Chemistry Blog

Aug 03

Two years in the life of a lab whiteboard


Two years ago my group and I shared a time-lapse video: A Year in the Life of a New Research Lab.  Shortly after, I picked up a new set of markers and directed the camera at our lab whiteboard. We stopped the camera last week and can now share two years in the life of our whiteboard condensed down to a 1 minute video. It contains one photo a day taken at 11:30 am for ~750 days.


 

 

Note: Some photos have been omitted due to inactivity or because there was proprietary information on the board.

Jul 12

Professor Anthony Russell Clarke  1959 – 2016


Anyone who has completed a doctoral thesis will testify to the almost parental like relationship a PhD supervisor has with their students. And so it is with great sadness that I heard my PhD supervisor Professor Anthony Russell Clarke, aged just 57, had passed away this week.

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Tony Clarke. Photo Credit. Emma Cordwell

To his friends, students and colleagues Tony Clarke was chaos incarnate. Anyone who worked with him can testify to the apparent disarray of his lab and life. The humdrum cycle of the working week didn’t impinge on Tony’s habits. For Tony there was no such thing as ‘work/life balance’, there was just Life. Sometimes the most appropriate thing to do with life was to head out to sea on his beloved boat, at other times the lab was the place to be. His wayward lifestyle made Tony a challenging person to work with; society doesn’t care for chaos, it prefers tidy plans, filed reports and scheduled meetings.

And so to many it was incredibly difficult to pinpoint how or why his group and indeed his mind worked so productively. It appeared to the outsider that disorder reigned. In fact true chaos ruled; chaos from which, as in nature itself, beauty and order emerges. Of course something is needed to trigger the emergence of order from a chaotic system. And in Tony’s case the attractor around which order condensed was his unwavering insistence on experimental rigour and reproducibility.

Inspiration, creativity, curiosity; Tony had these in spades. Everyone who ever worked with him couldn’t help but admire his intellect, wit, charm and passion. And so they overlooked, as best they could, his social transgressions. Most of his exasperated superiors let him get on with his research, content with his prolific outputs, the wise garnered his genius. Meanwhile his PhD and post-docs rallied around trying to keep his admin on track by digging out the most important forms and documents hidden in his office’s archaeological filing system (the deeper in a stack, the older the documents). This remained a workable system threatened only by the occasional  tectonic movements that disrupted the order.

Tony was an outstanding scientist. He received a SERC Personal Fellowship at 26, a Lister Fellowship at 36 and a personal chair at 41. Churning out seminal work in enzymology, protein engineering, protein folding and prion disease throughout his career. He retired through ill health at 55 with 183 papers, including 4 in Nature and 2 in Science, and an H-index of 49 under his belt.  But the numbers don’t do his achievements justice, his real legacy are the results of his infectious passion for science. He showed us that curiosity was key, that it was the exploratory process that was the interesting bit. Those that had the honour to work alongside him (for he always treated his charges as equals) are left with a life-long love of discovery. Tony burnt out early (his fondness for cigarette and a liquid diet hardly helped) but those of us whom he took along for the ride will benefit from his energy throughout our lives and careers.

It is perhaps worth noting that within hours of his death the hundreds of people whose lives he touched, spread as they were over decades of scientific discovery and thousands of miles, had all learned of his passing. The “Clarke-collective” had begun to grieve.

The world is a far less interesting place without Tony Clarke. His family, friends, students and colleagues will miss him greatly.

“We are able to find everything in our memory, which is like a dispensary or chemical laboratory in which chance steers our hand sometimes to a soothing drug and sometimes to a dangerous poison” Marcel Proust.

https://creativecommons.org/licenses/by-sa/4.0/

Jul 08

A Flash of Light: a popular science book written in a weekend.



Last autumn Andy Miah an I hatched a crack pot plan to write a popular science book in a weekend.

With the help of authors Chris Arridge, Wendy Sadler, Giuliana Mazzoni, Benjamin Burke, Juliette McGregor, Charlotte Stephenson, Kevin Pimbblet and Akshat Rathi along with illustrators Ian Morris, Heather Holst and Liz Bryan, plus The Conversation editors Miriam Frankel and Stephen Harris we did it!

A Flash of Light comes at a radical time in the history of scholarly publishing. With mobile and digital books capturing more of the attention of readers, the number of published scholarly articles doubling every decade, and a growing need to reimagine the book for the 21st century, our book is a product of these times.

Typically, when a scientist has the initial spark of an idea, it might be years before the fruits of their labour is read. In the between, grant proposals are written – and hopefully won – researchers are appointed to help carry out the work, papers are eventually written, peer reviewed, and finally, after what can be 5 years in total, these findings are published and have the chance of reaching the general population. Yet, even here, more work is needed by the publisher to ensure a wider audience and, typically, academics must take their work to intermediary platforms, such as the media, or book fairs.

The duration of this process, coupled with questions about the integrity of the peer review system have led some academics to interrogate and propose new working models for researchers and, perhaps since the digital age, academics have found outlets for their work to quench a growing desire to reach a wider public. In recent times, platforms like The Guardian’s science website, the Huffington Post and more, recently, the Conversation, have become spaces in which academics can write differently and reach new audiences.

At the same time, the rise of e-readers and e-publishing more widely provide greater opportunities to get ideas out fast. This was the pre-text for A Flash of Light, which aimed to turn the academic publishing model on its head and bring together some gifted writers and thinkers to fly in the face of established practices. The working hypothesis was that, if you could get a number of authors together in the same room for 2 days working intensively and without breaks or distractions from all of the other things that academic life brings, we could produce an amount of work equivalent to that which would otherwise take a year or two to accomplish.

 

The result of this frantic weekend was about 9 chapters comprised of around 30,000 words, supplemented by around 20 illustrations. Those chapters were messy, still needed editing, referencing and some tidying up, but they were good. They had a sense of pace and energy and they hung together into a fascinating story covering an incredible range of light related topics.

Flash of light crew

Flash of light crew. Illustration by Ian Morris.

Our book takes an epic journey starting to explore the colours of the universe and the sky above our heads. It covers light you never knew you could see and how light influenced the evolution of animals, we cover the psychology of colour and vision before looking at how humans have harnessed light for our own gains.

We learnt a fabulous amount in our weekend sitting around a table frantically researching and typing. Some fascinating material has not made it into the main text, but is worth mentioning. For example, we spent an hour or two brainstorming the topic of the book and, whilst we pretty much ended up writing what we wanted, we all got very excited about where colour is actually located. Discussions ventured from colour blindness, to the experiences of people who have had their sight restored and synesthesia. In the course of their discussion our facilitator, Mark Cutter,, noted that he is a governor of the Royal Institute for the Blind, and, 10 minutes later, he had Denise Leigh, a blind opera singer with synesthesia, on the phone talking to us. Her condition means that she can see sounds and she described the incredible ribbons of colour she sees whilst singing, the hues of her children and the blessing her synesthesia is. Denise’s story exemplify the brief and the rapid journey we went through during the course of the weekend, where the group sat around the table for 22 hours throwing stories, facts and figures at each other.

More often than not, edited books in academia are made without ever the authors coming together to work on a common core manuscript and this experiment sought to transform this model. However, it was not just an exercise in productivity and work flows. It was also an inquiry into how one makes the act of writing a performance and how this ritual of real-time collaboration can create a sense of history that can enrich our lives. Time will tell how our individual authors feel about the work they produced and the publication that resulted, but at the very least, we have shown that a lot more can get done, a lot quicker, by aggregating knowledge and focusing its discovery down in a very short amount of time.

Crucially, the book would not have happened without the additional support and belief in us by the Royal Society of Chemistry, particularly the hard work of Cara Sutton. We are tremendously grateful for the Society’s investment and willingness to try something completely unprecedented. Here again, we feel that this relationship was atypical where the publisher had a closely intellectual involvement with the generation of our words than is often the case.

 

Jun 11

The Periodic Table of Element Eytmologies



The seventh row of the periodic table is complete, resplendent with four new names for the elements 113, 115, 117 and 118. The International Union of Pure and Applied Chemistry (the organisation charged with naming the elements) has suggested these should be called nihonium (Nh); moscovium (Mc); tennessine (Ts) and oganesson (Og) and is expected to confirm the proposal in November.

Yuri Oganesyan.
Kremlin.ru, CC BY-SA

The three former elements are named after the regions where they were discovered (and Nihonium references Nihon the Japanese name for Japan). And “oganesson” is named after the Russian-American physicist Yuri Oganessian, who helped discover them.

After years of having to make do with temporary monikers while the elements were officially being added to the periodic table and evaluated by the IUPAC, these new names are much welcomed by scientists. Alas, those calling for names in tribute to great folk of popular culture have gone unheeded; Octarine (the colour of magic, according to Terry Pratchett), Ziggium (in tribute to David Bowie’s alter ego Ziggy Stardust) and Severium (in tribute to Alan Rickman and via Severus Snape) will not adorn the updated table.

Instead IUPAC have followed their rules which stipulate that “elements are named after a mythological concept or character (including an astronomical object); a mineral, or similar substance; a place or geographical region; a property of the element; or a scientist”.

But there wasn’t always such an organisation overseeing the names of the elements. Most of them have come about via contorted etymologies. So to give you an idea of the diversity of the most famous of scientific tables, I’ve turned it into an infographic and summarised a few of the eytmologies in numbers.

The Periodic Table of Elements’ Etymology.
Andy Bruning, Compound Interest, Author provided

Click here for a larger version.

Two of the elements stink. Bromine means “stench” and osmium means “smells”. France also appears twice on the periodic table in the form of francium and gallium (from Gaul) and its capital city, Paris, gets a mention (in the form of lutetium).

Three sanskit words – eka, dvi and tri, meaning one, two and three – were prefixed to elements and used as provisional names for those that had yet to be discovered. Eka- is used to denote an element directly below another in the table, dvi- is for an element two rows down and tri- is three rows beneath. Russian chemist Dimitri Mendeleev first used this nomenclature to fill in the gaps in his early periodic table, so element number 32 was known as eka-silicon until it was discovered and named germanium in 1886. Similarly, rhenium was known as dvi-manganese until 1926. Some 14 elements have had eka names including our four new additions which before their discovery were known as eka-thallium, eka-bismuth, eka-astitine and eka-radon.

Four of the elements are named after planets (Earth – in the form of tellurium, Mercury, Neptune and Uranus). A further two are named after dwarf plants (Pluto and Ceres), while one after a star (helium from the Greek for the sun – Helios) and another after an asteroid (Pallas) feature on the periodic table.

Five elements are named after other elements: molybdenium is from the Greek for lead, molybdos, while platinum comes from the Spanish platina meaning “little silver”. Radon is derived from radium, zirconium has its roots in the Arabic zarkûn meaning “gold-like” and nickle is from the German for “devil’s copper”.

Eight elements were first isolated from rocks quarried in a the small village of Ytterby in Sweden. Four of those elements are named in tribute to the village (ytterbium, erbium, terbium, yttrium).

15 are named after scientists, only two of whom were women: Marie Curie and Lise Meitner are immortalised in curium and meitnerium.

18 elements have had placeholder names derived from the Latin for the elements atomic number (for example ununoctium, now oganesson). This was introduced to stop scientists fighting over what their discoveries should be called. Nobody wants a repeat of the three-decade long “Transferium Wars” when battles raged between competing American and Russian laboratories over what to call elements 104, 105 and 106.

42 elements’ names are derived from Greek; 23 from Latin; 11 from English; five are Anglo-saxon; five German; five Swedish; two Norse; three Russian, and one apiece for Japanese, Sanskrit, Gaelic, Arabic and Spanish.

118 elements appear on the periodic table, and the seventh row is complete, but that doesn’t mean the table is finished. Laboratories around the world are busy smashing atoms together in an attempt to forge new even heavier elements. The hope is that before long these latter day alchemists will hit upon the fabled “island of stability”; a region of the table that harbours elements with half-lives much longer that the sub-second lives of nihonium, moscovium, tennessine, and oganesson.

Infographic for this article was made by Andy Brunning/Compound Interest

The Conversation

This article was originally published on The Conversation. Read the original article.

Dec 06

ACS LiveSlides: Another Step in Multimedia Science Publishing


Last March I introduced the Hanson research group’s five minute GEOSET videos. I’ve since learned that, in July 2013, Prashant V. Kamat (Deputy Editor), George C. Schatz (Editor-in-Chief) and their co-workers at the Journal of Physical Chemistry Letters announced ACS LiveSlides™, a user friendly mechanism for generating and sharing video slideshows for each manuscript. As noted in their editorial piece, they were motivated by the “changing publication landscape and the wide availability of new electronic tools have made it increasingly important to explore new ways to disseminate published research.”

We recently created an ACS LiveSlides™ presentation for our J. Phys. Chem. Lett. manuscript, “Photon Upconversion and Photocurrent Generation via Self-Assembly at Organic–Inorganic Interfaces.” The paper introduces self-assembled bilayers as a means of facilitating molecular photon upconversion and demonstrates photocurrent generation from the upconverted state. It’s arguably the first example of directly extracting charge from a molecular upconverted state if using the first submission date, first public disclosure, or the patent application date as markers. If using the manuscript acceptance date, Simpson et. al’s publication holds that distinction.

An invitation to create an ACS LiveSlides™ presentation immediately followed the message notifying us that our manuscript was accepted. All we needed to do was provide 5-8 Power Point Slides summarizing the manuscript (using a format provided by the ACS) and record an accompanying <10-minute mp3 audio file. The editors took the files (and a list of times for each slide transitions) and published our LiveSlides™ presentation in less than a week. It was an easy process and now anyone can view our presentation. No subscription necessary.

One drawback is that the video cannot be embedded on a webpage. As stated in their terms:

Files available from the ACS website may be downloaded for personal use only. Users are not otherwise permitted to reproduce, republish, redistribute, or sell any Supporting Information from the ACS website…

So we have a backup plan for those preferring an embedded video. Below you’ll find our GEOSET video summary presented by Sean Hill.

Oct 31

Halloween Chemistry: Cinder Toffee!




How about a spot of halloween chemistry? With nice simple explanations for the trick or treaters.

Cinder toffee!!

You’ll need:

  • Sugar
  • Golden syrup
  • A jam/jelly thermometer
  • Bicarbonate of soda
  • Grease proof paper
  • A baking tray
  • A saucepan

Safety:

The toffee mix gets very hot, be careful when handling in and make sure there’s an adult helping.


What to do:

1. Weigh out 100grams (3.5 oz) of sugar into the saucepan.
2. Add 3 tablespoons of syrup
3. Heat the mixture on a stove whilst stirring it.
4. Check the temperature of the mixture.
5. Carry on heating until it reaches 145-150oC (293-302).
6. Quickly stir in 1 teaspoon of bicarb. It will suddenly bubble up.
7. Now pour it into the baking tray, lined with grease proof paper.
8. Leave it to cool.

9. Break it all up (best done with a hammer) and enjoy!

What’s going on?
So that’s a nice simple recipe for a tasty treat but where is the science?

First off there’s the sugar and syrup. There are actually loads of different types of sugars, the stuff you put in your coffee and the granulated sugar used here is sucrose. It looks like this:

Sucrose
Golden syrup is a mixture of water, sucrose and two other sugars called fructose and glucose. They look like this:
Fructose
Glucose
Sucrose is actually made up of a fructose and glucose molecule that have been joined together.
So why do we need these three sugars to make the toffee? Well, when they are mixed all together they interfere with crystal formation. To explain how this works let’s represent each of the sugars with a different shape.
If we have one type of sugar then the molecules can pack together nice and neatly, like in the diagram. And that is exactly what happens in a crystal. But if you mix them all together they can’t form ordered patterns and so you don’t get crystals forming.
So if we tried to make the toffee with just one type of sugar then we’d end up with crystals forming which make for hard dense toffee (more like a boiled sweet). But by using 3 different sugars the crystals don’t form and instead you end up with a brittle, crunchy, glass like toffee.
Then there’s the bicarbonate of soda. You normally put this in cakes to make them rise. That’s because when you heat up the bicarb it turns to carbon dioxide gas (hence the bubbles in your cakes). The same thing happens here. When you spoon the bicarb into the hot sugar it almost instantly gets converted to carbon dioxide and causes the mixture to foam up.

Hope you enjoy the toffee and whilst you do you can find out more about the science of cinder toffer here.

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