The Computational Chemist said...what?

So I like cruising around Reddit.com's subreddit on chemistry from time to time because it's a generally useful place for seeing others' work, help out aspiring academics, and generally have a place to get extra help on advanced chemistry techniques. The atmosphere around there is full of polite, like-minded individuals all looking to have a good time in their field.
But sometimes people get a little too helpful, and step outside their comfort zone.

I took this little screen grab from a r/chemistry thread where a particular chemist has been asking about building his own inert atmosphere (nitrogen only) glove box. He wants to heat up some samples in it. So a computational chemist, a chemist that does all of their experiments inside a computer program, probably took this little gem of advice from their gen-chem lab when suggesting the original poster try to light a burner inside the glove box.

Now, Bunsen burners (named after the scientist Robert Bunsen) work from atmospheric oxygen being supplied to a pressurized stream of gas. That gas comes through a hose, mixes with the oxygen at the basal inlet of the burner, travels up the barrel, and is finally ignited at the top of the burner. If there's no oxygen around in the air, it won't light!

That's why quantum_mechanic's suggestion of "practice makes perfect" is silly- you can't practice making oxygen in a glove box where there is none!

Quotes from Chemistry...Part 9!

“We have a habit in writing articles published in scientific journals to make the work as finished as possible, to cover all the tracks, to not worry about the blind alleys or to describe how you had the wrong idea first, and so on. So there isn't any place to publish, in a dignified manner, what you actually did in order to get to do the work”. 
                   -Richard Feynman, in his 1965 Nobel speech

This is a matter that has plagued me throughout my whole time in academics as a researcher. In addition to that, I think it plagues science as a whole-- a problem where the actual story of scientific discoveries is lost amid the reporting of results.
Right now, science news report the results of some study that builds upon an earlier idea and the implications (far-reaching or near-sighted) for a greater audience. But there's a more exciting story to be told. To borrow from a fellow science communication colleague (and dashing gent in a bowler) Dr. Matthew Francis, "Science, is incremental. News, on the other hand, isn't."
News doesn't tell the full wandering story of how the discoveries are made. It doesn't tell about the failures, the frustrations, the late nights nor the moments where one is grasping at victory. You never hear in a news story-

 "Johnson was up until two in the morning running that analysis, because that machine is used so much it's the only time she could fit it in. The fumes of her 5pm coffee were just burning out and as the fuzziness of exhaustion began to close around her, the last scan completed sealing the confirmation of her hypothesis." HOW COOL WOULD THAT BE!?

"That's not an easy pipette, John. Jeez!"

Blind alleys, as Feynman calls them, are what drive scientists to keep asking new questions and probing new territory.

Granted, not all narratives are equally compelling. Many are downright dull without manufactured drama. But I think having added emphasis about the process of gathering results could add to the public perception about what scientists actually do. This could be beneficial in breaking down the caricature that has haunted popular perception for so long. It could paint scientists as the normal people we are, just doing our jobs too. Bill Bryson's book A Short History of Nearly Everything  is hands down, my favorite book ever. That's saying something for those that know my love of The Lord of the Rings and Redwall.
In the book, Bryson tells a number of anecdotes from many different disciplines of science from a really human perspective. These were people he was talking about. He painted the picture as such. He talked about where they were from, what piqued their curiosity, and about the context (most often accident) in which their big discovery was made.
That's a story I think is missing from a lot of science reporting. The "socially distant and awkward" researcher is (largely) a myth. The next time you read an article about a new scientific discovery, just take a moment to ponder how many ideas died on the chopping board, how many cups of coffee were consumed, and how many facepalms occurred in pursuit of that result.

Image (http://www.beyond.com/articles/top-schools-for-medical-lab-technicians-10959-article.html)

Conquering Westeros...the Chemistry of Fire Breathing Dragons

Literally rocket science. "Fire Breathing Dragon" by san dara [deviantart]

Dragons are riveting creatures. They have been a staple of fiction and mythology for all of written history, captivating our wonders and fears for millenia.  The mere mention conjures imagery of massive scaly beasts alighting dark caverns with the bodies of over-zealous knights. From ancient works like Beowulf to modern works like George RR Martin's A Song of Ice and Fire, dragons are known to spew fire "hot enough to weld steel or crack stone." But one part of the lore remains a fundamental mystery and topic of debate. What is dragon's fire? What is it made of and what makes it possible? A simple explanation is that the fire stems from their magical nature- but what if dragons really existed? What would it take to make dragons and their iconic fire-breathing real? Let's explore what it might take to make dragons possible- the chemistry, biology, and physics of this mythic beast.

A somewhat knowledgeable person might suggest that fire breath could be created by a pyrophoric compound. Pyrophoric compounds are certain chemicals that spontaneously burn in air and moisture. That, on the other hand, oversimplifies a more complicated question- how could a pyrophoric molecule possibly be made and moved within the body without resorting to some sort of magical or exotic material? It couldn't. With the exception of certain microscopic extremophile bacteria, the chemistry of living things is carried out in watery environments. This would mean the chemicals would burst into flame inside the dragon's body. Luckily, there exists within nature a model for small scale explosions within an animal.  

This lucky little bug is called the bombardier beetle! These beetles use a mix of hydrogen peroxide (the same as  the drug store disinfectant) and a chemical called para-hydroquinone. When mixed in the presence of catalysts called enzymes, these two chemicals undergo a reaction that produces a ton of heat and steam! Enzymes are proteins that act like little machines to help chemical reactions happen in the body. Though its result is certainly impressive, this little jet only reaches the boiling point of water though- it's no flame!

To melt steel, crack stone, or burn flesh we need something REALLY hot, so lets get back to basics. Any firefighter will tell you that you need three things for a fire: fuel, oxygen, and a source of ignition. For a fire to come out of a dragon, this rule still needs to hold true, but where do we find such a combination? The bombardier beetle gives us an interesting starting point- take two materials in separate sacs, mix them together and create a chemical reaction that is quick and violent. 

Another class of materials serves this exact purpose, hypergolic chemicals. Hypergolic chemicals automatically burst into flame when they come into contact with the right material. As shown in the video below, reactive nitrogen oxides provide a really neat example of the ignition of an organic (carbon containing) molecule with dinitrogen tetroxide. Nitrogen oxides of many different types are used as liquid propellants for rockets because of their high energy density and reactivity with various fuels. 

But if these reactive nitrogen oxides burst into flame in contact with anything organic, how could they exist inside the dragon's body he'll be hurt by it? Production of these chemicals inside the body would not be favored by evolution, so we'll have to find a way to quickly make these chemicals on demand. Fortunately, the two components of nitrogen oxides- nitrogen and oxygen- are incredibly abundant in the air! But how would such stable molecules, which exist in the atmosphere without complication, react to form these extremely reactive molecules? Simple! 

Using an enzyme inside of an internal air sac, the dragon could take nitrogen and oxygen gasses from the air and convert them into nitrous oxide N2O. You'd know this compound better as laughing gas- the same that you would get from the dentist! When N2O comes in contact with more oxygen, it gets converted into nitric oxide, NO. This is a very reactive molecule that would react with still more oxygen very rapidly to form nitrogen dioxide, NO2. This is where the chemistry gets exciting. 

NO2 can react with itself to form dinitrogen tetroxide N2O4, and normally a balance between these two molecules exists within a sample. Both are known to react explosively with organic matter (hydrocarbons) like you see in the video above. So this brings us to the next point- what do we use for fuel?

Dragons are voracious meat eaters and would therefore consume plenty of fats and oils. If they were known to eat vegetables, we could throw sugars and fiber into that mix as well, but we don't ever see dragons passing up a tasty horse for a salad now do we? These fats and oils from the dragon's meat intake, if combined with dinitrogen tetroxide serve as a perfect vehicle for lighting up the knight! If we leverage the dragon's serpentine nature and connect its digestive tract to a special sac inside the dragon's skull (like a snake's venom sac), the dragon could "exhale" the nitrogen oxide compounds, squirting a jet of grease would create the necessary environment to mix with air and ignite the fire!

Dragon Fire Anatomy, original sketch by Sara Spath

Combining biochemistry with fire clearly has never happened under any circumstances that science knows of at the moment, but if such a creature were to evolve or be engineered a la Jurassic Park, my bet would lay with a creature similar to this. Certain bacteria in the soil already produce nitrous oxide from the air, but it's obviously in very small amounts.  I, for one, am thankful that we don't live in constant fear of a gigantic, reptilian, fire-breathing beast. I'm glad that (for now) they exist solely in works of fiction. But what if...?

--------------------------------------------

Author’s notes:
Thanks to those who contributed conversation, expertise, and input on this post!

Previous examples[1] of this supposition[2] exist elsewhere, where the former example focuses on the ignition of methane and oxygen in the presence of a spark and the latter on platinum from the dragon's diet catalyzing a hydrogen flame. Clearly, no scientific consensus exists on the matter about what it is dragons breathe. 

I suggest this version over those provided in the earlier explanations for a variety of reasons. In the SciKat post, she suggests an actual spark be produced by the jaw or a “piezoelectric crystal” that ignited the flame inside the throat. Not only is this dangerous to the dragon, no real biological analogs exist for us to build from. It works on the idea of “exotic materials” too much for me. In the Animal Planet discussion, they use a platinum ore catalyst with hydrogen to produce the flame. It’s chemically accurate…but that would require the dragons to consume an amount of material that simply wouldn’t be sustainable for a healthy system. It’s why microbes eat rock, not animals.

There are some cool chemicals to look at that produce the hottest carbon-based flames, cyanogen NCCN and dicyanoacetylene NCCCCN (respectively), that I would have loved to include but there isn't any biologically applicable way of including them.

[1] http://sciencedaydreams.wordpress.com/2011/08/29/hello-world/

[2] http://www.animalplanet.com/tv-shows/other/videos/dragons-fire-breathing-dragons-explained.htm

[3] http://en.wikipedia.org/wiki/Dicyanoacetylene

Quotes from Chemistry, Part 8!

“Science, my lad, is made up of mistakes, but they are mistakes which it is useful to make, because they lead little by little to the truth.”


― Jules Verne, A Journey to the Center of the Earth

Image Courtesy of Wikipedia

Ten-Hundred Words Challenge

Can you write about what it is you do, using only the thousand most common words in English? I bet you can. With a little bit of thought, even a topic so rife with jargon as nanotechnology [1] can be simplified down to use really, really common terms. The "Up-goer-Five" [2] text editor takes whatever you put into it and checks against the list. Here's mine:

I like to think about and make really small stuff. Right now computer insides are made kind of small but soon that won't work anymore. Really Small Things work sort of different than Bigger Things and computer insides are too big. I am thinking about ways to make things even smaller but still work like the stuff we already know.
I can think about and make a thing the way I want to by using building blocks to put smaller things together to make a bigger Small Thing. With these Small Things I want to see how power moves through, to help understand what power does at such a small area. By changing the blocks that I use, I can make the Small Things act different from each other slightly so that I can know what change had what end.
Using these Small Things together with other small things will let humans make cool new things to do more new work with.

XKCD had a comic [3] that explained the Saturn V rockets (hence "up-goer five") and since being featured in a Scientific American [4] blog last year, a Tumblr called Ten Hundred Words of Science [5] collects submissions so that you can read in simple terms, what people really do!

At the Science Online Together 2014 Conference I attended last week in Raleigh, NC afforded me the opportunity to meet a lot of new and interesting people.
From that I met a woman who had participated in this challenge and she posed it to me. Thanks to +Gretchen Goldman for the inspiration!

[1] http://tenhundredwordsofscience.tumblr.com/post/41281268006/my-work-is-about-studying-really-small-things-it
[2] http://splasho.com/upgoer5/
[3] http://xkcd.com/1133/
[4] http://blogs.scientificamerican.com/guest-blog/2013/01/27/science-in-ten-hundred-words-the-up-goer-five-challenge/
[5] http://tenhundredwordsofscience.tumblr.com/

Dancing Dissertation Research

You do the hokey pokey and you turn yourself about....
Image courtesy of Kacey Deamer (@KaceyDeamer)

This week's "Picturing Science" post comes fresh from Science Online's Together 2014 conference in Raleigh, NC. While out to dinner one evening with some of the other conference attendees, I was asked by those around me to talk about the differences between a couple of the main biological molecules. The particular attendee asked me about the chemical difference between proteins and carbohydrates.
While the audience in general was a fairly savvy one, the woman in particular who had asked the question hadn't had chemistry since high school and had said so. Instead of breaking out the pens and bar napkins like I would do with someone intimately familiar with organic chemistry structures, I made do with what tools I had available: my body and a momentary lack of dignity.

I had a feeling this might cause a riot or food fight.[1]

I mean come on. The difference is so totally obvious duh. [2]

I explained that, in large part, carbohydrates were long chains of carbon rings stretched out like a necklace connected by oxygen and that a protein is a more complicated globular form that all depends on the way that its individual sections (called amino acids) are connected. To demonstrate this, I waved my hands like a hula dancer representing the carbohydrate chain and the protein structure was wrapped around my head like I was dodging a firefight. This got a lot of laughs because my forms got physically stranger as I was trying to communicate ideas with elbows, shoulders, wrists and fingers.

The folks around me had enjoyed the performance so much that I was asked to talk about my research....of course using the same odd demonstrations. While performing, one of the attendees took a series of photos with her phone and using some post processing in the phone itself produced the image you see at the top. I had been pantomiming the synthesis of a chemical and then talked about the future direction of my work. It got a fair amount of laughs as well and while it didn't teach any overarching concepts of science we had a good time. 

[1] Myoglobin http://upload.wikimedia.org/wikipedia/commons/6/60/Myoglobin.png
[2] Carbohydrate http://html.rincondelvago.com/000280467.png

What do food, creationism, and language have in common?

The day after the Bill Nye- Ken Ham debate [1] was a lively one online for extremists in both camps. Scientists shook hands, patted each others' (virtual) backs, and congratulated each other on the clearly superior position of science. Young Earth Creationists (YEC's, the people that believe the Bible as interpreted literally) too, held hands and praised the power of God to act through the voice of Ken Ham against the "secular humanist" view of Nye.
All of the people I personally know came away from watching that debate (mostly live) saying that Nye had stomped all over Ham. "Ham had no answers, no evidence, no proof," went the chorus. And online blogs largely followed suit. American Atheists, Inc. took only hours to release this "summary" [2] of the debate which excerpted from the Q&A section at the end.

Click link above for full image. Source: American Atheists, Inc.

Buzzfeed, too, released a listcicle* shaming creationists' reactions to the debate. While not representative of the population at large, it is meant to suggest YEC's inability to grasp reality and evidence. Its voice is tailored to say that YEC's are simpletons that won't change their minds because it is incompatible with their faith. A follow up to that article showing doctored (sarcastic) translations of those questions can be found on the web.
But there are a few writers that were unsure if Nye's goals were even compatible with the horse and pony show that Ham was setting up. Nye was in the lions' den, since the debate actually took place in the auditorium of the Creationist Museum.
Sean McElwee and Abigail Salvatore of Huffington Post [4] write, "The solution is not anti-theism but better theological and scientific awareness...The irony of debates like the one between Bill Nye and Ken Ham is that they pit two fundamentalist readers against each other."
Some writers supposed [5, 6] that Nye meeting Ham as an "equal" gave undue authority [7] to the YEC viewpoint against that of science. Each man came to the debate with a main point to make.

Analysis after the debate doesn't exactly show a thoughtful discussion about the differences between each philosophy. Name-calling and hyperpolarization are replete within each side. YEC's claim a moral superiority while "the humanists/atheists/rationalists/etc." claim a realistic or logical victory.

Ham contends that Nye's "Naturalism" will undermine all that religion stands for.

But this debate is a flash in the pan. At the end of the day it is unlikely that any YEC was impressed by evidence to leave faith behind and I have heard no stories about anyone deciding that YEC worldviews make more sense to them than factual evidence.
This is, however an interesting illustration about something else that parallels in chemistry today. Companies over the years are responding to public pressure- generated by marketing companies- to remove "chemicals" from their products. Chemists are famous for their long-standing and typical approach to this situation of a)mutual back-scratching and asking "Why does the public believe all this nonsense?" and b) trying to "educate" the public through dry and emotionless fact-based lecturing. This isn't limited to chemists, of course.
When Ham asked Nye to provide evidence for his assertions- Nye was obviously prepared for it. He presented evidence in droves. Much of the message of why it all matters was lost in the sheer volume of the science given, and it was all given at a high enough level that unless you're fairly proficient at science the "so simple a child can understand" points asserted by Ham gain traction. His "historical vs observational science" [debunked in 8] point is a perfect example of all this. It's a subtle trick that doesn't hold water under scrutiny.
How does this relate to the battle over chemophobia? It's all a matter of attention fatigue. When we don't specialize in an area of study we can easily be fool into thinking that the simplest explanations are the most reasonable. A blogger that calls herself "Food Babe"* recently took on Subway because she asserts a chemical in their bread (azodicarbonamide) should not be there. Since the chemical is also used in the production of "yoga mats and running shoes" she fearmongered until the company gave way. Battling chemophobia in the ways I mentioned above has historically been mostly ineffective. Recently a post [9] about what other chemicals Food Babe should ban "because they're used in plastics" made it onto reddit.com [10] but a comment in the thread points out "Of course none of this will be heard outside the chemist's community..." [11]

We need a new tactic. Science communication is a vicious battle. It has become clear that fighting fire with water is ineffective. We, as the scientific community need to start fighting fire with fire. Flashy marketing in the modern age will not yield to dispassionate facts. It may be time to put our money where our mouth is and counter those who would spread misinformation with marketing strategies of our own. I know that I won't win everybody over to my line of thought overnight. I don't care. We are losing ground on a slippery slope but the fight isn't over yet. The enemy predicts how we act and plans for that. Changing that pattern could turn the tide, and we could really learn something in the process.
We need to sell ourselves better. We're trained to believe that facts will stand for themselves in the wild, but it simply isn't true. Marketing needs to become a part of our new strategy.

Antoine Lavoisier once said noted, "As ideas are preserved and communicated by means of words, it necessarily follows that we cannot improve the language of any science, without at the same time improving the science itself; neither can we, on the other hand, improve a science without improving the language or nomenclature which belongs to it." [12]

If we improve the way we talk about science, we can improve the science along with it.


[1] http://www.youtube.com/watch?v=z6kgvhG3AkI
[2] http://i.imgur.com/T7Zz0R2.jpg
[3] http://www.buzzfeed.com/mjs538/messages-from-creationists-to-people-who-believe-in-evolutio
[4] http://www.huffingtonpost.com/sean-mcelwee/bill-nye-ken-ham-debate_b_4723766.html?utm_hp_ref=religion&ir=Religion
[5] http://www.csmonitor.com/Science/2014/0205/Bill-Nye-versus-Ken-Ham-Who-won-video
[6] http://scienceblogs.com/gregladen/2014/01/02/i-think-bill-nye-is-great-but-i-think-hes-making-a-mistake/
[7] http://www.richarddawkins.net/foundation_articles/2014/1/16/why-bill-nye-shouldn-t-debate-ken-ham
[8] http://ncse.com/creationism/analysis/historical-science-vs-experimental-science
[9] http://www.rheothing.com/2014/02/what-else-do-we-need-to-ban-besides.html
[10] http://www.reddit.com/r/chemistry/comments/1xm6yb/a_partial_list_of_other_chemicals_used_in_both/
[11] http://www.reddit.com/r/chemistry/comments/1xm6yb/a_partial_list_of_other_chemicals_used_in_both/cfcu01n
[12] http://www.nature.com/nchem/journal/v1/n5/full/nchem.302.html

*Yes, that's right. I'll link to a Buzzfeed article over her drivel. That's how bad it is. Normally I feel free to link to others' work that I reference but what she presents is so repulsive and toxic that I simply refuse to feed her click-through rate.

From http://urbanchristiannews.com/ucn/ken-ham-vs-bill-nye-DEBATE.jpg

Tweet Roundup From 3 Feb 2014

This is the first of the "Tweet Roundups", where I post either my top favorite tweets from other people or some of the tweets that I post myself- things that are too short to justify their own posts. "From: @[username]" means that the tweet was posted by someone else, "@[username]:" means I was tweeting at someone else, and everything else is just my own sundry thoughts.

The hidden environmental impact of feedstock, vitamins, and fertilizers. http://bit.ly/1eYDY4Z  from @Gizmodo [https://twitter.com/CrimsonAlkemist/status/431516286657380353] Feb 6

@SCStreet MT @EES_journal Doubly anchored adsorption gives better electronic properties than singly anchored for DSSC http://xlink.rsc.org/?doi=10.1039/C3CP54970D … [https://twitter.com/CrimsonAlkemist/status/431424897500196864] Feb 6
(Note: DSSC Stands for Dye-Sensitized Solar Cell)

@Sci_ents @RSC_EiC I would like for the first question after I say "I'm a chemist" to not be "so you blow stuff up?" Someday perhaps. [https://twitter.com/CrimsonAlkemist/status/431423878510809089] Feb 6

How do kindergarten teachers tell future chemists? The kids fail the alphabet "el-em-ENT-oh-pee" #chemistry #puns [https://twitter.com/CrimsonAlkemist/status/431234367051296768] Feb 5

What would change @Thescienceguy's mind? #creationdebate http://i.imgur.com/T7Zz0R2.jpg  [https://twitter.com/CrimsonAlkemist/status/431120556612911104] Feb 5

Well I guess if I wake up tomorrow and my experiment doesn't work, at least I can blame God. Thanks for the tip Ken Ham. [https://twitter.com/CrimsonAlkemist/status/430901077954019328] Feb 4

From @ZachWeiner: "I missed the first part of Bill Nye's speech, so I'm not sure it ever happened." [https://twitter.com/ZachWeiner/status/430859038167797761] Feb 4

Enjoy! @CrimsonAlkemist

https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiz8566sxPdIX-PKrMfgC24x-FN-l79O779j_JMCybEsThqLacF067zFhafokBovGfI6fxohfYVbuvCS86s0WhuwRU_k-06ngzrXU4jQ0Fx8jmSyKb76jSKylLMKnqog4uAtGFHO1J8qqM/s1600/600px-Ouroboros-simple.svg.png

Three Minute Thesis- now live!!!

The above video is my final competition entry into The University of Alabama's first-ever Three-Minute Thesis competition. The competition took place on November 11, 2013.

Molecular electronics is working on the further miniaturization of circuits for new devices and materials beyond what silicon can already do. Here's my little contribution!

NY Times "Debate", and my reaction to it. (Part 4)

Continuing the series that I started before Christmas is part 4 of the round-up of posts from the NYT [1] "Debate" [2], this post actually comes off as a little different because it's the first post [3] where I take a little bit of an issue. Luckily I don't disagree with the message, merely with the language in it.

The author, Tara Chklovski, reminds readers that teachers are busy enough trying to teach the basics and that "ongoing individual feedback to 20-plus students with 20-plus unique projects" is an unsustainable goal. To help remedy that situation and inspire kids to be excited exploratory thinkers, she shifts focus back to the home front...albeit softly. She says that "Parents can pick up the baton and lead their children on a journey of true exploration and discovery." Her entire post is sprinkled with cans and shoulds as if what seems (to me) like attentive parenting has become optional. Maybe I'm lucky. Maybe what I take for granted as my upbringing where the walks with dad, the kitchen time with mom, and the family outings to libraries and museums are special, not the norm.
Mrs. Chklovski links to her own blog over at Iridescent [4] outlining in more detail ways for parents to be active and engaging in their childrens' lives. Her language is stronger in that post, with less of a suggestive tone and offering real solutions. I don't understand why this kind of engagement should "surprisingly" (as she says in her closing sentence) lead to more enthusiastic learners and prepare them to ask deeper, more meaningful questions as they grow up. I would absolutely like to think that when I have kids I would naturally want to actively engage them at a matter of just being a parent. Of course, I say this now without kids or any experience of being a parent- I know how positively tiring it is, in theory. I guess we'll see how it goes when I actually settle down.

"'Children spend much more time at home than at school. Their parents know them intimately, interact with them one-to-one, and do not expect to be paid to help their children succeed. The home environment offers 'teachable moments' that teachers can only dream about.' -David Peterson" [4]

But because of this, Mrs. Chklovski, it's not something parents simply can do. It's something they must!


[1] http://www.nytimes.com/roomfordebate/2013/12/10/math-and-science-for-more-than-just-geeks
[2] http://jsphmeany.blogspot.com/2013/12/ny-times-debate-and-my-reaction-to-it.html
[3] http://www.nytimes.com/roomfordebate/2013/12/10/math-and-science-for-more-than-just-geeks/parents-can-help-their-kids-scientific-educations-simply
[4] http://iridescentlearning.blogspot.com/2013/11/a-case-for-parents-as-best-science.html#more

Watching paint dry

A common technique used in my lab....and by just about everyone else in an organic chemistry lab (sophomore undergraduates included)...is "elevated temperature, reduced atmosphere rotary evaporation." Nobody calls it that. It's just "rotovap." Much easier to say and since all models work under the heat and vacuum mode to distill off solvents those are really just assumed.
Basically, "rotovaping" or removing sovents by rotary evaporation is a fancy way of watching paint dry- literally if you happen to be in the paint business. Once a solution is put on the rotovap (the term is both a noun and a verb for those that are paying attention to my grammar) then it's a matter of having a dry sample afterwards. Naturally, this leads to a bit of down time. So I decided to take a picture to show off the pretty colors that can be chemistry. Enjoy!

NY Times "Debate", and my reaction to it. (Part 3)

Continuing coverage from Part 1 [1] of the series of my reactions to the NYT article on the future of STEM education in our country, Christopher Emdin [2] chimes in with a few cents to address his experiences with urban students from New York. His proposal, narrowly stated, wants to marry the pervasiveness of the hip hop culture in his area to the training of new scientific thinkers. In a video produced with NPR [3] he narrates the story of a group of young students writing and performing their own raps in a contest designed to promote multiple lines of thought and build confidence in the youth.

From [4]

"My father told me the program wasn't going to work and it was going to fail like every other program." says Victoria Richardson out of Bronx Compass High School [3]. She performed with two friends of hers on base pairing DNA and despite not winning the contest- they were still proud of what they were able to accomplish. Not only were they able to simply memorize rote base pairing schemes but they understood the material enough to create a work of art and communicate that knowledge enthusiastically.
Dr. Emdin says in the video, "Not every student a part of Science Genius will be a straight A student and go to college...and be the next Einstein. But you know what? We are definitely going to have more scientifically literate young people." [2]
That's a powerful point to note. In his article, he notes that the hip hop culture isn't completely general.
"I argue that the more teachers can consider the unique culture of their students, the more relevant and accessible their education will be." [2]
He basically says here that teachers should feel free to pull from whatever is popular in the kids' lives wherever they teach. Make it accessible and make it fun. Then, maybe a few, will ask those really probing questions that get them started down a really academic path. But no matter what field or endeavor these students choose- we will be all the better for a literate public.

[1] http://jsphmeany.blogspot.com/2013/12/ny-times-debate-and-my-reaction-to-it.html\
[2] http://www.nytimes.com/roomfordebate/2013/12/10/math-and-science-for-more-than-just-geeks/in-teaching-stem-use-hip-hop-as-a-bridge
[3] https://www.youtube.com/watch?v=YQrj4NPefd8
[4] http://www.tc.columbia.edu/i/media/9099_SciGenius-161_MarieCurieHighSchool.jpg

NY Times "Debate", and my reaction to it. (Part 2)

The first article in the lineup, as I briefly mentioned in Part 1 is by Miyaim Bilaik, who has her PhD in Neruoscience but is also now an actress most notably playing Amy Ferrah Fowler on the show "The Big Bang Theory ." (BBT)

I liked her thoughts on the matter, noting that "[t]he confines of a classroom, combined with teaching methods that are not engaging or inspiring..." [1] were not effective at getting young minds excited about the world around them but only fearful of what will be on the next exam. She posits the idea of using modern entertainment- television, movies, and games- to help supplement people in new and interesting ways to help people think about and grasp otherwise esoteric information. This is more than just bringing nerd culture into the limelight for shame [2]/ ridicule[3]. The battle over the net effect on "geek culture" by BBT is one that will wage like the battle at Helm's Deep outside of this discussion.

SOME PEOPLE ENJOY BBT DESPITE BOTH CHAMPIONING AND DEMEANING ITS CHARACTERS AND THEIR FLAWS!!!!

Science-literate producers and directors can wield incredible power in telling a story by not only the story elements it weaves, but the concepts it has the opportunity to explain. Think about it. If Glee or High School Musical could make singing in show choir cool again- what could we do with a show about kids making science interesting and approachable? Like Beau Lotto [5] and his "Blackawton Bees" [6] kids show us- ground breaking science can really be done.

I understand there will be limitations. Story will always take precedence. But breadcrumbs of learning are always better foundation than the black pits of despair that could be found on TV today.


Let's be real. Who would you rather your kid be watching?
[0] http://jsphmeany.blogspot.com/2013/12/ny-times-debate-and-my-reaction-to-it.html
[1] http://www.nytimes.com/roomfordebate/2013/12/10/math-and-science-for-more-than-just-geeks/use-hollywood-plots-and-characters-to-teach-stem
[2] http://butmyopinionisright.tumblr.com/post/31079561065/the-problem-with-the-big-bang-theory
[3] http://www.cracked.com/blog/4-reasons-2013-officially-marked-death-nerd/
[4] http://static4.wikia.nocookie.net/__cb20130117112538/lotr/images/b/b4/Theoden_leads_the_attack.png
[5] http://www.ted.com/talks/beau_lotto_amy_o_toole_science_is_for_everyone_kids_included.html
[6] http://rsbl.royalsocietypublishing.org/content/7/2/168.abstract

Quotes from Chemistry...part 2!

"Respiration is a combustion, truly very slow but otherwise perfectly similar to that of charcoal; it occurs in the interior of the lungs... and the heat developed in this combustion is communicated to the blood which traverses the lungs and is spread throughout the animal system."
-Lavoisier and Laplace, 1783

[1] http://en.wikipedia.org/wiki/File:Pierre-Simon,_marquis_de_Laplace_(1745-1827)_-_Gu%C3%A9rin.jpg 

Laplace, before his transform. [1]

Quotes from Chemistry...part 1

"...for nothing is created in the operations of either art or of nature, and it can be taken as an axiom that every operation an equal quantity of matter exists both before and after the operation, that the quality and quantity of the principles remain the same and that only changes or modifications occur. The whole art of making experiments in chemistry is founded on this principle: we must always suppose an exact equality or equation between the principles of the body examined and those of the products of it's analysis." -Antoine Lavoisier

(Partington, J.R., A Short History of Chemistry, third edition. 1965)

"My dear, is this entirely necessary right now? I'm trying to make the grocery list for once!"

NASA Trip in all its glory!

I mentioned briefly at the end of my Oct 25 2013 post that I was also getting ready for a big trip....NASA's Jet Propulsion Laboratory (JPL) had invited me and a slew of other lucky folk to gather at JPL for a two-day conference called "Year of Earth" [1] which previewed us to the various different missions that NASA JPL has in the works for the coming year [2]. Included in this highly immersive experience was a live public address from the NASA JPL auditorium where the project scientists in charge of these crucial Earth-based missions talked about the data being collected and, more importantly, the effects we hope it will have on current models used in predicting climate change. The video of the public address can be found on YouTube [3] and if you watch far enough into it, you can see my few seconds in the spotlight! (Okay, I was asking a question. But still, it was for science!)

In front of Mission Control!

We had a blast and the whole conference was full of people eager to talk about space, the Earth, and climate. Teachers, students, amateur enthusiasts and professionals all gathered to learn from each other and network all while cheering the banner of our beloved American space program. In fact, one of the "tweeps" (as we were called) has even created an infographic [4] about the online impact each of the participants had while at the event. The hashtags "#NASASocial" and "#EarthNow" even trended on twitter during the conference! Rachel Eddin, a blogger for WIRED wrote a story [5] that beautifully summarizes how incredibly passionate people are about having this mission of publicity succeed. She writes "There's a unity of purpose and generosity of resources...I was immediately inundated by offers for information and links...we were sharing data, educational resources."

Network Centrality Graph by Audun Utengen, from [5]

Many of the attendees had much better equipment (i.e. cameras) to capture the awesome campus that is JPL (like this shot from Rachel Eddin [6]). These people's work deserves to be seen. Veronica McGregor, in fact, helps to streamline this process by creating a powerful Storify feed [7] that highlights many of the stunning images people have uploaded. In the words of the one and only LeVar Burton, "Don't take my word for it!"

In addition to this, bloggers of all different ilk have thrown their hats in the ring to help publicize the exciting work coming out of NASA. This excellent photo-tour [8] of the event by Jennifer Kaplan has a great summary with equally quality photos of the facilities we were able to see. I know that I could have sampled only a small number of the amazing bodies of work that have come out of the two day event, to have tried would mean that this would never get published! It was absolutely unreal. The energy I can only describe as infectious.

None of this would have been possible without the tireless work of three key people spearheading the event planning. Veronica McGregor, Social Media Manager at JPL; Stephanie Smith, Social Media Specialist; and Courtney O'Connor, also Social Media Specialist; deserve a great deal of thanks for their hard work in coordinating the event. Their tireless dedication really showed in how smoothly and efficiently the event moved- and how even now, a week and a half after the event, activity and chatter flows between the attendees spanning continents.

"Goofy shot" of the tweeps. Source: NASA JPL Flickr [9]

[1] http://www.nasa.gov/content/nasa-invites-social-media-fans-to-preview-the-year-of-earth-at-jpl/#.UoRVSfkQbgw
[2] http://www.planetary.org/blogs/guest-blogs/bill-dunford/20131111-science-against-the-storm.html
[3] https://www.youtube.com/watch?v=MGGHwTQ-c9U&list=PL2aBZuCeDwlT56jTrxQ3FExn-dtchIwsZ
[4] http://www.wired.com/images_blogs/underwire/2013/11/NASASocial_CentralityGraph_AudunUtengen.jpg
[5] http://www.wired.com/underwire/2013/11/nasa-socials/
[6] http://24.media.tumblr.com/eda6529e8509192a313a3941f58a1b01/tumblr_mvum1ci0C81qgxab9o2_1280.jpg
[7] http://storify.com/VeronicaMcG/nasa-social-nasajpl-nov-4-5-2013/grid
[8] http://jenniferkaplan.me/2013/11/07/nasa-social-at-jpl/
[9] http://www.flickr.com/photos/nasa-jpl/ 

Get pumped....for SCIENCE!!!

So recently there has been a lot of activity going around me about science communication. And in this vein, it spawns from a number of different sources all with different intents- and these are all very good things. But the boiled down basics of it all comes back to one thing, and that's getting the public excited about science. Yes, the public, YOU!!!

I was watching a TED Talk the other day (Okay, it was more than one!) on a layover flight home from NASA (more on that later!) and there were two that really stuck out in their messages to me. Arthur Benjamin [1] was giving a lecture on the fascinating patterns hidden within the Fibonacci Numbers and how, "mathematics is used for three things: calculation, application, and last and unfortunately least- inspiration." He uses the illustrative nature of the Fibonacci sequence to make his single sentence point:

"Mathematics is not just solving for X. It's also figuring out Y." Source: [1]

A tangentially related video from Stuart Firestein [2] talks about the value of "high-quality ignorance" or, in other words, knowledge just beyond our current scientific understanding. His motivation behind this is to let non-specialists know that science is a lot less like the so-called scientific method we learn about in school but "more like farting around...in the dark."
These two messages, combined with the wonderfully inspirational video [3] from my new friend Saramoira Shields (@mathematigal on Twitter) point to a very simple statement that holds a lot of complicated weight. Science, math, engineering, whatever it may be- is hard. BUT! It's not impossible. It doesn't take some genius to whip up an answer to a problem on the fly or be the first kid to raise his or her hand in class. That's not the point. The point is to become a thinker, a rationalizer.
It takes patience. It takes perseverance. And it takes a little bit of caring attention to cultivate the knowledge base to make the leap from Calculation to Application. After a while and no short amount of effort, "farting around" can lead to wonderful "A-ha!" moments that make every bit of frustration well worth the trouble. And that, my friend, is where we can really reach Inspiration.

On a related note, my last post [4] was about the Three-Minute Thesis [5] competition going on at UA as I was soliciting some feedback for the Semi-Finals, as I was a representative for the Chemistry Department. I am pleased to report that not only I but the other two chemistry representatives, Greg Dye and Steven Kelley, have all been passed on to the UA 3MT Finals- competing for top thesis presentation at UA! Congratulations are in order for them as well as all of the other finalists.
We go on stage at 6pm next Wednesday, Nov. 20 in Russell Hall 159. So if you're in the Tuscaloosa area, come drop in! I and the other contestants would really appreciate the support! Next year will be even better with as excited as the administration is about this event. Click the link above to check out the original idea from the University of Queensland.

"The best thing to come out of Australia since me!" said Crocodile Dundee never. Source: [6]

I want to be able to talk about science. I want to talk TO YOU about science. And, maybe with a little bit of effort, we can feel the glee of discovery together.

[1] http://www.ted.com/talks/arthur_benjamin_the_magic_of_fibonacci_numbers.html
[2] http://www.ted.com/talks/stuart_firestein_the_pursuit_of_ignorance.html
[3] https://www.youtube.com/watch?v=Xs9aGVUZ3YA
[4] http://jsphmeany.blogspot.com/2013/10/after-hiatus.html
[5] http://www.uq.edu.au/grad-school/three-minute-thesis
[6] http://www.mnn.com/sites/default/files/main_hogan.jpg

After a hiatus...

It's been a while since I've contributed a post sadly and I attribute part of that to a jam packed teaching schedule and October being busy- Halloween is my favorite holiday after all!

Recently I participated in the first round of a competition being put on by my school, and competed for a nomination to the school-wide competition open to all PhD students at UA. This competition aims to increase the ability of graduate students to communicate their research to a varied and general audience. We are to translate our dissertations into a speech, 3 minutes in length or less that is able to be grasped by the public at large.

I thought to myself initially, "Oh yeah, piece of cake. I've been explaining my work to my family all along!" Trouble is, my family is full of scientists and engineers. I haven't really been trained to think outside of a wider perspective, which is my main driving force for this exercise. I thought I would post here the text of my speech, as "finalized" by the judges so that you, my readership, could offer comments and suggestions. I hope you enjoy it!

"When I was an undergraduate, my physical chemistry professor was one of those “back in my day”-type guys that would talk about his experiences at Los Alamos National Labs and the punch card computer he had to use- it was big as a whole room!  Consumer electronic devices are being made to fit into ever smaller packages and computers are being built with ever smaller circuits. Imagine sensors that can be eaten or medical devices implanted in the body without any impediment!

My project takes this to a new extreme. It focuses on the design and manufacture of molecules that will replace current electronic components. My strategy is to tailor a molecule's three-dimensional structure and thus custom-design molecules that behave the same as components already found in technology today, while cutting size by roughly 1000x and using energy much more efficiently. This would be like shrinking the function of a laptop to fit on a contact lens!

Specifically, I aim to make single molecule diodes, which carry electrical current in one direction, but prevent it from flowing in the opposite direction. Today, most diodes are made of silicon, which requires the device to be manufactured from a large base to a small finished product. This process has its limits and the building of molecular electronics focuses from a bottom-up design, which can reduce waste. I’ve asked the question- how small can we make these diodes? Where’s the limit? I’ve proposed one possible limit, a single bond between two carbon atoms. Up until now, construction of molecular diodes required three components to be made separately over several steps and then brought together as a final step- but I’ve simplified this process by producing a molecule in a single reaction with these three components all at once. The bridge component, key to function, is a single bond- no extra atoms involved at all!

From there, I’m able to take advantage of tricks within certain atoms’ properties to make these molecules attach themselves to metal surfaces much like an atomic version of alligator clips clipping to a battery and circuit.

Taking advantage of lower current flow and higher operating efficiency would lead to the production of smaller and faster circuits in future technology. This could lead to paper-thin flexible tablets, wearable electronics like contact lenses or even miniaturized pacemakers!

And then, someday in the future, I can complain to future chemistry students about how we had to suffer with flat, bulky, inflexible devices- back in my day."

Image Credit: PhD Comics

I have high hopes for this event, but I'm most excited about the possibility to talk about my research in a way that doesn't make people's ears smoke. It's been a trip so far, between this and the NASA visit next month I'll have plenty to talk about. 

What do you think? Where could it be more plain? 

Awesome Nicknames

So I'm reading J. R. Partington's "A Short History of Chemistry" (Harper Torchbooks, 1965) partly because it's an old book that I saved from destruction by a local library and partly because no chemistry course I've ever taken really touches on the development of the science that is so central to my life. I know it's dated and there are probably a lot of other texts that are more modern or may be more comprehensive- but I got it for a bargain. Get off my back alright? Okay. Thanks.

I'm working my way through the section right now that's basically discussing the high-times of alchemical study (which interestingly enough coincide with the European Middle Ages) and I've found that many of those researchers had names attributed to them, some based on scholastic significance while others have no evident origin and others just gave it to them[1]. Paracelsus, known also by his real name Theophrastus Bombast von Hoenheim, fits this latter description.

Theophrastus Bombast von Hoenheim...and his brother, Bombad Boss Nass von Hoenheim

Robert Bacon, and many of the other Franciscan Monks earned the scholarly titles, for example Bacon's Doctor Mirablis or Thomas Aquinas' Doctor Angelicus. Albert the Great, Albertus Magnus, was given his nickname by his peers during his lifetime because he brought to public attention many of the philosophical works which had become esoteric at that time.
From that, my question is- why can't we have cool nicknames again? I know it would complicate authorship attribution (which was rife in the Middle Ages), but how awesome would it be to be known as something other than your direct name? I guess that's what Twitter handles are for- I'm looking at you @SeeArrOh! But really. Can't we get a bit of grandiosity generated here? I mean something to really shed light on the SHEER AWESOME of the work that we do? Maybe something just  little bit more varied than Philosophiae Doctor!

What name might you choose, or what name do you think others might ascribe to you? Myself? I would choose Molectronicus.
+Joseph Meany

[1] http://www.naturasophia.com/Paracelsus.html Accessed 6 Aug 2013

Science and open policy

People complain about how science needs to be more open. I just realized I'm thankful for how open science is today, especially compared with the days of early science and alchemy where findings were encoded in such a form that only those specifically trained were able to unravel their meaning. Since science has progressed to a more standardized form, however, this leaves researchers of historical texts with a large job of decoding the past. With so much information available online, it is important that we are able to communicate thoroughly and openly- but most importantly- truthfully.


"This has always been a problem, however, because the texts that [the alchemists] have left us are very secretive. They're often very metaphorical they're often in a kind of code; and they're filled with all sorts of extravagant imagery- often very beautiful wood cuts but forbidding in the sense of...what does it all mean?"

This comes from Professor Larry Principe of Johns Hopkins University. He works as a science historian trying to decode many of the historical alchemy texts and the American Chemical Society recently put out a video overviewing some of his work. He explains that his main hurdles are decoding these metaphors and symbols, to repeat reactions done by "the ancients" using their methods and glassware to see what it is they actually made.

J.R. Partington, in his book, "A Short History of Chemisty" outlines that many texts from ~1200-1500 are "largely unintelligible" alluding to the secretive nature of this pseudoscience during the time, a contrasting discussion to his earlier elaboration on the treatises written by the Ancient Greeks, Arabs, and Egyptians. Shamefully, as well, "the later history of alchemy is often that of fraud."


While peer review is not perfect in its mission to vet what is "good science" and "bad science," I firmly support the system in place today opposing the search for the philosopher's stone of yesteryear. In the discussion of how to improve science communication we need to not forget- some control is better than none.

http://gizmodo.com/meet-the-man-who-decodes-the-ancient-secrets-of-alchemy-633187520

 http://fc02.deviantart.net/fs71/i/2013/111/7/c/alchemy_woodcut_duos_caputis_melior_quam_unus_est_by_dashinvaine-d62i1y6.jpg