Open science and "Encyclopedia of Life" - competition for projects

As we all know, our research field (ecology and evolutionary biology) are becoming increasing data-driven and to an increasing extent we are also using data collected by "others" from various internet sources. One such example is our recent paper in Ecology, where we used GBIF-data from thousands of species occurrence records, including from the Swedish source "Artportalen" ("The Species Portal") to model  and understand the environmental factors behind northern range limits in two Fennoscandian demoiselle species (the genus Calopteryx). 

Increasingly, evolutionary biologists interested in organismal biology and phenotypic evolution will use phenotypic data from sources like DRYAD, as has already been used for a long time for molecular data (DNA-sequences), where GenBank is now a common source of information when constructing phylogenies for comparative purposes. Thus, researchers will not only rely on data they have collected themselves (which is often expensive and it is logistically impossible to gather more than a limited amount of data in short time), but can to an increasing extent also use data from public open databases such as GBIF.

Now, another such initiative - Encyclopedia of Life (EOL) - announces a competition for project proposals (deadline November 15). One can propose data-driven projects - a "wish list" - of what kind of data one wants and in what form, and the "best" projects will be realized. This might be an opportunity for someone in our lab (Lesley?), provided that we can come up with a good project proposal to enter this competition. Think about it at least  until November 15.  

Odonates would be an example of a group where distribution data collected from amateur naturalists should ideally be compiled and become available for research projects through open databases. Unfortunately, the odonate research community is small, full of rivalry and have an unfortunate tradition of publishing in low-impact journals. Some odonate researchers and self-appointed experts are also extremely territorial about their collected occurrence data. This type of territoriality certainly hinders scientific progress and the establishment of odonates as respectable model organisms in ecology and evolutionary biology. Science should be characterized by openness and data-sharing - not by rivalry. 

Rapid evolution of rodents: another PLoS ONE study in the media

Some of you might be interested in this recent study published in PLoS ONE about rapid evolutionary changes in morphology in rodents. I served as an academic editor on this interesting paper, that has gained quite a lot of media attention, e. g. in Science News and in Los Angeles Times. Since I was academic editor for this article, I was interviewed about it and I briefly comment upon it in the Science News article.

Although media attention and coverage is not, and should certainly not be, the only criterion for scientific "quality" (whatever that is!), it is further testimony of the advantage to publish in "Open Acess"-journals in general, and PLoS ONE in particular. This study is also interesting because it shows the value of museum collections as a source for ecological and evolutionary research, a point that Shawn Kuchta has repeatedly emphasized in our lab-meetings (and which I completely agree with, of course).

Oliver Pergams and his colleague Joshua Lawler used a large data set consisting of thousands of museum specimens, collected from various places of the world and during a long time period (more than a century) to track changes in morphology of the skull of rodents. They analyzed statistically which traits that changed, and how much. They further linked these morphological changes to two ecological factors: increasing urbanisation (i. e. increasing local human population densities) and climatic factors.

They found that both urbanisation and climatic factors were statistically significantly related to the morphological changes they observed. Although not all these morphological changes are understood from a functional viewpoint, and the genetic basis of the changes are not known, the study is strongly suggestive. Rapid evolution in rodents might thus be a result of both humans directly, and possibly indirectly through anthroprogenic climate change.

"Ida": a new triump for PLoS ONE

In case you have not used the search engine "Google" today, I would just like to highlight that the image of today refers to an article published in PLoS ONE, about a 47 million-year old primate female specimen with the nickname "Ida". This article has created a large "buzz" in the bloggosphere and media, with over 700 links detected by Google News within 24 hours of the publication release!

It is another major publication and media triumph for PLoS ONE, as this remarkable paper would perhaps only a few years ago have been published in Nature or Science. These traditional, non-OA journals, now probably have to worry somewhat about their future as the PLoS-group is emerging more and more as a serious competitor when it comes to public outreach and news coverage. This is partly due to the advantage of the OA-format in general, although not the entire story. The PLoS staff are obviously very professional when it comes to media coverage and outreach, and almost every week there is one or several PLoS ONE articles that hit the news headlines and attract the attention of the mighty bloggosphere.

It is particularly interesting that it is the paleontologists who have taken PLoS ONE to their hearts, while ecologists and evolutionary biologists are extremely conservative and traditional, even hostile or suspicious in many cases (in my experience) towards this new journal. It is an interesting research question for a sociologist of science to find out this major difference in attitude between the paleontological and the ecological/evolutionary research communities. Perhaps it is because there are many more competing and good journals in ecology and evolutionary biology, compared to paleontology? Here you can read a short interview with the authors of this fossil-paper where they explain why they decided to publish their work in PLoS ONE, rather than a more traditional scientific journal.

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Rankings of "Open Access"-journals: PLoS ONE rocks!

As several of you might know, I have been complaining about how conservative attitudes some of my colleagues have towards "Open Acess"-publishing in general, and towards PLoS ONE in particular. This is quite frustrating, as me and several of my colleagues in the Editorial Board are doing our best to promote this new "revolutionary" journal, with the hope that it will in the long run change the entire publication landscape - to the benefit of both scientists, readers, taxpayers and the general public.

There are two classical objections against PLoS ONE by ecologists and evolutionary biologists. First, some of them are afraid to publish in PLoS ONE since it is not yet listed in Thomson's databases (ISI), such as "Web of Science". This is the database from which Impact Factors (IF:s) are calculated, and Thomson actually has a monopoly (!) on how to calculate IF:s. Since Thomson has up until now refused to list PLoS ONE in their data-base, some of my scientific colleagues are afraid that work published in that journal will be "forgotten" or not appreciated by the scientific community.

This objection partly shows a lack of knowledge and the misunderstanding about citation data-bases as reflecting some kind of "objective truth". In reality these data-bases are run by commercial companies with their own agendas. ISI is certainly not the only data-base, and it is one of the slowest to list new publications and it does only cover a small minority of all scientific journals. Scopus, for instance, covers more journals and so does probably also Google Scholar and PubMed. Thus, there is luckily severe competition among different data-bases, and hopefully ISI will soon become outcompeted and run out of business by better and faster alternatives with better litterature coverage. ISI is for the scientific world what Microsoft is for the computer world: a mean big company that we should all hate!

The second objection is that PLoS ONE has a publication policy that aims for "technical quality", rather than arbitrary and subjective criteria for acceptance of papers, such as "novelty". In that respect, PLoS ONE differs significantly from all other journals, including Science, Nature, PNAS and PLoS Biology. The philosophy of PLoS ONE is that it is the future scientific readership that should judge whether a paper is "significant" or not, not a few subjective referees or journal editors. The scientific process does not end with the publication of a paper, it starts. This is when a paper is read, discussed and (hopefully) gets cited and thus "accepted" as being important by other scientists.

Some researchers consider this as a weakness of PLoS ONE, and fears that it will become a "dumping ground" for poor quality papers that have not been published elsewhere. I, and many others, on the contrary view this as as strength of PLoS ONE, and I can honestly not say that I think that PLoS ONE has become such a vehicle for bad papers that some feared that it would become. But I am of course biased in my views, since I am involved in the journal, and it is up to others to decide about this.

Given the inherent problems with impact factors and how they are increasingly becoming "corrupt" and the arbitrary parts of traditional publication (biased referees, commercial data-bases, unfair editors etc.), I think we probably all agree that there is a need for newer ranking criteria of journals. These criteria could be based on things like number of downloads of articles, number of citations, more or less informal "ranking lists" by the scientific community, blog coverage, coverage in media etc. None of these rankings are likely to be perfect or reflect the final "truth", but they would provide a nice complement to the traditional measures, such as impact factors of journals.

The blogger "The Open Source Paleontologist" have done some such ranking lists of OA-journals, and you can read about them here, here and here. Although these ranking lists have their limitations and only deal with the paleontological science community, they are nevertheless interesting and revealing. I predict that we will see many more of these lists in the future, and I bet that the traditional "impact factor" hysteria, will soon go away (to the benefit of all science).

Not surprisingly, and pleasingly to me, PLoS ONE does very well in these ranking lists: it is always in the top 15 list of journals, and often among the top 5. Way to go, PLoS ONE!!! I am delighted. And the young scientists among you who reads this should of course not be afraid of publishing in PLoS ONE in the future, it will benefit your careers.