Deep Sea News

At the PLoS One Community blog I discuss why I joined PLoS One, believe in the open access mission, and contemplate how we view a paper’s novelty.

I was extremely flattered a year ago to be invited to join the academic editors at PLoS One. In that time I worked diligently to develop a Marine and Aquatic Science hub at the journal. I have accumulated what I consider to be an experienced team of academic editors who are both committed to open access but well respected researchers in their fields.  These include Zoe Finkel, Carlos Duarte, Geoffrey Trussell, John Bruno, Stuart Humphries, Stuart Sandin, and Steve Volmer, just to name a few.

Today the Marine and Aquatic Section is live. I am excited to introduce our first paper in the section.  Schmidt et al. examine the biogeography and population genetics of whale sharks demonstrating that disparate populations have considerable gene flow between them. Overall the paper cautions that conservation of whale sharks require global initiatives.

Please add Marine and Aquatic Science RSS feed to your readers!

Image credit: (c) 2006 MBARI / NOAA These this photograph shows three different types of sponges growing on the lava of Davidson Seamount: large yellow sponges, white frilly sponges, and white filamentous sponges which were previously thought to be a type of coral. The large yellow sponge provides a perch for several basket stars and pink shrimp.

About a month ago, I published my first paper at PLoS One. I believed an open access journal was the most appropriate place for the work so the group’s findings would be accessible to the public, scientists, conservationists, and policy makers.  I am delighted to say that this work, and the major finding of connectedness between the seamount and the surrounding deep sea, in part aided in efforts to include Davidson Seamount into the Monterey Bay National Marine Sanctuary.

I am delighted to see this work being discussed both locally at the Monterey Herald (Scientist See Movement of Marine Species) and internationally in a piece done for Conservation Magazine, a publication for the Society for Conservation Biology (A Seamount a Dozen).

Image credit: (c) 2006 MBARI / NOAA These large yellow sponges are of an unknown species, but researchers on the cruise have been calling them "Picasso sponges" because of their wild shapes. The yellow sponges grow to almost one meter (three feet) tall. Like the corals on Davidson Seamount, the sponges feed on tiny particles suspended in the currents.

Craig R. McClain, Lonny Lundsten, Micki Ream, James Barry, Andrew DeVogelaere (2009). Endemicity, Biogeography, Composition, and Community Structure On a Northeast Pacific Seamount PLoS ONE, 4 (1) DOI: 10.1371/journal.pone.0004141

Note: This was liveblogged at the time, but the wifi crashed under the weight of 200 simultaneous livebloggers.

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As many readers know, we are staunch proponents of open access. Craig being an academic editor at PLoS ONE and myself writing extensively on the benefits of open access, especially to taxonomy. Open Access is not just free of copyright and licensing fees but is a philosophy based on the “business” of doing science. Bill, one of the session moderators, said “it is a return on public investment”. In fact, universities are getting double dipped by journals because researchers often have to pay to publish their work, while university libraries must pay again to provide access to the journals that their faculty publish in. In fact, he presented a graph where the price of journal of subscriptions was increasing very fast in relation to Consumer Price Index and library salaries. Bjorn Brembs commented on an experience he had recently where he was asked to submit an article to a journal that then asked him for page charges. Unfortunately, his university didn’t subscribe to that journal and wasn’t able to get access to his own published article. The absurdity doesn’t stop there either.

Bob O’Hara, whom it was great to meet and talk with, had some criticisms, as well as others, that some aspects of open access are impractical and that the scientific community is not mature enough for it yet. He felt journal rankings in particular were a useful indicator of an applicant’s research quality. I disagree because you cannot compare journal quality across fields. If Bob, a statistician, was on a hiring committee for an ecologist would his experience and expectation with statistics journals be equivalent to that similar journals in ecology? Taxonomy has only 1 or 2 journals with impact factors above 5. I am excited that my anemones will be published in a journal with an impact factor above 1. Several science librarians in the audience commented that the impact factor was originally developed to help librarians determine which journals to spend money on. It had nothing to do with scientist per se, but seems to have been hijacked by the community to assess one another. Bob discusses his impression on his Nature Network Blog

You can find out which places are open access at ROAR and follow Peter Suber’s blog Open Access News.

- by Kevin Zelnio

Science is being revolutionized by the internet. More and more scientists are blogging, using wiki’s, special search engines, social networking sites and other online technologies to communicate with a broader audience or to enhance communication within their discipline or a small group of colleagues. Open access to information and source code for software is increasing. Much is being discussed about the future of science and the communication of science. It is very fascinating times we live in right now. More and more media sites, such as our Discovery Channel overlords, are recognizing the value in utilizing the communication experience, knowledge and enthusiasm of internet-savvy working scientists. This is a good thing.

For the last 2 years there has been a North Carolina Science Blogging Conference. I had the extremely good fortune of organizing and co-moderating a session called "Real-time blogging in the marine sciences" with Peter and my fantastic colleagues Rick, Jason and Karen. It was a great time and I also participated in a session on student blogging and open access in the developing world. I emphasize participated because these conferences followed an "unconference" format. This is a brilliant concept for conferences where sessions are moderated and discussion between everyone in the room is encouraged. This is in contrast to the traditional conference where a speaker gives a presentation to an audience, which is otherwise disengaged from the material being presented. In an unconference you walk away with the feeling that you were an important component of the discussion, and indeed, the second you raised your hand you were.

For the next Science Blogging Conference, there is a slightly new emphasis, reflecting its growth and the growth of interest in the role online technologies play in promoting, communicating, and enhancing science. This conference, and subsequent ones will be called ScienceOnline!

ScienceOnline’09 is the third annual science blogging
conference, to be held Jan. 16-18, 2009 at the Sigma Xi Center in
Research Triangle Park, NC.

Please join us for this free three-day event to explore science on the Web. Our goal is to bring together scientists, bloggers, educators,
students, journalists and others to discuss, demonstrate and debate
online strategies and tools for promoting the public understanding of
science.

I will be there, and hopefully as a presenter, but more importantly as a participant. If you are interested in the future of science, I encourage you register for this memorable and exhilarating conference. You can also see who else will be attending. There will also be four main conference tracks: Science blogging, Science communication and education, Doing and publishing science, and Show-and-tell quick sessions. Each
track will have sessions targeting different audiences (e.g., beginner
bloggers, experienced bloggers, scientists, students, teachers, etc.). Keep posted to Bora’s blog for updates

Additionally, if you are a person that wants to reach out to a few hundred scientists, communicators, media personnel, bloggers, writers, educators and internet-influential types, get in contact with the conference organizers or myself to showcase you organization’s mission, goals, products, samples, media, software, etc. Each conference participant will get a grab bag with you swag in it. Judging from mine last year, it was an AWESOME haul that kept me entertained for months afterwards.

Hope to see you there in January!

That is the common theme in marine biology. Clara Moskowitz has an article up at LiveScience describing how scientists are struggling to keep up with marine life discoveries. Here is a short snippet:

“Scientists figure there are at least 1 million species of marine organisms on Earth.

Of these, only about 230,000 are known to science now, and some of those have more than one name. To keep them all straight, 55 researchers from 17 countries are working on a new list, the ultimate tally of sea creatures great and small.

The list is about half done, the team announced today. So far, the scientists have counted 122,500 species, which puts them about halfway toward completing the inventory of known marine species by their goal of October 2010.

“Describing species without a universal register in place is like setting up a library without an index catalog,” said Philippe Bouchet, a scientist at the French National Museum of Natural History who is helping to compile the list. “

Much of the problem has to do with synonymy, a case when a species has more than one name. This happens for a variety of reasons. For instance, when a taxonomist describes and names a new species without consulting the full history of literature, two taxonomists describe the species around the same time independently, or the literature on a species is difficult to obtain or in obscure local journals. So far, the winner for most names is the “Breadcrumb Sponge”, Halichondria panicea, described as

“the marine world’s reigning champion of Latin aliases, with 56 synonyms appearing in taxonomic literature since its first description in 1766. Of no fixed address, it’s known to frequent floats, pilings, and the underside of rocks, smells like exploded gunpowder and takes on many guises.”

Cleaning up this mess is serious business. With over 250 years of species discoveries to sift through, scientists need a complete record of the literature to accomplish this task. In my opinion, much of the problem lies in obscurity of taxonomic works. Many scientists choose to publish their work in small local museum or society journals that most people wouldn’t know existed or are very difficult to get ahold of.

Open Access (OA) Taxonomy will alleviate much of this problem. The sooner we move to OA Taxonomy, the sooner we can start to keep better track of whats out there, the sooner everyone around the world with an internet connection can be on the same page.

See also the World Register of Marine Species.

I really love that quote from Alex Wild, by the way.

Brian Fisher (my former Evolution T.A. from ye ole UC-Davis days) and Alex Smith make open access history by publishing a taxonomic paper in PLoS ONE. It doesn’t matter that this paper is about ants, not deep sea ants either like those discovered from whale falls above. I mean really, everyone knows they are just derived crustaceans anyways, by extension they are honorary deep sea taxa. Some amazing blogger already discussed the paper anyways.

This is a huge step forward for taxonomy and PLoS ONE made the right decision to dive into taxonomy. After all, the International Institute for Species Exploration reported nearly 17,000 species were described in 2006 alone. That is quite a market if you ask me! I am looking forward to more open access species. See here, here and here for reasons why Craig and I support open access and open access taxonomy.