Life of a Lab Rat

I don't know if this is a good idea, whether people will like it, or even if I have the energy/inspiration to keep it up, but I thought a 'Weekly Protocol' feature might work.

Let's see how we go. I'll start with this one, for making splicing competent nuclear extracts. Cobbled together from a number of different sources, it's surprisingly easy and straightforward.

Printable: http://blogs.usyd.edu.au/labrats/pdfs/Nuclearextract.pdf

Some people just don't get it.

A reader wrote to me, on the horrors of MSDS and risk assessments etc., and suggested I look at something called 'Chemwatch'.

So I looked at the website, and BANG! Browser window resize! Choice of flash or non-flash! Eye-hurting design!

Wake up guys. That stuff is sooo last millennium. And because of it, I really can't be arsed.

A little bit off the wall, but for anyone who hasn't yet woken up to Stephen Fry's weblog, you should:

Imagine that one day someone hit himself lightly on the head with a parsnip. Instead of stopping (for this is a foolish thing to do) he carried on doing it. When he eventually did stop he went about his business but discovered, much to his surprise, that he had a sudden unconquerable urge to hit himself lightly on the head with a parsnip all over again. So he did. And the more he did it, the more he needed to do it. The act of doing it gave him a tiny surge of joy, a little rush of pleasure that had to be elicited, never mind what a twazzock he looked, parsnipping himself on the head all day.

Smoking is no less stupid than that. In fact it is a whole bicycle-shed more stupid, because it’s smelly, unsociable, carcinogenic etc etc etc. But the principle is the same: smoking has absolutely no point other than to stop the misery of not smoking

You see, this is why I hate the internets.

Just got back from a performance at the Pawns' school (Elder Pawn was first clarinet in a fantastic rendition of Pirates of the Caribbean) and am now supposed to be washing up, but I happened to stumble across Emma PeelTigtog's rant on paradigm shifts:

I’m not the only person to be annoyed over the years by the egregious overuse of the term “paradigm shift”. I knew people were misusing the term, but not having actually read Kuhn’s seminal work wherein he coined the term, I never had the properly grounded basis to articulate why.

"Paradigm shift" gets nearly fourteen hundred hits in PubMed. That's a lot of paradigms being overthrown. I really can't be arsed going through and thinking about which ones are really paradigms, but much like my own bugbear, "quantum leap" (111 hits in PubMed) — why people get so excited about the smallest possible discrete advance is beyond me —, I suspect that even (especially?) in the proper sciences the term is much abused.

I'd say more, but the suds are getting cold.

I just wanted to inform you that your samples arrived without sample volume left in the tube for a full sequencing reaction as stated on your order form. I refer to samples labelled XXXXA and XXXXB.

If you could resend these samples ensuring they are fully sealed and wrapped
up, we could sequence them for you as soon as possible by putting them on
the top of our list.

You dropped my bloody samples, dintcha?

I have refrained from commenting on the Craig Venter 'artificial life' brouhaha because, well, to be honest I couldn't think of anything sensible to say and this safety audit bollocks has been winding me up (having said that, the Head knocked on my door this morning and said "Are we still friends?" and we had a good chat, so I'm feeling less het up about it).

But in a far corner of the Internets, Bill Hanage explains just why Craig Venter's pronouncement is really all fur coat and no knickers. And it's worth the read:

I sure as hell recognise the advantage of a good PR machine. Clearly [Venter] does too.

It's all gone a bit George Smiley.

Peter is concerned about the American Chemical Society (ACS), as well as PRISM, Open Access, and stuff like that. I left a comment on his weblog recently, and from there I think someone at the ACS must have stumbled across the Labrats, because I have a received a second spam email from them, with yours truly in the 'Bcc:' — but this time 'To:' is someone at the NOAA.

My mystery correspondent begins

Dear Colleague and Friend,

Several of you contacted me
about a memo from Judith L. Benham which claimed that the American
Chemical Society is not protesting Open
Access in order to preserve profits and bonuses for the Society's executives.

S/he kindly attached the memo, and continues (I should make explicit that I am quoting from an email. These are the mystery author's opinion and claims, not mine),

Let me assure that I was not involved with last week's memo which is riddled with multiple misdirections typical of a slick political commercial. The most obvious falsehood is this passage: "Our Society's position is also represented by the Association of American Publishers, a non-profit organization whose membership encompasses the major commercial and non-profit scholarly publishers, including ourselves. ACS is not alone among scholarly publishers in reaching out to...."

The statement comes apart once you know the names of the players involved.
The position of the AAP was developed by Brian Crawford, who is chairman of
their scholarly division . Brian Crawford is also head of publishing at ACS. Big surprise.

So what we have are two organizations speaking from the same mouth.

This allows for clever gamesmanship by ACS executives..
Just last year, Rudy Baum wrote his second editorial in Chemical & Engineering
News where he called Open Access "socialized science."[1]

To buttress his argument, Rudy cited--who would have ever guessed!?--the Professional
and Scholarly Publishing Division of the Association of American
Publishers, which "has taken a strong stand" against the Open Access bill.

Rudy also wrote that the AAP's scholarly division had written letters to
senators opposing the bill.. What Rudy forgot to disclose to his
readers is that the letters were signed by the chairman of the AAP's
scholarly division, who is Brian Crawford, also head of publishing at
ACS.[2] Crawford is now apparently Rudy's boss.

Yes, Baum is that ridiculous. But it must be hard for a man to fully inform
readers when his wallet tugs at his conscience. Oh...it gets better.

Brian Crawford holds up his end of the bargain by penning letters against
Open Access on behalf of the AAP, such as the letter last year to the Los Angeles
Times. Brian wrote, "government bureaucracy continues to impede
participation and undermines the successful expansion of information access."
Crawford's byline was credited: "The writer chairs the executive council of the
professional and scholarly publishing division of the Assn. of American Publishers..[3]

I guess that Brian forgot to mention to the Los Angeles Times
that he is also a publishing executive at the American Chemical
Society. He might also have troubled editors with the minor fact that
his bonuses will plummet if ACS publishing profits drop..

So now you see how their political campaign against Open Access works.
First, Crawford creates the policy position at AAP's scholarly division; ACS
executives then point to AAP policy for cover with their members. But it is all a shell game that
quickly falls apart once anyone spends five minutes on Google. Links to the
appropriate information can be found [embedded by BK]. Look for yourself and have a giggle.

And just to prove that we're on the same team, a cheery wave goodbye

I hope everyone has a smashing week! Please keep sending in your emails with links and other bits of information that you find on the internet. And see the wiki for further information. It is only by demanding that ACS leadership becomes more accountable to members that we will see change.

Sincerely,
ACS Insider

No doubt the emails are flying today, because the US is, as I write this, about five hours from waking up, and it's a big day for Open Access over there:

URGENT CALL TO ACTION: Tell your Senator to OPPOSE amendments that strike or change the NIH public access provision in the FY08 Labor/HHS appropriations bill

not that we in the boonies can do anything about it, except maybe tell our friends.

Oh, and naturally, I will continue to report any further developments.

As Monday morning spam goes, this one's pretty interesting. I reproduce it here, unaltered (except for some formatting):

Hello,

I've been an ACS employee for many, many years, but I've
grown concerned with the direction of the organization. I'm sending
this email to alert you that ACS has grown increasingly corporate in
its structure and focus. Management is much more concerned with getting
bonuses and growing their salaries rather than doing what is best for
membership. For instance, Madeleine Jacobs is now pulling in almost
$1 million in salary and bonuses... That's almost 3X what Alan Leshner makes
over at AAAS, and almost double what Drew Gilpin Faust makes to lead Harvard.

I think Madeleine is smart, but I'm not quite sure if she's in the same
category as Dr. Faust. She doesn't even have a PhD!

What really concerns me is a move by ACS management to undermine the open-access
movement. Rudy Baum has been leading the fight with several humorous
editorials -- one in which he referred to open-access in the pages of
C&EN as "socialized science." ACS has also spent hundreds of
thousands of dollars in membership money to hire a company to lobby against
open-access.

What troubles me the most is when ACS management decided to
hire Dezenhall Resources to fight open-access. Nature got hold of some
internal ACS emails written by Brian Crawford that discussed how Dezenhall could
help us undermine open-access. Dezenhall later created a group called
Partnership for Research Integrity in Science and Medicine (PRISM),
which has this silly argument that open-access means "no more peer-review."

If you're wondering why ACS is fighting this, it's because people like Rudy Baum,
Brian Crawford and other ACS managers receive bonuses based on how much
money the publishing division generates. Hurt the publishing revenue;
you hurt their bonuses.

I'm hoping that sending out this email will get people to force ACS
executives to become more transparent in how they act and spend
membership money. Not to mention their crazy need for fatter salaries.

It's time for some change. If you want to check out the
sources for this information, there is a wiki site that has all the
articles and documents outlining what I've just written..

You can find it here:
http://www.sourcewatch.org/index.php?title=American_Chemical_Society

Those of us inside ACS know that it's time for things to change. But
management won't alter their behavior. The money is just too good.

Sincerely,

ACS Insider

I'd be fascinated to hear from anyone else who has received similar, and whether they know if the person in the 'To:' field is actually the author?

exonomics , n.

The scientific study of exons. A catch-all term for Black Knight's folder full of PERL scripts, microarray data, sequence alignments and random scribblings.

Actually, a google for 'exonomics' comes up with something financial, so the word is already in use. As I dislike any of the alternatives (exomics, etc.) I propose that we liberate this word from the oppressive regime of the economists and restore to it its birthright.

Tidying up the office, and came across this gel:

Whatever it meant, I didn't seem happy about it.

Adapted from an email I've just sent to the Head:

This is beyond ludicrous. If we are each to have a copy of the OHS paperwork, the maths looks like this:

Say 6 risk assessments, 6 SOPs. 20 MSDS sheets, at an average of 5 pages each. Four pages of policy document. Call it 115 pieces of paper. Thirty people in our group. That's three and a half thousand pieces of paper - best part of 7 reams. That's nearly half a tree, plus the toner used.

And that's just one quarter? one third if we're generous of Level N. I really, really think that this needs a rethink.

The first thing we do, let's kill all the lawyers.

Never one to mince his words, the Bard of Stratford obviously never had to deal with administrators, specifically administrators responsible for Occupational Health and Safety.

As I type, the Cage is gripped in a frenzy of OHS paperwork. Apparently there is to be an audit next week, and as there have been so many serious incidents in biological labs all over the world (um, not) we each have to generate and maintain a folder that contains vast acreage of processed rainforest, to comply with OHS regulations. Note that this does not make us actually any safer (because, frankly, concern for one's own skin is a pretty good incentive to not killing oneself at work); the entire exercise is to keep the lawyers happy.

The University has a policy of "eliminating conditions and incidents that could result in personal injury or ill health", which, as far as any of my fellow rats can work out, consists in actively preventing us doing any research.

Consider: The amount of paperwork to be analysed, filled in, printed off and filed is going to knock the lab for six for two working days at least. Then each time we do an experiment we're supposed to go to our personal folder and check that we're complying with whatever, further reducing the time available to do anything. But this, cunning as it is, is not nearly enough.

Each potentially hazardous chemical needs to have a corresponding Materials Safety Data Sheet in your personal folder. And the recommended site for downloading these MSDSs is broken:

.

Which means. . . because I can't download (and print) the MSDS, I'm not supposed to do the experiment. But I want to do the experiment (you know, I don't do this job for the money, I thought that should be obvious by now), so I'm forced to spend more time looking for the MSDSs on the individual suppliers' websites instead. Cunning.

But wait, there's more.

I've been reading the Cage's OHS website, — which you might think had actually been approved by someone who knows what it is we do — and, dumbly following instructions to the letter, we're supposed to mark each 'reaction' with a 'ChemAlert' label. Which means that for a standard tube containing one chemical, and the smallest available label, we get something that looks like this:

.

Now, imagine two, or three, potentially hazardous chemicals in there. It would be impossible to work with. Devilishly cunning, and further proof that the lawyers and administrators who dream up these schemes (a) have no idea about what we actually do and (b) don't care; because their purpose is not to save lives but to prevent the University getting sued.

What they fail to realize is that no amount of paperwork is going to make the lab safer, and is in fact counter-productive because people get so pissed off about the whole deal they treat the entire OHS section as a complete joke. Which might very well lead directly to personal injury or ill health (I watched this happen in Cambridge. It was not pretty then, and it is not pretty now).

Sod it all. I'm going to set up a PCR without having printed off a risk assessment, and bugger the lawyers.

(now the ears of my ears awake and
now the eyes of my eyes are opened)

When Ricardipus isn't whinging about his inability to manage his time, he's making comments on other people's weblogs.

He makes the very good point that the general public is never going to read science weblogs, but is tied to 'conventional' (as opposed to nuclear? I think we should be told) media. My thesis is that 'conventional' journalists probably are not going to have the time nor the inclination to use material from those same weblogs, so it all seems a bit pointless. However, I prefer e. e. cummings over Susan Musgrave and am more optimistic than Ricardipus, both when it comes to time management and the effects of science weblogs.

Journalists who report on science generally have to make do with press releases and interviews with heads of labs, from which they need to distill pithy soundbites. These are frequently misrepresented (deliberately or accidentally) and devoid of important context. We know that the scientific literature is impenetrable and execrably written and that this makes it difficult for scientists themselves, let alone the educated layman, to understand published work. Believe me, this week I am editing undergraduate theses and I know, I just know there must exist a compulsory Pompous and Ineffectual Writing 101 course.

What hope, then? What hope for the layman or the trained writer crafting a press release to understand the primary literature? What hope for editors of school textbooks to get the science right? What hope for seeing balanced and accurate science writing in the papers?

Weblogs.

Hang on a minute BK, what are you smoking? you might well ask. Bear with me.

Dr Ludbrook says

It seems to me that there are two components to writing well in science and medicine. The first, and most fundamental, is the need for a solid grounding in English grammar, usage and style.

This obviously starts at school, and we might in a moment of heady optimism imagine that universities offer writing courses that actually are effective. But this involves time and money, and is probably too late for most of us.

Ludbrook suggests that we should make use of freelance editors. This is obviously a marketing ploy and I shall pay it no further attention. But here's the crux:

The second is constant practice in writing, especially in the format required by biomedical journals.

"Constant practice in writing". Now we see how weblogs can be useful. Not necessarily as a means of direct or indirect (via traditional media) communication with 'the public', but as a tool for improving writing.

If practice makes perfect, then write to get better at writing. I don't know if he does it with this aim in mind, but Ian's weblog is a fantastic example of writing about science constantly, with no hope of reaching the 'general public'. But Ian has succeeded in making immunology more accessible to me, and I bet his writing has improved because he does it.

I'll be the first to proclaimadmit that a lot of the 'science' weblogs out there are terrible, and that the authors would rather take cheap shots at people who disagree with them than actually tackle anything with substance. But the beauty of the weblog format is the opportunity for feedback, for instant peer review. Which means that you and me, the readers, have the chance to point out that someone is being unintelligible, or overly verbose, or stupid, or narrow-minded. And maybe, when they learn to write betterer as a result, when they write their papers or their summaries for the PR office, they'll thank you.

In the meantime (because this won't happen overnight), if you're writing a weblog, or a paper, or a school newsletter, then check out this little Flesch-Kincaid readability gadget. I should run it on these theses and see if I can break it.

Pithy soundbite: Just because it's a blog doesn't mean it has to be crap.

Georg kindly sent me a link this morning, and although it is interesting, I've been wondering ever since about how to frame it.

I remember quite clearly the first time I realized that what you read in the newspapers (and by extension, what you see on news bulletins) is not necessarily what actually is. I had recently completed my thesis defence, and one Sunday morning my ex-supervisor rang me up to tell me that a member of my old lab had been murdered; shot at through his kitchen window. Come Monday, and the news had made the national dailies (and continued to do so).

And it wasn't that the incident itself had been misreported; it was the background, the little bitty details that made the victim a real person that were wrong.

That was just the start, of course. Soon I began to see details that were wrong all over the place. And yes, sometimes the stories were wrong too, or even non-existent (HT).

So when Georg says, hey, look at this:

Journalists and scientists at Monday's Scientific American sponsored panel discussion, "Does Science Get a Fair Shake in the Media?," hosted at USC Annenberg, unanimously agreed that while the public is consuming more science reporting now than ever before, mainstream journalism is doing a lousier job of covering the field

my inner cynic asks "Isn't all reporting like that? What's so special about Science journalism?"

I don't want to attack good journalism, or journalists. But there is a failure to realize, on the part of people like you and me, just how difficult it is to report factually, accurately and relevantly. I'm a hobbyist; it takes me as long as I want to write this, and I might still think 'to hell with it' and hit delete. But your professional journalist is trying to create a story, not write a scientific article, so that means she has to put in some 'human interest', to create a controversy or mystery if possible because within the looming deadline (that's redundant. All deadlines loom. It is in their very nature to loom. 'Loom': It rhymes with 'doom') she also has to get it past the editor who doesn't care about telling the truth but who does care about increasing circulation, or advertising revenue at least.

To approach science reporting with a traditional journalistic judgment of newsworthiness and objectivity is fundamentally incompatible with how science works

Our struggling journalist will, because she's good at her job, interview the locals, who range from the uselessly intellectual telling her that a modification in changing the dementia praecox concept to the more inclusive one of schizophrenia does nothing to weaken the fundamental dichotomy to the self-important constable who was proceeding to the Town Hall when the alleged miscreant did allegedly accost the alleged victim with what appeared to be a blunt instrument, allegedly, and finally sees the chance to get his name in the Scunthorpe Courier.

Which all means that it's a damned sight easier just to unthinkingly regurgitate the press release — which itself is expertly spun by someone with far more time to spare, if not just plain wrong.

Enough ranting. Even with good journalists and sympathetic editors, I think that science probably is worse off than, say, cricket coverage, because it is harder, LBW decisions and Duckworth-Lewis notwithstanding.

The media isn't doing its job to educate the public – most journalists have little to no background in science and statistics [...] Furthermore, due to traditional media's budget considerations, a science reporter is often responsible for several scientific disciplines, and that inevitably leads to a lack of intelligent, dependable coverage, or worse, over-coverage of wacky, pseudoscientific studies such as Jessica Alba's score in an index of female desirability.

Scientists must take some of the blame, too. When was the last time you read a scientific article that your mother, or even your sister, could understand?

On the other hand, many scientists cannot talk in layman's terms about what they do. Neither are they trained to do so. "No effort has been made to help us reach out or learn to talk to the media and to the public," Quick said

Which is one way of saying that you shouldn't be surprised when you discover that most science weblogs are about politics or badly written, or both. It's all a little bit pants, really.

The question remains,
"Can science blogs save science journalism?"
and I very much suspect that the answer is "No. But spending more on public education, especially in science, might".

There. Politics. Hope you're happy now.

This one's for the Whiffler:

From the ABC, I read

More acute for the Wallabies was that for the third time in tournament history it was bitter rivals England who were their World Cup executioner

and would like to comment that ultimately, England's verdugoship proved too much for the struggling Australian rugby team.

I thank you.

Back in the glory days of System 7 it seemed that everybody had a plasmid-drawing tool (I was originally going to say 'widget', but you'll see why I changed my mind in a minute). Then something went horribly wrong and all these useful little programs broke or went outrageously commercial (you know who you are) and consequently out of the reach of many of us.

So for a while there we were using Illustrator or similar to draw plasmid maps, which is a little bit like using a howitzer to take out a cockroach — it's expensive, there's a lot of collateral damage and you're never quite sure if you actually got it.

OK, so maybe that analogy is flawed. Never mind. Where was I? Oh, yes. Plasmid maps.

The incomparable but fairly well-hidden Ian York not only writes intelligently about immunology, thereby demonstrating that he is much, much smarter than I am, but I am reminded (because I promised to do this months ago) that he's written a little DNA-mapping program, XPlasMap, which as far as I'm concerned proves that he's superhuman.


I heartily endorse this product or service

This gadget (which would, I'm convinced, make an excellent OS X widget) slurps a sequence, finds the open reading frames and restriction sites, and makes a quickndirty plasmid (or linear) map in a mere couple of clicks. It is dead easy to insert fragments and to change the labels and colours, although removing sites you don't want to see is a little tiresome, and it would be nice to be able to zoom into crowded bits of the map. It also would be handy to be able to insert fragments by restriction site rather than base number, and to export the entire sequence (making the save file a package, as does EnzymeX, would help here), but for a simple to learn, easy to use tool for making records of all your plasmids, you can't really go wrong with XPlasMap.

Oh, and it outputs JPEG and PNG files for further furtling, although the reason for the JPEGs being 4,000 pixels wide is probably merely further proof of Ian's superiority.

The OED is a wondrous thing, and a source of great comfort and amusement to me. I recently stumbled across a little article on getting neologisms into the dictionary, and Ben Zimmer's Word of the Week feature.

It's all fascinating stuff, even if it's not as good as mine. Just imagine what I could do if they paid me.

Once, just once, it would be nice to have a simple project.

Image credit

I have been using siRNA to knock down the expression of my favourite protein (FP), in an attempt to figure out just what the heck it does. And the experiments have been looking pretty good — the message (RNA) goes 'phut' and the protein itself disappears within two days. We're assaying what affect this has on the cells by running exon microarrays (because we have reason to believe that FP is a splicing factor), which are expensive but potentially very powerful.

The first experiment worked well; we saw lots of changes when compared with an 'irrelevant' control (a lamin knockout) and got really excited. And then I did some n >1 and some more controls, and it all went a bit squiffy.

This is a graph showing the expression of lamin exons, on 12 microarrays representing triplicates of four conditions:

The three experiments on the very left are arrays of the lamin knockout experiment; the other 9 are (in triplicate, left to right) two different controls and the FP knockout. Note how the signals disappear almost completely from the lamin KO, but are pretty constant across the others. This is good, and right, and hopeful.

But then we look at the FP exons, and Oddness Occurs:

Look at the three right-most arrays (numbers 10, 11, 12). Number 12 disappears completely, which is what we'd hope for and expect. Ten is a bit meh (although it does go down a bit), but there is a huge uptick in four or 5 of the exons in experiment 11 (look at the orange line, for example).

I spent a goodly time renormalizing the data and trying to see if there was any systematic error in that particular experiment, but all the control exons (and indeed, the lamins) look good. Puzzling. Thinking about the experiment this morning, and what to do about it, I happened to read Jenny's ponderings on scepticism. And it struck me that what I am seeing is tantalizingly similar to that which Li and co. describe.

In other words, ignoring for the moment the obvious question of why supposedly the same cell line would behave completely differently in two presumably identical experiments, the squiffiness could be interesting.