosophy.

I've seen PIs before who tended to put students on TA quite frequently -- for their entire PhD, in many cases. But those have typically been groups with little-to-no funding, where available grant money wouldn't even cover a meager grad student stipend.

I've also seen well-funded PIs who limit their students to two semesters of teaching (or whatever the departmental requirement happened to be), regardless of external fellowships available to the individuals in their lab. In those cases, a large portion of the available grant money is devoted to stipend/tuition expenses.

So a lab that has plenty of cash that it needs to burn and decides to burn it by buying valuable (but not essential) upgrades--that's different.

It might be a subdiscipline thing. I suspect that "hard" synthesis groups -- methodology and total synthesis -- tend to rely more on a TA culture (perhaps the funding situation is less predictable here?). In contrast, most biologically-oriented organic groups seem to find the funding (from training grants and other sources) to keep their lab RA-based. Additionally, some grants have specifications.

Even so--can personnel costs be considered a "waste"? The word I would suggest is "investment." But it might be because I think a well-trained, happy chemist with decent instrumentation/supplies is more valuable than a slightly nicer MPLC.

Singers and musicians, apocryphal quotes, and chemists

Recently, I saw the following quote get shared widely among my acquaintances on a particular social media outlet:

Singers and Musicians are some of the most driven, courageous people on the face of the earth. They deal with more day-to-day rejection in one year than most people do in a lifetime. Every day, they face the financial challenge of living a freelance lifestyle, the disrespect of people who think they should get real jobs, and their own fear that they’ll never work again. Every day, they have to ignore the possibility that the vision they have dedicated their lives to is a pipe dream. With every note, they stretch themselves, emotionally and physically, risking criticism and judgment. With every passing year, many of them watch as the other people their age achieve the predictable milestones of normal life - the car, the family, the house, the nest egg. Why? Because musicians and singers are willing to give their entire lives to a moment - to that melody, that lyric, that chord, or that interpretation that will stir the audience’s soul. Singers and Musicians are beings who have tasted life’s nectar in that crystal moment when they poured out their creative spirit and touched another’s heart. In that instant, they were as close to magic, God, and perfection as anyone could ever be. And in their own hearts, they know that to dedicate oneself to that moment is worth a thousand lifetimes.
-David Ackert, LA Times

I kind of hate to reproduce it--not because it's pandering and indulgent*, necessarily, but because I can't find the original source, and as a scientist, that bothers me. It's attributed to David Ackert of the LA Times. No one seems to mention that the LA Times website doesn't even mention a David Ackert, much less this quote. So the authenticity/origin is dubious (that doesn't seem to matter to those who push it along). 

A quick search of the internet reveals several modifications of the quote, wherein people have substituted 'actors' and 'artists' for 'singers and musicians'. So, I figured: why not 'chemists'? (We do use instruments). Let's try.

[Chemists] are some of the most driven, courageous people on the face of the earth. They deal with more day-to-day rejection in one [group meeting] than most people do in a lifetime. Every day, they face the financial challenge of living a [STEM] lifestyle, the disrespect of people who think they should get real jobs, and their own fear that they’ll never work again. Every day, they have to ignore the possibility that the vision they have dedicated their lives to is a pipe dream. With every [column], they stretch themselves, emotionally and physically, risking criticism and judgment. With every passing year, many of them watch as the other people their age achieve the predictable milestones of normal life - the car, the family, the house, the nest egg. Why? Because [chemists] are willing to give their entire lives to a [synthesis] - to that [ring], that [stereocenter], that [functional group], or that [weird perfluorinated tail] that will [get them into JACS, or Org. Lett., or heck, Tet. Lett., it's gonna get ignored anyway]. [Chemists] are beings who have tasted life’s nectar in that crystal moment when they poured out their [organic layer by mistake] and [broke] another’s [favorite sep. funnel]. In that instant, they were as close to [unemployment] as anyone could ever be. And in their own hearts, they know that to dedicate oneself to that moment is worth a thousand lifetimes [...PSYCH! Hahahahahahaahahaah. Heh.].
-David Ackert, LA Times

Seems to fit.

Update: 11:05 PM. Re: source of original, for those interested (thanks to Chemjobber for the legwork). According to David Ackert:

@gravelpot I wrote the piece 15 years ago- it originally appeared in Backstage West. Don't think it ever appeared in LA Times.
— David Ackert (@DavidAckert) January 28, 2013

* Caveat: I've done a lot of music stuff myself; I'm not hating on musicians here. Just saying.

JACS comment section? Back to the future

It's been a very interesting couple of weeks in the realm of Blog Syn (the beginning of Blog Syn #003A has a roundup for anyone who hasn't been following). People across a number of blogs have noted the importance (or at the very least, usefulness) of chemists participating in social media and rapid web communication (indeed, even Phil Baran's lab has started a blog, despite hegemonic bias against blogging in the field of organic synthesis). 

How can chemists use social media to the greater benefit? Take, for instance, the first comment in Chemjobber's reply to the IBX+water conclusion. Polychem says (bold emphasis mine):

This work makes me think that every paper published on pubs.acs.org deserves its own comment section. I can imagine it being abused, but there may be some good insights by having essentially a wider peer review where you don't have to pay to print your rebuttal.
Good job Blog Syn people!

 Hmm... a comment section at JACS? Check out this 1996 editorial from the journal! For those stuck outside the paywall, an excerpt:

There is no question that digital computers have had a large impact on the publication of scientific research. JACS uses computers in the management of the journal data base and in production of the journal. Most manuscripts are now submitted in final form as floppy disks, and e-mail is often used for correspondence with authors and reviewers. Recently, especially with the wide accessibility and usage of the World Wide Web (WWW), interest has turned to electronic publishing, i.e., to the posting of manuscripts on the web rather than, or in addition to, producing a hard copy (print) journal. The advantages of electronic publishing include the faster appearance of a paper at a presumed lower cost than printing (with the attendant possibility of wider distribution) as well as the ability to provide materials, like computer programs, movies, color figures, and large amounts of experimental data, not available in the hard copy. Concerns about electronic publishing include the maintenance of the quality and integrity of the published literature, providing for the long-term archiving of papers, and assuring that financial support is available to carry out the needed peer review and maintenance of the archive. These points are discussed in a booklet available from ACS Publications: Will Science Publishing Perish?

Interesting that the ACS proposed lower cost and wider distribution--I wonder if that worked out that way? The last section of the editorial is also a fun read:

JACS Web Page -- An Experiment. The JACS web page (accessible via the ACS publications page at http://pubs.acs.org) displays instructions for authors, links to supporting information, and the table of contents for the latest issue of the journal. As an experiment we will also try out a section for selected correspondence and comments. Readers can submit, by way of a form available on the web page, scientific comments pertaining to recently published JACS papers. Authors will be asked to reply. Posting of comments will not be automatic. Comments for posting will be selected by the editors and they will not be sent out for review. There will be no appeals for comments not selected. Comments will not be published in hard copy or CD versions of the journal nor will they be archived. We hope these comments will generate interesting discussions and help amplify and clarify ideas and results published in JACS papers. They are not meant to discuss priorities or present still unpublished ideas or results. Additions and corrections will still be published in the printed version of JACS. We hope the level of discussion on the JACS page will be significantly higher than the average WWW newsgroup! This experiment will be terminated if the community feels it is not useful (or if it becomes too burdensome for the editors). At this time we cannot accept manuscripts submitted electronically for review; however, we are investigating the possibility of doing this in the future. As stated at the outset, the science publication field is evolving rapidly. The new possibilities are intriguing, but the community will best be served by an orderly evolution that involves the best features of both the print and electronic media.

It's quite revealing to see the difference between scientific publishing just 17 years ago (oh wow, 1996 was 17 years ago??) and now--after all, electronic submission is de rigueur not only for SI but for main text and for correspondence with reviewers.

More interesting, though: there was a comment section on JACS before the journal even started putting the manuscripts themselves online. Seems like unusually progressive thinking by the ACS!

But if you go to the JACS website now, there's no comment section. What happened to it? A search of editorials from the journal gives no relevant hits and a 2002 editorial discussing other web-based aspects of JACS makes no mention of it. Did it die a quick, fiery death?

Indeed, there's a lot of room for publishers to include the community in scientific discourse. Some do a little: Nature Chemistry, for instance, has a good metrics section that indexes blogs (but no comment section). The ACS journals don't have comments, nor do Taylor & Francis, the RSC journals, Elsevier, or PNAS.

Does anyone do comments?

Yes! Take a look at PLoS One (example article): they have comment section built in to a very slick web interface.

It'll be interesting to see how the face of scientific communication changes over the next few years.