Since 2006, PLOS ONE has published >200,000 articles, providing an inclusive home for primary research spanning all scientific disciplines and representing researchers from around the globe. As reflected in the journal’s publication criteria and policies,
“Open scholarship is growing in importance as a way of ensuring that there is global participation in research, improved quality and efficiency of education and science, and faster economic and social progress.
Over the next two years, the EIFL Open Access Programme will support open scholarship by focusing on four key areas: open access policies, open science training for early career researchers, sustainable open access journals and repositories, and Open Educational Resources….”
Openness is central to the research endeavor. It is essential to promote reproducibility and appraisal of research, reduce misconduct, and ensure equitable access to and participation in science. Yet, calls for increased openness in science are often met with initial resistance. The introduction of pre-print servers, open access repositories, and open data sets were, for example, initially resisted, but eventually adopted without adverse effects to the scholarly ecosystem. The launch of the Initiative for Open Citations (I4OC) is facing similar obstacles. This initiative has campaigned for scholarly publishers to make openly available the references found in articles from their journals. Many publishers, including most of the large ones, support the initiative and have opened their references. However, the initiative still lacks support from a minority of the large publishers.
Itzï is a hydrologic and hydraulic model that simulates 2D surface flows on a regular grid using simplified shallow water equations. It uses GRASS GIS as a back-end for reading entry data and writing results. It simulates surface flows from direct rainfall or user-given point inflows, and uses raster time-series as entry data, allowing the use of radar rainfall or varying friction coefficients.
Itzï is developed by Laurent Courty at the engineering institute of the National Autonomous University of Mexico.
The National Center for Ecological Analysis and Synthesis (NCEAS) at UCSB is co-sponsoring the Open Science Codefest 2014, which aims to bring together researchers from ecology, biodiversity science, and other earth and environmental sciences with computer scientists, software engineers, and developers to collaborate on coding projects of mutual interest.
Do you have a coding project that could benefit from collaboration, or software skills you’d like to share? The codefest will be held from September 2-4 in Santa Barbara, CA.
Inspired by hack-a-thons and organized in the participant-driven, unconference style, the Open Science Codefest is for anyone with an interesting problem, solution, or idea that intersects environmental science and computer programming. This is the conference where you will actually get stuff done – whether that’s coding up a new R module, developing an ontology, working on a data repository, creating data visualizations, dreaming up an interactive eco-game, discussing an idea, or any other concrete collaborative goal that interests a group of people.
Looks like a great program!
Sharks live in the vast, deep, and dark ocean, and studying these large fish in this environment can be difficult. We may have sharks ‘tweeting’ their location, but we still know relatively little about them. Sharks have been on the planet for over 400 million years and today, there are over 400 species of sharks, but how long do they live, and how do they move? Two recent studies published in in PLOS ONE have addressed some of these basic questions for two very different species of sharks: great whites and megamouths.
The authors of the first study looked at the lifespan of the great white shark. Normally, a shark’s age is estimated by counting growth bands in their vertebrae (image 1), not unlike counting rings inside a tree trunk. But unfortunately, these bands can be difficult to differentiate in great whites, so the researchers dated the radiocarbon that they found in them. You might wonder where this carbon-14 (14C) came from, but believe it or not, radiocarbon was deposited in their vertebrae when thermonuclear bombs were detonated in the northwestern Atlantic Ocean during the ‘50s and ’60s. These bands therefore provide age information. Based on the ages of the sharks in the study, the researchers suggest that great whites may live much longer than previously thought. Some male great whites may even live to be over 70 years old, and this may qualify them as one of the longest-living shark species. While these new estimates are impressive, they may also help scientists understand how threats to these long-living sharks may impact the shark population.
A second shark study analyzed the structure of a megamouth shark’s pectoral fin (image 2) to understand and predict their motion through the water. Discovered in 1976, the megamouth is one of the rarest sharks in the world, and little is known about how they move through the water. We do know that the megamouth lives deep in the ocean and is a filter feeder, moving at very slow speeds to filter out a meal with its large mouth. But swimming slowly in the water is difficult in a similar way flying slowly in an airplane is difficult. Sharks need speed to control lift and movement.
To better understand the megamouth’s slow movement, the researchers measured the cartilage, skin histology, and skeletal structure of the pectoral fins of one female and one male megamouth shark, caught accidentally and preserved for research. The researchers found that the megamouth’s skin was highly elastic, and its cartilage was made of more ‘segments’ than any other known shark, which may provide added flexibility compared to other species. The authors also suggest that the joint structure (image 3) of the pectoral fin may allow forward and backward rotation, motions that are largely restricted in most sharks. The authors suggest that this flexibility and mobility of the pectoral fin may be specialized for controlling body posture and depth at slow swimming speeds. This is in contrast to the fins of fast-swimming sharks that are generally stiff and immobile.
In addition to the difficulties in exploring deep, dark seas, small sample sizes present challenges for many shark studies, including those described here. But whether studying the infamous great white shark or one of the rare megamouths, both contribute to a growing body of knowledge of these elusive fish.
Tomita T, Tanaka S, Sato K, Nakaya K (2014) Pectoral Fin of the Megamouth Shark: Skeletal and Muscular Systems, Skin Histology, and Functional Morphology. PLoS ONE 9(1): e86205. doi:10.1371/journal.pone.0086205
Science magazine (a closed-access publisher) does a “sting” on crappy OA journals (and boy are there lots of these), and Michael Eisen points out how this sting is more about how crappy peer review is at catching bad science (even at Science). Here’s the best quote from Eisen’s response:
“To suggest – as Science (though not Bohannon) are trying to do – that the problem with scientific publishing is that open access enables internet scamming is like saying that the problem with the international finance system is that it enables Nigerian wire transfer scams.
There are deep problems with science publishing. But the way to fix this is not to curtain open access publishing. It is to fix peer review.”
After attending two recent scientific conferences, one which was gender balanced, and one which was so gender-imbalanced that it engendered snarky out-of-band twitter comments, it struck me that we might need a Bechdel Test for scientific workshops. The Bechdel test is a simple test for movies. To pass the test, a movie has to have:
- at least two [named] women in it,
- who talk to each other,
- about something besides a man.
Seems simple, right? You’d be amazed at just how few popular movies pass the test, including some set in universes that were originally designed for equality. (I’m talking about you, Star Trek reboot.)
Here’s an analogous test for scientific workshops or conference symposia. Does the workshop have:
- at least two female invited speakers,
- who are asked questions by female audience members,
- about their research.
Again, this seems simple, right? But you’d be shocked how few scientific conference symposia or workshops can live up to this standard. I suspect this depends strongly on specific research fields.
Rigoberto Hernandez has been talking about advancing science through diversity for quite a while. I finally got to hear him speak about the OXIDE project on this latest trip, and he’s got a lot of great things to say about how diversity can strengthen science. I think one great way to help is to point out the good conferences we attend which live up to this standard.
Rigoberto also happened to be one of the organizers of the gender-balanced conference, which was also one of the best meetings I’ve ever attended.