infiniflux!

sh*t scientists say

noreply@blogger.com (Joel Kelly) — Tue, 17 Jan 2012 18:34:00 +0000

Love it: "In conclusion more research is required"

the infiniflux 2011 infographic

noreply@blogger.com (Joel Kelly) — Fri, 06 Jan 2012 20:15:00 +0000

As I've discussed before (several times, in fact), I love beautiful scientific figures. Of course, the figure is only as good as the data it presents.

For the past year, I've been using the free web app Daytum, which combines Google's Chart APIs [1] with some elegant CSS/database scripting, allowing users to record various data in their lives according to whatever category they see fit. They have an iPhone app that makes recording entries quite easy. Daytum then displays the data in pretty, interactive plots.

As a grad student finishing my thesis, I thought it might be interesting to record my caffeine intake over the year to see how much I relied on chemistry's friendliest molecule:

(You can mouse over the charts to highlight a particular beverage.)

(If you're reading this in an RSS reader, the embedded graphs won't display correctly. Sorry!)

A legend for those of you keeping score at home:

- I averaged 1.96 coffees per day over the year, although you can see there was significant variation as required by my thesis writing schedule. The first rise happened in May when I was trying to write the first draft of my thesis. Caffeine consumption dipped slightly after I handed in the thesis to the committee, and I took some time off to get married and honeymoon (whoop whoop!). It then spiked pre-defense, tailing off during the move to Vancouver for my postdoc. It has since climbed steadily as we get settled in.

- My favourite coffeeshops were Transcend in Edmonton and Kafka's in Vancouver. Other highlights include Elm Cafe in Edmonton, Dark Horse in Toronto, and Blue Bottle in San Francisco.

- Most of the black coffee was made at home with my trusty French Press. My recipe is 30 g of coarsely-ground coffee to 16 oz water slightly cooled off the boil, steeped for 4 minutes. Delicious! Sometimes I cheated and added a little milk to cool the black coffee if I was in a rush in the mornings. Also, the volume of black coffee could vary significantly depending on the size of the beverage container.

- I made a lot of iced coffee using this NY Times recipe, which is DELICIOUS. It's way better than regular brewed coffee or espresso over ice, so I tracked it separately. You should make it too! Sometimes I added some cinnamon to the grounds as they steeped for extra deliciousness.

- Here's a list of espresso beverages for anyone not familiar. It's missing the flat white (a drink invented by Australians, in between a cappuccino and a latte), and the Gibraltar (a slightly gimmicky version of the cappuccino originating from San Francisco that is popular in Vancouver).

- The double double is Canada's signature coffee beverage from Tim Horton's, featuring two creams and two sugars. It is only to be consumed with greasy breakfast foods, in order to make the terrible coffee palatable.

It was fun to track my coffee consumption over the year, although I think I will try to find something new to quantify for 2012. Any suggestions?

[1] The Google Chart API looks amazing! Looks like there's some interesting work being done in Chemical Education in using it to make fancy plots.

happy halloween y'all!

noreply@blogger.com (Joel Kelly) — Mon, 31 Oct 2011 17:49:00 +0000

(by Grant Snider)

beautiful science!

noreply@blogger.com (Joel Kelly) — Fri, 07 Oct 2011 16:59:00 +0000

Here's two newish blogs dedicated to the art of scientific presentation (in posters and figures): NiceFigure.org, a tumblr devoted to beautiful figures in scientific publications, and Better Posters, a collection of pretty science posters and the reasons why they're effective. Neither seem to have much chemistry related content yet, but send them your examples of beautiful chemistry!

Edward Tufte approves.

(Previously: Scientific talks as gig posters)

I'm not dead yet! I'm feeling better!

noreply@blogger.com (Joel Kelly) — Wed, 05 Oct 2011 16:51:00 +0000

Hey-o!

My apologies for my long and unexplained hiatus round these parts. Between getting married, defending my thesis, moving to a new city and starting a postdoc, I've been a little busy.

My new research is something new and exciting involving liquid crystals! Which means all kinds of pretty pictures like this one:

I have a few posts planned for the next few weeks about the science-related parts of my crazy summer, and a few guest posts too. Hope you find them interesting!

PS- I am sad to say I lost $5 on my Nobel bet this year. Quasicrystals? What the heck! It sounds neat, I guess.

glassblowing

noreply@blogger.com (Joel Kelly) — Tue, 12 Apr 2011 20:42:00 +0000

Here's a nifty video on glassblowing produced by Etsy:

Handmade Portraits: Kiva Ford from Etsy on Vimeo.

Back to the thesis grindstone!

I've been published* in Nature Materials!

noreply@blogger.com (Joel Kelly) — Mon, 28 Mar 2011 17:45:00 +0000

So I wrote a letter to the fine editors of Nature Materials (one of the most respected and reputed journals in my field) on their recent editorial, "Transparency in peer review", and they up and published it in their April issue!

They're testing out new ways to make peer review more transparent, namely publishing the anonymous reviewers' reports as supporting documents alongside publications. As any history professor will tell you, these primary documents that describe the actual motivations and narrative of the authors, editors and reviewers are incredibly valuable in understanding the context within which this research was conducted.

My letter to the editors can be pretty much summed up as "Yes, yes, more of this sort of thing. Hurrah!"

But, let my experience be a lesson for all of you: if you are willing to put the 10 minutes of effort into responding to an interesting editorial or letter you come across, send it to them and you may just find yourself published!

*Having a colleague who just published an actual research letter in Nature Materials, I should warn you that trying to get your name in such a prestigious journal the normal way is much, much more difficult (and correspondingly more rewarding for her career).

more explosions!

noreply@blogger.com (Joel Kelly) — Wed, 09 Mar 2011 15:56:00 +0000

Update (March 20, 2011): Davin was interviewed by the RSC's Chemistry World. Go check it out!

You may recall a post from last November on a JACS paper on the explosive nature of nitrotetrazolate-2N-oxides. The paper also got some attention from the inimitable Derek Lowe in his popular series, "Things I Won't Work With."

Well, the Klapoetke group has gone one step further and published another paper in Inorganic Chemistry (subscription required) on crazy insane explosives, with probably the best TOC graphic of all time (of all time!):

That structure has a chain of 10 nitrogen atoms. That's right. 10.

Rather than try to explain the science behind this paper on my own, I emailed one of the co-authors, Davin Piercey for assistance. Davin did his undergrad research in our lab, and was happy to get back to me right away with an explanation (and a video!).

DGP: So within 24 h of the 1,1’-azobis(tetrazole) paper being online, there is already interest in this due to a combination of interesting properties and the scientific novelty arising from a chain of ten connected nitrogen atoms. Joel and I go way back so I agreed to write a guest post on this subject.

Describe the science behind this paper, and what makes this compound so explosive?

DGP: Generally explosive behavior results from one of two general sources, molecules containing fuel and oxidizer in the same molecule, or high heat of formation materials. Of course, both sources can be at play within one molecule. 1,1’-azobis(tetrazole) is an example of the latter type of material, where the high heat of formation results from mostly high nitrogen content, with minor contribution by strained bonds in the five-membered tetrazole rings. The reason high nitrogen content leads to explosive behavior, is the low thermodynamic stability of N-N bonds relative to the triple bond in nitrogen gas; explosives are metastable when compared to their detonation products (generalized: N2, CO2, CO, H2O).
The more N-N bonds present, the higher the higher the heat of formation and the lower the stability of the compound, where stability is manifested by both thermal and mechanical sensitivities.

As mentioned in the paper, 1,1’-azobis(tetrazole) has a heat of formation near that of 1,4-diazido-2,3,4,5-tetrazene, another exceedingly sensitive, high heat of formation material.

Eight-nitrogen chains were well known at the time, so preparing a longer chain was the academic motivation of this work.

What’s the craziest thing that’s happened to you in working with this stuff? How do you deal with it safely?

DGP: Safety is of course paramount when dealing with explosive materials, and the easiest way to be safe is to work on small scale. I was only working with 170 mg of precursor giving a maximum product yield slightly below this mass. However even 100 mg of quality explosive can punch a clean hole through 1mm aluminum so the next major factor is standoff: flasks containing explosives never get held in the palm of one’s Kevlar-covered hand, but rather are either held with a clamp, or by the neck a finger’s length away. With these two precautions taken, the remainder is personal protection equipment for potential shrapnel; Kevlar gloves and arm protectors work wonders, and basic body armour or leather, face shield, and hearing protection takes care of the rest. Another hidden danger with sensitive explosives is static discharge, so the experimenter is always electrically grounded.

Finally, for exceedingly sensitive materials such as this, keeping the material wet greatly reduces sensitivity, 1,1’-azobis(tetrazole) could not be repeatedly manipulated dry without exploding.

The craziest thing that happened while working with this stuff was once a raman tube was loaded with dry material, as it slid down the tube to the bottom it chose to explode. What was annoying was the filtercake of remaining material placed approximately 80 cm from the explosion must have got hit by the shrapnel, as it exploded concurrently; I was annoyed, I had grown tired of making it repeatedly. I switched to only handling it wet after that and no more incidents occurred.

Also amusing was the explosion while rotovapping an acetonitrile solution of it, it had been done several times before without incident, but this time I chose to slow it as it precipitated to watch. When the rotovap was slowed the flask exploded. The flask it was in is shown next to an intact flask on the paper’s table of contents image.

Due to proper protective measures, these explosions were only an inconvenience.

What drew you to study these explosive materials?

DGP: Their inherent awesomeness… well, that and pushing the limits of what can exist, and trying to stabilize compounds on the limits of existence.

Do you have any battlescars?

DGP: Nope… or at least not yet. :P ;)

Davin was also very gracious in sending along a video he recorded showing the explosion that generated one of the fractures in the above TOC graphic:

stay in school, kids

noreply@blogger.com (Joel Kelly) — Sat, 15 Jan 2011 21:37:00 +0000

Source: SMBC.

starting 'em early

noreply@blogger.com (Joel Kelly) — Wed, 22 Dec 2010 18:21:00 +0000

(via Metafilter)

A team of researchers publishing in Biology Letters have concluded "We also discovered that science is cool and fun because you get to do stuff that no one has ever done before."

The authors are 25 students at Blackawton Public School, aged 8-10, which I'm going go out on a limb and guess is the youngest age to be published in a peer reviewed journal ever.

The organizer and lead scientist is Beau Lotto, whose son Misha is in the class. I nominate Lotto for the title of ~~Dorkiest~~Best Dad Ever. Lotto has previously given a TEDglobal talk.

The study itself was on bees, concluding "bees use a combination of colour and spatial relationships in deciding which colour of flower to forage from."

Biological Letters is an RSC journal with a 2009 impact factor of 3.52. The authors tried to submit to Nature, Science, Current Biology and PLoS ONE, who were enthusiastic but declined to publish due to lack of referencing and simplistic writing style. Which, coincidentally, is a rejection that I've heard many a time. Maybe I should have gotten started in research a bit younger...

upstaged!

noreply@blogger.com (Joel Kelly) — Wed, 22 Dec 2010 02:38:00 +0000

Ahh! Professor Martyn Poliakoff, of the always entertaining Periodic Table of Videos, tries to upstage me by patterning a really tiny periodic table onto a strand of his own hair.

I'd like to point out that his pattern is still much, much larger than mine. And so I retain the title of world's smallest message for an internet blog thing!

merry christmas from infiniflux!

noreply@blogger.com (Joel Kelly) — Tue, 21 Dec 2010 22:09:00 +0000

Hey internet!

Hope you have a great and restful holiday break! The above image is a scanning tunnelling micrograph (STM) of a Si (111) wafer passivated with hydrogen under ultrahigh vacuum. The pattern of blackish dots arises due to the STM tip tunnelling current through the unfilled antibonding states of the surface atoms. Translated into layspeak, those little black dots are fairly good representations of individual Si atoms. Boo-yah. Let's see Hallmark do that.

In fact, the image above is about 100 nm x 100 nm, which is around 1.6 trillion times smaller than a 5 inch square Christmas card.

The white dots spelling out my very special christmas message (it helps if you squint)[1] were created in the surface by running the STM tip over the pattern with a high bias, ripping off hydrogen as it travels and leaving a dangling bond. This forms a midgap state, which is easier to pass current through; therefore the dangling bond shows up as a white dot on the image. This sort of patterning is much more useful than just making cheesy holiday cheer, and helps scientists to better understand the electronic properties of surfaces and interfaces. Such patterns may allow them to precisely create atomic wires for use in technologies such as spintronics. So cool!

The image was made by my friend and fellow grad student Marco, who is studying with Dr. Robert Wolkow at the University of Alberta. Marco is officially an honorary infinifluxer for life, an esteemed and exclusive club to which I am very happy to welcome him into. You too can join this club if you discover an element and name it after me. Act now in the next ten minutes and we'll throw in a complimentary Slap Chop. Operators are standing by.

Your Canadian tax dollars at work!
Joel

[1] I would have tried to write a more inclusive holiday message, but it's a huge pain in the rear to write large patterns. Sorry to all fans of Hanukkah, Kwanzaa and Festivus. We can still have an airing of the grievances if you want.
[1a] The largeish white blobs are gunk that tends to fall off of the tip when you are patterning. I definitely gained a lot of respect for people that work with STMs for their research in doing this. There are umpteen millions of different ways for things to go wrong when you're trying to manipulate atoms.

science jokes ahoy!

noreply@blogger.com (Joel Kelly) — Thu, 02 Dec 2010 23:50:00 +0000

Boingboing is having an open thread for science jokes, and there are some awesome groaners already:

A malacologist was chilling at home drinking a beer and watching Adventure Time. There was a knock at his door & he irritatedly stood to answer it.

On his porch was a haplotrema vancouverense. "Can I borrow your phone?" Piped up the snail.

"Fuck no." Said the scientist, kicking the snail off his porch.

TWO YEARS later the scientist was at home chilling out, drinking a beer and watching Regular Show. There was a knock at his door.

It was the very same haplotrema."What the fuck was that about?"

natural peppermint flavour

noreply@blogger.com (Joel Kelly) — Wed, 01 Dec 2010 08:17:00 +0000

I know what I'm using for my next column... I've been tired of the fruity odor of ethyl acetate, it's time for some "natural peppermint" flavour!

(spied in the health section of a grocery store in Edmonton)

i value my eyebrows and hearing, thank you very much

noreply@blogger.com (Joel Kelly) — Sun, 14 Nov 2010 00:13:00 +0000

Some of you may be followers of Derek Lowe's popular "Things I Won't Work With" series where he highlights especially nasty chemicals (y'know, above and beyond the ones that are preventing our river from freezing).

I am pretty pleased to nominate the below compound as worthy of a post from Lowe (and also a 6" thick blast shield):

The molecule comes from a JACS ASAP that was published by a former undergrad student in our group who has since gone on to do some crazy explosives chemistry in grad school in Munich (you'll need subscriber access to be able to read the article).

For any non-chemists in the house, one rule of thumb for judging the explosivity (a term I just made up) of an organic molecule is the ratio of C to N atoms. The more N, the more likely it is to blow sky-high. TNT (2,4,6-trinitrotoluene), the industry standard for a good explosive, has a C:N ratio of 7:3, whereas the above compound has a staggeringly low 1:5![1]

You'd have to have cojones made out of titanium carbide to be able to work with this stuff on a regular basis. Judging by the experimental, they take some serious precautions (and this is coming from a person who works with hydrofluoric acid every day):

5-Nitrotetrazole-2N-oxide and its salts are all energetic compounds with sensitivity to various stimuli. While we encountered no issues in the handling of these materials, proper protective measures (face shield, ear protection, body armor, Kevlar gloves, and earthened equipment) should be used at all times.

Congratulations, Davin! Don't explode your face off, ok?

[1] There are several other commercial explosive materials out there that have a much lower C:N ratio such as RDX, and even crazier compounds are out there in the literature. But Davin's lab is actually conducting explosion tests (i.e., going out of their way to actually blowing things up!). Cr-a-a-z-y.

schrodinger approves

noreply@blogger.com (Joel Kelly) — Thu, 11 Nov 2010 19:27:00 +0000

A friend has recently started an excellent organic chemistry blog[1] and offers the above kitteh-themed lesson on conformation and configuration. That, my friends, is a configurational isocat.

1. He is also offering organic chemistry online tutoring through Skype, which I think is a pretty great idea.

after which I set myself on fire.

noreply@blogger.com (Joel Kelly) — Mon, 25 Oct 2010 21:10:00 +0000

It snowed today in Edmonton. Just a little bit, enough to make the river valley all white and sparkly and awesome (boo to all the snow haters, by the way). It's still pretty nice out, just around -2 to 0°C.

Edmonton, by the way, has a gigantic river valley in the middle of it. The North Saskatchewan river is about 30-40 m wide and is fed by glaciers in the Rockies. Not exactly a tiny stream.

Sitting on the train into school this morning, I overheard the following conversation:

Small child: Mommy! Why is the river not frozen?
Mother: It's because that river doesn't freeze, honey. It's filled with chemicals that prevent it from freezing.
Small child: What are chemicals?
Mother: Chemicals are toxic pollution that ruin the water and make it not freeze.
Me: *head explodes*

I really hope that kid grows up to be a scientist.

DNA SPRAY.

noreply@blogger.com (Joel Kelly) — Tue, 19 Oct 2010 21:48:00 +0000

McDonald's is using a muggafuggin DNA SPRAY to prevent and track thefts!

The product, SelectaDNA, is a combined fluorescent dye and unique DNA strand that is sprayed upon activation of an alarm. This ties whoever comes into contact with the aerosol to the scene of the crime.

Someone over at metafilter pointed out some critical skeptics.

don't try this at home

noreply@blogger.com (Joel Kelly) — Tue, 19 Oct 2010 14:50:00 +0000

fun fact: synthetic microwaves can generate a lot of power. make sure to use an appropriately-sized vial for the scale of your reaction (not too big, or the above will happen; not too small or you'll generate too much pressure), or else you'll have learned nothing from joel's stupid mistake. nothing!

here's the protective sleeve that the vial sat in to protect the rest of the instrument from dolts like me:

the scientific process on the internet

noreply@blogger.com (Joel Kelly) — Sat, 14 Aug 2010 18:58:00 +0000

Hey internet, long time no see. Sorry I've been such a delinquent blogger!

Two things related to the peer-review process:

1. A new blog worth following: Retraction Watch, a blog that follows retractions from refereed journals:

The unfolding drama of Anil Potti — a Duke researcher who posed as a Rhodes Scholar and appears to have invented key statistical analyses in a study of how breast cancer responds to chemotherapy — has sent ripples of angst through the cancer community. Potti’s antics prompted editors of The Lancet Oncology to issue an “expression of concern” — a Britishism that might be better expressed as “Holy Shit!” — about the validity of a 2007 paper in their journal by Potti and others.

(via Metafilter)

2. I recently randomly stumbled across a really great and detailed experimental (PDF) for the collodial synthesis of bismuth sulfide nanowires, hosted on the personal site of a post-doc. For anyone that has tried nanomaterial synthesis, I think you'll appreciate the detail provided that is unfortunately missing from most nanomaterial experimentals. The author specifies which reagents you need to buy, how to set up the glassware, what to do if things go wrong, etc. You can compare to the published experimental here if you have access to Angewandte.

Everyday Scientist previously blogged about the trouble with Supporting Information.

synthetic bacteria

noreply@blogger.com (Joel Kelly) — Thu, 20 May 2010 18:06:00 +0000

Not that I have any idea what they're actually talking about, but apparently some dudes have made some sort of DNA synthetically that is self-replicating and will somethingsomethingbiofuelstakeovertheworld. Pretty sure this is all taken straight from the script of an in-development James Bond movie.

Original Sciencexpress article.

New York Times article.

noreply@blogger.com (Joel Kelly) — Mon, 17 May 2010 22:45:00 +0000

The newest CEO of Virgin Galactic: George T. Whitesides, former chief of staff of NASA.

If that name rings any bells, it's because he's the son of Professor George M. Whitesides, surface chemistry ninja and chemistry professor at Harvard. That is one geeky/so-very-powerful family!

He does have a brother, Ben Whitesides, who is a musician in "The Joggers", a Portland-based band known for its songs containing "elements of math rock which retain a pop sensibility."

fraud alert

noreply@blogger.com (Joel Kelly) — Wed, 07 Apr 2010 19:29:00 +0000

Someone is in some serious trouble over at Acta Crystallographica after some sleuthing discovered a whole whack of faked structures.

The editorial linked to above states the authors took a structure from the literature, and change metal centers and various functional groups with some tweaking of unit cell parameters and removal of reflections to make it look legit.

The accused authors come from Jinggangshan University, Jian, China. The count of retracted papers is at 70 and growing. Yikes.

The thing I don't really get is that the reward for going to all this effort of faking data to get publications is fairly small; Acta Cryst isn't a particularly glamourous journal by any stretch of the imagination. And the punishment (both likely coming to the authors from a destroyed reputation, and to other researchers who may have read these papers) seems really, really big.

Thanks to Ton Spek, who first discovered these frauds.

history!

noreply@blogger.com (Joel Kelly) — Sun, 04 Apr 2010 06:51:00 +0000

Hey internet,

I know most chemistry undergrad programs don't leave a ton of wiggle room for electives, but even if you find history to be not your cup of tea you should totally know about Lise Meitner!

Here are seom fun facts about Meinter:
1. She was a bad-ass physicist at a time when women were not allowed to get doctorate degrees, not viewed as capable of doing serious research and not able to hold a professorship (she worked for free as a "guest" until the age of 35-- sounds a lot like a really long, sexist postdoc).

2. She discovered the Auger effect in 1923. Coincidentally, Pierre Auger didn't discover the Auger effect until 1925, which is kind of funny given that they're named after him and everything.

3. She then teamed up with Otto Hahn to discover nuclear fission.

4. I'm going to repeat that: She helped friggin discover nuclear fission. Dudes!

4a. The way they discovered it was pretty dang clever, the perfect mix between chemistry and science. In studying the bombardment of uranium with neutrons, Hahn discovered the formation of barium via the formation of a organic barium salt. However, it was Meitner (and her nephew Otto Frisch, who coined the term fission and would go on to work at Los Alamos) who came up with the theoretical explanation for what was going on. She also realized this was in accordance with Einstein's famous E=mc^2, helping provide experimental proof for this most famous equation.

5. She also happened to do all this while on the lam from Nazi Germany, meeting covertly with Hahn, who stayed in Germany for the most part.

5a. As you may know, the discovery of fission led to the establishment of the Manhattan project and, um, atomic bombs. Meitner was offered a role working on the project but refused to work on a project with destructive intentions.

6. Hahn would go on to win the 1944 Nobel prize in Chemistry for the discovery, conspicuously without sharing any credit with Meitner. Sadly, Hahn never did fully acknowledge her role in the discovery of fission. Jerkwad. Hahn wasn't a total tool; he did help Meitner flee Nazi Germany by giving her a diamond ring to use as a bribe, and the initial reason he was not able to acknowledge her role in the initial publications was political, as a coauthorship would have admitted he was collaborating with a jewish refugee to the Nazis. But, anyway, he (and the Nobel committee) still comes off as a bit of a dink (collective dinks) for failing to give credit where credit was clearly due.

This concludes the history of chemistry lesson for today! Hope you enjoyed it!