This rather splendid piece of apparatus is sitting on a trolley just round the corner from my office. Mitch Guss uses it to demonstrate the use of the Ewald Sphere in indexing crystals for space group determination and data collection (for a tutorial on these concepts see Bernhard Rupp’s excellent Crystallography 101 course).

The printed web page (now there’s a slightly unphased concept) on top of the stack of overheads is from the Online Dictionary of Crystallography . In practise, we rotate the crystal using the goniometer (and see the annotation at Flickr ) and collect two diffraction patterns 90 degrees apart (about the axis of the incident beam) to index it. The whole thing rotates and twists quite pleasingly.

Writing and other forms of communication are also important to me in the day job as a science professional. After all, there’s no point doing all this stuff if you’re not going to share it, and if you’re going to do that it makes sense to be just as professional. This is not news, but I do have an eye for spelling mistakes and apostate apostrophes, etc. I often get asked to proofread manuscripts and slides, as well as for help with ‘the best way to say’ something.

It’s all right Gee, I’m not angling for a job as an editor at Nature (not yet, anyway). But I thought the community might enjoy this little jibe from Stuff White People Like . If you laugh half as much as I did, I will have laughed twice as much as you.

A well-written covering letter at least shows respect for the Editor who is handling your opus, and might actually be useful in persuading them to send the manuscript out to review instead of laughing hollowly and consigning it to the ‘ach, I can’t be arsed’ pile. But — just like writing papers and giving seminars — cover-letter writing is one of those things that we are, as far as I can tell, supposed to acquire by osmosis.

But I wondered if you have hints or advice you’d like to share. If so, you should leave a comment.

So. Please. Leave a comment .

This Dr Manhattan is a nuclear physicist — and a pawn of the US government. He has the ability to create duplicates of himself which can function independently of each other. The full implications of this become apparent when after an intimate moment with his girlfriend he goes back to the lab … and recombines with ‘himself’ who has been doing rather different sorts of experiments the whole time.

The thought sends a tingle down my spine. In the absence of an ‘intrinsic field’ deus ex machina, this is the best argument I’ve ever seen for human cloning (previous arguments on NN about what to do with excess bioinformaticians notwithstanding). I want a clone of myself. And I want the ability to imprint and transfer memories and experience.

Imagine.

I think I need three of me. One to work in the lab, one to write and do analysis and one to be a father/husband/social butterfly. At around 3 in the morning we’d all plug into the Neural Equalizer™ and synchronize our minds. The benefits – at an individual level – would be immeasurable. At a societal level imagine the progress we’d make. People would become essentially immortal, untiring — complete with ‘off-site’ backups.

All I have to do now is persuade the Wellcome to fund my research. I will of course be asking for volunteers to be experimental subjects, and as I can already see you rushing forward, I’d like you all to form an orderly queue behind Maxine.

Thank you.

”... these four-helix bundles are designed to bind substrate …”

I have no reason to believe that the chap is a closet IDer, but please, won’t someone think of the children?

Fun with ideas is (views the end of the sentence and chokes back the panic) fun.

However, in a place like this there’s no point in writing something unless you try to make yourself understood by the other person. When people are calling you a troll, or thinking “What the blazes are you trying to say, man?”, there’s a problem.

It’s called ‘communication’. Poetry is not communication in this sense — it does not invite dialogue. Not here on NN (and I disagree slightly with the sentiment that the audience should only be scientists).

But the rest of Rus’s comment deserves a civil response.

Scientists tend not to talk about ‘truth’. They prefer to think of things as ‘correct’, or ‘consistent with the evidence’. Evolutionary theory is consistent with the evidence, and is consistent with the philosophy of a rational, understandable Universe. It’s pretty difficult, these days, to think of an alternative to evolution that is scientific.

At least out-and-out Creationists don’t claim to be doing science, or have scientific backing for their (appalling) theology. I’ll grudgingly respect that position, as long as they don’t try to defend it scientifically.

Scientists do not study “the world poets have bequeathed to us”. Poetry is not amenable to measurement, to testing of hypotheses. Do we ask ee cummings to test his thankfulness? Since when did trees have leaping green spirits that could be observed with a microscope, or a LHC?

The thing, the real thing about science as a system is that it works. It makes predictions that can be tested, and gives us technology that does what we designed it to. The earth goes around the sun in a predictable fashion. All this talk of ‘dogma’ in context of something you don’t like probably reflects a failing of the public school system to get across the point that science is not about facts, but rather process. Talking about an “Age of Evolution” probably reflects a further failure — one of scientists to effectively engage poets (and sometimes the two come together in the one person).

I am not one of those who believes that science is the be-all and end-all. It is no substitute, and can not inform the things, the messy, sticky things like love and justice that make us human.

Science tells us how things work. Poetry (literature, faith) can tell us who we are.

Big money. Big science . A good example of why we need to explain ourselves:

“These scientists could trim $10 million if they would just cut out some of the purple and blue spheres,” said Rep. Roscoe Bartlett (R-MD), explaining that he understood the need for an abundance of reds and greens. “With all of those molecules and atoms going in every direction, the whole thing looks a bit unorganized, especially for science.”

This guy’s ignorance is shocking:

“Fifty billion dollars to buy atoms is too much,” Rep. Tom Feeney (R-FL) said. “Frankly, I don’t understand why they don’t just gather up all the leftover atoms in their test tubes and Bunsen burners. I think the scientists should have to use those up before getting new ones.”

(HT: Ian )

Over at Popsci, Henry advocates the murder of a reasonable percentage of the population. Elsewhere on the web this week I have read how over a million Londoners are quite obviously stupid for voting in Boris Johnson as Mayor of London. And just about everywhere we see nasturtians cast at the mental prowess of millions of people who — often through no fault of their own — fail to accept evolutionary theory as a mechanistic explanation for the immense beauty and variety of life around us.

This is a disturbing trend.

The biggest failure of (shudder) the blogosphere is the people behind it.

If you think Boris Johnson is bad for London or Gordon (is a moron) Brown is the worse thing since France, then calling people who voted for them stupid, or taxi-drivers, or Daily Mail readers, or pinko lefty commies is not actually going to win you many converts.

Equally, I seriously doubt for example that sciencey weblogs, especially those over at a certain place , are doing the perception of science and scientists any good at all when their major message seems to be “Creationists are stupid, and I’m a scientist, so you’d better shut up and believe me.”

Leave name-calling to the tabloids. We scientists are people, and we get things wrong — gloriously so with any luck. We are not intrinsically better than anyone else — maybe blessed with more neurons or lucky enough to get the right teachers at the right time — but not better, not more worthy of not being put up against a wall and shot. Those with whom we disagree, even if they are demonstrably wrong in some areas, are as worthy of respect as we are.

The sooner those of us who have this opportunity to spout off in public realize the immense harm we do in so many ways, maybe the sooner we’ll be able to have meaningful arguments — ones that actually persuade rather than beat down (and I am by no means holding myself guiltess).

Please excuse the rant. Maybe it’s just the excellent homebrew , and I’m feeling more expansive and loving today. Except towards hairy-footed, croc-wearing, male Nature editors, of course. (I’m sorry if I seem to be picking on you, Henry. This attitude has been niggling me for a while and your comments have merely lowered the activation barrier. You’re curmudgeonly but I love you.)

I know this because there was a chap on the train this morning, reading a magazine that had a picture of a rather sad-looking bovine on the front. The cover story was titled A world of alternatives. For a moment I thought, maybe even hoped, that here was a story about mad cow disease, or antibiotics in milk, or growth hormones or GMOs or any of a thousand and three things that might have made me try to get a closer look.

Nope. It was about defensive assets. As it says on the website (that I actually bothered googling it should be clear evidence of my dedication, or insanity (or both)),

When sharemarkets are volatile, investors run to defensive assets. These days there are plenty of alternatives to the more traditional fixed interest and bonds.

Cows as defensive assets? Hang on, this is thrill a minute stuff. Forget Star Wars , how about a “Ring of Beef” protecting our freedom? Sub-orbital Bovine Defence platforms, maybe? ICBMs (Inter-continental ballistic moo-ers)?

But sadly, no. Scrolling down I read

There are very good reasons for investing in agriculture. As the global population grows and wealth increases, demand for food is also on the rise, especially for premium products such as red meat, dairy products and grains such as wheat.

Expect all chartered accountants of your acquaintance to be investing in defensive livestock. Bah. Can’t even get a decent steak out of it.

Emma Hill and Mike Rossner take us on a journey that begins in 1787 and ends with the rather extraordinary statement (from a major scientific journal, at least) that they have now decided to return copyright to our authors, in return for the authors (that is, those of us who manage to publish in JCB) making the work available to the public.

In other words, article authors — scientists like you and me — grant JCB a licence to publish their work for six months.

There is a lot to think about in here, and I encourage you to read the entire statement . There is the thesis that six months is the monetary lifetime of a paper. There is the possibility that real data-mining will be made possible, a move that should make the likes of Peter Murray-Rust very happy (although the matter of format now becomes more pressing).

There is the intriguing thought that what appears to be a reclamation of the original premise of copyright might jump across to patents . Now that would be exciting, and good for science.

The vote closes today, but I don’t at all recommend that we all register and unduly influence proceedings.

There is a world of philosophy in that simple statement.

Not a summer’s day then, but a bronze one; russet incandescence cooled to gold, a last fling before winter froze out the year.

And another hero of science was there:

While we’re maudlin, in amongst the reprints I found the April 2002 issue of nature structural biology (as it was then), which contains Max Perutz’s obituary . Immediately following that is a paper from some of the ‘sons of structural biology’, one of whom might be familiar to this readership.

It’s all open access now: go look it up. One day I’ll tell you what’s interesting about that paper, how I almost lost my no-claims bonus in the writing of it, and what happened next.

Let me rephrase that: When I am World President, people will have ready access to all pertinent information. And do what I tell them into the bargain.

Inhabitants of Australia’s largest city (it has rained every day, heavily, for over a week) will laugh hollowly at a report from the BBC about the drought .

Yes folks, it’s the wettest drought on record. There is no denying that farmers are having a hard time of it. Farmers who grow – in this arid climate – crops such as rice. And cotton. That, um, use a lot of water. More than any other crop, in fact⁰. While apple growers celebrate a bumper harvest .

Meantime, urban terrorists citizens, who already behave as if it’s a police state (there are signs in every shop saying that it is a ‘condition of entry’ that you present your personal bags for inspection when requested. Not ‘requested by police’ – no, the checkout girl can ask. And people comply! I politely decline. I might live in a penal colony, but I refuse to be treated like a criminal), are being instructed to make further cuts in their water use. Never mind the social impact of this (the trains stink), my fast red sports car needs a wash:

More seriously, if you build a house and do not allow all rainwater that falls on your property to soak into the ground (by, for example, incorporating a ground-level rain storage tank) it used to be that you had to pay a charge – a tax (disclaimer: this particularly odd piece of legislation might have been repealed. Can’t find anything about it on teh intarwebs). And the population, scared of God-knows-what, is firmly opposed to any recycling of water at all.

But.

“The reality is that water is used wisely in the cities for a range of purposes, including high value-added industrial and commercial uses. Over the past 20 years there has been a substantial reduction in per capita urban consumption. Sydney, for example, has been able to accommodate an additional 700,000 people without using more water. In 2001, the urban-based manufacturing and services sector produced 89 percent of the nation’s gross value added. Agriculture, forestry and fisheries accounted for 2 percent. Yet in 2001 agriculture used 67 percent of Australia’s water.” [1]

Why would Australia want to spend so much, in social as well as economic terms, to save a drop in the proverbial ocean? Because people will do as they are told. Because it’s a damned sight easier to introduce taxes and legislation to piss off the famed Aussie Battlers than it is to seriously rethink the nation’s agricultural policy (most of Australia’s water-rich crops are exported. I’ve not seen cotton clothes made in Australia, nor ever bought Australian-grown rice).

And people might whine that it is a knee-jerk reaction to blame the cotton and rice farmers for Australia’s water shortage, but the fact of the matter is that there is a sparse fertile strip here, and when there is a glut of water, it should not be squandered for the sake of money, but managed for the dry times.

Rather than think seriously about stewardship and managing resources, a year ago the then Prime Minister urged Australians to pray for rain . When you pray you should be careful what you ask for, because less than two months later followed some quite spectacular floods .

And then, all good Aussies whined that the rain was ‘falling in the wrong places’. Away from the dams. Away from the catchment areas. Just as it has this year, in Sydney, the rain came down and the floods came up, and washed out to sea. I’ll remind you that this is Australia, where they built dams relatively recently and actually had the chance to locate the capital city somewhere that wasn’t dry, barren, and full of kangaroos.

What, I ask myself, is wrong with these people?

And then. And then.

The users of the dirtiest coal in the world, the biggest-engined cars (well, all right, maybe the Merkins have that honour) in the world, sitting on the most uranium in the world, don’t have the political will to do anything about climate change (which will probably actually increase global rainfall, but only in places where it is already wet. Like Manchester).

There is talk of building desalination plants to solve the water shortage (Australia, about the size of the continental US, is surrounded by sea. That’s a lot of potential potable water). These use energy. And in Australia we make energy by burning coal. That leads to global warming. Which makes more rain fall in the ‘wrong’ place.

Head hits desk

Like the rice and the cotton, we’re exporting the bloody uranium (that we can use to make ‘clean’ energy) to China. That epitome of stability, human rights and environmental respect.

I think … I think I need another drink. And seeing as the beer’s crap here (with notable exceptions ), it’ll have to be whisky. No CO₂ in that, right?

⁰ Rice requires twice as much water as any other crop in Australia, followed by cotton (which requires half that amount).

¹ WA Dept of Water, March 2006

And if you post two entries in succession the most interesting one disappears.

And you can’t edit the tags until you’ve published it.

This explains why one of my posts from last week disappeared, and I’d like a t-shirt please.

It probably also explains climate change, Intelligent Design and Henry Gee, but they’re not as interesting.

a post over at Lords of the Blog got me thinking. What do we say when we think a seminar speaker is mad, bad or dog, and don’t want to be rude?

We’ve swapped the girls’ bedrooms over, and now we’re thinking of exchanging sewing room with study (I sometimes working from home, and the current sewing room is more private than the study; and wouldn’t have the girls’ computer in it). In preparation for this mammoth task, I’m going through some boxes that have remained essentially untouched since we emigrated. I’m currently running at six piles of stuff:

1. rubbish
2. recycling
3. work-related
4. personal documents, memorabilia, stuff that we might need
5. RAF first day covers
6. things I don’t know where to put, yet

In one particular box I found some risk assessments, written when we were getting very ticked off with the whole unHealth & Safety Department nonsense. Here’s one, for example:

That’s easy to deal with – I’ll recycle the paper and take the binder to work. But a large proportion of that ‘work’ pile consists of reprints.

And I seriously don’t know what to do with them. The papers themselves are all available online. There is a rainforest the size of Wales worth of carbon locked in there. Do I sprinkle them like cherry blossom upon the poor unsuspecting students? Do I give them away so that when I’m (in)famous people will be able to hold a piece of my history in their hand? Do I instead sell them with the promise that I will be (in)famous one day?

Are there, somewhere in the world, seventy-eight people desperate for a copy of Structural basis for the interaction between the Tap/NXF1 UBA domain and FG nucleoporins at 1 Å resolution ?

Please, if you come across such a lost soul, send them to find me.

I’ll even share my risk assessments.

The SAS (hah) has a manager, who is getting a tad narked that no one is listening:

You may be aware that the nomination period for the 2008 Prime Minister’s Prizes for Science closes on 9 May.

Let’s pretend, for a minute, that I was.

To date, the number of nominations received has been disappointing, and is clearly not reflective of the number of potentially suitable nominees currently active in research.

Hey, this is Australia. We’re all drinking beer at the beach.

It continues

We had hoped, in fact, to see an increase in the number of nominations for the Malcolm McIntosh Prize for Physical Scientist of the Year and Science Minister’s Prize for Life Scientist of the Year, as a result of an amendment to the eligibility criteria for these Prizes.

The prize, I’ve discovered, consists of a shiny medallion and a lapel pin.

There is also a fifty grand ‘grant’ which apparently the winner is free to spend on anything they want, but it would take a brave indeed young post-doc to take that literally and buy, say, a sports car . (Hey, Henry posts pictures of his dog, I’m posting pictures of my car).

A shiny medallion and a lapel pin? Naw, chuck another prawn on the barbie, blue. What’s a ‘lapel’ anyway?

Go see it.

Laugh.

And then go and look at photographs of beautiful dogs.

Ligand binding induces a conformational change in ifnar1 that is propagated to its membrane-proximal domain

How gorgeous. Perhaps Apple should make a new application for iLife . . .

iFnar
Create doubles entendre that are more custom, more complete, more you.

Dear all

Please note that both the lifts are currently out of action.

In case one of them starts to work again, I advise not to use them this evening.

SNAFU.

Remember, if you are running 15N HSQCs on double labeled protein, you should use the -LABEL_CN option in the pulse program, which incorporates 13C decoupling, and will improve the look of your HSQC in the 15N dimension, as it removes the one-bond N-C coupling

You see, I recognize the words, but they make no sense to me.

Running through the Babelizer improves things, I feel:

They call it, if 15N executed HSQCs in double noticeable protein, if
that one he uses the option of LABEL_CN in the program of the
movement, that account decides that 13C to him and if flied the one of
its HSQC in the measurement of 15N becomes the end still to improve
the Vista inside ignited, from cancellations the connection an
obligation of GOLD

Stalag Luft III

Last year sometime, the University of Sydney (the SUstainable Campus ) in its asymptotic wisdom started a project to completely destroy the not unpleasant (and positively Elysian compared with the building itself, above) grounds outside my lab. This is, we are told, a necessary prerequisite to the completion of Sydney’s new $65 million⁰ Space Centre .

These things take some time, I’ll give you, but for the last six months the view from my tiny office window (if I could actually see through the grime) has been not unlike this:

Nevada nuclear test site

My regular readers (both of you) might remember on Monday it was my birthday I wrote that the two lifts in our building had broken . Again.

On Tuesday they were working, if you happened to use them between about 10:37 and 11:03, but today they were out of order again. This prompted one of our workshop staff to write to the departmental email list,

The University sees fit to spend millions¹ on unnecessary landscaping right in front of our building, but seems unwilling to pay for reliable lifts. That is, probably, new ones.

Why do we have to put up with this misguided priority?

I wondered for a moment if someone would propose a strike (what would be the point ?), but a prof upstairs chimed in with

What’s wrong with you man! Keeping up appearances to attract all those juicy full-fee paying International students is a very high priority. Always look on the bright side…they pay our salaries, besides, walking up and down seven floors each day keeps us all fit!

Don’t you just love optimists? That was followed up by a comment from an AP (on one of the lower floors) saying

As I sit here revising my manuscript (The effects of age, birth cohort and survey period on leisure time physical activity by Australian adults: 1990-2005² ) I thought you would like to know you can expend 250kJ (that is per day if you go up and down them 3 times) – that lets you have a wine at the end of the day guilt free.

(I never feel guilty about drinking wine, by the way: at least, not if you’re offering. Thanks very much. In fact, my dad was told to drink more wine to help him lose weight. Seriously).

An hour later, we got an email saying that the lifts were working, followed within minutes by another saying that number two had stopped. Precisely sixteen minutes after that another email informed us that lift number one had gone out in sympathy.

The Assistant Head subsequently issued a decree,

For your own safety (especially after hours) do NOT use the lifts. They are not WORKING just moving up and down occasionally.

It all got a bit silly after that, with the currently hypothesis being that zombies are nesting in Level One (the floors are number 2 through 8, with 2 being the ground floor. Yes. I don’t like to think about it either) and trapping unsuspecting µstudents so that they (the zombies) can feast on their (the students’) living brains (step away from the keyboard, Gee. And you, O’Hara).

All in all, I’m rather glad I was sat at home analysing microarray data. It might not be as exciting, but it suddenly seems a whole lot safer.

⁰ PDF (6.4 MB)

¹ I seem to recall that it was about $8 million. I wouldn’t worry about converting to £sd; once you start talking ‘millions’ the actual currency is almost irrelevant (except for Lira or Yen, I suppose).

² A catchy little tune, that.

has anyone seen my mobile phone last left in Lift #2

In our particular ivory rather drab concrete tower our lifts are a source of constant amusement . Getting into one of them is rather like taking a taxi in Hong Kong , except much, much slower. As my spy elaborated:

This morning I got stuck in the lift on Level 7 (which considering I get both vertigo and claustrophobia made me a tad anxious). After contacting the emergency line, I discovered that the only way I could keep in touch with the outside world was to hold the phone up a little. Since I wanted to say some last goodbyes to loved ones (and members of my family), I hung the phone up on the knobs… On being rescued, I completely forgot about the phone

He’s obviously very worried that his SIM card is going to be used to control a burning jeep crashing into Glasgow Airport, or something (given the Australian Plod’s record , this fear is probably not unreasonable).

Poor chap. But wait, there was a followup message, from another lecturer in the department:

I also got stuck this morning, along with 2 micro students, on level 5.
I couldnt get a mobile signal at all.

(Stuck with two microbiology students? How terrible – Ed.)

We pressed the emergency phone button, which goes to the lift company, and were told the “problem would be dealt with by someone on the site”.

which I’m sure must have been very reassuring.

The good news is that we now have a new CoSHH procedure for lifts:

I found that i could use my car key to wedge the door open enough to let our fingers open it the rest of the way.

So there you go. I’m just glad for their sakes that there were no spiders in there, too.

Now, resolution is one metric used to judge crystal structures: more objective information is obtained from the Free R , geometry deviations and other parameters . The ‘resolution’ does tell us what me might expect to ‘see’, however, and appears incredibly seductive to the professional scatterbrain.

And there is a bit of a hierarchy. Go to any talk in which there is a crystal structure described, and watch the speaker’s face when it comes to resolution. Although the Free R tells you how good the structure is, all the other crystallographers want to know the resolution. The speaker will mumble if the resolution is higher (i.e. worse) than about 3 Ångstrom, be pretty upbeat if it’s in the range 2.0 – 2.6 Å, and positively beam if the data is better (i.e. lower) than 2 Å. And then there’s the ‘Holy Grail’ of 1 Å structures, with low Free R, which quite frankly are rather neat because you can see that Kekulé was right.

You see the same in papers. A crystallographer with a better than 2 Ångstrom data set will want to skite in the title — and maybe they also wanted to let everyone know that they scored synchrotron time (as ‘in house’ X-Ray sets tend not to allow collection of data at better than ~ 1.8 Å resolution, although yours truly managed 1.6 Å once ).

It’s a matter of pride , I fear.

I’ve been keeping a semi-professional weblog at another place for a year and a half (and a personal weblog for more than six years, in one place or another). And I’ve learned a few things about the sort of post that attracts comments, especially in science.

The top three science weblog comment baits are probably religion pets, abuse of students , and silliness about comments. Serious posts that deal with the actual science, even the human story behind papers, are greeted with deafening silence. Indeed, it seems that the best way to get a lot of comments is to get students to make fun of creationists⁰.

So it’s a little strange to look at the comment précis (on the left, down there a bit) and see that the person attracting the greatest number of comments on Network Nature is the mild-mannered and completely offenceless Jennifer Rohn. What, I asked myself, is going on in her Gap Minding ?

And then it struck me. She (inadvertently, I’m sure) is cast as a damsel in distress, and, metaphorically, an entire Round Table of Bioinformatic Knights has sallied forth from their disparate Camelots (these days we might say ‘IKEA’) to rescue her from the clutches of Mordred Mordor Henry Microsoft Excel.

On their ivory iMacs chargers, lances in hand and colours fluttering like so many EST s, they crest the South Downs and ride towards Astolat (it sounds better than ‘Chelmsford’), to free Jenny (or whoever happens to be this week’s distresséd damsel) from the tyranny of the bench and bring to her the Holy Grail treasures of Computational Biology, blood-hewn from the the golden plains of Silico.

There’s only one thing for it.

I’m having trouble making some mutants.

That picture in my profile? I found it on the internets. In reality, I’m 23, blonde with blue eyes and a figure that Helen of Troy would have scratched my eyes out for. I’m trapped in this lab, which looks suspiciously like a tower, until my wicked stepfather marries me off to a biotech mogul (the genetically engineered and perfect son of Craig Venter, probably). I might even be able to imagine some dragons, and a moat.

Let’s chat.

(oh, and “Help! Help!”)

⁰ This is a bit like shooting fish in a barrel. Unsporting, perhaps: I don’t think anyone seriously thinks Creationism is science, so attacking it on those grounds is a bit silly. Like trying to swat a mosquito with one of these . You could probably get as many comments if you were to attack someone who really deserved it, like certain fundamentalist atheists, but they tend to have a lot of support so you’d have to be really brave. Or Henry.

I detect an undercurrent of insecurity in such discussions. Those of us who are practising scientists (I like ‘practising’; it implies we’re trying to get better at it) are very well aware that the rest of the world, when it thinks of us at all, views us with a mixture of scorn, pity and dread. We are reviled for having no dress or fashion sense, no cultural sensitivity, no social skills. We are scared that we are labelled as geeks, or — even worse — nerds.

Some of us make a conscious effort to counteract the public image of a scientist. We deliberately do not wear socks with sandals. We read (and sometimes write) poetry and prose , we are proud of our culinary , artistic , and other extra-curricular activities. Others, perhaps more bravely, intercede for us through weblogs; and yet others prefer to patronize (PUS ).

But sometimes it feels as if we are yelling into an empty room. We are resounding gongs or clanging cymbals, and nobody is listening. This can lead to dejection, despair and Australian lager.

To hell with it, I say.

Brothers and sisters, we are scientists. We hold the secret of life in our hands. We probe the very fabric of the Universe, and pick it apart thread by thread.

Why, then, do we cower in our labs and offices and dingy little seminar rooms, over-worked and underpaid, while our true worth is hidden under a bushel? I say we rise up, we activate our army of cloned bioinformaticians and mindless grad students, and hold the world’s governments hostage. We can build machines that make the Death Star look like a Lego toy (what is the power to destroy a planet compared to smashing really small things together really really fast and making black holes , hey?).

The Public Fear of Science. Now there’s something worth working for.

Now, if only my bloody cloning would work.

X. IT IS IMPORTANT THAT PARTS SEAL AT THESE LOCATIONS

I am fascinated by the English language, especially its inherent ambiguities. This email, from staff in our media kitchen, serves to illustrate:

hi everyone, there will be delays in autoclaving today due to building steam problems.

Perhaps he shouldn’t have had those beans for lunch.

If we take any pride in our vocation (or society), we have to lend a hand in taking out the trash. The doing of science in this particular incarnation depends on faithful peer reviewing. Upholding habeus corpus is a mainstay of our legal system (I like to think, recent atrocities committed by US and UK governments notwithstanding). Both depend on citizens doing their bit for the social collective. Not only should we do it, we should do it to the best of our ability.

We owe it to the community.

Just under two years ago I gave a talk to my group about some work I’d been involved with in Cambridge (where I had just left). The things that people remembered from the talk are me ping ing a marble across the room by squeezing it between my fingers, and two piles of cocktail sticks, one broken into small pieces but the other ‘full length’, as it were.

The point of these rather daft analogies was to demonstrate how actin might generate protrusive force in amoeboid motility. The cocktail sticks (and you can do the same thing with spaghetti or different lengths of copper wire, as in the above picture) showed my audience, I hope, that anything long and thin takes up more volume than the same mass of shorter ‘filaments’ of that thing.

What this has to do with amoeboid motility, and actin polymerization, is described in a paper from a collaboration between my previous boss in Cambridge and Tom Roberts at Florida State University, that is now available from PNAS. There will also be a short note about this finding in J Cell Biol (and I have discovered that there is a distressing lack of cell biologists in this building, so I have no one to skite to about it) sometime in the next week or two.

Briefly,

elongating filaments [contribute to] protrusion by generating an expansion of the cytoskeleton gel.

It’s all to do with packing volumes and aspect ratios, and there is a cute movie in the Supporting Information demonstrating what we mean.

The story of the paper itself is an interesting one. We sent it, two years ago, to a couple of ‘top rank’ journals because we believe that if it is not a paradigm, it is at least a new way of thinking about force generation in crawling cells. Unfortunately our manuscripts were savaged by cell biologists who essentially did not understand the physics, or by physicists who did not understand the biology: twice we had an incredibly hostile report and a quite favourable one.

At that stage we were quite frustrated because we accepted that we might be wrong in our conclusions, but were concerned that people were not getting the chance to test the hypothesis. None of the reviewers, it seemed, had any reasonable grounds for rejecting the work (the experiments were sensible and were done well, for example); it was mere prejudice against our experimental model that was keeping it back.

All our work was done with something called major sperm protein . This simple molecule is only found in nematode worms, and it, not actin, powers their sperm’s amoeboid crawling. It looks like actin-based crawling, it has similar kinetics and is based on polymerization, but it is not actin. It is much simpler, does nothing else in the cell that might interfere with motility, and appears to require fewer accessory factors. After we (that is the groups in Tallahassee and Cambridge) had been working on this for about ten years, we really were concerned that the actin guys were going to beat us to it.

The reviewers from PNAS however were favourable, and we were able to address their points and get the manuscript accepted. Now it is up to the rest of the world to tear it apart — I’m off to the pub. And there is no truth at all to the rumour that I was hired to place undue influence on Tom Pollard.

(And my catchphrase — I yearn to learn how the worm sperm turns — is now obsolete. Time to find another.)

“These laser beams are now so powerful they can shine up to five kilometres.”

Well, no, actually. They are “so powerful” that they can shine for infinity. As can the least powerful laser, if there’s nothing in the way. I suppose, in a way, I should be grateful that the police journalists people are stupid about physics and not just biology.

(And don’t get me started on the “XXXX can be used for ill, therefore let’s ban it”-type idiocy. Grrr.)

I’ve just seen this paper abstract, posted on another forum.

The speed of sound was measured in solutions of sucrose (0-70 wt/vol%), glycerol (0-30 wt/vol%) and orange juice (0-40 solids wt/vol%) as a function of temperature (10 °C to -13 °C). The velocity ( c ) in the unfrozen solutions, including the supercooled samples, could be modeled as a simple linear function of temperature (T, °C) and composition (x, wt/vol%): c = c[w] plus k[x]x plus k[T]T where c[w] is the speed of sound in water at 0 °C, and k[x] and k[T] are solute-dependant constants. There was a large increase in ultrasonic velocity corresponding to freezing in these samples (e.g., an unfrozen 10% sucrose solution has a speed of sound of 1416 m s[-1] at -5 °C while a similar frozen solution has a velocity of 1983 m s[-1]). The ice content was estimated from phase diagrams of similar samples and was a linear function of the change in ultrasonic velocity upon freezing for samples <8 °C. Some details of the effects of ice microstructure and possible theoretical approaches to its effects on ultrasonic properties are also discussed.

The speed of sound in frozen orange juice? What?

3. Hold the scientific community accountable for how it responds to misuse of its name. Instead of blaming Myers and Dawkins for doing what they do best, exert moral pressure on the rest of science to be clearer about what is and isn’t a legitimate invocation of the authority of science. Christians, after all are rightly suspected of moral failure when/if they fail to condemn outrages perpetrated in their name. Why should this not be expected of scientists? And while no human can find the time to answer every summons to repudiate the idiocy of fellow travelers, the world has a right to ponder whether relative silence signals tacit approval.

We have some loud atheists who like to pretend that it is science, and not unbelief, that is in conflict with belief. Shall we silence them? OF COURSE NOT. We should thank them for getting some important questions into the public square, then we should make it quite clear that their efforts have little to do with science, and everything to do with their perfectly legitimate but completely religious convictions.

You really should read the rest of the post too.

In EMBO Reports (part of the Nature group, so I’m allowed to talk about it here) we may have part of an answer. A rather tedious analysis¹ claims that there are not enough sensory descriptors in scientific writing.

[S]cientific prose should be enriched with sensory words, provided that they clarify the meaning rather than obscure it, in much the same way as a good statistical data visualization involves the mapping of abstract data into colours and three-dimensional shapes, to help the reader or viewer discover meaningful patterns.

Green! Purple! Parmesan! Silken!

And then, Frank Gannon says in an editorial²

If scientists were to use a more personal and forthright style, it might not only be more readable, but it could also force scientists to take more responsibility for their results and interpretations

Or, put another way

“the possibility could be considered, taking into account various relevant factors, that a modest alteration in the mode of expression could, in due course and after a preliminary and statistically relevant trial period, be phased into the scientific discourse, such as an alteration focusing on the first person, but not exclusively, or a measured change from the passive to the active mode of writing.”

All this ties in rather nicely with my previous rant , Martin Fenner’s new group and Linda Cooper’s recently revitalized weblog .

So, troops, I want to see excitement in your prose. I want to see wild speculation (and referees, take note: But referees also discourage speculative thinking with such withering lines as: “the extrapolations in the discussion are not supported by the data presented.”²). I want to be thrilled by your research as I know you are.

I want to see sentences such as Our neural system is therefore an eclectic ensemble of disparate pieces of hardware, which are perfected for solving specialized problems, such as the detection of potentially threatening bilateral vertical symmetry¹ written in actual English.

I also want a pony, but I’m not going to be too greedy.

¹ Rodriguez-Esteban & Rzhetsky

² Gannon

Yesterday we found a white-tailed spider on level 6 and a female red-back spider on level 2. It is possible these spiders are seeking refuge from the redevelopment outside. Both these spiders can give nasty bites, especially the red-back which is potentially lethal (and, in my experience, where there are females, there are usually egg-sacks).

While we were able to catch the one on level 6, the one on level 2 escaped, so be aware. (Probably as good a reason as any to be wearing closed shoes.)

I’ll just let all you arachnophobes run away screaming, now.

“Yes, they’ve been over-Westernized—”

and my first thought was

“What did you do, leave it in primary antibody too long?”

I really, really, really need to get out of here.

When something unusual happens, perhaps like for example (completely at random) one’s weblog post at NN getting 20 comments, an ordinary person might say, or think, “Cool! Lots of traffic!”.

A scientist, on the other hand, is more likely to rub his beard and say
“Hmm, I can think of an experiment. . .”

(Image from xkcd )

A small group of thoughtful people could change the world. Indeed, it’s the only thing that ever has. —Margaret Mead

Having, in the last three days, edited a manuscript when I should have only been checking for tyops [sic, Henry, sic], and similarly for an interminable chapter 4 of a PhD thesis, I have come to the following conclusion:

There is something rotten in the state of Denmark.

What?

Sorry, wrong parallel universe. Let’s try that one again:

‘Scientific’ writing is doomed unless we start with the students.

Maxine Clarke recently pointed out that Nature journal editors encourage authors to use ‘direct, plain prose’. Linda Cooper has written some very good articles, sadly not updated since the middle of last year. There are guidelines in the Author Services section of NPG and an excellent editorial in Nature Physics.

But still, on Monday, I banged my head against the desk in an exquisite mélange of grief and hilarity, at the following:

Triple resonance experiments give rise to three-dimensional datasets that contain three frequency dimensions;

The problem is not with teaching post-docs and PIs how to write. The problem is that students are never taught how to write directly and clearly. Indeed, we encourage them to write stilted, impenetrable prose in the third person and passive voice, because that is considered scientific.

And it’s pants.

A friend pointed out to me yesterday, after I had raved somewhat immoderately about this, that I was in a privileged position. As (through hard graft and a little bit of natural talent) I am able to write, it is my duty and responsibility to assist those who have difficulty. She’s right, of course; but it is a huge task.

By the time you get to reading editorials in learned journals, it’s far too late. One post-doc can do a little bit in his own lab, under the authority of a sympathetic PI of course, but really, this needs to start at undergraduate level, and continue throughout a scientist’s training. Ultimately, we are in the business of communication.

And I am not entirely disinterested: I’ll just beckon nonchalantly at Private Investigations, Part 1 .

I happen to disagree with the philosophy that says that the methods of doing research should be published according to those same methods — not least because actually, most of the stuff I do is not double- (or even single-) blinded.

My own take on the matter is that refereeing should be totally nonymous: in other words, the journals should tell the authors to whom they are sending the article for review, and the reviewer’s names be published along with the paper.

That is complete transparency, and would possibly make reviewers take responsibility for their comments.

We have had a number of complaints regarding the Nature Register page. After some thorough investigation we are pleased to announce that the problems have now been rectified.

Please visit My Account http://www.nature.com/nams/svc/myaccount where you can view your account and make adjustments accordingly.

If you would like to register with nature.com please click here:
Register file:///C:\Documents%20and%20Settings
\r.raymond\My%20Documents\My%20Pictures

“Oops”.

With me? No?

The Honours students gave their proposal talks last week. A random panel of academics assessed and made written comments that were passed on to the students on Monday. The students in turn had their own comments about the talks and the feedback process.

• They feel rather humiliated if their supervisor ‘answers’ a question for them

This point is completely fair. If a supervisor feels the need to answer a question on behalf of a student, then (assuming the student hasn’t completely frozen) this betrays a lack of confidence in the student, or even the project itself (and I’m not going to expand on that here, he said, darkly).

It’s part of the training: the student must be able to fend for themself, and, ultimately, make mistakes and live with them.

• They feel embarrassed if academics start to ‘squabble’ with each other over issues raised in their presentation

This one is less clear-cut. Rightly or wrongly, academics in seminars will disagree with each other, vocally and at length, while the speaker stands there like a lemon. Often you will find that certain antagonists have hated each other for years, and their feud spills over into public fora.

My advice? Either stand there looking amused or say something like “Maybe you two can talk about this later?” Coming from a student, that would be surprisingly effective.

• They really appreciate it when academics write legibly

Fair cop, guv. In our defence I will say that when you have 7 or 8 talks per session, it’s dark, and there isn’t much room on the form, copperplate can go right out the window.

Besides, would you trust a doctor with legible handwriting?

When I started writing a weblog I made a conscious decision to avoid the cesspit of stupidity that is both sides of the evolution:creationist ‘debate’ (it’s not a debate if there are no cogent arguments). But this is too beautiful to pass up.

(Shamelessly taken from Science )

Florida scientists declared victory last week after the state Board of Education approved science standards that for the first time explicitly embrace the teaching of gravity. But antigravity activists are claiming that the vote bolsters their position that gravity is a “just a theory” and therefore unproven.

In lieu of gravity, the standards now refer to “the scientific theory of gravity.” State education officials say the new wording was intended to appease conservatives without compromising on accuracy. To be consistent, officials applied the same wording to every other scientific concept mentioned in the standards, for example, changing “evolution” to “the scientific theory of evolution.”

Harold Kroto believes the new language allows scientists and teachers to make a clear distinction between scientific and unscientific theories. “The original standards were fine, but this might actually be better in the long run,” he says. “The phrase ‘scientific theory’ gives us leverage to differentiate between theories that are supported by evidence and those that aren’t.” The simple addition of “theory” would have been disastrous, he adds.

“Theories that are not scientific may be discussed in a humanities or a comparative religion course,” says Mary Jane Tappen, director of the education department’s Office of Mathematics and Science. But the difference may not be clear to everyone, concedes FSU gravitational theorist Juliet Travis. “If somebody wants to say a particular religious idea is a scientific theory, that’s another issue.”

Hard-liners unhappy with the standards don’t intend to let the matter rest. In the Florida Baptist Witness, the speaker of the state House of Representatives said he and other House leaders are considering introducing legislation to allow teachers to teach criticisms of gravitational theory.

Impressive.

For a born-again structural biologist like myself, this looks like an invaluable research and teaching aid. I shall follow its career with interest.

(via Peter MR , who reminds me what great fun BioMOO was, back in the day)

The post I wanted to write is at
http://blogs.usyd.edu.au/labrats/2008/03/on_randomization_monte_carlo_a_1.html

It describes how I took a Perl implementation of the Fisher-Yates shuffle and made it work for scalars, where the scalars in question are chromosomes.

When are Nature Network going to implement real HTML?

These talks are open to the entire Department, and people are encouraged to go along to see what everyone else is doing, as well as to support their own students. (I actually skipped our students’ talks; not just because their session was at an awkward time and I would have had to catch the cattle train, but also because if I am forced to listen to another LIM domain talk I might actually go quite Dagenham). A rolling panel of post-docs and academics assess these talks; comments are made on forms that subsequently disappear into Gareth’s office and — oh, I don’t know — get made into papier mâché models of Ayers Rock or something.

I was roped in to the assessment panel — I don’t really mind doing it, if only because it gives me a reason to stay awake — for two sessions (thirteen talks) on Thursday. This meant I got to sleep with my head on a desk on the front row of the audience while the plebs crowded in behind.

So, joking aside, I was doodling on my notepad at the end of one talk, desperately trying to think of something sensible to ask about UV-induced cell damage, when Prof C to my left queried the student’s proposed method of detecting apoptosis. Specifically, how was she going to distinguish ‘programmed cell death’ from necrosis? The student replied that she was going to use the DNA analysis method she had already described, but Prof C insisted that she would not be able to tell if it she was detecting apoptosis or merely necrosis.

This could have led to something of an impasse, but Prof C took pity and said, “What about caspases ?”

To which the student replied,

“Oh, do a Western?” as if someone had suggested she eat her own grandmother, “We could look at caspase 3 and nine, but that takes a long time and we’ve got kits to do the DNA assay.”

“Kits?” I said, somewhat more loudly than I had intended, “We’ve got news for you, sunshine,” which corpsed certain less ‘serious’ members of the assessment panel as well as not a few plebs behind me.

I can see we are going to have to invest in re-education this semester.

Is the answer to the ageless question “What does it mean?” precisely “Nothing”?

At least for this particular splicing factor, anyway. Damn, but I wish I had a simple project sometimes.

I don’t care what it does, I just love the name.

Back in Cambridge we used to have about 8 solid days’ worth of music in iTunes, as well as access to everyone else’s shared music and a (rather crappy, admittedly) radio. We had a lot to choose from, and the only fights occurred when a certain grad student got in early and played nothing but Coldplay and The Whitlams. I still shudder when I hear certain intro riffs. Oh, and when Trevor brought in jazz CDs. Ugh.

Here, music is banned from the main lab area and the offices. I have no problem with that; it does solve all sorts of arguments, even if sometimes you feel the need for Paint it Black when the RT-PCR fails yet again. We have a (clockwork!) radio in the gel room, which provides background hum (but the state of Sydney’s radio stations is abysmal, even if some of the adverts crack me up).

This does mean that people tend to wear iPods a lot. I know that some consider this to be antisocial and insular, but I’ve never really been bothered by this. Having received an iPod for Christmas, I’ve been able to appreciate the privacy that it gives you, and I wonder if there is a generally accepted etiquette for wearing them.

Let me explain. It’s probably obvious that a cove sitting in front of a culture hood is wearing an iPod because it’s better than the droning of the fans and putputputput of the suction. This means it is all right to talk to him, although don’t expect him to take an earbud out to listen to you (because his hands are aseptic).

I suspect that if someone is working at a bench in the wet lab then you have to look at how many earbuds are being worn. One means “Yup, I’m listening”. Two probably means “Do not disturb: I’ve already made a mistake setting up this PCR and if you talk I shall ignore you. If you persist, I shall stab you with my Gilson”. Whether the hands are gloved or not might have some bearing on the situation.

Of course, if someone is bopping along and singing “She never drinks the water and makes you order French Champagne” they’re fair game and you are allowed, indeed obliged, to interrupt before it’s too late.

In an office, someone with both earbuds in is also probably trying to concentrate and does not want to be disturbed, unless it is really urgent. Try sending him an email instead. Either that or he’s trying to drown out the power drill that’s been going outside the window all bloody morning.

Much of the time, scientists are to blame. Many scientists can not write clearly or succinctly, many can in their native tongue but not in English, and I suspect that the vast majority struggle of time-poor scientists with word limits (q.v. Pascal and others ).

And the copyeditors have to wade through the treacle of clumsy prose, malapropisms and mis-placed apostrophe’s, all to a strict deadline. It is evitable that mistakes will be made. There are dozens of manuscripts to process, proofmarks to decipher and screaming editors to placate. At this stage of the scientific process the content, the conclusions and the implications of the current work on the screen are irrelevant.

But from the point of view of the author, the scientist(s) who produced the paper, at this instant this paper is the most important thing in their life. It is the culmination of maybe three years’ work. On it depends grants, contract renewals, tenure, livelihood. It is inevitable that perfection is demanded.

To an editor, it may appear that this manuscript has been dashed off in an afternoon.

We know that is not true: it has been written and re-written numerous times. Words, lines, paragraphs have been typed, re-arranged, substituted, deleted, re-typed and shoe-horned into a seemingly draconian character restriction. Weeks have been spent on one sentence, as the manuscript crosses the Atlantic a dozen times, where each word serves a specific purpose, to deliver a precise meaning. And then it has faced the ennui of an Editor, and the wrath of hostile reviewers; it has returned for more crafting; a paragraph is lost here, and two new ones go there, this figure is enlarged at the expense of a table.

In the proofs, or if we’re really unlucky after the proofs have been sent back, one word gets changed, a comma is deleted or added, and that sentence fails to convey the precise sense the author intended. A figure is reduced so much it makes no sense, or is buried after the Materials and Methods section. And the author’s peers collar him at the next conference and demand to know what the hell he was thinking when he wrote that?

My latest JMB paper went online early December, but remained as a ‘corrected proof’ for nearly three months because the figures were all in the Materials and Methods section; four pages of dense text before a single figure, all following the results they illustrate. That makes Mike’s “Plant Homeodomain Fellowship” look positively cheery.

When I cock up an experiment, and have to repeat it, it’s a bloody pain. But I’ll do it, because it has to be right, and I (and my boss, and the reviewers) expect nothing less. If it’s not technically correct, then I do it again.

Scientists get very protective of their papers, with good reason. They are the currency of research, and we want, we need them to be perfect. Which is why sometimes, maybe, we’re not entirely rational about them.

You won’t have much luck obtaining a ‘Plant Homeodomain Fellowship’: the first author tells me that he decoded the abbreviation ‘PHD’ at the proof stage, but an over-zealous copy editor thought it also applied to ‘PhD’.

Bloody amateurs. What do they teach these people?

And they got better sandwiches at their induction than we ever do. Humph.

Alethea writes about the latest in personalized gene self-therapy, that wouldn’t be so bad, except . . . it’s self-healing . In the same way that Wikipedia is self-healing.

I’m going to hide in the cell room, and cry quietly into my media.

With a little effort, sandwiches can maintain their position as the lunch of choice for the postdoc on the go.

Guess who makes the lunches in our house?

Mico is scathing about ScientificMatch.com,

ScientificMatch.com—The Science of Love
A premier dating service that matches you by physical chemistry and mental harmony.

(I haven’t linked because the site appears to be down).

ScientificMatch looks harmless enough (if preying on the moronic classifies as ‘harmless’), and I have ranted previously about similar things. What is more worrying, to me at least, is places like this :

1. For only $985, we scan over one million variants in your genome
2. Calculate genetic risk for 18 diseases based on the current literature
3. Find out where your ancestors came from
4. Invite friends and family, compare your genomes
5. Get regular updates on future discoveries and a growing list of diseases and traits

(Hat tip )They say

For a low introductory price of $985, you can order a Genetic Scan of over one million variants across the genome. 2-4 weeks after we receive your sample you will have access to your personal genetic profile.

Is it just me, or is anyone else’s spider tense having a catatonic fit?

Then I checked some of the publications and realized that they are these guys , who essentially patented the entire Icelandic gene pool. Quite apart from the begged question of how well the Icelandic data maps onto less homogenous populations, there are a lot of ethical issues at stake.

Not least the one of how the directors of Hoffmann-La Roche will get very rich selling the drugs to treat whatever it is that deCODE tells you is wrong. . .

Not to be outdone by their father’s success (that, in case it wasn’t clear, talks about a paper I’ve just had accepted), the Pawns have been up for end of year (it’s Australia; we Do Things Differently here) awards at school.

The Elder Pawn (end of Year 5) was awarded an academic award for ‘Overall Excellence in English’, and the word on the street is that if the students at that school were not limited to one award each, she’d also have scored the OE in Music one. The Younger Pawn (end of year 2, i.e. 8 years old) got the ‘Overall Excellence in Science and Technology’ award. They both get nice certificates.

How’s that for a well-balanced family? We’re well chuffed with them.

Wikipedia has introduced a system of peer review, as if this solves anything. The problem is with the word ‘peer’. If articles were guaranteed to be edited by people who know what they’re talking about, then it would be fine. But you have no such guarantee, and in esoteric subjects (much of science, for example cough) you can not be sure that another student (a ‘peer’), for example, is not deliberately falsifying entries to steal a march on the competition. Paranoid, moi?

You betcha.

As my friend Mark puts it :

I am not in favour of citing Wikipedia as an “authority”, if by this we mean using it as a means of establishing points without any further discussion. I encourage my students, who are preparing for examinations at the moment, to engage critically with a range of secondary sources, one of which may indeed sometimes be Wikipedia.

And of course, with access to a University library, there is no excuse for not critically reviewing the primary literature, and doing your own fact-checking.

I’m all excited because my paper came out, and I’m all set up to do not one, but two cutting and incisive experiments, and go into the lab on Saturday to look after the stem cells, and I find that my HEKs are clumping together.

Bah. Low grade bacterial infection. Go back on Sunday to check the split from backup, and yes, it’s still there.

If you are not a cell culturist you have no idea how depressing this is.

Today I need to remake all my media and thaw some frozen cells, so I can do these experiments. Good job we’re not going away over Christmas.

For years the textbooks have viewed this process in three, discrete steps:

1. Transcription (DNA -> pre-mRNA) ref¹
2. Processing (pre-mRNA is capped, spliced, tailed and exported from the nucleus)
3. Translation (RNA -> protein)

Although we have long believed that these events happen almost simultaneously to any given ‘message’ in bacteria, the confounding presence of the nucleus has led us to believe that the same steps in real cells are spatially and temporally distinct. It turns out that this view is untenable.

Not only do bacteria have a nucleoid, the structure of which can influence gene expression in much the same way as eukaryotic chromatin, but the process of transcription-processing-translation in eukaryotes is much more coordinated than was once thought. Capping and splicing seem to be simultaneous with transcription, and export from the nucleus is similarly coupled to transcription and splicing.

Naturally, you only want your ribosomes to see to capped, spliced and polyA-tailed mesenger RNA, which then must be prevented from returning to the nucleus (see Ratcheting mRNA out of the Nucleus by Murray Stewart, and references therein). But how to do this?

The first thing you can do is let everything out of the nucleus, look for stuff that hasn’t been correctly spliced &c. and destroy it. A more efficient method, and the one that the cell seems to favour, is to stop incorrectly (or incompletely) processed RNA from getting exported in the first place:

There is a nuclear pore-associated protein called Mlp1 that retains intron-containing RNA, i.e. unprocessed mRNA, at the nuclear pore. This binds to something called Nab2, that in turns binds RNA itself and the mRNA export factor Gfd1 .

Nab2 is potentially a marker for ‘mature’ (processed and export-ready) mRNA. It has a compact N-terminal domain (i.e., at the start of the protein sequence) that despite looking like a well-characterized RNA-binding domain actually is necessary and sufficient for binding to Mlp1.

By using my NMR structure (left) as a starting point for molecular replacement, Murray was able to solve the phase problem for the 1.8Å dataset obtained from crystals of it. Furthermore, a single mutation in the middle of the domain, that did not negate its binding to Gfd1, completely knackers binding to Mlp1 (much thanks to the yeast people in Atlanta).

So know we have another little piece of the RNA export puzzle. You can read all about it (and what the reviewer said ).

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.

It used to work quite well (as long as we weren’t actually working together), and now, after several years working at different places, we’re back under the same roof. Gratifyingly, we have been able to collaborate on a piece of work and still talk to each other in the evenings. I’ll publish the results from this collaboration when we have them (and no, we’re not pregnant).

Related to this, FSP has some tips for couples being interviewed for faculty positions:

Don’t tell cute stories about each other, including revealing affectionate nicknames and embarrassing childhood episodes. Professors, especially those on search committees, prefer not to know any of this until after an interviewee becomes an actual colleague. Then we definitely want to know.

and I suspect that the ‘two jobs for the price of one’ imperative is actually rather common.

Do people here have experiences of 2-job hunting they’d like to share? Is your partner/spouse in the same trade, and if not, does it make things easier or more difficult? What are your experiences of finding jobs for you both in another country? (Our own experience was perhaps unusual.) Did your interviewing institute reimburse two travel claims? Arrange for childcare?

And what about other professions entirely? The cynic in me says that non-academic professions actually pay a living wage so that both halves of a couple don’t actually have to work, but that’s possibly unhelpful.

Ethidium bromide (EtBr), for the non mol-biologists among us, is used to stain nucleic acid so that we can actually see it in