Bioinformatics and experimentation

Russ Altman got a good discussion going on his blog. The many reactions were initiated by a post about bioinformatics people and whether or not they benefit from experience in the experimental lab.

See also: The blog of Russ Altman

I suck at math

More nerdy comics at xkcd.com

Help women stay in science

This article and graph from 2000 showing the proportion of women in academic positions is nearly unchanged when updated to figures of today.

An editors note "Help women stay in science" from The Scientist in September 2007, initated a flood of comments with interesting personal views and points on what it is that causes the heavy gender imbalance at top scientific leadership positions.

A quote from the comments:
"I don't know why some of the more seasoned members of the scientific community haven't realized the untapped potential of hiring mothers part time (is no one else aware of thier multitasking capabilities??)"

- The story continues in The Scientist January 2008 issue: "Why aren't there many women in the top spots in academia?"
- Tinyflame blogging on "Women in Science"
- SES Science diversity Meme: Women scientists

Zen and the art of microarray chip design

I have been reading a lot of books lately, correction: I am reading a lot of books at the moment. When in Norway I finished "Conversations with God" and "Zen and the art of motercycle maintenance". Both happen to be very philosophical of nature:
The first is about inward quality of life, how you can achieve more and be more satisfied by taking life in your own hands - create your Self by conscious choices in your life.
The second is about how you relate to the outside world. The author describes to contrasting ways of viewing the world, the classical and the romantic. The classical is the analytic way, where the solutions to problems are found by describing the object in minute detail until the description reveals the answer to the problem. The romantic, on the other hand, acts on feeling, on gut feeling about what is good Quality.

What I find a bit funny is that I have been working more than a year on a scientific project concerning Quality of microarray chip design. And when it came to the point where I wanted to draw the conclusion, finalise a hypothesis and confirm it, a new question showed up that could not be answered by analysing the data we had. Also, it was not possible in the scope of the project to provide the data that could give us the final answer. So to this problem I had to step out of the analytical way of thinking (it was practically a dead end) and zoom out and give a subjective solution to what will be the best way to deal with the new question. It may be unsatisfactory in a scientific way to solve problems by gut feeling, but in some cases (in science as well as in life), there is no analytical answer possible to a specific question, and then you have to do something else. At least I am entertained by the fact that I draw my own situation into the context I am reading to make it all make sense, hey, that is also why I am blogging this right now...

Encyclopedia of Life

The Encyclopedia of Life has taken on the amazing task of documenting all species of life on Earth. Their website states:
"Comprehensive, collaborative, ever-growing, and personalized, the Encyclopedia of Life is an ecosystem of websites that makes all key information about all life on Earth accessible to anyone, anywhere in the world."

Browse around or take a tour at the Encyclopedia of Life.

BMC good initiative

I would like to draw attention to this new electronic scientific journal by BioMedCentral:

"The aim of BMC Research Notes is to reduce the loss suffered by the research community when results remain unpublished because they do not form a sufficiently complete story to justify the publication of a full research article. A key objective of the journal is to ensure that associated data sets are published in standard, reusable formats whenever possible. Data sets published in the journal will be made searchable and easy to harvest for reuse."

In my opinion it is an excellent initiative, both to encourage publishing incremental and 'negative' results, as well as the focus on open and easy access to data sets and results.

Read more about BMC Research Notes.

Congress: Women in Science

On March 6th there is a congress at Radboud University about women in science. Please see the website for more information: http://www.ru.nl/viw/congres_women_in/

Illustration courtesy: Women in Science, German embassy of New Delhi

Wikispecies

The Wikimedia Foundation has launched yet another free and public access web encyclopedia: WikiSpecies. This directory of species contains pages on all forms of life, and as any wiki system, you can help expand the directory by adding pages and references. Actually, this project was started in August 2004, but I did not notice it until now, maybe because WikiSpecies now encompasses more than 100,000 articles. Go browse and discover how many species you never even heard about!

Illustration courtesy: Wikipedia - Animalia

Scooped again

It may look like my work has been scooped again, but hey - I look at it from the positive side: In order to publish my own work I have to focus on what is new, that noone else thought of doing before me. And there is plenty of it. It may even turn out to be a better paper now that the trivialities have been published already by someone else. Am I sounding too enthousiastic? Who said science would have to be easy to be fun?

Sugar greater lure than cocaine?

The newsbrief from Faculty of 1000 drew my attention to this new paper: Intense Sweetness Surpass Cocaine Reward. In this paper the research from Bordeaux show that 9 out of 10 rats choose saccharin-sweetened water over intravenous cocaine, when put in an either-or choice situation.

Interesting in itself, and next comes the question: How does this result compare to the human reactions to sweets and addictive drugs?

Illustration courtesy: Natural History Magazine - The Wild Rat

Redefining the gene

In a paper appearing in the June 2007 special ENCODE issue of Genome Research, Gerstein et al. update the definition of a gene while elaborating on the complexity of gene regulation that has been discovered in recent years. I love this comparison to computer operating systems (OS):
"The execution of the genomic OS does not have as neat a quality as this idea of repetitive calls to a discrete subroutine in a normal computer OS. However, the framework of describing the genome as executed code still has some merit. That is, one can still understand gene transcription in terms of parallel threads of execution, with the caveat that these threads do not follow canonical, modular subroutine structure. Rather, threads of execution are intertwined in a rather "higgledy-piggledy" fashion, very much like what would be described as a sloppy, unstructured computer program code with lots of GOTO statements zipping in and out of loops and other constructs."

Read the full paper in Genome Research
Illustration courtesy: KLV.nl

The coriolis myth

You may have heard, or you might even have been taught by your physics teacher, that the coriolis force is the rotational force that makes water rotate down the drain in one direction on the northern hemisphere and in the other direction in the southern hemisphere. However, I am sorry to tell you, it is a myth.
There is indeed a coriolis effect, and it does indeed affect particles in opposite direction on either hemisphere, but it is not strong enough to make the water run down the drain in a particular direction. The direction in which the water poured into the tub, the shape of the tub, and even small perturbance by objects in the tub all have a larger effect on the direction of rotation.

Read more about:
The Coriolis Effect - by wikipedia
Bad Coriolis - by Bad Meteorology
Does the water go down the drain...? - by Everyday Mysteries

Genomic insights

The ENcyclopedia Of DNA Elements (ENCODE) project has published the first assembly of their findings from high-throughput experiments concerning 1% of the human genome. The paper summarises the new knowledge of genome function and organisation that was found throught the experiments. One of the conclusions is that most of what we used to think of as 'junk DNA', actually does have a function in the genome, although it is not by carrying information on protein-coding genes.

Read the news on BBC: Human genome further unravelled and read the publication in Nature
Illustration courtesy: Universite de Geneve

New Center for Protein Research

In the news: The Novo Nordisk foundation has given a grant of 600 million Danish Kroner (approx 80,5 m) to the establishment of a new Danish centre for protein research. The new centre will be placed within the Panum Institute in Copenhagen. The first two scientific leaders of the centre have been appointed: Matthias Mann, a world leader in Mass Spec research, currently positioned at the Max Planck institute in Munich and Søren Brunak, the current leader of the bioinformatics facility CBS at DTU.

The Novo Nordisk Foundation Center for Protein Research is now in the news worldwide. Read the article in Nature News.

What do robots dream of?

Reading a Perspective article in Science, or actually reading a Letter responding to the article, brought to my attention once again the research on robot cognition and self-awareness. How can robots be programmed to learn independently? And can they be modeled by our knowledge of human learning?
The article 'Resilient Machines Through Continuous Self-Modeling' describes how a robot can model its own gait, and if it is injured by i.e. removing part of a limb, it can think up new ways of walking by a dream-like process. In the 'dream' it revisits its past experiences and recombines the knowledge to try out new solutions to the problem.

Reading:
'Resilient Machines Through Continuous Self-Modeling', Science Nov 2006
What do robots dream of?, Perspective article in Science Nov 2006
Do Androids Dream of Electric Sheep? by Philip K. Dick

Cold Spring Harbor

The surroundings here are tremendous. The Cold Spring Harbor Labs are situated on a hillside overlooking the bay. Huge trees are growing here, the cabins for accommodation of visitors are virtually in the forest. Squirrels run around the grounds, not at all afraid of the scientists walking about. I almost stepped on a rabbit crossing my path. He stopped to nibble at a tulip right in front of me, then walked off in no hurry.

New York - Part I

Safely arrived in Cold Spring Harbor. I enjoyed the flight, watched Casino Royale, watched the ice crystals forming on the window, watched Step Up, listened to laid back tango, and then I arrived at JFK airport. The shared cab I had booked beforehand came to pick me up at the terminal, and I had my evening meal at Cold Spring Harbor Labs. Most of the evening I spent talking with Celine about dancing (she is into tango) and dance shoes... and a little bit of science.