Patricia Brennan on bird genitalia

News from SCONC:

On Thursday, March 27 at 4 p.m., the Zoology Department at NCSU will host a seminar from Patricia Brennan of Yale University entitled “The Biology of Avian Genitalia: Form and Function.” Brennan’s work on the genital anatomy of waterfowl has revealed the existence of a “sexual arms race” between males and females. Unlike 97 percent of bird species, male waterfowl have a phallus, and it can range “from a half-inch to more than 15 inches long.” The seminar will be held in 101 David Clark Labs. Refreshments will be served in the lobby at 3:45.

Related:
Friday Weird Sex Blogging – The Birds Do It….
More on duck phalluses and uteri

Today’s carnivals

Linnaeus’ Legacy #5 is up on Catalogue of Organisms
Carnival of the Blue #10 is up on Switchboard
Carnival of Space #44 is up on Bad Astronomy
Friday Ark #181 is up on Modulator

ClockQuotes

You have to recognize when the right place and the right time fuse and take advantage of that opportunity. There are plenty of opportunities out there. You can’t sit back and wait.
– Ellen Metcalf

Mixed cats

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Orange Julius

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Marbles

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Biscuit

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New on…

…the intertubes. Busy week. Here are some good links:
Leaving your literary estate to the public domain:

This page has been circulating around the Web in recent days (apparently since February 26 or later). It depicts a sticker which an individual can apply to her ID card, in the manner of an organ donor sticker, indicating the individual wishes her copyrights to be released to the public domain upon her death.

The cloning of the bulls:

The story adds to last year’s discussion about horse cloning (horserace horse cloning?). But here the main theme is the affection that owners have for their bulls.

Hyena-Primate Convergence: The Social Brain Hypothesis:

They suggest that the intricate social dynamics of spotted hyena society has led to selection pressures on cognition which are analogous to primate brain evolution.

Why do people publish in Open Access journals?:

Just talked to a job candidate, who must remain nameless for now, whose work is involved in looking into who publishes in Open Access journals and who doesn’t and why? This got me to thinking of the various factors that academics weigh when deciding where to publish an article (also part of his work) and what kinds of things can be done to influence those choices.

Audubon’s Birds of America:

The University of Pittsburgh is fortunate to own one of the rare, complete sets of John James Audubon’s Birds of America. It is considered to be the single most valuable set of volumes in the collections of the University Library System (ULS). Indeed, only 120 complete sets are known to exist.
While Audubon was creating Birds of America, he was also working on a companion publication, namely, his Ornithological Biography. Both of these sets were acquired by William M. Darlington in the mid-nineteenth century and later donated, as part of his extensive library, to the University of Pittsburgh. Recognizing that the Darlington Library includes significant historical materials, such as rare books, maps, atlases, illustrations, and manuscripts, the ULS charted an ambitious course to digitize a large portion of Mr. Darlington’s collection, including the Birds of America.
We are pleased to present our complete double elephant folio set of Audubon’s Birds of America, accompanied by his Ornithological Biography, through this Web site. Together these sets comprise an unprecedented online combination.

All Peer Reviewers are Equal, But Some Peer Reviewers are More Equal Than Others:

Ok, so the journal has these lists of scientists on the Editorial Board. What are they doing?

Teachers Under Fire:

In other words, when it comes to teaching evolutionary biology in the public school classroom, the creationists have won the battle: They’ve forced evolution into a corner, surrounded it, eviscerated, driven it into the swamp.

Henry Gee: Against Stupidity (with which I vehemently disagree on almost every point):

It used to be that scientists did what they did, and would attempt to explain this to the uncaring multitudes, in as reasonable a way as possible, cognizant of the fact that whereas the multitudes might understand little of what the scientists were on about, the scientists had a duty to try to explain their activities nonetheless, gently, given that the multitudes, untimately, paid their wages.

Fortunately, Mike Dunford picked up on a small positive piece of it and responded:
Huns, Visigoths, and the Citadel of Science:

When there’s a horde of angry, armed people outside your walls, and they start settling in and making themselves at home, you might start to wonder if you’re looking at a siege. When the catapults come out and rocks, stones, jars of burning oil, and diseased animal carcasses start flying over the walls, the folks inside often feel besieged. By the time the attackers disappear in the middle of the night, leaving behind only the remains of their camp, a long-term sanitation crisis, and a large wooden rabbit, the full-fledged siege mentality has usually set in.

Henry responds: The Release Of Calcium From Intracellular Stores (And Other Stuff):

The problem, in my experience, is an attitude that whereas it might take years of training and a certain skill to write a scientific paper, any half-baked twit can write a press release, irrespective of experience. Writing press releases is often delegated to the most junior member of staff, when crafting an effective press release is extremely hard, requires a certain authorial skill and, if it is about science, the scientific knowledge equal to that of any science journalist.

And Mike responds again: Elephants, Mice, Red Flags, Bulls, and Science:

We don’t need to do a better job of talking to the general public. We need to start talking to the general public.

Related: The Scientist Delusion? Nature Column on AAAS Panel:

In the column titled “The Scientist Delusion,” Goldston notes that even very religious publics often strongly support many areas of science.

Why Opting Out Isn’t Really an Option:

So the system stinks. It demands the impossible of us. When we see a mom leave the lab bench, professoriate, engineering firm, or courtroom, she’s not gaily deciding to spend more time baking cookies. She’s agonized, stressed out, exhausted. She’s probably reached her breaking point. Given the unrelenting demands of her family and her job, she’s decided that the job has to go, because she has moral and legal obligations to take care of her family.

Puzzling Research Interpretations :

You may remember an earlier study which found an elevated breast cancer risk for women who had taken hormone replacement therapy at menopause, compared to a control group who took a placebo. Now a follow-up study suggests that the higher breast cancer risk remains, even after the women had ceased taking estrogen and progestin. I’m unhappy with some of the interpretations that this study has been given.

Social Science:

The stereotype that a lot of scientists are not well socially adjusted has a lot of supporting evidence. Some of the most awkward people I have ever met have been scientists. People who think that plaid on plaid makes for a well-matched outfit weird. No conversation skills kind of weird.

Why Republicans Reject Science:

To summarize, I think some Republicans do not reject science per se, rather what they reject is the tendency for scientific facts to be used for planning. By planning, I mean active organization of a system to achieve a desirable (to some) outcome. Planning can be applied to any complex system — societies, economies, climate, etc., and it is predicated on the assumption the knowledge of how a system works gives one the ability to control the outcome.

A win for the cetaceans:

I’ve been trying to monitor the situation involving the Bush administration’s attempts to bypass the law and proceed with its cetacean-killing sonar tests along the Pacific Coast. This week there was an important victory on this front, picked up by Hunter at Random — a court ruling requiring the Navy to stop with its current plans.

Prozac and Placebos:

Anyway, it turns out that this study was misinterpreted by the press more than most…

Should I be ABD before I have a baby? (and other questions about academic motherhood):

If I were comparing my emotional and mental well being during my grad school pregnancies and their aftermath to that of a normal human being, it might not be a favorable comparison. On the other hand, compared to my emotional and mental well being as a graduate student struggling to find a topic and write a dissertation prior to the pregnancy and parenting? Pregnancy and parenting may actually have been better for me.

Moths remember what they learn as caterpillars:

According to popular belief, within the pupa, the caterpillar’s body is completely overhauled, broken down into a form of soup and rebuilt into a winged adult. Richard Buckmister Fuller once said that “there is nothing in a caterpillar that tells you it’s going to be a butterfly.” Indeed, as the butterfly or moth quite literally flies off into a new world, it is tempting to think that there is no connection between its new life and its old existence as an eating machine. But not so.

Beef and dairy can be good for the planet: Making a case for cows:

For starters, cow farts aren’t really the problem; burps are. As it turns out, bovine burps are responsible for the vast majority of the methane released. But that is far from the only misconception about cows’ role in making the planet suitable–or not–for human habitation.

New adventures in science:

Back in the late 1980s, many gay men–like me–had two sets of medical records. At the outset of the HIV/AIDS epidemic, no one wanted his chart to show an HIV diagnosis, nor the fact that you had simply taken the HIV antibody test, because that meant–some way, some how–that you considered yourself at risk for the disease even if your results proved otherwise. Notably, we feared this information becoming known to health insurers, even our employers, sometimes our friends and families, because of the very real possibility of discrimination. That’s why my doctor kept two sets of records: the one on the right side of my chart was the official one; the other side harbored our secrets.

Colonization of the New World:

One of the problems I see in this sort of analysis is placing the evinced genetic splits in populations in space. This paper does a reasonably good job at arguing for an early split in Asia and subsequent population changes happening in the New World. However, if we change the timing of when the Ice Free Corrider was available to facilitate the movement of people, or if we change the rate of DNA mutation that is used to place population events in time, then the model may change fundamentally. I do not have lot of faith in the estimates used for DNA mutation rates. Nonetheless, this is a good, the best so far, synthesis of the available data with new information added.

My picks from ScienceDaily

‘Power Napping’ In Pigeons:

In humans, as in all mammals, sleep consists of two phases: deep, dreamless slow-wave-sleep (SWS) alternates with dream phases, called Rapid Eye Movement (REM)-sleep. Although several studies suggest that information is processed and memories are consolidated during sleep, this remains a hotly debated topic in neurobiology. Comparative studies in birds may help to clarify the function of sleep by revealing overriding principles that would otherwise remain obscure if we only studied mammals. This is because birds are the only taxonomic group other than mammals to show both SWS and REM sleep.
Interestingly, the independent evolution of similar sleep states in birds and mammals might be related to the fact that each group also independently evolved large brains capable of performing complex cognitive processes. In their actual study, researchers from the Max-Planck Institute of Ornithology in Seewiesen, Germany showed for the first time that birds compensate for sleep loss in a manner similar to humans.

Tree Of Animal Life Has Branches Rearranged, By Evolutionary Biologists:

A study led by Brown University biologist Casey Dunn uses new genomics tools to answer old questions about animal evolution. The study is the most comprehensive animal phylogenomic research project to date, involving 40 million base pairs of new DNA data taken from 29 animal species. The study, which appears in Nature, settles some long-standing debates about the relationships between major groups of animals and offers up a few surprises.

Hobbits May Be Human After All:

RMIT University researchers have joined the worldwide debate over the hobbit-like fossils found on the Indonesian island of Flores, with a controversial new theory suggesting their primitive features are the result of a medical condition.

But see what Greg, Afarensis and Brian have to say about that paper!
Television Shows Can Affect Racial Judgments:

A new study reveals that viewers can be influenced by exposure to racial bias in the media, even without realizing it. Led by Dana Mastro of the University of Arizona, the study exposed participants to television clips where Latinos were portrayed in both flattering and unflattering ways.

Lowly Icelandic Midges Reveal Ecosystem’s Tipping Points:

The midges that periodically swarm by the billions from Iceland’s Lake Myvatn are a force of nature. At their peak, it is difficult to breathe without inhaling the bugs, which hatch and emerge from the lake in blizzard-like proportions. After their short adult life, their carcasses blanket the lake, and the dead flies confer so much nutrient on the surrounding landscape that the enhanced productivity can be measured by Earth-observing satellites.

Secrets Of Cooperation Between Trees And Fungi Revealed:

Plants gained their ancestral toehold on dry land with considerable help from their fungal friends. Now, millennia later, that partnership is being exploited as a strategy to bolster biomass production for next generation biofuels. The genetic mechanism of this kind of symbiosis, which contributes to the delicate ecological balance in healthy forests, also provides insights into plant health that may enable more efficient carbon sequestration and enhanced phytoremediation, using plants to clean up environmental contaminants.

Oh, I am so taking Professor Steve Steve to see….

….this on the opening night!
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Watch Your Shoes! Interview with Suzanne Franks

Suzanne Franks, better known online as Zuska is a SciBling you do not want to make mad with mysogynist sentiments! At the second Science Blogging Conference in January she co-moderated a panel on Gender and Race in Science: online and offline.
Welcome to A Blog Around The Clock. Would you, please, tell my readers a little bit more about yourself? Who are you? What is your scientific background? What is your Real World job?
Well, right now I have no Real World Job because chronic migraines make it impossible for me to hold down a job. My education includes a PhD in biomedical engineering and a graduate certificate in women’s studies. In previous lives, I did basic cancer research in Germany and the U.S., I was a manager of medical writing in the pharmaceutical industry, and I was the founding director of the Women in Science and Engineering Program at Kansas State University. That last one is probably my proudest accomplishment.
I guess my Real-World job description now would be: blogging, gardening, reading, and playing with the cats. And having migraines.
What do you want to do/be when (and if ever) you grow up?
I’ve answered this question once before. What I said then still holds true: “Healthy. I can do pretty much whatever else I want, if I could just stop having migraines. Also, a mean banjo-picker.”
I guess I’d add that I really would like to be able to return to medical writing someday. Medical writing is rewarding work, professionally and financially. I highly recommend it as an alternative career for disillusioned postdocs.
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 got into blogging due to the incessant prodding of a good friend who is not a scientist. After I started, I thought “surely I can’t be the only one writing about gender and science!” So I started searching for blogs on women and science, blogs by women scientists, feminist blogs that discussed science… Some of the first ones I found were See Jane Compute (since today, found here) – which I fell in love with immediately, Adventures in Ethics and Science, Dr.Shellie, Naked Under My Lab Coat (which I adore, but she hasn’t blogged in a couple of months…I hope she’s doing okay with the thesis), Young Female Scientist, and Rants of a Feminist Engineer.
Before I moved to Scienceblogs I pretty much exclusively read women-and-science blogs. After the move I started reading other types of science blogs, just by virtue of reading what the other Sciencebloggers were writing. The conference allowed me to make contact with some bloggers I’ve already been reading, and that was a very useful and powerful experience.
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Immediately after the Conference, there were several posts up by female science bloggers about the issue of anonymity, e.g., this, this and this. You are one of the (minority?) of the female science bloggers who blogs under the full name. How does that restrict what you write about or not? Was that ever a source of any problems for you either online or offline?
Well, if I had a job, I’m not sure I would blog in the same way. I’d feel constrained by not wanting to jeopardize my job. For example, I can imagine that if I were in the pharmaceutical industry at present, I might want to blog more about things going on in that sphere…but I’d feel concerned about how that would come across at work.
Not being employed, I feel free to say whatever I want, and I have to tell you it is very liberating. I can finally express all the anger and frustration that so many women experience, but don’t feel free to talk about. I can be much more blunt about gender equity issues than I could when I worked at K-State, where my job required a more, shall we say, politesse approach to bring people on board with the vision of a more equitable world of science and engineering.
I do worry, on occasion, if I am able to go back to work, whether my outspoken blogging might hurt me. But I don’t worry enough about it to shut up. 🙂
The main annoyance I’ve experienced online comes from the umpteen million comments I get about how if I would just speak in a nice polite voice I’d be taken more seriously, usually from guys who actually mean “Your anger upsets me. Please be nice the way I think women are supposed to be.” Those people need to have their shoes puked on.
What does the expression “to puke on his shoes” mean? What is its origin?
The post that explains the genesis of “puke on his shoes” can be found here. Basically, when someone or some organization behaves in a manner that is so egregiously offensive that mere words cannot express all the outrage it engenders, then one wants to puke on someone’s shoes. And I’m generally willing to name the someone upon whose shoes puke should be deposited.
How do you see science blogs as tools in changing the culture of academia in regards to gender? Do you think that male science bloggers, by reading female science bloggers, are starting to “get it” and are becoming allies?
I don’t think science blogs have had much of an impact on the culture of academia with regards to gender equity, at least not yet. Most of the people positioned to enact institutional transformation are probably not reading blogs, let alone women-and-science blogs. I do think science blogs have helped create community for women scientists and engineers, in the sense that Janet Stemwedel of Adventures in Ethics and Science speaks of community.
Female science bloggers have created a community online where they can get and give advice on the myriad things they must cope with. So many women scientists and engineers are isolated, often the only one or one of few women in a department. They don’t have a peer group in the Real World to talk to about issues like childbearing, career/life balance, dealing with the daily grind of institutionalized sexism, and practicing effective moron management. They find their sisters online, and they realize “I’m not crazy, this really is screwed up and wrong.” They get their experience validated, and they learn how other women have coped with similar situations. This is really important for helping women persist in academia.
With regard to male readers of women-and-science blogs, there seem to be roughly three categories.
(1) Allies, who offer support and insight and want to know more about what they can do to be better allies. These guys more or less “get it” and want to improve their understanding of gender issues. They are not threatened by angry women.
(2) “Nice Guys” who do not think of themselves as sexist or biased but who have a hard time getting it about the extent of institutionalized sexism. They will often say “but I’ve never seen discrimination!” or “but I’m a Nice Guy! I don’t take advantage of women! Male privilege doesn’t apply to me!” or “are you sure that was an instance of sexism? Maybe it really can be explained by X [where X is Anything-But-Sexism]”. They will often open with something like “I accept that women are discriminated against, but…” and then go on to argue how whatever bit of discrimination or bias you’ve been talking about isn’t really the issue you think it is. They do not understand gender schemas and implicit bias and how those function to create disadvantage for women.
Nice Guys take a lot of work. A small percentage of them do really want to try and learn more about institutionalized sexism. The vast majority, however, while wanting to think of themselves as Allies, experience intense personal threat when gender equity is seriously discussed, which makes them defensive. They have trouble getting past taking it personally, and look at the big picture of institutionalized sexism, discrimination, and bias. How can I be biased? I’m a Nice Guy!
(3) Morons and trolls. Their main contribution is to clearly illustrate, far better than I ever could on my own, just exactly how bad things still are for women.
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?
Dave Munger’s presentation was very useful for me, full of practical tips that I hope to implement in some manner on my blog. Dave really emphasized blogging consistently, and having a regular weekly feature – two things that I have struggled with, in part because of my health issues. But I think some better organization of time on my part is called for here. 🙂
It was so nice to see you again and thank you for the interview.
Bora, it was a real pleasure! Thanks for everything you did to make the UnConference happen, and thanks for this interview!
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Check out all the interviews in this series.

Welcome the newest SciBling!

Go say Hello to Jane at See Jane Compute!

Today’s carnivals

I and the Bird #68 is up on Biological Ramblings
Change of Shift: Vol. 2, Number 18 is up on Emergiblog

Zoo School X-Press

Regular readers must be familiar by now with the ZooSchool in Asheboro, NC. Today’s news from the school – their students have put up the first issue of their online newspaper, the ZSX-Press. Go check it out!
In related news, and also at the Asheboro Zoo and related to education, The NC Zoo and NC Zoo Society will be hosting the No Child Left Inside Conference Thursday (today), March 6th, which will be held in the MPR [multi-purpose room] of the Stedman Education Building. I wish I could go. Perhaps someone there will write about it and post something online.

Reptile & Amphibian Day at the Museum

News from SCONC:

The NC Museum of Natural Sciences presents Reptile & Amphibian Day on Saturday, March 15 from 9 a.m. to 5 p.m. Dozens of displays, activities and presentations highlight reptiles and amphibians from North Carolina and around the world. Here’s your chance to get up-close and personal with hundreds of live animals, from giant pythons to bearded dragons. Meet reptile expert Dr. Brady Barr, the first person to capture and study all 23 crocodilian species in the wild.

ClockQuotes

It ever has been since time began, And ever will be, till time lose breath, That love is a mood – no more – to a man, And love to a woman is life or death.
– Ella Wheeler Wilcox

Genomics Blogger Dissed by the New York Times

Or, perhaps, the truth is more complicated, as revealed in the comments of that post.

Evolution: Education and Outreach

The second issue is now available online. Open Access. Most articles are highly ‘bloggable’.

Mel-Mel-Mel: it’s easy to remember in snowshoe hares

It has been almost three years since I promised to write a post detailing the photoperiodic response in mammals. (Birds are more complicated).
Now Shelley gives a good example – the snowshoe hare which changes color annually: it is dark in summer and white in winter. It is pretty easy to remember – it’s all the Mel-something molecules involved. So, here is a very simplified, but essentially correct description of how this happens:
Light is detected by the photo-pigment melanopsin in the retinal ganglion cells of the eye. The cells send a signal to the clock (in the suprachiasmatic nucleus, SCN).
SCN sends a signal to the pineal gland. During the night, when it is dark, the pineal gland responds to the SCN signal by synthetizing and releasing the hormone melatonin into the bloodstream. The duration of the melatonin release is an indicator of the length of the night: long night = winter, short night = summer.
Melatonin receptors are found in the SCN, in some other places in the brain, and in some other places in the body. In the snowshoe hare, one of the targets of melatonin is the hypothalamo-pituitary system that controls the deposition of the pigment melanin into the hair follicles.
Thus, in summer, melanin gets deposited into the hair follicles and the hair that grows out of them is dark. At the onset of winter, when the clock starts detecting the shortening of the day (i.e., lengthening of the night-time melatonin signal), melanin is supressed and the dark hair is replaced with white hair (and more of it) instead.

Blogrolling for Today

Trilobite Blog


Evolucija


Raw Dawg Buffalo


Znanost


Elle, phd


Diary of a PhD student


Education and Class


The field negro


See Jane in the Academy

Superhot beats supercold in a cloud of spectacular smoke!

Thermite annihilates liquid nitrogen:

Can teenagers be scared away from illicit drug use?

In 1986, 22-year-old Boston Celtics forward Len Bias died of a cocaine overdose. This week, DrugMonkey argued that Bias’ death–as opposed to educational programs like DARE–was the major reason why self-reported rates of cocaine use by 20-year-olds dropped from 20% in the mid-1980s to 7% in the early 1990s.

Now go and do the survey and check back in a week for the results.

My picks from ScienceDaily

Warming Climate May Cause Arctic Tundra To Burn:

Research from ancient sediment cores indicates that a warming climate could make the world’s arctic tundra far more susceptible to fires than previously thought. The findings are important given the potential for tundra fires to release organic carbon — which could add significantly to the amount of greenhouse gases already blamed for global warming.

Stop-And-Go Traffic: An Accident? Construction Work? No, Just Too Much Traffic:

A new study from a Japanese research group explains why we’re occasionally caught in traffic jams for no visible reason. The real origin of traffic jams often has nothing to do with obvious obstructions such as accidents or construction work but is simply the result of there being too many cars on the road.

See the video.
Most Physicians Sleep Fewer Hours Than Needed For Peak Performance, Report Says:

In a new survey, physicians report they are not getting the sleep they need to function at their best and current work schedules may contribute to their inadequate sleep. The survey, issued by the American College of Chest Physicians Sleep Institute (ACCP-SI), found that most physicians sleep fewer hours than needed for peak performance and nearly half of physicians believe their work schedules do not allow for adequate sleep. Results further indicated that, when compared to the general population, physicians reported more caffeine use but better overall health.

Today’s carnivals

Tangled Bank #100 is up on Archaeoporn
The Carnival Of Education: Week 161 is up on Education Wonks
The 114th Carnival of Homeschooling is up on PalmTree Pundit

Making the Data Public: Interview With Xan Gregg

Xan Gregg has also attended both the first Science Blogging Conference and the second one in January, where he co-moderated a session on Public Scientific Data. He blogs on FORTH GO.
Welcome to A Blog Around The Clock. Would you, please, tell my readers a little bit more about yourself? Who are you? What is your scientific background? What is your Real Life job?
I’m a software engineer working at SAS Institute on a desktop “statistical discovery” application called JMP. (Yes, we have a blog, and I sometimes post to it.) My primary interest is data visualization, and in 2006 I won a data visualization competition judged by author Stephen Few. My background is in math and computer science, and I use both fields as a team member at Project Euler, which is a site full of challenging math problems that usually require writing programs to solve.
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 wasn’t until I attended the first Science Blogging Conference that I knew about so much science blogging going on. Now I have trouble keeping up. I can hardly read as fast as you can blog! I like those blogs that provide good summaries of recent research, such as Cognitive Daily, Statistical Modeling, and one I discovered at the conference, ThankYouBrain by attendee Bill Klemm.
How did you get interested in public data?
Having a focus on data visualization, I’m always analyzing graphs and trying to think of ways to make them better. To really make a point, I need to actually produce a better visualization from the same data, and I have been disappointed to find that the data is not often readily available. I can sometimes to resort to programs like GraphClick that can scrape data from standard graphs, but even that doesn’t work for summary graphs where the real data is invisible.
xanhead.jpgWhy should scientists make their raw data public? What are the pros and cons?
The more I researched the subject, I found a disconnect between what scientists say and what they do. Almost every authority extolls the principles of public data, but few scientists practice it openly. I’ve found it to be primarily a question of when. Full open science labs like Jean-Claude Bradley’s UsefulChem publish data as it’s generated, but that model isn’t for everyone. I’d be happy to see data published with papers, whith the policy of the American Economic Review, but the usual answer to the question of when is “when somebody asks for it nicely enough.”
The pros and cons depend on your goals. If you’re trying to further public knowledge, then sharing data supports that goal. If you’re in a competitive situation, then sharing data could weaken your position. I guess that’s a philosophical issue on the nature of scientific research and the public good. In practical terms, publishing data encourages better review and new derivative research, and the only con is with confidential data that can’t be effectively anonymized.
Are there disciplinary differences?
The main disciplinary difference I’ve seen regards the quantity of data. Fields like astronomy and genetics have tons of data, which encourages central data respositories for archiving data.
How would you go about persuading a scientist to make his/her data public?
The idea is there already, so I’d focus on showing how easy it is to share data in a minimal way. Of course, most scientists take their cues from journals and funders, and we need more of them to require data. Some governments, including the US government, are moving in that direction for publicly funded research. It’d be nice to see PLoS adopt something like the data policy of American Economic Review. I’d be happy to work with someone on setting up a data repository site.
How should the raw data be presented online?
Anyway you can. Just a CSV (comma-separated values) file sitting on a web server is fine. Better is an independent site, such as Swivel or Google Docs. The important thing is to remember to include a description of the data fields and sources. Then use the URL of your data as a citation point.
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 whole conference makes me temporarily depressed. I find out that for every good idea I’ve had, not only has someone else already had it, but three sites are already implementing it!
It was so nice to see you again and thank you for the interview.
Thank you, Bora. Keep on tickin’.
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Check out all the interviews in this series.

Evil urban environmentalists don’t need to be evil, just smart

Common-sense environmentalism

I like to consider myself an environmentalist, but I almost never call myself one. Mainly because I really don’t want to be associated with a lot of the people who do.
Because environmentalists are usually right about the facts of the issues they attempt to confront: global warming is a reality, the rape of the world’s forests is a disaster in the making, corporate pollution is poisoning us, and the extinction of animal species is both an ecological and a human disaster. On the science and on most policy issues, the environmentalists are right.
But on the human front … they leave a lot to be desired. And this in turn has a lot to do with why their rightness fails to translate into effective action.

Another Story about Dick

Dave’s work was embraced by the locals because his research and interpretive skills gave them a new and broader respect and reverence for a place they already loved. Though he could easily has been the very kind of evil urban environmentalist that rural towns dread, he proved that this antagonism isn’t inevitable. Dave didn’t come on like an outsider coming in to show them a better way. His approach was more like that of a young, bookish pastor who made a permanent commitment to the community, and chose the place to be his own home. His job was to win hearts and minds for the preservation of the lake — and he understood that the first piece of that task was winning over the souls of Lee Vining and Mono County.

ClockQuotes

We lost the American colonies because we lacked the statesmanship to know the right time and the manner of yielding what is impossible to keep.
– Elizabeth II

Jane – the Journal/Author Name Estimator

Jane is the cool new tool that everyone is talking about – see the commentary on The Tree of Life, on Nature Network and on Of Two Minds.
In short, the Journal/Author Name Estimator is a website where you can type in some text and see which scientific Journal has the content closest to the text you input, as well as people who published on similar topics. If you click on “Show extra options” you can narrow your search by a few criteria, e.g., you can search only Open Access journals.
The idea is to discover journals to which you can submit your work. Most people know the journals available for their stuff, but this is the way to discover new journals, see which are Green or Gold OA, or find a place for a manuscript that has already been rejected by all of your usual venues 😉
Another use is for editors of broad-topic journals, to find relevant referees for the incoming manuscripts.
So, I did first the obvious test of the site – I copied and pasted the abstract of one of my papers. It gave the correct journal at 100% confidence, and all four co-authors at equal split of 25%. So, it works in that way. The other people mentioned down the list are also relevant researchers who would be appropriate for reviewing such a mansucript.
Then I copied and pasted a small chunk from my unpublished dissertation and got a list of potential reviewers that was pretty much perfect – people I’d suggest if asked.
Then, I typed in a bunch of terms that I know occur frequently in PLoS ONE in different papers, all mixed up – and PLoS ONE came up high on the list (and first among OA journals). So far so good.
Apparently, if you paste non-scientific text, you always get Harvard Business Review – they’ll take anything silly. Figures.
So, what would you use it for? Is it useful?

My picks from ScienceDaily

Giant Fossil Bats Out Of Africa, 35 Million Years Old:

When most of us think of Ancient Egypt, visions of pyramids and mummies fill our imaginations. For a team of paleontologists interested in fossil mammals, the Fayum district of Egypt summons an even older and equally impressive history that extends much further back in time than the Sphinx.

Are Wolves The Pronghorn’s Best Friend?:

As western states debate removing the gray wolf from protection under the Endangered Species Act, a new study by the Wildlife Conservation Society cautions that doing so may result in an unintended decline in another species: the pronghorn, a uniquely North American animal that resembles an African antelope.

Can Moths Or Butterflies Remember What They Learned As Caterpillars?:

Butterflies and moths are well known for their striking metamorphosis from crawling caterpillars to winged adults. In light of this radical change, not just in body form, but also in lifestyle, diet and dependence on particular sensory cues, it would seem unlikely that learned associations or memories formed at the larval or caterpillar stage could be accessible to the adult moth or butterfly. However, scientists at Georgetown University recently discovered that a moth can indeed remember what it learned as a caterpillar.

Today’s carnivals

Grand Rounds Vol. 4 No. 24 are up on ChronicBabe
Mendel’s Garden #24 is up on Bayblab

Three Exam System? Can we design something better?

That is what Anne-Marie asked after a week with seven mid-term exams. In a few weeks, she’ll have another bunch of exams all at the same time. And then a finals week in May.
This is, obviously, not the most efficient system. So, have you, as a student or a teacher, encountered a better system?

Linda Buck explains the sense of smell

News from SCONC:

Linda Buck is the Nobel-Prize winner that may live farthest from NC (but still in the U.S.). She will give a seminar Monday, March 10 at 4 p.m. in the Grand Ballroom of the Talley Center at NCSU. Buck won the Prize in Physiology or Medicine in 2004 for the discovery of olfactory receptors and subsequent work on the neurobiological basis for smell. The title of her talk is “Olfactory Sensing in Mammals.” Buck is based at the Fred Hutchinson Cancer Research Center in Seattle. This seminar is part of a series put on by the W.M. Keck Center for Behavioral Biology at NCSU.

ClockQuotes

You may search my time-worn face, You’ll find a merry eye that twinkles. I am NOT an old lady, just a little girl with wrinkles.
– Edythe E. Bregnard

String Spin Toy

Go here, draw a line, let it spin and click to fill it up:
stringspintoy.JPG

Welcome the newest SciBling!

Go say Hello to Josh Donlan, the new co-blogger on Shifting Baselines who will add a terrestrial component to the marine stuff already there. Josh’s arrival is also bound to provoke some interesting blogging around the scienceblogs.com, as his ideas of ‘rewilding’ the American West are greeted with a whole spectrum of responses by our resident bloggers and comenters (see this, this and this for some examples). This is going ot be fun!

New and Exciting in PLoS Medicine and PLoS Biology

Last week’s crop of PLoS ONE articles enjoyed quite a nice buzz in the media and on the blogs. But today is a new week, and we start, as always with new articles in PLoS Medicine and PLoS Biology – here are some of the article that caught my attention:
Could an Open-Source Clinical Trial Data-Management System Be What We Have All Been Looking For:

In Europe, it is a legal requirement to conduct clinical trials in accordance with the International Conference on Harmonisation’s guidelines on good clinical practice (see http://www.ich.org/). A recent editorial reported that this directive has led to a decline in the number of trials being conducted by independent academic groups [1]. One possible reason for this is that reporting and documentation requirements are now so burdensome that the process has become unnecessarily complicated [2]. This is rather ironic, given that well-designed clinical trials should be amenable to very simple data handling and analysis [3]. Indeed the flowchart established by the CONSORT (Consolidated Standards of Reporting Trials) statement [4] for carrying out a properly randomised controlled trial has just four steps, which supports the approach of keeping it simple.

Effects of Selection for Honey Bee Worker Reproduction on Foraging Traits:

In social insects, the evolution of the worker caste and the regulation of reproductive behaviour by workers are poorly understood. Evolution is conservative and often proceeds by adapting an existing gene network to a new function. The “reproductive ground plan” hypothesis (RGPH) suggests that social insects evolved their queen and worker castes by modifying a gene network that once regulated the foraging and reproductive phases of solitary ancestors. In this model, queens retain characteristics of insects in their reproductive phase, whereas workers retain characteristics of the foraging phase. Moreover, the foraging behaviour of workers may also be regulated by the same genes that once controlled the switch between foraging and feeding young in the nest. We evaluated the RGPH by studying a line of honey bees selected for high rates of worker reproduction. We show that in this line workers forage late in life and some may never forage, supporting the idea that genes related to reproduction are also related to foraging. However, we found no support for recent suggestions that genes related to reproduction also regulate the foraging behaviour of individual workers: once they start foraging, our highly reproductive workers forage in the same way that unselected workers do.

Assessing Evidence for a Pervasive Alteration in Tropical Tree Communities:

Recent studies have reported major changes in mature tropical forests, with increases in both forest biomass and net primary productivity, as well as shifts in plant species composition that favour fast-growing species over slow-growing ones. These pervasive alterations were attributed to global environmental change, and may result in dramatic shifts in the functioning of tropical forest ecosystems. We reassessed these findings using a dataset of large permanent forest plots on three continents. We found that tree biomass increased at seven of our ten plots, and showed a large decrease at a single plot. Overall, this increase was significant, albeit lower than reported previously for Amazonian forests. At three sites for which we had data for multiple census intervals, we found no concerted increase in biomass gain, in conflict with the increased productivity hypothesis. With the exception of one plot, slow-growing species gained more biomass than either fast-growing species or the tree community as a whole. Hence, our results do not support the hypothesis that fast-growing species are consistently increasing in dominance in tropical tree communities. Overall, our results suggest that our plots may be simultaneously recovering from past disturbances and affected by changes in resource availability.

How The Planets Got Their Names

Ah, the quirky world of science! Archy gives us a tour of history of how various objects in the Solar System got named, and the intrigue and politics around it.

Welcome Of Two Minds!

Retrospectacle and Omni Brain, as of now, have officially fused into the new, double-headed scibling – Of Two Minds. Go say Hello!

Today’s carnivals

Encephalon #40 is up on Mind Hacks
Carnival of the Green #117 is up on Confessions of a Closet Environmentalist

Biodiversity Heritage Library

Get yourself free PDFs of old biology/taxonomy books and papers courtesy of Biodiversity Heritage Library:

Ten major natural history museum libraries, botanical libraries, and research institutions have joined to form the Biodiversity Heritage Library Project. The group is developing a strategy and operational plan to digitize the published literature of biodiversity held in their respective collections. This literature will be available through a global “biodiversity commons.”
Participating institutions:
* American Museum of Natural History (New York, NY)
* The Field Museum (Chicago, IL)
* Harvard University Botany Libraries (Cambridge, MA)
* Harvard University, Ernst Mayr Library of the Museum of Comparative Zoology (Cambridge, MA)
* Marine Biological Laboratory / Woods Hole Oceanographic Institution (Woods Hole, MA)
* Missouri Botanical Garden (St. Louis, MO)
* Natural History Museum (London, UK)
* The New York Botanical Garden (New York, NY)
* Royal Botanic Gardens, Kew (Richmond, UK)
* Smithsonian Institution Libraries (Washington, DC)
The participating libraries have over two million volumes of biodiversity literature collected over 200 years to support the work of scientists, researchers, and students in their home institutions and throughout the world. The 10 member libraries of the Biodiversity Heritage Library (BHL) members now have over 1.124 million pages of key taxonomic literature available on the web.
The BHL will provide basic, important content for immediate research and for multiple bioinformatics initiatives. For the first time in history, the core of our natural history and herbaria library collections will be available to a truly global audience. Web-based access to these collections will provide a substantial benefit to people living and working in the developing world — whether scientists or policymakers.

Hat-tip: Anne-Marie

Oliver Smithies on stem cells and gene targeting

News from SCONC:

Oliver Smithies is the Nobel-Prize winner next door. A professor at UNC for almost 20 years, Smithies got the nod from Stockholm last fall. He will give a seminar at the Friday Center on Thursday March 6 at 6:30 p.m. in a lecture hosted by the Carolinas Chapter of the American Medical Writers Association.
Along with Mario Capecchi and Martin Evans, Smithies was recognized for his research on embryonic stem cells and DNA recombination in mammals. Their work on gene targeting in mice made it possible to study individual genes in health and disease–a fundamental breakthrough that affected all fields of biomedicine. Smithies has used gene targeting to develop mouse models for diseases such as cystic fibrosis, thalassemia, hypertension and atherosclerosis. A reception at 6:00 p.m. will precede the talk. The lecture will be held in the Redbud Room of the Friday Center in Chapel Hill

ClockQuotes

Words can sometimes, in moments of grace, attain the quality of deeds.
– Eliezer Wiesel

Make your own Jackson Pollock painting

Go here, click to change color, press Space to erase and start anew:
pollock.JPG

Blogs for Beginners

Under the fold, as the movie appears to slow down loading of my front page:

Continue reading

How Do You Shelve Your Books?

Wow! This is nuts! And this is nuts in a different way! Fortunately, Scott McLemee, Chad Orzel, Josh Rosenau and Brian Switek bring in some reality to the topic: what goes on the living-room bookshelf? Commenters chime in. Good stuff. Read it.
So, what are “rules” in the Coturnix house?
First, the house is too small to allow too much fine planning as to what the guests will see.
Second, we do not have guests very often (again, lack of space), so the bookshelves are not aimed at them.
Third, we have about 5000 books and they have to be stored somewhere, in some fashion.
Fourth, we have moved twice in the last 5 years, so the “rules” had to change, due to changes in available space.
Fifth, it never occured to me that a bookshelf is any kind of statement about me, though perhaps it is not true: I do like the rare guests to look at the books. It is not so much that I want to impress them with Great Literature, but I do like to brag about some rare gems I found serendipitously at second-hand bookstores and yardsales.
Sixth, I would never be so presumptuous to call the library mine – it is ours, we are a family, and all the books belong to each of us.
When people have a bad time and need to lift themselves up, or if they have good times and need to celebrate, they usually go out to eat at a good restaurant. My wife and I? We go to a bookstore. Food comes at one orifice and leaves on another. Books stay forever.
Do we ever get rid of books? Yes, we pack up a couple of boxes and sell them a few times a year. Kiddie books outgrown by our kids get sent to younger nephews and nieces. How do we choose what to get rid of? Books we did not like, and know will not like, and, importantly, do not think our kids will ever care to read.
How are the books organized? Right now, total chaos. Almost. Each kid has a shelf in his/her own room. All the physics book and chess books are in my son’s room, for instance. All the SF is on a shelf in our bedroom, next to my side of the bed. There is also a big “to read soon” shelf in our bedroom. There are also four other big shelves in our bedroom populated mainly by fiction, plus some books about the Balkans and some Judaica. Those used to be oganized in the alphabetical order by author, but are a mess right now – it’s a project for the near future. There are eight large and one small bookshelf in the living room, populuated by non-fiction, textbooks and reference books. Right now they are a mess, but they used to be organized by topic. An entire line of Darwin, another row is just SJ Gould, about two shelves are philosophy, lots of evolution, ecology, behavior, physiology, and also art, film, sociology, politics. It did make sense, trust me.
Oh, BTW, I built all the shelves myself.
So, what decides what books are kept? Books useful for reference, daily blogging, or study. Books we liked and hope our kids will read one day. Books of historical value. Book we intend to read. It’s actually pretty simple, and does not really involve impressing guests (though we appreciate it when the guests are impressed by the sheer numbers).
So, what’s your book-keeping/shelving method?

Blogrolling for Today

Perusing Science


Perusing Aardvarks


Adaptive Complexity


Exsisto Sane


Chimpanzees are not Monkeys


Mystery Rays from Outer Space


PTET


Exploring Our Matrix

See you at the SRBR meeting!

SRBR08splash.gif
The 11th Biennial Meeting of the Society for Research on Biological Rhythms will be held in Sandestin, FL on May 17th-21st, 2008. And I’ll be there. This meeting occurs every two years (on even-numbered years, the International Congress and the Gordon Conference are in odd-numbered years). I attended three or four of these when it was down on Amelia Island, FL. Then I skipped the one in Whistler, Canada, four years ago as I had no money to go, and the one in Sandestin two years ago as I was out of science. But I’ll be going back – with a mission: to explain Open Access to my colleagues, to get them to publish with PLoS, to get them to read my blog, to catch up with my field and to do some blog-interviews with the interesting people there. So, if you are chronobiologist and you’ll be there, please find me and say Hi.

Link Journalism

The proposal for link journalism is not a new concept, though the phrase is good. This is something that bloggers have been doing for years and have been imploring the corporate media to adopt for years. On paper, you can provide references in the footnotes or endnotes, or you can mention “unnamed sources”, but in the age of the Web, it is sheer blindness not to use links – nobody will trust you if they cannot click and instantly verify your statements. Remember – no links, no reputation.

SAGE keeps opening up….

I just noticed recently, when looking up a paper in the Journal of Biological Rhythms, that SAGE publishing group is starting to offer the Open Access option to the authors in some of its Journals:

Independent scholarly publisher, SAGE Publications, is now offering authors of papers published on SAGE Journals Online, the option to make their primary research articles freely available on publication. The ‘SAGE Open’ publishing option has been launched primarily to ensure that authors can comply with new stringent funding body requirements, (for example those now in place from the Wellcome Trust), and ensures that relevant journals are compliant with NIH/Wellcome Trust and other grant funder requirements.
The SAGE Open programme will initially operate across a number of biomedical journals in the SAGE portfolio. The fee per article for this service is $3,000USD/£1600GBP and excludes any other potential author fees levied by some journals (such as colour charges, which are additional) as well as taxes where applicable.
Under this scheme, SAGE will allow the deposition of the final paper, (post refereeing, copy-editing and proof-reading), to PubMedCentral and its international equivalents, such as UKPMC, or PMCI on publication. All other SAGE policies regarding open access archiving remain unchanged.
The SAGE Open option will be made available to authors of primary research articles only on acceptance of their paper for publication. This is in order to prevent any potential conflicts of interest, and to ensure that authors’ choice/funder requirements have no influence on the editorial peer review and decision-making.
Payment of the SAGE Open fee will enable articles to be immediately available on SAGE Journals Online to non-subscribers, as well as to subscribers to that journal. It will also permit authors to submit the final manuscript to their funding agency’s preferred archive if applicable.
Initially, this option will be made available for a selection of journals (see below for full list). These journals will publish articles in a hybrid manner. Those authors who do not wish to use this service will be under no pressure to do so, and their article will be published free of charge, in the usual manner. All existing policies on author posting of the final version will then apply.
The following list of journals participate in SAGE Open:
Adaptive Behaviour
Angiology
Chronic Respiratory Disease
Clinical and Applied Thrombosis/Hemostasis
Clinical Pediatrics
Clinical Rehabilitation
Clinical Trials
Human & Experimental Toxicology
Integrative Cancer Therapies
Journal of Biological Rhythms
Journal of Biomaterials Applications
Journal of Biomolecular Screening
Journal of Cardiovascular Pharmacology and Therapeutics
Journal of Oncology Pharmacy Practice
Journal of Pharmacy Practice
Lupus
Multiple Sclerosis
The Neuroscientist
Palliative Medicine
Perfusion
Seminars in Cardiothoracic and Vascular Anesthesia
Surgical Innovation
Toxicologic Pathology
Toxicology & Industrial Health
Trauma
Vascular Medicine
Please send questions or comments not covered by our list of frequently asked questions via e-mail to sageopen@sagepub.com

Very good, SAGE is actively looking for the best ways to adapt to the changing landscape of the science publishing world.

ConvergeSouth2008

Sue announces that the website will be up in two weeks, and the blog is already up and running. You can help with organization. In any case, mark you calendars:

ConvergeSouth 2008 will be held on October 16-17, 2008 in Greensboro, North Carolina. BlogHer will be held on October 18.