Clock Tutorial #12: Constructing the Phase Response Curve

Clock Tutorial #12:  Constructing the Phase Response CurveThe fourth post in the series on entrainment, originally written on April 10, 2005, explains the step-by-step method of constructing a PRC.

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Clock Quotes

If you spend too much time warming up, you’ll miss the race. If you don’t warm up at all, you may not finish the race.
– Grand Heidrich

Some hypotheses about a possible connection between malaria and jet-lag

Some hypotheses about a possible connection between malaria and jet-lagHypotheses leading to more hypotheses (from March 19, 2006 – the Malaria Day):

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Clock Tutorial #11: Phase-Shifting Effects Of Light

Clock Tutorial #11: Phase-Shifting Effects Of LightThe third post in the series on entrainment, first written on April 10, 2005, starts slowly to get into the meat of things…As always, clicking on the spider-clock icon will take you to the site of the original post.

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Clock Quotes

One of the things which danger does to you after a time is, well, to kill emotion. I don’t think I shall ever feel anything again except fear. None of us can hate anymore – or love.
– Graham Greene

Everything You Always Wanted To Know About Sleep (But Were Too Afraid To Ask)

ClockWeb%20logo2.JPG
This post is perhaps not my best post, but is, by far, my most popular ever. Sick and tired of politics after the 2004 election I decided to start a science-only blog – Circadiana. After a couple of days of fiddling with the templae, on January 8, 2005, I posted the very first post, this one, at 2:53 AM and went to bed. When I woke up I was astonished as the Sitemeter was going wild! This post was linked by BoingBoing and later that day, by Andrew Sullivan. It has been linked by people ever since, as recently as a couple of days ago, although the post is a year and a half old. Interestingly, it is not linked so much by science or medical bloggers, but much more by people who write about gizmos and gadgets or popular culture on LiveJournal, Xanga and MySpace, as well as people putting the link on their del.icio.us and stumbleupon lists. In order to redirect traffic away from Circadiana and to here, I am reposting it today, under the fold.

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Clock Tutorial #10: Entrainment

Clock Tutorial #10: EntrainmentThis is the second in a series of posts on the analysis of entrainment, originally written on April 10, 2005.

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Clock Quotes

I am now going to make you a gift that will stay with you the rest of your life. For the rest of your life, every time you say we’ve always done it that way, my ghost will appear and haunt you for twenty-four hours.
– Grace Murray Hopper

Circadian Rhythms, or Not, in Arctic Reindeer

Blogging on Peer-Reviewed Research

Circadian Rhythms, or Not, in Arctic ReindeerA January 20, 2006 post placing a cool physiological/behavioral study into an evolutionary context.

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New and Exciting in PLoS ONE

There are 19 new articles published last night and 22 new articles published today in PLoS ONE. 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:
Energy Stores Are Not Altered by Long-Term Partial Sleep Deprivation in Drosophila melanogaster:

Recent human studies reveal a widespread association between short sleep and obesity. Two hypotheses, which are not mutually exclusive, might explain this association. First, genetic factors that reduce endogenous sleep times might also impact energy stores, an assertion that we confirmed in a previous study. Second, metabolism may be altered by chronic partial sleep deprivation. Here we address the second assertion by measuring the impact of long-term partial sleep deprivation on energy stores using Drosophila as a model. We subjected flies to long-term partial sleep deprivation via two different methods: a mechanical stimulus and a light stimulus. We then measured whole-body triglycerides and glycogen, two important sources of energy for the fly, and compared them to un-stimulated controls. We also measured changes in energy stores in response to a random circadian clock shift. Sex and line-dependent alterations in glycogen and/or triglyceride levels occurred in response to the circadian clock shift and in flies subjected to a single night of sleep deprivation using light. Thus, consistent with previous studies, our findings suggest that acute sleep loss and changes to the circadian clock can alter metabolism. Significant changes in energy stores were also observed when flies were subjected to chronic sleep loss via the mechanical stimulus, although not the light stimulus. Interestingly, mechanical stimulation resulted in the same change in energy stores even when it was not associated with sleep deprivation, suggesting that the changes are caused by stress rather than sleep loss. These findings emphasize the importance of taking stress into account when evaluating the relationship between sleep loss and metabolism.

Explaining Lengths and Shapes of Yeast by Scaling Arguments:

Lengths and shapes are approached in different ways in different fields: they serve as a read-out for classifying genes or proteins in cell biology whereas they result from scaling arguments in condensed matter physics. Here, we propose a combined approach with examples illustrated for the fission yeast Schizosaccharomyces pombe.

Certainty in Categorical Judgment of Size:

The certainty of judgment (or self-confidence) has been traditionally studied in relation with the accuracy. However, from an observer’s viewpoint, certainty may be more closely related to the consistency of judgment than to its accuracy: consistent judgments are objectively certain in the sense that any external observer can rely on these judgments to happen. The regions of certain vs. uncertain judgment were determined in a categorical rating experiment. The participants rated the size of visual objects on a 5-point scale. There was no feedback so that there were no constraints of accuracy. Individual data was examined, and the ratings were characterized by their frequency distributions (or categories). The main result was that the individual categories always presented a core of certainty where judgment was totally consistent, and large peripheries where judgment was inconsistent. In addition, the geometry of cores and boundaries exhibited several phenomena compatible with the literature on visual categorical judgment. The ubiquitous presence of cores in absence of accuracy constraints provided insights about objective certainty that may complement the literature on subjective certainty (self-confidence) and the accuracy of judgment.

Decaying Raphia farinifera Palm Trees Provide a Source of Sodium for Wild Chimpanzees in the Budongo Forest, Uganda:

For some years, chimpanzees have been observed eating the pith of decaying palm trees of Raphia farinifera in the Budongo Forest, Uganda. The reasons for doing this have until now been unknown. An analysis of the pith for mineral content showed high levels of sodium to be present in the samples. By contrast, lower levels were found in bark of other tree species, and also in leaf and fruit samples eaten by chimpanzees. The differences between the Raphia samples and the non-Raphia samples were highly significant (p<0.001). It is concluded that Raphia provides a rich and possibly essential source of sodium for the Budongo chimpanzees. Comparison of a chewed sample (wadge) of Raphia pith with a sample from the tree showed a clear reduction in sodium content in the chewed sample. Black and white colobus monkeys in Budongo Forest also feed on the pith of Raphia. At present, the survival of Raphia palms in Budongo Forest is threatened by the use of this tree by local tobacco farmers.

Contemporary Parallel Diversification, Antipredator Adaptations and Phenotypic Integration in an Aquatic Isopod:

It is increasingly being recognized that predation can be a strong diversifying agent promoting ecological divergence. Adaptations against different predatory regimes can emerge over short periods of time and include many different traits. We studied antipredator adaptations in two ecotypes of an isopod (Asellus aquaticus) that have, diverged in parallel in two Swedish lakes over the last two decades. We quantified differences in escape speed, morphology and behavior for isopods from different ecotypes present in these lakes. Isopods from the source habitat (reed) coexist with mainly invertebrate predators. They are more stream-profiled and have higher escape speeds than isopods in the newly colonized stonewort habitat, which has higher density of fish predators. Stonewort isopods also show more cautious behaviors and had higher levels of phenotypic integration between coloration and morphological traits than the reed isopods. Colonization of a novel habitat with a different predation regime has thus strengthened the correlations between pigmentation and morphology and weakened escape performance. The strong signature of parallelism for these phenotypic traits indicates that divergence is likely to be adaptive and is likely to have been driven by differences in predatory regimes. Furthermore, our results indicate that physical performance, behavior and morphology can change rapidly and in concert as new habitats are colonized.

Sheril and Unscientific America at Quail Ridge Books

From Quail Ridge Books

Quail Ridge Books & Music
hosts author
Sheril Kirshenbaum
for a discussion of her book
UNSCIENTIFIC AMERICA: HOW SCIENTIFIC ILLITERACY THREATENS OUR FUTURE
Thursday, July 23 at 7:30 pm
Climate change, the energy crisis, nuclear proliferation — many of the most urgent problems of the twenty-first century require science-based solution. And yet Americans are paying less and less attention to scientists. Journalist and author Chris Mooney (The Republican War on Science) and Duke scientist Sheril Kirshenbaum explain how religious ideologues, a weak education system, science-phobic politicians, and the corporate media have all collaborated to create this dangerous state of affairs. They propose a broad array of initiatives that could reverse the current trend and call for the reintegration of science into public discourse.
Sheril Kirshenbaum is a marine scientist and research associate at Duke University. She has served as a congressional science fellow and pop radio disc jockey. She lives in Durham.
If you have any questions or would like more information please call the store at 828-1588 or go to http://www.quailridgebooks.com

I’ll be there.
I hear my copy arrived. I will not blog about it until I read it (I know the framing wars have already started, but I will resist for now).

Today’s carnivals

Twitter-friendly I and the bird #104 is up on A birding blog by Gunnar Engblom – part I and part II.
Friday Ark #251 is up on Modulator

Happy Birthday Nikola Tesla!

Three years ago it was a big round number.
This year, it’s the Google logo:
tesla09.gif

ScienceOnline’09: Interview with Bob O’Hara

The series of interviews with some of the participants of the 2008 Science Blogging Conference was quite popular, so I decided to do the same thing again this year, posting interviews with some of the people who attended ScienceOnline’09 back in January.
Today, I asked Bob O’Hara of the Deep Thoughts and Silliness blog to answer a few questions.
Welcome to A Blog Around The Clock. Would you, please, tell my readers a little bit more about yourself? Who are you? What is your (scientific) background?
My name is Bob O’Hara, but I comment on blogs and such places under the absolutely impenetrable pseudonym of Bob O’H. I have a blog on Nature Network, called Deep Thoughts and Silliness.
I’m a full time academic, which means I get to be both a nerd and as obscure as I can manage. I used to be a plant epidemiologist, but I now work in biostatistics, mainly in ecology and evolutionary biology.
What do you want to do/be when (and if ever) you grow up?
Senile.
BobO'Hara pic.jpgWhat is your Real Life job?
Butler to The Beast (pictured). It’s only a part-time position, and he pays me in cat hair, which the bank doesn’t accept. I think it must be because they don’t like Australian currency.
When I’m not acting as a resting place, I’m an Academy Fellow. The academy in question is the Academy of Finland: the position is basically that of a lecturer, only without the lecturing. I live in Helsinki, dodging the polar bears and itinerant OS developers.
What aspect of science communication and/or particular use of the Web in science interests you the most?
I really enjoy the pissing around, rather than taking the science too seriously. But I am now becoming more interested in using online tools for collaboration, for example wikis. A lot of my work is collaborative, so I’m looking for tools to make it easier. Emailing Word documents is hardy optimal.
How does (if it does) blogging figure in your work? How about social networks, e.g., Twitter, FriendFeed and Facebook?
I’ve used blogging to kick a few ideas around, getting one piece published, and stirring up interest with some others. I’m using wikis to help collaboration, but I think they don’t integrate well enough into usual work practices yet. I guess we’ll have to wait for Google Wave.
Other social networks don’t really figure in my work, except as excellent vehicles for prevarication. Few of my colleagues use them, so they don’t figure in my work. Hopefully that will improve.
When and how did you discover science blogs?
I can’t remember! I had looked at Panda’s Thumb a few times, but really started following it during the hilarities of the Dover trial. That dragged me into other science blogs (I know it’s not original, but Pharyngula was one of the first blogs I read – at least it was before ScienceBlogs started up).
What are some of your favourites? Have you discovered any new cool science blogs while at the Conference?
There are too many good blogs to plug! But a couple of blogs that I think should be better known are Prerogative of Harlots and Masks of Eris. Masks of Eris, in particular, should be required reading, especially if you want to understand Finland and the Finnish mentality.
I think I also have to plug Grllllllsciennntissssst, and her efforts to win a trip to Antarctica.
I didn’t discovered any new bloggers, but meeting Propter Doc reminded me to check out her blog more often.
Why did you come to the Conference?
It was mainly to meet people who I knew virtually in the flesh. I had met some poeple in London, but obviously not many Americans.
I was hoping to meet JanieBelle, but she didn’t attend, and sent her grouchy uncle Lou instead.
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?
Probably the main thing was the discussion of Open Access. It’s something I find interesting from the sociological point of view: the technology has opened up the possibilities for OA, but acceptance of it needs some changes in the way we pay for publication. On top of simply the finances, web based publishing makes it possible to try out some very interesting ideas.
What was clear to me was that there is a large gap between the idealism of some OA advocates, and the world that most scientists inhabit. So, the idea that journals shouldn’t have to judge importance when deciding whether to publish a piece of research seems naïve: there is certainly a place for that sort of journal (as readers of this blog are well aware!), but I think the importance of publishing in a “good” journal can’t be ignored: whether we like it or not, scientists use this as a marker for the quality of their work, for gloating to their colleagues, or for judging other researchers’ output. This is part of the sociology of science: it’s how we behave as scientists. My impression is that this simply isn’t appreciated by some OA advocates, and it can make their message sound irrelevant.
As an experienced denizen of the blogosphere, I know that I don’t have to provide any answers – I can criticise as much as I want!
It was so nice to finally meet you and thank you for the interview. I hope to see you again next January.
And you. I had a lot of fun in NC, so hopefully I’ll be able to visit again next year.
==========================
See the 2008 interview series and 2009 series for more.

Open Access in Belgrade

As you know, I gave two lectures here in Belgrade. The first one, at the University Library on Monday, and the second one at the Oncology Institute of the School of Medicine at the University of Belgrade. As the two audiences were different (mainly librarians/infoscientists at the first, mainly professors/students of medicine at the second) I geared the two talks differently.
You can listen to the audio of the entire thing (the second talk) here, see some pictures (from both talks) here and read (in Serbian) a blog post here, written by incredible Ana Ivkovic who organized my entire Belgrade “tour” this year.
The second talk was, at the last minute, moved from the amphitheater to the library, which was actually good as the online connection is, I hear, much much better in the library. Library got crowded, but in the end everyone found a chair. What I did, as I usually do, was to come in early and open up all the websites I wanted to show in reverse chronological order, each in a separate window. Thus, the site I want to show first is on top at the beginning. When I close that window, the second site is the top window, then the third, etc. Thus I do the talk by closing windows instead of opening them (and hoping and praying that would not take too much time).
Knowing how talks usually go in the States, I prepared to talk for about 50 minutes. But, when I hit the 50 minute mark, I realized that nobody was getting restless – everyone was looking intently, jotting down URLs of sites I was showing, nodding….so I continued until I hit 60 minutes as which time I decided to wrap up and end. Even then, nobody was eager to get up and leave. I was hoping I’d get a question anyway….and sure, I got 45 minutes of questions. Then another 20 minutes or so of people approaching me individually to ask questions….
I used the Directory of Open Access Journals as the backdrop to give a brief history of the Open Access movement, the difference between Free Access and Open Access and the distinction between Green OA and Gold OA.
Then I used the PLoS.org site to explain the brief history of PLoS and the differences between our seven journals. Of course, this being medical school, I gave some special consideration to PLoS Medicine.
Then I used the Ida – Darwinius massillae paper to explain the concept of PLoS ONE, how our peer-review is done and to show/demonstrate the functionalities on our papers, e.g., ratings, notes, comments, article-level metrics and trackbacks.
Then I used the Waltzing Matilda paper to enumerate some additional reasons why Open Access is a Good.Thing.
Trackbacks were also a good segue into the seriousness by which the scientific and medical community is treating blogs these days. I showed Speaking of Medicine and EveryONE blog as examples of blogs we use for outreach and information to our community.
I showed and explained ResearchBlogging.org (which they seemed to particularly be taken with and jotted down the URL), showed and explained the visibility and respect of such blogging networks as Scienceblogs.com and Nature Network and then Connotea as an example of various experiments in Science 2.0 that Nature is conducting.
I put in a plug for ScienceOnline conferences and the Open Laboratory anthologies as yet another proof how seriously Science 2.0 and science blogging is now being taken in the West. Then showed 515 scientists on Twitter, The Life Scientists group and Medicine 2.0 Microcarnival on FriedFeed as examples of the ways scientists are now using microblogging platforms for communication and collaboration. I pointed out how Pawel Szczesny, through blogging and FriendFeed, got collaborations, publications, and in the end, his current job.
Then I described Jean-Claude Bradley’s concept (and practice) of Open Notebook Science and showed OpenWetWare as a platform for such work. I pointed out that Wikipedia and wiki-like projects are now edited by scientists, showing the examples of A Gene Wiki for Community Annotation of Gene Function, BioGPS and ChemSpider and ended by pointing out a couple of examples of the ways the Web allows citizen scientists to participate in massive collaborative research projects
But probably the most important part of the talk was my discussion of the drawbacks of Impact Factor and the current efforts to develop Article-level metrics to replace it – something that will be particularly difficult to change in developing countries yet is essential especially for them to be cognizant of and to move as fast as they can so as not to be left behind as the new scientific ecosystem evolves.

Belgrade ’09

As the Universiade is happening in Belgrade right now, the city is full of young people from around the world and there is a lot of cool stuff in town, including a variety of clay figurines emerging out of asphalt:

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Clock Tutorial #9: Circadian Organization In Japanese Quail

Circadian Organization In Japanese QuailGoing into more and more detail, here is a February 11, 2005 post about the current knowledge about the circadian organization in my favourite animal – the Japanese quail.

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Clock Quotes

Better to strive and climb, And never reach your goal, Than to drift along with time – An aimless, worthless soul, Aye better to climb and fall Or sow, though the yield be small, Than to throw away day after day And never strive at all.
– Grace B. Hinkey

Seasonal Affective Disorder – The Basics

Seasonal Affective Disorder - The BasicsThis is an appropriate time of year for this post (February 05, 2006)…

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ScienceOnline’09: Interview with Stacy Baker

The series of interviews with some of the participants of the 2008 Science Blogging Conference was quite popular, so I decided to do the same thing again this year, posting interviews with some of the people who attended ScienceOnline’09 back in January.
Today, I asked Stacy Baker, everyone’s favorite Biology cyber-teacher, to answer a few questions.
Would you, please, tell my readers a little bit more about yourself? Who are you? What is your (scientific) background?
I’m a high school biology teacher. I’ve taught general, honors, and advanced placement biology for the past four years. Prior to teaching I worked as a biologist and studied seabirds in the Pribilof Islands and migrating seabirds off the Atlantic coast. I also worked a few years in wildlife rehabilitation. I have a BS in Zoology from Washington State University.
What do you want to do/be when (and if ever) you grow up?
When I was growing up I would answer, “Anything, but a teacher.” I’m serious! My mom’s a teacher and growing up watching her work long hours and get very little very financial reward turned me against the profession. Why on earth would anyone want to be a teacher?
Life has a funny way of making you eat your words. When I was working in the field I would occasionally have the opportunity to share what I was doing with local K-12 students. My colleagues said I had a gift for teaching and I suppose when enough people tell you you’re really good at something you start to wonder if it’s what you’re meant to do. I’ve really enjoyed teaching despite its many frustrations. The kids make it fun. Some days I feel like I’ve spent the whole day laughing.
What aspect of science communication and/or particular use of the Web in science interests you the most?
The web makes current science accessible to my students. The Open Access movement and science blogs make it easy to connect my students with scientists and original research. The web is a great way to make science exciting again. My students get tired of learning about what’s already been done and it excites them to talk with scientists about what is currently being researched. If a scientist talks with them about what they’re doing, my students often will (on their own without even being asked) research everything about that topic and learn all the content they need to know in the process. Some of these students are the ones who walked into my classroom saying they hate science. They walk out with a completely different attitude.
How does (if it does) blogging figure in your work? How about social networks, e.g., Twitter, FriendFeed, YouTube, Flickr, Ning, Facebook and others?
My students maintain and update our class blog, Extreme Biology. At the beginning of every school year, a new group of students is trained on how to use the blog. For most of my students this is the first introduction they’ve had into blogging so the learning curve is pretty steep. I’m hopeful that as the years go by, more students will enter my class having already used blogs and other web tools and I’ll be able to skip the time-consuming training and jump right into the science. As the year progresses, my students will discover new tools for us to try. They find current science research to blog about and then put a creative spin on the topic in order to educate their peers. Some of them write songs, create animations, make videos, and previous students return to share advice. We even had our own series of interviews of Science Online ’09 participants!
In addition to the blog we have a class wiki, youtube channel, twitter, and ning. The public twitter was only started at the end of the last school year so it hasn’t really taken off, yet. I also have a private twitter feed with my students.
The session about using the Web in the classroom which you led together with eight of your students was The Big Hit of the Conference. We all learned a lot from it. What did you learn from it, from the audience questions and comments?
First, I want to thank everyone in the audience for being so wonderful and treating my students like mini-celebrities! They floated on clouds for weeks afterward! We learned that kids really have a lot of power when it comes to how the web is being used. Their voices truly matter. My students arrived at the conference feeling unsure and a bit intimidated, but they left with a ton of confidence. The audience fired questions at them the entire time and the students did a remarkable job of answering.
I floated on clouds for weeks afterward!
When and how did you discover science blogs? What are some of your favorites? Have you discovered any new cool science blogs while at the Conference?
The details are too fuzzy because it’s been so many years now. Yours! But, in addition to yours there are too many great science blogs to pick favorites. I will say that my students have received a lot of positive feedback from bloggers they’ve interacted with here on ScienceBlogs and I’m really grateful for that. Many of the blogs mentioned at the conference I already knew about, but my students made a ton of new discoveries.
StacyBaker pic.jpgYou have some experience with research in the field. What motivated you to spend this summer in the lab, learning some of the most cutting-edge techniques in molecular and cellular neuroscience – not easy stuff to do by all means?
This summer I’m working in Michael Nitabach’s lab at Yale studying circadian rhythms in fruit flies. The project is funded by a NIH grant directed at getting science teachers involved in research. While I can’t share the details of the original research project Dr. Nitabach has me working on, I can say it’s very exciting and that I’m learning a lot. The lab is pretty fast-paced as its filled with post-docs, grad students, and undergrads. A lot of great ideas get thrown around in the “fly room” each day, during lab meetings, and department cookie breaks. I love all the Drosophila jargon that gets thrown around and I’m trying to convince the lab to make “fly pusher” shirts this summer. Fruit flies are a fun model to work with and they make genetics very accessible to students so I’m excited about taking everything I’ve learned back to the classroom. Check out the cool fly brain I dissected last week!
The experience I’m gaining in Dr. Nitabach’s lab is going to make me a better teacher. I didn’t enter the teaching profession in the traditional way. At the risk of upsetting the traditionalists, I believe there is total lunacy in allowing a person to teach science who has never actually practiced science. You can’t learn science by reading textbooks or taking educational methodology classes. Every science teacher needs to have the experience of participating in original research and they need to routinely refresh their skills. The last time I performed science in the field was five years ago. I feel quite rusty. In my perfect teaching ideal, science educators would teach for 4-5 years and then take one-year off to work on an original research project. I realize this is incredibly unrealistic thanks to the immobile system we have in place to train teachers, but due to my non-traditional background this type of ideal is possible for me.
The NIH grant was offered through the use of the ARRA money. Hopefully, NIH will seriously consider offering the grant every year. It would be a strong investment into the future of science education.
As you are applying for jobs, is the schools’ attitude towards the use of the Web in the classroom high on your list of criteria?
Absolutely! I was told in an interview recently that I wouldn’t be able to continue my blogging at that school. I politely ended the interview. It’s become so much a part of my methodology that I don’t think I could ever abandon it. Not every student has the luxury of having a home computer, but there is simply no excuse for a school to not have enough computer resources to offer their students. If a teacher has a detailed plan on how they use the Web safely in their classroom, they should be allowed to use it.
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 reception we received has motivated me to seek more ways my students can directly interact with practicing scientists. I also want to have my students more involved in participating in online conversations with scientists outside of just our blog. Some of them already do that, but I’d like to see more of them doing so. For example, I’d like them to have a journal club and discuss a paper on PLoS.
It was so nice to finally meet you in person and thank you for the interview (and say Hi to all your students). I hope to see you again next January.
It was wonderful to meet you as well! See you in January!
==========================
See the 2008 interview series and 2009 series for more.

Clock Tutorial #8: Circadian Organization In Non-Mammalian Vertebrates

Circadian Organization In Non-Mammalian Vertebrates This post was originally written on February 11, 2005. Moving from relatively simple mammalian model to more complex systems.

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Clock Quotes

One of the great things about books is sometimes there are some fantastic pictures.
– Governor George W. Bush

Today’s carnivals

Grand Rounds Vol. 5 No. 42 are up on Pharmamotion
Change of Shift Volume Four, Number One is up on Emergiblog

Oxytocin and Childbirth. Or not.

Blogging on Peer-Reviewed Research

From the Archives

Blogging on Peer-Reviewed Research

When teaching human or animal physiology, it is very easy to come up with examples of ubiqutous negative feedback loops. On the other hand, there are very few physiological processes that can serve as examples of positive feedback. These include opening of the ion channels during the action potential, the blood clotting cascade, emptying of the urinary bladder, copulation, breastfeeding and childbirth. The last two (and perhaps the last three!) involve the hormone oxytocin. The childbirth, at least in humans, is a canonical example and the standard story goes roughly like this:

When the baby is ready to go out (and there’s no stopping it at this point!), it releases a hormone that triggers the first contraction of the uterus. The contraction of the uterus pushes the baby out a little. That movement of the baby stretches the wall of the uterus. The wall of the uterus contains stretch receptors which send signals to the brain. In response to the signal, the brain (actually the posterior portion of the pituitary gland, which is an outgrowth of the brain) releases hormone oxytocin. Oxytocin gets into the bloodstream and reaches the uterus triggering the next contraction which, in turn, moves the baby which further stretches the wall of the uterus, which results in more release of oxytocin…and so on, until the baby is expelled, when everything returns to normal.

As usual, introductory textbook material lags by a few years (or decades) behind the current state of scientific understanding. And a brand new paper just added a new monkeywrench into the story. Oxytocin in the Circadian Timing of Birth by Jeffrey Roizen, Christina E. Luedke, Erik D. Herzog and Louis J. Muglia was published last Tuesday night and I have been poring over it since then. It is a very short paper, yet there is so much there to think about! Oh, and of course I was going to comment on a paper by Erik Herzog – you knew that was coming! Not just that he is my friend, but he also tends to ask all the questions I consider interesting in my field, including questions I wanted to answer myself while I was still in the lab (so I live vicariously though his papers and blog about every one of them).
Unfortunately, I have not found time yet to write a Clock Tutorial on the fascinating topic of embryonic development of the circadian system in mammals and the transfer of circadian time from mother to fetus – a link to it would have worked wonderfully here – so I’ll have to make shortcuts, but I hope that the gist of the paper will be clear anyway.

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ScienceOnline’09: Interview with Stephanie Zvan

The series of interviews with some of the participants of the 2008 Science Blogging Conference was quite popular, so I decided to do the same thing again this year, posting interviews with some of the people who attended ScienceOnline’09 back in January.
Today, I asked Stephanie Zvan of the Almost Diamonds and Quiche Moraine blogs and co-moderator of the session on Science Fiction on Science Blogs, to answer a few questions.
Welcome to A Blog Around The Clock. Would you, please, tell my readers a little bit more about yourself? Who are you? What is your (scientific) background?
I have one of the least scientific backgrounds of the people attending SO’09. What background I do have is in the social sciences, which makes me even more of an outlier. I have a degree in psychology that taught me a remarkable amount about research design, however, and I’ve never really gotten over that. In fact, it kept me from following my intended path of becoming certified for counseling. It turned out there just wasn’t any good evidence that most counseling had any lasting effect (which has since changed).
Aside from that, well, I’m terrible at describing myself and make no guarantees of consistency anyway.
What do you want to do/be when (and if ever) you grow up?
I don’t think I’ll ever be content to do just one thing, but I want to write more than I do. Writing brings in no income at this point, so it’s relegated to the sidelines more than I like. Ideally, my young adult science fiction novel will find a publisher and sell well to a bunch of kids who scream for more. We’ll see how that goes.
What is your Real Life job?
szvan.jpgAside from saying that I’m an analyst who works for a large corporation, I don’t talk about my job. The information I deal with is interesting enough that I see my work in the news sometimes, but ultimately, none of it is mine, and the clients I work with shouldn’t ever stumble across me online and worry that some of it might become public.
And apropos of the panel on blogging and employers, that was made clear to me when I started with my company. It’s a general policy, but it doesn’t take much imagination to apply it to blogging.
What aspect of science communication and/or particular use of the Web in science interests you the most?
I’m a communication geek, so it all interests me. It’s fascinating to watch the tower walls fall and see people collaborating, commiserating and debating simply because the informality of most blogs
How does (if it does) blogging figure in your work? How about social networks, e.g., Twitter, FriendFeed and Facebook?
For a fiction writer, some kind of dynamic online presence is a requirement these days. Well, that’s not true if your books debut on the NYT bestsellers list, but it is the standard advice. Blogging started as self-promotion for me, but I’m terrible at self-promotion. The blog didn’t really gel until I started talking about the social, political and economic topics I’m actually interested in. Discussion of contentious topics online may not be the best way to attract an audience for young adult fiction, but I’m not sure I can do anything else and still blog with any frequency or interest for others.
I’ve been on Facebook for over a year and Twitter for a couple of months. Both have ended up as a combination of news feed and free-ranging silly conversation. That suits me perfectly, but I have no idea how or whether that connects to my work beyond keeping me informed and entertained.
What are your thoughts on the never-ending debates between groups of people who are generally on the same side, but differ in one tiny detail, usually of strategy? For example, in the evolution/creation debate, silent vs. vocal atheists, or different strands of feminism (including the question of women in STEM), people who are on the same page 99% of the time, spend a lot of time aggressively arguing the remaining 1%?
This question is your revenge for me asking you about science journalism on the radio without giving you time to prep, isn’t it?
I think there’s a certain inevitability to this. There are lots of ways to talk about what’s going on, but being me, I’ll talk about it in terms of voice.
The places where I see these 1% arguments are in groups of people whose voices have traditionally been suppressed or marginalized. Feminists’, immigrants’, poor peoples’ and racial and sexual minorities’ voices have been ignored, cut off and dismissed. Atheists have been drowned out by the hue and cry the religious raise every time we’ve reminded them we exist.
Being heard has become easier and is becoming easier, but it is still not easy. Blogs, etc. give us a great place to speak, but speaking doesn’t guarantee that anyone will listen. Even the people who do read us won’t necessarily work very hard to understand us. In fact, since we’re saying unfamiliar and uncomfortable things, they have a vested interest in misreading us. We’ve all had a reader who comes along and leaves a comment that makes us say, “You thought I said what?”
99% of the time, those are the people who want to continue to suppress all our voices. The other 1%, they’re us. (Actually, considering how internet audiences self-select, it’s significantly more than 1%.) In the middle of an ongoing fight, it’s very difficult to remember that disagreeing about 1% means that we are in the same place on the fundamentals. We’re even in the same place on a great many of the details.
1% is noise. It’s nuances and connotations of words. It’s different cultural definitions of politeness. It’s varying priorities on a common to do list. It’s not restating all the things we have in common every time we want to speak. It’s shaping messages for different groups of people who still aren’t at 75%, much less 99%. It’s hauling one argument out of the common pile on any given day instead of another.
1% is not an attack, not even in the middle of a battle. In fact, it’s a sign that we’re winning and that we’re doing something very important as we win. We are, after all, trying to build a world in which it’s okay for people to disagree.
So what do we do about all the drama? Oh, hell, why ask me? Oh, right. Because I’ll answer.
Honestly, I don’t know what we do. I think the answer lies in spending some time picturing what a world in which everyone gets a voice really looks like. It’s a scary place in some ways. There aren’t any guarantees that it will make life better for any of us as individuals, although I have to uncomfortably admit that those of us with strong or persuasive voices will likely be disproportionally privileged.
One of the things that those of us who have those voices are going to have to figure out is how to balance being forceful (or charming or cutting) enough to overcome society’s dominant messages with creating an atmosphere in which the quieter and more awkward voices aren’t shouted down. I think some of the arguments that are happening are steps in the direction of figuring this out, but I don’t think anyone has the answers right now.
When and how did you discover science blogs? What are some of your favourites? Have you discovered any new cool science blogs while at the Conference?
I was hanging out in the science fiction and fantasy blogosphere, I don’t remember where, when someone posted a link to something cool at Cognitive Daily. My degree is in psychology, and I’m fascinated by the test required to tease out effects in cognitive psych. I was hooked.
Then I discovered there was more to ScienceBlogs and much more to the science blogosphere, and I was doomed. I didn’t really discover much new through the conference, but I did get a sense of just how widely I was already reading. One thing I did get to do at the conference was tell Greta and Dave Munger this story, which it had never occurred to me I’d be able to do.
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?
Aside from meeting so many very cool people, two events stand out for me. One was having dinner with Tom Levenson and discussing one of your journalism/new media posts, The Shock Value of Science Blogs. We both started off by saying there were parts of the post we disagreed with. Each of us was talking about a different part of the post, but as we went into more depth on the topic, neither of us really disagreed with the other. That really emphasized for me the level of detail at which some of these disagreements between allies happen.
The other thing that is imprinted on my memory is standing in the hallway as sessions were in progress. The door to one session opened, a session on impact factor or open access or one of the related issues on that topic, and a young woman came out. She said she needed more coffee to deal with the discussion. She walked that direction, stopped, and turned back toward me. She wasn’t quite crying.
“I want to support open access. I think it’s important, and I want to submit to open access journals. But if I don’t submit to the big journals with high impact factors, how will I end up with a job and funding to keep researching and submitting? My adviser is young and new. How will she get tenure if we do this?”
The young always fight our revolutions, and we always lose some to the cause.
It was so nice to meet you and thank you for the interview. I hope to see you again next January.
It was lovely and invigorating and exhausting to meet you too. I hope to be there.
==========================
See the 2008 interview series and 2009 series for more.

Science Cafe Raleigh – Energy for the Future

The Science Café for July (description below) will be held on July 21st at Tir Na Nog. This is the season when our utility bills begin to skyrocket. Our costly electric bills often bring into focus the high demand our community has for energy, as well as questions about where electricity will be coming from in the future as North Carolina’s population grows. This will be the subject of our next cafe. We will be meeting Dr. David McNelis from UNC-Chapel Hill’s Institute for the Environment. Dr. McNelis will give us information about options that we have for energy production in our future. What are the safest and most viable options that we have to choose from? Are there renewable energy sources that can meet our needs in North Carolina? Here is a link to a collection of articles from the New York Times that may help you begin thinking about this complex and very important topic. (http://www.nytimes.com/ref/science/earth/energy.html).
Energy for the Future
Tuesday July 21, 2009
6:30-8:30 p.m. with discussion beginning at 7:00 followed by Q&A
Tir Na Nog 218 South Blount Street, Raleigh, 833-7795
What does our energy future look like? As new options become available, how soon will we see a difference in transportation and in the supply and use of electricity in our homes and businesses? What are some realistic expectations we should have for the reduction of carbon emissions from energy use? Come to our café and join in on a discussion of energy sources for the future.
About the Speaker:
Professor David N McNelis has over 45 years of environmental sciences and engineering experience in federal government, university and industry settings. He served in research and research management positions with the U.S. Army, the U.S. Public Health Service and the Environmental Protection Agency; with the Department of Energy’s prime contractor for the Nevada Test Site; with the University of Nevada, Las Vegas; and now serves as the Director of the Center for Sustainable Energy, Environment and Economic Development in the University of North Carolina at Chapel Hill’s Institute for the Environment and as President of Nuclear Fuel Cycle Technologies, LLC. Currently he specializes in conventional, alternative and nuclear energy systems and technologies and the nuclear fuel cycle (including partitioning, transmutation, repository capacity and nuclear non proliferation).
This café is sponsored by Progress Energy.
RSVP to kateyDOTahmannATncdenrDOTgov

Who are you, dear readers?

I asked last year. And several other SciBlings also asked last year.
And now the fashion is starting again, I see. It started with Ed, and was picked up by DM and Sci. So, let me ask again:

Identify yourself in the comments. Even if you’ve never commented before, speak up. Who are you? Do you have a background in science? Are you interesting lay-person, practicing scientist, journalist, sentient virus, or something else? Are you a close friend, colleague, acquaintance or stranger?

Clock Tutorial #7: Circadian Organization in Mammals

Circadian Organization in Mammals This February 06, 2005 post describes the basic elements of the circadian system in mammals.

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Clock Quotes

Man is always more than he can know of himself; consequently, his accomplishments, time and again, will come as a surprise to him.
– Golo Mann

New and Exciting in PLoS ONE

There have been 19 new articles Monday night and 11 new articles Tuesday night in PLoS ONE. 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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A Huge New Circadian Pacemaker Found In The Mammalian Brain

Blogging on Peer-Reviewed Research

A Huge New Circadian Pacemaker Found In The Mammalian BrainIf you really read this blog ‘for the articles’, you know some of my recurrent themes, e.g., that almost every biological function exhibits cycles and that almost every cell in every organism contains a more-or-less functioning clock. Here is a new paper that combines both of those themes very nicely, but I’ll start with a little bit of background first.

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In the Serbian media

I gave a talk about Open Access at the University Library in Belgrade yesterday (listen to the audio here and see some pictures here).
I was just on TV a couple of hours ago, on Studio B – I talk fast so I had time to promote PLoS, Open Access, blogs and tomorrow’s lecture at Oncology Center at the University of Belgrade in just about 5 minutes on air. This was also probably a rare mention of Twitter and likely the very first mention of FriendFeed in Serbian media. I was wearing a PLoS ONE t-shirt which one of the anchors pointed out 😉
I am about to on the radio (Radio Belgrade 1) where the interview will be a whole hour long. Click on “Радио 1 уживо/RM” on the right margin to listen live at 9pm local (continental European time).

Linnaeus’ floral clock on the island of Mainau

As you may have noticed, I am quite fascinated with the earliest beginnings of my scientific discipline, which was almost entirely involving research on plants. The most famous story from that early period is the construction of a Flower Clock by Karl Linne, the father of taxonomy.
So, of course I got really exited when I saw, on the Mainau island last Friday, a reconstructed Linnaeus’ floral clock.

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Then I looked carefully – and noticed it was not telling the correct time. This was taken at 3pm.

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So I thought about it for a second….and, well, this is what I think is going on here.

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First, Linnaeus’ clock is a 12-hour clock, not a 24-hour one. It does not include plants that flower at night. The division of the daytime into 12 hours makes sense only during the equinox. As daylength changes during the year, each hour will become gradually longer than 60 minutes for six months, then shorter then 60 minutes for six months. Thus, such a clock will not be precise on any day except the (spring) equinox.

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Second, the latitude of Mainau in Germany is different from that in Upsalla in Sweden. And yet, the same species of flowers were used in both places. Thus, the photoperiod will be different and plants will flower at different times of day at these two places (again, except on the day of spring equinox).

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Very pretty – but not a precise time-piece….

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ScienceOnline’09: Interview with Katherine Haxton

The series of interviews with some of the participants of the 2008 Science Blogging Conference was quite popular, so I decided to do the same thing again this year, posting interviews with some of the people who attended ScienceOnline’09 back in January.
Today, I asked Katherine Haxton of the Endless Possibilities blog (see the archives of her Nature Network blog here), to answer a few questions.
Welcome to A Blog Around The Clock. Would you, please, tell my readers a little bit more about yourself? Who are you? What is your (scientific) background?
Hello! I’m Katherine and I’m a chemist. Don’t worry, I’m not just going to talk about molecules and things that might explode. I’ve been a chemist since I figured out that I was a poor excuse for a physics undergrad and have never looked back.
What do you want to do/be when (and if ever) you grow up?
I’m currently quite happy with the job I have, but don’t rule out the prospect of doing something else in the future. I don’t intend to grow up, I just plan on growing old.
What is your Real Life job?
In real life I am a lecturer in chemistry in Britain. It’s a bit of a strange job really because it includes all the research stuff that you’d expect of an academic, a large whack of teaching and a whole load of other stuff that I never expected to be doing. At the moment, I wouldn’t want to do anything else, well, except spend a little more time in the lab perhaps.
katharinehaxton pic.JPGWhat aspect of science communication and/or particular use of the Web in science interests you the most?
Good question! I think the web offers us an amazing opportunity to connect with people, information and ideas. It gives us the chance to communicate directly with all aspects of society (who use the web), and explain who we are and what we do. We also have the opportunity to work more effectively as scientists, sharing data and information, making things more freely available. The web hosts a wonderful array of collaborative tools for scientists, I’d like to see more tools being developed for scientists and ‘the public’ to engage with the issues and ideas that come up again and again.
How does (if it does) blogging figure in your work? How about social networks, e.g., Twitter, FriendFeed and Facebook?
I’m a bad blogger at the moment, struggling to find my writing voice now that I’ve gone to the trouble of setting up my own blog website. I’m having better luck with Twitter which was unexpected – I agreed to try Twitter for 30 days and see if I ‘got it’. Now I find it very useful for information gathering and satisfying my need for gossip! I see blogging and Twitter as forms of outreach – between chemists, scientists and just generally reaching out in general.
When and how did you discover science blogs? What are some of your favourites?
I stumbled on science blogs by accident a few years ago. I remember quite clearly reading the early NatureNetwork blogs like Anna Kushnir’s Blog, LabLife. My favourites include Highly Allochthonous and ScienceWomen, and it was a real privilege to get to meet the authors of those blogs back in January. I’m particularly enjoying this summer’s crop of conference blogging/twittering from various chemistry conferences and the Lindau meeting.
Have you discovered any new cool science blogs while at the Conference?
Since the conference I’ve started reading WhiteCoatUnderground, Skull in the Stars and Almost Diamonds. I’ve implemented a ‘one in one out’ Google reader policy – for every new blog I want to read,Ihave to remove a blog that isn’t updated often or that I no longer feel a connection with.
In many online discussions, especially on sensitive topics like politics, religion and feminism, the “tone argument” raises its head, where one side, usually representing traditional power, tries to silence the other by insisting on politeness, while the other side tries to undermine the traditional power structure by shocking with impoliteness. The former sees the latter as rude, the latter perceives the former as dishonest. Do you think there is also a geographical or cultural difference in where exactly the line lies between civil and uncivil discourse? Is there, for example, a set of words, phrases or “tones” that may be considered perfectly civil by (some of) the Americans, but horribly impolite by (some of) the Brits? And if so, is there a way to point out to cultural differences in order to resolve a debate?
This is a very complicated issue and really the tone argument just gets in the way. My personal opinion is that we could all do to be more tolerant of those who disagree with us, and more conscious of how our words and statements can be misinterpreted. There has been quite a bit of discussion about rules and protocols surrounding blogging, and that’s been quite fascinating. I believe that the blogger sets the tone for the comments thread, through moderation, counter-comment and other indicators of acceptable behaviour. And those standards of acceptable behaviour vary widely between blogs, as they should. I think some bloggers forget that the diversity of experience their readership brings to any issue is the most important aspect of using this medium to communicate, mainly through their desire to be agreed with. I dislike intensely those bloggers who inspire persecution against opinions different to their own, and those who incessantly use impolite shock tactics – like anything, impoliteness looses its impact when continually overused (no, it doesn’t become an iconic trademark of a particular blogger, it just gets old). Many bloggers (yourself included) have implied that their blog is like their living room, that to read a blog post and comment is to come into the living room and join the conversation. That implies a certain standard of behavior and politeness. The converse of the politeness argument is the need for rudeness. There are times and places where the most effective way to make a point is to be rude, to issue a short, sharp shock to the audience.
I don’t think that all debates need resolving – the beauty of having cultural differences is that there is frequently no right and no wrong, just varying degrees of interpretation. I think that’s seen quite plainly in arguments about feminism (I have no time for those about religion or politics). There seems to be a growing trend in labeling people as feminist or not, supportive or not, with no acknowledgement that everyone’s perspective is, and should be, different. Some of those differences are because of cultural issues between the US and the Brits, but we’re not the sole users of the internet, something we’d all do well to remember from time to time. We should welcome open and frank discussion of the origins of those differences rather than the creation of rules and codified behaviours to moderate, and ultimately suppress, those who disagree with us or express their viewpoint in a manner we would not have chosen ourselves.
I’d like to see a little more tolerance in these debates and a little more curiosity as to the origins of opinions, and acknowledgment that there may be cultural differences or misinterpretation. Words are, unfortunately, an imprecise method of communication and open to many interpretations. I don’t understand the need of a minority to take everything in the worse possible light. In an ideal world it should be possible to point out that a cultural difference or genuine misunderstanding has had an effect, but reality is usually somewhat less than ideal!
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 was overwhelmed by how friendly and open bloggers were in ‘real life’. I was amazed by the open and frank discussion in many of the sessions and felt reassured that such communities exist. It was a very good reminder that everyone does have different points of view, but that everyone can still come together and be welcoming and friendly. The conference inspired me to blog more (which I’m struggling to do), and work out new ways to include blogging in my job.
It was so nice to meet you in person and thank you for the interview. I hope to see you again next January.
Thank you Bora. It was lovely to meet you in January and I’m looking forward to next year!
==========================
See the 2008 interview series and 2009 series for more.

Clock Tutorial #6: To Entrain Or Not To Entrain, That Is The Question

 Clock Tutorial #6: To Entrain Or Not To Entrain, That Is The QuestionThis post from February 03, 2005 covers the basic concepts and terms on entrainment. This is also the only blog post to date that I am aware of that was cited in a scientific paper.

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The Curious Case of Balloon Animals!

On the way back from the Mainau island to Lindau island, we were entertained on the ship by a balloon magician. He started out with balloon molecules. Kind of a nifty way to demonstrate why you can write with graphite and not with a diamond.
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I am not sure the magician was aware that Dr.Kroto was sitting in the front row when he produced the bucky-ball (for which Kroto got his Nobel) but it worked out great in the end.
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But it got suspicious when the guy switched to making balloon plants and animals. Could it be? Is that a balloon magician or Stuart Pivar disguised as a balloon magician?
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And then he blew his cover – he made a tentacled balloon animal and placed it on PZ’s head. Yup, that must have been him!
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Clock Quotes

We need time to dream, time to remember, and time to reach the infinite. Time to be.
– Gladys Taber

Lithium, Circadian Clocks and Bipolar Disorder

Lithium, Circadian Clocks and Bipolar DisorderYou probably realize by now that my expertise is in clocks and calendars of birds, but blogging audience forces me to occasionally look into human clocks from a medical perspective. Reprinted below the fold are three old Circadiana posts about the connection between circadian clocks and the bipolar disorder, the third one being the longest and most involved. Here are the links to the original posts if you want to check the comments (especially the first comment on the third post):
January 18, 2005: Clocks and Bipolar Disorder
August 16, 2005: Bipolar? Avoid night shift
February 19, 2006: Lithium, Circadian Clocks and Bipolar Disorder

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The panel on Climate Change at Lindau Nobel conference

Ashutosh Jogalekar wrote the best summary of the panel on Climate Change held on the island of Mainau on the last day of the Lindau Nobel Meeting:
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Today’s carnivals

Scientia Pro Publica #7 is up on Greg Laden’s blog
Carnival of the Green #187 is up on Plant a Tree USA™
Carnival of the Liberals #94 is up on Submitted To A Candid World

The Butterfly House on the island of Mainau

A couple of German bloggers and I went to see the Butterfly House on the Island of Mainau. They had good cameras with lenses that allowed them to take extreme close-ups. I had to do with a little pocket camera, but a few pictures turned out decent enough to show:

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Animals on the island of Mainau are so tame, part 2

Here are some more pictures from the domestic and wild animal life on the island:

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ScienceOnline’09: Interview with Miriam Goldstein

The series of interviews with some of the participants of the 2008 Science Blogging Conference was quite popular, so I decided to do the same thing again this year, posting interviews with some of the people who attended ScienceOnline’09 back in January.
Today, I asked Miriam Goldstein of the Oyster’s Garter blog to answer a few questions.
Welcome to A Blog Around The Clock. Would you, please, tell my readers a little bit more about yourself? Who are you? What is your (scientific) background?
I am a graduate student at the Scripps Institution of Oceanography in La Jolla, California. I write the ocean science blog the Oyster’s Garter which has recently undergone a strange metamorphosis into a twice-weekly science column at the Slate spinoff Double X.
I grew up in New Hampshire and majored in biology at Brown University. Before starting graduate school, I worked in environmental consulting, outdoor education, taxidermy sales, and condominium construction.
MiriamGoldstein pic.jpgWhat do you want to do/be when (and if ever) you grow up?
I want to somehow make a living as a science educator and communicator, like a Borscht Belt version of Dr. Tatiana . The world is crying out for a Yiddish-spouting biological oceanographer with a love for naughty invertebrate hijinks, right?
What is your Real Life job?
My graduate research is in marine debris. I’ll be leading an expedition to the North Pacific Gyre (sometimes called the “Great Pacific Garbage Patch”) this summer. We’re going to try to accurately measure the distribution of the tiny bits of plastic floating out in the middle of the ocean, and get a sense of how they might be affecting the animals at the base of the food chain. There will definitely be an expedition blog and Twitter, too!
What aspect of science communication and/or particular use of the Web in science interests you the most?
I think the web is perfect for building community. While I started blogging to share my love of the spineless and slimy, I’ve found that a network of interested people can make your voice a lot louder. I’m interested in leveraging that for conservation. We’ve had some successes in the past, such as by debunking the iron fertilization company Planktos’ ridiculous claims that they were saving the ocean by throwing iron in it.
Of course, the trick in online communication is reaching people who don’t already agree with you. I’m trying to use my Double X column to reach people who don’t necessarily care about the ocean or environmental issues.
How does (if it does) blogging figure in your work? How about social networks, e.g., Twitter, FriendFeed and Facebook?
I’m SIO’s resident cheerleader for online outreach. I think online outreach is a powerful tool for getting a broad audience to remote places, like the middle of the ocean. It’s also great for building community, which you need to do if you work in conservation. After Science Online ’09 I gave a rousing presentation on the glory of blogging to my fellow students, though I’m not sure that I’ve convinced anyone!
I’m trying to explicitly incorporate blogging into my own research. I’m very excited about the potential for really awesome blogging on our upcoming marine debris cruise. And I have a pipe dream of creating a multimedia thesis chapter, but my committee probably won’t let me.
I have started running into the downside of blogging and social networking, which is that it takes time to do it well, and time can be pretty limited in graduate school. I had to put the main Oyster’s Garter blog on hold for the summer because organizing this cruise is so time consuming. I also discovered that I don’t have time to follow social networks much – it’s just too much media to read.
When and how did you discover science blogs? What are some of your favourites? Have you discovered any new cool science blogs while at the Conference?
It all started with an office job and a Metafilter addiction. I started by occasionally reading Pharyngula and Bitch PhD . Then I got hooked on ocean blogging (pun fully intended) with Deep Sea News, Blogfish, and Malaria, Bedbugs, SeaLice, and Sunsets. I wanted to be part of that community, so I started my own blog.
I came to the Conference explicitly to meet my ocean blogging buddies as well as the landlocked yet fabulous DN Lee. At the Conference, I did discover some wonderful new bloggers, particularly Glendon Mellow of the Flying Trilobite, Daniel Brown of Biochemicalsoul, and Mike Bergin of 10,000 Birds.
What is it about life out on the ocean and singing, anyway?
The United States oceanographic fleet is alcohol-free, so while at sea we compensate by singing about grog instead of drinking it. ARRRR!
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 particularly enjoyed learning about specific tools and techniques that incorporate online learning into the classroom. The “How the Facebook Generation Does It” session was absolutely fantastic. I have already given two presentations based on what I learned at Science Online, one to fellow scientists and one to teachers.
It was so nice to finally meet you and thank you for the interview. I hope to see you again next January.
Thanks for the opportunity, and I really hope I can attend!
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See the 2008 interview series and 2009 series for more.

ClockTutorial #5: Circadian Organization

ClockTutorial #5: Circadian Organization
I wrote this post back on February 02, 2005 in order to drive home the point that the circadian clock is not a single organ, but an organ system comprised of all cells in the body linked in a hierarchical manner:

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Lindau Nobel interview – Jennifer Murphy

A brief interview with one of the young researchers attending the Lindau Nobel conference – Jennifer Murphy from the University of California, Los Angeles, USA

Clock Quotes

Once upon a time a man dragged his father from their house and as they reached a tree his father cried Stop! I did not drag my own father past this tree!
– Gertrude Stein

Lindau Nobel – interview with Ghada Al-Kadamany

A brief interview with one of the young researchers attending the Lindau Nobel conference – Ghada Al-Kadamany from Jacobs University in Bremen, Germany

Flirting under Moonlight on a Hot Summer Night, or, The Secret Night-Life of Fruitflies

Flirting under Moonlight on a Hot Summer Night, or, The Secret Night-Life of FruitfliesAs we mentioned just the other day, studying animal behavior is tough as “animals do whatever they darned please“. Thus, making sure that everything is controlled for in an experimental setup is of paramount importance. Furthermore, for the studies to be replicable in other labs, it is always a good idea for experimental setups to be standardized. Even that is often not enough. I do not have access to Science but you may all recall a paper from several years ago in which two labs tried to simultaneously perform exactly the same experiment in mice, using all the standard equipment, exactly the same protocols, the same strain bought from the same supplier on the same date, the same mouse-feed, perhaps even the same colors of technicians’ uniforms and yet, they got some very different data!
The circadian behavior is, fortunately, not chaotic, but quite predictable, robust and easily replicable between labs in a number of standard model organisms. Part of the success of the Drosophila research program in chronobiology comes from the fact that for decades all the labs used exactly the same experimental apparatus, this one, produced by Trikinetics (Waltham, Massachusetts) and Carolina Biologicals (Burlington, North Carolina):
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This is a series of glass tubes, each containing a single insect. An infrared beam crosses the middle of each tube and each time the fly breaks the beam, by walking or flying up and down the tube, the computer registers one “pen deflection”. All of those are subsequently put together into a form of an actograph, which is the standard format for the visual presentation of chronobiological data, which can be further statistically analyzed.
The early fruitfly work was done mainly in Drosophila pseudoobscura. Most of the subsequent work on fruitfly genetics used D.melanogaster instead. Recently, some researchers started using the same setup to do comparative studies of other Drosophila species. Many fruitfly clock labs have hundreds, even thousands, of such setups, each contained inside a “black box” which is essentially an environmental chamber in which the temperature and pressure are kept constant, noise is kept low and constant (“white noise”), and the lights are carefully controlled – exact timing of lights-on and lights-off as well as the light intensity and spectrum.
In such a setup, with a square-wave profile of light (abrupt on and off switches), every decent D.melanogaster in the world shows this kind of activity profile:
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The activity is bimodal: there is a morning peak (thought to be associated with foraging in the wild) and an evening peak (thought to be associated with courtship and mating in the wild).
The importance of standardization is difficult to overemphasize – without it we would not be able to detect many of the subtler mutants, and all the data would be considered less trustworthy. Yet, there is something about standardization that is a negative – it is highly artificial. By controlling absolutely everything and making the setup as simple as possible, it becomes very un-representative of the natural environment of the animal. Thus, the measured behavior is also likely to be quite un-natural.
Unlike in the lab, the fruitflies out in nature do not live alone – they congregate with other members of the species. Unlike in a ‘black box’, the temperature fluctuates during the day and night in the real world. Also unlike the lab, the intensity and spectrum of light change gradually during the duration of the day while the nights are not pitch-black: there are stars and the Moon providing some low-level illumination as well. Thus, after decades of standardized work, it is ripe time to start investigating how the recorded behaviors match up with the reality of natural behavior in fruitflies.
Three recent papers address these questions by modifying the experimental conditions in one way or another, introducing additional environmental cues that are usually missing in the standard apparatus (and if you want to know what they found, follow me under the fold):

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Lindau Nobel interview – Jan Wedekind

A brief interview with one of the young researchers attending the Lindau Nobel conference – Jan Wedekind, formerly of University of Barcelona, Spain, and now with IRIS:

Waltzing Matilda – why were the three Australian dinosaurs published in PLoS ONE?

As I was traveling, I only briefly mentioned the brand new and exciting paleontology paper in PLoS ONE – New Mid-Cretaceous (Latest Albian) Dinosaurs from Winton, Queensland, Australia that was published on Thursday. Bex has written an introduction and will post a Media/Blog coverage (of which there was a lot!) summary probably tomorrow.
The fossils were discovered, cleaned and analyzed by the Australian Age Of Dinosaurs non-profit organization, with a help of thousands of volunteers – the ‘citizen scientists’. You can learn more from their press release.
The importance of the publication of this paper from the angle of its scientific significance has been covered by several bloggers already. Also, several notice how good it is that the paper was published in an Open Access online-only journal. For example, Andy Farke writes:

This paper is a fantastic example of the real benefits of an on-line, open access journal like PLoS ONE. Without page limitations, the authors were allowed to truly monograph the heck out of the bones. Virtually every element is illustrated from multiple angles (with high resolution photos downloadable from the website!) and accompanied by thorough text descriptions and measurements. The editors of most journals would freak out over such a “waste” of precious space – but I have a feeling that future researchers are going to thank the authors for their thoroughness. As a PDF, the paper weighs in at 51 pages – and this doesn’t include the supplementary information!

The lead author Scott Hocknull, in an interview for us, said:

“One of my major motivations for submitting to PLoS ONE was the fact that my research will reach a much wider community, including the hundreds of volunteers and public who gave their time and money to the development of natural history collections. They are the backbone of our work (excuse the pun) and they usually never get to see their final product because they rarely subscribe to scientific journals.”

In the comment on the post at Sauropod Vertebra Picture of the Week, Scott Hocknull said:

This project is almost a 100% volunteer effort, with thousands of volunteer preppers working endlessly to get the bones ready for publication. This was one of my main reasons for choosing PLoS ONE to publish in. One of my others was the opportunity to provide detail images and descriptions (as best I can).
Most of our volunteers have no access to scientific journal subscriptions, therefore having it online and free for them to look at meant that they could see for themselves the fruits of their labours. They need more credit for the beautiful bones than I.

And all of you can read it for free as well – all 51 pages of it, plus all the great images and supplemental information. And you can add ratings, notes, comments and trackbacks on the paper as well.