Recent activities...

Oh dear Chemically Cultured what has become of you. I seem to have neglected this poor blog for too long. But never fear, I've not been completely out of the loop.

I continue to write for the Chemistry World blog covering (pun intended) journal covers and their scientific impact. Recently, I wrote about  how to win a Nobel Prize with good cover art and I found out the secret to successful artwork from all the artists of last year's Chemical Science covers.

I also wrote a book review that was published in the March edition of Nature Chemistry. The review was for "Navigating the Path to Industry", a short book describing all (literally all) the steps to take when moving from academia into the chemical industry. In short, it's a great little step by step guide if you don't have contacts to mine for information or if you're a little lost on where to begin on your new career path. But of course go and read my review for more info.

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

55 applications later...

After countless alterations to my CV and a shameless outpouring of enthusiasm into numerous cover letters, I am finally about to start the next step of my career.

In my search for the perfect career move I sent out 55 applications in total. Many of these were actually for industry positions that I thought, "well I can do that, it would be ok and is kind of my skill set", and so I was not too surprised when I didn't get the job. But I was always optimistic and therefore always disappointed. I really wanted that perfect research position of five years to really develop a new idea that I was totally specialised for. But yeah, that doesn't actually happen.

In the meantime I began volunteering at a University. They were more than happy to have me work for free, which was very kind of them. In this time I did manage to get a couple small grants to help with the work and also to send me to talk at a conference. I did gain some great experience and some very helpful contacts. However, I learnt during this time that not having a stable, secure job is not something I would particularly recommend.

Out of all my 55 applications, I was invited six times for interviews. Three of which, much like the proverbial buses, came along at the same time. In the end I was in the most fortunate position of having a choice of where to go next and actually went to my final interview with an offer already in my pocket. I had been offered a position in industry (still in R&D), which was with a very exciting company and perfect for my expertise. My final interview was at a University and for a one year postdoc position. The research ideas were fantastic, the facilities amazing but the prospects and possibilities for the future were just that, prospects and possibilities.

After moving country a year ago and previously moving nine times in my eight years at University, I was ready to stay put for a change. I would love to continue research in a University atmosphere but not in the way that the traditional career path dictates or how the funding situation obliges people to continually move on after short projects. Therefore I said thank you very much, but no thank you to the academic path and willingly moved into industry.

I had already thought for a while that the long term academic plan was not what I wanted. I love research, I love exploring new ideas, discovering new things. But there are other options than the academic track. I like writing (obviously) and so publishing, editing and science communication is still something for future Tom to consider. But right now I still want to be part the doing science community not just the reporting about it part. So industry it is.

My final thoughts on the matter are on the similar difficulties facing other freshly graduated PhDs. In Holland, where I'm based, the funding situation in universities is not in good shape and industries are not doing much better either. I do feel that if I was able (and willing) to travel anywhere in the world, then I would have been much more likely to land something close to my dream job much more quickly. But the restrictions that come with staying put make things more difficult.

If you (like me) are intent on not moving then you better keep writing those applications and in the meantime improvise with what you do have, volunteer and ask for help. This last point being the most important. I wouldn't have got this far without a lot of support from friends and old colleagues.

Are there too many PhDs?

A recent competition from NatureJobs invited budding science writers to answer the above question. My (unsucessful and somewhat ranty) entry follows...

...

No, there are not too many PhDs. It’s that simple.

Can you imagine if everybody in the world studied for a PhD? The progress that would be made. The innovations in science and technology. The health benefits and developments in society would be beyond imagination. Everyone should be encouraged to do a PhD. The more PhDs there are, the better I would say.

In the current economic climate, the throng of PhDs fresh out of university are a beacon of hope for the future. More PhDs means, of course, more research. More research means greater advances and a push to really make a difference in the world. This can only be a good thing for society and for the individuals themselves. So let’s make everyone do a PhD.

But is this really practical? Sure, the advancement of knowledge and all that, it sounds fantastic. But can it be done, and then more importantly, how could it be done?

The reality of a PhD

If spending four years of your life obsessing over a tiny area of science until you are the world’s expert sounds fun to you, then go for it. But realistically, studying for a PhD is not everybody’s cup of tea. I’m sure there are many out there who would recoil at the thought. Some people are not cut out for the research life and many more simply have no wish to go down that road, so should I be so quick to encourage a worldwide research blitz? Probably not.

The number of PhD students has taken a sharp rise over the last 10-20 years. But what has the rise in numbers done for the current set that are studying? Having a PhD on your CV used to mean a more financially prosperous and successful career. It was the benchmark for a committed scientist and a firm footing for your future. However, this situation can only continue if, along with the rise in PhD numbers, there is an equal rise in the number of opportunities presented to these fresh PhDs. This is where the problem lies.

Keep the experts in science

The problem for a recently qualified PhD is where to go next. What options in science do these PhDs have after completing their research? The answer to that question is not very many. There is currently not the same level of investment in post-PhD options as there is in getting these students into the research faculties in the first place. This discrepancy leads to larger numbers of talented scientists leaving the area quickly after their hard fought efforts to perfect their research skills. Not everyone who completes a PhD wants to be a Nobel Prize winner but for those that do, the next steps are tricky. There are currently not enough jobs in science, not enough funding for further research and not enough support from governments.

The government has been promoting university more and more in recent years. If they want to encourage higher education and more people to study a PhD, or even keep the current set happy, there needs to be more of an investment in science. Everyone should be encouraged to learn and reach the best of their abilities. But more needs to be done to keep these young experts in science by putting a greater focus on funding further research. More needs to be done so that society can truly benefit from all these curious minds. Therefore, the answer to the question is simple. No, there are not too many PhDs, but we do need to do more to hold on to them.

To Chemistry World... and beyond!

I've started a new gig guest blogging for Chemistry World. Over there I'll be doing that thing where I praise (or poke fun at) academic journal cover art. So head on over there now and check out my first post about a crazy colour explosion in Chem Soc Rev.

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?!

Nature Chemistry Blogroll: Real Chemistry

I penned the latest edition of the Blogroll column in Nature Chemisty . Have a read and discover some other great blogs about "real chemistry".

What does it take to be a real scientist?

We read about the end results and look at the pretty graphs. But what was it actually like in the lab? The journey behind the data is often lost and the formal tone of a journal article cannot come close to conveying the love, suffering and fun that went into producing those results. However, bloggers and Twitter users are gradually breaking down that barrier and revealing a behind-the-scenes view of real chemistry.

A very open and engaging story of the work behind a Nature Materials article (£) was blogged by Sylvain Deville. ‘The Making of a Paper‘ takes us from the initial grant proposal, to the excitement of preliminary results and the pain of getting scooped. The Baran Lab also shares the stories behind their publications. Honestly stating “we had no idea we’d turn to electrochemistry” shows the success of an unexpected direction.

Elsewhere, the @RealScientists rotation-curation Twitter account continues to regale us with the daily activities of different scientists. Someone new is brought in each week to run the feed and showcase their own small slice of science. Previous curators include analytical and physical chemists and, at the time of writing, an evolutionary biologist has been delighting us all with the wonders of sex chromosomes.

It’s impossible to mention real science without talking about the Twitter phenomenon that is #RealTimeChem. This banner brings together chemists from all over the world and its creator, Dr Jay, is organizing the second annual RealTimeChem week. Your fellow chemists will be sharing more of their experiences and lab frivolity through blogs and tweets, and everyone can join in.