I was so happy to have published in May this year an invited perspectives article in a Nature Reviews journal. I considered Nature a prestigious place to publish and that they are highly organized and professional. However, sadly, this belief stand shaken after reading a slanted story in the recent issue of Nature, apparently attacking PLoS (that Nature sees as competitor!). I am kinda surprised; sometime back a similar slang on PLoS was passed by another group, although it was not heard aloud. Well that means PLoS is fast becoming a threatening success! Thanks to the cause that it bolsters and the public support that it enjoys globally.
As the matter currently dominantes blogosphere (see links below), I think I am not alone with my shaken belief; this should be sorrowfully the case of many who proudly published in journals of both Nature and PLoS. I wonder, if Nature risks alienating many of its well-wishers with such a stand it has taken against PLoS and Open Access.
I found the overall tone and spirit of the news article quite disturbing and distasteful. Especially, their painting of PLoS ONE journal as a ‘dumping ground’ and mention of its peer review process as ‘light’ is not at all correct and ignores facts. I see it as an unsuccessful attempt to dump all the ground-breaking work that PLoS ONE has been publishing since its launch in 2006 (see these posts for exmple; here, here and here). As I said in my response to the story, it is a simple fact that the ~300 scientists who publish in PLoS ONE every month and the 500 Editors who devote their time on rounds of peer reviewing are certainly not the fools out there.
The story referred PLoS as resorting to ‘bulk and cheap publishing’; what a slang! Apparently, however, the "bulk, cheap and lower quality papers" published by PLoS are not going unnoticed by Nature. Three of the ‘Research Highlights’ articles in the same issue report on articles published in PLoS journals (two from PLoS ONE! and one from PLoS Genetics). And I quote Scott Ramsey: ‘If it (the research that PLoS published) is not interesting enough to publish in Nature, at least it provides enough free copy to help round out an issue’!
Finally, I do not want to add more on my own perspective here as it is no different than what many others have already rolled out. There has been tremendous outrage to Nature’s self serving article (apparently all going in favor of PLoS!) in the blogosphere, as well as in the comments thread of the article itself. A summary of the relevant posts on the article can be found at: http://scienceblogs.com/clock/2008/07/on_the_nature_of_plos.php.
Links to other related posts are here:
http://phylogenomics.blogspot.com/2008/07/only-nature-could-turn-success-of-plos.html
http://tinyurl.com/6rdrvq
http://bjoern.brembs.net/news.php?item.381.11
http://scienceblogs.com/drugmonkey/2008/07/nature_offers_a_completely_obj.php
http://friendfeed.com/e/e731c5a7-2a55-40bb-895d-75ee14101f9b/PLoS-stays-afloat-with-bulk-publishing/
http://scienceblogs.com/gregladen/2008/07/nature_reattacks_open_access_a.php
http://alexholcombe.wordpress.com/2008/07/03/nature-targets-financial-weakness-of-plos-journals/
http://jdupuis.blogspot.com/2008/07/nature-vs-plos.html
Conflict of interest statement: I volunteer as Section Editor for PLoS ONE.
Sunday, July 6, 2008
Wednesday, July 2, 2008
New in PLoS ONE: Genetic structure of Adi tribes of North-East India
PLoS ONE today published a crop of 60 brand new articles, several of them are hitting the headlines. An interesting article from India by TS Vasulu and colleagues is also being talked about a lot since this morning (see below). The paper discusses 'Microsatellite based analysis of the genetic status of Adi tribes of Northeast India'.
Population biologists and anthropologists have been traditionally interested in aspects of human history and population migration in India -a homeland of a large number of genetic lineages of tribals and mainstream populations which speak 1600 different languages and dialects.
The article by Vasulu presents important genetic data from a number of closely related Tibeto-Burman speaking tribes from north-east India. The authors correctly present this region of India of utmost importance with respect to ancient human migration processes. In addition, the novel results obtained from these populations are compared with similar data from a range of other populations obtained from the literature.
Based on 15 autosomal microsatellite (STR) markers, the authors studied the genetic affinity, differentiation and sub-structuring among six Adi subgroups, as well as their genetic affinity with other neighbouring, Tibeto-Burman-speaking, tribes of India and with the linguistically divergent east and south-east Asian populations, with whom they share common ethno-historical and cultural attributes. The researchers investigated to what extent the six Adi subgroups are genetically divergent or affiliated. A comparison with the 16 Tibeto-Burman-speaking tribes of the neighbouring region in northern and north-eastern parts of the country as revealed by the cluster analyses indicates geographically proximate populations forming a close cluster. This is to be expected if these populations have indeed diverged from a common source after their settlement in different regions of the country in the recent past. In a comparison of the 50 populations (including populations from east and south-east Asia) for genetic diversity based on the autosomal loci, the resultant clustering tree showed some of the Tibeto-Burman tribes clustering with the populations from Tibet and China and whereas other Tibeto-Burman tribes of India cluster with linguistically different Southeast Asian populations. These results support the possibility that Tibeto-Burman populations were derived from more than one common source. Overall, the Adi and other Tibeto-Burman speaking populations of India are regionally well differentiated and exhibit genetic affinity with the neighboring populations of East/Southeast Asia, based on their shared ethno-history. However, a clearer picture may well emerge from the analysis of increased number of informative genetic markers and from the uniparental markers like mitochondrial DNA and Y chromosome.
You can read the news coverage about this study here and you may post your own reactions and comments directly on the article of Vasulu and colleagues by creating an account on the PLoS ONE website.
[Source: Press release of T S Vasulu, Indian Statistical Institute, Kolkata, India]
Population biologists and anthropologists have been traditionally interested in aspects of human history and population migration in India -a homeland of a large number of genetic lineages of tribals and mainstream populations which speak 1600 different languages and dialects.
The article by Vasulu presents important genetic data from a number of closely related Tibeto-Burman speaking tribes from north-east India. The authors correctly present this region of India of utmost importance with respect to ancient human migration processes. In addition, the novel results obtained from these populations are compared with similar data from a range of other populations obtained from the literature.
Based on 15 autosomal microsatellite (STR) markers, the authors studied the genetic affinity, differentiation and sub-structuring among six Adi subgroups, as well as their genetic affinity with other neighbouring, Tibeto-Burman-speaking, tribes of India and with the linguistically divergent east and south-east Asian populations, with whom they share common ethno-historical and cultural attributes. The researchers investigated to what extent the six Adi subgroups are genetically divergent or affiliated. A comparison with the 16 Tibeto-Burman-speaking tribes of the neighbouring region in northern and north-eastern parts of the country as revealed by the cluster analyses indicates geographically proximate populations forming a close cluster. This is to be expected if these populations have indeed diverged from a common source after their settlement in different regions of the country in the recent past. In a comparison of the 50 populations (including populations from east and south-east Asia) for genetic diversity based on the autosomal loci, the resultant clustering tree showed some of the Tibeto-Burman tribes clustering with the populations from Tibet and China and whereas other Tibeto-Burman tribes of India cluster with linguistically different Southeast Asian populations. These results support the possibility that Tibeto-Burman populations were derived from more than one common source. Overall, the Adi and other Tibeto-Burman speaking populations of India are regionally well differentiated and exhibit genetic affinity with the neighboring populations of East/Southeast Asia, based on their shared ethno-history. However, a clearer picture may well emerge from the analysis of increased number of informative genetic markers and from the uniparental markers like mitochondrial DNA and Y chromosome.
You can read the news coverage about this study here and you may post your own reactions and comments directly on the article of Vasulu and colleagues by creating an account on the PLoS ONE website.
[Source: Press release of T S Vasulu, Indian Statistical Institute, Kolkata, India]
Sunday, June 29, 2008
My picks from PLoS ONE: Malaria and tularemia – diagnostic markers and vaccine candidates
PLoS ONE published 54 new articles last week. I had a chance to thoroughly read two of them also because they were edited by me and that they have some real potential towards the development of diagnostics and vaccines for infection control.
The paper - Novel Peptide Marker Corresponding to Salivary Protein gSG6 Potentially Identifies Exposure to Anopheles Bites from Anne Poinsingnon’s group is highly relevant in the context of devising vector control strategies in malaria endemic regions. This study combined a bio-informatics approach with standard immunoepidemiological assays to identify an Anopheles specific salivary peptide that could be developed as a marker of exposure to Anopheles bites. Such an epidemiological tool would have direct application in identifying high risk areas for malaria transmission and areas where vector control strategies should be implemented. I really think that this work is of interest not only for those who work in malaria control and in the evaluation of vector control strategies but also in the field of the immune response to arthopod salivary components. If this approach proved to be succesful, it could be applied to the control of other vector-borne diseases.
Another study - A Francisella tularensis Schu S4 Purine Auxotroph Is Highly Attenuated in Mice but Offers Limited Protection against Homologous Intranasal Challenge from the group of Thomas Zahrt was another interesting article to recommend. It describes the use of type A and LVS-derived purine auxotroph mutants of Francisella as potential candidates for live attenuated vaccines against tularemia. The intranasal challenge approach taken by the investigators is new and is more representative of a real exposure than other studies, and was judged a major strength of the study. However, there are certain shortcomings of this study that would invite future research efforts by this and other groups working in the field of tularemia prophylaxis - the type A-derived mutant offered a little bit of protection of challenged animals in terms of lethality but the vaccinated animals still exhibited bacterial survival in the lungs, and many of them succumbed to infection. Nonetheless, the results clearly inform us that the development of next generation live attenuated vaccine for Francisella should be based on the use of less aggressive B type strains rather than the more reactogenic type A.
The paper - Novel Peptide Marker Corresponding to Salivary Protein gSG6 Potentially Identifies Exposure to Anopheles Bites from Anne Poinsingnon’s group is highly relevant in the context of devising vector control strategies in malaria endemic regions. This study combined a bio-informatics approach with standard immunoepidemiological assays to identify an Anopheles specific salivary peptide that could be developed as a marker of exposure to Anopheles bites. Such an epidemiological tool would have direct application in identifying high risk areas for malaria transmission and areas where vector control strategies should be implemented. I really think that this work is of interest not only for those who work in malaria control and in the evaluation of vector control strategies but also in the field of the immune response to arthopod salivary components. If this approach proved to be succesful, it could be applied to the control of other vector-borne diseases.
Another study - A Francisella tularensis Schu S4 Purine Auxotroph Is Highly Attenuated in Mice but Offers Limited Protection against Homologous Intranasal Challenge from the group of Thomas Zahrt was another interesting article to recommend. It describes the use of type A and LVS-derived purine auxotroph mutants of Francisella as potential candidates for live attenuated vaccines against tularemia. The intranasal challenge approach taken by the investigators is new and is more representative of a real exposure than other studies, and was judged a major strength of the study. However, there are certain shortcomings of this study that would invite future research efforts by this and other groups working in the field of tularemia prophylaxis - the type A-derived mutant offered a little bit of protection of challenged animals in terms of lethality but the vaccinated animals still exhibited bacterial survival in the lungs, and many of them succumbed to infection. Nonetheless, the results clearly inform us that the development of next generation live attenuated vaccine for Francisella should be based on the use of less aggressive B type strains rather than the more reactogenic type A.
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