Tag: science

Categories
nostalgia science

A visit to the ol’ lab…

I dropped in on my former DPhil supervisor, Nick Proudfoot at the Sir William Dunn School of Pathology yesterday. I don’t visit that much, even though we’re good friends now. The lab is a busy place, after all. You shouldn’t delay the progress of science.

I was there to take a photo of some lab equipment for the ARG we’re developing. Yes – there’s a clue. Part of the game will feature a virtual lab facility, where DNA experiments can be ordered over the Web and the results sent by email. It’s all part of the story…

Nick and I chatted – as we always do on these occasions – about recent progress in the field. Or not-so-recent progress, since I actually left molecular biology in 1992 and went into cell biology (the former is mainly about genes, the latter is mainly about proteins and cells). So my knowledge is fairly vague and out of date as it is…

Anyway, OMG! So may cool new techniques have been invented since I left! Eeee, kids today, they dun’t know how easy they’ve got it…in my day you really had to suffer for your science, with home-made apparatus and enzymes and techniques that barely worked…

The march of progress. And yet molecular biology labs are still fairly grungy, messy places to be. As the photo above proves!

Meanwhile, I also took a shot of my thesis, which is on a shelf in Nick’s office along with those of all the other students he’s shepherded through the process of becoming Dr. Scientist. Well done Nick! You’re a STAR. (Really – publishing eight scientific papers this year, in great journals too…)

(and so nice to see my first  ‘book’ in the company of those by my brother-in-law Paul and my good friend Becs!)

And spot the girl in the nerdy jumper, my official department photo from 1991 now displayed in one of the corridors of the labs.

Roll on the NJP Lab Reunion dinner in December!

(Photo above shows me, Alex Moreira, Joan Monks and Nick.)

Categories
science writing

Lab Rats – I so wanted it to be good

They finally set a sitcom in a research lab.

The idea is hardly original – I myself submitted a script for a lab sitcom (WHITECOATS) to the BBC and Channel 4 in 2004 only to have it a) rejected and b) ignored, respectively. A German TV producer got excited about it and pitched it to some German TV channel. I never heard from her again…

Well, if the brilliant Richard Herring gets his sitcom ideas rejected by the BBC then a total unknown writer who hasn’t even done the requisite ten years on the comedy circuit is NOT going to get taken seriously. I get that, I even agree. (And of course my script was the work of a screenwriting and comedy novice…)

I wrote WHITECOATS because I wanted to see a sitcom set in a lab. There wasn’t one, so I took a DIY attitude. Luckily for me it didn’t get taken up; I moved on to writing thrillers for children and wound up being paid what I’m guessing is more than a novice TV writer.

So LAB RATS – should have worked for me. I love Chris Addison in “The Thick of It”. He’s sweet and he’s a Manc, like me. I loved Geoffrey Perkins as Ford Prefect in the radio version of “The Hitch-Hiker’s Guide To The Galaxy”. I watched both the clips released prior to the show’s airing and laughed out loud.

But I’m afraid I watched with dismay yesterday. I’m not going to tear it apart – too many TV reviewers are doing that. I AM going to keep watching, but from such a beginning I don’t see that it ever reach any decent height. Unless they rejig the formula radically as was done with “Men Behaving Badly”.

The best thing I can say is that it’s sort of Goodies humour, but the Goodies has dated too. And the other thing I can say is that some of their conversations, sad and geeky though they were, are not far from the stupid kinds of things I remember we did talk about when I worked in a lab. The two clips of LAB RATS that made me laugh are here.

Okay, I’ve criticised another writer. Now I’ll offer myself up for the same treatment. Here is a snifter of my pilot script for WHITECOATS – the four-scene sample I entered in the BBC New Talent contest. Obviously I didn’t get anywhere or else I would never have written The Joshua Files.

Categories
nostalgia science

The immune system kicks a**

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Antigen presentation – the central tenet of immunology. Didn’t make any sense to me until I saw the crystal structures of MHC I, and the T-Cell receptor.

I emerged into the outside world today full the kind of renewed energy that only a post-viral recovery gives you.

The immune system is an amazing thing. Even moreso when you have some knowledge of how it works. I remember when they published the crystal structure of the Major Histocompatibility Complex I protein bound to a peptide antigen. Luckily for me this was the year that I took biochemistry finals at Oxford. I’d never understood the scientific evidence for molecular immunology properly until I actually saw those molecules interacting.

I’m just not good enough of an abstract thinker. The cellular evidence just befuddled me. I had to see something in 3D before I could catch on.

Immune system, amazing, hence I have made a whole load of antibodies and cytotoxic T-cells and other cell and molecular weapons and totally kicked that viruses ass and cleared it out of my system. And if anything like that comes round again, my B-cells will give it what for…

Oxford was warm and filled with shoppers, students and tourists. I heard some Brazilians speaking Portuguese and it cheered the part of me that still wants to be in Sao Miguel do Gostoso. I dropped into Waterstones and was relieved to see that ‘Invisible City’ survived the recent cull of children’s books on display in the window. Still on display and in the 3-for-2! Lots of books for older readers have been put aside to make way for picture books and other things for younger kiddies. Finally I share a window display with the wonderful Axel Scheffler!

Categories
Joshua Files science zero moment

Report from my sick-bed

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I should be in bed in bed but I’ve been there most of the day fighting off dengue fever. Okay it probably isn’t dengue fever but it’s plenty unpleasant enough and I brought it from Brazil. It’s my fifth day so I’m feeling a bit pathetic.

“How come you aren’t better yet, Mummy,” my six-year old asked. And then paused before adding, “Cos Daddy’s better. He got better right away. He’s been doin’ shoppin’ and cookin’ and other good things.”

It’s always got to be a competition, hasn’t it…?

I managed to rouse myself to beginning Joshua Book 3 today. Hurray! Only other writers can appreciate how big an achievement that is. I haven’t written for six months, astonishingly lazy underachiever that I am.

And before you cry ‘false modesty’ – University academic friends of mine are expected to write scholarly tomes whilst holding down a full-time college fellowship and University lectureships. Last year one of these friends, with four kids mind, published a book and also ended up delivering a speech at the Nobel Prize Award Ceremony. Another – who has two kids – was voted Woman Of the Year.

So – I know what I am. Lightweight and proud of it!

Gosh my head hurts. I only started this post really to alert you a recent issue of New Scientist, which I have been trying to read between bouts of languishing feebly. It could have been written for me! Articles about the possible collapse of civilisation, the real-life possible existence of time-travel and telepathy and a groovy little thing about an upcoming innovation in social networking Websites that neatly solves a plot problem for me.

Anyway. I’ve tried non-pharmaceutical remedies all day – cold compresses, cooling gel patches, Tiger Balm. Nothing. So I’m going to cave and take some proper medicine.

Ah. Sweet oblivion of an anti-histamine mild sedative combined with OTC analgesics.

That’s me out for at least 12 hours.

Categories
nostalgia science

Bioscience Nostalgia

Every so often I get all nostalgic for molecular biology. Ah, they were good days, so much work to do that you hardly had time to think about anything but science.

I found some videos on YouTube which made me smile. This has got nothing to do with Joshua Files, btw, but if you’ve half an interest in science geek humour, and the nostalgic musings of a former scientist then read on…


Here’s the PCR song. It’s from BIO-RAD, the manufacturer of the thermal recycling machine which makes the Polymerase Chain Reaction possible (at least optimal). Lucky BioRad, they had a bright employee named Kary Mullis who when faced with the dilemma that piqued many scientists in the 1980s, didn’t stop thinking. No; he took a long drive up to Marin County (or from…) and thought long and hard about it.

This was the dilemma: We were all using purified enzymes like DNA polymerase to amplify DNA ‘in vitro’ (as in, not in a cell but in a test-tube), but only on a small scale. We weren’t making enough DNA to use in DNA subcloning work or enough to see on a gel with the naked eye. It wasn’t possible.

We all knew that DNA can be replicated simply by melting the two strands, using DNA polymerase to fill in each strand. In theory, if you kept repeating the process 1 molecule would become 2, then 4, 8,16,32,64 etc. But the process of melting the DNA each time would destroy the enzyme. And it was a big hassle to keep swapping the DNA from water baths to ice baths to cycle the process of melting/annealing.

And that’s where most of us stopped thinking.

Kay Mullis, however, remembered that some bacteria exist at high temperatures (e.g. near volcanic vents under the sea), and have heat-stable enzymes. If he could use the DNA polymerase from such a bacteria, it should be possible to invent a machine that would heat-and-cool tubes for the optimum times so that small amounts of DNA could be melted and annealed 20,30,40 times.

And that would seriously amplify the molecules. That would make it possible to eventually detect teeny weeny amounts of DNA.

And so PCR was invented. As an employee Mullis didn’t get rich but he did invent a process that made the lives of all molecular biologists much easier, revolutionised forensic science and paternity suits.

For some reason I only once had a chance to use PCR. In my early days it wasn’t around and later it just wasn’t applicable to what I was researching, until the last month or so. And then I used it to detect a subcloned DNA molecule I’d made the day before. It was the fastest subcloning I ever did and the PCR worked first time, like a dream…and I thought Jeeeez…why wasn’t this around 6 years ago?!