Tuesday, 15 December 2009

ants in the sugar-bowl

In her brave, honest and funny book, The Wisdom of Whores, Elizabeth Pisani kicks a lot of asses and sacrifices quite a few sacred cows “on the untidy altar of Reality”. First-hand facts and elementary maths are there to expose myths such as that AIDS is necessarily “a development problem”. Or that “more premarital sex translates into more HIV”. The myths that cost billions of dollars. And human lives.

Sunday, 13 December 2009

more weasel words

From the Weasel Words Website by Don Watson:
To exchange business cards, glances etc. Have a drink, take tea, dine with. Do what’s necessary. (More if it’s agreeable.)

‘2.50pm. Coffee and Networking.’ — Governance seminar brochure.

‘I networked my arse off.’ — Participant in governance seminar.

(Watson’s Dictionary of Weasel Words, Contemporary Clichés, Cant & Management Jargon, page 222)
Right, that’s what bosses do on conferences etc. “Do what’s necessary.”

When I will be a boss (which is an euphemism for “never”), I’ll make it mandatory to play buzzword bingo during meetings and seminars. Including external seminars. That will keep ’em awake.

time (at this point in)
Now, then, before, earlier, later, next Wednesday, at the end of the day, etc.

‘But at the end of the day we have to say it is not appropriate at this point in time.’ (after
Alexander Downer); cf. ‘The whole life of man is but a point in time...’ (Plutarch)

‘At this point in time I lay me down to sleep.’

‘On a day like today,
We passed the points of time away.’

‘Excuse me, can you tell me the point in time?’

(Watson’s Dictionary of Weasel Words, Contemporary Clichés, Cant & Management Jargon, page 324)

Sunday, 6 December 2009

the fate of gurus

From The Ape and the Sushi Master by Frans de Waal:
Instead of marching onward with perfect vision, science stumbles along behind leaders who occasionally take the wrong alley, after which it turns to other leaders who seem to know the way, then corrects itself again, until sufficient progress is made for the next generation to either thrust aside or build upon. In hindsight, the path taken may look straight, running from ignorance to profound insight, but only because our memory for dead ends is so much worse than that of a rat in the maze.
Not surprisingly, leaders are treated with ambivalence. With the exception of those who have come up with absolutely invaluable insights, such as Einstein and Darwin, leaders first inspire and stimulate, then guide and protect their followers, but usually end up stifling further progress. They become major obstacles: the dinosaurs of fields that they themselves helped create. Hence the ugly practices in which a number of upstarts revolt and get rid of old guru. They never do so literally, of course, but instead wield the academic version of the long knife, such as disparaging jokes during lectures, critical footnotes, bad book reviews, and after all is said and done, deadly silence.
The Ape and the Sushi Master: Cultural Reflections of a Primatologist

Thursday, 3 December 2009

Feynman looks at the blueprints

The Pleasure Of Finding Things Out is a collection of Richard Feynman’s short works. Perhaps the most famous of these is his 1974 Caltech Commencement Address on Cargo Cult Science. My personal favourite there is Los Alamos from Below (slightly different version of this lecture appears here).
How do you look at a plant that ain’t built yet? I don’t know. So I go into this room with these fellows. There was always a Lieutenant Zumwalt that was always coming around with me, taking care of me, you know; I had to have an escort everywhere. So he goes with me, he takes me into this room and there are these two engineers and a loooooooong table, great big long table, tremendous table, covered with a blueprint that’s as big as the table; not one blueprint, but a stack of blueprints. I took mechanical drawing when I was in school, but I wasn’t too good at reading blueprints. So they start to explain it to me because they thought I was a genius.
The Pleasure Of Finding Things Out: The Best Short Works Of Richard Feynman (Helix Books)
And they start out, “Mr. Feynman, we would like you to understand, the plant is so designed, you see one of the things we had to avoid in the plant was accumulation.” Problems like — there’s an evaporator working which is trying to accumulate the stuff; if the valve gets stuck or something like that and they accumulate too much stuff, it’ll explode. So they explained to me that this plant is designed so that no one valve, if any one valve gets stuck nothing will happen. It needs at least two valves everywhere.

So then they explain how it works. The carbon tetrachloride comes in here, the uranium nitrate from here comes in here, it goes up and down, it goes up through the floor, comes up through the pipes, coming up from the second floor, bluuuuurp, from the blueprints, down, up, down, up, very fast talking explaining the very, very complicated chemical plant.

I’m completely dazed, worse, I don’t know what the symbols on the blueprint mean! There is some kind of a thing that at first I think it’s a window. It’s a square with a little cross in the middle, all over the damn place. Lines with this damn square, lines with the damn square. I think it’s a window; no, it can’t be a window, ’cause it ain’t always at the edge. I want to ask them what it is.

You must have been in a situation like this — you didn’t ask them right away, right away it would have been OK. But they’ve been talking a little bit too long. You hesitated too long. If you ask them now they’ll say, what are you wasting my time all this time for? I don’t know what to do. You are not going to believe this story, but I swear it’s absolutely true; it’s such sensational luck. I thought what am I going to do, what am I going to do????? I got an idea. Maybe it’s a valve? So, in order to find out whether it’s a valve or not I take my finger and I put it down in the middle of one of the blueprints on page number 3 down in the end and I said, “What happens if this valve gets stuck?” figuring they’re going to say, “That’s not a valve, sir, that’s a window.”

So one looks at the other and says, “Well, if that valve gets stuck,” and they go up and down on the blueprint, up and down, the other guy up and down, back and forth, back and forth, and they both look at each other and they turn around to me and they open their mouths — “You’re absolutely right, sir.”

So they roll up the blueprints and away they went and we walked out. And Lt. Zumwalt, who had been following me all the way through, said, “You’re a genius. I got the idea you were a genius when you went through the plant once and you could tell them about evaporator C-21 in building 90-207 the next morning,“ he says, “but what you have just done is so fantastic, I want to know how, how do you do that?” I told him, you try to find out whether it’s a valve or not.

Friday, 20 November 2009

say what you mean

Earlier this month, Sue Keogh gave a seminar entitled “Seven Steps to Great Web Copy” at the EBI. Good thing that EBI Interfaces published a round-up including the presentation and some useful notes. Most of it is just plain common sense (“it’s actually harder to be concise than to write a load of waffle”), but how many science-related websites actually use the common sense?

Thursday, 19 November 2009

not just drug design

Drug Design: Cutting Edge Approaches, published in 2002, is a collection of highly enlightening reviews, even if some of the approaches may be not so cutting-edgey any longer. (Really, one should never name a book like that.) The two chapters authored by Darren Flower (who is also an editor of the book) are a pleasure to read, not least because they put the drug design into fascinating historical and philosophical context.

From Molecular informatics: Sharpening drug design’s cutting edge:
‘Show me a drug without side effects and you are showing me a placebo,’ a former chair of the UK’s committee on drug safety once commented. As pharmaceutical products, of which Viagra is the clearest example, are treated more and more as part of a patient’s lifestyle, the importance of side effects is likely to grow. A recent study concluded that over 2 million Americans become seriously ill every year, and over 100,000 actually die, because of adverse reactions to prescribed medications.
On bioinformatics:
Academic bioinformaticians sometimes seem to lose sight of their place as an intermediate taking, interpreting, and ultimately returning data from one experimental scientist to another. There is a need for bioinformatics to keep in close touch with wet lab biologists, servicing and supporting their needs, either directly or indirectly, rather than becoming obsessed with their own recondite or self referential concerns.
On molecular similarity:
There is, ultimately, no ‘gold standard’ by which to judge the performance of different similarity measures. There is no consensus between chemists, or computer algorithms, and there isn’t one between receptors either. There is no universally applicable definition of chemical diversity, only local, context-dependent ones. The only correct set of rules would be those that a receptor chooses to select molecules: but these will vary greatly between different receptors. This has not discouraged the development of a large literature — comparing methods, primarily in the context of justifying the apparent superiority of a method that the authors have developed; these are often large, complex, yet discombobulatingly terse papers which assaults the reader with the weight of information rather than the arguments of sweet reason.
From Computational vaccine design:
Death, the pale horseman, comes in many guises, covering diverse causes from individual natural disasters to accidental injury. Natural disasters, or what insurance brokers are pleased to call acts of god, would figure highly on the average individual’s list of greatest causes of death and destruction.
One of the most significant events in the history of human disease interaction was the new world holocaust that affected South America in the century or so after its ‘discovery’ by the Spanish. <...> The catastrophic decline in the indigenous Indian population was on a scale unmatched even in the 20th century, and was likely to have been the greatest ever loss of an aboriginal population.
Drug Design: Cutting Edge Approaches

Monday, 9 November 2009

twenty years after

Just finished watching the BBC broadcast from Berlin, with giant dominoes falling and all that. I remember the euphoria at the time. Nowadays it is difficult to imagine anyone in right mind who’d say that the fall of the Berlin Wall was a bad thing. (Margaret Thatcher was famously opposed to it, but I am not sure she was in right mind.)

Still, I didn’t expect yesterday’s article in Guardian by Bruni de la Motte to cause such a torrent of (mostly right-wing) comments.

As a result of the purging of academia, research and scientific establishments in a process of political vetting, more than a million individuals with degrees lost their jobs. This constituted about 50% of that group, creating in east Germany the highest percentage of professional unemployment in the world; all university chancellors and directors of state enterprises as well as 75,000 teachers lost their jobs and many were blacklisted.
I don’t know how correct are the figures, but the article rings the right bells to me. Some of my colleagues from former GDR have lost their jobs as a result of Abwicklung (restructuring, or rather liquidation, of East German institutions). I think the biggest loser here was German science as a whole: East German scientists, educated to a high standard, had no problem finding jobs in the USA. But then, social revolutions, even velvet ones, are rarely good news for science.

Brigitte Young wrote in her 1993 paper:

Women are not only the first to lose their positions in the process of Abwicklung, they are also the last to be considered in the new stage of rebuilding the university system. Thus the politics of Abwicklung has to be understood as a microcosm of the gendered nature of German unification as a whole. Unification has provided German conservatives the opportunity to roll back not only the social policies of the east, but also the feminist achievements in the west.
But that was 16 years ago, right? Surely by now things should have got better. Yet the East-West divide still exists in German science. (In words of Fritz Stern, “the physical wall has been internalized”.) In last week’s Science, Gretchen Vogel wonders why the Max Planck Society, out of its 267 directors, has only one former East German who started a career before 1989. Not that it has many women directors either. Christiane Nüsslein-Volhard, Director at the Max-Planck-Institute of Developmental Biology, wrote that
in 1995, the society was able to boast that 25% of their female directors had received a Nobel prize.

Tuesday, 13 October 2009

science and photo doctoring

We all know that photo manipulation (aka photo doctoring, aka photoshopping) for the purposes of news reporting is, at best, controversial. We tend to forget though that the photographs were manipulated long before invention of computers.

Professor Hany Farid, the leader of the Image Science Group at Dartmouth College, compiled an entertaining guide to photo tampering throughout history, including the early composite photograph of Abraham Lincoln.

What about science? The recent Nature editorial says:

At a meeting on plagiarism in London last week, Virginia Barbour, chief editor of PLoS Medicine, a peer-reviewed journal published by the Public Library of Science (PLoS), which is headquartered in San Francisco, California, said that the problem of image manipulation has “crept up” on journal editors since the advent of software such as Photoshop.

Yeah, blame Photoshop. I am all for open access but the editing in open-access journals (including PLoS family) is already minimal. All the work is made by the (paying) authors and the (unpaid) reviewers. I don’t see why the authors would want to doctor their digital images, it looks to me like more work, even with Photoshop (which is not a cheap software), and they still have to pay. On the other hand, there always will be people who falsify their results, irrespectively of tools.

Emma Hill, Executive Editor of The Journal of Cell Biology, commented today:

At the JCB, we have screened all images of all editorially accepted papers since 2002. Over that time, we have consistently seen manipulations that affected the interpretation of the data in ~1% of accepted manuscripts. We have revoked the acceptance of those manuscripts. We find manipulations that violate our guidelines but do not affect the interpretation of the data in over 25% of accepted manuscripts. In those cases, the authors have to remake the figure(s) in question with a more accurate representation of the original data.
I say, 25% is a lot. How one can be sure that manipulations “do not affect the interpretation of the data”? Why the authors should bother with image manipulation otherwise? And then again, what is “more accurate representation of the original data”? (Back in my university days, we were taught that the artist’s impression of a microscopic view is often superior to a photomicrograph, because it is closer to what a human eye sees through the microscope.) Shouldn’t the editors just request the original data? Am I asking too many questions?

Monday, 12 October 2009

women Nobel prize winners 2009

I have mentioned earlier that women scientists are not featured prominently among the Nobel Prize winners. Now, within a week (from 5 to 12 October 2009), five women won Nobel Prizes.

So, a little correction to the statistics: now there are altogether 40 female Nobel Prize winners out of 802 individual laureates, i.e. 4.9%. Still, only 15 women got Nobels in science — unless you count Economic Sciences, in which case it will be 16.

However small the number of women Nobel Laureates remains, this year’s prizes make a bit of difference. Ada Yonath is only fourth (!) female Nobel laureate in Chemistry, the previous one was Dorothy Hodgkin in 1964. Elinor Ostrom is the first woman ever to receive The Sveriges Riksbank Prize in Economic Sciences “for her analysis of economic governance, especially the commons”, whatever that means. For the first time, two women biologists, Elizabeth Blackburn and Carol Greider, share the Nobel Prize in Physiology or Medicine.

In the latter case, there is a sort of explanation. In the telephone interview, Elizabeth Blackburn said that in her research field (molecular biology of telomere and telomerase) the ratio of men and women is “fairly close to the biological”, while all the other research fields are “aberrant” in this sense. Overgeneralisation? Maybe. Maybe not all the other fields. Simply vast majority of them.

There’s nothing particularly about the science per se which has any, sort of gender-like quality to it.
You want women to have access to science because it’s such a wonderful thing to do. Anything that makes it more feasible for women to be in science and do the science they like, that’s good.
I think that it doesn’t help to be a woman in science. Maybe now, but not when I was progressing.

Wednesday, 7 October 2009

the art of scientific writing

I got The Art of Scientific Writing (first edition) in early 1990s and it has been my trusty companion ever since. Although some parts of the books are a bit out of date (check out the section 5.2 Typewriter or Word Processor? and you’ll see what I mean), it remains an excellent read.

Appendix A, Oral Presentations, gives a no-nonsense advice how to deliver a good lecture, while Appendix B, Aspects of Scientific English, is a must read (I mean it: must read) for anyone who ever think of submitting a written communication in English. I can’t recommend it enough.

Much scientific writing is littered with idle words, awkward constructions, and inaccurate phrasing simply because few scientists take seriously the importance of good writing.
Readers of scientific prose are altogether too tolerant and too willing to shoulder an inappropriate amount of the burden. Perhaps this is a reflection of the scientist’s love of puzzle-solving, but it is certainly not conductive to effective communication.
We have frequently condemned the tendency to indulge in meaningless verbosity. The most obvious target is the pompous phrase hiding a simple idea:
  • a number of (many)
  • a majority of (most)
  • at this point in time (now)
  • despite the fact that (although)
  • due to the fact that (because)
  • for the purpose of (for, to)

Friday, 25 September 2009

just say no to multitasking

I recall a conversation between A, the director of the institute where I used to work many years ago, and D, a senior scientist in the same institute who was talking about his research. It was going like this:
D: “We did this and this.”
A: “Excellent.”
D: “We also did this and that.”
A: “Very good.”
D: “And last month we started the experiment on...”
A: “Good, but don’t you think you spread too thinly?”
D: “Well, no, I have a very talented PhD student, who also...”
A: “Wait, wait, let’s concentrate on the first thing for now. What was it, again?”
D: “It was this. While I was looking at the results of this compared with results of that, I thought I also should...”
A: “Oh, shut up. You can’t do everything at once.”
A bit too direct, perhaps, but that’s why A was a director. He did understand that multitasking is not always good for research; or maybe, never good for research. On the contrary, D thought that the more things you do simultaneously, the better. According to the excellent article by Christine Rosen,
In the late 1990s and early 2000s, one sensed a kind of exuberance about the possibilities of multitasking. Advertisements for new electronic gadgets — particularly the first generation of handheld digital devices — celebrated the notion of using technology to accomplish several things at once. The word multitasking began appearing in the “skills” sections of résumés, as office workers restyled themselves as high-tech, high-performing team players.
Are multitaskers any better than, er, monotaskers? The recent study conducted by Stanford scientists shows that no, not really.
“We kept looking for what they’re better at, and we didn’t find it.”
What a relief for people like me, low-throughput monotaskers. But is this “skill” as valuable now as it was ten years? You bet. Check it out: today’s search for multitask in Nature brings 23 hits, while New Scientist has 82 jobs featuring this keyword! (Charmingly, this latter resource adds that “the most relevant jobs are listed first”.)
A high level of multitasking ability over several projects is expected.
Must be adaptable to changing work requirements, and be willing to multitask.
Self-motivated, ability to multitask, and willingness to work in a start-up environment.
Strong communication (verbal and written), organizational and multitasking skills are essential.
And this is not just directors and managers, the people who you’d expect to be no good at anything. These “competencies” are expected from post-docs too. I can’t help thinking that it is nothing but greedy employers trying to get many for the price of one. Good luck to them.

Wednesday, 23 September 2009

Smilla meets professor

From Smilla’s Sense of Snow by Peter Høeg (translated by Tiina Nunnally):
Even though he omits his title, it’s still understood. Along with the fact that we must not forget that the rest of the world’s population is at least a head shorter than him, and here, under his feet, he has legion of other doctors who have not succeeded in becoming professors, and above him is only the white ceiling, the blue sky, and Our Lord — and maybe not even that.
He radiates courtesy and dominance, and I ought to be happy. Other women before me have been happy, and there will be many more. What could be better at life’s difficult moments than having six feet seven inches of polished medical self-confidence lo lean on?

We all live our lives blindly believing in the people who make the decisions. Believing in science. Because the world is inscrutable and all information is hazy. We accept the existence of a round globe, of an atom’s nucleus that sticks together like drops, of a shrinking universe — and the neccessity of interfering with genetic material. Not because we know these things are true, but because we believe the people who tell us so.

Friday, 18 September 2009

stroke of insight

Take 20 minutes off your busy schedule, pay no attention to anything else and watch Dr Jill Bolte Taylor telling an amazing story of a neuroscientist observing behaviour of her own brain. You will be impressed and moved with the courage and sense of humour of this lady. This video comes with a selection of subtitles in 23 languages, so really there is no excuse not to watch it.
...And in that moment my right arm went totally paralyzed by my side. And I realized, “Oh my gosh! I’m having a stroke! I’m having a stroke!” And the next thing my brain says to me is, “Wow! This is so cool. This is so cool. How many brain scientists have the opportunity to study their own brain from the inside out?”

And then it crosses my mind: “But I’m a very busy woman. I don’t have time for a stroke!” So I’m like, “OK, I can’t stop the stroke from happening so I’ll do this for a week or two, and then I’ll get back to my routine, OK.”

Sunday, 13 September 2009

карта звезды

When I was about four years old, I was drawing all the time. Once, in kindergarten, I was creating another masterpiece of an illustrated sci-fi book, which included the map of a star.

It took me quite a while to colour the centrefold of my wonderful book with a crayon. Eventually it looked more or less like this:

Map of a Star

(Alas, the original is lost, so this is just a weak imitation, you understand.) Somewhere in the middle of the map I put a circled black dot ◉, a flag ⚑, and the word Евсток (Evstok). In my view, it was a perfect name for a research station on the surface of a red giant.

Alas, my teacher did not quite understand what I was doing. When I explained, as patiently as I could, that this is the map of the red giant (everybody knows that red giants are orange), she congratulated me but crossed Евсток and wrote Восток (Vostok). What a stupid cow, I thought, but did not say so, because I was a polite boy. I was not about to give any more explanations.

All these years later, there’s still no sign of a research station on any star. Now, people of the earth, listen. When you finally manage to put one on the surface of a red giant, please name it Евсток.

Saturday, 12 September 2009

science is cool

Science is not all about the books. It can be cool, filled new and creative, fun ideas.
This blurb for Mitochondria video by Michelle Bell can be applied to all of ChloroFilms, a collection of “videos illustrating the remarkable aspects of plant life”. Don’t dismiss it as stuff for (or by) undergraduates: for example, The Science of Cool by Sharon Robinson is an overview of her original research in Antarctic mosses. My favourites are La Bloomba by Kris Holmes and The Fastest Flights in Nature by Hayley Kilroy.

Thursday, 10 September 2009

i felt like internet

From Girl Meets Boy by Ali Smith. How painfully familiar.
They all looked the same, the bosses with their slightly Anglified accents and their trendily close-shaved heads. They all looked far too old for haircuts like that. They all looked nearly bald. They all looked like they were maybe called Keith.
I was tired of being so young, so stupidly knowing, so stupidly forgetful. I was tired of having to be anything at all. I felt like Internet, full of every kind of information but none of it mattering more than any of it, and all of its little links like thin white roots on a broken plant dug out of the soil, lying drying on its side.

Monday, 17 August 2009

the summer is almost over

With all these warm sunny days, you wouldn’t say that the Summer is almost over. But it is. Academics are returning from vacations and clean their messy desks. Only this could explain the fact that within a week I have received three responses (all negative ones) re. my long-forgotten job applications. (One of the applications was submitted last December, another one this January, and the most recent one in March.) Interestingly, or maybe not, one of the letters contains a copy of the evaluation committee’s report (which looks like, well, a concise version of my CV, but at least it’s an evidence that somebody actually did read it) and a note that I am welcome to comment on this report not later than some day last month.

Needless to say, it doesn’t do much good to my ego. Even if I take the view that it is their loss. Which it is, but it is not my gain either. In any case, I am not getting paid for them losing me. (Hey, I’d like to develop this line of thought one step further. It seems that in some institutions people spend lot of time evaluating my applications. By not applying, I could save their time, effort, and valuable desk/disk space, so it’s only fair to get remunerated for that.)

Oh well. With these three off my Christmas card list, my potential employers are not exactly queuing outside. Which means I can go away again and not miss anything.

Sunday, 16 August 2009

cool badges

The Science Scouts develop some seriously cool badges. For all humankind.
Anyone is welcome to use these badges, although a link to this site (or the specific badge entry) is much appreciated. Even better is if you provide an anecdote in the comments section to explain your reasons for awarding yourself the badge.
Excellent. I allow myself to award myself a few.

Also, thanks to Science Scouts, I’ve got acquainted with The Science Creative Quarterly, which publishes some very nice articles, such as this review by Vince LiCata.
This is a large book. Weighing in at a solid 11.5 pounds (5.2 kg), this book is good for whacking things.
If you only have time to read one biochemistry textbook this year, Ezra Pound’s “On Biochemistry” is the book you want, unless you actually need to learn some biochemistry.

Saturday, 15 August 2009

she’s such a geek

You will be wanting to read my excellent essay, ‘Suzy the Computer’ vs. ‘Dr. Sexy’: What’s a Geek Girl to Do When She Wants to Get Laid? in She’s Such a Geek: Women Write About Science, Technology, and Other Nerdy Stuff.
It was this charming announcement on Zuska’s blog that prompted me to get hold of the said book. And what a book it is!

Personally, I don’t like the word ‘geek’ at all. Not everybody who is learning (works in, used to work in) science/technology is a geek. The truth is, however, that if you are a woman, you’ll be seen as a geek if you are interested in science, or maths, or technology, or computer games, or whatever else that happens to be a male-dominated field. Which is more or less everything except raising the children. Even in most egalitarian societies — and America, the home of this book’s authos, is hardly the one. OK, women may be allowed to be geeks, but even there their geekdom is considered largely incompatible with femininity, or sexual desirability. Boys don’t want to date smart girls. Mums want their daughters to behave like ‘normal’ girls (e.g. to join the cheerleading team rather than a math class). And so on.

I’d love to put a couple of quotes here — alas, there are 24 essays by very different authors, each one worth a quote or three, and I don’t have all night. Don’t be put off by the cover art. Get the book and enjoy.

She's Such a Geek: Women Write About Science, Technology, and Other Nerdy Stuff
P.S. There is an interesting blog by the same name and with contribution of some authors of the book; alas, it was not updated for more than a year.

Friday, 14 August 2009

a threat to scientific communication

Once again, I am getting spammed by Nature — this time it is an email with a modest subject “Impact Factor confirms Nature is top research journal”. It informs me that its Impact Factor is 31.434 now. The reason they bother to send me this?
To celebrate we are offering you an exclusive 30% discount if you
subscribe to Nature this week.
No thank you. I just read a brilliant review by Zoë Corbyn in Times Higher Education. Featuring opinions of scientists such as Peter Lawrence, Peter Murray-Rust, and Sir John Sulston, it is a wonderful read.
Noting that the medical journal articles that get the most citations are studies of randomised trials from rich countries, he <Richard Horton, editor-in-chief of The Lancet> speculates that if The Lancet published more work from Africa, its impact factor would go down.

“The incentive for me is to cut off completely parts of the world that have the biggest health challenges ... citations create a racist culture in journals’ decision-making and embody a system that is only about us (in the developed world).”
Horton believes the real crisis facing journals, and in particular the top health titles, is in defining the “purpose” of their role. While journals founded 300-odd years ago had an explicit mission, which was to “use knowledge to change society for the better”, today’s journals have “lost their moral compass”, he contends.
So, is it just the publishers to blame for the present situation? What about scientists themselves?
Unfortunately, say observers, there is no incentive for people on the inside to change things. The scientists who have learnt to play the “complicated game” of getting their papers into the top journals are reluctant to ditch it because they fear losing out.
Can anything be done by ‘ordinary’ scientists (i.e. those who do all the real work)? Yes!
A small but growing number of scientists are simply ignoring journals and putting their work on web pages and blogs, where there is no limit on the length of articles, raw data can be published with ease and peer review can take shape through discussions and comments.
Top universities, working together, could force the reform of copyright laws, Murray-Rust believes, but, given their inaction, he thinks that a better answer might be “civil disobedience on a mass scale”.

He envisages scientists focusing on one or two areas, such as medicine and climate change, where there are strong moral grounds for allowing science in journals to be reproduced — and “sticking the whole bloody lot” on their websites.
Even if you think you know all this (as I thought), read it.

Thursday, 13 August 2009

can accent damage your career?

We all know about racism, sexism and ageism, in the workplace or otherwise. But what about accentism? From A Plum in Your Mouth: Why the Way We Talk Speaks Volumes About Us by Andrew Taylor:

The BBC poll that so damned the Welsh accent was one of many over recent decades which have arranged regional accents in order how pleasant, prestigious, or socially desirable they are. A similar survey, carried out a few months later, reached much the same conclusions, with the added twist that Welsh found itself languishing around the bottom of a list of accents which supposedly gave the impression of hard work and diligence. It is significant that of the ten accents at the bottom of the poll, seven were those of big industrial cities or conurbations, namely Bristol, Swansea, Manchester, Glasgow, Liverpool, Black Country and Birmingham. There are other fairly clear prejudices against the other three, South African, German and Asian — but overall, the poll was simply a vote against urban working-class speech. It is probably not unduly cynical to point out that the second survey was carried out on behalf of the Aziz Corporation, a company which specializes in ‘executive communications’, and includes ‘voice development’ among the services it offers. It’s also noticeable that surveys such as these tend to tke place either in Summer or around Christmas, when news is in short supply.

Tuesday, 11 August 2009

what to tell my younger self

“If I knew then what I know now” is a regular column in The Big Issue magazine, in which celebrities tell us what they would tell their younger selves if they had a chance. It is, of course, impossible, that’s why I enjoy reading it.

What would I say — or rather, write in a column like this? I’d tell my younger self not to waste time in academy.” Knowing that there is absolutely no way to talk to my younger self: do I actually mean it? If I did not waste time in academy, I wouldn’t become what I am. So I would spend some time elsewhere, like in the army or medicine. Suppose I survive the army; I’d tell my younger self then not to waste time in army. Or medicine.

And would my younger self listen?

Not really.

Sunday, 19 July 2009

academic matters

Idly browsing the web (as usual), I came across Academic Matters, the open access Canadian magazine. The latest (May 2009) issue is devoted to Ethics in the Academy. Incidentally, this enjoyable article by Sergio Sismondo deals with issue of ghosts in some detail.
Academic authors are well versed in the art of multiplying papers and, also, with complaining about it. However, in the pharmaceutical industry each publication is part of a marketing campaign and has an expected return. The professionalization and commercialization of publishing makes a science out of the multiplication of papers.
Key opinion leaders (KOLs) <...> are well-known specialists who “can influence other physicians.” In practice, the term is applied to a specialist with existing relations to the industry, not simply to a prominent expert. Publication planners make KOLs their authors on articles and their speakers at conferences and other events. Actually, in the process they make KOLs themselves, by making some specialists more prominent as experts.
For as long as there has been academic publishing, some authors have found it convenient to copy work of others, and some authors have taken credit for work done by their students and juniors. For the most part, concern about plagiarism is about fairness, as some people’s work is exploited while other people gain unearned credit. The pharmaceutical industry, always an innovator, has developed a different form of plagiarism, involving only willing participants. Moreover, it has created new reasons for concern: the hiding of interests that drive research and publication and the possible harm to patients that this may create.
Is there anything that can be done? Yes, but the measures that Sismondo suggests in conclusion are highly unlikely to succeed out of goodwill alone, for both academia and pharma industry don’t want to lose financially.
Medical schools should punish plagiarists severely, for the usual reasons plus the fact that plagiarists put patients’ health at increased risk. They should also stop valuing pharmaceutical company sponsorship of research. Medical journals should require authors to describe in detail their contributions to articles and should scrutinize those descriptions. They should stop dealing with publication planners or anybody other than authors. They should also stop pandering to the industry for important manuscripts. More controversially, they should stop publishing sponsored research altogether: the 10 or so most important medical journals have such a lock on prestige that together they could step away from the pharmaceutical industry and show off their clean hands. Finally, governments should sequester drug research and marketing.

If you are still unsure whether open access is right thing, check out this Web Exclusive Article by Leslie Chan.
Citation has gradually became the primary scholarly currency, conferring authority and prestige in the academy, which in turn translates into tangible benefits such as career advancement, reputation, and grant funding. Broad dissemination of research results and points of view also serves the public good, which is a central mission of our public universities.
University administrations facing continual budget hardship and funding shortfalls, made worse by the global financial meltdown of 2008, are likely to dismiss Open Access and the suggested actions as a distraction rather than a priority. This would be a big mistake and a missed opportunity. If universities do not act while they still can, they will find themselves once again at the mercy of private entities, this time it may be Google, and their roles and relevance in society will be increasingly diluted.
Chan dispels the popular myths such as poor quality of Open Access journals or that majority of Open Access publishers are charging author fees. But he warns that
for Open Access to be widely adopted across the academy, institutional inertia, cognitive conservatism, and the culture of risk-aversion promoted by the academic reward system needs to be addressed. This may prove to be the biggest challenge to Open Access if university administrations remain largely silent, as they have been, on the question of Open Access.

Sunday, 12 July 2009

guests, ghosts, gofers

Thanks to this paper by Peter R. Mason from Zimbabwe, I got acquainted with an interesting classification of the authorship of (scientific) papers.
Guest authors are those “important” persons who insist that their names appear on the papers of their juniors, even when they have made minimum contribution to the research. Ghost authors are those who make a significant contribution to the writing of a paper, but their names do not appear as an author on the publication. This is often a situation found in clinical trials sponsored by pharmaceutical companies. A “gofer” is a name given to someone who is regarded as very junior and so is sent to “go for” something and bring it back to the more important members of a team.
Ostensibly, the article deals with the situation in developing world; in fact it talks about the universal problem. Check the recommendations of International Committee of Medical Journal Editors (ICJME):
Acquisition of funding, collection of data, or general supervision of the research group alone does not constitute authorship.
Mason quotes this passage and says:
Many instances of authorship from the developing world may not be compatible with these criteria.
As if in the “developed” world the situation is different. Show me a researcher who was never bullied into accepting uninvited co-authors. It looks like the only way to ensure that you don’t have guests/ghosts/gophers is to write and publish alone. Even three co-authors (which IMHO is an optimal number for scientific paper-writing) may be one or two too much.

In his essay The demise of the lone author, Mott Greene wrote:
The appreciation of Lotka’s law has allowed the continuation, in a world of clearly shared credit and hazily specified responsibility, of citation counting as the principal means of establishing scientific prominence and reputation. No matter how many co-authors you have, the more times your name appears on a scientific publication, the more productive you are assumed to be, and the more worthy of support.
At least, current system of scientific funding favours “more authors, more publications” scenario. (Greene says that Lotka’s law may be not applicable to those mass grave papers with 100+ co-authors. I don’t think it changes much: in his original paper, Lotka himself only counted the primary authors.) Commenting on Greene’s paper and follow-up by Kevin Hallock, Writedit suggests that if the ICMJE authorship rules were strictly enforced, there will be a lot more lone authors in scientific literature, which could be not a bad thing — except
perhaps that would be interpreted as not being collegial or collaborative rather than as being independent and tenacious.

Tuesday, 7 July 2009

how many scientists fabricate and falsify research?

Well, this illuminating study by Daniele Fanelli suggests that quite a few (without giving us any exact numbers of course). It all depends on how you formulate your question. For instance,
scientists were less likely to reply affirmatively to questions using the words “fabrication” and “falsification” rather than “alteration” or “modification”. Moreover, three surveys found that scientists admitted more frequently to have “modified” or “altered” research to “improve the outcome” than to have reported results they “knew to be untrue”.
That does not surprise me at all, but it’s good to have something like that published in peer-reviewed journal. Speaking of peers,
The grey area between licit, questionable, and fraudulent practices is fertile ground for the “Mohammed Ali effect”, in which people perceive themselves as more honest than their peers.
The decrease in admission rates observed over the years in self-reports but not in non-self-reports could be explained by a combination of the Mohammed Ali effect and social expectations. The level and quality of research and training in scientific integrity has expanded in the last decades, raising awareness among scientists and the public. However, there is little evidence that researchers trained in recognizing and dealing with scientific misconduct have a lower propensity to commit it. Therefore, these trends might suggest that scientists are no less likely to commit misconduct or to report what they see their colleagues doing, but have become less likely to admit it for themselves.
And now, from the past to the future (misconduct):
There seems to be a large discrepancy between what researchers are willing to do and what they admit in a survey. In a sample of postdoctoral fellows at the University of California San Francisco, USA, only 3.4% said they had modified data in the past, but 17% said they were “willing to select or omit data to improve their results”. Among research trainees in biomedical sciences at the University of California San Diego, 4.9% said they had modified research results in the past, but 81% were “willing to select, omit or fabricate data to win a grant or publish a paper”.
Now, really difficult question. Are San Diego guys more fraudulent than their San Francisco colleagues? Or more honest because thay admit being more dishonest?

Monday, 6 July 2009

we are all Iranians

Sometimes (and quite often) I wonder whether the “international scientific community” can do anything useful at all. Useful and noble. The recent editorial in Nature suggest that it can, actually that it has to.
The international scientific community has been laggard and passive in responding to the current situation <in Iran>. But Iranian scientists say that the solidarity of the international academic and scientific community is needed now more than ever.
Research bodies and universities — and perhaps a few Nobel laureates — need to speak out louder. They should encourage, rather than discourage, collaboration, and replace past discrimination by welcoming Iranian researchers and students.
Iran is not the only country in the region where human rights and democracy are violated; and the West has hypocritically been relatively silent on similar abuses by several of its allies in the Middle East. But in Iran at least, the country’s long traditions of democracy, education and free thinking — suppressed for decades by the regime, and in particular the current hard-line leadership — are now out in the open.

Monday, 29 June 2009

seven deadly sins

Unfortunately, I was not around last year when Carole Goble delivered her lecture “The Seven Deadly Sins of Bioinformatics” at the EBI. So, what are they?
  1. Parochialism and Insularity
  2. Exceptionalism
  3. Autonomy or death!
  4. Vanity: Pride and Narcissism
  5. Monolith Megalomania
  6. Scientific Method Sloth
  7. Instant Gratification
I think Carole is a bit harsh on bioinformatics, which, remember, is not even a science. Are these applicable to “Real Science™” though? Absolutely.

Saturday, 27 June 2009

studying is not about what’s worth it

This is one of my favourite scenes from My Neighbors the Yamadas.
Noboru: “Dad, do you think all this studying is really worth my time?”
Takashi: “Listen up! Studying is not about what’s worth it. Classes that seem worth it may turn out to be not worth it and therefore not worthwhile. But, sometimes things that are worthless may actually be worthwhile, worthless or not. So, it’s not about whether or not something is worthless or not!”
Matsuko: “What in the world are you talking about?”
Noboru: “That was so not worth it.”

Thursday, 25 June 2009

driven by a curiosity about nature

Here’s a portrait of a scientist I like — and envy. From H2O: A Biography of Water by Philip Ball:
Born in 1731, Henry Cavendish was an eccentric millionaire and a grandson of a duke, a self-financed natural philosopher whose social peculiarities did not prevent him from becoming a distinguished member of the Royal Society in London. He seems to have been driven by a curiosity about nature, which he pursued methodically to the exclusion of any curiosity about his fellow people. Cavendish seemed to care very little for the high esteem in which he came to be held; indeed, he seems to have been positively embarrassed by it.
Can you imagine anyone doing as much as him, without a need to write grants or publish? According to Wikipedia,
At age 18 (in 1749) he entered the University of Cambridge in St Peter’s College, now known as Peterhouse, but left four years later without graduating.
Nice. Probably got bored or something.

H20: A Biography of Water

Wednesday, 24 June 2009

science on Earth

About 15 years ago, I read the short sci-fi story entitled Mr. Tompkins and Candide Meet Their Ancestors. (It was written by Horace Drew, not by George Gamow.) I tried to find the full text on the web but without any success.
The arrogance of the human-Neanderthal hybrid was, to the Captain, its most amazing trait, after the sexual luster. Could the two be related? All of these big “science laboratories” were run by aggressive male primates in the same way that a gorilla kept his harem.
Visiting Caltech:
“Excuse me, is this place one of the great scientific labs, where Delbruck, Feynmann and Gell-Mann once worked?”
“Yes,” said the Professor, “but they are all gone now. Today we study astrophysics and cosmology, and string theory, and quantum chromodynamics, and many forms of mathematics.”
“But how do you know such studies are real,” asked the Captain, “if you can only look through a telescope and not go there, or if you do not really understand 4-D spacetime or the underlying structure of matter and energy, which are just two of your words for the same thing?”
“We are sure because we are sure, and certain because we are certain, even if there are no data. All of us agree, or we cut off the funding for the ones who don’t, because it would just be a waste of money if they have other views.” The Professor had written 100 papers in the most respected physics journals, on black holes, superluminal expansion, and cosmic strings, and now he was sure these were real things, and had convinced many others.
Learning about transcription:
He <Professor Dr. H.Q. Rotcaf> looked just like a male gorilla, as the Captain hoped. “Please ask my least-busy secretary to give you copies of my last 100 papers, from Science or Cell. I am a Leader in Transcription. I found many new factors, and factors upon factors. My grants total $10 million dollars a year. I write two papers a week. I lead the citation-indices in my field. I chaired six meetings and gave 22 lectures last year, in March alone. If a few in my group kill one another, that will just be Evolution of the Fittest, to make a stronger group. Now I must go to the airport, unless you are a newspaper reporter.”
Here the Captain had found what he wanted on Earth. What a classic example of the perversions that would result, from applying sexual-dominance principles to even an austere field such as science, which in all probability was the lowest of all Earth primate achievements, when measured against the existing knowledge and technologies on other civilized planets.
“Have you made any important medical advance or invention recently?”, asked Candide.
“I told you I published 123 papers last year in major journals, and led the nation in the Citation Index, and got the highest ratings in my Study Section. What more could you want?” said the great Professor Rotcaf. “Even the Boston transcription workers cannot match that, such as Professor Pool Ledom. I rule my group with an iron hand, when I see them between trips. I review 3 papers a day, and say what can and cannot be published about transcription. Here, look at how well I do that:”

“This paper presents important results, but is just not a Cell paper. I suggest the authors try some specialist journal such as Mol. Cell Biology which is really where they belong.”

“I have results in my lab which disagree with those proposed here, so their results cannot be correct, and I cannot recommend publication.”

“I have results in my lab which already precede those presented here, so they are not novel, and should in no way be published. Regrettably, my secretary mislaid this paper for several months, so the review is late.”

“These authors have never presented their results before in an American journal.”

“There are two kinds of paper from that group: results which have been done by others before and are not novel, and new results which have not yet been reproduced by others. I worry about both of them, and cannot recommend publication.”

you can’t push and write at the same time

In All the Great Writers, Charles Bukowski describes a conversation between a writer, James Burkett, and publisher, Henry Mason.
“look, Burkett, you’re a pusher. as a pusher, you’re great. why don’t you sell mops or insurance or something?”
“what’s wrong with my writing?”
“you can’t push and write at the same time. only Hemingway was able to do that, and then even he forgot how to write.”
(From The Most Beautiful Woman in Town & Other Stories)

Sunday, 21 June 2009

harmless, harmless

A couple of anecdotes from George Feher’s essay “The Development of ENDOR and other Reminiscences of 1950’s” (in Foundations of Modern EPR, pp. 548—556).

On visit of Wolfgang Pauli to Bell Labs in 1957:
The management of Bell Labs was always very proud and a bit self congratulatory on their fame and accomplishments. At the end of the day everybody connected with Pauli’s visit gathered in the conference room and formally said good bye to Pauli who, as usual, was nodding his head with closed eyes. “Professor Pauli, what do you think of our research?” asked the director, fully expecting a pat on the shoulder. The frequency of Pauli’s nods increased and after what seemed an interminably long time, he simply said: “Harmless, harmless”.
About Ernest Lawrence:
He considered labs and offices as sacred places in which strict standards (his) of behavior had to be followed. One day he entered an office and saw a young man with his feet on his desk munching a sandwich. Lawrence discretely closed the door to give the man a chance to shape up. Alas, when he reopened the door, the man had neither changed his position nor his activity. Lawrence became very irate, started shouting, and that’s when we students gathered in the corridor to witness the scene. During all this, the young man calmly continued to munch his sandwich with his feet on the desk. Finally, when Lawrence was close to apoplexy, the department chairman R.T. Birge arrived and quieted Lawrence. Upon which the young man calmly said: “I don’t know who you are, Sir, but I work for the telephone company”.

Tuesday, 16 June 2009

systems vs system

‘Systems biology’ is an annoyingly waguely-defined area. Its recent history illustrates the self-perpetuating nature of organised science really well. According to Wikipedia,
systems biology refers to a cluster of peripherally overlapping concepts rather than a single well-delineated field. However the term has widespread currency and popularity as of 2007, with chairs and institutes of systems biology proliferating worldwide.
And then:
As of summer 2006, due to a shortage of people in systems biology, several doctoral training centres in systems biology have been established in many parts of the world.
Isn’t it brilliant? We don’t know what it is exactly but we have a shortage of experts in it already. Why, we don’t even know how to spell it. For instance, this publication from ESF uses both ‘system biology’ and ‘systems biology’. For once, I can’t blame the ‘systems biologists’ (whoever they are) for the confusion: there is a long tradition of using plural, rather than singular, in variety of ‘systems sciences’. J. P. Van Gigch wrote in System Design Modeling and Metamodeling (p. 32):
The reader will note that, in this text, we use the term “system” in singular when it applies to only one theory, one paradigm, one approach, one theory of design as in system theory, system paradigm, system approach, or system design, respectively. By contrast, we still use “systems” in plural, when the term “system” applies to more than one system, as in the expression “hard systems domains”, “soft systems domains”, or in “various systems assumptions”. This notation agrees with that recommended by the so-called father of this discipline, L. von Bertalanffy.
Convinced? I am not, really. The construction (plural qualifier followed by a singular noun) seems ungrammatical. We say “star formation” and “pest control”, even though it is understood that we mean more than one star or pest. What is so special about systems?

Why do we even have to mention the systems? What is a system anyway? In thermodynamics, a system is the region of the universe under study. Thus, by definition, thermodynamics studies systems. I like that definition because it is perfectly applicable to every natural science. Therefore, every natural science studies systems.

Ross Ashby, English pioneer of cybernetics, gave another definition:
A system is a set of variables sufficiently isolated to stay constant long enough for us to discuss it.

Friday, 12 June 2009

curiosity as the driving force of science

Lev Landau once defined science as “the means to satisfy one’s personal curiosity at the state’s expense”. In my student days, we were made to understand this was a joke, but I think that Landau was dead serious. In Soviet Union, the state was the only source of money. Luckily, in Western society, scientists can satisfy their curiosity at the expense of state, academia, charities, private companies or mad financiers. (People skilled in grant writing are doing a good job of exploiting as many of these resources as possible, although the ‘curiosity satisfaction’ is not, as a rule, listed among the goals of the proposed research.)

Sure, there could be other reasons to go to science, but only one decent reason to do it is to satisfy one’s curiosity. Here’s the proof. When the Nobel laureates or some other prestigious award winners — in other words, the folk who is said to achieve something in science — give their Nobel Lectures or interviews for media, they always mention their curiousity (as a driving force of scientific endeavour). They never say “I always wanted to get a Nobel Prize” or “I like to be invited to give talks in nice locations” or “That will show them” or “I was dodging the army draft” or “I had nothing better to do”. No: “Since I was a child, I was curious about this and that”, etc.

Landau’s definition also can help to figure out what is science and what is not. Take, for example, bioinformatics and computational biology — some people think these are synonyms. No they are not. Computational biology is science. Bioinformatics is technology. Try to formulate a question which betrays a convincing degree of personal curiosity and you’ll see what I mean.

To finish for tonight, a couple of posts from Siris blog: Hume on Curiosity and the Value of Truth and Hume’s Philosophy of Mathematical Practice.

Curiosity, then, is the governing motive of mathematics, the one that shapes it into a pursuit and a passion. It is not, of course, the only motive; nor is it in every particular case the strongest motive. There is, for instance, vanity, the desire to make a name for oneself. And we should not pretend that academics are above such sordid desires; anyone who has ever had dealings with academics knows that they are often almost obsessed with the possibility of being well respected, and that this motivation in at least many cases overtops even curiosity as a driving force in their work. Academia is filled to the brim with vanity; on a Humean view, this is one of the reasons it works in the first place.

Wednesday, 10 June 2009


You know what, yesterday, as soon as I have published my previous post, the ever-vigilant blogger.com locked my blog. Here’s the explanation.
This blog has been identified as a potential spam blog. Your readers will see a warning page until the blog is reviewed.

This blog will be deleted within 20 days unless you request a review.
Naturally, I’ve requested the review, so hopefully it will be unlocked “within two business days”. I believe the list of weasel words in the previous post has caused the problem. As much as I’d like to say “Q.E.D.”, I think it is the sheer number of the words (rather than their low information content) that has triggered the spam alert. Which is a shame. I’d say, every page containing more than five words from that table should be flagged. (Well, one has to experiment to learn the truth.) Personally, I delete any email which has ‘innovative’ or ‘solutions’ in the subject line.

Tuesday, 9 June 2009

business weasel words

An essential table from my desktop guide to the real world: Dilbert and the Way of the Weasel (pp. 129—132).
You can disguise almost any level of ignorance via the clever use of weasel vocabulary. Try memorizing the words on this list and using them in alphabetical order the way they are shown here.
Business Weasel Words
action item
bells and whistles
best practice
bottom line
brand equity
bread and butter
breakthrough products
business case
business units
cash cow
caveat emptor
change agents
change management
compensation plan
competitive advantage
continuous improvement
core competencies
cross-functional teamwork
desktop environment
distribution channels
fast track
flow charts
focus groups
game plan
gap analysis
high level
human capital
inside-out organization
internal and external functions
key performance indicator
key strategic areas
lean manufacturing
lessons learned
line operation
living document
long term
management consultant
mission statement
movers and shakers
next steps
paradigm shift
quantifiable benefit
real-time basis
red tape
risk management
shareholder value
step change
strategic fit
technology platforms
thought leadership
track record
transaction flow
unquantifieable benefit
warm and fuzzy
war stories
whole nine yards
Ugly corporate speak? Well, show me a grant application or a report that does not have at least ten of these ‘keywords’ in it. Often a number of them are joined together in phrases like “develop an innovative knowledge resource” or “integrated platform”.

Dilbert: The Way of the Weasel