Life of a Lab Rat

I've been researching and writing a topic for a book chapter. This has been quite a bit of work — it's in a field with which I am vaguely familiar but there are lots of subtleties and gotchas — and has completely sucked my lab time away. A book chapter is nice, but sometimes I wonder whether I'm going to use all these hard-earned gobbets of information, wrested from the fires of PubMed: or even if anyone's going to read the damn thing and take something positive away from it.

I enjoy writing, and I enjoy learning new things, but sometimes you just need to go away and clone something. Anything. The first draft will be done this weekend, and then I can have a proper look at the microarray data that arrived this week. This week? Last week. I don't know. There was a long weekend somewhere, I remember that.

These microarray data are interesting. They're not in total accord with the first batch I did last year, which is actually quite reassuring because Beta Gal isn't haven't much luck getting data that are consistent with what they told us. Which means, and this is good or bad depending on the angle you approach it from, that I have to re-do about a month's worth of analysis.

In seven days. Because then I have to make a poster for a conference.

So. Yeah. A couple of extra days, please. Might make a difference.

Actin motility and force generation. Cast of thousands.

Went down to a seminar this afternoon, and saw my young apprentice helping the speaker set up the projector. I had just seen a reasonably interesting result fall out of my microarray data.

So I nicked a piece of paper from another postdoc, went back and stole her pen, and scribbled this:

My young apprentice was appropriately interested.

Now, after another couple of hours looking at more species, I'm seeing definite patterns. I still don't know what they mean, but at least there seems to be the possibility of an answer, and I'm beginning to be excited in my ignorance, rather than frustrated at it.

Science is supposed to be pretty. Not a lot of point in doing it, otherwise (for a range of values of 'pretty', at least).

So I was first pleased when I saw that an editorial Nature Cell Biology talked about the visual aspects of our work, and then disappointed when there were no accompanying pictures or movies to illustrate the point. Moreover, the link to 'further reading', which I clicked upon with great glee and haste, is empty.

Muppets.

Anyway, I got an email from Laura at the EMBO Journal last night. They are running a cover art competition;

The editors of The EMBO Journal are pleased to announce a new contest to select the best cover image for 2008.

As in the previous years, one winner will be selected from each of the two categories: Best Scientific Cover and Best Non-Scientific Cover. The prize for both winners will be a free one-year print and online subscription to both The EMBO Journal and EMBO reports.

This is a fantastic opportunity to indulge the artistic side of your scientific temperament. It's a shame that no one outside science will probably ever see your work, and the prize is hardly something that will appeal to someone with institutional access, but that's just quibbling. The closing date is 18 January 2008. Get snapping.

Last week, I asked a PhD candidate in our lab whether she'd got a date for her thesis defence. 'My what?' she asked. We looked at each other in mutual incomprehension before light dawned.

It turns out that there is no viva voce requirement for an Australian PhD.

I was shocked and stunned, and not to say a little amazed. No thesis defence? And no auditing of examiners. Well, well. Just how much do you think that little book is worth, then?

Today I read that there are calls to reinstate the viva voce, which raised a little cheer from me. But the whinging has started already:

Nigel Palmer, president of the Council of Australian Postgraduate Associations, said: "Students are always going to be cautious about anything that looks like a viva.

"Particularly towards the end of their candidature, PhDs are close to exhaustion. It's a very daunting proposition to come out and give a stunning presentation. Also, (a viva) disadvantages international students."

Poor wee grad students! Heaven forbid that an Australian PhD candidate should be daunted by anything. Won't somebody please think of the children?

In civilized countries it is not enough to be able to write something; you are called upon to answer criticism of your work and defend your conclusions, to be able to prove that you can contextualize and think independently, and — importantly — recognize when you've got something wrong and be able to reassess, to think on your feet. It's a public exam — and in some countries the defence really is public, the people who paid for your studentship can verify that you were worth it. International students are no more disadvantaged by a viva than they are when it comes to reading the literature (and writing the damned thesis in the first place). Someone who can not give a talk in the language of the country they do the lab work (I'm ignoring humanities/arts. Sticking to what I know) has a more fundamental problem than being able to defend a thesis. The argument about external examiners does not even get off the ground. Additionally, if someone can not complete a (non-coursework) PhD in three to four years, then serious questions about their ability, and that of their supervisor, need to be asked.

Look, a PhD is not about doing great science. It is about teaching you how to think like a scientist. That's why it is possible to fit it into three years. No one seriously expects a PhD to be your "life's work", or a new PhD to have a great publication record. We know the pressures of a PhD and we're looking to see if you have the nouse and the gumption and the sheer bloodymindedness to cope with real research. You do not actually start to be a scientist until you begin your first post-doc, when you will be expected to think for yourself and not have your hand held all the time, and cope with serious deadlines. In the real world, people are not going to wait for you not to be exhausted and daunted before doing something. And guess what boys and girls? Part of the training is to be able to give a full seminar, not just answer questions about your work.

And yes, a PhD is bloody hard work; exhausting and daunting. That is precisely why they are so valued.

This is Science.

You try. You push, you fight, you struggle. You take tiny, baby steps, and all the time you feel like you're running to stand still. Everyone else seems to be successful, and your plugging away only draws attention to to the void that waits where your next paper should be.

But still you try, hoping against hope, long ago going through the place where any sane person would have given up because deep in your heart you know that this is the only thing you can do; the only thing worth doing.

And maybe you look at the papers in the field and realize that the experiments that set you off on this wild goose chase were complete crap anyway, and the mechanistic interpretation, if there is one, is deeply, fundamentally flawed. You present a poster with your ideas, which, despite — or maybe because of — your lack of results, is very pretty and even enjoys a brief moment of glory on display alongside the prize-winners of this year.

Others need convincing, so you perform more experiments, and with tragic inevitability any data you generate are variable, standards don't and negative controls aren't. Little hints here and there suggest you might not be completely crazed, but you wonder if you've given your boss any reason at all to believe in you.

Then one afternoon you sit down to look at some very preliminary data: incomplete, waiting on the proper controls and still shy of the experimental nirvana that comes from n = 3; and you really don't know what you should be doing with this program but you fight it because by God it's not in you to give up, and you realize that you're reading the wrong strand of the chromosome but when you finally get the numbers to match six bases SHOUT at you from the Ensemble web site and you echo the shout to the office as you realize that here, indeed, is an Answer.

All your heartache and disappointments are forgotten in that sweetest of brief moments. You are the only person in the entire world to know what you do now.

You savour the exultation while your pulse recovers, then you grab your scribbled notes and a pencil and hotfoot it to the boss's office, where you try to keep the shaking out of your voice while you explain what you've just found. His reaction stuns you, as he leaps from his chair and calls in other members of the lab who have a vested interest in this project and whose own work has just been vindicated. You have to explain the result three times while phrases like "this is the best result" and "this is so fucking cool" are bandied around carelessly. The uninitiated look on, somewhat bemused.

Then comes the inquest, the 'whatifs' and the 'yeahbuts' and you have to explain how your model appears be right, pending further investigations and appeals and peer review. It's dark outside, it's late and you still need to set up a PCR before you can leave.

Nonetheless, they can not take it away from you:

For a Day, you were King.

Right, I promised to give a not-so-quick list of seminar do's and don'ts. The context for this is the Honours students giving their 'end of labwork' talks in a few weeks, and there's a few scribbles on a Post-It note I'd like to share.

The thing to remember through all this is the point of a talk (or lecture, or seminar, or whatever you want to call it). You are trying to convey a message, and most of the time that message is "Look how brilliant I am". Seriously. You are using your work to convince people in the audience to think "Hey! This cove deserves a degree!" or "Hey! I'd really like this person to work in my lab", or even "I'm glad I employed this person in the first place". Anything that distracts (or detracts) from your message is a bad thing.

That is why I've come down so heavily on the presentation aspect. It does matter, because people (being human) will focus on what they perceive to be wrong, and you do not want them thinking about the bad when they could (should) be focusing on your brilliance. Now, obviously you're not going to please everyone all the time, but you can certainly put your thumb on the scales.

All these points arise from sitting through various seminars. Unfortunately it's not just students who make basic errors; the pros do it too. A couple of weeks ago an email came round the 'academics' mailing list in the Cage, noting that our courses were getting a bad rap in the national press. We've all got something to learn.

The first point I'm going to make is so obvious I'm surprised it needs to be said. But if you get it wrong it's probably the one thing that will make people think "What a prat". It's so important that I'm going to put it on a separate line:

Spell check your slides.

Honestly, this is not difficult (and I'm not talking about technical terms, I'm referring to common words). On my computer at least, questionable words are automatically underlined, but the ability to check spelling in any document has been standard for essentially for ever in computing terms. And if a word looks all right to you but is flagged by your spell checker (Americanisms are a big gotcha, especially because the Americans themselves are deeply confused about -ise, -ize and -yse), then look it up. The OED is free to use from a USyd computer, so make use of it.

Related to this, if you're writing complete sentences rather than bullet points then check the grammar. This is slightly more difficult, but ask someone in the lab to check your slides for you. And if you're dyslexic you should do this anyway (spell checkers will not tell you if 'their' or 'there' is correct in context, for example).

Let's make that more formal. Even if you are an English geek, you should practise your talk in front of a friendly audience before you do it for real, so that they can spot any glaring errors that you have made. Proofreading shows respect for your intended audience. You can work out the implications of that for yourself.

Also remember that certain sad bastards (ahem) delight in looking for words in protein sequences. Find them yourself first; make a joke of it if you like.

Check that your slides are legible, from the back of the room in which you will give your talk. Easy to do, very few do it. Nigel makes a good point from the presentation point of view that serif fonts are generally bad when projected. Times New Roman is just one example of this.

Similarly, the use of colour can make or break a presentation. I still prefer plain black on a plain white background for clarity, with maybe an institutional crest in a corner and a coloured bar (horizontal or vertical) for relief. Recall that 10% of your audience might be colour-blind. Time spent on designing a flashy theme is time better spent on experiments, writing or going to the pub. You are not trying to sell pharmaceuticals to impressionable physicians, you are trying to demonstrate how clever you are. Just because Powerpoint and Keynote have these flashy templates does not mean you have to use them. Remember, you do not want to distract people from your message.

Which leads nicely into the next point: Transitions. I loathe Powerpoint transitions. Most of us have seen them all before and they're boring and, again, distracting. I have to admit that Keynote has one or two nice ones, but they're likely to become just as clichéd in a couple of years' time.

At the opposite end of the spectrum from yellow on blue Comic Sans with whizzing transitions is Sir Paul Nurse. Sir Paul gave a talk a couple of years ago at my institute in Cambridge, and boggled us all by hand-drawing his slides on the fly, on the OHP. Unless you are a very good artist, I do not recommend you try this, at least not until you're as famous as he is.

Keep your slides simple. One message per slide. One, at the most two, graphs or figures and no more than five bullet points — but not on the same slide as your graph! Highlight key points. Do not write out what you are going to say (more on this further down). Try to make all your slides legible without needing to turn down the room lights. This is difficult and not always possible.

The trick is to imagine that Professor Sleepy has dozed off during your talk, and wakes suddenly during a crucial data slide. She should be able to look at your slide and at a glance understand your point. Consider whether you really need to show a sequence alignment. These are notorious to get right, and it's often better just to leave them out. Think about how you are going to show data: It's good to see raw data, but it's also good to see controls versus experimental in a clear, striking graph.

When you finally give the talk for real — and I hate practising talks; I can never get into the swing of it without an audience but as I say, it is essential to get others to proofread your slides and your verbals — there are more things to remember.

Your talk should be structured. There should be a clear introduction; start large and focus in on your speciality. Contextualize. Explain why you did what you did, and what you were trying to find out. Concentrate on the data, and never, ever merely read from the slide. We can see and read that for ourselves; the slides are there to show data and to remind you what to say, to expand upon the core message that you are showing us. Conclude with a clear message.

I don't think it's important whether you give your acknowledgments at the start or the end, or during the talk. When I've described work that a few people have done I like to start by naming and thanking, so that the audience knows who I'm talking about when I say "David suggested we do this". It's possibly better that students save it for the end, but it's not something I'm worked up about.

So you're standing, giving the talk of your life, and you're facing the screen. Wrong, wrong, wrong. When we used glass slides and projectors this was more excusable, but the chances are that you'll have a laptop between you and the audience. So look at the audience, and glance down at the laptop. Ideally you should not even need the slides to give your talk, so except for pointing out things of interest you should never have to look at the screen. Talk to us! If you find yourself unable to remember your slides, and without a screen in front of you, then stand slightly to the side so you can see the screen out of the corner of the eye. Remember you're trying to impress us, not the screen.

Do not rush. Do not whisper, but neither should you shout; project your voice. This takes practice. Use simple terms, not jargon, whenever possible. Pace yourself, and make sure people can understand you. Look directly at members of the audience to confirm that they are getting it (and don't get too depressed if people are asleep. It happens to all of us). Work on your delivery, on capturing and holding people's attention. Consider what you're wearing; again, give no one an opportunity to focus on you or your foibles rather than your message.

"Hold the bloody pointer still", it says here. Most distracting when the little red dot is jerking all over the place while you're talking. Don't fiddle with change in your pocket (my biggest fault!) but don't be afraid, within reason, to use your hands to describe or emphasize. Don't 'um' and 'er', and don't say 'kinda', 'like' or 'sorta'. You may say 'innit' for comic effect. Don't be afraid to use humour, but you had better make sure it really is funny. Don't forget the names of collaborators and colleagues.

At the end of the talk, make it obvious you've finished. If someone asks a question and you can barely hear them, repeat the question (ask them to repeat it if necessary) so that the entire audience can hear. Address the questioner but talk to the rest of the audience as well (a difficult trick. I'm still working on it). If you don't understand the question, ask the questioner to rephrase or repeat, and then repeat your understanding back to them to check (this rephrasing the question in your own words is a useful trick. It lets the rest of the audience hear the question, confirms that you're answering the right question, and gives you time to think). Don't be afraid to stop and take a drink if you're dry; this also gives you more time to think.

I get a real blast out of giving talks, and one of the most important things to remember is to have fun. It's a crucial skill to learn if you're going to make a career out of this game, so you may as well enjoy it. Finally, realize that criticism of your talk is not aimed at you personally. Take criticism constructively, and learn from it.

I have been whining about Wikipedia, the free encyclopedia where you can write any old rubbish.

The major problem I have with the project is its assumed authority. It is treated as a reliable source by, I guess, most of the population. The problem is that if you're looking something up in an encyclopedia then the chances are you don't actually know much about the subject, and therefore can not tell if your source is correct.

Those of us who have some knowledge about some things are shocked to find that Wikipedia is often wrong about our speciality. And then we become very worried because we have no idea if this failing extends to things we know little, or nothing, about. But it is safe to assume that it does so extend. This is not just restricted to Wikipedia of course: I have read a few stories in newspapers (national and local) where I have had insider knowledge about the reported event. And approximately half of the statements of fact in those stories are just plain wrong.

This does not seem to concern the editors of Wikipedia. They are more worried about due process than truth. So if you are looking up something on Wikipedia, your assumption that the author of the article and the editors know anything about what they are talking about is false. All you know is that the article has been written and edited in accordance with some rather arbitrary principles. These arbitrary principles, rather than verifiable truths, are the authority upon which Wikipedia is based.

Now, this would not be a problem, except that increasingly, students and professional scientists are turning to Wikipedia for answers. And people are writing their own websites based on Wikipedia articles. It is a house built upon sand, and we, as publicly-funded scientists, are failing the public if we do nothing about it. Ian points out that it is not worthwhile to write or correct articles, because in some frenzied pomo notion of fairness and equality facts and evidence count for nothing, and the 'wikizombies' (thanks Ian!), with their 'citation needed's and 'balance' and due process 'liberate' (which my thesaurus has as an alternative for 'pillage') scholarship from antiquated notions of 'truth' and 'verifiability'.

Evil triumphs if good people do nothing. So what do we do?

The problem with, say , a 'professional' wiki-type encyclopedia is that the people who we would want to contribute are those who are probably the busiest in their field, doing experiments and writing papers and raising grants and teaching students (who contributes most to Wikipedia? Those with most time on their hands. Hmm). So what we need is some kind of payback to entice scholars to write scholarly articles. Scientists are attracted by the prospect of cold, hard cash, or publications they can put on their CV. The former would mean that any such project would have to cost money to use (let's not even think about advertising revenue), which defeats the purpose of a free resource. We do have something close to this, in HowStuffWorks.com, but again, where is the authority?

So what about a peer-reviewed WikiScipedia? Jenny suggested that contributors should have "a PhD from an accredited university and a current and credible scientific affiliation". That would be a nightmare to organize, and does not get around the quis custodiet ipsos custodes?[0] problem. Peer review works (mostly) for scientific journals, and is where textbooks (eventually) get their authority. Any scientist could contribute; all would be invited to write articles aimed at a reasonably educated (but pre-Bachelor's) adult, but all articles are reviewed by experts in the field. Articles could fall under 'Cutting edge' or 'Established dogma' categories. Maybe there should be two sections; a 'pending review' area where anyone could write/edit and an 'authoritative', peer-reviewed section. And while we're at it, let's at least have pseudonymous if not completely nonymous peer review, so that there is accountability and partisan conflicts can be avoided. And did I say it would be free access?

It would be invaluable to school children, and could also go a long way to increasing the level of scientific literacy in the general population (hey, if you're going to dream, aim high).

It would be hard work to get going, but no more so than any other learned journal. Contributors would be able to cite articles on their CVs, and funding agencies, who are increasingly waking up to the whole communicating with the public idea, should also be happy. We'd need a sponsor to get going, ideally a publishing house already committed to the principle of Open Access, with a competent editorial team that has marketing oomph and a sufficiently large and diverse scientific address book.

Oh, hullo Nature. Doing anything tonight?

And the reviewer says,

This is a well written and comprehensive article.  I have only a  few minor suggestions/corrections.

So that's nice.

Bit of a furore.

Unfortunately it's not in real life, but in the so-called 'blogosphere'. I'd like to take this opportunity to say that while I am not opposed to neologisms in general, the class of them that starts with 'blog-' is monstrously barbarous and should be avoided whenever possible. Sometimes, sickeningly, this is not possible. I apologize to my more discerning readers, both of you.

I have been wondering, myself, about the purpose of this weblog and sciencey weblogs in general. I am not totally sure on why I wanted to do this, except that 'it seemed a good idea at the time'. I know I had some noble notion that I could attempt to make science and the scientific way of thinking accessible to Bruce and Sheila Public, and some completely selfish motives that were to do with channelling my creative instincts. But I never thought that it was just about me, by me and for me — an exercise in self-gratification.

Funny thing, science. Most of us do experiments to show that something is so, but in reality we're excluding other possibilities. What we're doing, if we think about it, is trying to disprove hypotheses so that a theory is strengthened. Now that sounds a little odd, but it is the basis of the scientific method.

An observation leads to a hypothesis explaining that observation. We test that hypothesis by doing an experiment. We think of another hypothesis, and test that one. And we keep doing this, until we run out of testable hypotheses, to formulate a theory that is not contradicted by evidence, one that we say is 'supported' by experiment. Philosophically, it is difficult to be certain that any explanation of a phenomenon really represents reality, that is it is difficult to prove anything This is because someone with a good imagination can always come up with an explanation that fits the evidence but does not agree with your pet theory. It is much easier to disprove something.

We have Ockham, of course, but that is a philosophical concept and it although it might say something is likely or not, it does not tell us that something is. This is why good experiment design is important.

And yes, this is also why proponents of Intelligent Design do not make good scientists and and why it is bloody difficult to reason with them. They do not have any hypotheses in support of their position that are falsifiable. You can not prove them wrong, because everytime they are in a corner, puff of smoke! Dear old William can just go whistle.

But I did not want to argue about that today. I want to talk about proof, and faith.

A lot of people, and especially scientists and other rationalists, get very confused when talking about faith, and indeed proof. Is faith really a belief in the the improbable, the illogical or even the irrational? If you have evidence, does it stop being faith? If you have evidence is it necesarily proof? Surely you can only have faith in things that can not be proved, or that you know are not true? A few weeks ago someone opined that anyone who could have faith in the intangible was stupid. I wondered aloud where that left scientists, because let's face it friends, we all have faith in things we can not prove. Our experiments, our theories; we can only support from evidence, we can only prove, so much.

Question: If you can ask if you're delirious, does that automatically mean you're not?

It's all right, I've cut the analgesic dosage (mmm codeine) so I should be reasonably coherent now.

Went to the quack's on Friday, and fortunately did not get to see the muppet who managed to miss the pneumal party when I crawled into his office last Thursday, barely able to breathe and unable to stand. Instead I saw a nice lady doctor who continued my roxithromycin prescription and also prescribed a cephalosporin. That is because I said I did not want a penicillin, as we use beta-lactamases in the lab all the time and I did not want to take the risk that anything pathological in me had managed to acquire resistance. Unlikely I know, but always a worry.

I don't actually think she knew what I was talking about, but tried her best. She had never prescribed cephalosporins before, and knew nothing about them, but spent a good few minutes looking in various books before deciding what to do. She didn't even know who Ed Abraham was, which is a shame, because I did my DPhil in The Sir William Dunn School of Pathology, where the whole antibiotic story took off.

If anyone fancies a move to Cambridge, UK, they should get in touch with me, as my old boss has got some Wellcome funding. Yippee!

I spent a long time this afternoon thinking about the model upon which the set of experiments I have been doing for too many months is based. And I have come to the conclusion that the model is pants.

Which on the one hand is a shame, because I feel that I've wasted half the past year. On the other hand it does explain why the experiments are not showing what we expected — that is of course why we do experiments, to test models. The thing is that I can not make the model yield the result that was expected of it, even theoretically. That is, even if the model is correct it can not give the answer we were looking for. The best I can do is make half of the pre-messenger RNA transcripts behave and the remainder have ruddy great lengths of intron in them.

That is somewhat annoying, especially seeing as the effect I have been trying to reproduce was published a few years ago and appears to be accepted as true. That published work explains (but does not justify) why I had not previously assessed the model so critically.

W00t! Via Eva, we have the full length version of the teaser cell movie. Narrated in a very 1970s public hygiene announcement voice, but worth a look anyways.

Flash, unfortunately. . . sorry Nix.

Here is the microscope that was used to take those pictures:

One of my fellow Rats commented that she liked doing cell culture, because what with the laminar flow hood and everything it felt like she was doing Real Science. I know what she means, so here's another photograph of lab furniture; the cell culture, or laminar flow, hood.

There is an arrangement of fans and filters with the general idea that any nasty stuff inside the hood stays there and does not infect the operator, and everything on the outside stays there and does not infect whatever it is that the operator is working on. Obviously this theory breaks down a little bit because you have to put your hands and flasks of cells, solutions, pipettes and whatnot inside in order to actually do anything. We get around the problems this causes by liberally spraying 70% ethanol over the surface and anything that gets put inside (including hands, which are usually also washed with Hibiscrub first). There is also a reasonably high intensity ultraviolet lamp inside that gets turned on when the hood is not in use, to make life unpleasant for any nasties that do manage to find a way in.

And yes, you do get to feel like a real scientist doing real science, and most of us doing cell culture form an irrational emotional attachment to the cell line(s) we happen to be working with at the moment. We care for, feed and nuture our cells and it can be quite distressing (not just because of the time wasted) when, not if, you go to the incubator one morning and find your precious cultures swarming with bacteria, or fungi, or strange beings from the Planet Claire.

If you're as old as me, you might remember sometime in the early '90s being completely blown away by Tim Springer's wonderful videos of leucocyte extravasation. For some reason I seem to have a lot of non-science types reading these ramblings and I reckon I've probably just lost half my readership, so I'll step back a bit and put things into plain(er) English.

If you happened to pick up, say Jandl's Blood: Pathophysiology, you might find an opening paragraph that reads something like

Blood is a complex suspension in plasma of nondividing differentiated cells which continuously perfuses the vasculature. It contains a mixture of several very different kinds of cells, all of which stem from an oligarchy of progenitors that originate in marrow or lymph follicles.

Which is a rather complicated way of describing the red stuff that leaks out when you get a real bad paper cut. Essentially, blood is made up of red cells, white cells and little bitty things called platelets, all floating round in a kind of white wine sauce. And it gets everywhere. The red cells are the little fellas that carry oxygen and nutrients around, platelets help stop the red stuff leaking out, and white cells, like knights of old on armour'd chargers, fight infection. Depending on the sort of white cell you are, you can throw chemicals or antibodies at nasties, or actually muscle up and eat invading bacteria and other bits and pieces. Yummy.

This ties in with the 'why do we do it?' meme that's been bugging me recently.

Suz needs a hug, but she's written a very droll piece on scientists as, um, lab rats. Or mice, as she has it. The question is what happens when we apply the same criteria to ourselves as we do to our experimental models.

Her conclusion, that her experimental model (which I think by this stage is herself but I could be losing the plot myself at this point),

either has a learning defect or is masochistic

Shaun Cronin points to a polemic on the politicization of science by the current Australian administration.

I've got little to add aside from what I've already said in the comments, but you should go and have a read.

An interesting piece in the Grauniad last week (I know, I know, I'm sorry - I go to work, see an interesting article, try to remember it and the witticisms that spring to mind, finally come home on the mind-numbingly over-crowded Inner West line, have some dinner, the Younger Pawn is running around with a duvet cover on her head and making 'woo woo' noises and by then I've completely forgotten what I wanted to say) about the whole 'we're all doomed' thing.

(One reason I'm linking to it now is because I'm honestly not sure if any of my Australian readership read the Grauniard, possibly the last bastion of halfway decent professional reporting in the UK.)

The most effective countermeasure against zombie outbreaks has previously been shown to be aerial bombardment. Troops on the ground are not favoured because they are ineffective at the dismemberment – a prerequisite for zombie inactivation. However, carefully targeted high explosives successfully achieve this. A regrettable corollary is collateral damage, as nearby human life is inevitably destroyed. However, these innocent bystanders would, in the absence of intervention, would likely have become zombies – and a threat to their neighbours. This contingency is introduced into the model as a ‘user-directed interaction’ which destroys humans and zombies, making them functionally equivalent: in other words, non-infectious.

You may have seen the report that schools in the UK are 'producing too few scientists',a conclusion reached by the Confederation of British Industry (CBI). It is worth remembering that the CBI has an agenda, and that is to make money. Presumably they think that more scientists means more money for their member businesses country.

A little thought will show then that the CBI is not interested in science at all, rather technology; the appliance of science. The thing is that you do not get that technology unless you have first done basic research. And you need a hell of a lot of basic research to get a single money-spinning technology (if it were otherwise, research scientists would get richer a lot quicker).

Aside: There's a nice example of how politicians lie in that article. The CBI claims that the number of students taking 'A' Levels - the UK's 18+ exam/university entrance exam - in 'hard' sciences has decreased drastically in the last 20 years. One might think that this woould have an obvious knock-on effect on the number of hard science graduates. However, the Schools Minister says that school funding for physics and chemistry has increased, along with the number of science graduates, since 1997 - when the current mob got in. But if we take a look at the numbers it appears that most of that increase is accounted for by computer science and medical graduates, neither of which are famed for basic research (and computer science barely existed as a degree in 1994. No wonder there is such a large percentage increase.). The 110% increase for students taking 'biological sciences' seems hopeful, until you start to ask exactly what that means (I have no idea. I do know that there has not been a doubling in the number of biochemistry graduates). Lord Sainsbury keeps suspiciously quiet about social 'scientists', I note. I wonder if they are included in the statistics?

I am sure that most people in my lab could pass as perfectly normal members of society. I know that some of them even have real lives, and seem to be able to maintain relationships outside the lab.

Therefore I have been somewhat taken aback by the response to the Axygen 'eppendorf' tubes. A fair proportion of the lab rats have come up to me in the last week and raved - there is no other word for it - about these tubes. All right, they are good, but I never expected such an emotional excess.

The dangers of malnutrition in the unborn child, often leading to chronic disease in adult life, are well documented and the subject of much study. For example, searching Pubmed for Barker DJ turns up some 378 citations. However, it seems that over-nutrition can be just as bad, as the abstract below indicates.

Dorota Pawlak, Harvard Medical School and Children's Hospital Boston, is scheduled to give a seminar on Fetal over-nutrition and the risk for chronic diseases in childhood in the Human Nutrition Unit. If you want to come along, be in the School of Molecular & Microbial Biosciences Room 471 (Building G08, Maze Crescent) by 13:00 on Wednesday 30th August.

It is quite easy in this business to get disillusioned when you look around and see that, for example, the NIH only funds about 10% of RO1 grants and there is no career structure to speak of for postdocs. You begin to wonder if you are any good at all, especially when you reach a certain age and find that you are really enjoying the bench work but seem to have no luck at finding a real job.

"Hello, my name is John and I'm a scientist. I haven't been able to clone anything for three months. I'm taking it one day at a time."

The elder pawn (hmm, that sounds vaguely Lovecraftian) wanted to take her bicycle into school today. Turns out they're doing a project on machines. She asked if I had ever taken the back off a washing machine and when I said I had, she said

'Wow! What did it look like?'

I told her why I had taken the machine apart (to find out how it worked so that I could mend it) and from there went on to say actually, that's what I do at work. No, not mend washing machines — I take things apart to see how they work. I did not use the phrase 'the very fabric of Life' (I was tempted; that kind of thing does not faze nine year olds as much as you might think) but we did have an interesting discussion about dissection and atom bombs and all sorts of groovy stuff.

When I get to the bottom

I go back to the top of the slide

Where I stop and turn

and I go for a ride

A bit of a frustrating week.

The thermal cycler broke down just before it had completed a crucial experiment (but I think it went far enough to get some useful data), someone put agar plates with no antibiotic into the ampicillin plate bag (screwing up my cloning), a Western blot is tantalizingly inconclusive and a beautiful hypothesis appears to have been brutally slain.

Henry talks about some typical journalistic scare-mongering.

Now I'm not a developmental biologist, so I'm just basing my opinion on what I remember from seminars and distant lectures. Having said that, the article is an an interesting read, especially seeing as the question 'what does it mean to be human?' is closely related to 'what does it mean to be made in God's image?'.

Non-biologists look away for a couple of lines.

For some reason I got distracted by left-handed DNA earlier. It's a bit of a science geek joke, with a serious point.

Okay, you can look back now.

I then wanted to see what else Tom had to say and came across his Errata & Corrigenda page. And he makes the point very nicely that scientific research progresses through the identification of mistakes and falsification of hypotheses. Additionally, most research claims are false and are corrected by further experiment. There is nothing wrong with this; the observation-hypothesis-experiment cycle is how we do science, and some of those hypotheses will be wrong.

I should have written this up on Friday evening, but seeing as I was driving to Canberra it would have been inconvenient. I did pack the Queen's laptop, but it wouldn't have worked very well in the sauna. So, this post is a tad late. Apologies.

Friday is meeting day in our department. In the morning I set up a PCR reaction, helped a grad student next door with a cell culture problem, grabbed a coffee and went to our regular two-group lab meeting.

There's a misconception around that research — especially scientific research — is performed with a specific aim in mind. Ghassan makes this mistake:

Research is any project undertaken to reveal new knowledge. Research can be scientific; such as, testing to find cures for illnesses or improve medical treatments.

I heard on the radio a couple of minutes ago that Australia faces a severe scientist drought.

Julie Bishop is saying that Australia will be short of about 15,000 science and engineering professionals in six years' time. Tellingly, she has implied that the current (University, I presume) courses and career paths are not good enough. This in itself is progress, I feel; but although the government has admitted there is a problem, we have to ask what are they going to do about it?

The pledge of an extra 50 positions at CSIRO is a small step in the right direction, but there has to be a major rethink in the way science is supported if a real difference is to be made.

Oooh. This is a tough one.

I'm torn between

• Flexible working hours and a lot of job variety


• Open-minded yet skeptical approach useful for other aspects of life

After last week's little rant about the portrayal of science in the meeja, I thought it might be interesting to show you a couple of photographs.

This is the view from the lab door.

In one of my previous lives I pretended to be a crystallographer.

In other words, I would attempt to persuade concentrated protein solutions to get together and form ordered three-dimensional arrays - crystals - so that I could then shoot X-rays at them. The purpose of this was to determine their structure.

One of the things I was taught when I learned crystallography was to be very, very clean. No dust, human hair, bits of glass or other muck were allowed into the experiment. The most frustrating thing about crystallography is that all proteins are different, and will crystallize (if they crystallize) under different conditions, and there doesn't seem to be any pattern to this at all. The lab's insistence on cleanliness was an attempt to factor out one of the variables in the process. But I soon discovered that this may have been counter-productive. As with a lot of things in research, people disagreed with each other and there was a lot of intuition and opinion without a great deal of solid evidence. I realize that this might come as a surprise to some of you, to those who, perhaps, believe that 'scientists deal with facts'. The truth is that at the frontiers of science we don't know what's going on and we're trying to find out - that's why it's called 'research'. If you want facts, look in a text book (and they all contain mistakes, too).

So as I went on and got more experienced, I began to welcome small amounts of crud in my crystallization experiments. In fact, one recalcitrant protein only ever crystallized once, along what looked like an insect leg. I was never able to repeat that experiment; although I did have gothic fantasies about breeding every different sort of insect I could find and using various bodily insect parts as nucleants. A little too Shelley, perhaps.

I keep reminding myself of Sturgeon's Revelation (beware, that article is pretty tedious) that 90% of everything is crud. Nevertheless, I should point out some other weblogs that might be interesting to readers of this site.

Hot from Nature, we have Nature Protocols: Recipes for Researchers.

It's in beta, I'm getting a few 404s and the registration/sign in was weird (stealth login, anyone?) but it could be useful. One of those 'wait and see' projects I feel, and probably in direct competition with the protocols section of the OpenWetWare thing I wrote about last week.

What's interesting to me is that these are peer-reviewed methods, with user comments. So it's almost a Wiki-meets-journal type of thing. Hmm.

It's probably not a good idea to sneeze over your ice bucket while prepping RNA.