Category Archives: Science

Making science (part XVI): The perfect abstract

It can be considerably frustrating to have to summarize many years of work in just 150 words, but that is what scientists often have to do at the time of writing the Abstract section of their research papers. However, a well written Abstract is crucially important, as it is the first thing (sometimes the only thing!) that readers will read, including the journal Editors that will decide about its publication. It can really be a make-it-or-break-it for the success of the article. However, many young and budding scientists often struggle with this section, usually because of an inability to distill the single most important and essential part of the discovery in a clear and simple way. Read more...

Making science (part XV): Professional Editors

Once upon a time, science journals were run by scientific societies and their editors were active scientists. Very few of these remain today. Instead, nowadays most journals are own by private, usually very large, publishing companies and their editors are “professional”. That is, their only job is to be journal editors, they are not active scientists. Most of them were active scientists earlier in their career, but left academia to become “professional” editors, usually, shortly after their postdoctoral studies. Because of this, most professional editors are much younger (no problem there) and considerably more inexperienced (hmmm… ) than the principal investigators from whom they receive manuscripts for consideration. Typically, these “youngish” editors can get advice and (one would hope) guidance from more senior editors within the same journal or publishing organization, but they are pretty much in charge of the main decisions of the manuscripts assigned to them. Read more...

Interview with Singapore’s Straits Times

Today in The Straits Times:

NUS team develops man-made molecule that can ‘kill’ skin cancer cells

Professor Carlos Ibanez says the use of the molecule to activate the “death receptor” of melanoma skin cancer cells presents an option for a new treatment method for the remaining 45 per cent of melanoma skin cancer patients for whom current treatment fails. Photo: NUS Yong Loo Lin School Of Medicine.

Read the full article HERE.

Circadian rhythms

Presentation Speech by Professor Carlos Ibáñez, Member of the Nobel Assembly at the Karolinska Institute, Member of the Nobel Committee for Physiology or Medicine, 10 December 2017

Your Majesties, Your Royal Highnesses, Esteemed Nobel Laureates, Ladies and Gentlemen,

Phileas Fogg, the main character in Jules Verne’s acclaimed novel Around the World in Eighty Days, could not have suffered from jet-lag during his trip, despite crossing multiple time zones. His body had plenty of time – more than 3 days per time zone – to get adjusted to the time differences encountered along his journey. Today, in the era of jet travel, we can cross several time zones in only a few hours; but our bodies suffer, as they struggle to adapt to the new time at our destination. Many of our foreign guests this evening are surely experiencing this now. Why can’t our physiology adapt more rapidly? What keeps it behind?

Our physiology is regulated by an internal clock that generates daily rhythms known as “circadian”, from the Latin circadiem, meaning “around one day”. Circadian rhythms are ancient and exist in all forms of life. Life on Earth is adapted to the rotation of our planet, and the internal clock anticipates day/night cycles, helping organisms optimize their physiology and behavior. Although the existence of a biological clock has been known for nearly a century, only recently have we begun to understand what it is made of and how it keeps ticking.

Our story begins in 1729, when French astronomer Jean-Jacques de Mairan took a mimosa plant, which leaves are open during the day but close at night, and placed it in constant darkness. He observed that the leaves still opened and closed rhythmically at the appropriate time, suggesting an endogenous origin of the daily rhythm. Physiology is controlled by genes, and the biological clock is no exception. In 1971, Seymour Benzer and Ron Konopka isolated mutant flies that had alterations in their normal 24h cycle of activity. Fifteen years later, Jeffrey Hall and Michael Rosbash, working together at Brandeis University in Massachusetts, and Michael Young, at Rockefeller University in New York, isolated the mutated gene, called period.

As instrumental as this was, however, the isolation of the period gene did not tell very much about the mechanism of the biological clock. It was a remarkable series of discoveries made during the 1990s by this year’s Nobel Laureates that finally elucidated how our biological clock ticks. The basic principle, first proposed by Jeffrey Hall and Michael Rosbash, is deceptively simple. The period gene produces a protein that accumulates in the cell and, after reaching a certain level, blocks the gene and hence its own production. As protein levels subside, the gene becomes active again and the cycle resumes. As many things in biology, however, the devil is in the details; as it was still unclear how the period protein can be stabilized long enough and then enter the cell nucleus to inhibit its own production. Michael Young discovered two additional genes, he named them timeless and doubletime, that partner with period and together contribute to the generation of robust oscillations of approximately 24hs.

The discomfort of jetlag is evidence of the strength of our biological clock, as it takes time for the machinery to readjust to a sudden change in environmental conditions. Although sunlight is scarce this time of year in Stockholm, the good news is that food is also a strong resetting stimulus, so the banquet that follows after this ceremony will surely help towards adjusting our internal clocks.

The 2017 Nobel Laureates have uncovered a mechanism controlling a truly fundamental process in physiology, how our cells and bodies keep time. Such time-keeping is essential for our adaptation, and has important implications for human health; not just jetlag, but also the incidence of chronic syndromes, such as cancer, metabolic and sleep disorders, and several neurological conditions.

Professors Hall, Rosbash and Young:
Your brilliant studies have solved one of the great puzzles in physiology. Your discoveries have unraveled the cogs and wheels of the biological clock, an essential mechanism for the survival of life on our planet.

On behalf of the Nobel Assembly at the Karolinska Institute, I wish to convey to you our warmest congratulations. May I now ask that you step forward to receive the Nobel Prize from the hands of His Majesty the King.

Making science (part XIV): Journal Syndrome

The other day, I run into O.A., one of my former students who is now a  research group leader. O.A. is not the type that  lacks self-confidence, and although having a bit of a lazy attitude, he has some good ideas and a good feel for where the money is. I asked him how his research was going. He responded with a tepid smile, as if to indicate that I had asked the right question: “Very good. Next week I have a paper coming out in Nature, although I am only second last author in that one. I published a paper in EMBO Journal jus a few weeks ago. And we have also made some very interesting observations which will likely lead to a paper in a high-impact journal!”

I do not live in a bubble, so, in a disappointing way, I was not surprised. But it was difficult for me to keep myself from venting a remark of frustration, “O., you tell me where you are publishing your work, but you don’t tell me what the work was about, what you have discovered! Isn’t that the important thing?” Well, I did not actually make that last rhetorical question, but I should have.

Here is O.A., one of my former students, one of the promising ones, explaining his research in terms of the journals in which it is getting published, as if that were the only thing that matters in his science. Yes, he may have been trying to make an impression on his former mentor. But…  where did the science go? Isn’t that what really counts? The “Journal Syndrome” has advanced to such point that  the title of the journal in which the research is published becomes more important than the research itself and hence the preferred short-hand description for science output.

How did we get to this situation and can this trend be reversed? Without doubt, this is a direct product of the current addiction to Impact Factors, the mother of most curses in modern science.  However, while making Impact Factors disappear would appear very difficult at this time, avoiding the Journal Syndrome should be relatively simpler. When someone asks about your research, pretend he or she is a distant relative with no inside knowledge and simply tell them what you found in as few and simple words as possible. Journal Syndrome manifests most commonly when the other person is also a scientist.  In this case, you can allow yourself a bit more jargon and specifics, but the key point is always to keep the focus on your new findings. Try this next time. And if you are at the other end, as I was with my student O.A., don’t let them get away with the journal babble. Force them to tell you what they found. Hopefully, they’ll know…

Making science (part XIII): How not to make science

A newly recruited staff in a research group has her first meeting with the principal investigator, a full Professor,  to discuss projects and tasks to carry out in the lab. During the conversation, it becomes apparent that the so-called principal investigator is nothing more than a former clinician turned science administrator that pretends leading a research group. There are no new projects coming from the mind of this principal investigator.

“Go to PubMed and find something interesting to work on”, says the Professor.

Astonished, the newly recruited lab member becomes silent and after a few awkward minutes leaves the room, in shock.

“Go to PubMed and find something interesting to work on”. Now, we should point out that PubMed is the public repository of all scientific literature in the life sciences and biomedicine of the entire planet since the beginning of time. There are literary millions of papers in the repository. How does one find “something interesting to work on” there? Is this the best advice, the best guidance that this so-called senior scientist has to offer to his newly recruited lab member?

I could not believe when I first heard this, but it is a true story. It happened at the National University of Singapore, but the characters shall remain anonymous. There are likely people like that in most universities around the world.  Group leaders out there that have no clue whatsoever of what science is about, or what is to be an inspiring mentor. How their reputations survive is a total mystery.

Making science (part XII): The problem with impact factors

I have been around long enough to remember the time when there were no impact factors. (Don’t know what an impact factor is? Read HERE). We all knew that, say, Nature, was more prestigious (or sexy, hot, trendy, impactful, whatever you want…) than, say, JBC. And that JBC was better journal than many (actually many!) other (ie lower) journals. We did not need any impact factors to realise that. And of course this “intuitive” information was used to evaluate job candidates and assess tenure. A paper in Nature was very important, we all knew that, and did not need any impact factors. The problem now is that impact factors  put a hard number on what earlier was an intuitive, soft process. So, now we know that not only is Nature “better” than JBC, it is actually 10.12 times “better”. And PNAS is 2.23 times “better”. That is what has generated so many problems and distortions. The temptation to use those numbers is just too high, irresistible. For the journals, for the papers in them, and for individual scientists. And the numbers change every year. When applied to individual papers this gets totally crazy. Imagine. The “value” of a given paper can be higher (or lower) this year than, say,  3 years ago when it was published. The same paper, the same data. And let’s not get started with what the impact factor has done to innovaiton and creativity. (For a good view on this, read Sydney Brenner’s interview HERE Read more...

“A boring Noble Prize” (or a lesson in mediocre science journalism)

At the end of September each year, science journalists all over the world make their forecasts for the upcoming announcement of the Nobel Prizes that take place during the first week of October in Stockholm, Sweden. The week begins with the announcement of the winners of the Nobel Prize in Physiology or Medicine, awarded by the Karolinska Institute. It is followed by the Physics, Chemistry and Literature Prizes. As expected, this activity is all the more significant at Swedish newspapers and TV and radio stations, and this year of 2013 was no exception. Inger Atterstam, from the Svenska Dagbladet newspaper, is regarded as one of the most accredited science journalists in Sweden. Her 2013 forecast for the Physiology or Medicine Nobel Prize was vast and broad (to be on the safe side, presumably), and included scientists responsible for discoveries concerning the epidemiology of smoking, cochlea implants, treatments against malaria, rheumatoid arthritis, leukaemia and even Bill and Melinda Gates (!) (The nature of the discoveries made by the Gates couple which according to Ms. Atterstam deserved such a high honour was, however, not revealed).

Outside Nobel Forum, minutes after the announcement, Ms. Atterstam is visibly upset about the choice made by the Nobel Assembly for the 2013 Nobel Prize in Physiology or Medicine, and she makes no effort to hide her discontent in front of the cameras. The Prize went to James Rothman, Randy Schekman and Thomas Sudhof for their discoveries of the molecular mechanisms that control the specificity of trafficking, fusion and release of vesicles within and from cells. A long overdue award to one of the most influential and fundamental concepts in modern cell biology with direct relevance to a great number of human diseases including diabetes and neurological disorders. Incredibly important, but far away from any of the predictions made by Ms. Atterstam during the previous days. And it shows.

Microphone in hand, she confronts the unforgiving camera visibly distressed. Her eyes roll from left to right eluding the lens, her breath is heavy and agitated, her body swings back and forth. She does not pull her punches: “This was a  very traditional Nobel Prize, namely to three white, middle-class men coming from three of USA’s most prestigious and Nobel-awarded universities, Standford, Berkeley and Yale…” Wow! How about that for a bigoted statement? After a brief (and failed) attempt to explain some of the substance behind the discoveries, Ms. Atterstam revels in her own ignorance: “On the other hand, this is a very traditional and boring Nobel Prize because it is about very basic research that none really understands and that does not have any relevance, except in the realm of science.” Interesting words, coming from one of the leading science journalists in Sweden. Ms. Atterstam concluding remarks say it all: “The Nobel Committee has this time —once again— chosen not to give the Prize to applied research that concerns people [she chokes here] and which could thereby have drawn greater attention. We shall keep our hopes for the Higgs particle tomorrow.” Ms. Atterstam clearly considers the Higgs boson to be a discovery in applied science of immediate concern to people. 😉

Well, what else can be said? Here is one of the most prestigious science journalists of Sweden trying to explain basic research to the general public. As they say, with friends like Ms. Atterstam, who needs any enemies?

Making science (part XI): A perverted view of “impact”

Marc Kirschner is the John Franklin Enders University Professor and chair of the Department of Systems Biology, Harvard Medical School, Boston, MA 02115. He recently wrote an editorial for Science magazine published on 14 June 2013.

Kirschner debunks the notion of research “impact” as the likelihood that the proposed work will have a “sustained and powerful influence”. He writes that: “Especially in fundamental research, which historically underlies the greatest innovation, the people doing the work often cannot themselves anticipate the ways in which it may bring human benefit. Thus, under the guise of an objective assessment of impact, such requirements invite exaggerated claims of the importance of the predictable outcomes—which are unlikely to be the most important ones. This is both misleading and dangerous“.

Importantly, he says that “One may be able to recognize good science as it happens, but significant science can only be viewed in the rearview mirror. To pretend otherwise distorts science.”

Everyone preoccupied about the “impact” of current and future research should read Marc Kirschner’s full piece HERE.