Monthly Archives: May 2010

ScienceOnline2010 – interview with Fenella Saunders

Continuing with the tradition from last two years, I will occasionally post interviews with some of the participants of the ScienceOnline2010 conference that was held in the Research Triangle Park, NC back in January. See all the interviews in this series here. You can check out previous years’ interviews as well: 2008 and 2009.
Today, I asked Fenella Saunders from The American Scientist to answer a few questions.
Welcome to A Blog Around The Clock. Would you, please, tell my readers a little bit more about yourself? Where are you coming from (both geographically and philosophically)? What is your (scientific) background?
Fenalla Saunders pic.jpgI was born in England, raised in New York City, did my undergraduate at Duke University in North Carolina, went back to New York for 10 years, then came back to NC five years ago. I have a master’s degree in animal behavior from Hunter College of the City University of New York, where I did my thesis on the interactions of proboscis monkeys in captivity. My undergraduate degree is in computer science with a minor in Japanese, although I chose my major with the concept of going into science journalism.
While I was at college I discussed the education I would need with a number of science journalists, all of whom told me that an education in science, with outside projects to get journalism experience, was the best way to go. (I am from the era just before when it became pretty much standard for science writers to go to an MA program for science journalism.) A computer science major allowed me to study a broad range of sciences and technology, and it also gave me a backup plan in case journalism didn’t work out. At school I wrote for any venue I could get into (and I was lucky that in addition to a regular school paper with a health/medicine section, Duke had both a student-run science and a technology magazine), and in my senior year I wrote a couple of small pieces freelance for Popular Mechanics.
Tell us a little more about your career trajectory so far: interesting projects past and present?
My career started when I landed an internship at Discover Magazine, then got hired on. It was largely a matter of luck and timing: They had a lot of biology people and needed someone with a technology background. I stayed at Discover for about eight years, and ended up also being the online editor toward the end of that time. There were a ton of great moments at that job, but I would have to say my favorite one was when they allowed me to start writing about a different, new robot in each month’s news section. It was a series that lasted 2-3 years, and I never ran out of new robotics research to write about. During that time I freelanced a little, most notably as a co-author for a Time-Life book called “Space 2100.” I left Discover to work on publications for NYU School of Medicine for about two years, which was a very different experience. Probably the best part of that job was learning all about really high-powered MRI machines. For the past five years I’ve been at American Scientist, where I am now a senior editor. It is both fascinating and a challenge working with different scientists each issue, trying to get them to explain their own work for a general audience. I couldn’t even begin to pick a favorite from all of the articles I’ve helped bring to print–it could be anything from Champagne bubbles to snow flakes to honeybee nest relocation.
What is taking up the most of your time and passion these days? What are your goals?
American Scientist is published every two months, so we always confront the problem of remaining timely. We want to find more ways to keep in contact with our readers between issues. We recently relaunched our Web site, which allowed us to better keep up with technology in a few ways. We’re now able to embed video with the online versions of articles. We now also post podcasts of our lunch-speaker series. I am excited that I have been chosen as a fellow to attend on of the Knight Digital Media Center’s multimedia workshops, where I’ll learn more about how to edit audio, video and maybe program some Flash animation. I am hoping that after I attend that workshop, I will be better equipped to have us do more multimedia for the magazine online.
What aspect of science communication and/or particular use of the Web in science interests you the most?
The immediacy of the Web still is its biggest advantage in my mind. Something can be posted for all of the world to see within minutes, and if you are looking for information on a specific topic, a quick search will pull up enough reading to last hours. It’s a very democratic platform, as anyone can post on it, but that makes it all the more important to make sure that sources are reputable and verifiable–I am pretty sure that we all rely too much on the truthfulness of Wikipedia these days. I am also hopeful that the Web can make information, about science or anything, more accessible to people who, say, don’t have the luxury of going to college, or find themselves in a position of having to learn about something new that they never thought about doing.
That being said, I am still unsure of how the print vs. online debate is going to shake out. There is something to be said for picking up a whole magazine, not just a specific article you were looking for. It is broadening to be exposed to topics you might not have even realized existed. People are busy, so in some ways it’s faster just to pick up a print copy rather than have to search and dig online. Perhaps platforms such as the iPad will change all this. But I know that, when I have the time, just browsing through publications in the library is the best way for me to get new ideas.
How does (if it does) blogging figure in your work? How about social networks, e.g., Twitter, FriendFeed and Facebook? Do you find all this online activity to be a net positive (or even a necessity) in what you do?
It’s fairly bizarre for a publication not to use all social-media platforms possible these days. We send out a daily and a weekly conglomeration of science news, and we tweet about these entries daily as well. We also use twitter to talk about what’s in our latest issue, and we tweet about any news that relates to a past story that we have done. We have groups on Facebook and LinkedIn. We don’t have a set blog yet, although we are working on it, but our Computing Science columnist, Brian Hayes, has a regular one at bit-player.org.
When and how did you first discover science blogs? What are some of your favourites? Have you discovered any cool science blogs by the participants at the Conference?
Carl Zimmer is a former colleague of mine at Discover magazine, and he was an early entry into the blogosphere, so his was probably the first blog that I followed. I was happy to meet Ed Yong at the conference, and I follow his blog “Not Exactly Rocket Science.” I’ve also been following Rebecca Skloot’s blog about her book “The Immortal Life of Henrietta Lacks.”
What was the best aspect of ScienceOnline2010 for you? Any suggestions for next year? 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?
I really liked the fact that there were kids at the conference. Kids often are not brought into the dialogue when discussing science, particularly science journalism. Sometimes they are the target audience, but they are rarely part of the process. For a few years we did a mentoring program with a local middle school where we’d have kids come in for a week, but they’d rotate, so I’d get each student for only one day. I challenged them that they would write a whole science news story by the end of the day, and they all looked at me like I was crazy, but they all did it. Children can do amazing things if given the opportunity, and can provide unique insight. I found it particularly enlightening that the young students at ScienceOnline 2010 thought that Twitter was an adult thing–they saw no real use for it in their lives, preferring more interactive platforms such as Facebook.
I can’t say my usual “It was so nice to meet you in person” because I see you often, but certainly thank you for the interview. I hope to see you again soon.

Scott Huler – ‘On The Grid’ at Quail Ridge Books

huler 003.JPGAs I alerted you before, last night Scott Huler (blog, Twitter, SIT interview) did a reading from his latest book On The Grid (amazon.com) at the Quail Ridge Books in Raleigh.
The store was packed. The store sold out all the books before Scott was even done talking. The C-Span Book TV crew was there filming so the event will be on TV some day soon. Scott was also, earlier yesterday, on WUNC’s The State Of Things (the podcast will soon be online here) and the day before that he was on KERA’s Think with Krys Boyd (download MP3 podcast by clicking here).
Scott’s energy and enthusiasm are infectuos. He held the audience captive and often laughing. The questions at the end were smart and his answers perfectly on target. But most importantly, we all learned a lot last night. I think of myself as a reasonably curious and informed person, and I have visited at least a couple of infrastructure plants, but almost every anecdote and every little tidbit of information were new to me. Scott’s point – that we don’t know almost anything about infrastructure – was thus proven to me.
What Scott realized during the two years of research for the book is that people in charge of infrastructure know what they are doing. When something doesn’t work well, or the system is not as up-to-date as it could be, it is not due to incompetence or ignorance, but because there is a lack of two essential ingredients: money and political will. These two factors, in turn, become available to the engineers to build and upgrade the systems, only if people are persuaded to act. And people are persuaded to act in two ways: if it becomes too costly, or if it becomes too painful to continue with the old way of doing things. It is also easier to build brand new systems for new services than it is to replace old systems that work ‘well enough’ with more more modern ways of providing the same service.
huler 002.JPGThere are people who advocate for moving “off the grid” and living a self-sufficient existence. But, as Scott discovered, they are fooling themselves. Both the process of moving off the grid and the subsequent life off the grid are still heavily dependent on the grid, on various infrastructure systems that make such a move and such a life possible, at least in the developed world.
What is really astonishing is how well the systems work, even in USA which has fallen way behind the rest of the developed world. We are taking it for granted that the systems always work, that water and electricity and phone and sewers and garbage collection and public transportation always work. We get angry on those rare occasions when a system temporarily fails. We are, for the most part, unprepared and untrained to provide some of the services ourselves in times of outages, or to continue with normal life and work when a service fails. And we are certainly not teaching our kids the necessary skills – I can chop up wood and start a wood stove, I can use an oil heater, I know how to slaughter and render a pig, how to get water out of a well, dig a ditch, and many other skills I learned as a child (and working around horses) – yet I am not teaching any of that to my own kids. They see it as irrelevant to the modern world and they have a point – chance they will ever need to employ such skills is negligible.
grid_cover.jpgI got the book last night and am about to start reading it – very eagerly so. Scott started with his house in Raleigh and traced all the wires and cables and pipes going in and out of the house to see where they led. He compared what he learned in Raleigh and its various infrastructure experts and officials, to the equivalent services in other geographical places, and traced them back in history. I can’t wait to read the synthesis of all that research. I hope you will read it, too.
Cross-posted from Science In The Triangle

Serious Gaming at Sigma Xi

Last week I went to this season’s last American Scientist pizza lunch at Sigma Xi featuring Phaedra Boinodiris (Twitter, blog), Serious Games Product Manager at IBM.
I first saw Phaedra Boinodiris speak as the opening speaker at TEDxRTP (my review) back in March, but this was a different kind of talk, geared more towards scientists and science communicators.
I remember playing Pong when it first came out. I remember spending many hours back in 1980 or so playing The Hobbit on Sinclair ZX Spectrum. And I played many games at arcades (still not knowing which games started out as arcade games adapted to computers and which the other way round). Then I quit playing games for a couple of decades until my kids were ready for them. I loved Zoombinis – an amazing game of logic and a brilliant preparation for taking IQ tests! I loved Richard Scarry’s Busytown – the one and only game I know about infrastructure, where players build stuff and deliver it to others for the good of the town – from baking bread to paving roads – learning along the way how those things are done.
And sure, Phaedra Boinodiris started with a slide depicting Pong (to the chuckle of the audience) but soon got into the real stuff – the serious gaming and the story of how she got involved in developing such games, as well as about studies of gaming and how different kinds of games help develop different real-work skills, from eye-hand coordination to leadership to cooperation. Her first game – INNOV8 – was developed as a prototype, a proof of concept, in only three months and instantly became a huge hit. It is used by businesses and business schools around the world to teach Business Process Management. It is essentially a first person shooter game (without guns) in which the player is brought as an outside consultant into a company where s/he has to figure out the flow, the bottlenecks, etc. (including by interviewing employees, as well as data-sheets) and experiment in making it more efficient. The 2.0 version came soon after, adding such problems as traffic, customer service and supply chains.

The next game, recently announced and coming out in October 2010, will be a Sim-City-like serious game CityOne, designed to help city planners, town councils, citizens, and engineers plan better, more efficient infrastructure for their cities. Put in your city’s specs and start building new infrastructure, see how much it will cost, see what problems will arise, see what solutions are available – probably something you could not have thought of yourself and may be surprised.
As I am currently reading ‘On The Grid’ it occured to me that the developers of CityOne should read that book, and that Scott Huler should be given a test-run of the game, perhaps for him to review for Charlotte Observer and Raleigh News&Observer and the local NPR station. And for Science In The Triangle, of course.
Cross-posted from Science In The Triangle

Open Laboratory 2010 – submissions so far

The list is growing fast – check the submissions to date and get inspired to submit something of your own – an essay, a poem, a cartoon or original art.
The Submission form is here so you can get started. Under the fold are entries so far, as well as buttons and the bookmarklet. The instructions for submitting are here.

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Clock Quotes

The sheer rebelliousness in giving ourselves permission to fail frees a childlike awareness and clarity … When we give ourselves permission to fail, we at the same time give ourselves permission to excel.
– Eloise Ristad

Serious Gaming at Sigma Xi

Last week I went to this season’s last American Scientist pizza lunch at Sigma Xi featuring Phaedra Boinodiris, Serious Games Product Manager at IBM, and I filed my report over on Science In The Triangle blog.

Science Online London 2010

science-online2010 logo.jpgThe third Science Online London 2010 will be held at the British Library on September 3rd and 4th, 2010. You can follow it as a hashtag #solo10 on Twitter and add session suggestions to the wiki here.

Clock Quotes

As long as there is one upright man, as long as there is one compassionate woman, the contagion may spread and the scene is not desolate. Hope is the thing left to us in a bad time.
– Elwyn Brooks White

Ancestors and Offspring – evolution and synthetic biology (video)

A fascinating discussion with John Hawks and my Scibling Christina Agapakis about synthetic biology and other related topics – worth your time:

Is starting a science career a risk? (video)

Clock Quotes

There are victories of the soul and spirit. Sometimes, even if you lose, you win.
– Eliezer Wiesel

New and Exciting in PLoS ONE

There are 33 new articles in PLoS ONE today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:

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Today’s carnivals

I and the Bird #126 is up on Coyote Mercury.
This week’s edition of Change of Shift (Volume 4, Number 23) is up at The Makings of a Nurse.
Friday Ark #297 is up on Modulator.

Clock Quotes

It is easier to accept the message of the stars than the message of the salt desert. The stars speak of man’s insignificance in the long eternity of time; the deserts speak of his insignificance right now.
– Edwin Way Teale

New and Exciting in PLoS this week

Thursday – four out of seven PLoS journals publish new articles and I make my own picks. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:

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‘On The Grid’ by Scott Huler at Quail Ridge Books

Last night I went to the book reading of “On The Grid” by Scott Huler at Quail Ridge Books in Raleigh. It was a great event. I wrote a more detailed summary over on Science In The Triangle.

ScienceOnline2010 – interview with Jeremy Yoder

Continuing with the tradition from last two years, I will occasionally post interviews with some of the participants of the ScienceOnline2010 conference that was held in the Research Triangle Park, NC back in January. See all the interviews in this series here. You can check out previous years’ interviews as well: 2008 and 2009.
Today, I asked Jeremy Yoder from University of Idaho and the Denim and Tweed blog to answer a few questions. Jeremy came to ScienceOnline2010 as one of the two winners of the NESCent blogging contest.
Welcome to A Blog Around The Clock. Would you, please, tell my readers a little bit more about yourself? Where are you coming from (both geographically and philosophically)? What is your (scientific) background?
Jeremy Yoder pic.jpgHello, and many thanks for having me! I’m not sure how best to start this, so I’ll just go from the beginning:
I grew up very Mennonite in rural Pennsylvania (no, there were no buggies involved). I’m more-or-less an agnostic now, but my thinking is still strongly influenced by Mennonite values of peacemaking, simplicity, and independent inquiry.
I had my first taste of field biology in my senior year of high school, when one of my science teachers led the class through a forest survey in a woodlot adjacent to the campus. By cataloguing the trees according to their age class and species, we were able to deduce how mature the woodland was, and what it might look like in another hundred years. It opened up this vision of species jostling against each other, accommodating as well as competing to shape the landscape right outside my front door, and it seemed like a pretty cool thing to do for a living.
Tell us a little more about your career trajectory so far: interesting projects past and present?
From high school on I did my best to arrange to spend time outdoors. I majored in environmental science as an undergraduate, and then spent a year interning with the Western Pennsylvania Conservancy, working on plant community ecology among other projects. When I started to think about graduate school, I knew I wanted to study coevolution — the ways in which interacting species shape each other’s evolutionary history — and I was lucky enough to connect with Olle Pellmyr, who was looking for a new graduate student to work on his current study of Joshua trees and the moths that pollinate them.
Joshua tree populations are exclusively pollinated by one or the other of two different species of yucca moths. It turns out that trees from populations with different pollinators look pretty different themselves, and we now have good reason to think that the moths’ preferences for their “native” type of Joshua tree determines how often the two tree types can interbreed. A big part of my dissertation work is to use DNA sampling from Joshua trees across the whole Mojave desert to estimate how completely the two types of Joshua tree are isolated, and how much coevolution with the moths is responsible for the differences we see in the two types of tree. Before I started grad school, I’d never seen a North American desert — now I’ve been to just about every place Joshua trees grow, from the south rim of the Grand Canyon to the outer suburbs of Los Angeles and (I kid you not) just outside of Area 51.
Joshua Trees pic.jpg
What is taking up the most of your time and passion these days? What are your goals?
My dissertation is far and away my biggest preoccupation, you won’t be surprised to hear. I’ve just had a couple of projects accepted for publication — a literature review and an analysis that reconstructs some characteristics of the ancestors of yucca moths. I’m (hopefully) nearly done with a mathematical model that compares how different kinds of coevolutionary interactions affect the species involved, and I’m heavily occupied with the Joshua tree DNA analysis right now. My plan is to complete my doctorate by about this time next year, and I’m starting to think about possible postdoctoral work (hint, hint!).
I’m also keeping up with writing on Denim and Tweed for the time being, and I’m thinking about running what will be my second marathon sometime this fall. Hopefully, I’ll find some time to get out and enjoy the wilderness out here in the Pacific Northwest this summer, too, since this might be the last year I spend within a day’s drive of both Olympic and Glacier National Parks.
What aspect of science communication and/or particular use of the Web in science interests you the most?
Most academic biologists spend time teaching in addition to their research, and I really believe that telling the general public about my work is a logical extension of that principle — that being a scientist means communicating what you learn to others, not just accumulating knowledge to satisfy your own curiosity. The Web is a great venue for that, thanks to user-friendly blog hosting services and networks like Research Blogging and the Nature Blog Network that connect interested readers to my site. I now list D&T as a “broader impact” on all my grant applications.
How does (if it does) blogging figure in your work? How about social networks, e.g., Twitter, FriendFeed and Facebook? Do you find all this online activity to be a net positive (or even a necessity) in what you do?
I try to treat Denim and Tweed as an exercise in writing about science for a general audience — so it has that value for me even if no one reads it. In that sense, it’s a little like a one-man journal club, in which I sit down every week and read one paper carefully enough to explain it to someone else in about 700 words.
The blog is pretty heavily linked into my online social network as well — I have a public account on Twitter that I use regularly, and a FriendFeed profile that ties together the blog, my Flickr account, and my Facebook profile. And I interact with family, personal acquaintances, colleagues, and readers of D&T across all those platforms — over my last field trip, I’d post photos from Flickr to the blog, and have folks comment about them on my Facebook wall. It’s not very tidy, but every one of those networks seems to reach a slightly different set of people, so I guess I’m thoroughly enmeshed.
When and how did you first discover science blogs? What are some of your favourites? Have you discovered any cool science blogs by the participants at the Conference?
I’ve been reading science blogs since long before it occurred to me to start writing on my own — I don’t remember exactly how I got started, but my first contact was probably when someone sent me a snarky link from Pharyngula. I think I probably didn’t have a sense of the full scope of the science blogosphere before I found Research Blogging, though.
Through RB, I’ve found great sites like The EEB & flow, Conservation Maven, and Open Source Paleontologist, and even occasionally exchanged thoughts in the comments or via back-and-forth posts. Research Blogging is really a fantastic way to get started in writing about science on your own blog, both because it’s easy to add your posts to a feed lots of other science bloggers read and because it helps you find other people writing about the sort of science that interests you.
And then, after I’d been involved in RB for more than a year, I was lucky enough to be able to attend ScienceOnline 2010, and meet in person a number of folks I really only knew as text on the screen — and, yes, add a number of links to my RSS list, including Observations of a Nerd. I think I picked up far more Twitter feeds than blogs at ScienceOnline, though — so much of the conference conversation occurred on Twitter that it was basically unavoidable. And now I probably get more of my online science news via folks I’m following on Twitter than even through the RSS feeds I have bookmarked in Firefox.
What was the best aspect of ScienceOnline2010 for you? Any suggestions for next year? 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?
I think the biggest benefit I took from ScienceOnline2010 was a better sense of where I fit in the world of online science communication, in my role as a scientist with a blog. I saw some great models of how to draw the public into ongoing scientific work using online tools, and even how to engage the public in the actual science. I also saw some great sessions that addressed interactions among different groups of people involved in science communication — working scientists, educators, and science journalists. It was a really fun weekend all around, and it gave me a lot to think about as I work towards the (still pretty distant!) day when I’m ready to set up my own lab and research program.
It was so nice to meet you in person and thank you for the interview. I hope to see you again next January.

Clock Quotes

“I love my cats because I love my home, and little by little they become its visible soul.”
– Jean Couteau

New and Exciting in PLoS ONE

Another amazing serving of Wednesday sciencey goodness with 40 new articles in PLoS ONE today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:
A New Pterosaur (Pterodactyloidea: Azhdarchidae) from the Upper Cretaceous of Morocco:

The Kem Kem beds in South Eastern Morocco contain a rich early Upper (or possibly late Lower) Cretaceous vertebrate assemblage. Fragmentary remains, predominantly teeth and jaw tips, represent several kinds of pterosaur although only one species, the ornithocheirid Coloborhynchus moroccensis, has been named. Here, we describe a new azhdarchid pterosaur, Alanqa saharica nov. gen. nov. sp., based on an almost complete well preserved mandibular symphysis from Aferdou N’Chaft. We assign additional fragmentary jaw remains, some of which have been tentatively identified as azhdarchid and pteranodontid, to this new taxon which is distinguished from other azhdarchids by a remarkably straight, elongate, lance-shaped mandibular symphysis that bears a pronounced dorsal eminence near the posterior end of its dorsal (occlusal) surface. Most remains, including the holotype, represent individuals of approximately three to four meters in wingspan, but a fragment of a large cervical vertebra, that probably also belongs to A. saharica, suggests that wingspans of six meters were achieved in this species. The Kem Kem beds have yielded the most diverse pterosaur assemblage yet reported from Africa and provide the first clear evidence for the presence of azhdarchids in Gondwana at the start of the Late Cretaceous. This, the relatively large size achieved by Alanqa, and the additional evidence of variable jaw morphology in azhdarchids provided by this taxon, indicates a longer and more complex history for this clade than previously suspected.

Large-Range Movements of Neotropical Orchid Bees Observed via Radio Telemetry:

Neotropical orchid bees (Euglossini) are often cited as classic examples of trapline-foragers with potentially extensive foraging ranges. If long-distance movements are habitual, rare plants in widely scattered locations may benefit from euglossine pollination services. Here we report the first successful use of micro radio telemetry to track the movement of an insect pollinator in a complex and forested environment. Our results indicate that individual male orchid bees (Exaerete frontalis) habitually use large rainforest areas (at least 42-115 ha) on a daily basis. Aerial telemetry located individuals up to 5 km away from their core areas, and bees were often stationary, for variable periods, between flights to successive localities. These data suggest a higher degree of site fidelity than what may be expected in a free living male bee, and has implications for our understanding of biological activity patterns and the evolution of forest pollinators.

Helper Response to Experimentally Manipulated Predation Risk in the Cooperatively Breeding Cichlid Neolamprologus pulcher:

We manipulated predation risk in a field experiment with the cooperatively breeding cichlid Neolamprologus pulcher by releasing no predator, a medium- or a large-sized fish predator inside underwater cages enclosing two to three natural groups. We assessed whether helpers changed their helping behaviour, and whether within-group conflict changed, depending on these treatments, testing three hypotheses: ‘pay-to-stay’ PS, ‘risk avoidance’ RA, or (future) reproductive benefits RB. We also assessed whether helper food intake was reduced under risk, because this might reduce investments in other behaviours to save energy. Medium and large helpers fed less under predation risk. Despite this effect helpers invested more in territory defence, but not territory maintenance, under the risk of predation (supporting PS). Experimentally covering only the breeding shelter with sand induced more helper digging under predation risk compared to the control treatment (supporting PS). Aggression towards the introduced predator did not differ between the two predator treatments and increased with group member size and group size (supporting PS and RA). Large helpers increased their help ratio (helping effort/breeder aggression received, ‘punishment’ by the dominant pair in the group) in the predation treatments compared to the control treatment, suggesting they were more willing to PS. Medium helpers did not show such effects. Large helpers also showed a higher submission ratio (submission/ breeder aggression received) in all treatments, compared to the medium helpers (supporting PS). We conclude that predation risk reduces helper food intake, but despite this effect, helpers were more willing to support the breeders, supporting PS. Effects of breeder punishment suggests that PS might be more important for large compared to the medium helpers. Evidence for RA was also detected. Finally, the results were inconsistent with RB.

The Promise and Perils of Pre-Publication Review: A Multi-Agent Simulation of Biomedical Discovery Under Varying Levels of Review Stringency:

The Internet has enabled profound changes in the way science is performed, especially in scientific communications. Among the most important of these changes is the possibility of new models for pre-publication review, ranging from the current, relatively strict peer-review model, to entirely unreviewed, instant self-publication. Different models may affect scientific progress by altering both the quality and quantity of papers available to the research community. To test how models affect the community, I used a multi-agent simulation of treatment selection and outcome in a patient population to examine how various levels of pre-publication review might affect the rate of scientific progress. I identified a “sweet spot” between the points of very limited and very strict requirements for pre-publication review. The model also produced a u-shaped curve where very limited review requirement was slightly superior to a moderate level of requirement, but not as large as the aforementioned sweet spot. This unexpected phenomenon appears to result from the community taking longer to discover the correct treatment with more strict pre-publication review. In the parameter regimens I explored, both completely unreviewed and very strictly reviewed scientific communication seems likely to hinder scientific progress. Much more investigation is warranted. Multi-agent simulations can help to shed light on complex questions of scientific communication and exhibit interesting, unexpected behaviors.

Recurrent, Robust and Scalable Patterns Underlie Human Approach and Avoidance:

Approach and avoidance behavior provide a means for assessing the rewarding or aversive value of stimuli, and can be quantified by a keypress procedure whereby subjects work to increase (approach), decrease (avoid), or do nothing about time of exposure to a rewarding/aversive stimulus. To investigate whether approach/avoidance behavior might be governed by quantitative principles that meet engineering criteria for lawfulness and that encode known features of reward/aversion function, we evaluated whether keypress responses toward pictures with potential motivational value produced any regular patterns, such as a trade-off between approach and avoidance, or recurrent lawful patterns as observed with prospect theory. Three sets of experiments employed this task with beautiful face images, a standardized set of affective photographs, and pictures of food during controlled states of hunger and satiety. An iterative modeling approach to data identified multiple law-like patterns, based on variables grounded in the individual. These patterns were consistent across stimulus types, robust to noise, describable by a simple power law, and scalable between individuals and groups. Patterns included: (i) a preference trade-off counterbalancing approach and avoidance, (ii) a value function linking preference intensity to uncertainty about preference, and (iii) a saturation function linking preference intensity to its standard deviation, thereby setting limits to both. These law-like patterns were compatible with critical features of prospect theory, the matching law, and alliesthesia. Furthermore, they appeared consistent with both mean-variance and expected utility approaches to the assessment of risk. Ordering of responses across categories of stimuli demonstrated three properties thought to be relevant for preference-based choice, suggesting these patterns might be grouped together as a relative preference theory. Since variables in these patterns have been associated with reward circuitry structure and function, they may provide a method for quantitative phenotyping of normative and pathological function (e.g., psychiatric illness).

Coevolution in Action: Disruptive Selection on Egg Colour in an Avian Brood Parasite and Its Host:

Trait polymorphism can evolve as a consequence of frequency-dependent selection. Coevolutionary interactions between hosts and parasites may lead to selection on both to evolve extreme phenotypes deviating from the norm, through disruptive selection. Here, we show through detailed field studies and experimental procedures that the ashy-throated parrotbill (Paradoxornis alphonsianus) and its avian brood parasite, the common cuckoo (Cuculus canorus), have both evolved egg polymorphism manifested in discrete immaculate white, pale blue, and blue egg phenotypes within a single population. In this host-parasite system the most common egg colours were white and blue, with no significant difference in parasitism rates between hosts laying eggs of either colour. Furthermore, selection on parasites for countering the evolution of host egg types appears to be strong, since ashy-throated parrotbills have evolved rejection abilities for even partially mimetic eggs. The parrotbill-cuckoo system constitutes a clear outcome of disruptive selection on both host and parasite egg phenotypes driven by coevolution, due to the cost of parasitism in the host and by host defences in the parasite. The present study is to our knowledge the first to report the influence of disruptive selection on evolution of discrete phenotypes in both parasite and host traits in an avian brood parasitism system.

The Effects of Nutrient Dynamics on Root Patch Choice:

Plants have been recognized to be capable of allocating more roots to rich patches in the soil. We tested the hypothesis that in addition to their sensitivity to absolute differences in nutrient availability, plants are also responsive to temporal changes in nutrient availability. Different roots of the same Pisum sativum plants were subjected to variable homogeneous and heterogeneous temporally – dynamic and static nutrient regimes. When given a choice, plants not only developed greater root biomasses in richer patches; they discriminately allocated more resources to roots that developed in patches with increasing nutrient levels, even when their other roots developed in richer patches. These results suggest that plants are able to perceive and respond to dynamic environmental changes. This ability might enable plants to increase their performance by responding to both current and anticipated resource availabilities in their immediate proximity.

Bacterial Gut Symbionts Contribute to Seed Digestion in an Omnivorous Beetle:

Obligate bacterial symbionts alter the diets of host animals in numerous ways, but the ecological roles of facultative bacterial residents that colonize insect guts remain unclear. Carabid beetles are a common group of beneficial insects appreciated for their ability to consume insect prey and seeds, but the contributions of microbes to diet diversification in this and similar groups of facultative granivores are largely unknown. Using 16S rRNA gene clone libraries and terminal restriction fragment (tRF) length polymorphism analyses of these genes, we examined the bacterial communities within the guts of facultatively granivorous, adult Harpalus pensylvanicus (Carabidae), fed one of five dietary treatments: 1) an untreated Field population, 2) Seeds with antibiotics (seeds were from Chenopodium album), 3) Seeds without antibiotics, 4) Prey with antibiotics (prey were Acheta domesticus eggs), and 5) Prey without antibiotics. The number of seeds and prey consumed by each beetle were recorded following treatment. Harpalus pensylvanicus possessed a fairly simple gut community of approximately 3-4 bacterial operational taxonomic units (OTU) per beetle that were affiliated with the Gammaproteobacteria, Bacilli, Alphaproteobacteria, and Mollicutes. Bacterial communities of the host varied among the diet and antibiotic treatments. The field population and beetles fed seeds without antibiotics had the closest matching bacterial communities, and the communities in the beetles fed antibiotics were more closely related to each other than to those of the beetles that did not receive antibiotics. Antibiotics reduced and altered the bacterial communities found in the beetle guts. Moreover, beetles fed antibiotics ate fewer seeds, and those beetles that harbored the bacterium Enterococcus faecalis consumed more seeds on average than those lacking this symbiont. We conclude that the relationships between the bacterium E. faecalis and this factultative granivore’s ability to consume seeds merit further investigation, and that facultative associations with symbiotic bacteria have important implications for the nutritional ecology of their hosts.

The Nature of Working Memory for Braille:

Blind individuals have been shown on multiple occasions to compensate for their loss of sight by developing exceptional abilities in their remaining senses. While most research has been focused on perceptual abilities per se in the auditory and tactile modalities, recent work has also investigated higher-order processes involving memory and language functions. Here we examined tactile working memory for Braille in two groups of visually challenged individuals (completely blind subjects, CBS; blind with residual vision, BRV). In a first experimental procedure both groups were given a Braille tactile memory span task with and without articulatory suppression, while the BRV and a sighted group performed a visual version of the task. It was shown that the Braille tactile working memory (BrWM) of CBS individuals under articulatory suppression is as efficient as that of sighted individuals’ visual working memory in the same condition. Moreover, the results suggest that BrWM may be more robust in the CBS than in the BRV subjects, thus pointing to the potential role of visual experience in shaping tactile working memory. A second experiment designed to assess the nature (spatial vs. verbal) of this working memory was then carried out with two new CBS and BRV groups having to perform the Braille task concurrently with a mental arithmetic task or a mental displacement of blocks task. We show that the disruption of memory was greatest when concurrently carrying out the mental displacement of blocks, indicating that the Braille tactile subsystem of working memory is likely spatial in nature in CBS. The results also point to the multimodal nature of working memory and show how experience can shape the development of its subcomponents.

Bacterial Biodiversity-Ecosystem Functioning Relations Are Modified by Environmental Complexity:

With the recognition that environmental change resulting from anthropogenic activities is causing a global decline in biodiversity, much attention has been devoted to understanding how changes in biodiversity may alter levels of ecosystem functioning. Although environmental complexity has long been recognised as a major driving force in evolutionary processes, it has only recently been incorporated into biodiversity-ecosystem functioning investigations. Environmental complexity is expected to strengthen the positive effect of species richness on ecosystem functioning, mainly because it leads to stronger complementarity effects, such as resource partitioning and facilitative interactions among species when the number of available resource increases. Here we implemented an experiment to test the combined effect of species richness and environmental complexity, more specifically, resource richness on ecosystem functioning over time. We show, using all possible combinations of species within a bacterial community consisting of six species, and all possible combinations of three substrates, that diversity-functioning (metabolic activity) relationships change over time from linear to saturated. This was probably caused by a combination of limited complementarity effects and negative interactions among competing species as the experiment progressed. Even though species richness and resource richness both enhanced ecosystem functioning, they did so independently from each other. Instead there were complex interactions between particular species and substrate combinations. Our study shows clearly that both species richness and environmental complexity increase ecosystem functioning. The finding that there was no direct interaction between these two factors, but that instead rather complex interactions between combinations of certain species and resources underlie positive biodiversity ecosystem functioning relationships, suggests that detailed knowledge of how individual species interact with complex natural environments will be required in order to make reliable predictions about how altered levels of biodiversity will most likely affect ecosystem functioning.

Changing Patterns of Microhabitat Utilization by the Threespot Damselfish, Stegastes planifrons, on Caribbean Reefs:

The threespot damselfish, Stegastes planifrons (Cuvier), is important in mediating interactions among corals, algae, and herbivores on Caribbean coral reefs. The preferred microhabitat of S. planifrons is thickets of the branching staghorn coral Acropora cervicornis. Within the past few decades, mass mortality of A. cervicornis from white-band disease and other factors has rendered this coral a minor ecological component throughout most of its range. Survey data from Jamaica (heavily fished), Florida and the Bahamas (moderately fished), the Cayman Islands (lightly to moderately fished), and Belize (lightly fished) indicate that distributional patterns of S. planifrons are positively correlated with live coral cover and topographic complexity. Our results suggest that species-specific microhabitat preferences and the availability of topographically complex microhabitats are more important than the abundance of predatory fish as proximal controls on S. planifrons distribution and abundance. The loss of the primary microhabitat of S. planifrons–A. cervicornis–has forced a shift in the distribution and recruitment of these damselfish onto remaining high-structured corals, especially the Montastraea annularis species complex, affecting coral mortality and algal dynamics throughout the Caribbean.

The Power of Exercise: Buffering the Effect of Chronic Stress on Telomere Length:

Chronic psychological stress is associated with detrimental effects on physical health, and may operate in part through accelerated cell aging, as indexed by shorter telomeres at the ends of chromosomes. However, not all people under stress have distinctly short telomeres, and we examined whether exercise can serve a stress-buffering function. We predicted that chronic stress would be related to short telomere length (TL) in sedentary individuals, whereas in those who exercise, stress would not have measurable effects on telomere shortening. 63 healthy post-menopausal women underwent a fasting morning blood draw for whole blood TL analysis by a quantitative polymerase chain reaction method. Participants completed the Perceived Stress Scale (Cohen et al., 1983), and for three successive days reported daily minutes of vigorous activity. Participants were categorized into two groups-sedentary and active (those getting Centers for Disease Control-recommended daily amount of activity). The likelihood of having short versus long telomeres was calculated as a function of stress and exercise group, covarying age, BMI and education. Logistic regression analyses revealed a significant moderating effect of exercise. As predicted, among non-exercisers a one unit increase in the Perceived Stress Scale was related to a 15-fold increase in the odds of having short telomeres (p<.05), whereas in exercisers, perceived stress appears to be unrelated to TL (B = −.59, SE = .78, p = .45). Vigorous physical activity appears to protect those experiencing high stress by buffering its relationship with TL. We propose pathways through which physical activity acts to buffer stress effects.

‘Functional Connectivity’ Is a Sensitive Predictor of Epilepsy Diagnosis after the First Seizure:

Although epilepsy affects almost 1% of the world population, diagnosis of this debilitating disease is still difficult. The EEG is an important tool for epilepsy diagnosis and classification, but the sensitivity of interictal epileptiform discharges (IEDs) on the first EEG is only 30-50%. Here we investigate whether using ‘functional connectivity’ can improve the diagnostic sensitivity of the first interictal EEG in the diagnosis of epilepsy. Patients were selected from a database with 390 standard EEGs of patients after a first suspected seizure. Patients who were later diagnosed with epilepsy (i.e. ≥two seizures) were compared to matched non-epilepsy patients (with a minimum follow-up of one year). The synchronization likelihood (SL) was used as an index of functional connectivity of the EEG, and average SL per patient was calculated in seven frequency bands. In total, 114 patients were selected. Fifty-seven patients were diagnosed with epilepsy (20 had IEDs on their EEG) and 57 matched patients had other diagnoses. Epilepsy patients had significantly higher SL in the theta band than non-epilepsy patients. Furthermore, theta band SL proved to be a significant predictor of a diagnosis of epilepsy. When only those epilepsy patients without IEDs were considered (n = 74), theta band SL could predict diagnosis with specificity of 76% and sensitivity of 62%. Theta band functional connectivity may be a useful diagnostic tool in diagnosing epilepsy, especially in those patients who do not show IEDs on their first EEG. Our results indicate that epilepsy diagnosis could be improved by using functional connectivity.

The Brain Functional Networks Associated to Human and Animal Suffering Differ among Omnivores, Vegetarians and Vegans:

Empathy and affective appraisals for conspecifics are among the hallmarks of social interaction. Using functional MRI, we hypothesized that vegetarians and vegans, who made their feeding choice for ethical reasons, might show brain responses to conditions of suffering involving humans or animals different from omnivores. We recruited 20 omnivore subjects, 19 vegetarians, and 21 vegans. The groups were matched for sex and age. Brain activation was investigated using fMRI and an event-related design during observation of negative affective pictures of human beings and animals (showing mutilations, murdered people, human/animal threat, tortures, wounds, etc.). Participants saw negative-valence scenes related to humans and animals, alternating with natural landscapes. During human negative valence scenes, compared with omnivores, vegetarians and vegans had an increased recruitment of the anterior cingulate cortex (ACC) and inferior frontal gyrus (IFG). More critically, during animal negative valence scenes, they had decreased amygdala activation and increased activation of the lingual gyri, the left cuneus, the posterior cingulate cortex and several areas mainly located in the frontal lobes, including the ACC, the IFG and the middle frontal gyrus. Nonetheless, also substantial differences between vegetarians and vegans have been found responding to negative scenes. Vegetarians showed a selective recruitment of the right inferior parietal lobule during human negative scenes, and a prevailing activation of the ACC during animal negative scenes. Conversely, during animal negative scenes an increased activation of the inferior prefrontal cortex was observed in vegans. These results suggest that empathy toward non conspecifics has different neural representation among individuals with different feeding habits, perhaps reflecting different motivational factors and beliefs.

ScienceOnline2010 – interview with Jack, Staten Island Academy student

Continuing with the tradition from last two years, I will occasionally post interviews with some of the participants of the ScienceOnline2010 conference that was held in the Research Triangle Park, NC back in January. See all the interviews in this series here. You can check out previous years’ interviews as well: 2008 and 2009.
Today, I asked Jack from Miss Baker’s Biology class at Staten Island Academy, to answer a few questions. Jack wrote about his experience at ScienceOnline2010 here and wrote a blog post about video/computer games here.
Welcome to A Blog Around The Clock. Would you, please, tell my readers a little bit more about yourself? Where are you from?
Jack pic.jpgI’m Jack, a freshman student who went to Science Online 2010. I am one of Miss Baker’s students and I’m from NJ. I go to school at Staten Island Academy. I currently play the piano but I am planning to get a drum set to teach myself drums, too. I love making things whether it be some random contraption built out of paper or a game to be put online. I always liked making things since I built stuff with legos when I was in lower school.
What is taking up the most of your time and passion these days? What are your goals?
I enjoy using photoshop and flash together to make games. Recently, I decided to also write out my own music for the games. I am currently making a few games that have absorbed most of my free time. Between painstakingly creating graphics and filtering through code to thinking of music for the games, my free time is pretty much gone. As for my goals, I always wanted to design and create new devices or develop new software. I really want to go to M.I.T. for college, and I’ve been doing my best in and out of school to try and get there. On a completely different note, I also want to learn Japanese.
What particular use of the Web in science interests you the most?
I enjoy the amount of freedom that the web gives people, as anyone can access a world-wide database of knowledge for almost any subject. I currently surf the web to find aid in the programming world whenever I have trouble with a script. I also enjoy how the web can be used as a great device for gathering information and doing research. As I move along in developing my programming skills, it is great to talk with fellow programmers to brainstorm possible techniques of getting around difficulties like run time or complex functions.
How does (if it does) blogging figure in your work and school? How about social networks, e.g., Twitter, FriendFeed and Facebook? Do you find all this online activity to be a net positive (or even a necessity) in what you do and want to accomplish?
Using Facebook has helped me immensely as it is quicker and more open than e-mailing, so if I or someone else needs a little help with something, they can simply put it up and one of their friends can help out. I also think it is a great way to spread cool articles and facts. Twitter on the other hand has been abused by hundreds of people. No, I really don’t care that you are “enjoying your microwavable pizza” mrtwittrface. Because of all of the “eating this” or “listening to that” tweets on Twitter, I really can’t get into it.
As Miss Baker, when teaching the Biology class, gives you a lot of creative freedom, how does that affect your own interest in the subject? Do you think you learn better this way? What would you suggest to do differently to make it even better? What are some of your own projects you did for the class?
Of course, I found it easier to learn by writing a blog post and commenting on others. Having the creative freedom allowed me to learn what I wanted to, while also allowing the output of the project to be read and understood by people who aren’t just my classmates. Not only was I able to learn about how video games affect the brain, but I also got to make a game and work on my programming.
What was the best aspect of ScienceOnline2010 for you? Any suggestions for next year? 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?
I loved the fact that people were able to come together for a few days to talk about how the internet is used in science. It was cool to be one of the 8 kids there looking at everything from a different view than most of the other people there. I can’t believe that while I was presenting, Beth Beck (jokingly) asked, “Would you like a job at NASA?” but I was so focused on not messing up that the question just flew over my head. I didn’t want to ruin my opportunity to present at a conference in front of scientists and journalists and everyone else who was there, too. Because of that moment, I’m now working harder than before on my “occupation” of making flash games, as I realized that I could make a positive impact with my programming knowledge, but I need to keep working on getting better first.
It was so nice to meet you in person and thank you for the interview. I hope to see you again next January.

Clock Quotes

Those who think they have not time for bodily exercise will sooner or later have to find time for illness
– Edward Stanley

New and Exciting in PLoS this week

Tuesday night – time for four PLoS journals to publish new articles and for me to check them out and pick a few I consider most bloggable. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:

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ScienceOnline2010 – interview with Karyn Hede

Continuing with the tradition from last two years, I will occasionally post interviews with some of the participants of the ScienceOnline2010 conference that was held in the Research Triangle Park, NC back in January. See all the interviews in this series here. You can check out previous years’ interviews as well: 2008 and 2009.
Today, I asked Karyn Hede to answer a few questions:
Welcome to A Blog Around The Clock. Would you, please, tell my readers a little bit more about yourself? Where are you coming from (both geographically and philosophically)? What is your (scientific) background?
Karyn Hede pic.jpgI think of myself as a scientist who writes, even though I jumped out of research after graduate school. Most of my formal education is in science. I was biology/chemistry major and then studied genetics in graduate school at the University of North Carolina – Chapel Hill. I should have known I would end up a science communicator though. As an undergraduate, I performed in a “chemistry magic show.” We would go around to elementary and middle schools and get kids involved in the show. It was fantastic to see kids get engaged and to realize that science can be fun. After I committed to making the switch to writing about science and medicine, I studied journalism at UNC-CH. This was well before the medical journalism program existed. I was the oddball. I like to think I helped plant the seed for that program. I’ve spent my whole career telling stories about medicine, science and scientists.
Tell us a little more about your career trajectory so far: interesting projects past and present?
My first professional writing gig was for a local publication called Triangle Business Journal. I talked the editor into letting me write personality profiles of local scientists. My first interview was with George Hitchings, of the [now defunct] Burroughs Wellcome Co., who had just won the Nobel Prize in Medicine. He was so gracious, and I was so nervous! Many years later, I was working as communications officer at the Burroughs Wellcome Fund, a post now occupied by the inestimable Russ Campbell, when Dr. Hitchings passed away. We went over to the old Burroughs Wellcome offices to collect some of his memorabilia for display. They had his personal scrapbook there – he had cut out the article I wrote and put it in his scrapbook. That remains one of the best compliments I’ve ever been paid as a writer.
I was senior science writer at Duke Medical Center for four years. I learned how to put together broadcast-quality video and how to organize and run a news conference. It was a hectic job, and I spent a lot of my time responding to media requests. I discovered I prefer to be on the other side of the equation. I like to be the one asking questions.
Currently, I am a news correspondent for Journal of the National Cancer Institute and for the journal Science’s Careers site. I also write for magazines and science organizations.
What is taking up the most of your time and passion these days?
An undercurrent within my work has always been career development for scientists. When I was a graduate student, you were pretty much on your own as far as exploring career options and developing professional skills. I enjoy teaching and helping support the next generation of scientists. In the last couple of years I have done some consulting work with the North Carolina Biotechnology Center to promote professional science masters programs with the state. We organized a meeting around the issue in 2008. I’ve also been working with Russ Campbell on a series of professional development booklets for scientists. Recently, I started teaching scientific writing for biomedical graduate students at UNC. I taught two courses, one for first-year students and a second course I developed for students who are working their first grant or their dissertation. It’s my way of giving back.
What are your goals?
I am also into gardening and the local food movement. I subscribe to a local CSA at Maple Spring Gardens. A few years ago I organized a session at the National Association of Science Writers meeting to get science writers more interested in covering how our food is produced. Since then, the topic has gotten a lot of coverage, with Michael Pollan’s fantastic books and all the concern over outbreaks of food-borne disease. I’d love to write more about the intersection of science and food production.
What aspect of science communication and/or particular use of the Web in science interests you the most?
I think the wave of the future in science communication is going to be scientists engaging directly with people through their own blogs, videos and websites. Some people (like you!) are naturals and don’t need any help. I know scientists who would like to move more into this arena, but don’t know how to get started. I’d like to work with scientists to help them develop those communication and storytelling skills.
How does (if it does) blogging figure in your work? How about social networks, e.g., Twitter, FriendFeed and Facebook? Do you find all this online activity to be a net positive (or even a necessity) in what you do?
I read blogs and have gotten story ideas from blogs. I don’t have a blog (yet). I like to let ideas percolate for awhile before writing. The thought of having to produce coherent posts every day (or nearly so) is a bit daunting. My Facebook connections are mostly old friends from college and family. I like LinkedIn for work-related networking – it’s a bit more professional and I like having more control over the content.
When and how did you first discover science blogs? What are some of your favourites? Have you discovered any cool science blogs by the participants at the Conference?
I lived in Washington state for several years and moved back to North Carolina a couple of years ago. In my absence, I discovered an enthusiastic on-line science blogging community had grown up here. I wasn’t surprised. This has always been a science-rich area – blogging is just the latest incarnation of the local science communications community, but with a much wider reach now. I read your blog, Drugmonkey, Female Science Professor, The Intersection, and Terra Sigillata, among others.
What was the best aspect of ScienceOnline2010 for you? Any suggestions for next year?
This was my first time attending ScienceOnline. I was impressed with the sessions and particularly the workshops on Fri. The sessions on visualization in science were valuable, because I was teaching at the time and was able to gather a lot of incredible resources for my students. Meeting so many interesting people who are inventing the future of science communication was great. I’d love to see more of a mashup of working scientists and science communicators shaping the agenda next year.
It was so nice to see you again and thank you for the interview. I hope you can come again next January.

Cory Doctorow in Chapel Hill

Cory Doctorow, blogger at BoingBoing and author of several books, came to town last weekend and did a reading/signing of his latest novel For The Win at Flyleaf Books in Chapel Hill on Sunday.
I assume that, being bloggers and blog-readers, you all know who Cory is and what he does – if not, follow the links above as this post is going to be self-centered 😉
This is the first time I got to meet Cory in person, but he is pretty important person in my life. After I have been blogging about politics for a couple of years and my blog started being well known in the circles of the progressive blogosphere, Kerry/Edwards ticket lost and we all sunk into a collective state of depression. I wrote a few election post-mortems but the wind was out of my sails and I was tired of political blogging.
So I started a new blog in January 2005 and posted a longish blog post about circadian rhythms and sleep in humans. I installed Sitemeter on that one-post blog and went to sleep, only to wake up in the morning to an avalanche of traffic – coming from BoingBoing, linked to by Cory. Soon others linked to it as well, e.g., Andrew Sullivan. To this day, this is still one of the most visited posts in my blogging career and at least once a year it gets rediscovered by someone on digg, redditt or stumbleupon which brings in another mini-avalanche of traffic to it.
That was a wake-up call and an Eureka moment. Aha! Everyone can bash Bush and Cheney, but not everyone can write about science from a position of expertise! I can! On that day I became a science blogger. I knew a handful of science blogs at the time – Intersection, Loom, Pharyngula, Deltoid…but really, the space was still wide open at that time. Very soon, my science blog was receiving as high traffic as the political one, although I kept it very narrowly focused on just chronobiology – talk about a niche blog!
A year later, I was invited to join Scienceblogs.com which widened my audience and enabled me to organize the first science blogging conference (now known as ScienceOnline) and to put together the first science blogging anthology (Open Laboratory 2006). This broadened my audience even more and put my name out there into the media, the science publishing world and Science 2.0 world. As a blogger whose academic library password expired, I naturally became a proponent of Open Access and tended to blog a lot about PLoS papers because I could access them. All of this led to a job at PLoS which I got in the comments of a blog post of mine. That job then led to many other opportunities – speaking invitations, two trips to Europe, various consulting gigs, etc.
So, a single link from someone like Cory can completely alter one’s career trajectory. Just saying. Never hold your links back, you never know how that can help a person one day.
Oh, and you never know what exactly on your blog is interesting to other people. Cory says he loves the Clock Quotes. Go figure!
Anyway, I took a few murky photos at the reading – under the fold:

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Clock Quotes

You cannot make your opportunities concur with the opportunities of people whose incomes are ten times greater than yours.
– Edward S. Martin

New and Exciting in PLoS ONE

There are 28 new articles in PLoS ONE today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:
Torpor on Demand: Heterothermy in the Non-Lemur Primate Galago moholi:

Hibernation and daily torpor are energy- and water-saving adaptations employed to survive unfavourable periods mostly in temperate and arctic environments, but also in tropical and arid climates. Heterothermy has been found in a number of mammalian orders, but within the primates so far it seems to be restricted to one family of Malagasy lemurs. As currently there is no evidence of heterothermy of a primate outside of Madagascar, the aim of our study was to investigate whether small primates from mainland Africa are indeed always homeothermic despite pronounced seasonal changes in weather and food availability. One of the nearest relatives of Malagasy lemurs, the African lesser bushbaby, Galago moholi, which inhabits a highly seasonal habitat with a hot wet-season and a cold dry-season with lower food abundance, was investigated to determine whether it is capable of heterothermy. We measured skin temperature of free-ranging individuals throughout the cool dry season using temperature-sensitive collars as well as metabolic rate in captured individuals. Torpor was employed by 15% of 20 animals. Only one of these animals displayed heterothermy in response to natural availability of food and water, whereas the other animals became torpid without access to food and water. Our results show that G. moholi are physiologically capable of employing torpor. However they do not use it as a routine behaviour, but only under adverse conditions. This reluctance is presumably a result of conflicting selective pressures for energy savings versus other ecological and evolutionary forces, such as reproduction or territory defence. Our results support the view that heterothermy in primates evolved before the division of African and Malagasy Strepsirhini, with the possible implication that more primate species than previously thought might still have the potential to call upon this possibility, if the situation necessitates it.

Marginal Eyespots on Butterfly Wings Deflect Bird Attacks Under Low Light Intensities with UV Wavelengths:

Predators preferentially attack vital body parts to avoid prey escape. Consequently, prey adaptations that make predators attack less crucial body parts are expected to evolve. Marginal eyespots on butterfly wings have long been thought to have this deflective, but hitherto undemonstrated function. Here we report that a butterfly, Lopinga achine, with broad-spectrum reflective white scales in its marginal eyespot pupils deceives a generalist avian predator, the blue tit, to attack the marginal eyespots, but only under particular conditions–in our experiments, low light intensities with a prominent UV component. Under high light intensity conditions with a similar UV component, and at low light intensities without UV, blue tits directed attacks towards the butterfly head. In nature, birds typically forage intensively at early dawn, when the light environment shifts to shorter wavelengths, and the contrast between the eyespot pupils and the background increases. Among butterflies, deflecting attacks is likely to be particularly important at dawn when low ambient temperatures make escape by flight impossible, and when insectivorous birds typically initiate another day’s search for food. Our finding that the deflective function of eyespots is highly dependent on the ambient light environment helps explain why previous attempts have provided little support for the deflective role of marginal eyespots, and we hypothesize that the mechanism that we have discovered in our experiments in a laboratory setting may function also in nature when birds forage on resting butterflies under low light intensities.

Targeted Manipulation of Serotonergic Neurotransmission Affects the Escalation of Aggression in Adult Male Drosophila melanogaster:

Dopamine (DA) and serotonin (5HT) are reported to serve important roles in aggression in a wide variety of animals. Previous investigations of 5HT function in adult Drosophila behavior have relied on pharmacological manipulations, or on combinations of genetic tools that simultaneously target both DA and 5HT neurons. Here, we generated a transgenic line that allows selective, direct manipulation of serotonergic neurons and asked whether DA and 5HT have separable effects on aggression. Quantitative morphological examination demonstrated that our newly generated tryptophan hydroxylase (TRH)-Gal4 driver line was highly selective for 5HT-containing neurons. This line was used in conjunction with already available Gal4 driver lines that target DA or both DA and 5HT neurons to acutely alter the function of aminergic systems. First, we showed that acute impairment of DA and 5HT neurotransmission using expression of a temperature sensitive form of dynamin completely abolished mid- and high-level aggression. These flies did not escalate fights beyond brief low-intensity interactions and therefore did not yield dominance relationships. We showed next that manipulation of either 5HT or DA neurotransmission failed to duplicate this phenotype. Selective disruption of 5HT neurotransmission yielded flies that fought, but with reduced ability to escalate fights, leading to fewer dominance relationships. Acute activation of 5HT neurons using temperature sensitive dTrpA1 channel expression, in contrast, resulted in flies that escalated fights faster and that fought at higher intensities. Finally, acute disruption of DA neurotransmission produced hyperactive flies that moved faster than controls, and rarely engaged in any social interactions. By separately manipulating 5HT- and DA- neuron systems, we collected evidence demonstrating a direct role for 5HT in the escalation of aggression in Drosophila.

Loss and Recovery Potential of Marine Habitats: An Experimental Study of Factors Maintaining Resilience in Subtidal Algal Forests at the Adriatic Sea:

Predicting and abating the loss of natural habitats present a huge challenge in science, conservation and management. Algal forests are globally threatened by loss and severe recruitment failure, but our understanding of resilience in these systems and its potential disruption by anthropogenic factors lags well behind other habitats. We tested hypotheses regarding triggers for decline and recovery potential in subtidal forests of canopy-forming algae of the genus Cystoseira. By using a combination of historical data, and quantitative in situ observations of natural recruitment patterns we suggest that recent declines of forests along the coasts of the north Adriatic Sea were triggered by increasing cumulative impacts of natural- and human-induced habitat instability along with several extreme storm events. Clearing and transplantation experiments subsequently demonstrated that at such advanced stages of ecosystem degradation, increased substratum stability would be essential but not sufficient to reverse the loss, and that for recovery to occur removal of the new dominant space occupiers (i.e., opportunistic species including turf algae and mussels) would be required. Lack of surrounding adult canopies did not seem to impair the potential for assisted recovery, suggesting that in these systems recovery could be actively enhanced even following severe depletions. We demonstrate that sudden habitat loss can be facilitated by long term changes in the biotic and abiotic conditions in the system, that erode the ability of natural ecosystems to absorb and recover from multiple stressors of natural and human origin. Moreover, we demonstrate that the mere restoration of environmental conditions preceding a loss, if possible, may be insufficient for ecosystem restoration, and is scarcely cost-effective. We conclude that the loss of complex marine habitats in human-dominated landscapes could be mitigated with appropriate consideration and management of incremental habitat changes and of attributes facilitating system recovery.

Phylogenetic Evidence for Lateral Gene Transfer in the Intestine of Marine Iguanas:

Lateral gene transfer (LGT) appears to promote genotypic and phenotypic variation in microbial communities in a range of environments, including the mammalian intestine. However, the extent and mechanisms of LGT in intestinal microbial communities of non-mammalian hosts remains poorly understood. We sequenced two fosmid inserts obtained from a genomic DNA library derived from an agar-degrading enrichment culture of marine iguana fecal material. The inserts harbored 16S rRNA genes that place the organism from which they originated within Clostridium cluster IV, a well documented group that habitats the mammalian intestinal tract. However, sequence analysis indicates that 52% of the protein-coding genes on the fosmids have top BLASTX hits to bacterial species that are not members of Clostridium cluster IV, and phylogenetic analysis suggests that at least 10 of 44 coding genes on the fosmids may have been transferred from Clostridium cluster XIVa to cluster IV. The fosmids encoded four transposase-encoding genes and an integrase-encoding gene, suggesting their involvement in LGT. In addition, several coding genes likely involved in sugar transport were probably acquired through LGT. Our phylogenetic evidence suggests that LGT may be common among phylogenetically distinct members of the phylum Firmicutes inhabiting the intestinal tract of marine iguanas.

Morphological and Molecular Characterizations of Psychrophilic Fungus Geomyces destructans from New York Bats with White Nose Syndrome (WNS):

Massive die-offs of little brown bats (Myotis lucifugus) have been occurring since 2006 in hibernation sites around Albany, New York, and this problem has spread to other States in the Northeastern United States. White cottony fungal growth is seen on the snouts of affected animals, a prominent sign of White Nose Syndrome (WNS). A previous report described the involvement of the fungus Geomyces destructans in WNS, but an identical fungus was recently isolated in France from a bat that was evidently healthy. The fungus has been recovered sparsely despite plentiful availability of afflicted animals. We have investigated 100 bat and environmental samples from eight affected sites in 2008. Our findings provide strong evidence for an etiologic role of G. destructans in bat WNS. (i) Direct smears from bat snouts, Periodic Acid Schiff-stained tissue sections from infected tissues, and scanning electron micrographs of bat tissues all showed fungal structures similar to those of G. destructans. (ii) G. destructans DNA was directly amplified from infected bat tissues, (iii) Isolations of G. destructans in cultures from infected bat tissues showed 100% DNA match with the fungus present in positive tissue samples. (iv) RAPD patterns for all G. destructans cultures isolated from two sites were indistinguishable. (v) The fungal isolates showed psychrophilic growth. (vi) We identified in vitro proteolytic activities suggestive of known fungal pathogenic traits in G. destructans. Further studies are needed to understand whether G. destructans WNS is a symptom or a trigger for bat mass mortality. The availability of well-characterized G. destructans strains should promote an understanding of bat-fungus relationships, and should aid in the screening of biological and chemical control agents.

A Three-Dimensional Atlas of the Honeybee Neck:

Three-dimensional digital atlases are rapidly becoming indispensible in modern biology. We used serial sectioning combined with manual registration and segmentation of images to develop a comprehensive and detailed three-dimensional atlas of the honeybee head-neck system. This interactive atlas includes skeletal structures of the head and prothorax, the neck musculature, and the nervous system. The scope and resolution of the model exceeds atlases previously developed on similar sized animals, and the interactive nature of the model provides a far more accessible means of interpreting and comprehending insect anatomy and neuroanatomy.

The Bank of Standardized Stimuli (BOSS), a New Set of 480 Normative Photos of Objects to Be Used as Visual Stimuli in Cognitive Research:

There are currently stimuli with published norms available to study several psychological aspects of language and visual cognitions. Norms represent valuable information that can be used as experimental variables or systematically controlled to limit their potential influence on another experimental manipulation. The present work proposes 480 photo stimuli that have been normalized for name, category, familiarity, visual complexity, object agreement, viewpoint agreement, and manipulability. Stimuli are also available in grayscale, blurred, scrambled, and line-drawn version. This set of objects, the Bank Of Standardized Stimuli (BOSS), was created specifically to meet the needs of scientists in cognition, vision and psycholinguistics who work with photo stimuli.

Genomic Diversity and Introgression in O. sativa Reveal the Impact of Domestication and Breeding on the Rice Genome:

The domestication of Asian rice (Oryza sativa) was a complex process punctuated by episodes of introgressive hybridization among and between subpopulations. Deep genetic divergence between the two main varietal groups (Indica and Japonica) suggests domestication from at least two distinct wild populations. However, genetic uniformity surrounding key domestication genes across divergent subpopulations suggests cultural exchange of genetic material among ancient farmers. In this study, we utilize a novel 1,536 SNP panel genotyped across 395 diverse accessions of O. sativa to study genome-wide patterns of polymorphism, to characterize population structure, and to infer the introgression history of domesticated Asian rice. Our population structure analyses support the existence of five major subpopulations (indica, aus, tropical japonica, temperate japonica and GroupV) consistent with previous analyses. Our introgression analysis shows that most accessions exhibit some degree of admixture, with many individuals within a population sharing the same introgressed segment due to artificial selection. Admixture mapping and association analysis of amylose content and grain length illustrate the potential for dissecting the genetic basis of complex traits in domesticated plant populations. Genes in these regions control a myriad of traits including plant stature, blast resistance, and amylose content. These analyses highlight the power of population genomics in agricultural systems to identify functionally important regions of the genome and to decipher the role of human-directed breeding in refashioning the genomes of a domesticated species.

Jennifer Ouellette: Matchmaker for Hollywood and science (video)

Scientists: Don’t ask what Hollywood can do for you, ask what you can do for Hollywood!
Jennifer Ouellette is the Director of The Science & Entertainment Exchange, and a popular science writer. She also writes for her blog – Cocktail Party Physics.
She spoke with The Plainspoken Scientist about how scientists can best help Hollywood.

ScienceOnline2010 – interview with Sonia Stephens

Continuing with the tradition from last two years, I will occasionally post interviews with some of the participants of the ScienceOnline2010 conference that was held in the Research Triangle Park, NC back in January. See all the interviews in this series here. You can check out previous years’ interviews as well: 2008 and 2009.
Today, I asked Sonia Stephens to answer a few questions:
Welcome to A Blog Around The Clock. Would you, please, tell my readers a little bit more about yourself? Where are you coming from (both geographically and philosophically)?
Sure. I’m originally from Minnesota, but moved to Hawaii when I was young. Now I’m living in Florida. So geographically, I’ve been all over the place, but I probably consider Hawaii “home”. I was always interested in science and nature while growing up – while I was in Hawaii, that interest focused a bit on evolution and extinction. Hawaii is one of the evolution hotspots of the world, and now it’s unfortunately one of the extinction hotspots as well. There are many, many biological, political, social, and economic factors that have combined to create this situation in the Hawaiian Islands. Invasive species, climate change, and dwindling supplies of fossil fuels are some specific problems that make it really obvious that “culture” and “nature” are not, and can never be, separate. This idea made a big impression on me in college, so my interest in ecology now is in this interface of the human and natural worlds.
What is your (scientific) background? Tell us a little more about your career trajectory so far: interesting projects past and present?
Sonia Stephens pic.jpgAt the University of Hawaii, I studied the ecology of stream algae for my Master’s. After graduating, I worked for the National Park Service on a program to inventory and set up a long-term monitoring plan for Pacific Island park natural resources. I started out working on streams and other freshwater ecosystems, some of which are pretty funky, like anchialine pools. These are brackish systems found in rocky coastal areas in Hawaii, connected to both fresh and salty groundwater through crevices in the basalt substrate. They harbor a unique flora and fauna that can cope with tidal changes in salinity. They’re also culturally hugely important, as the only surface-level freshwater on these incredibly hot, dry coastal lava plains. Unfortunately, they’re also hugely threatened by groundwater pollution, coastal development, and invasive species. So these were some of the key resources that the NPS wanted to protect.
The point at which I started to get interested in science communication was when I began working more in-depth on the actual writing of the monitoring plan, as well as coming up with conceptual models and diagrams to illustrate ecosystems and processes (like anchialine pools). I found it really interesting and challenging to translate some of the complicated ideas into pictures as tools to communicate with the public. A whole different question, though, is how to actually get those explanations and illustrations out to people. Traditionally, the NPS creates park displays, which can only be visited in person, and reports and newsletters, which are now downloadable. But these aren’t necessarily the most far-reaching communication methods.
What I’m interested in doing is exploring how scientific organizations can use online tools to communicate with the public. Right now, I’m a PhD student at the University of Central Florida, in the Texts & Technology program. This is a humanities-based program that emphasizes study of digital media, so it’s pretty interdisciplinary in both methodology and subject matter. What I’d like to do is shed some light on what online tools work best for what purposes, and why some tools work better for some types of communication than others.
What is taking up the most of your time and passion these days? What are your goals?
Well, as a grad student, classes and teaching are definitely taking up most of my time. Since my program is based in an English department, I’m teaching college composition this academic year as part of my financial support, which has been quite a learning experience for me. This summer and next semester, I’ll be going into taking my candidacy exams and planning research (assuming the exams go well), so that will take up the majority of my time. In my research, I’m planning to use both visual and science communication theories to look at online science communication. I’m definitely interested in doing some empirical research, but those ideas are still taking shape.
How does (if it does) blogging figure in your work? How about social networks, e.g., Twitter, FriendFeed and Facebook? Do you find all this online activity to be a net positive (or even a necessity) in what you do?
I don’t have a blog, but I’ve been slowly dipping my toes into the social network aspect of the Internet. Facebook is a great way to keep track of what people are doing, but it does add to the occasional multitasking frenzy, so I’m not sure whether it’s a net positive yet… My main interest in these tools is more along the lines of asking what they’re good for, in terms of working on public understanding of science. I know a lot of writers like to use blogging as sort of a journaling tool, or a place to play with ideas. I’ve never really enjoyed journaling, but I’m starting to see how it might be useful in preparing for my exams (an idea I got from reading Christina Pikas’s blog), so that might be a good way to get started blogging. Right now, I have a fairly basic website online but I’m hoping to upgrade that soon…
When and how did you first discover science blogs? What are some of your favourites? Have you discovered any cool science blogs by the participants at the Conference?
I do read several of the blogs on the Science Blogs site, but honestly I usually just go to the 24-hour feed and look at what posts seem interesting. I do read a couple of nature blogs pretty regularly- one is by Julie Zickefoose, a nature writer & illustrator. and the other is by a birder, Sharon Stiteler. The rest of the blogs I read are generally politically oriented.
What was the best aspect of ScienceOnline2010 for you? Any suggestions for next year? 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?
Well, one of the questions that seemed to keep coming up at the meeting was: we have all these online tools to communicate with the public, but what tools work best in what situations? There’s a need for research on how well efforts at online science communication work in what situations. Which, obviously, is where I’m trying to go with my studies. I won’t promise to give a complete answer 🙂 but maybe I’ll be able to shed some light on this question.
I also saw a huge diversity of opinion about what science communication is, what blogging is for, whether we should be striving for science literacy vs. public understanding of science, etc. For these more philosophical questions, the answers really depend on the person doing the communicating. I think listening to the talks at the meeting and participating in some conversations helped me clarify some of those answers for myself and think about where I’d like to focus in my work. Personally, I’m involved in environmental activism, and I think that simply educating people about the science behind environmental issues is a huge step in creating sustainable social change. So my focus is on the public understanding of science, with the underlying goal of making the connections between “culture” and “nature” more obvious. Maybe in a few years, if I keep banging my head on a wall of public miseducation about statistics, for example, I’ll shift my focus to science literacy. But for now, I’ll try to start at least a little smaller!
It was so nice to meet you in person and thank you for the interview. I hope to see you again next January.

Open Laboratory 2010 – submissions so far

The list is growing fast – check the submissions to date and get inspired to submit something of your own – an essay, a poem, a cartoon or original art.
The Submission form is here so you can get started. Under the fold are entries so far, as well as buttons and the bookmarklet. The instructions for submitting are here.

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Clock Quotes

In answer to the question of why it happened, I offer the modest proposal that our Universe is simply one of those things which happen from time to time.
– Edward P. Tryon

Jay Rosen: How the News is Made Now (video)


Jay Rosen talks to World Bank, about “how the powerful cope with public scrutiny.” He talks for 30 minutes and the Q&A is another 30 minutes. Worth a watch.

Clock Quotes

There is a fifth dimension beyond those known to man. It is a dimension vast as space and timeless as infinity. It is the middle ground between light and shadow, between the pit of his fears and the summit of his knowledge. This is the dimension of imagination. It is an area called the Twilight Zone.
– Rod Serling

Diving Horses (video)

Related information:
The Diving Horses of Atlantic City
Wild Hearts Can’t Be Broken (movie)
Dedicated to The Diving Horses
Diving Horses (video)
The diving Horse (video)
Diving horse (Wikipedia)
A girl and Five Brave Horses (book)

Clock Quotes

Never bear more than one kind of trouble at a time. Some people bear three – all they have had, all they have now, and all they expect to have.
– Edward Everett Hale

Don’t Be a Sucker (video)

A 1947 movie made by the Department of War – as current today as it was then:

You can download the video or watch it bigger here.

Lots of news around PLoS these days

First big piece of news is the new PLoS Hub for Biodiversity – see the details on the PLoS Blog.
Second big piece of news is the New PLoS ONE Collection – Biodiversity of Saba Bank – the collection homepage, where all the articles are collected, is here and the overview article is here.
There is some movement on The Federal Research Public Access Act (FRPAA) in Congress. Keep up with the updates at the The Alliance for Taxpayer Access site, the Scholarly Publishing & Academic Resources Coalition (SPARC) site, or by following PLoS on Twitter.
There is ten days left for the April Blog Pick of the Month – keep those blog posts coming!
If you are not in a habit of checking the everyONE blog (and you should), note that I compile a weekly summary of the best blog and media coverage of PLoS ONE papers. See, for example, the collections of links for this week, last week and the week before it. As I noted before, the coverage by blogs is better and easier to collect (as bloggers link and cite the papers) than the coverage from MSM. Eh, one day they’ll learn, I hope…
I also occasionally choose a particularly cool image from a PLoS ONE paper and use it as a starting point (or center-piece) for a blog post about the paper. See the last two such posts here and here.
Finally, there are a number of new articles published in four out of seven journals yesterday and today and under the fold are those I find personally interesting or bloggable. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:

Continue reading

Clock Quotes

The need to be right all the time is the biggest bar to new ideas. It is better to have enough ideas for some of them to be wrong than to be always right by having no ideas at all.
– Edward de Bono

ScienceOnline2010 – interview with Antony Williams

Continuing with the tradition from last two years, I will occasionally post interviews with some of the participants of the ScienceOnline2010 conference that was held in the Research Triangle Park, NC back in January. See all the interviews in this series here. You can check out previous years’ interviews as well: 2008 and 2009.
Today, I asked Antony Williams from ChemSpider to answer a few questions.
Welcome to A Blog Around The Clock. Would you, please, tell my readers a little bit more about yourself? Where are you coming from (both geographically and philosophically)? What is your (scientific) background? Tell us a little more about your career trajectory so far: interesting projects past and present?
Tony Williams pic.jpgHi Bora…thanks for the invitation to connect! Where do I come from? When people meet me they’ll interpret my mongrel accent in many ways assuming that I am from Australia commonly (especially the Canadians) or from England (which is of course the common term for the United Kingdom over here). Well, I am from the UK but I am Welsh, not English. Earlier in life I was going to be a Welsh teacher but it’s been almost 30 years since I had a conversation in Welsh! I grew up in a small village in Wales of less than a hundred people. From there I went to Liverpool University to do a degree in Chemistry. I found Organic Chemistry very easy but really struggled with Physical Chemistry, especially spectroscopy. I found it very challenging but something in my personality, my friends call it a defect, has me prefer a challenge over something that it easy. I tend to take on those things that challenge me and push me rather than those things that are easy. So, naturally, I focused on physical chemistry, specifically spectroscopy, and in my final year of my degree did a summer project on NMR and got hooked. From there I went to London University to do my PhD looking at the effects of High Pressure on Lubricant Related Systems by Nuclear Magnetic Resonance, funded by Shell Oil. I engineered my own High Pressure Vessel made from non-magnetic titanium to stick into a magnet and apply pressures of up to 5kbar to liquids and look at the molecular dynamics under pressure. I was writing software to analyze the data and fit to specific models. Fun times – engineering, chemistry, computing – the type of diversity I like in a project.
From there I went to Ottawa, Canada to work at the National Research Centre (NRC) labs switching from Nuclear Magnetic Resonance to Electron Spin Resonance for about 18 months. It was a great place to work and I truly enjoyed the switch to a new type of spectroscopy. However, NMR definitely had more applications so I switched back to NMR and went to the University of Ottawa to run their NMR Facility, again for about 18 months. Lack of funding and the inability to get new equipment in to run even some of the more mundane modern NMR experiments had me look for other opportunities and move South to the United States to work at Kodak in Rochester as their NMR Technology Leader. There I had the responsibility to set the technology vision for NMR and manage a number of their NMR labs. During that period I was focused on the development of walk-up technologies to provide access to modern analytical technologies in the hands of chemists in a “walk-up” environment delivering robotic control, offline data access and processing and an “analytical LIMS” – a laboratory information management system to track samples, structure and spectra through our lab. We build the first web-based LIMS system, called WIMS (Web-based Information Management System) on Netscape Navigator (remember that?) and got a lot of attention and visits from the LIMS vendors. We developed software systems under the simple adage of “The Web is the Way”…how right we were. That work was done in 1996.
From Fortune 500 America I joined a small start-up chemistry software company called Advanced Chemistry Development. I joined as their product manager for NMR and over the next few years grew the product line into the industry leader for NMR prediction, for third party NMR processing and databasing and, one of the best undertakings of my scientific career, a platform for Computer Assisted Structure Elucidation. I had the opportunity to work with some of the best small molecule NMR jocks in the world, an incredible team of developers and scientists at ACD/Labs and then move my skill set outside of NMR. I managed the development of an entire analytical data management system (ADMS) covering Nuclear Magnetic Resonance, Mass Spectrometry, Chromatography, Infrared Spectroscopy and a myriad of other analytical techniques. I managed the structure drawing software, ChemSketch, that has had over a million downloads as it is now freeware, and the nomenclature product line for generating systematic names from structures and converting names to structures. The product lines became so successful that we had to bring in a group of other product managers who could focus on the individual product lines. I became their Chief Science Officer with a major focus on business development but always kept my hands in direct product management, marketing and sales. My passion remained the application of software to data handling, manipulation and delivery to scientists and trying to extract as much information as possible from available data.
A few years ago I floated an idea inside ACD/Labs regarding how it might be possible to index chemical compounds within an organization. Not just ones sitting inside a structure database but those represented in documents, reports, papers, publications, patents and represented by chemical names and structure images. It would require the culmination of multiple technologies including entity extraction techniques to find chemical identifiers, algorithms and look-up dictionaries to convert names to structures and software to convert structure images to structures. The intention was to index inside a central database and provide a tool to structurally index the network. We never moved the project forward because there was too much going on.
A couple of years later I was working extreme hours, focused a lot on sales, marketing and business. While it was fun there was a creative part of me not being exercised and I decided to start a hobby project to stress that particular muscle. I’d been watching what was going on with PubChem and a number of other online databases such as DrugBank. Web technologies had come a long way and I implicitly still believed in the “web is the way”. The concept of spidering an organization’s network had expanded to spidering the internet. Admittedly a major undertaking, a lot of the tools were coming together to allow it to happen. A few of my friends and I got together to create a platform for centrally indexing chemistry on the internet with the intention of linking chemical compounds to related resources on the web. And so ChemSpider was born.
ChemSpider logo.pngOnce ChemSpider went online as a structure searchable database of about 10 million chemicals we expanded the database by adding data from various other data sources, added functionality to query the data in various ways and added various services to allow organizations to tap into the resource we were building. Our target shifted over the next couple of years to one of building a structure centric community for chemists and, as we started to assemble and index the public chemistry on the internet it became clear that there was an enormous quality issue in the majority of the public compound databases we wanted to link too. There were so many errors in these databases it was quite shocking. As we assembled our database we were inheriting these errors and it was clear that we would need to curate these data in both robotic and manual ways. We built a curation platform to allow crowdsourced curation of the data so that users of ChemSpider could help us clean up the data. We added a deposition system for users to deposit their own chemistry and we added a series of tools to allow users to annotate the data and add supplementary information. The database today is almost 25 million unique entities assembled from over 300 data sources. We’ve truly built a community of chemists around ChemSpider with thousands of users coming to the site everyday and with a number of these users curating, annotating and adding data on an ongoing basis.
In June of last year the Royal Society of Chemistry acquired ChemSpider and that is where I am now as the Vice President of Strategic Development.
What is taking up the most of your time and passion these days? What are your goals?
Our focus remains consistent with the original goal of building a central portal for chemists to facilitate traversing the web to find chemistry related data, information and knowledge. At present we remain focused on linking together structure-based data and resources but will eventually expand this out to chemical compounds that cannot be explicitly defined by a chemical structure table…things such as polymers, minerals and mixtures (coal tar, mineral oil, etc.). We busy building curated disambiguation dictionaries and use them as the basis of chemical name (entity) extraction and recognition so that we can perform semantic markup and linking. We continue to expand the breadth and improve the quality of the data on the database with the intention of being able to query and link to every structure-based database that can be accessed via the internet. Chemists have different personae – there are synthetic chemists, analytical scientists, medicinal chemists, chemistry students and teachers to name just a few. While each of these would want to access different types of data for their work and research a Venn Diagram would provide a specific set of query overlaps – let them search by chemical name, chemical structure/substructure and properties. From there they would layer on different expectations about what to do with the result set. The goal is simple…make the internet structure-searchable and provide interfaces and services to allow chemists to query and use the results.
What aspect of science communication and/or particular use of the Web in science interests you the most?
Tony Williams pic2.jpgOne specific area of interest I have right now is to encourage crowdsourced collaboration in chemistry. My bias at present is to present an environment whereby members of the chemistry community can give/share/contribute/educate/enable/improve chemistry on the internet. In our terms this means allowing them to add their data to the ChemSpider database, annotate what’s already online, validate and curate out the junk. By applying their skills and contributing they can build their own professional profile in the community and bring benefit to other chemists. We are intending to layer on recognition and rewards systems and allow chemists to form connection networks of collaboration. We ourselves are already immersed into the network of Open Notebook Science providing access to services and data allowing others to perform their research. One of our areas of focus right now is ChemSpider SyntheticPages, an online database of synthetic procedures built for the community by the community. There is so much chemistry, so many chemical reactions that are performed in labs across the world but the synthetic details and associated analytical data never sees light of day and never gets published. It might make it into a thesis but then that will get put on the supervisors shelf or in a library somewhere. Despite the fact that these can be electronically enabled and discoverable the reality is it hardly happens. If we can get just a fraction of the chemistry community to donate one SyntheticPage a week the database will explode. As it’s a free resource chemists have much to benefit. The challenge is to how to encourage a chemist to invest some of their time in writing up their procedure and putting it online. Contributors to date have commented that if its already in electronic format it might add another 15-30 minutes to their day but the result is public exposure of the work, a permanent record of value to other chemists, a public profile for the submitted (including a digital object identifier for the resume!), and an opportunity to engage the community as they can provide feedback and comments. Everyone wins.
How does (if it does) blogging figure in your work?
I don’t blog as much as I used to simply because I don’t have as much time on my hands. When ChemSpider started I was “dragged” into blogging because of some attacks made on ChemSpider made by very vocal members of the blogosphere. I couldn’t figure out how to defuse some of the misinformation and accusations being made about our efforts with ChemSpider except to become a participant in the blogosphere. I found that blogging became a great way for me to engage the ChemSpider users and get their feedback on ideas for improving the service, to communicate new functionality in the system, to express my views of things going on in the community and to generally release creative expression again through writing.
The ChemSpider blog remains a way to communicate what we’re up to in terms of new developments on ChemSpider and other Cheminformatics projects internal to RSC. It also gives me a voice to comment on what’s going on in chemistry that interests me, what’s happening in the world of Open Science and engaging our users in dialog.
How about social networks, e.g., Twitter, FriendFeed and Facebook? Do you find all this online activity to be a net positive (or even a necessity) in what you do?
Facebook for me, at present, is more of a personal tool in terms of interacting with my friends and family in the UK and around the world. I use Twitter quite regularly (as @ChemSpiderman) and certainly while I am sitting in conferences and seminars. I have found Twitter surprisingly useful, more than I had ever imagined when it first showed up on the scene. My interactions via Friendfeed are certainly useful and I stay connected to certain groups of people on there and stay connected and informed. While each of these takes time it is definitely a net positive, though I would clarify, not a necessity for what I do. I am definitely an advocate for LinkedIn and find the networking aspects of that platform in particular very enabling.
When and how did you first discover science blogs? What are some of your favourites? Have you discovered any cool science blogs by the participants at the Conference?
I first discovered science blogs when I was dragged into the blogosphere by some particularly negative commentaries that were being made about ChemSpider. Lots of judgments, the majority of them not fact-based, were made about what we were trying to achieve with ChemSpider. As they say however, “no press is bad press” and once the fire was lit I entered the blogosphere to respond to the accusations. Without doing so I feel that our reputation would have been very negatively tarnished. It is one of the downsides of the blogosphere unfortunately…people get to say whatever they want, whatever they perceive and, in certain cases have no facts or data to back up their claims. That is when things get very interesting and engaging though!
My Google Reader follows a number of bloggers from my domain. I have a particular appreciation for the insights of Derek Lowe on his “In the Pipeline” blog. I follow Cameron Neylon, Jean-Claude Bradley, Egon Willighagen, Milkshake’s “Org Prep Daily“, Paul Docherty’s “Totally Synthetic” and many others of a similar nature. I had to slim down what was feeding the reader recently as following too many people was becoming overly distracting. I didn’t start following any particular blogs after the ScienceOnline conference but I do watch a lot more people via Twitter now and, when they tweet a post of interest, I navigate over to their blog. Twitter has become another way to link me into blogposts of interest without me overpopulating my reader.
What was the best aspect of ScienceOnline2010 for you? Any suggestions for next year? 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?
ScienceOnline was fun. I attend a lot of conferences in a year but the energy at ScienceOnline is simply contagious. The level of engagement and contribution far outweighs that I have experienced at any other conference other than the two SciFoo meetings I have attended. Participants at these types of meeting are there to do more than listen. They want to speak…they want to engage and they want to share their opinions. At many conferences there are blocks of time when I am not in sessions. At ScienceOnline there were too many sessions I wanted to sit in on and couldn’t. A much better situation! I walked out of the meeting with new connections, new collaborations and new possibilities. Definitely worth attending.
My one embarrassing moment was when I stood up to do the Lightning (Ignite) Talk at the dinner and hadn’t read the rules of engagement as it were. A pure oversight on my part regarding the flow of the Ignite Talk it actually worked for some strange and unknown reason. Keep the Ignite Talk format next year at the dinner…they were great fun.
It was so nice to see you again and thank you for the interview. I hope to see you again next January.

Clock Quotes

Time, when it is left to itself and no definite demands are made on it, cannot be trusted to move at any recognized pace. Usually, it loiters; but just when one has come to count on its slowness, it may suddenly break into a wild, irrational gallop.
– Edith Wharton

New and Exciting in PLoS ONE

There are 28 new articles in PLoS ONE today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:
Prestige Affects Cultural Learning in Chimpanzees:

Humans follow the example of prestigious, high-status individuals much more readily than that of others, such as when we copy the behavior of village elders, community leaders, or celebrities. This tendency has been declared uniquely human, yet remains untested in other species. Experimental studies of animal learning have typically focused on the learning mechanism rather than on social issues, such as who learns from whom. The latter, however, is essential to understanding how habits spread. Here we report that when given opportunities to watch alternative solutions to a foraging problem performed by two different models of their own species, chimpanzees preferentially copy the method shown by the older, higher-ranking individual with a prior track-record of success. Since both solutions were equally difficult, shown an equal number of times by each model and resulted in equal rewards, we interpret this outcome as evidence that the preferred model in each of the two groups tested enjoyed a significant degree of prestige in terms of whose example other chimpanzees chose to follow. Such prestige-based cultural transmission is a phenomenon shared with our own species. If similar biases operate in wild animal populations, the adoption of culturally transmitted innovations may be significantly shaped by the characteristics of performers.

Specific Appetite for Carotenoids in a Colorful Bird:

Since carotenoids have physiological functions necessary for maintaining health, individuals should be selected to actively seek and develop a specific appetite for these compounds. Great tits Parus major in a diet choice experiment, both in captivity and the field, preferred carotenoid-enriched diets to control diets. The food items did not differ in any other aspects measured besides carotenoid content. Specific appetite for carotenoids is here demonstrated for the first time, placing these compounds on a par with essential nutrients as sodium or calcium.

The Origin and Genetic Variation of Domestic Chickens with Special Reference to Junglefowls Gallus g. gallus and G. varius:

It is postulated that chickens (Gallus gallus domesticus) became domesticated from wild junglefowls in Southeast Asia nearly 10,000 years ago. Based on 19 individual samples covering various chicken breeds, red junglefowl (G. g. gallus), and green junglefowl (G. varius), we address the origin of domestic chickens, the relative roles of ancestral polymorphisms and introgression, and the effects of artificial selection on the domestic chicken genome. DNA sequences from 30 introns at 25 nuclear loci are determined for both diploid chromosomes from a majority of samples. The phylogenetic analysis shows that the DNA sequences of chickens, red and green junglefowls formed reciprocally monophyletic clusters. The Markov chain Monte Carlo simulation further reveals that domestic chickens diverged from red junglefowl 58,000±16,000 years ago, well before the archeological dating of domestication, and that their common ancestor in turn diverged from green junglefowl 3.6 million years ago. Several shared haplotypes nonetheless found between green junglefowl and chickens are attributed to recent unidirectional introgression of chickens into green junglefowl. Shared haplotypes are more frequently found between red junglefowl and chickens, which are attributed to both introgression and ancestral polymorphisms. Within each chicken breed, there is an excess of homozygosity, but there is no significant reduction in the nucleotide diversity. Phenotypic modifications of chicken breeds as a result of artificial selection appear to stem from ancestral polymorphisms at a limited number of genetic loci.

The Mediterranean Sea Regime Shift at the End of the 1980s, and Intriguing Parallelisms with Other European Basins:

Regime shifts are abrupt changes encompassing a multitude of physical properties and ecosystem variables, which lead to new regime conditions. Recent investigations focus on the changes in ecosystem diversity and functioning associated to such shifts. Of particular interest, because of the implication on climate drivers, are shifts that occur synchronously in separated basins. In this work we analyze and review long-term records of Mediterranean ecological and hydro-climate variables and find that all point to a synchronous change in the late 1980s. A quantitative synthesis of the literature (including observed oceanic data, models and satellite analyses) shows that these years mark a major change in Mediterranean hydrographic properties, surface circulation, and deep water convection (the Eastern Mediterranean Transient). We provide novel analyses that link local, regional and basin scale hydrological properties with two major indicators of large scale climate, the North Atlantic Oscillation index and the Northern Hemisphere Temperature index, suggesting that the Mediterranean shift is part of a large scale change in the Northern Hemisphere. We provide a simplified scheme of the different effects of climate vs. temperature on pelagic ecosystems. Our results show that the Mediterranean Sea underwent a major change at the end of the 1980s that encompassed atmospheric, hydrological, and ecological systems, for which it can be considered a regime shift. We further provide evidence that the local hydrography is linked to the larger scale, northern hemisphere climate. These results suggest that the shifts that affected the North, Baltic, Black and Mediterranean (this work) Seas at the end of the 1980s, that have been so far only partly associated, are likely linked as part a northern hemisphere change. These findings bear wide implications for the development of climate change scenarios, as synchronous shifts may provide the key for distinguishing local (i.e., basin) anthropogenic drivers, such as eutrophication or fishing, from larger scale (hemispheric) climate drivers.

Sequencing, Analysis, and Annotation of Expressed Sequence Tags for Camelus dromedarius:

Despite its economical, cultural, and biological importance, there has not been a large scale sequencing project to date for Camelus dromedarius. With the goal of sequencing complete DNA of the organism, we first established and sequenced camel EST libraries, generating 70,272 reads. Following trimming, chimera check, repeat masking, cluster and assembly, we obtained 23,602 putative gene sequences, out of which over 4,500 potentially novel or fast evolving gene sequences do not carry any homology to other available genomes. Functional annotation of sequences with similarities in nucleotide and protein databases has been obtained using Gene Ontology classification. Comparison to available full length cDNA sequences and Open Reading Frame (ORF) analysis of camel sequences that exhibit homology to known genes show more than 80% of the contigs with an ORF>300 bp and ~40% hits extending to the start codons of full length cDNAs suggesting successful characterization of camel genes. Similarity analyses are done separately for different organisms including human, mouse, bovine, and rat. Accompanying web portal, CAGBASE (http://camel.kacst.edu.sa/), hosts a relational database containing annotated EST sequences and analysis tools with possibility to add sequences from public domain. We anticipate our results to provide a home base for genomic studies of camel and other comparative studies enabling a starting point for whole genome sequencing of the organism.

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ScienceOnline2010 – interview with Emily Fisher

Continuing with the tradition from last two years, I will occasionally post interviews with some of the participants of the ScienceOnline2010 conference that was held in the Research Triangle Park, NC back in January. See all the interviews in this series here. You can check out previous years’ interviews as well: 2008 and 2009.
Today, I asked Emily Fisher from Oceana to answer a few questions.
Welcome to A Blog Around The Clock. Would you, please, tell my readers a little bit more about yourself? Where are you coming from (both geographically and philosophically)? What is your (scientific) background?
I grew up in Raleigh and Durham, North Carolina, and moved to Washington, DC about three years ago. I’m a writer and editor, not a scientist, but I’ve become more and more interested in science the last few years, which has surprised me. In school, science was always my least favorite subject and the one I did the worst in. The worst grade I ever got in high school was a C in physics, and that was after crying regularly during office hours. As an English major in college, I only took one science class: astronomy, and that was so I could go to UNC’s great planetarium.
I’ve always loved reading, writing and spending time in nature, so I’ve come around to science as an environmentalist. I want to spend my life helping protect the environment through writing and editing, so I’ve come to appreciate that I need to know the science behind what’s happening to the planet – and I’m increasingly curious about it. Scientific thinking doesn’t come easy to me, but maybe that’s also part of its appeal.
Tell us a little more about your career trajectory so far: interesting projects past and present?
My first job out of college was as an assistant editor for a small non-profit publisher that focused mostly on neuroscience. I learned a lot about the brain, though ironically I can’t remember most of it now…
After that I worked for a news aggregator web start-up called Brijit.com. We took long-form journalism (articles from the New Yorker, Atlantic, Harper’s, etc.) and published 100-word abstracts of the articles. It was like a thinking person’s Digg. It was a tremendously fun atmosphere — there were just a few of us editors, sitting around one big table in a one-room apartment in the Dupont Circle neighborhood of DC. We were churning out around 100 abstracts a day — we had it down to a science, really — and having a great time. We had a really cool thing going, but unfortunately the money ran out.
Emily Fisher pic.JPG
For the past two years I’ve worked for the ocean conservation organization Oceana as the web editor. I’ve learned so much about the threats facing the ocean, from ocean acidification to shark finning to bottom trawling, and I’ve become an ocean advocate myself.
Twice I’ve gone to the coast of North Carolina (Bald Head Island) to write about sea turtles for our blog and magazine — once I documented sea turtles hatching and once I wrote about nesting mothers. Both were incredible experiences.
What is taking up the most of your time and passion these days? What are your goals?
At Oceana, I’m focused on making our website and blog the most readable and engaging place for ocean conservation information. I would love to make us the number one place online for the oceans.
More specifically, right now in light of the Gulf of Mexico oil spill, we are trying to get 500,000 people to sign our petition to Obama and Congress stop new offshore drilling. So far we’ve gotten nearly 33,000 signatures.
I’m also passionate about sustainable food, so in my free time I spend a lot of time at the farmers’ market and trying out new recipes with friends. I also do a lot of yoga and am attempting to learn how to play the guitar.
How does (if it does) blogging figure in your work? How about social networks, e.g., Twitter, FriendFeed and Facebook? Do you find all this online activity to be a net positive (or even a necessity) in what you do?
Blogging is a big part of what I do on a daily basis. I aim to post one blog a day on Oceana’s blog, The Beacon, and sometimes I do more. In the last few weeks, for example, I’ve been posting two, three, four posts a day because of the oil spill. I think a lot of folks at Oceana have recognized what an asset the blog is at a time like this, when we want to react swiftly to the crisis and get our voice out there.
I started our Twitter account last year, and a friend and colleague of mine has pretty much taken it over along with Facebook. She’s doing a great job getting people engaged in our work.
I think blogging and social media are a crucial part of our communications work at Oceana — it’s our primary method of interacting directly with our activist base, or Wavemakers, and hearing their ideas, concerns and questions. Our CEO, Andy Sharpless, is even tweeting now, at @Oceana_Andy.
What was the best aspect of ScienceOnline2010 for you? Any suggestions for next year? 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?
I really enjoyed finally meeting people that I had online relationships with but never met in person, like Miriam Goldstein and the guys from Deep Sea News and Southern Fried Science. I also met some great new people, like the web editor from the New England Aquarium.
At the session about the future of science journalism, I realized that the line between blogger and journalist is truly blurred now. Similarly, at the session about social media from the Pacific Garbage Patch, I was impressed to see how science can be documented using social media tools like blogging and Twitter, even from the middle of the ocean. It was really striking to hear that the journalist’s New York Times story about the garbage patch was less effective and reached fewer people than her personal blog did.
I also really enjoyed the “blog to book” session. It’s my dream to write a book one day, and while a book project itself seems overwhelming, blogging doesn’t. It made a book seem like an achievable goal — some day.
It was so nice to see you and thank you for the interview. I hope to see you again next January.

Open Laboratory 2010 – submissions so far

The list is growing fast – check the submissions to date and get inspired to submit something of your own – an essay, a poem, a cartoon or original art.
The Submission form is here so you can get started. Under the fold are entries so far, as well as buttons and the bookmarklet. The instructions for submitting are here.

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Using Games to develop strategies and skills to thrive in a real-time world

If you can, join us at noon, Tuesday, May 25, here in Research Triangle Park for our final 2009-2010 American Scientist pizza lunch talk. (Don’t worry, we’ll launch a new season next fall.)
Our speaker will be Phaedra Boinodiris, a Serious Games Program Manager at IBM, where she helps craft IBM’s serious games strategy in technical training, marketing and leadership development. She’ll discuss: “Using Games to develop strategies and skills to thrive in a real-time world.” Boinodiris is the founder of the INNOV8 program, a series of games focused on business process management. An entrepreneur, she co-founded WomenGamers.Com, a popular women’s gaming portal on the Internet.
American Scientist Pizza Lunch is free and open to science journalists and science communicators of all stripes. Feel free to forward this message to anyone who might want to attend. RSVPs are required (for the slice count) to cclabby@amsci.org
Directions to Sigma Xi, the Scientific Research Society in RTP, are here: http://www.sigmaxi.org/about/center/directions.shtml

Today’s carnivals

Scientia Pro Publica #30 is up on Southern Fried Science.
Grand Rounds: Edition 6.34 is up on Better Health.

Clock Quotes

Contrary to general belief, an artist is never ahead of his time but most people are far behind theirs.
– Edgard Varese

New and Exciting in PLoS this week

PLoS Biology, Medicine, Neglected Tropical Diseases and ONE publish on Tuesday. What’s new today? As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:

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ScienceOnline2010 – interview with Amy Freitag

Continuing with the tradition from last two years, I will occasionally post interviews with some of the participants of the ScienceOnline2010 conference that was held in the Research Triangle Park, NC back in January. See all the interviews in this series here. You can check out previous years’ interviews as well: 2008 and 2009.
Today, I asked Amy Freitag from Southern Fried Science to answer a few questions.
Welcome to A Blog Around The Clock. Would you, please, tell my readers a little bit more about yourself? Where are you coming from (both geographically and philosophically)? What is your (scientific) background?
Well, first, the basics: I’m a PhD student at the Duke Marine Lab in Beaufort, NC. My research looks at different types of knowledge relating to water quality out here on the coast and how they do and don’t mesh to form a cohesive, scientifically-based policy to protect our estuarine resources for future generations. My scientific philosophy is a bit different than your standard empiricist, a discussion I and my co-bloggers have had in great detail and in print on the blog. Since humans and their behavior and decisions are a large part of my research, I tend to have a difficult time separating research from activism and have to pay constant attention to my role in my research community, as it extends far beyond just observation. This creates both opportunities and responsibilities.
Tell us a little more about your career trajectory so far: interesting projects past and present?
I’m interdisciplinary at heart. I never could decide if I’d rather be out talking to people or in the field counting critters. But really, the unifying factor is the observational, exploratory nature of the research, something I’d like to continue. Whether doing interviews or planting data loggers in the intertidal, it’s a field experience – a type of lifestyle where surprises are the norm. You set out with a mission to study one thing and your dissertation ends up being on something completely different that emerged from experiences during the research process. That’s what keeps me ticking – those surprises keep life interesting.
One of my favorite research projects arose from a “study abroad” experience in Alaska Native territory. The motivation initially was to get to Alaska and pay for my adventures by doing fieldwork. A forestry professor hired me to help with a prescribed burn about 45 minutes outside of Fairbanks that he and “the hotshots” from the forest service were planning. My role was to hike out every day for a few weeks and basically map out what the forest looked like pre-burn – size and types of trees, animal paths, type of understory, topography, etc. Fairly basic forestry science, which had been part of my academic history as I had spent a summer as an intern in a sugar maple plantation. However, the summer was a wet one and after I was done with all those measurements, the burn was declared postponed until the following summer. I was offered the opportunity to be a roving field hand and help with any of the projects going on at the University of Alaska, Fairbanks (UAF) that needed help.
After project-hopping for a few weeks, I was invited to come along to Venetie, a small village of roughly 200 people at the foothills of the Brooks Range in the Alaska National Wildlife Refuge that was concerned about their subsistence resources and had asked for research help from an anthropologist at UAF. I flew into town and got the tour, through a dusty general store and around the village, where there were no cars and the town activity for the day was to build a house for a recently married couple who had decided to move back to their hometown to raise their coming child.
The next day we met with the council of elders to discuss research needs and clarify the arrangement of intellectual property between UAF and the tribe. That evening, we went with one of the elders on a moose hunt, modern style – on the back of an ATV with a large rifle that could both spot and shoot across Big Lake. We didn’t see any moose that night, but did take home a duck for dinner. From a couple days’ experience, I became aware of the need for socially relevant research and collaboration with the residents in the area so carefully studied for the ecological literature. The project that resulted for me was a GIS analysis of changing subsistence resources (moose, caribou, berries, waterfowl, timber for wood stoves) under various models of increased fire due to climate change. From that, the tribe could predict which villages were the most vulnerable to resource shortages and plan for either moving them or subsidizing their needs from other villages.
Amy Freitag pic.jpg
What is taking up the most of your time and passion these days? What are your goals?
As for a lot of PhD students, most of my time goes towards my research, which is luckily also a passion of mine. I’m very much in planning stages for my life for the next three years, which is both exciting and a little bit nerve-wrecking as well. Part of that is making the friends and contacts I will need in order to get good interviews over the next few years, gaining rapport within the community. That’s often just a fun social science excuse to get out and do fun things 🙂 And hopefully, after my time here is done, I will have “an ethnography of water quality”.
What aspect of science communication and/or particular use of the Web in science interests you the most?
Science communication is crucial to both my research and commitment to broader impacts. It’s critical for transfer of knowledge and the collaboration that is necessary for effective policy. Beyond my particular interests, though, I’m often baffled by how many scientific articles are difficult to penetrate even for people who know the lingo. My undergrad advisor once said that if you can’t explain what you do to a fourth grader, taking into account their attention span, you aren’t doing good science. I’ve taken that as a mission in my life and the use of the Web is a great way to reach all the fourth graders out there.
How does (if it does) blogging figure in your work? How about social networks, e.g., Twitter, FriendFeed and Facebook? Do you find all this online activity to be a net positive (or even a necessity) in what you do?
I find blogging a good way for me to practice and refine my writing and keep my brain grounded in the real world in terms of the jargon I use. It’s a great way to extricate myself from the ivory tower. In addition, I find it super useful to have a blog up and running and respected when the time comes to write broader impacts statements. Through the summer, I will be blogging about my first time on a research cruise on the open ocean and potentially a trip to the Gulf of Mexico. In these cases, it’s both positive and necessary to blog and get immediate feedback. I credit our commenters and my Twitter friends for making me a better scientist.
When and how did you first discover science blogs? What are some of your favourites? Have you discovered any cool science blogs by the participants at the Conference?
I first discovered science blogs through friends, first the Cornell Mushroom Blog and then the one I now write for, Southern Fried Science. To be honest, I was more familiar with the political blogs, especially of the DC area where I grew up. It was a welcome find to discover science blogs and I am still surprised how welcoming the community has been. Like many before me have said, ScienceOnline is a great forum to put a face to a name on a blog and a personality behind the writing. It’s critical to keeping the community going and creating traditions and camaraderie between blogs (from singing sea shanties with the other ocean bloggers to planning Carnival of the Blue and swapping blog stories). I’ve met a number of awesome people just from one year attending ScienceOnline that are all easy to keep in touch with because we’re active over Twitter (like Jeff Ives of the New England Aquarium and Miriam Goldstein of Deep Sea News). These connections will definitely help me both professionally and personally in the future.
What was the best aspect of ScienceOnline2010 for you? Any suggestions for next year? 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 tweeting of all five parallel sessions by practically everyone in them was a change of conference culture for me, but one I would like to see occur elsewhere. It brought unity to the conference and made one fluid conversation happen as people drifted from session to session. I can’t wait to go back next year!
It was so nice to meet you in person and thank you for the interview. I hope to see you again next January.

Clock Quotes

Reading is like permitting a man to talk a long time, and refusing you the right to answer.
– Edgar Watson Howe

Now I am confused! Bye or Hello to a new Scibling?

Well, this is some kind of switcheroo!
Revere (or reveres) of Effect Measure has/have closed the doors. One of the best science/medicine blogs ever. One of those I point to when people snidely say that blogs can’t be trusted because they are all opinion and no substance. They can’t repeat that once they see Effect Measure.
But Revere(s) is/are not totally gone from the blogosphere. This is a smooth transition – from a single-person (or so we think) blog to a group blog to which Revere(s) sometimes contribute(s) – The Pump Handle. See the archives here and go say Hello at the new place here. Welcome Liz and Celeste (and yes, occasionally Revere) to the Borg!

Going Mad The American Way

New podcast and forum at PRI World Science:

Listen to a story by reporter Laura Starecheski, followed by our interview with Ethan Watters.
Our guest in the Science Forum is journalist Ethan Watters.
His latest book is Crazy Like Us: The Globalization of the American Psyche.
“America is homogenizing the way the world goes mad,” Watters writes. He contends that Americans are exporting their view of mental illness to the rest of the world.
Watters says culture influences not only how people deal with mental disorders but how mental disorders manifest themselves. Yet those cultural differences are disappearing as Western notions of mental health become popular worldwide.
Some examples Watters cites in his book:
• Anorexia nervosa, the eating disorder, is now common in countries with no history of the disease.
• Modern biomedical notions of schizophrenia are replacing the idea of spirit possession in places like Zanzibar.
• By selling pills for depression, pharmaceutical companies have caused a rise in the diagnosis of depression in Japan.
Bring your thoughts and questions about culture and mental illness to Watters. The discussion is just to the right.
* Is America’s view of mental health reflective of the nation’s individualistic culture?
* Have you or a family member been diagnosed with mental illness? Has your ethnic or religious background influenced your response?
* Would Americans benefit from importing ideas of mental health from other countries?

Related reading: The Americanization of Mental Illness.