Coming live from the lab

It's been a while since I've done this, I've been remiss, I apologise. Blogging takes a certain level of commitment, and I've slipped! But soon I will be presenting an opportunity for new bloggers to join me, so stay tuned.

In the meantime, today's lab meeting was interesting both because of the chocolate cupcakes and because it was the first time I'd been to the lab's "Journal Club" where one of the lab members picks an interesting journal paper they've found and discusses it. This time it was not one but two papers, both published in the same journal within a few months of each other and both seeming to deal with exactly the same question: Does a wound cause hair follicle stem cells to contribute to tumour formation? What is fascinating is both why the journal chose to publish two seemingly quite similar papers so close together, and also the fact that one has a much "sexier" title than the other although both actually mean the same thing!

I'm learning a lot here about publishing in journals - but to be honest I couldn't really even understand the introductory paragraph of either paper. The interesting detail I gleaned was that the possible relationship between injury and cancer was first thrown up in 1863... which just gives an indication of the evolution of scientific ideas, that nothing happens in a week or even a decade, sometimes a question is put out there and over 150 years later it is still be investigated.

The discussion of these papers also touched on something that is particularly interesting to me: what aspect of this research reached the "public"? The researcher in the lab mentioned how he had told his girlfriend about the papers and she had immediately panicked and said "Does that mean when I get a cut I could get cancer?" This might sound like an overreaction, but then I googled to see what the press has made of these publication and I found headlines such as:

How a paper cut could trigger skin tumors

which is not in the least alarmist, eh?!

But, I have to say, it's not such a stretch from the titles of these papers to the headline of this article. However, I'm sure the scientists involved would never want a wave of public panic about paper cuts! So, an interesting point to ponder about science communication. Where's the disconnect? Whose responsibility is it? Any comments?

 

Thought lab life was dull and boring? Think again!

One of the scientists at the lab I am writer-in-residence in sent this around yesterday and I think it's wonderful! It's for all of you non-scientists who think science is about hard fact, about right and wrong, about automatons in lab coats who reveal the truth of existence on a daily basis. Umm, no, not quite...

Tania's Tales from the Lab: Drink Me

I was commissioned to write a piece of "nanofiction" for the abstracts programme for the Nanoscience and Quantum Information Centre's recent nanoscience symposium - something a little odd that might stop people in their tracks as they realised it wasn't quite what they were expecting! This is the result:

Drink Me

He did and then he felt himself, felt himself, felt himself, down and down and down and there he was, on that pinhead, there he was. Looking around he found it all adjusted to his newly shrunken state and all was forests that had been only molecules and atoms. He in himself felt sameness and he walked amongst the tiny now turned giant and he saw the things he'd never seen, he'd only dreamed of when he was the one who probed, the one who studied. Look! he shouted but his shouts were not even squeaks of fruit flies, no-one there to hear, expect perhaps an ant but not here, not in this clean clean quiet room. 

After a while of wandering he saw himself to be some nanometres high at most and he delighted in this. Some others might have wept or sunk into some kind of blueness but he, being ever curious and scientific in his ways, knew that his journey here would teach him everything and so he did not look to grow again.

Why it's useful to have a writer-in-residence

So, having a writer-in-residence in your lab is clearly good for boasting about to other labs, something a little odd, a little quirky. And maybe your writer is useful because she asks silly questions that get you pondering something in a new way. But this writer-in-residence was useful this week on a practical level! I'd helped out in the lab last week when large amounts of counting of neutrophils (immune cells) was required. I was taking down the numbers as the researcher (who'd rather remain nameless so we will say his/her name is X) did the counting under the microscope. Then X inputted all the data into the software which produced very attractive graphs. So far so good.

That was last week. I said, Can I take the post-it notes on which I wrote down the numbers home as souvenirs? Sure, said X. Then today I arrive for my weekly visit and X is not quite so happy. Do you have those post-it notes? X says, rather frantically. Of course, I say. Writer-in-residence saves the day! says X, who somehow has managed to delete the files from last week, they've been swallowed up somewhere inside X's Mac...

Writer-in-residence saves the day! Get yourself one now, while stocks last.

Tania's Tales from the Lab: Lab Meditation

(I wrote this sitting in the lab recently.)

Lab Meditation

Look at a bottle.
Stare at some pipettes.
A tap.
The smooth cool bench.
No other signs of life.

Listen to the radio.
Breathe in.
Breathe out.
Watch a rocker.
Rock in time.

Examine a glove.
Sink into its purple.
Gaze at a clear liquid.
Listen to the hum of
the mammoth freezer.

Sit in the dark microscope cave.
Look at lit-up hair cells.
Listen to the turning of the
microscope magnification knob.
Touch the grey benchtop with
the back of your hand.

Squint as the sun floods in.

We Got Liminal....

I just wanted to write a quick blog about last week's Let's Get Liminal: Artistic Science and Scientific Art seminar (see previous blog post for details) which I found absolutely fascinating and I hope all those who came did too. The idea was to briefly showcase some of what's going on in Bristol University in that (liminal) "space between" arts and sciences - from the collaboration between a glaciologist and an artist, "artistic" images from research, and medical students' creative work about the practice of medicine.

Our visiting guest artists, Kira O'Reilly and Oron Catts, are in, it seems to me, another space entirely, a new and very exciting place where bioart is being done - artists learning about the tools used in biology labs and then using these methods and processes to produce art. 

The questions that Oron and Kira ask and then attempt to answer through their artworks are the basic questions of life that scientists  also ask. Kira, for example, says: What happens if I look at my own skin as just another type of material, just more stuff? (I am paraphrasing, forgive me). And she engages audiences with her installations, inviting them to also grapple with these issues. Oron - who gave us a detailed history of tissue culture, when it was first done and by whom - showed examples of how he and his collaborators have set up fully-functional labs in museum spaces to "grow" exhibits such as a leather jacket made from "victimless leather". 

It was a wide-ranging afternoon, and I found it both inspiring and moving, seeing these two monliths, ART and SCIENCE, so often kept apart by high walls and arbitrary definitions, actually merging harmoniously to produce something extraordinary which delights, informs and provokes. The first of many such meetings, I hope...!

Here are a few pictures of the proceedings (I didn't take pictures of every speaker - sometimes I was too engrossed and I forgot!):

Maggie Leggett, director of the University's Centre for Public Engagement, talks about plans for next year's Changing Perspectives exhibition in various Bristol galleries.

 Professor Jon Keating and Chrystal Chernwichan showed clips from the Mathematical Ethnographies films and the Science Faculty portraits, and talked about how people have reacted to using these media to put across something different about science - and about the concept of beauty and how it means something different, perhaps, to mathematicians and to artists!

Emily, a medical student, talks about a painting she did for the Creative Arts course she chose to take as part of her medical degree. I found it very moving, listening to her describe her painting of a woman with a spinal condition.

Dr Louise Younie (above) and Catherine Lamont-Robinson, artist and curator, talk about the Out of Our Heads project, showcasing creative work done by medical students. Louise talked about why she intiated the course and the hopes she has that integrating artistic practice into medical study will encourage greater empathy for patients amongst the medical students, who paint pictures, write poems, even create dance pieces inspired by their clinical practice.

Becky Jones showed us "beautiful" ( a word that had become a little controversial by this point in the seminar!) images from the labs which were entered for the 2009 Art of Science competition such as the one above, a confocal image showing communication between brain cells by Sam Lane. The 2010 competition opens shortly...

Dr Giles Brown and Emma Stibbon talked about their glacier-focused collaboration which resulted in artworks such as Emma's stunning picture, above, of the Aletsch Glacier. It was really interesting to hear how Emma went about researching her artworks, and that by drawing she is in many ways connected with the historical depictions of natural phenomena, harking back to the time before cameras, digital or otherwise. Giles pointed out that people approach and interact with Emma's 7ft drawing of a glacier hanging in his office in an entirely different way to the way they would approach a photograph of the same glacier.

Kira O'Reilly, giving us an overview of many of her astonishing and wonderfully provocative artworks and installations, and told us about her time in biology labs - how she tried to do inject something different into the atmosphere, wearing a striking crimson lab coat, for example!

Oron Catts introducing SymbioticA, A Centre of Excellent in Biological Arts, which runs workshops worldwide for artists, and invites artists to do residencies in the School of Anatomy and Human Biology at The University of Western Australia ... and even grants degrees in biological arts, making it unique. He was asked afterwards whether he wouldn't describe himself as a scientist, given the lab-based work he does, but he answered that he far preferred to be described as an artist. Another interesting issue to think about...

I don't think anyone would have failed to be stirred in some way by all these presentations. It caused me to look at my time in the labs in a different way, perhaps more visual... and so here's a little "art" of my own. I took this yesterday: What is it?! Leave a comment and the best answer wins... well, much glory!

 

Tania's Tales from the Lab: Part 3

I'm in the lab again today, I won't do a minute-by-minute live blog but I thought I'd write down some of my thoughts. After two months or so embedding in this lab, I feel now I have some kind of understanding of how difficult it is to ever assert that you know anything. Looking into science from the outside it seems that scientists run experiments to see if Z happens when Y is put with X, get results and hey presto, we have a new FACT. We think scientists have cutting-edge equipment on their lab benches, ultra-fast computers, powerful electron microscopes, so that they can see exactly what's what.
I mean, this is how it is on CSI, right?

Well, no.

The first thing I now have more of a grasp of is that you need to check, if not every step then every few steps and they might be many many steps in your experiment! - that you even have the right stuff in your test tubes! As one of the postdocs said to me last week, "It all looks like cloudy liquid" so how do you know what's in the cloudy liquid?

If you are interested in molecular biology, well, you run a gel... This, says Wikipedia, is:

a technique used for the separation of deoxyribonucleic acid (DNA), ribonucleic acid (RNA), or protein molecules using an electric field applied to a gel matrix

and this is the equipment:

Guess when this method was invented. Well, the first reports were some time in the 1930s. At least 80 years ago. And this is still, from what I understand, one of the best and most useful methods to figure out what's in your cloudy liquid. You have a wedge of gel in this bath contraption, you have a set of little wells into which you put your different samples - tiny drops of your cloudy liquid as well as control samples just to compare - and then you run an electric current which pushes the molecules of your liquid through the gel from top to bottom. Basically, the bigger molecules get stuck moving through the gel and the smaller molecules can move through a bit faster so get further. Like a race between very fat tortoises that get stuck getting down the corridor and skinnier tortoises - and all sizes in between!

After about 25 minutes or so, your gel is "done", your tortoises have moved as far as they're going to move. You take the gel out, stick it in another machine that shines UV light through the gel and you can take a photograph which looks something like this:

Clear now? Yup... I don't really know what it means either. The bands of light are molecules and some haven't moved far from the top, and some, like the guy in the bottom left corner, got pretty far...To the trained eye, this tells you everything.

Jut for fun - and a little education! - here is a 1930s concept brought into the 21st century with this cool animation about how to run a gel that I found on YouTube (with rock soundtrack):

When your gel tells you that there's stuff in your cloudy liquid that you didn't expect to be there, or something doesn't show up that's "supposed" to be there, then what do you do? Run the gel again - which involves preparing more samples etc.., can take a day or more. And if it happens again? Check all your equipment in case something snuck in. Check and re-check. And if still not...then you might need a complete rethink.

So, to sum up, to actually "see" in science isn't as simple as looking at a sample or sticking it in your fancy million-pound desktop machine. It often means using a technique developed in the 1930s and which can take days to prepare for. Anyone want to share gel stories? And talking of stories... more about the idea of "story" in science next time. Back to the lab!

Calling all potential bloggers!

I'm in the lab again today, but won't be blogging live, that was a little stressful! I might do it once a month or so. But here's the thing: this blog is not supposed to be just me me me. Ideally, there'd be a number of Bristol Uni science folk blogging here, so if you'd like to join in, do drop me an email at tania(dot)hershman(at)bris.ac.uk (replacing the (dot) and (at) with . and @). You don't need to know anything about blogs or blogging, I'm happy to help you get started. It's great fun - I very often find out what I'm thinking about something as I'm writing a blog post on my personal blog, TaniaWrites, so it can be useful! Try it, you might just like it...

Tania's Tales from the Lab Part 2: Live!

So today I'm the one who is experimenting - this blog post is coming to you live from the lab! Want to know what scientists actually do during the day? Or, if you are a scientist, is this lab more fun than yours? Only kidding...Please leave comments!

My laptop was stolen two days ago so I am blogging from my mobile phone, forgive any odd spelling.

12pm weekly lab meeting.

One person presents their work, everyone else eats lunch. Here goes...Ok, it's acronym city, and I've only heard of one of them so am a bit (very) lost. Like the idea of knockdowns. Sounds like cells meeting at High Noon!

12.25
Oooh, pretty pictures! Cells, I think. Hmm. Ah, once again, the word "story" is used in talking about the direction of research, what questions are going to be asked. Like this idea. And I like the word "vesicle".

12.40
Funding. It always comes down to money, doesn't it?

1.05
Meeting over, back in the lab office, and the post has arrived. What is it? Fish! M opens the square polystyrene box and there are two squarish clear containers, with blue liquid and dozens of baby zebrafish. They look happy, says M. How can you tell? And do you ever think that there are fish wandering around Royal Mail?

2.05
Having a fascinating discussion with E who is writing up her PhD thesis, and M, who did his PhD in Canada, where it took 6 years instead of the 3 here in the UK. Is a 6-year PhD an entirely different degree?

2.15

E is in a flat with three other women, all of whom are writing their PhD theses now and having such different experiences: one has a special desk assigned to her in the department so she can concentrate, one has a supervisor who won't get back to her with comments on her first chapter. E has a great supervisor but no good place to write: the lab office isn't quiet, her downstairs neighbours at home just had a baby and upstairs they are doing renovations!

Very interesting talk about supervisors - so much depends on who you get, you might even say that this relationship is vital for the course of science. If you get on well, if they are helpful, maybe a PhD student will continue on in science, or in this field, but if the relationship is fraught, difficult, your journey might take an entirely new direction.

2.55
E shows me her introduction, which is the size of my short story collection. This is just chapter 1! Am quite happy that I can sort of follow what it is talking about. We discuss how, plot-wise, the thesis doesn't really get into the action til Chapter 3, but of course that isn't the main consideration.


3.20
Am actually in the lab now as opposed to the lab office next door. When I first started embedding, Radio 2 was always on. Seemed like an odd choice. How did it affect experiments, I wondered. A few weeks later, I dared to change to Jack FM, which plays mostly 80s and 90s music and no talking! Will this affect anything? Then last week - no radio! No-one seemed to know who turned it off.... And today, Jack FM back on. Who is operating the lab radio?! (just heard Valerie by Steve Winwood. Nice.)

4.01

M has just shown me a new site he and Y recently discovered: The Journal of Visualized Experiments. It's totally amazing! It's like cookery shows for scientists:

How to dissect a fruit fly:
First, take specific-sized tweezers, then pull here...
shake twice for 3 minutes each...

And there's the postdoc, in his lab coat, being made to be the presenter, looking like he might burst out laughing as he talks to the camera. Is this the 40th time he's had to say this? Will future PhD students have to take a screen test? Next stop: Science TV? Love it! They have a Facebook group too.

4.24
B is having a bad day. She did something with gels and the result was completely baffling. Nothing appeared when something definitely should have shown up on the gel. A few week ago B had the opposite problem - too many things showed up on the gel in places they shouldn't. So M is helping out by testing the primer she used (do I sound like I know what all this means? Good!). M is just loading the gel - what will happen? Excitement is mounting! Jack FM is playing All I Need is A Miracle! Stay tuned....

bottle being filled with extra-pure water

4.34

Still waiting... M starting the electrophoresis. Will take 25 mins. Breath is bated.

4.45
Pipettes don't look like they did when I was at school. Bit scary, eh?

5.01
We head back into the lab. B watches as M gets the gel out and puts it in the machine which will show if there's something on it... And yes, there's something there!

But... wait.

It's not the right thing. Something's up. There's a stripe where there shouldn't be, and a blank space where there should be a stripe. It's inconclusive. M will have to do it all again. And this one test takes several days to prepare for.

Now this is science and it's not what you normally hear about - tests that when they work properly are "beautiful", says B, but can go wrong for so many different reasons. Some could be to do with the supplier who supplied the primer, say. Or a contaminated tube? There are so many steps involved in getting to the point where you even do the test, that doing it all again is a fairly exhausting and disheartening prospect. But there's no choice. B needs to see if a certain gene was present. She needs to know. So: one more time. Tomorrow is another day.

5.15 and I'm heading home. This has been great, but I think next time I will just scribble in my Moleskine, as I have been doing, and enjoy the tranquility involved in not being able to rush anything, having to wait. And then I will capture my reflections on the blog later. 

Tania's Tales from the Lab Part 1

I'm one of those people who gets a thrill from the smell of a chemistry lab. Talk to me of quarks and mesons, and my stomach is aflutter! But I wasn't cut out to be a scientist, it seemed. A BSc in Maths and Physics demonstrated that I didn't have what it took to dedicate myself to research – and I also realised that I wanted to work with words instead of elementary particles. So I became a science journalist. But fiction was my first love, and in 2008 my first short story collection, The White Road and Other Stories, was published. Half of the stories in the book were inspired by articles from New Scientist, because I just couldn't leave that science connection alone. I'm not the only one: there's quite a bit of science-inspired fiction out there, check this out.

So, the next natural step? Get inspiration directly from the place where science is being done. And that's what I did. Let me introduce Bristol University Science Faculty's first writer-in-residence. Nice to meet you.

I've only just begun, so there's not a great deal to report yet. I am headquartered in the brand-new and very beautiful Nanoscience and Quantum Information Centre (NSQI), but free to roam around the university, sniffing out those chemicals and large hadron colliders (alright, maybe only small hadron colliders.). The plan is to spend two days a week embedded in a lab, or perhaps several labs, asking lots of ridiculous questions, learning about how science is done, who does it, why they do it, what they do on a daily basis. And then my brain, which works in fairly odd ways, will stew on all of this, and somehow from it I will write short – and very short – stories. One of these stories will be published here each month, as well as regular blog posts so you can follow what I'm up to. I'm also aiming to get some of the lab rats writing fiction too, by running a few flash fiction workshops. (What is flash fiction? See my website here)

So far, I've been to a seminar on quantum tunnelling at the NSQI, and spent some time in the glass-walled “fishbowl” room there, intended to inspire interaction and encourage multi-disciplinary collaboration. And last week I spent a day and a half in Professor Paul Martin's biochemistry lab. I learned so much in just that time, there is so much that those outside the practice of science have no idea about. For example: how do you get to work in a lab? Do you answer a job ad? What radio station is best to have on in the background? Do scientists call themselves “scientists”? I will be visiting this lab more often, will report back on my findings! I also blog regularly about writing at TaniaWrites.

In the meantime, here's one I wrote earlier, a science-inspired flash story, The Painter and the Physicist. More tales from the lab soon. Blog post 2