The movie tries to argue that people supportive of intelligent design have been muzzled and persecuted.

It has activated the good people who are sadly called on too many times to “defend” evolution and Darwin and to expose intelligent design for what it really is. One of the stars in this arena is Kenneth Miller, a biology professor at Brown U. He has a nice op-ed in today’s Globe saying that not only is the movie full of lies, but is also a threat to science.

“Expelled” is a shoddy piece of propaganda that props up the failures of Intelligent Design by playing the victim card. It deceives its audiences, slanders the scientific community, and contributes mightily to a climate of hostility to science itself.”

The National Center for Science Education has a website devoted to debunking “Expelled”. They accuse the makers of the movie of being dishonest with the people they interviewed and in how they promoted it. The NCSE even recently ran a contest to pick the 5 best refutations of claims made in the documentary. The site says the winning entries will be posted soon, this month.

At last night’s NNB pub night, a couple of Harvard postdocs told stories about how they’ve felt the same effect at conferences or other places where they meet other scientists. (Being in a pub right across the street from the Longwood area in the company of other Harvard people felt like a safe place to be able to talk openly and to gain sympathy about this, rather than getting the predictable eyeball-rolls.)

They said that they go out of their way to not say their affiliation. “I’m from Boston.”

As one person put it, if people see that you’re from Harvard, they automatically think you’re a prick.

Where does this come from? Jealousy? Run-of-the-mill pettiness? A primordial urge to want to hate and take down the top dog? Is this any different from the Boston baseball fans who love to hate the NY Yankees? Does this happen in other parts of the world, like to the poor people at Cambridge or Oxford?

So the fact that one of those countries, the United Arab Emirates (UAE)—which sits on about eight percent of the world’s oil reserves, is trying to make a name for itself as an innovator and educator in renewable energy technologies and green urban planning is attracting attention. At a conference at MIT yesterday, the audience heard about a new six square-kilometer city that’s being built from scratch near Abu Dhabi, the capital of the UAE. The new city, which will be home to 50,000 residents, aims to be zero-carbon and zero-waste, thanks to solar technologies and the banning of cars.

Construction of the $22 billion Masdar City began earlier this year and is being financed in part by the government of Abu Dhabi through its Masdar Initiative, an economic development group created in 2006 with $15 billion from the government, aiming to put Abu Dhabi on the forefront of alternative energy R&D. (Incidentally, Fortune magazine last year called Abu Dhabi “the richest city in the world.”)

(See coverage of Masdar City from NPR, Boston Globe, NY Times and MIT Tech Review)

At the heart of Masdar City will be the Masdar Institute of Science and Technology (MIST), a graduate level research institute devoted to renewable energy. It was developed with the help of MIT and will open in September 2009 with 30 faculty and 100 master’s students. It will begin granting PhDs in 2011.

MIST faculty members (15 recruited so far, many of them MIT grads) are at MIT now working with MIT faculty on seven projects, funded by Abu Dhabi, that will be moved to MIST when it gets set up in its new home. Over the long term, MIT researchers can continue to collaborate with MIST researchers on MIST-funded projects, gaining access to Abu Dhabi’s wealth of resources.

I had a chance to sit down today with the Masdar Initiative CEO, Sultan Al Jaber, who was in town for the MIT conference and to promote MIST to Boston-area students.

(Credit: Masdar Initiative)

Why is oil-rich Abu Dhabi interested in developing sources of alternative energy?
Abu Dhabi recognizes that the global energy markets are evolving. If you look at the global energy demand curve, you’ll find that it’s increasing with substantial growth in renewable energy. Does that represent a threat or an opportunity? We believe that it represents a very unique opportunity for us to venture into.

Is this a way to prepare for the time when oil supplies run out?
It’s not only that. In order for the whole world to meet its energy requirements and demands, it can’t rely on one source of energy. It can’t. It’s not only going to be about hydrocarbons. We have to act now to find new sources of energy. We are believers that energy supplies should come from a portfolio of solutions. We prefer to go the clean energy route.

Why did you create MIST?
MIST is the centerpiece of this whole initiative. We saw how successful the Silicon Valley model has been, Singapore too and route 128 here in Boston. They all became successful because they have a university or research institute as the centerpiece of these clusters. They feed them with new technologies, enhance human capital and develop intellectual property. Based on that, we decided that we are going to build the home of alternative energy in Abu Dhabi. But in order for us to have a real home, we have to have a nucleus to provide the talent, the research and the technologies. That is MIST.

Will MIST students and faculty get to work on the development of Masdar City?
Definitely. We already have a few students accepted to MIST working on different activities within Masdar City.

I ran a news story here on NNB a couple of years ago about how theater could be used to bring science to the masses in an entertaining and enlightening way. On Friday, I decided to see a play about science to experience for myself whether theater could teach me a little (or at least increase my appreciation for) an area of science that I know little about: quantum physics (and basically, anything with the word “quantum” in front of it.)

QED brings us into the office of Feynman in 1986 at Caltech on a Saturday and the play is basically a long, meandering, sometimes moving, sometimes funny conversation between him and the audience. It’s interrupted by phone calls with his doctor (he was battling cancer at the time), friends, and officials from Washington DC, as well as a couple of visits from a keen student. Feynman, played by actor Keith Jochim, tells lots of stories in a chatty, jokey kind of way and talks about science, a little bit about his research, his work with the Manhattan Project, his first wife who died many years earlier, his efforts with the Presidential commission to investigate the Challenger disaster, and his recurring cancer. He also manages to squeeze in basic lessons about light (are they waves or particles or both?). Through that, we get a glimpse of what Feynman was like: mischievous, wacky, intensely curious about everything, fascinated with nature.

After the play, the actors came out to answer questions from the audience and they were joined by MIT physicist and emeritus professor Jerome Friedman, who won the Nobel Prize for physics in 1990 and who also knew Feynman. Friedman said the play “captured the essence” of Feynman as an irreverent, unconventional guy.

While I can’t say I learned a lot of physics, or gained any new understanding of quantum mechanics, I would say that what came through in the play was a sense for what science is (“tricking Nature into revealing her secrets”), how it’s done (“if you ask the right question, nature will give you the right answer”), and how fun, awe-inspiring, fascinating and exciting problem-solving and doing science can be. And who better to communicate that message than an eccentric and brilliant scientist like Richard Feynman.

Could such a play change the way a non-scientist audience member thinks about science and scientists? Possibly, given the experience of the actor who played Feynman. In the Q&A session, Jochim said that as a result of playing the part of Feynman and reading other books about him/by him, he found himself becoming more curious about the world around him, asking questions he probably wouldn’t have asked before.

I saw a couple of school kids in the audience with their parents. I think watching this sort of play about science should be a field trip for young science students. Science classes are good at teaching the facts and methods, but do they instill in students the fun and excitement of science? Because, as I wrote in another blog post, I think one of the things all people should know about science is that it can be fun. (I think such a play could benefit burnt out grad students/postdocs too—a good reminder of why they got into science in the first place.)

The Cambridge Science Festival wraps up today, but QED will be reopening again in July in Cambridge at the new Central Square Theater.

We need a logo for the event so we’re holding a competition to find the best one. For those of you who like to play in Photoshop, please help us out…send us your logo at network@nature.com by the end of May. Please try to include the name of the conference in it.

The winner will get some goodies from us, and we’ll wine and dine you when in London.

You can RSVP by posting a reply here.

Bring scientist-friends. We’ll be in the back room. Hope to see you then!

It looks like Washington DC will the first US city to introduce a bike-sharing program. You pay a yearly membership fee of $40 and then you can sign out one of 120 bikes parked at 10 locations in the city.

We in Boston need this. The T is slow, traffic is bad, and parking is nonexistent. The bikes could be especially useful to students and researchers. If there were bikes parked near all the major universities and campuses, students taking classes or doing research at different schools/campuses could more quickly get around. I wonder if researchers from different institutions around Boston would collaborate more if there were more and faster ways of getting across town? It seems so mundane but distance and commuting can be real barriers to collaboration.

Bike-sharing (and biking in general) could however be limited by two factors: snow (winter) and crazy Massachusetts drivers.

Lunch with a Laureate
Monday, April 28-Friday May 2, noon – 1pm
MIT Museum, 265 Mass. Ave.
An informal talk and Q&A session with one of the many local Nobel winners. Free.
Mon: Phil Sharp (Physiology/Medicine, 1993)
Tues: Wolfgang Ketterle (Physics, 2001)
Wed: Dudley Herschbach (Chemistry, 1986)
Thurs: Jerome Friedman (Physics, 1990)
Fri: Susumu Tonegawa (Physiology/Medicine, 1987) This Friday talk starts at 12:30pm.

Making Us Smarter? The Ethics of Neuronal Enhancement
Monday, April 28, 4:00 – 5:30pm
Novartis Auditorium, 220 Mass Ave.
Explore both the practical prospects and the ethical implications of various kinds of neuronal enhancement that are becoming possible as a result of current developments in the brain sciences. Harvard Provost and Neuroscientist Steven E. Hyman will moderate a panel and will be joined by Mark Bear, Director of the Picower Institute for Learning and Memory and Dr. Richard Wurtman, the Cecil H. Green Distinguished Professor of Neuropharmacology at MIT. Free.

Thinking Outside the Fossil Record: Explanations for the Cambrian Explosion of Animals.
Tuesday, April 29, 6:00pm
Harvard University, Geological Lecture Hall, 24 Oxford Street
There are many explanations for the Cambrian “explosion” – that flash of evolution 540 million years ago when the diversity of animal life exploded. Family after family of complex creatures with hard shells, spinal cords, and skeletons arose to dominate life on Earth and create rich, albeit incomplete, fossil record. What caused this diversity explosion and what makes this epoch unique in history? Come listen to Charles Marshall, Professor of Biology & Geology and Curator of Invertebrate Paleontology at Harvard. Free

Soap Box/Sociable Robots
Tuesday, April 29, 6:00 – 7:30pm
MIT Museum, 265 Mass. Ave.
What do sociable robots tell us about ourselves? First, we’ll hear from MIT professors Sherry Turkle and Cynthia Breazeal, then we’ll hear from you and the rest of the audience in this salon-style event. Who knows, a socialble robot or two may show-up to have their say! Free

Brewing Innovation
Wednesday, April 30, 6:30 – 9:30pm
MIT Museum, 265 Mass. Ave.
Join us for an evening of science and Sam (Adams)! Yeast has been used in the research of diseases from cancer to Alzheimer’s as well as cutting edge emerging energy work. Samuel Adams Beer Founder Jim Koch will talk about the science of brewing followed by Dr. Gerald R. Fink of the Whitehead Institute, who will lecture on breaking Biofuel research. Beer tasting and hors d’oeuvres will round out the evening. Strictly 21+ event. Cheers! Free but must pre-register, only 100 slots available. scitacular@gmail.com

QED/Underground Railway Theater
Wednesday, April 30 – Sunday, May 4
Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge
QED, Peter Parnell’s play about the brilliant and eccentric Richard Feynman, who won the Nobel Prize for his work on quantum electrodynamics. Directed by Jon Lipsky, starring Keith Jochim. Alternately very funny and surprisingly moving, QED is deeply inspirational about scientific inquiry and an expression of the human spirit. Performances will be followed by conversations with the public led by scientists of the MIT community, many of whom knew Feynman personally. This performance is a part of the Catalyst Collaborative@MIT, an on-going science/theater initiative between MIT and URT and follows up on the very successful production of Einstein’s Dreams which was part of the first Cambridge Science Festival. Cost: Tickets $20/$12 for students/seniors with ID.
Wed-Thurs, Sun: 7:30pm
Fri-Sat: 8pm
Sat and Sun: 3pm

Whitehead Institute Film Festival
Thursday, May 1, 7:00 – 9:00pm
McGovern Auditorium, Whitehead Institute, 9 Cambridge Center
Join us for a journey into the visual expressions of modern biology through a series of short films. Life-sustaining refreshments included. Free

Sci-Fi Camp-O-Rama: Sci-Fi Movie night at the Harvard Smithsonian Center for Astrophysics
Saturday, May 3, 7:00pm
Phillips Auditorium at the Center for Astrophysics, 60 Garden Street
Get ready for the yin and yang of sci-fi filmmaking. First we humbly offer one of Mystery Science Theater 3000’s funniest versions of the movie “Space Mutiny.” The second offering is “2010: The Year We Make Contact.” Unlike 2001, this sequel has a story that makes sense! It brings a whole new meaning to the words intelligent design. These films are a part of a special series, “Everything I Learned About Science, I Learned at the Movies!” that include free drawings and an enlightening science lecture. Free

Gov. Deval Patrick mentioned this news yesterday (Earth Day) in a speech he gave at MIT about all of the ‘green’ initiatives that he and his administration are pushing forward. He spoke as a pragmatic politician, saying that renewable energy was not only good for the environment, but also promised to create a new industry and new jobs in MA…not just for engineers and scientists but also in manufacturing and for blue collar workers (eg electricians to install solar panels). That seemed to really excite him.

So we can expect to see soon more programs and initiatives from state government to foster this industry and to encourage greater adoption of renewable energy technologies and energy efficiency. MA seems intent on competing with California on being the greenest and most energy efficient state. Given the lack of energy policy from the feds, it’ll be interesting to see what states can do and how much they can do to wean us off our oil addiction.

Update (Thurs, Apr 24): The governor, Senate president and House speaker said yesterday that Massachusetts would develop and adopt standards capping the amount of carbon in fuel. Again, another instance where Massachusetts is following the footsteps of California in developing clean energy initiatives.

At the upcoming Cambridge Science Festival, we’ll find out which scientists can best shake their stuff. As part of the festival later this month, the MIT Museum and the Boston Globe will host an evening on May 1 (7:30pm) where six finalists (chosen from videos submitted by dancing scientists) will perform in front of a panel of judges at the the MIT Museum.

The dances are supposed to somehow communicate a complicated scientific concept.

I have to admit to some skepticism about how well dance can depict science. (The best and only dance I’ve seen showing a scientific concept is the protein synthesis one from the 70s narrated by Paul Berg). But I’ll be in the audience May 1 with my camera to find out!

And today we released two major new features on Nature Network. Below is an excerpt of the announcement I just posted on the site.

The first new feature is affiliation networks. You’ll now be able to more easily find people from your institution. When you enter an affiliation in your profile, that affiliation is now a link that takes you to a page showing all the other NN members listing the same affiliation (eg Stanford University). You’ll find people who have entered it as their current affiliation, as well as alumni of your institution. You can also browse all the affiliations of NN members.

To make this work, we used the affiliation information that NN members had already provided in their profiles. But because members typed in their affiliations in such a variety of ways (eg “Broad Institute” is entered in four different ways), there are duplicates in our list of affiliations and people from essentially the same institution are appearing on separate affiliations pages.

We need your help. If you’re a NN member, please go to your profile; you’ll find that the affiliation you entered has been moved to a new section on the page. Next to each affiliation is an ‘edit’ link. Click on that to re-enter your affiliation. Use the full name of your institution (eg “Harvard University”, not just “Harvard”; “University College London”, not “UCL”).

You can now enter multiple affiliations separately, so if you are affiliated with two or more institutions, please enter them separately. Please also enter your past affiliations so that we can build strong alumni networks.

You can include more detailed information in your affiliation, such as the department, center or lab you’re in. Please do so using the following format:

• Jane Smith lab, Columbia University
• Center for Brain Science, Harvard University
• Department of Zoology, University of Oxford
• Jane Smith lab, Department of Zoology, University of Wisconsin, Madison
• Cognitive Psychology Lab, Duke University Medical Center

If you haven’t filled in the affiliation field in your profile, now’s your chance. Doing so will help you be better connected to people at the same institution and alumni.

This is only the first phase of the development of this feature. We will be rolling out more improvements over the coming months.

The second major new feature that went live today is two new tabbed views on the “Your network snapshot” page. On those two views, you’ll see the latest comments posted to the blogs and the forum threads that you’ve commented on. This way, you can see in one spot what others have said in response to your comments. It’s a quick and easy way to keep track of the conversations you’ve participated in.

Check these features out and let us know what you think. You can email us at network at nature.com or post to our feedback forum.

The Globe’s careers section this weekend had a nice article about how blogging (reading them, commenting on them, writing them) can help boost your career. The article was focused on careers in general (not on any particular type of career) but I thought the tips provided were relevant to many fields, including science.

Reading blogs can be a good way to keep up with latest events and trends in your area. Commenting on blogs is valuable too: “_The conversation is what forges relationships and before you know it, you have a much stronger network from blogging than you ever could from more conventional, nonidea based networking moments, like the exchange of business cards at a convention._”

And finally, I blogged a little while ago about wacky science videos making the rounds on Youtube. Well, one of those videos in particular has inspired Nature Publishing to launch…yup, you guessed it, its own science video competition! See the announcement below that’s going out today to members of Nature’s Facebook group:

What’s in your nature(.com)?

Calling all budding filmmakers! Inspired by BioRad ‘Scientists for better PCR’ video, ‘It’s in my nature.com’ is launching a video competition –enter for your chance to win a camcorder.

Make a video that sums up what the phrase ‘it’s in my nature.com’ means to you. It could be about why you love science, about your research, about you as a person, or it could be about www.nature.com! Be funny, be serious, be creative.

To enter: 1. Upload your video to the It’s in my nature.com Group on Facebook. 2. Email one of the ‘It’s in my nature.com’ Group admins your name, email address (so we can contact you) and link to your video and your Nature Network profile or Facebook profile.

File restrictions: under 100 MB and under 2 minutes, should comply with Facebook video rules.

Closing date: 12 May 2008.

Eligibility: Member of ‘It’s in my nature.com’ Facebook Group or a Nature Network registered user. Employees of NPG, Macmillan or their families are not eligible.

Restrictions: ‘It’s in my nature.com’ reserve the right to remove video that is obscene, libellous/slanderous, or is judged to be offensive. ‘It’s in my nature.com’ take no responsibility for the content of the videos.

Judging: Judges (the Facebook group admins and other employees of Nature Publishing Group) will choose a shortlist of 3 videos, which will be voted for by the ‘It’s in my nature.com’ Facebook group to choose a winner.

But what has always bugged me about this argument is: weren’t communities already polarized before the Internet came along? Haven’t we always stuck to talking and associating with people who think like us?

So I was glad to hear this question discussed at a talk last night at MIT called “Our World Digitized: The Good, the Bad and the Ugly.” Yochai Benkler, the co-director of Harvard’s Berkman Center for Internet and Society, and Cass Sunstein, a law professor from the University of Chicago debated (among other things) whether the Internet has deepened the divisions in society. Benkler talked about link analysis studies (looking at who on the Web is linking to who in specific types of discussions) and said that they show fragmentation but not as much as some have feared. However, he quickly qualified that this needs more study and better tools.

Sunstein then countered with evidence that people who talk with others sharing the same political opinions later become more extreme (eg people on the left move further to the left) and less diverse in their views. A quarter of Internet users say that they read things online that support what they already believe, according to the Pew Internet and American Life project. Benkler responded by saying that we see polarization with the ‘traditional’ media too like Fox News and that there are other cultural factors influencing this splitting of communities.

The conversation got more interesting when someone in the audience asked an astute question of whether polarization could be a good thing. Sunstein said there is evidence that by clustering with others who share their opinions, people build solidarity, feel empowered and are more likely to, basically, get off their butts. But he then argued that this clustering has a side effect: people don’t know, understand and can’t even engage with the “other side”. That, he said, was dangerous and unproductive for democracy.

So if we can’t say for sure that the Internet is leading to greater fragmentation, perhaps it’s safe to say that it doesn’t seem to be doing much to bring the fragments of society closer together. If that’s indeed the case, then what should we make of the efforts of scientists who so tirelessly blog with the aim of ‘educating’ the public or at the very least, battling the forces of misinformation (eg those who blog about topics controversial in the public sphere like evolution and climate change)?

Well done everyone.

If you’re not in Boston, London, NYC or Berlin, don’t feel left out. Organize your own pub nights for local scientists and feel free to use Nature Network as the website to bring people in your area together and to spread the word. Let us know what you’re planning and we can help you promote your event.

It’s something I’ve been thinking about a lot lately, both for a story I’m working on (one big reason I’ve been not-so-blogadelic here—more on that later) and for the future development of Nature Network. The recent formation of the collaboration group here on NN has further spurred my thinking.

So as a first step, let me open up the floor here for discussion.

1. What are some good examples of good, productive interdisciplinary collaborations that you’ve seen or actually experienced first-hand as something that really worked?

2. What were the key ingredients for making these collaborations successful? Ingredients can include funding and administrative mechanisms, the types of people involved, the types of questions and communications involved, culture, technology, websites, specific features of websites, etc etc.

3. What more can be done to encourage more such collaborations to happen?

I was in NYC last week giving a talk about online networking at Columbia. I mentioned that we would be launching new local hubs later this year and that inspired the creation of the NYC group, currently the fastest growing group. The admins of that group have taken the next step and organized a happy hour/meetup next week for local scientists. If you’re in NYC, please go! If you have friends in NYC, let them know about the event.

It also just so happens that the second fastest growing group on NN is the Berlin group, which coincidentally, is also organizing a Nature Network meetup next week too! So if you’re in Berlin, please go! If you know people there, let them know about it.

We at NN are really excited to see all this local activity associated and mediated by Nature Network and hope to see more.

Speaking of local events, I have been remiss in organizing the March pub night in Boston. Time flies and it’s already April. Apologies for that…I promise the next one will happen later this month.

A few of these grant winners quoted in the Nature story said that successful, productive labs should be allowed to earn as many grants as they can. One PI from MGH, Bruce Rosen, who received 8 NIH grants in 2007, was quoted in the Globe’s health blog saying that only one of his 8 grants was an individual investigator one. Others are training grants and more collaborative ones shared by other PIs. Senior PIs, he told the Globe, tend to be involved in lots of projects and centers.

I’m glad that reporters are looking deeper into where these grants are going and to whom, especially now with growing concern that young scientists unable to break into the NIH “club” are leaving academic science.

What I want to know is what percentage of all grants given out are renewals versus grants given to first-time applicants and how that has changed over time (we know that first-time applicants have a lower success rate in getting grants from the NIH than more seasoned researchers). Do those numbers exist out there? I’ll try to look around but if you’ve seen such numbers, please post a link here. If we’re seeing that a growing proportion of grants doled out are renewals, then that should be worth talking about.

I also wonder what the average number of renewals is for individual PIs. Has that number gone up or down over time?

Expect to see more discussion about this when the NIH announces changes to its peer review system this spring. We’ll see if the NIH decides to limit the number of grants each PI can receive each year.

Eva Amsen, a NN blogger, was one of the organizers and she led a mini-session called “10 things everyone should know about science.” She asked conference-goers to write down their ideas for what everyone should know about science on some bristol board.

Here are some of my favorites:

The key ingredients are intuition and imagination.
Evolution
Observations, like opinions, are based on your frame of reference.
“Theory”, “believe”, “random” and a few other words are used differently by scientists than by the general public.
Science is a human activity. Take from that what you will.
Science is based on testable hypotheses and replication.
It’s the only way to truth and understanding.
There is a lot of uncertainty in science—and that’s ok. (that was mine)

And my favorite favorite:
Science doesn’t have to be difficult, complicated, elite or engendered.

What would you write on this bristol board?

(This has already been a topic of conversation among other bloggers, including Larry Moran, Chad Orzel and Chet Raymo.)

In light of all this debate, I’ve just posted a story in NNB’s news section about an MGH researcher who’s found that pathological gambling activates the same reward region in the brain as cocaine addiction. The study suggests that compulsive gambling is an addiction, rather than just an impulse disorder as it’s currently classified today.

It describes the stories of 12 young researchers and their struggles to find funding. They talked about, for instance, how they couldn’t get grants because they had to wait at the back of the line while senior researchers got their renewals, and how they shied away from doing risky research in favor of more fundable projects.

• the average age of the first R01 grant recipient is now 43…last I heard, it was 42.
• the success rate for R01 applicants is particularly low for first-timers: 18 percent.

By the way, President Bush’s proposed 2009 budget calls for another year of flat funding for the NIH.

On a related topic, I posted yesterday about the HHMI’s approach to dealing with the problem. And Massachusetts is also chipping in with a funding program for new investigators.

Update (Mar 12): You can discuss the issues of the NIH funding crunch over in the Naturejobs careers forum.

Boston Skeptics is hosting its first event March 24. They describe themselves as: a group of critical thinkers who get together to talk, eat, drink, and be skeptical about things like homeopathy, creationism, psychics, aliens, alternative medicine, conspiracy theories, and whatever else catches our attention.

This program is designed to help junior professors cross that widening funding chasm (after the startup package runs out but before you get the first R01 grant) that NNB blogger Willy Lensch aptly called the “valley of death” in biomedical academic research. This HHMI initiative is one of a couple other fairly new ones I know of that try to help young researchers make key transitions in their careers (the NIH’s K99 “Pathway to Independence” program is another example).

Is this sort of funding mechanism a step in the right direction for young researchers? Is it enough? What more needs to be done?

In November, the National Research Council sharply criticized the NIH’s last review of the lab, saying that it failed to adequately look into worst-case scenarios of accidental release of pathogens from the lab.

The NIH press release said that the panel “may recommend scenarios to study.”

(Massachusetts’s highest court ruled in December that the state’s environmental review of the lab was also inadequate, saying that it “lacked a rational basis.”)

It’s much snazzier, shows off more of our lovely content and users, and gives a really quick guide on how to use the site.

Let me know what you think.

People were raving about a video from Biorad (the equipment supplier), which was so overflowing in cheese that I cringed. Who would have thought a PCR machine could illicit so much, er, emotion?

What are your favorite science videos? Post links to them here.

• for industry-sponsored research at universities/colleges—$250,000 per year for up to 3 years (must be matched 1:1 by industry partner)
• for “nationally prominent” faculty per year for up to 3 years (must be matched 1:1 by the research institution)
• for new investigators—$100,000 per year for up to 3 years (must be matched 1:1 by the research institution)

The bidders conference for the new investigators grants will be this Friday, Feb 29 in downtown Boston.

Deadlines can be found here

This new program is part of Gov Patrick’s $1B life sciences plan that is now being debated in the state House. Press reports have said that the bill should pass relatively unscathed pretty soon.

In time for this (or perhaps a little too late), the Globe has today an op-ed giving 10 reasons why the “biotech giveaway” is a “bad idea.” (Reminder: the plan includes $250M in tax breaks for the biotech industry) Jim Stergios, executive director of a Boston-based policy think-tank writes:

Attempting to stimulate the economy by buying jobs and subsidizing selected industries is the road to ruin. A far wiser path would be to leverage the skilled, educated workforce that is our greatest economic advantage by controlling the costs that chase jobs away from Massachusetts. That will take the hard work of reform and compromise, not more announcements about how the government is buying jobs.

Lately I’ve been giving talks about the importance of online networking for careers in science (see here for a previous post about this). We all know how networking can help you learn about opportunities and even help you get your next job. In my talks, I try to make the case that using networking websites can further expand your circle of contacts and get your name out there. We’re already seeing lots of examples of this on Nature Network.

Online networking is also being talked about more in the science press. The latest example: Naturejobs has a feature article out, rounding up a bunch of different community/networking sites for researchers, including Nature Network!

While on the subject of Naturejobs, they have launched a new careers advice forum on NN. I invite you to join it and sign up for the e-alerts, as the moderator, Paul Smaglik (former Naturejobs editor), will soon begin posting more regularly to it. He’s going to invite specialists in science careers to join the discussion.

If you’re a Nature Network fan, why not show your love by putting a NN sticker on your laptop

…or by putting on a button

or by sporting one our snazzy NN Sharpie pens (clicktop!)

To get your very own NN swag, email me with you mailing address at c.lok at boston dot nature dot com and I’ll send you some. We’ll just ask that you help us distribute some of the stuff around your campus. (Thanks Matt for the photos.)

Don Kennedy, Science’s chief editor, says that doing away with confidentiality in peer review would undermine the integrity of peer review and would go against the public interest of having a fair assessment of scientific and medical research. What do you think? Some have argued that reviewers’ reports should be made public after a specific period of time post-publication.

An NN blogger, Martin Fenner, has weighed in, saying that we should resist the temptation “to move the scientific argument from the editorial office to the courtroom” or else “the peer review process and the way we communicate science will never be the same again.”

To a very crowded room (I had to sit on the floor), Miller gave an energetic speech about the ways scientists should combat the intelligent design movement. First, they need to understand why so many Americans reject evolution. Miller said it’s because evolution to them means that humans came about by accident, randomly, and that idea is just not very acceptable.

So, Miller says, rather than deny the existence of design in nature (because ‘design’ has theological connotations), scientists need to embrace the word and concept and reclaim it as their own (without the religious overtones). Scientists should be saying that evolution isn’t an accident; it is part of nature. It happens as a result of the laws of the natural world. That, he says, should make evolution seem less random and will make it easier for scientists to communicate with religious people without alienating them right away.

Miller went on to argue how the genome, proteins and the human body have design to them. He spoke quickly and I, being on the floor, couldn’t see his slides very well, so I didn’t fully get all of those arguments. Which worried me. If Miller, who has had a lot of practice already communicating science to a general audience, couldn’t explain clearly to me how there’s design in biology, then how can we expect anyone else to make that argument convincing to the most skeptical of people? I think it would be easy to explain how evolution unfolds as a result of natural forces, but trying to show evidence of design in nature might be a tad difficult. Some might argue that this would be pandering to people who like the idea of a grand designer.

Open access: I’m sure I’m not the only one who’s getting tired of all the rhetoric, conjecture and emotion in the open access debate. Where’s the data to back up or weaken arguments on either side? This morning I heard a talk that did give some data. Phil Davis, a graduate student at Cornell (and a former librarian) talked about whether open access articles are cited and downloaded more than ones behind a subscription wall. He actually gave some data from a randomized control trial. If you can use that approach to study drugs or other medical interventions, why not open access? I thought it was clever way to cut through the OA rhetoric.

He worked with 12 journals published by the American Physiological Society to randomly assign about 1600 articles those journals were publishing to either an OA journal or a subscription based one. (Some of the APS journals were ‘converted’ to an OA model for this experiment). He then followed those papers over time, analyzing the number of clicks on the full-text HTML version, PDF downloads and citations. He even took into account possible confounding factors affecting readership, such as the number of authors (papers with long author lists get cited more) and whether the paper was publicized in a press release.

The results: OA articles (full-text) got more online views and were downloaded more as PDFs than nonOA articles, although the views increased more than PDF downloads. He also found that there were other factors that seemed to independently increase PDF downloads more: being cited in a review article, being press released, and being on the cover of the journal.

It gets more interesting: when he did the citation analysis, he found that OA articles were not cited more often 8 to 12 months post publication than non-OA articles.

What’s happening here? Davis speculated that most people who download such articles probably already have access via subscriptions and so don’t need and don’t cite OA articles. The higher jump in views among OA articles could be a result of people from the developing world and just casual browsers, he added. Davis said he was working to replicate his results in journals from other fields.

To commemorate, we’ve posted a special timeline showing how the website has grown and developed.

I wanted to throw in a few other interesting things that have happened on NN lately:

Blogs: The Nature Network bloggers forming a nice community. They recently voted on a nickname for themselves and have begun talking about organizing meetups.

Some of our bloggers have reported that by blogging on NN, they’ve gotten more and higher quality comments on their blog (from scientists) than they did when their blogs were hosted elsewhere. One person reported that he’s gotten several speaking invitations as a result of his posts. Anna Kushnir of Harvard wrote about how her experience on NN helped her get a part-time blogging job, a good thing as she is now wrapping up her PhD and looking for jobs outside of academia. And Massimo Pinto, a postdoc in Rome, says here that: “blogging on this platform is enriching me as a communicator, and is generating some constructive discussions with the readers.”

Groups/Forums: We’ve had activity in some forums really take off in membership and activity, such as Nature News and Opinion, Publishing in the New Millennium, Ask the Nature Editor and the India and Nature India groups, among many others. We hope to see more country/nationality based groups formed.

We’re also working on getting more groups to operate as online journal clubs. The Neuroscience group is taking the lead on this. The group’s moderator, Noah Gray, an editor with Nature Neuroscience and blogger on Action Potential, has gotten several scientists to post summaries of and questions about recent papers, asking for people to comment. If you’re a brain scientist, I invite you to join. If not, I invite you start up a similar online journal club for your field on NN.

I want to end on a quote from one of our users about his experience on Nature Network:

“Sometimes a brief outing to the forums takes your mind away from the proposals and paper writing. When you stroll back you may be a little inspired and a little refreshed with new ideas. Abraham Lincoln once said if he was given six hours to chop down a tree he would spend the first four hours sharpening his axe. We need to ponder what we do before we plunge ourselves into the chaos. The Network offers such opportunities for us to know what our peers are thinking and how excited or puzzled they feel about their research projects.” – Pu-Chun Ke, Assistant Professor of Biophysics, Department of Physics and Astronomy, Clemson University

Inside Higher Ed writes that Harvard stands out among other universities with similar initiatives by being more aggressive in getting professors to make their articles open-access. Professors with the FAS will need to opt out of having their articles posted online for free by filling out a waiver.

What’s not clear to me yet is what version of an article will Harvard require to be posted: Pre-peer-reviewed? Post-accepted but unedited? Fully edited? This is an important question because some journals allow only certain versions of a manuscript to be placed in public repositories (some don’t allow any versions at all to be freely posted). I checked, for example, Nature’s policy and here’s what it says:

When a manuscript is accepted for publication in an NPG journal, authors are encouraged to submit the author’s version of the accepted paper (the unedited manuscript) to PubMedCentral or other appropriate funding body’s archive, for public release six months after publication. In addition, authors are encouraged to archive this version of the manuscript in their institution’s repositories and, if they wish, on their personal websites, also six months after the original publication.

It remains to be seen what will happen if this new Harvard policy ends up not being compatible with the polices of journals. Who will budge first? Will the journals loosen their rules for fear that they won’t get submissions from Harvard researchers, who are presumably doing top work? Or will scientists, driven by their desire to publish in these journals, sign that waiver? It will be very interesting to see what happens here. Will other universities follow Harvard’s example?

My colleague, Hilary Spencer of Nature Precedings, has posted some commentary on this news in the Publishing in the New Millennium Forum. She has pretty much the same questions as I did and has given some more background on the widely varying policies of journals.

Update: The Scientist is reporting that the Harvard policy requires that papers be posted immediately after being accepted for publication. This sounds like it wouldn’t be compatible with some journals’ policies requiring that papers be posted online only a certain amount of time (6 months, in NPG’s case) after publication. The questions I raised above still stand. Will Harvard FAS researchers opt out of this policy so that they can get published in Nature and other journals incompatible with this OA requirement? Or will the journals change their policies? Will they wait to see if more universities will follow Harvard’s suit?

Update 2 (Feb 18): As Maxine has indicated below, Nature News published an article about this on Friday and says that Harvard still has to decide what the time limit is to submit papers for online posting (ie immediately or not?). And it also has to clarify what version of the paper must be posted (ie peer-reviewed or not? accepted for publication or not?). All very important questions that need to be answered to see if this new policy is compatible with the journals’ policies.

The Boston Herald is reporting today that the House and Senate will likely pass the bill in the next few weeks. The article quotes the Senate president saying that the bill will probably include incentives for not just the biotech industry but also technology and energy. This wouldn’t be a big surprise since many opponents have asked: why help out just one industry that by many measures is already doing pretty well on its own? (check out the NNB article on this very question.)

And the Globe takes a somewhat skeptical look at the potential impacts of large amounts of state funding for biological research, looking at the California stem cell windfall example. It makes a not-so-groundbreaking point that biology research takes time to yield results that the public can appreciate.

But it does try to delve into whether a funding bonanza results in a mass influx of researchers—a very good question that we should all be mindful of. James Thomson, the stem cell pioneer, has set up shop at UC Santa Barbara, according to the article, but still remains on faculty full-time at the U of Wisconsin, where he made his big discoveries. Advanced Cell Technology, the stem cell company, moved its headquarters to CA but it has more employees in Massachusetts where it got its start, the Globe says.

I did a Q&A with MGH’s Ken Chien a couple of years ago, not long after he moved from California to Boston to do stem cell research. When asked why he walked away from the promise of all that funding, he said:

One of the major attractions of Boston is the critical mass effort here in stem cell biology in general, and human embryonic stem cell biology in particular. From an outsider’s viewpoint, from a pure scientific stance, I would say that the Harvard and MIT communities combined are probably a minimum of two years ahead of everybody else in the area of human stem cell biology in the U.S…..I think the three most important ingredients in not just stem cell science, but almost any science, is people, people, and people.

My question is: does MA really need extra funding from the state to support the life sciences?

Based on the timing of the plaque’s formation, the researchers surmise that these clumps then trigger other changes in the brain that may lead to the disease. Whether plaques are a cause or an effect in Alzheimer’s has long been controversial. (From Nature News)

Along the same theme, a group of researchers from Children’s Hospital have created a zebrafish that remains transparent throughout its whole life. Zebrafish are a popular model organism because they are transparent as embryos. But as they grow into adults they become opaque. In their paper this week in Cell Stem Cell, the researchers, led by Leonard Zon, describe how they were able to watch tumors grow and metastasize in the fish.

For example, Ron Milo, a fellow in Harvard’s systems biology department told me about how he and his colleagues have created a new website called Bionumbers. Think of it as an almanac for biologists. You can look up answers to those burning questions, like:

What’s the average size of a protein in E.coli?

or

What’s the diameter of a human taste bud?

It’s a community website so you can add numbers, as long as you can back it up with a reference. Milo said this website was born out of frustration with literature searches that took a lot of time, but never produced the straight numbers he was looking for.

Then I spent some time with Andreas Mershin, an MIT postdoc, who told me about a website and program that he helps run, Molecular Frontiers, which aims to educate and excite children and teenagers about molecular science (it also organizes meetings for grownup scientists).

One of its projects is an online forum where kids can ask questions about molecules. Mershin, a postdoc, told me about how they’ll be awarding prizes to kids who ask the best questions.

The two authors of this study give plenty of qualifications on their work: without inspection of the full text, it was hard to see if proper attributions were made and if the duplications were from innocent intentions. But, they argue that this may be a growing problem and that journals and the scientific community need to better monitor and deal with the issue of plagiarism and self-plagiarism.

I posted a brief blurb about this in the Publishing in the New Millennium forum and it touched off quite an interesting discussion about whether they see this as a growing problem and whether there are legitimate reasons for an author to publish similar versions of his/her work in different places. One of the UT researchers, Errami, posted a short reply hinting that news of some fallout of their analysis (eg retractions) was on the way.

Well, here is one such development. On Friday, the Boston Globe reported that a Harvard/Beth Israel Deaconess physician/researcher was being investigated by Elsevier for allegedly duplicating in his 2004 review about half of the text from a review written by another author in 2003. The two papers were flagged in Errami’s and Garner’s analysis. The researcher, Lee Simon, was first named last week in the Dallas Morning News in its report of the Nature commentary.

I’ve received confirmation from an Elsevier spokesman that the review by Lee Simon is being retracted by the journal, Best Practice & Research Clinical Rheumatology.

But already, according to this Nature News story, there’s doubt about how accurate the sequences will be, given that the budget for it will be a mere $30 to $50 million. David Altshuler of MGH/Broad is one of the chairs of the consortium of researchers involved.

And later next week, the European Career Fair will be held at MIT (Feb 1-4). They call themselves the largest career fair in the US featuring employers based in Europe. About half of the companies are in the life science/engineering/technology sectors.

I had lunch a couple of weeks ago with one of the organizers, Wiep Klaas Smits, and he told me, to my surprise that most of the people registered to attend the fair are NOT homesick Europeans. According to the organizers’ stats, only about a third of registered attendees declare themselves to be from Europe. One third say they are American and the other third from other parts of the world.

I found that interesting. In science, the conventional thinking has been that you go TO the US (or STAY in the US) to further your career. Is the flow of traffic reversing now? Are more scientists finding Europe to be a more attractive place to work and live? Why? Is it just for the superior wine, cheese, bread? :)

Wiep Klaas has started a group here on NNB for anyone attending the career fair. Join the conversation there about why you might be interested in careers in Europe.

His work, showing that tumor growth is driven by its blood supply, touched off the development of cancer drugs that cut off tumor blood supply.

WBUR has a nice write-up of his life and achievements (correction/clarification: the write-up is from Children’s Hospital). I’ll update with links to obituaries as they come out.

I never met Dr. Folkman, but did see him give a talk once a few years ago to a very full room. If you knew him or worked with him, and if you care to, please post a comment here. What was he like?

Update (Jan 15): Stories are beginning to come out. This AP story and this blog post from the Scientist talk about how upset Folkman was when a NY Times article quoted Jim Watson saying that Folkman would ‘cure cancer’ in two years.

Update 2 (Jan. 16): The Globe today has a nice obituary of Dr. Folkman, describing him not only as a pioneering scientist who persisently pursued his his ideas about how tumor growth could be choked off by shutting down the tumor’s blood supply…even in the face of skepticism and criticism from his colleagues at the time. The article also portrays him as a loving husband and father and a mentor who trained many of today’s leading researchers.

Update 3 (January 18): The author of the 2001 book, Dr. Folkman’s War, wrote an op-ed in yesterday’s Globe, ending it by saying: “The Nobel committee at the Karolinska Institute in Stockholm moved too slowly. It doesn’t give the cherished prize posthumously.”

He’s posted two topics—commentary on two recent papers on some rather controversial topics: one about the “science” of ESP and the other about how a mutation in a transporter caused male Drosophila to court males as they would with females.

We’re inviting all those interested to have a look at the papers and then to answer some discussion questions that Noah has posted in each topic.

1. Work on an increasingly common disease whose cause remains a very controversial mystery
2. Find a genetic link that accounts for some of the cases, even if it’s just one percent of those cases
3. Collaborate with lots of people (scientists, clinicians and affected families) to collect, share, and analyze data from hundreds to thousands of patients
4. Get your work published in the New England Journal of Medicine

Newspapers and magazines (Boston Globe, NY Times, AP, Business Week, and more) are reporting the NEJM paper released yesterday describing the discovery of mutations in a section of chromosome 16 that appear to increase the risk of autism by 10 to 100 times and account for about 1 percent of cases. The senior author, Mark Daly of MGH and the Broad Institute, is part of the Autism Consortium, which is based in Boston and brings together 14 local institutions and dozens of PIs. They worked with colleagues across the US and in Iceland with Decode Genetics to analyze genotype data from 751 families affected by autism and from more than 800 people with autism.

Not to sound too cynical or anything with my ‘recipe’ and I’m certainly not implying that the researchers went out of their way to get publicity for their important work. (These articles quote scientists not involved in the project as saying how important this finding is.) But it goes to show just how hungry the public is for news about the causes of mysterious diseases, especially ones that affects children.

Glad to see that at least some of these articles have been responsible to stress that this is a result in basic science and isn’t going to lead right away to some kind of diagnostic test.

SciAm says that comments will influence the reporting, content and even point of view of the final version of the piece, which will appear in the print edition.

Nature is mentioned a fair bit in the article, including Nature Network and Connotea.

So I invite you to post your comments there.

Discussion was slow to get going, but things heated up when, over the weekend, a creationist said that life is too complex and beautiful to not have had some higher thought behind it. Oh my. I certainly couldn’t leave that point hanging. So I asked our resident evolutionary biologist, Henry Gee, an editor of Nature, to post a response, and the floodgates opened (Thanks Henry!). Take a look. Many of the commenters say that a belief in God and a subscription (not ‘belief in’) to evolution can co-exist and that science and religion shouldn’t be pitted against each other, as they are two different things.

It’s a timely discussion. The National Academies recently put out a report, “Science, Evolution and Creationism”. One of our newest bloggers, Pete Jordan, a postdoc with the NIH, has read the report and written a few comments on its strengths and weaknesses. It seems the report didn’t satisfy Pete in its discussion of how and why science and religion are separate human endeavors.

He argues that science is an oral tradition; because much biological data can’t always be standardized, biologists instead pass along valuable information through conversation. He gives an example of how he spent several weeks scouring the literature, trying to find an answer to a problem. He got his answer not through literature searches, but through a 15-minute conversation he had with two experts at a conference.

But he fears that biologists just don’t get together to talk to each other enough; here’s an excerpt:

I have found it extremely rare for anyone to take advantage of verbal information. Many scientists eschew scientific meetings as a waste of time, or are afraid of sharing their knowledge, out of concern of getting “scooped” by a competitor. I believe that open and free exchange of information is essential to drive progress in biology. Although good verbal communication skills might not be a formal criterion for career advancement, it can have a profound impact on your research. Talking with your colleagues might not be as esteemed as writing papers, but it can be just as valuable in helping everyone move their research forward.

What do you think? Do you agree that this is a problem? What can be done about it?

Previously, researchers had thought that differences in the type of bonds between the sugar molecules were important for human resistance to avian flu infection, but it turns out the shape of those molecules are important as well. An Emory scientist is quoted in this Wired story as saying: “People hadn’t really thought about the shape of the structures as being so relevant in this regard.”

According to Nature News, Sasisekharan says that an avian viral protein wouldn’t need to change much (just two or three amino-acid changes) in order to bind to our umbrella-shaped sugars. He added that testing the ability of an emerging avian flu strain to bind to these sugars could provide a sort of early warning of the virus’s ability to make a lot of people sick.

Some people were quite open about their or their colleagues’ use of these sorts of drugs. Lots of important issues were raised: regulation, long-term safety, fairness (should taking such a drug be any different as getting extra coaching or tutoring?) and efficacy (eg. just how effective are these drugs in improving cognitive performance in studies? An important question considering how many people are taking them!). One person, posting anonymously, even suggested that scientists would benefit more from the use of hallucinogenic drugs for ‘opening the mind.’

There’s also been a fair amount of chatter in the neuroscience blogosphere. On one blog is an informal poll, asking: If you could take a pill which enhanced your cognitive abilities with minimal side effects, would you?

When I checked the results today, they showed that 78 percent (43 people) responded yes.

Out of the more than 450 nominated entries, 52 were chosen by a panel of more than 30 judges; the winning posts include these from Nature Network bloggers:

Deanne Taylor, a research scientist with the Harvard School of Public Health, describes what changes need to be made to boost faculty diversity in science.

Kristin Stephan, a Tufts graduate student, discusses how difficult, but necessary, it is for PhD students in grad school to learn about careers outside of academic science.

Henry Gee, an editor with Nature, writes lovingly about his 9-year-old daughter with Asperger’s Syndrome and how having Asperger’s might help her become a good scientist.

Jennifer Rohn, a postdoc at University College London, documents in this series of four posts her return to the lab and academic science after four years as a journal editor. Required reading for anyone contemplating a career change.

Congratulations!

Thanks also to Anna Kushnir, another one of our bloggers, for being one of the judges.