Category Archives: Academia

Elites? That’s somehow bad?

This kind of he-said-she-said False Equivalence journalism is infuriating and is the prime reason why nobody trusts the corporate media any more which is why the newspapers are dying:
Academic Elites Fill Obama’s Roster:

…..All told, of Obama’s top 35 appointments so far, 22 have degrees from an Ivy League school, MIT, Stanford, the University of Chicago or one of the top British universities. For the other slots, the president-elect made do with graduates of Georgetown and the Universities of Michigan, Virginia and North Carolina.
While Obama’s picks have been lauded for their ethnic and ideological mix, they lack diversity in one regard: They are almost exclusively products of the nation’s elite institutions and generally share a more intellectual outlook than is often the norm in government. Their erudition has already begun to set a new tone in the capital, cheering Obama’s supporters and serving as a clarion call to other academics. Yale law professor Dan Kahan said several of his colleagues are for the first time considering leaving their perches for Washington.
“You know how Obama always said, ‘This is our moment; this is our time?’ ” Kahan said. “Well, academics and smart people think, ‘Hey, when he says this is our time, he’s talking about us.’ ”
But skeptics say Obama’s predilection for big thinkers with dazzling resumes carries risks, noting, for one, that several of President John F. Kennedy’s “best and brightest” led the country into the Vietnam War. Obama is to be credited, skeptics say, for bringing with him so few political acquaintances from Illinois. But, they say, his team reflects its own brand of insularity, drawing on the world that Obama entered as an undergraduate at Columbia and in which he later rose to eminence as president of the Harvard Law Review and as a law professor at the University of Chicago…..

What a load of bull!
A society builds Universities for a reason – as places where the best and the brightest, surrounded by the other best and brightest, gain knowledge, skills and wisdom, as well as humility that comes from having one’s ideas challenged by colleagues every day. These are the places explicitly built to train the new generations of leaders – people who have a good grasp of the way the world works and a good understanding of the best ways to deal with the curveballs that the world throws at people and societies. These are exactly the kind of people a country needs to lead it.
Where else can one gain such knowledge and skills? You can learn fist-fighting skills out on the street. You can learn how to fudge books in the business world. You can learn how to sing hymns in church. You can learn how to ignore reality, spin fairy tales and destroy the English language in right-wing “think” tanks. But the honest useful skills are learned only in the academia.
Why is Washington Post, in this piece (and most others, this is just the latest example), inserting irrelevant opinions of “conservatives” and so-called “skeptics” (really ‘pseudo-skeptics’)?
Over the past 28 years, and especially starkly over the past 8 years, every single “conservative” idea has been shown in practice to be wrong and dangerous. The conservatives, what’s left of them (although many of them erroneously, for historico-local reasons, think of themselves as conservatives although they are not, or label some liberal ideas as ‘conservative’ although they are not) are out wondering in the wilderness.
So, why should any media outlet ever ask any conservative for any opinion on any topic? They have been proven wrong on everything, their ideology is dead, and their opinions are irrelevant (except for the humor segments). Inviting a conservative (or a Republican, because these two terms are today, more than at any time in history, equal and interchangeable) on a show is just like inviting a Creationist on a show when the topic is a new finding in evolutionary biology. Quoting conservatives in a newspaper article is just like quoting a Global Warming Denialist in an article about climate change – irrelevant, laughable, wrong and, yes, dangerous because it gives the audience the wrong idea that conservatism still deserves respect. It does not.
With conservatism debunked and dead, the next opposition party to the Democrats will come from the Left, not Right.
No, it is not the loss of advertising that dooms newspapers. It is not the unruly, wild bloggers. It is their own dishonesty. Let them die. Now.

Douglas Baird, who hired Obama at the University of Chicago, noted that whizzes can also have too much faith in their answers. But he said Obama is confident enough in his own intellect to challenge others’ conclusions. He recalled watching Obama hold his own with erudite faculty members.
“He goes into a faculty club filled with Nobel laureates, and he talks to them on equal terms — there hasn’t been anyone in the White House like that for a long time,” Baird said. “So it’s not as if, when he’s given advice by powerful, smart people, that he’ll get swayed from his core principles. And if you’re confident you’re going to stick to your own principles, then you might as well surround yourself with smart people rather than dumb ones.”

Why does Impact Factor persist most strongly in smaller countries

The other night, at the meeting of the Science Communicators of North Carolina, the highlight of the event was a Skype conversation with Chris Brodie who is currently in Norway on a Fulbright, trying to help the scientists and science journalists there become more effective in communicating Norwegian science to their constituents and internationally.
Some of the things Chris said were surprising, others not as much. In my mind, I was comparing what he said to what I learned back in April when I went back to Serbia and talked to some scientists there. It is interesting how cultural differences and historical contingencies shape both the science and the science communication in a country (apparently, science is much better in Norway, science journalism much better in Serbia).
But one thing that struck me most and got my gears working was when Chris mentioned the population size of Norway. It is 4.644.457 (2008 estimate). Serbia is a little bigger, but not importantly so, with 7.365.507 (2008 estimate – the first one without Kosovo – earlier estimates of around 10 million include Kosovo). Compare this to the state of North Carolina with 9,061,032 (2007 estimate).
Now think – what proportion of the population of any country are active research scientists? While North Carolina, being part of a larger entity, the USA, can afford not to do some stuff and do more of other stuff, small countries like Norway and Serbia have to do everything they can themselves, if nothing else for security reasons, e.g., agriculture, various kinds of industry, tourism, defense, etc. Thus, North Carolina probably has a much larger percentage of the population being scientists (due to RTP, several large research universities, and a lot of biotech, electronics and pharmaceutical industry) than an independent small country can afford (neither Norway nor Serbia are members of the EU).
So, let’s say that each of these smaller countries has a few thousand active research scientists. They can potentially all know each other. Those in the same field certainly all know each other. Furthermore, they more than just know each other – they are all each other’s mentors, students, lab-buddies, classmates, etc., as such a country is likely to have only one major university in the capital and a few small universities in other large cities. It is all very….incestual.
With such a small number of scientists, they are going to be a weak lobby. Thus, chances of founding new universities and institutes, expanding existing departments and opening up new research/teaching positions in the academia are close to zero. This means that the only way to become a professor is to wait for your mentor to retire and try to take his/her place. This may take decades! In the meantime, you are forever a postdoc or some kind of associate researcher etc.
If each professor, over the course of the career, produces about 18 PhDs (more or less, depending on the discipline) who are indoctrinated in the idea that the academic path is the only True Path for a scientist, the competition for those few, rare positions will be immense. And they all know each other – they are all either best friends or bitterest enemies.
This means that, once there is a job opening, no matter who gets the job in the end, the others are going to complain about nepotism – after all, the person who got the job (as well as each candidate who did not) personally knows all the committee members who made the final decision.
In such an environment, there is absolutely no way that the decision-making can be even the tiniest bit subjective. If there is a little loophole that allows the committee to evaluate the candidate on subjective measures (a kick-ass recommendation letter, a kick-ass research proposal, a kick-ass teaching philosophy statement, kick-ass student evaluations, prizes, contributions to popularization of science, stardom of some kind, being a member of the minority group, etc.), all the hell will break loose at the end!
So, in small scientific communities, it is imperative that job and promotion decisions be made using “objective” (or seemingly objective) measures – some set of numbers which can be used to rank the candidates so the candidate with the Rank #1 automatically gets the job and nobody can complain. The decision can be (and probably sometimes is) done by a computer. This is why small countries have stiflingly formalized criteria for advancement through the ranks. And all of those are based on the numbers of papers published in journals with – you guessed it – particular ranges of Impact Factors!
Now, of course, there are still many universities and departments in the USA in which, due to bureacratic leanings of the administration, Impact Factor is still used as a relevant piece of information in hiring and promotion practices. But in general, it is so much easier in the USA, with its enormous number of scientists who do not know each other, to switch to subjective measures, or to combine them with experiments with new methods of objective (or seemingly objective) measures. From what I have seen, most job committees are much more interested in getting a person who will, both temperamentally and due to research interests, fit well with the department than in their IFs. The publication record is just a small first hurdle to pass – something that probably 200 candidates for the position would easily pass anyway.
So, I expect that the situation will change pretty quickly in the USA. Once Harvard made Open Access their rule, everyone followed. Once Harvard prohibits the use of IF in hiring decisions, the others will follow suit as well.
But this puts small countries in a difficult situation. They need to use the hard numbers in order to prevent bloody tribal feuds within the small and incestuous scientific communities. A number of new formulae have been proposed and others are in development. I doubt that there will be one winning measure that will replace the horrendously flawed Impact Factor, but I expect that a set of numbers will be used – some numbers derived from citations of one’s individual papers, others from numbers of online visits or downloads, others from media/blog coverage, others from quantified student teaching evalutions, etc. The hiring committees will have to look at a series of numbers instead of just one. And experiments with these new numbers will probably first be done in the USA and, only once shown to be better than IF, transported to smaller countries.
Related:
h-index
Nature article on the H-index
Achievement index climbs the ranks
The ‘h-index’: An Objective Mismeasure?
Why the h-index is little use
Is g-index better than h-index? An exploratory study at the individual level
Calculating the H-Index – Quadsearch & H-View Visual
The use and misuse of bibliometric indices in evaluating scholarly performance
Citation counting, citation ranking, and h-index of human-computer interaction researchers: A comparison of Scopus and Web of Science
H-Index Analysis
The EigenfactorTM Metrics
Pubmed, impact factors, sorting and FriendFeed
Publish or Perish
Articles by Latin American Authors in Prestigious Journals Have Fewer Citations
Promise and Pitfalls of Extending Google’s PageRank Algorithm to Citation Networks
Neutralizing the Impact Factor Culture
The Misused Impact Factor
Paper — How Do We Measure Use of Scientific Journals? A Note on Research Methodologies
Escape from the impact factor
Comparison of SCImago journal rank indicator with journal impact factor
Emerging Alternatives to the Impact Factor
Why are open access supporters defending the impact factor?
Differences in impact factor across fields and over time
A possible way out of the impact-factor game
Comparison of Journal Citation Reports and Scopus Impact Factors for Ecology and Environmental Sciences Journals
Watching the Wrong Things?
Impact factor receives yet another blow
Having an impact (factor)
In(s) and Out(s) of Academia
The Impact Factor Folly
The Impact Factor Revolution: A Manifesto
Is Impact Factor An Accurate Measure Of Research Quality?
Another Impact Factor Metric – W-index
Bibliometrics as a research assessment tool : impact beyond the impact factor
Turning web traffic into citations
Effectiveness of Journal Ranking Schemes as a Tool for Locating Information
Characteristics Associated with Citation Rate of the Medical Literature
Relationship between Quality and Editorial Leadership of Biomedical Research Journals: A Comparative Study of Italian and UK Journals
Inflated Impact Factors? The True Impact of Evolutionary Papers in Non-Evolutionary Journals
Sharing Detailed Research Data Is Associated with Increased Citation Rate
Measures of Impact

The 50 Most Important, Influential, and Promising People in Science

That is the Discover Magazine’s series of articles, which includes:
The 10 Most Influential People in Science
20 Best Brains Under 40
Teen Genius: 5 Promising Scientists Under 20
…and more (the series, as the numbers above do not add up to 50, must still be in progress).

Advice for potential graduate students

I wish every single laboratory web-page contained a disclaimer like this one:

We currently have room in the lab for more graduate students. Before you apply to this lab or any other, there are a few things to keep in mind. First, be realistic about graduate school. Graduate school in biology is not a sure path to success. Many students assume that they will eventually get a job just like their advisor’s. However, the average professor at a research university has three students at a time for about 5 years each. So, over a career of 30 years, this professor has about 18 students. Since the total number of positions has been pretty constant, these 18 people are competing for one spot. So go to grad school assuming that you might not end up at a research university, but instead a teaching college, or a government or industry job. All of these are great jobs, but it’s important to think of all this before you go to school.
Second, choose your advisor wisely. Not only does this person potentially have total control over your graduate career for five or more years, but he/she will also be writing recommendation letters for you for another 5-10 years after that. Also, your advisor will shadow you for the rest of your life. People will always think of you as so-and-so’s student and assume that you two are somewhat alike. Finally, in many ways you will turn into your advisor. Advisors teach very little, but instead provide a role model. Consciously and unconsciously, you will imitate your advisor. You may find this hard to believe now, but fifteen years from now, when you find yourself lining up the tools in your lab cabinets just like your advisor did, you’ll see. My student Alison once said that choosing an advisor is like choosing a spouse after one date. Find out all you can on this date.
Finally, have your fun now. Five years is a long time when you are 23 years old. By the end of graduate school, you will be older, slower, and possibly married and/or a parent. So if you always wanted to walk across Nepal, do it now. Also, do not go to a high-powered lab that you hate assuming that this will promise you long-term happiness. Deferred gratification has its limits. Do something that you have passion for, work in a lab you like, in a place you like, before life starts throwing its many curve balls. Your career will mostly take care of itself, but you can’t get your youth back.
If, after reading this, you want to apply to this lab, we would love to hear from you.

Hmmmmm, Nepal sounds good…..

Are more US students looking at studying in Canada?

This article made me think about this – it showcases two local examples, and it contains this statement:

Mary Gratch, the academic counselor for the junior and senior classes at CHS [Carrboro High School], was a counselor at Chapel Hill High School for 16 years before CHS opened. She said that about two of her students apply to Canadian universities every year.
“It’s a small number, but it kind of consistently happens,” she said. “In terms of people selecting schools, it’s the United States or Canada typically.”

But I am wondering if there are any trends occurring – do more (or less) students consider studying in Canada now than, let’s say, five or ten years ago?

Praxis #4!

Praxis #4 is up on The Lay Scientist. Enjoy!

A Modest Proposal

Tom Levenson has an interesting idea:
A Modest Proposal: A Science Initiative for the Obama Administration

But I’d like to lay down one relatively cheap marker that would, I think, have a significant impact on both the culture and the productivity of American scientific research to a degree disproportionate to the underlying amount of dollars. It’s not a new idea, and hardly original to me -but seeing as it has been completely out of court for almost a decade, I think it bears repeating, even if it is old news to veterans of the business.

More on a Modest Proposal

In this post, I laid out a first marker for what the new administration could do for science, calling for an expansion of support for young scientists and engineers — grad students, post docs and new principal investigators.
For the new PIs, I suggested an increase in the number and shift in the emphasis of what are now called Faculty Early Career Development Program grants, arguing that the availability of no-strings attached discretionary research funds for young scholars would have a disproportionate bang for the buck.

Read both posts (and comments) in their entirety. What do you think?

Are you still struggling with EndNote? How quaint….

Duncan Hull and colleagues just published an excellent, must-read article – Defrosting the Digital Library: Bibliographic Tools for the Next Generation Web:

Many scientists now manage the bulk of their bibliographic information electronically, thereby organizing their publications and citation material from digital libraries. However, a library has been described as “thought in cold storage,” and unfortunately many digital libraries can be cold, impersonal, isolated, and inaccessible places. In this Review, we discuss the current chilly state of digital libraries for the computational biologist, including PubMed, IEEE Xplore, the ACM digital library, ISI Web of Knowledge, Scopus, Citeseer, arXiv, DBLP, and Google Scholar. We illustrate the current process of using these libraries with a typical workflow, and highlight problems with managing data and metadata using URIs. We then examine a range of new applications such as Zotero, Mendeley, Mekentosj Papers, MyNCBI, CiteULike, Connotea, and HubMed that exploit the Web to make these digital libraries more personal, sociable, integrated, and accessible places. We conclude with how these applications may begin to help achieve a digital defrost, and discuss some of the issues that will help or hinder this in terms of making libraries on the Web warmer places in the future, becoming resources that are considerably more useful to both humans and machines.

The paper goes through each of the services, one by one, explains the pros and cons of each, and makes suggestions for the future development, as well as pointing out barriers and possible ways to overcome those. A couple of listed services are almost there – but are you using them? If so, why? If not, why not?

UnderTheMicroscope

ScienceWoman gives us a heads-up on a new and interesting organization – UnderTheMicroscope.com:

The Feminist Press with IBM have just launched UnderTheMicroscope.com, a new site to involve young women in science and to encourage them to pursue careers in science, technology, engineering and math. The site is part of the Women Writing Science, a project initiated by The Feminist Press at the City University of New York and funded by the National Science Foundation.
The site features personal stories of women scientists, role models, and mentors; tips for parents and teachers; links to related women and science sites; videos; and networking. Some of these features are available now, and others will come later this year as noted in the press release below

On the website they have also started a promising-looking blog.

Publishing and Communicating Science

The W. M. Keck Center for Behavioral Biology at North Carolina State University (which includes students, faculty and staff from Departments of Biology (formerly Zoology, my own Department), Genetics and Entomology) is a group I called home for a large chunk of my own graduate experience. Every year, on top of monthly discussion meetings for members, they organize other interesting events, including this one, coming up in two weeks:

The W. M. Keck Center for Behavioral Biology at North Carolina State University announces its 2008 Professional Development Workshop:
Publishing and Communicating Science
Orli Bahcall, Senior Editor of Nature Genetics: The Nature of Scientific Publishing
Peter Binfield, Managing Editor of PLoS ONE: PLoS ONE-Leading a Transformation in Academic Publishing?
John Rennie, Editor-in-Chief of Scientific American: How and Why Scientists Should Talk to the Public
Joe Palca, Science Correspondent for National Public Radio: How Much Can You Say in Three Minutes?
Saturday, November 8, 2008
8:30 am – 3:00 pm
Sigma Xi Conference Center, RTP
****registration required****
A registration fee of $20 is required. Registration after the deadline is $40. Payment by check only, made out to “NC Agricultural Foundation”.
The registration fee includes breakfast, served at 8:30 am, and a box lunch, and is non-refundable.

For more information, check the flyer. I’ll be there….

The Nobel Prize conundrum

I rarely jump on the blogging hype of noting the new Nobel Prize winners every year. Exceptions are cases when I have a different slant on it, e.g., when a Prize goes to someone in my neighborhood or if the winners have published in PLoS ONE and PLoS Pathogens (lots of loud cheering back at the office).
But usually I stay silent. Mainly because I am conflicted about the prizes in science in general, and Nobel in particular.
On one hand, one week every year, science is everywhere – in newspapers, on the radio, on TV, all over the internet. And that is good because it is a push strategy (unwilling consumers getting bombarded with information they did not specifically seek, but find interesting once exposed to) as opposed to the usual pull strategy (when already interested people actively seek information). The journalists usually have a tough job – the Nobels are often awarded for findings that are way beyond 6th grade level and explaining the science which requires quite a lot of background is not easy. Good science journalists prepare very well for the Nobels, though, and usually get the reporting done well. The general population gets to go beyond the basics and learn what’s new and exciting at the present moment. And Nobel winners are celebrities of sorts and people love celebrities. So this is a plus.
But the minuses are many as well.
First, sometimes a prize goes for a technique, not a fundamental discovery. This year’s prize in Chemistry is a case in point – discovery and cloning of the green fluorescent protein (GFP) from the jellyfish, Aequorea victoria. The 1993 prize for Chemistry was similar – it went to Kary Mullis and Michael Smith “for contributions to the developments of methods within DNA-based chemistry”, aka for the polymerase chain reaction (Mullis) and site-directed mutagenesis (Smith) – hmmm, both of these were biology prizes awarded for Chemistry: a pattern?
Like Larry, I think this is a bad idea. First, it reinforces the confusion that many people have – not being able to distinguish between science and technology. Second, I feel that a Nobel should go to discoveries that importantly affect the way we think about nature, rewrite the textbooks and perhaps have big implications for medicine (in the case of the Prize for Medicine). Technique in itself does not do this – it allows thousands of people to chip at nature’s secrets, experiment by experiment, one detail at the time, and perhaps collectively over time bring about fundemantal changes in our thinking about the way the world works. But the prize does not go to those thousands who actually discovered something new, it goes to people who provided the technical tools.
Second, it reinforces the popular notion that science is competitive and that scientists do research in order to gain fame and fortune – you all know the stereotype of the crazy anti-social scientist show spends decades in the basement laboratory dreaming of a Nobel Prize. Where is the usual reason people go into science – natural curiosity?
Third, it messes up with the new incoming scientists – it gives them a skewed idea of what science is all about. So, they do whatever it takes to get into a highfallutin’ school where they can join one of the enormous, faceless, gene-jockey labs with 25 postdocs where all the PI does is write grant proposals, the atmosphere is dog-eat-dog and one is tempted to doctor the data and do other unethical stuff. In that lab, the student is given a little detail to work on, while fostering the dreams of discovering a cure for cancer and getting a Nobel. There is an enormous pressure to produce lots of data quickly and to publish them in GlamourMagz.
What those students are not told is to go check the list of Nobel laureates and see what they got the prizes for. It was not one of the thousands of people working on C.elegans now, it went to the person who was the first to work on C.elegans. It was not one of the thousands of people working on zebrafish now, it went to the person who was the first to work on zebrafish. Likewise, it will not go to one of the thousands of people working on p53, or estrogen receptor, or using transgenic mice, or DNA-arrays, or whatever is the bandwagon now. All of that work needs to be done, but it is not revolutionary (at least not for a Nobel). It is “normal science”, incremental placing of pieces into the puzzle. Nothing wrong with that, but don’t get your hopes too high.
This brings me back to this year’s prize for the Green Fluorescent Protein. You have probably heard the story of Dr.Prasher, the guy who did not win the Nobel although he was the first to clone the GFP gene. He is now a shuttle driver for a garage (interestingly, Kary Mullis, the other guy who got a Nobel for a technique, is also now out of science: a surfer, womanizer and HIV denialist). Why? He could not get funding for the continuation of his work. When did this happen? In the late 1990s, at the time when the science funding started to go down.
So, if this is so revolutionary, why didn’t he get funding? The official notes on his grant proposals are probably official-sounding and diplomatic, but I can imagine what was going on through the reviewer’s head while reading Prasher’s proposal – something along the lines of “What on Earth is this jellyfish, Aequorea victoria? Why would anyone care about such an animal (is it an animal anyway, or what is it?)? Why not do something useful, in humans or mice, or at least in fruitflies? Why waste time and taxpayer money on this Discovery Channel crap?”
Being one of the thousands on a bandwagon is bad. Especially in the time of poor funding. But working on a non-bandwagon question, using non-molecular techniques, in a non-model animal is worse, much worse. At the time of the peak in funding, it was sometimes possible to get funding from NIH, but even then it was not easy for such research. Most biologists, though usually not covered by the media much, do that kind of stuff – just go to the SICB conference one year and see for yourself. Luckily, the research itself is usually not very expensive and a lab can “go on fumes” if needed for a year or so as long as it can keep its animals and rooms. There is alternative way of funding: instead of one large NIH grant, many of these labs have many small grants from NSF, NASA, US Army (or Airforce, or Navy), USDA, private foundations, etc. But at the time of low overall funding, even these sources dry up.
Some years ago, I listened to a very interesting talk by Knut Schmidt-Nielsen. The talk was in an unusual format and initially took some people aback. Instead of starting with a big question, gradually zooming in to the methods and results, then at the end zooming out again to the Big Picture, Knut started with an anecdote. Then, he told another anecdote. Then another. After an hour, we finally ‘got it’ – there was an undelying thread in all of these anecdotes. Each highlighted a piece of strange research by a strange person in a strange organism, marred by lack of funding and appreciation (and sometimes outright derision), yet in the end resulting in a ground-breaking discovery that shook our way of understanding the world, or provided a potent research tool (yes, GFP was one of the examples, tetrodotoxin was another). The take-home message was: do what you are passionate about, look at non-model organisms, let your curiosity take over, do not focus on application, tough out the lean financial times, and who knows, you may deserve a Nobel one day. For doing what you like, not what others told you is “hot”.
Look at that list of Nobel laurates in Physiology and Medicine again. Each one of them was a pioneer, doing something weird that nobody else thought made any sense at the time. They persisted and followed their hunches and finally overcome the resistance of their peers. And many thousands of others who did not win a prize, still retired happy with their career – they did something useful and had fun all along.
Not all of that research even required a lot of money, expensive equipment and large numbers of postdocs. Watson and Crick tinkered with pieces of metal and made a model. My favourite Nobel is the 1973 one: von Frisch used a fine paintbrush to mark the bees and a few dishes with sugar water; Lorenz walked around the yard followed by a flock of ducklings; Tinbergen had some fish in a tank, painted red dots on seagulls’ beaks, and moved some pine-cones around. And each one of them made revolutionary discoveries about the way the brain works. It is better to have a problem to solve and use one’s creativity to solve it in the simplest, cheapest, most decisive way, than to search for a question that you can address with the technique you are good at.
Often those simple, cheap, creative techniques provide more trustowrthy data. I know from my own work – I ran some gels and that’s an art, not science. I do not believe my own data (people around me in the lab did). What I got are hunches, perhaps something that statistics may say is relevant, but I dare you to try to repeat the experiment and get the same results! On the other hand, when I came up with a creative experimental protocol – all I needed to do is count eggs every day – the result I got was an all-or-none uber-conclusive response that does not need no steenkin’ statistics and simply over-rules a few decades of published literature (I really need to publish that stuff). Not all questions require, or could appropriately be addressed by running expensive molecular experiments. Each question is at a particular level of organization and requires the experiment to be done at that level, perhaps higher, not lower (as one can infer the behavior of parts from the behavior of the whole, but not vice versa).
There are many questions at the levels of molecules and cells that are worth asking, but that is not all there is in biology – and that is something that students need to be told. And some people will be really good at designing such experiments and answering important questions. But there are other levels in biology and other approaches, and some people will be better suited for those. And for saving money by designing and building one’s own equipment (my PI always told me if my PhD studies did not get me anywhere, I could always find a job using the skills learned in the lab – as an electrician or carpenter). At least in those other fields, the competitiveness is toned down a notch – no need to ask for millions of dollars every few years, no need to get into a GlamourSchool and publish in GlamorMagz – you can do it anywhere and publish wherever you want. Who can scoop you if you are studying deer in a particular forest? You have a couple of years of data in advance. You see if a competitor comes in – and you offer collaboration instead.
So, it’s up to one’s interests, talents and temperament. I was strongly advised (at the time when a PhD looked likely and such) to do a postdoc in a heavily molecular lab in order to get molecular techniques under my belt because that is “a necessity for getting a job”. So I tried – I went and spent a few weeks in such a lab (they even cleared up some space in the freezer for my samples) and decided that it was not for me. The PI was really nice, but part of that super-competitive atmosphere I detest. The lab consisted of 25 people who seemed really nice – on those rare moments when one could actually talk to them. Most of the time – and that is about 13 hours per day, 7 days a week – they were hunched over their benches, quiet, pale like Eloi. The specter of the Japanese hell-bent on scooping was hanging over everyone’s head. A saw postdoc, a really good, creative, smart guy with several excellent papers to his name, being told, on a Friday afternoon, to re-do his experiments and show the data first thing on Monday morning! WTF!? One thing I most appreciated in my old lab was time – I did my stuff when I wanted to. I did twice as much as asked because I was excited. Those who wasted their time left the lab after a year or less, but I persisted on my own. And nobody ever told me when to get the data or when to do my work. I did a lot of it at nights and over weekends because I am too social – would rather chat with people and attend seminars than work if others are around – but that was my own choice. Nobody tells me what to do.
Back to the topic. In non-bandwagon, non-molecular, non-medical biology, there is no need to rush, or to be secretive about one’s work, or to fudge the data, or not to do Open Notebook Science. No patents or big prizes or big money are at stake. But you have a nice, pleasant career in science suitable to those who are not of the A-type temperament. You have time for family and hobbies. And you enjoy the collegiality and collaborations and the growth in your own respect and authority over the years. That kind of stuff can sometimes even be done by amateurs. Nothing wrong with that.
So, the Nobel Prizes are used, in a way, to lead the students along the wrong paths – to jump on bandwagons. But being on a bandwagon, as history shows, does not result in winning a Nobel – quite the opposite. It is the weirdos, or people who moved from one discipline from another (thus avoiding thinking inside the box of the discipline) – the mavericks – who tend to hit on something really important, sometimes by intent, sometimes by serendipity.
So, go on and study what you are truly excited about in some emerging model system, or something weird like the platypus, or sea cucumbers, or ferns, or Venus flytraps, or silverslippers – who knows where that can end (more likely on science blogs or Discovery Channel where cool animals doing cool things are appreciated, than in Stockholm), but even if it does not, you’ll have fun all the way.

2008 Nobel prize in Physiology or Medicine

The 2008 Nobel prize in Physiology or Medicine was announced this morning.
The winners are HPV and HIV (OK, OK, the people who discovered them) – the year of the virus!
I don’t pay much attention to these, as biology I care about has not received the prize since 1973, but I was happy to hear about a different kind of connection I have with one of this year’s winners – Francoise Barre-Sinouss recently published a paper in PLoS ONE – this one: The CD85j+ NK Cell Subset Potently Controls HIV-1 Replication in Autologous Dendritic Cells
Well, if it’s good enough for a Nobel prize winner, it’s good enough for everyone, I’d say…. 😉

Zerhouni to step down

As you may have already heard, Alias Zerhouni will step down from his position of the NIH director in October, not waiting for the inauguration of a new Administration. He has been a strong and effective proponent of Open Access and I hope his successor will be as well. The blogospheric responses are all over the spectrum, from very positive to very negative, depending on what aspects of his tenure are the focus. Here are some examples:
Heather Morrison:

Dr. Zerhouni has led the NIH through the long process of the NIH Public Access mandate, first the voluntary policy, then the mandatory one, most recently speaking up forcefully for the NIH and against the absurd Conyers bill. The NIH is the world’s largest medical research funder, and from my viewpoint, this is one of the OA initiatives that has been the subject of the most intense lobbying efforts. Thank you, Dr. Zerhouni. Public access is a great gift to the world; it is appreciated, and you will be missed.

Charles W. Bailey, Jr.:

The National Institutes of Health has announced the resignation of its Director, Elias A. Zerhouni, M.D., from that post effective at the end of October 2008. Zerhouni has been a strong open access advocate.

Nick Anthis:

Eliot Zerhouni has overseen the NIH at difficult time, when its budget has been stagnant, leading to a precipitous decline in grant success rates. Two decent accomplishments, however, that occurred during his tenure were ethics reform and the NIH’s new policy on open access to publications funded by its research dollars. The legacy of what’s more commonly touted (at least by Zerhouni) as his major achievement–the NIH Roadmap–remains more dubious, as it is often blamed for siphoning funding away from more basic and higher-risk research.

Revere (also here):

Zerhouni presided over tumultuous years at NIH. The doubling of the NIH budget in the five years prior to 2003 created a pig in a python effect when the budget flatlined and all the new post docs, graduate students, laboratories and research projects stimulated by the doubling were left high and dry. Now the budget is at about what it was in real dollars before the doubling but there are many more mouths to feed and lab benches to maintain. Basic health research is facing its own financial meltdown as existing grants aren’t being renewed and the hands that do the work — the post docs and graduate students — are leaving the field and the research programs they were a part of are withering. This is creating a crisis in leadership in academic science in the US, as the post docs leave for other work and the mid level academics coming up for tenure can’t get their grants renewed and have to leave their institutions to look for other positions and start over or leave research altogether.

DrugMonkey:

Unsurprising since this is a political appointment and all. You did know that, right? More importantly and probably more concerning will be the dance of the IC Directors.
The directors of the NIH Institutes and Centers are slightly less political in nature but there are still allegiances. And the highly activist Directors can have immediate impact on what research grants get funded, etc. So the scientists who are funded by an IC which has a Director resign may want to pay some attention. A long interval of an Acting Director can, conversely, maintain status quo on the funding side but may seriously side-line Congressional advocacy for the IC’s mission.

writedit:

Given that the Great Zerhouni, like all political appointees, would have been submitting his resignation come January 2009, this is a bit odd he would bail a few months shy, especially since Kessler as FDA director set the precedent of straddling administrations (& parties in power; h/t BB). If the GZ had wanted to stay, it wasn’t out of the question. And with the CTSA Consortium just about to fill up and the T-R01s pouring in next January, I’m a bit surprised. Plus, if he truly wanted as minimal disruption as possible, he would have waited for the next appointed director to be approved by the Senate before stepping down. Someone will have the thankless job of serving as interim director for 6-8 months.

‘Advancing Science Through Conversations’ article – summary of the blogospheric responses

The PLoS Biology article about science blogs and their (potential) relationship to the academic institutions has, as expected, received quite a lot of coverage in the blogosphere. Nick collects the responses and responds to the responses – join in the conversation in the comments there. Update: So does Tara.
Update: Jessica’s post is what I would have written. Now I don’t need to – go read hers.

Dr. Mom, a book review in The Scientist

A new book explores the challenges of balancing motherhood and a career in science:

Editor Emily Monosson has collected the voices and personal stories of 34 mother-scientists working in various fields. In eloquent and often witty essays, these women directly address the challenges of being mothers in the scientific workforce.
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Essays in the book are arranged chronologically, according to the date by which the writer’s PhD was conferred. The book opens with scientists who received their PhDs in the 1970s, and marches onward through the 80s and 90s, ending with the voices of women who are in graduate school today. In this way, the book tracks the sweeping social changes of the past thirty years. Despite the great influx of women into science careers over the last decade, it is sobering to read that conflicts between work and family have not changed. Indeed, some of the essays in the last section read as though they could have been written decades ago.
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It is often said that motherhood is not for the faint of heart. The same could be said for a career in science. The debate over what causes the leaky pipeline, and remedies to address it, rages on. The pace of institutional and cultural change can seem glacial. In the mean-time, scientists who are also mothers can find support by sharing their stories with one another. Monosson’s book provides a valuable medium for doing so. As one woman writes in the opening pages of Motherhood: “In the final analysis, every woman finds her own way. It’s just good to know that none of us is alone.”

Read the whole thing (you have to log in, but the registration is free).

Why Is Academia Liberal?

Why Is Academia Liberal?When I posted this originally (here and here) I quoted a much longer excerpt from the cited Chronicle article than what is deemed appropriate, so this time I urge you to actually go and read it first and then come back to read my response.

Continue reading

Assault on (Higher) Education – a Lakoffian Perspective

Assault on (Higher) Education - a Lakoffian PerspectiveThis post was first written on October 28, 2004 on Science And Politics, then it was republished on December 05, 2005 on The Magic School Bus. The Village vs. The University – all in your mind.

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William James – The PhD Octopus

A century ago, yet nothing has changed: William James, March 1903:

…………..Human nature is once for all so childish that every reality becomes a sham somewhere, and in the minds of Presidents and Trustees the Ph.D. degree is in point of fact already looked upon as a mere advertising resource, a manner of throwing dust in the Public’s eyes. “No instructor who is not a Doctor” has become a maxim in the smaller institutions which represent demand; and in each of the larger ones which represent supply, the same belief in decorated scholarship expresses itself in two antagonistic passions, one for multiplying as much as possible the annual output of doctors, the other for raising the standard of difficulty in passing, so that the Ph.D. of the special institution shall carry a higher blaze of distinction than it does elsewhere. Thus, we at Harvard are proud of the number of candidates whom we reject, and of the inability of men who are not distingues in intellect to pass our tests.
America is thus a nation rapidly drifting towards a state of things in which no man of science or letters will be accounted respectable unless some kind of badge or diploma is stamped upon him, and in which bare personality will be a mark of outcast estate. It seems to me high time to rouse ourselves to consciousness, and to cast a critical eye upon this decidedly grotesque tendency. Other nations suffer terribly from the Mandarin disease. Are we doomed to suffer like the rest?
Our higher degrees were instituted for the laudable purpose of stimulating scholarship, especially in the form of “original research.” Experience has proved that great as the love of truth may be among men, it can be made still greater by adventitious rewards. The winning of a diploma certifying mastery and marking a barrier successfully passed, acts as a challenge to the ambitious; and if the diploma will help to gain bread-winning positions also, its power as a stimulus to work is tremendously increased. So far, we are on innocent ground; it is well for a country to have research in abundance, and our graduate schools do but apply a normal psychological spur. But the institutionizing on a large scale of any natural combination of need and motive always tends to run into technicality and to develop a tyrannical Machine with unforeseen powers of exclusion and corruption. Observation of the workings of our Harvard system for twenty years past has brought some of these drawbacks home to my consciousness, and I should like to call the attention of my readers to this disadvantageous aspect of the picture, and to make a couple of remedial suggestions, if I may…..

Read the whole story…
[Hat-tip]

Used postdocs

There is a new letter to Nature – Postdoc glut means academic pathway needs an overhaul – which I cannot read as I have no access, but others are discussing it on FriendFeed and there have been recent posts on the topic of endless/hopeless postdoc positions on DrugMonkey and The Alternative Scientist.
Bill sums it up the best graphically:
postdoc.jpg

Post-publication Peer-review in PLoS-ONE, pars premiere

Why is the letter P the most useful for alliterative titles?
But back to the substance. One thing that bugged me for a long time is that I often see on blogs or hear in person a sentiment that “there are no comments on PLoS ONE”. Yet I spend quite some time every week opening and reading all the new comments so I KNOW they are there and that there is quite a bunch of them already. Why the difference in perception? Is it due to the predictable distribution (a few papers get lots of comments, most get one or none, just like blog posts)?
So, when we saw this nice analysis of commenting on BMC journals by Euan Edie, we decided to take a look at our own numbers and see how they compare. We got the data together and sent them to a few people, mostly bloggers, to take a look. As they write their blog posts I will post the links here, especially when they do the nitty-gritty statistical analysis.
But for now, quickly out of the box, two of them have already posted their first impressions they took when they scanned the data.
Deepak Singh writes:

There people post a link and a whole discussion erupts (not always, but often enough). I would throw out this challenge (see the DOI suggestion above). Why should discussion be localized to PLoS One itself. If a paper pubished in PLos One is discussed in 20 other places, it would be considered a success. In other words, we shouldn’t limit our thinking to just on site commenting. Perhaps within the site, we should be focussed on ratings and perhaps tagging and notes.
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So what have we learned from this exercise. Quite frankly, I am not sure. Is the commenting on PLoS One at a level that we hoped it would be? Not quite. Is it as bad as some might like to believe? Not quite. What we have is a very very nascent (no pun intended) effort on the part of the scientific community using web publishing platforms as a communication medium. I’d like to ask those same scientists to think about newsgroups. Most scientists are fairly comfortable participating in newsgroups, and here you essentially have one, with very clearly defined thread titles.

Cameron Neylon says:

In that context, I think getting the numbers to around the 10-20% level for either comments or ratings has to be seen as an immense success. I think it shows how difficult it is to get scientists to change their workflows and adopt new services. I also think there will be a lot to learn about how to improve these tools and get more community involvement. I believe strongly that we need to develop better mechanisms for handling peer review and that it will be a very difficult process getting there. But the results will be seen in more efficient dissemination of information and more effective communication of the details of the scientific process. For this PLoS, the PLoS ONE team, as well as other publishers, including BioMedCentral, Nature Publishing Group, and others, that are working on developing new means of communication and improving the ones we have deserve applause. They may not hit on the right answer first off, but the current process of exploring the options is an important one, and not without its risks for any organisation.

There are also two quick responses on Nascent and Genome-Technology.
What is most interesting is that there are no comments on Nascent and Genome-Technology, only a couple on Deepak’s and Cameron’s posts, yet a very nice long discussion on FriendFeed (very much worth reading, and not just for compliments to me)! What can we learn from that fact alone?
Second, the comment (by ‘comment’ I mean Ratings+Notes+Comments) to article ratio on PLoS ONE has risen from 1.1 a year ago to about 1.5 today. For comparison, my own blog has 1.6. And I get lots of comments – on a few posts, while zero or one on most. And I am prolific with quick/short posts like Quotes, so it is a decent comparison: not every paper is exciting or controversial enough (just like most of my posts are not) to motivate people to say anything.
Also, a blog post usually gets comments immediately. After 24 hours it is deemed stale and people move on to the new stuff. A scientific paper will be expected not to get any for the first few months and to only gradually accumulate them over the years as new information comes in that sheds new light on that paper. And I see this every week – older papers get a nice share of comments every week, while papers published this week do not.
See what I wrote last year about this:

One thing to keep in mind is that a PLoS ONE article is not a blog post – the discussion is not over once the post goes off the front page. There is no such thing as going off the front page! The article is always there and the discussion can go on and on for years, reflecting the changes in understanding of the topic over longer periods of time.
Imagine if half a century ago there was Internet and there were Open Access journals with commenting capability like PLoS ONE. Now imagine if Watson and Crick published their paper on the DNA structure in such a journal. Now imagine logging in today and reading five decades of comments, ratings and annotations accumulated on the paper!!!! What a treasure-trove of information! You hire a new graduate student in molecular biology – or in history of science! – and the first assignment is to read all the commentary to that paper. There it is: all laid out – the complete history of molecular biology all in one spot, all the big names voicing their opinions, changing opinions over time, new papers getting published trackbacking back to the Watson-Crick paper and adding new information, debates flaring up and getting resolved, gossip now lost forever to history due to it being spoken at meetings, behind closed door or in hallways preserved forever for future students, historians and sociologists of science. What a fantastic resource to have!
Now imagine that every paper in history was like that (the first Darwin and Wallace letters to the Royal Society?!). Now realize that this is what you are doing by annotating PLoS ONE papers. It is not the matter so much of here-and-now as it is a contribution to a long-term assessment of the article, providing information to the future readers that you so wished someone left for you when you were reading other people’s papers in grad school and beyond. Which paper is good and which erroneous (and thus not to be, embarrassingly, cited approvingly) will not be a secret lab lore any more transmitted from advisor to student in the privacy of the office or lab, but out there for everyone to know. Every time you check out a paper that is new to you, you also get all the information on what others think about it. Isn’t that helpful, especially for students?

I hope more of you join in the discussion, and I will post links to other posts as they appear over the next week or two.

Organizing a conference

Why don’t *You* organize a conference?

A scientist should behave as a good citizen in the scientific community. You cannot expect that other colleagues perform all the unpleasant jobs and that you can spent all your time on science. I am referring to low-reward activities like reviewing papers, reviewing grant proposals, sitting on review panels, being an editor of a scientific journal, sitting on program committees and – which is the subject of my present post – really organizing a conference.
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My Advice
Try to stay away from organizing a conference. I have always been quite successful in not organizing them.

Ha! I organized two. And am in the midst of organizing the third. And it is not bad at all!

How to moderate a conference panel

Jeremiah Owyang: How to Successfully Moderate a Conference Panel, A Comprehensive Guide
Not all of it is applicable to an unconference like ScienceOnline’09, but lots of nuggets of wisdom in there.

Praxis #1

PraxisWelcome to the first experimental issue of the newest science blog carnivalPraxis. Why experimental? Because we still have to see where to set the boundaries. If it is “Life in Academia”, then pretty much everything on science blogs is eligible and the effect is diluted. If we narrow it down to one topic, e.g., Open Access publishing, then there will not be sufficient posts and sufficient interest to keep the carnival alive. We’ll have to define a happy middle. We want people to find each other here – folks that write about the business of science, about publishing and Science 2.0, about survival in the Academia, as we can all learn from each other and help each other. So, we would appreciate your feedback about this so the future hosts (and I hope you will volunteer to be one – just e-mail me) can tighten it up for everyone’s enjoyment.
I have received a number of entries and have added a few more of my own choice. As is often the case with the very first edition of a carnival, old classic posts were eligible so quite a few of those are presented here. Starting with edition #2 next month, only posts written in the interim time will be eligible so get busy writing!
Doing Science
Peter Dawson Buckland: …only limited by imagination.” An interview with Kevin Zelnio:

It’s hard to say. I think it lots of cases there is a culture that teaches young scientists that it is a waste of time. Your time is better-spent writing grants and papers. That is what gets you jobs. Sure, after working all morning, day and night most scientists don’t want to go home and then write about science for free or for few readers whom they do no know. There is no reward structure for communication. Many funding agencies have requirements for “broader impacts”, but a lot of it BS. Some well-known scientists have excellent programs in place. I’m lucky enough to have an advisor who supports communication to a certain degree. He definitely doesn’t approve of me blogging, but we do tours and talks for teachers and grade school students, I judge science fairs, that sort of thing.

Cameron Neylon: A new way of looking at science?:

I’ve spent a long time talking about two things that our LaBLog enables, or rather that it should enable. One is that by changing the way we view the record we can look at our results and materials in a new way. The second is that we want to enable a machine to read the lab book.

Anne-Marie: Belize Update #2:

Lesson 3: I have discovered the wonders of Machete Therapy. If you have anything bothering you, stressing you out, weighing on your mind, just take on 100 m transects of jungle with a machete. It is astoundingly cathartic. Not sure what this says about me? I do hate that we have to leave even a small swath of destruction to do the habitat surveys, but all the data is being put towards conservation research.

Career Choices and Getting Funded
DrugMonkey: NIH Basics: The Study Section:

Let’s start with the NIH study section and how you should go about educating yourself with the information that you need to guide your own grant writing.

Pawel Szczesny: Freelancing science – today and tomorrow:

In response to recent Neil’s comment and questions that repeat in emails, I’ve decided to describe in little more detail my status as a freelancing scientist. However keep in mind that I have no idea about such arrangement outside of Poland, so it is likely that some things may look different in other countries.

Cath@VWXYNot: Finding the alternative within academia:

Hopefully the advice above will help you to make that first step into your new career. But don’t stop now! Your first non-academic position is unlikely to be the amazing dream job that you will do for the rest of your life, but it will expose you to another, broader, range of experiences. For example, as well as the grant writing that is my day-to-day focus, my new job also gets me involved in public relations, website design and intellectual property issues. I haven’t quite figured out which parts I enjoy the most (definitely not intellectual property!), but you can bet that as soon as I do, I’ll start volunteering for more of it.

Alex Palazzo: A way to break out of the pyramid scheme:

One obvious way to prevent such pyramid schemes is to stop the flow of postdocs going up by providing them with career paths at the postdoc level. The result – fewer PIs, more bench scientists, more stability for junior scientists.

Samia: HERRRP ME.:

I could give you all the boring background, but it all boils down to choosing between two labs.

DrugMonkey: Are Stable Research Career Tracks the Solution to “Structural Disequilibria” in the NIH Racket?:

The fact of the matter is that many, many Ph.D. wielding individuals are in the process of serving out such a career. The trouble is that it is not a stable, formal job category. So anyone who makes it to retirement, does so by matter of a series of accidental or lucky steps in joining a lab or labs that can sustain the stable level of funding that is required to maintain very senior Ph.D. level non-PI scientists. This makes this particular ambition a fairly dodgy one.

Presenting Data
Scicurious: And Now, a Powerpoint Presentation:

In the afternoon session, I got bored. And in my boredom and jetlag, I have compiled a list. A list of things that you shall NOT do during your big presentation in front of 350 people.

David Ng: The ‘speaking publicly’ list formulized (plus a bit with some clown humour):

The response for the “Things to avoid at all cost when speaking publicly” post was awesome, and so, I’ve tried to formalize the suggestions into a fairly definitive list. The ones that didn’t make it tended to be more debatable, although admittedly, there are few in the list right now that sort of sit on the threshold of that parameter (I’m think about stuff like “winging it” or being “arrogant”).

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

But even apart from one’s own interests, there are some posters that remain forever in one’s memory. I tried to think what was it about those particular posters that made them so memorable to me and to see if any general rules can be drawn out of them.

Sharing and Networking
Cath@VWXYNot: Networking: the basics:

People. People connected to you and to each other. Even if your primary network is quite small, each person in it will connect you to others who you may never have met or even heard of.

Michael Nielsen: The Future of Science:

An ideal collaboration market will enable just such an exchange of questions and ideas. It will bake in metrics of contribution so participants can demonstrate the impact their work is having. Contributions will be archived, timestamped, and signed, so it’s clear who said what, and when. Combined with high quality filtering and search tools, the result will be an open culture of trust which gives scientists a real incentive to outsource problems, and contribute in areas where they have a great comparative advantage. This will change science.

Shirley Wu: Envisioning the scientific community as One Big Lab:

The idea behind One Big Lab is that the scientific community should act as, well, one big lab, sharing resources when it makes sense, and everyone, especially the community as a whole, benefits.

Cameron Neylon: The science exchange:

Turning the funding system on its head is probably not viable and while it makes a nice thought experiment I’m sure there are many reasons why its a terrible idea. What we need to do is find research funders who are serious about increasing their return on investment; not in terms of money, but in terms of results; in terms of science. I think if we can do that, and convince someone of the case for a return on their investment, the rest of the technical problems will be pretty straightforward to crack.

Coturnix: The Scientific Paper: past, present and probable future:

Science has some very conservative elements (in a non-political sense of the term) that will resist change. They will denigrate online contributions unless they are peer-reviewed in a traditional sense and published in a reputable journal in the traditional format of a scientific paper. Some will retire and die out. Others can be reformed. But such reforming takes patience and careful hand-holding.

Pedro Beltrao: Post-publication journals:

No single individual wants to go through all published literature to find the useful information but together we effectively do this. The challenge is how to evaluate specific articles by a combination of metrics to promote them to wider audiences in a way that is not easy to exploit. Kevin Kelly said recently in a Ted Talk that “The price of total personalization is total transparency”. Would this bother scientists ? Lets say that a few science publishers get together with some of these scientific social sites (social networks, bookmarking sites) to mimic the Frontiers model in a larger scale. Users would install a browser plugin that would link their scientific profile and social contacts with their reading activity. The publishers could then use this information to create personal reading hubs for users.

John Wilbanks: On the Erosion of the Public Domain:

The public domain is not contractually constructed. It just is. It cannot be made more free, only less free. And if we start a culture of licensing and enclosing the public domain (stuff that is actually already free, like the human genome) in the name of “freedom” we’re playing a dangerous game.

Jean-Claude Bradley: Open Notebook Science:

It does not necessarily have to look like a paper notebook but it is essential that all of the information available to the researchers to make their conclusions is equally available to the rest of the world. Basically, no insider information.

Cameron Neylon: Facebooks for scientists – they’re breeding like rabbits! and An open letter to the developers of Social Network and ‘Web 2.0’ tools for scientists:

I will also be up front and say that I have an agenda on this. I would like to see a portable and agreed data model that would enable people to utilise the best features of all these services without having to rebuild their network within each site. This approach is very much part of the data portability agenda and would probably have profound implications for the design architecture of your site. My feeling, however, is that this would be the most productive architectural approach. It does not mean that I am right of course and I am prepared to be convinced otherwise if the arguments are strong.

Ethan Zuckerman: The complexity of sharing scientific databases:

Under US law, pretty much anything you write down is copyrighted. Scrawl an original note on a napkin and it’s protected until 70 years after your death. Facts, however, are another matter – they can’t be copyrighted. So while trivial but creative scribblings are copyrighted, unless you choose to release them into the public domain, the information painstakingly discovered about the human genome – DNA sequences, for instance – aren’t. But the containers they’re stored in – the databases they’re held in – can be copyrighted.

Deepak Singh: The commons and the anticommons:

I am not quite sure I agree with the entire premise. While in certain areas, I do believe in the tragedy of the commons, that is not true for the fundamental scientific data talked about on this blog. The only tragedy that can occur there is not allowing people to use the underlying data to not just innovate, but also learn. What we do with the discoveries we make, perhaps a new drug, an innovative idea on how we can leverage nature’s blueprint, is where we need to develop “property rights”, but we should not forget the anticommons when we do so.

Chad Orzel: Peer Review Does Not Define Science:

Peer review is an important part of the modern scientific establishment, but peer review is not the core of science. Holding peer review as the only standard for what counts as doing science is a step toward making a scientific guild system, which is something we absolutely do not want.

Dr. Free-Ride: Peer review and science and Objectivity and other people:

What’s the point of the peer review process? The goal is to figure out what we agree upon and to filter out the influence of subjective preference as much as possible. Which parts of how the world seems to me are due to the world, and which are due to my subjective preferences? The parts we tend to agree on might be the best candidates for the features of our experience that correspond to real features of the world.

Getting Published
Jonathan Eisen: Why I am ashamed to have a paper in Science:

So I just had a paper published in Science last week. In many ways, it has all the makings of one of those papers I should be really proud of….

Rock Doctor: Publish well or perish??:

The long and short of it is that it is no longer good enough to do good research and publish, now you must publish properly or you may become so much chattel alongside the academic road.

Pawel Szczesny: By any measure I’m average at most:

Reputation-wise I’m going to be in the middle unless I will make something extraordinary. But honestly to make a scientific breakthrough the last thing I need is a number describing quality of my thinking.

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

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.

The Publishing Business
Bill Hooker: The Future of Science is Open, Part 1: Open Access, The Future of Science is Open, Part 2: Open Science and The Future of Science is Open, Part 3: An Open Science World:

I’ve never had an idea that couldn’t be improved by sharing it with as many people as possible — and I don’t think anyone else has, either. That’s why I have become interested in the various “Open” movements making increasing inroads into the practice of modern science.

Richard Akerman: My article on peer review for Nature:

One of my main concerns is that Wisdom of Crowds is sometimes oversold, in the way that Service-Oriented Architecture (SOA) is. Just put together a system, sprinkle some magic Wisdom of Crowds dust on it, and hey presto, the system is continuously improved by everyone who uses it.

Frank Norman: Who needs information skills?:

In my early days as a librarian I envied the information wizards who performed online literature searches – they had mastered the arcane system commands and database indexing and could react quickly to adjust their search as results came through. Then I became a wizard myself and enjoyed being able to pull bibliographic rabbits out of digital hats. When disintermediation hit, searching moved from the esoteric to the commonplace. Everyone could have a go at it and they did.

Bjoern Brembs: Journals – the dinosaurs of scientific communication:

Today’s system of scientific journals started as a way to effectively use a scarce resource, printed paper. Soon thereafter, the publishers realized there were big bucks to be made and increased the number of journals to today’s approx. 24,000. Today, there is no technical reason any more why you couldn’t have all the 2.5 million papers science puts out every year in a single database. It doesn’t take an Einstein to realize that PLoS One is currently the only contender in the race for who will provide this database. For all the involved, it is equally clear what the many advantages of such a database would be. Consequently, traditional publishers are rightfully concerned that their customerbase is slowly dissappearing.

Kevin Zelnio: Free Access to Internet Resources Helps Conservation:

There were several conclusions drawn about plant conservation, but here is a tidbit about how free access to information helped in assessing conservation status.

Bill Hooker: An Open Access partisan’s view of ‘Electronic Publication and the Narrowing of Science and Scholarship’:

In fact, the comparison between print and online access is barely even possible when considering Open Access information. The same considerations of cost — who can afford to read what — apply to commercial print and online publications, but free online information has essentially no print ancestor or equivalent. Few if any scholarly journals were ever free in print, so there’s a huge difference between conversion from commercial print to commercial online on the one hand, and from commercial print to Open Access on the other.

Coturnix: Historical OA:

In discussions of Open Access, we always focus on brand new papers and how to make them freely available for readers around the world as well as for people who want to mine and reanalyse the data using robots. But we almost never discuss the need to make the old stuff available. Yet we often lament that nobody reads or cites anything older than five years. Spending several years reading everything published in the field in the 20th century up until about 1995 (as well as some 19th century stuff) helped me greatly in my own research. It would help others, I’m sure, especially those who are now revisiting old questions with new techniques. How are the classical papers going to be made available for today’s students?

Science Communication and Education
John Hawks: How to blog, get tenure and prosper: Starting the blog, Graduate students and blogging and How to blog, get tenure and prosper: A very useful engine:

Science is ultimately a social activity that progresses toward greater understanding. Blogging is also a social activity, which can serve the ends of science, if you apply your expertise. What is more, by incorporating the content management paradigm into your workflow, you can maintain a blog with very minimal work.

Maddox2: Advice on Freelance Science Writing:

I know some of these seem like no-brainers, and I hope I haven’t offended anyone. If I did, I apologize in advance 🙂 But as I said, I have had freelance writers violate every single one of the points above at one point or another…so maybe they’re not as no-brainer as we’d like to think.

Coturnix: Scientists are Excellent Communicators (‘Sizzle’ follow-up):

Or should we just leave the MSM to rot and die, and put our efforts into new media, the kind in which there is no intermediate (who may believe that he-said-she-said journalism is the way to go) but the communication is many-to-many with instant feedback? Because in such an environment scientists are experts and seen as authorities and listened to and believed.

Abel Pharmboy: Is organic chemistry still relevant in the pre-medical curriculum?:

An old professor bud of mine compared professional education to building a retaining wall. One first digs a trench and put several layers of pilings in the whole which are then covered up. No one sees them, but they are the foundation upon which the rest of the wall stands. How easy is it then to decide what pilings are needed for success in today’s physicians?

Panthera studentessa: Reducing research culture shock in undergrads:

Research is so fundamental to a science education that I don’t know why we aren’t being taught how to do it much earlier. Our brains are filled with facts about what other people have already discovered, but many of us aren’t learning how to make our own discoveries as well. Instead of learning to know and regurgitate the right answer, maybe we should be learning how to figure it out on our own.

Jennifer Rohn: In which I am utterly Fooed:

The chaotic nature of the entire event was equally evident in the session I helped organize with SF novelist John Gilbey and pseudoscience basher Ben Goldacre called ‘Seducing the Public with Science. (Ben wanted to call it ‘Pimping Science’ or ‘Seducing the Pubic’ but was gently overruled.) Someone spontaneously decided to summarize the unfolding discussion on the white board and, as you can see from the figure above, what it lacked in coherence it made up for in raw enthusiasm.

Academic Atmosphere
Zuska: Locking the Barn Door:

You are a university president. You naturally wish to avoid scandal and negative publicity during your administration. The time to make it mandatory for all faculty and staff to undergo training in how to avoid sexual harassment is:
A: When you take office, or shortly thereafter.
B: After one of your professors is caught emailing female students a quid pro quo: A’s if they would expose their breasts and allow him to fondle them.

Anna Kushnir: Horror Stories, of the Scientific Variety:

A few questions came to mind after listening to these stories (they weren’t really delivered as stories. More like ranty monologues with shaking hands and dangerously-tilted wine glasses). The first question had too many expletives to reproduce here. The second was, “How do you do that?” How do you scoop people you see on a daily basis? I understand that the funding crisis really is, at this point, a crisis. I understand that jobs are painfully difficult to come by. What I don’t understand is when and where ethics and common decency slip out the door.

Sunil: Postdoc personalities:

Postdocs come in all shapes, sizes and characters, but there are a few character types you want to avoid hanging out with (even if you are one of them), in order to remain sane and content. Surprisingly, like most normal people, postdocs too fit into some characteristic groups (including those you want to avoid). So here are some of the classes of postdocs whom I do my best to avoid (and hope never to become).

Rhea Miller: Vow to never become Jaded…:

I really only notice these attributes in young scientists, i.e. graduate students and post-docs. Does this mean that the Jaded ones eventually give-up, get use to it, change their prospectives, or do they hide that inner Jaded color as they progress?? Or maybe it’s just that grad students/postdocs can’t seem to see the light at the end of the tunnel until they get there??

Special topic of the month: Animal Research
DrugMonkey: Animals in Research: The conversation begins, Animals in Research: IACUC Oversight and Animals in Research: Guide for the Care and Use of Laboratory Animals:

This brings me to what may be a personal view. I believe that everyone that works with research animals has not merely the right, but rather the obligation to report situations that appear to compromise the health and welfare of the research animals.

Dr. Free-Ride: When the tactics become the message:

Maybe some of the groups involved in firebombing and other violent attacks used to have a point worth taking seriously. At this point, their violent tactics have become their message.

Orac: Animal rights terrorists firebomb a researcher’s house:

Also, comparing animal rights terrorists with civil rights advocates in the 1950s and 1960s is an insult to the memory of those nonviolent protesters who, sometimes at great personal risk, spoke out against injustice. Vlasak’s cowardly little band of animal rights terrorists are far more akin to the Ku Klux Klan and white power rangers who used violence to try to stop the civil rights marchers. They’re far more akin to the criminals who bombed the 16th Street Baptist Church in 1963 and other thugs who tried to stop the civil rights movement through violence and terrorism. They are scum.

Abel Pharmboy: Escalating lunacy:

Yes, Capt Clark, a logic transplant would indeed be necessary.

Matt Springer: Defending Science:

But as far as I can tell, there’s only one research subject that has a real chance of getting a scientist murdered.

Scicurious: Animal Research:

Animal research is a necessary part of medical progress. But that doesn’t give us the right to go cutting into any animal we like. There are strict rules in place to ensure that the animals we use are treated in the best possible way. The researchers I work with are incredibly compassionate people, but there is also a practical reason. A suffering animal is not going to give you good data, and an animal that is not healthy can show a different reaction to a drug. It is in the best interest of science that the animals we use be well treated.

Acmegirl: Support the People Who Do Animal Research:

I don’t work with animals. But I have done so in the past, and I can honestly say that it is not like what you see in the movies. There is training, protocols to be evaluated, logs, etc. A researcher doesn’t just have cages and tanks with random animals hanging around for them to tinker with for no good reason than a whim. Everything is planned, regulated and overseen.

drdrA: Firebombings and such:

Drugmonkey has a nice post up about this topic- and well, since I actually teach a couple of hours on the ethical use of animals in research to graduate students in biomedical sciences, medical students and sometimes undergraduates, I thought I would add my two cents worth as well. First, there is a very useful chapter about this very subject in a book entitled ‘Scientific Integrity’ by Francis Macrina… I believe that the operative section is chapter 6- ‘Use of Animals in Biomedical Experimentation’, much of what I have written below is taken from this chapter. I would like to have students leave my class with a basic understanding in a couple of areas.

Sandra Porter: Support animal research, save lives, Book review: ‘The Animal Research War’, Handling research animals: taking courses and learning how to be kind and More thoughts on animal research: Pets and wild animals benefit, too:

What do these cases have to do with animal research? In the United States, animal vaccines are regulated by the U.S. Department of Agriculture’s Animal and Plant Health Inspection Service (APHIS), Center for Veterinary Biologics (CVB). Like the vaccines produced for humans, the vaccines produced for animals must be pure, potent, safe, and they must work. This means that all the vaccines that are given to your pets, agricultural animals, and wild animals were tested on lab animals to make sure that the vaccines are safe and that they work.

The next edition of Praxis will alight on Life v. 3.0 blog on 15th of September, 2008, so get writing and submit your posts.

Next thing, they outlaw cooking at home: it’s chemistry, after all….

Robert Bruce Thompson is the author of Illustrated Guide to Home Chemistry Experiments, a book I have and like, but cannot really use as it is hard to get the chemicals. Thompson now writes a guest popst on MAKE blog: Home science under attack

The Worcester Telegram & Gazette reports that Victor Deeb, a retired chemist who lives in Marlboro, has finally been allowed to return to his Fremont Street home, after Massachusetts authorities spent three days ransacking his basement lab and making off with its contents.
Deeb is not accused of making methamphetamine or other illegal drugs. He’s not accused of aiding terrorists, synthesizing explosives, nor even of making illegal fireworks. Deeb fell afoul of the Massachusetts authorities for … doing experiments.

So, even if you can find chemicals, you can have the cops coming and confiscating them?!
As NNadir says, It Must Have Been Beautiful to Do Science In Those Days, but not any more. I used to have a decent chemistry kit, and a good little microscope, and bought some additional glassware from a lab store downtown. Can’t get any of that any more:

These days science involves heavy duty – and often expensive – instrumentation, software programs with arcanely programmed guts – LIMS systems, speed, speed, speed, dense arrays of information, and all too narrow focus.
But all this was brought here on the shoulders of giants well after Newton, giants who labored maybe in more obscurity.
Some of what I was looking at today was science from the 50’s and the 70’s, the men and women of the time who first moved beyond this planet’s atmosphere and gravity. And I was struck by the beauty of their jury-rigged lives, where they built stuff from scratch.

Or, as John Wilkins says:

Kids today have emasculated chemistry sets that do precisely nothing interesting. And if Mythbusters has taught us anything, it’s that kids love explosions. That is the route to an educated population of science loving psychopaths. But we didn’t turn out to be psychopaths, we turned out to be lovers of science. We have lost something important. If a frigging chemist, who knows how to work safely, cannot do science at home, the west can pretty well forget about the next few generations of kids ever learning anything useful.

Which now feeds to the entire question of amateur science – can people outside science institutions do science any more (apart from Christmass bird count, I guess)? Janet has written two posts recently that touch, in a way, this question: Peer review and science and Objectivity and other people. Who is a scientist? Who are the peers, and what forms peer-review can take? If you play with a chemistry kit at home, and discover something new, and post it on a blog, and other chemists come by and read your detailed descriptions, and replicate the findings – was that peer-reviewed? How many people would negate this is science because it was not peer-reviewed in a formalized fashion in a scientific journal? How many would understand that peer-review can have many forms? See the comment thread on Chad’s post on this topic.
But if you cannot even do science in the basement, the whole question of peer-review of home-made science gets murky.

Praxis #1 – last call for submissions

PraxisThe new blog carnival, covering the way science is changing (or not changing enough) in the 21st century – Praxis, is about to start. The call for submissions is now open – send them to me at Coturnix AT gmail dot com by August 14th at midnight Eastern so I can post the carnival on the 15th in the morning.
The business of science – from getting into grad school, succeeding in it, getting a postdoc, getting a job, getting funded, getting published, getting tenure and surviving it all with some semblance of sanity – those are kinds of topics that are appropriate for this carnival, more in analytic way than personal, if possible (i.e., not “I will cry as my minipreps did not work today”, but more “let me explain the reasons why I chose to work with advisor X instead of Y” or “how to give a good talk”, or “why publish OA” or “how does an NIH section work?”) and perhaps most importantly how the new technology – mainly the Internet – is changing the world of science. I expect a LOT of entries about Open Access, of course…. 🙂

Paperless Office? Bwahahahaha!

Today, I have everything I need on my computer, and so do most working scientists as well. Papers can be found online because journals are online (and more and more are Open Access). Protocols are online. Books are online. Writing and collaboration tools are online. Communication tools are online. Data collection and data analysis and data graphing and paper-writing tools are all on the computer. No need for having any paper in the office, right? Right.
But remember how new that all is. The pictures (under the fold, the t-shirt is of Acrocanthosaurus at the NC Museum of Natural Science) of my old office are only five years old! You know I am a Web junkie. If I could have survived without paper, I would have ditched it all. But I could not (and the pictures show only half of the office – there were two large file cabinets full of reprints behind the photographer – my brother – and much, much more, plus more in the lab itself):

Continue reading

Praxis #1 – second call for submissions

PraxisThe new blog carnival, covering the way science is changing (or not changing enough) in the 21st century – Praxis, is about to start. The call for submissions is now open – send them to me at Coturnix AT gmail dot com by August 14th at midnight Eastern.
The business of science – from getting into grad school, succeeding in it, getting a postdoc, getting a job, getting funded, getting published, getting tenure and surviving it all with some semblance of sanity – those are kinds of topics that are appropriate for this carnival, more in analytic way than personal, if possible (i.e., not “I will cry as my minipreps did not work today”, but more “let me explain the reasons why I chose to work with advisor X instead of Y” or “how to give a good talk”, or “why publish OA” or “how does an NIH section work?”) and perhaps most importantly how the new technology – mainly the Internet – is changing the world of science.

Praxis #1 – call for submissions

PraxisThe new blog carnival, covering the way science is changing (or not changing enough) in the 21st century – Praxis, is about to start. The call for submissions is now open – send them to me at Coturnix AT gmail dot com by August 14th at midnight Eastern.
The business of science – from getting into grad school, succeeding in it, getting a postdoc, getting a job, getting funded, getting published, getting tenure and surviving it all with some semblance of sanity – those are kinds of topics that are appropriate for this carnival, more in analytic way than personal, if possible (i.e., not “I will cry as my minipreps did not work today”, but more “let me explain the reasons why I chose to work with advisor X instead of Y” or “how to give a good talk”, or “why publish OA” or “how does an NIH section work?”) and perhaps most importantly how does new technology – mainly the Internet – is changing the world of science.

Innumeracy and related academic turf-defenses….

Chad: Innumeracy by John Allen Paulos
Tom: What Does the Public Really Need To Know?: Science/Math edition.
Chad: The Innumeracy of Intellectuals
Janet: Fear and loathing in the academy.
Join in the fray….

Rise and Fall of HIgher Education

Here is just a brief excerpt from Why I am Not a Professor OR The Decline and Fall of the British University:

The more prosaic truth emerges when you scan the titles of these epics. First, the author rarely appears alone, sharing space with two or three others. Often the collaborators are Ph.D. students who are routinely doing most of the spade work on some low grant in the hope of climbing the greasy pole. Dividing the number of titles by the author’s actual contribution probably reduces those hundred papers to twenty-five. Then looking at the titles themselves, you’ll see that many of the titles bear a striking resemblance to each other. “Adaptive Mesh Analysis” reads one and “An Adaptive Algorithm for Mesh Analysis” reads another. Dividing the total remaining by the average number of repetitions halves the list again. Mozart disappears before your very eyes.
But the last criterion is often the hardest. Is the paper important? Is it something people will look back on and say ‘That was a landmark’. Applying this last test requires historical hindsight – not an easy thing. But when it is applied, very often the list of one hundred papers disappears altogether. Placed under the heat of forensic investigation the list finally evaporates and what you are left with is the empty set.
And this, really, is not a great surprise, because landmark papers in any discipline are few and far between. Mozarts are rare and to be valued, but the counterfeit academic Mozarts are common and a contributory cause to global warming and deforestation. The whole enterprise of counting publications as a means to evaluating research excellence is pernicious and completely absurd. If a 12 year-old were to write ‘I fink that Enid Blyton iz bettern than that Emily Bronte bint cos she has written loads more books’ then one could reasonably excuse the spelling as reflective of the stupidity of the mind that produced the content. What we now have in academia is a situation where intelligent men and women prostitute themselves to an ideal which no intelligent person could believe. In short they are living a lie.
It was living a lie that finally put an end to my being a professor. One day in 1999 I got up and faced the mirror and acknowledged I could not do the job any more. I quit; and from the day I quit, though things were often tough, I never experienced the sense of waste and futility that accompanied working in a British university. By stroke of fate, I am living only a few hundred yards from the institution at which I worked. Sometimes when walking past I see the people I worked with and they look old. Living a lie does that to you.

It is bitter, bitter, bitter, but also revealing and thought-provoking….
[Hat-tip: Deepak over on FriendFeed]

In(s) and Out(s) of Academia

Bjoern Brembs is on a roll! Check all of these out:
Incentivizing open scientific discussion:

Apart from the question of whether the perfect scientist is the one who only spends his time writing papers and doing experiments, what incentives can one think of to provide for blogging, commenting, sharing? I think because all of science relies on creativity, information and debate, the overall value of blogging, commenting and sharing can hardly be overestimated, so what incentives can there be for the individual scientist?

Journals – the dinosaurs of scientific communication:

Today’s system of scientific journals started as a way to effectively use a scarce resource, printed paper. Soon thereafter, the publishers realized there were big bucks to be made and increased the number of journals to today’s approx. 24,000. Today, there is no technical reason any more why you couldn’t have all the 2.5 million papers science puts out every year in a single database. It doesn’t take an Einstein to realize that PLoS One is currently the only contender in the race for who will provide this database. For all the involved, it is equally clear what the many advantages of such a database would be. Consequently, traditional publishers are rightfully concerned that their customerbase is slowly dissappearing.

Post-publication paper assessment:

The more variables there are to game, the more difficult it becomes. Now we have one variable (IF) and we all know who is gaming it ad nauseum. In this thread we have 5 measures, add ratings and comments and you have 7. This should be impossible to game for anyone but the hacker who can get thousands to machines on the net to just hype this one paper.
All of these measures are relevant even long after publication. Some papers ignored by the media may later turn out to harbor the most important discovery of the century, while some of those tossed around everywhere turn out to be completely irreproducible. Having these measures in place, if nothing else, would allow us to quantify and study such events.
But again, no matter how many numbers you have, these measures cannot substitute for actually reading the papers! The numbers barely give you a rough idea of where a paper or a scientist can be placed with respect to others in the same field. Yet, these measures would be light-years ahead of any one-dimensional, irreproducible, obviously manipulated and corrupt measure such as the IF.

Building a scientific online reputation:

For me, this basically means that all the expertise and technical prerequisites are there to bring the scientific community into the 21st century. The advantages of the new system need to be succinctly summarized and widely publicized at the same time as the current system’s disadvantages and idiosyncracies need to be pointed out and publicized along with the new proposal. And because criticizing is always easier than advertising, I’ll start by summarizing why Thomson’s Bibliographic Impact Factor (BIF) is dead.

Why Thomson’s Bibliographic Impact Factor (BIF) is dead:

Despite the recent downpour of evidence against the use of Thomson’s BIF, I still get comments from people such as “However, IFs are still the most used way of evaluating a researcher’s career and value. Even if we find this ridiculous, it’s just the way it is.” or “in our institution, every researcher has to publish in journals whose BIF is at least 5.”. In the light of the current state of affairs concerning the BIF, this is just embarrassing. So here are the top three reasons why the BIF is dead:
1. The BIF is negotiable and doesn’t reflect actual citation counts (source)
2. The BIF cannot be reproduced, even if it reflected actual citations (source)
3. The BIF is not statistically sound, even if it were reproducible and reflected actual citations (source)
Now go and spread the information so I don’t have to suffer from these ridiculous statements any more.

Then, on Nature Network blogs and Nature blogs, discussion about the “manners” in the science blogosphere:
Corie Lok: What is fair play in the blogo/commentosphere?:

Now, maybe it’s a generational thing. Those of us who didn’t ‘grow up’ with blogs might be more easily taken aback by what goes on in them. Those of us who did grow up with them perhaps have learned to take the bad with the good.

To which I commented:

A lot depends on one’s prior experiences. If one comes to science blogging out of academia with its highly formalized and ritualized kabuki dance of language-use, extremely polite on the surface, yet often very vicious in the subtext, then one sees blogs as very uncourteous and unpleasant – the things that are supposed to be hidden between the lines and now said openly.
Many of the most popular science bloggers have a different history – many years of battling Creationist and other pseudoscience crusaders on Usenet groups in the early 1990s, people who, if they can use language at all, use it in a very vicious way, sometimes with threats of bodily harm. I spent the early 90s on Balkans usenet groups, battling heatedly nationalist Serbs, Croats and Bosnians who do not just voice empty threats but would, if they could find you, really kill you. Others cut their teeth on political blogs or feminist blogs, which are very blunt and heated. Just try not supporting Howard Dean in the 04 primaries or Obama in 08 – you get your fill of human nastiness. And that is nothing compared to what Republicans say once the general election starts!
My first blog was political – I wrote highly opinionated and strongly-worded posts. And of course, I got, let’s put it diplomatically, some highly opinionated commenters. I never deleted. Sometimes I responded (politely at first – that is unusual and disarming – I turned some trolls into friendly and polite commenters that way), sometimes I ignored, sometimes my other commenters took care of trolls.
Then, after the move to Sb, I gradually reduced writing about politics and religion and my threads are now quite nice and polite most of the times. Various heated debates about “framing” or the latest “Nature vs. PLoS” kerffufle are sweet lullabies compared to most of the stuff I saw and suffered over the years online. One grows a thick skin, understands that people behave strangely online, laughs at the most egregious examples, and moves on.
There is no single definition of a “science blog”. Blog is a piece of software. You do what you want with it. If you are a scientist with a blog, or if you write more-or-less regularly about science (or meta-stuff, e.g., life in the lab, women in academia, politics of science funding….), then you can claim that your blog is a science blog. And your blog is going to be different from all other science blogs out there, as it is what you want it to be, reflecting your own interests, goals and personality. Nobody can tell you how to do it. There is no, and there should be no “template” or “definition” of a science blog – that is the beauty of the beast.
Thus, some blogs are serious, others not. Some are nice, some are inflammatory. Some focus 100% on latest peer-reviewed research. Others are a smorgasbord of everything the blogger feels like posting at any given time (like my blog, for instance). There is no recipe, no straightjacket, no “one right way” to do it. And that is what makes the science blogosphere so exciting and vibrant – so many cool voices, interesting personalities! Who says that scientists are socially-inept or bad communicators?!

The discussion there continues:
Noah Gray: Getting into and out of character:

We seem to be at a critical juncture concerning the intersection of blogs and other Web 2.0 technologies with science. This is no time to poison the atmosphere and turn away the more “relaxed” or “casual” participants. Polarized communities refusing to tolerate rival positions, or unwilling to engage in a civil debate over any topic, from publication business models to the role of Ca2+-permeable AMPARs in LTP, will shut out many would-be contributors and stunt the growth or slow the adoption of blogs, commenting, and other web-based technologies dedicated to the pursuit of scientific collaboration. If such technologies are ever really going to work for science, it will be because of inclusivity, not exclusivity.

Maxine Clarke: Manners in the blogosphere:

The anonymity of cyberspace provides protection to both share honest opinions and participate in mud-slinging without repercussion, he notes. Yet interaction on the Internet is more personal. “So why should some choose to check their manners at the door before logging on?” He argues that intolerant online communities unwilling to engage in a civil debate — whether on publication business models or the role of glutamate receptors in long-term potentiation of neurons — will turn off would-be contributors and stunt the growth of online scientific collaboration. Web-based collaborative technologies will not work for science if they become dominated by exclusive, aggressive types. Gray isn’t calling for “communal singing of Kum Ba Yah during scientific debates”, but simply a certain level of restraint and professionalism online.

This is an interesting segue to Michael Nielsen’s latest instalment of his future book about the future of science: Shirky’s Law and why (most) social software fails:

Shirky’s Law states that the social software most likely to succeed has “a brutally simple mental model … that’s shared by all users”.
If you use social software like Flickr or Digg, you know what this means. You can give friends a simple and compelling explanation of these sites in seconds: “it’s a website that lets you upload photos so your friends can also see them”; “it’s a community website that lets you suggest interesting sites; the users vote on submissions to determine what’s most interesting”. Of course, for each Flickr or Digg there are hundreds of failed social sites. The great majority either fail to obey Shirky’s Law, or else are knockoffs that do little not already done by an existing site.
To understand why Shirky’s Law is important, let’s look at a site where it’s violated. The site is Nature Network, one of the dozens of social networking sites aspiring to be “Facebook for scientists”. Like other social networks, Nature Network lets you connect to other users. When you make a connection, you’re asked whether you would like to connect as a “friend” or a “colleague”. Sometimes the choice is easy. But sometimes it’s not so easy. Furthermore, if someone else connects to you, you’re automatically asked to connect to them, but given no immediate clue whether they connected as a friend or as a colleague. The only thing shared in the users’ mental model at this point is acute awkwardness, and possibly a desire to never connect to anyone on Nature Network again.
I don’t mean to pick on Nature Network. It’s the most useful of the social networks for scientists. But it and most other social websites (apart from the knockoffs) don’t even come close to obeying Shirky’s Law.
Why is Shirky’s Law so hard for developers to obey? I’ll give three reasons.

Interesting…. We here at Sb are often accused of being cliquish and insular. But if you look at our 70+ blogs and dig through the archives, you will see that we rarely comment on each other’s blogs – most (99%?) of the comments come from outside readers. Also, most of our links point to outside of Sb. On the other hand, NN is specifically designed to be a community (not a platform for independent players) and almost all of the comments there are from each other. Thus, it is easy for them to maintain a high level of politeness there (this is not a bad thing – this is how they designed it on purpose). It is much harder to harness the hordes of pharyngulites that spill over to all of our blogs – and I do not mind them at all, I think they make the debate spirited and in a way more honest by bypassing superficial niceness and going straight to the point. This may also have something to do with NN bloggers mainly being in the academia, while a large proportion of SciBlings are ex-academia, journalists, artists, etc. with a different rhetoric. The rhetoric of academia is a very formalized kabuki dance, while the rhetoric of the blogosphere has shed all formalities and is much more reminiscient to the regular everyday oral conversation.
Moving on to other, related topics…
Jocalyn Clark: Is the NIH open access policy regressive?:

Panellists noted that the recent NIH public access policy emphasises free not open access. That is, the policy may lead to freely accessible publications (for which publishers or organisations may reap profits from charging authors a fee to deposit their manuscripts), but these will remain under restrictive licenses (thus limiting text-mining).
This, Cockerill argued, makes the NIH policy regressive.

NASA to launch OA image collection:

Nasa is to make its huge collection of historic photographs, film and video available to the public for the first time.

Rhea Miller: Vow to never become Jaded…:

But I do NOT understand why it is socially accepted to be a Jaded student…to be completely negative about the research he/she does, to avoid showing up to journal clubs/seminars, or to never participate in scientific discussions. What does being burnt out do for you in becoming the best you can be?? How does it help your science, your field, or your coworkers??
I really only notice these attributes in young scientists, i.e. graduate students and post-docs. Does this mean that the Jaded ones eventually give-up, get use to it, change their prospectives, or do they hide that inner Jaded color as they progress?? Or maybe it’s just that grad students/postdocs can’t seem to see the light at the end of the tunnel until they get there??

Panthera studentessa: Letting fear take over:

As time goes on, I’m becoming more and more concerned that I don’t have what it takes to hack it in graduate school. In every community, every blog, every forum that I read, people always talk about how stressful and all-consuming grad school is. To be perfectly honest, my mental health isn’t exactly the best it’s ever been. I just worry that I won’t be able to handle the mental and physical stress.
——-
I suppose there’s always the option of just not going to graduate school, but that really throws a wrench in my career plans. I don’t even know what kind of jobs a person can get with a bachelor’s in zoology. And anyway, I don’t want to let my fear determine what I do with my life. I just wish I knew how to begin to get over it.

Maddox2: Advice on Freelance Science Writing:

Caveat: I am writing this advice from the perspective of an editor who regularly works with freelance science writers. However, the market in which I work may not be the same as some of you out there work in, or want to work in. Therefore, I can guarantee that following the advice below will endear you to K-12 educational publishers (and to companies like mine who work for educational publishers). I can’t speak to journals, newspapers, etc…but I can’t imagine they’d mind if you follow this advice! And given that a lot of people here have expressed an interest in freelance writing, I thought I might be able to provide a bit of a different perspective on things.

Mad Hatter: Networking Nuts And Bolts:

I think the most important thing to keep in mind when networking is that your contacts are much more likely to help you if they like you. My personal philosophy on networking is this: when my networking contact turns on her computer and sees an email from me, I want her to click on the email thinking, “Hey, I remember Mad Hatter. I liked talking to her. I wonder what she’s been up to?” What I don’t want her to do is groan and think, “Oh, no…it’s Mad Hatter again. What does she want now?” So with that in mind, here are some tips on networking that have worked for me.

John Hawks has posted first two of a 4-piece series on Blogging And Tenure: How to blog, get tenure and prosper: Starting the blog:

Last month, the University of Wisconsin officially granted me tenure. So, I can say without any doubt (if other examples had not been sufficient), it is absolutely possible to write a daily, high-profile blog and still be recognized by your colleagues as a scholar. In fact, it is possible to blog, do good research, and earn tenure at a Research I university.
That seems like progress, compared to the situation four years ago when I began blogging. A few high-profile tenure denials in late 2005, including physicist Sean Carroll and political scientist Daniel Drezner, made it seem like a blog might be the kiss of death for a research reputation. Inside Higher Education ran a story on the subject, as did Slate, with the melodramatic title, “Attack of the Career-killing Blogs”. Since I was interviewed in that article, I suppose I should have been a little nervous (I wrote about it here).
Happily things have changed.

…and: Graduate students and blogging:

As far as I know, there are no data concerning blogging and career success — or, for that matter, between any kind of public outreach and success in research careers (as opposed to teaching or industry careers that directly involve outreach). Anecdotally, there are some people who spend a lot of effort on outreach who have very well-respected research careers, and others who don’t. I’d say it’s up to the individual to chart her own course.
——————–
I’d like to advocate for a model of blogging that many graduate students might find useful. If I were starting out today, I’d blog my dissertation. Why not? Is there really anything so secret in your history and literature review that it couldn’t be read by the few hundred people who will find your blog?

The importance of stupidity in scientific research

Now this is a title of a paper in a scientific journal that will make one’s eyebrows go up: The importance of stupidity in scientific research (by Schwartz J Cell Sci.2008; 121: 1771) :

I recently saw an old friend for the first time in many years. We
had been Ph.D. students at the same time, both studying science,
although in different areas. She later dropped out of graduate school,
went to Harvard Law School and is now a senior lawyer for a major
environmental organization. At some point, the conversation turned
to why she had left graduate school. To my utter astonishment, she
said it was because it made her feel stupid. After a couple of years
of feeling stupid every day, she was ready to do something else.
I had thought of her as one of the brightest people I knew and
her subsequent career supports that view. What she said bothered
me. I kept thinking about it; sometime the next day, it hit me. Science
makes me feel stupid too. It’s just that I’ve gotten used to it. So
used to it, in fact, that I actively seek out new opportunities to feel
stupid. I wouldn’t know what to do without that feeling. I even
think it’s supposed to be this way. Let me explain.

I am not sure what he wrote is really what she meant, but anyway, this was a nice way for him to start the article. What he is talking about is not really stupidity. I’d call it ignorance. And grad school teaches you to cherish and relish in your ignorance, as that is the main motivator in working every day to diminish it a little bit at a time by discovering something new, a little bit of information about the way the world works that in some reduces your own and everyone else’s ignorance. If you are successful in acquiring this mindset – enjoying the ambiguity of science, having ease with saying “I don’t know….and, by the way, nobody does” – you feel good. If you are a different kind of person, you may as well feel stupid:

Productive stupidity means being ignorant by choice. Focusing
on important questions puts us in the awkward position of being
ignorant. One of the beautiful things about science is that it allows
us to bumble along, getting it wrong time after time, and feel
perfectly fine as long as we learn something each time. No doubt,
this can be difficult for students who are accustomed to getting the
answers right. No doubt, reasonable levels of confidence and
emotional resilience help, but I think scientific education might do
more to ease what is a very big transition: from learning what other
people once discovered to making your own discoveries. The more
comfortable we become with being stupid, the deeper we will wade
into the unknown and the more likely we are to make big
discoveries.

Science To Life hits a big milestone!

Go there right now and congratulate Karen Ventii on her shiny new PhD!

Electronic Publication and the Narrowing of Science and Scholarship. Really?

Electronic Publication and the Narrowing of Science and Scholarship by James A. Evans, ironically behind the paywall, has got a lot of people scratching their heads – it sounds so counter-intuitive, as well as opposite from other pieces of similar research.
There is a good discussion on FriendFeed and another one here.
A commentary at the Chronicle of Higher Education is here, also ironically behind the paywall.
Here is the press release and here is the abstract:

Online journals promise to serve more information to more dispersed audiences and are more efficiently searched and recalled. But because they are used differently than print–scientists and scholars tend to search electronically and follow hyperlinks rather than browse or peruse–electronically available journals may portend an ironic change for science. Using a database of 34 million articles, their citations (1945 to 2005), and online availability (1998 to 2005), I show that as more journal issues came online, the articles referenced tended to be more recent, fewer journals and articles were cited, and more of those citations were to fewer journals and articles. The forced browsing of print archives may have stretched scientists and scholars to anchor findings deeply into past and present scholarship. Searching online is more efficient and following hyperlinks quickly puts researchers in touch with prevailing opinion, but this may accelerate consensus and narrow the range of findings and ideas built upon.

For now, let’s see what others say:
Peter Suber:

* It’s hard to say much based on a newspaper summary and a press release. But at first glance, Evans’ results conflict with the many studies showing that OA articles are cited significantly more often than non-OA articles. These studies differ from one another on how to explain the correlation between OA and increased citation counts, but they agree on the correlation. However, there may be ways to reconcile the two sets of results. For example, authors may cite fewer articles when they have more to choose from, but they may still cite OA articles relatively more often than TA articles. Or the average number of citations per article may decline with the growth of the total number of articles accessible to authors, but OA articles might bring the average up, and TA articles might bring it down. Or the multiplication of ejournals may be narrowing the scope of the average paper, and therefore shortening the average reference list, but citations may be growing overall and the of citations of OA articles may be growing faster than the citations of TA articles. (On the other side, the Economist said that “the same effect applied whether or not a journal had to be paid for” –though without specifying exactly which effect.)
* Evans’ results also appear to conflict with a recent study by Arthur Eger, Database statistics applied to investigate the effects of electronic information services on publication of academic research – a comparative study covering Austria, Germany and Switzerland, GMS Medizin – Bibliothek – Information, June 26, 2008. Eger found that “a larger content offering coincides with a dramatic increase in Full Text Article requests, and an increase in Full Text Article requests, after about 2 years, coincides with increased article publication.” If Evans is right that “less is sampled”, then the two studies are definitely incompatible. But if look only at Evans’ conclusions about citations, the two studies may be compatible. Evans is saying that access to more literature reduces the number of different sources one cites, and Eger is saying that it increases (“dramatically” increases) the number of articles one requests or samples. Researchers may be viewing more articles but citing fewer. Are they using their enhanced access to browse neighboring topics? Are they exploring serendipitous discoveries, only some of which turn out to be citable? Does their wider reading help them zero in on citable research?

Brandon Keim asked (and commenters are answering):

What do you think, scientist and scholar Wired Science readers, especially those whose careers have spanned the jump from paper to screen? What have you gained — or lost — from the internet’s rise?

Philip Davis:

In other words, it is not the additional online access that this causing the change in citation behavior but the tools that accompany the online access — tools that allow readers to link to related articles, rank by relevance, times cited, etc. It is these tools that signal to the reader what is important and should be read. The result of these signals is to create herding behavior among scientists, or what Evans describes as consensus building.
A highly-efficient publication system can come with unanticipated consequences — the loss of serendipity. In an earlier blog post, we discuss how the Internet is changing reading behavior in general, reducing the depth of inquiry. In another blog, we discuss how signaling can help readers save time.

David Crotty:

Evans brings up a few possibilities to explain his data. First, that the better search capabilities online have led to a streamlining of the research process, that authors of papers are better able to eliminate unrelated material, that searching online rather than browsing print “facilitates avoidance of older and less relevant literature.” The online environment better enables consensus, “If online researchers can more easily find prevailing opinion, they are more likely to follow it, leading to more citations referencing fewer articles.” The danger here, as Evans points out, is that if consensus is so easily reached and so heavily reinforced, “Findings and ideas that do not become consensus quickly will be forgotten quickly.” And that’s worrisome-we need the outliers, the iconoclasts, those willing to challenge dogma. There’s also a great wealth in the past literature that may end up being ignored, forcing researchers to repeat experiments already done, to reinvent the wheel out of ignorance of papers more than a few years old. I know from experience on the book publishing side of things that getting people to read the classic literature of a field is difficult at best. The keenest scientific minds that I know are all well-versed in the histories of their fields, going back well into the 19th century in some fields. But for most of us, it’s hard to find the time to dig that deeply, and reading a review of a review of a review is easier and more efficient in the moment. But it’s less efficient in the big picture, as not knowing what’s already been proposed and examined can mean years of redundant work.

Martin Fenner:

The greater availability of research papers in recent years thanks to electronic publication (and open access) should broaden and not narrow the papers that we read and ultimately cite in our own publications. But looking at my own behavior when reading papers or writing a publication, and thinking about many discussions we had on related topics, these findings make perfect sense.
Today’s technology allows us to make the distribution of scientific papers in electronic form very efficient, and thanks to this technology we have new business models (author-pays) and an ever-increasing number of journals. Access to research articles is now easier, cheaper and for a broader audience than in ever was before. This is of course a wonderful development, but unfortunately creates a new problem: information overflow and how to filter out the relevant information.
Twenty years ago the typical researcher would use the personal or institutional journal subscription to regularly follow the important papers in his field. Index Medicus and Current Contents were used to find additional articles, but they were cumbersome to use. Today few researchers regularly read printed journals. Most papers are found by searches of online databases and by subscriptions of tables of content by email or RSS. There are many clever tools to facilitate this, but most people probably are overwhelmed by the information and stick to some very specific research interests and high-profile journals.

Thomas Lemberger:

In any case, the study highlights two complementary strategies in information retrieval: finding relevant papers by targeted searches versus staying informed on a broad range of topics by systematic browsing. In our Google-driven era, we may have the tendency to forget the importance of good old-fashioned ‘table-of-content-skimming’ to stimulated cross-disciplinary thinking, widen our horizon and cultivate scientific curiosity.
Perhaps it is a specificity of printed media to provide “poor indexing” and therefore enforce broad exposure to unrelated areas of research. On the other hand, some web technologies already help to browse through vast amounts of online publications (for example an RSS aggregator helps me to generate a daily literature survey; this can be further combined, for example here at Frienfeed, with other community-centered feeds; other aggregators highlight information by automatic clustering: Postgenomic and Scintilla). However, these tools remain imperfect and, in our reflection on the future of scientific publishing, we will need to find the right balance between the two strategies above and think of how the increasing efficiency of searching engines can be complemented by means providing continuous exposure to diversity.

Bill Hooker does the most detailed analysis of the paper so far (so click and read the whole thing, graphs and all):

What this suggests to me is that the driving force in Evans’ suggested “narrow[ing of] the range of findings and ideas built upon” is not online access per se but in fact commercial access, with its attendant question of who can afford to read what. Evans’ own data indicate that if the online access in question is free of charge, the apparent narrowing effect is significantly reduced or even reversed. Moreover, the commercially available corpus is and has always been much larger than the freely available body of knowledge (for instance, DOAJ currently lists around 3500 journals, approximately 10-15% of the total number of scholarly journals). This indicates that if all of the online access that went into Evans’ model had been free all along, the anti-narrowing effect of Open Access would be considerably amplified.
In fact, the comparison between print and online access is barely even possible when considering Open Access information. The same considerations of cost — who can afford to read what — apply to commercial print and online publications, but free online information has essentially no print ancestor or equivalent. Few if any scholarly journals were ever free in print, so there’s a huge difference between conversion from commercial print to commercial online on the one hand, and from commercial print to Open Access on the other.
Indeed, I would suggest that if the entire body of scholarly literature were Openly available, so that every researcher could read everything they could find and programmers were free to build search algorithms over a comprehensive database to help the researchers do that finding, then in fact the opposite effect would obtain. Perhaps it’s true that the more commercial online access you have, the less widely a researcher’s literature search net is cast, but as I mentioned above I see no reason to attribute that more to the mode of access than to its cost.

Perhaps with greater accessibility, people have quit citing old papers which they used to cite just because everyone always cites those papers without even reading them. Those who have the least access, tend to cite very old stuff, textbooks, popsci articles, e.g., these guys. Those who have good access can both browse and search and find what is truly relevant to their work. They cite only stuff that they have actually read and found useful. Perhaps people are just getting more honest.

Cool bloggy miscellanea

Scientific Collectivism 1: (Or How I Stopped Worrying and Loved Dissent):

I want to bring up a discussion about what I perceive is a dangerous trend in neuroscience (this may be applicable to other areas of science as well), and that is what I will term “scientific collectivism.” I am going to split this into two separate posts because it is so long. This first post is the weaker arguments, and what I see are the less interesting aspects of scientific collectivism-however, they deserve a discussion.

What will you be? and the related Friday Poll: Tinker, Tailor, Biologist, Researcher. So, how do you call yourself when you are introduced to a stranger?
A little muddled (especially in not making sufficient distinction between peer-reviewed Journals and pop-science magazines), but an interesting look from the outisde in: The High Cost Of Science:

Let’s say, for the sake of argument, that you are interested in science and you want to learn more about it. Maybe you’re tired of creation vs evolution debates and you want to do the research yourself, or maybe you just want to become a more informed citizen. Whatever your reasons, you have a few options but none of them are all that appealing.

Online Alarm Clock which, once set, does not need to be online in order to ring on time. Does it work on an iPhone?
Fair Use Rights:

Intellectual property, copyright, creative commons, copyleft, open access… These are all terms high on the science and other agenda these days. For example, public-funded scientists the world over are calling for research results to be available free to them and their peers for the public good and for the good of scientific advancement itself. Librarians likewise are also interested in the fullest dissemination and sharing of knowledge and information, while user-creators and the new breed of citizen journalists that are the result of the Internet Age are also more liberal in their outlook regarding the proprietary nature of creative works.

Survival of the Abudant: Mutational Networks Constrain Evolution:

What has been found over the last few years is that these neutral mutations occur in networks. That means that there are little fleets of genotypes, all of the same “fitness”, that have overlapping series of neutral mutations. Most of these fleets are small, but a few are larger, and its the larger fleets of genotypes that the researchers in this study focused on. The large networks tend to be adjacent to a pretty large number of phenotypes. So you have all these little neutral mutations, next to RNA with a wide variety of phenotypes. Do these little neutral mutations influence evolution after all?

The Kudlow Year:

We’ve had a terrible year. Obvious problems remain, along with whatever else lurks beneath the waterline. Wall Street showed some optimism about the future yesterday, but we’ve still got a long way to go. A lot of this boils down to arithmetic. Pay more attention to the numbers and less to ideologues on teevee or the web who try to tell you different.

Scribd and Lulu partner:

Print-on-demand publisher Lulu (which offers an OA option for content providers) and document sharing site Scribd are partnering, according to ReadWriteWeb. Lulu will begin making some of their OA content available in Scribd’s iPaper format (a “sort of a YouTube for PDFs”), including utilizing iPaper’s ability to embed AdSense ads within the documents.

Rational Voters?

The underlying assumption, of course, is that issues matter, that voters are fundamentally rational agents who vote for candidates based on a coherent set of principles. In other words, they assume that my political preferences reflect some mixture of ideology and selfish calculation. I’ll vote for the guy who best matches my geopolitics and tax bracket.
The problem, as political scientist Larry Bartels notes, is that people aren’t rational: we’re rationalizers. Our brain prefers a certain candidate or party for a really complicated set of subterranean reasons and then, after the preference has been unconsciously established, we invent rational sounding reasons to justify our preferences. This is why the average voter is such a partisan hack and rarely bothers to revise their political preferences.

I Like My Facts Well Done and Humorless. The funny take on Sizzle.
PhysioProf rants and raves on Feministe for a couple of weeks or so. Check the tribal wars in the comments!
A pierced scientist? AKA, I need a mentor:

It occured to me yesterday that I have a lot of questions to ask and nobody to go to for answers. I really need a mentor of some kind. I mean, I have an academic advisor, but he’s an old white man who doesn’t make any attempt to engage me in conversation. He’s very standoffish and business-oriented whenever I meet with him, which I think has been once a year for the last three years. I doubt he knows my name. And I have Dr. Calhoun, my research advisor, who I’m starting to warm up to a little bit but I’m not really at the point where I can ask him the kinds of personal questions that are the most burning. I doubt I’ll ever be able to not be intimidated by him, especially since I found out he’s the chair of the graduate admissions committee.

How to read a scientific paper

Here is a good example. Step-by-step.

Open Textbooks

Georgia Harper saw an interesting article in USA Today about Open textbooks and, among else, says:

Open access is just one part of a much bigger and more complex picture. I am very optimistic that open access will find its way into the book market (or what we call books today), but again, it’s not like that will cut off the flow of revenues. Quite the contrary. It just makes it possible for a lot more people to benefit from the work of authors while authors and those who help them ready their works for public consumption still reap sufficient financial rewards to make creating worthwhile. Maybe the biggest stumbling block is understanding that as a copyright owner, you don’t have to appropriate every cent of public benefit from your work. There’s viability in skimming off the top and letting some of the benefit go to those who never would have been able to buy your book anyway. That concept seems really counter-intuitive to many authors and publishers, but I think it’s what makes open access a successful competitor — authors and publishers can still get paid (if that’s what they want) but people who would not have had access also derive benefit.
So, back to copyright law: we make and distribute copies of others’ works; we license others’ works; we buy others’ works. We (educators) are very big consumers of and producers of educational, research and scholarly materials. This is big, big business. And it’s got copyright as a major component of its engine. But a bundle of copyrights, no matter how big, becomes worth less and less over time. New works get created every single day. And every single new author has choices today about how to distribute, market and benefit from his or her work that were simply not available even a decade ago. That’s what makes authoring and creating so exciting today: the chance to reach an audience of any size is within reach for many more of us than in the past. How will you handle your copyrights? Open access has an awful lot to recommend it. Look into it! Creative Commons licensing is a good example of how you can make your work widely and freely available while still maintaining the degree of control that fits with your overall goals in writing or creating in the first place.

Amen.
Hat-tip: Gavin Baker

The Graduate Junction

Graduate Junction is a new social networking site designed for graduate students and postdocs. I looked around a bit and found it clean, easy-to-use and potentially useful. This is how they explain it – give it a try and let me know what you think:

The Graduate Junction is a brand new website designed to help early career
researchers make contact with others with similar research interests,
regardless of which department, institution or country they work in. Designed
by two graduate researchers at the University of Durham, The Graduate Junction
has proved very popular with research students and academics alike. Within the
first two weeks after our launch in early May 2008 over 2000 researchers in the
UK had registered and the news had spread across 40 countries.
Currently research students have two main sources of information, published
literature and academic conferences. Whilst published literature is
essential, it can only ever reveal completed work. Relevant academic
conferences provide a forum for students with similar research interest to
interact but occur infrequently. It is very easy to become isolated, overly
focused on the specifics of one’s own work and lose a sense of what other
related work is being done.
The Graduate Junction hopes to prevent that isolation and allow early career
researchers to start forming the networks which can stay with them throughout
their careers. The Graduate Junction aims to provide an atmosphere similar to
that at academic events and through the use of the internet aims to establish
an on-line worldwide graduate research community.
The Graduate Junction is unique because it links researchers based on ‘research
keywords’, promoting interdisciplinary relationships. By simply registering a
few basic details, users can search for fellow researchers by keyword,
institution, department, supervisor or name. Alternatively, users can search
The Graduate Junction’s on-line research groups which allows them to find and
communicate with a number of other researchers sharing their research
interest. The Graduate Junction has been designed to be simple and provide
only information and functionality that is relevant to researchers.
The Graduate Junction is useful for all Master, Doctoral and Postdoctoral
researchers at any stage of the research process, and allows them to start
building networks and stay informed about current developments in their field.
With the addition of conference and postgraduate job listings imminent, The
Graduate Junction aims to be one of the most useful resources available for all
graduate researchers.

An alarming picture of scientific misconduct in the USA

Repairing research integrity:

Misconduct jeopardizes the good name of any institution. Inevitably, the way in which research misconduct is policed and corrected reflects the integrity of the whole enterprise of science. The US National Academy of Sciences has asserted that scientists share an ‘obligation to act’ when suspected research misconduct is observed1. But it has been unclear how well scientists are meeting that obligation. In the United States, the Office of Research Integrity (ORI) evaluates all the investigation records submitted by institutions and plays an oversight role in determining whether there has been misconduct at institutions that receive support from the Department of Health and Human Services (DHHS). The reported number of investigations submitted to ORI has remained low: on average 24 institutional investigation reports per year2.
ORI focuses resources, not only on evaluating institutional reports of research misconduct but also on preventing misconduct and promoting research integrity through deterrence and education. To evaluate these initiatives, we investigated whether the low number of misconduct cases reported to ORI is an accurate reflection of misconduct incidence, or the tip of a much larger iceberg. The latter seems to be the case.
The 2,212 researchers we surveyed observed 201 instances of likely misconduct over a three-year period. That’s 3 incidents per 100 researchers per year. A conservative extrapolation from our findings to all DHHS-funded researchers predicts that more than 2,300 observations of potential misconduct are made every year. Not all are being reported to universities and few of these are being reported to the ORI.

Read the rest

Impact Factors 2007

If anyone is interested, Thompson has just released the new Impact Factors for scientific journals. Mark Patterson takes a look at IFs for PLoS journals and puts them in cool-headed perspective.
One day, hopefully very soon, this will not be news. What I mean by it is that there soon will be better metrics – ways to evaluate individual articles and individual people in way that is transparent and useful and, hopefully, helps treat the “CNS Disease”. Journals will probably have their own metrics based on the value they add, but those metrics will not affect individual researchers’ careers the way they do now.

Why do Academics do this blogging thing?

A number of my SciBlings (and their commenters) try to explain:
Janet
Chad
Martin
PhysioProf
DrugMonkey
Brian Switek
Alice
Jeremy Bruno
Grrrrrl

Revisiting academic blogging

It’s always interesting to hear what Eszter has to say about academics and blogging. She is right that the environment has changed and that more and more people know what blogs are and appreciate them (not everyone, though, but those are not academics, really).
She is also right that the term “blog” is not very useful – a blog is a piece of software: it is what you do with it that affects how you are perceived by peers, which in turn can affect your career trajectory. There are examples of people who lost prospects due to their blogging, but that was either because they were foolish (their loss) or the prospective employees were (the employees’ loss).
But there are also many counter-examples of people who got their jobs because of their blogging, or it was helpful. For instance, Deepak got a job with Amazon over twitter, I was a witness when Jason Calacanis hired a programmer via twitter, Anne-Marie, an undergrad, has been approached by potential graduate advisors due to her lovely blogging, and you know I got my job in the comments thread of a post on my blog.
Anyway, it is an interesting post and comment thread to read.

Search for PPT slideshows by keyword

Go to http://www.slideworld.org, type in a keyword, and it will do a search of slideshows that contain that word. I typed “circadian” and found a lot….
Hat-tip: Ana

Congratulations!

Jarred aka The Urochordate is a PhD as of today.

Columbia Book Sale

I got an interesting e-mail yesterday:

Columbia White Sale goes through May 31st. For more information, please visit: http://cup.columbia.edu/sale/23. We are offering up to 80% off on more than 1,000 titles in all subjects. (There are some really great deals). I hope this will be of interest to you and your readers. Please feel free to pass the word to friends and colleagues.

Hmmmmm, shiny!

Ettiquette for blogging a scientific meeting – a question

I will be going to a scientific conference next week. Believe it or not, this will be the first purely scientific meeting I’ll attend since I quit grad school and started blogging (all the others had to do with science communication, blogging, technology, journalism, Internet, publishing…). So, I am thinking….
I remember going to scientific meetings meant going to a nice little Florida resort and spending a couple of days with one’s friends and colleagues, isolated from the rest of the world, talking about science 24/7. It is an opportunity to share your latest work and ideas with an inner circle of the field. Seeing one’s findings and words plastered all over the Internet is probably not what most people there will expect to happen and some may get dismayed. Has this world changed since the last time I went there? Are the people more aware nowadays that everyone in the audience may be a journalist or a “journalist”? Do they like seeing their ideas disseminated more widely?
So, what is the proper behavior in regard to liveblogging conferences these days? I will see a bunch of talks and posters and will probably find some of them exciting enough to want to write about. I can always approach the speaker afterwards and ask (or warn) or even do a semi-formal interview. But some I just want to quickly liveblog in passing, as things happen. I will bring a notepad, a few good pens and will take good notes, and will have my laptop with me in case I want to liveblog directly into the computer.
The program is publicly available, including all the abstracts. Some posters or slides may even show up online afterwards. There is nothing illegal about blogging about it, but is it against any new unwritten rules?
How about hallway chats? Hotel-room drunken hypothesis-spinning? Beach-side frolicking with crazy geeks who cannot talk about anything but science? Should I warn people that a blogger is in the room?

New UNC Chancellor is a scientist. w00t!

Holden Thorp is a chemist and an overall great guy. Good news for NC science and education.

Colleges should not discriminate against Martians and Tralfamadorians

Our governor agrees. At least in the print version of this article which has a somehwat different title: “Easley supports college for aliens”. I wonder why they changed it for the Web version – is the editorial position that having green or purple skin disqualifies one from higher education?

Congratulations!!!!!

Anna Kushnir is now to be referred to as Doctor Anna Kushnir!

Open Humanities Press

Peter Suber relays the announcement (and add some more) of the Open Humanities Press, a collection of seven Open Access journals (a humanities PLoS of sorts) in critical and cultural theory.
Humanities bloggers have been way ahead of science bloggers in regards to posting their own work (including ideas, hypotheses and rough drafts) online, yet official humanities publishing has lagged behind natural sciences and medicine when it comes to adopting Open Access, so this is a very positive move on their part.