Scooped

Being scooped is every researcher’s worst nightmare.
It happened to me, once; less than three days before submitting my first paper from my postdoctoral lab, I spotted a new paper in press at my target journal, with substantially overlapping conclusions. Luckily I was so close to publication myself that there could be no doubt the work was independent – and there were some conclusions that were unique to my paper. This meant that we did still get the paper published (in a different journal), but not without some very stressful times. One of my labmates was not so lucky a year later; he was completely scooped (by a different lab to the one that got me), and didn’t get a chance to even submit his paper.
So my heart goes out to Professor Laura Bierut at Washington University in St. Louis, the victim of a scoop that made the news section of Science this week.
For those of you who don’t have access to the original article, the story is that Professor Bierut had contributed data to a shared database. The federally funded project had a publication embargo in place, so that while other researchers could access and analyse the data, the contributors would get the first shot at publication. However, a researcher at a different institute breached the terms of this agreement, and submitted a paper based on Professor Bierut’s data a full six months before the embargo was due to expire.
The offending paper has since been retracted, but it can’t be unpublished, and it remains available in the journal’s online archives. The NIH are investigating, and have frozen the other researcher’s access to the shared database until their review is complete.
There have been some discussions of data sharing around these parts recently (see Bob’s recent post for an example). There is obviously a great reluctance that needs to be overcome before free and open data sharing becomes widespread, and incidents like this one (even if unintentional) represent a major obstacle.
So, assuming that data sharing is A Good Thing, who should shoulder the responsiblity of protecting the people who generate the data?

  • The goverment and its funding bodies? Well, it seems as if they tried in this case.
  • The journals? Can they really be expected to vet every single submission to ensure that no embargoes were breached?

A better system for removing retracted papers from the literature might help, but what’s the point of treating the symptoms?
My feeling is that researchers will be keeping their cards close to their chests for the forseeable future.

Posted in Uncategorized | 25 Comments

Data Ducks?

Here’s a gem from the Microsoft Word Thesaurus:

No, I didn’t accidentally insert a space there; I actually clicked a link from the entry for “data”. And this was all that popped up.

I’m sure there’s a joke in there somewhere. Maybe about getting your ducks in a row before using a thesaurus.

Posted in English language, silliness, technology | 3 Comments

BRING IT ON!!!!!

The pre-season Flames tickets are part of my birthday gift to Mr E
Man; he’ll probably take his BFF. But I’m going to the Blues game for
sure!

Posted in photos, sport | 10 Comments

Tuesday pet peeve: the wrong kinds of ignorance

(This post could potentially get me into trouble at work – a rarity on this blog! I therefore wrote it without using any of the keywords that might cause the people involved to find it on Google. My apologies if this makes it unclear).

I have no problem with good old-fashioned, honest ignorance – as long as it comes served with healthy portions of a) awareness of said ignorance and b) willingness to own up to and address the knowledge deficit.

But then there are the other kinds of ignorance:

“I already know how to do this. I don’t need to pay attention to these instructions”.

“I don’t know how to do this, but I’d better not tell anyone – they might be mad at me. I’ll just guess”.

and, of course, “I don’t know, and I don’t care”.

I’ve encountered examples of all four recently. Not from my immediate colleagues, but from people who work for various collaborators at different sites across the country. Here’s how the story unfolded…

What I needed, Part I:

A PDF from each person, generated by Website 1 in a way that attaches metadata (necessary for recognition by and and upload to Website 2).

What I got, Part I:

1) One email saying “I’m sorry, I have no idea how to do this”.

2) One PDF that had been printed out and then scanned back in, rather than just saved (i.e. no metadata).

3) One scanned print-out of various pages from Website 1 (i.e. not only was there no metadata, but half the information was missing).

4) A couple of actual correct PDFs, with metadata.

How I responded, Part I:

1) “No problem, call me and I’ll walk you through it”.

2) “Grrrrrrr”.

3) “Grrrrrrrrrrrrrrrrrrrr. Are you fucking kidding me??!!”

4) Grateful weeping.

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What I needed, Part II:

A Word document from each person, with the required sections in the correct order, and following various formatting guidelines I’d provided by email.

What I got, Part II:

A Word document from each person, with some or all of the required sections in more or less the right order. Each one followed a subset of the formatting guidelines, with a unique combination in each document.

How I responded, Part II:

“Am I on TV? Where did you guys hide the camera?”

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What I needed, Part III:

Corrections to the above.

What I got, Part III:

A few apologies, and a couple of doses of attitude along the lines of “I don’t have time for endless revisions”.

How I responded, Part III:

“Fuck this for a game of soldiers, I’ll just do it myself”.

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What I needed, Part IV:

A signature from each person’s boss.

What I got, Part IV:

All the required signatures. BUT three people neglected to put my name on the courier envelope*. Hundreds of people work in my building. Our mailroom guys are not allowed to open unaddressed mail.

How I responded, Part IV:

By spending an hour in the mail room, sorting through all the piles and piles of unaddressed mail, and swearing and complaining to the mailroom guys, who fortunately were hilarious and awesome.

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Look.

If I ask you to do something, and you don’t know how, just tell me. I will help you. I didn’t know how to to this stuff when I started, either (no-one does – it’s not exactly the most intuitive system in the world). So I asked people who did know, and they helped me. And I kept the instructions. And now I know how to do it, and how to help you.

If you frustrate me enough with your incompetence and learned helplessness that I end up doing it myself, well, at least the damn thing gets done. But you don’t learn a thing, and I’ll no doubt see you for Round Two next year.

A plague of clowns upon the wilfully ignorant! And not the good kind, the annoying and/or creepy kind!

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*Yes, this is technially incompetence rather than ignorance. But I really need to vent about it anyway.

Posted in career, grant wrangling, plagues, rants | 6 Comments

Fun with lasers

This video popped up on the Best of YouTube podcast. The developers describe the system as follows:
a prototype musical instrument capable of generating sound in real time from the lines of doodles as well as from the contours of three-dimensional objects nearby (hands, dancer's silhouette, architectural details, etc). There is no camera nor projector: a laser spot explores the shape as a pick-up head would search for sound over the surface of a vinyl record - with the significant difference that the groove is generated by the contours of the drawing itself.

I don’t pretend to understand the underlying technology – I just know that
a) The “music” needs some work.
b) I want one anyway.
c) So do my cats.

Posted in Uncategorized | 4 Comments

Remember the world’s worst courtroom sketches?

I think the artist is now doing the Victoria police’s composite sketches:

Posted in silliness | 8 Comments

Friday night horror

I saw this freak of nature on PZ Myers’ Pharyngula blog, and since I don’t want to be the only person with nightmares, I thought I’d share the photo.
(beyond the jump so as to protect the squeamish)

Continue reading

Posted in Uncategorized | 11 Comments

Disorient express

The Canada Line, the latest addition to Vancouver’s SkyTrain rapid transit system, has been up and running for a couple of weeks now*. It connects downtown to the airport, and my favourite bus route to a station one block from my work. Given that I usually only take transit in atrocious weather, I’ll be very happy to transfer to the SkyTrain part way to work and avoid the extra five blocks walk from the bus stop down a treacherous icy hill.

This week has been an exception to the weather rule; I rode my bike in the torrential rain on Tuesday and Wednesday, but took the bus and SkyTrain yesterday and today, in blazing sunshine (I’m saving my legs for a planned assault on the Grouse Grind tomorrow). The crowds of confused people around the ticket machines and TransLink employees seemed to suggest that a lot of people are using the Canada Line (and the SkyTrain in general) for the first time this week – and an encounter this morning confirmed my suspicion.

I got off the bus and descended into the station, and was halfway down the stairs just as a train arrived at the closest platform. Three or four of us, including a woman with a small suitcase, made a run for it and bolted through the doors just as they closed.

As the train moved off, the woman turned to me and said, “which way is this train going?”

“Erm, downtown”, I replied.

“Oh… I’m heading to the airport. It’s my first time on this thing. Guess I’ll be getting off and turning around at the next station…”

I hope she didn’t get on the very first plane she saw at the airport.

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*On budget and three months ahead of schedule. Now that the schools are back in session it’s busy, but not overcrowded. An unqualified success. BITE ME, NIMBYS.

Posted in silliness, travel, Vancouver | 14 Comments

The ties that bind

This BBC article about school tie styles brought back lots of memories!

Many British schools are apparently introducing clip-on ties in order to force their students into monotonous conformity “ensure consistency” and “provide an atmosphere of discipline”. I think this is a terrible shame; while I agree with the underlying reasons for school uniforms (principally to minimise bullying due to discrepancies in how much parents can afford to spend on branded clothing), there is a proud British schoolkid tradition of subverting uniform codes to rebel against authority and express individuality, and diverse tie styles are a large part of that.

The BBC says “No-one can be precisely sure when the process started – it may even have been decades ago – but it’s clear that it’s reached crisis point.” Decades ago sounds about right to me!

My primary school didn’t have a uniform while I was there, and it was only when we moved up to secondary school that we had to learn to tie a proper tie knot. Our uniform consisted of black shoes (not trainers/sneakers), white socks, a navy blue skirt or trousers*, white or pale blue shirt or blouse, navy blue cardigan or V-neck sweater – and a navy blue tie with thin yellow diagonal stripes.

The official uniform code didn’t mention shoelaces, and so we expressed ourselves chiefly through that medium. I remember having tartan and then fluorescent laces, while one of my male friends had laces printed with “left” and “right” (and insisted on wearing them on the wrong feet). Our shoes sported a veritable rainbow of individuality.

The official code also neglected to specify tie style, other than saying we had to have our top button done up and the tie knotted just below it. I turned up on my first day, age 11, sporting the traditional tie style that my Dad had taught me and that I’d spent hours perfecting. Only the first-years without older siblings were wearing our ties in this “kipper” style, which immediately marked us out as targets for ridicule.

On the second day, I tied my tie back-to-front, with the narrow part in front and worn long enough to tuck into the waist band of my skirt, and the wide part tucked inside the shirt – just the way the older kids did. My parents both protested, so I retied it the “proper” way – and promptly switched back as soon as I left the house. I wore my tie in this way most days for the next five years, occasionally experimenting with the 1-inch-long-narrow-tie that was the most popular alternative. A few of my friends went for the 2-inch-long-super-wide-tie look, and even unpicked the tie’s seams and spread the edges out to get it even wider. (This was, of course, an “ironic” response to the narrow ties of most of their peers). Some of the stricter teachers would make us fix our ties at the start of their classes, but as soon as the bell rang, the styles would magically revert…

Sixth-formers (those of us who stayed on for the optional final two years, from age 16-18) didn’t have to wear the uniform. And the school ditched the ties not long after I left, anyway, and switched to a more modern trousers-polo shirt-sweatshirt combo instead. Most kids were pretty happy with the change, but – and here’s the important thing – they continued to rebel through the medium of shoelaces.

As the BBC article says, “there will just be other ways to rebel.”

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*For my first couple of years at the school, girls were only allowed to wear trousers from November to March. This unpopular restriction was finally overturned when we got our first ever female Muslim classmate.

Posted in education, silliness, UK | 14 Comments

Over the moon about collaboratinos

Another day, another science typo: this time, I emailed a colleague to ask for a “letter of collaboratino”.
(Well, I almost did – previous experience caused me to activate Outlook’s “always check spelling before sending” option long, long ago).
I wonder what a collaboratino might look like. Clearly, it’s a subatomic particle that facilitates interactions between larger entities. But is it involved with weak or strong forces? Is it ever possible to simultaneously measure both its motivation and its benefits? How much spin is involved?
What I do know is that when a collaboratino meets an anti-collaboratino, the effects are sure to be more devastating than Dan Brown could ever imagine.
And what adjectives might one use to describe a collaboratino?
Drafting another letter for a different project, I started with the suggested phrase “I am delighted to collaborate with you on your grant application titled ‘really important science'”. It is indicative of the importance of measuring collaboratino spin that the word “delighted” cropped up again in the next paragraph. Unable to come up with an appropriate synonym on the spot, I hit shift-F7 for suggestions – but didn’t think that “charmed”, “enchanted”, “thrilled”, “elated”, or indeed “overjoyed” were quite suitable.
I was pleased to finish that draft and send it off for long-distance approval; a quantum of solace in a frantic and over-caffeinated week.

Posted in Uncategorized | 20 Comments