Monday, 29 June 2009

seven deadly sins

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

Saturday, 27 June 2009

studying is not about what’s worth it

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

Thursday, 25 June 2009

driven by a curiosity about nature

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

H20: A Biography of Water

Wednesday, 24 June 2009

science on Earth

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

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

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

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

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

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

you can’t push and write at the same time

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

Sunday, 21 June 2009

harmless, harmless

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

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

Tuesday, 16 June 2009

systems vs system

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

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

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

Friday, 12 June 2009

curiosity as the driving force of science

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

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

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

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

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

Wednesday, 10 June 2009


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

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

Tuesday, 9 June 2009

business weasel words

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

Dilbert: The Way of the Weasel

Monday, 8 June 2009

Weingarten’ dilemma

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.

Thursday, 4 June 2009

women in science

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:
  1. young men strive to achieve high status among their peer group
  2. 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.

Wednesday, 3 June 2009

amateur, pet, student

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.