Category Archives: Science

Making science (part VII): On the utility of science

In a recent interview for the podcast series of the Proceedings of the National Academy of Sciences of the USA, Ira Mellman of Genentech expressed his views on the utility of science practiced at academic institutions. After an academic career at Rockefeller and Yale University, Mellman joined Genentech in 2007 where he is Vice President of Research Oncology. Mellman is a member of the National Academy of Sciences since 2011. The interview is about current challenges in the field of cancer immunotherapy. But things get a bit more controversial at the end. Scroll the audio featured below to -0:35 and you’ll hear this:

PNAS: “I asked Mellman whether his move from academia to industry has brought him closer to his goal of practicing people-centered science.” Read more...

Making science (part VI): Ignorance

There are known knowns; there are things we know we know. We also know there are known unknowns; that is to say, we know there are some things we do not know. But there are also unknown unknowns, the ones we don’t know we don’t know.
— D. Rumsfeld, 2002

The scientific literature increases exponentially with thousands of papers added daily. As the day has only 24 hours, what this means is that every time we sit down to read a paper, we have —consciously or unconsciously— decided to neglect thousands of others which we will most likely never read, ever. Agonizing as this may sound to some, it is equally inevitable. The assurance that we feel when moving a paper to our “to-read” list can be self deceptive, however, and so it is crucial that we choose which papers to read with great care. Or rather, that we carefully decide which papers not to read. In fact, better to do this consciously than as a default consequence of the limited number of hours in the day. The art of selectively ignoring sets of facts has been called “controlled neglect” and it is a crucial tactic to cope with the vast mountain of facts that keeps growing by the day. Read more...

Intriguing clinical meta analysis of a unique dataset in traumatic brain injury from the “Asterix” comic books

Researchers from Heinrich-Heine University in Düsseldorf, Germany, have published an intriguing study on traumatic brain injury using a dataset taken from the Asterix comic series. The report appeared in Acta Neurochir (2011) 153:13511355.

We learn that the goal of the study was to “analyze the epidemiology and specific risk factors of traumatic brain injury (TBI) in the Asterix illustrated comic books. Among the illustrated literature, TBI is a predominating injury pattern.” One of the major strengths of the study is that clinical data were “correlated to information regarding the trauma mechanism, the sociocultural background of victims and offenders, and the circumstances of the traumata, to identify specific risk factors.” Read more...

Making science (part V): Bad project

“I want good data, a paper in Cell
But I got a project straight from Hell”

“I wanna graduate in less than five years
But there ain’t no getting out of here”

“Oh oh oh… caught in a bad project”

Crazy mice. Smelly brain cells. Empty Western blots. It’s a bad project alright. Or… is it? There are indeed bad projects out there. Research projects begin with a question that is to be answered. If no question has been formulated, however general, and experiments are being done only because they are doable, then a bad project is on the horizon. With a question at hand, hypotheses have to be made as to the posssible answers, ideally covering all logical possibilities. Lack of hypotheses in a project is not a good sign. The question posed may not be answereable. (We’ve all heard about hypothesis-free studies. That’s okey for a group leader with 50 postdocs and lots of other projects. Not recommended  to anyone that wants to graduate and get a job in less than five years!) Hypotheses help designing the experiments that are going to distinguish between them. Experiments are typically designed to systematically disprove them one by one. A neat, key experiment to prove one of the hypothesis upfront is more difficult to come by. Some experiments may just add support to a particular hypothesis, but not prove it or disprove it outright. So far so good. But a good project should also allow for serendipitous discoveries. Paradoxically, serendipity is one of the most common ways of advancement in science. Alas, serendipity can not be planned. But it can be encouraged. In addition to concrete goals and defined questions, research projects that allow some amount of open-ended possibilites have greater chances to extend into (positively) unexpected directions. It’s a fine balance, in which informed intuition plays a vital role. (For a discussion of intuitive thinking, see Making Science Part III.) Lady Science in the video above seems to be having more problems than just a bad project. But those are topics of other discussions. Read more...

Making science (part IV): Good science, good writing

Can a good scientist be a bad writer? The answer, in my opinion, is nope. Here is the story.

The registrator office at the Karolinska Institute has recently received a request to release the full texts of several of their successful grant applications to the European Research Council (ERC) as well as the texts of their respective evaluations and referee comments. ERC grants are both generous and prestigious awards that have come symbolize the success of the European scientific elite. Under Swedish freedom of information legislation, the Karolinska Institute -which is ultimately under state jurisdiction- is obliged to release these documents, as astonishing as this may sound. (A topic that surely deserves a post of its own.) Needless to say, such a request has come down as nothing short of controversial among the scientists involved, since grant applications contain unpublished data and detailed confidential information about their future research programs. Who could have made such a preposterous request? Read more...

Making science (part III): Intuition

Intuition is as important in science as it is in the arts and any other creative activity. Intuition can allow the formulation of novel ideas or solutions to complex problems that would otherwise be difficult or improbable to reach via conventional, logical reasoning. Although the popular term “gut feeling” would appear to indicate that intuitive processes take place outside the brain, it is a misplaced metaphor, as intuition is very much a mental activity.

As in conventional reasoning, intuitive thinking computes the odds of competing ideas or solutions. Unlike the former, however, the intuitive process is largely unconscious. We are only aware of the result of the computation but not the process by which it was obtained. It is nevertheless a mental calculation like any other: it utilizes data stored in memory to deduce connections, predict missing bits of information, or generate new hypotheses. Read more...

Making science (part II): The making of a scientist

Former postdoc fellow Svend Kjaer has today published his first first-author paper after leaving the lab. It has appeared online at the Nature Structure and Molecular Biology website. He’s got the first glimpse of the three-dimensional structure of the extracellular domain of the RET receptor, giving insights into how it binds ligand and how its mutation causes disease. Something we were striving to see for several years while he was at our lab has now been achieved and it’s one of the great success stories of making science. It took a lot of perseverance, a good measure of ingenuity and the crucial guidance and support of Svend’s current mentor and common friend Neil McDonald from the CRUK institute in London. As if by coincidence, from Svend comes also this link to the one-hour film “Naturally Obsessed: The Making of a Scientist” telling the story of three graduate students in a crystallography lab at Columbia University, NYC and their road to success (or failure) through “years of trial and error and unflinching dedication”. It gives good insights into real science making in a lab, the elusive thrill of its ups and downs, and what it takes to get to the finish line. Link from the picture above. Read more...

Making science (part I): Discovery

Making science is about being where none else has been. Seeing what none else has seen. Walking on an unknown planet for the first time, without leaving the walls of the lab.

This is the essence of being a scientist. Of course, day to day life in a research lab can be difficult. We don’t walk on a new planet everyday. Reagents that don’t work, mice that don’t breed, experiments that don’t make sense… Many things can get on our way to the answers we are looking for. Sometimes we get answers to questions we have not asked. It’s a journey into uncharted territory. And like any journey, it is prone to surprises. Discovery is the driving force. But not every question asked leads to a discovery. How to know what questions to ask? That’s another matter altogether… Read more...

Vijay Iyer Trio

FASCH10_0828A remarkable concert featuring Vijay Iyer Trio live at Fasching on April 13 2010 in full power. Here is Vijay in full concentration at the piano (pic taken with my EOS 7d and the 100-400 L, which I took by mistake thinking that it was the 70-200L 2.8!). In addition to Iyer on piano, the trio includes Stephan Crump on bass and Marcus Gilmore on drums. Their most recent album is “Historicity” (2009) on the ACT label. Several of the pieces of that album were featured at the Fasching concert. Vijay Iyer uses thick chords sweeping across the keyboard generating an orchestral backdrop onto which melodic lines navigate. Improvisation remains the central theme. From Vijay Iyer’s website: “his powerful, cutting-edge music is firmly grounded in groove and pulse, but also rhythmically intricate and highly interactive; fluidly improvisational, yet uncannily orchestrated; emotionally compelling, as well as innovative in texture, style, and musical form.” Read more...