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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.

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By July 12, 2016 44 comments Uncategorized

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.

 

By July 8, 2016 0 comments Uncategorized

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.

By June 11, 2016 4 comments Uncategorized

The chrome plated mystery of the Terracotta army’s swords



QIMG_6487in the 1st Emperor of China prepared well for the after-life. Throughout his reign he commissioned and built an eternal army of some 6000 soldiers, charioteers and cavalry. The  warriors stood in formation, buried at the foot of his tomb, there to guard the Emperor for eternity.

But all did not go as planned. Shortly after Qin was entombed chaos descended on his newly united China. Qin’s heirs, wishing to defeat him (even after his death) attacked his after-life defences. History tells that the underground barracks that housed the vast army of terracotta warriors were set alight. Fires smouldered for 90 days, structures around the ornate statues collapsed smashing the exquisite army. The broken soldiers and their bronze weaponry lay buried in ash and rubble. The great mausoleum was forgotten. Two millennia passed. Until in 1974, a peasant farmer, whilst digging a well, found fragments of a crushed warrior. And excavations began.

The thousands of individual Qin dynasty soldiers, have been painstakingly pieced together and placed back in formation. They are an awe inspiring sight. But I marvelled just as much when I saw no less incredible bronze weapons that armed the officers. Their swords are still sharp and largely unaffected by the 2200 years that have passed since they were forged. Instead of the green corrosion you’d expect on bronze artefacts the blades actually appear gun metal grey. Why this is the case is something of a mystery.
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There are reports of an analysis of the artefacts conducted by the Chinese Research Institute of Nonferrous Metals and Chinese Academy of Geological Sciences (although I am unable to find the primary data). The suggestions is that a 10-15 micron coating containing chromium oxide (at up to 2% chromium) was found. The conclusion; for millennia this thin layer protected objects from the ravages of time and chemistry.

So where did the chromium oxide layer come from? Did the ancient Chinese metallurgists, as suggested by curators of the Terracotta army, really have chrome plating technologies thousands of years before it was developed in the west? Over the intervening time did the chromium shine lose its lustre as it slowly oxidised, resulting in the grey we see today? Is a 10 micron, dilute layer of chromium oxide really enough to impart anti-corrosion properties?  Or is there another explanation for the immaculate swords?

This isn’t the first time someone’s asked these questions. Its been discussed on a sword forum where suggestions include forgeries and serendipitous impurities in the alloy. The latter seems to be supported by Prof Frank Walsh, an electrochemist now at Southampton University, when he was interviewed for an ABC documentary back in 2003 where:

Professor Walsh notes that the heat from the fires and the presence of carbon would have provided a reducing environment in which chromium atoms could have migrated to the surface of the weapons. There they’d oxidise and form a protective coating … Metals do diffuse over time, so this ‘natural’ explanation is plausible.

For me this isn’t a totally satisfying explanation. Largely since it appears, from the items on display, that only the blade is free of corrosion. The hilt has clearly corroded. If the slow migration of chromium to the surface of the blade is responsible why didn’t this mechanism occur elsewhere on the swords? But the idea that Qin’s weapon smiths knew how to apply anti-corrosion layers to their creations seems rather fanciful.

Which leaves the above questions unanswered. So chemists, time to reopen discussions. What do you think is going on? Can anyone come up with a way that the ancient Chinese might have deliberately or accidentally protected the weapons?  Or what else might have resulted a corrosion free blade, whilst the rest of the weapon is tarnished?

P.S. Any Chinese chemists/metallurgists out there who might be able to track down the analysis of the blades?

By September 22, 2015 11 comments Uncategorized