low-throughput

an absolute sinecure

2012-01-21T20:40:00.002Z

From Dirk Gently’s Holistic Detective Agency by Douglas Adams:

Indeed, it was not entirely clear if Reg had ever taught anybody at all and what, if anything, he would have taught them. His professorship was an obscure one, to say the least, and since he dispensed with his lecturing duties by the simple and time-honoured technique of presenting all his potential students with an exhaustive list of books that he knew for a fact had been out of print for thirty years, then flying into a tantrum if they failed to find them, no one had ever discovered the precise nature of his academic discipline. He had, of course, long ago taken the precaution of removing the only extant copies of the books on his reading list from the university and college libraries, as a result of which he had plenty of time to, well, to do whatever it was he did.

Since Richard had always managed to get on reasonably well with the old fruitcake, he had one day plucked up courage to ask him what, exactly, the Regius Professorship of Chronology was. It had been one of those light summery days when the world seems about to burst with pleasure at simply being itself, and Reg had been in an uncharacteristically forthcoming mood as they had walked over the bridge where the River Cam divided the older parts of the college from the newer.

“Sinecure, my dear fellow, an absolute sinecure,” he had beamed. “A small amount of money for a very small, or shall we say non-existent, amount of work. That puts me permanently just ahead of the game, whichis a comfortable if frugal place to spend your life. I recommend it.”

sniff talks to the professor

2011-12-30T20:20:00.001Z

From Comet in Moominland by Tove Jansson:

“But how do you know that the Observatory is on that peak especially?” asked Sniff, craning his neck to see the top, but without success as it was hidden in the clouds.
“Well,” answered Snufkin, “you only have to look at the ground just here. It’s covered with cigarette ends which have obviously been thrown out of the windows by those absent-minded scientists up there.”

“According to my reckoning it should hit the earth on the seventh of October at 8.42 p.m. Possibly four seconds later,” said the professor.
“And what will happen then?” asked Sniff.
“What will happen?” said the professor in surprise. “Well, I hadn’t thought about that. But I shall record the events in great detail you may be sure.”

to collaborate or not to collaborate

2011-11-01T22:00:00.008Z

A few quotes from a fascinating new book, Collaborative Computational Technologies for Biomedical Research (Wiley, 2011):

Even within an institution — which should be legally, strategically, and financially incented for alignment, and for maximizing the opportunities for internal collaboration — barriers still exist. The subunits of the institution: its departments, its divisions, its components produce collaboration “walls” of varying substantiality. Organizational lore and personal relationships add another layer of “not-invented here” (NIH) culture, and allegiances to local agendas, even to the point of disadvantaging the larger institutional unit. In fact, if we wish to pursue the elimination of collaboration barriers we have to realize that many barriers are not institutional at all. Choices to collaborate or not collaborate are sometimes based not just on current affiliations but on past affiliations, degrees obtained, reputations, and even a less than rational bias as to just who our collaboration partners should be.

Alpheus Bingham (Foreword)

Many people who enter the field of scientific research are inherently introspective or shy; others possess minds that are highly logical and analytic. Many scientists were loners at school, perhaps never participating in team activities, such as sports or group governance. <...> People without great collaborative skills may engage in criticism, blame, negativity, and back-biting, often when under high stress. They may horde information for fear it will be used improperly. They may withdraw when others need them most or engage in manipulative behavior to get the attention or credit they yearn for. They many not communicate well, especially listening carefully, and may not understand the human side of technical information.

Robert Porter Lynch (Chapter 2)

...Large-scale voluntary collaboration systems show remarkably consistent patterns in contributors’ behavior within scientific collaborations in the pharmaceutical industry and extending to every other company and industry examined. This behavior has all the signatures of a power law, driven by positive feedback from the individual and the group, and with a “long tail” such that approximately half of all contributions come from people who contribute only once to any given campaign. Interestingly the evidence also suggests that networks of acquaintanceship are not an essential driving force, which makes us revise our concept of “community”.

Robin W. Spencer (Chapter 6)

So, not surprisingly, what has happened in the past 20 years or so is biologists and chemical biologists (chemists working in biology) have resorted to data collecting. Genomics, proteomics, metabolomics, structural biology [X-ray and nuclear magnetic resonance (NMR)], chemical libraries, high-throughput assays, and so on, have been essentially data-collecting exercises. The “exciting discoveries” are made by robots, machines, and computers which collect enormous amounts of data. In the process human thought often seems to have become of secondary importance. At the same time, creative collaborations between chemists and biologists are often marginalized and starved for the resources...

Victor J. Hruby (Chapter 7)

Charles Darwin is an example of someone who acquired vast amounts of biological data from his correspondence with fellow naturalists and others with intimate knowledge of the natural world. Although the Victorian postal service that he used was comparatively efficient compared with today’s “snail mail” (and Darwin’s correspondence was prodigious), the need to communicate by letter writing inevitably slowed the development of his ideas on evolution. A modern Darwin alive today would be able to condense decades of networking into a few years, but it is interesting to speculate whether this speed would come at the expense of deep critical thought undertaken at a more leisurely pace.

Edward D. Zanders (Chapter 10)

discoveries today are really not expected

2011-10-05T21:01:00.004+01:00

From the telephone interview with Dan Shechtman, the winner of The Nobel Prize in Chemistry 2011:

Q: What do you think your experience of discovering quasicrystals taught you about science?

A: Oh, it taught me... This is a very good question! You know, it taught me that a good scientist is a humble scientist, somebody who is willing to listen to news in science which are not expected. Because discoveries today are really not expected – if they were expected they would have been discovered a long time ago. So something new, that is forbidden by some laws... people have to listen to this. In most cases, the news is not really news. But in some cases, discoveries are made and should be listened to.

blogging

2011-09-11T14:14:00.000+01:00

I have no illusions as to how many people read my blog. True, it was never meant to be read by many, but it is always nice to be reassured. Thank you Despair, Inc.! What about you?

19 August 1991

2011-08-19T15:00:00.000+01:00

Do I remember August Putsch? Yes. Vividly. Early morning Monday, 19 August 1991, I heard the news on the radio. The classical music followed. On the telly, interminable Swan Lake, just like when Brezhnev (later: Andropov) died. I can’t stand Swan Lake ever since.

I was working on my Ph.D. thesis then. Just a couple weeks before the putsch, I did a presentation at the International Conference on Cytochrome P450 hosted by my institute. Some guys were interested and there was even talk of a postdoc stint somewhere in the States or Japan. The future looked bright.

I took a suburban train to Moscow. As I was walking from Park Kultury towards my lab, I saw the tanks on the streets: not-so-gentle reminder what country I was living in. This latter circumstance was about to change in two days though.

inflated importance, unreal deadlines

2011-07-25T22:08:00.000+01:00

From Structured Procrastination by John Perry:

The list of tasks one has in mind will be ordered by importance. Tasks that seem most urgent and important are on top. But there are also worthwhile tasks to perform lower down on the list. Doing these tasks becomes a way of not doing the things higher up on the list. With this sort of appropriate task structure, the procrastinator becomes a useful citizen. Indeed, the procrastinator can even acquire, as I have, a reputation for getting a lot done.

The trick is to pick the right sorts of projects for the top of the list. The ideal sorts of things have two characteristics, First, they seem to have clear deadlines (but really don’t). Second, they seem awfully important (but really aren’t). Luckily, life abounds with such tasks. In universities the vast majority of tasks fall into this category, and I’m sure the same is true for most other large institutions.

One needs to be able to recognize and commit oneself to tasks with inflated importance and unreal deadlines, while making oneself feel that they are important and urgent.

fit for nothing

2011-06-15T11:11:00.000+01:00

From The Solitude of Prime Numbers by Paolo Giordano (translated by Shaun Whiteside):

He was dressed anonymously and had the posture of someone who doesn’t know how to occupy the space of his own body. The professor thought he was another of those who do well in their studies because they are unable to make much headway in life. The ones who, as soon as they find themselves outside the well-trodden paths of the university, always reveal themselves to be fit for nothing.

He looked at the scroll that he held rolled up in his hand, on which it was written in beautiful cursive script that Mattia Balossino was a graduate, a professional, an adult, that it was time for Mr Balossino, B.Sc., to face up to life, and that this meant he had reached the end of the track that he had blindly followed from the first year of primary school to his degree. He was still only half breathing, as if the air didn’t have enough momentum to accomplish the complete cycle.

What now? He wondered out loud.

that’s what the degree was about

2011-05-12T15:30:00.000+01:00

From Studies in the Park by Anita Desai:

My father laid his hand on my shoulder. I knew I was not to fling it off. So I sat still, slouching, ready to spring aside if he lifted it only slightly. “You must get a first, Suno,” he said through his nose, “must get a first, or else you wont get a job. Must get a job, Suno,” he sighed and wiped his nose and went off, his patent leather pumps squealing like mice. I flung myself back in my chair and howled. Get a first, get a first, get a first — like a railway engine, it went charging over me, grinding me down, and left me dead and mangled on the tracks.

I felt as if we were all dying in the park, that when we entered the examination hall it would be to declared officially dead. That’s what the degree was about. What else was it all about? Why were we creeping around here, hiding from the city, from teachers and parents pretending to study and prepare? Prepare for what? We hadn’t been told. Inter, they said, or B.A. or M.A. These were like official stamps — they would declare us dead. Ready for a dead world. A world in which ghosts went about, squeaking or whining, rattling or rustling. Slowly, slowly we were killing ourselves in order to join them. The ball-point pen in my pocket was the only thing that still lived, that still worked.

chair of comparative ambiguity

2011-04-14T17:00:00.001+01:00

In the introduction to The Oxford Hysteria of English Poetry, which appears in his book Greatest Hits: His 40 Golden Greats, Adrian Mitchell wrote:

I spent three years at Oxford studying Modern English Literature (500—1815). Allegedly. So I thought I should pass on the fruits of my enhanced brainbox to all and sundry especially the latter. Most of my audience is pretty sundry. It is meant to be spoken by a very old battered poet who has survived from the days when we had pterodactyls instead of critics.

There hasn’t been much time
For poetry since the Twenties
What with leaving the Communist Church
To join the Catholic Party
And explaining why in the C.I.A. Monthly.

Finally I was given the Chair of Comparative Ambiguity
At Armpit University, Java.
It didn’t keep me busy,
But it kept me quiet.
It seemed like poetry had been safely tucked up for the night.

scientifically produced antiscience

2011-03-12T14:00:00.002Z

From Zen and the Art of Motorcycle Maintenance (1974) by Robert M. Pirsig:

If the purpose of scientific method is to select from among a multitude of hypotheses, and if the number of hypotheses grows faster than experimental method can handle, then it is clear that all hypotheses can never be tested. If all hypotheses cannot be tested, then the results of any experiment are inconclusive and the entire scientific method falls short of its goal of establishing proven knowledge.

It looked as though the time spans of scientific truths are an inverse function of the intensity of scientific effort. Thus the scientific truths of the twentieth century seem to have a much shorter life-span than those of the last century because scientific activity is now much greater. If, in the next century, scientific activity increases tenfold, then the life expectancy of any scientific truth can be expected to drop to perhaps one-tenth as long as now. What shortens the life-span of the existing truth is the volume of hypotheses offered to replace it; the more the hypotheses, the shorter the time span of the truth. And what seems to be causing the number of hypotheses to grow in recent decades seems to be nothing other than scientific method itself. The more you look, the more you see. Instead of selecting one truth from a multitude you are increasing the multitude. What this means logically is that as you try to move toward unchanging truth through the application of scientific method, you actually do not move toward it at all. You move away from it! It is your application of scientific method that is causing it to change!

What Phaedrus observed on a personal level was a phenomenon, profoundly characteristic of the history of science, which has been swept under the carpet for years. The predicted results of scientific inquiry are diametrically opposed here, and no one seems to pay too much attention to the fact. The purpose of scientific method is to select a single truth from among many hypothetical truths. That, more than anything else, is what science is all about. But historically science has done exactly the opposite. Through multiplication upon multiplication of facts, information, theories and hypotheses, it is science itself that is leading mankind from single absolute truths to multiple, indeterminate, relative ones. The major producers of social chaos, the indeterminacy of thought and values that rational knowledge is supposed to eliminate, is none other than science itself. And what Phaedrus saw in the isolation of his own laboratory work years ago is now seen everywhere in the technological world today. Scientifically produced antiscience — chaos.

America, Britain

2011-02-07T23:23:00.002Z

From Faster Than the Speed of Light (2003) by João Magueijo:

Regrettably, people are often most proud of their most appalling attributes, and indeed many American scientists appear to be more appreciative of bandwagons than of their Feynman legacy. I once met a girl in New York who was thrilled to find out I was a physicist; but she became terminally disappointed upon hearing that I lived in England and harbored no ambitions to move to the United States. She simply couldn’t understand that. When I asked why, she tried to reply with an example, but she couldn’t remember the name of the physicist in point. She asked me, “Who was the physicist who was better than Einstein, but never came to the U.S. so he never made it?”

To this day I have no idea who this mythical character might be.

Britain has a unique ability to let its talent go. People like to say that it’s because its academic institutions cannot financially compete with the United States, but I find that a poor excuse. In fact the British “brain drain” is totally self-inflicted, the product of a culture in which accountants, lawyers, consultants, politicians, and financial morons of all varieties are prized well above teachers, doctors, nurses, etc. It’s considered bad taste in Britain to do anything useful these days.

work is overrated

2011-01-20T22:06:00.000Z

From New Rules For Writers by Anis Shivani:

Find ways to be unemployed, doing nothing, finding enough time on your hands, after you’ve met your basic needs, to wander into unknown realms of thought and imagination. You can’t do it when you’re busy working like everyone else, collecting a paycheck, keeping regular hours, depending on the goodwill and collegiality of customers, coworkers, bosses — if you choose employment in academia, it’s no different, you still have clients and bosses to please. Avoid this gentle poison by figuring out ways you can mock the system by taking from it what it needs to give you to maintain your writing, and give it nothing back in return.

What it wants from you is your time — your only irreplaceable commodity, the only thing you can’t ever get back. Every minute spent teaching a student or hiring out your talents in any other way is an insult to your writing potential, and each such moment degrades you so that you can never attain greatness. They’re more than happy to give you a paycheck. Heck, there are tens of thousands of writers “teaching” writing to others, dissatisfied with their own work, and they wonder why? Refuse their devil’s bargain. Refuse them the blood and toil they want from you in return for allegiance. Work at something that mocks the bourgeois idea of work, and make it pay off. You don’t have to work for nothing. You don’t have to live on nothing. You just have to figure out how to turn work on its head so it becomes a means to feed your writing, not the other way around. Work is overrated. It’s the only overrated thing in the whole human realm.

you start to think it’s normal

2010-12-29T23:23:00.001Z

From The Time I Heard the Private Donald J. Rankin String Concerto with One Discordant Violin, by the American Composer John Morton by Yann Martel:

I hate this place. I hate it because whenever I come here during the day I like it and nearly fall for it. It’s comfortable and warm, the people are nice, and you know what’s expected of you. I say to myself, You should get a daytime job here. The pay’s good, better than what you make now anyway, you work with people, the hours are sane — hey, why not?

Then I catch myself. This place is dangerous it’s so cunning. It crawls up on you stealthily. You get used to it, the routine, you know. You start to think it’s normal. Finally you think there’s nothing else. Then you blink, forty years have gone by, and your life’s over. Sometimes I come here during the day and I look in from the outside and I ask myself, Why don’t these people ask for more?

scientists and bureaucrats

2010-12-12T17:30:00.002Z

From the book A Journey of the Imagination: The Art of James Christensen; captions by the author.

Three Scientists Debating the Aerodynamic Capabilities of the Dynastes Beetle

The beetle flies for two miles at a stretch, but these self-important egos are debating it “scientifically”. You may notice that their feet don’t match up and it’s very hard to tell where one leaves off and another begins. They have, in effect, lost their personal identities in their quest for self-importance.

The Old Scholar

Every university has an old scholar or two, professors whose learning stopped years ago, here symbolized by the wormy apple and the snuffed-out candle. The tatty, stuffed owl on wheels, the Ptolemaic (earth-centered) solar system, and the Leonardian sketch that’s all out of kilter symbolize wisdom that has become outdated or obsolete.

Life-Size Portrait of a Very Minor Official

I have an ongoing battle with the rigidity of bureaucracy. This is an officious little minor dignitary. If we use hieratic scaling — that is, the most important person in an image is the largest — then this tiny little portrait is life-sized.

the science of snowballing

2010-11-28T17:00:00.003Z

Continuing with the Arctic exploration theme: a scene from hilarious Belgian animation Panique au village (see the clip from 6:27 onwards). The three mad scientists, operating a giant mechanical penguin and entertaining themselves with long-distance snowballing. Where do they hire for jobs like that?

from annals of adult psychophysics

2010-11-22T19:02:00.006Z

Now about the scientific expeditions — in words of a certain Humbert Humbert:

One of my favourite doctors, a charming cynical chap with a little brown beard, had a brother, and this brother was about to lead an expedition into arctic Canada. I was attached to it as a ‘recorder of psychic reactions’.

I had little notion of what object the expedition was pursuing. Judging by the number of meteorologists upon it, we may have been tracking to its lair (somewhere on Prince of Wales’ Island, I understand) the wandering and wobbly north magnetic pole. One group, jointly with the Canadians, established a weather station on Pierre Point in Melville Sound. Another group, equally misguided, collected plankton. A third studied tuberculosis in the tundra. Bert, a film photographer — an insecure fellow with whom at one time I was made to partake in a good deal of menial work (he, too, had some psychic troubles) — maintained that the big men on our team, the real leaders we never saw, were mainly engaged in checking the influence of climatic amelioration on the coats of the arctic fox.

I left my betters the task of analysing glacial drifts, drumlins, and gremlins, and kremlins, and for a time tried to jot down what I fondly thought were ‘reactions’ (I noticed, for instance, that dreams under the midnight sun tended to be highly coloured, and this my friend the photographer confirmed). I was also supposed to quiz my various companions on a number of important matters, such as nostalgia, fear of unknown animals, food-fantasies, nocturnal emissions, hobbies, choice of radio programs, changes in outlook and so forth. Everybody got so fed up with this that I soon dropped the project completely, and only toward the end of my twenty months of cold labor (as one of the botanists jocosely put it) concocted a perfectly spurious and very racy report that the reader will find published in the Annals of Adult Psychophysics for 1945 or 1946, as well as in the issue of Arctic Explorations devoted to that particular expedition; which, in conclusion, was not really concerned with Victoria Island copper or anything like that, as I learned later from my genial doctor; for the nature of its real purpose was what is termed ‘hush-hush’, and so let me add merely that, whatever it was, that purpose was admirably achieved.

Vladimir Nabokov, Lolita (1955)

a general disinclination to work of any kind

2010-11-01T17:00:00.004Z

From Three Men in a Boat by Jerome K. Jerome:

In the present instance, going back to the liver-pill circular, I had the symptoms, beyond all mistake, the chief among them being “a general disinclination to work of any kind.”

What I suffer in that way no tongue can tell. From my earliest infancy I have been a martyr to it. As a boy, the disease hardly ever left me for a day. They did not know, then, that it was my liver. Medical science was in a far less advanced state than now, and they used to put it down to laziness.

“Why, you skulking little devil, you,” they would say, “get up and do something for your living, can’t you?” – not knowing, of course, that I was ill.

actually working

2010-10-21T01:00:00.002+01:00

My favourite quotes from the Work section of The Lazy Person’s Guide to Life by Gray Joliffe, a truly wonderful book which seems to be out of print. If I ever get back to regular employment, I have to make sure that I can reach my full lazy person’s potential there.
actually working

Some people like making work complicated because it gives them a sense of identity and importance. Those of use who are secure enough not to need this reassurance attempt to simplify everything, and get through it quicker.

The easiest thing to be at work is the boss, because then you can delegate everything and concentrate on important things like lunch and going home early.

business travel

After all, that amount of iron isn’t entitled to fly.

commuting

The lazy person’s philosophy is this: as most of us work with our brains it is ludicrous to transport our bodies from one place to another, home to office.

getting fired

Getting fired is harmful to the self-esteem, but only for the first five or six times, after which you give up on yourself and make your fortune painting abstracts under an assumed name.

meetings

Meetings are for the most part unnecessary, but if you are dragged into one, you can catnap surreptitiously and that beats working. Don’t let key people see your eyes snap shut, though, because it looks amateur.

self-employment

Lazy people are never unemployed, as they prefer to call it freelance or self-employed.

For more quotes, go here.

budget cuts vs Nobel prizes

2010-10-12T21:50:00.002+01:00

Science is Vital has got its official website and a bunch of celebrity supporters, including Sir Patrick Moore and the Nobel laureate Sir Paul Nurse. More than 30,700 have signed the Petition to be delivered to Downing Street this coming Thursday. (You still have a few hours to sign it!) Who knows, this time it may work. Or may mot. I just read on Exquisite Life blog that

To pay for a Conservative—Liberal deal on student fees, ministers are considering the possibility of a second wave of extra cuts to science budgets after the Comprehensive Spending Review.

And speaking of Nobels: isn’t it good news that four of this year’s Nobel crop (Robert G. Edwards, Andre Geim, Konstantin Novoselov and Christopher Pissarides) are based in Britain? That undoubtedly will help the argument. As Lord Rees, President of the Royal Society (quoted here) put it,

Just this week two Russian scientists <Geim and Novoselov>, working in the UK for the last ten years, won Nobel Prizes. Would they have chosen the UK today, when cuts are threatened?

On the other hand, and quite in contrast to last year, there were no women Nobel prize winners this time. Shame.

science is vital

2010-09-18T20:00:00.003+01:00

Britannia used to rule the world but does not any longer. It doesn’t have much in terms of natural resources, the public transport is awful and more or less everything here is overpriced. Which is understandable, since this country produces very little. London may host the next Olympics but a great sports nation Britain is not. And don’t even start me on weather.

Let’s face it, the only two things Britain is any good at are science and gardening. Some people would disagree and insist that British gardening is excellent, rather than “any good”. That’s fine with me. More to the point, I am told that a lot of scientific research in the UK is world-class. I won’t argue with that either, even though I myself never was involved in world-class research. You would expect the world-class research attract at least some decent funding, and then some more funding to add more class to “just” research, right? A man can dream. But then the government tells us that there is a huge budget deficit “that we inherited” (from the previous government, of course) and science funding also must be cut, which reminds me that we are still surrounded by idiots. I can’t agree more with Robert M. May writing in New Scientist that

the current thinking is not just wrong, it’s mad.

Now I am not a big fan of joining the Facebook groups, but I am prepared to make an exception for a good cause when I see one. Science is Vital is actually doing something: organising a March for Science on Saturday 9th October in central London, and will be lobbying Parliament on Tuesday 12th October. If you are reading this, please join the group, spread the word, plan a day out in London... speak up against the madness.

Of course, there always will be gardening.

not afraid to say “we don’t know”

2010-09-06T22:00:00.001+01:00

From The Housekeeper and the Professor by Yoko Ogawa (translated by Stephen Snyder):

“Solving a problem for which you know there’s an answer is like climbing a mountain with a guide, along a trail somebody else has laid. In mathematics, the truth is somewhere out there in a place no one knows, beyond all the beaten paths. And it’s not always at the top of the mountain.”

Among the many things that made the Professor an excellent teacher was the fact that he wasn’t afraid to say “we don’t know”. For the Professor, there was no shame in admitting you didn’t have the answer, it was a necessary step toward the truth. It was as important to teach us about the unknown or the unknowable as it was to teach us what had already been safely proven.

shortlisted

2010-09-01T18:00:00.003+01:00

“Shortlisted” (or even longlisted) “for Booker / Pulitzer / Orange Prize...” Did you ever wonder why it is OK for fiction authors to put these credentials on the book covers while listing the failed job interviews on your CV is deemed off-limits? Once upon a time, last century, I was shortlisted for a lectureship. On the interview, I had a chance to meet two other candidates, one of whom was eventually offered the position. That means, at some point I had 33% chance to get that job. And yet I feel that it won’t do me much good if I put this fact (that I blew my chance, that is) in my CV. Because in this sport only the wins count.

Frankly, this is ridiculous. If I were lucky and got that or other job, I wouldn’t send my CVs around any longer, right? So it shouldn’t really harm to mention that some of the previous applications resulted in interviews. Same goes for grants. You are expected to include the successful grant proposals in your CV. Why only successful? The writing of unsuccessful grant application is as time-consuming — and as important.

Do you know what helps to get a grant? That’s right: being employed. Therefore, being employed helps being employed, and having grants helps getting grants.

logy, logue, logia

2010-08-04T23:00:00.003+01:00

First published 3 August 2010 @ just some words

Contrary to what you read in Wikipedia, -logy is not a suffix. If anything, it is a root. It is derived from Greek word logos (λόγος) which has a lot of meanings:

speech, oration, discourse, quote, story, study, ratio, word, calculation, reason.

The Concise Oxford Dictionary says:

-logy /ləʤɪ/ comb. form forming nouns denoting: 1 (usu. as -ology) a subject of study or interest (archaeology; zoology). 2 a characteristic of speech or language (tautology). 3 discourse (trilogy). [F -logie or med. L. -logia f. Gk (as Logos)]

I like “a subject of study or interest” better than “science”, because “logies” in a sense (1) also include astrology, phrenology and pyramidology. (One former colleague of mine used to say that there are real sciences, like chemistry and physics, and phony ones, which all end on “ology”.) There is a tendency (at least as far as renaming of university departments goes) to substitute well-established terms of Greek etymology with pluralised English equivalents: “earth sciences” instead of “geology”, “life sciences” instead of “biology” and so on. I can’t help thinking that, by using plurals, they try to get more funding. But what on earth is “biological sciences” if not a tautology? Does not biology sound scientific enough? Apparently not.

Since there are too many fields of study and people know only so many Greek words, it is inevitable that quite a few “logy” (1) terms are hybrid words which mix Latin and Greek parts. For example, sociology (the corresponding Greek word is κοινωνιολογία) and scientology (both contemporary and early usages of which sound tautological). Similarly, Italian, Russian and other Slavic languages have a hybrid word algologia (альгология) — phycology, a branch of botany dealing with algae. The (non-hybrid) English term algology means something else: study of pain.

Then there is philology. It does not mean “study of love” but the other way round: “love of study”. Really, it should be logophilia, and indeed such a word exists, meaning “love of words”, with a vague hint of a medical condition.

“Logies” (2) include dilogy, palilogy, phraseology, terminology — you name it.

Apology and eulogy belong to the third group of “logies”. These two can be made into verbs (apologise, eulogise) — something you really cannot do with “logies” of (1) and (2) types. “Logy” (3) is very similar to -logue as in dialogue, monologue, catalogue, Decalogue...

What about analogy and homology? They don’t belong to any of these three categories. They are derived from the same Greek root logos but use another meaning of it: ratio, proportion.

Many European languages retained the Greek spelling, -logia of their -logies (see the table below). In English, logia (Greek λόγια), a plural of logion, refers to collection of sayings of Jesus, especially those which did not end up in the Gospels. In Spanish, logia (from Italian word loggia) means either lodge (as in Logia Masónica) or, er, loggia.

English	analogy	pharmacology	tautology	trilogy
French	analogie	pharmacologie	tautologie	trilogie
German	Analogie	Pharmakologie	Tautologie	Trilogie
Greek	ἀναλογἰα	φαρμακολογία	ταυτολογία	τριλογία
Italian	analogia	farmacologia	tautologia	trilogia
Portuguese	analogia	farmacologia	tautologia	trilogia
Russian	аналогия	фармакология	тавтология	трилогия
Spanish	analogía	farmacología	tautología	trilogía

just some words

2010-08-04T22:55:00.002+01:00

Three months ago, I started another “low-throughput” blog, just some words. I wanted to have not-Blogger blog. But why did I choose to host it on Maneno? First, Maneno is multi-lingual, and I want to have an option to publish in more than one language. Second, Maneno is African.

It allows those with limited or narrow-bandwidth internet to use a system that is lightweight and straightforward in functionality.

One day I move to Africa and will need this! Last but not least: “maneno” means “words” in Swahili, and my new blog is all about words. From different languages.

Now I read on its Site Blog that Maneno is

going to gradually stop hosting blogs on the system as well as not accept any new joins.

That means, “somewhere down the road” I will have to move just some words somewhere else. In the meantime, I’d like to reproduce here one of my articles.

i don’t know how to teach

2010-06-14T19:00:00.002+01:00

Professor Farnsworth is my all-time favourite mad scientist. I don’t know in which field he is a professor but since he is teaching at Mars University, it is not even relevant. Professor does not care either in which field he wants the Nobel Prize: “They all pay the same”.

Fry: “Hey, professor. What are you teaching this semester?”
Farnsworth: “Same thing I teach every semester: the mathematics of quantum neutrino fields. I made up the title so that no student would dare take it.”
Fry: “Mathematics of wonton burrito meals. I’ll be there!”
Farnsworth: “Please, Fry, I don’t know how to teach. I’m a Professor!”

tragedy of the immigrants

2010-06-03T22:03:00.002+01:00

From Brick Lane by Monica Ali:

‘This is the tragedy of our lives. To be an immigrant is to live out a tragedy.’
‘What are you talking about?’
‘The clash of cultures.’
‘I beg your pardon?’
‘And of generations,’ added Chanu.
‘What is the tragedy?’

Mrs Azad, the doctor’s wife, is puzzled and annoyed by Chanu’s incessant talk of a tragedy.

‘Of course, the doctor is very refined. Sometimes he forgets that without my family’s help he would not have all those letters after his name.’
‘It’s a success story,’ said Chanu, exercising his shoulders. ‘But behind every story of immigration success there lies a deeper tragedy.’
‘Kindly explain this tragedy.’
‘I’m talking about the clash between Western values and our own. I’m talking about the struggle to assimilate and the need to preserve one's identity and heritage. I’m talking about children who don’t know what their identity is. I’m talking about the feelings of alienation engendered by a society where racism is prevalent. I’m talking about the terrific struggle to preserve one's own sanity while striving to achieve the best for one’s family. I’m talking—’
‘Crap!’

‘The society is racist. The society is all wrong. Everything should change for them. They don’t have to change one thing. That,’ she said, stabbing the air, ‘is the tragedy.’

drive

2010-05-22T16:55:00.001+01:00

An amazing animation by RSAnimate, inspired by Dan Pink’s talk at the RSA and his latest book, Drive.

As long as the task involved only mechanical skill, bonuses worked as they would be expected: the higher the pay, the better the performance. But once the task called for even rudimentary cognitive skill, a larger reward led to poorer performance.

is brevity my sister?

2010-04-24T12:24:00.012+01:00

I don’t know about you, but I can’t stand people who constantly talk on their mobiles. Back in 1995, Bill Bryson wrote in his Notes from a Small Island:

These people are getting to be a real nuisance, aren’t they? This one was particularly irritating because his voice was loud and self-satisfied and littered with moronspeak, and his calls were so clearly pointless: ‘Hello, Clive here. I’m on the 10.07 and should be at HQ by 1300 hours as expected. I’m going to need a rush debrief on the Pentland Squire scenario. What say? No, I’m out of the loop on Maris Pipers. Listen, can you think of any reason why anyone would employ a total anus like me? What’s that? Because I’m the sort of person who’s happy as a pig in shit just because he’s got a mobile phone? Hey, interesting concept.’

Then a few moments of silence and: ‘Hello, love. I’m on the 10.07. Should be home by five. Yes, just like every other night. No reason to tell you at all except I’ve got this phone and I’m a complete fuckwit. I’ll call again from Doncaster for no reason.’ Then: ‘Clive here. Yeah, I’m still on the 10.07 but we had a points failure at Grantham, so I’m looking now at an ETA 13.02 rather than the forecast 1300 hours. If Phil calls, will you tell him that I’m still a complete fuckwit? Brill.’ And so it went on all morning.

Fifteen years later: what has changed? Clive got a smartphone, learned how to text and tweet, even how to post hideous photos at Facebook, but the gist remains the same.

Maybe that was the reason of my initial dislike of Twitter? Of course, it’s not Twitter’s fault that most tweets appear to be as semantically rich as blather of Bryson’s “Vodaphone Man”. On the other hand, the 140-character limit poses quite a challenge. If you have anything interesting to say at all, say it in a few words. Because the papers, patents, grant applications, grant reports, CVs and associated documents, like “teaching philosophy”, even blogs (including this one), all suffer from logorrhoea. I’m sure both authors and reviewers will benefit from shorter, um, whatever.

Imagine a grant proposal in a tweet. Sounds interesting — has value. Boring — goodbye, end of story. As an experiment, I’ve created a Twitter account, ecologicalniche, just to see what it may look like. I promise not to fill it with my daily minutiae. Just with some silly ideas. In a faint hope that one sunny day somebody agrees to fund them.

crowdsourcing

2010-03-26T20:00:00.005Z

There are only a few buzzwords which irritate me more than this one. But what exactly is crowdsourcing? According to Wiktionary, it means “delegating a task to a large diffuse group, usually without substantial monetary compensation”. While Jeff Howe, who coined this horrid word back in 2006, gives us two definitions:

The White Paper Version: Crowdsourcing is the act of taking a job traditionally performed by a designated agent (usually an employee) and outsourcing it to an undefined, generally large group of people in the form of an open call.

The Soundbyte Version: The application of Open Source principles to fields outside of software.

Thus, according to the White Paper Version, crowdsourcing is kind of outsourcing. Which, like it or not, is a means to increase capitalist exploitation by paying less for the same job. I like the the Soundbyte Version better even though it is a bit too vague. But what it has to do with crowdsourcing?

Folk music is not created by some amorphous Volk mass but by the individual musicians, most of whom do have names. Similarly, the open content is not created by a crowd. In words of Dan Woods,

There is no crowd in crowdsourcing. There are only virtuosos, usually uniquely talented, highly trained people who have worked for decades in a field. Frequently, these innovators have been funded through failure after failure. From their fervent brains spring new ideas. The crowd has nothing to do with it. The crowd solves nothing, creates nothing.

Take this call to the community regarding stereochemistry of digitonin (mentioned on my other blog). Where is a crowd? Everyone who responded is an expert. (Yes, that includes me, even if I say so myself.) And was the problem solved? No.

Wikipedia’s list of crowdsourcing projects include Wikipedia itself, “despite objections by co-founder Jimmy Wales to the term” (and, I bet, to the annoyance of many authors of Wikipedia articles); InnoCentive, Goldcorp and other companies which give cash prizes to individual solvers responding to a challenge; a few nice examples of citizen science; and, wait, some bona fide crowdsourcing:

In January 2008, the State of Texas announced it would install 200 mobile cameras along the Texas-Mexico border, to enable anyone with an Internet connection to watch the border and report sightings of alleged illegal immigrants to border patrol agents.

Now you’d think that this latter initiative, being not as intellectually challenging as, say, virtual protein folding, may actually work. But no: all these millions of web hits so far failed to translate “into much law enforcement work”.

my yawning gap year

2010-02-28T17:00:00.007Z

28 February 2009. I woke up in the morning (hey, that sounds like blues!) realising that I am not going to work today, or next week, or next month. Freedom!

When I were a lad, the concept of gap year was unheard of. After the school, young men were facing a choice of either university or a two-year spell in the army — or, with any luck, three-year spell in the navy. As exciting as it was, the military stint never appealed to me; six years in the university looked so much more prudent. I started working full-time couple months after graduation (and I was working part-time for almost three years before that). Work, work, work. Work.

We were taught that regular employment is good and absence thereof is bad. I don’t know, I quite enjoy the fact that I can sleep as much as I want while I am, er, on me career break. Speaking of which: according to Wikipedia,

The <gap year> market demographic is split into those aged 18—24 (pre, during and post university), 25—35 (‘career gap’, also known as ‘Career Break’ and ‘Career Sabbatical’) and 55—65 (pre and post retirement gappers).

Now I know: mine is post-sabbatical pre-preretirement gap — apparently underoccupied ecological niche.

no landing cards for me

2010-02-19T21:37:00.004Z

Yesterday, while waiting in a queue to the passport control at Stansted airport, I was pondering how lucky I am to have British passport. I don’t have to fill the landing card anymore. I cannot tell exactly how many of these I have completed during my first ten years in this country. A lot. I never could understand what is the point of these scraps of paper in the era of computer-readable passports. And yet, according to Wikipedia,

Failure to complete a Landing Card when this is required is a crime punishable by a fine or 6 months in prison.

I wonder how determined one should be to end up in prison. I mean, they just won’t let you in unless you complete it, right?

One has to do that even after obtaining indefinite leave to remain in the UK. I remember the first time I entered the country with my brand new ILR stamp in the passport.

“For how long are you going to stay?”
“Forever.”
“For EVER?!”

You had to see the immigration officer’s face. It turned out that he never saw the (then) new-style ILR stamp before.

If I still had to fill this form, what would I put as “occupation”? Probably “none”. I can only guess what would be the reaction. Alas, my Russian passport has expired so I am postponing this experiment. Indefinitely.

back in my student years

2010-02-12T22:28:00.005Z

Circa 1986. The professor at our department of biophysics is saying (to nobody in particular):

«Я только что сказал моим студентам что работать в науке надо много. А теперь я надеваю пальто и иду домой.»

“I just told my students that in science one has to work a lot. And now I put on my coat and go home.”

what’s wrong with science blogging?

2010-02-08T22:17:00.006Z

There was an interesting post by David Crotty entitled Science and Web 2.0: Talking About Science vs. Doing Science on The Scholarly Kitchen blog.

Even without new online technologies, scientists already spend a substantial portion of their time communicating. They share results with peers, plan future experiments with collaborators, give talks, write papers, teach, etc.

Frankly, I don’t see why any of these activities are incompatible with blogging. Quite the reverse: blogging can be a way to improve the communication. If you give a presentation, whether at a conference or in a classroom, why not to post it online? And is there any better way to share your results than to blog about them?

New social media endeavors ask scientists to devote even more time to communication, but it’s unclear where participants are supposed to find that time. Every second spent blogging, chatting on FriendFeed, or leaving comments on a PLoS paper is a second taken away from other activities. Those other activities have direct rewards towards advancement. It’s hard to justify dropping them for activities backed by vague promises that “you will be one of the early adopters and will be recognized and respected for this in the future.” That’s a tough gamble for most to take, and scientists are unlikely to risk current status for a leg up in the event that sweeping societal changes occur in how we fund, employ, and judge scientific achievement.

Thus, it is inherent conservatism of those who are “unlikely to risk current status” that prevents the scientific community from embracing new technology. If so, then that’s too bad for science. But really, should we worry?

The author discriminates between scientists and people who talk about science, for example... teachers. Excuse me. I heard there are many people in academia whose positions include a lot of teaching. On the one hand, “scientists are no different than other humans” (and most people don’t blog, ergo most scientists shouldn’t either). On the other hand, it is implied that they require the communication tools different from “mainstream” ones. I do recall that in 1980s there was a belief that scientific computing should be done on specialised workstations, not PCs or Macs. Now most of the scientific computing is done exactly on the same PCs and Macs.

The blogging in science may never become a mainstream activity. Or maybe it is the future of scientific communication. Consider this: people blog because they like blogging, not because they have nothing else to do. Also, people go to science because science is fun. While writing grant proposals and, in most cases, writing research papers is not fun. (That also explains why reading grant proposals and most research papers is not fun either.) The sooner scientists leave these not-fun activities behind, the better. Or so one can hope.

i use the eighty/twenty rule

2010-01-31T12:00:00.003Z

The Pareto principle, widely known as 80-20 rule, has been used, abused and ridiculed innumerable times. Perhaps the funniest joke involving the rule is this one:

Chicago Driving 80/20 rule: 80% of your waving will be done with 20% of your fingers.

To quote Dilbert and the Way of the Weasel:

Another good utility phrase is “I use the eighty/twenty rule”. Toss it into conversation at any time. This will generate strong agreement because it fits any situation where you have no data. It doesn’t even matter what part is eighty and what is the twenty. It just always sounds right.

For example, if you’re waiting for people to arrive for a meeting you could say, “For any business meeting, eighty percent of the people come on time and twenty percent are late”. That sounds totally reasonable. But if you say it the other way around it sounds just as reasonable: “For any business meeting, twenty percent of the people come on time and the other eighty percent are late”. It’s like magic.

Granted, it may sound reasonable to those who never heard about the Pareto principle, but the business meeting example is not the illustration of the 80-20 rule.

The Pareto principle is a special case of the Pareto distribution. The two numbers do not have to add to 100 because they apply to different things entirely. In the example graph below, “20” correspond to 20% of whatever the horizontal axis stands for, while “80” corresponds to the green area above it which takes 80% of all area.

Back in 1998, Sidney Redner analysed “popularity” of scientific papers in terms of citation. It turns out that there is no such thing as a typical number of citations received by a published paper. He counted the citations for the ISI list of papers published in 1981 (783,339 papers) and found that

most publications are minimally recognized, with ≈47% of the papers in the ISI data set uncited, more than 80% cited 10 times or less, and ≈.01% cited more than 1000 times. The distribution of citations is a rapidly decreasing function of citation count but does not appear to be described by a single function over the entire range of this variable.

Couple of years later, two Brazilian scientists, Constantino Tsallis and Marcio de Albuquerque, analysed the same data set and, contrary to Redner’s conclusion, found that there exists a single power law-type function N(x) along the entire range of the citation number x.

What, if anything, does it tell us? If scientific papers exhibit universality, that is, behave in the same fashion as sand piles or earthquakes or stock markets (and it looks like they do), then there is no way to predict whether a paper will be popular or not. Moreover, this kind of distribution has nothing to do with scientific qualities of a paper. The authors should stop worrying — or boasting — about impact factors and concentrate on important things, like getting a life.

i ask too many questions

2010-01-24T20:29:00.007Z

I am getting tired of constant rewriting of my CV. (Not that I did any this year, you understand, but this is besides the point.) But then, I am easily tired of any repetitive useless work. Why don’t they have an analogue of OpenID in the world of CVs? That would save everybody’s time and effort, right? Right. And the answer is: maybe they (whoever “they” are) don’t want to save anybody’s time and effort. That will put all those CV writing agencies out of business, and it’s bad for the economy.

Consider this template for application for employment. The template itself is only six pages, however I guess the complete application should be the size of a short monograph. Here are some highlights (colouring is mine).

The application must be structured as specified by the template below,

or else.

4 DECLARATION OF INTENT/VISION

Describe your vision and your plans for the future with respect to both scientific and educational activities, within the framework of the employment sought (maximum one page).

5 SCIENTIFIC EXPERTISE

5.1 Description of research activities (maximum two pages). <...> The description should include an assessment of the applicant’s independence and productivity.

6 TEACHING EXPERTISE

6.1. Self-reflection over the role of teacher
The description of teaching expertise should make clear not only what the applicant has done but also how it has been done, why it was done in just this way, and the results. The applicant is to state his or her fundamental educational principles and the way these are expressed in practice.

What could be the “results” I wonder. “90% of my students became managers”?

The self-reflection is to have a maximum length of five pages when applying for employment as professor or senior lecturer, and a maximum length of one page when applying for employment as postdoctoral research fellow or associate senior lecturer.

You see, even poor research post-docs are not free from writing this nonsense.

9 PERSONAL ASSESSMENT

The applicant should describe his or her own personality in a manner that makes it possible to assess the ability to work with others, and the suitability for employment as described in the job announcement.

(Isn’t it the job of the evaluation committee to decide on the suitability for employment? Is anyone going to write “I am not suitable for employment” anyway?)

My first reaction was: are they bonkers? I mean, who is going to write all this rubbish? And perhaps more importantly: who is going to read it?

Calm down, I tell myself, there must be some sense in it. I can think of two reasons to insist that the application conforms to this template. First: to reduce the number of applicants. Most people have better things to do and therefore won’t even bother. Second: to pre-select those candidates who are ready to sacrifice a few days of their lives to write a long meaningless document that nobody is going to read. It gives the prospective candidates a taste of things to come. In academic world, it is not reading that counts, it’s writing.

loose ends

2010-01-07T21:21:00.009Z

Ten years ago or so, I attended the lecture of Sydney Brenner. And what a treat it was. He managed to keep the audience’s attention for an hour without showing a single slide or using any other prop. I remember his notion that bioinformatics is to theoretical biology as accountancy is to economics. I don’t think it went particularly well with that (sizeable) part of audience which was comprised of bioinformaticians. Including me. Ten or so years later, I tend to agree with Dr Brenner.

Loose Ends is a collection of columns written by Brenner for Current Biology between 1994 and 1997. I got this book as a gift, back in 1998. Apparently, it is out of print now, which is a shame. It should be made a compulsory reading for every biologist.

Molecular biology has been a great leveller and has made thinking unnecessary in many areas of modern biology. With the disappearance of theory has also come the decline of experimentation, and the practice of science by hypothesis and testing is not known by many students in the field. So powerful are contemporary tools for extracting answers from nature that pausing to think about the results, or asking how one might find out how cells really work, is likely to be seen as a source of irritating delay to the managerial classes, and could even endanger the career of the questioner.
(In Theory)

The best publication list I have ever seen was that of a candidate for some official post who was engaged in defence research. The two first papers were: Landing aeroplanes on aircraft carriers I & II, Restricted circulation. The remaining items, numbered 3 to 9, were labelled “Secret”. I would have been tempted to inflate the list of secret publications to 19.
(Citation matters)

For better or for worse, some of Brenner’s predictions of nineties became reality in the noughties. Mostly for worse, I’m afraid.

Before we develop pseudoscience of citation analysis, we should remind ourselves that what matters absolutely is the scientific content of a paper and that nothing will substitute for either knowing it or reading it.
(Citation matters)

Nowadays, the said pseudoscience is flourishing.

I predict that very soon every grant application will have to include a strategic mission statement and a business plan, as well as an organogram outlining the structure of the laboratory with a clear definition of who reports to whom. Perhaps as time goes on and science gets more difficult to do, the actual research project will come to be a smaller part of the application. Eventually it may disappear all together. This would fulfil the ultimate dream of every manager and administrator, which is simply to have pure management with no content...
(A tiresome business)

debating tenure

2010-01-04T19:56:00.005Z

In one of Friends episodes, Ross is getting tenure and is very excited about it. (You can tell that the series was drawing to the end.)

“You know what the best part about this is? I can never be fired.”

Here is another thing Ross gets wrong, although he simply repeats a popular myth. But what exactly is tenure? The latest (October/November 2009) issue of Academic Matters is dedicated to this strange creature, and I thoroughly enjoyed reading it.

In words of Michiel Horn,

Tenure is not without drawbacks. But these are the price that has to be paid to protect the innovative, the unconventional, and the unpopular, those whose fields of academic specialization have fallen into disfavour and, most of all, those who do work, sometimes very important work, that takes a long time to complete and leads to no commercially useful results.

On the contrary, Michael Bliss argues that

The claim that tenure is a necessary precondition of academic freedom is inherently and monstrously unjust to non-tenured academics. These are the scholars, often more adventurous and outspoken than the old and established, who most need academic freedom. To them the institution of tenure is as though society offered a guaranteed annual income to everyone but the poor. Words like “hypocrisy” and “dishonesty” come to mind.

The essay of Mark Kingwell is probably the best-written one:

All in all, tenure remains sacrosanct because nobody with any standing has a stake in criticizing it. There is another major factor in tenure’s culture of belief and that is simple psychology, exacerbated by the rampant professional envy of the academic world. The main reason people want tenure is because other people have it. Many academics do not admit this, maybe not even to themselves, because standard arguments about academic freedom are available to them, arguments that make tenure’s critics look crass.

But now try offering a few deeper objections. Who needs academic freedom in a constitutional democracy, where freedom of expression is already guaranteed? Or, more slyly, what possible objection could there be to speaking frankly about topics in which most people have utterly no interest?

In his view, instead of protecting academic freedom, tenure actually stifles it:

Unfortunately, but to nobody’s surprise, the institution of tenure tends to make academic departments conservative. Since tenure decisions are made by senior faculty, all of them tenured themselves, there is a natural tendency to reproduce the status quo. Academics deny this, but their acts betray them.

Sandra Acker investigates whether the tenure is still a gender issue.

The various forms of appraisal and evaluation may incorporate unacknowledged gendered norms. Most of the assessors (senior faculty) are men, and the reward system is biased toward research and publications rather than teaching and service. In one study, the “successful academic” was described in interviews as “someone whose first priority was research, who worked long hours, who defined themselves in terms of their work, who had experienced no break in career, and who had an uninterrupted forward movement in their career profile.”

Pat Finn advocates the abolition of tenure in favour of granting academics the same job security as ejoyed by other professionals.

Academic freedom is special, prized, and to be defended at all costs. Tenure is not.

She acknowledges, however, that her opinion is unlikely to be embraced by academia anytime soon:

So tenure will likely remain unchanged. And academics will continue to defend it when challenged by critics who believe in the myth of “a job for life”.

ants in the sugar-bowl

2009-12-15T12:00:00.010Z

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.

On UN agencies:

The six founding members of UNAIDS have now swelled to ten, and ants from elsewhere in the UN system are making their way to sugar-bowl, too. The Standing Committee on Nutrition has its HIV programme. So do peacekeepers. And fisheries. Why fisheries?

Chatting with my friend Bert who works for the World Bank, I marvelled that almost every UN agency was on the AIDS bandwagon. Bert gave me a weary look. ‘The UN institutions are professional beggars, and beggars go where money is’, he said. ‘So you get “culture and AIDS”, “kids and AIDS”, “fish and AIDS”. I’m just waiting for “climate change and AIDS”.’

On American funding of HIV programmes:

The biggest funder of all, the United States, decides in Washington how its money will be spent. It actively discourages investing in ways that will maximize lives saved in most of the world.

On articles of faith:

The demonization of condoms, now fairly common in Muslim countries, seems to be a relatively recent contaminant from Catholic doctrine.

On scientific honesty:

A few years ago, the British Medical Journal floated the idea of including an ‘honesty box’ in each of its articles — a space for researchers to record the ‘warts’ in their data, the little things that go wrong in the field. Because let’s face it, things go wrong even when you’re going door to door asking people what they ate for breakfast. In HIV research you’re going from brothel to gay bar asking about behaviours that are often illegal or embarrassing and collecting specimens to test for an unspeakable fatal disease in countries with erratic vigilante movements and an irregular power supply. The honesty box can fill up quite quickly.

On AIDS conferences:

Once upon a time, these conferences were about science. Nowadays they are about institutional posturing, theatrical activism and money. Lots of money. The Bangkok conference cost US $18.5 million. Nearly 19,000 people rocked up to it, scrummaging for the goodie back-packs given out by pharmaceutical companies. Big pharma paid handsomely to nab the best real estate, the exhibition booths in the center of the main hall. They paid again to get their booths dressed to impress, with cappucino bars, and indoor waterfall and larger-than-life photos of gleaming Western labs and grateful African children.

more weasel words

2009-12-13T12:00:00.011Z

From the Weasel Words Website by Don Watson:

networking
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)

the fate of gurus

2009-12-06T13:30:00.008Z

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.

Feynman looks at the blueprints

2009-12-03T17:12:00.008Z

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.

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.

say what you mean

2009-11-20T18:30:00.008Z

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?

not just drug design

2009-11-19T18:41:00.006Z

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.

twenty years after

2009-11-09T21:39:00.012Z

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.

science and photo doctoring

2009-10-13T22:51:00.010+01:00

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?

women Nobel prize winners 2009

2009-10-12T13:30:00.005+01:00

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.

(From the interview with Elizabeth H. Blackburn)

I think that it doesn’t help to be a woman in science. Maybe now, but not when I was progressing.

(From the interview with Ada E. Yonath)

the art of scientific writing

2009-10-07T00:00:00.009+01:00

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)

just say no to multitasking

2009-09-25T11:00:00.006+01:00

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.

Smilla meets professor

2009-09-23T15:41:00.007+01:00

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.

stroke of insight

2009-09-18T22:00:00.007+01:00

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.”

карта звезды

2009-09-13T12:00:00.007+01:00

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:

(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.

science is cool

2009-09-12T21:00:00.007+01:00

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.

i felt like internet

2009-09-10T22:29:00.005+01:00

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.

the summer is almost over

2009-08-17T19:00:00.007+01:00

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.

cool badges

2009-08-16T21:11:00.011+01:00

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.

she’s such a geek

2009-08-15T21:30:00.008+01:00

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.

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.

a threat to scientific communication

2009-08-14T22:22:00.013+01:00

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.

can accent damage your career?

2009-08-13T21:56:00.008+01:00

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.

what to tell my younger self

2009-08-11T18:50:00.006+01:00

“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.

academic matters

2009-07-19T15:46:00.005+01:00

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.

guests, ghosts, gofers

2009-07-12T18:35:00.005+01:00

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.

how many scientists fabricate and falsify research?

2009-07-07T17:08:00.005+01:00

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?

we are all Iranians

2009-07-06T21:21:00.003+01:00

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.

seven deadly sins

2009-06-29T21:21:00.005+01:00

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?

Parochialism and Insularity
Exceptionalism
Autonomy or death!
Vanity: Pride and Narcissism
Monolith Megalomania
Scientific Method Sloth
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.

studying is not about what’s worth it

2009-06-27T21:35:00.007+01:00

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.”

driven by a curiosity about nature

2009-06-25T16:49:00.007+01:00

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.

science on Earth

2009-06-24T23:59:00.005+01:00

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

2009-06-24T14:00:00.005+01:00

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)

harmless, harmless

2009-06-21T18:53:00.007+01:00

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”.

systems vs system

2009-06-16T20:39:00.004+01:00

‘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.

curiosity as the driving force of science

2009-06-12T21:49:00.009+01:00

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.

Q.E.D.?

2009-06-10T13:17:00.002+01:00

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.

business weasel words

2009-06-09T17:50:00.010+01:00

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
accountable
action item
alignment
applications
architecture
ballpark
bells and whistles
benchmark
best practice
bottom line
brand
brand equity
bread and butter
breakthrough products
B2B
business case
business units
capability
cash cow
caveat emptor
challenge
change agents
change management
channels
cherry-picking
client-centric
collaboration
compatble
compensation plan
competitive advantage
consumer-driven
contingencies
continuous improvement
contribution
core competencies
cost-effective
cost-reduction
cross-fertilization
cross-functional teamwork
customer-focused
day-to-day
deliverables
delta
deployments
desktop environment
develop
digital
discipline
disconnects
disengaged
distribution channels
documentation
dotcom
e-business
efficiencies
empower enterprise
e-services
e-tailers
eyeballs
facilitates
faster
fast track
flow charts
focus
focus groups
framework
functional
game plan
gap analysis
goal-directed
goals
guesstimate
hardball
hardware
high level
human capital
identified
implementation
incentivize
incremental
information
initiatives
innovative
inside-out organization
integrated
interactive
interface
internal and external functions
intranet
key performance indicator
key strategic areas
leadership
lean manufacturing
lessons learned
leveraging
line operation
living document
long term
management consultant
maximizing
metrics
milestones
mission-critical
mission statement
mobile
movers and shakers
next steps
objectives
off-line
operationalize
opportunity outsourcing
paradigms
paradigm shift
parallel
partner
performance
positioning
proactive
process
product
profitability
quality
quantifiable benefit
real-time basis
reciprocal
red tape
requirements
reseller
resource
responsive
results-driven
revisit
rightsizing
risk management
robust
service
shareholder value
showstoppers
software
solutions
specifications
standardization
step change
strategic fit
suboptimal
synergies
teamwork
technology platforms
thought leadership
tools
track record
traction
transaction flow
transforming
turnkey
unquantifieable benefit
utilizing
value-added
values
viral
vision
warm and fuzzy
war stories
whole nine yards
win-win
world-class

Business Weasel Words
accountable action item alignment applications architecture ballpark bells and whistles benchmark best practice bottom line brand brand equity bread and butter breakthrough products B2B business case business units capability cash cow caveat emptor challenge change agents change management channels cherry-picking client-centric collaboration compatble compensation plan competitive advantage consumer-driven contingencies continuous improvement contribution core competencies cost-effective cost-reduction cross-fertilization cross-functional teamwork customer-focused day-to-day deliverables delta deployments desktop environment develop digital discipline disconnects disengaged distribution channels documentation dotcom e-business efficiencies empower	enterprise e-services e-tailers eyeballs facilitates faster fast track flow charts focus focus groups framework functional game plan gap analysis goal-directed goals guesstimate hardball hardware high level human capital identified implementation incentivize incremental information initiatives innovative inside-out organization integrated interactive interface internal and external functions intranet key performance indicator key strategic areas leadership lean manufacturing lessons learned leveraging line operation living document long term management consultant maximizing metrics milestones mission-critical mission statement mobile movers and shakers next steps objectives off-line operationalize opportunity	outsourcing paradigms paradigm shift parallel partner performance positioning proactive process product profitability quality quantifiable benefit real-time basis reciprocal red tape requirements reseller resource responsive results-driven revisit rightsizing risk management robust service shareholder value showstoppers software solutions specifications standardization step change strategic fit suboptimal synergies teamwork technology platforms thought leadership tools track record traction transaction flow transforming turnkey unquantifieable benefit utilizing value-added values viral vision warm and fuzzy war stories whole nine yards win-win world-class

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”.

Weingarten’ dilemma

2009-06-08T15:22:00.009+01:00

As usual, I was looking for something else entirely when I came across the book entitled Theory of Technology. It contains a chapter written by Thomas E. Clarke. I allow myself a couple of quotes:

Protestations to the contrary, most organizations are not looking for creative output from their employees. They want employees that can follow instructions and operate within a very narrow band of decision-making authority.

In many cases, when scientists move to the managerial ladder just to get more financial compensation, the organization loses a productive, highly motivated scientist and gains an unfulfilled, mediocre manager.

Personally, I would correct the latter passage by removing “just to get more financial compensation”: whatever the motivation, more often than not the scientist is lost. For good. The author himself explains why the scientists do not make good managers:

Unlike many other professionals, scientists and engineers do not seek out promotion to the ranks of management as this would force them to interact with people to a greater degree and detract from their focus on their scientific profession.

In their sci-fi novel За миллиард лет до конца света (Definitely Maybe in English translation), Arkady and Boris Strugatsky describe a series of unexplained phenomena that occur around several scientists, who are all working on unrelated problems. A working hypothesis is that there is some sort of natural force preventing the humankind from discoveries which may threaten the “Homeostatic Universe”. Weingarten, a molecular biologist, is facing a tough choice: either to continue his groundbreaking experiments on reverse transcriptase (and incur the wrath of Homeostatic Universe) or to become a director of a brand new research institute, knowing that he will not be able to return to his potentially Nobel Prize-winning work. Naturally, Weingarten chooses the directorship (he is arguing that, as a director, he will be able to conduct research worth ten Nobel Prizes; somehow, his friend Malianov is not convinced.)

Of course, the Homeostatic Universe of Strugatsky brothers is just a metaphor for scientific bureaucracy. (Or maybe the scientific bureaucracy is just one of manifestations of the Homeostatic Universe. It does not matter.)

In science, one either does science, or makes a career.

women in science

2009-06-04T18:20:00.012+01:00

Thanks to the recent post in Women in Science blog, I got acquainted with this Nature editorial and the actual EC report. (I had no time to read all 136 pages of it yet, but I am doing my best.) All interesting stuff, but, in the end, did they come with anything that we did not know before?

In conclusion, it appears clear that even the most gender-aware countries in Europe do not escape strong gender imbalance at the level of highly prestigious grants, positions or prizes.

Really? Well, I heard there was a bit of gender imbalance among the Nobel Laureates (there are altogether 35 female Nobel Prize winners out of 789 individual laureates, i.e. 4.4%; only 12 women got Nobels in science). But wait, read this:

What does clearly emerge is that application behaviour differs between men and women. Women apply or re-apply less, apply to less prestigious sources, requesting less funding, and for shorter duration.

So now we know who to blame: it is the women themselves. Instead of concentrating on important things like grant writing, they take career breaks or work part-time to raise their children etc.

Forget the EC report: this article by Philip Greenspun was written three years ago but is every bit as relevant now as in 2006. Don’t be deceived by the title: it is not only about women in science. It is about men in science too. (Granted, he talks about American science, but it is equaly applicable to the ‘Western’ science in general.) On the contrary, the section titles speak for themselves: ‘Why does anyone think science is a good job?’, ‘For whom does academic science as a career make sense?’, ‘What about the excitement and fun of science?’, and finally, ‘Why do American men (boys, actually) do it?’.

A lot more men than women choose to do seemingly irrational things such as become petty criminals, fly homebuilt helicopters, play video games, and keep tropical fish as pets (98 percent of the attendees at the American Cichlid Association convention that I last attended were male). Should we be surprised that it is mostly men who spend 10 years banging their heads against an equation-filled blackboard in hopes of landing a $35,000/year post-doc job?

Having been both a student and teacher at MIT, my personal explanation for men going into science is the following:
young men strive to achieve high status among their peer group
men tend to lack perspective and are unable to step back and ask the question “is this peer group worth impressing?”

It may be not always politically correct but a great read anyway.

amateur, pet, student

2009-06-03T13:50:00.008+01:00

Most (maybe all) of what is now called ‘bioinformatics’ grew from amateur projects, pet projects or student projects. In any case, at the time (20—25 years ago), it was near impossible to get any funding to do it. Never mind that, the bioinformatics had a distinct advantage over experimental biology that it did not require much in terms of ‘materials’ (as in ‘Materials and Methods’) except access to a computer and, increasingly, Internet. That allowed people to do whatever they wanted to do without any need to go to the lab. The chemoinformatics could have been like that — except it was not. There was no chemical databases in public domain, period. When we just started to work on ChEBI in 2003, we were told that we shouldn’t really bother since “all useful chemical data is commercial”. Boy, the times have changed. For an instant reference on any topic, we look up Wikipedia, not Britannica.

In my view, ChemSpider was one of such amateur (in a best sense of this word) enterprises — that is, until it was acquired by the Royal Society of Chemistry last month. (Good thing it was not acquired by CAS.) There was a lot of excitement in blogosphere; I found comments by John Wilbanks and Rich Apodaca most interesting. Undoubtedly, the chemical community as a whole should be a winner. And yet... According to Antony Williams,

“What originally started as a hobby project to give back something to the chemistry community has become one of the primary internet resources for Chemistry. And this from home built computers in a basement, with no funding and a team of volunteers. With the resources, reputation and vision of the RSC to support ChemSpider our long term goal is to deliver the primary online platform where chemists will resource information and collaborate with a worldwide community of scientists.”

Exactly: a hobby project became a leading chemoinformatics resource. Something that the RSC, in spite of its great “resources, reputation and vision”, has failed to deliver.

So, amid much congratulations and celebrations, I allow myself to privately mourn a loss of a brilliant amateur project.

question and hope

2009-05-24T23:09:00.008+01:00

A couple of quotes from Knots: Mathematics with a Twist by Alexei Sossinsky.

So the arithmetic of knots has not helped us to classify them. But there is scant reason to talk of failure here: Schubert’s theorem <that every knot decomposes uniquely into prime knots> does not need any applications; it is mathematical art for art’s sake, and of the most exalted kind.

Research always begins with a question, and hope.

the anarchy and oligarchy of science

2009-05-24T00:27:00.008+01:00

Part 3 of The new information ecosystem: cultures of anarchy and closure by Siva Vaidhyanathan was written some six years ago but remains as relevant now.

Science has always been global, cosmopolitan, messy, inefficient, and troublesome.

Yes, inefficient (or “low-throughput”, as in this blog’s name). All these aspects of science attract me.

Despite some elements of oligarchy, science as a practice succeeds because of, not despite, its ideology of relative openness. Credentialism is more an imperfection rather than a corruption of science.

Of course, credentialism is not a corruption of science: it is its inherent feature. The golden age of science free of credentialism never existed, thus nobody could corrupt it in that way. Still, the other possibilities of corruption are always abound.

As in so many other areas of life — from music to political action — just as communicative technology has allowed the flowering of a new scientific revolution, the oligarchic concerns of commerce and national security have crowded out these democratic values at their sources — the university and laboratory.

working full-time in science

2009-05-23T21:58:00.007+01:00

For the last 20 years, I was working full-time in science. I mean, if molecular biology is a science, then I was working in science. It does not automatically mean I was doing science. Let me elaborate on this a little.

There are very few people out there actually doing Science. A lot of people are said to be “working in science” though. Maybe they are working in places which have scientificky-sounding names, for instance “Department of Molecular Biology”. Here, “working” means they are get paid for being there. (Check Wikipedia for many other meanings of work.) When one has a chance to leave this kind of employment for something less esoteric but never uses this chance, (s)he is said to choose “staying in science”. I like the expression “staying in science” more than “working in science” because it, obviously, does not imply any work.

I am not employed any longer full-time (or part-time for that matter) in science or otherwise. Therefore, I can write whatever I please, about science and other stuff one always wants to write while in full-time employment but never has any time.

I mean, they can’t kick me out.