Between classical and ideal: enhancing wildland fire prediction using cluster computing

One of the challenges still open to wildland fire simulators is the capacity of working under real-time constrains with the aim of providing fire spread predictions that could be useful in fire mitigation interventions. We propose going one step beyond the classical wildland fire prediction by linking evolutionary optimization strategies to the traditional scheme with the aim of emulating an “ideal” fire propagation model as much as possible. In order to accelerate the fire prediction, this enhanced prediction scheme has been developed in a fashion on a Linux cluster using MPI. Furthermore, a sensitivity analysis has been carried out to determine the input parameters that we can fix to their typical values in order to reduce the search-space involved in the optimization process and, therefore, accelerates the whole prediction strategy. Baker Abdalhaq received the BSc. Computer Science from Princess Sumaya University College, Royal JordanianSocieaty, Amman Jordania in 1993. In 2001 and 2004, he got the MSc and PhD in Computer Science from Universitat Autónoma de Barcelona (UAB), respectively. His main research interest is focused on parallel fire simulation and, in particular, how to take advantage of the computational power provided for massively distributed systems to enhance wildland fire prediction. Ana Cortés received both her first degree and her PhD in Computer Science from the Universitat Autonoma de Barcelona (UAB), Spain, in 1990 and 2000, respectively. She is currently assistant professor of Computer Science at the UAB, where she is a member of the Computer Architecture and Operating Systems Group at the Computer Science Department. Her current research interests concern software support for parallel and distributed computing including algorithms and software tools for the load-balancing of parallel programs. She has also been working on enhancing wildland fire prediction by exploiting parallel/distributed systems. Tomàs Margalef got a BS degree in physics in 1988 from Universitat Autónoma de Barcelona (UAB). In 1990 he obtained the MSc in Computer Science and in 1993 the PhD in Computer Science from UAB. Since 1988 he has been working in several aspects related to parallel and distributed computing. Currently, his research interests focuses on development of high performance applications, automatic performance analysis and dynamic performance tuning. Since 1997 he has been working on exploiting parallel/distributed processing to accelerate and improve the prediction of forest fire propagation. He is an ACM member. Germán Bianchini received the BSc. Computer Science from Universidad Nacional Del Comahue, Argentina, in 2002. In 2004 and 2006, he got the MSc and PhD in Computer Science from Universitat Autónoma de Barcelona (UAB), respectively. His main research interest is focused on parallel fire simulation and, in particular, how to take advantage of the computational power provided for massively distributed systems to enhance wildland fire prediction. Emilio Luque received the Licenciate in physics and PhD degrees from the University Complutense of Madrid (UCM) in 1968 and 1973 respectively. Between 1973 and 1976 he was an associate professor at the UCM. Since 1976 he is a professor of “Computer Architecture and Technology” at the University Autonoma of Barcelona (UAB), where he is leading the Computer Architecture and Operating System (CAOS) Group at the Computer Science Department. Professor Luque has been the Computer Science Department chairman for more than 10 years. He has been invited lecturer/researcher in Universities of USA, Argentina, Brazil, Poland, Ireland, Cuba, Italy, Germany and PR of China. He has published more than 35 papers in technical journals and more than 100 papers at international conferences and his current/major research areas are: computer architecture, interconnection networks, task scheduling in parallel systems, parallel and distributed simulation environments, environment and programming tools for automatic performance tuning in parallel systems, cluster and Grid computing, parallel computing for environmental applications (forest fire simulation, forest monitoring) and distributed video on demand (VoD) systems.     

Nutrition proteomics and biomarker discovery

Baukje de Roos is a principal investigator at the University of Aberdeen, Rowett Institute of Nutrition and Health. She investigates mechanisms through which dietary fats and fatty acids, and also polyphenols, affect parameters involved in the development of heart disease in vivo. This is achieved not only by measuring their effect on conventional risk markers for heart disease but also by assessing their effect on new markers that are being developed through proteomic and mass spectrometry methods. She obtained her PhD in Human Nutrition at Wageningen University, The Netherlands, in January 2000, after which she was appointed as a post-doctoral research fellow at the Department of Vascular Biochemistry, Glasgow Royal Infirmary, in collaboration with GlaxoSmithKline. In June 2001 she joined the Rowett Research Institute in Aberdeen. She is currently working for the University of Aberdeen, where her research is funded by the Scottish Government Rural and Environment Research and Analysis Directorate (RERAD). She is an active member of the European Nutrigenomics Organisation (NuGO), an EU-funded Network of Excellence, which merges the nutrigenomics activities of its 23 partners across Europe.     

From observations to paradigms; the importance of theories and models. An interview with Hans Meinhardt by Richard Gordon and Lev Beloussov

Hans Meinhardt received his PhD in physics from the University of Cologne at 1966. For a postdoctoral fellowship, he went to the European High Energy Laboratory CERN in Geneva where he joined a group working on the leptonic decay of the Xi-minus particle. One of his duties was to perform computer simulations to optimize the complex experimental setup -- a skill which turned out to be helpful later on. In 1969 he switched to biology and joined the department of Alfred Gierer at the Max Planck Institute for Developmental Biology (formerly Virus Research) in Tubingen. His interest was focused on mechanisms of biological pattern formation. Using computer simulations as a tool, he developed models for essential steps in development. Most fascinating for him was the possibility to recapitulate and to reconstructusing the computer the genesis of structures where no structures were before and to see how these emerging structures become subsequently further refined. In addition to the interaction with Alfred Gierer and his group working on hydra development, the Max-Planck Institute as a whole provided a very stimulating environment. In the seventies, the work of Klaus Sander on gradients in early insect development was highly influential. Collaboration with Martin Klinger in the eighties revealed that the pigmentation patterns on tropical sea shells are convenient to study highly dynamic patterning processes. The variability and the asthetic beauty of these patterns turned out to result from the chaotic nature of the underlying reactions. Mechanisms deduced from shell patterns became a key to understand other developing systems such as orientation of chemotactic cells or phyllotaxis. Officially Hans Meinhardt retired at the end of 2003. At present he works on refinements and extensions of models which account for the different modes of embryonic axis formation in different phyla from an evolutionary point of view.     

Exploiting redundancy to boost performance in a RAID-10 style cluster-based file system

While aggregating the throughput of existing disks on cluster nodes is a cost-effective approach to alleviate the I/O bottleneck in cluster computing, this approach suffers from potential performance degradations due to contentions for shared resources on the same node between storage data processing and user task computation. This paper proposes to judiciously utilize the storage redundancy in the form of mirroring existed in a RAID-10 style file system to alleviate this performance degradation. More specifically, a heuristic scheduling algorithm is developed, motivated from the observations of a simple cluster configuration, to spatially schedule write operations on the nodes with less load among each mirroring pair. The duplication of modified data to the mirroring nodes is performed asynchronously in the background. The read performance is improved by two techniques: doubling the degree of parallelism and hot-spot skipping. A synthetic benchmark is used to evaluate these algorithms in a real cluster environment and the proposed algorithms are shown to be very effective in performance enhancement. Yifeng Zhu received his B.Sc. degree in Electrical Engineering in 1998 from Huazhong University of Science and Technology, Wuhan, China; the M.S. and Ph.D. degree in Computer Science from University of Nebraska – Lincoln in 2002 and 2005 respectively. He is an assistant professor in the Electrical and Computer Engineering department at University of Maine. His main research interests are cluster computing, grid computing, computer architecture and systems, and parallel I/O storage systems. Dr. Zhu is a Member of ACM, IEEE, the IEEE Computer Society, and the Francis Crowe Society. Hong Jiang received the B.Sc. degree in Computer Engineering in 1982 from Huazhong University of Science and Technology, Wuhan, China; the M.A.Sc. degree in Computer Engineering in 1987 from the University of Toronto, Toronto, Canada; and the PhD degree in Computer Science in 1991 from the Texas A&M University, College Station, Texas, USA. Since August 1991 he has been at the University of Nebraska-Lincoln, Lincoln, Nebraska, USA, where he is Professor and Vice Chair in the Department of Computer Science and Engineering. His present research interests are computer architecture, parallel/distributed computing, cluster and Grid computing, computer storage systems and parallel I/O, performance evaluation, real-time systems, middleware, and distributed systems for distance education. He has over 100 publications in major journals and international Conferences in these areas and his research has been supported by NSF, DOD and the State of Nebraska. Dr. Jiang is a Member of ACM, the IEEE Computer Society, and the ACM SIGARCH. Xiao Qin received the BS and MS degrees in computer science from Huazhong University of Science and Technology in 1992 and 1999, respectively. He received the PhD degree in computer science from the University of Nebraska-Lincoln in 2004. Currently, he is an assistant professor in the department of computer science at the New Mexico Institute of Mining and Technology. He had served as a subject area editor of IEEE Distributed System Online (2000–2001). His research interests are in parallel and distributed systems, storage systems, real-time computing, performance evaluation, and fault-tolerance. He is a member of the IEEE. Dan Feng received the Ph.D degree from Huazhong University of Science and Technology, Wuhan, China, in 1997. She is currently a professor of School of Computer, Huazhong University of Science and Technology, Wuhan, China. She is the principal scientist of the the National Grand Fundamental Research 973 Program of China “Research on the organization and key technologies of the Storage System on the next generation Internet.” Her research interests include computer architecture, storage system, parallel I/O, massive storage and performance evaluation. David Swanson received a Ph.D. in physical (computational) chemistry at the University of Nebraska-Lincoln (UNL) in 1995, after which he worked as an NSF-NATO postdoctoral fellow at the Technical University of Wroclaw, Poland, in 1996, and subsequently as a National Research Council Research Associate at the Naval Research Laboratory in Washington, DC, from 1997–1998. In 1999 he returned to UNL where he directs the Research Computing Facility and currently serves as an Assistant Research Professor in the Department of Computer Science and Engineering. The Office of Naval Research, the National Science Foundation, and the State of Nebraska have supported his research in areas such as large-scale scientific simulation and distributed systems.     

Q & A. [interview

Elaine and Gary Ostrander spent their youth in New Jersey and New York before heading to Nebraska for their teen years and eventually Washington State for High School and college, as their father moved around in library administration. Elaine was an undergraduate at the University of Washington, a graduate student at the Oregon Health Sciences University and a postdoc with James Wang at Harvard, studying DNA supercoiling. She next went to Berkeley, where she began the canine genome project, initiating the meiotic linkage map and working on human chromosome 21 at the Lawrence Berkeley National Labs. In 1993 she moved to the Fred Hutchinson Cancer Research Center where she is now a Member of the Divisions of Clinical Research and Human Biology. She is also an Affiliate Professor of Genome Sciences and Biology at the University of Washington, and heads the Program in Genetics at the Hutchinson Center. Gary completed his undergraduate degree in Biology at Seattle University, a M.S. degree at Illinois State University and a Ph.D at the University of Washington in Ocean and Fisheries Science. He went on to be a postdoc in the Department of Pathology at the University of Washington Medical School while being mentored by Senitroh Hakomori of the Fred Hutchinson Cancer Research Center and Eric Holmes of the Pacific Northwest Research Foundation. His work focused on using novel aspects of the biology of fishes to address fundamental questions about cancer. He subsequently held both faculty and administrative positions at Oklahoma State University. Since 1996, he has been at the Johns Hopkins University, where he currently holds academic appointments in the Departments of Biology and Comparative Medicine and is the Associate Provost for Research.     

Jonathan Hodgkin

Jonathan Hodgkin graduated from Oxford in 1971 and then did a PhD with Sydney Brenner at MRC LMB in Cambridge, studying behavioural genetics in the nematode Caenorhabditis elegans. Later, after a couple of years working with myxobacteria as a postdoc in Dale Kaiser's lab at Stanford, he returned to LMB as a staff member, where he remained for most of the subsequent two decades. In the year 2000, he moved to Oxford as Professor of Genetics in the Department of Biochemistry, switching his major research interests from developmental genetics and sex determination to the study of host-pathogen interactions in the worm. For the past ten years, he has acted as curator of the C. elegans genetic map and gene nomenclature, and he is currently President of the Genetics Society of Great Britain.     

Anna Fraentzel Celli (1878-1958)

This paper provides a short history of Anna Fraentzel Celli life, from her arrival in Italy in 1898 to her death in 1958, reviewing available documents and written testimonies. Anna Fraentzel was born in Berlin in 1878, third of four daughters from a bourgeois family; her maternal grandfather, Luigi Traube, was a very well known physician, as well as her father Oscar, and she developed an early interest in medicine that she couldn't fulfill: actually after her father's death she was forced to shorten her education, she couldn't enter the medical school, as she would have liked to, and she attended the nursing school, instead, displaying a lot of good practical sense. As a nurse in Hamburg in 1896 she met Prof. Angelo Celli, who was there on a professional visit, and who assisted the young nurse in finding a job at the city hospital. She was much younger than him, who was already a middle aged respected scientist; anyhow, even after his departure, they kept in touch and eventually fell in love. They married in 1899 and she moved to Rome to work at the S. Spirito Hospital joining a brilliant group of physicians and researchers as Tommasi-Crudeli, Marchiafava, Bignami, Bastianelli, Dionisi, Grassi, and her husband Angelo. They had long been studying the mode of transmission of the malaria infection and in 1898 they had identified the mosquito Anopheles as the vector of the malaria parasite. She got enthusiastically involved both in the scientific work and in the antimalarial campaign which Celli promoted in the Agro Romano. The strong personality of Anna Celli, her active involvement in social problems, her passionate dedication to her work, her peculiar way of being feminist, expressed fully her commitment to the struggle against malaria and illiteracy in the Agro Romano and in the Paludi Pontine at the beginning of the twentieth century. She must be credited as a major force in the creation and functioning of the Peasant Schools, as well as in the organisation of the experimental antimalarial health clinics. After her husband's death in 1914 she continued as a promoter of the antimalarial campaign, co-operating with the Red Cross and other institutions. Moreover, she edited the scientific and historical papers which Angelo Celli had collected and written during his life. She was also a prolific writer and lecturer on these issues and gained widespread appreciation both in Italy and in Germany. Toward the end of her life she retired to a nursing home in Rome where she died almost alone in 1958.     

T. R. R. Stebbing:A bibliography with biographic notes

T. R. R. Stebbing (1835–1926), a specialist on the systematics of amphipod Crustacea, was raised in London in a literary family and studied classics, law and history at Oxford. After his ordination as a priest in 1859 he was a schoolmaster, then, after he married, a private tutor at Torquay. About 1863 he read Darwin's Origin of species and was convinced by it; by 1868 he had become a naturalist and systematist. In 1877 he moved to Tunbridge Wells where he spent the rest of his life studying Crustacea, active in scientific societies, and writing essays and reviews.
Stebbing's Darwinism was not particularly original, though he marshalled some good examples from the invertebrates to indicate the importance of variation within and between species. He regarded natural selection as a directing force by which God's plan for organisms was being worked out, and credited it with the origin of language, morality and religion. In taxonomic practice, Stebbing advocated priority of names, simple rules of transliteration and gender, and publication of new names only in a few easily-accessible journals. After the publication of the Regies internationales de la nomenclature zoologique in 1905 his writings on taxonomic practice were confined to minor issues.
A bibliography of Stebbing's 242 publications concerned with carcinology, Darwinism, nomenclature and miscellaneous subjects has been compiled.     

Walk-In Bridge Scheduling in Bluetooth Scatternets

Bluetooth scatternets may be operated in a loosely coupled mode, called Walk-In Bridge Scheduling, in which the master polls all of its slaves and bridges using E-limited service. Using the theory of queues with vacations, we derive the stability criteria for packet queues in piconet masters, slaves, and bridges. We show that the stability of the slave queues is more critical under high traffic locality, whereas the stability of the bridge queues becomes progressively more important as the non-local traffic increases. Our analysis shows that the limited exchange mode, in which the bridge residence time in a piconet is limited, performs better and has a wider stability region than the complete exchange mode in which the bridge stays in the piconet until all queued packets are exchanged. Simulations show that this scheduling approach offers good performance and excellent scalability, while maintaining scatternet stability.Vojislav B. Mii received his PhD in Computer Science from the University of Belgrade, Yugoslavia, in 1993. He is currently Assistant Professor of Computer Science, at the University of Manitoba in Winnipeg, Manitoba, Canada. Previously, he has held posts at the University of Belgrade, Yugoslavia, and the Hong Kong University of Science and Technology. His research interests include systems and software engineering and modeling and performance evaluation of wireless networks. He is a member of ACM, AIS, and IEEE.Jelena Mii received her PhD degree in Computer Engineering from the University of Belgrade, Yugoslavia, in 1993. She is currently Associate Professor of Computer Science at the University of Manitoba in Winnipeg, Manitoba, Canada. Previously, she has been with the Hong Kong University of Science and Technology. Her current research interests include wireless networks and mobile computing. She is a member of IEEE Computer Society.Ka Lok Chan received his MPhil degree in performance of Bluetooth networks at the Hong Kong University of Science and Technology.     

Better than CD: Eugénie Cotton (1881-1967)

Aimé Cotton is known for his invention of circular dichroism spectroscopy. In 1913, he married Eugénie Feytis, a scientist who studied physics with Marie Curie. Following the Second World War, Eugénie Cotton was determined to advance the rights and standing of women, sure in the belief that doing so was necessary not only because it was just but also because a world with women in the forefront would be more secure and less susceptible to the catastrophe worldwide military conflict. She was a cofounder of the Women's International Democratic Federation and served as its first president. In 1951, she was awarded the Stalin Peace Prize, and in 1961, the gold medal from the World Peace Council. The extraordinary life of Eugénie Cotton is reconstructed in a new biography by Loukia Efthymiou, Eugénie Cotton (1881-1967) (Éditions Universitaires Européennes, 2019) that is reviewed here. Among the contributions of Eugénie Cotton of particular interest to the Chirality readership is the biography she wrote of her husband, Aimé Cotton, l'optique et magneto-optique (Éditions Seghers, 1967), the most complete source of information on the founder of the science of circular dichroism. This biography is also discussed here, thereby building two reviews of books, one new and one old, one about Eugénie Cotton and one by her, into a single essay.     

Q & A

Gregory A. Petsko is Gyula and Katica Tauber Professor of Biochemistry and Chemistry and Director of the Rosenstiel Basic Medical Sciences Research Center at Brandeis University. He did his undergraduate work at Princeton and his graduate work as a Rhodes Scholar at Oxford University. He held faculty positions at Wayne State University School of Medicine and MIT before moving to Brandeis in 1990. A structural biologist, he is best known for his work, together with his colleague Dagmar Ringe, on the structural basis of enzyme catalytic power and the role of protein dynamics in protein function. He writes a regular opinion column for the journal Genome Biology.     

Jonathon Howard.

Jonathon 'Joe' Howard (Fig. 1) is Group Leader and Director at the Max Planck Institute of Molecular Cell Biology and Genetics; he and his research group moved to Dresden, Germany, in July 2001. Howard received his PhD in neurobiology in 1983 from the Australian National University in Canberra. He did postdoctoral research there and also at the University of Bristol, UK, and at the University of California, San Francisco. In 1989, he joined the faculty at the University of Washington. His book "Mechanics of Motor Proteins and the Cytoskeleton" was published earlier this year. [interview by Mari N. Jensen]     

Q & A. [interview

Joel Rosenbaum was born and grew up in Massena, New York state, on the St Lawrence River border with Ontario, Canada. He received his undergraduate and PhD degrees from Syracuse University, and a Masters Degree in high school biology teaching at St Lawrence University. His PhD work was done with the protozoologist, George Holz Jr, and his post doctoral research on cilia and flagella was at the University Of Chicago with Frank Child and Hewson Swift. He has been at Yale University for 37 years where he has taught Cell Biology. His research has been on the synthesis and assembly of the proteins of cilia and flagella, showing that the flagellar axoneme assembles at the distal tip and that detachment of the flagella upregulates the genes for flagellar proteins. More recently his group has shown that this tip assembly process is facilitated by a rapid kinesin and cytoplasmic dynein-mediated motility underneath the flagellar membrane called ‘intraflagellar transport’. He is a runner with more than 20 marathons under his belt.     

Schweingruber’s cosmos of inspiration

Born 29^th February 1936 near Bern, Switzerland, Fritz Hans Schweingruber worked as a teacher until 1965, obtained a PhD in botany from the University of Basel in 1972 (where he also obtained a Professorship in 1976), and started his lifelong career at the Swiss Federal Research Institute WSL in Birmensdorf right afterwards. Fritz developed a dendrochronological network across much of the Northern Hemisphere, expanded wood (xylem) science beyond forests, implemented wood anatomical techniques into dendroecology and paleoclimatology, and enthusiastically trained thousands of students, of which hundreds remained actively involved in the still emerging field of tree-ring research. Though Fritz died 7^th January 2020 after an extraordinary academic career, his intellectual legacy will continue to inspire scholars around the world.     

Known by the society he keeps: an interview with Robert Ruffolo

By his own admission, Robert R. Ruffolo, Head of Research and Development at Wyeth-Ayerst, is a bit of a nerd. Opting to spend seven nights per week with his textbooks at the expense of all else, he earned his pharmacy degree summa cum laude, and his PhD in pharmacology in just over three years. He speaks with unabashed enthusiasm for the pharmaceutical industry, for biomedicine, and particularly for the future of pharmacology. Even if you don't know Ruffolo, you've probably seen him-if not at a science symposium, then surely as the lead "actor" in televised promotions that ran throughout 1999 on behalf of the Pharmaceutical Research and Manufacturers of America (PhRMA; scenes reproduced here, with permission). "Actor" belongs in quotation marks, because if there is such a thing as type casting, then Ruffolo is certainly an example in the PhRMA ads: passionate about good drugs and the people who need them; proud of his profession and his contributions; dedicated to science as well as to his colleagues; and grateful for the opportunities he has had to contribute. The commercial's requisite happy ending, where three generations of a coronary-prone farm family ride off into the sunset, reflects Ruffolo's own success story in helping to bring carvedilol to market. In all of this, however, Ruffolo's sincerity transcends the hokey as well as the nerdy. His devotion to science includes a mission to help others, and he would argue that in this and most ways, he is not so different from his academic colleagues.     

Q & A. Philip Ingham

Philip Ingham grew up in Liverpool and graduated from Cambridge University in 1977. He did his D.Phil in Developmental Genetics at Sussex University and postdoctoral work in Strasbourg, France before joining the laboratory of David Ish-Horowicz at the ICRF Mill Hill Laboratories. Here he applied the emerging technique of tissue in situ hybridisation to the analysis of the Drosophila segmentation genes. After a short spell at the MRC Laboratory of Molecular Biology in Cambridge, he rejoined the ICRF as a Research Scientist at the Developmental Biology Unit in Oxford. His group pioneered the analysis of the Hedgehog signalling pathway in Drosophila and in collaboration with the labs of Andy McMahon and Cliff Tabin at Harvard University, discovered the Hedgehog gene family in vertebrates. In 1996 he was appointed Professor of Developmental Genetics at the University of Sheffield where he has established the Centre for Developmental Genetics.     

More than a blog

Blogging is circumventing traditional communication channels and levelling the playing field of science communication. It helps scientists, journalists and interested laypeople to make their voices heard.Last December, astrobiologists reported in the journal Science that they had discovered the first known microorganism on Earth capable of growing and reproducing by using arsenic (Wolfe-Simon et al, 2010). While media coverage went wild, the paper was met with a resounding public silence from the scientific community. That is, until a new breed of critic, science bloggers, weighed in. Leading the pack was Rosie Redfield, who runs a microbiology research lab in the Life Sciences Centre at the University of British Columbia in Vancouver, Canada. She posted a critique of the research to her blog, RRResearch (rrresearch.fieldofscience.com), which went viral. Redfield said that her site, which is typically a quiet window on activities in her lab got 100,000 hits in a week.Redfield said that her site, which is typically a quiet window on activities in her lab got 100,000 hits in a weekThis incident, like a handful before it and probably more to come, has raised the profile of science blogging and the freedom that the Internet offers to express an opinion and reach a broad audience. Yet it also raises questions about the validity of unfettered opinion and personal bias, and the ability to publish online with little editorial oversight and few checks and balances.Redfield certainly did not hold back in her criticism of the paper. Her post said of the arsenic study: “Lots of flim-flam, but very little reliable information. [...] If this data was presented by a PhD student at their committee meeting, I''d send them back to the bench to do more clean-up and controls.” She also opined on why the article was published: “I don''t know whether the authors are just bad scientists or whether they''re unscrupulously pushing NASA''s ''There''s life in outer space!'' agenda. I hesitate to blame the reviewers, as their objections are likely to have been overruled by Science''s editors in their eagerness to score such a high-impact publication.”Despite the fervor and immediacy of the blogosphere, it took Science and Felisa Wolfe-Simon, the lead author on the paper, nearly six months to respond in print. Eventually, eight letters appeared in Science covering various aspects of the controversy, including one from Redfield, who is now studying the bacteria in her lab. Bruce Alberts, editor-in-chief of Science, downplayed the role that blogging played in drumming up interest in the controversial study. “I am sure that the number of letters sent to us via our website reflected a response to the great publicity the article received, some of it misleading [...] This number was also likely expanded by the blogging activity, but it was not directly connected to the blogs in any way that I can detect,” he explained.Bloggers, of course, have a different take on the matter, arguing that it was another example of a growing number of cases of ''refutation by blog''. The blogging community heralds Redfield as a hero to science and science blogging. By now, more traditional science media outlets have also joined the bloggers in their skepticism over the paper''s claims, with many repeating the points Redfield made in her original blog response.Jerry Coyne, an evolutionary geneticist at the University of Chicago in the USA, writes the blog Why Evolution is True (whyevolutionistrue.wordpress.com), which is a spinoff from his book of the same name. He said that bloggers, both professional scientists and journalists, have been gaining a new legitimacy in recent years as a result of things such as the arsenic bacteria case, as well as from shooting holes in the 2009 claims that the fossil of the extinct primate Darwinius masillae from the Messel Pit in Germany was a ''missing link'' between two primate species (Franzen et al, 2009). “[Blogging has] really affected the pace of how science is done. One of the good things about science blogging, certainly as a professional, is you''re able to pass judgment on papers instantly. You don''t have to write a letter to the editor and have it reviewed. [Redfield] is a good example of the value of science blogging. Claims that are sort of outlandish and strong can be discredited or at least addressed instantaneously instead of waiting weeks and weeks like you''d otherwise have to do,” he said.“... you''re able to pass judgment on papers instantly. You don''t have to write a letter to the editor and have it reviewed”Perhaps because of the increasingly public profile of popular science bloggers, as well as the professional and social value that is becoming attached to their blogs, science blogging is gaining in both popularity and validity. The content in science blogs covers a wide spectrum from genuine science news to simply describing training or running a lab, to opinionated rants about science and its social impact. The authorship is no less diverse than the content with science professionals, science journalists and enthusiastic amateurs all contributing to the melting pot, which also has an impact on the quality.Carl Zimmer is a freelance science journalist, who writes primarily for the New York Times and Discover Magazine, and blogs at The Loom (blogs.discovermagazine.com/loom). “Most scientists have not been trained how to write, so they are working at a disadvantage,” he said. “[Writing for them] would be like me trying to find a dinosaur. I wouldn''t do a very good job because I don''t really know how to do that. There are certainly some scientists who have a real knack for writing and blogs have been a fantastic opportunity for them because they can just start typing away and all of a sudden have thousands of people who want to read what they write every day.”Bora Zivkovic, who is a former online community manager at Public Library of Science, focusing mainly on PLoS ONE, is one of those scientists. A native of Belgrade, he started commenting in the mid-1990s about the Balkan wars on Usenet, an Internet discussion network. He began blogging about science and politics in 2004 and later about his interest in chronobiology, which stems from his degree in the topic from North Carolina State University. He still combines these interests in his latest blog, Blog Around the Clock (blogs.scientificamerican.com/a-blog-around-the-clock). Last year, Scientific American named Zivkovic its blog editor and he set up a blogging network for the publication. “There isn''t really a definition of what is appropriate,” he said. “The number one rule in the blogosphere is you never tell a blogger what to blog about. Those bloggers who started on their own who are scientists treasure their independence more than anything, so networks that give completely free reign and no editorial control are the only ones that can attract interesting bloggers with their own voices.”“The number one rule in the blogosphere is you never tell a blogger what to blog about”Daniel McArthur, an Australian scientist now based in the UK, who blogs about the genetic and evolutionary basis of human variation at Genetic Future (www.wired.com/wiredscience/geneticfuture), and about personal genomics at Genomes Unzipped (www.genomesunzipped.org), said that it is difficult to define a science blog. “I think it''s semantics. There are people like me who spend some time writing about science and some time writing about industry and gossiping about things in the industrial world. Then there are the people who write about the process of doing science. There are many, many blogs where [...] the content is much more about [the blogger''s] personal voyage as a scientist rather than the science that they do. Then there are people who use science blogging as an extra thing that they do and the primary purpose of their blog is to add political advocacy. I think it''s very hard to draw a line between the different categories. My feeling is that science bloggers should write about whatever it is they want to write about .”The ability to distribute your opinion, scientific or otherwise, online and in public is raising difficult questions about standards and the difference between journalism and opinion. Sean Carroll, who writes for the physics group blog Cosmic Variance (blogs.discovermagazine.com/cosmicvariance), is a senior research associate in the Department of Physics at the California Institute of Technology in the USA. “Some blogging is indistinguishable from what you would ordinarily call journalism. Some blogging is very easily distinguishable from what you would ordinarily call journalism,” he said. “I think that whether we like it or not, the effect of the Internet is that readers need to be a little bit more aware of the status of what they are looking at. Is this something reputable? Anyone can have a blog and say anything, so that one fact is both good and bad. It''s bad because there is a tremendous amount of rubbish on the Internet [...] and people who have trouble telling the rubbish from the good stuff will get confused. But it''s also good because it used to be the case that only a very small number of voices were represented in major media.”Zimmer contrasts the independence of blogging with traditional journalism. “You really get to set your own rules. You''re not working with any editor and you''re not trying to satisfy them. You''re just trying to satisfy yourself. In terms of the style of what I do, I will tend to write more—I think of [my blog posts] as short essays, as opposed to an article in the New York Times where I''ll be writing about interviewing someone or describing them on a visit I paid to them. One of the great things about a blog is that it''s a way of making a connection with people who are your readers and people who are following you for a long time.”One of the world''s most popular scientist bloggers is Paul Zachary Myers, known as PZ, a biology professor at the University of Minnesota in the USA. He blogs at Pharyngula (scienceblogs.com/pharyngula), a site named for a particular stage in development shared by all vertebrate embryos. “Passion is an important part of this. If you can communicate a love of the science that you''re talking about, then you''re a natural for blogging,” he explained. “[Pharyngula] is a blog where I have chosen just to express myself, so self-expression is the goal and what I write about are things that annoy me or interest me.”“Passion is an important part of this. If you can communicate a love of the science that you''re talking about, then you''re a natural for blogging”Myers'' blog, which is driven by a mix of opinion, colourful science writing, campaigning against creationism and an unflinching approach to topics about which he is passionate, draws about 3 million visitors a month. He said his blog attracts more traffic than other blogs because it is not purely about science. “I do a lot of very diverse things such as controversial religious stuff and politics, and whatever I feel like. So I tap into a lot of interest groups and that builds up my rank quite a bit. I''d say there are quite a few other science blogs out there that are pure science blogs, but pure science blogs—where they just talk about science and nothing but science—cannot get quite as much traffic as a more broadly based blog.”In an example of his sometimes-incendiary posting, Myers recently took on the Journal of Cosmology regarding an article on the discovery of bacteria fossils in a meteorite. He said that the counterattack got personal, but that he usually enjoys “the push back” from readers. “That''s part of the argument. I would say that everyone has an equal right to make their case on the web. That''s sometimes daunting for some people, but I think it''s part of the give and take of free speech. It''s good. It''s actually kind of fun to get into these arguments.”Beyond the circus that can surround blogs such as Pharyngula, scientist bloggers are debating whether their blogging counts as a professional activity. Redfield said that blogging can be taken into account among the outreach some governments now require from researchers who receive public funds. She said that some researchers now list their blogging activity in their efforts to communicate science to the public.Coyne, however, does not share his interest in blogging with other senior faculty at the University of Chicago, because he does not believe they value it as a professional activity. Still, he said that he recognizes the names of famous scientists among his blog readers and argues that scientists should consider blogging to hone their writing skills. “Blogging gives you outreach potential that you really should have if you''re grant funded, and it''s fun. It opens doors for you that wouldn''t have opened if you just were in your laboratory. So I would recommend it. It takes a certain amount of guts to put yourself out there like that, but I find it immensely rewarding,” he said. In fact, Coyne has had lecture and print publishing opportunities arise from his blogs.“It opens doors for you that wouldn''t have opened if you just were in your laboratory [...] It takes a certain amount of guts to put yourself out there like that...”Redfield said she finds blogging—even if no one reads her posts—a valuable way to focus her thoughts. “Writing online is valuable at all levels for people who choose to do it. Certainly, by far the best science writing happening is in the community of writers who are considered bloggers,” she said.In terms of pay, science blogging usually remains in the ''hobby zone'', with pay varying widely from nothing at all to small amounts from advertising and web traffic. ''GrrlScientist'', an American-trained molecular evolutionary biologist based in Germany, who prefers to go by her nom de blog, has been blogging for seven years. She writes the popular Punctuated Equilibrium blog (www.guardian.co.uk/science/punctuated-equilibrium) for The Guardian newspaper in the UK, as well as Maniraptora (blogs.nature.com/grrlscientist) for the Nature Network, and is co-author of This Scientific Life (scientopia.org/blogs/thisscientificlife) for the science writing community Scientopia. She said she earns a small amount from ad impressions downloaded when her blog is viewed at The Guardian. On the other end of the scale is Myers, who declined to disclose his income from blogging. “It''s a respectable amount. It''s a nice supplement to my income, but I''m not quitting my day job,” he said.Yet bloggers tend not to do it for the money. “I know that when I go to give talks, the fact that I have the blog is one of the first things that people mention, and lots of students in particular say that they really enjoy the blog and that they''re encouraged by it,” Carroll explained. “Part of what we do is not only talk about science, but we act as examples of what it means to be scientist. We are human beings. We care about the world. We have outside interests. We like our jobs. We try to be positive role models for people who are deciding whether or not this is something that they might want to get into themselves one day.”The rise of the science blogosphere has not all been plain sailing. Although the Internet has been hailed as a brave new world of writing where bloggers can express themselves without interference from editors or commercial interests, it has still seen its share of controversy. The blogging portal ScienceBlogs was the launchpad for some of the best and most popular writers of the new generation of science bloggers, including Myers and Zivkovic. But an incident at ScienceBlogs shook up the paradise and raised journalistic ethical quandaries.In July 2010, a new site, Food Frontiers (foodfrontiers.pepsicoblogs.com), appeared on ScienceBlog, sponsored by PepsiCo, the makers of the popular drink. The blog featured posts written by the beverage maker''s representatives and was blended in with the other blog content on the portal. “Pepsi''s blog looked like my blog or PZ''s blog,” Zivkovic explained, “with no warning that this was paid for and written by Pepsi''s R&D or PR people [...] talking about nutrition from a Pepsi perspective, which is a breach in the wall between advertorial and editorial. The moment the Pepsi blog went live, about 10 bloggers immediately left.” He said that the journalist-bloggers in particular pointed to a break of trust that would sully the reputation of ScienceBlogs writers and confuse readers.In his final blog at the site, titled ''A Farewell to Scienceblogs: the Changing Science Blogging Ecosystem'', Zivkovic nailed the danger of the ''Pepsigate'' incident to the validity of the blogosphere. He wrote: “What is relevant is that this event severely undermined the reputation of all of us. Who can trust anything we say in the future? Even if you already know me and trust me, can people arriving here by random searches trust me? Once they look around the site and see that Pepsi has a blog here, why would they believe I am not exactly the same, some kind of shill for some kind of industry?” (scienceblogs.com/clock/2010/07/scienceblogs_and_me_and_the_ch.php). Myers, who at the time was responsible for more than 40% of the traffic at ScienceBlogs, went ''on strike'' to protest. In the aftermath, the Pepsi blog was pulled.Redfield raises another interesting word of caution. “Most scientists are extensively worried about being scooped, so they''re scared to say anything about what''s actually going on in their lab for fear that one of their competitors will steal their ideas,” she said. In this context, social networking sites such as ResearchGate (www.researchgate.net; Sidebar A) might be a more appropriate avenue for securely sharing ideas and exchanging tips and information because it enables users to control who has access to their missives.“... they''re scared to say anything about what''s actually going on in their lab for fear that one of their competitors will steal their ideas”

Sidebar A | ResearchGate—social media goes pro

Whenever she is looking for ideas for a research project, biologist Anne-Laure Prunier, who works in the Department of Cellular Biology and Infection at the Institut Pasteur in Paris, has recently turned to ResearchGate (www.researchgate.net), the scientists'' version of the social networking site Facebook. “Every time I have used ResearchGate, I found it really useful,” she commented.ResearchGate, based in Berlin, Germany and Cambridge, USA, is a free service that launched in January 2009. It was co-founded by Ijad Madisch, who earned his MD and PhD from the University of Hannover''s medical school in Germany and is a former research fellow at Harvard Medical School. He explained that his goal in starting the network was to make research more efficient. “During my research in Boston, I noticed that science is very inefficient, especially if you''re doing an experiment and trying to get feedback from people working on the same problem. You don''t have any platforms, online networks where you can go and ask questions or if you''re trying to find someone with a specific skill set. So I decided to do that on my own.”As a result, the site offers researchers functionality similar to Facebook—the modern template for social networking. Through ResearchGate, members can follow colleagues, be followed by those interested in their research, share their conference attendance and recent papers—their own or those that interest them—and most importantly, perhaps, ask and answer questions about science and scientific techniques.“You can get in touch with a lot of different people with a lot of different backgrounds,” Prunier explained. “When I have a very precise technical question for which I don''t find an answer in my institute, I turn to ResearchGate and I ask this question to the community. I have done it three times and every time I have gotten a lot of answers and comments, and I was able to exchange information with a lot of different people which I found really useful.”By May 2011, ResearchGate had reached one million members across 192 countries. The largest numbers of registrations come from the USA, the UK, Germany and India. Biologists, who are second only to medical doctors on the site, make up more than 20% of members. In addition to blogging, ResearchGate is just one example of how the Internet—originally invented to allow physicists to share data with one another—is changing the way that scientists communicate and share information with each other and the public.Carroll, on the other hand, who has been blogging since 2004, said that physicists are very comfortable about publicly sharing research papers with colleagues online. “The whole discussion gets very heated and very deep in some places about open access publishing. Physicists look on uncomprehendingly in fact because they put everything for free on line. That''s what we''ve been doing for years. It works.” But he said they are more cautious about blogging for a general audience. By contrast, he believes biology is especially well-suited to being blogged. “[Biologists are] actually more comfortable with talking to a wider audience because biology, whether it is through medicine or through debates about creationism or life on other planets or whatever, gets involved with public debate quite often.”Zivkovic agrees: “PZ [Myers] and me and a number of others are interested in reaching a broad lay audience, showing how science is fun and cool and interesting and important in various ways. Connecting science to other areas of life, from art to politics and showing the lay audience how relevant science is to everyday life”. Even so, he pointed out that although blogging is popularizing science with the public, there is a less-mainstream sphere serving professional scientists as a forum for surviving the cut and thrust of modern science. “There is a strong subset of the science blogosphere that discusses a life in science, career choices, how to succeed in academia [...] A lot of these are written by people who [...] believe that if their real names were out there it could jeopardize their jobs. They''re not interested in talking to lay audiences. They are discussing survival techniques in today''s science with each other and providing a forum for other young people coming into science.”Ultimately, whether you read popular science blogs, trawl deeper for survival tips, or write your own, the science blogosphere is expanding rapidly and is likely to do so for years to come.     

Shigeo Yamanouchi (1876–1973): A noted Japanese phycologist

Dr Shigeo Yamanouchi was born in Yamagata Prefecture and completed his secondary education at Tokyo Higher Normal School (THNS) where he was also a professor until 1904. In 1905, he went to the University of Chicago in the USA and earned a PhD in Botany in 1907. He is best noted for his excellent research on the cytology and life histories of the marine algae Polysiphonia, Fucus, Cutleria, Aglaozonia and Zanardinia, published between 1906 and 1921 while he was associated with the University of Chicago. He also described the freshwater green alga Hydrodictyon africanum. In 1910, he returned to THNS as a Professor and wrote several botanical textbooks, receiving his DSc degree in 1911 and traveling in England and the USA as an advisor for the Japanese Ministry of Education during 1911–1913. For much of the time between 1920 and 1942 he remained in the USA, returning to Japan following the advent of World War II, During his later life, he was in obscurity, and sadly there is very little recorded of his activities in the post-war years. He died in Tokyo on 2 February 1973 at the age of 96.     

Jordan Raff

Jordan Raff is a Cancer Research UK funded group leader at the Wellcome/CR-UK Gurdon Institute in Cambridge, England. He obtained his PhD from the Department of Biochemistry at Imperial College, London, and he worked as a Post-doctoral fellow at the Department of Biophysics and Biochemistry, University of California, San Francisco. He is currently a Director of the Company of Biologists, and on the committee of the British Society of Cell Biology. He has studied centrosomes and cell division in fruit flies throughout his scientific career.     

Introduction to the Nigel Barlow Symposium

Dr Nigel Barlow died on 4 June 2003 aged 53 in Christchurch, New Zealand. Nigel completed his PhD at the University of East Anglia in 1977 and emigrated to New Zealand in 1979 where he worked initially at Palmerston North and for the last 12 years for AgResearch at Lincoln. Nigel made an enormous contribution to New Zealand ecological science through the use of mathematically based models. In particular, he worked on insect pests such as grass grubs and vertebrate pests such as possums and rabbits, producing over 130 papers. Nigel’s models of bovine tuberculosis underpinned the current strategies and expenditure of over $50 million each year on the control of wildlife vectors on this disease. Nigel’s capabilities as a scientist were not only in the applied field but also reflected in his ability to win funds with his student John Kean from the prestigious Marsden Fund for basic research on the causes of rarity. He was Editor of the New Zealand Journal of Ecology from 1985 to 1990 and of the Journal of Applied Ecology. Nigel was awarded the New Zealand Ecological Society Award for his outstanding contribution to applied ecology in 1996 and posthumously in 2003 the Caughley Medal for lifetime contributions to wildlife management and ecology by the Australasian Wildlife Management Society. Nigel was a true polymath and enthusiast about all natural history. He had an interest in bird-winged butterflies and regularly vanished into the jungles of Indonesia and Papua New Guinea to study them. He was fascinated by crocodilians and anacondas, mountain climbing, landscape painting, and malt whisky. At work he was resistant to bureaucratic interference but happy to pass on his abilities and insights to his students and numerous colleagues.