Category Archives: Academia

What makes a memorable poster, or, when should you water your flowers?

What makes a memorable poster, or, when should you water your flowers?Being out of the lab, out of science, and out of funding for a while also means that I have not been at a scientific conference for a few years now, not even my favourite meeting of the Society for Research on Biological Rhythms. I have missed the last two meetings (and I really miss them – they are a blast!).
But it is funny how, many years later, one still remembers some posters from poster sessions. What makes a poster so memorable?

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The Scientific Paper: past, present and probable future

From the ArchivesA post from December 5, 2007:
Communication
Communication of any kind, including communication of empirical information about the world (which includes scientific information), is constrained by three factors: technology, social factors, and, as a special case of social factors – official conventions. The term “constrained” I used above has two meanings – one negative, one positive. In a negative meaning, a constraint imposes limits and makes certain directions less likely, more difficult or impossible. In its positive meaning, constraint means that some directions are easy and obvious and thus much more likely for everyone to go to. Different technological and societal constraints shape what and how is communicated at different times in history and in different places on Earth.
Technology – Most communication throughout history, including today, is oral communication, constrained by human language, cognitive capabilities and physical distance. Oral communication today, in contrast to early history, is more likely to include a larger number of people in the audience with whom the speaker is not personally acquanted. It may also include technologies for distance transmission of sound, e.g., telephone or podcasts. This is the most “natural” means of communication.

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NIH public access law is now being implemented

As many of you may be aware, yesterday was the first day of the implementation of the new NIH law which requires all articles describing research funded by NIH to be deposited into PubMed Central within 12 months of publication. Folks at SPARC have put together a list of resources one can consult when looking for answers about the implementation of the access policy.
Bloggers on Nature Network as well as here on Scienceblogs.com will write posts about the NIH bill and its implementation throughout the week (the ‘OA week’), informing their readers about the implementation, the next steps to be worked on in the future, and related topics. NIH is collecting public comments on the policy until May 1 so feel free to chime in yourself.
This law is not something that just appeared out of thin air a couple of months ago. As Liz Allen explains:

It’s been a long and winding road to get to this point and PLoS has been closely involved from the very beginning. Inspired by the desire to harness the potential of the internet to foster faster, freer exchange of biomedical knowledge, Harold Varmus, then director of the National Institutes of Health, proposed an electronic publishing site called E-biomed that would provide barrier-free access to the peer-reviewed and pre peer-reviewed scientific literature. After a period of public review (during which E-biomed met with fierce opposition from established publishers, sound familiar?), Dr. Varmus announced the creation of PubMed Central. Launched in February 2000, PMC is the NIH’s free digital archive of biomedical and life sciences journal literature and is the repository into which all NIH funded research articles must be deposited from today.

Of course, if you publish with PLoS, you do not have to worry about any of this – we know what to do and we do it for you automatically. The moment your paper is published, it is immediatelly deposited in PubMed Central, so you can go on with your work without worrying about the new law. In today’s issue of PLoS Biology, Harold Varmus exlains:

In contrast, open-access journals, like those published by PLoS or BioMed Central, make their articles immediately and freely available in PMC, eliminating any extra work by the authors and any delay before the articles are fully accessible. Furthermore, these journals permit far greater use of their articles, by allowing readers to explore and reuse the texts under the terms of a Creative Commons license. These degrees of freedom are possible because access and use do not diminish revenues: open-access publishers recover their costs upfront, frequently by charging a publication fee that is paid from research expenses, rather than with subscription charges to libraries and readers. Thus the distribution and reuse of open-access content can be without limit, just as scientists and the public would wish.

Print and Misprint

Obligatory Reading of the day: Why I feel so strongly about redundant digitization

NIH getting serious about brain doping

There have recently been several articles in the media about brain enhancers, so-called Nootropics, or “smart drugs”. They have been abused by college students for many years now, but they are now seeping into other places where long periods of intense mental focus are required, including the scientific research labs. Here is a recent article in New York Times:

So far no one is demanding that asterisks be attached to Nobels, Pulitzers or Lasker awards. Government agents have not been raiding anthropology departments, riffling book bags, testing professors’ urine. And if there are illicit trainers on campuses, shady tutors with wraparound sunglasses and ties to basement labs in Italy, no one has exposed them.
Yet an era of doping may be looming in academia, and it has ignited a debate about policy and ethics that in some ways echoes the national controversy over performance enhancement accusations against elite athletes like Barry Bonds and Roger Clemens.

And here is a recent article in the Baltimore Sun:

Despite the potential side effects, academics, classical musicians, corporate executives, students and even professional poker players have embraced the drugs to clarify their minds, improve their concentration or control their emotions.

It is apparently used in business:

I’ve long thought that the use of performance enhancing drugs, typically associated with professional sports, would spread to other endeavors as science progresses. Arguably, many professionals already use chemicals to improve their performance. Constant nicotione and caffeine consumption has been endemic in the business world for a long time, and more recently prescription drugs such as Adderall have been used and abused by white collar professionals to improve focus and concentration. Chemical-assisted performance is by no means a panacea. It carries with it a host of medical and ethical questions. Yet as we gain deeper insight into the way the human brain works, we’ll inevitable be confronted with new opportunities and dilemmas such as these.

Nature also recently had a discussion on the use of brain enhancers by the academics:

Barbara Sahakian and Sharon Morein-Zamir from the Department of Psychiatry at Cambridge University argue that the increased usage of brain-boosting drugs by ill and healthy individuals raises ethical questions that cannot be ignored. An informal questionnaire Sahakian and Morein-Zamir sent to some of their scientific colleagues in the US and UK revealed fairly casual use by academics, and we now want to hear your views on the topic..

The problem is getting serious enough that an international organization has recently been founded, the World Anti-Brain Doping Authority:

The agency works to help individual academic federations implement testing procedures in the fields of academic research. It also produces a list of prohibited substances that academics are not allowed to take and maintains the World Anti Brain-Doping Code.

This is pretty scary stuff. On one hand, these drugs have not been tested very well, so nobody knows what nasty side-effects they mat have with repeated and prolonged use, so this is certainly a worry. But I thought that it was a little bit too much, or at least premature, that the NIH is jumping in on this bandwaggon, with, IMHO, quite drastic proposed measures:

The National Institutes of Health (NIH) today announced three new initiatives to fight the use of brain enhancing drugs by scientists. The new initiatives are (1) the creation of the NIH Anti-Brain Doping Advisory Group (NABDAG), a new trans-NIH committee, (2) a collaboration with the World Anti-Doping Authority (WADA) and the European Commission to create the World Anti-Brain Doping Authority (WABDA) and (3) the adoption by the NIH of the World Anti-Brain Doping Code – a set of regulations on the use of brain enhancing drugs among scientists.
“These new initiatives are designed to level the playing field among scientist in terms of intellectual activities,” said NIH Director Elias A. Zerhouni, M.D. “These three activities are designed to get NIH ahead of the curve in terms of performance enhancing drug use among scientists.”
NABDAG will serve to coordinate activities across different NIH agencies in terms of regulating the use of brain enhancing drugs. The trans-NIH group will be directed by internationally renowned doping authority Jonathan Davis, Ph.D., current director of research at WADA.
“The priority of NABDAG will be to seek out input from the scientific community and from within NIH,” Davis said. “The availability of tremendous expertise and the remarkable infrastructure at NIH will make our activities more robust and will allow us to tackle questions about brain doping that were not possible to address in the past. For example, new testing procedures will need to be developed and we will be able to bring the entire NIH infrastructure to this task.”
While “doping” is now accepted as a problem among athletes, it is less widely known that so-celled “brain doping” has been affecting the competitive balance in scientific research as well. It is for this reason that NIH is collaborating with the World Anti-Doping Authority (WADA), which has led the fight against doping in athletics, to create the World Anti Brain Doping Authority (WABDA). “Because brain doping is not just an American problem,” said Richard Pound, the current Director of WADA and acting Director of WABDA until a permanent head can be found, “we are working with the European Union’s research funding agency, the European Commission Research, to make sure WABDA is effective.
NABDAG will be established within the NIH Office of Intramural Research and administered by the National Institute of Mental Health (NIMH). Additional support for the center will come from the NIH Office of the Director, the National Institute on Drug Abuse (NIDA) and the Center for Scientific Review (CSR). The research activities of NABDAG will take place on the NIH Bethesda campus. An additional focus of NABDAG will be to provide training opportunities for students and established scientists from developing countries and from minority groups in the United States.
Together with WABDA, NABDAG will work to develop the international rules for the use of performance enhancing drugs among scientists as well as testing and punishment procedures. Most importantly they will administer the World Anti Brain-Doping Code, a set of uniform anti-brain doping rules. The NIH and European Commission have formally adopted this Code for the conduct of all scientists which receive funding in any form (intramural or extramural) from these agencies. The Code includes regulations on which drugs are prohibited, what the recommended testing procedures should be, and what the punishments should be for positive tests. More information on the WABDA Code can be found at http://wabda.org/. We note that the implementation will include testing of all NIH funded scientists both at the time they receive funding as well as at random times during the course of working on an NIH funded project. Testing will also be implemented at all NIH-funded or NIH-hosted events such as conferences and workshops and at grant review panels.
NIMH, NIDA, and CSR are among the 27 institutes and centers at the NIH, an agency of the Department of Health and Human Services. The NIMH mission is to reduce the burden of mental and behavioral disorders through research on mind, brain, and behavior. More information is available at the NIMH website http://www.nimh.nih.gov. The National Institute on Drug Abuse is a component of the National Institutes of Health, U.S. Department of Health and Human Services. NIDA supports most of the world’s research on the health aspects of drug abuse and addiction. The Institute carries out a large variety of programs to ensure the rapid dissemination of research information to inform policy and improve practice. Fact sheets on the health effects of drugs of abuse and further information on NIDA research can be found on the NIDA web site at http://www.drugabuse.gov. The Center for Scientific Review organizes the peer review groups that evaluate the majority of grant applications submitted to the National Institutes of Health. CSR recruits about 18,000 outside scientific experts each year for its review groups. CSR also receives all NIH and many Public Health Service grant applications — about 80,000 a year — and assigns them to the appropriate NIH Institutes and Centers and PHS agencies. CSR’s primary goal is to see that NIH applications receive fair, independent, expert, and timely reviews that are free from inappropriate influences so NIH can fund the most promising research. For more information, visit http://www.csr.nih.gov.
The National Institutes of Health (NIH) — The Nation’s Medical Research Agency — includes 27 Institutes and Centers and is a component of the U.S. Department of Health and Human Services. It is the primary federal agency for conducting and supporting basic, clinical and translational medical research, and it investigates the causes, treatments, and cures for both common and rare diseases. For more information about NIH and its programs, visit http://www.nih.gov.

That’s pretty harsh, don’t you think? And if egalitarianism is the goal, this will backfire due to inherent differences between people – an insomniac like me can certainly get more done than someone else who actually gets 8 hours of sleep every day. Back in the day I did experiments that lasted 24 hours, sometimes 36 hours, a couple of times even 72 hours straight. Not everyone’s physical and mental constitution would allow for such exertion. This would actually favor people like me. And the others? Let them eat Provigil!
Then, is the next step going to be to force morning people to work only in the morning and the evening types only in the evenings?
Will research that involves mental rotation of 3D objects be limited only to female researchers, or will the men have to be handicapped in some way, perhaps by having more than 0.08% blood alcohol so the 3D objects spin faster?
There is also a dangerous potential for going down the slippery slope. Will they start adding new chemicals to the list? In my long experiments, I was also aided by copious amounts of chocolate, Coca Cola and junk food from the vending machine (and who knows what chemicals are in those!). If NIH bans caffeine, the entire business of science in the USA will grind to a halt. No coffee, no data, sorry, sir.
Environment is known to affect our cognitive abilities as well. A factor that probably helped me the most during my long experiments was the radio tuned to a local station specializing in reruns of the Rush Limbaugh show. Our technician thought it was great that Rush was speaking the Truth to the Power, while I was inclined to scream but held back as I did not want to stress my birds and thus get unreliable data (hmmm, in retrospect, does listening to Rush affects a bird directly?). Will NIH ban radios? iPods? If it does try to completely control the environment, say Good Bye to all the field work, not to mention all the research going on up on the Space Station.
But all of this is besides the point – who ever said that science should be egalitarian!? Scientists are selected and self-selected for their intelligence, curiosity and overall geekiness. It is in the interest of scientific progress that scientists always do their best, so if they want to use brain enhancers, that’s fine, its their own choice and their own sacrifice for the greater good.
I think that NIH thinks of science like running. On an even playing field, the best runner will win. But why limit oneself to running speed. Give runners additional equipment and they go faster and soon enough you will have another exciting sport – NASCAR! I think of science as NASCAR! The spoils go to the one with the best brain enhancer! And next, we will have people racing their small personal spaceships, just like in Star Wars!
And that is just how it should be. The competition should not really be between scientists, but between Science and Nature (not talking about the journals here, as anyone knows there PLoS wins, of course). And Nature is powerful, autonomous from NIH, and as we all know, loves to play dirty. So, we should use everything we can come up with to speed ourselves up. As Nature tries to hide her secrets from us, we need to deploy all our armamentaria to snatch them from her.
And that is why we need Open Access. Just sayin’ (they pay me to do this, you know?). And I even did not have my coffee yet!
Hat-tip to Jonathan who has more.

Update:

Anna has more….
Blake puts it in proper context.
Chris has a good point.
Update 2: There is more from:
Pedro
Howard
Jenna
Martin
Bob
Hsien
Steve
Andy
Genome Technology

Broken Pipeline

Check the website and download the PDFs:

An unprecedented five consecutive years of stagnant funding for the National Institutes of Health is putting America at risk–slowing the pace of medical advances, risking the future health of Americans, discouraging our best and brightest researchers, and threatening America’s global leadership in biomedical research. Unfortunately, President Bush’s budget proposal recommends a sixth year of flat funding for the NIH in 2009.
On March 11, 2008, a group of seven concerned academic research institutions, released a new report–A Broken Pipeline? Flat Funding of the NIH Puts a Generation of Science at Risk (http://brokenpipeline.org/brokenpipeline.pdf) –warning that America stands to lose a generation of young researchers and the cures they could discover if current NIH funding trends continue. The report features the voices of 12 junior researchers from institutions across the country who, despite their exceptional qualifications and noteworthy research, attest to the funding difficulties they and their peers are experiencing. Such difficulties, they say, are negatively impacting their work as well as science in general, and causing many young scientists to abandon academic research.

Post-doc with a leading Sleep research group

POSTDOCTORAL FELLOWSHIP OPPORTUNITY in SLEEP MEDICINE
Charles A. Czeisler, Steven W. Lockley, Christopher P. Landrigan, Laura K. Barger
Harvard Work Hours, Health and Safety Group
Division of Sleep Medicine, Brigham & Women’s Hospital, Harvard Medical School
The Harvard Work Hours Health and Safety Group focuses on understanding the consequences of extended work hours and disordered sleep schedules on health and safety across a range of professions and populations. We also develop and test countermeasures to prevent the increased risk of accidents and injury for both worker health and public safety with the long-term aim of providing data to inform evidence-based policy and legislative decisions. Recently, we have addressed the impact of reducing extended duration (>24 h) work shifts on physician health and patient safety and developed and tested a comprehensive sleep disorders screening and fatigue management program in several police forces.
We seek a post-doctoral fellow to join our team who will participate in ongoing projects and develop new research initiatives. These projects will primarily be ‘field-based’ programs involving data collection under real-world conditions but conducted using robust clinical trial designs. The Division of Sleep Medicine is interdisciplinary, with members from backgrounds in physiology, psychology, medicine, and mathematics and the successful candidate will be encouraged to collaborate within and outside the Division as they pursue their research interests. The rich environment of the Division of Sleep Medicine (http://sleep.med.harvard.edu) offers many opportunities for career development and education.
The candidate will have knowledge of clinical study design and experimental statistics. Candidates with experience in field- and/or laboratory based clinical trials are encouraged to apply. A background in Sleep Medicine is desirable but not required. An educational program in Sleep Medicine will be provided which the candidate will be expected to attend. The initial appointment will be for 2 years, renewable annually thereafter.
Interested candidates should send a letter of interest, curriculum vitae, and contact information for three references in hard copy and electronic format to:
Steven W. Lockley PhD
Division of Sleep Medicine
Brigham and Women’s Hospital
221 Longwood Ave
Boston MA 02115
Email: slockley@hms.harvard.edu

The so-called Facebook Scandal

[rant]So, if you organize a study-group online instead of in meat-space, the old fogies who still remember dinosaurs go all berserk. A student is threatened by expulsion for organizing a Facebook group for studying chemistry. Moreover, as each student got different questions, nobody did the work for others, they only exchanged tips and strategies. See the responses:
The Star:

Yet students argue Facebook groups are simply the new study hall for the wired generation.

Yes, they are.
Greg:

How much of this is a matter of administrative fear of the internet?

100%.
Larry:

Today, that sense of “honor” seems horribly old-fashioned. To most students it will not seem like cheating if they ask their friends for help with the assignments and share information. That’s what happened on the Facebook study group.

Old-fashioned is too nice a term. It is outdated and anachronistic.
Post-Diluvian Diaspora:

Honestly, do you not see the difference between studying together and exchanging answers on a graded assignment?

The problem is in a stupid professor who thinks in terms of “graded assignments” in the 21st century.
This all stems from the old German universities of a couple of centuries ago, where getting a degree was essentially a hazing process. Toughening the individual. For what? For replicating and preserving the hierarchy, both within the academia and in society as a whole. The educational systems around the world, at all levels, are still based on such outrageous ideas.
No individual can know everything needed knowing. No individual can make the necessary societal changes on one’s own. So why teach them as if it is all up to an individual? Both learning and social change are communal processes. What we need to be teaching is how to be a member of a community, how to network, how to contribute, how to share, how to pull together in order to increase the global knowledge and, by using this knowledge, to increase the global welfare.
Science is supposed to be a collaborative activity. Why is it organized (and taught) as if it was a competitive activity? How does that affect science? Negatively, by increasing secretiveness and sometimes outright fraud.
The Web is changing all this. The teenagers already grok that the old selfish notions of intellectual property are going by the way of the dodo. They naturally think in terms of networks, not individuals. And thinking in term of newtorks as opposed to a linear, hierarchical, individualistic focus, is necessary for speeding up the advancement of knowledge and societal good.
In other words, it is not important what each individual knows or does, it is important what the interactions between individuals can do, and how the group or community (or global community) learns and acts upon the knowledge.
Thus, education, especially science education, from Kindergarden through post-doc and beyond, should be organized around collaborations, teaching people and letting them practice the networking skills and collaborative learning and action. Individuals will make mistakes and get punished by the group (sometimes as harshly as excommunication). They will learn from that experience and become more collaborative next time. The biggest sin would be selfish non-sharing of information.
If I could, I would not give individual students grades on their individual performance at all. I would give a common grade for the entire class. Each individual will then get that same grade. If the last semester’s cohort got an A, do you think that this semester’s group would settle for anything less? And how do they get an A? By pooling their resources, sharing all the information, closely collaborating on all assigned projects, and coaxing/teaching/punishing individuals who are not pulling their weight. Neither the reward nor the punishment would be meted out by some outside self-appointed ‘authority’, but by peers – the people who matter the most.
Then, they would take this approach to the Real World, where such things really matter, where sucess is that of a community, not that of any individual.
So, if you do not get this, if you are not mentally ready for the 21st century, if you still harbor the outdated competition-based, individualistic mindset, you should not be in the teaching business. Quit today. Save yourself the embarassment of being laughed at by your students. Save your students from having to deal with an authoritarian. Save the society from promulgating the counter-productive, anti-social methods of knowledge-acquisition and knowledge-use.[/rant]

A 40-hour workweek?

In academia? See what they say:
Mad Hatter
EcoGeoFemme
ScienceGirl
Jennie
Mad Hatter again
DrugMonkey
Laurie Granieri
ScienceWoman
Telecommuting has its perks. But working only 40 hours is not one of them. Especially in my case in which the line between work, blogging, schmoozing and fun is blurry. Is posting this weekend post to be considered work (building and keeping my own community that, tomorrow, will click on a link to PLoS) or pleasure (doing what I always did – reading interesting stuff online and sharing with my readers)? Both? Who’s to tell? I have fun doing it. But I have fun doing my job, too.
And back when I was in grad school, my gregariousness/sociability was a drawback (wasting my time chatting with colleagues), so I did most of my work at night and on weekends (the Big Holidays were the best as there was absolutely nobody to talk to). And the nature of my research was such that I could not possibly work 9-5. I had to do big campaigns, i.e., experiments that lasted 24, 36 or even 72 hours straight, followed by a couple of days I am not expected to be seen on campus at all.

Jane – the Journal/Author Name Estimator

Jane is the cool new tool that everyone is talking about – see the commentary on The Tree of Life, on Nature Network and on Of Two Minds.
In short, the Journal/Author Name Estimator is a website where you can type in some text and see which scientific Journal has the content closest to the text you input, as well as people who published on similar topics. If you click on “Show extra options” you can narrow your search by a few criteria, e.g., you can search only Open Access journals.
The idea is to discover journals to which you can submit your work. Most people know the journals available for their stuff, but this is the way to discover new journals, see which are Green or Gold OA, or find a place for a manuscript that has already been rejected by all of your usual venues 😉
Another use is for editors of broad-topic journals, to find relevant referees for the incoming manuscripts.
So, I did first the obvious test of the site – I copied and pasted the abstract of one of my papers. It gave the correct journal at 100% confidence, and all four co-authors at equal split of 25%. So, it works in that way. The other people mentioned down the list are also relevant researchers who would be appropriate for reviewing such a mansucript.
Then I copied and pasted a small chunk from my unpublished dissertation and got a list of potential reviewers that was pretty much perfect – people I’d suggest if asked.
Then, I typed in a bunch of terms that I know occur frequently in PLoS ONE in different papers, all mixed up – and PLoS ONE came up high on the list (and first among OA journals). So far so good.
Apparently, if you paste non-scientific text, you always get Harvard Business Review – they’ll take anything silly. Figures.
So, what would you use it for? Is it useful?

Three Exam System? Can we design something better?

That is what Anne-Marie asked after a week with seven mid-term exams. In a few weeks, she’ll have another bunch of exams all at the same time. And then a finals week in May.
This is, obviously, not the most efficient system. So, have you, as a student or a teacher, encountered a better system?

Books on careers in science

Anne-Marie reviews two books that appear to be useful in thinking about one’s career in science: The Beginner’s Guide to Winning a Nobel Prize, by Peter Doherty, and The Chicago Guide to Landing a Job in Academic Biology, by Chandler, Wolfe, and Promislow. Read the review and, if you think this is something you need, buy the books.
And, if you have additional recommendations, let Anne-Marie know in her comments.

Discovering scholarly information and data

Next Generation Discovery: New Tools, Aging Standards
March 27-28, 2008
Chapel Hill, NC
Discovering scholarly information and data is essential for research and use of the content that the information community is producing and making available. The development of knowledge bases, web systems, repositories, and other sources for this information brings the need for effective discovery — search-driven discovery and network (or browse) driven discovery — tools to the forefront. With new tools and systems emerging, however, are standards keeping pace with the next generation of tools?

Richard Akerman and my SciBling Dave Munger are among the participants. I’ll try to make it…

How to have your papers deposited into PubMed Central

Are you confused with the new NIH Policy and unsure as to what you need to do? If so, Association of Research Libraries has assembled a very useful website that explains the process step by step. But the easiest thing to do is to publish with a journal that does the depositing for you free of charge and here is the list of such journals. Of course, PLoS automatically does that for you as well.

Open Access Beer!

What is the difference between Free Access Beer and Open Access Beer?
You go to a bar to get your Free Access Beer. You sit down. You show your ID. The barista gives you a bottle. You don’t need to pay anything for it – it’s free, after all. You take your own bottle-opener from your pocket and open the bottle. You drink the beer from the bottle. You return the empty bottle to the barista. You go home.
You order you Open Access Beer online or by phone. You pick what kind of beer you want. It gets delivered to your door really fast. The delivery man opens the bottle for you. You are not carded, nor do you have to pay. That beer is now yours to do whatever you want with it – you can drink it out of the bottle, or pour it into a glass. You can use it for cooking or you can use it to water your plants. You can do a chemical analysis of it in your lab and use the knowledge to produce an even better homebrew.
See the difference?
Unfortunately, there is no such thing as Open Access Beer, or even Free Access Beer. Which, it turns out, may be a Good Thing. For science, at least. Especially if you are Bohemian kind of guy. You need to read this very Grim report (from Emmett, via Kevin):
A possible role of social activity to explain differences in publication output among ecologists:

Publication output is the standard by which scientific productivity is evaluated. Despite a plethora of papers on the issue of publication and citation biases, no study has so far considered a possible effect of social activities on publication output. One of the most frequent social activities in the world is drinking alcohol. In Europe, most alcohol is consumed as beer and, based on well known negative effects of alcohol consumption on cognitive performance, I predicted negative correlations between beer consumption and several measures of scientific performance. Using a survey from the Czech Republic, that has the highest per capita beer consumption rate in the world, I show that increasing per capita beer consumption is associated with lower numbers of papers, total citations, and citations per paper (a surrogate measure of paper quality). In addition I found the same predicted trends in comparison of two separate geographic areas within the Czech Republic that are also known to differ in beer consumption rates. These correlations are consistent with the possibility that leisure time social activities might influence the quality and quantity of scientific work and may be potential sources of publication and citation biases.

beer%20and%20science.JPG

Generally, inhabitants of Bohemia (western region of
the Czech Republic) are known to drink more beer than
people from Moravia (eastern region of the country). This
difference was confirmed for my sample of researchers:
researchers from Bohemia drank significantly more beer
per capita per year (median 200.0 litres) than those from
Moravia (median 37.5 litres; Mann-Whitney test: U17,17
2.84, p0.005). Therefore I predicted lower measures of
publication output for the former in comparison to latter
group of researchers (I could not include nominal variable
”region” in regression models because of its significant
interdependence with another effect variable, the beer
consumption). Indeed, researchers from Bohemia published
fewer papers per year (U17,172.32, p0.02), were less
cited per year (U17,172.99, p0.003), and showed lower
citation rate per paper per year (U17,172.30, p0.02).

The question is: do you do less science because you drink too much, or do you drink too much because your science sucks? And, is 200 liters of beer per year too much? Who’s to judge? Moravians? Is there a similar correlation with wine and other drinks? Other non-alcoholic social activities?
Or is beer-drinking one of the possible symptoms of the Impostor Syndrome (see mrswhatsit’s series on it: Part I, Part II, Part III, also Zuska, Sciencewoman, Revere, Laelaps and DrugMonkey to learn more about it).

New and Exciting in PLoS Computational Biology

I found two articles interesting to me in today’s issue of PLoS Computational Biology – the first one about becoming a good scientist, the other on circadian rhythms:
On the Process of Becoming a Great Scientist:

In the vein of promoting further debate and discussion, I provide here a different and perhaps deeper look at what makes a successful scientist. While I can’t claim to have the reputation of Hamming, I grew up in a family of well-known scientists, and have had plenty of chances to observe the trajectories of scientific careers over my lifetime. Based on that experience, I propose the following as a somewhat distinct set of guidelines for doing the best research:

Modeling an Evolutionary Conserved Circadian Cis-Element:

Life on earth is subject to daily light/dark and temperature cycles that reflect the earth rotation about its own axis. Under such conditions, organisms ranging from bacteria to human have evolved molecularly geared circadian clocks that resonate with the environmental cycles. These clocks serve as internal timing devices to coordinate physiological and behavioral processes as diverse as detoxification, activity and rest cycles, or blood pressure. In insects and vertebrates, the clock circuitry uses interlocked negative feedback loops which are implemented by transcription factors, among which the heterodimeric activators CLOCK and CYCLE play a key role. The specific DNA elements recognized by this factor are known to involve E-box motifs, but the low information content of this sequence makes it a poor predictor of the targets of CLOCK/CYCLE on a genome-wide scale. Here, we use comparative genomics to build a more specific model for a CLOCK-controlled cis-element that extends the canonical E-boxes to a more complex dimeric element. We use functional data from Drosophila and mouse circadian experiments to test the validity and assess the performance of the model. Finally, we provide a phylogenetic analysis of the cis-elements across insect and vertebrates that emphasizes the ancient link between CLOCK/CYCLE and the modeled enhancer. These results indicate that comparative genomics provides powerful means to decipher the complexity of the circadian cis-regulatory code.

Obligatory Reading of the Day

Mythbusting Canadian Healthcare, Part II: Debunking the Free Marketeers by Sara Robinson
Scientific Careerism 101: Yes, grad students and postdocs it IS your fault by DrugMonkey
The project of being a grown-up scientist (part 2) by Janet D. Stemwedel
The Well Dressed Professor… by Thomas Levenson
Your massive credit card debt means you’re doing great! by Amanda Marcotte
Barack Obama’s Achilles Heel by Jon Swift
The Cult of Obama by Sara Robinson

New on….

….Scienceblogs.com
Busy today. What are the others writing about?
Abel Pharmboy and DrugMonkey discuss the causes of death of Heath Ledger.
Nature had some articles about ScienceDebate 2008 and got it all wrong. I agree with what John Lynch wrote.
PhysioProf explains the brave new world of NIH Grants – not what I remember from the times of plentiful funding.
Angry Toxicologist on animal testing.
Obligatory Reading of the Day: Janet on the project of being a grown-up scientist.
The awesomest movie of a gigantic shark.
Shelley and Steve are Of Two Minds…

Who’s scooping whom and why this matters?

Aetosaurs. No, I have not heard of them until now. But that does not matter – the big story about them today is the possibility – not 100% demonstrated yet, to be fair – that some unethical things surround their discovery and naming. And not just Aetosaurs. Some other fossils as well.
As I am not on the inside loop of the story, you need to first read the background story on Aetosaurs by Darren Naish – Part 1 and Part 2.
Then, carefully read Darren’s today’s post and responses by Laelaps, Cryptomundo and Paleochick.
For the ethical side of the story, read Janet’s take.
For the gory details of the story, read the timeline, the entire collection of information and the brief summary of it.
Finally, this was all made public today in an article in Nature. In short, it appears that a group of people have made it a habit to scoop their colleagues by publishing other people’s information (shown by colleagues in private) and naming species faster by using their in-house Journal.
Now imagine a world in a not-so-distant future….
You just spent a long, hard, but exciting day in the Gobi desert. You finally get to eat dinner and shower and get back to your tent and turn on your computer. You post on your blog:
“Gobi. Day 23. It was a very exciting day today – we struck gold: an apparently well-preserved fossil of something that is clearly in the X family, and perhaps related to Y species, but astragalus is so weird – look at this picture of it [insert a photo of the bone]. This is most certainly a new species. It will take a year or two to dig this thing out, clean it up, analyze it and publish the full description, but for now, we name it Blogosaurus….”
And there is a time-stamp on the blog post. And a bunch of palaeo-colleagues post congratulations in the comments. And it is aggregated by a bunch of sites (ResearchBlogging.org, Connotea, etc.).
Scoop that if you can!
Everyone knows that you, indeed, are in the Gobi, as they know about your grant proposal for it and they have been following your blog daily, including all the pictures from the trip. They know they did not just see you two hours ago sipping tea in the faculty lounge at your University. They post congratulatory posts on their own blogs. They discuss the pictures and early descriptions that you posted. Over the next months and years, they keep up with the digging, cleaning and analysis by reading your blog. They come to visit and help with analysis. They teach about it in their classes. Finally, when you publish the official description of the Blogosaurus, they add comments on the paper itself.
Of course, as they all also keep blogs, they have changed the official rules of naming, allowing for official publication no matter how many times the name has been mentioned elsewhere, offline or online (as long as the description was not published in another taxonomy journal). And if they discovered that you kept another fossil find a secret, at least for a while, that would raise all sorts of red flags: was there something fishy about the fossil? Why didn’t you immediately tell the world about it if everything was legit? That kind of secretive behavior is automatically suspect, and considered unethical and anti-social.
Sunlight is the best disinfectant…

Open Education Declaration

On the heels of David Warlick’s session on using online tools in the science classroom, this initiative is really exciting:

Teachers, Students, Web Gurus, and Foundations Launch Campaign to Transform Education, Call for Free, Adaptable Learning Materials Online
Cape Town, January 22nd, 2008–A coalition of educators, foundations, and internet pioneers today urged governments and publishers to make publicly-funded educational materials available freely over the internet.
The Cape Town Open Education Declaration, launched today, is part of a dynamic effort to make learning and teaching materials available to everyone online, regardless of income or geographic location. It encourages teachers and students around the world to join a growing movement and use the web to share, remix and translate classroom materials to make education more accessible, effective, and flexible.
“Open education allows every person on earth to access and contribute to the vast pool of knowledge on the web,” said Jimmy Wales, founder of Wikipedia and Wikia and one of the authors of the Declaration. “Everyone has something to teach and everyone has something to learn.”
According to the Declaration, teachers, students and communities would benefit if publishers and governments made publicly-funded educational materials freely available online. This will give students unlimited access to high quality, constantly improving course materials, just as Wikipedia has done in the world of reference materials.
Open education makes the link between teaching, learning and the collaborative culture of the Internet. It includes creating and sharing materials used in teaching as well as new approaches to learning where people create and shape knowledge together. These new practices promise to provide students with educational materials that are individually tailored to their learning style. There are already over 100,000 such open educational resources available on the Internet.
The Declaration is the result of a meeting of thirty open education leaders in Cape Town, South Africa, organized late last year by the Open Society Institute and the Shuttleworth Foundation. Participants identified key strategies for developing open education. They encourage others to join and sign the Declaration.
“Open sourcing education doesn’t just make learning more accessible, it makes it more collaborative, flexible and locally relevant,” said Linux Entrepreneur Mark Shuttleworth, who also recorded a video press briefing. “Linux is succeeding exactly because of this sort of adaptability. The same kind of success is possible for open education.”
Open education is of particular relevance in developing and emerging economies, creating the potential for affordable textbooks and learning materials. It opens the door to small scale, local content producers likely to create more diverse offerings than large multinational publishing houses.
“Cultural diversity and local knowledge are a critical part of open education,” said Eve Gray of the Centre for Educational Technology at the University of Cape Town. “Countries like South Africa need to start producing and sharing educational materials built on their own diverse cultural heritage. Open education promises to make this kind of diverse publishing possible.”
The Declaration has already been translated into over 15 languages and the growing list of signatories includes: Jimmy Wales; Mark Shuttleworth; Thomas Alexander, former Director for Education at the Organization for Economic Cooperation and Development; Lawrence Lessig, founder and CEO of Creative Commons; Andrey Kortunov, President of the New Eurasia Foundation; and Yehuda Elkana, Rector of the Central European University. Organizations endorsing the Declaration include: Wikimedia Foundation; Public Library of Science; Scholary Publishing and Academic Resources Coalition; Canonical Ltd.; Centre for Open and Sustainable Learning; Open Society Institute; and Shuttleworth Foundation.
To read or sign the Cape Town Open Education Declaration, please visit: http://www.capetowndeclaration.org.

Go and sign the Declaration!

Update:
David Wiley of the USU Center for Open and Sustainable Learning has more.

Life Sciences in North Carolina

OK, this may not be very new, but for all of you taking a look at science in North Carolina next week due to the focus on the Science Blogging Conference, The Scientist has published a number of essays looking at every aspect of Life Science in the state – check it out: The State of Life Sciences.
For the latest news on life science in North Carolina, visit the Bioscience Clearinghouse, a very useful website hosted by The North Carolina Association for Biomedical Research.

My SciBling speaks at NESCent

From an e-mail from the Science Communicators of North Carolina:

At noon on Friday, January 18, the National Evolutionary Synthesis Center (NESCent) in Durham will host a seminar by Josh Rosenau, the Public Information Project Director at the National Center for Science Education. Rosenau, who is in town for the Science blogging conference, will opine on the subject of “Talking to the Media about Evolution and Creationism.” The discussion is sure to be lively.

Science Advisor

Following his (excellent) article in Seed on the topic, my SciBling Chris Mooney blogs about the future of the position of the Science Advisor to the President, suggesting some potential names, and Matt Nisbet, RPM, Blake Stacey, Brian Switek, Scott Hatfield, Lila Guterman, Larry Moran, Mike Dunford, Flavin, c4chaos, Gordon Watts and PZ Myers chime in with their own opinions on the potential candidates.
For some reason, all the bloggers are focusing on popularizers of science and charismatic figures. But the job of a Science Advisor to the President is not really that public (unless the next President completely changes this role).
For a few decades, since the position has first been formed, the role of the Science Advisor was, well, to advise the President on scientific topics. Mooney is correct that there has been a shift in topic since then, i.e., what the most important science-related issues of the day are – from atomic energy that was really big in the 50s and 60s to the biotechnology and climate science today.
GW Bush waited almost a year – during which he did a LOT of assaults on science – before appointing poor Dr.Marburger for the role. Then, he demoted the role – the Science Advisor no longer has the ear of the President, but is relegated to some backroom to play rummy with the Origami Advisor, Interior Decorating Advisor and Dog-Grooming Advisor. Every now and then, when the Administration does something particularly egregious and the science community attacks them for it, someone goes to the back room and drags Marburger out to the microphones and cameras and instructs him to say something along the lines of “But, George Bush is a nice guy. Really. And he really likes science. He really enjoyed watching that nature show – did you see it the other day? – especially when the pack of hyenas ripped into that wildebeest. Wasn’t that cool?”
In the unlikely event that a Republican wins the elections in November, it is highly unlikely that the role of Science Advisor will get reinstated to the former level, not even by the least insane candidate, the only one who concedes that global warming is real and may be a bad thing and perhaps, just perhaps, humans may have something to do with it (McCain). When everything you stand for is against the empirical reality, why have some scientist keep reminding you that you are basing your policy decisions on fairy-tales, wishful thinking and gut-feeling?
On the other hand, all the Democratic candidates have indicated, at least indirectly, that they would reinstate the position back to the Cabinet level. Mooney reports:

The top democratic presidential contender, Hillary Clinton, has officially pledged to right the wrongs against Marburger–or at least, against his office. If elected, Hillary says, her science adviser will be named early, get the “Assistant to the President” title back, and report directly to her.

Thus, in the next Administration, the new Science Advisor will be a member of the Cabinet, will be present at all the Cabinet meetings, will talk to the President daily, and will have a direct influence on policy on a day-to-day basis. I do not see the Science Advisor as a public figure, though a public appearance may happen occasionally, perhaps to announce major science-related news from the White House. In other words, the person will not be responsible for selling science to the people, but explaining science to a reality-based President. A very, very different role.
All of the people mentioned by bloggers are completely unprepared for such a job. What is needed is someone who is well versed in science policy and politics and has a track record in administration of science and in dealing with the Congress. It does not even matter if the person is famous or a complete unknown to the general public, a highly controversial figure or someone universally liked, a theist or an atheist – none of those things are likely to ever affect the job (or the initial nomination) at any time.
So, my personal pick for the job is Harold Varmus, who won the Nobel Prize in physiology and medicine for his discovery of oncogenes and is a prolific researcher. He spent six years as the Director of NIH during which time he managed to persuade the Congress to double the NIH budget. He really got PubMed going, is a big proponent of Open Access, is now the President of Sloan-Kettering and he turned a dream into reality by founding the Public Library of Science. He has testified in Congress and is a very likable person and an effective speaker. He has no negatives I can possibly think of, knows his science, knows his policy/politics and is persuasive and passionate. I think he would be perfect.

The most exciting job in science publishing can be yours!

PLoS ONE is the first and (so far) the most successful scientific journal specifically geared to meet the brave new world of the future. After starting it and bringing it up from birth to where it is now one year later, Chris Surridge has decided to move on.
Do you think you have the skill and experience to pick up where he leaves off? Do you want to be at the cutting edge of scientific publishing? If so, take a look at the new job ad for the Managing Editor of PLoS ONE:

The overall responsibility of this position, which will be located in the San Francisco office, is to lead the editorial staff and editorial board who run PLoS ONE — a ground-breaking online-only publication covering the full breadth of scientific and medical research. PLoS ONE was launched one year ago, and is already publishing over 150 peer-reviewed research articles each month.

While other PLoS journals have a narrower scope (Biology, Medicine, Pathogens, Genetics, Computational Biology, Neglected Tropical Diseases), ONE is supposed to be the ONE place for all areas of science. Thus, your scientific background does not necessarily have to be in biomedical research to be eligible and welcome for this job, if your experience and organizational skills are a perfect match for the job.

New on…..Publishing

In the wake of the signed omnibus bill that funds NIH and ensures open deposition of NIH-funded research, here are some thoughtful questions:
Why the NIH bill does not require copyright violation:

The great advantage of the requirement to deposit in Pubmed (rather than simply to expose on a publisher or other website) is that the act is clear. You can’t “half-deposit” in Pubmed. They have the resources to decide whether any copyright statement allows the appropriate use of the information or is suffiently restrrictive that it does not meet the NIH rules.
At some stage the community will get tired of the continual drain on innovation set by the current approach to publihing. Whether when that happens many publishers will be left is unclear.

What does USD 29 billion buy? and what’s its value?

So, while Cinderella_Open_Access may be going to the ball is Cinderella_Open_Data still sitting by the ashes hoping that she’ll get a few leftovers from the party?

What is peer review, anyway?

A final question is perhaps the most difficult: How do we identify journals offering acceptable levels of peer review? Who’s to say whether a given journal is good enough? After all, even the most rigorous scholarly journals sometimes make errors — indeed, one of the most important parts of the scientific process is identifying and correcting problems in earlier work. Indeed, too rigorous a standard of peer review can stifle research just as much as too lax a standard.

The Impacted Factor in need of Cleansing

I buried this among a bunch of other cool links yesterday, but there was a study the other day, in the Journal of Cell Biology, that seriously calls in question the methodology used by Thompson Scientific to calculate the sacred Impact Factor, the magic number that makes and breaks lives and careers of scientists.
Apparently, it is really a magic number calculated in a mysterious way, not in the way that Thompson Scientific claims they do it. Who knows what subjective factors they include that they do not tell us about?

When we examined the data in the Thomson Scientific database, two things quickly became evident: first, there were numerous incorrect article-type designations. Many articles that we consider “front matter” were included in the denominator. This was true for all the journals we examined. Second, the numbers did not add up. The total number of citations for each journal was substantially fewer than the number published on the Thomson Scientific, Journal Citation Reports (JCR) website (http://portal.isiknowledge.com, subscription required). The difference in citation numbers was as high as 19% for a given journal, and the impact factor rankings of several journals were affected when the calculation was done using the purchased data (data not shown due to restrictions of the license agreement with Thomson Scientific).
Your database or mine?
When queried about the discrepancy, Thomson Scientific explained that they have two separate databases–one for their “Research Group” and one used for the published impact factors (the JCR). We had been sold the database from the “Research Group”, which has fewer citations in it because the data have been vetted for erroneous records. “The JCR staff matches citations to journal titles, whereas the Research Services Group matches citations to individual articles”, explained a Thomson Scientific representative. “Because some cited references are in error in terms of volume or page number, name of first author, and other data, these are missed by the Research Services Group.”
When we requested the database used to calculate the published impact factors (i.e., including the erroneous records), Thomson Scientific sent us a second database. But these data still did not match the published impact factor data. This database appeared to have been assembled in an ad hoc manner to create a facsimile of the published data that might appease us. It did not.
Opaque data
It became clear that Thomson Scientific could not or (for some as yet unexplained reason) would not sell us the data used to calculate their published impact factor. If an author is unable to produce original data to verify a figure in one of our papers, we revoke the acceptance of the paper. We hope this account will convince some scientists and funding organizations to revoke their acceptance of impact factors as an accurate representation of the quality–or impact–of a paper published in a given journal.
Just as scientists would not accept the findings in a scientific paper without seeing the primary data, so should they not rely on Thomson Scientific’s impact factor, which is based on hidden data. As more publication and citation data become available to the public through services like PubMed, PubMed Central, and Google Scholar®, we hope that people will begin to develop their own metrics for assessing scientific quality rather than rely on an ill-defined and manifestly unscientific number.

Of course, this was written in a polite language of science. But on a blog, I can say that this is at least very fishy and suspect. And several other bloggers seem to agree, including Bjoern Brembs, The Krafty Librarian, Eric Schnell, Peter Suber and Stevan Harnad who each dissect the paper in more detail than I do, so go and read their reactions.

Open Grant Review?

If scientific papers can be publicly reviewed either pre-publication or post-publication, and if one day soon the public can have a voice on the patents, then why not also grant proposals? Now, Michael does not go that far – he only proposes a more direct communication between the researcher and the reviewer – but, why not? Some people write good proposals. Others can sell them better in a different way: by talking about them. I would certainly like to be able to try to sell my grant proposal by shooting a video and posting it on a site like Scivee.com, where both the reviewers and the public can add their commentary.

Boston trip – Part 1

OK, back home and rested – it’s time for a pictorial report, in two parts. This one is social, the other part will be about the conference itself. All of it under the fold…

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On my last scientific paper, I was both a stunt-man and the make-up artist.

Cannot. Resist. Funny. Titles. Sorry.
But seriously now, the question of authorship on scientific papers is an important question. For centuries, every paper was a single-author paper. Moreover, each was thousands of pages long and leather-bound. But now, when science has become such a collaborative enterprise and single-author papers are becoming a rarity, when a 12-author paper turns no heads and 100-author papers are showing up more and more, it has become necessary to put some order in the question of authorship.
Different scientific areas have different traditions. In one discipline your contribution to the work would place you at the first author spot, in another at the last spot. Who can make heads and tails out of it all? And what about all those people who are middle-authors? Are they not worthy of getting a job?
Now that everyone is exploring alternatives to Impact Factors of journals, some are focusing on a metric for evaluating individual papers, while others are trying to figure out how to measure contributions of individual people. Both are important! A good measure of the impact of a paper is needed for the progress of science (and to historians of science). A good measure of the impact of people is needed for making sound career decisions: who gets a post-doc where, who gets a job, promotion and tenure, who gets lecture invitations and prizes.
Setting aside the possibilities of including contributions other than paper authorship (e.g., teaching, writing reviews and editorials, science popularization, books, lectures, political activity/advisory, expert witness role in courts, administrative duties, peer-reviewing, blogging, vigorous and high-quality activity online, e.g., in comments on articles published on platforms that allow interactivity, such as PLoS ONE, PLoS Neglected Tropical Diseases, PLoS Hub for Clinical Trials, etc.) and narrowing it down to just authorship on peer-reviewed research articles, it is obvious that the ambiguous system in place right now is not coming even close to what is needed for a fair evaluation of individuals engaged in the scientific endeavors.
As the authorship system affects so many people personally, in terms of their careers, it is no surprise that the discussion of this topic can get quite heated. And that is aside from the fact that some people still adhere to the silly notion that authorship has something to do with the typing of words of the final article (just see the hot exchanges in the comments on this post and this post if you don’t believe me). Authoring is creating. Or contributing to a creation of something new, regardless of the verbal description of that creation that must come at the end of the process (and can be done by hired writing professional, unless he/she is on strike right now).
Some journals require more detailed descriptions for each author’s contribution to the work. That is definitely a move in the right direction, but is not yet perfect.
Now, there is a new proposal that, at first reading, sounds ridiculous but if you stop and read it again and think about it should make you reconsider – a credit list. Yes, just like in the movies, when the credits roll at the end. Each person is listed, some people more than once, and each person’s contribution is very well defined. Everyone knows exactly what a “producer” does, what the “director” does and what the “2nd camera assistant” means. Look at the Oscars – they give awards for music composition, animation, special effects, writing, acting, directing, and all the possible roles in what it takes to make a movie.
How is science different? Someone is good at getting money, another one at having creative ideas, another at experimental design, another has a great “touch” with the animals or pipetters, while another is brilliant with statistics or making beautiful graphs. Why not reward each contribution in its own right?
Make your comments here.

Blogging on Peer Reviewed Research Icons Inauguration Day!

If you are a regular reader of this blog, you may have seen this, this and this, i.e., an effort to design an icon that a blogger can place on the top of a post that discusses peer-reviewed research. The icon makes such posts stand out, i.e., the readers will know it is not a discussion of a press release or media reporting, or fisking of a crackpot, a meme, or showing a cute animal picture.
So, I am please to announce that the icons are here! Dave Munger explains.
BPR3%20icon-samples.png
Pick up the codes for icons on this page. Carefully read the Guidelines before you start using the icon.
See who is using the icon already, by visiting this page so you can see the examples.
The blog-posts that use the icon will be aggregated in the nearest future on the BPR3 blog. So, get started today!
I went back last night and added the icon to a number of appropriate posts of mine – I have linked to them again under the fold. You can see that I actually sometimes write (or at least used to) about REAL science!

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How to build a better peer-review system

Mark Patterson writes in Bringing Peer Review Out of the Shadows:

———————–
Hauser and Fehr propose a system for holding late reviewers to account by penalizing them when it’s their turn to be an author. A slow reviewer’s paper would be “held in editorial limbo” for a length of time that reflects their own tardiness as a reviewer. The short article was intended to provoke a discussion about how to improve peer review – an opening card as Hauser and Fehr put it.
So far, 16 responses have been added from readers, and the general view seems to be that incentives would be more effective than the punishment that Hauser and Fehr propose. As for an incentive, quite a number of respondents favour a system whereby reviewers are paid for their efforts – although not to a level that would fully reimburse the time spent.
——————–snip——————-
As an editor, I’ve been privileged to be party to some incredibly thoughtful and constructive discussions between authors and reviewers. It’s not always that way of course, but when it works, it’s fantastic. I’ve often felt that it’s a pity that these exchanges haven’t been shared more broadly, and as pointed out by others in the discussion, there are many who feel that greater transparency in peer review is the way to go – pre- and post-publication.
———————-snip——————
The formula for more transparent peer review might not be perfect yet, but there is great potential and further experimentation is a must. Ultimately, improving the peer review process will take the same kind of thoughtful and constructive discussions that help researchers identify the extra step that will maximize the significance of their results. We invite you to join in that discussion.

Please go there and add your thoughts!

ASIS&T update

A quick update on the Milwaukee events….
The first time I went to Mocha’s (much better wifi than the hotel and it is free) I saw a familiar face walk in – from Scifoo! World is small. She promised to come to the Science Blogging Conference (I am leaving the name out so not to play Gotcha later if she manages not to come in January). Jean-Claude, Janet, Christina Pikas and I went to dinner at Water Street Brewery last night – all four of us will meet again in January at the Science Blogging Conference. Janet, Jean-Claude and I had lunch at 105-year old German Mader’s Restaurant. Back at Mocha’s waiting for some time to pass until I go to the airport to go back home….
There is a lot of people from UNC here, including Jeffrey Pomerantz, Tessa Sullivan and Fred Stutzman. Nice to see some familiar faces here. As Janet noted, this is not our tribe. They all know each other and there is a lot of social stuff going on that we are looking at from outside in.
Christina is liveblogging all the sessions she attended, including our session this morning so you can get some more details from someone who was not on the panel itself.
We went to an interesting session this morning, where Phillip Edwards presented his research proposal (pdf) on the decision-making process as to where to publish one’s work (especially the choice between Closed and Open Access journals). Christina liveblogged this as well.
I finally got to meet danah boyd whose blog I’ve been reading for many years now. It is actually one of the first blogs I ever discovered. She was on two panels yesterday afternoon and I went to both of them. Jeffrey blogged about one of them on research methodologies in the study of online social networks. How similar, yet how different from the way the same topic was covered by non-academics at ConvergeSouth the other day.
The best session was the one before it, about online behavior, i.e., types and personas (eg.., trolls, flame warriors, questioners, answerers, connectors, diplomats, etc…). That was actually quite useful for my job as it looks at motivations people have when they post comments and get engaged in online communities.

Opening Science to All at ASIS&T

Back at delightful Mocha’s cafe on the corner…
We just finished our session at the ASIS&T conference: Opening Science to All: Implications of Blogs and Wikis for Social and Scholarly Scientific Communication, organized by K.T. Vaughan, moderated by Phillip Edwards. Janet Stemwedel, Jean-Claude Bradley and I were the panelists. There were about 50-60 people in the audience who asked some excellent questions afterwards.
I started off with defining science blogs and various uses they can be put to, in particular how they interact with other ways of scientific communication such as Open Access publications. Jean-Claude then focused on Open Notebook science and his experience in using blogs, wikis and other online tools in his own research and building research collaborations. Janet finished the session with a look at the way science blogging is changing the structure and culture of the world of science (or not – she is sitting next to me typing her own version of this so see what she say about it).
The entire session was recorded in a couple of different media and I will tell you once it appears online somewhere. I am aware of only two pictures taken, though, right after the session – Janet is showing us another one of the many sides of her multi-faceted nature as she responds to a question by an NIH guy…
ASIS%26T%20001.jpg
ASIS%26T%20002.jpg
The links from my presentation are under the fold:

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How to write a successful grant in behavioral sciences

On the Oxford University Press Blog, two useful articles:
Grant Writing: Things That You Can Do To Learn Scholarship
Behavioral Science Grants: Surefire Tips and Pointers

Felice Frankel wins The Lennart Nilsson Award for science photography

Nobel Prizes are not the only awards given in Stockholm these day. Karolinska Institute also gives an annual Lennart Nilsson Award for photography. This year’s prize has just been announced and I am happy to report that the recepient is a friend of mine (and Scifoo camper), Felice Frankel for her amazing science photography. From the Press Release:

Felice Frankel, a scientific imagist and researcher at Harvard University’s Initiative in Innovative Computing, has been named the recipient of the 2007 Lennart Nilsson Award. Frankel was sited for creating images that are exquisite works of art and crystal-clear scientific illustrations – both fascinating and valuable to the general public and scientific community alike.
The Lennart Nilsson Award is given out annually in honour of the internationally celebrated Karolinska Institutet photographer. As with the Swedish photographer’s own images, Felice Frankel’s work reveals previously invisible aspects of the world in unique, novel ways. Her subjects range from nanotechnology to magnetism and the surface tension of water droplets.
“In studying Ms. Frankel’s work, I recognize my own way of looking at the world. We share the same passion for using images to explain and communicate science,” says Lennart Nilsson.
In selecting Felice Frankel, the board of the Lennart Nilsson Foundation stated: “Those viewing Ms. Frankel’s images are initially captivated by their form and colour. No sooner is their curiosity aroused than they want to know what the photograph depicts. She has thus fulfilled a scientific reporter’s paramount task: to awaken people’s interest and desire to learn.”
Felice Frankel began her academic career in biology, but then moved on to architectural and landscape photography. During a fellowship year at Harvard’s Graduate School of Design, she turned once again to science, beginning work in her present specialty. Today, she is a Senior Research Fellow at the Initiative in Innovative Computing at Harvard University and also holds an appointment as a research scientist at the Massachusetts Institute of Technology (MIT).
Throughout her professional life, Felice Frankel has worked to make visual imagery a key tool in scientific communication. Her photographs, like Nilsson’s, have often been reproduced on the covers of leading science magazines like Nature and Science. She writes a regular column in American Scientist, and has published a series of books. Her latest — Envisioning Science: The Design and Craft of the Science Image (MIT Press, 2002) — is a guide to creating visual scientific images that convey research to a wider audience. Felice Frankel lectures regularly about scientific photography and new methods of using images to improve the teaching of science.
The Lennart Nilsson Award was established in 1998 and is administered by Karolinska Institutet in Stockholm, Sweden. The Award of 100,000 SEK (approximately 15,600 USD) will be presented in Berwaldhallen concert hall in Stockholm on the first of November 2007. The occasion will also host the annual installation of professors at Karolinska Institutet, Sweden’s largest centre for medical research and training and the home of the Nobel Assembly. Lennart Nilsson will be present at the ceremony.

HarvardScience

Today, Harvard has launched a new website – HarvardScience – showcasing the depth and breadth of science, medicine, and engineering at all of Harvard’s schools and affiliated hospitals:

The site provides a comprehensive resource for anyone interested in science in general, and particularly what’s happening at Harvard in the sciences and engineering.

How much does pharmaceutical industry control what appears in medical literature?

Ghosts, drugs, and blogs:

By its hidden nature, it is obviously a challenge to determine the exact prevalence of “ghost management,” defined by Sismondo as the phenomenon in which “pharmaceutical companies and their agents control or shape multiple steps in the research, analysis, writing, and publication of articles.”

Of course they fight against Open Access Publishing – too much sunshine scares them and would make them scurry away in panic…

Science 2.0 at SILS

Yes, I’ll be there this Friday. Come by and say Hello if you are in the building or close at lunchtime.

Help make NIH-funded research findings freely available to everyone!

Back in July, the House of Representatives passed a bill that requires all the NIH-funded research to be made freely available to the public within at most 12 months subsequent to publication.
The equivalent bill has passed the Senate Appropriations Committee earlier this summer and will be up for vote in the Senate very soon! In advance of this important vote, The Alliance for Taxpayer Access has issued a Call for action:

As the Senate considers Appropriations measures for the 2008 fiscal year this fall, please take a moment to remind your Senators of your strong support for public access to publicly funded research and – specifically – ensuring the success of the National Institutes of Health (NIH) Public Access Policy by making deposit mandatory for researchers.
Earlier this summer, the House of Representatives passed legislation with language that directs the NIH to make this change (http://www.taxpayeraccess.org/media/release07-0720.html). The Senate Appropriations Committee approved a similar measure (http://www.taxpayeraccess.org/media/release07-0628.html). Now, as the Appropriations process moves forward, it is critically important that our Senators are reminded of the breadth and depth of support for enhanced public access to the results of NIH-funded research. Please take a moment to weigh in with your Senator now.

Read the rest for talking points and the contact information of your Senators, then do your part and contact them! And spread the word – by e-mail, posting on your blog or website, on forums and mailing lists. Let’s get this bill passed this month and thus ensure that taxpayer-funded research is freely available to its funders – the taxpayers.
This needs to be done no later than Friday, September 28, 2007, when the bill is slated to appear in the Senate.

Textbooks

There have been a couple of recent posts about textbooks lately. Jim Fiore started it all with a look at the textbook business from the perspective of the authors and students, looking primarily at the problem of money. One sentence really hit me, though:

The problem with a large, institutionalized used book market is that it completely cuts out the publisher and the author.

In a larger economy, it is called ‘stock market’. When you buy stocks, most often you will be buying them from a broker, not directly from the company. In other words, you are entering the used-stocks market. You are investing, but not into the company. Yet, the worth of a company is measured by the way its stocks are doing on this second-hand stock market. Only about 6% of the stocks in any given year are sold by the businesses themselves, i.e., the money invested in those stocks go back to the company which can then use it for R&D or for PR or for salaries, etc. Many old, well-established companies have not sold any new stocks in decades. This is as if the performance of, for instance, Ford is measured not in the sales of new cars, but in the re-sale value of the second-hand cars. Ford does not get a penny out of any of those transactions, can do very little to influence that market, yet it is required to do whatever it takes to increase the worth of its stock despite of no money coming in. The stockowners demand it, without ever giving back anything to the company. So, the CEOs slash and cut left and right, trying to get growth without having anything coming back in with which to water the plant. This is much better explained in this book (written by a small business owner and no enemy of capitalism) by Marjorie Kelly.
But, back to the textbooks. PZ Myers looks at the business from the perspective of a teacher:

It makes it difficult for students to sell off their used textbooks, it gives faculty the headache of having to constantly update their assignments, and if you allow your students to use older editions, it means we have to maintain multiple assignments. It’s extraordinarily annoying, and to no good purpose at the university (to great purpose at the publisher, though).

Jim responds:

In the arena of science and engineering there are issues with the fairly narrow audience and resultant low volume, and some difficulties with the used book market. There is, of course, the issue of the publishers. I am going to risk having my snout slapped by biting the hand that feeds me, but hey, I noticed something the other day that has my head spinning anyway.

But David Warlick goes further. If you decide to abandon or downgrade the textbooks for your classes, and start using the Web instead, you cannot just let the students go on a wild hunt. They will come up with stuff of questionable quality. With a textbook, it’s easy – it is a text that is approved by you as a teacher and by your colleagues who wrote it, edited it, and promoted it to institutions and school districts. Students know that the textbook is to be trusted, thus they do not need to learn the skills of critically evaluating it. But if they have to find their own sources, they need to learn how to separate the wheat from the chaff:

We teach from textbooks, from reference books, from journals, online databases, and from our own educated expertise. It’s part of our arsenal, as teachers, to help us instill confidence in the sources of that which we are teaching. I’m not saying that textbooks, reference books, and commercial databases are bad, and that we shouldn’t use them. They are enormously valuable. But we’re missing something that’s very important when we rely so exclusively on carefully packaged content and then lament that our students and children rely so readily on Google.
We have to practice what we preach, and we have to practice it out loud!
At the same time that we continue to use our textbooks (or what ever they evolve into), reference works, databases, and our own expertise, we should also bring in, at every opportunity, content and resources that we have found, evaluated, processed, and prepared for teaching and learning, and that we should include conversations about how we found it, evaluated, and processed it. If the are seeing us, every day, asking the questions that are core to being literate today, then perhaps they will not only develop the skills of critical evaluation, but also the habits.

The discussion in the comments is quite contentious there, actually. What do you think?

A kick-ass Conference: Autonomy, Singularity, Creativity

Unfortunately, due to the Murphy’s Law of conference dates, I will have to miss this fantastic meeting, because I will at the time be at another fantastic meeting, but if you can come, please do – registration will be open online in a few days.

Autonomy, Singularity, Creativity

The conference theme is about bringing scientists and humanities scholars to talk about ways that science is changing human life.

November 8th, 9th, and 10th, the National Humanities Center will host the second ASC conference.

And the program features a Who’s Who list:

Thursday, November 8th
Frans de Waal
Martha Nussbaum
Friday, November 9th
Dan Batson
Margaret Boden
Joseph Carroll
Frans de Waal
Evelyn Fox Keller
David Krakauer
William Lycan
Martha Nussbaum
Steven Pinker
Paul Rabinow
Margery Safir
Robert Sapolsky
Saturday, November 10th
Terrence Deacon
Daniel Dennett
Alex Rosenberg
Mark Turner

Of those, I have seen Sapolsky, Fox Keller and Deacon speak before, and I know Alex Rosenberg, and for each one of them alone, it is worth showing up!

Qualitative vs. Quantitative Research (in Medicine and elsewhere)

In a commentary and a blog post, the editors of PLoS Medicine ask:

….is there still a reluctance to accept that anything useful can be learned from research without numbers?

An old question that tends to generate a lot of heat. Where do you stand on it, within medicine or within your own area of research?

What is an “Author”?

There are some die-hards in the comment thread of this post on Evolgen who assert that the only thing that makes one an author of something is the act of writing, i.e., using writing materials to commit language to paper. Preferably English language… Thus, in their minds, there is something fishy about multi-author scientific papers, i.e., only the individual who crafted the sentences of the paper should be considered an author of that paper.
But…
Leonardo painted Mona Lisa. Leonardo is the “Author” of Mona Lisa. People who named it, framed it, marketed it, hung it up in The Louvre and described it in the Catalogue – all of them are equivalent to editors and publishers. They are not authors. Leonardo is. Although, note that he never commited language to paper. For all practical purposes he could have been illiterate, he would still be the Author.
Mozart composed The Little Night Music. Mozart is the “Author” of The Little Night Music. He wrote it down in musical notation, but for all practical purposes he could have just played it and had some court musician (Salieri?) jot down the notes on paper. In any case, Mozart is the Author. Although, note that he never committed language (German, English or any other) to paper. For all practical purposes he could have been illiterate, he would still be the Author.
Many modern music bands are composed of musically illiterate people. They get together and start playing their instruments. After a while and many fits and starts, they come up with something that actually sounds good. They then practice it and in the end they record it. The music is never written down, but it is distributed in the form of a digital file, perhaps as a CD. They are collectively Authors of the piece. Others – producers, recording engineers, marketers, etc. are not Authors. The band members are. No language was committed to paper in the entire process, not even musical notation. For all practical purposes they could all have been illiterate, they would still be the Authors.
When a bunch of scientists get together and talk, they may come up with an idea, which they then refine and develop. They contact other scientists who possess particular skills or expertise needed for the project. The work gets done, with each person doing his/her own part. They all participate in data production, data analysis and/or interpretation. Finally, almost as an afterthought, one unlucky member of the group is assigned the tedious job of writing the paper, i.e., the textual part of the paper. This one person commits language to paper, though the statistics and graphs are a much more important parts of the paper (and much more difficult to produce than text). All the people involved in the process are Authors of that piece of work. If the group hired someone else, e.g., a professional writer (and yes, some labs do that), to write the textual part of the paper, the ONLY person who is NOT an Author of that paper is the ONLY person who actually committed language to paper.
So, where does the confusion arise from? Authorship has NOTHING to do with language. It has everything to do with the creative process. People who produce something new, be it art, music, ideas (including stories) or knowledge are the authors of it. The writing is just one of the many possible ways that the authored thing is recorded for others to enjoy. A novelist is an author not because she typed, but because she creatively invented the story she subsequently typed.
Imagine if 20 or 50 years from now there is no scientific paper in the current form at all. All of science is reported in the video format on places like SciVee or JoVE. The authors of the work turn on the camera and talk about their initial idea and background, then show around the lab, demonstrate their techniques, put up a short clip of something relevant to the work (e.g., animal behavior), display the data and the analysis, then again turn to the camera and talk about their conclusions and the directions for the future research. The YouTube generation, now in their 50s and 60s and with long white beards, watches this and, if intrigued, clicks on another button that shows all the raw data sitting there ready to be mined. No writing is involved at all. No putting language on paper. Yet, all the people who participated in the creation of this piece of knowledge are Authors. For all practical purposes they could all be illiterate, they would still be the Authors.

Nature mission (sic) statement

Maxine Clarke:

In printing the statement verbatim every week as we have done, making it clear when it originated, we have hitherto assumed that readers will excuse the wording in the interests of historical integrity. But feedback from readers of both sexes indicates that the phrase, even when cited as a product of its time, causes displeasure. Such signals have been occasional but persistent, and a response is required.

Suzanne Franks:

Who needs outright discrimination? It’s so much more pleasant and civilized to discriminate while pretending to be inclusive. It’s just one tiny step sideways, but in the right direction to deflect real and meaningful change. It’s just our small way of saying “patriarchy RULES!”

Chris Surridge:

I had always thought it was a disclaimer when quoting text letting me indicate that I know there is an error in the text but that I am quoting verbatim. Basically [sic] says “I didn’t make a mistake, the error is in the original”. Now it seems we can use it to indicate that we disagree with the original wording and are sure that the author would too if they were around to ask.

Bill Hooker:

So now at least I know what it is that I disagree with. I don’t think NPG should link to the 1869 statement, at least not without going through the modern version, as Nature (the journal site) does. I think the print journal should print the modern mission statement — with, if they want a nod to their impressive history, a comment to the effect that apart from updating sexist and exclusive language, not much has changed from the original (which is visible on our website, etc etc).

Suzanne Franks 2:

Well, I’m sorry, but much of my original critique remains unchanged. I don’t care if you have a nice new online mission statement. If you want to keep printing your old sexist one every week then contextualize it as a historical document and explain that it is sexist and outdated and was outdated at the time it was published and is included here only as another example of how women were explicitly excluded in the past. And contextualize it that way every time you print it, every week, not once in an editorial. That tiny little [sic] does not do the job. What it does is say “we know this is wrong but we don’t care, we are going to keep printing it anyway”. Continuing to print it uncontextualized each week says “we revere this bit of our history so much that we want you to read it every week. And we don’t really care all that much that it is sexist, ’cause we think it rocks so much!”
As I said in a comment, imagine the historical mission statement said “for scientific white men”. Would you still feel comfortable printing it every week? Would you feel that just inserting a little [sic] after it was a sufficient gesture to allow you to keep printing it unmodified? I’m guessing it’s less likely the answer would be yes.

Thoughts?

Alone in the lab…and you get hungry!

So, you look around to see if there is anything edible!
Of course, it’s easy if you work with tasty animals….(just ask the guys in the next door lab who work on lobsters, crayfish and oysters…or wait until you get some brains out of quails and notice the plump breastmeat….just joking).

Jobs: Managing Editor, PLoS Biology

I am not sure if blogging about it is enough – in this case a very strong Resume may be more important – but if you think you have sufficient experience and expertise to be a Managing Editor of a major biology journal, PLoS Biology (and are not too intimidated to be stepping into Hemai’s shoes), check the job ad and apply:

The Public Library of Science (PLoS) seeks an experienced editor and manager to lead its flagship life science journal – PLoS Biology. Since its launch in 2003, PLoS Biology has rapidly become established as both a high impact journal and a leader in the open-access publishing movement. This is a unique opportunity to develop a ground-breaking journal, and to shape a fundamental transition in scientific publishing. The managing editor could be based in either of our editorial offices in San Francisco, USA or Cambridge, UK.

Sorry, the Chapel Hill office in my bedroom is too small for such a big position, but San Francisco is a gorgeous city and the folks at PLoS are great to work with.

An interesting case of plagiarism

The Purloined Bibliography:

My training in medieval history had acquainted me with the practice of identifying dependencies among manuscripts by tracing the repetition of errors. By analogy, I thought, if there were additional idiosyncratic errors on my Web site that also appeared in the book, each instance would be a discrete piece of evidence showing that the volume had lifted material from my work.
I found myself in the unusual position of hoping that I had made more mistakes. Could I find more evidence than just two bizarrely placed asterisks?

Congratulations to Rob!

My SciBling Rob Knop is leaving the academic circus for a cool job: designing Universes or some such astronomical stuff on Second Life. Just as he is about to leave his University, though, he got a nice parting gift from the academic world for his work on the expansion of the Universe – the Gruber Prize in Cosmology. Please go and say Hello and Congratulations to Rob!
Related:
Farewell and Hail
Science blogger (and soon to be former academic) shares Gruber Prize.
Is getting tenure Mission Impossible?
Kudos for Rob
I have shilled

Does tenure need to change?

There is a long and interesting comment thread on this article on The Scientist blog. What do you think?
(Hat-tip: Tanja)

Science Envy

I missed this by weeks, but Dave asked a set of questions that I was pondering on, but found no time and energy to answer until now.
PZ, Janet, Martin, Chad and RPM responded (I am assuming some people outside SB did as well) and their responses (and their commenters’) are very interesting.

1. What’s your current scientific specialty?

Chronobiology, although I have not seen the inside of the lab for three years now. So, scientific publishing, education and communication – does that count?

2. Were you originally pursuing a different academic course? If so, what was it?

Yes, I went to vet school before I came to the States. Finished 3.5 out of 5 years of it, too.

3. Do you happen to wish you were involved in another scientific field? If so, what one?

It took me a while to respond to this, because it was really hard for me to answer this question. I love my field and would do it all over again. Yet, I also love evo-devo. And animal behavior. And comparative animal physiology. And palaeontology. And neuroscience. And evolutionary theory. And marine biology. And….well, pretty much everything in biology.
If I could go all the way back to early childhood and got to start all over again, no other science is completely out of the question, form math, physics and chemistry, to archaeology and psychology.
I also agree with some of my SciBlings on the Math/CS envy. I was REALLY good at math until I was about 18 or so. Decades of unuse, and now I can do little more than balance my checkbook.
In 1980 or so I had all the opportunities to turn myself into a computer programmer, but I decided that playing games was more fun, so, beyond basic HTML, I now know nothing about computers, code, and anything related and I really feel a big gap in my knowledge and ability to function bacause of this.
Another envy is philosophy – I never had an opportunity to take a single philosophy course, not even in high school, so I am completely self-taught and it shows.
But after all this thinking, I realized someting else – I am really envious of 19th century scientists! They felt no need to specialize. Why have to pick and choose, when you could do everything?
Just look at Darwin! He got to travel the world. He wrote papers, technical monographs, popular science books, a travelogue and memoirs. He did geology, palaeontology, taxonomy, comparative anatomy, natural history, plant physiology, animal behavior. Oh, yes, I heard he also dabbled in theory, so he could subsequently do evolutionary biology as well. And many consider him a philosopher.
Perhaps that is why I am so gung-ho about Science 2.0. I see a possibility that the new technology will give rise to new ways to do, publish and communicate science, forming connections between fields that were difficult or impossible to do in the 20th century, when a separate graduate degree may have been needed for such a thing.