Monthly Archives: July 2008

Fun stuff on the Web….

Food-shaped USB flash drives. Pizza for me…. [Via]
Under The Effluence. Human sewage used for cereals?!
Great Opening Sentences From Science Fiction. Any other suggestions?
Another surgical liveblogging experience: Which Is the Safe Side?

Governmental Corporate Media


From Alex (the whole post worth reading).

Today’s carnivals

Carnival of the Green #138 is up on Allie’s Green Answers
Carnival of the Elitist Bastards #3 is up on Pharyngula
Gene Genie #34 is up on ScienceRoll
Berry Go Round #7 is up here on A Blog Around The Clock

Carnival of Science/Academia/Publishing?

Martin saw this comment of mine and sprung into action: Name the new ‘Carnival of Scientific Life’!

The two big questions are what to call it, and how often to host it, so I’d like your input in the comments below please. I’ll be making the final decision on August 1st.
What would be a good name for the carnival? (Ideally something without “carnival” in the title.)
Should it be held monthly, or at some other frequency?
The carnival is intended to cover all aspects of life as a scientist, whether it’s the lifestyle, career progress, doing a Ph.D., getting funding, climbing the slippery pole, academic life as a minority, working with colleagues and students, dealing with the peer-review process, publishing, grants, science 2.0, amusing anecdotes, conference experiences, philosophical musings, public engagement, or even historical articles about what life was like in the good (or bad) old days.
In other words, anything related to the experience of living the scientific life. Not blogging about research, but blogging about everything that goes with being a researcher. A sort of “meta-science” carnival if you like.
I’ll be putting together a hosting schedule here in the coming days. If you’re interested, let me know at editor@layscience.net.

This is how he describes it: About the Carnival of Academic Life

The carnival is intended to cover all aspects of life as an academic, whether it’s the lifestyle, career progress, doing a Ph.D., getting funding, climbing the slippery pole, academic life as a minority, working with colleagues and students, dealing with the peer-review process, publishing, grants, science 2.0, amusing anecdotes, conference experiences, philosophical musings, public engagement, or even historical articles about what life was like in the good (or bad) old days.

On the same day, there was a thread on ‘Plausible Accuracy’: Open Science blog carnival – The interest seems to be there, so what about the details?, where I left the following comments:

I’ve seen carnivals come and go, and at this point I do not think there is enough people out there to sustain a carnival on such a narrow topic as OA alone. I would rather have a carnival on all things meta-science, with an OA section in it.
———-
This also means that people who write/read about other aspects of life in science will get to read the OA stuff (people always check out who else is on the carnival they are in, and also link to the carnival), many for the first time, and get introduced to the idea which they can spread to others. Makes the topic less insular when it rubs shoulders with others who write about science but never gave a thought to the business of publishing before. A way to bring in more people to the cause.

I would think that something like this would be OK. Not “I am bummed because my mini-prep did not work today” kinds of posts, but analytic posts about the way science works, the way academia is organized, the internal and external politics of science, discrimination, funding, promotion, careers, the business of publishing, the Science 2.0 and science blogging issues, etc., but with a special emphasis on the way the Web is changing science practice in all of its aspects.
What do you think?

MedBlogging under scrutiny

The Health Blogosphere: What It Means for Policy Debates and Journalism:

The Kaiser Family Foundation is sponsoring a discussion about the growing influence of blogs on health news and policy debates. Only in the past few years has the blogosphere become mainstream. In the health policy arena, we now see policymakers, journalists, researchers and interest groups utilizing this new media tool to deliver information to their audiences. The briefing will highlight how the traditional health policy world has embraced blogging and will feature a keynote address by U.S. Department of Health and Human Services Secretary Michael Leavitt, the first cabinet officer to author an official blog, followed by a moderated discussion with a variety of health policy bloggers and a media analyst.
Questions to be explored with the panelists include: Why do individuals and organizations blog? How does blogging impact the broader work of an organization? Are there different standards used when blogging versus other writing? Have blogs impacted the news business significantly? What kind of influence are blogs having on political and policy debates?

Unfortunately, the panel is heavily skewed toward Rightwing, Bush-loving, business-only types, with the brave exception of Ezra Klein.
Annie has a lot more information worth checking out. But you should tune in tomorrow at 1pm Eastern time and pitch in. Let’s reframe their discussion so it actually gets honest.

It’s just not fair!

All this attention on Juno! Millie is depressed:
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Biscuit is outraged:
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The movie with the longest title ever

Night of the Day of the Dawn of the Son of the Bride of the Return of the Revenge of the Terror of the Attack of the Evil, Mutant, Alien, Flesh Eating, Hellbound, Zombified Living Dead Part 2: In Shocking 2-D:

DonorsChoose

Like we did the last two years, SciBlings will have a month-long fundraising drive for educational projects via DonorsChoose. More info soon.
For now, check out Janet’s first teaser for some info.
Also checkk out the DonorsChoose blog for their information.
For the locals – there is an exciting NC part of this all:

The Burroughs Wellcome Fund, an independent private foundation in North Carolina, will support $25,000 in inquiry-based science and mathematics projects through DonorsChoose.org during the 2008 / 2009 school year.
These funds are only available to North Carolina teachers, so take advantage of this opportunity and submit your project today! All eligible projects will automatically be considered. See the sticky-notes below for a few project ideas that would qualify for Burroughs Wellcome Fund support.

Lee Siegel – who let him into a media room again?

Lee Siegel was on NPR’s On The Media the other day, defending his sockpuppetry and painting all bloggers as unwashed hordes of fascists. Boo hoo.
I listened to the podcast and it was too short to be of much substance. The interviewer has no idea how big of an offense sockpuppetry is, and Siegel demonstrated that, apart from comments on his own blog, he has never really taken a look at the blogosphere as a whole. If the comments on his posts are all he knows, he really knows nothing about blogs. The quip about editors who wink about nobody reading comments is just another proof how ignorant they are of the New Media and what it does. The idea that journalists losing jobs will now turn against bloggers instead of “pandering” to them is just ridiculous – laid off journalists tend to become bloggers and harbor ill feelings towards giant media houses that laid them off in pursuit of profits and reduction of news value.
Siegel has been covered by SciBlings before. Also see Ed Cone and Josh Marshall.
Possibly related:
Old vs. New Media Redux
Those on the Losing End are always the Loudest
Another hit-job on blogs
Michael Skube: just another guy with a blog and an Exhibit A for why bloggers are mad at Corporate Media
Are we Press? Part Deux

Today in OA

Citation Statistics (pdf):

This is a report about the use and misuse of citation data in the assessment of scientific research. The idea that research assessment must be done using “simple and objective” methods is increasingly prevalent today. The “simple and objective” methods are broadly interpreted as bibliometrics, that is, citation data and the statistics derived from them. There is a belief that citation statistics are inherently more accurate because they substitute simple numbers for complex judgments, and hence overcome the possible subjectivity of peer review. But this belief is unfounded.

Information Liberation:

If your child has a life-threatening disease and you’re desperate to read the latest research, you’ll be dismayed to learn that you can’t — at least not without hugely expensive subscriptions to a bevy of specialized journals or access to a major research library.
Your dismay might turn to anger when you realize that you paid for this research. Through the National Institutes of Health alone, American taxpayers funnel more than $28 billion annually into medical research. That’s leaving aside the billions more in public spending on state universities or the tax exemptions granted for gifts to private campuses.

Open Access and the NIH

In 1978, in enacting Section 105 of title 17, Congress faced a choice about what to do with copyrighted works that result from government funding, including basic research funding of scientific, technical, and medical (“STM”) journal articles. One approach was simply to preclude any assertion of copyright, treating such works the same way as works created by government employees within the scope of their employment. That approach would have been simple to apply, but might have inhibited the publication of some STM journals, at a time when hard copy ruled as the method of distribution. Congress chose a middle approach, discussed here in the 1976 House Judiciary Committee report:, which begins by referring to the definition of “work of the United States government”:

An Interview with Heather Joseph:

Heather Joseph talks about her career with SPARC and BioOne. She discusses the NIH mandate that NIH-funded research will be deposited into PubMed Central, and she shares her views on some of the controversial issues the mandate has raised about copyright, peer review, and embargo periods. She also addresses the recent decision by the Harvard faculty to make their scholarly output accessible through the university’s institutional repository, and she suggests ways that librarians can help their faculties prepare for open access.

Heather must be dismayed that her interview is behind the pay-wall.

Big Biology

What Alex and commenters say….

The Beautiful Mind: Making Memories

Science Communicators of North Carolina:

Thursday, August 7
7 p.m.
The Beautiful Mind: Making Memories
Dr. Kelly Giovanello of the UNC-CH Cognitive Neuroscience of Memory Lab. Part of the Morehead Planetarium Current Science Forum.
250 E. Franklin St., Chapel Hill, (919) 962-1236

Juno

Due to popular demand:
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ClockQuotes

Gardening is an exercise in optimism. Sometimes, it is the triumph of hope over experience.
– Marina Schinz

Berry Go Round #7

Welcome to the seventh edition of Berry Go Round, the carnival about all things botanical.
The previous edition was last month at Seeds Aside and the 8th issue will be at the end of August on Not Exactly Rocket Science.
The tradition for this carnival is to make it colorful (well, the plants are pretty), so I did what several other hosts of various carnivals did recently and used the LOLCat Builder to make it pretty and fun.
Since this makes the post very image-heavy and may slow down loading of the page for people with slower connections, I have placed them all under the fold.
To see from which blog the post comes from, hover your mouse/cursor over the image.
To go and read the entry, click on the image.
Also, I know, I know, there is no mycological carnival yet, so Berry Go Round has a subsection for that other sub-Domain of fungi, the Hyphae Go Round carnival, added on the bottom (last three entries). Enjoy:

Continue reading

Daddy blogging….

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Web-literacy – essential for 21st century?

Literacy debate: Online, r u really reading?:

As teenagers’ scores on standardized reading tests have declined or stagnated, some argue that the hours spent prowling the Internet are the enemy of reading — diminishing literacy, wrecking attention spans and destroying a precious common culture that exists only through the reading of books.
But others say the Internet has created a new kind of reading, one that schools and society should not discount. The Web inspires a teenager like Nadia, who might otherwise spend most of her leisure time watching television, to read and write.

G Protein Receptor


(Via, on FriendFeed)

Old vs. New Media Redux

Scoble: The blog editing system in action (also check out the discussion on FriendFeed):

Journalists who fight this system (and readers who don’t check out the comments) are missing the point. This is a participatory media, not a one-way one, and, while it has a different editing system (the editing is done post publishing, not pre publishing) it’s pretty clear to me that this system arrives at the truth a lot faster than anything on paper does.

I thought Bloggers vs. Journalists was Over. I guess not, as long as dinosaurs are still extant and capable of mouthing words…
Related…and somewhat related….

My picks from ScienceDaily

Diversity In Primary Schools Promotes Harmony, Study Finds:

For the first time, children as young as 5 have been shown to understand issues regarding integration and separation. The research confirms that the ethnic composition of primary schools has a direct impact on children’s attitudes towards those in other ethnic groups and on their ability to get on with their peers.

Who’s More Likely To Do Sports? White, Middle Class, And Middle-aged:

The comfortably off, white, and middle aged are the most likely to participate in sporting activities, reveals a 10 year study published ahead of print in the British Journal of Sports Medicine.

Older People May Need Less Sleep, Study Finds:

Along with all the other changes that come with age, healthy older people also lose some capacity for sleep, according to a new report published online on July 24th in Current Biology. When asked to stay in bed for 16 hours in the dark each day for several days, younger people get an average of 9 hours of shuteye compared to 7.5 for older people, the researchers report.

Frequent Family Meals Might Reduce Teen Substance Use:

Parents who have regular meals with their adolescent children might help lessen the chances they will start drinking or smoking later in their teen years, according to new research.

Energy Drinks Linked To Risk-taking Behaviors Among College Students:

Over the last decade, energy drinks — such as Red Bull, Monster and Rockstar — have become nearly ubiquitous on college campuses. The global market for these types of drinks currently exceeds $3 billion a year and new products are introduced annually.

New Roadside Beautification Concept Studied:

Travel America’s highways or drive down any city street this summer and you’ll probably see them. From small, manicured beds of flowers maintained by community volunteers to extensive landscaping projects along America’s byways, roadside gardens are taking root.

Podcast on Open Science

Watch it here:
The Extraordinary Everyday Lives Show #053 – Open Science:

This show is all about the intersection of Technology and Human desire. This year Dave and I have been focusing on ‘deepening connections’ with those we subscribe to via RSS. Having a chat on a podcast is a remarkable way of doing that we have found. Agenda is loose guide only, we are very stream of consciousness, no edits, no script kinda guys.

The Giant’s Shoulders – call for submissions

The second edition of The Giant’s Shoulders, carnival of history of science, will be hosted by The Lay Scientist on August 15th. Check out the first edition to see what it is all about, then submit your stuff. If you appeared in a previous edition, you need to write something new, but if this will be your first time, you can sneak in some of your best old stuff, I’m sure that will be OK…

ClockQuotes

Every time I close the door on reality it comes in through the windows.
– Jennifer Unlimited

Long time to hang around at home

I had to cancel my trip to Toronto in September so, after the SciBling meetup I have nowhere to travel all the way until ConvergeSouth in October, which will be fun (this year co-organized with BlogHer), so I hope you consider showing up if you can.
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Picture of the day

Newspaper misspells its own name in the front-page header:
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Hat-tip: Sue

Potential abuse of users’ privacy in Serbia

Serbia: New Instructions and Law Regulations on Online Privacy:

On July 21, RATEL, Serbia’s Republican Agency for Telecommunications, posted a Document of Instructions for Technical Requirements for Subsystems, Devices, Hardware and Installation of Internet Networks on their official web site. This news didn’t go unnoticed yesterday in Serbian blogosphere and internet community, as many bloggers expressed various opinions as well as disapproval because of the potential abuse of users’ privacy.
This document of instructions defines technical requirements for authorized monitoring of some specific telecommunications and provides a list of duties for telecommunication operators, which are obligated to act according to the Constitution Law of Republic of Serbia as well as elements of it.
According to element 55 (Law of Telecommunications), subpart 3, these Instructions were issued by RATEL in cooperation with public telecommunication operators and the governmental body responsible for immediate conduct of electronic monitoring.
This means implementation of massive tracking and archiving in all forms of electronic communications for the purposes of the national agency for the security.

Via
Check the blogospheric responses there….

Innumeracy and related academic turf-defenses….

Chad: Innumeracy by John Allen Paulos
Tom: What Does the Public Really Need To Know?: Science/Math edition.
Chad: The Innumeracy of Intellectuals
Janet: Fear and loathing in the academy.
Join in the fray….

An eye-catching yet flawed bar graph

Discussed at these sites, among others:
Chart junk-ies
When bar charts go bad
World’s Most Expensive Places to Have Sex.
Catch the flaw(s).
Click here to see large.
Go under the fold to see small:

Continue reading

Now that’s old!

Pandagon is six years old today! How many is this in dog years? Congrats Amanda, Pam, Jesse and the crew!

What is ‘citizen journalism’?

From Jay Rosen:

Save this movie as a reference when someone asks you to define a Citizen Journalism in the future….

Left vs. Right online

There has been a lot of chatter on the interwebs (for years, but again now) about the differences between the ways the political Left and Right use the Internet and blogs:
GOP losing the new-media war:

…….The right is engaged in the business of opining while the left features sites that offer a more reportorial model.
At first glance, these divergent approaches might not seem consequential. But as the 2008 campaign progresses, it’s becoming increasingly clear that the absence of any websites on the right devoted to reporting — as opposed to just commenting on the news — is proving politically costly to Republicans.
While conservatives are devoting much of their Internet energy to analysis, their counterparts on the left are taking advantage of the rise of new media to create new institutions devoted to unearthing stories, putting new information into circulation and generally crowding the space traditionally taken by traditional media. And it almost always comes at the expense of GOP politicians.
While online Republicans chase the allure of punditry and commentary, Democrats and progressives are pursuing old-fashioned shoe-leather reporting, in a fashion reminiscent of 2004……..

A different view on the left versus right online debate:

In the regular debate about about how the right can catch up online, several points are often missed. The first is that the left has developed a movement based on the interconnectedness of people inside the movement. People get recruited, energized, and leveraged. This may or may not be as much a function of larger demographic and political trends, as it has something to do with the netroots specifically.
At the same time, the right has often been better at campaign mechanics, especially in recent years. Our assumption seems to be that if we get enough people to go and vote in this country — which we still believe is just right of center — then we can win.

Rebranding via Blogging:

The web is conducive to insurgency movements. That’s been the Democrats for the last eight years. They were out of power and needed different tools. Progressives perceived that the political culture had shifted, but the Democratic Party did not shift with it, so they began telling a story about a different vision of the Democratic Party and the political system. They made fundamental criticisms of both parties and the media, and rallied a lot of people to them. They erected a very effective mechanism for bringing the party in their direction, they created a gravitational pull so the political leaders and the money people had to come to them. That has fundamentally reshaped the Democratic Party. The Republican Party, on the other hand, was perceived by most in its base as being a more effective machine.

Via Ed Cone:

What the left does better online: report, rather than just opine.
Why they had to do it: the mainstream media was “browbeaten” into ineffectiveness.

Read the entire articles for more.
Well, an anti-democratic party cannot allow its lowly prole members to do anything but follow orders. It is a hierarchical structure where all the information (hmm, talking points and lies) flow from the top down. And how much fun is it to read second-hand lies on some blog instead of first-hand lies straight from Cheney? No amount of re-branding will ever change the basic core worldview of the GOP-ers, thus they can never have anything like a bottom-up online movement, independent from the party elders, working at reshaping the party from within.

Rise and Fall of HIgher Education

Here is just a brief excerpt from Why I am Not a Professor OR The Decline and Fall of the British University:

The more prosaic truth emerges when you scan the titles of these epics. First, the author rarely appears alone, sharing space with two or three others. Often the collaborators are Ph.D. students who are routinely doing most of the spade work on some low grant in the hope of climbing the greasy pole. Dividing the number of titles by the author’s actual contribution probably reduces those hundred papers to twenty-five. Then looking at the titles themselves, you’ll see that many of the titles bear a striking resemblance to each other. “Adaptive Mesh Analysis” reads one and “An Adaptive Algorithm for Mesh Analysis” reads another. Dividing the total remaining by the average number of repetitions halves the list again. Mozart disappears before your very eyes.
But the last criterion is often the hardest. Is the paper important? Is it something people will look back on and say ‘That was a landmark’. Applying this last test requires historical hindsight – not an easy thing. But when it is applied, very often the list of one hundred papers disappears altogether. Placed under the heat of forensic investigation the list finally evaporates and what you are left with is the empty set.
And this, really, is not a great surprise, because landmark papers in any discipline are few and far between. Mozarts are rare and to be valued, but the counterfeit academic Mozarts are common and a contributory cause to global warming and deforestation. The whole enterprise of counting publications as a means to evaluating research excellence is pernicious and completely absurd. If a 12 year-old were to write ‘I fink that Enid Blyton iz bettern than that Emily Bronte bint cos she has written loads more books’ then one could reasonably excuse the spelling as reflective of the stupidity of the mind that produced the content. What we now have in academia is a situation where intelligent men and women prostitute themselves to an ideal which no intelligent person could believe. In short they are living a lie.
It was living a lie that finally put an end to my being a professor. One day in 1999 I got up and faced the mirror and acknowledged I could not do the job any more. I quit; and from the day I quit, though things were often tough, I never experienced the sense of waste and futility that accompanied working in a British university. By stroke of fate, I am living only a few hundred yards from the institution at which I worked. Sometimes when walking past I see the people I worked with and they look old. Living a lie does that to you.

It is bitter, bitter, bitter, but also revealing and thought-provoking….
[Hat-tip: Deepak over on FriendFeed]

Today’s carnivals

Tangled Bank #110 is up on Pharyngula

ClockQuotes

I will not eat oysters. I want my food dead – not sick, not wounded – dead.
– Woody Allen

Blog Carnivals – what is in it for you?

I keep getting asked: why should I participate in blog carnivals?
The Wikipedia page about blog carnivals is not really accurate (it includes things that are not carnivals), and also suffers from overzealous, obsessive-compulsive, self-important administrators (who have probably never seen a carnival, never submitted a post to one, never hosted one, never started or managed one, ah well…).
I have written a lot about carnivals in the past (see especially this, this, this, this and this) so you should check those out for more “meaty” treatments, though some of the stuff in there is a little out-of-date (and some links may be broken).
So, let me try to state this briefly here (newbie bloggers first, oldie bloggers below).
Let’s say you consider yourself to be a new science blogger by some reasonable criteria. You tend to write about various topics in science, nature, medicine, environment, you debunk pseudoscience or muse about the life in the academia. If you are a new blogger, nobody knows about you, your traffic is 3 visits per day, and you have no idea who else out there writes stuff you are interested in – carnival is a place for you. How?
Step I – find the appropriate carnivals
Here, let me help you – a list of good current science-related carnivals (hover over the titles to see what they are about):
Tangled Bank
Grand Rounds
Scientiae
Skeptics’ Circle
Carnival of the Blue
Carnival of the Green
The Giant’s Shoulders
Cabinet of Curiosities
Linnaeus’ Legacy
Circus of the Spineless
I And The Bird
Berry Go Round
Festival of the Trees
Encephalon
Molecular and Cell Biology Carnival
Oekologie
Change of Shift
Bio::Blogs
Philosophia Naturalis
Four Stone Hearth
The Accretionary Wedge
Boneyard
Mendel’s Garden
Gene Genie
Cancer research blog carnival
Carnival of Space
Carnival of Mathematics
Friday Ark
Hourglass
Medicine 2.0 Blog Carnival
Step II – read the carnivals
Once you find the carnival(s) that are close to your interests, go and check out the homepage to see what are the official criteria and “rules”, then go to the very latest edition (or two, or dozen or 200, as far back into the past as you have stamina to go). Click on every link and open every post. Read them.
First, you will find things you did not know before – you will learn something new.
Second, you will get the feel for what kinds of posts are appropriate for the carnival. You will see which posts you like and which ones you don’t, which posts have a lot of comments and which ones have none, which blogs are popular (and why) and which ones are not. You will quickly develop your own ‘taste’ and from it your own ‘style’.
Third, when you really like a post, click around that blog to see what else is there on the front page and in the archives. Bookmark and blogroll the blogs you like the best. Start posting nice, intelligent, polite comments on the blogs you like and on specific posts you like. Start making connections….
Also, start linking to the new editions of your favourite carnivals as they get published – sometimes the trackbacks will show up and bring you some back-traffic, but even if not, the host will come to pay you a visit and may look around to see who you are.
Step III – submit to carnivals
Some hosts are picky, but most will include pretty much every decent post in the edition of the carnival they are hosting. Thus, once you write a post that you think satisfies the criteria for the inclusion in the carnival, submit it. You are likely to be included if your stuff is worth anything. If you were unlucky with a picky host the first time, try again next week. You’ll get in there eventually. This is not a peer-reviewed journal, it’s a community magazine. Peer-review will come later, in the comments on your post.
When the carnival edition containing your post gets published, quickly link to it. Post a ‘thank you’ note in the comments of the carnival (with your name linking back to your blog, as always). Enjoy the traffic (you do have some kind of sitemeter or traffic tracker, don’t you?) and be prepared to politely respond to the comments that may show up on that post even if the comments seem a little harsh at first (you’ll get used to the blunt tone of the blogosphere after a while and your polite tone will mellow some of the blunter commenters’ tone – feel free to just delete obvious trolls and spam).
Most of the visitors will come once and leave as soon as they are done reading that one post. But a few will stay longer and look around. If they like what they see, they will keep coming back. You should be getting a more permanent bump in the traffic as well as some more comments than usual. You will notice (you do check on Technorati who is linking to you, don’t you?) that some people may put you on their blogrolls or in their RSS feeds.
Do it again next week (or fortnight or month or whatever) and monitor how people respond to your posts. Learn from the experience.
Step IV – host a carnival
Once your posts have been included in several carnivals, consider volunteering to host an edition. First read the posts linked inside this post to prepare. Take the job seriously – read all the entries carefully, publish the carnival on time, make it neat, check that all links are working correctly, notify all the participants (as well as regular promoters of carnivals like PZ, Greg Laden, Grrrrl, me etc.) by e-mail as soon as the carnival is up.
Then enjoy the increased traffic and comments. You are now really, truly, on the list of “who is who in the science blogosphere”!
Consider doing it again….
But still, ….why?
Because this is the best way to build a community around a particular topic – the quickest, easiest way for people who are harboring similar interests to find each other, decide if they like each other, to boost each other’s rankings and traffic, and, if needed, to organize together for some kind of action. In best cases, you will meet some of those bloggers in person and forge new friendships, or even scientific collaborations.
Then, there is a special case – American atheists. For decades almost every U.S. atheist thought that he/she was the only one, or at least the only one in town. It felt unsafe to say anything about it. But the Web changed this. First on Usenet groups, and later on forums and blogs. With the current explosion of blogs and blog readers, suddenly atheists realized they are not alone, not even in their towns, and that their numbers are much greater than the polls and censuses suggest. With the safety in numbers, it is now possible to come out of the closet.
And I would argue that Carnival of the Godless played a key role in this development as a venue for atheists to find each other, eye-ball their numbers, exchange ideas, and plan action – how to make atheism OK in the United States, how to make it OK to analyze/critique/criticize religion, how to pull together to counter the eggregious influences of religion on politics and society. Yes, some find it unpleasant to hear vocal atheists – after all, Americans have always been enculturated that criticizing religion is not something done in polite company so some sensibilities are hurt, but that is exactly what happened in the past in the matters of race, gender and sexual orientation. Nothing changes until someone fights for it. And the fight makes some people uncomfortable. It is their discomfort that eventually results in change for the better, even if it is because they are sick and tired of hearing it so they succumb to the persistent noise and start supporting the cause so it will stop! And nobody gets out of the closet until there is a perception of numerical advantage. And the Carnival of the Godless provided that perception for a lot of people.
How about the old-timers?
If you are an older, already prominent blogger, your participation will not likely affect your traffic, popularity or rate of commenting. But, you are prominent at least in part because you were an early adopter – one of the first science bloggers around. It is almost a duty, or pay-back time, to promote those who are good but new and need our help and promotion. It is not hard to link to new editions of carnivals, occasionally host one, sometimes send an entry to one or another carnival. It boosts other people’s traffic, it boosts their confidence (“I was in the same carnival with PZ!”), and helps build the community. You/we should all do it sometimes.

Blogrolling for Today

The path forward


Maxwell’s Demoness


Science Matter


The Technium


The Wobbling Mind

New and Exciting in PLoS this week

Isolation-by-Distance and Outbreeding Depression Are Sufficient to Drive Parapatric Speciation in the Absence of Environmental Influences:

A commonly held view in evolutionary biology is that new species form in response to environmental factors, such as habitat differences or barriers to individual movements that sever a population. We have developed a computer model, called EvoSpace, that illustrates how new species can emerge when a species range becomes very large compared with the dispersal distances of its individuals. This situation has been called isolation-by-distance because remote parts of the range can take different evolutionary paths even though there is no particular place where we would expect different populations to separate. When the extent of genetic difference between individuals is coupled with decreasing offspring viability (e.g., resulting from developmental problems), EvoSpace predicts that sharp spatial boundaries can emerge in arbitrary locations, separating subpopulations that occasionally persist long enough to become reproductively incompatible species. The model shows an inherent tendency toward spatial self-organization, in contrast with the traditional view of environmentally forced origins of new species. We think that isolation-by-distance is a common aspect of the evolutionary process and that spatial self-organization of gene pools may often facilitate the evolution of new species.

The Interplay between Entamoeba and Enteropathogenic Bacteria Modulates Epithelial Cell Damage:

In amoebiasis, a human disease that is a serious health problem in many developing countries, efforts have been made to identify responsible factors for the tissue damage inflicted by the parasite Entamoeba histolytica. This amoeba lives in the lumen of the colon without causing damage to the intestinal mucosa, but under unknown circumstances becomes invasive, destroying the intestinal tissue. Bacteria in the intestinal flora have been proposed as inducers of higher amoebic virulence, but the causes or mechanisms responsible for the induction are still undetermined. Mixed intestinal infections with Entamoeba histolytica and enteropathogenic bacteria, showing exacerbated manifestations of disease, are common in endemic countries. We implemented an experimental system to study amoebic virulence in the presence of pathogenic bacteria and its consequences on epithelial cells. Results showed that amoebae that ingested enteropathogenic bacteria became more virulent, causing more damage to epithelial cells. Bacteria induced release of inflammatory proteins by the epithelial cells that attracted amoebae, facilitating amoebic contact to the epithelial cells and higher damage. Our results, although a first approach to this complex problem, provide insights into amoebic infections, as interplay with other pathogens apparently influences the intestinal environment, the behavior of cells involved and the manifestations of the disease.

In(s) and Out(s) of Academia

Bjoern Brembs is on a roll! Check all of these out:
Incentivizing open scientific discussion:

Apart from the question of whether the perfect scientist is the one who only spends his time writing papers and doing experiments, what incentives can one think of to provide for blogging, commenting, sharing? I think because all of science relies on creativity, information and debate, the overall value of blogging, commenting and sharing can hardly be overestimated, so what incentives can there be for the individual scientist?

Journals – the dinosaurs of scientific communication:

Today’s system of scientific journals started as a way to effectively use a scarce resource, printed paper. Soon thereafter, the publishers realized there were big bucks to be made and increased the number of journals to today’s approx. 24,000. Today, there is no technical reason any more why you couldn’t have all the 2.5 million papers science puts out every year in a single database. It doesn’t take an Einstein to realize that PLoS One is currently the only contender in the race for who will provide this database. For all the involved, it is equally clear what the many advantages of such a database would be. Consequently, traditional publishers are rightfully concerned that their customerbase is slowly dissappearing.

Post-publication paper assessment:

The more variables there are to game, the more difficult it becomes. Now we have one variable (IF) and we all know who is gaming it ad nauseum. In this thread we have 5 measures, add ratings and comments and you have 7. This should be impossible to game for anyone but the hacker who can get thousands to machines on the net to just hype this one paper.
All of these measures are relevant even long after publication. Some papers ignored by the media may later turn out to harbor the most important discovery of the century, while some of those tossed around everywhere turn out to be completely irreproducible. Having these measures in place, if nothing else, would allow us to quantify and study such events.
But again, no matter how many numbers you have, these measures cannot substitute for actually reading the papers! The numbers barely give you a rough idea of where a paper or a scientist can be placed with respect to others in the same field. Yet, these measures would be light-years ahead of any one-dimensional, irreproducible, obviously manipulated and corrupt measure such as the IF.

Building a scientific online reputation:

For me, this basically means that all the expertise and technical prerequisites are there to bring the scientific community into the 21st century. The advantages of the new system need to be succinctly summarized and widely publicized at the same time as the current system’s disadvantages and idiosyncracies need to be pointed out and publicized along with the new proposal. And because criticizing is always easier than advertising, I’ll start by summarizing why Thomson’s Bibliographic Impact Factor (BIF) is dead.

Why Thomson’s Bibliographic Impact Factor (BIF) is dead:

Despite the recent downpour of evidence against the use of Thomson’s BIF, I still get comments from people such as “However, IFs are still the most used way of evaluating a researcher’s career and value. Even if we find this ridiculous, it’s just the way it is.” or “in our institution, every researcher has to publish in journals whose BIF is at least 5.”. In the light of the current state of affairs concerning the BIF, this is just embarrassing. So here are the top three reasons why the BIF is dead:
1. The BIF is negotiable and doesn’t reflect actual citation counts (source)
2. The BIF cannot be reproduced, even if it reflected actual citations (source)
3. The BIF is not statistically sound, even if it were reproducible and reflected actual citations (source)
Now go and spread the information so I don’t have to suffer from these ridiculous statements any more.

Then, on Nature Network blogs and Nature blogs, discussion about the “manners” in the science blogosphere:
Corie Lok: What is fair play in the blogo/commentosphere?:

Now, maybe it’s a generational thing. Those of us who didn’t ‘grow up’ with blogs might be more easily taken aback by what goes on in them. Those of us who did grow up with them perhaps have learned to take the bad with the good.

To which I commented:

A lot depends on one’s prior experiences. If one comes to science blogging out of academia with its highly formalized and ritualized kabuki dance of language-use, extremely polite on the surface, yet often very vicious in the subtext, then one sees blogs as very uncourteous and unpleasant – the things that are supposed to be hidden between the lines and now said openly.
Many of the most popular science bloggers have a different history – many years of battling Creationist and other pseudoscience crusaders on Usenet groups in the early 1990s, people who, if they can use language at all, use it in a very vicious way, sometimes with threats of bodily harm. I spent the early 90s on Balkans usenet groups, battling heatedly nationalist Serbs, Croats and Bosnians who do not just voice empty threats but would, if they could find you, really kill you. Others cut their teeth on political blogs or feminist blogs, which are very blunt and heated. Just try not supporting Howard Dean in the 04 primaries or Obama in 08 – you get your fill of human nastiness. And that is nothing compared to what Republicans say once the general election starts!
My first blog was political – I wrote highly opinionated and strongly-worded posts. And of course, I got, let’s put it diplomatically, some highly opinionated commenters. I never deleted. Sometimes I responded (politely at first – that is unusual and disarming – I turned some trolls into friendly and polite commenters that way), sometimes I ignored, sometimes my other commenters took care of trolls.
Then, after the move to Sb, I gradually reduced writing about politics and religion and my threads are now quite nice and polite most of the times. Various heated debates about “framing” or the latest “Nature vs. PLoS” kerffufle are sweet lullabies compared to most of the stuff I saw and suffered over the years online. One grows a thick skin, understands that people behave strangely online, laughs at the most egregious examples, and moves on.
There is no single definition of a “science blog”. Blog is a piece of software. You do what you want with it. If you are a scientist with a blog, or if you write more-or-less regularly about science (or meta-stuff, e.g., life in the lab, women in academia, politics of science funding….), then you can claim that your blog is a science blog. And your blog is going to be different from all other science blogs out there, as it is what you want it to be, reflecting your own interests, goals and personality. Nobody can tell you how to do it. There is no, and there should be no “template” or “definition” of a science blog – that is the beauty of the beast.
Thus, some blogs are serious, others not. Some are nice, some are inflammatory. Some focus 100% on latest peer-reviewed research. Others are a smorgasbord of everything the blogger feels like posting at any given time (like my blog, for instance). There is no recipe, no straightjacket, no “one right way” to do it. And that is what makes the science blogosphere so exciting and vibrant – so many cool voices, interesting personalities! Who says that scientists are socially-inept or bad communicators?!

The discussion there continues:
Noah Gray: Getting into and out of character:

We seem to be at a critical juncture concerning the intersection of blogs and other Web 2.0 technologies with science. This is no time to poison the atmosphere and turn away the more “relaxed” or “casual” participants. Polarized communities refusing to tolerate rival positions, or unwilling to engage in a civil debate over any topic, from publication business models to the role of Ca2+-permeable AMPARs in LTP, will shut out many would-be contributors and stunt the growth or slow the adoption of blogs, commenting, and other web-based technologies dedicated to the pursuit of scientific collaboration. If such technologies are ever really going to work for science, it will be because of inclusivity, not exclusivity.

Maxine Clarke: Manners in the blogosphere:

The anonymity of cyberspace provides protection to both share honest opinions and participate in mud-slinging without repercussion, he notes. Yet interaction on the Internet is more personal. “So why should some choose to check their manners at the door before logging on?” He argues that intolerant online communities unwilling to engage in a civil debate — whether on publication business models or the role of glutamate receptors in long-term potentiation of neurons — will turn off would-be contributors and stunt the growth of online scientific collaboration. Web-based collaborative technologies will not work for science if they become dominated by exclusive, aggressive types. Gray isn’t calling for “communal singing of Kum Ba Yah during scientific debates”, but simply a certain level of restraint and professionalism online.

This is an interesting segue to Michael Nielsen’s latest instalment of his future book about the future of science: Shirky’s Law and why (most) social software fails:

Shirky’s Law states that the social software most likely to succeed has “a brutally simple mental model … that’s shared by all users”.
If you use social software like Flickr or Digg, you know what this means. You can give friends a simple and compelling explanation of these sites in seconds: “it’s a website that lets you upload photos so your friends can also see them”; “it’s a community website that lets you suggest interesting sites; the users vote on submissions to determine what’s most interesting”. Of course, for each Flickr or Digg there are hundreds of failed social sites. The great majority either fail to obey Shirky’s Law, or else are knockoffs that do little not already done by an existing site.
To understand why Shirky’s Law is important, let’s look at a site where it’s violated. The site is Nature Network, one of the dozens of social networking sites aspiring to be “Facebook for scientists”. Like other social networks, Nature Network lets you connect to other users. When you make a connection, you’re asked whether you would like to connect as a “friend” or a “colleague”. Sometimes the choice is easy. But sometimes it’s not so easy. Furthermore, if someone else connects to you, you’re automatically asked to connect to them, but given no immediate clue whether they connected as a friend or as a colleague. The only thing shared in the users’ mental model at this point is acute awkwardness, and possibly a desire to never connect to anyone on Nature Network again.
I don’t mean to pick on Nature Network. It’s the most useful of the social networks for scientists. But it and most other social websites (apart from the knockoffs) don’t even come close to obeying Shirky’s Law.
Why is Shirky’s Law so hard for developers to obey? I’ll give three reasons.

Interesting…. We here at Sb are often accused of being cliquish and insular. But if you look at our 70+ blogs and dig through the archives, you will see that we rarely comment on each other’s blogs – most (99%?) of the comments come from outside readers. Also, most of our links point to outside of Sb. On the other hand, NN is specifically designed to be a community (not a platform for independent players) and almost all of the comments there are from each other. Thus, it is easy for them to maintain a high level of politeness there (this is not a bad thing – this is how they designed it on purpose). It is much harder to harness the hordes of pharyngulites that spill over to all of our blogs – and I do not mind them at all, I think they make the debate spirited and in a way more honest by bypassing superficial niceness and going straight to the point. This may also have something to do with NN bloggers mainly being in the academia, while a large proportion of SciBlings are ex-academia, journalists, artists, etc. with a different rhetoric. The rhetoric of academia is a very formalized kabuki dance, while the rhetoric of the blogosphere has shed all formalities and is much more reminiscient to the regular everyday oral conversation.
Moving on to other, related topics…
Jocalyn Clark: Is the NIH open access policy regressive?:

Panellists noted that the recent NIH public access policy emphasises free not open access. That is, the policy may lead to freely accessible publications (for which publishers or organisations may reap profits from charging authors a fee to deposit their manuscripts), but these will remain under restrictive licenses (thus limiting text-mining).
This, Cockerill argued, makes the NIH policy regressive.

NASA to launch OA image collection:

Nasa is to make its huge collection of historic photographs, film and video available to the public for the first time.

Rhea Miller: Vow to never become Jaded…:

But I do NOT understand why it is socially accepted to be a Jaded student…to be completely negative about the research he/she does, to avoid showing up to journal clubs/seminars, or to never participate in scientific discussions. What does being burnt out do for you in becoming the best you can be?? How does it help your science, your field, or your coworkers??
I really only notice these attributes in young scientists, i.e. graduate students and post-docs. Does this mean that the Jaded ones eventually give-up, get use to it, change their prospectives, or do they hide that inner Jaded color as they progress?? Or maybe it’s just that grad students/postdocs can’t seem to see the light at the end of the tunnel until they get there??

Panthera studentessa: Letting fear take over:

As time goes on, I’m becoming more and more concerned that I don’t have what it takes to hack it in graduate school. In every community, every blog, every forum that I read, people always talk about how stressful and all-consuming grad school is. To be perfectly honest, my mental health isn’t exactly the best it’s ever been. I just worry that I won’t be able to handle the mental and physical stress.
——-
I suppose there’s always the option of just not going to graduate school, but that really throws a wrench in my career plans. I don’t even know what kind of jobs a person can get with a bachelor’s in zoology. And anyway, I don’t want to let my fear determine what I do with my life. I just wish I knew how to begin to get over it.

Maddox2: Advice on Freelance Science Writing:

Caveat: I am writing this advice from the perspective of an editor who regularly works with freelance science writers. However, the market in which I work may not be the same as some of you out there work in, or want to work in. Therefore, I can guarantee that following the advice below will endear you to K-12 educational publishers (and to companies like mine who work for educational publishers). I can’t speak to journals, newspapers, etc…but I can’t imagine they’d mind if you follow this advice! And given that a lot of people here have expressed an interest in freelance writing, I thought I might be able to provide a bit of a different perspective on things.

Mad Hatter: Networking Nuts And Bolts:

I think the most important thing to keep in mind when networking is that your contacts are much more likely to help you if they like you. My personal philosophy on networking is this: when my networking contact turns on her computer and sees an email from me, I want her to click on the email thinking, “Hey, I remember Mad Hatter. I liked talking to her. I wonder what she’s been up to?” What I don’t want her to do is groan and think, “Oh, no…it’s Mad Hatter again. What does she want now?” So with that in mind, here are some tips on networking that have worked for me.

John Hawks has posted first two of a 4-piece series on Blogging And Tenure: How to blog, get tenure and prosper: Starting the blog:

Last month, the University of Wisconsin officially granted me tenure. So, I can say without any doubt (if other examples had not been sufficient), it is absolutely possible to write a daily, high-profile blog and still be recognized by your colleagues as a scholar. In fact, it is possible to blog, do good research, and earn tenure at a Research I university.
That seems like progress, compared to the situation four years ago when I began blogging. A few high-profile tenure denials in late 2005, including physicist Sean Carroll and political scientist Daniel Drezner, made it seem like a blog might be the kiss of death for a research reputation. Inside Higher Education ran a story on the subject, as did Slate, with the melodramatic title, “Attack of the Career-killing Blogs”. Since I was interviewed in that article, I suppose I should have been a little nervous (I wrote about it here).
Happily things have changed.

…and: Graduate students and blogging:

As far as I know, there are no data concerning blogging and career success — or, for that matter, between any kind of public outreach and success in research careers (as opposed to teaching or industry careers that directly involve outreach). Anecdotally, there are some people who spend a lot of effort on outreach who have very well-respected research careers, and others who don’t. I’d say it’s up to the individual to chart her own course.
——————–
I’d like to advocate for a model of blogging that many graduate students might find useful. If I were starting out today, I’d blog my dissertation. Why not? Is there really anything so secret in your history and literature review that it couldn’t be read by the few hundred people who will find your blog?

Happy birthday, PLoS Genetics!

PLoS Genetics is celebrating its third birthday this month! Let’s see what’s new this week, among else…
PLoS Genetics Turns Three: Looking Back, Looking Ahead:

PLoS Genetics is three years old this month–a milestone worth celebrating! As we do, and as we recognize all who have helped us reach this point in time, we thought this would be a good opportunity to share with you a summary of our brief history and a look ahead.
Our original intent was to provide an open-access journal for the community that would “reflect the full breadth and interdisciplinary nature of genetics and genomics research by publishing outstanding original contributions in all areas of biology.” Now, three years later, all of us on the Editorial Board are very pleased with the breadth of topics covered and with the diversity of approaches, organisms, and systems. Going forward, PLoS Genetics will continue to be a journal by and for the entire genetics and genomics community.

The Status of Dosage Compensation in the Multiple X Chromosomes of the Platypus:

Dosage compensation equalizes the expression of genes found on sex chromosomes so that they are equally expressed in females and males. In placental and marsupial mammals, this is accomplished by silencing one of the two X chromosomes in female cells. In birds, dosage compensation seems not to be strictly required to balance the expression of most genes on the Z chromosome between ZZ males and ZW females. Whether dosage compensation exists in the third group of mammals, the egg-laying monotremes, is of considerable interest, particularly since the platypus has five different X and five different Y chromosomes. As part of the platypus genome project, genes have now been assigned to four of the five X chromosomes. We have shown that there is some evidence for dosage compensation, but it is variable between genes. Most interesting are our results showing that there is a difference in the probability of expression for X-specific genes, with about 50% of female cells having two active copies of an X gene while the remainder have only one. This means that, although the platypus has the variable compensation characteristic of birds, it also has some level of inactivation, which is characteristic of dosage compensation in other mammals.

Pain Genes:

Pain, which afflicts up to 20% of the population at any time, provides both a massive therapeutic challenge and a route to understanding mechanisms in the nervous system. Specialised sensory neurons (nociceptors) signal the existence of tissue damage to the central nervous system (CNS), where pain is represented in a complex matrix involving many CNS structures. Genetic approaches to investigating pain pathways using model organisms have identified the molecular nature of the transducers, regulatory mechanisms involved in changing neuronal activity, as well as the critical role of immune system cells in driving pain pathways. In man, mapping of human pain mutants as well as twin studies and association studies of altered pain behaviour have identified important regulators of the pain system. In turn, new drug targets for chronic pain treatment have been validated in transgenic mouse studies. Thus, genetic studies of pain pathways have complemented the traditional neuroscience approaches of electrophysiology and pharmacology to give us fresh insights into the molecular basis of pain perception.

Stable in a Genome of Instability: An Interview with Evan Eichler:

We like to think that our genome is rock-solid, that it is dependable, there for us when we need it. The truth is far from that. By fits and starts, our species’ collective genome is undulating, reshaping itself with eruptions of genomic lava and clashes of sequence tectonics, at once both marvelous and unsettling. We are unaware of this tumult within us until we are confronted with disease in ourselves, our friends, or our family.
Evan Eichler is a man obsessed with this process, and to speak with him is a study in contrasts (Image 1). An unassuming Canadian, Eichler is a student of genomic architecture, the arrangement of sequences in our genome, and their evolution. Eichler grew up on a farm in Manitoba, married his college sweetheart, and now lives together with her and their four children in the mountains east of Seattle. As we walked up the hill to my office during his recent visit to UCSF, he talked about being an early riser, taking his son to band practice before school, and then driving the 30 miles to work in his Toyota. Eichler is a man bristling with excitement for his discoveries, but holding it in check by a tradition of modesty. He has consistently followed his own path, chosen career opportunities that were dictated not by politics or peer pressure but rather by what feels like a good fit for him.

Today’s carnivals

Friday Ark #201 is up on Modulator

Sex, Gender, Reproduction

I have not done a Friday Weird Sex Blogging post in ages, and I won’t do today either, but others did some cool blogging on various related topics: from gender disparities, to gynecological procedures, to weird animal/plant sex, so here is a little collection for this weekend:
My take on Mr. Tierney’s article:

Again, I can’t predict what the gender breakdown of any profession would be if we didn’t live in a rather patriarchal society. Maybe it wouldn’t be 50/50 if everything else was equal. But it’s not. I hate to use the P-word, but consider the environment our girls are being raised in. Until societal pressures can really be controlled for, I’m not sure that we can really say what people’s “natural tendencies” are. And that goes for men, too. Gender stereotypes are stupid. And Tierney’s insistence that girls just don’t like some things isn’t terribly inspiring (or new).

Blogging my mammogram:

At the urging of my colleague Abel, who liveblogged his own vasectomy, I’m documenting my first mammogram. Given that I had pretty much no idea what to expect going into this, I’m hopeful that this post will demystify the experience a little for those who know they probably should get mammograms but have been putting it off.

The pros and cons of screening mammography: reading my ‘patient instructions’:

However, to the extent that most of us who are getting regular health care in the U.S. are doing it within the context of some kind of insurance, we aren’t generally making this call individually. We’re working within the framework of our health care provider’s policy, which usually tracks what insurance will cover.

Why Not? Blogging My D & C:

And that’s it! Now I am officially one of those people who shares every intimate detail of their lives with total strangers on the internet. You know, just like I promised myself I would never do. If you had asked me, when I first took up blogging, whether I’d be posting pictures of the inside of my uterus on my blog, I’m pretty sure I’d have answered “what the hell are you talking about?” And yet, here we are. Just don’t tell my mom.

World Wide Web Abortions:

In theory, I think it’s pathetic (not to mention potentially high-risk) that some patients have to resort to DIY specialized medical care just because they happen to be pregnant. In practice, when your reality is that your access to proper medical care is at the mercy of strangers, it’s preferable to obtain care from (apparently) competent strangers like Women on Web, rather than some unqualified black marketeer.

Sex and the over seventies – what the research really said:

Media coverage has stuck to this, although a lot of coverage has focused on the ooo-isn’t-it-shocking-that-wrinklies-are-having-sex angle, and in many places misquoting or misunderstanding the study data. This is probably because most journalists didn’t read the original research or editorial, and based their stories on the press release. Of the journalists I spoke to who were writing their coverage yesterday the majority were not interested in getting reportage of the study right, but simply wanted me to find them a seventy year old couple who didn’t mind talking about their sex lives or having their photograph included in the paper.

Lonesome George not so lonesome:

George, a Pinta island tortoise who has shown little interest in reproducing during 36 years in captivity, stunned his keepers by mating with one of his two female companions of a similar species of Galapagos tortoise.

This Friday’s Weird Science: Foot-binding:

This is where Dr. McGeoch got his idea. He notes that ancient Chinese historians who lived during the Tang Dynasty talked about women with their feet bound, noting that they were, perhaps, a little more “sensitive” in bed than those who had big feet. So foot binding was considered conducive to a better sex life. Dr. McGeoch hypothesizes that, because the girl’s feet were kept small, broken, and atrophied, she might get a structural reorganization in her somatosensory cortex, where neurons were recruited from the feet to the genetalia, resulting in a stronger signal from the genitals. Of course, this would remain to be seen (and I would not want to be the lab rat for that experiment), but it’s an interesting idea.

Not quite viagra!:

…It’s a penis shaped fungus! A Stinkhorn in the family Phallaceae. I came across this in a unit about fungi I did last year and just found it funny… a bit immature perhaps…

Botanical posts – you have 8 hours left!

Next edition of Berry Go Round, the carnival about all things related to plants, will alight here at A Blog Around The Clock tomorrow (probably late afternoon), so please send your submissions tonight by midnight EDT to: Coturnix AT gmail DOT com

The importance of stupidity in scientific research

Now this is a title of a paper in a scientific journal that will make one’s eyebrows go up: The importance of stupidity in scientific research (by Schwartz J Cell Sci.2008; 121: 1771) :

I recently saw an old friend for the first time in many years. We
had been Ph.D. students at the same time, both studying science,
although in different areas. She later dropped out of graduate school,
went to Harvard Law School and is now a senior lawyer for a major
environmental organization. At some point, the conversation turned
to why she had left graduate school. To my utter astonishment, she
said it was because it made her feel stupid. After a couple of years
of feeling stupid every day, she was ready to do something else.
I had thought of her as one of the brightest people I knew and
her subsequent career supports that view. What she said bothered
me. I kept thinking about it; sometime the next day, it hit me. Science
makes me feel stupid too. It’s just that I’ve gotten used to it. So
used to it, in fact, that I actively seek out new opportunities to feel
stupid. I wouldn’t know what to do without that feeling. I even
think it’s supposed to be this way. Let me explain.

I am not sure what he wrote is really what she meant, but anyway, this was a nice way for him to start the article. What he is talking about is not really stupidity. I’d call it ignorance. And grad school teaches you to cherish and relish in your ignorance, as that is the main motivator in working every day to diminish it a little bit at a time by discovering something new, a little bit of information about the way the world works that in some reduces your own and everyone else’s ignorance. If you are successful in acquiring this mindset – enjoying the ambiguity of science, having ease with saying “I don’t know….and, by the way, nobody does” – you feel good. If you are a different kind of person, you may as well feel stupid:

Productive stupidity means being ignorant by choice. Focusing
on important questions puts us in the awkward position of being
ignorant. One of the beautiful things about science is that it allows
us to bumble along, getting it wrong time after time, and feel
perfectly fine as long as we learn something each time. No doubt,
this can be difficult for students who are accustomed to getting the
answers right. No doubt, reasonable levels of confidence and
emotional resilience help, but I think scientific education might do
more to ease what is a very big transition: from learning what other
people once discovered to making your own discoveries. The more
comfortable we become with being stupid, the deeper we will wade
into the unknown and the more likely we are to make big
discoveries.

My picks from ScienceDaily

‘Snow Flea Antifreeze Protein’ Could Help Improve Organ Preservation:

Scientists in Illinois and Pennsylvania are reporting development of a way to make the antifreeze protein that enables billions of Canadian snow fleas to survive frigid winter temperatures. Their laboratory-produced first-of-a-kind proteins could have practical uses in extending the storage life of donor organs and tissues for human transplantation, according to new research.

Freedom’s Just Another Word For Less Sexually Active Teens:

Sophisticated statistical research is providing more evidence of a link between rigid parenting and increased sexual activity in older teens. Although it is difficult to confirm that controlling mothers and fathers cause kids to have more sex, the findings suggest it is wise to give children freedom, said Rebekah Levine Coley, lead author of a new study of nearly 5,000 U.S. teenagers. Coley is an associate professor of applied developmental and educational psychology at Boston College.

Costs Of Climate Change, State-by-state: Billions, Says New Report:

Climate change will carry a price tag of billions of dollars for a number of U.S. states, says a new series of reports from the University of Maryland’s Center for Integrative Environmental Research (CIER). The researchers conclude that the costs have already begun to accrue and are likely to endure.

It Takes Nerves For Flies To Keep A Level Head:

The nerve connections that keep a fly’s gaze stable during complex aerial manoeuvres, enabling it to respond quickly to obstacles in its flight path, are revealed in new detail in research published today (22 July 2008).

Various Species’ Genes Evolve To Minimize Protein Production Errors:

Scientists at Harvard University and the University of Texas at Austin have found that genetic evolution is strongly shaped by genes’ efforts to prevent or tolerate errors in protein production.

Prevailing Theory Of Aging Challenged: Genetic Instructions Found To Drive Aging In Worms:

Age may not be rust after all. Specific genetic instructions drive aging in worms, report researchers at the Stanford University School of Medicine. Their discovery contradicts the prevailing theory that aging is a buildup of tissue damage akin to rust, and implies science might eventually halt or even reverse the ravages of age.

Outdoor Enthusiasts Scaring Off Native Carnivores In Parks:

Even a quiet stroll in the park can dramatically change natural ecosystems, according to a new study by conservation biologists from the University of California, Berkeley. These findings could have important implications for land management policies.

UNDERCURRENTS: the voice of undergraduate research

The July issue of our e-newsletter is now available.
http://snipurl.com/34wgh
Highlights:
* Social Networking For Researchers
* Do Research and Teaching Mix?
* Undergrads Create New Science
* Writing An Undergrad Thesis
* Research Conferences Update
* Ongoing Items database and conferences database
* Please contribute to Undercurrents

ClockQuotes

Work expands so as to fill the time available for its completion. General recognition of this fact is shown in the proverbial phrase “It is the busiest man who has time to spare.”
– C. Northcote Parkinson

Is there an ornithologist in the house?

If so, go help Michael identify this bird he took a picture of earlier today. If you can, post a comment here.

WALL-E

I finally found some time to go and see a movie theater from the inside. My daughter and I went and saw Wall-E tonight.
Like everyone says, it is a beautiful movie.
Get some popcorn and sit back.
Take in the fantastic graphic design.
Play the “spot the cultural reference” game.
Enjoy the sweet love story.
Laugh.
Leave the social analysis for later, if you insist on doing one at all.

Blogrolling for Today

Moss Plants and More


The Wild Side (Olivia Judson)


The Phytophactor


Mendeley Blog


The Apprenticing Lab Rat

Today’s carnivals

I and the Bird #80 is up on Hawk Owl’s Nest
The 181st edition of The Carnival of Education is up on The Education Wonks