the DNA journey

Yesterday, I came across this short film, as usual, looking for something completely different at Film English.

“This should be compulsory”, says one of its protagonists, talking about the DNA test. I am not sure about that. Danish scientists questioned the logic behind these tests (as any scientist would do). In absence of national reference datasets (what is “100% Icelandic”, for example?), the results of comparison do not seem to make much sense.

Still, I think it’s a great, if scientifically flawed, short. I did show it today to my students (all in their early 20s) and saw tears in their eyes. They might have not understood half of the language used in the film but they’ve got the message. Watch it.

hand wash

Last night I put this, presumably, hand-wash only jumper into a washing machine. On a hand wash cycle, cold water. The machine stopped in the middle of the cycle because the filter was blocked. I left it overnight. This morning, I took the filter out (a minor flood followed). It looked as if someone was trying to stuff a felt hat into it and partially succeeded. The rest of the hat is all over the drum. Mopped the floor. Decided to repeat the rinse. The machine stopped in the middle of the cycle. Took the filter out. Mopped the floor. Took the dripping jumper out to the garden. Washed my hands from fluff. Cleaned more serious fluff from the washer’s drum. Run the rinse. Took the filter out. Mopped the floor. Cleaned some further fluff from the drum. Run the rinse. Checked the jumper. My, this hand wash involves a lot of hand washing. Took the filter out. Mopped the floor.

This reminded me of my early or, indeed, my later days (and nights) in “biocomputing”, now known as “bioinformatics”. True, the machine does something, eventually, but cleaning the mess is left up to you.

to collaborate or not to collaborate

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.

loose ends

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.

not just drug design

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

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.

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’ve been 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.

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 were 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.