Faculty council approves new course evaluation service | Campus | Indiana Daily Student

“IU’s [Indiana University’s] Open Access policy was also discussed at the meeting. The Library Committee of the Bloomington Faculty Council [BFC] researched open access to make a recommendation to the BFC as to whether IU should adopt an active open access policy. The committee did not recommend an active policy, said Jason Jackson, Library Committee chair. IU currently has a passive policy in which professors can publish their articles open access if they prefer. “Our concern, instead, was open access that’s achieved through the deposit of scholarly articles and manuscripts into a repository, such as IU Scholar Works,” Jackson said….”

Satellite Telemetry Uncovers the Tracks of Tiny Ocean Giants

Pygmy Blue Whale

The pygmy blue whale, cousin to the more well-known Antarctic blue whale, has an enigmatic history. Pygmy blue whales dwell in vast expanses of the Indian and southern Pacific oceans, and are a highly mobile species. The species was identified in 1966—although it’s likely to have been confused with its cousin the “true” blue whale prior to 1966—so it’s only in recent years that we’ve been able to catch glimpses of these elusive cetaceans during their migrations to and from breeding and feeding grounds. The researchers of a recent PLOS ONE paper tested out a new method of tracking these whales: satellite telemetry (described below). Using this method, the researchers mapped the migration of pygmy blue whales as they moved from the coast of Australia to the waters of Indonesia. We caught up with author Virginia Andrews-Goff to get some additional details on what it’s like to track these tiny giants.

How did you become interested in pygmy blue whales, and how did you get involved in mapping their migratory movements?

This research was carried out by the Australian Marine Mammal Centre, a national research centre focused on understanding, protecting and conserving whales, dolphins, seals, and dugongs in the Australian region. The work we carry out aims to provide scientific research and advice that underpins Australia’s marine mammal conservation and policy initiatives. We, therefore, have a keen interest in all whales that migrate through Australian waters including pygmy blue, right and humpback whales.

Pygmy blue whales are of particular interest, however, as so little is known in regard to their movements and population status.  Large scale movements of whales are particularly hard to study and what we do know about pygmy blue whales we have mainly learnt from examining whaling records. Fortunately, pygmy blue whales were targeted by the whaling industry for only a very short period of time in the late 1950s and early 1960s just prior to the IWC banning the hunting of all blue whales in 1966.

What are the challenges of better understanding whale migration in general?

Large-scale, long-term whale movements are challenging to study as it is impractical to do so by direct observation. Therefore, we need to use devices, such as satellite tags, that can be attached to the whale to provide real-time location information.

What is satellite telemetry and how did it enable your findings?

In this case, satellite telemetry refers to the use of a satellite-linked tag attached to the whale. This tag communicates with the Argos satellite system when the antenna breaks the surface of the water. A location can then be determined when multiple Argos satellites receive the tag’s transmissions. We then receive this location data in almost real time via the Argos website, which allows us to track the movement of the tagged whale.

Pygmy Blue Whale 2

Based on your tracking, you found that the pygmy blue whales traveled from the west coast of Australia north to breeding grounds in Indonesia. Can you give readers a sense of why they travel this route?

Generally, whales migrate between productive feeding grounds (at high latitudes) in the summer to warmer breeding grounds (at low latitudes) during the winter. The exact reason for this general pattern is unclear, though quite a few theories exist, including to avoid predators, to assist the thermoregulatory ability of the calf, and to birth in relatively calm waters.  Because of the timing of this migration, we believe these animals travel to Indonesian waters to calve. Usually it is assumed that whales fast outside of the summer when no longer located in the productive feeding grounds. Interestingly, these pygmy blue whales travel from productive feeding grounds off Western Australia to productive breeding grounds in Indonesia and therefore, probably have the opportunity to feed (and not fast) on the breeding grounds.

Filtered satellite tag derived locations of pygmy blue whales (n = 11) by month.

Satellite tag derived locations of pygmy blue whales by month.

You’ve mentioned that pygmy blue whale migratory routes correspond with shipping routes. How does this interaction impact the whales?

Baleen whales (whales that use filters to feed instead of teeth) use sound for communication and to gain information about the environment they occupy. When pygmy blue whale movements correspond to shipping routes, there is potential for the noise generated by the ships to play some role in altering calling rates associated with social encounters and feeding.

Why is it important for us to better understand pygmy blue whale migration, and how does mapping their migratory movements help conservation efforts for this endangered animal?

Our coauthor, Trevor Branch, hypothesised in 2007 that pygmy blue whales occupying Australian waters traveled into Indonesian waters. However, prior to this study, we didn’t actually know that this was the case. As such, conservation efforts relevant to the pygmy blue whales that use Australian waters are required outside of Australian waters too. We can also now gain some understanding of risks within the pygmy blue whale migratory range, such as increased ambient noise from development, shipping, and fishing, and therefore assist in mitigating these risks.

What’s next for you and your research team?

A question mark still remains over the movements of the pygmy blue whales that utilise the Bonney Upwelling feeding grounds off southern Australia. Genetic evidence indicates mixing between the animals in the feeding areas of the Perth Canyon (the animals that were tagged in this study) and the Bonney Upwelling. This indicates the potential for individuals from the Bonney Upwelling to follow a similar migration route to those animals feeding in the Perth Canyon. However, it is also thought that Bonney Upwelling animals may utilise the subtropical convergence region south of Australia. We plan to collaborate on a research project that aims to tag the pygmy blue whales of the Bonney Upwelling and ascertain whether these animals move through the same areas and are therefore exposed to the same risks as the Perth Canyon animals.

Pygmy Blue Whale 3

We look forward to seeing more from Dr. Andrews-Goff and her team in the future. In the meantime, read more about the elusive worlds of southern Pacific Ocean whales here at the EveryONE blog.

Citation: Double MC, Andrews-Goff V, Jenner KCS, Jenner M-N, Laverick SM, et al. (2014) Migratory Movements of Pygmy Blue Whales (Balaenoptera musculus brevicauda) between Australia and Indonesia as Revealed by Satellite Telemetry. PLoS ONE 9(4): e93578. doi:10.1371/journal.pone.0093578

Image 1: IA19847 Blue pygmy whale

Photograph © Mike Double/Australian Antarctic Division

Image 2: IA19850 Blue pygmy whale

Photograph © Mike Double/Australian Antarctic Division

Image 3: pone.0093578

Image 4: IA19851 Blue pygmy whale off Western Australian coast near Perth, Western Australia, Australia Photograph © Mike Double/Australian Antarctic Division

The post Satellite Telemetry Uncovers the Tracks of Tiny Ocean Giants appeared first on EveryONE.

Scholars in action

Recently Dutch legal scholars sent an open letter to Kluwer, the most important publisher of legal books and journals. Sixty two professors urgently request a reduction of the costs this publisher charges universities. They calculated that annually Dutch universities pay 5 million euros to Kluwer for access to and reusage of legal publications they wrote themselves. Kluwer does not permit availability of the publications in Open Access. Those who signed the letter consider this to be undesirable.
The process leading up to publication is paid for by public money and commercial publishers force universities to sign expensive contracts for access to those publications.

TheContentMine: Progress and our Philosophy

TheContentMine is a project to extract all facts from the scientific literature. It has now been going for about 6 weeks – this is a soft-launch. We continue to develop it and record our progress publicly. It’s a community project and we are starting to get offers of help right now.  We welcome these but we shan’t be able to get everything going immediately.

We want people to know what they are committing to and what they can expect in return. So yesterday I drafted an initial Philosophy – we welcome comments.

Our philosophy is to create an Open resource for everyone created by everyone. Ownership and control of knowledge by unaccountable organisations is a major current threat; our strategy is to liberate and protect content.

The Content Mine is a community and we want you to know that your contribution will remain Open. We will build safeguards into The Content Mine to protect against acquisition.

We are a meritocracy. We are inspired by Open communities such as the Open Knowledge Foundation, MozillaWikipedia and OpenStreetMap all of whom have huge communities who have developed a trustable governance model.

We are going ahead on several fronts – “breadth-first”, although some areas have considerable depth. Just like Wikipedia or OSM you’ll come across stubs and broken links – it’s the sign of an Open growing organisation.

There’s so much to do, so we are meeting today to draft maps, guidelines, architecture. We’re gathering the community tools – wikis, mail lists, blogs, Github, etc. As the community grows we can scale in several directions:

  • primary source. Contributors can choose particular journals or institutions/theses to mine from.
  • subject/discipline. You may be interested in Chemistry or Phylogenetic Trees, Sequences or Species.
  • technology. Concentrate on OCR, Natural Language Processing, CrawlingSyntax or develop your own extraction techniques
  • advocacy and publicity. A major aim is to influence scientists and policy makers to make content Open
  • community – its growth and practice.

We are developing a number of subprojects which will demonstrate our technology and how the site will work. Hope to report more tomorrow.


Latest Article Alert from Reproductive Health

The following new articles have just been published in Reproductive Health

For articles using Author Version-first publication you will see a provisional PDF corresponding to the accepted manuscript. In these instances, the fully formatted Final Version PDF and full text (HTML) versions will follow in due course.

Metabolic effects of the contraceptive skin patch and subdermal

Latest Article Alert from Environmental Health

The following new articles have just been published in Environmental Health

For articles using Author Version-first publication you will see a provisional PDF corresponding to the accepted manuscript. In these instances, the fully formatted Final Version PDF and full text (HTML) versions will follow in due course.

Urinary and breast milk biomarkers to assess exposure to naphthalene in

Latest Article Alert from Malaria Journal

The following new articles have just been published in Malaria Journal

For articles using Author Version-first publication you will see a provisional PDF corresponding to the accepted manuscript. In these instances, the fully formatted Final Version PDF and full text (HTML) versions will follow in due course.

Use of a semi-field system to evaluate the efficacy of topical repellents

Latest Article Alert from Respiratory Research

The following new articles have just been published in Respiratory Research

For articles using Author Version-first publication you will see a provisional PDF corresponding to the accepted manuscript. In these instances, the fully formatted Final Version PDF and full text (HTML) versions will follow in due course.

Vitamin D deficiency in community-acquired pneumonia: low levels of

Is Elsevier going to take control of us and our data? The Vice-Chancellor of Cambridge thinks so and I’m terrified

I am gutted that I missed the Q+A session with Professor Sir Leszek Borysiewicz the Vice-chancellor of  Cambridge University. It doesn’t seem to have been advertised widely – only 17 people went – and it deserves to be repeated.

The indefatigable Richard Taylor – who reports everything in Cambridge – has reported it in detail. It was a really important meeting. I’ll highlight one statement, which chills me to the bone (note that this is RT’s transcript):

“the publishers are faster off the mark than governments are. Elsevier is already looking at ways in which it can control open data as a private company rather than the public bodies concerned.”

Now I know this already – I’ve spent 4 years finding out  in detail about Elsevier’s publishing practices. It’s good that the VC realises it as well. Open Access is a mess – the Universities have given part of their priceless wealth to the publishers and are desperately scrabbling to get some of it back. The very lack of will and success makes me despondent – LB says:

“And I know disadvantaging the individual academic by not having publication in what is deemed to be the top publications available? So it’s a balance in the argument that we have.”

in other words we have to concede control to the publishers to get the “value” of academics publishing where they want.

Scholarly publishing costs about 15,000,000,000 USD per year. Scholarly knowledge/data is worth at least ten times that (> 100,000,000,000 USD/year).  [I’ll justify the figure later]. And we are likely to hand it all over to Elsevier (or Macmillan Digital Science).

I’ve done what I can to highlight the concern. This was the reason for my promoting the phrase “Open Data” in 2006  – and in helping create the Panton Principles for Open Data in Science in 2008. The idea is to make everyone aware that Open Data is valuable and needs protecting.

Because if we don’t Elsevier and Figshare and the others will possess and control all our data. And then they will control us.

Isn’t this overly dramatic?

No. Elsevier has bought Mendeley – a social network for managing academic bibliography.  Scientists put their current reading into Mendeley and use it to look up others. Mendeley is a social network which knows who you are, and who you are working with.

Do you trust Mendeley? Do you trust Elsevier? Do you trust and large organisations without independent control (GCHQ, NSA, Google, Facebook)? If you do, stop reading and don’t worry.

In Mendeley, Elsevier has a window onto nearly everything that a scientist is interested in. Every time your read a new paper Mendeley knows what you are interested in.  Mendeley knows your working habits – what time are you spending on your research?

And this isn’t just passive information. Elsevier has Scopus – a database of citations. How does a paper get into this? – Scopus decides, not the scientific world. Scopus can decide what to highlight and what to hold back. Do you know how Journal Impact Factors are calculated? I don’t because it’s a trade secret.  Does Scopus’ Advisory Board guarantee transparency of  practice? Not that I can see. Since JIF’s now control much academic thinking and planning, those who control them are in a position to influence academic practice.

Does Mendeley have an advisory board? I couldn’t find one. And when I say “advisory board”, I mean a board which can uncover unacceptable practices. I have no evidence that anything wrong is being done, but I have no evidence that there are any checks against it. Elsevier has already created fake journals for Merck, so how can I be sure it will resist the pressure to use Mendeley for inappropriate purposes? Is Mendeley any different from Facebook as far as transparency is concerned?  Is there any guarantee that it is not snooping on academics and manipulating and selling opinion? “Dear VC – this is the latest Hot Topics from Mendeley; make your next round of hirings in these fields”.

I’m also concerned that Figshare will go the same way. I have have huge respect for Mark Hahnel who founded it.  But Figshare also  doesn’t appear to have an advisory board. Do I trust Macmillan? “we may anonymize your Personal Information so that you cannot be individually identified, and provide that information to our partners, investors, Content providers or other third parties.” Since information can be anonymised or useful but not both are you happy with that?

There aren’t any easy solutions.  If we do nothing, are we trusting our academic future to commercial publishers who control the information and knowledge flow. We have to take back our own property – the knowledge that *we* produce. Publishers should be the servants of knowledge – at present they are becoming the tyrants.






Stripe’s Open Source Retreat

rechargeThe Open-Source Retreat that is being sponsored by stripe looks quite intriguing.  Stripe relies on a lot of open source software, and they’ve announced a program to give a grant to a small number of developers to come to San Francisco to work full-time on an open-source project for a period of 3 months. The awardees will have space in Stripe’s SF office, and will be asked to give a couple of internal tech talks over the course of the program, but otherwise it’ll be no-strings-attached.

This is a clever model for supporting open source development, and I hope this idea catches on with other companies that benefit from open source. I can think of a number of academic developers who would love the idea of a sabbatical to work on an open source code project, to meet new people who might use their code, and to get a fresh perspective in new surroundings – an open source sabbatical.  This could be a great way for companies that benefit from open source scientific software to help encourage and influence the development of the tools they use.

The deadline for applying to the Stripe program is May 31st, and the program will run from September 1st through December 1st.