# Blog

• ### Legislation in the United States seeks to keep research findings behind paywalls

Post date: 6 years 1 month ago
Citation for this post:

Do exorbitant profits need to be protected at the expense of transparent and freely available publicly-funded research?
This is the question to which academic publishers say emphatically “Yes”, while one hopes all researchers and the public say “No”.

Two bills in the United States, SOPA (Stop Online Piracy Act, HR3261, ; background-color: transparent; font-weight: normal; text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;">text of the bill) and the RWA (Research Works Act, HR3699, ; background-color: transparent; font-weight: normal; text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;">text of the bill), have taken the web by storm, outraging open source fans, hackers, scientists, and public access advocacy groups, and surely pleasing supporters (read: publishers).   ; background-color: transparent; font-weight: normal; text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;">The Guardian has even suggested that academic publishers make Rupert Murdoch look like a socialist.

; background-color: transparent; font-weight: normal; text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;">A letter in response to the pending RWA legislation from ESA’s Katherine McCarter has sparked reactions from ; background-color: transparent; font-weight: normal; text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;">Jonathan Eisen, ; background-color: transparent; font-weight: normal; text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;">Michael Eisen, ; background-color: transparent; font-weight: normal; text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;">Casey Bergman, ; background-color: transparent; font-weight: normal; text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;">Alex Golub, the ; background-color: transparent; font-weight: normal; text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;">Univ. of Michigan Library (and many more ; background-color: transparent; font-weight: normal; text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;">here).

The most salient point here is that the United States public pay through taxes for (1) many salaries at public universities, then (2) pay for research grants for those same scientists, and then (3) have to pay again to see results of the research.  It is the third time the public pays that is of concern here.  If taxpayers pay for something in the US, they should own it.

Financing scholarly publishing
It does cost money to publish scientific papers.  What are the costs?  BioMedCentral (BMC) has compiled a table of these costs for some publishing houses.  In this BMC table, article-processing (i.e., page) charges range from about $900 to$5000 (although some journals have no page charges, so the $900 should be$0) ; background-color: transparent; font-weight: normal; text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;">[1].  What are publisher profits?  On her blog, Heather Morrison reports that profits in various time periods were huge for Elsevier (2011: 1.1 billion US dollars, or profit margin of 36%), Springer (2010: 294 million, 33.9%), John Wiley & Sons (Q1 of 2012: 106 million, 42%), and Informa (1st half 2011: 72 million, 32.4%).  Part of the profit to publishers is charging increasing amounts for subscriptions to libraries (or, the ‘; background-color: transparent; font-weight: normal; text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;">serial crisis’).  Even though for-profit publishers charged libraries many times more than non-profit publishers in 2005, this price difference is not reflected in citation rates ; background-color: transparent; font-weight: normal; text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;">[2].

What are the international consequences?
SOPA and RWA are bills in the United States.  Do these bills influence international publishing?  SOPA and RWA no doubt, if passed, will slow down the open access momentum.  For the RWA bill, there appears to be no specification as to whether the bill applies to publishers in the United States only, or also international publishers.  Presumably, it doesn’t matter who publishes the paper - the point is RWA says government agencies can not make papers published by private publishers be freely available.

What should we do?

• Get social:
• Follow knowledgeable supporters of open access, including ; background-color: transparent; font-style: normal; text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;">Heather Piwowar, ; background-color: transparent; font-style: normal; text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;">Jonathan Eisen, ; background-color: transparent; font-style: normal; text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;">William Gunn, and ; background-color: transparent; font-style: normal; text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;">Cameron Neylon.
• Publish ONLY in open access journals:
• ; background-color: transparent; font-style: normal; text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;">DOAJ is a useful place to look.
• Data driven action
• Find out who’s getting money from SOPA lobbyists, and how they might be likely to vote on SOPA using ; background-color: transparent; font-style: normal; text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;">SOPA Track (uses data from Sunlight Labs APIs).  Is there a similar tool for the RWA?
• A few APIs (Application Programmatic Interfaces) - the ; background-color: transparent; font-style: normal; text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;">Sunlight Labs APIs or ; background-color: transparent; font-style: normal; text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;">New York Times Congress API  - allow you to research what United States elected representatives are saying and where the money is coming from.  Sunlight Labs serves up data on what United States representatives are saying, where they get donations, and what they are voting.  Their APIs are also behind the MapLight site that shows contributions from publishers to representatives (; background-color: transparent; font-style: normal; text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;">see here), which reveal that Rep Carolyn Maloney (D-NY), one of the two sponsors of the RWA bill (along with Rep Darrell Issa [R-CA]),  is the largest recipient of donations from Reed Elsevier.  There are numerous libraries for the Sunlight Labs APIs, including Python, Ruby, and R if you want to do your own mashup.
• Make noise:
• Blog, tweet, post, yell, scream, and occupy to let everyone know that you support open access / open science.

[1] ; background-color: transparent; font-weight: normal; text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;">http://www.biomedcentral.com/about/apccomparison/
[2] ; background-color: transparent; font-weight: normal; text-decoration: underline; vertical-align: baseline; white-space: pre-wrap;">http://www.econ.ucsb.edu/~tedb/Journals/EcologyJournals.pdf

• ### The flexibility to seize opportunities.

Post date: 6 years 5 months ago
Citation for this post:

With the dust settling on this week's British Ecological Society's , it seems a good idea to draw together the early careers advice from various workshops, evening events and academic talks.

The opening evening's centrepiece (no, not the ) was the "unlocking your potential" event featuring a distinguished panel of , ,  and  and chaired by the redoubtable . The take-home message was the need to flexible and to seize opportunities: all five told tale of the struggle to get permanent positions, how national and international networks can get you experience of new ways of working in new places. The key factor in locating that crucial stepping stone to a successful career was frequently nothing more subtle than simply good luck. Gary Player's adage certainly holds here: the more you practise, the luckier you get. So keep going, try new things and don't give in to defeatism if those early phd or fellowship applications don't get off the ground.

One way to boost the chances of success with applications is to ensure we're all reaching as many other ecologists as possible. Conversation around the  dinner table revolved around how to stand out from the crowd and so get that elusive phd: the benefits of fieldwork or software experience (GIS and R being the most discussed). The same idea holds for postdocs and fellowships: use every opportunity to enhance an international profile. In , there are many more opportinities: blog posts can become replies published in Science. If you're doing a Masters project and know the organiser of a session, try and get a talk in it: (a Masters student in Andrew MacColl's lab) did just that and gave an excellent talk on "The ecological causes of evolution". As mentioned on an , the judicious use of blogging and tweeting can also grow your network and enhance your impact.

We live and work in an age when there are many ways of having a distinctive voice that can, in the words of Georgina Mace, find the area of science we want to own, and make sure others know we own it.

• ### Maximising impact and effectiveness of our science in a digital world

Post date: 6 years 5 months ago
Citation for this post:

An emergent theme of diverse components of BES 2011 is that you don't have to be at the top of your chosen profession to have a profound influence on ecology and ecological thinking.

In the BES lecture, argued for a stronger integration of ecology in agricultural science, a goal which a promotes actively. Of many fine case studies, the to facilitate the transfer of knowledge among interested parties to maximise social capital. Without the inclusion of farmers or stakeholders in any regimes (a theme explored in depth by the research of the 2011 Marsh Award winner ), new ideas have a much harder time in affecting real change, no matter how well-received in the scientific literature.

These benefits of shared knowledge were also clear in the afternoon workshop on . and emphasised that the best way to learn how to communicate effectively using new media is simply to have a go! Regardless of mistakes or different opinions, there is wisdom in crowds in or . The self-correcting nature of wikipedia sites means that one person can remove a wikipedia entry that they do not agree with; it also means that half of these mass deletions are rectified and reposted within 3 minutes []. As noted, in a world where, we all have an opportunity to communicate with more people than ever before to maximise the impact of our research.

As Ross Mounce (, ) emphasised and on this site previously, making data available is one key way of doing this, and more of that later in the week.

• ### Changing government policy from the bottom up

Post date: 6 years 5 months ago
Citation for this post:

The 2012 annual is up and running at the University of Sheffield. At the time of writing the room is filling up for the "" early career researcher event, ahead of the by now traditional ceilidh and sessions on .

Elsewhere, the continues to launch new initiatives. One such example, conceived and inaugurated by , was to summarise the most prescient events of the last Year in Ecology. Necessarily taking a British perspective, Bill began with the sobering events of climategate and government proposals to sell off forests. The former issue has been dealt with extensively elsewhere (e.g., ), but the latter is perhaps less well known outside the UK. The idea was to raise capital by selling off tracts of forestry land that are especially valuable to local communities living near them. After much opposition, the government backed down over the sell off thanks in a large part to the success of the campaign.

is a people-powered movement, which campaigns on multiple issues to affect real change in the lives of millions of people. Its efforts on the forestry issue highlight how new technologies are changing the way that campaigns can be run. The reach of the Internet connected previously-disparate local interest groups, which made the campaign front-page, national news. It is these sorts of networks that aims to build, helping early career researchers establish links with like-minded individuals to maximise the impact of our research. Bill concluded by echoing the that  and to ensure that prevail over rumours and untruths. Early career researchers have a strong role to play in disseminating this message, and the success of 38 Degrees emphasises how bottom-up organisations can affect real change at the top.

• ### Next-Generation Ecologists and Open Data

Post date: 6 years 5 months ago
Citation for this post:

The next generation of ecologists have the opportunity to affect a shift in the culture of ecology. The shift that we need is to make ecology open. Why? In short, there are significant benefits to open science seen in other fields - suggesting that ecology can benefit from the shift.

We live in an increasingly connected world, which means that ecologists can make this shift to open ecology relatively rapid, especially through use of social media such as Facebook and Twitter. Below I lay out what I think are advantages of open ecology, some challenges to open ecology, some solutions, and some promising trends.

## Why should ecologists share data?

Here are a few reasons to share data: 1) sharing data should increase the pace of ecological discovery; and 2) sharing data may increase citations of your own research (Piwowar et al. 2007).

## Open data: challenges and solutions

"Although it is challenging to develop new technological solutions to data sharing in ecology, the social and cultural barriers may be even more onerous." - Reichman et al. 2011, Science

### Social and cultural challenges

1. Tradition! Ecologists are not used to sharing data. The predominant method to retrieve original data likely involves emailing the author. Should you personally request data from an ecologist, you are not likely to get the data! A recent study (Savage & Vickers 2009) asked 10 scientists that published in PLoS Journals for their raw data, citing PLoS's explicit requirement that authors share data, and only one of 10 authors shared their data - 10%! This is admittedly a very small sample size, but if it is at all representative of scientists, lack of willingness to share data may be the biggest challenge to open data.

Solution:

• Easy - wait for the pool of ecologists to turnover to a cohort that are more open to data sharing. Just kidding, sort of. Large systemic changes probably take time. US NSF is at least requiring that grant recipients have a data management plan (see ), and projects are appearing to create data management plans easily (e.g., ), but unfortunately NSF does not require grant recipients to make data open source.
2. Ecological data can be cheap, but time consuming, to collect. Given how cheap ecology data can be to collect (admittedly, costs can be great if studies occur across sites, countries, etc.), many ecologists work alone or just with their graduate students or a few colleagues. This leads to the data dispersion problem discussed below, and makes data acquisition difficult.

Although sometimes cheap, collection of ecology data can be time consuming. This is partly a reflection of the nature of ecology groups in which only a small number of people are collecting a data set, leading to more time needed to collect data than if large teams were involved. In addition, ecologists strive to gain generality, and uncover temporal trends, if any. Thus, we like to collect data over many generations/years of our study organism/location. Given the sometimes long periods of time data collection requires, ecologists may be understandably protective of their efforts.

Solutions:

• Data cost: It is great that ecology data is relatively cheap to collect, and is not likely to change, at least with field ecology data. The solution must be to make data sharing endemic in ecologists.
• Time: An increase in funding for ecology would decrease time of data collection within seasons, but the likelihood of increased funding is not high given the state of the global economy. However, we still strive to collect data over many years to seek generality, etc., so this remains a constraint on open data in ecology.
3. Lack of a reward system for data sharing. Ecologists generally can not get credit if they share their data sets.

Solution:

• One promising example is that provides a citation for a deposited data set on their system. Do ecologists use these in their CV's? Do hiring/tenure committees value these data sets?
• Another interesting solution for rewards was brought up by Kueffer et al. (in press) in a recent Trends in Ecology and Evolution commentary. They suggested that when meta-analyses are published, the papers used in the analyses are often not indexed by ISI and other indexing services. If journals allow more generous space for citations, the papers included in the meta-analysis can be inserted into the references section - leading to their indexing in ISI, counting towards citations that would be noticed by hiring/tenure committees.

### Technological challenges

1. Data dispersion. Ecology data is dispersed among thousands of researches around the world, making it hard to get to this data. However, efforts such as Dryad for data sets and TreeBASE for phylogenetic trees are making the data dispersion problem less of a stumbling block.

Solution:

• Many web services serve as repositories for different types of data (e.g., phylogenetic trees: ; specimens: ), but these are still fragmented sources and do not "talk" to each other. is a recent initiative that seeks to link data sets, and should go a long way towards solving data dispersion (given ecologists can come around to allowing access to their data). Also, see the project for a way to find ecological data sets, and .
2. Data heterogeneity. Ecology data does not share an alphabet (e.g., DNA, RNA, amino acids), making it logistically difficult to make data easily available in one location, and in easily available formats. However, we can overcome data heterogeneity in ecology by clever use of metadata (think ).

Solution:

• This impediment to open data is a hard one to fight because ecological data will always be really diverse, making a single coherent data source such as probably impossible. However, some projects like are archiving diverse data formats. Creating really good metadata to go along with datasets is really important, and can make ecological data so much easier to use. You can use tools like software to help you create metadata.
3. Data acquisition. Ecological data is not very open, and is hard to access. In fact, Reichman and colleagues estimated that only 1% of ecological data collected is accessible after publication (Reichman et al. 2011)! For the ecological data that is accessible, there aren’t great tools for data exploration (but see below for some promising examples). The lack of a unifying alphabet of ecological data resulted in each branch of the field developing its own indexing and archival practices.

Solution:

• In addition to data repositories, there are a few efforts to make open source data easy to access for scientists. One awesome project is , which seeks to provide a single node which will connect to many data providing nodes, making it easier to find ecological data. Another project, , seeks to develop R-based tools for facilitating open science. is an open-source statistical/modeling/data visualization environment. Using an open-source environment will integrate open-source data sets from across scientific disciplines, allowing reproducible research on open-source data, phylogenetic trees, citations, and even full-text literature through open-source journals such as and .

See Reichman et al. (2011) for more discussion on open data and open science.

## Promising signs

Although sharing is may not be a habit for ecologists yet, we are making progress towards open data in ecology. Many projects come to mind:

In addition, a number of ecology and evolution journals require raw data to be archived in various locations (e.g., Dryad), including:

• American Naturalist
• Evolution
• Evolutionary Applications
• Heredity
• Molecular Ecology
• Molecular Phylogenetics & Evolution
• PLoS Journals
• Systematic Biology
• and more...

## The way forward

The next generation of ecologists need to pave the way for a new generation of ecology that is open and transparent, facilitating collaboration, and accelerating the speed of ecology (Piwowar et al. 2007, Costello 2009).

Open and transparent ecology will also make our science less open to criticism, especially the controversial fields of ecology such as climate change. See these stories (, ) for examples of calls to increase openness in science as a way to increase public trust in science. Allowing any interested parties access to the same data we ecologists have can only increase trust among the public and policy makers.

The most immediate task we have to undertake is to make all of our data open source. Post your datasets on or , your phylogenetic trees on , etc.

Finally, what do you think? What do you think are the major hurdles to open ecology? What are the solutions? Please let us know what you think with a comment below, on Twitter (), or on .

#### References

• Costello, M. J. 2009. Motivating online publication of data. Bioscience 59: 418-427.
• Kueffer, C., Ü. Niinemets, R. E. Drenovsky, J. Kattge, P. Milberg, H. Poorter, P. B. Reich, C. Werner, M. Westoby, I. J. Wright. In press. Trends in Ecology & Evolution, doi:10.1016/j.tree.2011.07.007
• Piwowar, H. A., Day, R. S., and D. B. Fridsma. 2007. Sharing detailed research data is associated with increased citation rates. PLoS One 2(3): e308.
• Reichman, O. J., Jones, M. B., and M. P. Schildauer. 2011. Challenges and opportunities of open data in ecology. Science 331: 703-705.
• Savage, C. J. and A. J. Vickers. 2009. Empirical study of data sharing by authors publishing in PLoS journals. PLoS ONE 4(9): e7078.

#### Notes

Thanks to and the for feedback on early drafts of this post.

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