Board games - science style

Last week I was at Spiel, the largest board game convention of Europe in Essen, Germany. I played a shed load of board games with concepts ranging from collecting the most bananas to hanging up life sized washing. I also played a couple games with a scientific theme, which is a rare event in the board gaming world.

Can you save humanity?

One game that I played at the convention is really going viral at the moment (pun intended). This was Pandemic: Contagion. The game is a spin off from the board game Pandemic and you play as a specific disease attempting to rid the world of that troublesome humanity.

Whilst diseases are of course not sentient beings, it is a pretty novel idea to take on the role an infection. The game itself was ok, it didn't grab me at the first play, but maybe it will grow on me (yes, another intended pun). What I did really like with the game was the artwork, as accurate as you ever get with cartoon viruses. The components were also really cool as you get to play with petri dishes and to hold a fist full of viruses.

The original Pandemic is one of my favourite board games ever. A cooperative game where you fight the diseases together as a crack team of operatives and scientists, this time to save humanity! Again, the artwork is great and the four diseases are kinda realistic representations of microbes and viruses. The "Scientist"" character is also a fine example of promoting diversity in science, a white coated lady analysing her latest data. There are also a couple expansions to the base Pandemic game, one being called In the Lab. I've not played it myself but understand that here you can take a pause from racing around the world to enter the laboratory and develop new cures, cool!

Stereotypical spies

Another game I played at Spiel was the party game Spyfall. In this Russian produced game (just saying) there is of course a spy, who must uncover the location of the other players, whilst they each attempt to unmask the spy. The players are given cards with a location on them, one of which being a university. Now a university has many different departments as well as countless other student hangouts and from all these options Spyfall chooses to use a science lab. I say "science lab" as I'm actually not quite sure if it is a chemistry lab or more like a botanist's greenhouse. So let's just say it is something in the biological sciences area.

Unfortunately, the creators of Spyfall decided to go for the stereotypical depiction of an old crazy scientist for their game. The spy in the picture is disguised with a wig of white unkempt hair. One further point is that if this was a real situation then the spy would instantly be caught. Anyone that has worked in a university lab will know, old professors never set foot in the labs and would certainly not be seen getting their hands dirty doing some actual research.

An old board game that surely everyone knows is Cluedo. One of the characters/suspects in this game is Professor Plum. This learned man was first depicted as an absent minded, aged scientist. Not really pushing the imagination of the players here or indeed the boundaries of science. The character has, however, gone through a number of transformations over the years in different editions. His job has varied from archaeologist to psychiatrist to video game designer. In the latest interpretation he has lost his academic title and with it has perhaps lost the chance to persuade generations more of impressionable young scientists to solve murders, perhaps.

The portrayal of scientists in board games has come a long way since Plum's days but maybe still has a way to go. I do really believe that chemistry and science is a massively under used theme for games. What could be more fun than beating your friends in the hunt to synthesise a new molecule or to write the best grant proposal, oh yeah I see it now. If anyone else knows of any other science themed board games then please let me know, I'd love to try them out.

Autumn leaves

Autumn is upon us. The rain is coming, the temperature is dropping and the trees are changing from their summery greens into their autumnal reds and golds.

I saw Compound Chem had made a wonderful infographic about the chemicals that produce the brilliant coloured leaves this time of the year and so I sent the link to my Dad, an avid gardener. He then replied to me with a poem, another of his hobbies, that he'd written a few years ago describing the changes to the leaves with a chemical insight.

The colours in the leaves

Once the green of chlorophyll,

Didst verdant scenes on yonder hill,

Fill with glowing hues its summer’s glory,

And leaves shine forth to tell a chemist’s story.

As leaves do turn to feed from moistened light,

And deadly gas from which these leafy leaves will soon take flight.

How silently, as autumn ushers in bright days yet frosty nights,

These many-hued greens give way to other sights.

Other forms usurp the molecular green-maker’s robe,

And from their secret lair these tribes with ear-harsh names do probe.

So chlorophyll succumbs to xanthophyll,

No more such verdant scenes on yonder hill,

And carotene and anthocyanins do hold the day,

And orange, yellow, red and gold do sway.

Yet does not summer green pass to autumn splendour,

And to us cold breezes crispness render. 

Peter Branson 2007

Just who's been talking about your work?

Want to know who's been tweeting about your work, or what news articles are out there on that latest bit of research? Altmetric are now making that easier than ever. 

Article level metrics

Wiley are piloting an "article level metric score" with Altmetric for every one of their articles in the Wiley online library. These scores give a level for how much the article is shared online. I only recently noticed this development after seeing a Tweet from Matteo Cavalleri (@physicsteo) about these Altmetric ratings. A pretty cool idea.

Next to each article is a little Altmetric icon and a score for that article. In their FAQ section, they explain how it's all figured out in three easy steps:

1: Volume - Your score rises as more people mention it, which makes sense. But you only get 1 mention from each person per source, so you can't fake boost the score by tweeting the same thing over and over.

2: Sources - Different sources contribute different amounts. So a newspaper article is worth more than a blog post (even a fine one such as this), but then a blog is worth more than a mere tweet.

3: Authors - The score depends on who is saying it. So loud-mouths talking about every article under the sun are worth less than a specialist sharing with their specialist peers.

So with this new information at hand, I went to check out my latest paper.

Looking at this article recently published in Angewandte Chemie, it has a score of 28, which to me sounds pretty good. Clicking on the link then gives you a breakdown of what that all means. So for this particular paper there were three news articles and five Twitter mentions. The news stories were all new to me. Being an author of the work you think I might have known, but no. A break down of the tweets states that four were from the public and one from a scientist. I'm pretty sure all the tweets came from scientists so I'd love to know whose work Altmetric doesn't think is worthy of scientist status! 

The news articles were all based on the same press release from an Angewandte but one link was to a Chinese website. A (possibly bad) Google translate of the opening sentence gave, "Eye for an eye, but also treat the person in his body", which was definitely not in the original English press release!

But hey Altmetric, I also talked about the paper on my own blog recently, so that's another one to add to the list, maybe need to expand your search a little. (--Update-- This blog is now recognised! Nice one Altmetric, sorry for ever doubting you.)

Alternate versions

Interestingly, Angewandte also does a German version of the journal (technically this is the original and the other is an international version). Looking at the paper in the German edition tells another story. The score is up to 34!

There are four news outlets this time and one blog. No tweets for this one but one extra blog (still not mine). Two of the same news pieces from the international version were there and one of the new ones was from a German website (a faithful translation this time).

So Angewandte is actually artificially lowering their scores by having two versions. Maybe something for the Altmetric team to consider here; combining the mentions somehow. Or I could just do it for them and add up the scores, which gives me an impressive looking 28 + 34 = 62. That's how science works right?

The making of a cover

I'm on the cover! One of my scientific ambitions has just been fulfilled.

From the moment I began my PhD I had but one aim... finish the PhD. Well I managed that last year, but I also had other ambitions for my scientific career and one of them was to have my work featured on a journal cover. The first time I dived into the scientific literature and saw these cover designs, I knew straight away that I had found my calling in life. Ok, so this is a slight exaggeration, but I do think they are really cool.

Authors use all sorts of ways to demonstrate their work visually. But obviously some fields of research lend themselves more easily to the use of pretty pictures than others. My work with protein interactions was certainly one of these areas.

The first sketch

It was in July last year that I had a break through. My proteins were binding in the way that I wanted and things were finally all coming together. As a quick summary, the work involved attaching 5 carbohydrates to a non-toxic mutant of the cholera toxin protein. That modified protein could then be used as an inhibitor of matching size to the original toxin. The carbohydrates of the inhibitor bind to the wild-type cholera toxin, therefore inhibiting the wild-type from sticking to your cells.

I was sat in the back of a seminar a week or so after getting my latest results, when my thoughts wandered onto how I could visualise the work. In my mind there was only one way to show the interactions and that was by anthropomorphising the proteins. I sketched down a first rough cartoon. The noble inhibitor was obviously going to try to catch the evil toxin. I don't remember much of the seminar, but I think this was still time well spent.

The modified protein, our hero, had 5 large arms to catch the bad guy, oh and a police badge giving him the authority to hunt down these no-good toxins. As for his nemesis, well this guy had to wear the stereotypical black stripes and face mask of a robber as well as holding onto a swag bag to keep all his loot. As if this did not yet make it completely clear that he was not to be trusted, he also has evil eyebrows, a sure sign of a villain.

My initial sketch was not complete fantasy. The 5 arms represented the addition of carbohydrates to the protein. The swag bag represented for the toxic subunit that the wild-type protein possesses. The big googly eyes represented, oh no wait, they were just big googly eyes.

Writing the paper for this work was put on a list of things to do for quite a while and with it went the protein policeman. I was away at international conferences (holidays), I then had my thesis to write and after that a change of country. So it wasn't until February that the first draft of the paper appeared and as with any publication, a TOC (table of contents) image was needed. Here, the protein enemies resurfaced.

From notebook to TOC

The cholera toxin protein is fairly well known, with many crystal structures. Therefore, it was quite an easy task to scan through the protein data bank and pick out a nice structure as a starting point. A ribbon representation of the protein structure was chosen to start with as I believe this is the most recognisable protein depiction. Using Pymol, I then built in the alkane chains and added the carbohydrates around the protein. There was no choice for the colours, there is a standard scheme in the Turnbull lab; red = cholera toxin, orange = non-toxic mutant. The proteins were structurally accurate, the eyes and mouths were added for effect.

The initial design got the thumbs up from the lab group although it certainly needed a little refining. So after trying a few different positions and angles, the protein ribbon was changed in favour of a surface representation and a decent image was taking shape. The mask was added back in for the villain. A whistle and a police badge were given to our hero. Not the most serious piece of work, but we were confident that the actual research was good enough so that we could relax a little with a silly image.

From TOC to cover

I really wanted to try for a journal cover. We had some great work (I thought) and a great idea to build the TOC image into a full picture. The paper had been submitted to Angewandte and so the image had to be based on their standard circular design.

We went through 15 versions of bacteria for a background. Red, yellow and blue bacteria, some more realistic than others. I also tried out a Petri dish with bacteria growing across the plate but a consensus was made for an image with some large green bugs. The proteins stood out in the foreground and the colours worked well. Bacteria was used because the work is about protein modification and binding, and of course we couldn't perform any of the work (or have need to) without some little E. coli factories churning out all that protein.

A final change was to put some actual science into the image. Straight through the middle, separating the two enemies is a curve from one of the ELLA (enzyme-linked lectin assay) experiments reported in the paper. It gives the inhibitory potential of our good guy binding to the baddie. A fitting central divide.

All the best pictures have something a little bit ambiguous about them and here I feel that confusion is provided subtly by the police badge. The acronym refers to the top detective agency at Leeds University. CTPD, of course, standing for the Cholera Toxin Police Department. At this institution they only hire the most specialised proteins to catch the toxins.

The paper was accepted with great reviews and even recommended as a VIP paper. Excellent news! After much celebration we submitted the cover design. The editors were very quick to respond and accepted our image. More excellent news! I was amazed by how incredibly smoothly everything had gone. For my first first-author research paper this was fantastic.

I'm not sure if the image is quite bad enough to make it into TOCROFL, that will be the aim for my next paper. And after that my next scientific ambition is to get an SI unit named after myself, so we'll see how that works out.

You can find the paper "here" and our awesome cover design "here".

That love-hate supervisor relationship

 
What? I've not even started this blog post yet and you've already got a problem.

Supervisors

A mentor, a role model, a leader, a helping hand. These are all terms that could describe that voice of reason encouraging your next step. But when it came to reports and manuscripts, my supervisor always made me see red. Red pen that is.

Just wait a minute I'll get on to it soon.

 

No, I'm saying what you did. That's the point.

My PhD supervisor kept a certain red pen that he saved especially for colouring in my reports. Don't get me wrong, I was very grateful for all the feedback and insightful comments. Only it was sometimes quite hard to pick out the wise words amongst all the scribbles that appeared in the margins, on the figures and generally in any part of the paper with the smallest bit of blank space available. I spent hours writing up my work and of course felt some pride when presenting good results. All I ever wanted was just the smallest sign of approval, a pat on the back, a simple 'well done'.

Thanks! Finally some approval.

Ok I'll move on.

Corrections

Thanks to comments from my supervisor, I have learnt the proper use of a semicolon and when it is wise to avoid 74 word sentences. I'm sure (I'm almost sure) that he always wanted the best for me, but the criticism sometimes gets hard to take. Yes, he has years more experience than me, but come on, when was the last time he did a real experiment? There's no way he could still actually get in the lab and create the data that I was producing, right?

What! But I think you actually mean "your data are crap"?

 Are you sure? It looks correct to me.

Ok, ok. Maybe I'll scrap it all. I should never have started this blog post in the first place.

I actually had a very good working relationship with my supervisor and he tells me it was only for this reason that he felt able to fully unleash when it came to marking my work. Likewise, I was comfortable taking the criticism, knowing (hoping) that it would only make my writing better in the end.

I wanted to end by pointing out your obvious superiority and how indebted I am for all your help...

Thanks, thought I would just give it a stab and see where it went.

What?!

Pint of Science

Last week the pubs were even more crowded than usual. Not because of a special drinks offer, but instead to meet a group of scientists. Across 6 countries and in 21 cities, everyone was enjoying their “Pint of Science”. Guest blogger Amanda helped organise the event in York and is here to explain all.

To the pub

Almost a year ago I received an email looking for volunteers to help organise an international outreach festival, Pint of Science. The event combined two of my favourite things, hearing about exciting new research and going to the pub! It later became apparent this wasn’t going to be a small event. The festival was running 12 events within each city involved, over 3 evenings. Last year, Pint of Science was run in London, Oxford and Cambridge, stimulating and engaging the public about current research and why science is relevant to their everyday lives. Now, a team of York postgraduates were challenged with extending the festival up to the north of England.

What really excited me about the festival was removing science outreach events from lacklustre venues and into a relaxed environment that is well known for fuelling the generation of many great scientific ideas. For example, James Watson admitted that many crucial discussions between him and Crick were at pubs in Cambridge during their discovery of the DNA alpha helix.

In the 10 months leading up to the event we put together a programme of talks covering all areas of science. The talks included mind reading using MRI, plasma science as sustainable energy sources and fish and (computer) chips for understanding Parkinson’s disease.

My personal highlight was a talk at Brigantes bar, given by Professor Dave Smith, a previous lecturer of mine and famous for his YouTube videos. In “From G&T to TLC – how chemistry helps you feel better”, he demonstrated the healing properties of tonic water, and his own research on gene delivery using self-assembly techniques in an engaging an interactive talk. Other highlights across the pubs in York included a very large and loud plasma reactor and a Gangnam Style dancing robot!

A great success of the festival was the interaction between the audience and the speakers. The informal environment really encouraged discussions around the topics being presented, with a pint in hand.

The Journal of Let's Get Physical Chemistry

A new journal has been announced filling a much needed hole in the science publishing market. Are you a super cool prof that just can't wait to showcase your latest sexy undergrads or make up for your scientific inadequacies with macho bravado? If so then this is the place for you!

For more amazing sexy science and other communication failures then check out the Journal of Proteomics (now without that TOC image).

Elemental errors

Every writer should be prepared to take a step back sometimes, hold their hands up and say "I'm sorry, I was wrong". Some startling information has just come to my attention and I feel compelled to share it. If this misjudgement on my behalf leads to a loss of trust, I understand and I thank those of you who still support me.

Last year I wrote a post about one of my favourite films and how it was almost perfect. Avatar is that film and there was one aspect that saddened me and which I deemed to be a major flaw in the film. This flaw was enough to take away that 5th star from the rating, to knock it off the top of the all time great list. 

Not so ridiculous after all

Therefore now, with much pleasure, I can announce that Avatar has been rerated and is now deemed perfect. Hooray! Yes I know it has giant blue people and floating mountains, but let's move on. Avatar centres on the hunt for unobtainium. That wonderfully named element, that unprecocious and most mature name for an element was previously my focus of distaste. But I now embrace the simplicity and accuracy with which the name came about.

You see, there are already not one but two elements, real elements, that have names as ridiculous as our unobtainium and  I have shamefully only just uncovered this informationfound. These culprits are lanthanum and dysprosium. These two elements, however, escape the derision and ridicule that was focussed on unobtainium simply because they are not English words. Lanthanum comes from the Greek meaning "to be hidden" and dysprosium, also from the Greek, meaning "hard to get".

So why don't we have hiddenium and hardtogetium on the periodic table? Well, quite frankly it's probably because they are stupid names that everyone would laugh at. But why should we laugh? Those names simply describe a property of the elements. Why do scientists feel the need to use fancy obsolete languages to describe the world? Is the universe not grand enough by itself? What's wrong with plain old English? Maybe if the names were in a more common language then it might make the science a little more informative and a little more accessible to the non-Greek speaking community.

Revamp for the shining dawn

Therefore I have decided to revamp a few other elements that would benefit from a new name. Bromine is the first one, named from the Greek for stench (because it smells bad) and so I will henceforth refer to it simply as stinkium. Another that needs changing is technetium. The name sounds quite futuristic, rather technical and that would be because it is radioactive and is not often found naturally. The man-made version has been around for less than 100 years and the name comes from the Greek for artificial. So this element will now be called fake-ium. Finally, there is gold. Yes gold, that most precious of metals has the chemical symbol Au, which is short for aurum (from Latin this time) meaning "shining dawn". So the next time somebody flashes their new jewellery at you just tell them what a nice piece of shinyum they have.

p.s.
I couldn't end this post without mentioning that sometimes using obscure words and languages can be beneficial to avoid embarrassment. Copper nanotubes really could do with a new name. Although Cu does originally come from the Latin...

Opening lines

My PhD thesis was submitted back in September. Then two months later, after almost forgetting everything I had done in the previous four years, I faced my viva. I felt a combination of a little bit of panic, a little bit of calm, a little bit of self-doubt and a little bit of over confidence. This mix left me feeling happy with what I had produced and only hoped that my examiners would be happy too.

In the end, it turned out to be a surprisingly enjoyable encounter, with compliments from the examiners on my titles and images at the start of each chapter. All those hours spent playing on ChemDraw and Pymol were not wasted after all. I like to go for grand sweeping statements and so my introduction was entitled,
"From the wilds of Nature to the confines of the lab".

The opening few paragraphs of my thesis introduction are shown below. It is pretty general to begin with as I wanted to write it so that anybody would be able to come along and pick up this volume and have a chance at understanding something before their brain started to hurt...

   "Taking a minute to think about the great variety of life on this planet can only leave you with a feeling of awe. The multitude of complex and beautiful forms that have covered our world seem to be innumerable in their differences. On the nanoscale these differences can become even more apparent. Even within a single species many different tissues are present and each may comprise many different types of cell.

   There is structure to everything. On every scale a new level of appreciation can be found, from the straight, solid trunks of huge redwood trees, to the flexible muscle tissue allowing our movement and to the delicate, helical DNA that encodes all existence. The huge variety of natural structures is easy to see around us and on the nanoscale bioarchitecture can be just as impressive.

   It took billions of years for the natural universe to be shaped around us, yet it is only in the last hundred years or so that humans have truly began to understand the fundamental principles that hold this world together. We are starting to better understand the complex mechanisms that govern how all these systems interact and scientists can now use this information to change and add to what nature has already created.

   A central goal of synthetic biology is to learn from nature and take inspiration. This knowledge can then be used to create bioinspired and novel artificial architectures and systems that meet our needs, demands and are limited only by our own imagination."

When checking over this, my supervisor wrote in the margin, "Camera pans out to reveal Tom standing on top of mountain. Roll credits..." Did anybody else try to go for something general or grand or just stick to the technical stuff for their thesis? I didn't hide anything funny in the text, like Labsolutely, but I managed to reference a YouTube video that I'm in and my very first reference was a tweet.

The PhD that was

After having submitted my thesis last week, I thought it time to retire the PhD page from my blog. So here it is for posterity...

I had the pleasure of working with Dr Bruce Turnbull at Leeds. My project was to develop general strategies towards controlling protein self-assembly into designed nanostructures.

Taking advantage of weak protein-carbohydrate interactions we aim to construct three-dimensional nanoscale virus-like particles and other nanoarchitecture (my new favourite word). Ligands of various lengths, and with different carbohydrate moieties of varying affinity, have been covalently attached to the cholera toxin B‑pentamer (CTB). The carbohydrate units bind into the natural binding pocket of another CTB pentamer, bringing the proteins together to form different aggregates and particles. Analysis of the structures can be performed with AUC, MS, AFM, SEC, ITC, DLS and any other acronym you can think of.

So what does it all mean?

Well, to simplify things just imagine a brick. Now stick some velcro to that brick. Then get a load of these in a bag, shake them about a bit and hopefully out should pop a discrete spherical object. If this sounds unlikely and a bit crazy then you've grasped the idea perfectly.

If we can build organised, controlled structures on the nanoscale then this opens up possibilities for nanomachines, templated reactions and drug delivery vehicles.

PhD life

Doing a PhD is stressful, hard work and immensely fun. The work differs day to day with massive highs when your reactions unexpectedly work and terrible lows when your proteins commit suicide. There is a lot of self-motivation and commitment needed to complete a successful PhD, and it also helps having a great team around you and a kind word of encouragement every now and then (cheers Bruce). All for the advancement of the human race, and maybe also for the title of Dr before your name.

 

Geek week communication

It is geek week on Youtube and so I thought as science falls firmly into this category I'd highlight a few short videos I'd class as great science communication. They are all quite different and show the variety of things possible in front of a camera. I wrote a post not long ago about how words are important for communication, but of course that is not the only medium available for telling your story. Videos can be a great source of information and far more appealing in some cases. 

The complex life of sugars

This film was made for the Royal Society Summer Science exhibition that took place in London earlier in July. It's a nice whizz through all the areas of normal life where carbohydrates are found. The graphics are amazing, it keeps things very simple from tree bark to microarrays. Importantly also, the chemical structures are accurately shown which is unfortunately not always the case in popular science.

Conference call

The second film is a discussion of what is synthetic biology and where is it going. The film was produced at a conference of the Synthetic Components Network and nicely combines interviews, discussions and fancy images of proteins. Make sure you pay attention at 1.30 for a cameo appearance from yours truly. As a finger is pointed towards my poster, Beth Bromley says, "...they have no idea of what's impossible". Thanks Beth.

An extreme sport

The third video here might have been just a bit of fun, but it is really fantastic and a great example of how anyone with a camera can make an exciting and engaging short film (about chemistry!). I bet you've never seen a camera on a rotavap before...

For more great science videos have a look at Kyle Hill's round up for Scientific American and of course for all the ladies out there I couldn't write this post without mentioning the amazing awful "science: it's a girl thing".

Conference tweeting

At the recent International Symposium on Macrocyclic and Supramolecular Chemistry conference (ISMSC8) there was a distinct lack of interactions through social media.

Whilst coffee breaks and poster sessions were full of interesting chats and discussions, the internet was almost completely ignored by the attendees. The ISMSC website encouraged the use of the hashtag #ISMSC before the conference began. But in the book of abstracts and throughout the conference there was no mention at all of Twitter, I was disappointed.

There were a couple tweets in the build up before the conference, giving hope of a social (media) bunch of people.

On my way to #ismsc ! I will present the last development of the peptide synthesising molecular machine. See you there.
— Guillaume De Bo (@GuillaumeDebo) July 6, 2013

But during the conference I found myself a little lonely with only Ivan Aprahamian and Guillaume De Bo really contributing. Ivan summed up the twitter experience calling the crowd "technologically challenged".

300+ plus chemists at #ismsc and only ~10 tweets
— Ivan Aprahamian (@aprahamian) July 10, 2013

With sponsorship from Nature Chemistry and the National Science Foundation, both pretty big in Twitterland, you might have expected some input from them. But alas no, it was left to Chem Comm to join us at the end to publicise the poster prize they were sponsoring.

Big congratulations to Brandon Hirsch (Indiana) winner of @ChemCommun grand poster prize - he won a future front cover of ChemComm! #ISMSC
— ChemComm (@ChemCommun) July 11, 2013

Another chemistry conference, ISACS11 is taking place this week with around 50 tweets just from yesterday, although mostly dominated by one Chemistry World journalist. Whilst this is not a huge amount it is still much better than at ISMSC8. Derek Lowe is also present and so he's busy blogging through some of the talks.

But what is going on here? Is it just a generation difference and the young folks need to step up or are some conferences missing a trick? Get the discussions going over some coffee sure, but continue it and spread it further on the internet.

My first conference talk

The chemistry postgraduate conference was at Leeds last week and I gave my first ever proper conference talk. Being in the last couple months of my PhD and therefore extra busy, extra stressed and with no time for distractions like these silly presentations, I left things to the last minute.

So it was only an internal meeting and the audience mostly made up of other postgrads from the organic section, but speaking to a full room is never an easy task.

The build up

A hash together of group meeting slides and figures from previous reports gave me something to practice in front of the lab group, with 3 days to go. I tend to think I am quite good at winging it and this is generally my theory for life, but in this case it wasn't great. I realised this was kind of a big deal and therefore I should put a bit of effort in. Therefore next couple days were spent creating ChemDraw schemes, making cartoon figures and in 3 hour meetings with my supervisor.

Athene Donald wrote a great blog post about the pitfalls of conference presentations, with the key point being practice, practice, practice! I can only agree with her. I also got a handy tip from my supervisor to make sure it started well. he suggested that I learnt a script for the first couple slides of introduction so that I knew exactly what to say at the beginning and wouldn't stumble through incomprehensible mumbles.

Amazingly, it all went rather well. I knew what I wanted to say and said it. I spoke confidently and even managed to get a couple small laughs in, thankfully no tumbleweed moments. I handled some probing questions, avoiding anything too deep on the synthesis or too general on the reasons (applications are overrated). Shown above is one of my slides giving the (one day) infamous cartoon depiction of the cholera toxin protein, everyone knows that it's red right? In our lab, every protein has its own colour.

And relax

My talk was the last one of the day, a potentially awful slot if everyone is fed up by then and itching to get to the wine reception. But it was nice afterwards to not have to sit through any more pretending to listen whilst going over my notes. I had some great feedback from friends and academics and then got in to the bitching about some of the other talks.

Blue background and then blue data points on a graph, bad idea. Switching to a second presentation because you left out or forgot to talk about something, bad idea. Talking in a voice so deep you make the floor vibrate, bad idea (maybe I'm just jealous about not having a deep manly voice for this point).

I now know what to expect next time around and what to do better. I'll always remember this as a first effort and maybe with some feeling of nostalgia. The conference was followed by a ball in the evening that was also a memorable event, or not so for those of us overindulging in the free wine.

What am I on about?

Seriously, what on earth am I going on about?

When trying to get your point across, have a debate or tell a story it is very important to say the right words. Communication is all about language and used well can be an incredibly powerful tool.

First some common words

I wanted to have a look at the language I've been using on this blog and see if I'm saying the right things or in fact (more likely) saying some very strange things. I thought that a quick trip over to Wordle, a nice website for making fancy word displays, could tell me what I wanted to know. The 75 most frequently used words from my last 10 blog posts are displayed below.

The most obvious and bizarre thing is that I apparently say first an awful lot! I say first more than any other word. Why? I don't see second in the wordle. Maybe I don't think second is important. Maybe I get so distracted with the first thing that I ramble on and then start talking about other questions like oh look questions is pretty big on the picture too.

Science is up there, journal, work, cover (I do talk about covers a lot) but there are other surprising big ones such as one. When do I say one? Am I talking about unique occurrences or again get bored after the first? I'd like to see more superlatives being used. Great is there, but I have much better words than that in my vocabulary. I think science is wonderful and we should use equally wonderful words to describe the amazing world we live in.

There's no point doing ground breaking work and not telling anyone about it and that's where words come in. Language can not only be useful but also fun. Playing around with your split infinitives can allow you to boldly go where no scientist has gone before.

Chemical poetry

This week on Twitter has been all about Real Time Chem, if you've somehow missed it then you are spending too much time in the lab.

 

Real Time Chem is a great community project on Twitter using the hashtag #RealTimeChem. Chemists all over the world have been sharing their daily experiences, lab work, cool articles and finding solace in the fact that they are not the only one failing to purify that unknown black mess.

Amongst other things this week, I have been doing some isothermal titration calorimetry (ITC). A wonderful technique (when it works) of measuring the binding enthalpies and association constants for non-covalent interactions. It's one of my favourite pieces of kit to use; it can give great insight into the success (or failure) of synthesised ligands and makes some pretty graphs.

 
After setting the experiment going I had about 30 minutes to procrastinate before the run was finished. So the internet gets fired up and through a strange connection of aimless link clicking, on websites including "Facebook", "Chemistry World" and "Jet2 cheap flights" (possibly not in that order), I came across Nobel prize winner Roald Hoffmann. Whilst obviously being a great scientist, Professor Hoffmann is also the author of a large number of poems. Some of his work focuses on chemistry and I thought what a fantastic medium poetry is for expressing the wonder and excitement of uncovering nature. I'm sure it would work equally well for portraying the torment and anguish at failed reactions, but let's stick to the wonder for now.

Back at the ITC, a flash of inspiration hit me and I came up with a poem all about the technique...


Isothermal Titration Calorimetry

Separate they contemplate their lives alone
But this the only thought they share
Not knowing their worlds are about to collide
Never loneliness will they again bear

One passively waits for an injection of life
Floating in their own little cell
The other poised to mix at the first chance
That stirring sensation will tell

But it takes another to set their paths
One who knows what makes them attract
To turn up the temperature, wait for the calm
Push the right buttons, see them interact

An initial touch, not sure where it will lead
At first you can never quite know
But a second feel, a larger reach
The heat given off starts to show

As if they had always been as one
They're together and will never part
The creator watches his successful work
Plotting their lives as a chart

Their story lives on for others to see
An example for anyone that looks
To find a guest for that elusive host
Written down in the wisest of books

Get me out of here!

What a great couple of weeks it's been and finally I now have a chance to rest. My fingers are aching from typing so much and my brain hurts from puzzling over hundreds of queries. After participating in "I'm a scientist, get me out of here", was it all worthwhile?

The gloves are off

The first week started as a bit of fun, chatting to some kids and quite simply being amazed by the variation of questions that kept popping up on the screen. As the second week began however, things started to get a little more serious.

The fairly sedate pace of the first week saw 3 live chat sessions spread out over the 5 days. By comparison, at the end of the second Tuesday another 4 chat sessions were done. And the end of Tuesday meant it was time for the first eviction. It was Jon that fell at the first hurdle. He admitted that his demise was probably attributed to missing that day's chats due to work. The loss of a fellow scientist made the event suddenly all so real. Could I afford to miss a question so I had time to purify some protein? Could I afford to delay purifying some protein so I had time to answer more questions?

Wednesday saw the loss of Yalda. We had all been in the chats, we had all been quick to get a share of the all important (or not so) first response to questions posted online. So what had made the difference this time? No eye contact in her profile picture was the best suggestion I heard. Did the students want short, straight answers, did they want some humour? Was a question as a reply the best way to engage them, or would a detailed essay be preferred? My guess was a good mix of it all and that's what I went for, although not the easiest thing to pull off.

4 chats were scheduled for Thursday; it was going to be a busy day. The culmination was an exchange with an all girls school, that included arguments over animal testing and inquiries into how many children we all wanted. This may have been the deciding factor of why Claire was next to leave.

So, I was in the final! It was now just me and a fellow PhD student Jack. I was so relieved to have made it through to the end. But after coming so far, my only thoughts were now on the win. Jack obviously felt the same, with some (fairly light) fighting talk on Twitter.

The winner of the Drug Development zone is...

After 2 weeks of grilling the scientists, asking questions that they either never dared or never had the chance to in normal classes and actually getting to know the scientists with some (sometimes too) personal questions, the winners were undoubtedly the students. What a fantastic event it has been, with great credit of course going to the organisers and moderators who kept everything running smoothly. Hopefully I have played some small part in sparking the students' interest in science and maybe even hooking a few in for life.

The results of the all the zones were announced one by one in the "staffroom" on the website, with many of the nervous scientists then expressing their joy and congratulations to their peers. After finishing off the nails on all my fingers, the Drug Development zone was the last to be declared. Jack and I had made that final push for the student votes, there were no more questions to answer and no more opinions to sway. The votes were counted. It was a tie! Equal votes, both winners. A wonderful end to a brilliant event. We congratulated each other and now both have the chance to use the £500 prize for further outreach events. So again, the real winners are the students.

The scheme is running again in June and I would highly recommend it to anyone wanting to get experience explaining theories and concepts to a different audience or just wanting a break from talking to their boring old professor.

I'm a scientist...

After a week of struggling to answer mind-bending questions and not pass out in manic live chats, I've come to the conclusion that 13 year-olds are actually a fairly intelligent and extremely inquisitive bunch.

Like X factor for scientists

I was picked to be part of the national on-line event "I'm a scientist, get me out of here"! It's an excellent initiative run 3 times a year, where school kids can literally ask a scientist anything they want.

The event has been running for a few years and this March they have 11 zones each with 25 school classes, which means a lot of kids to contend with. The places for scientists were 6 times oversubscribed and this time they have added more zones in an attempt to accommodate more schools. It's popular, but why?

I've been involved in outreach programs before. I've helped out at Uni open days and demonstrated experiments for school kids coming in. A year ago I took part in (the now defunct) Researchers in Residence, where I went into a year 11 class for a number of weeks. During this time I talked to them about my work, arranged for a trip for them into university and naturally tried to encourage them all to become scientists. These schemes were great at showing children a human side to science and allowing them to see what a university and an actual "scientist" are really like. This is where I'm a scientist excels.

The kids get to post questions on the website and then bombard us with yet more in the live chats. Most so far are real science queries with most of them based on drugs (me being in the Drug Development zone). The real novelty of this project however, is that in the following week I may be kicked out. Every day the children will vote for their favourite scientist out of our group of 5; who answered their questions best, who sounded most intelligent or simply who told the best joke. At the end of each day one will leave and by Friday only one will remain victorious held aloft by their teenybopper fans.

Hello why do you like science

So the kids can connect with scientists and ask all the questions they never get to in their normal science lessons. But as I said, not all of the questions are sciencey. The others include gems such as, "waffles or pancakes?" and "how tall are you?". But these questions are equally important as they allow the scientists to become real, human people. We are not a bunch of deranged lab rats nor are we an elitist, higher intelligence (even if I'd like to think so sometimes). Connecting with the school children through these silly questions lets them see us for what we really are; just like them. With this in mind, hopefully they will realise that science is for them and in a few years they'll be the ones changing the world and inspiring the next generation.

As for me, I'm thoroughly enjoying the experience. I've answered all the questions I could and even answered some that I had no idea about before. My enthusiasm for science and engagement has rocketed and my lab work has suffered immensely. But with my supervisor away this next week I may get a little obsessed answering questions and reading ones from the different zones, that is unless I get evicted...

Posting a winning formula

Last week the Masters students in Leeds presented posters on their work as part of their degree course. For the few weeks beforehand (yes it took them a few weeks) they were mostly hidden away behind a computer changing fonts, images, headings and references until they had something resembling a five-year-old's first attempts at potato printing.

Winning is not so blue and white

After a little bit of tweaking, arguments over font size and drastically changing the colour scheme, the butterfly finally emerged from its chrysalis. But no, they were not actually all that bad, especially for a first attempt. Few people realise how difficult it is to make something scientifically accurate and also visually stimulating.

As an example, below are 2 posters that came out of my lab from PhD students. So which do you think won a prize when presented at a conference?

To put you out of your misery, the answer is both. Both designs won best poster awards at different meetings. But they are obviously quite different. Nature Journal believes a good poster could "change your career", so what is the secret formula for success?

Well in my opinion the poster on the left looks a lot better. It has more colour, lots of different images, not much writing and easy to follow sections for different parts of the presentation. But I would say all this, as I created it. By contrast, the poster on the right has a lot of small writing, it's very white and appears overly crowded. But they both were winners.

They both do have many images and diagrams, they both have a fair amount of data presented and they are both blue, not so different as it might first seem. A poster has to be eye-catching in some way or at least grab your attention for long enough so that you read a few lines and get hooked. From then on in it has to be ordered, easily understood, not overloaded with information and with a few pretty pictures thrown in for good measure.

The designer of the right poster is also one of the best talkers that I know. She can talk about anything and make it sound interesting (even her research). And this is a great skill that you can't show on a piece of paper. Being able to verbally communicate with your audience, to not confuse them or bore them, is vital. Knowing your audience and being able to change the language you use and the way you describe things can really make the difference. This might be between someone just saying hi to be polite as they quickly walk past, or being drawn in by a few well chosen words.

Teacher knows best

So back to the masters students. It took me a lot of effort to convince one student that brown and pink perhaps didn't make the most pleasing of background colours. The text was cut down by half; no one wants to stand there for an hour reading. We removed the empty white space by increasing image sizes and rearranging text boxes. And I even got my name squeezed into the acknowledgements. But I did fail to make him increase the font size, even after much pleading and threatening to sabotage his work. It was perfectly readable on the computer screen, but when printed and up on a large stand he admitted that you probably get a better view if you don't have to stand with your face 10 cm from the board.

Being bold and confident in your abilities is great. And in the end you have to be comfortable with what you've produced otherwise you won't be able to talk about it effectively. But one thing I've learned over the last few years, is that I don't always know best (many will be amazed to hear me say this). Take advantage of any help you can get. Use other people's knowledge. Seek a different opinion. Do this and you will better yourself. I never thought poster design could be so philosophical.

Cover Art

Science is art

At first glance, academic journals may seem to be all seriousness and impersonal facts. But at the very front of every edition lies an artistic outpouring. The cover is the place for scientists to highlight their work and at the same time show off their skills with Photoshop.

Here, researchers have a chance to show off the essence and ingenuity of their fantastic work, or so they hope. Creativity, imagination and communication are core principles of art and design. These same attributes are also vital in science.

Many journal covers have caught my eye over first few years of my fledgling academic career and so here I shall promote some of the best (and worst) examples. The scientists deserve some recognition for what they have produced after hours slaving away, perfecting their art.

The importance of cover art

There is a certain prestige to having your work plastered on the front a shiny little book. However, with the movement to electronic editions with fewer people ever seeing a paper copy and therefore not starting from the cover, have they lost significance? In the last 3 years I can count on one hand how many paper journals I’ve flicked through. It is far more normal now to jump straight to a pdf of the specific article you are searching for. Altmetric investigated this further with discussion in a recent blog post.

At The University of Leeds we have a common room that has cover art from the latest publications by Leeds academics posted around the walls. And whether these images have helped gain funding, entice the smartest undergrad or simply aroused the interest of a lost history student, there is a certain something to them that is worth talking about.

Bringing scientific information to life

The cover of Science this month exemplifies the importance of this art. It showed the winning illustration in the 2012 “Science NSF International Science & Engineering Visualization Challenge”. A stunning image of a “wiring-diagram”, which represented long-distance neural connections in the brain of a macaque. The outcome was that the visualisation could provide guidance for forming a brain-like network from multiple computer chips.

Science magazine is found at: Science2013, 339, 6119, 481-616

The goal of the competition is nicely stated as,

"to encourage new ways to visualize data ... for conveying scientific principles and ideas across disciplines and to the general public, and for revealing the hidden beauty of structures on scales from nanometres to the cosmos."

Fun, informative and about monkeys (sort of), what more could you want?