Scienceblogs.com readers Meetup

If you attended the Science Blogging Conference or read what people blogged about it, or said about it in subsequent interviews, you know how much fun it is to meet your favourite bloggers in real life. You gain a new perspective, you read them more diligently, you understand them better, and you have some calamari and beer.
So, we would like all the readers of Scienceblogs.com to organize local meetups. The organizing has already started (see here, here, here, here and here for examples). Rare are the people who read only one of us – most of our readers are shared across at least a few scienceblogs. Let’s all meet in many locations around the country and the world.
How to organize? Join the Scienceblogs.com Facebook fan group and use the Wall and the Discussion Board to organize. The idea is for readers to organize this, not bloggers (we’ll just show up if we live close by). So, if you are a reader, fan, commenter – do this, see who else in the group is from your area and decide on the place, date and time and let us know.
Recent new additions to scienceblogs.com may have changed this, but I think that North Carolina, with seven SciBlings, is still in the numerical lead over any other state or country. Thus, I expect there may be quite a lot of readers here as well. Heck, there are three of us hugging the few miles of US15-501 in the middle of the Triangle so even if just Sheril, Abel and I show up, it is already quite a meetup! And if it grows big, perhaps the other four will come from the western part of the state as well (or alternatively, organize another meetup in Charlotte).
Oh, and while you are on Facebook anyway, you might just as well join the A Blog Around The Clock readers’ group, or the PLoS fan group, or just make me your friend.

Today’s carnivals

Boneyard XIV is up on Self-designed Student
Accretionary Wedge #6 is up on the Lounge of the Lab Lemming
Carnival of the Green #116 is up on The EcoLibertarian

Darwin Quotes

Charles_Darwin.jpgAs for a future life, every man must judge for himself between conflicting vague probabilities.
– Charles R. Darwin
Support The Beagle Project
Read the Beagle Project Blog
Buy the Beagle Project swag
Prepare ahead for the Darwin Bicentennial
Read Darwin for yourself.

My picks from ScienceDaily

Early Experience Affects Where Birds Breed For Life: What Happens If Habitat Changes?:

How young migratory birds choose the nesting location of their first breeding season has been something of a mystery in the bird world. But a new University of Maryland/National Zoo study of the American redstart suggests that the environmental conditions the birds face in their first year may help determine where they breed for the rest of their lives, a factor that could significantly affect the population as climate change makes their winter habitats hotter and drier.

Ancient Puzzle Solved In Fossils From Canadian Rockies, Dating To Cambrian Explosion:

Geologists at the University of Leicester have solved a puzzle found in rocks half a billion years old. Some of the most important fossil beds in the world are the Burgess Shales in the Canadian Rockies. Once an ancient sea bed, they were formed shortly after life suddenly became more complex and diverse — the so-called Cambrian explosion — and are of immense scientific interest.

Python Snakes, An Invasive Species In Florida, Could Spread To One Third Of US:

Burmese pythons–an invasive species in south Florida–could find comfortable climatic conditions in roughly a third of the United States according to new “climate maps” developed by the U.S. Geological Survey (USGS). Although other factors such as type of food available and suitable shelter also play a role, Burmese pythons and other giant constrictor snakes have shown themselves to be highly adaptable to new environments.

Small Sea Creatures May Be The ‘Canaries In The Coal Mine’ Of Climate Change:

As oceans warm and become more acidic, ocean creatures are undergoing severe stress and entire food webs are at risk, according to scientists at a press briefing this morning at the annual meeting of the American Association for the Advancement of Science in Boston.

Space Tourism To Rocket In This Century, Researchers Predict:

Seeking an out-of-this-world travel destination? Outer space will rocket into reality as “the” getaway of this century, according to researchers at the University of Delaware and the University of Rome La Sapienza. In fact, the “final frontier” could begin showing up in travel guides by 2010, they predict.

Bacteria Can Be Made To Spin Spider Silk Through Understanding Of Big Molecules:

Biological and medical research is on the threshold of a new era based on better understanding of how large organic molecules bind together and recognise each other. There is great potential for exploiting the molecular docking processes that are commonplace in all organisms to develop new drugs that act more specifically without adverse side effects, and construct novel materials by mimicking nature.

Worm Defecation Holds Clues To Widespread Cell-to-cell Communication Process:

The focus of two recent Nobel prizes, a species of roundworm has made possible another advance in the understanding of how cells talk to one another, according to a study published online Feb. 21 in the journal Current Biology. In 2002, researchers won the Nobel Prize for Medicine for work in the roundworm Caenorhabditis elegans (C. elegans) on the genetics of how cells “decide” to self-destruct, a topic now central to human cancer research. Another team won in 2006 for the discovery in C. elegans of an ancient defense mechanism against attempts by viruses to disrupt cells’ genetic machinery.

Inside The Head Of An Ape:

Do apes have imagination? How do they understand pictures? A years-long study of apes performed by cognitive scientist Tomas Persson shows, among other things, that it doesn’t take a human brain to understand pictures as being a representation. Persson’s dissertation, which is now being submitted at Lund University, is the first one in Sweden to focus entirely on the thinking of apes.

Unveiling The Underwater Ways Of The White Shark:

It’s hard to study a creature when you only catch fleeting glimpses of it. Up until recently, that was one of the big stumbling blocks for marine biologists and ecologists, but advances in electronic tracking technology have allowed them to peer farther across, and deeper under, the surface of the oceans than ever before.

Obsolete Lab Skills

You may remember a few days ago I posted a link to the list of Obsolete skills (the links were to this post, this wiki and this wiki). The growing list is certainly fun to read and check off your own skills against it. Archy adds some more.
But, what I really liked, especially since this is a science blog, was this comment by Barn Owl, suggesting we list our science-related and laboratory skills that are either useless outside of the lab or now obsolete even in a science lab.
For instance, Anna has developed strength in in the muscles used in vial opening as well as the ability to eye-ball minute volumes of liquid.
Well, I can use, if you wake me up in the middle of the night, the 1982 program called Circadia. It is to this day the best software for analysis of circadian data, but the latest Mac OS’s cannot run it as it is so old. It is Open Source now and I would love to see someone do an upgrade on it and make it more modern.
I hope I never have to do an RPA (RNase Protection Assay) again – it takes back-breaking 3-5 days to do three of those in parallel for just a few data-points. There are better techniques these days.
The way IACUCs are going these days, I doubt I will ever again be allowed to put my surgical skills to use – if you want your quail’s ovaries or pineals removed, optic nerves severed, or radiotransmitters implanted, I can do it, but only if you get the IACUC approval for it first.
Some of the old melatonin radioimmunoassays are a pain in the behind. I hope someone’s developed something simpler and more reliable lately.
Catching a runaway quail in a pitch-dark isolation room using sound only.
Changing food, water and paper in complete darkness.
Giving i/m injections into the birds’ breastmeat in complete darkness.
Taking blood samples from miniature wing-veins of quail using military infrared goggles.
OK, your turn: what are some of the lab skills that are either useless outside of the lab or so outdated to be useless in the lab today?

James McCarthy on ScienceDebate2008

Get the embeddable video clips here.

The Cool Aunt of the scienceblogging community: Interview with Janet Stemwedel

Janet Stemwedel a.k.a. Dr.Free-Ride is the blogmistress of Adventures in Ethics and Science and the Science Blogging Conference last month was her second appearance here – last year she was the Keynote Blogger-Speaker and this year she led a session on Science Blogging Ethics.
Welcome to A Blog Around The Clock. Would you, please, tell my readers a little bit more about yourself? Who are you? What is your scientific background? What is your Real Life job?
Hi Bora, thanks for having me!
I’m a middle-aged, almost mid-career academic who came from the East Coast to the San Francisco Bay Area for grad school and ended up staying. I’ve been teaching for more than half my life, parenting for going on nine years, and constantly renegotiating my relationship with the tribe of science without being able to quit it entirely.
I used to think I was going to be a chemist when I grew up — and went so far as to finish a Ph.D. in chemistry (focused on the dynamics of far-from-equilibrium chemical systems that display interesting behaviors like oscillations). But on the verge of packing up and starting a postdoc, it became clear to me that the questions that really captivated me weren’t so much questions in chemistry as questions about chemistry, and about science more generally.
Luckily, since I had double majored in chemistry and philosophy as an undergraduate, I knew that the kind of question keeping me up at night actually had a field of its own: the philosophy of science. The hard part was realizing that if I wanted to be a philosopher of science, I had to go back and do another Ph.D. There is nothing quite as surreal as defending your dissertation and then, two weeks later, sitting for the GREs.
Currently, my real life job title is Assistant Professor of Philosophy at San Jose State University. See Mom, I didn’t end up living on your couch!
What do you want to do/be when you grow up?
I’d like to be tenured. (Ask about that again at the end of May and I should know whether that aspiration was successful.)
Beyond that, I’d like to be a sort of “cool aunt” to the scientific community, especially to the people training to be scientists and trying to imagine themselves as grown-up scientists.
What do I mean by that? I’d like to give the advice and encouragement that people need to navigate the community, but that they feel awkward talking directly to their scientific “parents” about. (Don’t forget, sometimes it’s your relationship with the cool aunt that makes it possible for you to communicate better with your parents.) And I’d like to get that community of scientists talking to each other more than they seem to now about all sorts of things — like ethics, and different ways the scientific enterprise could be set up that might make life better for everyone.
Once I have that under control, I’d like to learn how to play drums.
When and how did you discover science blogs? What are some of your favorites? Have you discovered any new cool science blogs while following the Conference?
I first came to science blogs by way of philosophy blogs — I found Panda’s Thumb through the dear departed Philosophy of Biology blog, and Pharyngula through Brian Leiter’s blog. I think Bitch Ph.D. was probably where I started coming across the more personal blogs by scientists about the patterns of academic life.
There are so many great science blogs that I’d be hard pressed to come up with a list of favorites shorter than my blogroll. Some that I started reading in earnest after SBC ’08 are I Love Science, Really, The Inverse Square Blog, and Pondering Pikaia.
JanetPic.jpgHow are science bloggers different from all the other bloggers in regards to ethical behavior online (and offline).
My sense is that the science-y neighborhoods of the blogosphere show a tendency to want to back up claims with evidence, and to want to “show the work” on the inferences drawn from the evidence. This isn’t to say that only the folks blogging about science do this, mind you, but it feels like this is part of our identity as scientists or friends of science. Reality is where we live, and we think it’s a pretty nice place most of the time.
I’m not sure I could say anything sensible about offline behavior without a much larger network of informants than I have in place at present.
A couple of years ago, there were attempts to write a Bloggers Code of Ethics, which were overwhelmingly rejected by bloggers of all kinds. More recently, some suggested writing a Science-Bloggers Code of Ethics. Why is this a bad idea?
I’m deeply suspicious of the power of codes per se to influence behavior. Most professions have professional organizations whose websites proclaim a list of principles to which members of those professions are officially committed. I’m willing to bet most people who belong to those organizations couldn’t tell you what’s in their code.
More than that, I don’t know that a particular set of rules can make people ethical. It may coax some letter-of-the-law compliance, and it will encourage folks to find loopholes, but robust ethical behavior comes from people who are in touch with their own values and in an ongoing conversation with the other people in their community about the shared interests, goals, and values that define them as a community. A code may sometimes capture the shared commitments that come out of such an ongoing dialogue, but I doubt that a code can force individual buy-in to the values or to the community.
What is the goal of the Science Blogging Ethics wiki?
The hope is to have a place for a continuing dialogue about our values as community of people blogging about science (in lots of different ways).
I think we can gain a lot by being in an ongoing discussion about what practices are better ones for our various aims, which seem to range from explaining scientific theory or research results to non-experts, to talking about methodology, or career development, or teaching, or what science has to do with everyday life, or what the everyday life of a scientist looks like. We can learn from each other’s experiences, including the mistakes. And one good outcome of such a discussion might be for people blogging about science to start seeing themselves as a community.
I noticed something interesting. Whenever there is a blog-war between sciblings, once it gets really red-hot and nasty, we all start checking out your blog, waiting for you to post about it. Then, when you do, and you tell one scibling to sit in the corner for 30 minutes and the other scibling to write “I will be nice to my sciblings” a hundred times on a piece of paper, everything calms down. Where does that authority of yours come from? The Friday Sprog Blogging? We are all very hot-headed and independent folks, yet we always agree that Janet has the last word. How come?
I don’t know that I have any special “authority” — certainly, the sprogs would dispute the assertion that I do — and I’m pretty sure I never literally sent anyone to the corner or to the chalkboard.
But, I do have this thing I do where I try to understand the source of disagreements, and to figure out where the different sides in the argument are coming from. At least in spats within the community of science bloggers, it’s hardly ever the case that one side is wrong about everything — the bloggers involved are too smart, and too committed to some kind of intellectual honesty. So I generally go in trying to work out what each side is trying to get across, and why the other side isn’t getting it.
This probably comes from my philosophical training to come up with the least crazy thing your opponent could be claiming before you offer a good argument against it. Maybe there’s also a little bit of parental patience in there, too. But I’d guess that what really motivates me to try to be the voice of reason heading off blogwars in the science district of blogtopia is that I feel like I *know* a lot of the people involved well before the shouting starts. I start from the assumption that these people I know and like and respect can find some common ground, and that they’re more interested in working out how things actually are than in just winning the argument.
Obviously, this doesn’t mean there aren’t disagreements that persist. But I think we can find ways to engage each other and explore these disagreements that aren’t just shouting matches.
Is there anything that happened at this Conference – a session, something someone said or did or wrote – that will change the way you think about science communication, or something that you will take with you to your job, blog-reading and blog-writing?
The student blogging panel — especially, the discussion on that panel of advisors who take a dim view of blogging graduate students — made me think hard about what part we professorial types should play in changing the academic culture. If any time away from work is seen as an indication of insufficient commitment, that’s either going to convince budding scientists (or academics of other stripes) that they’re not allowed to have other facets of their lives, or that they have to hide them. We can do better. I hope that openly having a life beyond my research and teaching, and arguing in my tenure dossier that my blogging is a kind of engagement with the larger world that enhances my professional activities rather than undercutting them, will start to shift the expectations in a more humane direction.
It was so nice to see you and thank you for the interview.
It’s always fun to see you, Bora! I hope that one of the next times we see each other we can celebrate your defending your dissertation.
Gulp…
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Check out all the interviews in this series.

Darwin Quotes

Charles_Darwin.jpg…doing what little one can to increase the general stock of knowledge is as respectable an object of life, as one can in any likelihood pursue.
– Charles R. Darwin
Support The Beagle Project
Read the Beagle Project Blog
Buy the Beagle Project swag
Prepare ahead for the Darwin Bicentennial
Read Darwin for yourself.

Open Laboratory

Reed and I met this morning and shipped off the authors’ copies of the OpenLab 2007 to the international addresses, then packaged and addressed the US ones which I will send out on Monday.
We already got our first submission for the Open Laboratory 2008. You can get started, too – the submission form is here.

BluSci interview now online

I%20Blog%20You.JPGMico Tatalovic of Blue Sci, the Cambridge’s popular science magazine, interviewed me back in April 2007 and wrote an article on science blogging based on that interview. It came out in the Issue #9 as a PDF in October, and is finally found online on Blue Sci.

Annie Get Your Gun

Last night we went to Raleigh Memorial Auditorium and saw the opening (“student”) night of “Annie Get Your Gun”, starring Larry Gatlin, who is apparently some big name in country music, and Raleigh-born Lauren Kennedy who we last saw as Lady Of The Lake in Spamalot when we went to NYC two years ago (btw, Spamalot is coming to Raleigh in April, but the Lady will be played by someone else).
It was fun (a couple of minor glitches that they skillfully masked or played for laughs, the biggest being when Larry forgot his line in one of the songs and Lauren saved him by singing them for him without missing a beat and he recovered with the next line – some of the kids in the audience probably never knew that this was not how it was supposed to go).
Lauren has so much energy and a great presence on stage – she makes it look easy and fun. And of course, they both sing phenomenally.

Kids with ‘Dr’ in front of their names: Interview with Ryan Somma

Ryan Somma is a software developer from coastal North Carolina who blogs on Ideonexus. It’s all a blur now, but I think the Science Blogging Conference last month was his second.
Welcome to A Blog Around The Clock. Would you, please, tell my readers a little bit more about yourself? Who are you? What is your scientific background? What is your Real Life job?
Scientific Background? (Looking around nervously.) Why do you wanna know? Ummm… My father was head of the Microbiology Department at ODU, and my mother teaches Nursing there. I rebelled against them by majoring in English and smoking lots of pot… The security guards at my high school nicknamed me “Professor.” Does that count?
I fell in love with science when I experienced an iconoclasm after reading Carl Sagan’s Demon-Haunted World, which I picked up to learn why religious beliefs were silly and unsupportable, instead I learned that my belief in alien abductions was silly and unsupportable. I wanted to learn what else I was wrong about, and Science, while not “truth” with a capital-T, is the closest approximation to it. Really, my science background is immersing myself in online resources, like ScienceBlogs.
During the day I write Aviation Logistics Management Software for the Coast Guard… poorly..
You are a volunteer at The Port Discover Science Center. Can you tell us more about The Port Discover Science Center and what you do there?
Yes! The Port Discover Science Center is one-room in downtown Elizabeth City that brings daily science activities to the children of this small town, where I’ve ended up. They run on a yearly budget of less than $60k, which is amazing considering all the activities they host there.
My role has been largely one of benefactor. I’ve donated and maintained computers for the center, set up a flight simulator, provided DVDs, software, a projector, sound-system, build exhibits, etc, etc. I’ve done what I can to ensure they have a wide variety of daily exhibits. There should be little Science Centers like this all over the place. They should be like churches, building community bonds everywhere.
What do you want to do/be when you grow up?
Vice President of Cool. Duh.
Ryan%20Somma%20interview%20pic.jpgWhat is the role of Azrael in the Tragedy of the Commons?
Hmmmm… sustaining herself off her master’s scraps… subservient to a greedy and decrepit old man… flee-ridden… I think Azrael represents George Bush. He’s pretty-much the Oil Industry’s and Dick Cheney’s pet, and Gargamel does a good job of representing those interests.
Only, a pet nematode would more accurately reflect George Bush’s intelligence and invertebrate nature, don’t you think?
(Sidenote: I recieved a lot of hate mail for that article, which I’m cultivating a thick skin towards. I aspire to one day handling criticism with PZ Meyer’s sharp wit.)
When and how did you discover science blogs? What are some of your favorites? Have you discovered any new cool science blogs while following the Conference?
That’s the best part of the conference! Discovering all these new leads for information. I’ve been very impressed with the intellectual content and classical references in Thomas Levenson’s Inverse Square Blog as well as Eric Roston’s Carbon Nation, and the Bibliophilism of John Dupuis’ Confessions of a Science Librarian. It’s so cool to find so many like-minded intellectuals.
Meeting you kids in person gave me deeper insight and appreciation of blogs I was familiar with, but not always reading intensely. The sessions with Dr Rundkvist’s Aardvarchaeology gave me a new outlook on his blog’s voice, while the session with Dr. Stemwedel of Adventures in Ethics and Science gave me a better appreciation for one of her blog’s main subjects.
I think Science Blogs has been awesome. You guys have made scientists accessible, while maintaining your oftentimes-erudite-incomprehensibility. On my blog I started collecting Science Proponents in my FaceBook friends, like you, Bora, which is like collecting sports cards, only scientists.
Your blog posts are quite provocative, yet in person you seem quite shy. Now that you have met a bunch of bloggers in person, do they behave differently than what you could guess from their online personas? Is this ability for people to experiment and be who they want to be online a positive transformative experience that, for instance, teenagers should experience as a part of growing up?
Figuring out who you are online is a fantastic experience. I was figuring it out in Elementary School on the BBSes (before the Webbernets) using my Commodore 64. Online, you can be whatever you want to be in a world of pure ideas. My only concern for teens is that they should do it anonymously. There’s more freedom that way, and you don’t have to worry about something stupid you posted in the heat of the moment haunting you years later when you’ve grown out of it.
The biggest thing that really got me meeting all these Science Blogging heroes was that so many of them are kids with “Dr” in front of their names. I thought people with doctorates were supposed to be old and feeble and smoke pipes and wear cardigans!!! How dare you all be human?!?! : )
It was so nice to see you and thank you for the interview.
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Check out all the interviews in this series.

Darwin Quotes

Charles_Darwin.jpgThe fact of evolution is the backbone of biology, and biology is thus in the peculiar position of being a science founded on an improved theory, is it then a science or faith?
– Charles R. Darwin
Support The Beagle Project
Read the Beagle Project Blog
Buy the Beagle Project swag
Prepare ahead for the Darwin Bicentennial
Read Darwin for yourself.

Totally obligatory reading of the day!

Chez describes how and why CNN fired him for blogging and then piles on!
Spread the word. The old media needs to learn to respect the people formerly known as audience.

Excellent, excellent!

This blog has just been notified that a bank in Sierra Leone has…nope, no millions of dollars in spam-money. Something much better – Maryannaville gave us the Excellent Blogger Award! Thank you!
Recepients of this award can proudly place this image on their side-bars:
excellentblog.jpg
And now, I need to pick ten recipients. Ten!? Per minute? Yikes – this is hard. Let’s just assume that all of my SciBlings are Excellent by definition and take a look at some good ones outside of The Borg:
Malaria, Bedbugs, Sea Lice, and Sunsets
The Beagle Project Blog
Sandwalk
The INFO Project Blog
The Inverse Square Blog
Mind the Gap
Creek Running North
Pondering Pikaia
Archy
The Natural Patriot

The Warlord in the Library: Interview with John Dupuis

John Dupuis has been writing Confessions of a Science Librarian since the time blogging software was really physically soft, being made of clay and shaped like a tablet. We finally got to meet face-to-face at the Science Blogging Conference last month – a meeting long overdue until then.
Welcome to A Blog Around The Clock. This is going to be an interesting reversal – it is usually you who gets to ask the questions in blog interviews. Would you, please, tell my readers a little bit more about yourself? Who are you? What is your background?
Yes, it is a bit of a reversal. But I’m not crazy enough to try and interview 40 people in 40 days, more like one every other month or so. And don’t worry, Bora, I will get around to returning the favour and interviewing you!
As for me, I’m currently the Head of the Steacie Science & Engineering Library at York University in Toronto, Ontario, Canada. I’ve been at York since August 2000. However, like with so many librarians, this is my second career. My first career was as a software developer for a large multinational insurance broker, something I did for over 12 years. That was in Montreal, where I was born. I also have a undergraduate degree in Computer Science from Concordia University. Ultimately, I noticed that the thing I liked best about the software developer job was helping people with their information needs, to find the stuff they need to make decisions in their jobs. So, when various takeover and downsizing exercises began to wear me down a bit, I had a chance to really think about what I wanted to do: get a new job in the same industry or change careers entirely.
After some deep thought, I decided that it was time for a career change. Having some family and close friends already in library biz, it seemed like a natural progression for me. So, it was back to school for a Library and Information Science degree at McGill; while there I worked at the McGill Physical Sciences & Engineering Library for a practicum placement and got bitten by the science librarian bug. It was a great place to work with a passionate, commited staff
dedicated to helping faculty and students. Luckily, when I graduated a job came open at York in the science library and the rest, as they say, is history. Okay, the process of relocating from Montreal to Toronto was a bit more complicated than that but there are some things I’ll only tell over beer in a hotel bar.
I’ve been writing my blog, Confessions of a Science Librarian, since October 2002. It really started as a bit of a lark. One day I was sitting in my office wondering what these new-fangled blogs were all about. Something strange possessed me and I went to the Blogger site and started my own blog. I wish I could take credit for the title, but I have to admit it was suggested to me by my friend and York colleague Patti Ryan. I don’t think I ever expected it to have the long life that it’s had — 5.5 years is quite ancient by blog standards. It’s made me a lot of friends and opened a few doors that might otherwise stayed closed. I feel priveledged to be part of two wonderful blogging communities, science blogs and library blogs.
What is your Real Life job? What does it mean to be a Science Librarian?
My real life job is helping people. The people I help are mostly undergraduate students and I help them mostly with how to find scholarly, peer reviewed resources in science and engineering. (Okay, I also help them to find the bathroom and clear paper jams in the photocopier.) I sit at our Help Desk answering questions, I buy books and decide what journals and databases to subscribe to, I advocate for Open Access resources, I give Literature Search Skills sessions in science and engineering classrooms, I sit on committees and go to meetings. I try not to shush rowdy students too often, but my library is pretty small and we get complaints if it gets too noisy. Yes, the modern student still appreciates a bit of peace and quiet.
The great thing is that we librarians at York have faculty status so I also have a form of tenure and get to take sabbaticals every seventh year. I just came back from my first last August.
And I think a lot about what it will mean to be a science librarian in the future. But more on that in a couple of questions.
What do you want to do/be when you grow up?
Well, when I was a little kid, I wanted to be Jean Beliveau. And then a little later I wanted to join The Legion of Super-Heroes or perhaps become The Warlord. Somehow those desires morphed into programming and libraries. What would the future hold, in the perfect world? I’ve always dreamed of having one of those big, cluttered, cozy, serendipitous used bookstores, just hanging out with others that love books, science, science fiction, mysteries, comics, and all the rest. However, I’m not too sure what kind of future those venerable institutions have these days, so I’ll probably have to come up with something else for my retirement.
Internet has turned the job of a librarian upside down. What does that mean specifically for science librarians?
The future of my particular profession is an issue that has really obsessed me over the last couple of years. I’ve written about it extensively on my blog and I’ve even given a presentation on it at a recent conference. Whipping through those conference slides is probably the best way to get an overview of what my current thinking is.
In fact, the more I think about it, the less I seem to have a grasp about what the future brings. There are big challenges ahead for academic libraries. How do you get your physical layout just right, the balance between computer workstations, relaxing comfy chairs with coffee, group study rooms, informal collaborative spaces and, perhaps the thing that gets lost in the shuffle, quiet space for study and contemplation.
The other question that really obsesses me is what’s worth paying for? We libraries have pretty significant budgets, mostly dedicated to journal and database subscriptions. Ultimately, what do we want to be spending this money on? For sure, more people to embed in labs and research groups, like Peter Murray-Rust suggests. People to build a compelling web presence, to make the stuff we buy more visible on the free web (we call this “discovery at the network level”), people to work with faculty on teaching students about scholarly communication. But what about stuff? Surely, we won’t be buying a lot of paper books in the future but products like Morgan & Claypool’s Synthesis, Knovel ebooks and O’Reilly’s Safari are fantastic products, well worth paying for. It’s no coincidence that I’ve interviewed people from all three of those companies: Mike Morgan, Sasha Gurke) and CJ Rayhill. I want to understand what makes them tick and how they’re going to adapt and change in the future.
But how to let people know we have all those great products and how much time and effort they can save students and researchers? It seems to me that outreach, liaison and marketing are huge parts of what a librarian has to do these days.
Other things probably worth paying for are online journal backfiles like Nature back to the first issue. Now that’s expensive, but probably worth every penny. There are also a lot of datasets and other databases that are proprietary and well worth paying for. Are abstracting and indexing databases like Web of Science or INSPEC still worth paying for? Just barely, but that might change in the future. How about SciFinder Scholar? Sure, they add a lot of value to the data they use with cool structure search and the like.
And look at what’s happening in the High Energy Physics field with the SCOAP3 project! Imagine a world where libraries could band together to pay publishers to make their journals all Open Access. It’s almost a utopian dream.
So, as the information landscape continues to get more and more complicated, the life of a science librarian hurtles on into the future surrounded by uncertainty but still finding ways to contribute to the scientific enterprise and make a difference in the lives of students and researchers.
dupuis1colour.jpg
In discussions of Open Access on science blogs, at meetings, between scientists and publishers, most people talk about Gold, while librarians appear to prefer Green approach to Open Access. Can you explain to my readers what is the difference between the two and if you could speculate why people with different backgrounds may prefer one or the other?
First, Definitions. And I have to admit that being colour-challenged (see below), I tend to have a hard time remembering stuff associated with colours anyway. Green Open Access is promoting OA via encouraging authors to self-archive a version of their acticles in some sort of Open Access venue, whether it be their own web page, an Institutional Repository or some sort of disciplinary repository (such as the physics arxiv). Here Open Access to scholarship isn’t dependant on the whims of the publishers, but on the intentions of the authors. And this is pretty important because not all fields have access to a wide range of OA journals or even disciplinary repositories. Of course, authors do need to respect the copyright rules of the publishers; Sherpa RoMEO is a good source for the various rules used by different journals and publishers.
Gold Open Access is publishing in Open Access journals. This is obviously the best way to go, as all the articles published in OA journals are free to the world. But, like I said, some disciplines are poorly served here. Most of the humanities and social sciences and pretty well all the engineering fields, for example. Although, even some of these areas are seeing improvement.
As for librarians vs the rest, I have to admit I’ve never really thought about it this way. I guess librarians see Green as something we can have a more direct role in implementing and promoting, although many libraries now host Open Access journals on their own servers (York’s hosted journals are here, although they’re not all OA). I think librarians are also maybe somewhat resigned to the fact that it’ll still be quite some time before we see a majority of all scholarly articles published in OA journals and in the meantime Green OA is a good way to get stuff out there. Computer Science, for example, is a field where maybe 80-90% of recent articles are posted on the authors’ web pages. On the other hand, in fields that don’t already have a strong tradition in Green OA, it’s almost impossible to get people to post their articles in, say, Institutional Repositories.
Realistically, I think it’ll be at least 5 to maybe 10 years before we see a widely dispersed OA tipping point, and a variety of publishing business models will still exist beyond that point. I hope I’m wrong, but I think my New York Giants were a better bet to win the Super Bowl.
As for researchers, well, read Peter Suber’s Trends Favoring Open Access, I think he makes a good point on item #29:

Researchers themselves control the rate of progress toward OA, but after all these years most of them are still oblivious to its existence and benefits. As I’ve noted above, there is a trend toward greater familiarity and understanding. But there is also a longstanding counter-trend of impatience with anything that distracts attention from research. This preoccupation is generally admirable and makes researchers good at what they do. But even from the narrow perspective of what advances research, it is having perverse consequences and limiting the audience, impact, and utility of the research on which scholars are so single-mindedly focused.

I think the situation is more complex than an either/or with librarians and researchers working in different directions and more of a situation where if we all work together we can make more progress.
If Jorge Luis Borges lived today and was Internet-savvy, how do you think he would envision and describe the Library of Babel? Something like Gordon R. Dickson’s The Final Encyclopedia or more like Vernor Vinge’s Libraeorome Project in The Rainbows End? What is your own vision?
Good question. Kind of a cross between YouTube and Wikipedia? With half the shelves filled with porn, a quarter with news on Britney Spears, 12.5% with creationism and woo, 6.25% with racist sites, 3.125% with pirated music, 1.5625% with videos of teenagers lip-syncing pop songs and the rest with something useful.
My own vision? You know that old Star Trek episode where Spock goes back in time and hooks up with a cave woman (All Our Yesterdays)? They pass through a kind of library-like portal into the past. That’s where I’d like to work!
If you could tell scitech faculty and students one thing about your job, what would it be.
Basically, I’m here to help you.
For faculty, I would say, “let my colleagues and me help you teach your students about the literature of science, where it is, how it’s created and how to find it.” There’s a bit of a vacuum these days. So often it seems to me that faculty members just assume that new grad students (for example) know how to find the good stuff, but they don’t. Interestingly, it’s often the newest faculty members that are the most open to collaborating with librarians to teach students about these things. We’ve made a lot of inroads at York the last few years, collaborating with science and engineering faculty to help students learn about finding scholarly resources. Believe it or not, I even have a blog where I host pages for the courses I help with! (http://www.yorku.ca/yul/cse/) Take a look and you can see some of the kinds of things I talk about. It’s been quite successful with students and faculty seem to like it too. Some days I’ve had as many as 5 or 6 messages or chat sessions with students using the Meebo plugin.
For students, I’d say, “Don’t be shy!” I’d like to tell them that your librarian is your best friend.
For grad students, you may not believe it, you may be getting by just fine, but especially at the beginning of your career we can really help. There may be things your supervisor assumes you know about, assumes you understand, assumes you know how to find. There’s nothing wrong with not knowing. Every year I get the new Computer Science grad students at York for an hour as part of their orientation and that’s what we talk about. What’s a journal, what’s a conference, what’s the best and easiest way to find the peer reviewed stuff your profs expect you to find. And, while we’re at it, what’s peer review, the invisible college, all that stuff. They appreciate it and the faculty appreciate it too.
And the same kind of message for undergrads: Don’t be shy. Come to the reference desk, chat with me on Meebo or send me an email or a message on FaceBook. When your prof asks you to find 3 peer reviewed articles on recycling asphalt, I can connect you with some full text online pretty fast.
When and how did you discover science blogs? What are some of your favourites? Have you discovered any new cool science blogs while at the Conference?
Well, I actually discovered library blogs first. I was reading some before I started my blog, like EngLib, STLQ, LISNews and (Library Stuff and a few others. I think the first science blog I started reading was See Jane Compute, and probably Chris Leonard’s dear departed Computing Chris blog when he was at Elsevier (My recent interview with Chris, now at PhysMath Central). I don’t think I got into science blogs in a big way until the first iteration of ScienceBlogs came online a couple of years ago. It seems to me that a big part of my job is to understand how science and scientists tick and science blogs are a really important part of that for me.
As for favourites, I don’t think I need to plug any of the ScienceBlogs stable here! In any case, the ones I follow the closest are in computer science and software development:
See Jane Compute by Jane (Whom I also interviewed)
Adventures in Applied Math by Rebecca
Knowing and Doing by Eugene Wallingford
Computational Complexity by Lance Fortnow and Bill Gasarch
Coding Horror by Jeff Atwood
Joel on Software by Joel Spolsky
The Yourdon Report by Ed Yourdon
At the conference itself, a couple of the really interesting new ones I discovered are The Inverse Square Blog by Tom Levenson and Science and Religion News by Salman Hameed. Tom’s getting mentioned in a lot of these interviews — I think he owes us all a beer at the next conference for all the free publicity.
Of course, my newest favourite is the blog my 15-year-old son has started for a school project: Space Exploration and Us! If he keeps it up, maybe I’ll bring him to the conference next year.
Is there anything that happened at the Conference – a session, something someone said or did or wrote, a new friendship – that will change the way you think about science communication, or something that you will take with you to your job, blog-reading and blog-writing?
A couple of things really stood out for me. The first was the incredible sense of community among the bloggers. Everybody was so open and friendly and willing to talk about just about anything, at the restaurant, the conference and at the hotel bar. For example, did you know that Bill Hooker and I share red-green colour blindness? And talking about community, believe it or not I was chatting with a fellow science blogger right up until the very minute I boarded my plane for Toronto! That would be Deepak Singh, who was stuck at the airport at the same time waiting for his flight. The other thing that stood out was a sense of possibilities, that with enough ingenuity and elbow grease, we could use blogs for just about anything. The great discussions in David Warlick’s session were genuinely inspirational. Hearing about what Salman Hameed is doing with blogs in his Science & Religion course was great, and then getting to sit down and talk to him about it in depth was even better.
It was so nice to finally meet you and thank you for the interview.
Thanks for the opportunity to unleash my geeky librarian soul on the world. Oh yeah, there are two of my blog interviews that I didn’t plug yet: Timo Hannay of Nature and Richard Akerman of CISTI. Both great interviews!
============================
Check out all the interviews in this series.

Today’s carnivals

I and the Bird #69 is up on Living the Scientific Life (Scientist, Interrupted)
Change of Shift Volume Two, Number Seventeen, Murphy’s Law is up on Crzegrl.net
Friday Ark #179 is up on Modulator

Olduvai George on NPR

I was lucky to be in the car at the right time this morning to catch a story about Mastodons in Manhattan: A Botanical Puzzle, i.e., why honey locust trees in NYCity have long thorns – an interesting story (click on the link and click on “Listen Now”) which, among others, features our blog-friend Carl Buell.

Darwin Quotes

Charles_Darwin.jpgThe very essence of instinct is that it’s followed independently of reason.
– Charles R. Darwin
Support The Beagle Project
Read the Beagle Project Blog
Buy the Beagle Project swag
Prepare ahead for the Darwin Bicentennial
Read Darwin for yourself.

Lessig for Congress!

Lawrence Lessig is running for Congress and blogging about it. It would be sooooo nice to have him elected. Join the Facebook group and donate.

Discovering scholarly information and data

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

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

The miniLegends mentoring program – using blogs in the classroom.

Wow! Al Upton teaches kids aged 8 and 9 and he is teaching them how to run their own blogs. Each young blogger also gets an adult mentor and you can sign up to be a mentor if you want. Sue Waters, who provides some good tips on classroom blogging, provides more detail about Upton’s work and points to two of his good posts: Class blogs – management, moderation and protection and Class blogs – personalise your blog, a sequence of settings, which are full of good information and advice for any age students.

The miniLegends mentoring program – using blogs in the classroom.

Wow! Al Upton teaches kids aged 8 and 9 and he is teaching them how to run their own blogs. Each young blogger also gets an adult mentor and you can sign up to be a mentor if you want. Sue Waters, who provides some good tips on classroom blogging, provides more detail about Upton’s work and points to two of his good posts: Class blogs – management, moderation and protection and Class blogs – personalise your blog, a sequence of settings, which are full of good information and advice for any age students.

The Parenting Beyond Belief seminar in Raleigh

Seminar on Secular Parenting Coming to Raleigh, March 15
Presented by Dale McGowan
Editor/co-author, Parenting Beyond Belief: On Raising Ethical, Caring Kids Without Religion
* How does moral development really work?
* My mother-in-law wants our kids baptized. How can I respond without causing a rift?
* How can I ease my son’s fears about death without pretending there’s an afterlife?
* How can kids learn about religion without being indoctrinated into religion?
Over nine million parents in the U.S. are raising children without religion. The Parenting Beyond Belief seminar, a unique, interactive half-day workshop with author and educator Dale McGowan, offers encouragement and practical solutions for secular parenting in a religious world. Based on the freethinking philosophy of the book Newsweek called “a compelling read,” the Parenting Beyond Belief seminar is empowering secular parents across the country to raise ethical, caring, confident kids without religion.
Participants will learn effective ways to:
* Encourage religious literacy without indoctrination;
* Help kids interact productively with a religious world;
* Help kids develop active moral reasoning;
* Weigh church-state issues in the public sphere;
* Address sensitive issues constructively with religious relatives using the principles of nonviolent communication;
* Help children develop a healthy understanding of death and a joyful love of life;
* Build a family atmosphere of fearless questioning and boundless wonder;
* …and much more.
————————————————
Location: Unitarian Universalist Fellowship of Raleigh
Date/Time: Sat. March 15, 9:00am-12:30pm
Registration is $40 per person or $60 per couple
Registration and additional information at:
http://www.parentingbeyondbelief.com/sem_raleigh.htm

Dude liveblogs own vasectomy

Internets are interesting places. One finds all sorts of strange things people post on there. But I hope that Abel’s vasectomy liveblogging will make many more men realize that the operation is quick, easy and painless. Perhaps more guys will elect to do it due to reading this post.

My picks from ScienceDaily

Saving The Rainforest With … Toys?:

Villagers in tiny communities including Guayabo, Sawacito and Mahor, in the rainforest of northeastern Honduras, used to take part in the rampant illegal trade in mahogany, but recently they have formed a cooperative and learned to harvest the prized wood in sustainable ways. Now, they mostly use trees that have fallen naturally or harvest them in a sustainable way from around the fringes of the nearby Rio Platano Biosphere Reserve, and remove planks from the forest, first on their backs, then on muleback to avoid the disruption caused by heavy machinery.

Can Exposure To Intense Underwater Sound Result In Death Of Whales?:

NOAA Fisheries Service is looking at how marine mammals react to underwater sound. Increasing evidence suggests that exposure to intense underwater sound in some settings may cause certain marine mammals to strand and ultimately die. Some of these strandings are associated with mid-frequency active (MFA) military sonar, and most have involved beaked whales; the dominant species is Cuvier’s beaked whale (Ziphius cavirostris), but the genus (Mesoplodon) has also been involved.

Mysterious Sea Creatures Found In Antarctic Waters:

The return of the last of three Antarctic marine science research vessels marks the culmination of one of Australia’s most ambitious International Polar Year projects, a census of life in the icy Southern Ocean known as the Collaborative East Antarctic Marine Census (CEAMARC). Australia’s Aurora Australis and collaborating vessels L’Astrolabe (France) and Umitaka Maru (Japan) have returned from the Southern Ocean, their decks overflowing with a vast array of ocean life including a number of previously unknown species collected from the cold waters near the East Antarctic land mass.

No Easy Answers In Evolution Of Human Language:

The evolution of human speech was far more complex than is implied by some recent attempts to link it to a specific gene, says Robert Berwick, professor of computational linguistics at MIT. Berwick will describe his ideas about language in a session at the annual meeting of the American Association for the Advancement of Science on Feb. 17. The session is called “Mind of a Toolmaker,” and explores the use of evolutionary research in understanding human abilities.

Is That Sea Otter Stealing Your Lunch — Or Making It?:

Hunted to near extinction, sea otters are making a steady comeback along the Pacific coast. Their reintroduction, however, is expected to reduce the numbers of several key species of commercially valuable shellfish dramatically, such as sea urchins and geoducks.

Like Owner, Like Dog: One Third Of US Dogs Are Obese, Cats Also Suffer:

Obesity in pets mirrors that of humans, as do the reasons — decreased physical activity, age, and an increased caloric intake, even genetic predisposition. Like humans, there are also many health problems associated with being obese, such as diabetes mellitus.

Congratulations to the good people of Greensboro

Greensboro is the only North Carolina town on the ‘Popular Science’ list of the America’s 50 Greenest Cities. We still have a lot of work ahead of us until we catch up with the West Coast.
(Hat-tip)

Blogrolling for Today

Women’s Bioethics Blog


InnoBlogger


Bench Marks


Synthesis


Urban Science Adventures!


Diary of a phd student

The Future is Here and it is Bright: Interview with Anne-Marie Hodge

I discovered Pondering Pikaia less than a year ago and it has immediately become one of my favourite daily reads. Thus, I was very happy that Anne-Marie Hodge could come to the Science Blogging Conference last month so she could meet with all the other science bloggers in person.
Welcome to A Blog Around The Clock. Would you, please, tell my readers a little bit more about yourself? Who are you? What is your background? What is your Real Life job?
Thanks, Bora, I feel really honored to be an interviewee! Let’s see, who am I…I grew up in a military family, so I moved around quite a bit and don’t really have a home town. My parents are originally from Tennessee, though, and we generally think of ourselves as being from the south. My Real Life job is currently “student,” although I prefer to think of myself as a zoologist-in-training. I’m an undergrad, in my junior year, majoring in Zoology/Conservation and Biodiversity and minoring in Anthropology. I work as a research assistant on various projects in the biology department, and I earn grocery money tutoring, mostly genetics but other random biology classes also.
For a long time I actually planned on pursuing a law career, but after I took AP Biology in high school I realized that I definitely belong in science. I haven’t looked back since. I started college as a pre-vet major (actually Zoology/Pre-Vet, my school has five or six tracks in Zoology), but I had some opportunities to do field research and realized that the questions I am most interested in answering are more related to ecology, conservation, etc than to medicine, and I switched my Zoology concentration from Pre-Vet to Conservation and Biodiversity, and added an Anthropology minor. One thing about conservation that often gets overlooked is how people-oriented any policy has got to be. I think studying anthro has definitely helped me in how I think about different problems facing biodiversity. You can know your organism/ecosystem inside out and have an amazing management plan, but if you aren’t effective at understanding and working with the local people you’re never going to maximize your potential for success.
So that is my background, what else…I have a dog, Charlie. He outsmarts me on a daily basis, but that’s one of the fun things about owning German shepherds, they keep you on your toes! He was actually a rescue case, he was severely abused by his previous owner. It has taken a lot of work and time but he’s made a total 180 since I first got him. We like to hike, and I rock climb when I have time, although time is pretty hard to come by these days: I am carrying 18 hours of classes in addition to work and being an officer in a couple of organizations, I’m still trying to figure out how to squeeze more than 24 hours into a day. My favorite activity outside of class is working on projects (volunteer clean-ups, educational outreach, monthly speakers, etc) with my school’s chapter of Society for Conservation Biology. I started the chapter here last year and we’ve been growing steadily. It’s been a lot of work getting it off the ground, but I am really happy with how it is turning out!
What do you want to do/be when you grow up?
After grad school I plan on trying to find a position as a faculty member at a university, so I can continue to do field research while also doing my part to help train the next generation of biologists. I can see myself working for a conservation organization for a few years right after grad school if the opportunity arises, but my ultimate plan is to settle in to a life in academia. I’m interested in doing research on the behavioral ecology and population dynamics of carnivores, especially canids, and how those patterns can be used to more effectively manage populations to prevent declines/extinctions.
I have always loved writing, and I feel pretty strongly about the importance of promoting science awareness, so I also plan to continue the habit of writing about science as a side project, either in blog form or otherwise in the future.
When and how did you discover science blogs? What are some of your favourites? Have you discovered any new cool science blogs while at the Conference?
My story is similar to Brian’s answer in his interview: I was a Pharyngula reader originally, and he was my gateway drug to the blogosphere. I followed him when he joined SB and discovered a whole world of fascinating science bloggers. The community has definitely grown since I first started reading!
It’s very hard to pick favorites, some of the ones most related to my own interests (zoology and evolution) are Laelaps, Tetrapod Zoology, Evolving Thoughts, Catalogue of Organisms, and Gene Expression, but I really enjoy reading posts from other fields as well. Since I’m hoping to have a job as a professor someday, I always enjoy reading Adventures in Ethics and Science, On Being a Scientist and a Woman, and Female Science Professor. Right now my perspective is from the student side of university life, but I am always very interested in reading tales from the other side of the lecture podium.
SBC%20Saturday%20017.jpgYour blog is quite new, yet your series on Science of Harry Potter was very popular and a post of yours won its entry into the Open Laboratory 2007. Did this fast success take you by surprise? Can you explain it?
I first started my blog a little over two years ago, just as a place to mention science news stories I found interesting, and in the beginning stages entries were pretty sporadic. This past summer I really increased my posting activity, which is when I began to start making connections and getting more notice. The Harry Potter Science series was definitely an attention-grabber, and I think that’s when I started to really accumulate some links and become more known (thanks in great part to Bora’s enthusiasm about the series!).
I was surprised at how fast my readership grew once it finally did start to increase. I think that all bloggers should read Malcolm Gladwell’s The Tipping Point. He discusses how big shifts in success or recognition can result from meeting just a few of the right people, “hubs” that can bring notice to you on a much wider scale. My blog was already beginning to increase its readership when I read that book, but if I’d read it sooner I think I would have been smarter about finding more outlets for promoting my blog in its early days (carnivals, more linkbacks, more comments on other blogs, etc).
You often write about the topics related to the classes you take at any given moment. Are you using your blog as a “learning tool” in a sense? Grappling with new knowledge, simplifying its complexity, and clarifying it to yourself by putting it in writing?
I do sometimes get material for posts from classes, usually when I find a case study or example especially interesting and want to research it further. This semester I’m taking fewer zoology classes than I did last fall, so there has been less of that (plus I’ve had less time for posting in general this spring!). But yes, writing a blog post based on course material does definitely help me to master the material better, because I do have to reorganize and resynthetise the information in order to create my own narrative. Also, I always look up extra information and often the post snowballs quite a bit because the farther I get into the details, the more fascinated I become.
I make an effort not to turn Pondering Pikaia into a “this is what I learned in school today” series, but making occasional posts that were inspired by class lectures definitely has benefits. On more than one occasion I have taken exams that featured essay questions on an exact topic that I posted about! The dicyemida story, from Invertebrate Biodiversity, and the two gynogenesis and a hybridogenesis posts, from Vertebrate Biodiversity, are all examples of this. That ended up working out great for me: I nailed the essay questions because I had already looked up a lot of supporting information and composed a written explanation of the topics.
At your session (Student Blogging) you mentioned that you have been contacted by potential graduate advisors? Why do you think they are interested in taking you in as a graduate student? Do you think this reversal of roles (they are knocking on your door instead of you knocking on theirs) is something we will see more often in general, or is this the particular case of the openness of the ecological community, or is it something about the way you write on your blog?
A couple of professors have dropped me notes in comments or e-mails. None have made official offers, usually it is just a brief message saying that I appear to have ideas and interests that could fit into their research programs, and to drop them an e-mail when I am shopping around for schools. This has definitely been exciting and a little intimidating! I always assume that *everyone* reads anything that I post, so I am not nervous about what anyone might find in the content of my blog, but I do sometimes fear that people with misconceptions about blogs in general might be turned off if they find out an applicant is a blogger. Having some positive feedback from Real Live Professors has eased my mind about this a little.
I do think that the internet is changing the way applications and recruitment are handled. I’m definitely a member of the “Facebook generation,” and among my peers it’s pretty much taken for granted that everyone has some presence on the internet, whether it’s Facebook, Myspace, a blog, a LiveJournal, or any other of the millions of personal accounts/pages people can accumulate. This makes it much easier to check people out when they apply, which is something to be aware of (keep your drunken party pictures to yourself!). That may hurt some people if they’re irresponsible about how they portray themselves, but having the chance to represent yourself and your career goals to the public also increases the chance that someone will come across your information and become interested in you. So I think that everyone involved can benefit from the new dynamics, professors have a chance to get MUCH more information on applicants than they could in the past, and students/job-seekers have a much higher visibility and many more ways to communicate their qualifications, provided they’re smart about keeping their content professional.
Is there anything that happened at the Conference – a session, something someone said or did or wrote, a new friendship – that will change the way you think about science communication, or something that you will take with you to your job, blog-reading and blog-writing?
One thing that has been an issue for me in the past is a slight inferiority complex. I am extremely aware that I am younger and have less formal education than most of the other science bloggers and blog readers. I always worry about not being taken seriously, that people will assume my opinions are naive (and thus not take the time to really read them) or dismiss me as just a silly college kid. Meeting everyone at the conference, though, definitely helped to assuage those fears. Everyone was extremely friendly, and I was definitely made to feel like “one of the crowd,” I had a great time and came back feeling more like a peer in the blogging community.
As far as topics that were covered at the conference, I thought the sessions about open access issues were very important, especially the one about how to make science literature more available in developing nations. I am so glad that PLoS has taken off recently. This semester I’ve tried to do my part in the open access movement by blogging more papers from open-access sources and also making a point of using PLoS for class assignments, and a couple of my professors have been very excited to learn about the site. They’ve made announcements about PLoS in class, hopefully it will help the upcoming generation of scientists to see open access as more of the norm. Like I mentioned above, it’s pretty much taken for granted that we all have information free to the public via online memberships and accounts, I hope that in the future open access science will become the default instead of an exception.
Let’s see, other pivotal conference experiences…I managed to get my picture taken with Professor Steve Steve. At that moment, my entire trip became a success. 😉
One last slightly random note, I know the bad weather made travel a little stressful that weekend, but I have been living in the southeast for a long time now and it was the first time I had seen a single flake of snow in over four years, it was a big deal! Here in Alabama, I kid you not, I have literally seen people taking pictures of frosty windshields because freezes are such novelty.
It was so nice to finally meet you and thank you for the interview.
Thank you, I really appreciate the opportunity!
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Check out all the interviews in this series.

Bush promises $350 million for Neglected Tropical Diseases

World Health Organization announced a $350 million initiative as a five-year plan to control seven major tropical diseases in Africa:

Statement by WHO Director-General Dr Margaret Chan
I warmly welcome the initiative, announced today by United States President George W. Bush, to vastly increase funding for the integrated treatment of seven of the most important neglected tropical diseases: lymphatic filariasis, schistosomiasis, blinding trachoma, onchocerciasis, and three soil-transmitted helminthiases. These are blinding, deforming, and debilitating diseases that affect the poorest of the poor. An intensified attack on these diseases delivers a blow against the poverty of millions of people.
I further welcome the ambition behind this enhanced commitment: to reduce dramatically and eventually control and eliminate diseases that have caused misery and sapped productivity since antiquity. The time is ripe for ambitious initiatives like the one announced today.
WHO and its multiple partners, including USAID, have established a firm foundation for moving forward with unprecedented speed – and the best-yet prospects for success. Highly effective drugs are available, and many are being donated by industry in large quantities. Strategies for integrated delivery have been devised, streamlining operational requirements and reducing costs. Moreover, the drugs are safe and simple to administer and all at-risk populations can be treated – an approach to mass prevention similar to that of childhood immunization. Efforts to increase coverage can begin immediately.
I welcome the challenge, made by President Bush today, for other donors to complement this US commitment of US$ 350 million over five years to treat these diseases.

Hey, even Bush can occasionally do what’s right, so give him the credit for it. Perhaps, with all this attention, we should not be calling these diseases “neglected” any more? Perhaps we should rename our youngest journal?
I hope other sponsors pitch in to complement the Bush offer and raise the fund to $700 mil.

How to have your papers deposited into PubMed Central

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

Darwin Quotes

Charles_Darwin.jpgIf the misery of the poor be caused not by the laws of nature, but by our institutions, great is our sin.
– Charles R. Darwin
Support The Beagle Project
Read the Beagle Project Blog
Buy the Beagle Project swag
Prepare ahead for the Darwin Bicentennial
Read Darwin for yourself.

Today’s carnivals

Tangled Bank #99 is up on Greg Laden’s blog
Cabinet of Curiosities #4, The Choose Your Own Adventure Edition, is up on Archaeoporn.

My picks from ScienceDaily

Do Animals Think Like Autistic Savants?:

When Temple Grandin argued that animals and autistic savants share cognitive similarities in her best-selling book Animals in Translation (2005), the idea gained steam outside the community of cognitive neuroscientists. Grandin, a professor of animal science whose best-selling books have provided an unprecedented look at the autistic mind, says her autism gives her special insight into the inner workings of the animal mind. She based her proposal on the observation that animals, like autistic humans, sense and respond to stimuli that nonautistic humans usually overlook.

Antarctic Life Hung By A Thread During Ice Ages:

Frozen in time… frozen in place… frozen solid… All of these phrases have been used to describe Antarctica, and yet they all belie the truth about this southerly point on the globe. Although the area is covered in ice and bears witness to some of the most extreme cold on the planet, this ecosystem is dynamic, not static, and change here has always been dramatic and intense. A report published in the March issue of Ecology argues that the extreme cold and environmental conditions of past Ice Ages have been even more severe than seen today and changed life at the Antarctic, forcing the migration of many animals such as penguins, whales and seals. Understanding the changes of the past may help scientists to determine how the anticipated temperature increases of the future will work to further transform this continent.

Evolutionary History Of SARS Supports Bats As Virus Source:

Scientists who have studied the genome of the virus that caused severe acute respiratory syndrome (SARS) say their comparisons to related viruses offer new evidence that the virus infecting humans originated in bats.

Fish Devastated By Sex-changing Chemicals In Municipal Wastewater:

While most people understand the dangers of flushing toxic chemicals into the ecosystem through municipal sewer systems, one potentially devastating threat to wild fish populations comes from an unlikely source: estrogen. After an exhaustive seven-year research effort, Canadian biologists found that miniscule amounts of estrogen present in municipal wastewater discharges can decimate wild fish populations living downstream.

Sleep Apnea Doubles Car Crash Risk, Study Shows:

People with sleep apnea — a breathing disorder that disrupts sleep — are at double the risk of being in a car crash, a new study by Vancouver Coastal Health Research Institute and University of British Columbia respirologists finds.

Isopods At The Gate: Interview with Kevin Zelnio

Kevin Zelnio celebrates invertebrates on his blog The Other 95% and, at the second Science Blogging Conference four weeks ago, it was announced that he has joined the Deep Sea News blog and thus officially became a SciBling (with all the associated hazing rituals involving beer).
Welcome to A Blog Around The Clock. Would you, please, tell my readers a little bit more about yourself? Who are you? What is your scientific background? What is your Real Life job?
I’m a PhD student at Penn State hopefully in my final year. My scientific training is in invertebrate zoology and marine ecology. I study the ecology of deep-sea hydrothermal vent communities at the Eastern Lau Spreading Center which is conveniently situated between Fiji and Tonga! I am also into taxonomy and describe some of the many new species we find there.
What do you want to do/be when you grow up?
A jack of all trades. I want to be a writer, a museum curator for inverts, a taxonomist, gentleman naturalist, a folk musician and work in the open access publishing movement.
You went down in the submersible Alvin. Can you tell us how did that happen and what did you do there?
I was an overenthusiastic undergraduate at University of California – Davis where i majored in Evolution and Ecology and (almost) Geology. I was taking a 1-unit seminar course in hydrothermal vents for fun. My professors were invited to go on a cruise to the East Pacific Rise, which is off the coast of Central America and Mexico, to run the night operations using a towed camera. This was a biological cruise headed by Janet Voight, a curator at the Field Museum. They asked if I wanted to come along for a little month long boat ride in the middle of my fall quarter. Of which I replied HELL YEAH!! As the undergrad, I was affectionately referred to as the “ship’s bitch” and worked a lot with the video and helping other researchers with their work. I found my talent of sorting through muck to find critters. A talent that basically became my PhD now. There were only a limited number of Alvin dives on the expedition and only 2 scientists can dive a day, pending no severe weather (of which we undoubtedly had a few days of). I wasn’t really expecting I’d ever get to go down, but always hoping. I even shaved off my beard for the time since I could grow facial hair in preparation (so the emergency oxygen masks makes an airtight seal around the face – a requirement to dive). Eventually I was approached and asked if I wanted to dive the next day. Of which I replied HELL YEAH!! After locking me in the sub with a pilot to make sure I didn’t have any claustrophobic tendencies, and double checking to make sure the oxygen mask fit my face, I was briefed and ready to go!
It was an 8 hour ride in total and U N B E L I E V A B L E in every way. It took 45 minutes to descend 2.5 kilometers. The color of the ocean turns a darker and darker shade of blue until you reach the maximum depth limit of light and nothing but blackness all around you. I saw fish and luminous jellies and plankton on the way down. After a while the sub pilot put the lights on and within minutes I could see the ocean bottom approaching. It was barren and lifeless and as we touched down a puff of sediment was kicked up by Alvin’s thruster and I felt as if I had just landed on the moon. Eventually I saw fish here, a sea whip there. Then BAM! An enormous black smoker appeared before me brimming with 2 meter tubeworms with red plumes wavering in the current. We were just centimeters from the 300C hydrothermal fluid and toxic metals and gases. One error and you can “burn” a hole right throw the plexiglass portal. Thankfully the Alvin sub pilots are exceptionally skilled. Our objectives were to retrieve some experiments left on the seafloor for a graduate student and retrieve water samples of the hydrothermal fluid for a chemist that was also in the sub with me. I also video-taped as much as I could trying to find unusual behaviors, predation, just taking it all in and taking notes for the other senior scientist. At the end of the dive we dropped weights and the ascent took an hour and half. I still have a vivid image of that day. It was a turning point in my life.
Kevin%20Z%20interview%20pic.jpg
[Image from here]
When and how did you discover science blogs? What are some of your favourites? Have you discovered any new cool science blogs while at the Conference?
I guess I never really knew what blogs were until maybe a little over a year ago. I had been reading Deep Sea News irregularly for awhile because when I googled something I was interested in about the deep sea it always came up! Eventually I started commenting on the site and about that time I realized that this was a blog.
I have so many favorites, I keep track of them in Google Reader. I read my co-moderators (from the Real Time Blogging in the Marine Sciences session) blogs religiously: Cephalopodcast; Malaria, Bedbugs, Sea Lice and Sunsets; The Beagle Project and Deep Sea News. I love Snail’s Tales, I guess his was one of the first blogs I found when I started my own blog. Since the conference I’ve gotten much more into reading some of my fellow sciblings blogs. Quite a few blogs have made it into my Reader of people I met and had good interactions with at the Conference. The Inverse Square blog, Pondering Pikaia and Museum of Life + Science blog are 3 that jump out at me right now.
Most people classify blogs into personal, political, tech, medical, etc. Your classification divides blogs into two categories: above and below 200m. Care to explain?
Deep Sea News is all about reporting on the largest environment on earth. By somewhat arbitrary definition, “deep” is characterized by roughly everything under 200-400 meters. Photosynthesis is really hampered beyond 200 and light is virtually gone by 400. There is easily enough going on down there to cover a post a day minimum. Its a very exciting and dynamic place to be!
If it was technically feasible, would you blog WHILE diving?
Probably not. Maybe Twitter updates though. You can’t waste too much time since you got only one shot at getting your research or observations done and the sub is pretty expensive to operate. The last objective of our dive plan is always “Don’t F@#$ up!” If I had my own sub then naturally! Craig, Peter and I at Deep Sea News are in the process of obtaining a blog submersible.
What are your personal experiences about the pros and cons of blogging as a science graduate student?
Its a tough balance. I really like writing and communicating my passion and enthusiasm about the ocean and invertebrates. This is my outlet for me to do what I want to do for no other reason than I want to. I do not have the support of advisor, he views blogs as a waste of time and career stopper. I respectfully disagree of course and view writing a blog post as no more a waste of time as watching an hour or two of TV or reading a book. Blogging has also given me greater confidence and understanding in science. I am famously known in my lab as the most up to date person on research in the marine environment. That’s because I am reading and then blogging about all this great research being produced by other scientists. Writing about something helps me to retain that information and treat it more critically.
Is there anything that happened at the Conference – a session, something someone said or did, a new friendship – that will change the way you think about science communication, or something that you will take with you to your job, blog-reading and blog-writing?
The whole conference was a real eye-opener for me. I’ve been to several science conferences in my field of research but that was by far the best conference I’ve attended. I came away from it all with a revitalized interest and several ideas of which to improve myself. I will definitely take it more seriously, meaning that I will edit my posts, write more clearly and succinctly, and make better use of online tools and technologies. I must say though the student blogging panel was a great discussion and I am impressed of the caliber of knowledge of breadth that these undergrads and grad students have and how well they communicate. It gives me hope for the future.
It was so nice to see you in person and thank you for the interview.
The pleasure was truly mine and I look forward to making SciBlogCon a regular thing.
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Check out all the interviews in this series.

EEB in PLoS ONE

ONE%20publish_center.jpgThe word ‘ONE’ in PLoS ONE indicates that the journal publishes articles in all areas of science. This is not as easy as it sounds, of course. The majority of papers published so far have some kind of biomedical connection to them, which is not a surprise as the biomedical community was the first to embrace PLoS and as the other six PLoS journals are either specifically targeting this community (PLoS Medicine, Pathogens and Neglected Tropical Diseases) or are welcoming to such papers (PLoS Biology, Genetics and Computational Biology).
The support of patient advocate groups, PLoS openness and non-acceptance of advertising from the pharmacological industry, led to a wealth of articles describing clinical trials, leading to our first PLoS Hub – Clinical Trials where the community can post comments on these papers.
But we want PLoS ONE to go beyond and to, eventually, publish equally in all areas of science. We have to do it incrementally. We understand that it is not easy to be the pioneer, the ice-breaker, the first person in one’s field to publish in PLoS ONE and subsequently get asked “you published WHERE?”. Such people, we understand, have to be at a secure point in their careers, as well as strong proponents of Open Access. And such people are key to our success – they tell their colleagues about us and provide the seed – that first paper in the field that gives the others the opening to also submit their manuscripts to us. If you recognize yourself in this description, contact me ASAP!
Eventually, in a year or two, we may see a lot of physics, astronomy, math and chemistry published in ONE. Areas like geology, meteorology and archaeology may come before that. But the best way to expand is to work with what we have – ask people to publish papers that are somewhat related to papers we have already published. So, we may go from biomedical science through Computational Biology to Mathematics, or from biomedical science through Biophysics to Physics.
So, we took a look to see which areas of the Life Sciences have already gravitated to PLoS ONE and it was obvious that we have quickly (in only one year and 1600 papers) become quite a journal-of-choice for the EEB community – that is: Ecology-Evolution-Behavior.
We have already published 159 papers in the Ecology category (see this for a good recent one).
There are already 269 articles tagged as Evolutionary Biology and those include forays into anthropology, invertebrate and vertebrate paleontology and even philosophy of evolutionary biology (we are also capable of publishing taxonomical new-species-description monographs).
Finally, Behavioral Biology (which probably deserves its own category) can be found under the ecology and evolution tags, as well as among the 250 articles categorized as Neuroscience. Check out some cool papers on the behavior of fruitflies, honeybees, iguanas, birds, bats, pikas, chimps and humans, to point out just a few.
Those are large numbers! And we want more! Look around those categories – is there something that is somewhat similar to your own research? If so, why not publish with us?

Viruses in the Oceans: join the latest Journal Club

Brendan Bohannan, Richard W. Castenholz, Jessica Green and their students and postdcos at the Center for Ecology and Evolutionary Biology at University of Oregon are currently doing a Journal Club on the PLoS ONE article The Sorcerer II Global Ocean Sampling Expedition: Metagenomic Characterization of Viruses within Aquatic Microbial Samples, which is part of the PLoS Global Ocean Sampling Collection. Please join in the discussion.

Darwin Quotes

Charles_Darwin.jpgWithout speculation there is no good and original observation.
– Charles R. Darwin
Support The Beagle Project
Read the Beagle Project Blog
Buy the Beagle Project swag
Prepare ahead for the Darwin Bicentennial
Read Darwin for yourself.

New and Exciting in PLoS ONE

There are 50 new articles in PLoS ONE this week – here are some of my picks for you to check out (and post comments, ratings, etc.):
Clocking the Lyme Spirochete:

In order to clear the body of infecting spirochetes, phagocytic cells must be able to get hold of them. In real-time phase-contrast videomicroscopy we were able to measure the speed of Borrelia burgdorferi (Bb), the Lyme spirochete, moving back and forth across a platelet to which it was tethered. Its mean crossing speed was 1,636 µm/min (N = 28), maximum, 2800 µm/min (N = 3). This is the fastest speed recorded for a spirochete, and upward of two orders of magnitude above the speed of a human neutrophil, the fastest cell in the body. This alacrity and its interpretation, in an organism with bidirectional motor capacity, may well contribute to difficulties in spirochete clearance by the host.

Measuring the Meltdown: Drivers of Global Amphibian Extinction and Decline:

Habitat loss, climate change, over-exploitation, disease and other factors have been hypothesised in the global decline of amphibian biodiversity. However, the relative importance of and synergies among different drivers are still poorly understood. We present the largest global analysis of roughly 45% of known amphibians (2,583 species) to quantify the influences of life history, climate, human density and habitat loss on declines and extinction risk. Multi-model Bayesian inference reveals that large amphibian species with small geographic range and pronounced seasonality in temperature and precipitation are most likely to be Red-Listed by IUCN. Elevated habitat loss and human densities are also correlated with high threat risk. Range size, habitat loss and more extreme seasonality in precipitation contributed to decline risk in the 2,454 species that declined between 1980 and 2004, compared to species that were stable (n = 1,545) or had increased (n = 28). These empirical results show that amphibian species with restricted ranges should be urgently targeted for conservation.

Revealing Historic Invasion Patterns and Potential Invasion Sites for Two Non-Native Plant Species:

The historical spatio-temporal distribution of invasive species is rarely documented, hampering efforts to understand invasion dynamics, especially at regional scales. Reconstructing historical invasions through use of herbarium records combined with spatial trend analysis and modeling can elucidate spreading patterns and identify susceptible habitats before invasion occurs. Two perennial species were chosen to contrast historic and potential phytogeographies: Japanese knotweed (Polygonum cuspidatum), introduced intentionally across the US; and mugwort (Artemisia vulgaris), introduced largely accidentally to coastal areas. Spatial analysis revealed that early in the invasion, both species have a stochastic distribution across the contiguous US, but east of the 90th meridian, which approximates the Mississippi River, quickly spread to adjacent counties in subsequent decades. In contrast, in locations west of the 90th meridian, many populations never spread outside the founding county, probably a result of encountering unfavorable environmental conditions. Regression analysis using variables categorized as environmental or anthropogenic accounted for 24% (Japanese knotweed) and 30% (mugwort) of the variation in the current distribution of each species. Results show very few counties with high habitat suitability (≥80%) remain un-invaded (5 for Japanese knotweed and 6 for mugwort), suggesting these perennials are reaching the limits of large-scale expansion. Despite differences in initial introduction loci and pathways, Japanese knotweed and mugwort demonstrate similar historic patterns of spread and show declining rates of regional expansion. Invasion mitigation efforts should be concentrated on areas identified as highly susceptible that border invaded regions, as both species demonstrate secondary expansion from introduction loci.

Healthy Lifestyle Behaviour Decreasing Risks of Being Bullied, Violence and Injury:

Bullying and violence are problems of aggression in schools among adolescents. Basic daily healthy practices including nutritious diet, hygiene and physical activity are common approaches in comprehensive health promotion programs in school settings, however thier relationship to these aggressive behaviours is vague. We attempted to show the advantages of these healthy lifestyle behaviours in 9 developing countries by examining the association with being frequently bullied, violence and injury. A cross-sectional cross-national survey of 9 countries using the WHO Global School Based Student Health Survey dataset was used. Measurements included experiences of “being frequently bullied” in the preceding 30 days and violence/injury in the past 12 months. Association of risk behaviours (smoking, alcohol, sexual behaviour) and healthy lifestyle (nutrition, hygiene practices, physical activity) to being bullied, and violence/injury were assessed using multivariate logistic regression. Hygiene behaviour showed lower risks of being frequently bullied [male: RR = 0.7 (97.5CI: 0.5, 0.9); female: RR = 0.6 (0.5, 0.8)], and lower risk of experiences of violence/injury [RR = 0.7 (0.5, 0.9) for males], after controlling for risk behaviours, age, education, poverty, and country. Healthy lifestyle showed an association to decreased relative risk of being frequently bullied and violence/injury in developing countries. A comprehensive approach to risk and health promoting behaviours reducing bullying and violence is encouraged at school settings.

Shrimps Down Under: Evolutionary Relationships of Subterranean Crustaceans from Western Australia (Decapoda: Atyidae: Stygiocaris):

We investigated the large and small scale evolutionary relationships of the endemic Western Australian subterranean shrimp genus Stygiocaris (Atyidae) using nuclear and mitochondrial genes. Stygiocaris is part of the unique cave biota of the coastal, anchialine, limestones of the Cape Range and Barrow Island, most of whose nearest evolutionary relations are found in coastal caves of the distant North Atlantic. The dominance of atyids in tropical waters and their food resources suggest they are pivotal in understanding these groundwater ecosystems. Our nuclear and mitochondrial analyses all recovered the Mexican cave genus Typhlatya as the sister taxon of Stygiocaris, rather than any of the numerous surface and cave atyids from Australia or the Indo-Pacific region. The two described Stygiocaris species were recovered as monophyletic, and a third, cryptic, species was discovered at a single site, which has very different physiochemical properties from the sites hosting the two described species. Our findings suggest that Stygiocaris and Typhlatya may descend from a common ancestor that lived in the coastal marine habitat of the ancient Tethys Sea, and were subsequently separated by plate tectonic movements. This vicariant process is commonly thought to explain the many disjunct anchialine faunas, but has rarely been demonstrated using phylogenetic techniques. The Cape Range’s geological dynamism, which is probably responsible for the speciation of the various Stygiocaris species, has also led to geographic population structure within species. In particular, Stygiocaris lancifera is split into northern and southern groups, which correspond to population splits within other sympatric subterranean taxa.

Poor Reporting of Scientific Leadership Information in Clinical Trial Registers:

In September 2004, the International Committee of Medical Journal Editors (ICMJE) issued a Statement requiring that all clinical trials be registered at inception in a public register in order to be considered for publication. The World Health Organization (WHO) and ICMJE have identified 20 items that should be provided before a trial is considered registered, including contact information. Identifying those scientifically responsible for trial conduct increases accountability. The objective is to examine the proportion of registered clinical trials providing valid scientific leadership information. We reviewed clinical trial entries listing Canadian investigators in the two largest international and public trial registers, the International Standard Randomized Controlled Trial Number (ISRCTN) register, and ClinicalTrials.gov. The main outcome measures were the proportion of clinical trials reporting valid contact information for the trials’ Principal Investigator (PI)/Co-ordinating Investigator/Study Chair/Site PI, and trial e-mail contact address, stratified by funding source, recruiting status, and register. A total of 1388 entries (142 from ISRCTN and 1246 from ClinicalTrials.gov) comprised our sample. We found non-compliance with mandatory registration requirements regarding scientific leadership and trial contact information. Non-industry and partial industry funded trials were significantly more likely to identify the individual responsible for scientific leadership (OR = 259, 95% CI: 95-701) and to provide a contact e-mail address (OR = 9.6, 95% CI: 6.6-14) than were solely industry funded trials. Despite the requirements set by WHO and ICMJE, data on scientific leadership and contact e-mail addresses are frequently omitted from clinical trials registered in the two leading public clinical trial registers. To promote accountability and transparency in clinical trials research, public clinical trials registers should ensure adequate monitoring of trial registration to ensure completion of mandatory contact information fields identifying scientific leadership

Transparent Meta-Analysis of Prospective Memory and Aging:

Prospective memory (ProM) refers to our ability to become aware of a previously formed plan at the right time and place. After two decades of research on prospective memory and aging, narrative reviews and summaries have arrived at widely different conclusions. One view is that prospective memory shows large age declines, larger than age declines on retrospective memory (RetM). Another view is that prospective memory is an exception to age declines and remains invariant across the adult lifespan. The present meta-analysis of over twenty years of research settles this controversy. It shows that prospective memory declines with aging and that the magnitude of age decline varies by prospective memory subdomain (vigilance, prospective memory proper, habitual prospective memory) as well as test setting (laboratory, natural). Moreover, this meta-analysis demonstrates that previous claims of no age declines in prospective memory are artifacts of methodological and conceptual issues afflicting prior research including widespread ceiling effects, low statistical power, age confounds, and failure to distinguish between various subdomains of prospective memory (e.g., vigilance and prospective memory proper).

The Effect of Inappropriate Calibration: Three Case Studies in Molecular Ecology:

Time-scales estimated from sequence data play an important role in molecular ecology. They can be used to draw correlations between evolutionary and palaeoclimatic events, to measure the tempo of speciation, and to study the demographic history of an endangered species. In all of these studies, it is paramount to have accurate estimates of time-scales and substitution rates. Molecular ecological studies typically focus on intraspecific data that have evolved on genealogical scales, but often these studies inappropriately employ deep fossil calibrations or canonical substitution rates (e.g., 1% per million years for birds and mammals) for calibrating estimates of divergence times. These approaches can yield misleading estimates of molecular time-scales, with significant impacts on subsequent evolutionary and ecological inferences. We illustrate this calibration problem using three case studies: avian speciation in the late Pleistocene, the demographic history of bowhead whales, and the Pleistocene biogeography of brown bears. For each data set, we compare the date estimates that are obtained using internal and external calibration points. In all three cases, the conclusions are significantly altered by the application of revised, internally-calibrated substitution rates. Collectively, the results emphasise the importance of judicious selection of calibrations for analyses of recent evolutionary events.

A Non-Human Primate Model for Gluten Sensitivity:

Gluten sensitivity is widespread among humans. For example, in celiac disease patients, an inflammatory response to dietary gluten leads to enteropathy, malabsorption, circulating antibodies against gluten and transglutaminase 2, and clinical symptoms such as diarrhea. There is a growing need in fundamental and translational research for animal models that exhibit aspects of human gluten sensitivity. Using ELISA-based antibody assays, we screened a population of captive rhesus macaques with chronic diarrhea of non-infectious origin to estimate the incidence of gluten sensitivity. A selected animal with elevated anti-gliadin antibodies and a matched control were extensively studied through alternating periods of gluten-free diet and gluten challenge. Blinded clinical and histological evaluations were conducted to seek evidence for gluten sensitivity. When fed with a gluten-containing diet, gluten-sensitive macaques showed signs and symptoms of celiac disease including chronic diarrhea, malabsorptive steatorrhea, intestinal lesions and anti-gliadin antibodies. A gluten-free diet reversed these clinical, histological and serological features, while reintroduction of dietary gluten caused rapid relapse. Gluten-sensitive rhesus macaques may be an attractive resource for investigating both the pathogenesis and the treatment of celiac disease.

Colouration and Colour Changes of the Fiddler Crab, Uca capricornis: A Descriptive Study:

Colour changes in animals may be triggered by a variety of social and environmental factors and may occur over a matter of seconds or months. Crustaceans, like fiddler crabs (genus Uca), are particularly adept at changing their colour and have been the focus of numerous studies. However, few of these studies have attempted to quantitatively describe the individual variation in colour and pattern or their adaptive significance. This paper quantitatively describes the colour patterns of the fiddler crab Uca capricornis and their ability to change on a socially significant timescale. The most dramatic changes in colour pattern are associated with moulting. These ontogenetic changes result in a general reduction of the colour pattern with increasing size, although females are more colourful and variable than similarly-sized males. Uca capricornis are also capable of rapid colour changes in response to stress, but show no endogenous rhythms associated with the semilunar and tidal cycles commonly reported in other fiddler crabs. The extreme colour polymorphism and the relative stability of the colour patterns in Uca capricornis are consistent with their use in visually mediated mate recognition.

Early Development of the Central and Peripheral Nervous Systems Is Coordinated by Wnt and BMP Signals:

The formation of functional neural circuits that process sensory information requires coordinated development of the central and peripheral nervous systems derived from neural plate and neural plate border cells, respectively. Neural plate, neural crest and rostral placodal cells are all specified at the late gastrula stage. How the early development of the central and peripheral nervous systems are coordinated remains, however, poorly understood. Previous results have provided evidence that at the late gastrula stage, graded Wnt signals impose rostrocaudal character on neural plate cells, and Bone Morphogenetic Protein (BMP) signals specify olfactory and lens placodal cells at rostral forebrain levels. By using in vitro assays of neural crest and placodal cell differentiation, we now provide evidence that Wnt signals impose caudal character on neural plate border cells at the late gastrula stage, and that under these conditions, BMP signals induce neural crest instead of rostral placodal cells. We also provide evidence that both caudal neural and caudal neural plate border cells become independent of further exposure to Wnt signals at the head fold stage. Thus, the status of Wnt signaling in ectodermal cells at the late gastrula stage regulates the rostrocaudal patterning of both neural plate and neural plate border, providing a coordinated spatial and temporal control of the early development of the central and peripheral nervous systems.

Food and Guilt – questions about some extraordinary claims

There is a lot of stuff one hears about food, sustainability, environment, etc., and it is sometimes hard to figure out what is true and what is not, what is based on science and what is emotion-based mythology.
For instance, some things I have heard over the years and have no means to evaluate if they are even close to plausible:
Claim #1: if we used every square inch of arable or potentially arable land, clearing the rainforest, turning deserts into fields, removing cities, malls and highways, killing all the animals, destroying all natural ecosystems, moving all humans to the Moon and planting all of the Earth’s landmass (except, perhaps Antarctica and Mt.Everest), there would still not be enough grain, fruits and vegetables to feed the entire current human population. True or False? Source?
Claim #2: if we used all the available technology to maximize the production of fish, shellfish, sea-weed, etc., the entire production on the oceans would still not be able to feed the entire current human population. True or False? Source?
Claim #3: if all of the suitable (and unsuitable but convertable, e.g,. cities, deserts) land was converted into small farms where chickens really freely roam and peck around the yard, there would not be enough chicken meat to feed the entire current human population. True or False? Source?
I guess if any or all of those are even close to true, the idea is that we have to trade-off and compromise: we cannot eat just plants, or just seafood, or just free-range chicken, but have to combine all (plus farm-raised animals of several species raised as humanely as possible, plus a little bit of game meat) of these in some way that can feed all of us without destroying the environment.
So, anyone know any answers, or at even educated guesses as to the veracity of any of the three above claims?

Food and Guilt

…from different points of view:
Anne-Marie: Culinary revelation
Mark Powell: Saving the ocean with guilt or desire? and Does the sustainable seafood movement rely on guilt? (blogfish poll)
Miriam Goldstein: Guilty as charged
Amanda Marcotte: Save your soul with recycling

My picks from ScienceDaily

Identical Twins Not As Identical As Believed:

Contrary to our previous beliefs, identical twins are not genetically identical. This surprising finding may be of great significance for research on hereditary diseases and for the development of new diagnostic methods. How can it be that one identical twin might develop Parkinson’s disease, for instance, but not the other? Until now, the reasons have been sought in environmental factors. The current study complicates the picture.

Genome Of Marine Organism Tells Of Humans’ Unicellular Ancestors:

The newly sequenced genome of a one-celled, planktonic marine organism, reported Feb. 14 in the journal Nature, is already telling scientists about the evolutionary changes that accompanied the jump from one-celled life forms to multicellular animals like ourselves.

Fruit Flies Show Surprising Sophistication In Locating Food Source:

To a fruit fly, a piece of rotting fruit or the food in your picnic basket is a little slice of heaven. It’s where the tiny animal–not much more than a speck on your fingertip can find food and a mate, the two passions of its short, two-month lifespan. But the odor plume of a food source can be very slight, subject to the vagaries of wind and other weather, in a world that looms large to this tiny bug. Yet the fly is uncanny in finding a meal. How? By using more than just its sense of smell.

Oral Contraceptives Could Work For Dogs, Cats, Pigs, Maybe Even Deer And Coyotes:

If you’re a land owner and animals such as coyotes or wild pigs are driving you hog wild, help may soon be on the way to control their numbers in a humane way — in the form of a birth control pill for animals being developed at Texas A&M University’s College of Veterinary Medicine & Biomedical Sciences. The concept would be to get it to wild animals through baited food, researchers say.

Giant Frog Jumps Continents, May Have Eaten Baby Dinosaurs:

A giant frog fossil from Madagascar dubbed Beelzebufo or ‘the frog from Hell’ has been identified by scientists from UCL (University College London) and Stony Brook University, New York. The discovery of the 70 million year-old fossil frog, of a kind once thought unique to South America, lends weight to a new theory that Madagascar, India and South America were linked until late in the Age of Dinosaurs.

Living Corals Thousands Of Years Old Hold Clues To Past Climate Changes:

New research shows that the second most diverse group of hard corals first evolved in the deep sea, and not in shallow waters. Stylasterids, or lace corals, diversified in deep waters before launching at least three successful invasions of shallow water habitats in the past 30 million years. This finding contradicts a long-established theory that suggests corals and other marine animals all evolved in shallow water before migrating into deeper habitats.

ConvergeSouth08

Sue and Ed are starting to plan the fourth ConvergeSouth and are asking the community to help with the planning.

New and Exciting in PLoS Medicine and PLoS Biology

Are Animals Autistic Savants:

Do animals have privileged access to lower level sensory information before it is packaged into concepts, as Temple Grandin has argued for autistic savants? Giorgio Vallortigara and colleagues critique this perspective, and Grandin responds.

see also.
Maternal Death, Autopsy Studies, and Lessons from Pathology:

Clara Menendez and colleagues analyze 139 complete autopsies following maternal deaths in Maputo, Mozambique and find a predominance of infectious and preventable causes. Sebastian Lucas discusses the study in a related perspective.

Blogrolling for Today

SES: Science, Education & Society


The Natural Patriot


Patently silly


Evolved and Rational


A Fat Question


Stuff White People Like


Running the Numbers

Blogger Wins a Prestigious Journalism Award!

Congratulations to Josh Marshall for winning the George Polk Award!
(Hat-tip)

Anna Kushnir interviews Rose Reis

In my daily interviews I always ask: what new blogs did you discover at the Conference? If anyone asked me that question – and you know it’s hard to surprise me! – one I’d pick would be the INFO Project blog run by Rose Reis, now my daily read.
Now, Anna (where did she get the idea, I wonder?) interviews Rose over on the JoVE Blog and the interview is worth your time. And yes, sooner or later, Rose Reis will be interviewed here as well – stay tuned.

Future Science Cyberstructure

Earlier today I went to UNC to talk about Science On The Web in Javed Mostafa’s graduate course on Enabling Usability of Cyberinfrastructures for Learning, Inquiry, and Discovery. I showed and talked about the following sites:
The rapidly growing List of Open Access journals and how the recent NIH law and Harvard vote are pushing publishing inexorably towards the OA model.
PLoS, Open Access, the TOPAZ platform for a new breed of journals like PLoS ONE (and a couple of examples of user activity on ONE papers), as an example of the leader of OA publishing (and also the story of how I got to work there).
Nature Precedings, and comparison to arXiv, wikis and blogs.
Jean-Claude Bradley’s open notebook chemistry blog and wiki (including a Master’s thesis being written there) and how they used Second Life to do an experiment.
Rosie Redfield’s Vancouver lab with open notebook blogs, and a little about age/generation effect on the adoption of Science 2.0, and about being a “pioneer”.
Science video, in particular SciVee and JoVE as the leaders and how important they are.
Recent advances in science blogging.
My article on the future of the scientific paper – we discussed the SF-like ideas about the future of science communication and the way science will be done, as well as the role of Information Scientists in such an ecosystem.
I did not have time to touch on blog carnivals – a kind of bottom-up, community driven online magazines.
It was fun for me – I hope it was as fun (and useful) to the students as well.

Good news

The Florida Board of Education passed new science standards.

Plus ca change,….

While I was busy, I heard Castro resigned, Musharaff’s party lost the elections, and Kosovo declared independence. Wake me up when something really important happens, e.g., Bush leaves the White House….