Public Library of Science - PLoS ONE Blog

New Academic Editor Interview - Niyaz Ahmed

Peter Binfield — Tue, 18 Nov 2008 10:17:47 -0800

At the end of October 2008, Niyaz Ahmed (PLoS ONE Section Editor for Microbiology and Genomics) passed the milestone of 50 papers handled for PLoS ONE and by the time I caught up with him to congratulate him, he had reached almost 60. Given this great achievement, I thought it would be a perfect excuse to interview him for our ongoing series of ‘Discussions with PLOS ONE Editors”.

Niyaz is a group leader, in charge of a team of 10, at the “Centre for DNA Fingerprinting and Diagnostics” in Hyderabad, India. His lab is interested in the molecular basis of the acquisition and adaptation of chronic pathogens to their host niches, and the outcome of that adaptation in the long run. He kindly took time out of his schedule to speak to me at 11.30 in the evening (just 9 am in San Francisco, with a 13 ½ hour time difference) - this was a time when he would normally be working on PLoS ONE submissions!

PB: Niyaz – tell me what it is like to do research in India?

NA: Being based in India is a huge advantage for my work. India is unfortunately a hot spot for infections such as TB and enteric diseases where my main interests lie. In addition, there is a great deal of cultural and genetic diversity here that broadly influences the acquisition, maintenance and eradication of the diseases. . Therefore, my location is important from a host point of view as well as from a pathogen’s point of view. In addition, in the post genomic era there is a great deal of resources and collaborative interests percolating through to India. My group extensively collaborates with laboratories in Europe and elsewhere and we have a long term collaborative program running at the University of Sassari, Italy.

PB: What do you feel makes PLoS ONE relevant to scientists?

NA: I have spoken to many of the young leaders in science, and most of them think that PLoS ONE is making new headway in science communication, and that its’ most important function is to provide an inclusive forum (by which I mean one can publish topics between the disciplines and across the disciplines). This is the main thing that makes PLoS ONE so distinct. I would also highlight the tools that it provides for rating, evaluation, and post publication commenting, as well as the journal clubs. It is a very open, very inclusive, and yet very smart independent system of publishing – that is what attracts the attention of the new generation. Also some people are very interested in the swift speed at which papers are published. So I think the inclusive scope, the speed and being a platform for discussion are three of the most important things in my opinion.

PB: And tell me about your blog that you write - BLoG ONE

NA: I felt that I would like to air my own ideas about the papers that I am accepting and that I should somehow put what I feel about each particular paper on the web. And that is how I started the blog – as a way to highlight the best of those papers that I have been accepting. This was my way to advocate for PLoS ONE, and each post clearly links back to PLoS ONE. But I don’t just highlight papers that I handle, I also highlight many of the other PLoS ONE papers that are published every week. Although the sole intention of the blog is to advocate for PLoS ONE, I do feel that it highlights the contemporary approach to the OA debate that PLoS ONE represents.

PB: Well, we thank you for doing this – your blog is a very nice example of how to re-promote Open Access content. And what is your opinion on our acceptance criteria?

NA: As a journal we are promoting article level evaluation in the light of new generation, post publication metrics (cites, trackbacks, blog posts, media coverage, ratings, social bookmarking and journal clubs). Impact Factor only matters for the journal level evaluation of the literature. Here, we are inclusive in the sense that if the research is sound, it has adhered to the community standards, and it has been performed with a rigorous methodology then it should be accepted in the literature. So long as the research qualifies to be included in the literature, then we are not worried about its impact because its impact will be determined by the readers and the community. In this way, it is our part to let the content go before the readers and the community and only then to sit and analyze the trends.

PB: How many hours a week would you say you devote to PLoS ONE?

NA: Mostly in the evenings, after I come back from the lab I will be working on my editorial assignments. I typically spend 2 hours a day on my tasks as Section Editor and then for manuscripts that I am personally reviewing, I may work on them for more than a week before being able to submit a review. My institute gives me the freedom to make myself available for this work. They consider my time spent on editorial activities to be part of professional activity, and that is very supportive of them.

PB: What would you say is the ‘best’ paper you have handled and why?

NA: Well, all the articles that I accept are carefully considered after a rigorous peer review. The most noteworthy, however, is the case of a set of two related manuscripts on the topic of coral reef conservation (by Dinsdale and colleagues and Sala and colleagues) that I edited in February this year. My impression is that these papers would have been otherwise published in any of the frontline science journals if they were not fielded in PLoS ONE. Both the articles were based on the Scripps Institute expedition findings and were enthusiastically received by the international media. A commentary on these articles was simultaneously published in PLoS Biology and the articles were evaluated in Faculty of 1000. I have separately indicated why I have recommended publication of these articles and why I liked to handle these articles.

PB: And finally, what would you say is the thing about Open Access that most excites you?

NA: Developing countries are in great need of Open Access. The fruits of the scientific and technological revolution are not reaching them because they have to pay to receive the content. In an Indian case scenario, while the library budgets are dwindling, internet access has become affordable for masses, thanks to our technology driven economy. And that is where OA comes to enhance research productivity as well as the pace of discovery. Finally, I will say, that knowledge should not be kept bound. Knowledge is created to be open. It’s a free world!

PB: That is a great note to end on. Thank you for your time Niyaz, and congratulations again on handling so many papers for PLoS ONE.

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Academic Editor Interview - Ivan Baxter

Peter Binfield — Thu, 6 Nov 2008 10:36:07 -0800

To kick off our series of interviews with PLoS ONE Editiorial Board Members, I started with a phone call to one of our longer standing Academic Editors - Ivan Baxter, who is currently the Section Editor covering Plant Biology. Ivan is a Senior Research Associate at the Bindley Bioscience Center at Purdue University.

PB. I’d like to start with a bit more detail on your scientific background.

IB. I am a computationally oriented plant biologist and I am interested in how plants interact with their environment to regulate the mineral content of their tissues. I’ve been doing plant biology for 8 years now; looking at mineral nutrition for the last four, and before that I was working on ion transporters. Before getting into plants, I worked on RNA biochemistry. I am currently the Plant Biology Section Editor for PLoS ONE in addition to being an Academic Editor and I have been on the PLoS One Editorial Board since the summer of 2006.

PB. What was it that attracted you to PLoS ONE in the first place?

IB. I liked the fact that we don’t worry about trying to define what is significant – that attracted me right from the start as I’ve always felt that was extremely arbitrary. I’ve always been excited about the whole idea of Open Access, and another strong feature that attracted me to PLoS ONE was the fact that you can make the paper as long as you wanted as long as it is good and cohesive.

PB. How does the peer-review process on PLoS ONE work?

IB. Since joining the Board, I have also acted as a reviewer for three of the top plant journals, and the review process is similar at all of those journals. A paper is submitted to PLoS ONE and the PLoS Editorial team review it for formatting and quality control issues. Then they work to find an Academic Editor, frequently, this involves a section editor like myself. As a working plant biologist, I am able to identify which of the 15+ (and growing) plant researchers on the editorial board is the best match for the paper. Our plant biology editors span a wide variety of disciplines within plant biology and are located on five continents. Once a board member agrees to review a paper they also accept responsibility for ensuring the quality of the manuscript if it is going to be published in PLoS ONE.

PB. What is the standard of peer-review on PLoS ONE?

IB. The standards that we apply to papers are the same as I apply as a reviewer at other plant journals, with one major exception. We look for papers that present primary research that has been conducted to a high technical standard where the conclusions are supported by the experiments. We also, of course, insist that the experiments are conducted in an ethical manner, that the underlying data has been deposited in the appropriate repository, and that the writing is intelligible. What we don't do is apply an arbitrary significance standard (i.e. this paper is in the top 27.465% of those in its field), which is a highly subjective judgment. As a result of our strict standards, most papers are either rejected or returned to the authors for revisions. Some of the revisions end up as de facto rejections if the authors are not able to correct the identified deficiencies. However, a majority will be published after the authors address the reviewers' comments and concerns. Like the review process at other journals, the review process at PLoS ONE improves the quality of the papers that we publish, however since we will publish any paper that meets our standards, authors know they won't have to go through multiple rounds of reformatting and revision to resubmit to multiple journals.

PB How quickly does this process move?

IB. Regarding the speed of our processes, I think we are as good as any journal I know of, if not better and that overall it moves faster than anywhere else. I think we have established a different process and that it is good and rigorous.

PB. What’s the general quality of submissions like?

IB. I also think that in general we are getting very good quality submissions. Obviously there is a range, but I have handled several papers which I feel could have been published in the top journals in my field and for whatever reason were not.

PB. Why do you think so many scientists submit to PLoS ONE?

IB. I feel that these papers come to PLoS ONE because of the speed, but also the fact that if an author is confident that their science is good then they should feel that there is no reason why their paper would not be published in PLoS ONE. That is very reassuring because at most other journals you go to, you can persuade the reviewers to agree that the paper is correct and still even after making all their corrections they may come back to you and say that is it “not quite right for our journal". We are never going to say that, so if you go to PLoS ONE and you are confident that your science is good then you can be confident that you will be published. You may be wrong, of course, and you will find that out through our review process, however the knowledge that you’re not going to have to reformat, resubmit to multiple journals is very attractive to people.

If you think that you have the skills and expertise to join the Editorial Board of PLoS ONE, please let me know (pbinfield@plos.org). If you want to experience this process for yourself, please send us your work.

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New interview with PLoS ONE author

Liz Allen — Mon, 27 Oct 2008 09:18:54 -0700

We are continuing our series in which we look at PLoS ONE articles that have a combination of good publicly available article level metrics (usage data: page views; citations (from Google), media coverage, comments and ratings etc).

Another such article is Aversive Learning in Honeybees Revealed by the Olfactory Conditioning of the Sting Extension Reflex. I asked the Author (and Editorial Board member of PLoS ONE) of this article Martin Giurfa of the Research Centre on Animal Cognition (CNRS), University Paul-Sabatier, France, about why he chose PLoS ONE to publish his work and what his experience was like. This is what he said:

Q. Please briefly describe the topic of this paper and how you went about the research?
A. For almost 100 years the honeybee has been a traditional invertebrate model for the study of learning and memory but so far a single modality was investigated: appetitive learning in which bees were always rewarded with sugar to support learning. In this paper we overcome this limitation and provide the first controlled demonstration of aversive learning in honeybees. We showed that this learning is amenable to the laboratory and explored its cellular basis. Using odorants paired with electric shocks, we conditioned the sting extension reflex, which is exhibited by harnessed bees when subjected to a noxious stimulation. In parallel, we identified dopamine as the biogenic amine that substitutes aversive reinforcement in the bee brain, as opposed to octopamine that was shown to substitute for appetitive reinforcement.

Q. Why do you think this paper attracted interest and what are you investigating now?
A. This would be too long to go into here. Suffice to say that people have realized that aversive learning can now be studied in bees for the first time and that it is possible to access the brain simultaneously. In my opinion a very important step in the case of an animal that for decades has been the model for just appetitive learning

Q. Why did you choose PLoS ONE?
A. Because I wanted to support the PLoS ONE initiative by sending what I considered to be one of my best works. Because I thought that PLoS ONE could become an extremely important and recognized journal where the fashion ("we are not sending your paper to reviewers because it is not of general interest...") is excluded.

Q. What was your experience of publishing with us like?
A. The experience was very positive. Good editor, good reviewers, constructive criticisms, etc.

If this experience sounds good to you and you’ve not tried PLoS ONE yet or you’ve only published with us once or twice, we would welcome your work .

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Interview with a PLoS ONE author

Peter Binfield — Mon, 20 Oct 2008 12:47:29 -0700

We've been looking at PLoS ONE articles that have a good combination of important article level metrics (usage data: page views; citations, media coverage, comments and ratings etc). One such article is On the origin and Functional Architecture of the Cortex which was also featured in a journal club discussion at The Sydney University Visual Physiology Group.

I asked the Author of this article, Dario Ringach of the University of California Los Angeles, why he chose PLoS ONE to publish his work and what his experience was like. This is what he said:

Q. Why did you choose PLoS ONE?
A. It allowed a venue to publish a controversial theory about the origins of the functional architecture of the cortex. PLoS would make these ideas widely accessible and also provided a forum for discussion which, in my mind, was very useful to get constructive criticism to guide the further development of the theory.

Q. Why do you think this paper attracted interest and what are you investigating now?
A. The paper has likely attracted some attention because some predictions of the theory have now been verified (a) the dependence of orientation bandwidth with the location of neuron within the orientation map, (b) the clustering of on/off afferents in layer 4, and (c) a direct relationship between the clusters of on/off afferents and the preferred orientation of cells at that site. Our theoretical work has concentrated on expanding and working on this model to come up with new predictions and tests that could be experimentally tested with available techniques.

Q. What was your experience of publishing with us like?
A. It was a piece of cake... rapid turn around, almost no mistakes in typesetting (despite the heavy math). I will likely do it again!

If this experience sounds good to you and you’ve not tried PLoS ONE yet or you’ve only published with us once or twice, we would welcome your work.

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Bats eat birds - join the discussion

Bora Zivkovic — Tue, 30 Sep 2008 15:43:13 -0700

As the month of September is coming to a close, and the topic of the month in PLoS ONE is bats, we decided to end the focus with a Journal Club.

Starting today, and lasting a week, there will be a Journal Club on this PLoS ONE article - Bats' Conquest of a Formidable Foraging Niche: The Myriads of Nocturnally Migrating Songbirds by Ana G. Popa-Lisseanu, Antonio Delgado-Huertas, Manuela G. Forero, Alicia Rodriguez, Raphael Arlettaz and Carlos Ibanez:

"Along food chains, i.e., at different trophic levels, the most abundant taxa often represent exceptional food reservoirs, and are hence the main target of consumers and predators. The capacity of an individual consumer to opportunistically switch towards an abundant food source, for instance, a prey that suddenly becomes available in its environment, may offer such strong selective advantages that ecological innovations may appear and spread rapidly. New predator-prey relationships are likely to evolve even faster when a diet switch involves the exploitation of an unsaturated resource for which few or no other species compete. Using stable isotopes of carbon and nitrogen as dietary tracers, we provide here strong support to the controversial hypothesis that the giant noctule bat Nyctalus lasiopterus feeds on the wing upon the multitude of flying passerines during their nocturnal migratory journeys, a resource which, while showing a predictable distribution in space and time, is only seasonally available. So far, no predator had been reported to exploit this extraordinarily diverse and abundant food reservoir represented by nocturnally migrating passerines."

Folks in the The Kalcounis-Ruppell lab, Hershey lab and O'Brien lab in the Department of Biology at UNC Greensboro, have read and discussed the paper and posted their comments here.

You know what to do - go there, register/login and join the conversation.

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At PLoS ONE we're batty about Bats

Peter Binfield — Tue, 9 Sep 2008 09:57:25 -0700

Every month, PLoS ONE focuses on a particular topic where we publish a significant volume of work. This month we are focusing on Bat research which broadly falls into 2 categories, Physiology/Behaviour and Disease/Epidemiology - we have analyzed our top papers in the field in terms of viewing patterns, citations and media/blog coverage.

From this analysis, the paper entitled Marburg Virus Infection Detected in a Common African Bat by Towner et al, was the most viewed of this group (Source: Google Analytics) and the most cited by other scientists (Source: Google Scholar). It also received nice blog coverage, for example, this post by Tara C. Smith in the blog Aetiology

From the same analysis, the paper entitled Accelerated FoxP2 Evolution in Echolocating Bats by Li et al, had our second highest number of unique page views of all Bat papers and also received a good deal of coverage in the blog community:

As the Managing Editor of PLoS ONE, I am always interested to know what motivates our authors to publish with us and find out more about their research. A good way to do this is to interview the authors of these high profile papers, and so we asked Stephen J. Rossiter, from the University of London (the corresponding author of this paper) why he and his team chose PLoS ONE to publish this work. He said:

“We were attracted to PLoS ONE for its quick publishing, open source ethos and the lack of limit on the manuscript length. We are pleased that in spite of being published only last year, our paper has already been cited three times”.

We are also always interested in learning about the publication process that our authors experienced and whether they would do it again. In this case, the reply was:

“When we first submitted our paper to PLoS ONE, we were slightly concerned that its content might not be reviewed beyond an appraisal of its methodological competency. Not a bit of it - the paper received two very thorough and constructive reviews by leaders in the field, which were as rigorous as any that we have seen from top-ranking journals”.

Finally, we sought the author’s perspective on why they think that a paper is so highly read; the impact it made on the field at the time and how the field and their role in it has moved on since publication:

“The story of FoxP2 exemplifies how genes of medical significance can help shed light on evolutionary processes, and vice versa. Variation in FoxP2 is linked to speech coordination defects in humans, but seems to correlate with the origin of echolocation in bats. These results then led us to discover that the cochlea gene Prestin, which underpins high frequency hearing in mammals and is linked to human deafness, has undergone convergence in lineages of echolocating bats”.

Overall, we clearly delivered an excellent publishing experience for these authors, and we are certainly pleased that their work is receiving so much positive attention in the community.

Naturally, I wanted our Bat focus to either coincide with the release of the latest Batman movie or with Halloween, but like a small mammal flapping just out of reach, both dates eluded us. We hope that this won’t put you off from sending your work to us and receiving a similarly satisfying publication experience.

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The Neuroscience of Things That Make You Go "Ew!"

Rebecca Walton — Mon, 18 Aug 2008 12:04:22 -0700

Paul Sereno’s paper wasn’t – by any means – the only PLoS ONE paper published last week to have been covered by the press and by bloggers.

Reporting in PLoS ONE on August 13, Matt Finer, of Save America's Forests, and colleagues at Duke University and Land Is Life tracked hydrocarbon exploration projects across the western Amazon and generated a detailed map of oil and gas activities across the region, which, the researchers found, overlaps considerably with the latest biodiversity maps for amphibians, birds and mammals. Unlike the eastern Brazilian Amazon, the western region is still largely intact but large reserves of oil and gas lie below the landscape of the latter and growing global demand is leading to increased exploration and development in the region. There were news stories on the study in The Guardian, New Scientist and The Associated Press and it was blogged by Daily Kos, The Intersection and DigitalJournal.com.

Another study raising environmental issues – this one by Alex Pyron and colleagues at The City University of New York – outlined the potential effects of climate change on Burmese python populations in the United States. The PLoS ONE study found that, contrary to previous research, the pythons were unlikely to spread beyond the Floridian everglades in which they make their homes. The researchers used records on the distribution of pythons in their native range along with high resolution global climate databases to predict the potential extent of the python’s distribution in the U.S. and model the possible effects of global warming on the snakes. The results suggest that the pythons are restricted to the vicinity of the Everglades in extreme south Florida. The study was featured on Live Science and was also picked up on some of the wires.

As an ophidiophobic, reading Pyron’s article and some of the news stories (especially those with accompanying images) made me feel a little uneasy. In their article published in PLoS ONE last week, Mbemba Jabbi at the National Institutes of Mental Health, along with colleagues at the University Medical Center Groningen, shed some light on how reading a book or watching a film can invoke in us the same emotions as if we were experiencing the events ourselves. Focusing on the emotion of disgust, the researchers used an fMRI scanner to measure the participants’ brain activity while they: had drops of an unpleasant, bitter liquid placed on their tongue; watched a video of “disgusting” behaviour; and read a passage of disgusting text. They found that the same areas of the brain – the anterior insula and adjacent frontal operculum – were activated both when the participants tasted the liquid and when they watched the video and read the passage. The article was covered by New Scientist (although, note the disclaimer – “Warning: this story contains a paragraph of disgusting text” at the top of the story), Wired, PsychCentral and Discount Thoughts.

Finally, researchers led by Daniel Perez at the University of Maryland studied the H9N2 strain of the influenza virus, publishing their findings in a paper entitled, Replication and Transmission of H9N2 Influenza Viruses in Ferrets: Evaluation of Pandemic Potential. The scientists used ferrets (whose biology is very close to humans when it comes to flu) to characterise the mechanism of replication and transmission of recent avian H9N2 viruses and, according to the paper, the results suggest that, “the establishment and prevalence of H9N2 viruses in poultry pose a significant threat for humans.” There were news stories about the study in Reuters, AFP, Science News and Discover Magazine.

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Digging into the "Green Desert" of Niger's Holocene Past

Rebecca Walton — Mon, 18 Aug 2008 11:47:14 -0700

After the massive media buzz surrounding the last paper published in PLoS ONE by Paul Sereno, in which he and colleagues described the anatomy and behaviour of Nigersaurus taqueti (dubbed “the Mesozoic cow” by the press), you can imagine that we were quite excited to receive another paper from the University of Chicago Palaeontologist and National Geographic Explorer-in-Residence.

Sereno and his team had originally been on a dinosaur-hunting expedition in the Ténéré Desert in Niger (which is where the Nigersaurus fossil was discovered) when they happened on a large, Stone Age graveyard. In the new PLoS ONE article, Lakeside Cemeteries in the Sahara: 5000 Years of Holocene Population and Environmental Change, the researchers outline the findings from a series of new archaeological sites at Gobero, dating from the Holocene and preserving the earliest Saharan cemetery from around 9500 years ago, as well as burials from two separate periods of occupation spanning more than 5000 years. Arid conditions forced the initial occupants to abandon the area a little over 8000 years ago but with the return of more humid conditions, around 6600 years ago, the region was repopulated by a more gracile people who left behind elaborate grave goods, including animal bone and ivory ornaments, many of which are pictured in the paper.

One of the graves contained the skeleton of a small Tenerian woman facing the skeletons of two small children (a photograph of this by Mike Hettwer, captioned Stone Age Embrace, has been widely used alongside many of the news stories on the article). Samples from the grave contained pollen clusters, suggesting the individuals had been laid to rest on a bed of flowers.

Some of the accompanying images are part of the published paper (and so can be reused in line with the terms of the Creative Commons Attribution License); other images, along with more information about the expedition can be found on the Project Exploration website (Project Exploration being a nonprofit science education organization that makes science accessible to the public—especially minority youth and girls—through personalized experiences with scientists and science). Any users registered on the PLoS ONE site can, of course, post notes and comments and rate the paper online.

Understandably, the article received huge amounts of coverage in the media and in the blogosphere (despite “Bigfoot”’s efforts to steal the spotlight). As well as making the front page of Slashdot, the story was the top Associated Press science story on Thursday (it was also one of the overall top stories), it was in Yahoo science news’s most viewed list on Friday, and in the New York Times most-emailed list. There were several hundred news stories on Google News, so here are a few highlights of the coverage (see also Knight Science Journalism Tracker and A Blog Around the Clock):

News:

New York Times – Graves Found From Sahara’s Green Period
Washington Post – Excavations Show a Lush Life in the Sahara
Los Angeles Times – Archaeologists get a glimpse of life in a Sahara Eden
Reuters – Stone Age graveyard shows Sahara was once green
National Geographic – Ancient Cemetery Found; Brings "Green Sahara" to Life
Scientific American – Paleontology's Indiana Jones
New Scientist – Stone Age mass graves reveal green Sahara
Nature News – Back when the desert was green

Blogs:

Wired – Saharan Snapshot of Stone Age Life
Pharyngula – I Wish I Was a Paleontologist
Greg Laden’s Blog – Stone Age Graveyard Reveals Lifestyles of a Green Sahara
Stones, Bones ‘n’ Things – Paleontology Meets Archaeology
Anthropology.net – The Kiffian & Tenerean Occupation Of Gobero, Niger: Perhaps The Largest Collection Of Early-Mid Holocene People In Africa
Metafilter – Lost Tribes of the Green Sahara

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ONE journal, two birthdays

Liz Allen — Fri, 1 Aug 2008 10:32:43 -0700

The English Monarch has two birthdays – their real date of birth is celebrated in private with family and friends and the official date (which could historically be moved should their real birthday fall at a time of year when the weather was inclement) which is celebrated in public through the Trooping of the Colour Ceremony and a fly-past over Buckingham Palace in London.

PLoS ONE also celebrates twice (but far less grandly) – first there’s the date we opened our doors for submissions, 4 August 2006 (the date of our conception) and then there’s the date we launched (our birth), 20th December 2006.

Within less than 3 weeks of opening our doors we had received 70 manuscripts which represented far more papers flowing far faster than we’d ever experienced before. Now, two years later, we receive approximately 350 submissions per month. Not surprisingly, the PLoS team has grown since then to cope with the increased workload.

Two folks who deserve special mention for being there at the start and still being on board now - they are Bex Walton and Lindsay King.

Two years on, the person who still sums up our publishing philosophy well is the author of the first paper accepted for PLoS ONE, Andrej Romanovsky of St. Joseph's Hospital, Phoenix, Arizona, USA. He said "A traditional publisher uses complex rules to determine who, when, how, and at what price will be allowed to see your results. You can continue supporting this system ... or you can submit your next paper to PLoS”.

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Happy, er, conception-day?

from A Blog Around The Clock on Mon, 2008-08-04 04:55

Two years ago on this day, PLoS ONE opened for submissions (and surprisingly many manuscripts - 70 - got submitted immediatelly)....

Tyrannosaurus Re-examined

Rebecca Walton — Fri, 1 Aug 2008 08:38:54 -0700

This week saw the publication of another dinosaur study in PLoS ONE. In the article, entitled, Dinosaurian Soft Tissues Interpreted as Bacterial Biofilms, Thomas Kaye, at the Burke Museum of Natural History, and colleagues reported that material recovered from dissolved dinosaur bones by palaeontologists in 2005 (and believed to be dinosaurian soft tissue) may actually have been slimy biofilm created by bacteria that coated the voids once occupied by blood vessels and cells.

This study has already generated a large number of news articles and blog posts, including the following: New Scientist (T. rex 'tissue' may just be bacterial scum), Scientific American (Presumed dinosaur flesh may just be bacterial sludge), National Geographic (Dinosaur Slime Sparks Debate Over Soft-Tissue Finds), USA Today (New study has a bone to pick about dinosaur soft tissue), Aetiology (Dinosaur soft tissue--just bacterial biofilm?) and Pharyngula (Tyrannosaur morsels).

Several comments have already been posted on the published article and you can join in the discussion once you have created an account on the PLoS ONE publication website.

On the topic of biofilm, Carsten Matz’s paper, Marine Biofilm Bacteria Evade Eukaryotic Predation by Targeted Chemical Defense, published last week also picked up some coverage in the Washington Post (Social Lives of Bacteria May Yield Benefits for Humans) and Chemistry World (Biofilms deploy chemical weapons).

Also on a watery theme was Natalia Ospina-Álvarez and Francesc Piferrer’s paper on the potential effects of climate change on sex determination in fish. In vertebrates with separate sexes, sex determination can be genotypic (GSD) or temperature-dependent (TSD). The Spanish researchers used field and laboratory data to critically analyze the presence of TSD in the 59 species of fish where this type of sex determining mechanism had been postulated and found that increasing temperatures invariably resulted in highly male-biased sex ratios and that even small changes of just 1-2°C can significantly alter the sex ratio from 1:1 (males:females) up to 3:1 in both freshwater and marine species. Time Magazine covered the article (Global Warming's Fish-Sex Effect) and the story has also been Dugg several times.

Danish palaeontologist Per Christiansen compared the evolution of skull and mandible shape both in modern cats and in (the now extinct) sabercats; Greg Laden has posted a nice write-up of the study on his blog and there also posts on The Dragon’s Tales and on Counter Minds.

Finally, here is a quick round-up of some of coverage of several papers published in PLoS ONE on July 23^rd: Does Pathogen Spillover from Commercially Reared Bumble Bees Threaten Wild Pollinators? (New Scientist, Reuters, Greg Laden’s blog); Sample Size and Precision in NIH Peer Review (The Scientist, Mike the Mad Biologist); and Changes in Gray Matter Induced by Learning—Revisited (Mind Hacks).

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