On the Journal with No Name

There was a little bit of kerfuffle a week or two ago. Apparently some rather well-respected institutions (and the Max Planck Institute) decided to announce they were thinking of launching a journal. Maybe. In a year’s time. With no editor-in-chief and no business plan.

But! This is going to be the best journal ever! And you won’t need to pay to submit! Or read it! And you’ll never have to do a reviewer’s experiment again! and did we say it is going to be top tier?!

Anyway, thanks to a conversation at the day job today with one of my cow-orkers, I think I see where this is heading. Mark Walport, head honcho at the Wellcome Trust (about whom I have only good things to say, by the way), hath decreed that the aforementioned WT shall fund only the best research.

And obviously this new Journal with No Name will publish only the best research.

Which means that Wellcome-funded researchers will publish in this journal, and this journal only—obviously, because this is the best journal, and they are the best researchers.

In this way, the Wellcome stops paying researchers to publish in lesser open impact journals (which it does as a matter of course, and must cost an absolute stink), and instead saves that money by allowing, nay encouraging these excellent researchers to publish in the Wellcome’s own journal, for free. Because they are doing the best science, and this is going to be the best journal. And of course, not needing to do extra pesky experiments means they have time to publish even more papers, making the Journal with No Name even better!

What could possibly go wrong?

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Big angry macrophage

Those of you who know anything about British popular culture will no doubt be familiar with Benny Hill. The Benny Hill Show was long-running and immensely popular—although it was often accused of being sexist, it was the men who were usually shown up to be idiots (admittedly in the presence of scantily clad females). Very intelligent and witty, the show’s trademark finish was a chase scene, to the tune “Yakety Sax”.

David Rogers, who died two years after Benny Hill, was a scientist and physician, interested in infectious diseases and medical education. He made a famous video of a big angry macrophage neutrophil chasing down and engulfing a Staph aureus bacterium.

Here, in honour of them both and all things Friday (and because I’m going on holiday now), is something that I hope amuses you. Watch out for the twist.

Posted in Science, Video | Tagged , , , , | 3 Comments

On the hairy nature of light—redux

A while ago I reported on an experiment. Using my laser beam I demonstrated the wave nature of light, by measuring its diffraction. One of the referees, for reasons of poetry, wanted to see the experiment repeated with a different wavelength laser.

So, like a good little peer-reviewed scientist I toddled off and repeated the experiment with a red laser beam that very evening. And here, finally, are the results. No surprises: the red laser was refracted more than the green one. About 20% more, which is what I’d have predicted given the difference in rated wavelengths.

But here are the pictures, and the maths. The working for the green laser is given in my earlier post.

First, here’s the experimental set up:

Laser with flash

Note the high-tech use of a peg and Scotch Tape to hold the hair (human, brunette) in place. There’s also a slightly fuzzy photo, taken under ambient light (one of those dreadful energy-saving bulbs) in which you can see the beam itself thanks to Rayleigh scattering and the dust in the spare room.

Green laser, ruler
Measuring the green laser

For the red laser, I had to turn off the lights (it only being rated at 1 mW); I also bounced it off a mirror to give me a longer path length and therefore a better node measurement.

Red laser, wall

Using this method, I measured the third maximum at 13 cm from the central spot. I measured the path length at 6.75 m. Given

nλ = xd/L
where

n = # of maximum
x = distance of maximum
d = slit distance (i.e. the hair width–approximately 100 microns)
L = length of beam

then

nλ = (0.13 m 100 x 10-6 m) / 6.75 m

so

λ = (1.9259 x 10-6 m) / 3

therefore the wavelength is 642 nm.

QE, as they say, D.

Green laser, mirror & path

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Another one

Moth

This is a classic.

Posted in Science-less Sunday | Tagged | 3 Comments

Flutterby

Identify this.

Flutterby

Posted in Science-less Sunday | Tagged | 6 Comments

Apocalypse Penguin

Number five.

Apocalypse Penguin

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The Chain

Listen to the wind blow, watch the sun rise

At this time of night, if the lights on the Addenbrookes roundabout are kind to me—and they usually are, because the sensors pick me up as I approach—three minutes and two seconds after putting the car into first gear I’m turning off the Babraham Road.

It was the last full week before Christmas. I’d come back to the lab after dinner—cycling home in the dark, and then coming back in the car. We’d had the referee reports back, and I had to do some more NMR titrations, this time on the 800 MHz machine. This meant getting a sample to Ji-Chun in the morning, which meant desalting it overnight, which in turn meant picking the right tubes from off the S-100 column and getting them all into the Centriprep before I went to bed.

Listen to the wind blow, down comes the night

I change down from fourth to second, easing the clutch back in and letting the engine brake into the turn, half an empty mile of straight country lane rising gently in front of me.

Blinking back the itch behind my eyeballs I emptied the last 8 ml aliquot into the Centriprep. I’d been concentrating the protein, ten millilitres at a time, for the last couple of hours. One more fifteen minute spin, and I could fill it to the brim with deionized water; in the morning I’d have a protein that was so concentrated it was almost solid. I’d then be able to dilute it in phosphate buffer at pH 6, and add heavy water for field frequency lock.

Damn the dark, damn the light

It’s best doing this at night, as I can see headlights a mile off, well beyond the rapidly approaching horizon. Even cyclists and pedestrians show up as I flip on the main beam. I plant my right foot to the floor as the bass line kicks in.

I closed the lid of the refrigerated centrifuge, set the speed to 500 rpm and pressed start. I washed my hands in the tiny sink, dried them and turned the lights off as I closed the door to the lab behind me. Downstairs in the harshly lit loading bay car park, I turned the ignition, looked over my shoulder and—

Crunch.

Swinging out, my front nearside bumper had scraped the wing of the sporty yellow Toyota parked next to me. There were still some lights on upstairs, but I had no idea whose car it was. I parked the car and went back into the building to find a pen and paper. This is what insurance is for, after all.

Run into the shadows

On a clear night like this I’m doing a good 80 as I approach the bend at the top of Granham’s Road, Lindsey Buckingham’s guitar screaming to the redline. I slip into neutral and crest the ridge, the wheel going slack in my hands as the tyres lose their grip. Then I coast down to the level crossing, only touching the brakes as I approach the 30 limit, safe on the other side of the hill.

Posted in Lab ratting, War stories | Tagged , , , , , | 4 Comments

I won’t apologize

But I have every sympathy with John Rennie.

Read it, please. And forgive me.

Posted in meta | Tagged | 7 Comments

Darth Penguin

Darth Penguin

There are no words.

Posted in Penguins | Tagged | 2 Comments

On peer review, part 451 (b)

I had a conversation on twitter last night with m’learned friend Nige, who runs the most ethical small business I know of.

He pointed me at this blog post by Richard Smith at the BMJ, What is post publication peer review?.

You know, there are days when I wish I hadn’t used the phrase ‘post-publication peer review’ to describe what F1000 does. It’s inevitably misunderstood. Post-publication peer review, as I intended the phrase, is not and never could be a replacement for peer review ‘proper’ (if you like). What F1000 does is look at papers after they’ve been published and say “Hey guys (and gals), this one’s worth reading. Here’s what it purports to say,” dot dot dot.

Peer review ‘proper’ (if you like) says “Yeah, they did the right stuff here, but there are a couple more experiments they should do to be sure,” or something like that. And if you’re reviewing for a glamour mag, you might also get a comment along the lines of “ARE THEY OUT OF THEIR TINY LITTLE MINDS?” or similar. That, especially the first part (whether the experiments were done right, the controls are appropriate, the relevant literature has been reviewed and cetera, &c., etc.) is not going to happen ‘post-publication’. No way, no how, not ever, uh-uh, over Karl Popper’s dead body [check that Popper is dead—Ed.].

You see, the thing is, the real, incontrovertible and indisputable thing is about science, is that it’s all provisional. (Henry has made this point somewhat forcibly several times in the past, most famously by asserting “Everything Nature publishes is wrong”.) Findings reported in papers only ever become less provisional when somebody repeats the experiment in a different lab and gets the same (or similar) results. (Nige and I discussed clinical trials briefly, which is where the ethics thing came up, but even there you should be able to decide on what’s ‘true’ through meta-analyses and Cochrane Reviews and whatnot.)

Reproducibility.

That, and only that, is true post-publication peer review.

Not chatting about a paper on blogs or in Nature; not commenting on a manuscript thrown up on a pre-print server; not talking about posters; not even F1000.

So, please, can we drop all this nonsense about doing away with peer review (‘proper’—if you like)? It’s not big, and it’s not clever.

Posted in Literature, Nonsense, The stupid, it burns | Tagged , | 14 Comments