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Archive for the ‘Journals’ Category

Molecular Ecology cover imageWe are pleased to report that Molecular Ecology is now the first journal to surpass 1000 data packages in Dryad! Our latest featured data package is the one that took Molecular Ecology past the goalposts:

  • Bolnick D, Snowberg L, Caporaso G, Lauber C, Knight R, Stutz W (2014) Major Histocompatibility Complex class IIb polymorphism influences gut microbiota composition and diversity. Molecular Ecology doi:10.1111/mec.12846
  • Bolnick D, Snowberg L, Stutz W, Caporaso G, Lauber C, Knight R (2014) Data from: Major Histocompatibility Complex class IIb polymorphism influences gut microbiota composition and diversity. Dryad Digital Repository doi:10.5061/dryad.2s07s

Why so many data packages from Molecular Ecology?  It is likely due to a few factors.  One, Molecular Ecology publishes a lot of papers (445 in 2012 according to Journal Citation Reports) and have had integrated data and manuscript submission with Dryad since 2010.  Two, the field works with many datatypes for which no specialized repository exists.  Three, Molecular Ecology not only began requiring data archiving in 2011 when it adopted the Joint Data Archiving Policy, but actually goes beyond JDAP by requiring a completed data availability statement in each article, something that managing editor Tim Vines and his colleagues have shown to be associated with very high rates of data archiving. Four, since Dryad introduced Data Publishing Charges, Molecular Ecology has been sponsoring those charges on behalf of its authors.

Other journals looking to support data archiving in their fields would do well to look at Molecular Ecology as a model.

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A number of notable publications have been added to the growing list of those integrating submission of data and manuscripts with Dryad.

The recently adopted Data Policy of Royal Society Publishing now requires that data sets “be deposited in an appropriate, recognized, publicly available repository” and that authors “disclose upon submission of the manuscript any restrictions on the availability of research materials or data.” To support this policy, the Royal Society now sponsors the Data Publication Charge to Dryad for data associated with any of its publications Proceedings of the Royal Society, Proceedings B, the Royal Society’s flagship biological research journal, has joined Biology Letters in integrating submission with Dryad.  Currently, submission of data occurs prior to manuscript review for Proceedings B, and following acceptance for Biology Letters.  Watch this space for further efforts to support the data archiving needs of Royal Society Publishing.

BMCEcologyBMCEvolBiology

In an editorial entitled ‘An open future for ecological and evolutionary data?’, recently published jointly in BMC Ecology and BMC Evolutionary Biology, authors Amye Kenall, Simon Harold and Christopher Foote announce the integration of manuscript submission for these two journals with Dryad in order “to encourage a more widespread adoption of open data sharing in the fields of ecology and evolutionary biology by facilitating this process for our authors.”  Now that the technical work has been accomplished for these two journals, submission integration can be easily extended to other BMC series titles at the request of the editors.

SciData_new_logo

Scientific Data is a newly launched open access publication from Nature Publishing Group that aims to promote the accessibility and reuse of scientifically valuable data sets. This is supported by both a strong data deposition policy and a novel publication type called a Data Descriptor.

Data Descriptors will provide detailed descriptions of the experiments and procedures involved in generating important datasets, including essential information needed for scientists to assess the technical quality of the data, reproduce key methods or analysis workflows, and ultimately reuse the data to address important research questions. In addition, every publication at Scientific Data will be supported by metadata describing key properties of the experiments and resulting data, which will be checked by an in-house curator and released in the ISA-tab format, and hopefully other standard formats in the future. These metadata will aid data mining, and will help scientists find and reuse high-quality datasets stored across multiple data repositories.

NPG sponsors data submissions associated with Scientific Data, and data are submitted to Dryad prior to review.

Together with a number of previously integrated journals from German Medical Science and Pensoft Publishers, on subjects ranging from subterranean biology to reconstructive surgery, the total number of titles now integrated with Dryad exceeds 50. Authors may consult this list to see which journals are integrated, when to submit data (either before review of after acceptance), whether the journal allows an optional data embargo, and whether Data Publication Charges are sponsored for that publication.Submission integration is a free service, and can be implemented with a wide variety of manuscript submission systems. We encourage publishers and editors to contact us about integration of additional titles, and we encourage authors to let editors know if this is a feature that they would value.

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Ecology and Evolution is the latest journal to integrate submission of manuscripts with data to Dryad.  Ecology and Evolution is a Wiley open access journal supported by other journals published by Wiley, including journals owned by the British Ecological Society, the European Society for Evolutionary Biology and the Society for the Study of Evolution.

Ecology and Evolution’s integration with Dryad means that all authors will be invited to archive the data supporting the conclusions in the article, and their process of depositing data files has been simplified by the behind-scenes-coordination between the journal and the repository. Authors are invited to submit data to Dryad when their manuscript is accepted, and have the option to set a one-year embargo on the availability of their data files. There are already 50 articles in the journal with their underlying data archived in Dryad.

EcologyEvolution_DryadThe journal has a strong data policy, requiring “as a condition for publication, that data supporting the results in the paper should be archived in an appropriate public archive, such as GenBank, TreeBASE, Dryad, the Knowledge Network for Biocomplexity or other suitable long-term and stable public repositories.”

Editor-in-chief Allen J. Moore  says “We are fully behind Dryad… and I think things are going well.”  Moore is a strong proponent of open data, a former Dryad Board member, and an experienced data depositor.

The journal covers Data Publishing Charges for its authors.

 

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We are pleased to announce that Elementa is the latest journal to integrate submission of manuscripts with data to Dryad.  Elementa’s integration with Dryad means that all authors will be invited to archive the data supporting the conclusions in their article, and their process of depositing data files has been simplified by the behind-scenes-coordination between the journal and the repository. Authors will be invited to submit data to Dryad when their manuscript is accepted, and will have the option to set a one-year embargo on the availability of their data files.

The journal has a strong data policy, requiring “all major datasets associated with an article to be made freely and widely available.” The journal is also a Dryad member, and will be covering the charges for its authors when Dryad begins assessing Data Publishing Charges (DPC) on September 1.

Elementa: Science of the Anthropocene is a new open access scientific journal publishing original research reporting new knowledge of the Earth’s physical, chemical, and biological systems.

logo The journal is a nonprofit collaborative involving BioOne, Dartmouth, the Georgia Institute of Technology, the University of Colorado, the University of Michigan, and the University of Washington. Elementa is comprised of six inaugural knowledge domains: Atmospheric Science, Earth and Environmental Science, Ecology, Ocean Science, Sustainable Engineering, and Sustainability Transitions.

The journal is now welcoming article submissions, and the first articles will be published in September.

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We are pleased to announce that Ecology Letters is the latest journal to integrate submission of manuscripts with data to Dryad.  In this process, the journal and repository communicate behind the scenes in order to streamline data submission for authors, and also to ensure that the article contains a permanent link to the data.

EcolLettCover copyEcology Letters is published by The French National Center for Scientific Research (CNRS), a public basic-research organization that defines its mission as producing knowledge and making it available to society. Marcel Holyaok, the journal’s Editor-in-Chief, has been actively involved with Dryad since 2009, serving on the Consortium Board from 2009-2011, and currently on the elected Board of Directors.

There are already a number of articles in Ecology Letters with associated data in Dryad, including the most frequently downloaded data file in Dryad, The Global Wood Density Database, which has been downloaded nearly 6000 times:

Zanne AE, Lopez-Gonzalez G, Coomes DA, Ilic J, Jansen S, Lewis SL, Miller RB, Swenson NG, Wiemann MC, Chave J (2009) Data from: Towards a worldwide wood economics spectrum. Dryad Digital Repository. doi:10.5061/dryad.234

Article:

Chave J, Coomes D, Jansen S, Lewis SL, Swenson NG, Zanne AE (2009) Towards a worldwide wood economics spectrum. Ecology Letters 12: 351-366. doi:10.1111/j.1461-0248.2009.01285.x

Dryad is delighted to welcome Ecology Letters to the growing group of journals that have taken this important step to support and facilitate their authors’ data archiving.

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We are pleased to share below the text of a press release from Elsevier, announcing use of this image to direct viewers of online articles to the underlying data in Dryad. Dryad_web_banner_small_v4eSee below for sample articles; the image displays on the right sidebar, under Applications and Tools. This Dryad widget may be used by any publisher or journal to facilitate access to related publicly available data that authors have archived in Dryad.

Elsevier, a world-leading provider of scientific, technical and medical information products and services, and the Dryad Digital Repository, a leading archive for scientific and medical research data, today announced that they have implemented two-way linking between their respective content.

The Dryad Digital Repository provides facilities for archiving, discovery and accessibility of data files associated with any published article in the sciences or medicine, as well as software scripts and other files important to the article. Dryad is a nonprofit organization committed to its mission of making data publicly available for research and educational reuse. All data files stored in Dryad receive persistent, resolvable Digital Object Identifiers (DOIs) to ensure their proper citation.

Scientific and medical research datasets stored by Dryad for research articles published in 28 Elsevier journals can now be immediately accessed from the online articles on ScienceDirect and vice versa. This allows readers to easily find the background information they need in order to develop a deeper understanding of the article, and also helps to place the article in a larger context.

Dr. Todd Vision, Associate Director for Informatics at the National Evolutionary Synthesis Center and Principal Investigator on the primary NSF grant funding Dryad since 2008, said, “We are delighted to work with Elsevier in cementing the union between scientific articles and research data. Molecular Phylogenetics and Evolution was one of the first journals that joined the Dryad consortium and we would like to applaud them for recognizing that the integrity, rigor, and long-term impact of the science published by the journal is strengthened by archiving the associated data at the time of publication. We also believe that authors themselves will ultimately benefit, in the form of increased citations and other forms of professional credit, for making their data available for others to reuse.”

Dr. Derek Wildman, Editor in Chief of Molecular Phylogenetics and Evolution, a journal which has successfully incorporated and uses the reciprocal linking option between Dyrad and ScienceDirect, said, “DNA sequence data serves as the basis for the majority of the studies we publish. Dryad has done an excellent job in establishing a public archive for all types of data used in evolutionary biology. By making these data sets public and allowing for direct linking between a published research papers, scientists can more efficiently build on the work of their predecessors, strengthening scientific research enterprise. We see the incorporation of the two-way linking as a win for all parties.”

The first 28 journals hosted on ScienceDirect to feature the reciprocal linking option, displayed in the right hand sidebar of the online article page view, are:

  • Animal Behaviour
  • Applied Soil Ecology
  • Behavioural Processes
  • Biological Conservation
  • Comparative Biochemistry and Physiology. Part D, Genomics and Proteomics
  • Ecological Indicators
  • Environmental Pollution
  • Fisheries Research
  • Fungal Genetics and Biology
  • Gene
  • Hormones and Behavior
  • Infection, Genetics and Evolution
  • International Journal for Parasitology
  • Journal of Biomedical Informatics
  • Journal of Human Evolution
  • Journal of Informetrics
  • Marine Genomics
  • Molecular and Biochemical Parasitology
  • Molecular Phylogenetics and Evolution
  • Palaeogeography, Palaeoclimatology, Palaeoecology
  • Protist
  • Quaternary Science Reviews
  • Science of the Total Environment
  • Soil Biology and Biochemistry
  • Theoretical Population Biology
  • Toxicon
  • Trends in Ecology and Evolution
  • Virus Research

This type of linking between articles and data is one of the pillars of Article of the Future, Elsevier’s on-going program to improve the format of the scientific article. Elsevier collaborates with more than thirty data repositories, and is continually looking to collaborate with other relevant organizations.

View article examples on ScienceDirect:

R. Alexander Pyron, John J. Wiens, A large-scale phylogeny of Amphibia including over 2800 species, and a revised classification of extant frogs, salamanders, and caecilians, Molecular Phylogenetics and Evolution, Volume 61, Issue 2, November 2011, pp. 543-583, http://dx.doi.org/10.1016/j.ympev.2011.06.012.

Peter J. Unmack, Gerald R. Allen, Jerald B. Johnson, Phylogeny and biogeography of rainbowfishes (Melanotaeniidae) from Australia and New Guinea, Molecular Phylogenetics and Evolution, Volume 67, Issue 1, April 2013, pp. 15-27, http://dx.doi.org/10.1016/j.ympev.2012.12.019.

James Starrett, Marshal Hedin, Nadia Ayoub, Cheryl Y. Hayashi, Hemocyanin gene family evolution in spiders (Araneae), with implications for phylogenetic relationships and divergence times in the infraorder Mygalomorphae, Gene, Volume 524, Issue 2, July 2013, pp. 175-186, http://dx.doi.org/10.1016/j.gene.2013.04.037.

Mercy Y. Akinyi, Jenny Tung, Maamun Jeneby, Nilesh B. Patel, Jeanne Altmann, Susan C. Alberts, Role of grooming in reducing tick load in wild baboons (Papio cynocephalus), Animal Behaviour, Volume 85, Issue 3, March 2013, pp. 559-568, http://dx.doi.org/10.1016/j.anbehav.2012.12.012

# # #

About Dryad

The Dryad Digital Repository is a curated resource that makes the data underlying scientific and medical publications discoverable, freely reusable, and citable. By providing a general-purpose home for a wide diversity of data types, Dryad benefits individual researchers, educators and students as well as a diversity of stakeholder organizations. Dryad is a member-based nonprofit organization incorporated in North Carolina, USA with users around the world.

About Elsevier

Elsevier is a world-leading provider of scientific, technical and medical information products and services. The company works in partnership with the global science and health communities to publish more than 2,000 journals, including The Lancet and Cell, and close to 20,000 book titles, including major reference works from Mosby and Saunders. Elsevier’s online solutions include ScienceDirect, Scopus, Reaxys, ClinicalKey and Mosby’s Suite, which enhance the productivity of science and health professionals, and the SciVal suite and MEDai’s Pinpoint Review, which help research and health care institutions deliver better outcomes more cost-effectively.

A global business headquartered in Amsterdam, Elsevier employs 7,000 people worldwide. The company is part of Reed Elsevier Group plc, a world leading provider of professional information solutions. The group employs more than 30,000 people, including more than 15,000 in North America. Reed Elsevier Group plc is owned equally by two parent companies, Reed Elsevier PLC and Reed Elsevier NV. Their shares are traded on the London, Amsterdam and New York Stock Exchanges using the following ticker symbols: London: REL; Amsterdam: REN; New York: RUK and ENL.

Media contact

Dale Seaton
Executive Publisher, Journals
Elsevier
+1 212 633 3862
d.seaton@elsevier.com
 
**Update: In addition to DOIs, the banner widget also works with PubMed IDs

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Dryad is pleased to announce that a diverse array of new partner journals have completed submission integration during the first quarter of 2013.  Authors to these journals will benefit from streamlined data deposition, while the journals will benefit from enhancement of the articles through a tighter linkage to the underlying data.

Submission integration is completely free, and can be implemented with a wide variety of manuscript submission systems.  We welcome inquiries from other journals that wish to integrate submission with Dryad, and encourage authors from non-integrated journals to let their editors know if it is a service that they would value.

gms2

  • eLife is a prestigious new open-access journal published by the Howard Hughes Medical Institute,  the Max Planck Society, and the Wellcome Trust.
    elife
  • Journal of Open Public Health Data (JOPHD) is a new journal from Ubiquity Press that publishes peer-reviewed data papers describing public health datasets with high reuse potential.  The data itself must be made freely available in a public repository.

jophd

Each journal that integrates with Dryad chooses whether to have authors archive their data prior to peer review or after manuscript acceptance.  Of these six journals, GMS Medical Sciences, eLife, and the Journal of Open Public Health Data chose to have their authors submit data prior to peer review.

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We are pleased to announce that Biology Letters is the latest journal to integrate submission of manuscripts with data to Dryad.  In this process, the journal and repository communicate behind the scenes in order to streamline data submission for authors and ensure that the article contains a permanent link to the data.

It is particularly apt because Biology Letters is published by the Royal Society, which invented the idea of sharing knowledge through a scientific journal back in 1665.  Scientific communication has come a long way from those early letters among gentleman natural philosophers to the current conception of Science as an Open Enterprise conducted in the public interest.  Reflecting these changes in science and technology, the Royal Society recently strengthened its policy on the availability of research data:

To allow others to verify and build on the work published in Royal Society journals it is a condition of publication that authors make available the data and research materials supporting the results in the article.

Datasets should be deposited in an appropriate, recognized repository and the associated accession number, link or DOI to the datasets must be included in the methods section of the article. Reference(s) to datasets should also be included in the reference list of the article with DOIs (where available). Where no discipline-specific data repository exists authors should deposit their datasets in a general repository such as Dryad.

There are already a healthy number of articles in Biology Letters with associated data in Dryad, including one of last year’s hit data packages, Monsters are people too.  The first to be published via integrated submission is:

Article:

Jevanandam N, Goh AGR, Corlett RT (2013) Climate warming and the potential extinction of fig wasps, the obligate pollinators of figs. Biology Letters 9(3): 20130041. doi:10.1098/rsbl.2013.0041

Data:

Goh AGR, Corlett RT, Jevanandam N (2013) Data from: Climate warming and the potential extinction of fig wasps, the obligate pollinators of figs. Dryad Digital Repository. doi:10.5061/dryad.hj7h2

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The following guest post is from Tim Vines, Managing Editor of Molecular Ecology and Molecular Ecology Resources.  ME and MER have among the most effective data archiving policies of any Dryad partner journal, as measured by the availability of data for reuse [1].  In this post, which may be useful to other journals figuring out how to support data archiving, Tim explains how Molecular Ecology’s approach has been refined over time.

newsman

Ask almost anyone in the research community, and they’ll say that archiving the data associated with a paper at publication is really important. Making sure it actually happens is not quite so simple. One of the main obstacles is that it’s hard to decide which data from a study should be made public, and this is mainly because consistent data archiving standards have not yet been developed.

It’s impossible for anyone to write exhaustive journal policies laying out exactly what each kind of study should archive (I’ve tried), so the challenge is to identify for each paper which data should be made available.

Before I describe how we currently deal with this issue, I should give some history of data archiving at Molecular Ecology. In early 2010 we joined with the five other big evolution journals in adopting the ‘Joint Data Archiving Policy’, which mandates that “authors make all the data required to recreate the results in their paper available on a public archive”. This policy came into force in January 2011, and since all five journals brought it in at the same time it meant that no one journal suffered the effects of bringing in a (potentially) unpopular policy.

To help us see whether authors really had archived all the required datasets, we started requiring that authors include ‘Data Accessibility’ (DA) section in the final version of their manuscript. This DA section lists where each dataset is stored, and normally appears after the references.  For example:

Data Accessibility:

  • DNA sequences: Genbank accessions F234391-F234402
  • Final DNA sequence assembly uploaded as online supplemental material
  • Climate data and MaxEnt input files: Dryad doi:10.5521/dryad.12311
  • Sampling locations, morphological data and microsatellite genotypes: Dryad doi:10.5521/dryad.12311

We began back in 2011 by including a few paragraphs about our data archiving policies in positive decision letters (i.e. ‘accept, minor revisions’ and ‘accept’), which asked for a DA section to be added to the manuscript during their final revisions. I would also add a sticky note to the ScholarOne Manuscripts entry for the paper indicating which datasets I thought should be listed. Most authors added the DA, but generally only included some of the data. I then switched to putting my list into the decision letter itself, just above the policy itself. For example:

“Please don’t forget to add the Data Accessibility section- it looks like this needs a file giving sampling details, morphology and microsatellite genotypes for all adults and offspring. Please also consider providing the input files for your analyses.”

This was much more effective than expecting the authors to work out which data we wanted. However, it still meant that I was combing through the abstract and the methods trying to work out what data had been generated in that manuscript.

We use ScholarOne Manuscripts’ First Look system for handling accepted papers, and we don’t export anything to be typeset until we’re satisfied with the DA section. Being strict about this makes most authors deal with our DA requirements quickly (they don’t want their paper delayed), but a few take longer while we help authors work out what we want.

The downside of this whole approach is that it takes me quite a lot of effort to work out what should appear in the DA section, and would be impossible in a journal where an academic does not see the final version of the paper. A more robust long-term strategy has to involve the researcher community in identifying which data should be archived.

I’ll flesh out the steps below, but simply put our new approach is to ask authors to include a draft Data Accessibility section at initial submission. This draft DA section should list each dataset and say where the authors expect to archive it. As long as the DA section is there (even if it’s empty) we send the paper on to an editor. If it makes it to reviewers, we ask them to check the DA section and point out what datasets are missing.

A paper close to acceptance can thus contain a complete or nearly complete DA section. Furthermore, any deficiencies should have been pointed out in review and corrected in revision. The editorial office now has the much easier task of checking over the final DA section and making sure that all the accession numbers etc. are added before the article is exported to be typeset.

The immediate benefit is that authors are encouraged to think about data archiving while they’re still writing the paper – it’s thus much more an integral part of manuscript preparation than an afterthought. We’ve also found that a growing proportion of papers (currently about 20%) are being submitted with a completed DA section that requires no further action on our part. I expect that this proportion will be more like 80% in two years, as this seems to be how long it takes to effect changes in author or reviewer behavior.

Since the fine grain of the details may be of interest, I’ve broken down the individual steps below:

1) The authors submit their paper with a draft ‘Data Accessibility’ (DA) statement in the manuscript; this lists where the authors plan to archive each of their datasets. We’ve included a required checkbox in the submission phase that states ‘A draft Data Accessibility statement is present in the manuscript’.

2) Research papers submitted without a DA section are held in the editorial office checklist and the authors contacted to request one. In the first few months of using this system we have found that c. 40% of submissions don’t have the statement initially, but after we request it the DA is almost always emailed within 3-4 days. If we don’t hear for five working days we unsubmit the paper; this has happened to about only 5% of papers.

3) If the paper makes it out to review, the reviewers are asked to check whether all the necessary datasets are listed, and if not, request additions in the main body of their review. Specifically, our ‘additional questions’ section of the review tab in S1M now contains the question: “Does the Data Accessibility section list all the datasets needed to recreate the results in the manuscript? If ‘No’, please specify which additional data are needed in your comments to the authors.”  Reviewers can choose ‘yes’, ‘no’ or ‘I didn’t check’; the latter is important because reviewers who haven’t looked at the DA section aren’t forced to arbitrarily click ‘yes’ or ‘no’.

4) The decision letter is sent to the authors with the question from (3) included. Since we’re still in the early days of this system and less than a quarter of our reviewers understand how to evaluate the DA section, I am still checking the data myself and requesting that any missing datasets be included in the revision. This is much easier than before as there is a draft DA section to work with and sometimes some feedback from the reviewers.

5) The editorial office then makes sure that any deficiencies identified by myself or the reviewers are dealt with by the time the paper goes to be typeset; this is normally dealt with at the First Look stage.

I’d be very happy to help anyone that would like to know more about this system or its implementation – please contact me at managing.editor@molecol.com

[1] Vines TH, Andrew RL, Bock DG, Franklin MT, Gilbert KJ, Kane NC, Moore JS, Moyers BT, Renaut S, Rennison DJ, Veen T, Yeaman S. Mandated data archiving greatly improves access to research data. FASEB J. 2013 Jan 8. Epub ahead of print.  Update: Also available from arXiv.

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Our guest post today is from Mohamed Noor of Duke University, president of the American Genetic Association. The AGA is a scholarly society dating back to 1903.  AGA, together with Oxford University Press, publishes the Journal of Heredity, which is a charter member in the Dryad organization and one of the first journals to integrate manuscript and data submission with the repository.  The society just held their annual symposium in Durham, North Carolina, not so far from Dryad’s NESCent headquarters, and has some excellent news to report from the Council meeting.

The American Genetic Association is pleased to announce that it has now fully adopted the Joint Data Archiving Policy (JDAP) for the Journal of Heredity.  The Journal of Heredity had previously required that newly reported nucleotide or amino acid sequences, and structural coordinates, be submitted to appropriate public databases. For other forms of data, the Journal “endorsed the principles of the Joint Data Archiving Policy (JDAP) in encouraging all authors to archive primary datasets in an appropriate public archive, such as Dryad, TreeBASE, or the Knowledge Network for Biocomplexity.”

This voluntary archiving policy was facilitated by the direct link between the Journal of Heredity and Dryad, in effect since February 2010.

To further support data-sharing and data access, in July 2012, the AGA Council voted unanimously to make data archiving a requirement for publication, under the terms specified in the JDAP.

The requirement will take effect by January 1, 2013. The American Genetic Association also recognizes the vast investment of individual researchers in generating and curating large datasets. Consequently, we recommend that this investment be respected in secondary analyses or meta-analyses in a gracious collaborative spirit.

Many other leading journals in ecology and evolutionary biology have adopted policies modeled on JDAP over the past two years, and other journals are invited to consider it as a policy that has attracted wide support among scientists.

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