Congratulations….

….to PZ Myers for getting a monthly writing gig in The Guardian. This is going to be fun to watch! The other three science writers they hired also sound interesting.

Jay Rosen on the Science Writers in New York Panel for Social Media

A must-watch video clip:

Science publishing also suffers from its curmudgeons

I’ve been having fun lately watching this guy struggle with the 21st century realities of scientific publishing which has a lot of parallels with the struggle that journalistic curmudgeons have – too steeped in the 20th century model to have the courage to think in a new way:
Socialism in science, or why Open Access may ultimately fail:

OK. So here’s the argument: Science needs to be made known through publishing. In order for science to be published, we need a team of people who will do the job of supervising the review process, editing, storing, and distributing bite-sized pieces of science called papers. These people need to be paid. Traditional closed access (CA) journals pay their employees from revenues they generate by selling their journal or the right to access it online. OA journals accomplish the same through selling space in their journal to people who want to publish in them. The main question is “Can OA journals publish high impact science, and also break even financially?”.

Good people, like Peter Suber and Stevan Harnad respond to some of those misconceptions in the comments. This is followed by the second post:
Socialism in science – Part 2 – I am wiser but not quite convinced:

Thus, it is with sadness that I must conclude I am still skeptical about the chances of the diverse OA initiatives to completely substitute for the current CA publishing models. Call me doubting Thomas, but I want to see proofs of the feasibility of profitable high-impact open access publishing before I jump on the bandwagon and sing songs in praise of OA. All I can see right now is a lot of unfounded hope and plenty of examples to the contrary. Convince me if you can.

Cameron Neylon tries to respond on his blog: What is the cost of peer review? Can we afford (not to have) high impact journals? (FriendFeed discussion here):

The question I would like to ask though is different. The Molecular Philosophy post skips the zeroth order questions. Can we afford high impact publications?

Now the third post is up (with a plea to me personally to post the links and send some traffic): Socialism in science – Part 3 – the Utopian system of post-publication peer review:

Last, but not least, I, and many people I know, like to peruse tables of contents of the most prestigious journals just to get the idea of what is currently at the very forefront of scientific discovery. The papers published in these journals are usually very good science and are a pleasure to read, whether they are directly related to my research, or not. I don’t want to give that pleasure up and get a scientific del.ic.ious-like sexiness contest instead.
OK. So I think I know why you guys don’t get it. You are good, noble people and you think, after a Greek philosopher or another, that if you show people the right thing to do, they will do it, just like you would. Well surprise, surprise: You are WRONG! Modern psychology makes it clear that people need a stick or a carrot to move anywhere and counting on their intrinsic goodness and noble instincts will get you nowhere. Sure, there will be people like yourselves who will do the RIGHT THING, but if you are set out to take over the world, you’d better have your stick and carrot business sorted out. As an unquestionable authority in the art of rant, Comrade PhysioProf, once said “Academic science is not a Care Bears fucking** tea party!”. I’ll Amen to that.

Sounds like journalistic curmugeons, doesn’t it: “But I like the smell of ink and paper! And you can’t live without us!”
Join the discussion on FriendFeed….

ACTION: Senators blocking key science nominations and need to hear from you today!

‘Holds’ on NOAA Administrator & Science Advisor Confirmations. Call Senators Now.:

The Washington Post is reporting that Senate votes to confirm Jane Lubchenco as NOAA Administrator and John Holdren as Science Advisor are currently being obstructed by a Democratic Senator. Quoting multiple unnamed sources, the Post says that New Jersey Democrat Robert Menendez has placed an “anonymous hold” on the nominations in order to try to gain leverage for some issues related to Cuba that he’s interested in.

The Latest Outrage: Holds on Holdren, Lubchencho:

The Washington Post (the news part) reports that the man who is now one of my senators, Robert Menendez of New Jersey, has placed a hold on the nominations of John Holdren and Jane Lubchencho, and won’t allow them to be voted on. Reportedly, “Menendez is using the holds as leverage to get Senate leaders’ attention for a matter related to Cuba rather than questioning the nominees’ credentials.”
What a complete outrage. These nominees need to work on climate change, science advising, and much else; they have no role in Cuba policy. Obama named them back in December–they should be in their offices by now. This is the most shallow form of politicking, and prevents the new administration from getting going.

Science in the Senate: It’s Not Just Menendez; Full Court Press Badly Needed.:

It appears that yesterday’s reports that New Jersey Democrat Robert Menendez was holding up the confirmation of both the Science Advisor and the NOAA administrator were not entirely correct. He may well be delaying these confirmations, but he’s apparently not the only one. CQ Politics is now reporting that the nominations are being held by multiple members of the Senate. Due to the holds, there is currently no confirmation vote scheduled on the floor.
This is a very reliable report. CQ Politics is not basing this on anonymous sources. They are quoting Commerce Committee Chairman John Rockefeller. Rockefeller’s committee has jurisdiction over the nominations, and held a confirmation hearing for both nominees last month. Given his position, it’s very unlikely that Rockefeller is wrong.

The above posts have contact information – let’s clog their phones, faxes and e-mail with calls until they unblock this!

Tim O’Reilly makes the argument for Open Publishing @ TOC 2009

From here:

Tim O’Reilly makes the argument for Open Publishing @ TOC 2009 from Open Publishing Lab @ RIT on Vimeo.

Drawing upon his real world experiences, Tim O’Reilly shares his thoughts on Open Publishing, why its a good idea, and how to make it work. This video was taken on the floor of the 2009 O’Reilly Tools of Change conference in New York City.
For more information on Tim O’Reilly (and why he knows what he’s talking about), head to oreilly.com/ or follow him at: twitter.com/timoreilly
You can read (and download) “What is Web 2.0” at:
oreillynet.com/pub/a/oreilly/tim/news/2005/09/30/what-is-web-20.html

My picks from ScienceDaily

First Fossil Brain: Shark Relative That Lived 300 Million Years Ago Yields Very Rare Specimen:

A 300-million-year-old brain of a relative of sharks and ratfish has been revealed by French and American scientists using synchrotron holotomography at the European Synchrotron Radiation Facility (ESRF). It is the first time that the soft tissue of such an old fossil brain has ever been found.

Evidence Appears To Show How And Where Brain’s Frontal Lobe Works:

A Brown University study of stroke victims has produced evidence that the frontal lobe of the human brain controls decision-making along a continuum from abstract to concrete, from front to back.

Physical Fitness Improves Spatial Memory, Increases Size Of Brain Structure:

When it comes to the hippocampus, a brain structure vital to certain types of memory, size matters. Numerous studies have shown that bigger is usually better. Now researchers have found that elderly adults who are more physically fit tend to have bigger hippocampi and better spatial memory than those who are less fit.

Sex Is In The Brain, Whether It Be Lack Of Sexual Interest Or Hypoactive Sexual Desire Disorder:

More than 40 percent of women ages 18-59 experience sexual dysfunction, with lack of sexual interest — hypoactive sexual desire disorder, or HSDD — being the most commonly reported complaint, according to medical researchers. While some question the validity of this diagnosis, a multidisciplinary team from the Stanford University School of Medicine is devoted to objective investigation of such problems.

Wave Of Brain Activity Linked To Anticipation Captured:

Neuroscientists at Georgetown University Medical Center have, for the first time, shown what brain activity looks like when someone anticipates an action or sensory input which soon follows.

New And Unexpected Mechanism Identified How The Brain Responds To Stress:

Chronic stress takes a physical and emotional toll on our bodies and scientists are working on piecing together a medical puzzle to understand how we respond to stress at the cellular level in the brain. Being able to quickly and successfully respond to stress is essential for survival.

How Microscopic Changes To Brain Cause Schizophrenic Behavior In Mice:

Disrupting the function of a key molecule in the brain leads to microscopic brain abnormalities and schizophrenia-like behavior in mice. These abnormalities are similar to those seen in the autopsied brains of people who diagnosed with schizophrenia in life, according to a team of scientists at the Scripps Research Institute.

Clock Quotes

There are two times in a man’s life when he should not speculate: when he can’t afford it, and when he can.
– Mark Twain

How to Use the Facebook Privacy Features – A Video Tutorial

…from Blog on the Side:

New and Exciting in PLoS ONE

There are 16 new articles in PLoS ONE today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites.
First, one for our new Palaeontology Collection:
Bird-Like Anatomy, Posture, and Behavior Revealed by an Early Jurassic Theropod Dinosaur Resting Trace:

Fossil tracks made by non-avian theropod dinosaurs commonly reflect the habitual bipedal stance retained in living birds. Only rarely-captured behaviors, such as crouching, might create impressions made by the hands. Such tracks provide valuable information concerning the often poorly understood functional morphology of the early theropod forelimb. Here we describe a well-preserved theropod trackway in a Lower Jurassic (~198 million-year-old) lacustrine beach sandstone in the Whitmore Point Member of the Moenave Formation in southwestern Utah. The trackway consists of prints of typical morphology, intermittent tail drags and, unusually, traces made by the animal resting on the substrate in a posture very similar to modern birds. The resting trace includes symmetrical pes impressions and well-defined impressions made by both hands, the tail, and the ischial callosity. The manus impressions corroborate that early theropods, like later birds, held their palms facing medially, in contrast to manus prints previously attributed to theropods that have forward-pointing digits. Both the symmetrical resting posture and the medially-facing palms therefore evolved by the Early Jurassic, much earlier in the theropod lineage than previously recognized, and may characterize all theropods.

An Indicator of the Impact of Climatic Change on European Bird Populations:

Rapid climatic change poses a threat to global biodiversity. There is extensive evidence that recent climatic change has affected animal and plant populations, but no indicators exist that summarise impacts over many species and large areas. We use data on long-term population trends of European birds to develop such an indicator. We find a significant relationship between interspecific variation in population trend and the change in potential range extent between the late 20th and late 21st centuries, forecasted by climatic envelope models. Our indicator measures divergence in population trend between bird species predicted by climatic envelope models to be favourably affected by climatic change and those adversely affected. The indicator shows a rapid increase in the past twenty years, coinciding with a period of rapid warming.

Serial Position Learning in Honeybees:

Learning of stimulus sequences is considered as a characteristic feature of episodic memory since it contains not only a particular item but also the experience of preceding and following events. In sensorimotor tasks resembling navigational performance, the serial order of objects is intimately connected with spatial order. Mammals and birds develop episodic(-like) memory in serial spatio-temporal tasks, and the honeybee learns spatio-temporal order when navigating between the nest and a food source. Here I examine the structure of the bees’ memory for a combined spatio-temporal task. I ask whether discrimination and generalization are based solely on simple forms of stimulus-reward learning or whether they require sequential configurations. Animals were trained to fly either left or right in a continuous T-maze. The correct choice was signaled by the sequence of colors (blue, yellow) at four positions in the access arm. If only one of the possible 4 signals is shown (either blue or yellow), the rank order of position salience is 1, 2 and 3 (numbered from T-junction). No learning is found if the signal appears at position 4. If two signals are shown, differences at positions 1 and 2 are learned best, those at position 3 at a low level, and those at position 4 not at all. If three or more signals are shown these results are corroborated. This salience rank order again appeared in transfer tests, but additional configural phenomena emerged. Most of the results can be explained with a simple model based on the assumption that the four positions are equipped with different salience scores and that these add up independently. However, deviations from the model are interpreted by assuming stimulus configuration of sequential patterns. It is concluded that, under the conditions chosen, bees rely most strongly on memories developed during simple forms of associative reward learning, but memories of configural serial patterns contribute, too.

Genetic Structure of the Polymorphic Metrosideros (Myrtaceae) Complex in the Hawaiian Islands Using Nuclear Microsatellite Data:

Five species of Metrosideros (Myrtaceae) are recognized in the Hawaiian Islands, including the widespread M. polymorpha, and are characterized by a multitude of distinctive, yet overlapping, habit, ecological, and morphological forms. It remains unclear, despite several previous studies, whether the morphological variation within Hawaiian Metrosideros is due to hybridization, genetic polymorphism, phenotypic plasticity, or some combination of these processes. The Hawaiian Metrosideros complex has become a model system to study ecology and evolution; however this is the first study to use microsatellite data for addressing inter-island patterns of variation from across the Hawaiian Islands. Ten nuclear microsatellite loci were genotyped from 143 individuals of Metrosideros. We took advantage of the bi-parental inheritance and rapid mutation rate of these data to examine the validity of the current taxonomy and to investigate whether Metrosideros plants from the same island are more genetically similar than plants that are morphologically similar. The Bayesian algorithm of the program STRUCTURE was used to define genetic groups within Hawaiian Metrosideros and the closely related taxon M. collina from the Marquesas and Austral Islands. Several standard and nested AMOVAs were conducted to test whether the genetic diversity is structured geographically or taxonomically. The results suggest that Hawaiian Metrosideros have dynamic gene flow, with genetic and morphological diversity structured not simply by geography or taxonomy, but as a result of parallel evolution on islands following rampant island-island dispersal, in addition to ancient chloroplast capture. Results also suggest that the current taxonomy requires major revisions in order to reflect the genetic structure revealed in the microsatellite data.

Big Genomes Facilitate the Comparative Identification of Regulatory Elements:

The identification of regulatory sequences in animal genomes remains a significant challenge. Comparative genomic methods that use patterns of evolutionary conservation to identify non-coding sequences with regulatory function have yielded many new vertebrate enhancers. However, these methods have not contributed significantly to the identification of regulatory sequences in sequenced invertebrate taxa. We demonstrate here that this differential success, which is often attributed to fundamental differences in the nature of vertebrate and invertebrate regulatory sequences, is instead primarily a product of the relatively small size of sequenced invertebrate genomes. We sequenced and compared loci involved in early embryonic patterning from four species of true fruit flies (family Tephritidae) that have genomes four to six times larger than those of Drosophila melanogaster. Unlike in Drosophila, where virtually all non-coding DNA is highly conserved, blocks of conserved non-coding sequence in tephritids are flanked by large stretches of poorly conserved sequence, similar to what is observed in vertebrate genomes. We tested the activities of nine conserved non-coding sequences flanking the even-skipped gene of the teprhitid Ceratis capitata in transgenic D. melanogaster embryos, six of which drove patterns that recapitulate those of known D. melanogaster enhancers. In contrast, none of the three non-conserved tephritid non-coding sequences that we tested drove expression in D. melanogaster embryos. Based on the landscape of non-coding conservation in tephritids, and our initial success in using conservation in tephritids to identify D. melanogaster regulatory sequences, we suggest that comparison of tephritid genomes may provide a systematic means to annotate the non-coding portion of the D. melanogaster genome. We also propose that large genomes be given more consideration in the selection of species for comparative genomics projects, to provide increased power to detect functional non-coding DNAs and to provide a less biased view of the evolution and function of animal genomes.

Lip-Reading Aids Word Recognition Most in Moderate Noise: A Bayesian Explanation Using High-Dimensional Feature Space:

Watching a speaker’s facial movements can dramatically enhance our ability to comprehend words, especially in noisy environments. From a general doctrine of combining information from different sensory modalities (the principle of inverse effectiveness), one would expect that the visual signals would be most effective at the highest levels of auditory noise. In contrast, we find, in accord with a recent paper, that visual information improves performance more at intermediate levels of auditory noise than at the highest levels, and we show that a novel visual stimulus containing only temporal information does the same. We present a Bayesian model of optimal cue integration that can explain these conflicts. In this model, words are regarded as points in a multidimensional space and word recognition is a probabilistic inference process. When the dimensionality of the feature space is low, the Bayesian model predicts inverse effectiveness; when the dimensionality is high, the enhancement is maximal at intermediate auditory noise levels. When the auditory and visual stimuli differ slightly in high noise, the model makes a counterintuitive prediction: as sound quality increases, the proportion of reported words corresponding to the visual stimulus should first increase and then decrease. We confirm this prediction in a behavioral experiment. We conclude that auditory-visual speech perception obeys the same notion of optimality previously observed only for simple multisensory stimuli.

And one from yesterday:
A Genome Wide Survey of SNP Variation Reveals the Genetic Structure of Sheep Breeds:

The genetic structure of sheep reflects their domestication and subsequent formation into discrete breeds. Understanding genetic structure is essential for achieving genetic improvement through genome-wide association studies, genomic selection and the dissection of quantitative traits. After identifying the first genome-wide set of SNP for sheep, we report on levels of genetic variability both within and between a diverse sample of ovine populations. Then, using cluster analysis and the partitioning of genetic variation, we demonstrate sheep are characterised by weak phylogeographic structure, overlapping genetic similarity and generally low differentiation which is consistent with their short evolutionary history. The degree of population substructure was, however, sufficient to cluster individuals based on geographic origin and known breed history. Specifically, African and Asian populations clustered separately from breeds of European origin sampled from Australia, New Zealand, Europe and North America. Furthermore, we demonstrate the presence of stratification within some, but not all, ovine breeds. The results emphasize that careful documentation of genetic structure will be an essential prerequisite when mapping the genetic basis of complex traits. Furthermore, the identification of a subset of SNP able to assign individuals into broad groupings demonstrates even a small panel of markers may be suitable for applications such as traceability.

Welcome the newest SciBling!

Kim Hannula of ‘All of My Faults Are Stress-Related ‘ has just moved today from her old blog to her new blog here on Scienceblogs.com. Is this the fourth geoblogger here? I think so.
Anyway, go and say Hello!

Lawrence Lessig on Open Access, Copyright and the nasty Conyers bill

John Conyers and Open Access:

Pushed by scientists everywhere, the NIH and other government agencies were increasingly exploring this obviously better model for spreading knowledge. Proprietary publishers, however, didn’t like it. And so rather than competing in the traditional way, they’ve adopted the increasingly Washington way of competition — they’ve gone to Congress to get a law to ban the business model they don’t like. If H.R. 801 is passed, the government can’t even experiment with supporting publishing models that assure that the people who have paid for the research can actually access it. Instead, if Conyers has his way, we’ll pay for the research twice.
The insanity in this proposal is brilliantly described by Jamie Boyle in this piece in the FT. But after you read his peace, you’ll be even more puzzled by this. For what possible reason could Conyers have for supporting a bill that 33 Nobel Prize Winners, and the current and former heads of the NIH say will actually hurt scientific research in America? More pointedly, what possible reason would a man from a district that insists on the government “Buying American” have for supporting a bill that basically subsidizes foreign publishers (for the biggest players in this publishing market are non-American firms, making HR 801 a kind of “Foreign Publishers Protection Act”)?
Well no one can know what goes on the heart or mind of Congressman Conyers. But what we do know is what MAPLight.org published yesterday: That the co-sponsors of this bill who sit on the Judiciary Committee received on average two-times the amount of money from publishing interests as those who haven’t co-sponsored the bill.

Lawrence Lessig Answers Your Questions on Copyright, Corruption, and Congress:

A decade’s work against IP extremism taught me two things: first, that people — teachers, parents, archivists, entrepreneurs, and many many artists — recognized the insanity in the current war; and second, that members of Congress didn’t even understand the issue. Some say that’s because they’re clueless. I don’t think that’s right. Instead, I believe Congress doesn’t get it because it cares less about making sense of copyright policy and more about raising dollars for political campaigns. When you recognize (as it took me way too long to recognize) that this is the same in a wide range of public policy contexts, including some of the most important (e.g., global warming), you realize the root cause here — corruption — is the problem that has to be addressed.
——————————–
I think the big story that the press doesn’t cover well is just how ordinary the corruption of government is. The serious problem, in my view, is not members using government to feather their own nests (though as one member put it to me, Congress has become a “farm league for K St.,” which is extremely serious). The most serious problem is instead good people living in a corrupt system. In my view, these “good people” have a moral obligation to change this corrupt system. They have a moral obligation to take a stand against it. We have seen enough to see just how much harm this system is producing. To stand by and let it continue — indeed, to encourage it to continue in its current form — is an act of extraordinary cowardice.

Lessig is urging people to take action here — joining his reform organization’s ‘donor strike’ to pressure Congress to fix the underlying corrupt system that resulted in Conyers doing what he did. After you sign, they’ll email you a number to call your representative in Congress (and Conyers) about this specific bill.

How to filter all that enormous scientific information

Chris Patil and Vivian Siegel wrote the first part of their thoughts on this problem, in Drinking from the firehose of scientific publishing:

The fundamental question is this: can the wisdom of crowds be exploited to post-filter the literature?
————–snip————
A lioness doesn’t bother eating individual blades of grass – she lets the antelopes do that drudgery, and then she eats the antelopes. It is similarly tempting to assign the post-filtering task to hordes of enthusiastic volunteers – intrepid, pajama-clad souls, armed only with keyboards and search engines, who would wade through the jungle of the literature and return to us only the choicest prizes. But this is a fantasy. For bloggers to provide an efficient and efficacious post-filter service, they would have to meet an imposing list of qualifications: sufficiently well-trained to make wise judgments about the papers most worthy of attention; sufficiently idle to have nothing better to do than read papers all day; free of idiosyncrasy or agenda that might bias their choices; and willing to work continuously for free. (In other words, there won’t be ‘hordes’.) Add to that the need for competition between bloggers -comparative prestige being the coin of that murky realm – and soon we’ll find ourselves combing through myriad blogs in order to make sure we’re reading the best one. And then we’ll write a column about the need to post-filter the blogosphere.

Chris, on his blog, adds:

Obviously I wouldn’t blog if I thought it were totally pointless, but I have come to believe that even the most well-intentioned scientific bloggers are probably not going to be able to revolutionize their colleagues’ relationship with the literature. In part, as we say in the excerpted passage, this is because it’s unlikely that a single individual will rarely have both the relevant expertise and the required amount of free time. But are also other reasons, the most important one being that “one size does not fit all”, e.g., any given blogger’s survey of the recent literature involves judgment calls about what is interesting and important, which may or may not correspond with the judgments that would be made by any given individual reader.

Harold Varmus on Daily Show last night

Under the fold:

Continue reading

My picks from ScienceDaily

Continue reading

Clock Quotes

One of the sad signs of our times is that we have demonized those who produce, subsidized those who refuse to produce, and canonized those who complain.
– Thomas Sowell

Nowhere.com

Rural communities have big troubles persuading broadband (and wireless) providers to bring their services to them. Read this excellent article both for the compelling story and for the details of technical, economic and political angles on this problem.

ScienceOnline’09 still reverberates

I am sorry – I failed to link to the Coast to Coast Bio, podcast #10, where Deepak and Hari discuss ScienceOnline09
Also, there is now an article in French about Miss Baker and her students.

The Matthew effect in science

Douglas Kell: The Matthew effect in Science – citing the most cited:

The Matthew effect applies to journals and papers too – a highly cited journal or paper is likely to attract more citations (and mis-citations), probably for the simple psychological reasoning that ‘if so many people cite it, it must be a reasonable paper to cite’ (and such a paper is, by definition, more likely to appear in the reference list of another paper). Clearly that reasoning can be applied whether the paper has been read or otherwise. Simkin and Roychowdhury (2005 and 2007) note that a clear pointer to the citation of a paper one has not read is if it copies a mis-citation, and an analysis of the frequency of such serial mis-citations allows one to estimate, statistically, what fraction of cited articles have actually been read – at least at or near the time of writing a paper – by the citing author. Their analyses show (at least for certain physics papers) that “about 70-90% of scientific citations are copied from the lists of references used in other papers”, and that a typical device is to start with a few recent ones plus their citations. Some aspects of this tendency in bibliometrics, especially with highly cited papers, can be detected from the power law form of the distribution of citation numbers, as in the Laws of Bradford and Lotka that I discussed before. Of course the mindless propagation of errors without checking sources properly is hardly confined to Science – a famous recent example with spoof data showed how some journalists simply copied Obituary material from Wikipedia!

I know people do this. Drives me crazy! Every paper I ever cited I read and re-read and re-read. Heck, I even tried to slog through papers in German (which I don’t speak) if I thought they were relevant. But copy+paste just because others did? Nope.

Did I see that?

I forgot! But they say it was in a movie.
Mo explores the portrayal of Amnesia in the movies. Lovely!

Why Scientists won’t use Twitter?

Asks Nachiket Vartak:

Twitter doesn’t need an introduction. The microblogging service is widely popular, and most Twitter users swear by its wonderful utility. It is a “Social Commons”, as one enthusiastic web junkie put it. But a few months into using Twitter, I realised that there are very few scientists – and I mean natural scientists, on Twitter. For instance, at the time of writing this post, the Twitter account science had 2,247 followers , while some popular individuals have followers 10-fold that number.

Here are 211 scientific twitterers you may be familiar with – definitely a good start!

Introducing: The Replacements!

Jay Rosen, on Twitter:

“Hey @Boraz: Scientists (mainly, me) are close to announcing a branching off from the curmudgeons, a new species, almost. The Replacements.”

My response on Twitter:

@jayrosen_nyu I am all ears! The Replacements! Sounds like a superhero comic strip, a movie one day!

Jay, on FriendFeed:

The Replacements are those who mistakenly believe that crowing for the 1,000 time that bloggers cannot replace journalists is an important and insightful act. Identifying feature: they make a show of disagreeing with the hordes of writers who think bloggers CAN replace (newspaper) journalists but fail to quote or link to any. Recent case: http://is.gd/llQa
Another example: http://is.gd/ls5v

My response on FriendFeed:

An important part of their argument, which usually comes out clearly if they engage in the discussion with the commenters, is the sudden switch in the meaning of the word “blog”. As we know, blog is software. What one uses it for is a different story. But….
…invariably some commenter mentions HuffPo, TPM, Firedoglake or a good local blog that does investigative reporting. Those sites originated as blogs, and have a bloggy look and feel (and use blogging software), but they have grown into New Media organizations, with paid reporters and interns and editors, etc.
As soon as that happens, they jump on it and switch to their preferred meaning of ‘blog’ – the small individual site full of LOLCats and adolescent angst. No, nobody suggested those kids will do investigative journalism, so this is a hijack of the meaning. Josh Marshal does not have adolescent angst, as far as I can tell.
What most bloggers say in these discussions is that they don’t want to become journalists, that a small number of really good bloggers may want to become professional journalists, and that many laid-off journalists will become bloggers but only in the sense of “doing their stuff online instead of in print”.
There is also the sense that a lot of journalism is (usually botched) transcription of what the sources or experts say, while today sources and experts can talk directly to the public.
Finally, there are accidental journalists – people who happen to be at the right place at the right time and report the news (e.g., the guy who lives next to the Minnesota bridge that fell) for a few days, then go back to their normal lives.
Nobody ever said that little bloggers with LOLcats and adolescent angst are going to replace journalists. But the method and style of journalism, as it abandons the expensive paper and moves to the Web, will have to change. Also, both the hyperlocal and the huge global papers will survive with some good paper/Web combo. The medium-sized city/state papers owned by chains are those that will die.
And many bloggers are worried that there will be a period of vacuum after the papers die and before New Media manages to take over with a new model and be able to cover everything the papers covered till now.

Open Access in the developing world – yes, it is a Good.Thing.

A few days back a paper came out (not OA, sorry), with a keen grasp of the obvious: Open Access is useful for those living in countries where they do not have much access. Duh! Furthermore, those who barely do any science at all, i.e., in the least developed countries, don’t cite, so there is no difference between OA and TA there. And yet more, their methodology was fraught with errors galore. I am happy to report that this paper was debunked by several people already – so check them out:
Evans and Reimer greatly underestimate effect of free access
Research highlights from Dr. Obvious: Tracking the citation advantage of open-access publication in the developing world
A Global Perspective On The Open Access Effect
The Evans & Reimer OA Impact Study: A Welter of Misunderstandings
Perils of Press-Release Journalism: NSF, U. Chicago, and Chronicle of Higher Education
Especially those last two by Stevan Harnad are thorough and detailed. Don’t believe something just because it has been published!
Also a discussion here.

Harold Varmus is everywhere!

A Hurdle for Health Reform: Patients and Their Doctors:

Dr. Harold Varmus, the president of Memorial Sloan-Kettering Cancer Center in New York and a former director of the National Institutes of Health, said increasing public access to the findings of medical research would be important for health care reform to succeed.
“One obvious goal is getting information out to health care practitioners about effectiveness experiments,” said Dr. Varmus, a Nobel Prize-winning cancer biologist and the author of the new book “The Art and Politics of Science” (Norton). “This is going to be crucial, because if the government’s going to spend $1.1. billion from the stimulus bill on comparative effectiveness research, you want that stuff to be in the public domain.”

Experts Seek Intellectual Property Reform:

Nobel laureates Sir John Sulston and Harry Varmus, College of Physicians and Surgeons ’66, provided a scientific perspective, suggesting that life sciences research has been hampered by commercial concerns.
“It’s not just about IP [intellectual property], it’s about rebalancing the way we fund things,” said Sulston, a pioneering geneticist, complaining that too much private funding tends to “short circuit” research by subjugating scientific discovery to the short-term profit motive. He criticized privately-funded research for hindering the free dissemination of results, adding that for effective progress to occur, “everybody needs to see all of the data at once, not just some of it.”
Varmus picked up on this point, explaining that scientists’ collective obsession with publishing their work in prestigious journals has led to a biased system that only publicizes a small subset of useful scientific results.

Now it’s our job to keep the Democrats’ toes to the fire

Senator Tom Harkin luvz him some alternative medicine. And he hates when the studies demonstrate those things don’t work, so he tries to push them into the Obama Administration’s health care plan by force. Read Orac, PalMD and PZ for details (and for info what you can do). This administration is supposed to be reality-based – let’s make sure the wackos don’t change that….

A very brief history of plagiarism

Archy does an amazing detective job on who stole what from whom in the old literature on mammoths, going back all the way to Lyell!
Then, as much of that literature is very old, he provides us with a history and timeline of the ideas of copyright and plagiarism so we could have a better grasp on the sense of the time in which these old copy+paste jobs were done.

Cromer Is So Bracing is now over

But there is plenty of digital evidence it really happened!
Check out the #CISB hashtag on Twitter, the CISB’09 room on FriendFeed, and the blog posts:
Cromer Is SO Bracing ’09 – Day One
Cromer Is SO Bracing ’09 – Day Two
Cromer is SO Bracing – Friday Lunchtime update
Cromer Is SO Bracing – Pier Review
Cromer is SO Bracing – Saturday Afternoon
Cromer is SO Bracing – Sunday
Sorry to have missed this, but my ghost that “slept on that sofa” was there!

Make sure all your important statements fit in 140 characters or less.

Pros and cons of your audience at a conference following you live on microblogging services:
How to Present While People are Twittering
Project Management helped by MicroBlogging
Conference technology planning
Discussion on FriendFeed

‘Blogs firmly established as means of scientific communication’

A voice from Latin America:

Many scientists use science blogs to post information on their work and receive comments from other scientists and from people outside the usual circle of readers. Some authors even suggest posting in blogs part of their works before publishing them, in order to exchange ideas and bring new perspectives. Scientists who use blogs consider them a complement to – not a replacement of – scientific journals, since they represent documents that do not substitute articles, but that establish a maturing stage of scientific work preparation, which is static and limited in terms of scope. However, many scientists still see blogs as a distraction from the real world and believe they do not gain much by commenting their work with lay people or specialists from other fields. Some consider attractive the possibility of communication through blogs, but do it anonymously, afraid of being deemed as not serious, or criticized for dedicating time to tasks that are not acknowledged as academic activities.

Harold Varmus on Daily Show tonight

So says Jonathan. Will watch.

Video of the Open Science panel at Columbia…

…is now online.
See summaries by Caryn Shechtman, Arikia Millikan and me. Update: Also see Talia Page both on Space Cadet Girl and TalkingScience.

Today’s carnivals

Circus of the Spineless Issue 36 is up on Invertebrate Diaries
Encephalon Edition 65 is up on PodBlack Cat
Berry Go Round #14 is up on Gravity’s rainbow
Four Stone Hearth #61 is up on Moore Groups Blog
Carnival of the Liberals LXXXV is up on The Lay Scientist

My picks from ScienceDaily

Underlying Sleep Problem Linked To Attention-deficit/hyperactivity Disorder In Children:

A study in the March 1 issue of the journal SLEEP suggests the presence of an intrinsic sleep problem specific to attention-deficit/hyperactivity disorder (ADHD) and supports the idea that children with ADHD may be chronically sleep deprived and have abnormal REM sleep.

Butterfly Found To Be New Species, Because Of Its Mustache:

After nearly a century in the Natural History Museum collections, a new butterfly species has been discovered because of its mustache.

Coffee Cultivation Good For Diversity In Agrarian Settlements But Not In Forests:

Coffee shrubs, both in themselves and because they are most often cultivated in the shade of large trees, can have a positive impact on plant and animal diversity in those parts of the landscape that are deforested and dominated by agriculture. What constitutes a dilemma for consumers wishing to shop ecologically is that when coffee is grown in a forest, which is also common, the impact on diversity is negative.

Clock Quotes

History teaches that grave threats to liberty often come in times of urgency, when constitutional rights seem too extravagant to endure.
– Thurgood Marshall

Snow

Taken from my porch a few minutes ago:
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snow 003.jpg
snow 004.jpg

Happy Birthday Dr.Seuss – from Google

Google Dr.Seuss.gif

Memo to self-described sane, rational, science-loving Republicans

You have been Expelled.
No, not by me, by your own party.
The Republican party is now a clown car.
The sane, thoughtful conservatives have left it over the years, some prominent ones quite publicly last year, either more openly by stating they are leaving GOP, or a little more carefully, by endorsing Obama for President.
What is left are racist, sexist, homophobic, femiphobic, xenophobic, Creationist, authoritarian, theocratic, cowardly scuzbuckets like Rush Limbaugh, Michele Bachmann, Bobby Jindal, Steve Sailer, Sarah Palin, Newt Gingrich, Sean Hannity, Anne Coulter and Joe The Plumber.
And the lowlife that came to Palin events to drool at her.
And the most insane Republicans in Congress. The sane ones lost their elections. None of them are left in the House. A couple of them still in the Senate, but will have to switch to Independent if they want to get re-elected in their Blue states. The brand is THAT damaged.
Their platform? Make fun of everything that normal people want.
Good luck with that.
People are judged by who they are friends with. Do you want to be associated with those lunatics?
Why didn’t you get the memo you were Expelled? Because they are too high on endogenous hallucinogens. And they still hope to get your vote. One thing they have no interest in whatsoever are your ideas.
Think about it. What can you do?
Get together with other sane conservatives and try to wrestle the party from those cretins? Good luck.
Get together with other sane conservatives and try to take over another party, e.g., Libertarians? Good luck.
Get together with other sane conservatives and try to form another party? Good luck.
Each of the above three scenarios will produce a party that is almost indistinguishable from the Democrats, who have firmly taken the Center. Tough to compete with a copycat against the Real McCoy. Anything even a little to the right of them is, right now, bordering on insane and totally unpopular because all those ideas have been tried over the past 40 years and each one of them failed miserably.
Join the Democrats? As they are so corporate and straight in the middle, and unlikely, constitutionally (in the sense of their own mindset, not the highest law of the country), to ever move Left, that may be your best bet.
Or just go Independent and watch as the US political ecosystem evolves.
Obama has been the President for just a month. Give it a few more months and watch. It is quite possible that we are entering a very different world.
In this new world, we will have to forget the idea that there are two opposing parties keeping each other in check (even if one of them is full of shit on everything). In it, it will be us keeping check on our elected representatives. In such a world, parties and party affiliation will not be as important as they have been to date. It will take us some time to get used to the idea and to start using it well.
People who get this new world will be relevant in it. Those who don’t will be left behind. GOP will continue to be irrelevant as their modus vivendi is the hating of Democrats and laughing at words they think are funny.
The MSM will be irrelevant as they are still paying attention to what GOP-ers say (as if anyone cares), give them equal time (as if their opinions touch reality), or wonder how the Republicans will stage a come-back (as if this is some kind of inevitable Law Of Nature that this will ever happen).
In the meantime, if you don’t want to be laughed at, quit the GOP. You REALLY don’t want to be associated with that amount of hate, idiocy and obstructionism, do you?

Positive Emotions and Psychophysiology

From SCONC:

Thursday, March 5
7 p.m.
What Good is it to Feel Good? The Science of Positive Emotions
From our “what the world needs now” file, Dr. Barbara Frederickson, head of the Positive Emotions and Psychophysiology Lab at UNC will share thoughts from her new book, Positivity. You can strengthen relationships, relax the mind and relieve stress by thinking positively. Part of the Current Science Forum at Morehead Planetarium, UNC.

Today’s carnivals

Carnival of Evolution #9 is up on Moneduloides
March Scientiae: Role Models is up on Liberal Arts Lady
Festival of the Trees #33 is up on Local ecologist
Skeptics’ Circle #106 is up on Disillusioned Words
Friday Ark #232 is up on Modulator

The Best of February

In February I posted 166 times. This includes two BPR3-icon-worthy posts about science! The first was on Circadian Rhythm of Aggression in Crayfish with the longish addendum on citing blog posts in scientific literature. The second was An Awesome Whale Tale, and, related to this paper, I announced the new Palaeontology Collection in PLoS ONE in Fossils! Fossils! Fossils!. I also did an interview with Dr.Adam Ratner.
I have covered another session in ScienceOnline’09 – Saturday 3:15pm – Blog carnivals. Miss Baker and her students were on NPR and one of the students wrote a Malaria Song that spread virally across the Web.
I gave an hour-long radio interview about ScienceOnline’09, science blogging and science journalism, and you can listen to the podcast.
Carl Zimmer was in town for Darwin Day so we had great fun at his talk and after.
I was on the Media roll again, starting with D.C. press corps dissed again – but this time for good reasons, continuing with A Quick Note to Huffington Post and Incendiary weekend post on bloggers vs. journalists, then noted that Carrboro Citizen won six NC press awards, and ending with Why good science journalists are rare? and two linkfests of good related stuff: A smorgasbord…. and On the Media – your weekend reading (instead of the hardcopy NYT you are not subscribed to anyway) (plus several more link and copy+paste posts on the topic).
On blogging and social media, there were, as usual, several posts. First, I asked Do you comment on your own blog?. Then, relating it to politics, Who has power?. Then I traced The Evolution of Facebook, announced the North Carolina group on Nature Network, pointed to the analysis of User activity on PLoS ONE, announced an amazing inaugural Diversity in Science Carnival and noted a two-fer from the Nature Publishing group on the same day: Nature: It’s good to blog and Nature Methods: It’s good to blog.
I also listed several meetings I’d like to go to: Part I, Part II, Part III, Part IV, Part V and Part VI.
I went to NYC and participated in a panel on Open Science, then had coffee with Jay Rosen, lunch with John Timmer, dinner with a bunch of bloggers and another dinner in a Serbian restaurant before coming home.
Next week I’ll be in Boston, so if you are there, meet me.

My picks from ScienceDaily

Continue reading

Clock Quotes

So much of our time is preparation, so much is routine, and so much retrospect, that the path of each man’s genius contracts itself to a very few hours.
– Ralph Waldo Emerson

On the Media – your weekend reading (instead of the hardcopy NYT you are not subscribed to anyway)

Actually, Journalists do take some of the blame for the death of newspapers:

But why is the business model dying?
Competition is a factor, and blogs are obviously part of that mix. But again, if I’d started a business and someone else opened up down the street and offered a more appealing product, and I lost customers, would it be fair to blame the other guy alone for my problems?
In a free market, we have competition. Yes, it can suck when you’re not on the winning side. But there’s nothing saying that you can’t start a new business, or reform your existing one to compete.
Newspapers remain wedded to print in a market that is switching to an all digital model. Newspapers offer a variety of news in a market that has moved strongly towards specialization (not exclusively, but more so than in the past.)
If more and more people are no longer buying newspapers because the content has no appeal vs the competition, wouldn’t at least some of the blame lie with the people who produce the newspaper content that fewer people now want to read?

Ice, Ice Baby: When Fact-Checking Is Not Fact-Checking:

I know that I may be sounding a bit Talmudic by spending so many blog posts on this one bit of information, but examining how these Post editors have dealt with it has proven to be very revealing. They never bothered to check with scientists about the validity of a statement in a column, and after thousands of people have complained, they recognize that there was something so amiss that should have called the scientists. But they still can’t manage to make a decision about whether the statement requires a correction.
What’s more, they continue to ignore the broader, more important problem with Will’s discussion of sea ice: the facts that picking out two days from a thirty-year time series is not a meaningful way to look at climate trends, and that climate models do not, in fact, lead you to expect a decrease in global ice cover. And they have not even taken any notice of all the other errors in Will’s two columns.

The George Will Affair:

A wide variety of scientists, journalists, bloggers, and pundits has refuted Will’s arguments many times over in the week and a half since. A comprehensive list of those rebuttals, including an early entry from CJR, can be found here.
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But his point about the wiggly, lawyerly language is especially germane because this is a classic case of evidence versus inference. The Post can argue that, technically, all of the evidence Will presents passed fact-checking; and Will can then infer what he wants about that evidence–even if his inferences differ drastically from those of the scientists who collected the evidence–without journalistic foul.

George Will, the Washington Post, and the Death of Newspapers:

Some bloggers seem to think this piece is hard on them; precisely the opposite was intended. I think it’s amazing that bloggers have basically destroyed the credibility of both George Will and the Washington Post editorial page. Both seem to deserve it; bloggers gave it to them. Bravo. But I also lament the decline of our newspapers–even though much of it is their own fault, as in this instance–and worry that without them, we won’t be better off.

The George Will Scandal:

Something striking has happened over the past week in the dynamical relationship between the blogosphere and the rather gaunt-looking “mainstream media,” or MSM, with respect to a science controversy. And watching it unfold makes one wonder if we aren’t seeing a kind of turning-point moment in the transition–for better or worse–away from newspapers as the dominant source of opinion, commentary, and thoughtful analysis in our society.

Unchecked Ice: A Saga in Five Chapters:

I guess I don’t understand editorial pages. The laws of physics must be different there.

The reality of fact-checking at daily newspapers: George Will is no exception:

First, contrary to what many non-journalists seem to believe, George F. Will is a journalist. Just because he gets to add interpretation and value judgment to the factual material that serves as his raw material doesn’t mean he gets to flout the ethical parameters of the business. In other words, he is obliged to represent the source material he cites fairly and accurately. If he doesn’t then he’s violating his contract with his employer and his obligation to his readers.

Does what George Will thinks about climate change really matter?:

I was trying to be polite, but the conversation quickly slid into the frustration so many in the room, not just me, have with climate science denialism. Here’s the thing: If Will is right, and there is no global warming, then much of what we think we know about chemistry and biology and ecology and thermodynamics and geology and physics is wrong. If Will is right, then thousands of climatologists are not only wrong, but participating in a global conspiracy to conceal the truth about the state of the planet’s ecosystem. The climatologists have nothing to gain from perpetuating the “lie” of anthropogenic global warming, but they’re doing it anyway, just to be mean.
And if that isn’t the silliest idea since the 8-track tape, I don’t know what is.

George Will Lies; His Editor Does Nothing:

There are many problems with this philosophy, but those are irrelevant, since George Will made factual errors rather than debatable inferences. Once again, he wrote that “according to the U.N. World Meteorological Organization, there has been no recorded global warming for more than a decade.” There is no inference there. Will isn’t saying he disagrees with the WMO’s interpretation of the data, he’s saying the WMO thinks there’s been no recorded warming for more than a decade. The WMO doesn’t think this. No serious scientific organization thinks this.
It’s a sad display from one of our great papers. The Post still has a lot of talented and hardworking writers; this is a slight to them all. In these difficult times, the paper ought to be striving to show it’s still relevant. Instead, it shows us that at least at the editorial/oped page, they don’t choose well between the truth on the one hand, and making such an eminence as George Will retract on the other.

Once more into the breach:

How do I put this politely?
It is not possible for a reasonable person equipped with a secondary education to read the material George F. Will cites in his columns arguing against the scientific evidence for global warming and come to the conclusions that Will reaches.

My Email to Fred Hiatt of the Washington Post:

Dear Mr. Hiatt, [Introductory Comments]…I believe what I’ve called the “Republican War on Science” continues, and the George Will saga represents a stunning example. In my opinion, the Post editorial/oped page makes a terrible mistake by not correcting his manifest errors; but leave that aside–you’ve said people should instead “debate him.” Would you publish an oped by me exposing Will’s egregious errors, misrepresentations, and distortions of the science of global warming, and thus further debate?

In Defense of Walter Sullivan:

When I was trying to learn the craft of writing about the earth, a geologist who was serving as my guide said I had to read Walter Sullivan’s Continents in Motion. The book was a revelation to me – for the skill with which Sullivan explained the science of plate tectonics, but more importantly for the nuance with which he explained how science works: the fits and starts, the struggle to find data, the even greater struggle to find theory to structure and think about what that data is telling us.
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I spent a great deal of time recently studying climate science during that time period (see here for the result). If newspaper journalism is the first draft of history, Sullivan’s work needs very little editing. It is anything but a megaphone of global cooling alarm, but rather a rich account of the complex science of the day.

Come back to tell you all, I shall tell you all: The Chicago Journalism Town Hall:

A lot of the people newspapers pay to write are not just competing against people who write for free, they are competing against people who write better than they do, and those people are compelled to write because they are experts, which they are paid to be.
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Now anyone with a computer can read those, and thousands of other professional and amateur equivalents. You can also use this thing called Twitter and it’s kind of like reading a Richard Roeper column (you can even follow Richard Roeper on Twitter, but it’s less interesting than most Twitter feeds). Look at it economically: the value of Richard Roeper, star columnist, has declined due to market forces. There are a lot of people offering the same or better service. The Roeper Bubble has burst. And I don’t mean to pick on Richard Roeper. Well, actually I do, but there are more grave examples. Take David Brooks.
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More simply: journalists have historically been paid by newspapers to call up experts and talk to them (I have done this many times), and to then relay that information back to the reader. Now many of those experts write. For readers. It saves them time, and usually a lot of stupid questions.
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Some of these people writing for free are better at writing than many of the people who are paid to write.

The future of news:

It’s getting close to a week after the Chicago Journalism Town Hall, on which I was a panelist along with 13 other of the city’s media luminaries (that there were far more watching us supposed experts from the audience speaks to the depth and breadth of talent in Chicago — any number of them could have taken our place.) You can listen to the three hour discussion in two parts on chicagopublicradio.org. I’d hoped to jump right into the fray here on the blog, but work has kept me from getting my thoughts out in print.

Gore, Will, Climate and Complexity:

Many climate scientists, bloggers and readers have weighed in this morning online and in my in-box to complain about my short print story assessing the risk of overstatement or inaccuracy facing everyone pressing an argument about climate science and policy. (I’ll include some examples in the comment thread this morning.)

NPR and Twitter:

It is Saturday morning. I turn on my laptop and check various websites; new friends to add on Facebook, Tweets to reply to on Twitter. I grab a cup of coffee and tune in Weekend Edition on NPR. I am not alone. NPR has just run a story about Twitter, and Andy Carvin’s efforts to get Dan Schorr to use Twitter. In the world of Twitter, it is a big story.

Editorial: The 32% Theory:

When you break down the percentages, that means a full 37% percent of what was in the paper was either shit you could get anywhere or shit you’d never want at all. And among the remaining 63%, let’s charitably assume that half of that news had been available prior via TV, radio, or Internet. That leaves you with a daily newspaper that is — again, charitably — 32% relevant. That’s not good.
Now, let’s plug the human element back in. The fact of it is simple: Print media is fast becoming a boutique medium — it will always be around, but will never again employ the number of people it does today, and certainly never again the number that it did thirty years ago. Some — many, even — of these people are talented, and all of them, as human beings, deserve jobs. What will become of them? Some will hang on until the house burns down completely, some will find other fields of employ, others will strike upon a new model, one that is desperately needed as news itself continues to dumb itself down throughout all media.

BREAKING: Press Corps Incredulous That Obama Budget Reflects Campaign Promises:

It felt like a primal whine from rich reporters. Hasn’t Barack Obama considered that maybe John McCain’s tax policy is the right one? Does Obama not realize that the best way to be a Democrat is preserve conservative Republican tax policy?
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In a remarkable scene, Gibbs patiently and repeatedly explained that, no really, Obama actually won the election, that he’d explained exactly what he was going to do during the campaign, the American people understood and voted on it, and now he’s doing it. During the campaign, Obama had pledged to cut taxes for 95% of American workers and end the catastrophic non-workingness of George Bush’s trickle-down tax policy. Now, among some questioners, there seems to be confusion and alarm that Obama intends to implement that policy.
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The sour mood of the elite press corps was apparent from the first question, by the Associated Press’ Jennifer Loven. Noting Obama’s quote from earlier today, “There are times when you can afford to redecorate your house and there are times when you have to focus on rebuilding its foundation,” Loven asked whether it was appropriate that the Obamas conduct any re-decorations in the White House as they settle in.
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As one reporter observed after the briefing, “Did you notice all the questions about taxes came from reporters making over $250,000 a year, especially the TV guys?”

The [Monday] Papers:

“A column is based on the length of a column of type!” Ann Marie Lipinski once explained to me in frustration, when explaining why one of her former columnists was at odds with the paper because he wanted his columns to jump. (And many newspaper columnists today still act as if that artificial length was handed down by God as optimal, or that there is something valuable about news stories filed at 6 p.m. that sit around until 6 a.m. before anyone sees them.)
Yes, but not only is that an artificial constraint, but columns are of different lengths in different-sized publications. And besides that, aren’t journalists the ones who should know better than any that rules are made to be broken?
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One scenario discussed on Sunday was a city without a newspaper. Inherent in the discussion was the false notion that that meant a city without news. Somehow I think chicagotribune.com – or its remnants – will stay alive if the rest of the company sinks. And if not, that’s a whole lot of reporters and business folk who could re-band together immediately on the Web. It’s just not a useful discussion.
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But more unbelievable is the notion that somehow serendipity is lost in the Internet. The Internet is a case study in serendipity! Ever hear of the term surfing? That’s serendipity! But then, I seem to remember reading that the youth of America were wasting their lives surfing the Internet. Better to surf the newspaper?
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I love Carol Marin, but when she said that you could create something, but how would you drive traffic to it I almost had to revoke my membership in her fan club. Meanwhile, Nate Silver reports that folks are “throwing money” at him. A year ago, Silver’s site didn’t exist and he had no traffic.

The [Eric Zorn] Papers:

Robust local online news operations aren’t going to spring up fully formed. But the examples I’ve listed are indeed going concerns. Online sites have been included in the Pulitzer Prize competition for the first time this year. It takes time. But newspapers should already be there; they have squandered their tremendous advantage, and I don’t think anyone in the industry seriously argues otherwise. And why does a concern have to be self-sustaining through advertising? There are other models. Maybe MinnPost and other new sites are the newspapers of the future. Would that be so wrong?

The [Thursday] Papers:

Besides that, limiting access to your product is madness. Thanks to the Internet, the Tribune now has more readers than it’s ever had in its history. And the ability to know something about those readers to tell advertisers, to tailor editorial content, to create community, to interact, and to sell services and products to is virtually unlimited.
Finally, as I’ve said and written before, if you want to try to put your crappy feature stories behind a firewall, go right ahead. I recommend not writing them instead and focusing on unique content, which means local reporting first and foremost, though not merely conducted in the same crappy traditional way. And this reporting should never have a price tag put on it – not in a democracy. There are many other revenue streams to tap; just look around.
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“I would say that you can’t just put up your existing print content and park ads around them and expect that to be the model. The new business model is a new CONTENT model . . . the nature of content can and should change on the web in all sorts of ways, and that creates new ad models too . . . I don’t know why everyone is so quick to declare online advertising dead except as wish fulfillment; to the contrary, it’s just in its infancy! We don’t even know what metrics to use yet, advertisers are still unknowledgeable about the web, sales forces largely aren’t selling it, and the new media products still haven’t been developed . . . the Web model is every bit a new content model as anything; the advertising model will follow, but the only thing different about the business model itself will be a wider array of revenue streams available.”
To expand and reiterate, you can’t just put your old content on the Web and think you can slap ads around it and that’s that. Your old content, by and large, sucks. And it’s not reported, written or edited for the Web. You might as well slap radio transcripts on the Web and think you’re now doing Internet journalism; you’re not.

Could bloggers be sued for telling the truth?:

If you’ve ever worked in journalism, you’ve probably heard the expression, “Truth is the ultimate defense against libel.”
Well, maybe not, according to a new court decision that could leave countless bloggers and other citizen journalists exposed to libel suits for true statements.

West Seattle Blog Is So Hot Right Now:

I know I’m stating the obvious, but if I brought anything away from last night’s journalist mash-up, No News Is Bad News, it’s that West Seattle Blog is HOT, HOT SHIT right now.
The premise of the event was … well, I don’t remember. But, what it became was a chance for 150ish journalists and a few of their subjects to come together in one room, talk about the state of the industry, pontificate on how we got where we are and who’s to blame, and toss around ideas for how to save QUALITY JOURNALISM (not necessarily ink and paper). West Seattle Blog, perhaps more than any other voice in the room, is demonstrating an idea, a business model, and a way to preserve local journalism. They have skin in the game. They’re making it work. They’re not just talking about it, they’re doing it. And doing it well. But they’re not saying they’ve found the digital news solution, either. They’ve found something that works in West Seattle, not necessarily the rest of the country or even the city.

Journalism’s fatal disconnect with business:

By splitting journalism and business into two buckets separated by a longstanding cultural divide, the two groups fail to collaborate on ideas that tap the strengths of both. And neither have a track record of understanding how technology enables community, the greatest opportunity of all. In fact, nearly three-quarters of local online news consumers say newspapers have failed in providing a sense of community and “connective tissue” in their local cities and neighborhoods (Forrester Research 2009). After all, most journalists want to control the conversation. So do the sales folks. So you need a third element: creative technology folks, empowered with resources, who can infuse community in content and revenue generation, providing value to both users and businesses.

Crisis in the US newspaper industry :

Whatever model the newspapers of the future adopt, the current crisis is likely to put at least some titles out of business, with only the strongest surviving.
Less competition could mean more business for the survivors and the industry is likely to consolidate, with cities and regions being served by fewer newspapers; we could perhaps see a truly national newspaper market develop in the US.
But with US newspapers competing with one another, as well as with international news providers (including the BBC), there would still be plenty of choice for news consumers.
“With even half a dozen papers, the American newspaper industry will be more competitive than it was when there were hundreds,” writes Michael Kinsley. “Competition will keep the Baghdad bureaus open and the investigative units stoked with dudgeon.”
The “crisis” in the newspaper industry may, therefore, be more of a crisis for the journalists and publishers who are currently facing job losses and bankruptcy.
But if it is merely the quantity, but not the quality, of journalism that declines then – for readers – there may not be a crisis at all.

No, The Death Of Newspapers Does Not Mean An Age Of Corruption:

A few folks have sent in Paul Starr’s long but thoughtful article in The New Republic, which worries that, thanks to newspapers dying, we’ll be entering a new age of corruption, since no one will be watching government officials like investigative reporters have in the past. The article is well worth reading, and brings up a number of interesting points — but, in the end, fails to make a compelling case for a number of reasons — most specifically that it relies on both a faulty model of news production and a faulty understanding of economics. This isn’t to knock Starr or the article, because the mistakes are subtle, but important.
The first mistake is in looking at news production itself — and specifically investigative reporting. Starr seems to significantly overestimate how much investigative reporting newspapers do. In fact, investigative reporting is a fairly new phenomenon and has never been a major focus of newspapers. Those bemoaning the supposed “loss” of this function don’t seem to recognize how little money has been put towards such investigative reporting in the past. As that second link suggests, most newspapers spend more on their comics pages than on investigations.

The Powers That Were:

Indeed, the tradition of great journalism that many pundits seem to romanticize is a relatively recent development. Before Woodward and Bernstein, for instance, there wasn’t a lot of investigative journalism at most papers; it really exploded in the ’80s. The financial success that Chris cites also allowed the professionalism of a lot of newsrooms that were pretty crummy a generation ago. We need to find new ways to preserve quality journalism-but it’s anything but a divine right, and btw, there’s no reason why newspapers should think they have a monopoly on it.

Who’s watching the Watchdogs?:

Goose a few newspaper journalists these days and they’re likely to exclaim something about why Americans should care about saving their industry. And it’s likely to sound something like this: “Without us protecting the public as investigative watchdogs, government corruption is going to run amok!”
Which might be a compelling point, were it not for five little things:
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So let’s try this another way, shall we? Sure, there’s nothing intrinsically wrong with newspapers conducting investigative journalism — in fact, I hope they choose to do more of it. But let’s consider for a moment the possibility that newspapers have done at least as much to encourage bad behavior by government and business as they’ve done to curb it.
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Ever wonder who does most of the public-policy grunt work in America? For the good guys, it’s typically underpaid crusaders at civic-minded non-profit groups, people who care about clean water and safe food and healthy children other such left-wing nonsense. Newspapers count on these scruffy muckrackers, even though they typically distance themselves from their “radical” agendas.
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Much of what passes for watchdog investigative reporting is based on studies conducted by these pesky non-profits, or by anonymous government underlings in some state auditor’s office, or the federal GAO, and so on. They produce the proof, editors build stories around their findings, and each year on press awards night, some reporters get plaques that credit them with the whole enterprise.
Is there newspaper reporting, investigative or otherwise, that takes on a public-policy issue and challenges ruling orthodoxy without a boost from an interest group? Probably. But newspapers generally refuse to poke the status-quo without being able to cite some interest group for raising the issue. Wanna know why? Because the status quo is where the money and power are. Do the math.
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In journalists’ romantic private world, they are working-class heroes confronting the powerful on behalf of the powerless, and that happy myth is hard to give up. In truth, they are effectively limited by the compromises inherent in their business and our society. Newspapers simply will not long engage in unpopular whistleblowing, or in watchdogging that hurts their circulation. Medicare watchdogging isn’t sexy, and the people who benefit from it aren’t valuable to advertisers, yet newspaper advocates promote a system that leaves the watchdogging function to a secretive guess about which stories will be the most valuable to the paper, not society. Is this supposedly important role really something that’s best left to such furtive whims?
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Today’s mediascape is a remnant of a collapsing 20th century system in which most of the journalistic infrastructure belonged to newspapers. Their current argument for their social value oozes irony because it reverses the way newspapers have valued themselves for a generation — not for their civic-mindedness, but for their bottom line. And if that bottom line is less than 20 percent profit, you can bet they’re laying off reporters, not offering stockholders smaller dividend payments.
Somebody should investigate that.

25 ideas: Creating An Open-Source Business Model For Newspapers :

I’m just one of many people coming up with business ideas for saving newspapers. There are a lot of posts being published on this subject.
Someone should collect all the advice because it’s turning into some kind of open source business model. And the beauty of this approach is that only a few newspapers need to have the courage to try new ideas–if any one of them succeeds then the rest can piggyback. They win and we win.
Here are my 25 ideas on how newspapers might be able to survive and become innovative media businesses:

Failing: The NY Times And Andrew Revkin Blow The George Will Story:

But there aren’t two sides to this, just because Will and company want there to be, or because the American population doesn’t know what to think. 40% of Americans don’t believe in evolution, but the NY Times doesn’t portray that as a scientific debate. Likewise, 25% of Americans think the Sun circles the Earth, but that doesn’t warrant 4 inches in the newshole.
Revkin — and the NY Times — had another chance to say that public opinion on climate change, perhaps the most critical issue we face, is simply and clearly wrong. Climate change is not a topic debated by serious scientists anymore: it is taken as a given that the climate is changing, faster than we expected, and it is speeding up. This is due to human impact, principally in the form of CO2 emissions. No debate left.
The media have an obligation to get to the real scientific bottom of these stories, not just offer up the arguments of two hypothetical sides, and leave it to the reader to figure out whether Will is right or Gore was wrong.

The Five Question Interview – Jay Rosen:

The program in which I got my PhD at NYU (1986) was the kind of program McLuhan said he wanted to establish. In it, we studied the history of communication systems from speech-the first medium-through writing, printing, telegraph, telephone, radio, TV, looking not at the devices themselves but at, say… the problems of cultural memory in an oral culture, or “craft literacy” where a group controls access to the writing system and thus to priestly authority. The democratizing influence of print in the Protestant reformation. The disruptive influence of photography on realism in painting. The information science of code breaking- where I first met my friends, signal and noise. It was a great subject to study and very good preparation for the Web.
McLuhan and Postman were both creatures of print civilization, masters of literacy, who were able to break the page. They were ready to “unlearn dead concepts,” a phrase from Postman’s books. I was also influenced by the semiotics of Roland Barthes, a French critic who was big when I was in grad school. McLuhan and Barthes were doing something very similar in the 1950s: short essays about advertisements and myth. (Appreciate the simple definition for myth that Barthes had: “many signifiers, one signified.”) I made my first acquaintance with the curmudgeons of the world in studying the reactions McLuhan got from “big literature” around 1964-67.

A Wrinkle In Ice (or Not):

There’s been a wrinkle in the global warming fact-checking saga I’ve been following this week.
Just to recap-George Will wrote a column claiming that global warming’s a lot of hype. He made a number of misleading statements, including one that was rejected by the very scientists he claimed as his source.

Washington Post Stands By Climate Change Denialism:

This started as a problem for Will, his direct supervisors, and the Post’s ombudsman. But now that the Post as a paper is standing behind Will’s deceptions, I think it’s a problem for all the other people who work at the Post. Some of those people do bad work, which is too bad. And some of those people do good work. And unfortunately, that’s worse. It means that when good work appears in the Post it bolsters the reputation of the Post as an institution. And the Post, as an institution, has taken a stand that says it’s okay to claim that up is down. It’s okay to claim that day is night. It’s okay to claim that hot is cold. It’s okay to claim that a consensus existed when it didn’t. It’s okay to claim that George Will is a better source of authority on interpreting the ACRC’s scientific research than is the ACRC. Everyone who works at the Post, has, I think, a serious problem.

A Birders’ Guide to Facebook

Gunnar Engblom explains Facebook to newbies.
Just go to Facebook and search for ‘Birding’ – people, groups, events.

Why The Onion is the best news organization?

Because they are more realistic than the MSM – this clip is even more relevant today than it was when first released:

My picks from ScienceDaily

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Clock Quotes

Sometimes you are overwhelmed when a thing comes, and you do not realize the magnitude of the affair at that moment. When you get away from it, you wonder, did it really happen to you?
– Marian Anderson

Fossils! Fossils! Fossils!

You may be aware that PLoS ONE has started making Collections of papers in various areas of research. The older PLoS journals have been making collections for a long time. PLoS ONE is just starting. Last month we put together the first such collection – Stress-Induced Depression and Comorbidities: From Bench to Bedside.
Today, we are happy to unveil our second collection – the PLoS ONE Paleontology Collection!
It is important to keep in mind that there are two types of collections: the first type is a one-off, closed collection, often associated with a conference, where we ask for or are offered a whole set of manuscripts (10-20 papers) which are all submitted roughly at the same time, peer-reviewed in a normal fashion, then, if accepted, published roughly at the same time. Then, the collection is closed – there are no more additions to it.
The Paleontology Collection is different – it is an open collection. This means that all of our papers to date (PLoS ONE only, not other PLoS journals) that deal with fossils in any way, 26 of them so far, are included in the collection. Furthermore, all the future palaeo papers will be automatically added to the Collection as soon as they are published. Thus, such papers will always be placed together, prominently displayed and easy to find – just a single click is needed to get there.
We are hoping that the open style of this Collection will motivate people in the field to submit palaeo papers to us in the future.
A second note: as it’s my job to check all the user activity on PLoS ONE, I have noticed that palaeo folks are unusually willing to use the comments/notes/ratings tools. Several of our fossil papers already have quite a lot of comments, notes, ratings and/or trackbacks (you should go to this blog post to see the examples). So, I would like to use this occasion to try to urge people to register, login and post comments, notes or ratings on palaeo papers, or send trackbacks if their blogging platforms allow it (Blogger.com can’t do it). I think that the palaeo community can be an example to others for the good and vigorous use of these tools. So, if you blog about this new Collection (and I hope you will help us spread the word) I would appreciate it if you would also encourage your blog readers to start using these tools on our fossil papers.
Greg Laden immediatelly understood why Collections are so useful:

PLoS ONE is a veritable fire hose of OpenAccess research. Which is nice, but how do you browse a fire hose?
By using the PLoS ONE collections you can track your favorite topic or delve into the earlier literature or just browse around. And now, starting just moments ago, there is a PLoS collection on paleontology.

Andy adds:

Why should we care? Speaking selfishly, this will allow us to easily access all articles in our field. All future articles are automatically added to the collection. This means that if you don’t want to wade through all of the other contributions on the PLoS ONE list (although there are some very interesting ones!), you can just keep an eye on the paleontology collection for any and all exciting developments. In a broader sense, this collection will help paleontologists to reach an even broader audience.
And once again–take advantage of the comment, note, and rating features at PLoS ONE (as outlined in my previous post). It’s really a unique opportunity to interact with authors, make your thoughts known, and help science march onward. If you have that really cool piece of research, submit your manuscript!

Finally, a word or two on my own musings about this Collection. As these 26 papers were published over the past two years, I knew I personally liked them very much, but only now that they are all in one place I realized why: they are all incredibly inter-disciplinary! These papers are not just simple descriptions of new species. They tend to combine insights and techniques from several disciplines, e.g., comparative anatomy and molecular systematics, biogeography and physiology and more. These are kinds of papers that don’t readily find home in other, more specialized journals, except in Science and Nature. PLoS ONE is, almost by definition, a perfect place for publication of such works. And Open Access ensures that such papers are widely read, covered by media and blogs, and later, hopefully, more often cited than papers hidden behind pay-walls.
So, go ahead and enjoy – introducing the PLoS ONE Paleontology Collection!

My picks from ScienceDaily

What Is A Virus? Research Suggests A Broader Definition May Be Needed:

The strange interaction of a parasitic wasp, the caterpillar in which it lays its eggs and a virus that helps it overcome the caterpillar’s immune defenses has some scientists rethinking the definition of a virus. In an essay in the journal Science, Donald Stoltz, a professor of microbiology and immunology at Dalhousie University, in Halifax, Nova Scotia, and James Whitfield, a professor of entomology at the University of Illinois, report that a new study also appearing in Science shows how the diverse ways in which viruses operate within and among the organisms they encounter may not be fully appreciated. The study, from a team of researchers led by the Université François Rabelais, in Tours, France, found that the genes that encode a virus that helps wasps successfully parasitize caterpillars are actually integrated into the wasps’ own chromosomes. These genes, which they show to be related to those from another known group of viruses, are an indivisible part of the wasp’s genetic heritage; they are passed down from one generation to another of parasitoid wasps.
While it is not unusual for virus DNA to become embedded in the chromosomes of their hosts, in this case the wasp is not the only “host” of the virus. The viral genes do replicate (copy themselves) inside the wasp (the permanent host), but they actually target – and act upon – the immune system of the caterpillar (a more transient host).

Birds’ Movements Reveal Climate Change In Action:

The northward and inland movement of North American birds, confirmed by thousands of citizen-observations, has provided new and powerful evidence that climate change is having a serious impact on natural systems, according to a new report by Audubon (BirdLife in the USA). The findings signal the need for dramatic policy changes to combat pervasive ecological disruption.

More…..

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Clock Quotes

Sometimes being a friend means mastering the art of timing. There is a time for silence. A time to let go and allow people to hurl themselves into their own destiny. And a time to prepare to pick up the pieces when it’s all over.
– Octavia Butler

Nature Methods: It’s good to blog

Another editorial about science blogging today, this time in Nature Methods: Lines of communication:

The public likes science stories it can easily relate to, and we have to admit that most science, including that published in Nature Methods, is unlikely to get more than a snore from nonscientists. In contrast, science stories that have a human interest or other emotionally charged angle require the concerted efforts of both journalists and scientists to ensure that the public understands the story well enough to make an informed personal decision. A failure in this regard can lead to a crisis that is difficult to resolve.
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A powerful aspect of blogs is their capacity to put a human face on science and related health issues by allowing scientists to discuss how these things affect them personally in a format in which regular readers feel as though they know the writer. Analysis of the MMR vaccine incident suggests that emotional arguments like a scientist talking about vaccinating his or her own children might be more powerful than the rational arguments that form the basis of normal scientific discourse. The public’s emotional response to genetically modified food in some countries might also have been very different if people could see numerous online blog entries from scientists discussing why they were not concerned about the scenarios being promulgated in the press. But can enough scientists be convinced of the potential benefits of blogging to make this a reality?
Conferences such as Science Blogging 2008: London, organized by Nature Network, and ScienceOnline’09 are exploring the role of blogging in science and trying to get more scientists involved. Nature Network just concluded their Science Blogging Challenge 2008–won by Russ B. Altman–where the goal was to get a senior scientist to start blogging. Altman’s colleague Steve Quake also just started blogging in a guest stint for the New York Times. One hopes that examples of prominent scientists blogging will convince others of the benefits. When a blog author is not a prominent scientist with a reputation to maintain, the quality of information on the blog can be a concern, but scienceblog tracking sites such as http://blogs.nature.com/ can help alleviate this problem.

w00t for the mention of ScienceOnline09! I wish they also mentioned ResearchBlogging.org as a means to track good science blogging (mention of carnivals would be too much to expect from a short article like this, I understand).

In the spirit of leading by example, Nature Methods will convert its online commenting site, Methagora, into a proper blog in preparation for later this year when commenting capabilities will be incorporated into published papers. Methagora will allow us to highlight and comment on papers that we feel are of interest to a larger readership and discuss the impact we see them having on science and hopefully society. We invite you, our readers–scientists and nonscientists alike–to share your thoughts and concerns, including your thoughts on this editorial. See you in the blogosphere!

I am happy to hear this. I guess the PLoS ONE example is emboldening others to start the experiment as well. This is a Good Thing. More journals allow the commenting on the papers, more ‘normal’ this will appear to scientist, more quickly it will become normal for scientists to use this. You remember when Nature tried this experiment a couple of years ago, then quit and proclaimed the experiment to be a failure after only six months? When they did that, I was, like, WTF? Who ever expected such a big shift in the entire scientific culture to happen in six months?! But give it another five years and it will start getting there. And remember that a scientific paper is not a blog post – do not expect a bunch of comments over the first 24 hours: they will slowly accumulate over the years and decades.
Finally, let me just notice that both Nature and Nature Methods published pro-blog editorials on the same day. And they also interviewed me this week for a topical issue on the state of science journalism/communication they are planning for a couple of weeks from now. I don’t think this is a coincidence – Nature group is cooking something and we’ll have to wait and see what that is.