Author Archives: Bora Zivkovic

The Wolfram Demonstrations Project

This was released to public today:

Conceived by Mathematica creator and scientist Stephen Wolfram as a way to bring computational exploration to the widest possible audience, The Wolfram Demonstrations Project is an open-code resource that uses dynamic computation to illuminate concepts in science, technology, mathematics, art, finance, and a remarkable range of other fields.
Its daily-growing collection of interactive illustrations is created by Mathematica users from around the world, who participate by contributing innovative Demonstrations.
Interactive computational resources have typically been scattered across the web–requiring specialized programming knowledge that’s made them difficult and expensive to develop. As a result, their coverage has long been limited, and progress has been slow.
In many ways, The Wolfram Demonstrations Project introduces a new paradigm for exploring ideas. The power to easily create interactive visualizations, once in the domain of computing experts alone, is now in the hands of every Mathematica user.
Demonstrations can be created with just a few short lines of readable code, powered by the revolutionary advances in Mathematica. This opens the door for researchers, educators, students, and professionals at any level to create their own sophisticated mini-applications and publish them online.
From elementary education to front-line research, topics span an ever-growing array of categories. Some Demonstrations can be used to enliven a classroom or visualize tough concepts, while others shed new light on cutting-edge ideas relevant to high-level workgroups and thesis research. Each is reviewed for content, clarity, and presentation, edited by experts at Wolfram Research to ensure quality and reliability.
All Demonstrations run freely on any standard Windows, Mac, Unix, or Linux computer. In fact, you don’t even need Mathematica to benefit. Anyone can preview a Demonstration online, and interact with it using the free Mathematica Player. Those with Mathematica can also experiment with and modify the code on their own computers.

I looked around a little bit and, although there is nothing related to my own field, I found lots of cool stuff, from maps to oscillations to the Long Tail. Give it a try. Play with some of the demonstrations. See if they are useful for you in your teaching.

Nursing Blogging of the fortnight

Change of Shift: Vol. 1, Number 23 is up on Emergiblog.

BirdBlogging of the Fortnight

I and the Bird # 48 is up on Greg Laden’s blog.

Science Blogging Conference ’08 and The Open Laboratory 2007

2008NCSBClogo200.pngAs the 2007 Science Blogging Conference was such a great success, we are already in full swing in organizing the 2008 conference and hoping to make it even bigger and better than the first one.
Our beta-version wiki is up – check out the homepage and the first, rough outlines of the program (feel free to edit the page and add your idea at the bottom or in the comments). At this point we are trying to get more sponsors so if you and your organization/company/magazine is interested, let us know soon.
Check out our blog for updates.
Open%20Laboratory%20cover%20image.jpgLast time, almost in time for the conference, we edited and published the first-ever science blogging anthology, the Open Laboratory 2006, which was an instant hit. Thus, we are already collecting nominations for the next years’ edition. Send us your best posts (or best posts written by others) of the year by using this submission form and help us spread the news by adding this code to your blog or website.

Open Classroom – learning about Holocaust by making a podcast

Survivor Testimonies Engage Students in Holocaust History:

Through a program funded by the Claims Conference, a group of 8th graders in Philadelphia, Pennsylvania who had never before learned of the Holocaust found themselves deeply affected by these first-person narratives during a month-long educational unit on the Shoah.
Victoria Monacelli, a teacher of reading and language arts at the Warren G. Harding Middle School, incorporates technology into her curriculum in order to engage students. As part of her literacy program, her students produce a monthly “podcast,” a recorded oral presentation on a specific topic for which the students conduct extensive research in order to produce a script. The podcasts are reproduced on websites and can be downloaded into MP3 players.

Click here to listen to the podcast. More info here.
Related: Storyblogging
Hat-tip: Mom

My Picks From ScienceDaily

Corals — More Complex Than You?:

The humble coral may possess as many genes – and possibly even more – than humans do. And remarkably, although it is very distant from humans in evolutionary terms, it has many of the immune system genes that protect people against disease. In fact, it is possible some of these were pioneered by corals.

Continue reading

Blogrolling for Today

Eye On DNA

Democrats Now

PSoTD

Bakachanaileen’s journal

Paleo-Future

Smooth Pebbles

Minor Revisions

Recent Carnivals

Scientiae Carnival: 5th Edition is up on Clarity.
Festival of the Trees #11: Trees in the Concrete is up on Flatbush Gardener
Bio::BLogs #10 is up on Nodalpoint
The 117th Carnival of Education: The Carnival of One Liners is up on Dr. Homeslice
Grand Rounds Vol. 3, No. 32 are up on Shrink Rap.
Carnival of the Green #75 is up on Enviropundit: Green Building Blog.
Radiology Grand Rounds XI are up on Sumer’s Radiology Site.
Carnival of Homeschooling #70: The Yes, No, Yes! Edition is up on Dewey’s Treehouse.

ClockQuotes

You’ll have time to rest when you’re dead.
– Robert De Niro

Circadian Meditation?!

How does one fisk a medical quackery when there is no attempt whatsoever to explain what it is all about – not even a string of New-Age mumbo-jumbo, nonsensical, vaguely English-sounding words. All it says is: Buy The Book. Yeah, right…
Related: Circadian Quackery

Obligatory Readings of the Day

Combat Clintonism! and Mysteries.
Bookmark that blog! (hat-tip)

Creating slow-wave sleep on demand

Press-release just in – Deep Sleep: Researchers Discovery How To Simulate Slow Wave Activity:

———-snip————-
During slow wave activity, which occupies about 80 percent of sleeping hours, waves of electrical activity wash across the brain, roughly once a second, 1,000 times a night. In a new paper being published in the scientific journal PNAS, Tononi and colleagues, including Marcello Massimini, also of the UW-Madison School of Medicine and Public Health, described the use of transcranial magnetic stimulation (TMS) to initiate slow waves in sleeping volunteers. The researchers recorded brain electrical activity with an electroencephalograph (EEG).
A TMS instrument sends a harmless magnetic signal through the scalp and skull and into the brain, where it activates electrical impulses. In response to each burst of magnetism, the subjects’ brains immediately produced slow waves typical of deep sleep, Tononi says. “With a single pulse, we were able to induce a wave that looks identical to the waves the brain makes normally during sleep.”
The researchers have learned to locate the TMS device above a specific part of the brain, where it causes slow waves that travel throughout the brain. “We don’t know why, but this is a very good place to evoke big waves that clearly travel through every part of the brain,” Tononi says.
Scientists’ interest in slow waves stems from a growing appreciation of their role in sleep, Tononi says. “We have reasons to think the slow waves are not just something that happens, but that they may be important” in sleep’s restorative powers. For example, a sleep-deprived person has larger and more numerous slow waves once asleep. And as sleep proceeds, Tononi adds, the slow waves weaken, which may signal that the need for sleep is partially satisfied.
Creating slow waves on demand could someday lead to treatments for insomnia, where slow waves may be reduced. Theoretically, it could also lead to a magnetically stimulated “power nap,” which might confer the benefit of eight hours sleep in just a few hours.
Before that happens, however, Tononi must go further and prove that artificial slow waves have restorative benefits to the brain. Such an experiment would ask whether sleep with TMS leads to greater brain restoration than an equal amount of sleep without TMS.
Although an electronic power-napper sounds like a product whose time has come, Tononi is chasing a larger quarry: learning why sleep is necessary in the first place. If all animals sleep, he says, it must play a critical role in survival, but that role remains elusive.
———-snip————-

Once the paper shows up on the PNAS site, I’ll see if there is more I need to add to this story.

Big Circadian Changes at UVA

One chronobiological pioneer is leaving and another one is coming in. Gene Block is going to UCLA and Joe Takahashi is leaving Northwestern (What are Fred Turek and others going to do there without him? What happens to the Howard Hughes institute?) and coming in to head the new Center for Circadian and Systems Biology. A very interesting game of musical chairs. Stay tuned.

My Picks From ScienceDaily

Famous Galapagos Tortoise, Lonesome George, May Not Be Alone:

“Lonesome George,” a giant Galapagos tortoise and conservation icon long thought to be the sole survivor of his species, may not be alone for much longer, according to a multinational team of researchers headed by investigators at Yale University. New research led by biologists Adalgisa Caccone and Jeffrey Powell in the Department of Ecology and Evolutionary Biology at Yale, with the strong support and cooperation of the Galápagos National Park and Charles Darwin Research Station, has identified a tortoise that is clearly a first generation hybrid between the native tortoises from the islands of Isabela and Pinta. That means, this new tortoise has half his genes in common with Lonesome George.

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Undergraduate Research – some examples

Jake, Chad, Rob, Janet, Chad again and Chad again. have already written everything important about today’s Buzz topic – the undergraduate research. What I will do is add a few examples and you draw conclusions why this worked (or not) for each one of them.
A Self-Starter
Kevin Messenger loved snakes all his life. He did his own research in high school, a standard survey of herps in the Sandhills area of North Carolina. He presented that at a meeting of the Herps society while a high-school senior. He went to college to NCSU because he wanted to work with Hal Heathwole. He got his own first grant as a college freshman which resulted in a really nifty (I think still not published, but presented) paper on the effects of moonlight on nocturnal snake activity. He breezed through college. Nobody really cared if he got Ds in English or Chemistry classes – he aced all biology classes though, including some graduate level courses he took quite early on. He also got involved in some gecko research with my lab-buddy Chris. He barely graduated when he already had a grant to go to China to do a herps survey of a previously unsurveyed (and rarely visited by Westerners) are of China. He reported his findings in a series of guests posts on this blog. What a fun way to get a Masters…
A Surprise
Laura Jolley was considered by some of our faculty here to be a bookish type – excellent grades, but perhaps growing up with too sheltered life to want to get dirty with research. So when she applied for a hard-to-get grant to go to Africa to do AIDS research most were reluctant to sign a letter of support for her. Dr.Nick Haddad, who saw her in actiuon in his ecology core course, gladly signed and was delighted when she actually got the money. You have to scroll down here (one should think NCSU folks would learn the notion of permalink by now!) to read about her accomplishments and I have also mentioned her in this post. She spent two summers in Ghana and one in Lesotho living with the locals, doing the research on local attitudes and knowledge about sex and AIDS and devising strategies for education and prevention. She is in graduate school up in DC right now studying public health and epidemiology.
A Hidden Gem
Amy Hughes was my student in a physiology lab which, as its most important component, has an independent project. Amy is smart, but was shy and not with the greatest of the GPEs in the world at the time. She had no idea what to do for her project except that she liked handling crayfish in one of the lab exercises and wanted to work alone (i.e., not teamed up with another student or two). I have no idea how and why I figured out that she would be just the right person to do this long and tedious study, but she did brilliantly and when I showed the data to a professor he promptly got some funding for Amy to repeat and continue the work as her honors project. The result is the first ever study published on a blog – the famous crayfish circadian/melatonin/aggression post. She went on to Minnesota where she got a MS in epidemiology (I think her work there should be published by now), came back to NCSU for some more fun and classes and will start medical school next semester. Oh, and she came to the Science Blogging Conference.
Obvious from the beginning
Elizabeth Daubert was one of those straight A students who ran out of classes and had to take all graduate-level courses in her senior year, including the extremely tough two-semester General Physiology with Bob Grossfeld (NCSU is a big campus yet it is eerily quiet on the days when there is an exam in this course). My PI did not do any undergraduate research, but when Chris and I were running the lab (and far too many experiments) he let us hire undergrads to help us. Most of the people we hired were pretty much content to be paid to feed the animals, but Elizabeth wanted to do research. And she did. She got fully involved in several of my experiements – all aspects of it, not just the drudgery work. Now, my boss is a brutally honest person and, if he is not prepared to write a stellar letter of recommendation for you, he’ll politely refuse to write one at all. But he wrote a letter for Elizabeth when she started applying to grad schools. Every place she applied to (except Stanford) called her for an interview and wherever she went she was referred to as the “candidate with the Underwood letter”! I have no idea what he wrote, but people in the field understand that if he writes one, it is to be taken seriously. She got accepted/invited everywhere. She is happily enjoying (scroll down) her neuroscience graduate studies at University of Virginia right now.
Now go read what others have written about the theory of undergraduate research and think how Kevin, Laura, Amy and Elizabeth fit in there.
Update: Kate, Propter Doc, Guru, Laelaps, Jason and Kayhan add their experiences.
Update: Jenna and Larry add their perspectives.

Monday Weird Sex Blogging….

…because weird sex does not only happen on Fridays….
Remember this? Many have asked themselves (I did) where does it go, i.e., what kind of female genital tract can accomodate such a large penis. But one person actually did not stop at wondering but set out to find out. You can find out who and how and why in Carl Zimmer’s today’s NYTimes article about today’s PLoS-One paper.

More Godless Blogging of the Week

Out in the real world, especially in the Red States and the Bible Belt, atheists tend to go on with their lives without actively tooting their horns every day everywhere. But online, the Internets are teeming with atheists suggesting that there may be more of us in the general population than what the various censuses show, even if one controls for such things as self-selection, i.e., repressed atheists tending to vent their atheism online if prohibited from doing so offline. The Carnival of the Godless has been going on for some time now and it has grown really big, to the point of unweildy. So, a new carnival has just started and it looks good – check out the Humanist Symposium and its Inaugural Edition. Considering how crowded the atheist blogosphere has become, I doubt that the two carnivals will be in competition with each other – both will be equally big and good.

My Serbian readers will die laughing when they read this….

A guy ‘jebo jeza’, ahem, literally fucked a hedgehog in Serbia and ended up in the ER. Do kids there these days don’t even know their slang? ‘Jebo jeza’ means something along the lines of ‘being in big trouble’ or ‘having everything go wrong for you’. This guy accomplished that for himself, I guess….unless this is, as is likely, an urban legend.

Happy Labor Day!

In a large proportion of the surface of our planet, people are not supposed to go to work today. Not here, though. Eh, the good old days back home when my parents would go off for a ten-day vacation on May Day and leave my brother and me to rule the house and host parties…

Monday

I am teaching tonight (and preparing for the lecture today) so there will be very light blogging today, naked or not (tune in tomorrow).
I am also struggling with writing the cover letter for PLoS. I have never written (or even read) a cover letter before so I asked some friends for samples of theirs and it makes me really uncomfortable how self-advertising they are supposed to be: me, me, me. I have as big ego as anyone, but writing a couple of pages about how great I am just rubs me wrong. I’ll keep trying…

Welcome a new SciBling!

Go say Hello to Mark and Chris Hoofnagle at Denialism blog.

ClockQuotes

Time, which changes people, does not alter the image we have retained of them.
– Marcel Proust

Godless Blogging of the Fortnight

Carnival of the Godless #65 is up on Light Remembered.

Circadian Skyline

The word ‘circadian’ has a certain mystique about it for people not in the know, thus it is not surprising that there are several bands around with that word incorporate in their names. I know I blogged about it before but I am too lazy right now to search my archives for it. Anyway, here is the newest addition to the lineup, an Ohio band called the Circadian Skyline.

Tomorrow

Are you going to blog dressed or in the nude?

My Picks From ScienceDaily

Wing Morphing Of The Swift Could Inspire New Aircraft Designs:

A swift adapts the shape of its wings to the immediate task at hand: folding them back to chase insects, or stretching them out to sleep in flight. Ten Dutch and Swedish scientists, based in Wageningen, Groningen, Delft, Leiden, and Lund, have shown how ‘wing morphing’ makes swifts such versatile flyers. Their study, published as cover story in Nature on April 26, proves that swifts can improve flight performance by up to three-fold, numbers that make ‘wing morphing’ the next big thing in aircraft engineering.

Continue reading

ClockQuotes

Art is long, and Time is fleeting,
And our hearts, though stout and brave,
Still, like muffled drums, are beating
Funeral marches to the grave.

– Henry Wadsworth Longfellow

Blogrolling for Today

Life of a Labrat

Open and Shut?

Open…

Open Access News

Recurring Decimals…..

T. taxus

Under the Dome

Journalology

Blogging Teach-in

Just came back from the first Durham blogging teach-in of the year. Pam, Brian and Anton were there and we introduced some new interesting people to the wonderful world of blogging (and they started their own new wordpress blogs).
If you are in the Triangle NC area, we are doing the same thing next week – same place and time: Durham public library 10am-12noon.

Curse Words

Last week’s Casual Friday study on Cognitive Daily tried to look at the way various curse words are used and perceived by their blog readers.
Today, the results are in and, though not surprising, they are quite interesting. The sample is probably skewed towards well-educated folks interested in cognitive science, as well as towards the US readers (or at least English-speaking readers), but they had a large enough sample this time to get significant differences between sexes, if not races.
Do you find “bitch” less offensive if you are a dog breeder? Or if you are a regular reader of Bitch, PhD blog?

Physics Blogging of the Week

Philosophia Naturalis #9 is up on Science And Reason.

Classroom Blog

I am starting my BIO101 for adults course again on Monday and this time I am deteremined to use a blog in the classroom. To begin with, I copied my lecture notes here (still needs some fiddling and editing before Monday) and we’ll see how it works out.

My Picks From ScienceDaily

Dogs Copy Other Dogs’ Actions Selectively, The Way Humans Do:

A distinguishing feature of human intelligence is our ability to understand the goals and intentions of others. This ability develops gradually during infancy, and the extent to which it is present in other animals is an intriguing question. New research by Friederike Range and Ludwig Huber, of the University of Vienna, and Zsofia Viranyi, of the Eötvös University in Budapest, reveals striking similarities between humans and dogs in the way they imitate the actions of others. The phenomenon under investigation is known as “selective imitation” and implies that dogs–like human infants–do not simply copy an action they observe, but adjust the extent to which they imitate to the circumstances of the action.

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ClockQuotes

I think scientists should stop wasting valuable resources trying to cure cancer and focus on more important issues, like keeping me from drooling in my sleep.
– Bill Hewins

New science-related carnival!

The first edition of Carnival of Space is up on Why Homeschool.
Submit your entries for the next edition here and volunteer to host here.

Happy Birthday, John James Audubon

John James Audubon was born on his father’s plantation in Haiti on this day in 1780. Despite being born of his father’s mistress, he was raised in France by his father’s wife and educated with other young aristocrats. He took an early interest in drawing birds, when he found himself without an income he proceeded to paint some of the finest images of North America’s avians. The modern Audubon Society approves of his art but would hardly approve of his methods: He got the birds to pose for him by first shooting them.

It is not only fine feathers that make fine birds.
– Aesop
The birds I heard today, which, fortunately, did not come within the scope of my science, sang as freshly as if it had been the first morning of creation.
– Henry David Thoreau, 1817 – 1862
I value my garden more for being full [of] blackbirds than of cherries, and very frankly give them fruit for their songs.
– Joseph Addison, 1672 – 1719
The bird has an honor that man does not have. Man lives in the traps of his abdicated laws and traditions; but the birds live according to the natural law of God who causes the earth to turn around the sun.
– Kahlil Gibran, 1883 – 1931
God loved the birds and invented trees. Man loved the birds and invented cages.
– Jacques Deval, 1895 – 1972
To a man, ornithologists are tall, slender, and bearded so that they can stand motionless for hours, imitating kindly trees, as they watch for birds.
– Gore Vidal

From Quotes of the Day

The Future of the Interview

Excellent article by Jeff Jarvis: The obsolete interview (hat-tip: Anton). As I’ve been interviewed several times this year, I agree. The world is changing: media, just like science publishing (see below) and getting a job (see further below) will change….

Three labs simultaneously discover a new clock gene!

Thus reports The Scientist:

Researchers from three different labs have identified a new circadian gene in the mouse, according to two papers in Science and one paper in Cell published online this week. Mutagenesis screens revealed that mutations in a protein called FBXL3 lengthen the mouse circadian period by several hours, and biochemical analyses showed that FBXL3 is necessary for degradation of key circadian clock proteins.

I’ll probably have something more to say once I get hold of the actual papers.
In a perfect world, the three groups would have done Open Notebook science, found each other, collaborated, minimized waste of parallel work, and ended with a kick-ass monster paper in PLoS-Biology that would get cited hundreds of times within a year. Ah well….

A great interview with Elizabeth Edwards

With Bob Geary of The Independent Weekly. Listen to the whole thing here or read an excerpt here.

Dont’ forget tonight!

I’ll have to find my remote control and remember how to use it, because the 08 campaign season is officially starting tonight with the first Democratic presidential debate in South Carolina, at 7pm ET on MSNBC. You all know who I am rooting for.

Second Science Blogging Conference

Yes, we are working on it. Anton just put up the new wiki and the first scaffolding for the program. At this point in time we certainly invite your suggestions, but mostly are looking for sponsors in order to see how ambitious we can be next year in comparison to the First Conference.
Oh, and don’t forget to submit your nominations for the second edition of The Open Laboratory.

Looking for good educational biology movies

I am teaching my BIO101 again starting this Monday. The class is very small, so the discussions and student presentations will not last very long. Thus, I will have extra time at the end of each lecture. This can be a good time to show some videos. So, if you know of good movies available online or that can be ordered as CDs or VHS tapes, let me know in the comments (check the link for the topics I need to cover). I have a couple of ancient tapes whcih will do in a jiffy, but I am looking for more recent and better stuff. Keep in mind that this is VERY basic biology. Thus, the cool Harvard movie of the inside of the cell won’t work – too many molecules I do not cover and nothing is labelled anyway.

Skeptical Blogging of the Fortnight

The 59th Skeptics’ Circle is up on Pooflingers Anonymous

My Picks From ScienceDaily

Horses Suffer From Obesity, Just Like Humans:

Horses are inheritably couch potatoes. An overeating, slothful horse leads to an obese horse. Unlike humans, however, horse owners often don’t see the dangers of an obese horse. Caretakers may see no harm in giving their horses rich foods, but obesity in horses is just as unhealthy as obesity in humans and can lead to fatal diseases.

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TIME’s most influential people of the year

They are asking you to rate them here.
I have never heard of about half the people on the list – perhaps they are ‘influential’ in their small circles. Others are celebrities, and they may be influential in distracting people from things that matter. Some used to be influential in the past, or are influential abroad but not here. PZ suggests everyone gives Dawkins a 100%. Sure – the only scientist on the list (although they call him, gasp, an “evolutionist”!!!!).
Watch out – the stuff loads really slowly and it is too easy to give a 50% when your intention is to give a different rating. I have only voted for Elizabeth Edwards (who have since slipped from 14th to 34th place!) because she is the only one I know in person and the only one to have commented on my blog.

ClockQuotes

In three minutes, 98 percent of all the matter there is or will ever be has been produced. We have a universe. It is a place of the most wondrous and gratifying possibility, and beautiful, too. And it was all done in about the time it takes to make a sandwich.
– Bill Bryson

Fair Use and Open Science

Update: The issue has been resolved amicably and Shelley has some further thoughts. And some even more further thoughts. The discussion will continue here on Scienceblogs and elsewhere in the follwoing days….
If you read other Scienceblogs and not just me, you are likely quite aware of the “Wiley Affair”, but if you are not here is a quick summary:

Continue reading

Fighting Malaria in Southern Mali

It is the malaria week right now, isn’t it? Check out this nifty website about the efforts to fight malaria in Kangaba, Mali. Just click and drag on each picture and you can swing it around full 360 degrees.
Hat-tip: Anton

Oh, how I wish I could go there…

Cold Spring Harbor 72nd Symposium: Clocks & Rhythms, May 30 – June 4, 2007. Abstract deadline is way past due, but just to go and be there (and blog from there) would be super-awesome.

Blogger Perceptions on Digital Preservation Survey

If you have a moment, this is a useful study to participate in:

Do you blog? If yes, then please consider participating in an online survey from the University of North Carolina at Chapel Hill’s School of Information and Library Science. The study, Blogger Perceptions on Digital Preservation, is being conducted under the guidance of the Real Paul Jones. The study team is interested in hearing from all bloggers on their perceptions on digital preservation in relation to their own blogging activities, as well as the blogosphere in general. To hear more about this survey, please visit the study’s fact sheet at http://www.ils.unc.edu/~hcarolyn/blogsurvey/. From there, you can link out to the web-based survey. The survey will be available from April 25 through May 23, 2007. We believe blogs are valuable records of the human experience. Help to contribute to continued access to these important records by participating in our study. If you have any questions, feel free to contact Carolyn Hank, the study Principle Investigator, at hcarolyn AT email DOT unc DOT edu. Thanks!