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!

The falsehood of the perpetual candle

“Oh ye seekers after perpetual motion, how many vain chimeras have you pursued? Go and take your place with the alchemists.”
         – Leonardo da Vinci, 1494

Found in an article about a "perpetual candle" and a designer's ill-fated attempt at creating a renewable candle by recycling mass/energy

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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)

The Crimson Alkemist and Patreon

So I know there are a few readers out there that are fans of what I've been writing, and I've been introduced recently to a service called Patreon recently. It offers the ability for fans of a creator's work to donate to their cause instead of polluting a webpage with tons of ads.
Crimson Alkemist is a labor of love aside from research, but I'd like to be able to contribute a lot more quality material while no longer pillaging (or pillaging less) from Google Images for my posts. I could use these extra funds to pay graphic artists to help with new images- content exclusive here! This could really take the blog to a new level- would that interest my readers? I'm always looking for new ways to make this better for you- help me make it possible!

Thanks for reading, you rock.
+Joseph Meany

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

Chemistry Cake for real?

I just absolutely had to share this incredible birthday cake that some friends of a woman I met at a conference last year, made her. The picture itself is a couple of years old and they were revisiting the nostalgia of it for her recent birthday but I had to make sure the world knew that Samantha Gascan has awesome friends for creating this. The "smoke" effect comes from dry ice and water in a cup at the top of the cake itself. 

Eat your heart out, Cake Boss.

The Good News is Come!

With this week's special twitter update I have the announcement to make that The Crimson Alkemist is finally using original artwork on the twitter account and will be ravamping the layout in weeks to come to put a "not-default" appearance onto the site. I started the blog to engage undergraduates in extracurricular information that would be hopefully interesting and fulfilling to them as they progressed in their careers in science- but I projected that their interaction would be minimal at best and decided not to tweak layouts too much. And as far as using my own pictures? Nope. I'll just link to where I pull the images.
When I decided that I wanted to continue this as a little side pet project I knew that it would be a bad idea to spend tons of time away from my research on it- after all, I'm trying to get a PhD on time here! So I kept the Google Images on both here and Twitter, even keeping the basic Blogspot layout. But then something changed. People have started noticing the blog and I'm actually going to conferences for science communication. Next week will be a flurry of tweets while I'm at the conference. I'll have to find a way to make that into a presentable format here.
So I decided to tap my family's talent and ask Kendra Meany to help me design a logo for The Crimson Alkemist. She does me better. Based on the original design idea I had submitted to her, she was able to create an incredible piece of art that is going to be used across the board for promoting my writing here. You can see it below. She also created a bit of heading text that you see above with that incredible O.

But with that, here's this week's Twitter Round-up!

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

Quotes from Chemistry...Part 7!

via Google Images

"When we are there, and whilst we exercise
Our implike craft, we seem so wondrous and wise,
our terms they are all so learned and so quaint."
- Geoffrey Chaucer, The Canterbury Tales

This excerpt is taken from The Tale of Canon's Yeoman and is, oddly enough, poetically descriptive of even contemporary academic life. I'd have never seen it before, except having been a part of it for ten years now. A fuller picture can be drawn from the whole of Yeoman, so if you're interested (as I am), go take a look.
I found a version of this quote in Nature Chemistry 1, 334 - 335 (2009) Stretching Topology [1]

[1] http://www.nature.com/nchem/journal/v1/n5/full/nchem.302.html

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

Where did it go?

I used to have a labmate who what notorious for sneaking things away from my space when I wasn't looking. stir rods, flasks, chemicals, especially spatulas. They would disappear into some void and reappear only in his sink, covered in some weird waxy gunk a week later. Who knows what horrors they might have encountered on their way to the sink.

This fortune I got yesterday at lunch made me think of him and all I could do was laugh because of the connotation of "solution" in chemistry. I'll be on the lookout for my solvent bottles, Bruce.

Lifehacking...the Jerry Seinfeld way

Quoted directly from The Seinfeld Strategy [1]

""He said the way to be a better comic was to create better jokes and the way to create better jokes was to write every day.
He told me to get a big wall calendar that has a whole year on one page and hang it on a prominent wall. The next step was to get a big red magic marker. He said for each day that I do my task of writing, I get to put a big red X over that day.
"After a few days you'll have a chain. Just keep at it and the chain will grow longer every day. You'll like seeing that chain, especially when you get a few weeks under your belt. Your only job is to not break the chain."

You'll notice that Seinfeld didn't say a single thing about results.
It didn't matter if he was motivated or not. It didn't matter if he was writing great jokes or not. It didn't matter if what he was working on would ever make it into a show. All that mattered was "not breaking the chain."
And that's one of the simple secrets behind Seinfeld's remarkable productivity and consistency. For years, the comedian simply focused on "not breaking the chain.""

I figure this is helpful, but I should put more preliminary ideas down on paper and not necessarily here! I thought this might help out someone as well!

[1] http://www.entrepreneur.com/article/231023

SOME BIG NEWS...and a couple changes.

Little stuff first.

This sporadic posting thing is just not good. It gets in the way of the creative process that is both writing and my research- which definitely needs to stay on track. So I'm putting myself on a schedule beginning next week. Tuesdays are dedicated to finishing the NYT editorial piece, and when that's finished I'll use that as the real creative outlet and general blogging day. Wednesdays will be dedicated to "Picturing Chemistry"- bringing art into the lab and onto your screens. And late Friday is dedicated to a "Tweet Round-up", as I realize that many followers of this blog don't have Twitter and I don't deluge this site during the week with my 140-character musings. I'll round up some of my favorite posts by myself and others for you to enjoy!
Of course, "Quotes from Chemistry" will be updated as I find them and more interesting but time-sensitive news posts (think WV chemical spill) will update as I can get them on the site. I missed a big break this week which I'm sad about but hey- I was dealing with "snowpocalypse!"
I hope the new schedule keeps me on my toes and keeps you all thoroughly entertained!

Alright, now the bigger stuff.

When I was in Pasadena for the NASA trip, I sat at my group table with a very nice lady. Her name was Karyn and I didn't happen to catch her occupation at the time but we all had a lot more on our minds. Fast forward to the end of the conference and I was speaking with Veronica McGreggor, one of the people in charge of the NASASocial conference. I mentioned to her that it was because of a group called Science Online [1] that I found out about the social in the first place. Veronica says to me "Well Joe, you do know you were sitting at the table with Karyn Traphagen, the Executive Director of Science online- right?"
My jaw dropped. I had no idea that I had been exchanging small talk all weekend with the person basically responsible for my participation at NASA JPL. I resolved to rectify that and sent a nice email to Karyn bascially gushing like a fanboy thanking her for what she does and offering my assistance if ever I could be of help.

Well I got an email from her last Sunday that absolutely blew. my. mind.
She was inviting me to be an attendee at the Science Online Together conference in Raleigh, NC from February 26th-March 1st. The Executive Director HERSELF reached out to invite little ol' me. So over the course of the next month I'll be working my butt off to get together the necessary materials for the conference and bring The Crimson Alkemist to a wider crew. Celebrities like Veritasium [2] and MinutePhysics [3] (who was quoted recently in Part 6 [4] of Quotes from Chemistry) will be there. This isn't entirely devoid of chemistry though- even Carmen Drahl [5] of Chemistry and Engineering News will be there. I'll get the chance to meet people who have helped inspire me in keeping this blog running beyond its original purpose.

I'm sure I'll have a story or two to tell when I make it back from that. I know I'll learn plenty from the people who have been-there-done-that before me.

Seriously. Visit these guys and get excited.

Because of this exciting opportunity, I'm taking advantage of some specific skill to come out with my own BRAND LABEL!!! I'm not going to release any teasers on this yet, but the Crimson Alkemist Twitter is going to have a new profile photo and I'm going to try to work on getting this site updated as well. It's like cleaning up your apartment in anticipation of having new company over! Stay Tuned!

[1] http://scienceonline.com/
[2] https://www.youtube.com/user/1veritasium
[3] https://www.youtube.com/user/minutephysics
[4] http://jsphmeany.blogspot.com/2014/01/quotes-from-chemistrypart-6.html
[5] http://cen.acs.org/static/about/staff_landing/biocd.html

Quotes from Chemistry...Part 6!

"A bond of any sort, whether between planets, molecules, atoms, nuclei or quarks, is just a happenstance when when two or more particles together have a lower total energy than when they were apart. Like if you're married, and your taxes go down."

-Henry Reich of Minutephysics

This West Virginia issue is getting out of control.

I am going to lead this post with a big disclaimer.
Much of what I am about to write is speculation. I will cite where I can back up an idea but beyond that none of what I say should be taken as gospel.
Chemophobia is a thing. People are scared of "chemicals" in their food, in their clothes, in the air. Chemists often times quietly chuckle to themselves in private company about the ignorance of the public and how everything is made up of chemicals and how you can't really have a chemical-free banana.
Most chemicals people encounter on a day-to-day basis are benign or helpful. The oxygen we breathe, the wood of my desk, the chocolate in my cake. It's when accidents happen that cause chemicals that aren't supposed to be in contact with us that "chemical" takes on it's malicious tone and people become acutely aware of dangerous substances.

On January 9, 2014, 7,500 gallons of 4-methylcyclohexane methanol[1] (MCHM) was spilled into the Elk River in West Virginia from a leak in a tank owned by a company called Freedom Industries. This spill was so tremendous that people in the area couldn't use the tap water in their homes for over a week[1]- it was unsuitable for anything other than flushing down the toilet. The company was brought in for questioning because safety data for the chemical in question was lacking. The company stood by its assertion that the chemical was only toxic in large quantities and that the problem could be dealt with easily. Too bad reality doesn't bend to the whims of businessmen the way they might like. This cleanup my fold the company.[2]

Today it has come to light, however, that MCHM wasn't the only chemical in those tanks. The Charleston Gazette[3] reports that a "source" gave them a tip about this second chemical known by its' trade name PPH glycol ether.The company "Freedom Industries has claimed the exact identify of the substance is "proprietary.""[3] and that, "data about the potential health effects of the chemical "PPH" are -- like the information on Crude MCHM -- "very limited."" [3] While the information is technically proprietary, I thought I would do a little digging to see what I could find about this new chemical. "PPH glycol ether" is all the article calls the chemical and they mention it's made by Dow.
Do a Google search for "Dow DiPPH Glycol Ether" and you come up with a patent [4] for some of its blends as well as a published Material Safety Data Sheet[5] for the propylene glycol ethers. In this MSDS (page 4) as well as a Sales Flyer [6] for the chemical, Dow asserts that these chemicals are biodegradable and do not persist in the environment. Document [6] asserts that 60% elimination occurs after about 7 days and [5] makes the assumption that it will be taken care of in the water treatment plants.

This is where things get dicey. It's not enough to just assume something like this when you're talking about people's drinking water. Granted, Dow makes sure to say that the glycols aren't supposed to be in contact with people, but the Gazette paints a big question mark over why the public wasn't notified about the "real" contents of the spill before and why the glycols didn't show up in the water tests (post treatment plant) prior to this. They say:
"State officials said late Tuesday that, after consulting with West Virginia American Water Co., they believe the water company's Elk River plant would likely have removed the chemical from drinking water during its normal treatment process. Additional testing of some of the original water samples from the first days after the incident is being conducted to confirm that, officials said."[3]

So let me get this straight. A company spills a bunch of toxic chemicals into the drinking water system of a major metro area. At first, the company owns up to one chemical but now after two weeks we know that it's no less than three. And we don't know where the last two went in the water quality tests that have already been performed. MCHM has little (and poor) data about itself available for the public and regulators to talk candidly about how to proceed. The company has potentially poisoned thousands of kids. And now these two additional chemicals are exposed and their data is still slightly better...but still not good. Especially the line from [5] that says, "When introduced to water, they will have a tendency to remain in water."

If I were a West Virginian, I would be looking for a way out. Now. Outrage all aside.

[1] http://www.businessinsider.com/parents-are-afraid-for-their-kids-in-west-virginia-2014-1
[2] http://www.wvgazette.com/News/201401210034
[3] http://www.wvgazette.com/News/201401220031
[4] http://www.google.com/patents/WO2012075320A1?cl=en
[5] http://msdssearch.dow.com/PublishedLiteratureDOWCOM/dh_02bd/0901b803802bdec3.pdf?filepath=productsafety/pdfs/noreg/233-00601.pdf&fromPage=GetDoc
[6] http://msdssearch.dow.com/PublishedLiteratureDOWCOM/dh_08ec/0901b803808ecba6.pdf?filepath=fsc/pdfs/noreg/805...&fromPage=GetDoc

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!

Quotes from Chemistry...Part 5!

"I often think what interesting history we are making for the student of the twenty-first century."
-William Carey Jones, 1908 (via http://www.xkcd.com/1311/)

This isn't strictly chemistry, but the same could be said for the future students of the twenty-second century. What amazing marvels are we creating today that will be looked back upon as fundamental to students a hundred years from now?

As an aside, WC Jones was a politician from Washington State, and a sharp dresser. Just look at that tie!

Image courtesy of wikipedia

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!

A little tardy but...Quotes from Chemistry Part 4!

Christmas Spirit is a neutral chemical that builds new compounds and rejuvenates old. It is a reversible compound, for Christmas Spirit returns to its original state, ready to begin anew.

It has an affinity for good, and attacks the bad. Large or small quantities of it can be handled, depending on the capacity of the mind that dispenses it. Let us analyze the chemical and physical properties of Christmas Spirit as we do any chemical, element, or compound. It has, at times, an odor of frankincense and myrrh, the odor of evergreens or of burning tapers. This depends on the place and the heat of reaction. On mixing, it has a tinkling, joyful sound, full taste of all good things.

Its energy is unbounding, dividing itself a million times, it becomes more powerful, creating in most all it meets a feeling of light-heartedness; in some, a wistful sadness. More often it is like new wine—it refreshes, stimulates, makes happiness and smiles, increasing generosity and good nature.

-Howard A. Marple, “The Chemistry of Christmas”

Chemical & Engineering News, December 10, 1929 [1]

[1] The Watch Glass, C&ENews http://cen.watchglass.org/day/2013/12/25