Now there are more ways to connect, communicate, and collaborate on the ACS Network, the premier online network for ACS members and the global chemistry community. Check out the latest networking tools in the ACS Network: Bookmark and share your favorite links; tag and categorize content more effectively; send and receive in-system private messages; participate on the go with email digests and alerts; collaborate and share documents in private or open groups, and stay engaged on the latest discussions in your communities of interests. Log on at www.acs.org/network, create your profile, and see for yourself!

Whether you're job-hunting or just trying to stay competitive in a tough market, you can rev up your career at the ACS Career Fair, to be held Sunday, Aug. 22, through Wednesday, Aug. 25, in the Boston Convention & Exhibition Center, at the upcoming 240th ACS National Meeting. The Career Fair provides ACS members the opportunity to meet with employers and discuss potential job opportunities, as well as enhance their professional development by participating in mock interviews, resume reviews and attend over 30 career-oriented workshops. The Career Fair is open to ACS members who are registered for the meeting; unemployed members who qualify for a 2010 ACS dues waiver can request a waiver of meeting registration fees. Visit ACS Careers for more details, and give your career a boost at the Boston meeting!

As a synthetic chemist the first thing I usually want to know about a chemical compound is “How did they make it?” and then “How do they know they made it?” However, synthetic procedures and characterization data for compounds are often found lurking in an article’s Methods section or in the depths of the Supplementary Information.

Not any more! We are now testing a new feature for the Nature Chemistry website that displays the procedure for making a chemical compound on its compound information page. Our first example of this can be found in Howard Colquhoun’s article in the August issue of Nature Chemistry which is live online today.

Compound pages – which display lots of other useful information about the structure – are easily accessed by clicking on hyperlinked bold compound numbers in the HTML version of an article. Where the paragraphs of text describing the synthesis and characterization of the compound are provided by an author, they will be displayed under the heading “Synthetic Procedure” on these pages. From the procedure you can view any other structures mentioned by bold number and navigate to their compound pages by hovering or clicking on the hyperlinked numbers respectively. This makes it really easy to follow the chain of the reaction you are interested in.

Following the links at the top of the compound pages you can still jump back to the article to find the full experimental details in the Methods section or Supplementary Information. We also encourage authors to provide us with raw data files – such as CIF files – which can be displayed on the compound pages.

We hope that including synthetic procedures and data on the compound pages makes it faster to browse for what you are looking for. Pulling all this information together in the article HTML will not only feed OSCAR the journal-eating robot, but also make life easier for over-worked lab-rats bench-monkeys post-graduate students.

Have a play and see what you think - this is only at quite an early stage, so any feedback would be gratefully received.

Laura

Laura Croft (Technical Editor, Nature Chemistry)

What kind of lab is this? An anonymous commenter came close with "Biochem/Natural products isolation? "

It's a kitchen. The clue is on the cabinet where it says "3 TBS Sugar". Read here how chef Dave Arnold of the French Culinary Institute in NYC got Buchi to tweak a rotovap for some cool chemistry in the kitchen.

I'm fairly sure the stuff in the beaker is mint.

When I was in elementary school we lived in a small town outside of Chicago. The local rec department had a terrific summer program, drop-in arts & crafts, boating lessons and field trips galore. My favorite trips (besides the outings to Cubs' games) were to the Museum of Science and Industry - what I called the "push-button" museum for all the interactive exhibits. I could go again and again...and did. We were on our own in the museum, something that is probably unthinkable in these hypervigilant days, trusted to return on time to our yellow school bus for the long trip back home.

When I read From the Mixed-Up Files of Mrs. Basil E. Frankweiler I didn't dream of running away to the Met in New York, I dreamed of hiding out in the Museum of Science and Industry. I would have slept in the U-boat.

My brother Pat (who I think I could have counted on to be my co-conspirator in such an adventure) sent me an announcement for a competition to spend a month living my all time favorite museum. Alas, I'm not on sabbatical, and am so committed for the fall that there is no way I could go, even if I could survive the competition. But a girl can dream, can't she?

---

Photo of The Museum of Science and Industry, Chicago, IL. Photographed 9 April 2006. © Jeremy Atherton, 2006. Used under CC license.

I've been doing some research for home renovation projects this summer (new cabinets for the kitchen) and came across this quiz to determine "your decorating style". (For the record, I don't have one!) It got me thinking about lab spaces and how they reflect the work done in them, as well as the scientists.

Labs and research spaces have a certain aesthetic to them. Biochem labs have a different "style" than synthetic labs than laser labs than...right down to a preferred palette of wall colors (for some reason, I associate white with biochem labs, black or deep blue with laser labs) and what sort of signs you'll find on the doors going in (eye protection required) and going out (did you remember to fill the trap?).

Take a look at the bench in the photo and see if you can correctly identify the research field. Organic, inorganic, or....

Look for the answer tomorrow!

---

Is your lab an architectural or decorating wonder? Could we identify your field from a photo of your bench or lab? Want to play? Send me a photo.

Link to the photo will come tomorrow (otherwise I'd give away the answer...)

There were many great talks yesterday at the Belgian Organic Synthesis Symposium, but as I have time to describe just one, I’ll mention Eric Jacobsen’s tour de force about hydrogen-bonding catalysis. This seems to be an area that’s really kicking off right now.

His thesis is that hydrogen-bonding catalysts shouldn’t be thought of in the way that chemists tend to conceptualize asymmetric catalysts in general - that is, as molecules or complexes that bind to substrates in order to block the approach of reactants from certain directions. Instead, he made the case that hydrogen-bonding catalysts act more like enzymes, activating and/or stabilizing the substrate (or the substrate's transition state)through hydrogen bonding. That’s not to say that steric interactions are unimportant, clearly they still have an impact. But to fully understand how hydrogen-bonding catalysts work, he argues that you need to look first at the stabilizing effects of non-covalent interactions.

He backed this up with many case studies of hydrogen-bonding catalysts from his own lab (such as those for Claisen rearrangements, polyene cyclizations and Strecker-like reactions), in each case providing a detailed analysis of how each catalyst works. It’s all beautiful stuff, and you find some it in JACS (see the abstract for his analysis of the Strecker reaction here).

Today is the last day of the meeting, so this is where I’ll sign off from Belgium. I’ve only been able to discuss a handful of the presentations, but there were many other highlights at this meeting. I can only encourage organic chemists out there to come to the next meeting in the BOSS series, in 2012 - you won’t be disappointed.

Andy

Andrew Mitchinson (Senior Editor, Nature)

Day three of the Belgian Organic Synthesis Symposium, and the heat wave continues. That means there have been plenty of excuses for conference attendees to drink Belgian beer, as the title of this blog implies. But we were also treated to a spectacular talk today by Kenichiro Itami, who presented (among other things) his latest research towards the bottom-up synthesis of carbon nanotubes.

Itami’s grand strategy is to prepare nanorings of benzenes, known as cycloparaphenylenes (CPPs), then to stack them up into cylinders and join them together in aromatization reactions - hey presto, you get a carbon nanotube. He’s not the only person pursuing this strategy, as both Carolyn Bertozzi and Shigeru Yamago seem to be trying the same thing.

The first problem to overcome in this approach was how to make the inherently ring-strained CPPs - Bertozzi published her solution in 2008 (you can see the abstract for the JACS paper here), closely followed by Itami in 2009 (in Angewandte, abstract here), then by Yamago this year (also in Angewandte, abstract here). Itami is now concentrating on finding a scaleable route for making CPPs, so that he has sufficient material to attempt the all-important aromatization reaction. He’s not quite there yet, but he has come up with an impressively concise synthesis of a CPP, and just needs to optimize the yields.

In the mean time, he’s also devised a general, modular synthesis that allows access to CPPs of different sizes, and he presented some rather beautiful crystal structures of a CPP - interestingly, the molecules stack up in much the way you would need them to if you wanted to fuse them together into a nanotube.

No doubt Bertozzi and Yamago are also making advances of their own, so I’ll certainly be following the progress in the race for a bottom-up synthesis of carbon nanotubes.

Andy

Andrew Mitchinson (Senior Editor, Nature)

I enjoyed the Belgian Organic Synthesis Symposium in 2008 so much that I decided to go to another one. So, here I am in Namur, capital of the Wallonian region of Belgium, where they’ve been having a mini-heatwave - and where my hotel room has no air conditioning. So, forgive me if this turns out to be a short entry, but it’s hard to concentrate on blogging when the temperature is 30 °C.

The meeting has got off to a terrific start, with Dave MacMillan undergoing the usual rite of passage as the recipient of the ‘Tetrahedron Chair’ prize - he gave four lectures today on organocatalysis. The lectures are billed as a one-day course, and so unsurprisingly there wasn’t much in the way of new results. But there were a few teasers of things to come from the MacMillan lab. Look out for Dave’s forthcoming synthesis of strychnine, completed in an amazing 12 steps. I think this might be the shortest route ever, but feel free to correct me. Dave also mentioned that his lab is currently looking for alternatives to Hantzsch esters as hydride sources for organocatalytic reductions, and briefly described a soon-to-be-published method for the alpha-amination of aldehydes.

You might think that a whole day listening to one person speak would be wearing, but Dave has such a conversational style that his lectures feel more like one-to-one chats, in which he gives you the inside scoop on how his greatest discoveries were made. Even the lure of free Belgian beer (given away as a freebie at the end of today’s programme) didn’t deprive him of any of his audience.

And speaking of Belgian beer, the thought of a cold, frosty one is extremely appealing from my oven of a hotel room. So I’m going to go and get one.

Andy

(Andrew Mitchinson, Senior Editor, Nature)

This was great! I am so impressed with the students and their creativity. This actually lets me know there are professors out their like myself trying to reach the youtube generation. Well done!!!

Dr. Pamela M. Leggett-Robinson
Department Chair, Sciences
Associate Professor of Chemistry
Georgia Perimeter College

My sailboat's name is the Fiat Lux — "let there be light" in Latin — drawing from both my theological and scientific personae. I sail a Laser, an Olympic class racing dingy, which is an apt boat for a quantum mechanic. The ability to amplify light by stimulating an existing emission process was first predicted by quantum mechanics, then the apparatus to actually do it was built. Laser is really an acronym: Light Amplification by Stimulated Emission of Radiation. The radiation is electromagnetic radiation, not the radioactive radiation.

There's been a smattering of conversation about light production around my house this weekend between sailing the Laser, setting off fireworks and observing fireflies. One of my teen guests wondered how the fire in fire flies was different from the fire in fireworks. All light is not created in quite the same way....though there are some fundamental similarities.

There are really two fires in fireworks, the thermal explosives that send them skyward, and the "rockets red glare" — the glittering burst of color in the sky. The heat from the thermal explosion (usually blackpowder or a similar substance) is what trigger the colors.

If you ever done a flame test, putting a solid substance or a concentrated solution on a wire loop and placing it in a flame to see what color is produced, you've done the same chemistry. The extreme heat excites electrons in an atom or molecule, and as they fall back down to their lowest energy, or ground state, emitting a photon (a bit of light) that just exactly matches the difference in energy between the excited state and the ground state. An orange flame meant you had sodium on the wire, while a violet flame suggested potassium. More properly this technique is called atomic emission spectroscopy.

For atoms the picture you usually see in a high school text of this process is of a ladder, where electrons are shown moving from rung to rung. The larger the distance between the two rungs (or states) the higher the energy of the photon emitted. If the distance corresponds to photons in the visible region, you see a color, otherwise you have to use something fancier to figure out the energy of the photons being released.

Different atoms have different spacings between states and so the colors they emit when heated to high temperatures are likewise different. There are in fact many states, and so many types of photons can be emitted, but few are in the visible region.

If you click here, you can see a simulation of the photons you'd expect to see when an excited sodium atom returns to the ground state. Are you surprised that sodium can be used for yellow-orange in fireworks? Some urban legends suggest that lead (or radioactive barium) are used in fireworks, but if you look at the line spectrum of lead you can see why it can't be true -- there is no rung to rung jump in lead that corresponds to a visible photon. So a lead firework would be invisible! (Lead used to be used to make the fireworks "crackle"...)

(And it's true that barium salts are used in fireworks, but they are not radioactive. There are no naturally occurring radioactive isotopes of barium.)

---

Read more:

An article at C&E News on the chemistry of fireworks

Related posts:

Jello lasers
Romancing the stone (lasers in the plot line of a romance novel)

Image from Wikimedia.

your advisor doesnt seem to be a very sympathetic person! Good luck with that stipend.

[Posted on behalf of Materials Girl]

Three years ago, while still an undergrad with zero notion of “research”, I wrote a post that briefly pondered the summer life of a grad student. The following year I discovered that summer = vacation for the younger masses only. Now that the regular school year is over, I’m experiencing my first summer as a graduate researcher. So far, this has been time to catch up on the research that I neglected during the school year. (Apparently, a grad school B– = undergrad C– = failure + retake class = extra motivation to maintain straight As! Plus, TAing is awesome, even if in an often painful manner.)

Grad students resemble “normal” working people, only we work longer hours (and/or organize time poorly/try to make up for the time wasted during regular work hours), have a lower salary, and get away with wearing hole-filled jeans and t-shirts from high school. Or as in my case, we get paid nothing. Last week I offhandedly asked “our beloved supervisor” to start paying me during the summer; my financial aid and TAing contract from the department ended in June. He laughed/chuckled/smirked(?) and mentioned that I should apply for the NSF fellowship* again, then changed the subject. Ummm, time for more student loans? This might be a reason to find a wealthier advisor, if only I didn’t genuinely like my projects and group – a recent, but decisive development… The combination of happiness and grad school seems a rare commodity. I’m hanging onto my 7am–10pm motivation for dear life.

*They only gave me an honorable mention this year — and thus no money. /grumbling

So, the summers are for good work – and a couple of good breaks. And, apparently, we never work enough. The internet, among other things, provides countless horror stories of advisors deporting international students who fail to meet some absurdly high standards, brusquely demanding work 20/7** (a useless gesture, as this likely results in lower quality results and inefficient time management), etc. I have little problem with working unspeakably hard, assuming that the projects are worthwhile. However, I want to be the one motivating myself and scheduling my own time, instead of having an irate PI taking attendance and cracking the whip. As it is, one reason I’ve learned to be happy in grad school is that my PI doesn’t micromanage us from day-to-day – he generally just picks on our data and masterminds numerous ideas to try [which may or may not be of value, but that’s a different issue!]. Besides, with all the random assignments, it is not even necessary for him to demand nights and weekends – if I am to present anything decent at our weekly group meetings! Motivation by necessity is much more enjoyable than by direct force.

**20 hours a day, 7 days a week. They do, at least, acknowledge that we are primarily human and need SOME sleep. During my first or second month in the group, my advisor mentioned that getting over 4 hours a night means I’m not working hard enough. He was grinning, and to this day I haven’t figured out if that was a joke or a passive-aggressive communication regarding my work ethic.

At the end of the day, I’m enjoying my serfdom/hermithood, and I even take occasional nights off to… umm… I actually don’t know what to do with “spare time”… Still, though, can I get a stipend already?

Ideally one should try taking up science related jobs for a while before embarking on a phd. In an ideal world, one should be able to devote a couple of years to discover that real passion for doing research. If this is not possible, be ready to quit grad school if you find that there is something else out there that is more fun and better paying.

In my opinion, many real jobs are not all that interesting - they involve a lot of routine and while some of them can be quite paying, an awful lot of them are taxing and underpaid (translation for example).

"the world’s hottest pepper — in an aerosol spray to disperse unruly mobs or immobilize rioters non-violently"

Not in the least bit non-violent! A good dose of well aimed curry powder can kill a person by asphyxiation.

Curry powder is one of the few chemicals available in the home that can act as a pH tester. Curry powder turns red as the solution grows acidic.

I have always wanted to be a scientist since I can remember. You are still in the beginning of your academia life. For me, I am nearing the "end" of my PhD. Looking back, I am not so sure about my "dream" anymore.

Self-reflection is important. To be able to keep the passion alive is a skill. Not everybody will be able to sustain it. For what ever reason that prompt you to stop at Master, when you walk out of the lab and you must never, ever doubt your decision.

I can tell you this much, academia, to some, might look like a nice cocoon, but it is really different looking from the inside. Inside, outside, they are the same.

A PhD is not everything, but it is something.
Think about it. Good luck to you.

What elements of academic culture are hindering scientific progress?

How often are important scientific developments overlooked by industry?

What stories about science do you tell at cocktail parties?

Posted on behalf of Lou Woodley

What question would you ask a Nobel Laureate in science if you could? This is one of the competitions that forms part of the social media aggregation site for this year’s Lindau Nobel Laureates Meeting which takes place from 27th June to July 2nd. The annual Meeting on Lake Constance is celebrating its 60th anniversary this year and will bring together 61 Nobel Laureates across the sciences with almost 700 young researchers for a week of lectures and networking.

To follow what happens at the event, the aggregation site brings together an official blog in English and German with Twitter, Flickr and videos from the event. There are also two competitions: in the first you can submit and vote for potential questions to ask the Laureates. The most popular questions will be answered and featured in a special Nature Outlook supplement in the autumn. The second competition invites you to submit and tag photos of Nobel Laureates for a chance to win a Flip HD camera. More details can be found here. You can also find additional content on Facebook or meet other attendees in the Nature Network forum.

We recently published an interesting Thesis article by Bruce Gibb called "Life is the variety of spice" and have since received a comment that seeks to extend the ideas originally discussed.

Gavin Armstrong (Associate Editor, Nature Chemistry)

*****************************************

In an insightful article in the January 2010 issue of Nature Chemistry, Bruce Gibb proposed the addition of curry-making to undergraduate organic chemistry labs. Curry-making is a classic example of a practical aspect of chemistry (molecular gastronomy) that laymen tend to ignore. Initially the reagents (spices) are heated (fried) in oil so as to overcome the different activation barriers. After that, water is added to the mixture and boiled, driving the reaction towards equilibrium. There are many rate constants in the first step which is one of the reasons that the ingredients must be heated stepwise at various temperatures. During the final reflux, multiple equilibrium constants are set up. Hence the concentrations of the different spices assume immense importance. A little on the higher side and the curry can become extremely spicy. In fact, the science is delightfully complex and it is astonishing that curry making works more often than not.

While seconding the author’s proposal, we also feel that one should consider adding part of the culinary class to the biochemistry curriculum. The author discusses the essential structural implications of the different curry ingredients and their mutual physico-chemical interactions while it is being prepared. Additionally, one needs to appreciate the biochemical interactions of the curry after consumption and how it’s different ingredients stimulate a diverse array of distinct receptors (often simultaneously) [Gerhold & Bautista, 2009]. Capsaicin, black pepper and garlic all stimulate the TRPV1 receptor [McNamara et al., 2005] whose activation leads to the typical burning sensation. Various oils and cloves stimulate the TRPV3 receptor (highly expressed in the nose) [Xu et al., 2006]. It is the combined downstream effect of these various taste and olfactory receptor stimulations that leads us to appreciate the flavor of curry coupled with the aroma and warmth of cloves.

It is interesting to note that this is not the only way that the TRPV receptors have been put to use in society. In eastern India, plans are underway to equip the police with ‘bhut jolokia’ [Liu & Nair, 2010 and Bosland & Baral, 2007] — the world’s hottest pepper — in an aerosol spray to disperse unruly mobs or immobilize rioters non-violently. Gibb noted that peppers evolved to produce capsaicinoids to ward off herbivores, today these peppers are being used by human intruders as ‘smoke bombs’ to keep wild animals at bay in remote forests.

Culinary science has for a long time been treated as an art by cooks around the world and they are mostly ignorant of the science lurking behind a good recipe. Most programs in gastronomy do little to emphasize its molecular aspects. While good food is certainly aesthetic, it is the chemists who can also appreciate the science behind it. While chemists might not become dedicated cooks, a basic culinary education does have implications in the real world; and trained individuals might cherish the opportunity to apply it in their daily lives and career. Thus there are multiple reasons why we would like to highlight the contribution made by biochemists in understanding culinary science.

Finally, a comprehension of the science behind the curry will certainly make a better cook and good food is a universal healer.

Arnab De [Department of Microbiology and Immunology, Columbia University Medical Center]
Subho Mozumdar [Department of Chemistry, University of Delhi, India]
Rituparna Bose [Department of Geological Sciences, Indiana University, Bloomington; e-mail: ribose@indiana.edu]

Spoof music videos offer the chance for ageing chemistry geeks such as myself to relive both their chemical and musical past. This video in particular was the cause of much hilarity within the Nature Chemistry team. This video is great – although one of the early lyrics ‘in the lab, working alone’ is a cause for concern – so let’s hope that it is there for artistic reasons rather than anything else. But can such videos serve any useful purpose?

Well, this would be a fairly boring blog post if the answer was “No”, so I was delighted this weekend to hear from Neil Garg at UCLA about a small video project set as part of the sophomore organic chemistry course. For a small extra credit, Garg asked his class to make music videos highlighting aspects of the course.

No less than 140 out of 240 enrolled students took part and made a total of 61 videos – I’ll be interested to hear from Neil when the exam results are in! Although the videos are worth very little in the final score, it’s hard to believe that the students failed to learn something useful in the way of organic chemistry from making them.

Steve

Stephen Davey (Associate Editor, Nature Chemistry)

Genetic discoveries from a shrub called the burning bush, known for its brilliant red fall foliage, could fire new advances in biofuels and low-calorie food oils, as per Michigan State University scientists. New low-cost DNA sequencing technology applied to seeds of the species Euonymus alatus - a common ornamental planting - was crucial to identifying the gene responsible for its manufacture of a novel, high-quality oil. But despite its name, the burning bush is not a suitable oil crop........

Dhiren Barot was an al Qaeda operative involved in plots to blow up the London subway, among other targets. To maximize the damage and the terror, he planned to pack some of his bombs with toxic gas. Fortunately, in August 2004, British authorities nabbed Barot and his accomplices before they could carry out their attacks........

[Posted on behalf of Materials Girl]

Some say that you go to college to find out who you really are, but I say that undergrad is just the starting point. Maybe you agonized for the first couple years about your major, or you had your next ten years planned out since high school — give or take changes once actually reaching university. For those who end academia at a Bachelor's, sure, that's enough to get a job and to establish a career. From there, real life, and the real you.

However, for the poor wretches who choose to stay in the protective cocoon of Academia, even grad school may only be a step in development. We are expected to have a solid background in our department, knowledge in all subfields (or the ability to cram it in the week before prelims), and a fund-able project to pursue for the next 4–8 years. We are expected to work much, sleep little, and produce small miracles on a small salary. It is doable, yet it also feels as though we are kept too busy to take a step back and evaluate our lives. Being grounded only by science is a precarious situation — what if your research fails? Any amount of intelligence cannot force nature to act otherwise. Is self-reflection a necessity? No, not to your adviser. Past age 25 or so, though, we really are in the regime of adulthood. (Then again, many "real" adults haven't a clue about what to do with THEIR lives, either.)

Sometimes it also feels as though grad school is simply a rite of passage. Our superiors went through the same process, with varying degrees of pain and toil. We are then expected to have that PhD and list of publications on our resumés — the stamp of approval that magically reflects our capabilities as researchers, multi-taskers, and not-completely-insane individuals. It isn't for everyone, but I can already feel the disdain of some "higher-ups" if I announce my decision to leave academia with only a Master's. (The reasons why are for a future post.)

It's been less than a year since I became a grad student, and there's still much to learn. For now, my most far-reaching question remains: Is it worth pursuing a PhD? Either I haven't found the right project or group to excite me, or research just isn't my thing...

My 10 favorite things about Polymer Chemistry

Well, some of mine overlap with others that have been posted, but it doesn't stop them being my favourites. I also noticed a distinctly experimental flavour to a lot of them, so I tried to come up with some more closely related to my current position:

1. New reactions that run ‘spot to spot’ on TLC
2. Freshly made Pd(PPh3)4
3. A well packed flash chromatography column (which results in tight and well separated bands of compounds)
4. Gas-tight microsyringes
5. Old fashioned mechanical shakers that make the whole lab move
6. A full set of clean NMR spectra
7. RIDICULOUS – acronyms for NMR experiments
8. Rapid responses from reviewers (even when they say ‘no’)
9. A well balanced referee report
10. A good pun (with the emphasis on good)

Given the popularity of Derek Lowe's 'Things I won't work with' (http://pipeline.corante.com/archives/things_i_wont_work_with/), how about some things he does like? And how about some thoughts from Prof. Like Substance (http://proflikesubstance.blogspot.com/) - perhaps he could add some flavour from being a young academic?

I've propagated the meme ...

http://www.sciencebase.com/science-blog/my-favourite-chemistry-things.html

An SF fan from the moment I discovered Heinlein's Have Spacesuit -Will Travel in the minuscule public library in the small (population 2500) Midwest town I grew up in, it's probably not a surprise that I would have been an avid watcher of SF on TV. When I get various 'urgent warnings' in my inbox, I often hear the Lost in Space robot's voice in my head, "Warning, Dr. Smith! Warning!"

A few days ago, this warning about the dangers of taking business cards from strangers appeared. Take one of these drug laden cards in your bare hands and soon you will be easy prey for swindlers and worse. Is such a thing possible? Can you be drugged against your will by briefly touching a drug?

In principle, yes. Unbroken skin, though a good way of keeping your insides in, is not an absolute barrier to molecules entering the body. Some molecules — such as DMSO — are better at getting in than others.

When I teach mathematical modeling, one topic we look at is ways to model diffusion. An application that many of my students find interesting are passive drug delivery systems that capitalize on diffusion. In other words - patches. To me this warning sounds like a folkloric riff on drug patches. In fact, delivery through a patch is a pretty complex system, it's not just a matter of soaking the equivalent of a gauze pad in a drug and taping it to your arm.

The drug cocktail purported to be on the business cards is burundanga - a mixture of two plant alkaloids, atropine and scopolamine. Both can be administered through the skin, when I had surgery a couple of years ago, the anesthesiologist use a scopolamine patch to manage my post-op nausea. But he didn't hand me a "don't throw up" card to hang onto for a few minutes in pre-op - that patch he applied behind my ear was a marvel of pharmaceutical engineering!

Burundanga has been used criminally but by slipping into a victim's food or drink. Incidental contact with atropine or scopolamine won't incapacitate you — though the prescribing information for the scopolamine patch points out that you should avoid touching the patch and then your eyes - resulting in dilated pupils and blurry vision.

___
Scopolamine was used as an amnesia inducing agent during labor and delivery in the 60's. I suspect Betty Draper's halucinations during labor and delivery on Mad Men (The Fog, Season 3, episode 5).

Image is of belladona, from which atropine and scopolamine can be extracted.

We've been enjoying the 'favourite things about chemistry' meme started by ChemJobber and continued by Azmanam and the C+EN team - who have now challenged us!

So the London-based team put their heads together and came up with this list:

1. The smell of ethyl acetate (in the morning) [SC]
2. A rainbow of Keck clips [SC]
3. A good graphical abstract that perfectly sums up the paper [SC]
4. CPK models (the proper physical things, not just pretty pictures) [SC]
5. Peter Atkins' textbooks [GA]
6. Awesomely symmetrical (and pretty) crystal structures [NW]
7. Chemistry sets [GA]
8. The elements song [GA/NW]
9. Curly arrows [LC]
10. Freaky glassware and the prowess of glassblowers [All]

We'll also throw the baton on to the Chemistry World gang, David Bradley of ScienceBase and Michelle Francl of Culture of Chemistry — and our Boston- and Tokyo-based teammates Steve and Anne.

Neil

Neil Withers (Associate Editor, Nature Chemistry)

Uh-oh, looks like we need to reinforce the fact that it's always and will continue to be like this. Science has increasingly been a bad career starting in 1970. After the Cold War, People's Revolution, easy access to information over the internet, etc., the long training imposed upon the practitioners of science is severely outdated.

First thing to do is abolish the PhD. A lot of egos will be bruised by that, I know. But this will make a career in science far less costly and finally get rid of the serfdom factor. People can enter the field more quickly, smart people can move up, not-so smart people can find their final positions and those with other passions can use their science knowledge in productive ways. That third class of people is usually turned into bitter, balding Post-Docs after ten years, before entering the work force and poisoning the industry with their sadness. All that energy and imagination blown on the pursuit of soft-money, what a shame. There are many other solutions, but abolishing the PhD is the first one that must be done, or else no improvement could ever occur.

If that doesn't happen, scientists will find themselves in Greenspun's scientific dystopia:
http://philip.greenspun.com/careers/women-in-science

Katz warned of this long ago also:
http://wuphys.wustl.edu/~katz/scientist.html

and these pictures might become a bit more true:
http://philip.greenspun.com/careers/

You've been warned. We can continue this profession in shame now and change later, but I have a feeling shame will give way to change anyway. Once enough smart, imaginative people are scared away, science will enter stagnation.

Start the Abolition!!! Down with the PhD!!! Down with soft money serfdom!!!

[This post is based on the editorial in the May issue - read here for the full text, available for free to all registered users. We welcome feedback on our editorials in the comments section below.]

Cuts in pharmaceutical R&D jobs might provide short-term improvements to the bottom line, but do not bode well for the industry in the long run.

Right now does not seem to be a good time to be a pharmaceutical researcher. In January and February this year some of the world's biggest pharmaceutical companies seemed to be competing to see who could lay off the most staff. The background to all of this is the low numbers of compounds that the companies have in their pipelines and the soon-to-expire patents of their highest selling drugs. The drug companies' response has been the same for several years — merge and try to make cost savings.

So where is the industry headed? Are we witnessing a wholesale restructuring of the way these companies perform research? For many years, the large pharma companies have been outsourcing parts of their R&D. It is often the same scientists who used to work directly for big pharma who now work at (and run) the contract research organisations.

Smaller salaries and less regulation are an easy way to cut costs. It is thus no surprise that the only part of GSK neuroscience research to survive the cuts is the neurodegeneration area based in Shanghai. Another option has been to in-license drugs developed by smaller companies. The approach is popular — it removes much of the risk from the early stages of development.

There seems to be a fundamental problem with either approach. Big pharma has always played a role as a training ground in medicinal chemistry. Furthermore, having experts within the company is absolutely necessary and taking part in ongoing research is a major part of that expertise. For evidence of the problems with in-licensing, one needs to look no further than the ongoing uncertainty over the GSK deal for Sirtris.

Big pharma and small start-up companies might have very different criteria for taking a drug candidate into clinical trials. Clinical trials are a costly venture and big pharma must see a reasonable chance of positive results before proceeding. For start-ups simply reaching this stage might be enough to bring in the buyers.

Whether this is a short-term lull in the industry, or whether it is a sign of things to come, it is important to consider what these vast numbers of trained chemists will now do. Governments worldwide repeat calls for more science graduates — and in many ways it's not the new graduates who have the problem. The typical pharma job advert seeks a PhD graduate with 0-5 years of experience — so the really bad news is for those more experienced chemists who have just been laid off.

It would now seem to be a tough task to convince a potential graduate student that this industry is so attractive. Who would invest years of their life and a lot of money into gaining a graduate degree if it offered only five years of employment before forcing a complete career change?

...has just gone live. You can find it here.

It features: a pretty eye-catching cover, a PHD cartoon in the Thesis article on making science experiments more public and a review of the fun but dangerous-sounding book Mad Science: Experiments You Can Do at Home — But Probably Shouldn't.

This month's research papers cover carbene-stabilised P2 radical ions, intefacial structure rearrangements induced by charge-transfer, some synergistic organocatalysis, organic redox electrolytes for solar cells and much more.

And don't forget to check out the atomic-emission-spectra scarves mentioned in Blogroll too!

Neil

Neil Withers (Associate Editor, Nature Chemistry)

In principle, you are right.

...but from time to time I hear lectures in poor English (like mine), in a noisy place, with bad ppt slides, and in uncomfortable seminar room. Those lectures are so interesting that they capture the attention of all the audience. Nothing, except the lecture, does matter.

Is it a talent or a fortunate chance? How can we learn this?

Nongjian (NJ) Tao is in the Center for Bioelectronics and Biosensors, Biodesign Institute, and also affiliated with Electrical Engineering, Physics and Chemistry at Arizona State University. His current research interests include molecular electronics, chem- and bio-sensors.

1. What made you want to be a chemist?

I am probably not a typical chemist on Nature Chemistry's blog because my training is in biophysics. I have been attracted to chemistry because it serves as glue between physics, biology and engineering, which is critically important for interdisciplinary research, such as molecular electronics and sensors.

2. If you weren’t a chemist and could do any other job, what would it be - and why?

I would like to be a geologist or astronaut, who can explore new frontiers, a remote desert or a distant planet, while getting paid. I don’t really regret my career decision because I find that exploring research areas between different traditional disciplines is just as exciting (and challenging).

3. What are you working on now, and where do you hope it will lead?

I am looking for ways to place a single molecule between electrodes, to probe and control its chemical and physical properties, and to explore device applications. I am also developing chemical sensors that can fit in a cell phone, allowing one to excess not only internet and email, but also chemical information. I believe that such a function would expand our capability to solve many real world problems, such as security, environmental protection, and disease prevention and diagnosis.

4. Which historical figure would you most like to have dinner with - and why?

Richard Feynmann would be at the top of a long list. “Feynmann’s Lectures in Physics” helped me to pass an important Physics exam that sent me to study for a Ph.D. in the US. “Surely, you’re joking, Mr. Feynmann” once made a 12-hour oversea flight quite enjoyable and unforgettable. His “plenty of room” lecture has been a constant source of inspiration for my research.

5. When was the last time you did an experiment in the lab - and what was it?

That was last week – when I was experimenting three different glues to fix my broken glasses. Over time, I find myself spending less time doing lab work, and more time reviewing or writing proposals. Fortunately, I am surrounded by many young talents who can do better jobs in lab than myself.

6. If exiled on a desert island, what one book and one music album would you take with you?

I will bring books that can teach me how to survive in a desert island or break out of prison. Entertaining books and CDs would be nice, but I would have to save the space for water and food.

7. Which chemist would you like to see interviewed on Reactions – and why?

Stuart Lindsay – my Ph.D. mentor. He taught me how to do science. I am sure that younger readers will benefit from interacting with him.

Junichiro Yamaguchi is in the Department of Chemistry at Nagoya University, and works on the synthesis of biologically active molecules and natural products - particularly through C-H bond functionalization. Discovery and development of new chemical reactions in order to aim for the “ideal organic synthesis” are his ultimate goals. He also co-runs Chem-Station, a famous chemistry website in Japan.

1. What made you want to be a chemist?

When I first entered university, I had absolutely no interest in chemistry. However, I am fortunate to have met Prof. Yujiro Hayashi at the time, who completely changed my mind and who eventually became my Ph.D. supervisor. He had an unusual, almost excessive passion for chemistry, and particularly for organic chemistry, which he seemed to enjoy purely out of curiosity. I simply started chemistry in order to try to see what he thought was so incredibly interesting – by that time, his passion had already transferred onto me!

2. If you weren’t a chemist and could do any other job, what would it be - and why?

I guess I would be a salesman of some business or medical firm because I am drawn by the strength of interpersonal communication, and I think that selling merchandise is based on trust and relationships between people. In this vein, I am also interested in working on the World Wide Web. I would have set up an independent online-based company, although I cannot tell if such a plan would have enjoyed success or not.

3. What are you working on now, and where do you hope it will lead?

I am working as an Assistant Professor with Prof. Kenichiro Itami in chemical synthesis. I have partaken in natural product total synthesis, and I have been fortunate enough to be involved in the synthesis of many bioactive natural products during my graduate and postdoctoral research. However, natural product synthesis requires so many complex strategies, such that only fellow scientists in this field could understand the extent of its tortuous and complex nature. In order to realize the “ideal chemical synthesis”, the main emphasis of my research regards the development of new synthetic methods, strategies, and concepts to solve challenging synthetic problems. I would like to make molecules as if one were to construct architectures using LEGO blocks.

4. Which historical figure would you most like to have dinner with - and why?

I would like to have dinner with Prof. Robert Woodward, widely recognized as the best synthetic chemist of the 20th century. Having achieved such tremendous total syntheses in an age when purification techniques and spectroscopic analyses were so limited, is nothing short of extraordinary. I would like to talk to him about chemical synthesis and the future of the field of organic chemistry.

5. When was the last time you did an experiment in the lab - and what was it?

I am still running experiments routinely in the lab, and trying to share time with my students in the fumehood. Therefore, I cannot even conceptualize the last experiment I could run, and in fact I do not even want to think about it! Over time, my efforts in the fumehood will have to be gradually reduced, but I would like to keep doing chemistry with my own hands as much as possible.

6. If exiled on a desert island, what one book and one music album would you take with you?

Could I cheat and bring a laptop, or at least an iPhone? If I had to be disconnected from the world, I would simply like to enjoy various pieces of literary works and music, as well as various scientific papers, little by little, until the end of time.

7. Which chemist would you like to see interviewed on Reactions – and why?

I actually have two chemists in mind – the first one is Prof. Phil Baran of The Scripps Research Institute, my postdoc advisor as well as good friend. He is only one year older than me, and yet his ability to synthesize natural products keeps astonishing the chemical community. The second chemist would be Prof. Kenichiro Itami, who I currently share my days with. I would have refused to go back to Japan for my career had I not had the opportunity to meet him and if he did not have such a splendid personality and intellectual talent.

[Posted on behalf of Materials Girl, who is blogging from the Spring 2010 Materials Research Society meeting.]

There often exists an unfortunate lack of connection between presenter and audience. What with non-native English speakers – bless them – insufficient amplification, convoluted PowerPoint, and all the rest, we all may find ourselves itching to be at another symposium. Unfortunately, leaving mid-talk constitutes disruption and some insult to the presenter. (I’ve made it a habit to sit unobtrusively in a corner, and to only sneak out of large, full rooms when the speaker’s back is turned.)

This introduces the subject of attendee etiquette. Half of the audience may walk in late or leave midway through a presentation, although that can be excused in light of travel considerations, lack of personal relevancy, etc. Much less forgivable is the making of excess noise during talks, or squeezing past people to reach a seat near the front. (It’s really not hard to stay in the back, and to wait until questions are finished to move around! Most people do, but occasionally someone bustles about loudly.) Perhaps the worst offence is maintaining noisy conversations outside in the hall, or even in the room. The perpetrators’ voices might be at their normal speaking volume, but everything is loud to the audience of a silent room. All of these annoyances can be avoided with a little bit of consideration…

We might also consider direct interaction, where occasionally some poor young graduate gets ripped apart by a cantankerous researcher, or a combative questioner harasses speakers over minor details. Probing questions and challenging ideas are helpful, but personal/professional/political issues are best left for private debate! As Tim Miller noted in his excellent seminar, Mastering Science Presentations, it is best for all parties to maintain complete civility and to firmly disregard unscientific impoliteness.

On another note, the clothing ranges from business suits and dress shirts, to jeans and t-shirts – sometimes even flip flops! Personally, it feels awkward to wear anything short of a black coat, slacks, heels/boots, etc. (So I generally resemble a character from the Matrix. Or a dude.) Attire is a minor issue, though, particularly since most attendees are males whose formalwear is relatively comfortable and easily come by.

So, considering general dress and behavior (aside from interpersonal relations), conference etiquette boils down to a major question: how stiff and formal are we expected to be?

Paul Krugman has a piece on climate change on his blog at the NY Times. One commenter responds:

"One thing they are "gong" [sic] to do is point out that if the ppm increase in atmospheric CO2 is solely due to man-made combustion of fossil fuels, laws of chemistry and physics have been violated. For every molecule of carbon, two molecules of oxygen are consumed. Therefore, if the rise in CO2 is due to such combustion, then we should observe a decrease in atmospheric O2 by a factor twice as great. I have seen no evidence to suggest that global O2 is decreasing at all." (H. Muhlphart )

Ouch! My response:

No law of chemistry and physics has been violated by assuming that the increasing CO₂ comes from combustion of fossil fuels. The reason no decrease in O₂ is "noticed" is because the loss due to the formation of carbon dioxide is very small compared to the total amount of oxygen. If you increase the amount of CO₂ by 100 ppm (more or less what's predicted in the next 50 years), the decrease in O₂ is from 209,460 ppm to 209,360 ppm. That's the equivalent of being at the top of less than a 30 foot hill. You certainly don't notice any change in the oxygen levels between the basement and second floor of a house, do you?

And I didn't even bother with the notion that carbon dioxide "eats" two oxygen atoms no matter what carbon source you make it from - fossil fuel or respiration. Or that it's one carbon atom to one oxygen molecule. At this level of understanding of the basic science, you are not simply not entitled to an opinion on the matter.

What does the p in pH stand for?

The term pH has been in use for more than a century. It is a logarithmic measure of the hydrogen ion concentration ([H+]): pH = -log10[H+]. (Technically, there aren't bare protons (H+) floating around in solutions, but that wasn’t known when pH was introduced!) The original symbol used by Sorensen was p_H⁺.

Theories vary as to the origin of the p - most agree it means power but whether in Latin, French or German, seems in dispute. Thinking it would be either French or Latin as the original paper was published in French, I was surprised to find that it's neither, though the legend is both old and persistent. By 1920, many authors were assuming that it meant “power”, but Jens Norby returned to the original sources and points out that it was the arbitrary choice of the letters p and q for two variables in the work-up of the experimental data. The variable p eventually ends up in the formula arrived at for the concentration of the hydrogen ion.

The modern form pH was introduced in 1920, "as a matter of typographical convenience".

For the full explanation, see Jens G. Norby, The origin and the meaning of the little p in pH, Trends in Biochemical Sciences 25, 36-37 (2000). The illustration is a selection from the original paper: Sorensen, Compt. redn. du Lab. de Carlsberg 8 1-168 (1909).

Open Laboratory 2009 - a juried anthology of the best of the science blogosphere from last year has appeared. Edited by scicurious, it's available here. I have a piece in it - a cleaner version of this post on the use of helium to preserve documents. I'm fascinated with the interplay between web and print that ultimately produces this volume.

Want a copy? Order one -- or if you're feeling lucky, de-lurk and leave a comment before March 5th and I'll draw a winner at random. The rest of the pieces look great - on everything from the flu to charismatic megafauna (whales and chimps) to the statistics of human milk production.

I vividly remember the first time I met a Nobel Prize winner. I was a graduate student in my 3rd year, and Roald Hoffman had recently won the Prize in chemistry (1981). A group of us went up with our research advisor (who had worked with Hoffman as an undergraduate) to hear him speak at a symposium at USC. On the drive up we were briefed as to behavior - do not speak unless spoken to. Frankly, we were happy enough to be out of the lab as well as treated to lunch (and to a terrific speaker). Lunch was at picnic tables in an outdoor courtyard - the grad students all clustered at a table on the edge. Imagine our surprise (and delight) when Hoffman joined us at the table, and spent lunch asking us what we were doing for research, and what excited us most about chemistry. I, at least, left with the sense that I was an interesting part of the chemical community -- even if a very junior one.

The Noble organization and Honeywell are offering the opportunity to anyone to ask a question of Nobel winners. The next live broadcast is Tuesday, March 2 at 11:15am (-6hrs GMT), when you can hear Robert Grubbs, who won the chemistry prize in 2005 for his discovery of olefin metathesis (a method to rearrange carbon-carbon double bonds using metal catalysts). I wrote my oral exam proposal on olefin metathesis in 1982 - I was fascinated then, and am still, with these atomic level architectural changes.

The best part? You can ask questions - email them to question@honeywellscience.com or go through Twitter or Facebook.

In the early part of the 19th century, the word scientist had yet to be coined. As the scope of materials and phenomena that natural philosophers and historians dealt with increased, there was a growing sense that these terms were inadequate to describing the task of this new breed of inquirers. In the 1830s, the British Association for the Advancement of Science explored potential candidates, but ultimately rejected various proposed terms, including scientist:

"Philosophers was felt to be too wide and too lofty a term,..; savans was rather assuming,..; some ingenious gentleman proposed that, by analogy with artist, they might form scientist, and added that there could be no scruple in making free with this termination when we have such words as sciolist, economist, and atheist — but this was not generally palatable."

The need remained, however, and a decade later, William Whewell, a philosopher and biologist pushed the issue again: “We need very much a name to describe a cultivator of science in general. I should incline to call him a Scientist.” This time it stuck.

Once the name stuck, an image quickly became attached -- wild hair, lab coats and odd apparatus all became part and parcel of what it means to be a scientist. My most recent Thesis columnin Nature Chemistry -- Men of Mystery -- takes up popular images of scientists, and considers the impact the images might have on public discourse about science.

UPDATED: See Snail's Tails post about philosophy and philosophical instruments. The ad for the "philosophical instrument makers" is fascinating!

In 2006, Bora Zivkovic brought us the first edition of Open Laboratory, a print collection of the best science blogging of the year. Now in its 4th year, the 2009 edition, guest edited by scicurious at Neurotopia is going to press soon. A record 760 posts were nominated, winnowed down to fifty by scicurious and her panel of judges.

One post of mine (The Pressure to Preserve) will be included! While you're waiting for this edition to come out, I heartily recommend browsing the earlier editions. Who says scientists can't write?

'tis the season for baking on the home front. It's been mostly biologically based leavening (yeast) at my house, but some strictly chemical rising has been going on as well. For an interesting mix of chemistry and biology in the kitchen check out Not So Humble Pie's science cookies: zebrafish, drosophila, gel electrophoresis and atoms are on the menu. Something to keep in mind for the next snow day around here...

When I was lecturing on lasers this week, I was surprised to discover how many of my students were unaware that laser was an acronym (Light Amplification by Stimulated Emission of Radiation). Science is replete with acronyms - Ira Levine once essayed that if you knew enough acronyms you could pretend you knew computational chemistry - good, bad, really funny and occasionally unfortunate.

On my desk is a paper which refers (with as near as I can tell with a straight face) to "PUS research." Public Understanding of Science. I swear this is true.

If you've got a favorite one - funny, famous or truly unfortunate - leave it in the comments for all of us to enjoy...

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Related Posts
Science in the kitchen: Jello lasers
Romancing the stone (steampunk lit and lasers)

Scientists from the University of California, Irvine have found that Nitrogen Dioxide (NO2) and Ozone (O3) react with surfaces painted with lead based paint to increase the release of lead from said paint posing an even greater risk for children. By Roberta Barbalace

Stephen Davey, associate editor for Nature Chemistry, blogged at the Sceptical Chymist about visiting the National Archives and seeing the Declaration of Independence, the Constitution and the Bill of Rights. He was surprised to find that the documents were stored under helium as opposed to argon - and wondered why. That started me wondering as well, particularly since the inert gases are not interchangeable in all circumstances (you can use helium to dilute the air mixture for diving, but not argon, for example.)

Helium is both more expensive (not an issue in this context, the cost of the gas inside the cases has got to be the least expensive piece!) and difficult to work with than argon. It can leak out through materials that seem air and water "tight". That's why those latex balloons that looked so cheery on the day of the party are withered and droopy by the morning. They're waterproof, but not helium proof.

In the 1950s the US National Bureau of Standards (now NIST) was charged with deciding on the best way to preserve the Charters of Freedom (the three founding documents of the United States of America). (You can read the full report here.) Helium was chosen, despite its propensity to leak through many materials, partly because a high purity, local source was readily available but most because of its thermal conductivity.

The designers of the encasements wanted a way to measure the pressure of the helium within the cases without having to open them, or remove a sample. Since the thermal conductivity of helium is very different than that of air, changes in the thermal conductivity (how heat moves between the panes) could be used to detect leaks. Argon's thermal conductivity is similar to air, so if argon leaked out and air in, the change would be hard to detect.

New casements were designed about ten years ago, with argon as the gas of choice this time. Sapphire ports are embedded to allow the atmosphere inside the cases to be monitored spectroscopically - by passing a beam of light through the port. Since the new methods of monitoring don't require the inert atmosphere to have a different thermal conductivity, it allows argon - which can't wiggle its way out the way helium can - to be used.

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The photo is from The Science News-Letter, vol. 62 (Dec. 6 1952), p. 359.

(Cross posted at my other blog.)

I am in the midst of writing an essay for Nature Chemistry - about why people are so curious about stereotypes of scientists, but seem less so about other fields. There is the DAST (draw a scientist test), but not as far as I can discover similar instruments to assess the images of other professions. Where are the DATTs (draw a teacher test) and DACTs (draw a chef test)? On the other end of the cultural spectrum there is the Big Bang Theory.

The earliest anthropological study I can find dates to the late 1950s and is by Margaret Mead (yes, that Margaret Mead) and Rhoda Metraux under the auspices of the AAAS. They analyzed thousands of essays, drawn from a set of 35,000 written by US high school students. The 1 page essays were written in response to one of three prompts. Prompt I read "When I think about a scientist, I think of..."

What took my breath away was Prompt II (italics are not mine, but as given in Mead's original paper - Science 126, 384-390 (1957)):

If you are a boy, complete the following statement in your own words.
If I were going to be a scientist, I should like to be the kind of scientist who...

If you are a girl, you may complete either the sentence above or this one:
If I were going to marry a scientist, I should like to marry the kind of scientist who..."

Math Man points out that I did both.

UPDATE: So there is a draw-a-teacher test (DATt) (H/T to Neil who commented on drawing God - another area that has been explored by educators and psychologists)

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Images are from K.D. Finson, J.B. Beaver, B.L. Cramond, "Development and Field Test of a Checklist for the Draw-A-Scientist Test" School Science and Mathematics 95, p. 195 (1995).

Dear Gentle Readers,

For a long time I have been an author and outlet for many in the chemistry community and the run was, to say the least, more than I could have ever expected.  It was through this blog that I found a cathartic release of frustration, anger and, most importantly, the insatiable curiosity I have always had for science.

Some time ago, a reader named Bethany Halford asked me a question about why I blog and I framed my answer in as quotable of a context as I could – because I wanted to see how far I could push this thing.  I think I have pushed it far enough and I have reached the end of my intellectual interest and now wish to divest myself from blogging so that I may completely free myself for the pursuit of other things.  No doubt you have noticed that the frequency of posting has diminished as my other projects have begun to take off and my fullest efforts are required there.

Now that blogging appears to be an activity which is regulated by the FTC, I think it’s safe to say that it has finally arrived.  I now know (or at least I think I know) what it takes for someone to develop a successful web presence and what sort of innovations are needed to build on that presence.  My programming skills are also none the worse for the endeavor.

In any regard, this is the end.  The lights will be shut off next month, the gmail account will no longer be answered and the chemblog store with its catchy EJ cup and functional group poster will be deleted.

Good bye, world.

Yours,

Kyle Finchsigmate

Pew tracks American's familiarity with the news of the day - my kids took the latest quiz (and each scored in the top quartile for adults and so were quite pleased with themselves). I played with something similar for science...it's definitely NOT rocket science, so if you've any science background at all -- you should score 100%.

If you're looking for the answers - they are here.

Today I constructed a brand new shelf in my hood.  I love hood shelves.  You can put chemicals on them, solvents, glassware… all kinds of things that would ordinarily go somewhere else more… public.   After I was done constructing my masterpiece I began to admire my handiwork and populate it with things (mostly chemicals) but, while I was standing there talking with my hood neighbor, the consensus was reached that the new shelf begged a novel hood design:  it needed hood Feng Shui.

While I have no idea what Feng Shui actually is, I’m 99% certain it has something to do with colorful fish or those lucky bamboo things they sell at Target and since 99% is basically 100% I figured my hood needs a fish inside of it.

Of course, I’m a realist.  I can’t put a whole aquarium in my hood – that would be chest slappingly short bus retarded.  Since I don’t want to run an air pump through my hood I need a labyrinth fish.  The king of such fish is the betta fish or the Siamese fighting fish.  And  because I’m 99% sure Feng Shi also means making sure your shit matches, it needs to be in a round bottom flask.  (That useless 29/42 ground glass is suddenly less useless!)

So, I’m thinking about something like this:

I would put the fish in a flask on my shelf, where I would feed it and it could watch my reactions for me at night (and tell me who the fuck keeps turning my hood’s airflow alarm back on).

Alternatively, I could set up an ant farm and run the ant tubes all over my hood.  That would prolly kick ass, too.

This energy audit was conducted on our house as part of our 70s house eco renovation project to help us prioritize weatherization and energy efficiency projects. This is one in a series of articles documenting the eco renovation of our house. By Erik North, Free Energy Maine LLC.

After I won a Nobel Prize I suddenly turned into an omniscient sage, whereas formerly I was simply a workaholic.

Richard Ernst, Chemistry 1991

(H/T to Nature Chemistry's October editorial)









Photo of Dirac's Nobel Medal is from: rubberpaw at Flickr

I am at the ACS meeting in Washington DC, here as "press" rather than chemist. It's a very different way to see the meeting. I went to a press briefing this morning - on the first phases of development of aresol vaccines for measles (Robert Sievers). The press center is tucked away next to the registration, and has everything a writer might want: food, wireless access and a steady stream of caffeine and conversation.

The briefings are being streamed live on the web and journalists watching can send their questions in to be asked. Miss something the first time round? Watch the replay here.

Listening as a scientist to a talk, and as a writer to the briefing turn out to be slightly different experiences. Both require critical listening, but listening as a writer prompts me to think far more about the words the science is coming wrapped in. The shorthand scientists use sounds almost staccato in this context. "Measles naive" instead of "never exposed to the measles virus" or "no evidence of viremia" instead of "no measurable virus in the bloodstream".

We try to be both precise and concise, but I wonder how often the combination in giving a talk, or even reading a paper in the literature leads to attentional processing deficits? An interesting experiment in attentional processing is to present subjects with a rapidly changing sequences of letter, interspersed with numbers. If two numbers are placed too close together, subjects can "miss" the second letter while their brain is busy processing the first. Pack too much into a sentence, and your "subjects" might miss bits.

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My Thesis column in Nature Chemistry this month, Stretching Toplogy, takes a slightly different tack in thinking about the ways words wrap around science.

My youngest and I are heading into Philadelphia tonight for a chocolate dessert feast, so it seems apt that a friend sent me this bit of mathematical magic this morning - with a plea to explain how it works.

Chocolate Calculator:

This is pretty neat. Don’t say your age; you will probably lie anyway!

DON’T CHEAT BY SCROLLING DOWN FIRST

It takes less than a minute. Work this out as you read.

Be sure you don’t read the bottom until you’ve worked it out!

1. First of all, pick the number of times a week that you would like to have chocolate (more than once but less than 10)
2. Multiply this number by 2 (just to be bold)
3. Add 5
4. Multiply it by 50 — I’ll wait while you get the calculator
5. If you have already had your birthday this year add 1759. If you haven’t, add 1758.
6. Now subtract the four digit year that you were born.

You should have a three digit number

The first digit of this was your original number (i.e., how many times you want to have chocolate each week).

The next two numbers are YOUR AGE! (Oh YES, it is!!!!!)

THIS IS THE ONLY YEAR (2009) IT WILL EVER WORK, SO SPREAD IT AROUND WHILE IT LASTS!

So how does it work?
Expressed algebraically, the procedure if you have had your birthday can be written as:
50 (2n +5) + 1759 - y
where n is the number you chose and y the year you were born

The author asserts that this will produce a number where the digit in the 100's place is n and the remaining digits are your age or 100*n + age. If you have had your birthday this year, your age in 2009 can be written in terms of your birth year, y, as
age = 2009 - y
So the formula should produce 100*n + (2009 - y).

It is trivial (I love saying that) to show that

50 (2n +5) + 1759 - y = 100*n + (2009 - y)

This will not work if your age is greater than 99, but as long as you are younger than that, the last two digits will always be your age even if the number of times you want to eat chocolate in a week is greater than 10 -- so in either case eat all the chocolate you want!

I was playing Scrabble online the other day and when a z materialized on my rack near the end of the game was desperate enough to try "azo". Good news, what I thought was chemist's shorthand, the dictionary thinks is a word. "Azo" has been part of my vocabulary since I was very young. My dad's graduate work was on azides - molecules that contain three linked nitrogen atoms (N₃) tagged at the end and that are notoriously unstable (a fancy chemistry term for "could explode at any time" - at a dinner for his PhD adviser some 25 years later the number of people around the table lacking fingers was astounding). Azo compounds are molecular relatives of the azides - molecules that have an two linked nitrogens in the middle (R-N=N-R). Some azo compounds are brightly colored and generally they are more stable than azides.

As a rule of thumb, if you see "azo" in a compound's name, it's likely to have nitrogen in it somewhere. Why? French chemist Lavoisier dubbed the fraction of air that cannot support life "azote" from the Greek azotos: without + life. We now know that roughly 80% of the air we breathe is nitrogen gas - hence the connection between azo and nitrogen.

Lavoisier's alternate terms was "mephitic air" -- another Greek import, this time from the name of the goddess who prevented noxious smells from arising from sewers: Mephitis. Ironically, while many nitrogen compounds smell awful (dead fish anyone?), nitrogen gas, Lavoisier's mephitic air, is odorless. That goddess has lent her name to smellier pursuits though - the striped skunk's Latin name is Mephitis mephitis. I can personally attest to the smell.

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Photo used under Creative Commons license. Credit to Kevin Bowman.

My youngest son, Barnacle Boy, swims like a fish. When he was small, he could stay under water just a second longer than I though he should be able to -- I'd be ready to reach under and haul him to the surface, and then up he would pop. I began to wonder if he had gills.

Nowadays I'm certain he has no gills, though he can still hold his breath for a long time. He's not quite completely adapted to an aquatic life, though. He suffers from water in the ears. And he hates to hear himself sloshing...

The standard remedy for water stuck in the ears is "SwimEar" - an ad for which reads in part:

"Once water enters this tube...surface tension will cause this water to adhere firmly to the walls of the canal, thereby blocking it. Why is this water so difficult to remove? This is due to surface tension effect as well as the fact that it is extremely difficult to break the vacuum that is created behind the trapped water in the ear canal."

Despite the popping sensation you can get when your ears finally clear from water, there is no vacuum behind the water (really, I'm certain). As the ad implies, the trouble is that water is clingy, and therefore has a high surface tension. The high surface tension is what impedes the flow of water out of the ear canal -- think of getting the water out of a thin straw. The ear canal is behaving like a capillary. Reduce the surface tension and the fluid will release.

SwimEar is just a solution of isopropyl alcohol with a dash of glycerin added for comfort. (Ethanol, or ethyl alcohol, is what we drink - but to a chemist, an alcohol is a molecule that has a "tail" of (mostly) carbons and hydrogens topped off by a hydroxyl group: OH. Ethanol is CH₃CH₂OH, isopropyl alcohol is (CH₃)₂CHOH.) The isopropyl alcohol lowers the surface tension of the water (so will a bit of soapy water for that matter).

Horror of horrors - the Romans used lead to sweeten their fruit. No wonder Rome fell! Except that I was willing to read a 1883 paper (in German with healthy helpings of Greek and Latin) to discover that it may be lead and it may be sweet, but the lead doesn't lead it to be sweet.

In a time when mercury was regularly used as a remedy for maladies as serious as syphilis and as commonplaces as constipation, it doesn’t surprise me that lead compounds were in the pharmacopeia. (In all fairness, some modern antibiotics and most chemotherapy agents are at least as toxic as these less old remedies; they just have a better risk-benefit ratio.) Sugar of lead, or as it’s called in the 19th century medical literature, saccharum saturni, is lead acetate: Pb(CH₃COOH)₂. It was once prescribed for intestinal troubles, an odd choice, since one symptom of acute lead poisoning is an upset stomach. Lead poisoning is also known as painter's colic.

Sugar of lead really is sweet, roughly as sweet per spoonful as sugar. In the 18th and 19th century, lead shot was often dropped into bottles of port, purportedly to make it sweeter - though the more likely effect is anti-bacterial. Why? Lead does dissolve well in alcohol and juices (crystal decanters to store your port are a bad idea) - but I can't find anything that suggests solutions of lead ions are sweet.

The Romans were reputed to use lead acetate as a sweetener. They produced a syrup called sapa by boiling down mildly fermented grape juice in kettles made from lead alloys. (The hydrates of lead acetate are far less soluble in alcohol solutions - you are more likely to get a suspension of crystals in the syrup.) I am suggesting that it’s unlikely that the syrup was sweet because of the lead acetate it certainly contained. An 1883 analysis of sapa produced according to recipes dating from the classical Roman period, in kettles of similar metallic content to those found at Pompeii and other sites, suggested that the lead content of sapa was roughly 850 mg per liter. The equivalent amount of table sugar would be roughly a teaspoon - hardly enough to taste sweet in a liter of liquid. On the other hand, the sugars (glucose and fructose) in the concentrated grape must are the equivalent of 1 cup of table sugar per liter and would certainly swamp any sweetness coming from the lead acetate. It's still not all that sweet. To get a sense of how sweet this is, simple syrup, which has similar culinary uses to sapa, has about 4 cups of sugar in a liter.

I still wouldn't use sapa to poach my pears, but I think it unlikely that the sweet taste of sapa has much to do with lead.

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Photo is c. 2009 John4kc. Used with permission.

I was wandering the Cape Anne historical museum this winter and noticed in a 19th century ship's medical kit a vial labeled "sugar of lead." This is lead acetate, which tastes sweet -- and is reputed to have been used as a sweetener is days past. Other metal salts are sweet as well - yttrium salts and beryllium salts can both taste sweet.

Beryllium was first identified in 1798 by chemist Louis Vauquelin as an oxide in beryl and emeralds (emeralds are beryls with a bit of chromium added!). Since the chloride salt of the new element tasted sweet, the editors of the journal which published Vauquelin's findings suggested he call the oxide (or earth) glucina from the Greek, glyks (γλυκυς) for sweet. The elemental symbol used was Gl.

Beryllium was suggested as alternative once other sweet metal salts were found, for the gemstones in which the element was first identified. It took until 1949 for this to become the official IUPAC name of the element with four protons.

Beryls were used to make "reading stones," magnifying glasses, then eventually ground into lenses for eyeglasses.

The recipe for pulled pork called for 1/2 cup of brown sugar to be dissolved into 1 1/2 cups of apple cider vinegar. What I had in the cabinet was solid as a rock - there was no way I was packing this into a measuring cup. (Yes, I know I could have done this in the microwave...) My scale came to the rescue. I hacked off chunks until I had the correct mass of brown sugar (110 grams more or less). I dumped the three large hunks into the vinegar in a 2 cup glass measure, and noted that the total volume was just about 2 cups. Nice job.

Then I stirred it to dissolve the sugar. And watched the volume decrease to just over 1 1/2 cups of solution! Have I just proved Archimedes wrong? The volume of sugar at first seemed to have displaced the equivalent volume of liquid, but then seemed to vanish...well not exactly into thin air, but vanish nonetheless. As my 15-year old might say, "What's up with that?"

Yes, Archimedes was correct, but his theory did not address substances that dissolve in the liquid. This is a good demonstration of how much "empty "space is in a liquid. The sugar molecules (and other things in brown sugar, which is not terribly pure as chemicals go) insert themselves between water molecules, without needing to push the water molecules further apart. To a good first approximation the volume of a solution made from a solvent and soluble solid is the volume of the solvent used, not the sum of the two volumes.

Try it...it's fun to watch, and it still intrigues me to think about the amount of unused space there is in a liquid that seems so substantial at the macroscopic level!

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The pulled pork was a keeper...though the kids found the BBQ sauce too spicy for their taste. Try it on challah rolls!