Author Archives: Bora Zivkovic

Social Networking for Beginners

Related:
Wiki for beginners
Blogs for Beginners

Gaming Systems

From here (click if you need help identifying the gaming systems – or candidates for that matter):
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ScienceOnline’09 – individual session pages

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If you check out the Program, you’ll see that I have started making pages for individual sessions – just click on “Go here to discuss” next to each session. Over the next few days I will do this for all the sessions and the session leaders will use those pages in whichever ways they want. For now, I have made pages for these sessions – check them out:
Science Fiction on Science Blogs?
Science blogging without the blog?
Science online – middle/high school perspective (or: ‘how the Facebook generation does it’?)
Transitions – changing your online persona as your real life changes
Semantic web in science: how to build it, how to use it
Using the Web in teaching college science
How to search scientific literature

Today’s carnivals

Four Stone Hearth #51 is up at Clashing Culture
192nd Carnival of Education is up on Detention Slip
The new edition of the Carnival of the Liberals is up on Clashing Culture

DonorsChoose 2008 Challenge – update 4

My DonorsChoose board includes challenges like this one, for example: Animal Life Cycles Up-Close:

Change you can believe in! That seems to be the motto these days. I want to teach my 2nd grade students about real change… animal life cycles.
My goal is to provide students with hands-on opportunities for observation and discovery. Students will compare and contrast various life cycles, recording changes in their learning logs.
I teach at a magnet school which has a strong Spanish emphasis. Our 2nd grade team shares most science materials so over 100 students will benefit from your contribution. We do not have any science textbooks or adopted curriculum guides; we simply teach the state standard course of study using whatever resources we can find.
These materials will bring excitement into the classroom and engage students in the world of science. As students safely explore live animals up-close, learning becomes more meaningful. Content can be integrated into many different subject areas such as writing, math, and reading. Your gift will motivate students as they grow in their respect for life and care for the environment. Thank-you for your consideration.
My students need to observe different animal life cycles (ladybug, frog, ant) in 5 different stations for each.

Just click here and donate as little as 5$ and make some kids happy.

The Invisibility Cloak

From SCONC:

Tuesday, Oct. 14
7 p.m.
Science Cafe Durham (aka Periodic Tables): The Invisibility Cloak
Steve Cummer of Duke’s Pratt School of Engineering discusses acoustic materials that might hide a submarine or improve an auditorium’s performance. Broad Street Café, 1116 Broad Street, Durham. http://www.ncmls.org/periodictables

Clock Quotes

Time is a fixed income and, as with any income, the real problem facing most of us is how to live successfully within our daily allotment.
– Margaret B. Johnstone

DonorsChoose 2008 Challenge – SciBlings need some urgent help

Perhaps you are still waiting on contributing to my projects, but these projects of my SciBlings cannot wait much longer!

Today’s carnivals

The 24th edition of the Boneyard is up on The Other 95%
The 145th Carnival of Homeschooling is up on Corn and Oil

What insect is this?

This insect has been sitting on my window, completely motionless, all day. It is about 2in long in the body, probably around 5-6in if one includes the stretched legs. What is this? Does it sting or can I handle it safely, put it on a sheet of white paper to take a better picture?
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New and Exciting in PLoS ONE

There are 9 new articles in PLoS ONE today (as well as another 3 articles published last night). As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. Here are my own picks for the week – you go and look for your own favourites:

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ScienceOnline’09 – Duke University

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Again, let me introduce a bunch of people who have registered to attend and participate in ScienceOnline09 in January. Today – folks associated with Duke University.
Anton Zuiker, one of the organizers of this conference, is a long-time blogger, the founder of BlogTogether.org, and manager of Internal Communications at Duke Medicine, which involved designing and running the Web-based Inside Duke Medicine as well as re-designing their print newsletter.
Andrea Novicki is the Academic Technology Consultant at the Center for Instructional Technology, Duke University Libraries.
Marsha Penner is a postdoc in the Department of Psychology & Neuroscience.
Karl Leif Bates is is the Manager of Research Communications at Duke University and the Editor of Duke Research
David Palange is a student and blogger in the Nicholas School of the Environment
Clinton Jenkins is an ecologist and researcher in the Pimm group at the Nicholas School of the Environment.
April L. MacKellar is a doctoral student in the Department of Biochemistry.
Constance Johnson is doing cool educational stuff in the School of Nursing.
Lenore Ramm works at Duke and is a prolific food blogger.
Carmen Yeung is part of the Real Oceans Project of The Nicholas Institute for Environmental Policy Solutions
Benjamin Landis is a student in Nicholas School of the Environment
Eugenia Tsamis is a doctoral student in Biochemistry
Kevin Zelnio writes on Deep Sea News and The Other 95% and just started working in the Duke Marine Lab.
Robyn Walker is the Communications Assistant at the Duke University Nicholas School of the Environment
Anthony So is the Director of The Program on Global Health and Technology Access at the Terry Sanford Institute of Public Policy
Heidi Koschwanez is a student at the Center for Biomolecular and Tissue Engineering
Tong Ren is a Ph.D student in the Department of Electrical and Computer Engineering, Pratt School of Engineering.
Mary Jane Gore is the Senior Science Writer for The Duke Medicine Office of News and Communications
Mollie Minear is a PhD student in the Program in Genetics and Genomics.
Yuanjie Jin is a graduate student in Biology.
Zakiya Whatley is a student in the Program in Genetics and Genomics
Kristian Lum is a student of Statistics.
Andrew Thaler is a PhD student in the Duke University Marine Lab
Erica Tsai is a doctoral student in the Department of Biology, the developer of PhyloGeoViz, and, as one of the leaders of WiSE is in charge of the Friday program at ScienceOnline09.
Do you want to meet them? Sure, it’s easy and free. Just register.

My picks from ScienceDaily

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Diabetes Mellitus Explained

By SciCurious.

Open Laboratory 2008 – submissions so far

We are busy preparing for The Open Laboratory 2008. The submissions have been trickling in all year, and a little bit more frequently recently, but it is time now to dig through your Archives for your best posts since December 20th 2007 and submit them. Submit one, or two, or several – no problem. Or ask your readers to submit for you.
Then take a look at your favourite bloggers and pick some of their best posts – don’t worry, we can deal with duplicate entries. Do not forget new and up-coming blogs – they may not know about the anthology – and submit their stuff as well.
As we did last year, we encourage you to also send in original poems and cartoons.
Keep in mind that the posts will be printed in a book! A post that relies heavily on links, long quotes, copyrighted pictures, movies, etc., will not translate well into print.
The deadline is December 1st, 2008.
Below are submissions so far. Check them out and get inspired. If you see that one of your posts is at an old URL and you have since moved, re-submit with the new URL (perhaps re-post it if necessary):
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Springer buys BMC

Open access publisher BioMed Central sold to Springer:

Those in the open access movement had watched BioMed Central with keen interest. Founded in 2000, it was the first for-profit open access publisher and advocates feared that when the company was sold, its approach might change. But Cockerill assured editors that a BMC board of trustees “will continue to safeguard BioMed Central’s open access policy in the future.” Springer “has been notable…for its willingness to experiment with open access publishing,” Cockerill said in a release circulated with the email to editors.

Today’s carnivals

Linnaeus’ Legacy #12 is up on PodBlack Cat
Grand Rounds Vol. 5 No. 3 are up on M.D.O.D.

DonorsChoose 2008 Challenge – update 3

My DonorsChoose board includes challenges like this one, for example: Smile….We love science!:

I teach special need students in an Inclusion Kindergarten setting in North Carolina. Our school is a Title One campus and we serve many low income families.
I would like to increase and enhance my student’s knowledge of science. The Simple Science Exploration tubs will include 4 fun, hands on experiments with simple picture direction as the student’s work independently. Having these tubs will provide the student’s with engaging hands on activities. Currently, I have a limited amount of material to teach science in a scientific way.
The Simple Science tubs will provide student’s with simple investigations. making comparisons among objects and making predictions. My students will benefit from the tubs because they offers a varieties of ways to increase their interest in science.
Your support will ensure that my student’s will have the opportunity to enjoy science. I appreciate all that you will do for children and families.
My students need one (1) Simple Science Exploration Tubs to gain an understanding of basic scientific principles as they create a variety of experiments.

Just click here and donate as little as 5$ and make some kids happy.

The Behavior and Misbehavior of Dogs

From SCONC:

Tuesday, Oct. 14
6:30-8:30 pm
Science Cafe Raleigh: The Behavior and Misbehavior of Dogs
Barbara Sherman, of NC State’s College of Veterinary Medicine and president of the American College of Veterinary Behaviorists (pet whisperers) discusses dog behavior, and misbehavior. Tir Na Nog, 218 South Blount St, Raleigh

Clock Quotes

A man’s penmanship is an unfailing index of his character, moral and mental, and a criterion by which to judge his peculiarities of taste and sentiments.
– Philip Dormer Stanhope, 4th Earl of Chesterfield

Why Current Publication Practices May Distort Science

Published today in PLoS Medicine:

This essay makes the underlying assumption that scientific information is an economic commodity, and that scientific journals are a medium for its dissemination and exchange. While this exchange system differs from a conventional market in many senses, including the nature of payments, it shares the goal of transferring the commodity (knowledge) from its producers (scientists) to its consumers (other scientists, administrators, physicians, patients, and funding agencies). The function of this system has major consequences. Idealists may be offended that research be compared to widgets, but realists will acknowledge that journals generate revenue; publications are critical in drug development and marketing and to attract venture capital; and publishing defines successful scientific careers. Economic modelling of science may yield important insights.

Today’s carnivals

The latest edition of Medicine 2.0 Blog Carnival is up on USMLE blog for smart people
Carnival of the Green #148 is up on Sustainablog.

Silent Alarm Clock

See here. Found on GearCrave:
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GearCrave says:

If you are anything like me, you do not find anything as annoying as being jolted awake by a high-pitch electronic sound in the morning. Today, we bring you a soothing alternative. “Silence” is a conceptual alarm clock that will wake you up without emitting any sound. If you need to be awoken, you simply wear a special wireless rubber ring. When the designated alarm time comes, the clock will send a signal to the ring which will generate a tactile alarm. If you wish to continue your sleep, just shake your hand to activate the snooze function. As time goes on, further snoozes will be harder to generate, requiring more vigorous shaking each time.

Yankodesign says:

Alarm clocks usually jolt us awake leading us to reach for the almighty snooze button. Silence is a conceptual alarm clock that allows you to program multiple alarms and wakes you without any sound. Each person wears a wireless rubber ring with an integrated vibration device that generates a tactile alarm. The snooze function is engaged by shaking your hand. However, each successive time you want to snooze, more movement is required, making sure you get to work on time.

Cool physics on Bloggingheads.tv

Jennifer Ouelette and Julianne Dalcanton chat about space, physics and science education:

Science Saturday: Our Humongous Sky:
Julianne lays claim to a comet (14:18)
The scientific sensibility infiltrates television (05:03)
Woes and wonders of the Hubble Space Telescope (08:38)
How astronauts prepare to go into space (09:00)
Jennifer defends corpse museums (04:15)
The right way to teach science to kids (04:12)

My picks from ScienceDaily

Gene Expression In Alligators Suggests Birds Have ‘Thumbs’:

The latest breakthrough in a 120 year-old debate on the evolution of the bird wing was published in the open-access journal PLoS ONE, October 3, by Alexander Vargas and colleagues at Yale University, the University of Wisconsin-Madison and Yale Peabody Museum of Natural History.

Galloping And Breathing At High Speed:

The coordination of two systems are key for any horse to walk, trot, gallop or win a race. The first are the lower limbs, which allow the animal to move along on a “spring-like” tendon. The second is a complicated respiratory system, which allows a horse to take in one breadth for every stride they make while racing.

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ScienceOnline’09 – Education sessions

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Today, instead of introducing people, I will introduce a session, or two or three.
Feedback from participants of the last two conferences indicated a lot of interest in sessions relevant to science educators at all levels. At both the 1st and the 2nd conference, we had one session on using blogs in the classroom. But this time, we want to heed the calls and provide, if possible, three such sessions, each targeting a somewhat different audience.
So, if you go to the conference wiki and check the Program page, you will see the following three sessions listed there:
Online science for the kids (and parents) — moderated by Janet Stemwedel:

Even little kids are online these days. They are curious about the world. What kind of scientific information is there on the Web that is suitable for the littlest ones? How does one find the good stuff? What works and what doesn’t for that age group? What can one do to add quality science material for kids and parents? How to write blog posts with little kids in mind?

And also:
Using the Web in teaching college science — moderated by Andrea Novicki and Brian Switek:

What are the strategies, methods and pitfalls of using the online technologies in science education in college? The importance of Open Access to primary research. The willingness of students to post on blogs. Text-messaging as communication. The problem of the “creepy treehouse”.

And finally – and I am really excited about this:
Science online – middle/high school perspective (or: “how the Facebook generation does it”?) — moderated by Stacey Baker and her students:

How does middle/high school science education differ from that in college? There are also institutional problems: a) Most US pub. school networks firewall out major sources of info, such as all of scienceblogs.com, all of blogspot.com, all of youtube, etc. A teacher who finds something on a blog can’t use it directly in classroom. b) Conceptually linked posts and comment threads, ads, external links, etc. are often inappropriate for PS K-12 settings (which is perhaps why ‘a’ is true). c) yet, some bloggers want to have some of their work used in this setting. Are the younger kids different from college students in their use of online tools? Many school are experimenting with new technologies but do not have a clear idea how to do it – did they ask the kids themselves for advice? If not, we’ll ask the students in this session.

And if you look at the list of registered participants so far, you will see quite a lot of teachers and education specialists, as well as a few high school and college students, e.g., Kim Gainer and her duaghter Patti, John Dupuis’ son Sam, Elissa Hoffman and a number of others. We are also expecting some teachers and students from the Zoo School and from the Duke’s summer student research blogging program. Keep checking the wiki for more information….

For the first time, Chaffinches outnumber Starlings in the Netherlands

According to this article: Fascinating birds migration at EuroBirdwatch 2008:

Over the past weekend, 50.000 adults and children from over 30 European countries took up EuroBirdwatch 2008, BirdLife’s invitation to observe the fascinating migration, as birds move south across Europe for the winter.
BirdLife Partners across Europe were involved – from Portugal to Turkey; Malta to Norway – between them putting together 2.700 different events.
And once again birds didn’t disappoint: attendees counted 2.3 million of them passing overhead.

hat-tip

2008 Nobel prize in Physiology or Medicine

The 2008 Nobel prize in Physiology or Medicine was announced this morning.
The winners are HPV and HIV (OK, OK, the people who discovered them) – the year of the virus!
I don’t pay much attention to these, as biology I care about has not received the prize since 1973, but I was happy to hear about a different kind of connection I have with one of this year’s winners – Francoise Barre-Sinouss recently published a paper in PLoS ONE – this one: The CD85j+ NK Cell Subset Potently Controls HIV-1 Replication in Autologous Dendritic Cells
Well, if it’s good enough for a Nobel prize winner, it’s good enough for everyone, I’d say…. 😉

DonorsChoose 2008 Challenge – update 2

My DonorsChoose board includes challenges like this one, for example: Science Trip For Our Amazing Urban Students:

The he students deserve this. I teach 5th grade at an urban, diverse, 86% free & reduced lunch school. Our school is 55% latino population, many who do not speak English and many who were born in another country. Our school has about 12 different languages spoken throughout it. Our students come from families that are very limited financially and we want to offer them an opportunity to go on a trip that will change their lives. This trip is a once in a life time trip for most of our students.
When teachers at our school introduce a unit on the beach or the zoo, most of our students stare at us blankly because these are not experiences that they have ever had. These are common experiences that most American students come to school with. Having these experiences allows students to make connections to the curriculum they see through elementary school. Our students, not having these experiences, are very limited in what they can connect to our curriculum concepts. This prevents them from meaningful learning.
We are planning a 5th grade trip to Seabrook Island on the Atlantic Ocean. This trip will be filled with so many new and exciting experiences for our students to have. It will broaden their understanding of America and our world.
While at Seabrook Island students will be continually learning and exploring our North Carolina Science Curriculum.
Students will…
-explore ecosystems of the ocean, wetlands, and forest.
-observe jellyfish, dolphins, crabs, snakes, alligators, etc.
-connect weather concepts with observable patterns over the weekend.
-connect concepts of different clouds and the weather they bring.
-explore the landforms of the coastal region of our country.
-explore forces of the wind and waves using tools and kits.
Your help will ensure that our students can afford this experience. Being a school with 86% free & reduced lunch means most of our parents will not be able to afford a trip like this. Our goal is to provide this trip to any student and family interested. By providing snacks and supplies, we will be able to bring our costs down on the families so that more students can have the trip of their lifetime.

Whither (wither?) Science Journalism?

From SCONC:

Tuesday, Oct. 14
6 to 8 p.m.
SCONC monthly meeting – Whither (wither?) Science Journalism
Durham science journalist Cathy Clabby, formerly of the N&O now of American Scientist, discusses the sorry state of her craft in U.S. newspapers and magazines and shares some of the new venues that journalists are finding to publish their work. NC Biotech Center, #15 Alexander Drive, RTP. Congressional Room. Please rsvp@ncbiotech.org

Clock Quotes

It’s only when we truly know and understand that we have a limited time on earth – and that we have no way of knowing when our time is up – that we will begin to live each day to the fullest, as if it was the only one we had.
– Elisabeth Kubler-Ross

Politics of Animal Protection

Politics of Animal Protection
Originally written on September 1, 2006, re-posted today to raise more dust 😉

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Happy blogiversaries!

Shakesville (formerly known as Shakespeare’s Sister) is four years old.
Afarensis is four years old.
Highly Allochthonous is three years old.
What is it about October and all those blogiversaries? What were all those people doing nine months prior….

Wikipedia, just like an Organism: clock genes wiki pages

ResearchBlogging.orgThe October issue of the Journal of Biological Rhythms came in late last week – the only scientific journal I get in hard-copy these days. Along with several other interesting articles, one that immediately drew my attention was Clock Gene Wikis Available: Join the ‘Long Tail’ by John B. Hogenesch and Andrew I. Su (J Biol Rhythms 2008 23: 456-457.), especially since John Hogenesh and I talked about it in May at the SRBR meeting.
Now some of you may be quick to make a connection between this article and its author Andrew Su and A Gene Wiki for Community Annotation of Gene Function, published in PLoS Biology back in July, where one of the authors is also Andrew Su. And you would be right – it’s the same person and the two articles are quite related.
In the PLoS Biology article, they write:

A loose organization of Wikipedia editors has spearheaded the creation and expansion of several thousand articles related to molecular and cellular biology (the “MCB Wikiproject”), including many gene-specific pages. These articles vary widely in quality, format, and completeness, ranging from relatively complete encyclopedic entries (e.g., “enzyme,” “oxidative phosphorylation,” and “RNA interference”) to very short collections of information called “stubs” (e.g., “amphinase” and “glomus cell”). As an example of the collaborative writing process, the article on RNAi has been edited 708 times by 232 unique editors since its initial creation in October 2002. On the subject of human genes, generally only the most well-characterized of genes and proteins have highly developed entries (e.g., “HSP90” and “NF- B”).
In principle, a comprehensive gene wiki could have naturally evolved out of the existing Wikipedia framework, and as described above, the beginnings of this process were already underway. However, we hypothesized that growth could be greatly accelerated by systematic creation of gene page stubs, each of which would contain a basal level of gene annotation harvested from authoritative sources. Here we describe an effort to automatically create such a foundation for a comprehensive gene wiki. Moreover, we demonstrate that this effort has begun the positive-feedback loop between readers, contributors, and page utility, which will promote its long-term success.

In the JBR paper, the authors focus on the development of Wikipedia pages describing genes involved in circadian rhythms, probably the first genes to be done comprehensively there, as an example for others as to how to do this kind of thing:

Why use Wikipedia for this? First, Google and Wikipedia have already become scientific research tools. When you Google an unfamiliar gene you usually end up at common sites of gene annotation such as the National Center for Biotechnology Information. Though these sites have expert curators who do the best they can, they are usually not domain experts and are so overloaded that they frequently fall behind in accurately summarizing the literature. (It’s actually amazing what they accomplish given available resources.) For confirmation, research your favorite gene. Using Wikipedia will allow our community to build and evolve living, up-to-date summaries on the function of important genes in the circadian network. Check out the pages on Arntl (http://en.wikipedia.org/wiki/ARNTL) and Rev-erb-alpha (http://en.wikipedia.org/wiki/Rev-ErbA_alpha). Second, in part due to Wikipedia’s past success, its pages appear near the top of search engine lists such as Google, and consequently attract viewers. Finally, our field competes with other disciplines for the best and the brightest young scientists. These people use Wikipedia. High quality pages on annotated clock genes will attract their attention, and attract them to our field.

Importantly, the gene pages need not be extremely long. What is much more important is that they be well referenced. See, for instance Wikipedia pages they mention, those for ARNTL gene (also known as Bmal1 or Mop3), or Rev-ErbA alpha (I have written about some of these genes before, e.g., Lithium, Circadian Clocks and Bipolar Disorder, Tau Mutation in Context and The Lark-Mouse and the Prometheus-Mouse if you want more background). That is all that is needed – if I wanted to be silly, I could say that since genes are small, their wiki pages need to be small as well. But that is only half-silly, really.
This is just like in the real world. Genes don’t really do anything. They are coded descriptions of parts in a catalog. To explain a biological function, one needs to go from genes to their mRNAs to proteins, then to look at protein modifications and how multiple proteins interact with each other. Then see how such protein interactions affect the behavior of a cell. Then see how the altered behavior of a cell affects the entire tissue and how the changes in that tissue affect distant organs. Finally, one gets to explain the function once one understands how a collection of organs, interacting with the external environment, results in changes in biochemistry, development, physiology or behavior of the organism, and how this function evolved.
In the same way, gene pages on Wikipedia are not supposed to be stand-alone. Knowing everything about a clock gene does not mean one knows anything about circadian rhythm generation and modulation (not to mention its evolution). The value is in links – to all the other clock genes, to genes that do similar things (e.g., other transcription factors or nuclear receptors), to primary literature on the proteins coded by these genes and their interactions, and to higher-level functions, e.g., the Circadian Rhythms page and links within.
Some would ask – Why Wikipedia (I know, there are still some people out there who don’t like it):

What’s the downside? The major criticism is poor annotation. Actually, we argue that no annotation is worse than poor annotation, as the latter tends towards self-correction by provoking experts to intervene. In fact, a recent study concluded that Wikipedia was as accurate as Encyclopedia Britannica, and unlike Britannica, growing at a rate of 1500 articles per day (Giles, 2006). Another potential downside is non-consensual or controversial entries. We would argue that these are better addressed in real time via Wikipedia than in journal articles, where they remain fixed for years. Wikipedia even has tools to deal with controversial topics (for examples, see entries on “Intelligent Design,” evolution, “Swift-boating,” or climate change).

And, I’d argue, clock gene pages are not as contentious as those on climate change or creationism. Very few Wikipedia pages are so controversial as to be continuously suspect. Almost all of the pages are on non-controversial subjects, written and edited by experts on the topic, and are as reliable, or better, as anything else one can find out there, not to mention the fastest to get updated once new information comes in.
The effort is starting with the focus on mammalian genes, for obvious reasons of medical relevance and the existence of a wealth of information. But there is just as much, if not more, information on Drosophila clock genes. And comparative analysis of clock-genes in a variety of organisms is the key to understanding the circadian function and its evolution, so if your strength is in other old or emerging model organisms (did you see Japanese quail on that list?!), don’t hesitate to add the pages and information on those.
Finally, I’d like to urge you to contribute – I know that many chronobiologists read this blog (though most are silent types who never comment). It will take 30-60 minutes of your time to make or edit a page on the gene (or a higher-level process) in circadian biology and this effort will have much bigger audience and much broader impact than all of your peer-reviewed papers put together. It’s worth your time even if probably will have no effect on your getting tenure. But the tenure committee is not your only audience – there are researchers around the world (many in developing countries), teachers and students and lay audience, who will be affected by your contribution in a much more lasting and important ways than the inner circle of your department. Isn’t this why you are doing science in the first place?
If you want to discuss this more, come to ScienceOnline09, where John Hogenesh, one of the authors of the JBR article, will demonstrate Wiki Genes, answer questions, and deeply internalize your suggestions 😉
References:
John B. Hogenesch and Andrew I. Su, Clock Gene Wikis Available: Join the ‘Long Tail’, J Biol Rhythms 2008 23: 456-457.
Jon W. Huss, Camilo Orozco, James Goodale, Chunlei Wu, Serge Batalov, Tim J. Vickers, Faramarz Valafar, Andrew I. Su (2008). A Gene Wiki for Community Annotation of Gene Function PLoS Biology, 6 (7) DOI: 10.1371/journal.pbio.0060175

Talk to the hand

Actually, Hey Sarah, talk to the paw! – the Polar Bear paw!
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The voter registration deadline in North Carolina is this Friday, October 10th.

Are you registered? Do you know where to vote? You can find information and register (if you are not) here (this is an Obama site, but it works for everyone):

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ScienceOnline’09 – NIEHS

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I said I was going to introduce the participants at ScienceOnline09 in non-daily but larger batches. So, today, I introduce a large contingent of people coming from the National Institute of Environemental Health Sciences (NIEHS):
NIEHS News Director Robin Mackar
Web Manager Cheryl Thompson
Biomedical Librarian Stephanie Holmgren
Signal Transduction researcher Ren Rongqin
Signal Transduction researcher Danielle Duma
Signal Transduction researcher Daniel Brown
Signal Transduction researcher Erica Lannan
Blood-Brain Barrier researcher Brian Hawkins
And Pediatric Epidemiology researcher Yang Cao

The best illustrations of…

…current politicians and events can be found here. Unfortunately, I cannot whet your appetite by posting one of the pictures here as:

All images copyright Zina Saunders – do not use without permission

DonorsChoose 2008 Challenge – update

My DonorsChoose board includes challenges like this one, for example: Media Literacy in Science:

I am a high school science teacher in North Carolina who wishes to move his students into the 21st century with the skills necessary to become lifelong learners in the global environment.
All too often information presented in textbooks can be less than exciting to students and can even be out dated by the time the textbooks reach the students hands. The articles presented in Current Science are more in the style of those published in popular magazines and newspapers with the student audience in mind. Our students are practiced at reading literary materials such as stories from their English classes, however they need practice in the skills necessary to comprehend the type of material found in factual writings such as newspapers and magazines. These skills are extremely important in keeping up to date with advances in science, medicine and many other topics in todays media rich world.
I would like to supplement our classroom instruction with a subscription to Current Science Magazine. The topics presented are up to date and written in a style that makes them relevant to the student audience. The magazine has a long reputation for presenting accurate information from all disciplines of science and can be used with my biology classes as well as physical science.
Your contribution will help to empower my students to become critical readers and to gain practice in a skill that they can carry with them into productive, informed futures.

This is difficult time to do satire….

….as Real Life is just as crazy. There is not that much difference between the Thursday’s debate and the SNL sketch, is there?
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Today’s carnivals

Carnival of Space – NASA birthday edition – is up on Alice’s Astro Info
And write and submit posts for Mendel’s Garden (on the first Sunday of November on evolgen), for Praxis (on October 15th, at The Other 95%) and for The Giant’s Shoulders (on October 15th at Second Order Approximation).

My picks from ScienceDaily

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Clock Quotes

It’s not easy having a good time. Even smiling makes my face ache.
– Dr. Frank N. Furter

My picks from ScienceDaily

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Offal is Good

The offal refers to….

….those parts of a meat animal which are used as food but which are not skeletal muscle. The term literally means “off fall”, or the pieces which fall from a carcase when it is butchered. Originally the word applied principally to the entrails. It now covers insides including the HEART, LIVER, and LUNGS (collectively known as the pluck), all abdominal organs and extremities: TAILS, FEET, and HEAD including BRAINS and TONGUE. In the USA the expressions “organ meats” or “variety meats” are used instead.
Offal from birds is usually referred to as GIBLETS.
Another, archaic, English word for insides, especially those of deer, was “umbles”, a term which survives in the expression “to eat humble pie”, meaning to be apologetic or submissive.

Growing up in Yugoslavia, I was a very picky eater. But I absolutely loved offal. I loved liver and, although just a kid, I had developed 2-3 different recipes for preparing livers from various animals: pork, calf, veal, beef, lamb, duck, turkey and goose (I did not like chicken liver). My Mom fixes fantastic bread-battered brains which were treated as a special delicacy in our house. Yum! I loved to suck the marrow out of beef bones. I always picked hearts and gizzards from my chicken soup. When we had chicken, I would often eat necks and feet. Oxtail is fantastic. Beef tongue in tomato sauce is one of the best things to eat ever, in my mind.
Also, whenever we castrated a stallion, that was an excuse to get together for dinner – the fried horse testicles. All the best restaurants in Serbia serve ‘white kidneys’, i.e., pig testicles. I never really liked the blood sausage, but beef knees or pig tongues and ears served cold in aspic were a staple in our household.
So, when I came to the United States, I was quite surprised to see that people here generally do not eat any of that stuff. Not even liver! I was quite excited when I went to San Francisco and got to try the duck fries at Incanto.
A few months ago, when Chris put up braised Kobe-beef oxtail as a dinner special at Town Hall Grill, I had it every day that week – it was that good! – yet Chris said that it did not sell very well. And oxtail is not even offal – it is skeletal muscle, and the tenderest of all as it does not need to move a big, heavy animal around, or chew tons of bulky food – just swat an occasional fly. So, not even here in the Triangle, where there is a powerful food culture, and the locavore food scene is amazing, do people easily overcome their cultural barriers to eating meat that is not steak. And yes, this is a cultural barrier:

The type of offal used in any given culture depends on the favoured meat animal, which may in turn depend on religious dietary laws. Muslim countries use much lamb offal. The Chinese have numerous ways of dealing with organs from pigs.
Offal is a good source of protein, and some organs, notably the liver and kidneys, are very valuable nutritionally. In most parts of the world, especially the less developed countries, it is valued accordingly. In the English-speaking world, however, the pattern is different. In North America, there has been and still exists a squeamish attitude which prompted the title Unmentionable Cuisine for the book by Schwabe (1979). In Britain, where there used to be no, or anyway few, qualms about eating offal, overt consumption has declined in the last half of the 20th century, although the offal is in fact still eaten in processed foods where it is not “visible”.
Squeamish attitudes may be explained on various grounds. Heads and feet remind consumers too directly that the food is of animal origin. Ambivalence about eating certain bits of an animal”s anatomy, such as TESTICLES, is expressed through the used of euphemistic names. Some internal offal has surreal shapes and strong flavours, which are not to everyone’s taste. The meat of feet and ears is characterized by textures which are gelatinous and crunchy at the same time, a combination which is generally disliked in the western world, although appreciated in the Orient.

Another dimension in the USA is historical – for a very long time, whenever an animal at a farm was slaughtered, the owners got the steaks, and the slaves got the offal. Thus, there is a racial differentiation here as well – the whites do not have a tradition of cooking offal and tend not to have family recipes and cookbooks about it, while the blacks do have such a tradition and the recipes come down through generations, from mothers to daughters. I have noticed especially here down South, that the country-club-whites especially look down their noses with disdain at offal dishes and their almost visceral disgust with them has more than a little of a classist and racist tinge to it.
Which is unfortunate. There are many places on this planet in which there is not much money going around, and the environment is not too conducive for raising sufficient amounts of grains, fruits and vegetables to feed everyone. Thus, many (probably most) cultures in the world have to be predominantly meat-eating. And growing animals for food is also not very easy or cheap either. So, it makes sense – economic sense if nothing else – to use every last edible bit of an animal. That way, each animal provides more meals to more people than if just steaks were to be eaten. This, in turn, means that fewer animals need to be grown and slaughtered.
In such places – and I have seen that in rural Serbia myself growing up – there is an almost spiritual connection to the farm animals – the slaughter is not something done lightly. It usually involves the entire large family (and friends and neighbors), the slaughter is performed with utmost care, almost ritually. And the greatest care is made not to let any piece go to waste.
At the time when the food business is straining the economy in the USA, ruining the farmers, endangering the people eating meat, done in a way very nasty to the animals, and using far too much energy (aka Oil), a little efficiency may help, including a change in culture in ways that allow us to better utilize each individual food animal (see this, this, this, this, this, this, this, this, this, this, this and this for background and additional information about the economics and politics of food).
It is not a surprise to me that the first cookbook ever to focus on just one type of offal – the testicles – was written by a Serbian chef – The Testicles Cookbook – Cooking with Balls by Ljubomir Erovic:

The Testicles Cookbook – Cooking with Balls is a multimedia cookbook complete with how-to videos on cooking testicle dishes. Including Testicle Pizza, Testicle Goulash and White Wine Testicles, this is a short teaser taken from the full cookbook, written by Serbian testicles chef, Ljubomir Erovic. The full book is available to buy on YUDU in English and Serbian.

Guardian: Cooking with balls: the world’s first testicle cookbook

Everyone’s very excited about a new e-cookbook launched today, by online publishers YUDU. It’s been compiled by a Serbian fellow called Ljubomir Erovic who has apparently been a testicular cook for some 20 years.
“The tastiest testicles in my opinion probably come from bulls, stallions or ostriches, although other people have their own favourites,” says Mr Erovic. He also uses those from pigs and turkeys in his cooking and points out that “all testicles can be eaten – except human, of course”. Glad to hear it Ljubomir.
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While the ingredient is fairly challenging, most of the dishes in the book are less adventurous, from testicle pizza, goulash, battered testicles to barbecued testicles and giblets. To be fair though, it doesn’t hurt to keep it simple, and there are a couple of more demanding recipes in there, for instance, calf testicles in wine (white or red but not sweet) and testicles with bourguignon sauce.

Daily Mail: On the ball: Introducing the world’s first testicle cookbook :

Erovic also organises the World Testicle Cooking Championship, held annually in Serbia since 2004. It draws in chefs from Australia, Bosnia-Herzegovina, Finland, Greece, Hungary, Norway and Serbia. One metric tonne of testicles are prepared.
“When not cooking or eating testicles, or helping others to do so, (Erovic) now runs a company involved in the maintenance of medical and dental equipment,” the book says.

We need to eat and we need to systematically change the way the food industry is organized, but this also means we need to ‘try some new foods’ and be more efficient and less wasteful about it. You can start by frying a testicle or two one of these days. It’s not bad at all, I can guarantee you.

Clock Quotes

What country can preserve its liberties, if its rulers are not warned from time to time that the people preserve the spirit of resistance? Let them take arms…. The tree of liberty must be refreshed from time to time, with the blood of patriots and tyrants. It is its natural manure.
– Thomas Jefferson

Emerging Nanotechnology: A New Risk Factor for Lung Diseases?

From Sigma Xi:

Greetings everyone. We meet again at noon on Wednesday, Oct. 15 in RTP to hear NCSU associate professor James Bonner discuss “Emerging Nanotechnology: A New Risk Factor for Lung Diseases?” As you know, the commercial use of nanomaterials has outpaced scientific assessments of any potential health or environmental risks. Jamie Bonner is one of the scientists working to catch up.
Sigma Xi’s Pizza Lunch speaker series is free and open to science journalists and science communicators of all stripes (free to forward this message to anyone you would like to be included). RSVPs are required to cclabby AT amsci DOT org.
Directions to Sigma XI:
http://www.sigmaxi.org/about/center/directions.shtml.

Can you raise sea-water blue crabs in fresh-water ponds?

Apparently yes: Freshwater Farm Ponds Turning into Crab Farms:

North Carolina’s native blue crab population has been at historic lows since 2000. Dr. Dave Eggleston, director of NC State’s Center for Marine Sciences and Technology (CMAST) and professor of marine, earth and atmospheric sciences, looked at various methods for helping the population recover. He hit upon a solution which not only reduces pressure on existing crab populations, but also benefits farmers looking to diversify their crops: using irrigation ponds on farms to grow blue crabs.
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Eggleston and his fellow researchers discovered that crabs can tolerate a salinity level of only .3 parts per thousand, which is about the same level found in coastal tap water. They did further work to determine the best set of circumstances for raising crab: population density, food rations, and habitat structure in ponds.
This past July, Eggleston and Ray Harris, NC State director of cooperative extension for Carteret County, had the opportunity for a large-scale test when they stocked a 10-acre lake with 40,000 hatchery-raised crabs, and a smaller pond with 4,000 crabs. The crabs will take approximately 105 days to reach maturity, and so far the endeavor looks successful.
With the rapid rate of growth for pond-raised crabs, Eggleston expects that in a given year, a farm could produce two to three harvests, as crabs don’t do well in freshwater during the winter months.
“If you look at a 2 1/2 -acre pond, you could stock it with 50,000 hatchery-raised crabs and expect to harvest around 20 percent, or 10,000 fully grown crabs. At $3 per crab, that’s $30,000 – and multiply that times three. It definitely adds up.”

New and Exciting in PLoS ONE

There are 12 new articles in PLoS ONE today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. Here are my own picks for the week – you go and look for your own favourites:
Importance of Achromatic Contrast in Short-Range Fruit Foraging of Primates:

Trichromatic primates have a ‘red-green’ chromatic channel in addition to luminance and ‘blue-yellow’ channels. It has been argued that the red-green channel evolved in primates as an adaptation for detecting reddish or yellowish objects, such as ripe fruits, against a background of foliage. However, foraging advantages to trichromatic primates remain unverified by behavioral observation of primates in their natural habitats. New World monkeys (platyrrhines) are an excellent model for this evaluation because of the highly polymorphic nature of their color vision due to allelic variation of the L-M opsin gene on the X chromosome. In this study we carried out field observations of a group of wild, frugivorous black-handed spider monkeys (Ateles geoffroyi frontatus, Gray 1842, Platyrrhini), consisting of both dichromats (n = 12) and trichromats (n = 9) in Santa Rosa National Park, Costa Rica. We determined the color vision types of individuals in this group by genotyping their L-M opsin and measured foraging efficiency of each individual for fruits located at a grasping distance. Contrary to the predicted advantage for trichromats, there was no significant difference between dichromats and trichromats in foraging efficiency and we found that the luminance contrast was the main determinant of the variation of foraging efficiency among red-green, blue-yellow and luminance contrasts. Our results suggest that luminance contrast can serve as an important cue in short-range foraging attempts despite other sensory cues that could be available. Additionally, the advantage of red-green color vision in primates may not be as salient as previously thought and needs to be evaluated in further field observations.

Transplantation of Human Umbilical Mesenchymal Stem Cells from Wharton’s Jelly after Complete Transection of the Rat Spinal Cord:

Human umbilical mesenchymal stem cells (HUMSCs) isolated from Wharton’s jelly of the umbilical cord can be easily obtained and processed compared with embryonic or bone marrow stem cells. These cells may be a valuable source in the repair of spinal cord injury. We examine the effects of HUMSC transplantation after complete spinal cord transection in rats. Approximately 5×105 HUMSCs were transplanted into the lesion site. Three groups of rats were implanted with either untreated HUMSCs (referred to as the stem cell group), or HUMSCs treated with neuronal conditioned medium (NCM) for either three days or six days (referred to as NCM-3 and NCM-6 days, respectively). The control group received no HUMSCs in the transected spinal cord. Three weeks after transplantation, significant improvements in locomotion were observed in all the three groups receiving HUMSCs (stem cell, NCM-3 and NCM-6 days groups). This recovery was accompanied by increased numbers of regenerated axons in the corticospinal tract and neurofilament-positive fibers around the lesion site. There were fewer microglia and reactive astrocytes in both the rostral and caudal stumps of the spinal cord in the stem cell group than in the control group. Transplanted HUMSCs survived for 16 weeks and produced large amounts of human neutrophil-activating protein-2, neurotrophin-3, basic fibroblast growth factor, glucocorticoid induced tumor necrosis factor receptor, and vascular endothelial growth factor receptor 3 in the host spinal cord, which may help spinal cord repair. Transplantation of HUMSCs is beneficial to wound healing after spinal cord injury in rats.

Refinement of Light-Responsive Transcript Lists Using Rice Oligonucleotide Arrays: Evaluation of Gene-Redundancy:

Studies of gene function are often hampered by gene-redundancy, especially in organisms with large genomes such as rice (Oryza sativa). We present an approach for using transcriptomics data to focus functional studies and address redundancy. To this end, we have constructed and validated an inexpensive and publicly available rice oligonucleotide near-whole genome array, called the rice NSF45K array. We generated expression profiles for light- vs. dark-grown rice leaf tissue and validated the biological significance of the data by analyzing sources of variation and confirming expression trends with reverse transcription polymerase chain reaction. We examined trends in the data by evaluating enrichment of gene ontology terms at multiple false discovery rate thresholds. To compare data generated with the NSF45K array with published results, we developed publicly available, web-based tools (www.ricearray.org). The Oligo and EST Anatomy Viewer enables visualization of EST-based expression profiling data for all genes on the array. The Rice Multi-platform Microarray Search Tool facilitates comparison of gene expression profiles across multiple rice microarray platforms. Finally, we incorporated gene expression and biochemical pathway data to reduce the number of candidate gene products putatively participating in the eight steps of the photorespiration pathway from 52 to 10, based on expression levels of putatively functionally redundant genes. We confirmed the efficacy of this method to cope with redundancy by correctly predicting participation in photorespiration of a gene with five paralogs. Applying these methods will accelerate rice functional genomics.

Adaptive Threonine Increase in Transmembrane Regions of Mitochondrial Proteins in Higher Primates:

The mitochondrial (mt) gene tree of placental mammals reveals a very strong acceleration of the amino acid (AA) replacement rate and a change in AA compositional bias in the lineage leading to the higher primates (simians), in contrast to the nuclear gene tree. Whether this acceleration and compositional bias were caused by adaptive evolution at the AA level or directional mutation pressure at the DNA level has been vigorously debated. Our phylogenetic analysis indicates that the rate acceleration in the simian lineage is accompanied by a marked increase in threonine (Thr) residues in the transmembrane helix regions of mt DNA-encoded proteins. This Thr increase involved the replacement of hydrophobic AAs in the membrane interior. Even after accounting for lack of independence due to phylogeny, a regression analysis reveals a statistical significant positive correlation between Thr composition and longevity in primates. Because crucial roles of Thr and Ser in membrane proteins have been proposed to be the formation of hydrogen bonds enhancing helix-helix interactions, the Thr increase detected in the higher primates might be adaptive by serving to reinforce stability of mt proteins in the inner membrane. The correlation between Thr composition in the membrane interior and the longevity of animals is striking, especially because some mt functions are thought to be involved in aging.

Variation in the Large-Scale Organization of Gene Expression Levels in the Hippocampus Relates to Stable Epigenetic Variability in Behavior:

Despite sharing the same genes, identical twins demonstrate substantial variability in behavioral traits and in their risk for disease. Epigenetic factors-DNA and chromatin modifications that affect levels of gene expression without affecting the DNA sequence-are thought to be important in establishing this variability. Epigenetically-mediated differences in the levels of gene expression that are associated with individual variability traditionally are thought to occur only in a gene-specific manner. We challenge this idea by exploring the large-scale organizational patterns of gene expression in an epigenetic model of behavioral variability. To study the effects of epigenetic influences on behavioral variability, we examine gene expression in genetically identical mice. Using a novel approach to microarray analysis, we show that variability in the large-scale organization of gene expression levels, rather than differences in the expression levels of specific genes, is associated with individual differences in behavior. Specifically, increased activity in the open field is associated with increased variance of log-transformed measures of gene expression in the hippocampus, a brain region involved in open field activity. Early life experience that increases adult activity in the open field also similarly modifies the variance of gene expression levels. The same association of the variance of gene expression levels with behavioral variability is found with levels of gene expression in the hippocampus of genetically heterogeneous outbred populations of mice, suggesting that variation in the large-scale organization of gene expression levels may also be relevant to phenotypic differences in outbred populations such as humans. We find that the increased variance in gene expression levels is attributable to an increasing separation of several large, log-normally distributed families of gene expression levels. We also show that the presence of these multiple log-normal distributions of gene expression levels is a universal characteristic of gene expression in eurkaryotes. We use data from the MicroArray Quality Control Project (MAQC) to demonstrate that our method is robust and that it reliably detects biological differences in the large-scale organization of gene expression levels. Our results contrast with the traditional belief that epigenetic effects on gene expression occur only at the level of specific genes and suggest instead that the large-scale organization of gene expression levels provides important insights into the relationship of gene expression with behavioral variability. Understanding the epigenetic, genetic, and environmental factors that regulate the large-scale organization of gene expression levels, and how changes in this large-scale organization influences brain development and behavior will be a major future challenge in the field of behavioral genomics.

Today’s carnivals

The Festival of the Trees #28 is up on Arboreality
Friday Ark #211 is up on Modulator
The latest Change Of Shift is up on NurseLinkUp