From Financial Times:

In a study published on Wednesday in PLoS ONE we found that testosterone had little to do with trading skill. Traders with higher testosterone did indeed do better at this type of trading, because they took more risk. But there was no link between the hormone and their trading skills, as measured by the Sharpe ratio (of which more later). Testosterone alone was not enough.

One day Open Access Workshop was organized on November 18, 2009 at the University of Hyderabad at the initiative of the Indira Gandhi Memorial Library of the University. Professor Seyed E Hasnain, Vice-Chancellor, inaugurated the workshop and delivered his keynote speech. He stressed for the need to make the scientific literature open and free of cost. The university is planning to usher into green open access very soon.

Although the benefits of probiotics have been postulated for more than 100 years, there has been an increasing interest in the effects of probiotics on ill health and general well being over recent years.
Studies have shown positive outcomes of probiotics in the treatment and prevention of gastrointestinal infections and disease. But are generic probiotics enough? In the review “Probiotics and gastrointestinal disease: successes, problems and future prospects” published in Gut Pathogens, Eamonn Culligan et al. review the treatment of various GI disorders with specific probiotic strains. They also discuss whether the future lies with designer probiotics, which are engineered to specifically target a particular toxin or pathogen, but raise concerns of a negative public reaction to the development of this possible course of treatment.

Will designer probiotics be the future treatment of GI disorders? Or will public resistance for genetically modified organisms hinder its progress? (Source: Biomed Central Blog)

A Rapid and Economic In-House DNA Purification Method Using Glass Syringe Filters

Kim Y-C, Morrison SL

PLoS ONE 4(11): e7750. doi:10.1371/journal.pone.0007750

Background
Purity, yield, speed and cost are important considerations in plasmid purification, but it is difficult to achieve all of these at the same time. Currently, there are many protocols and kits for DNA purification, however none maximize all four considerations.

Methodology/Principal Findings
We now describe a fast, efficient and economic in-house protocol for plasmid preparation using glass syringe filters. Plasmid yield and quality as determined by enzyme digestion and transfection efficiency were equivalent to the expensive commercial kits. Importantly, the time required for purification was much less than that required using a commercial kit.

Conclusions/Significance
This method provides DNA yield and quality similar to that obtained with commercial kits, but is more rapid and less costly.

Yellow fin tuna (Thunnus albacares) and short-beaked common dolphin in a diorama of the eastern tropical Pacific at the AMNH's Milstein Family Hall of Ocean Live. (Image/R. Mickens/AMNH)

Next time you head out to your favorite sushi restaurant, you might want to think twice about ordering the tuna. There’s a good chance the fish on your plate could be an endangered species.

A new study by the American Museum of Natural History conducted DNA investigations on tuna at restaurants in New York City and Denver and found that nearly 30 percent of the tuna tested was actually endangered bluefin, and less than half of that was labeled as such.

A single bluefin tuna can sell for tens of thousands of dollars at market, a popular draw for the fishing industry. But that popularity comes with a price. Western stocks of northern bluefin tuna now hover around 10 percent of their “pre-exploitation” numbers. And last October, the country of Monaco nominated northern bluefin tuna for a listing under a complete international trade ban by the Convention on International Trade in Endangered Species (CITES), according to a press release.

The serving up of a critically endangered fish is not necessarily on the shoulders of the restaurants. They might not know they’re doing it, just as consumers might not know they’re eating it. This is because the eight species of tuna are so genetically similar – closer than humans are to chimpanzees – that even with DNA testing, it’s hard to distinguish the difference, and once tuna arrives to the U.S. market, the U.S. Food and Drug Administration-approved marketing label is simply “tuna.” A new and improved method of genetic detective work just might help change all that.

“When you eat sushi, you can unknowingly get a critically endangered species on your plate,” says Jacob Lowenstein, a graduate student affiliated with the Museum and Columbia University in the press release. “But with an increasingly popular technique, DNA barcoding, it is a simple process for researchers to see just what species are eaten at a sushi bar.”

DNA barcoding can be used to identify what animal became which product, even down to the origin of a leather handbag, according to the press release. In the case of the bluefin tuna, DNA barcoding defines a genetic key of 14 nucleotides exclusive enough to identify whether the tuna being served is bluefin. A similar method has been used to identify endangered whales on the Asian market and wildlife being sold in the African bushmeat trade.

With any luck, researchers will develop a handheld barcoding machine that can be used to identify fish on-site.

This study can be found in the current issue of PLoS ONE.

Als je buitenlandse films – in een taal die je redelijk beheerst – bekijkt met ondertitels in dezelfde taal, leer je de taal extra goed verstaan. De visuele hulp van de ondertitels maakt namelijk dat je persoonlijke uitspraakverschillen of dialectvariaties snel op de juiste manier gaat interpreteren. Zet je Nederlandse ondertitels aan, dan is het effect omgekeerd: je begrijpt de taal in de film slechter.

Deze ontdekking publiceren Holger Mitterer van het Max Planck Instituut voor Psycholinguïstiek (MPI) en James McQueen (MPI en Radboud Universiteit Nijmegen) vandaag in het tijdschrift PLoS ONE. In de studie lieten ze studenten 25 minuten kijken naar Engelse films met vreemde accenten, zoals Schots of Australisch. Keken ze met Engelse ondertiteling dan was hun begrip van het gesproken Schots of Australisch na die 25 minuten al verbeterd. De ondertitels helpen je namelijk om te begrijpen hoe de woorden zouden klinken in standaard-Engels zodat je razendsnel de klankverschillen leert herkennen.

Nederlandse ondertitel: minder begrip
De controlegroep zag de films met Nederlandse ondertitels en moest het dus zonder leerhulp doen. Dat was te merken. Na het experiment begrepen de proefpersonen de regionale varianten zelfs slechter.

De onderzoekers vinden het een goed idee om mensen die een vreemde taal leren zoveel mogelijk ondertitels te presenteren in de taal die in een programma gesproken wordt. Op dvd’s is dat vaak geen probleem. En ook op de Nederlandse televisie zou je de taal van de ondertiteling zelf moeten kunnen kiezen. Het zal nog wel even duren voor dat dat mogelijk is. Voor wie niet wachten kan om al tv-kijkend zijn Engels te verbeteren: Kies teletekstpagina 888 bij de BBC. TV5 heeft Franse ondertitels in de aanbieding.

Bron: Radboud Universiteit

(Image via USGS)

Albatrosses are very special animals. Not only are they up there on the list of largest flying birds, they also have the largest wingspan compared to any other living animal. Albatrosses have only one mate for their lives. The male and female find each other through an intensely elaborate dance ritual that takes years to perfect. They then lay one egg only and raise the chick together. Unlike other animals, the albatross does not raise a group of young, instead choosing to focus solely on one. Albatrosses have been known to spend most of their lives in the air, only landing to mate and nest.

Scientists wanted to find out what exactly the albatross do on these long journeys gliding around in the air. Unable to follow them around in a boat all the time, they attached small, lipstick sized camera’s to the birds.

Here are the results:

(Image via PLoS One)

A: a ‘featureless’ sea, B: an iceberg encountered, C: a killer whale breaking the ocean surface, apparent from its dorsal fin (white arrow) and three black-browed albatrosses attracted to the whale, D: two albatrosses flying in association with the camera-mounted bird, E: a fisheries vessel in the distance (white arrow) with an aggregation of birds, F: a bright light source during the night, possibly a vessel or the moon.

Amazing perspectives! It’s great that through the pursuit of scientific research, art is created along the way.

(via TreeHugger via PLoS One)

Impressed by PLoS style, our university here decided to teach Open Access, creative reuse and article level metrics to entry level PhD students in Life Sciences. I am grateful to the university authorities for enabling us to direct such a timely and important course for the first time in the history of graduate teaching in India; see the course curriculum approved by the university below. I hope many other universities and institutes will be able to replicate this course:

Course name: Scientific writing; Course director: Dr Niyaz Ahmed; Course credits: 1 (12 lectures in a semester)

• 1. Documentation of scientific observations and maintenance of raw data in a biology lab
• 2. Primary research articles and secondary content – commentaries, reviews, book length evaluations
• 3. Creative re-use, semantic enhancements and reproduction of open access scientific material
• 4. Copyright and Creative Commons attribution licences
• 5. Publication ethics
• 6. Malpractices in scientific reporting – examples and case studies
• 7. Citations, evaluations, article-specific metrics and impact factors
• 8. Scientific deliberations

Espanjalaiset tutkijat ovat huomanneet yhteyden endokannabinoidien ja tulehduksen välillä.

Colitis ulcerosa (CU) eli haavainen paksusuolen tulehdus on krooninen tulehduksellinen suolistosairaus. Espanjassa sijaitsevan Barcelonan yliopiston tutkijoiden mukaan endokannabinoidijärjestelmä on muuttunut niissä paksusuolen kudoksissa, jotka kärsivät haavaisesta paksusuolen tulehduksesta.

Tutkijat päättelivät, että “endokannabinoidien signaalin välitysreitti läpi CB2 -reseptorin voi vähentää colitikseen liittyvää tulehdusta. Tämä viittaisi siihen, että se voisi olla potentiaalinen kohde lääkekehitykselle Colitis ulcerosan ja Crohnin taudin hoitoihin.”

Colitis ulcerosa esiintyy paksusuolessa tai peräsuolessa. Sen oireita ovat muun muassa veriripuli, kivut (ennen ulostusta), väsymys, laihtuminen ja kuume. CU todetaan peräsuolen tai paksusuolen tähystyksessä.

Crohnin tauti esiintyy yleisimmin paksusuolessa sekä erityisesti ohutsuolen loppuosassa. Tauti voi kuitenkin esiintyä missä tahansa ruoansulatuskanavan alueella.

Crohnin taudin oireita ovat muun muassa ripuli tai ummetus, kivut (usein oikealla alavatsassa), väsymys, laihtuminen ja kuume. Tauti voi näkyä suussa olevina haavaumina eli aftoina. Tauti todetaan mahalaukun tai paksusuolen tähystyksessä, tutkimuskeinona voi olla myös ohutsuoliröntgentutkimus.

Lähde:

Marquéz L, et al. PLoS  One 2009;4(9):e6893.

http://www.unboundmedicine.com/medline/ebm/record/19730730/abstract/Ulcerative_colitis_induces_changes_on_the_expression_of_the_endocannabinoid_system_in_the_human_colonic_tissue_

PLoS ONE achieved yet another milestone yesterday by receiving an award from the ALPSP (the Association of Learned and Professional Society Publishers) for Publishing Innovation of the Year, 2009. The award is given in recognition of a truly innovative approach to any aspect of publication as adjudged from originality and innovative qualities, together with utility, benefit to the community and long term prospects. This prestigious industry award is therefore, a proof of the hard work of all the editors, managers, staff, authors, and reviewers! The award is a formal recognition of the fact that PLoS ONE has spearheaded a radical departure from traditional scientific publishing in a number of ways, from its pioneering editorial policies to its regular technical innovations, including the commentary and rating features available on all of its articles—in short, PLoS ONE now means ‘new generation scientific publishing in a most innovative and interactive style’.

It is heartening to note that 200th article from PLoS ONE has now been evaluated at the Faculty of 1000 Biology. Last year on July 17, a report on the evaluation of 100th article from PLoS ONE was posted on this blog. It is about in a year’s time that further one hundred articles were evaluated; a remarkable achievement despite a very high volume publishing in diverse areas. Since the number of articles almost tripled in a year (6000 in August 2009 versus 2600 in July 2008), the number of evaluations touched almost 10 per month (3.3% of total articles published). For a broad based and high volume journal such as PLoS ONE, the F1000 evaluations serve as an important quality index for individual articles.

By – Elio (Moselio Schaechter)

"How does anthropocentrism apply to microbiologists? In a current commentary in the new journal Gut Pathogens, Ramy Aziz reminds us that it shows up all over the place. Take the very term microbe, meaning small living thing. ‘Small,’ says who? Not the microbes. To them, other microbes would be of ‘normal’ size and we humans Rabelaisian gargantuas. This wouldn’t much matter if it stopped there, with our choice of words alone. Aziz points out that anthropocentrism in microbiology can have serious consequences. For instance, ‘pathogens’ have been considered to be special group of microbes, separate from the rest. Nothing could be farther from the truth, and nothing could be more objectionable than to consider the human body to be anything but another habitat.

In recent years, it has been increasingly realized that pathogenic microbiology is merely another branch of microbial ecology. However, a gentle reminder in Aziz’ well-turned words is welcomed. A truly integrated view of the microbial world, or of the biological world in general, cannot be anthropocentric but can only be, as Aziz says, biocentric".
[In syndication with ASM blog - 'Small things considered', original post here]. Ramy K Aziz is an Editorial Board Member of PLoS ONE.

A recent study coming out of the University of Paris Nord has expanded on the results of an 1874 experiment which saw teams of ants lend a mandible to colony-mates submerged in sand by digging them out and dragging them to safety. This time, the operation got far more complex as researchers tied nylon threads around the waists of individual desert ants (specifically Cataglyphis cursors), half-buried them in sand, and watched as teams of five ants set out to rescue them. If the rescuers came from the same colony as the tethered ants, they would shift the sand away, gnaw through the nylon, and drag their relatives out by their limbs.

Importantly, this study has revealed that the altruistic mechanism in these ants is not just a simple find-and-dig response to a chemical released by distressed individuals. That they understood the solution to be digging out and biting through the nylon thread suggests a far more sophisticated mental process is being used. What was also clear from this study is the highly selective nature of this behaviour, which sees the rescuers work in ernest to free trapped individuals from their own colony, but threaten, dismember, and spit acid at individuals from different species, or ants from different colonies.

Now, this is all seems pretty reasonable, and so some unfortunate individuals might get sprayed with acid or severely bitten on occasion, it’s no big deal in the grand scheme of things. It is nature afterall. But what could become a serious issue is the fact that if all these rescue teams are doing is wandering around, scouting for ants in distress, saving some and dismembering others, pretty soon they’re going to get a serious case of the God Complex. Like they’ll be marching through the desert on a routine expedition, passing the time by exchanging really explicit stories of past sexual exploits and discussing which hot females they’d fully like to ruin, before suddenly picking up on a chemical alarm signal which sends them scampering towards the source. And then they’ll start digging the trapped individual out and it’ll be like, “Man, I can’t believe you did it with Gloria. Isn’t she like your cousin or something?  Ahh, anyone know who this is? Have you guys seen him around before? Patrick? No? Anyone…? ACID!! ACID IN THE FACE!! KEEP GOING, HE’S GETTING WEAKER!!”

And then the expedition will move on, Steve will be talking about the time he did it with some female in the sink at Subway before Edgar interrupts with a, “Do you guys smell that?” And they’ll run over to this horrific scene where like three ants are trapped under a marbled velvet gecko carcass they thought they could carry but obviously couldn’t. So the rescuers will start digging furiously all like, “Whatever, man. You think that’s badass? Trying doing it in a proper restaurant that hasn’t put a hungover fifteen-year-old in charge of keeping the surfaces clean. Then we’ll all be impre- Shit. Hey Pierce, isn’t this that guy who hooked up with your little sister on New Years Eve that time your mum told you to keep an eye on her…? Yeah? LEGS! OFF WITH HIS LEGS!! Same colony? Whatever! Plenty more workers where you came from, buddy!”

And then they’ll start digging another one out and Piece will be like, “You know what? I’m pretty sure this is that arsehole who tried to steal my coffee table in woodwork once because we have the same initials and his was fully shit and crooked and… BITE HIM! BITE HIS HEAD!!” And meanwhile Bryce will be pulling the legs off some other colony-mate he thinks might have given his girlfriend the eye once at some party last year, gleefully dislocating the last leg with a, “How do you like me now, bitch?!”

PLoS One // Not Exactly Rocket Science // Alex Wild Photography

- bec

Photo by cudmore on Flickr

In science, much significance is placed on peer-reviewed publication, and for good reason. Peer review, in principle, guarantees a minimum level of confidence in the validity of the research, allowing future work to build upon it. Typically, a paper (the current accepted unit of scientific knowledge) is vetted by independent colleagues who have the expertise to evaluate both the correctness of the methods and perhaps the importance of the work. If the paper passes the peer-review bar of a journal, it is published.

Measuring impact

For many years, publications in peer-reviewed journals have been the most important measurement of someone’s scientific worth. The more publications, the better. As journals proliferated, however, it became clear that not all journals were created equal. Some had higher standards of peer-review, some placed greater importance on perceived significance of the work. The “impact factor” was thus born out of a need to evaluate the quality of the journals themselves. Now it didn’t just matter how many publications you had, it also mattered where.

But, as many argue, the impact factor is flawed. Calculated as the average number of citations per “eligible” article over a specific time period, it is highly inaccurate given that the actual distribution of citations is heavily skewed (an editorial in Nature by Philip Campbell stated that only 25% of articles account for 89% of the citations).  Journals can also game the system by adopting selective editorial policies to publish articles that are more likely to be cited, such as review articles. At the end of the day, the impact factor is not a very good proxy for the impact of an individual article, and to focus on it may be doing science – and scientists – a disservice.

In fact, any journal-level metric will be inadequate at capturing the significance of individual papers. While few dispute the possibility that high journal impact factors may elevate some undeserving papers while low impact factors may unfairly punish perfectly valuable ones, many still feel that the impact factor – or more generally, the journal name itself – serves as a useful, general quality-control filter. Arguments for this view typically stem from two things: fear of “information overload”, and fear of risk. With so much literature out there, how will I know what is good to read? If this is how it’s been done, why should I risk my career or invest time in trying something new?

What is clear to me is this – science and society are much richer and more interconnected now than at any time in history. There are many more people contributing to science in many more ways now than ever before. Science is becoming more broad (we know about more things) and more deep (we know more about these things). At the same time, print publishing is fading, content is exploding, and technology makes it possible to present, share, and analyze information faster and more powerfully.

For these reasons, I believe (as many others do) that the traditional model of peer-reviewed journals should and will necessarily change significantly over the next decade or so.

Article-level metrics at PLoS

The Public Library of Science, or PLoS, is leading the charge on new models for scientific publishing. Now a leading Open Access publisher, PLoS oversees about 7 journals covering biology and medicine as well as PLoS ONE, on track to become the biggest single journal ever. Papers submitted to PLoS ONE cover all areas of science and medicine and are peer-reviewed only to ensure soundness of methodology and science, no matter how incremental. So while almost every other journal makes some editorial judgment on the perceived significance of papers submitted, PLoS ONE does not. Instead, PLoS ONE leaves it to the readership to determine which papers are significant through comments, downloads, and trackbacks from online discussions.

Now 2 1/2 years old, PLoS ONE boasts thousands of articles and a lot of press. But what do scientists think of it? Clearly, enough think highly of it to serve on its editorial board or as reviewers, and to publish in it. Concerns that PLoS ONE constituted “lite” peer review seem largely unfounded, or at least outdated. Indeed, there are even tales of papers getting rejected from Science or Nature because of perceived scientific merit, getting published in PLoS ONE, and then getting picked up by Science and Nature’s news sections.

Yet there is still feeling among some that publishing in PLoS ONE carries little or no respectability. This is due in part to a misconception of how the peer review process at PLoS ONE actually works, but also in part because many people prefer an easy label for a paper’s significance. Cell, Nature, Science, PLoS Computational Biology – to most people, these journals represent sound science and important advances. PLoS ONE? It may represent sound science but it’s up to the reader to decide whether any individual paper is important.

Why is there such resistance to this idea? One reason may be tied to time and effort to impact: while citations always have taken some time to build up, a journal often provides a baseline proxy for the significance of a paper. A publication in Nature on your CV is an automatic feather in your cap, and easy for you and for your potential evaluators to judge. Take away the journal, and there is no baseline. For some, this is viewed as a bad thing; for others, however, it’s an opportunity to change how publications – and people – are evaluated.

Whatever the zeitgeist in particular circles, PLoS is clearly forging ahead. PLoS ONE’s publication rates continue to grow, such that people will eventually have to pay attention to papers published there even if they pooh-pooh the inclusive – but still rigorous – peer review policy. Recently, PLoS announced article-level metrics, a program to “provide a growing set of measures and indicators of impact at the article level that will include citation metrics, usage statistics, blogosphere coverage, social bookmarks, community rating and expert assessment.” (This falls under the broader umbrella of ‘post-publication peer review’.) Just how this program will work is a subject of much discussion, and certain metrics may need a lot of fine-tuning to prevent gaming of the system, but the growing consensus, at least among those discussing it online, is that it’s a step in the right direction.

Essentially, PLoS believes that the paper itself should be the driving force for significance, not the vehicle it’s in.

The trouble with comments

A major part of post-publication peer review such as PLoS’s article-level metrics is user comments. In principle, a lively and intelligent comment thread can help raise the profile of the article and engage people – whether it be other scientists or not – in a conversation about the science. This would be wonderful, but it’s also wishful thinking; as anyone who’s read blogs or visited YouTube knows, comment threads devolve quickly unless there is moderation.

From rustylime.com

For community-based knowledge curation efforts (think Wikipedia), there is also a well-known 90-9-1 rule: 90% of people merely observe, 9% make minor or only editorial contributions, and 1% are responsible for the vast majority of original content. So if your audience is only 100 people, you’ll be lucky if even one of them contributes. Indeed, experiments with wiki-based knowledge efforts in science have been rocky at best, though things seem to getting better. The big question remains:

But will the bench scientists participate? “This business of trying to capture data from the community has been around ever since there have been biological databases,” says Ewan Birney of the European Bioinformatics Institute in Hinxton, UK. And the efforts always seem to fizzle out. Founders enthusiastically put up a lot of information on the site, but the ‘community’ — either too busy or too secretive to cooperate — never materializes. (From a news feature in Nature last September on “wikiomics”.)

Thus, for commenting on scientific articles, we have essentially two problems: encouraging scientists to comment, and ensuring that the comments have some value. An experiment on article commenting on Nature several years ago was deemed a failure due to lack of both participation and comment quality. Even now, while many see the fact that ~20% of PLoS articles have comments as a success, others see it as a inadequate. Those I’ve talked to who are skeptical of the high volume nature of PLoS ONE tend also to view their comments on papers to be a highly valuable resource, one not to be given away for free in public but disclosed in private to close colleagues or leveraged for professional advancement through being a reviewer.

Perhaps the debate simply reflects different generational mindsets. After all, people are now growing up in a world where the internet is ubiquitous, sharing is second-nature, and almost all information is free. Scientific publishing is starting to change, and so it is likely that current incentive systems will change, too. Yet while the gulf will eventually disappear, it is perhaps at its widest point now, with vast differences in social norms, making any online discourse potentially fraught with unnecessary drama. As Bora Zivkovic mentions in a recent interview,

It is not easy, for a cultural reason, because a lot of scientist are not very active online and also use the very formalised language they are using in their papers. People who have been much more active online, often scientists themselves, they are more chatting, more informal. If they don’t like something they are going to say it in one sentence, not with seventeen paragraphs and eight references. So those two kinds of people, those two communities are eyeing each other with suspicion, there’s a clash of cultures. The first group sees the second group as rude. The second group views the first group as dishonest. I think it will evolve into something in the middle, but it will take years to get there.

When people point to the relative lack of comments on scientific papers, it’s important to point out the fact that online commenting has not been around in science for very long. And just as it takes time for citations to start trickling in for papers, it takes time to evaluate a paper in the context of its field. PLoS ONE is less than three years old. Bora notes, “It will take a couple of years, depends on the area of science until you can see where the paper fits in. And only then people will be commenting, because they have something to say.”

Brush off your bullshit detector

The last argument I want to touch on is that of journals serving as filter for information. With millions of articles published every year, it can seem a daunting task keeping up with the literature in your field. What should you read? In a sense, a journal is a classifier, taking in article submissions and publishing what it thinks are good and important papers. As with any classifier, however, performance varies, and is highly dependent on the input. Still, people have come to depend on journals, especially ones with established reputations, to provide this service.

Now even journals have become too numerous for the average researcher to track (hence crude measures like the impact factor). So when PLoS ONE launched, some assumed that it would consist almost entirely of noise and useless science, if it could be considered science at all. I think it’s clear that that’s not the case; PLoS ONE papers are indeed rigorously peer-reviewed, many PLoS ONE papers have already had great impact, and people are publishing important science there. Well, they insist, even if there’s good stuff in there, how am I supposed to find what’s relevant to me out of the thousands of articles they publish every year? And how am I supposed to know whether the paper is important or not if the editors make no such judgment?

Here, I would like to point out the many tools available for filtering and ranking information on the web. At the most basic level, Google PageRank might be considered a way to predict what is significant and relevant to your search terms. But there are better ways. Subscribing to RSS feeds (e.g. through GoogleReader) makes scanning lots of article titles quick and easy. Social bookmarking and collaborative filtering can suggest articles of interest based on what people like you have read. And you can directly tap into the reading lists of colleagues by following them on various social sharing services like Facebook, FriendFeed, Twitter, and paper management software like Mendeley. I myself use a loose network of friends and scientific colleagues on FriendFeed and Twitter to find interesting content from journals, news sites, and blog posts. The bonus is that you also interact with these people, networking at its most convenient.

The point is that there is a lot of information out there, you have to deal with it, and there are more and more tools to help you deal with it. It’s no longer sufficient to depend on only one filter, and an antiquated one at that. It may also be time to take PLoS’s lead and start evaluating papers on their own. Yes, it takes a little more work, but I think learning how to evaluate papers critically is a valuable skill that isn’t being taught enough. In a post about the Wyeth ghost-writing scandal, Thomas Levenson writes:

… the way human beings tell each other important things contains within it real vulnerabilities.  But any response that says don’t communicate in that way doesn’t make sense; the issue is not how to stop humans from organizing their knowledge into stories; it is how to build institutional and personal bullshit detectors that sniff out the crap amongst the good stuff.

From nitot on Flickr

Although Levenson was writing about the debate surrounding science communication and the media, I think there’s a perfect analogy to new ways of publishing. Any response that says don’t publish in that way doesn’t make sense; the issue is not how to stop people from publishing, it is how to build personal bullshit detectors – i.e. filters. People should always view what they read with a healthy dose of skepticism, and if we stop relying on journals, or impact factors, or worse to do all of our vetting for us, we’ll keep that skill nicely honed. At the same time, we are not in this alone; leveraging a network of intelligent agents – your peers – will go a long way.

So continue leading the way, PLoS. Even if not all of the experiments work, we will certainly learn from them, and keep the practice and dissemination of science evolving for the times.

Quite by chance, I stumbled on this interesting paper [1] yesterday by Philip Campbell who is the Editor-in-Chief of the scientific über-journal Nature [2]. Here is the abstract:

As Editor-in-Chief of the journal Nature, I am concerned by the tendency within academic administrations to focus on a journal’s impact factor when judging the worth of scientific contributions by researchers, affecting promotions, recruitment and, in some countries, financial bonuses for each paper. Our own internal research demonstrates how a high journal impact factor can be the skewed result of many citations of a few papers rather than the average level of the majority, reducing its value as an objective measure of an individual paper. Proposed alternative indices have their own drawbacks. Many researchers say that their important work has been published in low-impact journals. Focusing on the citations of individual papers is a more reliable indicator of an individual’s impact. A positive development is the increasing ability to track the contributions of individuals by means of author-contribution statements and perhaps, in the future, citability of components of papers rather than the whole. There are attempts to escape the hierarchy of high-impact-factor journals by means of undifferentiated databases of peer-reviewed papers such as PLoS One. It remains to be seen whether that model will help outstanding work to rise to due recognition regardless of editorial selectivity. Although the current system may be effective at measuring merit on national and institutional scales, the most effective and fair analysis of a person’s contribution derives from a direct assessment of individual papers, regardless of where they were published.

It’s well worth reading the views of the editor of an important closed-access journal like Nature, a world champion heavyweight of Impact Factor Boxing. So their view on article-level bibliometrics and novel models of scientific publishing on the Web like PLoS ONE is enlightening. There are some interesting papers in the same issue, which has a special theme on the use and misuse of bibliometric indices in evaluating scholarly performance. Oh, and the article is published in an Open Access Journal too. Is it just me, or is there a strong smell of irony in here?

References

1. Philip Campbell (2008). Escape from the impact factor Ethics in Science and Environmental Politics, 8, 5-7 DOI: 10.3354/esep00078 see more commentary on this paper over at friendfeed
2. Philip Campbell (1995). Postscript from a new hand Nature, 378 (6558), 649-649 DOI: 10.1038/378649b0
3. John Sturges (1963) The Great Escape

Via our daily Google Alert email we learned of some interesting research into ancient barley at the University of Warwick, where ‘boffins’ have recovered significant DNA information ‘from a lost form of ancient barley that triumphed for over 3000 years seeing off: 5 changes in civilisation, water shortages and a much more popular form of barley that produces more grains’.

The press release, which summarises a paper entitled “Archaeogenetic Evidence of Ancient Nubian Barley Evolution from Six to Two-Row Indicates Local Adaptation”,  has just been published in PLoS One, although a search for the paper there was fruitless (if someone can point us to the paper we’d appreciate it)!

Written by Dr Robin Allaby, Sarah A. Palmer and Jonathan D. Moore from the University of Warwick’s plant research arm Warwick HRI; Alan J. Clapham from Worcestershire Historic Environment & Archaeology Service at the University of Worcester; and Pamela Rose fromThe McDonald Institute for Archaeological Research, University of Cambridge, it describes the results of their examination of archaeobotanical remains of ancient barley at Qasr Ibrim in Egypt’s Upper Nile.

Qasr Ibrim was once a cliff-top fortress standing at the edge of the Nile in what is now the far south of Egypt, in the region known as Lower Nubia. Today, it is a tiny island in Lake Nasser, the lake created by the construction of the Aswan High Dam some forty years ago.

Photo used under Creative Commons from Chericbaker

According to Wikipedia ‘human habitation at the site dates from the Late Kingdom (the last flowering of native Egyptian rulers after the Third Intermediate Period from the 26th Saite Dynasty into Persian conquests ending with the death of Alexander the Great. It ran from 664 BC until 323 BC.) but it reached its greatest prominence in the Middle Ages. Qasr Ibrim is the source of the largest collection of Old Nubian documents ever found. The site was occupied for over 3000 years by 5 successive cultures: Napatan, Roman, Meoitic, Christian and Islamic (more info on Qasr Ibrim here).

According to the press release;

‘The first surprise for the researchers was that throughout that period every culture seemed to be growing a two rowed form of barley. While natural wild barley tends to be two rowed most farmers prefer to grow a much higher yield 6 row version which produces up to 3 times as many grains. That 6 row version has grown for over 8000 years and that was certainly grown in the lower Nile over the same period as Qasr Ibrim was occupied. It was thought that despite the fact that the rest of Egypt used 6 row barley that the farmers of Qasr Ibrim were perhaps deliberately choosing to import 2 rowed barley but the researchers could not understand why that would be so.

The plant scientists were pleased to find that the very dry conditions at Qasr Ibrim meant that they were able to extract a great deal of DNA information from barley samples from the site that dated back 2900 years. This was far better than would normally be expected from barley samples of that age. This led to the researchers to a second and much bigger surprise. They found that the DNA evidence showed that the two rowed barley at the site wasn’t the normal wild two eared barley but a mutation of the more normally cultivated six rowed barley that had changed into a two ear form that had continued to be cultivated for around three millennia.

“There may have been a natural selection pressure that strongly favoured the two-row condition. One such possible cause we are currently investigating is water stress. Qasr Ibrim is located in the upper Nile which is very arid relative to the lower Nile where six-row remains are found, and studies have shown that two-row can survive water stress better than six-row”’

Dr Robin Allaby concludes that:

“This finding has two important implications. Such strong selection pressure is likely to have affected many genes in terms of adaptation. Archaeogenetic study of the DNA of such previously lost ancient crops could confirm the nature of the selection pressure and be very valuable in the development of new varieties of crops to help with today’s climate change challenges. Secondly this crop’s rediscovery adds to our respect for the methods and thinking of ancient farmers. These ancient cultures utilized crops best suited to their environmental situation for centuries, rather than the much more popular six rowed barley they used a successful low grain number yield crop which could cope far better with water stress.”

We’d venture to suggest that the authors have a look at brewing techniques.com here.

Particularly this bit:

‘It is widely believed that two-row barleys are the best barleys for malting and brewing. In fact, outside North America most of the world’s brewing nations exclusively use two-row barley for malt. Six-row barleys, if produced overseas at all, are largely used only for feed.’

Or this bit:

‘The historical preference for two-row barley is based on the fact that two-row barley yields malts with 1-2% greater theoretical extract, meaning that brewers can brew more beer..’

Or this table:

And as the people at brewing techniques point out – it should be mentioned that every barley cultivar, whether six-row or two-row, can have distinct effects on the organoleptic (flavor, aroma, color) characteristics of beer. Two-row malts are generally believed to yield a mellower flavor (our emphasis).

Perhaps there’s a very good reason why the researchers have discounted selection in order to produce a better beer. But at first glance it seems to be a very simple solution to the mystery as to why these ancient Egyptian farmers specifically choose to grow the 2 row variant.

Addendum: Via a third party we’re told that Alan  Clapham, one of the paper’s authors,  thinks it is more likely that it was environmental pressures that forced them into using two row barley (and he points out that it is  six row barley which has reverted to two row) – the arid nature of the site -but suggests we have a look at the work of Delwen Samuel on her experimental brewing at Tell el-Amarna. Apparently the product of this experiment was once produced commercially by Scottish and Newcastle.

Additionally, the full article we were referring to is available here…

]]> http://openlogic.wordpress.com/2009/07/04/the-journal-of-biosciences-india-struggling-to-exist-or-to-make-a-difference/ Sat, 04 Jul 2009 13:10:41 +0000 Niyaz Ahmed http://openlogic.wordpress.com/2009/07/04/the-journal-of-biosciences-india-struggling-to-exist-or-to-make-a-difference/

The Journal of Biosciences is the only ‘high impact’ journal of life sciences published from India under the aegis of the Indian Academy of Sciences. The journal has established an impressive rapport among life sciences communities in India and elsewhere. Sadly, however, it was flagged recently in a meeting (read ahead) that not many of its well-wishers themselves consider to publish their best of the best research in J Biosci. I attended the meeting of the Editors of the J Biosci recently wherein all interested to the cause of the journal were invited. I found morale of the associates of the journal and the authors quite upbeat, also in the aftermath of recently released ‘journal impact factors’ – JIF 2008; the J Biosci has recorded a ‘comfortable’ IF of 1.7! However, I think they need to be careful on the statistics part because the number of papers published by the journal has been traditionally very low; it published about 70 citable articles in a 2 year period. Given this, I thought it will not be appropriate to celebrate the jacked up IF, but to introspect as to why the acceptance rate is so low (just 7%) and why so many commentaries and secondary content being published and not much original research? I guess the board members, might as well consider following the example of PLoS journals wherein many of the PLoS advocates first published their high quality (the so called ‘Nature, Cell, Science, PNAS quality’ of stuff??) research in the journals they stood for. Well, this proposition didn’t go well – there were arguments in favor and against and the excuses given were vivid. We can understand the hesitation, but as someone said, ‘charity begins at home’! Other hindering things could be the extraordinarily long time taken by the journal, as told, for completing the peer review (somewhere near 3-4 months) and for eventual publication after acceptance (2 more months). Keeping aside these deficiencies, I think we are looking at an emerging journal coming up from a developing country domain and I am all in favor of publishing there as long as the journal follows an Open Access policy although Springer has already started selling the contents through paid views/downloads under an agreement with the journal/academy.

Ramy Aziz, one of the most enthusiastic members of the PLoS ONE Editorial Board has very nicely commented on a recently published PLoS ONE article which highlights the failures of the so called ‘impact factor’ based rating of the value of science journals. The journal impact factors were released last week itself and thus the analysis presented in the article is very timely, indeed. Below are Ramy’s comments to which I agree 100%:

“The presented results pertain to what we believe to be the largest and most thorough survey of usage- and citation based measures of scientific impact.”

I agree with the above statement and I definitely like this thorough comparison of a large number of “impact measures.” The article is also informative and has introduced in detail many methods for evaluation of scientific literature with which I was not familiar.

However, on reading the article, I had the following concerns regarding its reliability:

1) Most of the readers will only read the abstract, especially because the article is full of statistical and technical terms. The conclusion of the abstract is not so informative and poorly represents the insightful discussion at the end of the article.
In particular, I would have preferred a positive than a negative conclusion. I would have preferred a recommendation of which measures correlate better with each of the multiple dimensions of scientific attributes (e.g., quality, prestige, impact, immediacy, etc.) rather than the–rather obsolete–conclusion that JIF is not optimal and should be “used with caution.” I have read more than 20 articles and editorials (including those in Science, JBC, JCI, PLoS) written in the past two years and stating that JIF should be used with caution.

2) I agree with the authors that JIF is misused; however, a value cannot be blamed for what it does not stand for. I believe the authors have given more importance to JIF (probably because of its “impact” on the scientific community), and I think that this has affected the objectiveness of the paper.

3) As the authors state in the introduction, until now I’m not sure whether how “scientific impact” is defined. Is it “journal impact”, “article impact”, or “scientist impact”? And which of these matters more? However, the authors seem to have committed the same unfair comparison that JIF and SJR do: measuring articles, scientists, and even “science” itself by the journals rather than by the articles. Journal-level metrics simply mean that an article is evaluated mostly prior to its publication. Once a scientist “makes it to Science or Nature,” he or she celebrates even if the article will never be cited again!

4) Once more I declare my agreement with the authors that JIF is neither the most accurate nor the fairest way to measure scientists, articles, or even journals. However, this “conclusion” is clearly stated in the introduction (quoted below). Why the analysis then?

“The JIF is now commonly used to measure the impact of journals and by extension the impact of the articles they have published, and by even further extension the authors of these articles, their departments, their universities and even entire countries. However, the JIF has a number of undesirable properties which have been extensively discussed in the literature [2], [3], [4], [5], [6]. This had led to a situation in which most experts agree that the JIF is a far from perfect measure of scientific impact but it is still generally used because of the lack of accepted alternative”

5) One final concern/question.
Citation-based metrics take into consideration journals that are technologically behind (for many “non-science-related” reasons, including funding problems, poor management, being published in a developing country, etc.) and thus do not have well established web sites but are still citable and cited. Do the “usage-based metrics” just ignore those journals?

Here comes a new PLoS ONE article describing one of the most authoritative analyses of the research impact – by none other than the Wellcome Trust. The research conducted by experts of the Trust summates that authoritative opinions about a published research finding constitute important benchmark of the quality of biomedical research. These data vindicate stand of the advocates of post publication peer review (and I am one humble volunteer) that modern day qualitative indicators are extremely necessary to judge the impact of biomedical research findings. Not only that this article supports and strengthens cause of the ‘Faculty of 1000’ but also that of PLoS ONE, although indirectly. The latter is no doubt the most successful forerunner of the idea of post-publication peer review and qualitative assessment while harnessing the web2.0 based semantic tools for such purposes. At this critical juncture, it is time for the concerned institutions to retrospect about their practices of evaluating research productivity of scientists based on bibliometric indices (such as the ‘impact factor’) alone.

A new PLoS ONE article describing whole genome sequence of a contaminating mycobacterial species, Mycobacterium abscessus is the most recent addition to the ‘PLoS ONE Prokaryotic Genome Collection‘.

The article presents most important observations such as those related to the presence of several novel virulence determinants of non-mycobacterial origins and that these were perhaps acquired from other environmental organisms and pathogens including Rhodococcus sp., Streptomyces sp., pseudomonads and Burkholderia cepacia.