Yearly Archives: 2007

My picks from ScienceDaily

Generosity May Be Genetically Programmed:

Are those inclined towards generosity genetically programmed to behave that way? A team of researchers, including Dr. Ariel Knafo of the Psychology Department at the Hebrew University of Jerusalem, believes that this could very well be the case.

Like Humans, Monkey See, Monkey Plan, Monkey Do:

How many times a day do you grab objects such as a pencil or a cup? We perform these tasks without thinking, however the motor planning necessary to grasp an object is quite complex. The way human adults grasp objects is typically influenced more by their knowledge of what they intend to do with the objects than the objects’ immediate appearance. Psychologists call this the “end-state comfort effect,” when we adopt initially unusual, and perhaps uncomfortable, postures to make it easier to actually use an object.

In Fruit Flies, Homosexuality Is Biological But Not Hard-wired, Study Shows:

While the biological basis for homosexuality remains a mystery, a team of neurobiologists reports they may have closed in on an answer — by a nose.

Bacteria Employ Type Of DNA Modification Never Before Seen In Nature:

A team of MIT researchers and others has discovered that bacteria employ a type of DNA modification never before seen in nature.

‘Smart’ Flower Bulbs Pull Themselves To Deeper Ground:

Confused about the right planting depth for flower bulbs? Trust the bulbs! Researchers have discovered that some flower bulbs are actually “smart” enough to adjust themselves to the right planting depth. A recent study published in the Journal of the American Society for Horticultural Science proved that bulbs can adjust their planting position by moving deeper into the ground, apparently in search of moister, more conducive growing conditions.

Today’s carnivals

Mendel’s Garden #21 is up on The Inoculated Mind
Carnival of the Green #107 is up on LiveGreen

Science Blogging Conference – who is coming? (Duke University)

2008NCSBClogo200.pngThere are 40 days until the Science Blogging Conference. The wiki is looking good, the Program is shaping up nicely, and there is more and more blog and media coverage already. The anthology should be published in time for the event. There are already 178 registered participants and if you do not register soon, it may be too late once you decide to do so (the maxium capacity of the venue is about 200). Between now and the conference, I am highlighting some of the people who will be there, for you to meet in person if you register in time.
Kendall Morgan is the senior public relations specialist at Duke University. She has a Ph.D. in biology from the University of Oregon and a graduate certificate in science writing from the University of California, Santa Cruz.
Mark Schreiner is the managing editor of the Inside Duke Medicine employee newspaper.
Anthony So is the Senior Research Fellow of Public Policy and Law, and the Director of the Program in Global Health and Technology Access at Duke University
In order to meet them, you know what you have to do: register! Registration is free. Check the map for nearby hotels. And sign up for the Friday dinner.
If you are coming, find hotel information, exchange information about where you are staying, if you are offering a ride, need a ride, or want to carpool on the Ride Board – just edit the wiki page and add the query or information.
Our Friday lab tours are now in place, so you can start signing up to join one of them.
Get updates and get in touch with other participants via our Facebook Event group (I see that some who originally responded “Maybe attending” are now registered).
Please use ‘scienceblogging.com’ as your tag when writing blog posts about it or uploading pictures. You can also download and print out the flyers (PDF1 and PDF2) and post them on bulletin boards at your office, lab or school.

ClockQuotes

The trouble with born-again Christians is that they are an even bigger pain the second time around.
– Herb Caen

Golden Compass – it’s about sex, really

This weekend, with 70 degrees F in Chapel Hill, it would have bin a sin to remain indoors. So I didn’t. But in the end, at twilight today, my daughter and I went to see Golden Compass, the movie whose first-weekend box-office earnings I wanted to boost.
I made sure not to read any reviews of the movie beforehand. I am, unlike most people who already wrote about it, one of those people who has never read the Pullman books on which the movie is based. Thus, like the majority of the target audience, I was a Pullman “virgin” and I wanted to watch it just like anyone else going out to see a movie on a weekend, with no big expectations.
Of course, there was no escaping knowing at least something about it. Before seeing the movie, I knew that:
– the books are supposed to have a strongly anti-religious sentiment, growing stronger as the story moves to the third book. But, I have no idea if the anti-religious sentiment is against the religion in the sense of belief in the supernatural, or the mythology, or the ceremony, or the community-building aspects (“us versus them”), or the top-down hierarchical structure of the religious organization.
– Pullman is a first-generation (“born-again”) atheist. This gives him a different view of religion than someone like me who was born and raised an atheist, in an atheist family, in an atheist country. His childhood religion colors him as a person, and his adult rebellion against religion also colors him as a person. He knows how it feels to be religious. I don’t. For me, religious people are curiousities, perhaps interesting as potential subjects to study: how is it possible for a human being to believe obvious untruths and how does such belief result in particular anti-social behaviors? It is like starting one’s research career by studying cockroach behavior because you want to eradicate the pest, but after decades of study you realize that you quickly forgot the fact they are pests and got fascinated by their brains, how they work and how they lead to particular cockroach behaviors. Having Gregor Samsa join your research group would be fascinating as he would bring new angles, yet also would bring biases that a merely human researcher cannot have.
– there was a controversy before the movie came out. Atheist groups protested the watering-down of the anti-religious sentiment compared to the books. The most extremely anal political organizations that like to voice their opinions publicly as if they speak for religion, voiced their disapproval of the movie and called for boycotts.
So, that’s all I knew. We got popcorn and sodas and went in.
And then, I loved the movie. It was fast-moving, it was fun, it has great acting, great characters, great scenery, great special effects and a fun story. My daughter loved it as well. We both now want to read the books (we have all three, sitting on the shelf right next to the Harry Potter series, still unread by anyone in the household, but that is soon to change).
Of course, the story is a typical fantasy story – it has all the elements such a story has to have. There is the main protagonist who is an unlikely hero, too young and inexperienced for the job, yet nobody else can do. Events thrust the protagonist into the role of the hero. This involves a journey. An older, wiser character serves as a teacher. There is a funny, yet also wise sidekick. The enemy is a jealous authoritarian (surrounded by a slimy posse of thugs) who wants to rule the world. An object is lost and needs to be retrieved. The hero finds help and shelter from a group at the edge of society that cherishes freedom. The journey is perilous, and each dangerous event on the road teaches the hero something new and adds crust and courage to the character (i.e., the character is built). Unexpected family ties are discovered (“I Am Your Father, Luke!”). The crescendo of events leads to the final battle between Good and Evil in which Good triumphs and the hero, irreversibly changed, rides off into the sunset.
So yes, all the archetypes are in the movie. And so they are in every adventure, fantasy, coming-of-age story in history. From Illiad to Winnie-the-Pooh and Alice in Wonderland to James Bond. From 1984 and Fahrenheit 451 to Brave New World. From Hobbit and The Lord Of The Rings to Star Wars and Harry Potter. And so they are in the Golden Compass as well. Does it make the movie bad? Of course not – there is a reason why those elements are always in the story – they work! They appeal to something in all of us, make us identify with the hero and makes the adventure exciting!
So, what is special about Golden Compass? It’s sex. Everything in the movie has an interesting sexual or gender connotation. The hero is a heroine – a smart and brave girl. And, although there are many, many characters in the movie, very few are female. The society is entirely patriarchal. Thus, it is not just the age and the spunk, but also the gender of the heroine that rubs many other characters wrong (on both sides of the Good/Evil divide).
The place-time looks Victorian – I actually recognized the scenes filmed at Queens College and the Radcliffe Square in Oxford. And the society is Victorian as well. The school where Lyra goes to employs only men. The students, apart from her, are all men. White men. The only other female character at the college is the maid.
The Gyptians, while Billie’s mother appears to be a prominent member of the group, are still led by a group of old bearded men – she does not sit at their table when they make decisions.
With the polar bears it is hard to tell who is male or female, but there is no question that the King has to be male.
And of course, the Magisterium is led by a bunch of ugly, old, nasty, white guys who are the prime target audience for the Viagra commercials, if they only had anyone to use the blue pill with. Their sexual frustration, combined with the fear of death, turns them into power-hungry control freaks. If they can’t get it, nobody will! Thus, nobody, especially children, shall even know about sex, …er, Dust. Familiar?
In this world, every person has a daemon. Daemon is an animal and it is the place where the person’s soul resides. It is also a representation of the person’s sexuality. In kids, deamons are innocent and cute and change shape and form (aka species) all the time. At puberty, the species gets fixed. The soldiers have wolves. The farmers’ souls are horses. The servants’ daemons are dogs – higher in hierarchy, bigger the dogs, with the top servants walking around with Great Danes. And what are the daemons of the top leaders of the Magisterium? All are Great Cats. Now, why do you think these middle-aged guys are walking around with black panthers and snow leopards? Of course, for the same reason that their modern counterparts drive Jaguars to the grocery store.
And the very top dog, the leader of the cult? His daemon is a snake. Yes, really – a snake. The guy is constantly holding and playing with his python!
The king of the bears, the guy who likes to play with the dolls, is stupid enough to fall for the trick because the sweet-talking was delivered by a pretty girl who knows how to stroke his masculine insecurity.
The other bear, the good guy, also has some issues – he is a loner, a drunk, and a warrior. And as macho as can be. “Are you sure you want to ride me?” he asks, not being able to believe his good luck!
The other major female character, the ice-cold Mrs. Coulter – the brilliant stroke of lucky coincidence in naming, useful at pointing out to the dense what her role in the society is – is between the rock and a hard place. While the leaders of the Magisterium, all men, can sit around with stern faces, fluffing each others’ self-importance, Mrs. Coulter, being a woman, is supposed to actually do the work. She is doing the cleaning of the house. Being a woman, she is judged by her performance. Being a woman, she is dispensable if she screws up or becomes too uppity for their taste. They lust after her, and they hate her because they cannot have her. So, they own her and play with her destiny. And she, an independent spirit when younger, decided to play within the system, by their rules, choosing to have some power and temporary safety within their hierarchy in return for obedience. And she does it with a vengeance. If they are nasty, she has to be ten times as nasty just to be tolerated in their society.
Her project, an experimental splitting between kids and daemons, is a form of castration. Which she does with gusto. Except in one instance when her own offspring is to be rendered infertile. Her genetic immortality is more important to her than anything else in that moment of weakness.
So, is this movie anti-religious? Yes and no. It is primarily anti-authoritarian, so, as much as all organized religion is authoritarian, it is anti-religion. I do not know how the books are, but the movie does not mention God or even mention even a little bit of their beliefs and theology. We do not see anything from their sacred texts, do not hear the liturgy or see the ceremony. All we see is the social organization of the Magisterium which is decidedly authoritarian and bigoted, and on the other side, the Good side, the people are free-thinking and all-inclusive. The wiches, the bears, the Gyptians (who look like sea-faring Gypsies, the most despised and oppressed and simultaneously most romanticized nation in the world – for their love of freedom), the funny guy with a Texas accent – they never eye each other with suspicion for a split-second. Tolerance is in their blood.
But an authoritarian, hierarchical organization need not be limited to religious organizations. Political organizations, and others, can also be organized in the same way, motivated by greed, fear and sexual repression. Just because the leaders of the Magisterium wear funny robes, does not mean that the movie attacks priesthood in just religious organizations. Other, secular organizations also have their priests and uniforms. And of course the leaders of such organizations will want to headquarter their operations in as big and phallic buildings as possible, thus the cathedrals shapes in the movie. Again, the brilliant coincidence of the name of the second major female character….
And just because the audience is expected to want a “big one” as well, this little questionnaire produces, in about 90% of the trials, a Big Cat:

My picks from ScienceDaily

Young Chimps Top Adult Humans In Numerical Memory:

Young chimpanzees have an “extraordinary” ability to remember numerals that is superior to that of human adults, researchers report.

Artificial Jellyfish, Explosives Sensor Among Projects Being Developed At Undersea Technology Center:

Artificial jellyfish, explosives sensors and seabed batteries are among the diverse research projects under way just nine months after the creation of a Center of Excellence in Undersea Technology in collaboration with the Naval Undersea Warfare Center in Rhode Island.

Heads Or Tails? Scientists Identify Gene That Regulates Polarity In Regenerating Flatworms:

When cut, a planarian flatworm can use a population of stem cells called neoblasts to regenerate new heads, new tails or even entire new organisms from a tiny fragment of its body. Mechanisms have been sought to explain this process of regeneration polarity for over 100 years, but until now, little was known about how planaria can regenerate heads and tails at their proper sites.

Today’s carnivals

Friday Ark #168 is up on Modulator
The latest edition of the Carnival of the Godless is up on The Jesus Myth
Cancer Research Blog Carnival #4 is up on /weblog

Science Blogging Conference – who is coming? (UNC)

2008NCSBClogo200.pngThere are 41 days until the Science Blogging Conference. The wiki is looking good, the Program is shaping up nicely, and there is more and more blog and media coverage already. The anthology should be published in time for the event. There are already 174 registered participants and if you do not register soon, it may be too late once you decide to do so (the maxium capacity of the venue is about 200). Between now and the conference, I am highlighting some of the people who will be there, for you to meet in person if you register in time.
Berrie Hayes is the Bioinformatics Librarian at the Health Sciences Library at University of North Carolina – Chapel Hill
Peter Charles is the Director of the Cardiovascular Functional Genomics Laboratory at the University of North Carolina – Chapel Hill.
David Ketelsen is a cancer researcher at UNC and a blogger.
In order to meet them, you know what you have to do: register! Registration is free. Check the map for nearby hotels. And sign up for the Friday dinner.
If you are coming, find hotel information, exchange information about where you are staying, if you are offering a ride, need a ride, or want to carpool on the Ride Board – just edit the wiki page and add the query or information.
Our Friday lab tours are now in place, so you can start signing up to join one of them.
Get updates and get in touch with other participants via our Facebook Event group (I see that some who originally responded “Maybe attending” are now registered).
Please use ‘scienceblogging.com’ as your tag when writing blog posts about it or uploading pictures. You can also download and print out the flyers (PDF1 and PDF2) and post them on bulletin boards at your office, lab or school.

ClockQuotes

Our theological Church, as we know, has scorned and vilified the body til it has seemed almost a reproach and a shame to have one, yet at the same time has credited it with the power to drag the soul down to perdition.
– Eliza Farnham

Ten Years Since The Kyoto Agreement….

Indy has the entire issue devoted to the topic of Global Warming, with some excellent articles:
10 years after Kyoto: You’re getting warmer by Bill McKibben
10 years after Kyoto: Winners and losers by Sena Christian
James Hansen won’t be quiet by Lisa Sorg
Ryan Boyles, state climatologist by Matt Saldana
Energy interests fund Duke University’s research on climate change policy by Matt Saldana
State senator parades dubious ‘global warming experts’ before commission by Mosi Secret

Video Games and Aggression

My son is working on a paper for school and he picked the topic of video games and how they affect behavior. He primed himself by playing Assassin’s Creed for a couple of days, so he could aggressively look for sources and he found these:
Most Middle-school Boys And Many Girls Play Violent Video Games
Children’s Personality Features Unchanged By Short-Term Video Play
Study Examines Video Game Play Among Adolescents
Surgeons With Video Game Skill Appear To Perform Better In Simulated Surgery Skills Course
Online Multiplayer Video Games Create Greater Negative Consequences, Elicit Greater Enjoyment than Traditional Ones
How Violent Video Games Are Exemplary Aggression Teachers
In Video Games, Not All Mayhem Is Created Equal
Violent Video Games Can Increase Aggression
In Which Art Intimidates Life
This is your brain on violent media
Repeated Exposure to Media Violence Is Associated with Diminished Response in an Inhibitory Frontolimbic Network
Brain Changes When Viewing Violent Media
Media violence and the brain: when movies attack
This is Your Brain on Violent Media
Now he can start furiously typing his essay.
If only this image (from here) was not photoshopped, but reflected the real excitement of doing science instead of shooting at everything that moves….
laracroft%20and%20mario%20scientists.jpg

The long and heroic history of LOLcats

http://view.break.com/392548 – Watch more free videos
Hat-tip: Maru

Science Blogging Conference – who is coming? (More locals)

2008NCSBClogo200.pngThere are 42 days until the Science Blogging Conference. The wiki is looking good, the Program is shaping up nicely, and there is more and more blog and media coverage already. The anthology should be published in time for the event. There are already 169 registered participants and if you do not register soon, it may be too late once you decide to do so (we’ll cap at about 200). Between now and the conference, I am highlighting some of the people who will be there, for you to meet in person if you register in time.
Steve Thiedke is the owner of IVC, Inc.
Nathan Walls and Robin Walls work for McClatchy Interactive.
Bruce Bair is a Physician Assistant in NC.
In order to meet them, you know what you have to do: register! Registration is free. Check the map for nearby hotels. And sign up for the Friday dinner.
If you are coming, find hotel information, exchange information about where you are staying, if you are offering a ride, need a ride, or want to carpool on the Ride Board – just edit the wiki page and add the query or information.
Our Friday lab tours are now in place, so you can start signing up to join one of them.
Get updates and get in touch with other participants via our Facebook Event group (I see that some who originally responded “Maybe attending” are now registered).
Please use ‘scienceblogging.com’ as your tag when writing blog posts about it or uploading pictures. You can also download and print out the flyers (PDF1 and PDF2) and post them on bulletin boards at your office, lab or school.

ClockQuotes

No one from the beginning of time has had security.
– Eleanor Roosevelt

New on…. Open Access and Science 2.0

Subscription-supported journals are like the qwerty keyboard:

Are there solutions? One reason for optimism is that changing how we pay the costs of disseminating research is not an all-or-nothing change like switching from qwerty to Dvorak keyboards. Some new open-access journals are very prestigious. Granting agencies are giving strong ‘in-principle’ support to open access publishing, and my last grant proposal’s budget included a hefty amount for open-access publication charges. And libraries are looking for ways to escape the burden of subscription charges.

This is an interesting idea: an Open Access journal for brief notes and updates, i.e., parts of papers.
Is the End of the Print Journal Near?: New ARL Report Examines This Issue
Related to the three posts above: The Scientific Paper: past, present and probable future
Open Access and Accessibility for the Print Disabled. Of course. Open for Everyone!
Sharing, Privacy and Trust in a Networked World “on the potential roles of social networks for libraries”.
At this lab, everyone is required to maintain a science blog, and response: Why take the risk of writing a research blog? Read the comments on both posts as well.
The Ethics of Being an Open Access Publisher
WHO embargoes health information
Listen to Peter Murray-Rast’s talk at Berlin5 on Open Access.
Listen to the recording of Jean-Claude Bradley’s talk on Open Notebook Science.
Sequence the genomes of microbes or yourself, then plug the genomes into the Interactive Tree of Life.
Nurturing your talent in academia – some good ideas to think about.
CC, Open Access, and moral rights and Intellectual Property Rights: Wrong for Developing Countries?.
Re-writing for Proseminar:

It’s time to share another round of student writing! I asked students in the Proseminar course at USU (in which all faculty take three week turns introducing students to their research interests) to put together a paper about issues related to open education. The twist (there always is one) is that they were to write as little of the paper as possible. You see, wholesale plagiarism is discouraged, but weaving together a coherent piece from ten or fifteen different extant sources is tough and an excellent chance to get some first hand experience with reuse. =) Here are links and some summaries to these re-writing exercises, in which students assembled papers from pre-existing pieces:

Behold! The New Anti-Open Access FUD
Both this article and this article completely forget that scientists at universities are also academics and also bloggers (just look around scienceblogs.com for a start)!!! Why such focus on the humanities blogs in the first place? Where did that come from?
Dancing with words:

There is a great attraction to publishers in finding ways to describe Restricted Access as open. Carried to its logical conclusion, all publications thus become Open Access. Some are Delayed-For-A-Bit Open Access, others are Quite-A-Lot-Delayed Open Access, some are Very-Delayed Open Access and the rest – where the publisher never intends to make them freely available at all – are simply Permanently-Delayed Open Access. You see, what is there to complain about?

Open Science project on domain family expansion
Bursty work. Sort of… how science works, too. Not detectable from publications, though.
Corie Lok: Bringing science out of the dark ages
John Wilbanks: No tenure for Technorati: Science and the Social Web and Seeding the Social Web for Science
Is knowledge ‘property’?

New and Exciting in PLoS Community Journals

Each week, there are new articles published in PLoS Neglected Tropical Diseases, Pathogens, Computational Biology and Genetics. Check them out. Today’s pick:
The Role of Carcinine in Signaling at the Drosophila Photoreceptor Synapse:

During signaling in the nervous system, individual nerve cells transfer information to one another by a complex process called synaptic transmission. This communication involves the release of a specific neurotransmitter into the synaptic cleft, which then triggers signaling in the downstream neuron by binding to and activating specific cell surface receptors. In order to terminate the neuronal signal, the neurotransmitter must be rapidly removed from the synaptic cleft. This is done by two mechanisms: the neurotransmitter can be degraded or modified, or the transmitter can be taken up by the presynaptic neuron and packaged into vesicles for reuse. In the compound eye of the fruitfly D. melanogaster, the photoreceptor cell responds to light and releases histamine into the synaptic cleft. This signal is terminated by the removal of histamine from the synapse and the enzymatic conversion of histamine to carcinine. We have shown that it is not sufficient just to modify the histamine neurotransmitter, but it is also important to remove carcinine from the photoreceptor synapse. The failure to adequately remove carcinine results in defects in the visual transduction process. Moreover, the work suggests that carcinine itself modulates vision by regulating histamine release into the synapse.

My picks from ScienceDaily

Humans Appear Hardwired To Learn By ‘Over-Imitation’:

Children learn by imitating adults–so much so that they will rethink how an object works if they observe an adult taking unnecessary steps when using that object, according to a new Yale study.

Subliminal Smells Bias Perception About A Person’s Likeability:

Anyone who has bonded with a puppy madly sniffing with affection gets an idea of how scents, most not apparent to humans, are critical to a dog’s appreciation of her two-legged friends. Now new research from Northwestern University suggests that humans also pick up infinitesimal scents that affect whether or not we like somebody.

Free Software Brings Affordability, Transparency To Mathematics:

Until recently, a student solving a calculus problem, a physicist modeling a galaxy or a mathematician studying a complex equation had to use powerful computer programs that cost hundreds or thousands of dollars. But an open-source tool based at the University of Washington won first prize in the scientific software division of Les Trophées du Libre, an international competition for free software.

Brain Systems Become Less Coordinated With Age, Even In The Absence Of Disease:

Some brain systems become less coordinated with age even in the absence of Alzheimer’s disease, according to a new study from Harvard University. The results help to explain why advanced age is often accompanied by a loss of mental agility, even in an otherwise healthy individual.

Pass The Popcorn! Study Finds That Film Enjoyment Is Contagious:

Loud commentary and cell phone fumbling may be distracting, but new research suggests that the presence of other people may enhance our movie-watching experiences. Over the course of the film, movie-watchers influence one another and gradually synchronize their emotional responses. This mutual mimicry also affects each participant’s evaluation of the overall experience — the more in sync we are with the people around us, the more we like the movie.

Optimism Isn’t Always Healthy:

People are generally optimistic, believing they’ll do better in the future than they’ve done in the past. This time around, I’ll actually use that gym membership. I’m sticking to the diet this time. Now is the time to start saving for a down payment on a house. However, a new study reveals that this “optimism bias” can lead us to make immediate choices that go against our long-term goals.

This is how MSM should handle scientific “controversies”

Praise where praise is deserved – Dan Abrams handled this segment perfectly, foregoing the he-said-she-said false equivalence, and even remembering to ask for the origin of the supposedly scientific study trotted out by the utterly dishonest proponent of the abstinence-only education:

Let’s hope that his colleagues were paying attention and will try to emulate him in the future, whenever they have a liar on the show (both scientific and non-scientific topics, of course).
Thanks, Amanda.

‘Tis the giving season, parts 2 and 3

Way back when there were just a handful of liberal political bloggers, The American Street was one of them. Kevin Hayden has, over the years, helped and promoted many a blogger, gathered round all those lone voices and built a community out of them – a community that is quick to help one of its own when needed (and it helped me a couple of times in the past). Now it is time to pay back – Kevin was hurt by the collapsing housing bubble and needs your help. Not much – a couple of bucks each.
And once you are done there and still have some cash to spare, there is another good cause. While Pandagon and Shakesville are busy group blogs, and Echidne, Majikthise and Feministe are not exactly single-voice blogs any more either, Feministing is going a step further – building a big community, you know, like a feminist version of DailyKos, with diaries and stuff. But that effort needs your help. You know what to do.
[‘Tis the giving season, part 1]

Wiki for beginners

Hat-tip: Greg

Encouraging authors to place their papers into open repositories

How to move an article from TA to OA? It does not even have to be from a peer-reviewed journal. Graham Steel explains: he contacted the author and asked him to deposit the article into an open repository. So, now you can read it either here (and pay) or here (for free).

Rep. Brad Miller on Blogging

You may remember that a couple of weeks ago, a bunch of us bloggers got to meet Rep. Brad Miller (D – NC13) and talk about the effects of new media on politics. Now you can read two accounts of the meeting by Seth Wright and Emily Burns.

The benefits of Open Access Publishing for students in higher education

The benefits of Open Access Publishing for students in higher education (video):

Most students in higher education have some experience with Open Access when doing their deskresearch. They appreciate the free access of scholar publications on the World Wide Web.
But students in higher education also develop their competences as junior researchers and publishers. Can Open Access Publishing help them to get some reputation in the international academic society? And how appreciate they the readers’ feedback on papers published on the internet?
The Millennium Generation has grown up with free accessible information. They are supposed to embrace the idea of Open Access Publishing. However, students also may be anxious for publishing (preprints of) their papers, for instance for copyright reasons. It seems that good communication about the possibilities of Open Access Publishing by their educators (tutors, professors and librarians!) is very important. Peter Becker and Jos van Helvoort, professors teaching Library and Information Science in the Netherlands, would appreciate to discuss these topics with an international public.

Hat-tip and commentary: Peter Suber

Creationism is Paganism, says Vatican

Archy reports that the papal official astronomer said so:

Believing that God created the universe in six days is a form of superstitious paganism, the Vatican astronomer Guy Consolmagno claimed yesterday.
Brother Consolmagno, who works in a Vatican observatory in Arizona and as curator of the Vatican meteorite collection in Italy, said a “destructive myth” had developed in modern society that religion and science were competing ideologies.
He described creationism, whose supporters want it taught in schools alongside evolution, as a “kind of paganism” because it harked back to the days of “nature gods” who were responsible for natural events.

And, as Archy reminds us, Intelligent Design Creationism is just one form, the slickest and most dishonest, of Creationism. Now, who will tell the Protestants….

The New Primitives

This year I have no time to follow even the Democratic primary race (in which I am interested) and am certainly not going to waste my time on the GOP race. I took a brief look once they all announced and picked up some news here and there on the blogs or NPR, and realized they are just a circus car full of clowns.
But I could not resist reading (thanks, Ed) this WSJ commentary on the reception of the Romney religion speech by his target audience, the hopelessly brainwashed:
Romney Address Wins Mixed Evangelical Reviews:

Some Christians didn’t want to hear such preaching about plurality. The speech didn’t win the vote of Republican Steve Carlson, a Pentecostal Christian and a consultant for the nonprofit voter-education organization Iowa Christian Alliance. “If my choice is between Mike Huckabee, who I know is saved, and Gov. Romney, who as a Mormon…I’m going to pick Mike Huckabee,” Mr. Carlson said.

Sure they don’t want to hear about plurality – it’s their way or highway. They were never interested in tolerance and why should they change now?

A sizeable group of voters remain mystified by Mormonism. Bernie Hayes, a 52-year-old from Cedar Rapids, Iowa, said he finds the religion’s tenets illogical and too different from mainstream Christianity. “I don’t want a president who believes something so off-base,” he said. The fact that Mr. Romney doesn’t want to discuss his faith “makes it worse,” said Mr. Hayes, who supports Mr. Huckabee.

Oh, Mr.Hayes, and when was the last time your religion met logic? And you support a Creationist without your head exploding?

“I don’t think it answered any questions about the Mormon religion and how it plays into his candidacy,” said Joe Mack, director of the office of public policy for the South Carolina office of the Southern Baptist Convention. “I’m not sure it changed the minds of South Carolina Baptists.” Mr. Mack said he will choose a candidate based on where he stands on abortion issues.

We now know the subject of Mr.Mack’s recurring nightmares – vagina dentata. He is eager to put those scary women back into shackles so he can make sure that her sacred blastocyst officially becomes his.

Janis Groves, a Baptist from Bryan, Texas, who attended the address, was pleased that Mr. Romney didn’t delve into specifics. “No,” Ms. Groves, 59 years old, said curtly when asked if she wanted to learn more about the religion. “We are leery.”

Leery? Word.

Science Blogging Conference – who is coming? (Local Scientists)

2008NCSBClogo200.pngThere are 43 days until the Science Blogging Conference. The wiki is looking good, the Program is shaping up nicely, and there is more and more blog and media coverage already. The anthology should be published in time for the event. There are already 168 registered participants and if you do not register soon, it may be too late once you decide to do so (we’ll cap at about 200). Between now and the conference, I am highlighting some of the people who will be there, for you to meet in person if you register in time.
Bonnie Blake is Research Assistant Professor in the Department of Pharmacology at UNC.
Tom Hoban is a Professor of Sociology at NC State University.
Tammy Ren is a graduate student in the Department of Electrical and Computer Engineering at Duke University and a blogger
Evelyn Lynge is the Co-President of the Jacksonville branch of the The American Association of University Women
In order to meet them, you know what you have to do: register! Registration is free. Check the map for nearby hotels. And sign up for the Friday dinner.
If you are coming, find hotel information, exchange information about where you are staying, if you are offering a ride, need a ride, or want to carpool on the Ride Board – just edit the wiki page and add the query or information.
Our Friday lab tours are now in place, so you can start signing up to join one of them.
Get updates and get in touch with other participants via our Facebook Event group (I see that some who originally responded “Maybe attending” are now registered).
Please use ‘scienceblogging.com’ as your tag when writing blog posts about it or uploading pictures. You can also download and print out the flyers (PDF1 and PDF2) and post them on bulletin boards at your office, lab or school.

ClockQuotes

The function of genius is not to give new answers, but to pose new questions which time and mediocrity can resolve.
– H. R. Trevor-Roper

My picks from ScienceDaily

Fighting Diseases Of Aging By Wasting Energy, Rather Than Dieting — Works For Mice:

By making the skeletal muscles of mice use energy less efficiently, researchers report that they have delayed the animals’ deaths and their development of age-related diseases, including vascular disease, obesity, and one form of cancer. Those health benefits, driven by an increased metabolic rate, appear to come without any direct influence on the aging process itself, according to the researchers.

Gene Implicated In Human Language Affects Song Learning In Songbirds:

Do special “human” genes provide the biological substrate for uniquely human traits, like language?

Chipmunks And Shrews, Not Just Mice, Harbor Lyme Disease:

A study led by a University of Pennsylvania biologist in the tick-infested woods of the Hudson Valley is challenging the widely held belief that mice are the main animal reservoir for Lyme disease in the U.S.

Flies’ Evasive Move Traced To Sensory Neurons:

When fruit fly larvae are poked or prodded, they fold themselves up and corkscrew their bodies around, a behavior that appears to be the young insects’ equivalent of a “judo move,” say researchers. They now trace that rolling behavior to neurons resembling those that sense pain.

Pheromones Identified That Trigger Aggression Between Male Mice:

A family of proteins commonly found in mouse urine is able to trigger fighting between male mice, a new study has found. The study is the first to identify protein pheromones responsible for the aggression response in mice. Pheromones are chemical cues that are released into the air, secreted from glands, or excreted in urine and picked up by animals of the same species, initiating various social and reproductive behaviors.

Today’s carnivals

Four Stone Hearth XXIX is up on Remote Central
The 75th Meeting of the Skeptics’ Circle is up on Pro-Science.

Roo to Moo turns Goo into Poo – is that Woo?

Eco-friendly kangaroo farts could help global warming: scientists:

Australian scientists are trying to give kangaroo-style stomachs to cattle and sheep in a bid to cut the emission of greenhouse gases blamed for global warming, researchers say.
Thanks to special bacteria in their stomachs, kangaroo flatulence contains no methane and scientists want to transfer that bacteria to cattle and sheep who emit large quantities of the harmful gas.

And if we give cows jumping beans and jumping genes along kangaroo bacteria, perhaps they’ll really start jumping over the moon….

Brain, Symmetry and Sleep

Hmm, I did not know this – apparently the left hemisphere of the human brain falls asleep first, and the right one a little bit later in most people.
I wonder if that has any connection with the reason we tend to focus on the right side of the face when someone is talking to us – checking the vigilance/sleepiness state of the person?

Reading classical papers as an educational tool

Using a classic paper by I. E. Lawton and N. B. Schwartz to consider the array of factors that control luteinizing hormone production:

Two significant benefits derived from reading and discussing classic scientific papers in undergraduate biology courses are 1) providing students with the realistic perspective that science is an ongoing process (rather than a set of inarguable facts) and 2) deepening the students’ understanding of physiological processes. A classic paper that is useful in both of these regards is by I. E. Lawton and N. B. Schwartz (A circadian rhythm of luteinizing hormone secretion in ovariectomized rats. Am J Physiol 214: 213-217, 1968). The primary objective of the study is to determine whether tonic (pulsatile) secretion of luteinizing hormone (LH) from the pituitary gland exhibits a circadian rhythm. While this hypothesis seems relatively straightforward, its in vivo investigation necessitates an awareness of the multitude of factors, in addition to the circadian clock, that can influence plasma LH levels (and a consideration of how to control for these factors in the experimental design). Furthermore, discussion of the historical context in which the study was conducted (i.e., before the pulsatile nature of LH secretion had been discovered) provides students with the realistic perspective that science is not a set of facts but rather a systematic series of attempts by scientists to understand reality (a perspective that is difficult to convey using a traditional textbook alone). A review of the historical context in which the study was conducted, and a series of discovery learning questions are included to facilitate classroom discussions and to help deepen students’ understanding of the complex nature of pituitary hormone regulation.

Oh yes, I remember the Lawton and Schwartz paper – I have read it a couple of times in my life. And I agree that reading classical papers is a great educational tool. It will be even better in the future when then classical papers will also have years of comments, links, trackbacks and annotations added to them, right there on the paper, for everyone to see how the thinking about the paper changed over time and how the science of the topic progressed since it was first published.

Now this is a serious crisis!

Workers in the Ivory Coast, producer of about 40% of world cocoa, are on strike! As chocolate is the Fifth Food Group, this may lead to global malnutrition of cataclismic proportions (how big are your hidden stashes?)

Dinosaurs! At National Geographic

As usual, they made a great website and you can have fun with the “hidden camera” and try to figure out how many little movies did they have to make for the trick to work (i.e., try to “roar” when the people are on different places on the screen):

In support of this upcoming special, National Geographic has asked that I invite you to experience Dino Central Park [http://www.dinocentralpark.com]. Featuring a hidden “webcam” in Central Park, the website allows users to scare the pants off of unsuspecting New Yorkers walking through the park by controlling a virtual Dino hidden in the bushes.
Dino Death Trap, premiering Sunday December 9th at 8:00 pm, digs up brand new species of dinosaurs from a lost age of the early Jurassic. Join National Geographic as they travel to western China, deep in the dry and desolate Junggar Basin, when the graves never-before-seen Dinos are uncovered. Some scientists are calling it “The Pit of Death”, others, “Dinosaur Pompeii”. Envision dinosaur corpses stacked one on top of each other, piled four and five high. A bizarre T. Rex ancestor, a Triceratops ancestor, an ancient Crocodilian, and nearly 40 more different species dating back 160 million years ago are uncovered in front of National Geographic cameras. Follow a team of paleontologists, led by Dr. Jim Clark, of George Washington University, and Dr. Xu Xing, of the Chinese Academy of Sciences as they unearth answers to a virtual black hole in dinosaur evolution. Watch as the bones are examined, reconstructed and brought back to life, using high resolution CGI, and slowly probe the mystery of who these dinosaurs were, how they died and what they can tell us about the Lost Age of the Dinosaurs.
Want more Dinosaurs? From DinoCentralPark.com, head over to NGCDinos.com [http://www.ngcdinos.com] where you’ll find 3-D Dino renderings, a fossil hunt game, a Dino mummy timeline, and six video previews of the show. National Geographic even created a “Dino Widget” to help you and your friends determine what kind of Dino they are!
*Disclaimer: Dino Central Park is for entertainment purposes only, and does not feature an actual webcam.

Science Blogging Conference – who is coming? (Scientists are coming from all over the place!)

2008NCSBClogo200.pngThere are 44 days until the Science Blogging Conference. The wiki is looking good, the Program is shaping up nicely, and there is more and more blog and media coverage already. The anthology should be published in time for the event. There are already 167 registered participants and if you do not register soon, it may be too late once you decide to do so (we’ll cap at about 200). Between now and the conference, I am highlighting some of the people who will be there, for you to meet in person if you register in time.
Linda MacDonald Glenn teaches medical ethics at the Alden March Bioethics Institute and the University of Vermont school of nursing.
Salman Hameed teaches Astronomy at Hampshire College and blogs at Science and Religion News
Elisabeth Montegna is a graduate student in molecular genetics and cell biology at Univeristy of Chicago.
Alexander P. Roubian is a student of political science at Rutgers University.
In order to meet them, you know what you have to do: register! Registration is free. Check the map for nearby hotels. And sign up for the Friday dinner.
If you are coming, find hotel information, exchange information about where you are staying, if you are offering a ride, need a ride, or want to carpool on the Ride Board – just edit the wiki page and add the query or information.
Our Friday lab tours are now in place, so you can start signing up to join one of them.
Get updates and get in touch with other participants via our Facebook Event group (I see that some who originally responded “Maybe attending” are now registered).
Please use ‘scienceblogging.com’ as your tag when writing blog posts about it or uploading pictures. You can also download and print out the flyers (PDF1 and PDF2) and post them on bulletin boards at your office, lab or school.

ClockQuotes

I wake to sleep,
and take my waking slow.
I feel my fate in what I cannot fear.
I learn by going where I have to go.

– Theodore Roethke

Today’s carnivals

Tangled Bank #94 is up on Life before death
Linnaeus’ Legacy #2 is up on Laelaps
Carnival of the Liberals #53: Best Of 2007 is still in progress, but will soon alight on Neural Gourmet
The 148th Carnival of Education is up on So You Want To Teach?
Carnival of Homeschooling #101: Snowed-In Edition – is up on Dewey’s Treehouse

The Scientific Paper: past, present and probable future

Communication
Communication of any kind, including communication of empirical information about the world (which includes scientific information), is constrained by three factors: technology, social factors, and, as a special case of social factors – official conventions. The term “constrained” I used above has two meanings – one negative, one positive. In a negative meaning, a constraint imposes limits and makes certain directions less likely, more difficult or impossible. In its positive meaning, constraint means that some directions are easy and obvious and thus much more likely for everyone to go to. Different technological and societal constraints shape what and how is communicated at different times in history and in different places on Earth.
Technology – Most communication throughout history, including today, is oral communication, constrained by human language, cognitive capabilities and physical distance. Oral communication today, in contrast to early history, is more likely to include a larger number of people in the audience with whom the speaker is not personally acquanted. It may also include technologies for distance transmission of sound, e.g., telephone or podcasts. This is the most “natural” means of communication.
Smoke signals and tom-toms introduced new constraints to communication – the messages had to be codified, short and simple and much of verbal and non-verbal communication had to be eliminated. Invention of writing, on stone tablets, clay tablets and papyrus, and later on paper and in print, changed the constraints further, making some aspects of communication easier and others more difficult, leading to the development of universal rules and norms of written communication. Unlike oral communication, the written communication is unidirectional, from one to many, making feedback from the audience difficult or impossible. Thus, it is necessarily linear. Its permanence also requires greater care be taken about the form and content. Finally, physical constraints (i.e., the size of a book) impose a structure to written communication, e.g., breaking down the work into chapters, subheadings and paragraphs, placed in a particular order. Also, written communication introduces the concept of authorship (and readership) while oral communication is “owned” by all the participants in the conversation.
Society – What and how is communicated differs dramatically if the audience is small and familiar (e.g., one’s children or neighbors) or large and unfamiliar (speaking at a conference). Written communication is, by definition, aimed at a large and unfamiliar audience, which has an effect on form, style and content of communication. Local habits and traditions further determine the forms and styles of communication.
Conventions – Different types of communication within particular groups of people are often officially codified, often precisely defining the language, style and format. Legal and scientific literature are probably the most extreme examples of a very strict code imposed by official societies. Such strict formalization of communication was initially very useful, imposing order (positive meaning of “constraint”) to an otherwise chaotic and undependable mish-mash of communication forms, allowing all the members of the community to understand and trust each other. However, when such strict forms last for decades and centuries, they are often made out-dated by the passage of time, invention of new technologies and societal changes, thus making the negative meaning of ‘constraint’ more and more obvious.
Scientific Communication
Development of communication of science reflects the development of science itself. Communication of information about the facts about the world did not differ much from other forms of communication for most of history until science itself started distinguishing itself as a special type of human endeavor, different from philosophy and religion. The way science communication evolved parallels the changes in our thinking about the scientific method. At the time when trips to the countryside and armchair thinking were still regarded as science, much of communication was in the form of books. When the hypothetico-deductive aspect of the scientific method “won” as the scientific method, the fledgling scientific societies, led by the Royal Society in the UK and the Academy in France, designed the form and structure of the scientific paper – the form we still use today: title, author, abstract, introduction, materials and methods, results, discussion and references.
Today, we understand that the hypothetico-deductive method is just one of several elements of the scientific method (see this) and that the standard format of the scientific paper is perfectly unsuitable for publication of findings reached through other methods.
Description of new species (extant or extinct) requires a monograph format, for which specialized journals exist that cater to this particular format. Ecological surveys are often straight-jacketed into the standard format, with addition of unwarranted mathematization – not all science requires numbers and statistics. Finally, science is getting more and more collaborative – single-author papers are becoming a rarity, while the papers boasting 10, 20, 50 or even 100 authors are becoming a norm, which challenges the way authorship in science is determined (see this and links within).
But what really made the limitations of the standard format obvious is the genomic revolution. Sequencing a genome is not hypothetico-deductive science – it is akin to an ecological survey: apply a technique and see what you get! Now that the excitement of publication of the first few genomes has receded, the existing journals are inadequate platforms for publication of new genomes. While sequencing is getting easier with time, it is still expensive and time-consuming. Yet, the techniques have been standardized and there is really not much to say in the introduction, materials and methods or discussion sections of a genome paper. All that is needed is a place to deposit the raw data as tools for future research in an easily-minable format that makes such future research easy. The data would be accompanied by the minimal additional information: which species (or individual) was sequenced, which standard method was used (and if it was modified), and who did the work. It is not, any more, an intellectually creative endeavor, as useful as it is for the progress of biology and medicine.
Science On The Web
When e-mail first became popular as a communication method, some people understood it as an extension of the written communication (letters) while others took it to be a new form of oral communication (telephone). Of course, it is both and more. Two people can rapidly exchange a large number of brief personal messages (as in a phone conversation), or one can send a long e-mail message to a large group of people, written with proper grammar, capitalization, punctuation and formatting (as a pamphlet). And yet, it is also neither – unlike oral communication, there is no way to convey non-verbal communication (thus the invention of emoticons 😉 ). Unlike written communication, it is fast, informal, not usually taken very seriously or read carefully, and is easy to delete. E-mail is now a communication form of its own.
The communication on the Web is, likewise, a whole new form. Again, some people see it as written communication (putting an article or book online in order to reach more readers and nothing more), while others see it as a more personal, oral communication that is written down (and such people, unlike the first group, love podcasts and videos which add the non-verbal components of communication to the text). The former prefer static web-pages with their ‘feel’ of permanence. The latter prefer Usenet, livejournals and blogs. The latter perceive the former as stodgy, authoritarian and boring. The former perceive the latter as wild, illiterate and untrustworthy. Again, they are both right and they are both wrong – it is a whole new way of communicating, fusing and meshing the two styles in sometimes unpredictable ways – it is a mix of written and oral communication that combines permanency and authority with immediacy, honesty and the ability for rapid many-to-many communication. The younger generation will use it naturally (though this does not mean that many senior citizens today did not grasp it already as well).
So, how will the constraints (both positive and negative) imposed by the new technology and new social norms alter the formality of the scientific communication, including the format of the scientific paper?
Online, the constraints of the paper and printing press will be gone. No more need for volumes, or issues, or page numbers, or, for that matter, for the formal scientific papers.
The standard format of the scientific paper will become just one of many (and probably not the dominant or most frequent) form of scientific communication. Different people have different talents and inclinations. One is analytic, another synthetic. One is creative, another a hard worker. One has great hands with the equipment or animals, while another is good with computers and statistics. One has a lot of space and money and a network of collaborators at a prestigious institution, another is stuck in a small office somewhere in the developing world with no research funds at all. And each can make a valid and useful contribution to science. How?
One will have a great idea and publish it online. The other will turn the idea into an experimental protocol that tests the idea and will publish it somewhere online. The next will make a video of the experimental method. The next person will go to the lab and actually follow the protocol and post raw data online. The next person will take the data an analyze it and post the results somewhere else online. The next person will graph and visualize the data for easier understanding. The next person will write an essay that interprets the findings and puts them into the broader context (e.g., what does it mean?). The next one will write a summary that combines several of those findings (a review). The next will place that entire research program into the historical or philosophical context. The next will translate it into normal language that lay-people can understand.
They are all co-authors of the work. Each used his/her own strengths, knowledge and talents to contribute to the work. Yet they did not publish together, simultaneously or in the same online space, though all the pieces link to each other and thus can be accessed from a single spot. That single spot is the Scientific Journal, a place that hosts all of the pieces and links them together (also see Vernor Vinge’s vision of the science of the future, combining laboratories at universities with online boards where ideas and results are rapidly exchanged).
In the future, journals will be online hosts for all styles of scientific contribution and ways to link them together (within and betwen journals) – from hypotheses and experimental methods, to data, analyses, graphs to syntheses and philosophical discussions. The peers will review each other in real time and assign each other portions of the available funding according to the community perceptions of the individual’s needs and qualities. Universities will be places for teaching/training the next generations of scientists and for housing the labs. The PhD will be needed for becoming a professor, but not for becoming a worthy and respected contributor to science – that evaluation will be up to peers.
This may sound like science fiction, but we are already living in it. Repositories (like arXiv and Nature Precedings), science blogs, OA journals, Open Notebook Science (what Rosie Redfield and Jean-Claude Bradley do, for instance) are already here. And there is no going back.
So, how do we prepare for this future? Word: slowly but smartly. Science has some very conservative elements (in a non-political sense of the term) that will resist change. They will denigrate online contributions unless they are peer-reviewed in a traditional sense and published in a reputable journal in the traditional format of a scientific paper. Some will retire and die out. Others can be reformed. But such reforming takes patience and careful hand-holding.
The division of scientists into two camps as to understanding of the Web is obvious in the commentary on PLoS ONE articles (which is my job to monitor closely). Some scientists, usually themselves bloggers, treat the commentary space as a virtual conference – a place where real-time oral communication is written down for the sake of historical record. Their comments are short, blunt and to the point. Others write long treatises with lists of references. Even if their conclusions are negative, they are very polite about it (and very sensitive when on the receiving end of criticism). The former regard the latter as dishonest and thin-skinned. The latter see the former as rude and untrustworthy (just like in journalism). In the future, the two styles will fuse – the conversation will speed up and the comments will get shorter, but will still retain the sense of mutual respect (i.e., unlike on political blogs, nobody will be called an ‘idiot’ routinely). It is important to educate the users that the commentary space on TOPAZ-based journals is not a place for op-eds, neither it is a blog, but a record of conversations that are likely to be happening in the hallways at conferences, at lab meetings and journal clubs, preserved for posterity for the edification of students, scientists and historians of the future.
PLoS ONE is a good example of the scientific journal of the future that I have in mind – the ONE place where all the data will be deposited. The commentary space and the Hubs are where all the really interesting stuff will be happening before and after publication of data: hypotheses, methods, videos, podcasts, blogs, debates, discussions, user-user peer-review, etc. The other PLoS Journals will be places, closely connected to ONE and the Hubs, of course, where works of special value will be highlighted – high-quality, media-worthy and large/complete pieces of work, plus editorials, news, etc. – the added value. They are a necessary link between the present (past?) and the future – the showcase of the quality that we can provide and thus hopefully change the minds of the more resistant members of the scientific community.

Science Blogging Conference – who is coming? (Science 2.0)

2008NCSBClogo200.pngThere are 45 days until the Science Blogging Conference. The wiki is looking good, the Program is shaping up nicely, and there is more and more blog and media coverage already. The anthology should be published in time for the event. There are already 164 registered participants and if you do not register soon, it may be too late once you decide to do so (we’ll cap at about 200). Between now and the conference, I am highlighting some of the people who will be there, for you to meet in person if you register in time.
Ryan Sasaki is coming all the way from Nova Scotia to demostrate the ChemSketch from ACD/Labs
And Amy Brand will tell you all how to use CrossRef to find and manage your references.
In order to meet them, you know what you have to do: register! Registration is free. Check the map for nearby hotels. And sign up for the Friday dinner.
If you are coming, find hotel information, exchange information about where you are staying, if you are offering a ride, need a ride, or want to carpool on the Ride Board – just edit the wiki page and add the query or information.
Our Friday lab tours are now in place, so you can start signing up to join one of them.
Get updates and get in touch with other participants via our Facebook Event group (I see that some who originally responded “Maybe attending” are now registered).
Please use ‘scienceblogging.com’ as your tag when writing blog posts about it or uploading pictures. You can also download and print out the flyers (PDF1 and PDF2) and post them on bulletin boards at your office, lab or school.

ClockQuotes

The illusion that times that were are better than those that are, has probably pervaded all ages.
– Horace Greeley

New and Exciting in PLoS ONE

Tuesday night – time to see what’s new in PLoS ONE – 28 new papers:
Reporting Science and Conflicts of Interest in the Lay Press:

Forthright reporting of financial ties and conflicts of interest of researchers is associated with public trust in and esteem for the scientific enterprise. We searched Lexis/Nexis Academic News for the top news stories in science published in 2004 and 2005. We conducted a content analysis of 1152 newspaper stories. Funders of the research were identified in 38% of stories, financial ties of the researchers were reported in 11% of stories, and 5% reported financial ties of sources quoted. Of 73 stories not reporting on financial ties, 27% had financial ties publicly disclosed in scholarly journals. Because science journalists often did not report conflict of interest information, adherence to gold-standard recommendations for science journalism was low. Journalists work under many different constraints, but nonetheless news reports of scientific research were incomplete, potentially eroding public trust in science.

Structure of the Scientific Community Modelling the Evolution of Resistance:

Faced with the recurrent evolution of resistance to pesticides and drugs, the scientific community has developed theoretical models aimed at identifying the main factors of this evolution and predicting the efficiency of resistance management strategies. The evolutionary forces considered by these models are generally similar for viruses, bacteria, fungi, plants or arthropods facing drugs or pesticides, so interaction between scientists working on different biological organisms would be expected. We tested this by analysing co-authorship and co-citation networks using a database of 187 articles published from 1977 to 2006 concerning models of resistance evolution to all major classes of pesticides and drugs. These analyses identified two main groups. One group, led by ecologists or agronomists, is interested in agricultural crop or stock pests and diseases. It mainly uses a population genetics approach to model the evolution of resistance to insecticidal proteins, insecticides, herbicides, antihelminthic drugs and miticides. By contrast, the other group, led by medical scientists, is interested in human parasites and mostly uses epidemiological models to study the evolution of resistance to antibiotic and antiviral drugs. Our analyses suggested that there is also a small scientific group focusing on resistance to antimalaria drugs, and which is only poorly connected with the two larger groups. The analysis of cited references indicates that each of the two large communities publishes its research in a different set of literature and has its own keystone references: citations with a large impact in one group are almost never cited by the other. We fear the lack of exchange between the two communities might slow progress concerning resistance evolution which is currently a major issue for society.

Repeated Exposure to Media Violence Is Associated with Diminished Response in an Inhibitory Frontolimbic Network:

Media depictions of violence, although often claimed to induce viewer aggression, have not been shown to affect the cortical networks that regulate behavior. Using functional magnetic resonance imaging (fMRI), we found that repeated exposure to violent media, but not to other equally arousing media, led to both diminished response in right lateral orbitofrontal cortex (right ltOFC) and a decrease in right ltOFC-amygdala interaction. Reduced function in this network has been previously associated with decreased control over a variety of behaviors, including reactive aggression. Indeed, we found reduced right ltOFC responses to be characteristic of those subjects that reported greater tendencies toward reactive aggression. Furthermore, the violence-induced reduction in right ltOFC response coincided with increased throughput to behavior planning regions. These novel findings establish that even short-term exposure to violent media can result in diminished responsiveness of a network associated with behaviors such as reactive aggression.

Time Processing in Huntington’s Disease: A Group-Control Study:

Huntington’s disease (HD) is a genetically inherited neurological disorder. The disease affects circuits in the brain that are involved in timing tasks. Beste and colleagues report that HD patients performed worse than healthy controls in both time estimation and time discrimination tasks. However, individuals who carried the gene variant responsible for HD but who did not have symptoms did worse than controls only in time estimation tasks. These results help elucidate the progression of disease in HD and suggest possible outcomes for evaluating disease status in clinical trials.

Infectious Offspring: How Birds Acquire and Transmit an Avian Polyomavirus in the Wild:

Avian polyomaviruses, a group of DNA-based viruses, are known to cause disease in some bird species. In this study, Potti and colleagues show that such viruses follow an “upwards vertical” route of transmission in a host population of pied flycatchers. The virus seems to spread from the parasitic fly larvae that infect the nests to the nestlings, which, in turn, pass on the virus to their parents through the parents’ disposal of the nestlings’ feces. The results suggest a possible cost associated with parental care; this cost may differ between the sexes as a result of their different roles in breeding tasks.

Oxygen Reperfusion Damage in an Insect:

The effects of oxygen reperfusion damage to organs and tissues following periods of oxygen starvation are well documented in higher organisms like mammals. In this study, Lighton and colleagues induced oxygen reperfusion in Drosophila melanogaster, to determine the resulting functional damage in an invertebrate. The results show the potential of Drosophila as a model organism for further research into reperfusion injury.

Dynamic Perceptual Changes in Audiovisual Simultaneity:

The timing at which sensory input reaches the level of conscious perception is an intriguing question still awaiting an answer. It is often assumed that both visual and auditory percepts have a modality specific processing delay and their difference determines perceptual temporal offset. Here, we show that the perception of audiovisual simultaneity can change flexibly and fluctuates over a short period of time while subjects observe a constant stimulus. We investigated the mechanisms underlying the spontaneous alternations in this audiovisual illusion and found that attention plays a crucial role. When attention was distracted from the stimulus, the perceptual transitions disappeared. When attention was directed to a visual event, the perceived timing of an auditory event was attracted towards that event. This multistable display illustrates how flexible perceived timing can be, and at the same time offers a paradigm to dissociate perceptual from stimulus-driven factors in crossmodal feature binding. Our findings suggest that the perception of crossmodal synchrony depends on perceptual binding of audiovisual stimuli as a common event.

Is a parthenogenetic female a ‘group of one’?

A few weeks ago John Wilkins wrote a long and thoughtful 5-part review of a recent paper by E.O.Wilson and D.S.Wilson:
The two Wilsons on sociobiology
Sociobiology 2: Theoretical foundations
Sociobiology 3: Kin selection and pluralist explanations
Sociobiology 4: individuals as groups, and a summary
Sociobiology 5: What is at issue
Since I always thought of group selection in the Unto Others sense of the term, I am not as confused as some others who are familiar with some older, unrealistic models. I still think that the best explanation is by Robert Brandon in, I think, fifth chapter.
Sexual reproduction is a pretty important component of hierarchical view of units/levels of selection, so one may wonder how parthenogenesis (virgin birth) affects that theoretical construct. Here are some recent thoughts on parthenogenesis:
Sandra Porter: Did she or didn’t she? Genetic testing and virgin birth
RPM: What’s the deal with ‘virgin birth’ (parthenogenesis)?
Greg Laden: The Bible as Ethnography ~ 05 ~ The Virgin Birth
Martin Rundkvist: Sacred Parthenogenesis
Zuska: Are Men Necessary? ‘Ask a Science Blogger’ Wants To Know!
Anne-Marie: Gynogenesis redux: Return of the Clones (and earlier: Hybridogenesis: Who’s your daddy? Who cares! and Gynogenesis: Attack of the clones)
Now you put the two topics together….mind boggles.

Debate

I had to miss several of the past televised Dems presidential debates, though I read the post-mortems on them on blogs afterwards just to learn that the MSM is still not serious about doing their job. Thus, today’s radio debate on NPR was quite refreshing – they had more-or-less equal time for each of them, and sufficient time for them to develop their ideas beyond the sound-bites. The questions, while not as good as they should have been, were miles ahead of the stuff CNN, for instance, decided to ask.
You can listen to the podcast of the entire debate here.
Here are some of the early summaries:
Ezra Klein
Chris Cillizza
Mark Halperin (excerpts) (in more detail here)
Discussions on DailyKos here, here and here.

Congratulations to Enloe students!

For winning the second place at the Siemens science competition:

Mentored by N.C. State University professors Donald Bitzer and Anne-Marie Stomp, the students developed a computer model that helps scientists determine which gene sequences to use to produce specific proteins. The research could provide a cost-effective method of commercially producing useful proteins such as insulin.

Cost of publishing in OA journals

Bill Hooker:

But the next time you hear someone talk about the “cost” of publishing in OA journals, please point ’em here.

And the ‘here’ of that sentence is this post which should disabuse you, once for all, of the idea that publishing in OA is more expensive than publishing with the dinosaur publishers. Bookmark that post and have the link ready for whenever you hear that myth pop its head up.

Zotero Translator for PLoS Articles

Zotero is a Firefox plug-in that allows you to manage and cite research papers. They just announced that Zotero now works with PLoS papers. If you have no idea what I am talking about, Rich Cave explains.

Today’s carnivals

December Scientiae Carnival is up on A k8, a cat, a mission
The 21st edition of Gene Genie is up on BayBlab
Bio::Blogs #17 is up on Blind.Scientist
The latest Grand Rounds are up on Doctor Geek, M.D.

David Cohn on Science Journalism and Web 2.0

David writes:

Community is no longer a dirty or scary word. Sciam, Seed, in the US, Germany and all over the world. Online communities are becoming understood and a valued commodity. When Google bought YouTube I said the price they payed wasn’t for the technology (they already had Google Video) what they bought was the community. News organizations realize that creating niche communities is a way to stay relevant to advertisers and readers.
And science journalism, which de-facto covers a “boring” subject to lots of people, can only benefit by creating a vibrant community of people who have a passion for the subject. What science journalism needs are people who criticize science because they love science (as opposed to people who criticism because they don’t believe in science). That’s what these communities can offer – and how they will improve science journalism.

Welcome to scienceblogs.com

Dinosaurs! Friday night at the Museum

Every first Friday of the month, there is something fun going on at the NC Museum of Natural Science. This week, Friday December 7th, the theme is Dinosaurs!!!
6 PM Parenthood and Life’s Hazards for Dinosaurs – presentation by Dr. Dale Russell, Senior Curator of Paleontology
I took a class on Dinosaur Osteology with Dale Russell and went to the Carnegie Museum on a December trip as a part of the course some years ago. He took us down to the vaults at dawn before the museum opened and started pulling stuff out of drawers testing our knowledge on the spot. He pulled a little oval-shaped bone from a drawer with no processes or much other distinguishable about it except a hole in the middle of it and asked me what it was – I immediately excitedly shouted “occipital bone of the Diplodocus!” and he was very pleased – he said he knew I would know it because of the pineal opening….
7 PM Natural Horror Picture Show, First Feature – The Lost World (1925)
Now, that’s a classic! Have you not seen it yet?
7:30 PM Thelonius Monk tribute by the University of North Carolina-Greensboro jazz ensemble
Jazz? Enjoy!
8:30 PM Natural Horror Picture Show, Second Feature – Mad Max 2: The Road Warrior
I guess this can be somehow construed as having to do with Dinosaurs LOL!
But if you want to skip Mad Max, you can always go downstairs to see the permanent dino exhibit and see Acrocanthosaurus and Willo, the dinosaur with a heart (all permanent exhibits are free). Or you can pay (only $5 after 5pm) and see the traveling exhibit Dinosaurs: Ancient Fossils, New Discoveries.
Anyone want to go as a group and liveblog the event?

Richard Smith on Open Access

Graham Steel, a vocal Open Access supporter, alerts me that the latest Mansbridge One on One interview on CBC features Richard Smith. You can watch the video here – the talk about Open Access starts about seven minutes into the interview.