My Picks From ScienceDaily

Oh, how I hate this (mis)use of the term!
Male Biological Clock Also ‘Ticking’: Fertility Problems Greater For Men Over 35:

Pregnancy rates decrease and miscarriages increase when a father is over 35 years of age, a scientist will tell the 24th annual conference of the European Society of Human Reproduction and Embryology on July 7. Dr. Stéphanie Belloc, of the Eylau Centre for Assisted Reproduction, Paris, France, will say that this is the first time that such a strong paternal effect on reproductive outcomes has been shown.

Nature Reserves Attract Humans, But At A Cost To Biodiversity:

Rather than suppressing local communities in developing nations, nature reserves attract human settlement, according to a new study by researchers at the University of California, Berkeley.

When Using Gestures, Rules Of Grammar Remain The Same:

The mind apparently has a consistent way of ordering an event that defies the order in which subjects, verbs, and objects typically appear in languages, according to research at the University of Chicago.

Simple Life Form May Have Existed 700 Million Years Earlier Than Previously Thought:

The accepted timeframe for the beginnings of life on Earth is now being questioned by a Curtin University of Technology led team of scientists, after finding a key indicator to the earliest life forms in diamonds from Jack Hills in Western Australia.

Birds Migrate Together At Night In Dispersed Flocks, New Study Indicates:

A new analysis indicates that birds don’t fly alone when migrating at night. Some birds, at least, keep together on their migratory journeys, flying in tandem even when they are 200 meters or more apart.

Special Horseshoes Measure Acceleration In Horses, Evaluate Methods of Rehabilitation:

The most frequent injuries that horses suffer are derived from pressure exerted by riders, and knowing which forces are involved when horses move can prove highly informative when considering treatment for such injuries. A team of scientists from Wageningen University, led by Professor Johan van Leeuwen, has carried out studies both into the advantages of different rider techniques in reducing injury risk, and into the benefits of a method of equine rehabilitation.

Brain Noise Is Good: New Study Overturns Notion That Brain Noise Quiets Down With Maturity:

Canadian scientists have shown that a noisy brain is a healthy brain. “Brain noise” is a term that has been used by neuroscientists to describe random brain activity that is not important to mental function. Intuitive notions of brain-behaviour relationships would suggest that this brain noise quiets down as children mature into adults and become more efficient and consistent in their cognitive processing.

Children Overestimate Cute Animals In Rainforests, While Underestimating Insects And Annelids:

Globally, natural ecosystems are being lost to agricultural land at an unprecedented rate. This land-use often results in significant reductions in abundance and diversity of the flora and fauna as well as alterations in their composition.

Ancient Marine Invertebrate Diversity Less Explosive Than Thought:

Diversity among the ancestors of such marine creatures as clams, sand dollars and lobsters showed only a modest rise beginning 144 million years ago with no clear trend afterwards, according to an international team of researchers. This contradicts previous work showing dramatic increases beginning 248 million years ago and may shed light on future diversity.

Today’s carnivals

Encephalon #49 is up on Neuroscientifically Challenged
The 61st Carnival of Space is up on The Bat Page
Carnival of the Godless #95 is up on The Atheist Blogger
The 68th edition of Carnival of the Liberals is up on Globally Rational

ClockQuotes

Character isn’t inherited. One builds it daily by the way one thinks and acts, thought by thought, action by action. If one lets fear or hate or anger take possession of the mind, they become self-forged chains.
– Helen Gahagan Douglas

New and Exciting in PLoS

Circadian Phase Resetting via Single and Multiple Control Targets:

The robust timing, or phase, of the circadian clock is critical in directing and synchronizing molecular, cellular, and organismal behaviors. The clock’s failure to maintain precision and adaption is associated with sleeping disorders, depression, and cancer. To better study and control the timing of circadian rhythms, we make use of systems theoretic tools such as sensitivity analysis and model predictive control (MPC). Sensitivity analysis is used to identify key driving mechanisms without having to fully understand or investigate the detailed mechanistic interconnections of the large complex circadian network. Contrary to intuition, sensitivity analysis of the circadian model highlights several non-photic control inputs (such as transcriptional regulation) that outperform light-based circadian phase resetting – light is known to accelerate protein degradation. Aside from targeting individual parameters as control inputs, our methods identify combinations of control targets that may further the efficiency of entrainment. We compare the phase resetting performance of our MPC algorithm among cases involving individual and multiple simultaneous control targets (in wild-type simulations). We then tailor the algorithm to correct continuously the phase mismatch that occurs in short and long period mutant phenotypes. Through use of the presented tools, our algorithm is robust in the presence of model mismatch and outperforms the natural in silico sun-cycle-based phase recovery strategy by nearly 3-fold.

Increased Brain Signal Variability Accompanies Lower Behavioral Variability in Development:

Intuitive notions of brain-behavior relationships would suggest that because children show more variability in behavior, their brains should also be more variable. We demonstrate that this is not the case. In measuring brain signal variability with EEG and behavior in a simple face recognition task, we found that brain signal variability increases in children from 8-15 y and is even higher in young adults. Importantly, we show that this increased brain variability correlates with reduced behavioral variability and more accurate performance. A brain that has more variability also has greater complexity and a greater capacity for information processing. The implication of our findings is that variability in brain signals, or what some would call noise, is actually a critical feature of brain function. For the brain to operate at an optimal level, a certain amount of internal noise is necessary. In a certain way it could be stated that a noisy brain is a healthy brain.

On the Extent and Origins of Genic Novelty in the Phylum Nematoda:

The high-throughput sequencing of messenger RNA from parasitic organisms has permitted large-scale sequence analyses typically reserved for complete genome studies. Such expressed sequence tags (ESTs) have previously been generated for 37 species from the phylum Nematoda, of which 35 were from parasitic species. These datasets were combined with the complete genomes of Caenorhabditis elegans and C. briggsae. The sequences were assembled into 65,000 protein families, and decorated with 40,000 distinct protein domains. These annotations were analysed in the context of the nematode phylogeny. We identified massive gene loss in the model nematode, C. elegans, as well as plant-like proteins in nematodes that cause crop damage. Furthermore, many protein families were found in small groups of closely related species and may represent innovations necessary to sustain their parasitic ecologies. All of these data are presented at NemBase (www.nematodes.org) and will aid researchers working on this important group of parasites.

An Integrated Approach for the Analysis of Biological Pathways using Mixed Models:

In microarray data analysis, when statistical testing is applied to each gene individually, one is often left with too many significant genes that are difficult to interpret or too few genes after a multiple comparison adjustment. Gene-class, or pathway-level testing, integrates gene annotation data such as Gene Ontology and tests for coordinated changes at the system level. These approaches can both increase power for detecting differential expression and allow for better understanding of the underlying biological processes associated with variations in outcome. We propose an alternative pathway analysis method based on mixed models, and show this method provides useful inferences beyond those available in currently popular methods, with improved power and the ability to handle complex experimental designs.

Is there a herpetologist in the house?

This snake was sighted about a week ago in Burlington NJ by one of my readers. Can anyone here identify the species? Please place your guesses in the comments:
snake%201.JPG
snake%202.JPG

ClockQuotes

I like the man who faces what he must,
With steps triumphant and a heart of cheer;
Who fights the daily battle without fear.

– Sarah Knowles Bolton

Weekend in NY City

Too busy all week to write about this, but last weekend we went on a family trip to NYC. Old-timers here may remember that we took the kids there two years ago, so they were eager to visit again. We spent four days there, flying JetBlue (always happy with their service), and generally having great fun. We did touristy things, mainly whatever the kids wanted to do. No online access at all!
So we shopped at F.A.O.Schwartz and at Macy’s:

Continue reading

My Picks From ScienceDaily

Agriculture Linked To Frog Sexual Abnormalities:

A farm irrigation canal would seem a healthier place for toads than a ditch by a supermarket parking lot. But University of Florida scientists have found the opposite is true. In a study with wide implications for a longstanding debate over whether agricultural chemicals pose a threat to amphibians, UF zoologists have found that toads in suburban areas are less likely to suffer from reproductive system abnormalities than toads near farms — where some had both testes and ovaries.

Music Went With Cave Art In Prehistoric Caves:

Thousands of years later, we can view stone-age art on cave walls, but we can’t listen to the stone-age music that would have accompanied many of the pictures. In many sites, flutes made of bone are to be found nearby.

Undergraduates Forge New Area Of Bioinformatics:

A group of undergraduate students from the University of California San Diego have forged a new area of bioinformatics that may improve genomic and proteomic annotations and unlock a collection of stubborn biological mysteries. Their work will be published in the July issue of the journal Genome Research.

Scientists Set Out To Measure How We Perceive Naturalness:

Natural products are highly valued by consumers yet their properties have been difficult to reproduce fully in synthetic materials, placing a drain on our limited natural resources. Until now …

Rare Plants And Endangered Species Such As Tigers At Risk From Traditional Medicine:

Two reports from TRAFFIC, the world’s largest wildlife trade monitoring network, on traditional medicine systems in Cambodia and Vietnam suggest that illegal wildlife trade, including entire tiger skeletons, and unsustainable harvesting is depleting the region’s rich and varied biodiversity and putting the primary healthcare resource of millions at risk.

Wild Orangutans Declining More Sharply In Sumatra And Borneo Than Thought:

Endangered wild orangutan (Pongo spp.) populations are declining more sharply in Sumatra and Borneo than previously estimated, according to new findings published this month by Great Ape Trust of Iowa scientist Dr. Serge Wich and other orangutan conservation experts in Oryx – The International Journal of Conservation.

Looking For The Founatain Of Youth? Cut Your Calories, Research Suggests:

Want to slow the signs of aging and live longer? New Saint Louis University research suggests cutting back on calories could be a promising strategy.

SCONC: Podcasting 101

Thursday, July 10
6:00 – 8:00 PM
With support from our friends at Burroughs Wellcome Fund, SCONC (Science Communicators of North Carolina) is hosting an introduction to podcasting (think of it as radio over the Internet). National authority Ryan Irelan of Podcast Free America will lead a two-hour session at Sigma Xi on NC 54 in the Research Triangle Park. (click here for directions) Please RSVP to Ernie Hood no later than Tuesday, July 8, or you might go hungry. (bkthrough AT earthlink DOT net)

The coolest picture of the year, I predict

Last night I thought I had fun, hearing both thunder and fireworks, but these guys could not just hear but also see not two but three spectacular things simultaneously – fireworks (left), comet McNaught (center) and lightning (right). And this was all captured in one of the most exciting photos I have seen recently, bound to win all sorts of “Picture of the Year” contests come December:
Comet Between Fireworks and Lightning, picture taken by Antti Kemppainen:
Australian%20sky.jpg
Click here to see it really big!
Explanation:

In January 2007, people from Perth, Australia gathered on a local beach to watch a sky light up with delights near and far. Nearby, fireworks exploded as part of Australia Day celebrations. On the far right, lightning from a thunderstorm flashed in the distance. Near the image center, though, seen through clouds, was the most unusual sight of all: Comet McNaught. The photogenic comet was so bright that it even remained visible though the din of Earthly flashes. Comet McNaught has now returned to the outer Solar System and is now only visible with a large telescope. The above image is actually a three photograph panorama digitally processed to reduce red reflections from the exploding firework.

You.Will.Be.Assimilated!

Yes, this is me, Bora Borg, at least parts of it. Ably photoshopped by McDawg:
Bora%20Borg.jpg

Books on Open Access

As expected, most of them are free to download. Peter Suber has all the relevant links:
Open Access Opportunities and Challenges: A Handbook (PDF) by Barbara Malina (ed.).
Science Dissemination using Open Access by Canessa and Zennaro.
Understanding Open Access in the Academic Environment: A Guide for Authors (PDF) by Kylie Pappalardo.
I also have Scholarly Journals Between the Past & the Future by Martin Rundkvist.

OA student projects available

Heather Morrison just finished teaching her class on Open Access and the student projects are now all online for you to see.

More you can see, more you click

That is, in a nutshell, the conclusion of this study. If you have free access to a lot of literature, you are much more likely to click on links and download PDFs (which hopefully means you will read the papers, learn from them, improve your science, and cite them when writing your own manuscripts). If you know that most of the time you will see a “pay $60” page instead, you don’t bother clicking anyway.
Also, this mainly applies to the new papers – the older papers are rarely looked at – so there is no real need to keep archives TA for any lengthy periods of time.
Peter Suber comments.

NIH Public Access Policy instructions on PubMed home page

Thanks to Heather for the heads-up:

Instructions for NIH-funded authors have been prominently placed on the PubMed home page.
There is a link to a list of journals that will manage the submission process with the NIH guidelines on behalf of authors – very handy! – as well as instructions for authors who publish in journals that do not provide this service.

Storm

Last night, the skies opened. And that sky-opening business is always kinda tricky – the sky-trap-door engineer has to make sure that everything goes well. And last night, as Jesse Helms was going up in the sky to meet his Maker, the trap-door kinda got stuck. Or perhaps ol’e Jesse wanted to send one last fart at ‘Liberal Zoo’ as he used to call Chapel Hill.
The thunderstorm was very sudden and powerful and much of the area lost electricity. We were without power for about 5 hours – from 8:30pm till 1:30am.
So, we lit up the candles. Kids played Monopoly. I, being offline, read a book – yes, I finished a real, physical, hardcopy book!
Someone donwtown set off the fireworks anyway (although officially they are postponed for tonight), so we had fun trying to distinguish the sounds – which loud ‘craaaack’ was thunder, and which was fireworks. That was a lot of fun.

Today’s carnivals

Scientiae Carnival is up on PodBlack blog

ClockQuotes

If your daily life seems poor, do not blame it; blame yourself that you are not poet enough to call forth its riches; for the Creator, there is no poverty.
– Rainer Maria Rilke

Fun to watch: the Edwards-Rove debate

Edwards, Rove to face off in UB debate:

Sens. Barack Obama and John McCain might not burn up the campaign trail around Western New York this election year, but the University at Buffalo may have scheduled the next best thing.
GOP strategist Karl Rove and former Democratic vice presidential candidate John Edwards will debate the issues of the presidential campaign Sept. 26 as part of the university’s Distinguished Speakers Series, The Buffalo News has learned.
As surrogates for the parties’ standard bearers, the two also could square off more than once at other locations around the nation.

[hat-tip: MLDB]

My Picks From ScienceDaily

Body’s Own ‘Cannabis (Marijuana)’ Is Good For The Skin, Scientists Find:

Scientists from Hungary, Germany and the U.K. have discovered that our own body not only makes chemical compounds similar to the active ingredient in marijuana (THC), but these play an important part in maintaining healthy skin.

Experimental Philosophy Movement Explores Real-life Dilemmas:

Imagine a business executive who thinks: “I know that this new policy will harm the environment, but I don’t care at all about that — I just want to increase profits.” Is the business executive harming the environment intentionally? Faced with this question from a University of North Carolina at Chapel Hill philosopher, 82 percent of people polled said yes.

Going Green: Savings And Comfort Are The Best Incentives:

Would shrinking your carbon footprint, recycling more, and going green be easier if you could monitor your household’s environmental impact? That’s the question a team of Canadian industry consultants set out to answer.

In Vitro Fertilization: New Method Predicts Which Women WIll Get Pregnant:

Researchers at the Stanford University School of Medicine have identified a method that can predict with 70 percent accuracy whether a woman undergoing in vitro fertilization treatment will become pregnant. This information may someday help the tens of thousands of couples who want to undergo IVF each year, and their doctors, decide on their course of action.

To Multiply, Ant Colonies Adapt To Environmental Conditions:

By combining field work in Australia with mathematical modeling, three scientists from the laboratoire Fonctionnement et évolution des systèmes écologiques (CNRS/Université Pierre et Marie Curie/ENS Paris) have shown that the quality and quantity of winged queens produced by colonies of the Rhytidoponera ant vary according to environmental conditions. In certain cases, colonies even stop producing founding queens and spread solely by splitting up the colony.

Two-ton, 500 Million-year-old Fossil Of Stromatolite Discovered In Virginia, U.S.:

Virginia Museum of Natural History scientists have confirmed that an approximately 500 million-year-old stromatolite was recently discovered at the Boxley Blue Ridge Quarry near Roanoke, Virginia. This specimen is the first-ever intact stromatolite head found in Virginia, and is one of the largest complete “heads” in the world, at over 5 feet in diameter and weighing over 2 tons.

Jesse Helms has died

There is no need to say anything at this moment because it is not nice to say ugly stuff about the dead.
Before coming to the US, as a kid not interested in politics, and certainly not in US politics, Helms was one of the rare American politicians I have heard of – mostly as an example how the US electoral system sometimes enables utterly unfit people to reach high levels of power. We laughed.
Ten years ago, one of the questions I had to answer when becoming a US citizen, was “who are the current US senators representing NC?” I said “Jesse Helms and Lauch Faircloth, hopefuly not for much longer.” A couple of months later, my first vote in any US election was against Faircloth who was defeated then by John Edwards. Helms resigned later.
What is interesting to watch today is how news media and blogs are trying mightily to say something, anything nice about the guy. For instance, Powerline blog starts a ridiculous eulogy with “Former Senator Jesse Helms, the great anti-Communist, has died.” Anti-Communist? Is that what is important? The ghosts of Red Scare? Who cares any more? How is that more important to point out than all the other “anti”s that Helms was?
See how this was covered by NYTimes, Raleigh News & Observer and Charlotte Observer. Compare to Pam Spaulding.

Today’s carnivals

Four Stone Hearth #44 is up on Greg Laden’s blog
The 90th Meeting of the Skeptics’ Circle is up on The Millenium Project
Friday Ark #198 is up on Modulator

ClockQuotes

The sky is the daily bread of the eyes.
– Ralph Waldo Emerson

My Picks From ScienceDaily

Secret Of The Sweet-Sounding Stradivarius: Wood Density Explains Sound Quality Of Great Master Violins:

The advantage of using medical equipment to study classical musical instruments has been proven by a Dutch researcher from the Leiden University Medical Center (LUMC). In collaboration with a renowned luthier, Dr. Berend Stoel put classical violins, including several made by Stradivarius, in a CT scanner. The homogeneity in the densities of the wood from which the classical violins are made, in marked contrast to the modern violins studied, may very well explain their superior sound production.

Resveratrol, Found In Red Wine, Wards Off Effects Of Age On Heart, Bones, Eyes And Muscle:

Scientists have found that the compound resveratrol — found in red wine and grape skin — slows age-related deterioration and functional decline of mice on a standard diet, but does not increase longevity when started at middle age.

Species Extinction Threat Underestimated Due To Math Glitch:

Extinction risks for natural populations of endangered species are likely being underestimated by as much as 100-fold because of a mathematical “misdiagnosis,” according to a new study led by a University of Colorado at Boulder researcher.

Prevalence Of Religious Congregations Affects Mortality Rates:

LSU associate professor of sociology Troy C. Blanchard recently found that a community’s religious environment — that is, the type of religious congregations within a locale — affects mortality rates, often in a positive manner. These results were published in the June issue of Social Forces.

Sleep Problems Associated With Menopause Vary Among Ethnic Groups:

Difficulty falling asleep and staying asleep increase as women go through menopause according to research by Rush University Medical Center. Waking up earlier than planned also increases through late perimenopause but decreases when women become postmenopausal. The study is published in the July 1 issue of the journal Sleep.

Does This Make Me Look Fat?:

The peer groups teenage girls identify with determine how they decide to control their own figure. So reports a new study by Dr. Eleanor Mackey from the Children’s National Medical Center in Washington DC, and her colleague Dr. Annette La Greca from the University of Miami. Also influencing weight control behavior is girls’ own definition of normal body weight and their perception of what others consider normal body weight.

Evolutionary Origin Of Mammalian Gene Regulation Is Over 150 Million Years Old:

Scientists at the Babraham Institute, the Sanger Institute, the University of Cambridge and the University of Melbourne and the University of Texas at San Antonio (all part of the SAVOIR consortium) have found that a complex, highly conserved and extremely important mechanism of controlling genes is over 150 million years old.

Get Smart About What You Eat And You Might Actually Improve Your Intelligence:

New research findings published online in The FASEB Journal provide more evidence that if we get smart about what we eat, our intelligence can improve. According to MIT scientists, dietary nutrients found in a wide range of foods from infant formula to eggs increase brain synapses and improve cognitive abilities.

Attitudes Toward Consumption And Conservation Of Tigers In China:

The potential market for tiger products in China is enormous, but a vast majority of the Chinese public would rather have wild tigers than tiger-bone wine, according to new research.

Tummy’s Taste For Red Wine With Red Meat:

What happens when red wine meets red meat? If the rendezvous happens in the stomach, scientists in Israel are reporting, wine’s bounty of healthful chemical compounds may thwart formation of harmful substances released during digestion of fat in the meat.

Happy Birthday!

pone_ed_logo.jpgHappy birthday to Elizabeth Edwards, the most inspiring person on the US political scene since I started paying attention a couple of decades ago….

On the Nature of PLoS….

I know that you know that I work for PLoS. So, I know that a lot of you are waiting for me to respond, in some way, to the hatchet-job article by Declan Bucler published in Nature yesterday. Yes, Nature and PLoS are competitors in some sense of the word (though most individual people employed by the two organizations are friendly with each other, and even good personal friends), and this article is a salvo from one side aimed at another. Due to my own conflict of interest, and as PLoS has no intention to in any official way acknowledge the existence of this article (according to the old blogospheric rule “Do Not Feed The Trolls”), I will only send you to the responses by others who felt compelled to comment about the article. You can also, if you wish, post a comment on the article itself.
Peter Suber:

Declan Butler last used tax records to investigate PLoS’ finances in June 2006. See some of the comments (first set, second set) generated by his investigation.

DrugMonkey:

Since they are in science however, we can expect Nature to be totally objective and to eschew blatantly self-serving editorials and news focus pieces that gratuitously bash the competition. Can’t we? Yeah right.

Jonathan Eisen:

So why is the success of PLoS One a problem? Well, because it allows Nature to do the old good cop bad cop routine and to write, again, about the “failings” of the PLoS publication model. Now, mind you, the article does not quote a single source for what the PLoS publication model is. But they do say it has failed.

Vanya:

Hmmm…but tell us how you really feel. In case you’re wondering, the “bulk, cheap publishing of lower quality papers” takes place in PLoS ONE. Sigh. I’m an author on one such “lower quality paper”. I’d break down and cry if it weren’t for the feedback, citations and media coverage we received on that paper.
In the words of my labmate who chooses to go unnamed:
“maybe Nature, at the end of their articles, should write Competing Interests: The authors have declared that competing interests exist and we like to talk bad about a competitor’s economic model”
Seriously though, I wonder if Nature realises that their article comes across as being extremely one-sided and very childish.

Greg Laden:

Some will say that the Nature piece by Butler is negative or even cynical regarding PLoS. Maybe. But on close examination, perhaps Butler is just doing his job as a journalist, asking questions, probing, seeking clarity. In the mean time, PLoS clearly stands up well against these questions.
One thing that does bother me a bit about the Nature piece is this: To the extent that it can be seen as negative, it must be seen as negative about a competitor. Normally one would expect a discloser statement indicating that where PLoS loses financially, Nature gains. The sources cited by Butler who have negative things to say about PLoS are also either competitors or simply anti-OpenSource.
I am absolutely confident that Butler and Nature will address (or even redress) this apparent misstep.

Razib:

I won’t really get into the details here. I think the article makes some good factual points, but they’re stitched together in a manner to depict PLoS in a rather unfavorable light. The kicker of course is that Nature has some major conflicts of interest here.’

Razib:

PLoS, does it suck? (check the comments thread)

GrrlScientist:

Wow, have you read Declan Butler’s nasty little hatchet job that was just published in Nature about the Public Library of Science (PLoS)? My jaw hit the top of the table in my little coffee shop where I am ensconced — why would Nature demean their journal by publishing such a snotty little screed where they attack the normal, but probably painful, financial ups-and-downs of a new journal?

Alex Holcombe:

Nature has published a news item by Declan Butler on the finances of one of its competitors: the open-access PLoS journals, using language that puts the organisation and its journals, especially PLoS ONE, in a negative light.
The fact that PLoS does not meet its costs exclusively from the author publication fees, as Nature focuses on, is interesting, especially from the point of view of an organization like Nature Publishing Group, whose purpose is to make a profit. But….

Mike Dunford:

A story that fairly examined what PLoS ONE has done so far, how it’s perceived by other scientists (or even how aware other scientists are of it), and whether the increased number of articles appearing there means that more scientists are using the journal’s articles as resources would be an interesting read. It’s sad that Butler and the editors at Nature decided to go with the snide hatchet job instead.

PlausibleAccuracy:

Ok, so I think I agree that the article is sort of unnecessarily rude and demeaning, but I wouldn’t really expect anything different from a for-profit publisher. The worst part is that everything Dr. Butler tries to imply is a failing of PLoS has been done many times over in the closed-access for-profit journal community. Right, so let’s try to look past the blatant attack and take a look at the actual facts, shall we?

Insilico:

Nature has some news to tell the world about their rival PLoS (Public Library of Science). Open source publishing by PLoS thrives on charity funding. Does the business model needs a redesign of it’s aims, goals and strategies? Or is it a cheap trick from scared Nature publishing? Judge yourself….

Bill Hooker:

This clumsy hatchet job from Nature reporter Declan Butler is beneath him, a poor excuse for journalism and an affront to the respect with which many of his colleagues are regarded by the research community.
Let’s start with the title: “PLoS stays afloat with bulk publishing”. Loaded rhetoric, anyone? The clear implications are that PLoS is floundering (Butler’s own numbers show otherwise!), and that “bulk” is somehow inferior (to, one presumes, “boutique” or some such). PLoS is “following an haute couture model of science publishing” sniffs our correspondant, who goes on to clarify: “relying on bulk, cheap publishing of lower quality papers to subsidize its handful of high-quality flagship journals”.
This emphasis on “quality” and the idea that the same somehow equates with scarcity continues throughout: “the company consciously decided to subsidize its top-tier titles by publishing second-tier community journals with high acceptance rates”, “the flood of articles appearing in PLoS One (sic)”, “difficult to judge the overall quality”, “because of this volume, it’s going to be considered a dumping ground”, “introduces a sub-standard journal to their mix”.
The intent is obvious, and the illogic is boggling. Where does Butler think the majority of science is published? Even if you buy into this nebulous idea of “quality” (one knows it when one sees it, does one not old chap? wot wot?) there can be no “great brand” journals without the denim-clad proletarian masses. All the painstaking, unspectacular groundwork for those big flashy headline-grabbing (and, dare I say it, all too often retracted) Nature front-pagers has got to go somewhere.

Greg Laden:

My own criticism of “peer review” is really meant to be a broader critique of the publishing process overall. Furthermore, my belief is NOT that the situation with science publishing is totally screwed up, but rather, that there are some real problems that must be addressed, and PLoS as Open Access and PLoS as on line is an important model for what I see as a good approach to solving some of these problems.

Dave Munger:

My goodness! PLoS has received $17 million in grants! This is obviously a signal that things are going badly for the revolutionary open-access publisher. They’re resorting to handouts! When a charitable organization continues to earn the respect of more and more foundations, increasing its bottom line year after year, it’s clearly a sign of impending doom!
——————-
Clearly this demonstrates that Harvard is in dire circumstances, just like PLoS. Don’t let Harvard and PLoS’s impeccable reputations fool you. When granting institutions and other donors want to give non-profits large sums of money, it’s a sign of their inevitable decline. Fortunately we have private institutions like Nature, the University of Phoenix, and DeVry University to take their place.

ocmpoma:

Several blogs over at ScienceBlogs are discussing a recent review of PLoS, a major open access organization, in Nature. Their opinions of the piece are not very high. Here’s Gene Expression, whose post lists out several others on the subject; here’s Greg Laden’s Blog, which brings a broader discussion of peer review into the discussion; and here’s Living the Scientific LIfe, which has what I think is the best summary of the main points in the review, and the problems with them.

janeblum:

Personally, I think Nature has as much right as any business to take potshots at the competition. Whether they are wise to do so remains to be seen. I doubt that true believers on either side of the open access movement are going to persuaded by the article or the reactions to it, so it’s difficult to see what they gain. And as Britannica learned when it challenged wikipedia, such challenges can come back to haunt you later. Britannica endured an extended comparison of the accuracy of its articles versus those in Wikipedia, and now includes wikipedia-like features. Will we see Nature Publishing Group journals change as a result of this discussion?

SciCurious:

I wouldn’t know one thing or another about PLoS’ financial status. I can barely keep my own bills straight without looking at other people’s. But I do know that there’s no shame to be had in publishing in one of PLoS’ “lower level” journals. They’re pretty well respected in my department. As for PLoS ONE, my own advisor told me just yesterday that she’d LOVE to have a PLoS ONE article. Grad students in my department present PLoS ONE articles in Journal Clubs, and many of the respected people in my field send papers there.

Richard:

Nature does really well at the first section but does it really ensure that the results are rapidly disseminated to the public throughout the world? Or does charging for access fulfill the ‘fashion that conveys their significance’? if you pay for something does that enhance its significance?
Interestingly, Nature did not make a profit for more than 30 years:

juniorprof:

In closing, I’d just like to say a few words about science in developing countries and open access. I hope that as scientists we can all recognize the important role that science and researchers can play in helping developing countries achieve their goals. Research is a powerful tool in the repertoire of education. Moreover, many developing countries have urgent research needs that don’t register on the radar of countries that have reached industrialized status. Even if institutions in developing countries receive discounted access to pay journals it is money spent that could be dedicated to other aspects of research or education. These researchers must have access to literature to succeed and they must also have as many research dollars as they can get their hands on. Open access can be a powerful tool in this fight. My personal opinion is that open access journals, and PubMed Central in particular, can and should be key aspects of how we can bring science, education and research to developing countries. Think about that when you’re putting off depositing your papers in PubMed Central or when you’re considering the appropriate venue for your next publication

Bruce Sterling:

I also really love it when scientists abandon all reserve and objective dignity and start backstabbing and eyegouging in public.

Bjoern Brembs:

It needs to be pointed out here that publishing in these “non-light” journals decides over grants, tenure, promotions and thus peoples’ careers and livelyhoods. So one could paraphrase the current system of publishing in science in the following way: If the scientific community were a large corporation, it would be out-sourcing it’s hiring and firing to a group of ex-employees who either left the corporation because they didn’t like it or were fired themselves. Now how many managers would implement such a system in their company?
Instead, we should have one single, decentralized, publicly accessible database where the current assessment by editors (i.e., the “non-light” component of peer review in e.g. Nature) comes after publication as one of many measures of post-publication review and assessment. The first review should be done by scientists on the science – whatever happens to the paper afterwards is open to debate. I, for one, value the input of professional editors and their expert judgement of scientific newsworthyiness and would not want to miss it.

John Dupuis:

As most science librarians, I am somewhat critical of Nature’s tendency to charge boatloads of money for their journals and journal backfiles, but I do accept that what they do costs money and that they have a right to run their company as they see fit. I don’t have a problem paying for stuff that has real value.
However, I do have to say I am very disappointed with this turn of events. Notwithstanding their journal business, I have always been very impressed by the web group at Nature and the fine work they have done on products like Scintilla, PostGenomic, Precedings, Connotea, Nature Network and others. Those are, for the most part, fine products that are really pushing the edges and trying new and exciting things. They are of of the few commercial publishers that really seems to get doing science on the web and I’ve been happy to promote those products and services in my community here and to present about them to a wider audience. Of course, OA is a very important piece of the puzzle of doing science on the web and PLoS is also trying new and exciting things and really seems to get it. There’s a real conflict there. Perhaps Nature’s left hand should be telling it’s right hand what’s really going on out here.

Hank (this one is difficult to understand as it is full of misunderstandings of who the players are, how they operate, what the relationships between them are, etc. – the tacit knowledge that people on the inside take for granted and do not realize sometimes that people on the outside do not know – yet sometimes those on the outside feel compelled to comments as if they know – welcome to the blogosphere, this is what makes it vibrant and good! Who knows, someone may take time out of the holidays and go there and explain the complex networks of publishers, bloggers, etc, and who is who, and how Nature works, how PLoS works, etc., though all that information is findable on the web via, for instance, Google search):

Should Nature writers with integrity be a fan of all open access publications? Well, no, not if it is a free-for-all just to make money. Nor should we. Declan Butler taking what he knew what would be an un-popular stand, especially given his employer and the claims of bias it would engender, is to be applauded. Not saying anything would have been the easier, diplomatic road. And completely wrong.

Timo Hannay:

To look on the bright side, none of this may matter very much in the longer run since truly widespread open access to scientific content is coming about through funder-mandated archiving, not open-access publishing. Nevertheless, the ironies and misunderstandings are just too stark to pass them by without comment.

Greg Laden:

A number of bloggers, including myself, had suggested that Delcan Butler’s anti-PLoS writup in nature constituted an attack of one company against another. How silly of us to have done so. Here’s what we should have been thinking instead:

PhysioProf:

Notice how this dude unquestioningly equates the “lowness” or “highness” of a journal with the quantity of “editorial input”? This is totally fucking ridiculous. Journal editors do the best job when they identify good reviewers who understand the importance and reliability of a particular piece of work, and then stay the fuck out of the way.

Michael Meadon:

I like open access. In my opinion, the serials crisis is an absolute travesty and, despite my ‘capitalist’ instincts, the spectacle of huge companies making profits from the efforts of academics who (a) are not in the companies’ employ and (b) are funded (largely) by taxpayers, utterly disgusts me. So it rather pisses me off that the august Nature magazine (which, I should note, I have difficulty accessing because my institution can’t afford the subscription fee) has published a bloody screed against PLoS, the best known open access suite of journals. The screed opens thusly:

Greg Laden:

The flap that started with the ill advised commentary by Delcan Butler started out looking like it MIGHT be an Orwellian, perhaps Nixononian attempt by a well established publishing icon in the fields of science to damage an up and coming competater, the Public Libary of Science in particular, and the Open Access Movement more generally. As time goes by, however, I start to get the impression that it does not merely look this way, but may actually be this way.

Lars Juhl Jensen:

I want to be the first to point out the caveats of this analysis. First, the analysis above did not take into account that each journal does not publish the same number of papers. However, weighting the journals by number of papers when calculating average impact factors shifts the balance in favor of PLoS (9.79 for PLoS vs. 9.46 for NPG). Second, the journal PLoS ONE does not have an impact factor yet and was thus not included in my analysis. Third, the criticism by Declan Butler was mainly targeting the fact that much of PLoS’ revenue is due to PLoS ONE. However, until NPG chooses to make available detailed financial reports like PLoS does, it is impossible to tell how much of their revenue comes from lower-impact journals.

Greg Laden:

The House of Commons (U.K.) Select Committee on Science and Technology investigated Open Access publishing alternatives, and pursuant to this obtained written evidence from Nature Publishing Group consisting of answers to specific questions about “pay to publish.” Here are excerpts from the document. Given the current discussion on Open Access publishing, this may be of interest to you.

Mike Dunford:

Timo Hannay just responded, over at one of Nature’s blogs, to the hordes of bloggers who were somewhat displeased with the tone and content of Declan Butler’s recent Nature article. Now that someone from Nature has returned fire, and other bloggers have fired back, it’s likely that this whole thing is going to turn into one of those multi-day, multi-article kerfuffles that do so much to maintain blogging’s reputation as the WWE of the scientific world. Which is cool, as far as I’m concerned. It’s been a while since I’ve grabbed a folding chair and climbed into the Cage of Death. I’m ready to go.

Pedro Beltrao:

Going back to one of Timo’s main points, I don’t agree that PLoS creates barriers to market entry to other OA publishers. At least certainly not because they used philanthropic grants until they reached break even point. If there are barriers in the market they are due to perception of quality and strong brand name. Here OA publishers have the added advantage that creating a strong brand is easier when most people perceive OA as something good. From the example of PLoS and to some extent BMC there are now clear paths for any publisher (specially one with a strong brand name) to set up a viable business OA model.

Mario Pineda-Krch:

It’s nice to hear Timo Hannay’s view of open content (actually rather refreshing after reading Declan Butler’s tantrum piece). I am a bit puzzled, however. Does Hannay’s views represent the view of the Nature Publishing Group as a whole or do they represent only his own views? And, how does all of this fits in with the Nature vs. PLoS runaway train of Declan Butler that has been whipping up a storm in the blogosphere over the last few days (see Bora’s post for a succinct summary). The pieces by Declan Butler (he actually has two stories, the second and the first) unequivocally give a impression that Nature is (as Timo puts it in the clip) on of those “hostile” and “reactionary” publishers that are in a “defensive mode” towards the Open Access publishing model that “give the whole industry a disservice”.

floatingnotes:

Many critics are complaining about either the appropriateness of Nature criticizing a competing journal (without explicitly discussing conflict of interest) or for criticizing open-access in general. I think it is entirely appropriate for Nature to write well-argued, well-reasoned articles on science publishing, even discussing competing models critically, but the Butler article under question does not pass these criteria IMO.

Niyaz Ahmed:

I found the overall tone and spirit of the news article quite disturbing and distasteful. Especially, their painting of PLoS ONE journal as a ‘dumping ground’ and mention of its peer review process as ‘light’ is not at all correct and ignores facts. I see it as an unsuccessful attempt to dump all the ground-breaking work that PLoS ONE has been publishing since its launch in 2006 (see these posts for exmple; here, here and here). As I said in my response to the story, it is a simple fact that the ~300 scientists who publish in PLoS ONE every month and the 500 Editors who devote their time on rounds of peer reviewing are certainly not the fools out there.

Zen:

My only comment for now is to repeat the mantra that led me to start this website. Ideas that spread, win.

Stevan Harnad:

Nature’s reply states that “Nature isn’t anti-open access,” but it neglects to mention that Nature back-slid in 2005 — from having at first been Green on OA self-archiving by its authors to rejoining instead the minority of journals who still try to embargo access. Nature’s reply also misses the real growth region of Green OA mandates, which is now institutional and departmental mandates like Southampton’s, QUT’s, Minho’s, CERN’s, Liege’s, and now Harvard’s and Stanford’s, rather than just funder mandates.

Greg Laden:

The following are excerpts from the journal Nature regarding the Public Library of Science. These were located with a simple search for the phrase “Public Library of Science.” For each item, I provide the source, and a selected bit of text. I have no selection criteria to report, but I do have a reason for doing this: To give an interesting view of the history of PLoS as a concept and an entity, and to some extent, the reactions to PLoS from various quarters.

Peter Suber:

Stevan is right to correct the impression that all OA is gold OA (through journals), and to remind everyone of green OA (through repositories). But “free online access” is itself only part of the story. Stevan links from that phrase to a more complete discussion. But because he doesn’t elaborate in his post, I’ll elaborate a little. The term “OA” is now used in at least two ways: (1) to remove price barriers alone (“free online access” or gratis OA) and (2) to remove both price and permission barriers (libre OA, which includes BBB OA). The gratis/libre distinction is not the same as the gold/green distinction. The former is about rights or freedoms, and the latter is about venues. Gold OA can be gratis or libre, and green OA can be gratis or libre. Just as we can’t afford to forget about green OA, we can’t afford to forget libre OA.

Oca sapiens:

Cosa gli ha preso a Declan Butler sull’ultimo Nature, di attaccare in quel modo la Public Library of Science? Che il gruppo open access non faccia profitti, si sa, ma davvero PLoS ONE rastrella qualunque articolo, senza tener conto del suo valore? O pubblica risultati interessanti e qualche volta discutibili, ma dando la possibilità a tutti di discuterne? Commenti.
Be’, vado a Modena, dove “Oltre i giardini” mi ha messa nella sezione scienza, ma dev’essere un errore.

ob:

Mittwoch publizierte der renommierte NatureNews-Redakteur Declan Butler eine – allgemein als nasty bezeichneten – Artikel über PLoS: PLoS stays afloat with bulk publishing: Science-publishing firm struggles to make ends meet with open-access model. Die Kommentare dort sind mehr oder weniger einhellig der Ansicht, dass Nature einen Wettbewerber “gedisst” hätte. Stellvertretend hier zwei Kommentare:

Bjoern Brembs:

Editors of schorarly, peer-reviewed journals often claim that somehow their choosiness is the most important verdict on the quality of a scientific manuscript. Points in case are Nature Neuroscience’s peer-review policy, a recent Nature News article or a follow-up on the Nature blog “Nascent”. However, data on the ‘impact’ or quality of papers published in these very choosy journals varies greatly. Therefore, I have a suggestion on how to judge the performance of an editor. My suggestion requires that all peer-reviewed scientific primary literature is deposited in some database before any subjective editorial choice has been made. An example would be PLoS One, but any such database would do. Then, editors can thumb up or thumb down papers after they have been vetted by peers and promote or demote papers according to their judgement, very similar to acceptance and rejections in so-called high-end journals of today. Since all choices (also rejections!) are recorded, each editor (or goup of editors) will establish a track record. In a way, this is similar to the concept of the Faculty of 1000. Obviously, this will provide a great incentive to maximize their reliability as gatekeepers of scientific quality. How can their performance be measured? By counting downloads, citations, trackbacks, comments, ratings, media coverage, Fac1000 mention or any other measure deemed relevant of the papers they accepted/rejected.
That way, everybody would get their cake and eat it too: seemingly objective performance measures for both scientists and editors. Wouldn’t that be fair?

Ricardo Vidal:

What I find to be the most notorious aspect in this whole string of events is that there is quite a large community of science bloggers that are ready to offer their “peer-review” in situations such as these. Is this a good thing? I would like to believe so…

Philip Davis:

In an expository news piece released in last week’s issue of the journal Nature, Declan Butler describes how the Public Library of Science is attempting to stay afloat by using lower-cost, “bulk publishing” with PLoS One to offset mounting costs of publishing PLoS Biology and PLoS Medicine.

Bjoern Brembs:

I’m sure nobody ending up on this obscure blog could have missed the current frenzy about a Nature news article by Declan Butler attacking PLoS. In the meatime, there has been a follow-up by Nature publishing director Timo Hannay, also with comments and a reply by Timo. I think what we see here are the labor pains of a new scientific publishing model. People realize that things are not working effectively, some would maybe even claim that the entire system is broken and needs to be replaced. A good overview can be had from Coturnix in his post, but there are also comments worth noting individually such as Pedro Beltrao, Greg Laden, Lars Jensen, Mario Pineda-Krch, DrugMonkey or Bill Hooker.

Mike the Mad Biologist:

That’s why I almost never review articles for these journals anymore (as opposed to Open Access journals, which I do–two in the last month alone, and that’s during grant season). Seriously, if they ever did want me to review, then they have to pay me just like any other business who wanted to consult my expertise would. If enough of us did that, well, things would get very interesting….

donham nise:

If you haven’t already, take a look at the PLoS Biology or the new journal PLoS One (a direct competitor for Nature since it accept all sorts of articles). From an occasional reader perspective, the articles are authoritative, attractive, and visually appealing.
While Nature remains one of two pre-eminent science journals (the other is Science), it is clear that “the times they are a changin.” The Nature editorial staff clearly recognizes this-and maybe they are a bit worried.

DrugMonkey:

A recent foofaraw (including offerings from YHN and PhysioProf) arose over an ill-advised tone struck in an attack editorial thinly veiled as an analytical news item published in Nature. The discussion has brought Open Access science [several tomes on OA linked here] back to the blog-table for discussion. I have another thought, beyond my reaction to the sneering tone of the aforementioned attack editorial. One of the ways I think the Nature piece may possibly have gone astray is in not recognizing the depth to which their customers, research scientists, are reflexively sympathetic to the notion that our product–the primary scientific observation–should be freely available to all. I have been interested to hear some perspectives on why Open Access trips the trigger from some bloggers not previously on the OA Nozdrul or wackaloon lists.

John Wilbanks:

And, speaking as an entrepeneur, criticizing a startup for high-flying rhetoric and missed revenue projections in its first five years of operations is kind of ridiculous. If we did this kind of fisking on every web company – or even on Nature’s web 2.0 operations, which I doubt pay their own bills with ads and revenue – we wouldn’t have very many startups left to kick around.
——————-
The final takeaway is that everybody involved probably needs a deep breath or five. The article wasn’t that bad. Inartful, yes. Inaccurate, probably not. But the real story here is that the data in the article tell us PLoS is figuring out a path to making it, and has investors in it for the long run. How can that be bad?

Greg Laden:

This item is to be found at the blog called The Scholarly Kitchen. This is a blog of the “Society for Scholarly Publishing” … which is presumably a trade organization supporting the evil, pirate-like publishers. The piece makes a couple of absurd points and one major, major mistake. I have visited the blog and corrected it. They may not like it.

My Biotech Life:

I like the idea of PLoS as a startup that is keeping to it’s original goal while trying to work out the kinks regarding the open-access publishing model. And I agree, they have produced high quality peer reviewed science.

Stevan Harnad:

In other words, while appearing to be doing OA a service, this Nature policy is actually doing Nature a service and only giving OA the minimal due that is already inherent in the NIH and kindred mandates.

Anders Norgaard:

One perspective which has been overlooked a bit, as far as I can tell is that Nature has managed to frame the debate. Intentionally or not.
The framing can be summarized as “the problem is that top tier journals can’t be profitable as open access – author pays, in competition with Toll-Access journals”. This framing is advantageous to Nature as it implies that “the author-pays principle must generate all revenue for OA journals – subsidies are not ok”. Equally advantageous is it when “top-tier journal” is defined not only as “high rejection-rates” but also “high overheads”. Nature has an interest in making the two things seem inseparable.
For society and everyone who is not Nature (or other Toll-Access, high overhead journals) the framing does not make sense. The debate is part of a broader debate of the future of scientific publishing. And it is unreasonable to assume that a future of efficient digital publishing must be hobbled to serve to needs of businesses adapted to the past of high cost of paper distribution. Or that it must be measured by the same criteria of success (high profit from monopoly priviledges) as old businesses.

Georgia Harper:

Well, I will leave it to all of you to figure out if you have sufficient “rights” to read the article itself, but do go read the comments. Too bad about whatever data supports the whole conversation. We pobrecitos don’t have access to that, just to the rants about the results. Ah, transitions.
Of course, I could spend some of my very limited time today clicking my way through the variety of screens I must click through to get to my library’s walled garden where I suspect this article is cached away. Maybe it’s worth it. Maybe not. Today it’s not. It’s summer, I’m on vacation. Only minimally attentive to tedious things like journal article search interfaces. And why is it that publishers do this to libraries? Oh, yes, I’m so sure they have their very good reasons. And I have mine for ignoring authors and their writings whose publishers make their work hard to find and read. So much to read, watch, listen to. So little time. There’s the basic fundamental of Open Access. The business models will follow.

David Crotty:

It’s certainly good news that PLOS has found a way to cover their costs and continue the noble experiment they’ve undertaken. I’m not sure how good the news is for other publishers interested in experimenting with open access and author-pays models. Publishers and societies may not be able to drum up the large amount of donation funding needed to keep a highly selective journal in the black. They may not be all that interested in running streamlined, higher-volume journals to cover costs. It’s also very unclear how many of these type journals the market will bear-if every publisher starts one, will there be enough material/interest to continue to cover costs in other ventures?

Corie Lok:

Reading through some of the comments and blog posts about the article reminded me of a real-live discussion I sat in on at Scibarcamp back in March in Toronto. One senior, high-profile physicist at the event said how disillusioned he was with the science blogosphere. He said he’s been really turned off by the nastiness and divisiveness he’s seen. He said the science blogosphere has not fulfilled its promise of being a forum for serious scientific discussion. (Not to say that all blog posts and comments about the Nature article were mud-slinging; I saw some very good discussions. And not to say that all science bloggers engage in ranting. I’ve seen plenty of blogs that do engage in high-quality conversations but I’m sure many bloggers have stories to tell about the nastiness they’ve read or experienced online.)
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.
But still, I wonder how many other scientists out there would agree with this physicist? If there is a critical number of them out there agreeing with him, what does this mean for science blogging?

Charles W. Bailey, Jr.:

What the Nature article misses is that the scholarly evaluation of PLoS ONE articles does not end with the initial screening review for compliance with the stated Criteria for Publication. Rather, it begins there. PLoS ONE is using a radically different model of peer review than traditional journals. Whether it is a success or failure is not primarily determined by how many articles it publishes, but by the effectiveness of its post-publication review system in assessing the value of those papers.
If PLoS can reduce costs in what the article terms its “second-tier community journals” by using larger academic editorial staffs, there does not appear to be anything intrinsically wrong with that. To the contrary. The issue is not the editorial strategy, rather it’s whether the author fees are unjustifiably high in relation to journal costs and whether the excess profit is being siphoned off to support other publications. Although comparative author fee data is given in the article, there is not enough economic evidence presented in the article to make any informed judgment on the matter.
Regarding grant support, I presume that Jerram understands the issue better than outsiders, and, if he believes that PLos can become self-sustaining in a few years, then there is no reason to doubt it, barring unforeseen circumstances.

Annalise Paaby:

Perhaps I am biased–perhaps my work is generally free of serious methodological flaws–but my experience revealed the PLoS One editorial process to be the most rigorous of the three journals to which I sent my first paper.
It was disappointing to get rejected twice before publishing in PLoS One. But the real frustration was that of the five reviews from the first two journals, three of the referees did not understand the work. (One was downright insulting.) The two reviews from PLoS One, however, were thorough, detailed and clearly by researchers who understood the work. A reflection of an editorial process of high integrity, certainly, and not an unusual one.

ob:

Da kann man als Wettbewerber wirklich neidisch werden und als Bibliothek durchdrehen… War Nature nicht auch derjenige Verlag, der seine kürzlichen exorbitanten Preisanstiege (40% in einem Jahr, gnädig verteilt auf 2-3 Jahre für Konsortien) mit dem Argument verteidigte, man wäre mit zu niedrigen Preisen am Markt eingestiegen und müßte diese nun nach oben anpassen, weil man sein Marktziel (sprich Profitmarge) nicht erreicht hätte. Oh, könnte ich nur mit meinem Dekan auch mal so sprechen!! Aber dafür muß man wohl 3 Jahre auf eine Sprachschule für Marketingdeutsch…

Joseph J. Esposito:

Declan Butler’s recent piece on the PLOS business model was cited
on this list. I think Butler is attempting to hold PLOS to a
standard that few publishers attain, including Butler’s own
employers at the Nature Publishing Group.
What PLOS is doing (whether you like the practice or not) is
simple brand extension. There are highly presitigious and
selective PLOS publications, whose aura is being transferred to a
new program, PLOS One, which has a different editorial
methodology. We are all familiar with this; most members of this
list work with Microsoft Windows, Microsoft Internet Explorer,
Microsoft Word, and Microsoft Excel; renegades may own an iMac,
iPod, and and iPhone. The Nature Publishing Group has been among
the most aggressive STM publishers in extending its brand to new
publications. Indeed, a rival of Nature wryly remarked to me
(enviously, perhaps?) that Nature had put its name onto so many
publications that he was awaiting the announcement for “Nature
Nature.”
PLOS is not above criticism, but let’s not insist that an OA
service compete with toll-access publishers on what are truly
spurious grounds.

Tobias Maier:

In einem Nature Artikel der vergangenen Woche wurde der Rivale PLoS hart angegangen. Nature behauptet, PLoS (sieben unterschiedliche Journals werden von PLoS ausschliesslich open-access verlegt) würde ihr Konzept damit finanzieren, dass sie Artikel niederer Qualität ohne ausreichenden peer-review Prozess für einige Magazine akzeptieren, um mit Hilfe der so eingesammelten Publicationfees ihre Flagship – Journals PLoS Biology und PLoS Medicine, finanzieren zu können.
Einen guten Überblick über die Blogreaktionen zu der Debatte auf der ScienceBlogs.com Schwesterseite bietet Bora Zivkovic, Online Community Manager des kritisierten PLoS Jounrnals, hier auf seinem Blog around the Clock.
Mein Kollege Anders Norgaard liest viel auf ScieceBlogs.com, und hat einen besseren Überblick über die Debatte als ich. Er findet, dass Nature mit der Debatte eigentlich aussagen möchte, dass es für profitable high-profile Journals nur ein gutes Konzept gibt, nämlich das von Nature. Er ist damit nicht einverstanden:

Juan Carlos Lopez:

First, having previously commented on open-access publishing in this forum, I explicitly want to distance my journal and myself from any pejorative descriptors that might have been applied to the science published by the PLoS journals. I’m not an advocate of open access, but the quality of what open-access journals publish has never been an issue I have cared to discuss in public.

ClockQuotes

All brave men love; for he only is brave who has affections to fight for, whether in the daily battle of life, or in physical contests.
– Nathaniel Hawthorne

Today’s carnivals

The 25th edition of the Festival of the Trees is up on Earth, Wind and Water
The 178th Carnival of Education is up on An (aspiring) Educator’s Blog
The 131st Carnival of Homeschooling is up on Beverly’s Homeschooling Blog
And don’t forget to submit your entries to the inaugural edition of The Giant’s Shoulders

Innovation 2008: 14 questions for Presidential Candidates regarding Science and Technology

Check this out, from the ScienceDebate 2008 team: 14 Questions the candidates for President should answer about Science & America’s Future.
Compare to my questions (1, 2, 3, 4, 5, 6).

If you thought that OA-evangelism is an intellectual game – think again!

Yes, I know, Gavin is a dear colleague and a friend, but his latest article, Excluding the poor from accessing biomedical literature: A rights violation that impedes global health, is just brilliant. A must-read for all concerned with healthcare, medical information and OA publishing:

In this article, I take a rights-based view of this current crisis of restricted access to the results of scientific and medical research. Such research is conducted in the interests of the public, and yet the results are largely kept out of the public domain by traditional corporate publishers who own them, subject them to extremely tight copyright restrictions, and sell them in a market worth about US$5 billion. The results of biomedical research have unfortunately been privatized, monopolized, and concentrated in the hands of a tiny number of multinational corporations.
This article considers how exclusion from accessing the biomedical research literature harms global public health. I argue that this literature should be considered a global public good and base my argument upon long-standing and recent international declarations that enshrine access to scientific and medical knowledge as a human right. I present an emerging alternative publishing model, called open access, and argue that this model is a more socially responsive and equitable approach to knowledge dissemination. I situate open access publishing within a broader movement that has emerged in the digital era to create a public “knowledge commons,” which can play a crucial role in supporting an informed citizenry in its efforts to promote human rights. Finally, I propose that Health and Human Rights itself, as an open access journal, could help to catalyze the creation of an online “health and human rights commons.”

My Picks From ScienceDaily

Malagasy Chameleon Spends Most Of Its Short Life In An Egg:

There is a newly discovered life history among the 28,300 species of known tetrapods, or four-legged animals with backbones. A chameleon from arid southwestern Madagascar spends up to three-quarters of its life in an egg. Even more unusual, life after hatching is a mere 4 to 5 months. No other known four-legged animal has such a rapid growth rate and such a short life span.

Newcomer In Early Eurafrican Population?:

A complete mandible of Homo erectus was discovered at the Thomas I quarry in Casablanca by a French-Moroccan team co-led by Jean-Paul Raynal, CNRS senior researcher at the PACEA laboratory (CNRS/Université Bordeaux 1/ Ministry of Culture and Communication). This mandible is the oldest human fossil uncovered from scientific excavations in Morocco. The discovery will help better define northern Africa’s possible role in first populating southern Europe.

New Evidence That Ancient Choanoflagellates’ Form Evolutionary Link Between Single-celled And Multi-celled Organisms:

What do humans and single-celled choanoflagellates have in common? More than you’d think. New research into the choanoflagellate genome shows these ancient organisms have similar levels of proteins that cells in more complex organisms, including humans, use to communicate with each other.

An Impossible Coexistence: Transgenic And Organic Agriculture:

The cultivation of genetically modified maize has caused a drastic reduction in organic cultivation of this grain and is making their coexistence practically impossible. This is the main conclusion reached in one of the first field studies in Europe carried out by a researcher of the Institute of Environmental Science and Technology of the Universitat Autònoma de Barcelona, who has analysed the situation in Catalonia and Aragon, Europe’s main producers of transgenic foods.

Eating Broccoli May Keep Prostate Cancer Away, Study Suggests:

Eating one or more portions of broccoli every week can reduce the risk of prostate cancer, and the risk of localised cancer becoming more aggressive.

Worms Do Calculus To Find Meals Or Avoid Unpleasantness:

Thanks to salt and hot chili peppers, researchers have found a calculus-computing center that tells a roundworm to go forward toward dinner or turn to broaden the search. It’s a computational mechanism, they say, that is similar to what drives hungry college students to a pizza.

Mammoth Hunting: does the memory still survive in the Native American oral folklore?

Archy tackles that question expertly. He’s on a roll these days! And this is the mammoth story, so of course, his blog is the place to go for such answers.

New and Exciting in PLoS ONE

There are 62 articles published this week in PLoS ONE. There are also two Journal Clubs going on right now – here and here. Here are some of my picks for the week – go read, rate, comment and send trackbacks:
A Comparison of Wood Density between Classical Cremonese and Modern Violins:

Classical violins created by Cremonese masters, such as Antonio Stradivari and Giuseppe Guarneri Del Gesu, have become the benchmark to which the sound of all violins are compared in terms of their abilities of expressiveness and projection. By general consensus, no luthier since that time has been able to replicate the sound quality of these classical instruments. The vibration and sound radiation characteristics of a violin are determined by an instrument’s geometry and the material properties of the wood. New test methods allow the non-destructive examination of one of the key material properties, the wood density, at the growth ring level of detail. The densities of five classical and eight modern violins were compared, using computed tomography and specially developed image-processing software. No significant differences were found between the median densities of the modern and the antique violins, however the density difference between wood grains of early and late growth was significantly smaller in the classical Cremonese violins compared with modern violins, in both the top (Spruce) and back (Maple) plates (p = 0.028 and 0.008, respectively). The mean density differential (SE) of the top plates of the modern and classical violins was 274 (26.6) and 183 (11.7) gram/liter. For the back plates, the values were 128 (2.6) and 115 (2.0) gram/liter. These differences in density differentials may reflect similar changes in stiffness distributions, which could directly impact vibrational efficacy or indirectly modify sound radiation via altered damping characteristics. Either of these mechanisms may help explain the acoustical differences between the classical and modern violins.

Children’s Perceptions of Rainforest Biodiversity: Which Animals Have the Lion’s Share of Environmental Awareness?:

Globally, natural ecosystems are being lost to agricultural land at an unprecedented rate. This land-use often results in significant reductions in abundance and diversity of the flora and fauna as well as alterations in their composition. Despite this, there is little public perception of which taxa are most important in terms of their total biomass, biodiversity or the ecosystem services they perform. Such awareness is important for conservation, as without appreciation of their value and conservation status, species are unlikely to receive adequate conservation protection. We investigated children’s perceptions of rainforest biodiversity by asking primary-age children, visiting the University Museum of Zoology, Cambridge to draw their ideal rainforest. By recording the frequency at which children drew different climatic, structural, vegetative and faunal components of the rainforest, we were able to quantify children’s understanding of a rainforest environment. We investigated children’s perceptions of rainforest biodiversity by comparing the relative numbers of the taxa drawn with the actual contributions made by these taxa to total rainforest biomass and global biodiversity. We found that children have a sophisticated view of the rainforest, incorporating many habitat features and a diverse range of animals. However, some taxa were over-represented (particularly mammals, birds and reptiles) and others under-represented (particularly insects and annelids) relative to their contribution to total biomass and species richness. Scientists and naturalists must continue to emphasise the diversity and functional importance of lesser-known taxa through public communication and outdoor events to aid invertebrate conservation and to ensure that future generations are inspired to become naturalists themselves.

Relationship between Quality and Editorial Leadership of Biomedical Research Journals: A Comparative Study of Italian and UK Journals:

The quality of biomedical reporting is guided by statements of several organizations. Although not all journals adhere to these guidelines, those that do demonstrate “editorial leadership” in their author community. To investigate a possible relationship between editorial leadership and journal quality, research journals from two European countries, one Anglophone and one non-Anglophone, were studied and compared. Quality was measured on a panel of bibliometric parameters while editorial leadership was evaluated from journals’ instructions to authors. The study considered all 76 Italian journals indexed in Medline and 76 randomly chosen UK journals; only journals both edited and published in these countries were studied. Compared to UK journals, Italian journals published fewer papers (median, 60 vs. 93; p = 0.006), less often had online archives (43 vs. 74; p<0.001) and had lower median values of impact factor (1.2 vs. 2.7, p<0.001) and SCImago journal rank (0.09 vs. 0.25, p<0.001). Regarding editorial leadership, Italian journals less frequently required manuscripts to specify competing interests (p<0.001), authors' contributions (p = 0.005), funding (p<0.001), informed consent (p<0.001), ethics committee review (p<0.001). No Italian journal adhered to COPE or the CONSORT and QUOROM statements nor required clinical trial registration, while these characteristics were observed in 15%-43% of UK journals (p<0.001). At multiple regression, editorial leadership predicted 37.1%-49.9% of the variance in journal quality defined by citation statistics (p<0.0001); confounding variables inherent to a cross-cultural comparison had a relatively small contribution, explaining an additional 6.2%-13.8% of the variance. Journals from Italy scored worse for quality and editorial leadership than did their UK counterparts. Editorial leadership predicted quality for the entire set of journals. Greater appreciation of international initiatives to improve biomedical reporting may help low-quality journals achieve higher status.

An Automated Phylogenetic Tree-Based Small Subunit rRNA Taxonomy and Alignment Pipeline (STAP) (Jonathan Eisen explains):

Comparative analysis of small-subunit ribosomal RNA (ss-rRNA) gene sequences forms the basis for much of what we know about the phylogenetic diversity of both cultured and uncultured microorganisms. As sequencing costs continue to decline and throughput increases, sequences of ss-rRNA genes are being obtained at an ever-increasing rate. This increasing flow of data has opened many new windows into microbial diversity and evolution, and at the same time has created significant methodological challenges. Those processes which commonly require time-consuming human intervention, such as the preparation of multiple sequence alignments, simply cannot keep up with the flood of incoming data. Fully automated methods of analysis are needed. Notably, existing automated methods avoid one or more steps that, though computationally costly or difficult, we consider to be important. In particular, we regard both the building of multiple sequence alignments and the performance of high quality phylogenetic analysis to be necessary. We describe here our fully-automated ss-rRNA taxonomy and alignment pipeline (STAP). It generates both high-quality multiple sequence alignments and phylogenetic trees, and thus can be used for multiple purposes including phylogenetically-based taxonomic assignments and analysis of species diversity in environmental samples. The pipeline combines publicly-available packages (PHYML, BLASTN and CLUSTALW) with our automatic alignment, masking, and tree-parsing programs. Most importantly, this automated process yields results comparable to those achievable by manual analysis, yet offers speed and capacity that are unattainable by manual efforts.

A Microsatellite Guided Insight into the Genetic Status of Adi, an Isolated Hunting-Gathering Tribe of Northeast India:

Tibeto-Burman populations of India provide an insight into the peopling of India and aid in understanding their genetic relationship with populations of East, South and Southeast Asia. The study investigates the genetic status of one such Tibeto-Burman group, Adi of Arunachal Pradesh based on 15 autosomal microsatellite markers. Further the study examines, based on 9 common microsatellite loci, the genetic relationship of Adi with 16 other Tibeto-Burman speakers of India and 28 neighboring populations of East and Southeast Asia. Overall, the results support the recent formation of the Adi sub-tribes from a putative ancestral group and reveal that geographic contiguity is a major influencing factor of the genetic affinity among the Tibeto-Burman populations of India.

Attitudes Toward Consumption and Conservation of Tigers in China:

A heated debate has recently emerged between tiger farmers and conservationists about the potential consequences of lifting the ban on trade in farmed tiger products in China. This debate has caused unfounded speculation about the extent of the potential market for tiger products. To fill this knowledge gap, we surveyed 1880 residents from a total of six Chinese cities to understand Urban Chinese tiger consumption behavior, knowledge of trade issues and attitudes towards tiger conservation. We found that 43% of respondents had consumed some product alleged to contain tiger parts. Within this user-group, 71% said that they preferred wild products over farmed ones. The two predominant products used were tiger bone plasters (38%) and tiger bone wine (6.4%). 88% of respondents knew that it was illegal to buy or sell tiger products, and 93% agreed that a ban in trade of tiger parts was necessary to conserve wild tigers. These results indicate that while Urban Chinese people are generally supportive of tiger conservation, there is a huge residual demand for tiger products that could resurge if the ban on trade in tiger parts is lifted in China. We suspect that the current supply of the market is predominantly met by fakes or substitutes branded as tiger medicines, but not listing tiger as an ingredient. We suggest that the Traditional Chinese Medicine community should consider re-branding these products as bone-healing medicines in order to reduce the residual demand for real tiger parts over the long-term. The lifting of the current ban on trade in farmed tiger parts may cause a surge in demand for wild tiger parts that consumers say are better. Because of the low input costs associated with poaching, wild-sourced parts would consistently undercut the prices of farmed tigers that could easily be laundered on a legal market. We therefore recommend that the Chinese authorities maintain the ban on trade in tiger parts, and work to improve the enforcement of the existing ban.

Trait-Like Brain Activity during Adolescence Predicts Anxious Temperament in Primates:

Early theorists (Freud and Darwin) speculated that extremely shy children, or those with anxious temperament, were likely to have anxiety problems as adults. More recent studies demonstrate that these children have heightened responses to potentially threatening situations reacting with intense defensive responses that are characterized by behavioral inhibition (BI) (inhibited motor behavior and decreased vocalizations) and physiological arousal. Confirming the earlier impressions, data now demonstrate that children with this disposition are at increased risk to develop anxiety, depression, and comorbid substance abuse. Additional key features of anxious temperament are that it appears at a young age, it is a stable characteristic of individuals, and even in non-threatening environments it is associated with increased psychic anxiety and somatic tension. To understand the neural underpinnings of anxious temperament, we performed imaging studies with 18-fluoro-deoxyglucose (FDG) high-resolution Positron Emission Tomography (PET) in young rhesus monkeys. Rhesus monkeys were used because they provide a well validated model of anxious temperament for studies that cannot be performed in human children. Imaging the same animal in stressful and secure contexts, we examined the relation between regional metabolic brain activity and a trait-like measure of anxious temperament that encompasses measures of BI and pituitary-adrenal reactivity. Regardless of context, results demonstrated a trait-like pattern of brain activity (amygdala, bed nucleus of stria terminalis, hippocampus, and periaqueductal gray) that is predictive of individual phenotypic differences. Importantly, individuals with extreme anxious temperament also displayed increased activity of this circuit when assessed in the security of their home environment. These findings suggest that increased activity of this circuit early in life mediates the childhood temperamental risk to develop anxiety and depression. In addition, the findings provide an explanation for why individuals with anxious temperament have difficulty relaxing in environments that others perceive as non-stressful.v

Maternal Feeding Controls Fetal Biological Clock:

It is widely accepted that circadian physiological rhythms of the fetus are affected by oscillators in the maternal brain that are coupled to the environmental light-dark (LD) cycle. To study the link between fetal and maternal biological clocks, we investigated the effects of cycles of maternal food availability on the rhythms of Per1 gene expression in the fetal suprachiasmatic nucleus (SCN) and liver using a transgenic rat model whose tissues express luciferase in vitro. Although the maternal SCN remained phase-locked to the LD cycle, maternal restricted feeding phase-advanced the fetal SCN and liver by 5 and 7 hours respectively within the 22-day pregnancy. Our results demonstrate that maternal feeding entrains the fetal SCN and liver independently of both the maternal SCN and the LD cycle. This indicates that maternal-feeding signals can be more influential for the fetal SCN and particular organ oscillators than hormonal signals controlled by the maternal SCN, suggesting the importance of a regular maternal feeding schedule for appropriate fetal molecular clockwork during pregnancy.

Avoiding Costly Conservation Mistakes: The Importance of Defining Actions and Costs in Spatial Priority Setting:

The typical mandate in conservation planning is to identify areas that represent biodiversity targets within the smallest possible area of land or sea, despite the fact that area may be a poor surrogate for the cost of many conservation actions. It is also common for priorities for conservation investment to be identified without regard to the particular conservation action that will be implemented. This demonstrates inadequate problem specification and may lead to inefficiency: the cost of alternative conservation actions can differ throughout a landscape, and may result in dissimilar conservation priorities. We investigate the importance of formulating conservation planning problems with objectives and cost data that relate to specific conservation actions. We identify priority areas in Australia for two alternative conservation actions: land acquisition and stewardship. Our analyses show that using the cost surrogate that most closely reflects the planned conservation action can cut the cost of achieving our biodiversity goals by half. We highlight spatial differences in relative priorities for land acquisition and stewardship in Australia, and provide a simple approach for determining which action should be undertaken where. Our study shows that a poorly posed conservation problem that fails to pre-specify the planned conservation action and incorporate cost a priori can lead to expensive mistakes. We can be more efficient in achieving conservation goals by clearly specifying our conservation objective and parameterising the problem with economic data that reflects this objective.

Mating with Stressed Males Increases the Fitness of Ant Queens:

According to sexual conflict theory, males can increase their own fitness by transferring substances during copulation that increase the short-term fecundity of their mating partners at the cost of the future life expectancy and re-mating capability of the latter. In contrast, sexual cooperation is expected in social insects. Mating indeed positively affects life span and fecundity of young queens of the male-polymorphic ant Cardiocondyla obscurior, even though males neither provide nuptial gifts nor any other care but leave their mates immediately after copulation and die shortly thereafter. Here, we show that mating with winged disperser males has a significantly stronger impact on life span and reproductive success of young queens of C. obscurior than mating with wingless fighter males. Winged males are reared mostly under stressful environmental conditions, which force young queens to disperse and found their own societies independently. In contrast, queens that mate with wingless males under favourable conditions usually start reproducing in the safety of the established maternal nest. Our study suggests that males of C. obscurior have evolved mechanisms to posthumously assist young queens during colony founding under adverse ecological conditions.

Open access and the last-mile problem for knowledge

Peter Suber, a thoughtful essay, as always:

In telecommunications the “last-mile problem” is the problem of connecting individual homes and businesses to the fat pipes connecting cities. Because individual homes and businesses are in different locations, hooking up each one individually is expensive and difficult. The term is now used in just about every industry in which reaching actual customers is more difficult than reaching some location, like a store or warehouse, close to customers.
We’re facing a last-mile problem for knowledge. We’re pretty good at doing research, writing it up, vetting it, publishing it, and getting it to locations (physical libraries and web sites) close to users. We could be better at all those things, but any problems we encounter along the way are early- or mid-course problems. The last-mile problem is the one at the end of the process: making individualized connections to all the individual users who need to read that research.
The last-mile problem for knowledge is not new. Indeed, for all of human history until recently it has been inseparable from knowledge itself and all our technologies for sharing it. It’s only of interest today because the internet and OA give us unprecedented means for solving it, or at least for closing the gap significantly.
The problem is not that librarians “warehouse” knowledge in the pejorative sense of that term. On the contrary, they go out of their way to help users find and retrieve what the library has to offer, and often do the same for much beyond the library as well. The problem is to make individualized connections between knowledge, wherever it lies, and users, wherever they are. Even a well-stocked and well-organized library staffed by well-trained librarians can only solve a subset of that problem and connect a subset of users with a subset of knowledge.

Read the whole thing – it is excellent and thought-provoking.

Video Archive from Workshop on New Communication Channels for Biology

All the usual suspects were there (I was supposed to go but I could not possibly fit it into my calendar) and now you can watch all the videos from all the presenters – just click here and choose:

San Diego, CA, June 30, 2008 — More than 20 experts presented their views on the future and use of new media and communications in the biological and other sciences. The New Communications Channels in Biology Workshop at UC San Diego was organized by the Calit2-based Community Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis (CAMERA) with funding from the Gordon and Betty Moore Foundation. Talks ranged across topics in e-science communications, including science blogs, semantic Web tools, authenticated wiki-like research discussions and analysis, as well as the potential to formalize community-level contributions. Calit2 speakers included CAMERA executive director Paul Gilna and the developer of the Research Intelligence portal, Jerry Sheehan. Calit2 offered a live webcast of the workshop; the individual talks are now archived for on-demand viewing

ClockQuotes

You do not need the bible to justify love, but no better tool has been invented to justify hate.
– Richard A. Weatherwax

Blogrolling for today

Bad Astronomy


The Loom


Discoblog


80 beats


Better Planet

Kevin is in China again

For those of you who remember the adventures of Kevin in China from two years ago, he is there again, doing his herpetology fieldwork and reporting regularly. Instead of this blog, he is posting his adventures and pictures on a herp forum – probably the best way to follow is to check out his posts there.

My Picks From ScienceDaily

New Map IDs The Core Of The Human Brain:

An international team of researchers has created the first complete high-resolution map of how millions of neural fibers in the human cerebral cortex — the outer layer of the brain responsible for higher level thinking — connect and communicate. Their groundbreaking work identified a single network core, or hub, that may be key to the workings of both hemispheres of the brain.

Neuroscience Teaching Using Multi-Media:

The National Science Foundation (NSF) has awarded Williams College $228,987 to redesign the way introductory science of the brain is taught.

New Study Is First To Look Beyond General Attitudes About End-Of-Life Options And Ask Older People What They Would Do:

It used to be that when you had a life-threatening illness you waited it out. Nowadays you have options. A new study in the just-released March issue of Psychology and Aging, published by the American Psychological Association (APA), looks at the factors that influence older adults end-of-life decisions.

The Suspect Confessed. Case Closed? Not Necessarily, Researcher Says:

Even Modern Non-Violent Interrogation Techniques Can Produce False Confessions.

United States Has Highest Level Of Illegal Cocaine And Cannabis Use:

A survey of 17 countries has found that despite its punitive drug policies the United States has the highest levels of illegal cocaine and cannabis use. The study, by Louisa Degenhardt (University of New South Wales, Sydney, Australia) and colleagues, is based on the World Health Organization’s Composite International Diagnostic Interview (CIDI).

New carnival – ‘Hourglass’: biology of aging

Chris Patil wrote:

Ouroboros’ second anniversary is coming up this weekend, and I thought it might be nice to do something special to commemorate the occasion.
There’s enough good science blogging about the biology of aging that the community deserves its own monthly carnival (along the lines of the general-biology carnival Tangled Bank, or the neuroscience carnival Encephalon, both of which we’ve hosted here before). So let’s start one. I thought long and hard about names and settled on “Hourglass,” which is topical enough to be appropriate, but general to be inclusive.
I’ll host the first installation next Tuesday, July 8th, and organize the hosting arrangements thereafter — sometime after the first issue I’ll create a page here devoted to past, current and future hosts.
Topics of posts should have something to do with the biology of aging, broadly speaking — including fundamental research in biogerontology, age-related disease, ideas about life extension technologies, your personal experience with calorie restriction, maybe even something about the sociological implications of increased longevity. Opinions expressed are not necessarily those of the management, so feel free to subvert the dominant paradigm. If in doubt, submit anyway. About the only sorts of things I’m going to turn away are quackery or promotions of a commercial product. So, no growth hormone commercials or glowing reviews of your own book, please. 🙂
In terms of original publication date — for future issues we’ll probably want to limit contributions to articles published within the last month. Since this is the first issue, however anything published prior to July 8 (i.e., anything ever published) would be great.
So if you’re a biogerontology blogger, a science blogger with one great post about aging, or anyone else who wants to make a relevant submission to Hourglass I, please email me. (Do the same if you’d like to host a future Hourglass, as well.) With your submission, I would also welcome any appropriate images that you’d like to accompany your submission — see here for an example of what I’m talking about.

Natural Selection anniversary podcast

You can listen to the short and sweet Takeaway podcast:
A look at Charles Darwin’s legacy as the theory of evolution turns 150:

One hundred and fifty years ago, Charles Darwin’s theories of evolution and natural selection were presented at the Linnean Society of London. A year and a half later, Darwin published what is now a monumental work: “The Origin of the Species.” The Takeaway looks at Darwin’s legacy and the continuing debate surrounding evolution.

By John Hockenberry and Adaora Udoji.

Harvard Summer Course on Circadian Biology

Came to my e-mail inbox:

The Harvard Summer School is pleased to announce the addition of a
three-day special seminar for teachers in the sciences. Based on the
well-known “Chautauqua Seminars” model, there is no cost to participants
other than a $50 registration fee. The course is taught by distinguished
Harvard faculty and provides an opportunity for invited scholars to share
new knowledge, concepts, and techniques directly with teachers in ways
which are immediately beneficial to their teaching. The primary aim of
this rejuvenating session is to enable teachers to keep their teaching
current with respect to both content and pedagogy.
This course will be of interest to graduate students considering teaching,
high school teachers, and college professors in the sciences.
THE COURSE
Circadian Biology: From Clock Genes and Cellular Rhythms to Sleep Regulation
August 20 through 22, 2008
With J. Woodland Hastings, professor of molecular and cellular biology at
Harvard University; and Steven W. Lockley, assistant professor at Harvard
Medical School
Application should be made as early as possible and will be considered on
a space-available basis until the start of each course.
For more information: http://www.summer.harvard.edu/2008/news/seminars.jsp

Science Blogging 2008: London

Finallogo.jpgConference Programme for the Science Blogging 2008: London is now online. I wish I could afford to go – it looks delicious! I hope everyone there takes and posts a lot of pictures, videos, podcasts and blog-posts so we can all vicariously participate.

My Picks From ScienceDaily

Penguins Setting Off Sirens Over Health Of World’s Oceans:

Like the proverbial canary in the coal mine, penguins are sounding the alarm for potentially catastrophic changes in the world’s oceans, and the culprit isn’t only climate change, says a University of Washington conservation biologist.

Evolution Of Fruit Size In Tomato:

Domesticated tomatoes can be up to 1000 times larger than their wild relatives. How did they get so big?

Carbon Hoofprint: Cows Supplemented With RbST Reduce Agriculture’s Environmental Impact:

Milk goes green: Cows that receive recombinant Bovine Somatotropin (rbST) make more milk, all the while easing natural resource pressure and substantially reducing environmental impact, according to a Cornell University study.

Mate Choice In Plants:

Plants are very selective when it comes to choosing mates. Flowering plant pollination systems are clever devices for attracting pollinators like birds, ants, and insects, but there are also mechanisms for keeping out unwanted pollen. Some plants happily self-fertilize with their own pollen but others reject such pollen because of the deleterious effects of inbreeding. In these plants, their own pollen or that of close relatives is rejected if it lands on the female stigma.

Shiitake Mushrooms May Improve Human Immune Function, Especially If Grown On Old Oak Logs:

Shiitake (Lentinula edodes) mushrooms are good for you–and shiitake byproducts can be good for other crops.

Carl and Phil – Discovery bloggers!

You have probably already heard that Carl Zimmer has moved his blog The Loom from scienceblogs.com to a new URL (which, of course, you need to bookmark) of the new The Loom.
As he started his journalistic career at the Discover magazine, this was a hard invitation to reject. Discover has just started their own blog network. Carl is not the only celebrity to move – Phil Plait has also moved his Bad Astronomy blog from here to the new Bad Astronomy site.
As of now, it is impossible to see all of their blogs – there is no blogroll yet – but so far I could see Discoblog, 80 beats, Better Planet and Reality Base. We’ll be discovering the others, no doubt, over the next few weeks and months. It appears at the first glance that all the new bloggers there are already established science writers and journalists, no amateurs there like me 😉
Now, there is no hiding the fact that I am disappointed, as all the other SciBlings must be as well, to see Carl leave us. We SciBlings here have quite a sense of community and it is always sad to see one of us leave. And although scienceblogs.com is The Borg, difficult to displace from the top, I am guessing that the Overlords at Seed Media Group are watching with some trepidation as other organizations, journals and magazines start their own blog networks.
It is a Darwinian world, after all. But the term “Darwinian world” means more than just ‘nature red in tooth and claw’, with the biggest, meanest, most aggressive competitor hunting down, dismembering and eating all the others. Darwinian world is also the world of ecosystems in which various species find balance among themselves, cooperate, and strengthening of one population helps other populations get bigger and stronger.
The science blogging world is rapidly growing, but it is still small. WIRED has WIRED Science and Correlations. Nature has Nature Network with its blogs, as well as their ‘official’ Nature Blogs. There is ScientificBlogging.com. Scientific American has its own stable of blogs. TIME has a science blog. New York Times has a science blog. And there are now thousands of independent science blogs (and thousands of medical, nursing, healthcare, nature, birding and environmental blogs), some of which form informal blogging communities, circles or aggregators, find each other on blog carnivals, etc. Some send their posts on peer-reviewed research to the ResearchBlogging.org aggregator. And as we all get to know each other, we’ll link to each other more, increasing each others’ Google and Technorati rankings, and generally making science blogging more and more visible to the people who are not specifically looking for us, just searching the web randomly.
And while money-counters at each of the sponsoring organizations may be worried by all this competition, the overall growth of science blogging can only be a good thing. More networks – more chances for individuals with writing talent to get on and obtain a bigger soapbox. More visible science bloggers get, better it will be for the science popularization, science education and science-related policy around the world. More people get interested in science, more they will visit all of these blogs and networks and make their money-counters happy. It is a win-win situation. It is a Darwinian world in an ecological sense, not Spencerian, at least at this point in time.
So, you know I will continue reading Carl and Phil wherever they are. And I will now get to know their new co-bloggers as well. And it is all good. More the merrier.

Today’s carnivals

Berry Go Round #6 is up on Seeds Aside
Grand Rounds, Vol 4, No. 41 are up on The Covert Rationing Blog

ClockQuotes

A man can believe a considerable deal of rubbish, and yet go about his daily work in a rational and cheerful manner.
– Norman Douglas

Happy 150th Birthday to the Principle of Natural Selection!

On this day 150 years ago essays by Alfred Russel Wallace and Charles R. Darwin were read at the meeting of the Linnean Society in London. This was the first time in history that the idea of natural selection was presented to the world.
George Beccaloni and Wesley R. Elsberry wrote excellent pieces commemorating the anniversary.

A video about the new co-working space in Los Angeles


Hat-tip: Brian

Blogrolling for today

The Alternative Scientist


RepositoryMan


Bonnie J. M. Swoger


Marine Depot Blog


Curiosities of Biological Nomenclature


Gossamer Tapestry