A legal workaround idea for non #openaccess ecology articles – university library #openpaper #outreach days

The access paywall of many scientific journals is a significant barrier to a rapid, efficient process of securing many peer-reviewed ecology and science articles. Recently, I needed to assess the state-of-the-art for animal camera trapping in wildlife ecology. I used google scholar and web of science to populate a list of papers to read. I was ‘behind the paywall’ at a university IP address. Even with this barrier removed, it was a challenge.  I wanted to pull down a total of 20 papers, and only 60% of these were readily available because even with the exorbitant subscription fees the university library pays, some journals were not included. I realized that few wildlife ecologists and managers have even the limited level of access that I had to these very applied papers. This is a problem if we want evidence-based conservation and management of natural systems to prevail. There are numerous solutions of course including contacting the authors directly, searching for it online and hoping you get lucky to find it posted somewhere, checking researchgate, and joining a few other similar access author-based portals. There are two other simple solutions of course to engage managers – share with them directly when it is in print and encourage them to join a service like researchgate. Identifying managers interested in our work and sending it to them is a form of scientific communication and outreach. We need to do it. However, I had an even more broad public outreach idea – use university libraries as public access research portals.

University libraries pay subscription fees to many publishers. Leverage this access to run open science or open paper days.  In my experience, even with a temporary guest ID on wifi at most university campuses, one is able to access their full offerings of peer-reviewed publications. Universities could use this access and do even more – educate on peer review and show off all the incredible research that more often than not taxpayer dollars fund.

University-library solutions
1. DayUse Research-IDs. University libraries are increasingly digital repositories of information. Show this off to the public, the parents, and local applied researchers by offering guest-research IDs for a day at time for the public to browse holdings.
2. Notifications for digital research content. University libraries are increasing more like digital cafes than physical holdings of books. Advertise the resources that are available behind this paywall to all users, regularly, when they are online. Notifications/alerts, additional linking to primary research from courses and less on textbooks, and potential (non-obtrusive) pop-ups within the network for students on new research developments.
3. Open-paper public days. University libraries should run access days to teach the public about modern bibliometric search tools, explain the peer-review process, explain the publishing process, and show/allow folks to look up primary research that interests them. There will always be a topic someone needs to know about and a journal for it. Most importantly, these days will promote scientific literacy and also potentially provide fuel to new pay models or even better different profit models for academic publishers. If non-academics that pay taxes fully comprehended how much awesome research is out there in this academic stream that they never get to see, access, and pay for through tax dollars, it is hard not to imagine they would not want to see big changes.

The function of a university library
University libraries can still look like this.


More often that not university libraries instead look like massive digital cafes or computer labs.


The problem with all the information in the ether and behind these paywalls is that this intangibility hides the depth of the resource and extent that information could and should be available more broadly.  I love the ‘learnings common’ philosophy that is evolving in many university libraries. I am just concerned that it is not reaching far enough out – at least to the parents of the students that attend the university.

University library websites have improved dramatically and feel more contemporary. However, there is a limited signal of the extent of the digital research that are held and no indication of how the public might access even a tiny bit of this infrequently to learn. I recognize public libraries and university libraries are not quite the same thing, but why do they have to be so different. Can they partner, co-evolve, and reduce the paywall limitation to the research that matters for better decisions at least for health and the environment?


My best guess is that university libraries thus provide three significant functions in this domain.
1. Provide access to research.
2. Provide a space to access and do research.
3. Train and educate on how to do research.

As a researcher, the first is the most critical to me. As an educator, all three are important to my students.

I recognize all of this misses the point – research should be open. Primary researchers should strive to be OA all the time with our work, but I recognize that there are reasons why we can not necessarily achieve this goal quite yet. Journals can also work towards this end too.

In interim, much of research needed to make the best possible decisions is out there now – i.e. where and how to deploy animal cameras for conservation this field season for my team – and the natural now is changing rapidly.
I want science to help. To do so, we need to be able to see it. Now.

Break-up letter you can use with VW

Dear VW,
Our relationship is over. You lied to us. When we entered into this partnership, I agreed to look after you, and you agreed to look after me, my family, and the environment we share. All these years you were however silently, sneakily lying. I cleaned you, looked after you, bought you new things when you needed them, and cared for you. All you had to do was be honest and help me get where I needed to be. I do not even want to see you anymore. I am stuck with you now until your family decides what to do. Trust is earned not bought. I cannot stay in a relationship with someone who does not realize that we have only one chance to make the world a better place.


‘#Elementary’ ecology and the value of red herrings


At first, I resented the postmodernism of Elementary. However, I now enjoy the human dimension associated with character development and for its challenges to my thinking about the science of interactions and hypothesis testing. The most recent episode was a brilliant piece for me in terms of my struggles with a paper I am working on with a collaborator that includes contrasting predictions. The episode was entitled ‘Hemlock’, and it is a very apt metaphor (for me at least) for some of the challenges that modern ecologists face.

Here are the elements that inspired me to think about how we sometimes approach ecological interpretations to evidence.

1. Sherlock and Watson investigate the disappearance of a lawyer. Unlike most episodes in contemporary detective/police shows (and even this show), this episode does not begin with a macabre crime scene or body. We never do see the body. Sounds like ecology. Species disappear, and we need to know why. Dramatic global change is occurring, but frequently, the effects are evident only in the gradual loss of a species or process and not through a disaster with a grisly, photographic opportunity for collection of evidence or political leverage. There is no smoking gun. In ecology, we rarely happen upon outcomes that are not driven by complexity or sets of interactions with processes emergent from interdependence.  There can be a smoking gun, but sometimes, it is the indirect interactions with the gun/agent that are real driver of change and not the direct effects. Positive interactions can also have negative effects on ecosystems (i.e. no gun at all but smoke).

smoking gun

2. Sherlock generates both numerous hypotheses (explanations of how the system/phenomenon works) and associated predictions (testable, specific outcomes with evidence) that are refuted as mostly immaterial evidence accumulates in this episode. This is fascinating to me. There are many more failures to support predictions than the usual episode, and it is refreshing. I get the sense that many contemporary experimental community ecology studies certainly generate the hypothesis a priori but refine/adjust the predictions post hoc. I recognize that we have moved beyond strict Popperian falsification, but we are talking about single studies that have associated prediction sets within each paper reported as perfectly satisfied. This seems a bit convenient. My collaborator and I set up the particular experiment we are writing up now with a hypothesis to describe the system but with opposing predictions. Given that ecology embraces complexity, I realized that I have read few papers recently that have contrasting predictions sets that alternatively support or refute the hypothesis. I want that complexity back, and I want to include some of it my papers from now on to highlight the importance of judgment and fair evidence handling alongside appropriate statistics. I know there is a very real bias against non-statistically significant findings and failure to support dominant hypothesis within a subdiscipline, nonetheless, the red herrings we chase make the instances of support all the more robust, honest, and reproducible.

I propose there are at least conceptions of the red herring from the detective genre for ecology.

1. Red herring as distraction. RED HERRING

In the most reviled sense from a publication-bias perspective, failure to support is a distraction at best, a hindrance to scientific progress at worst.  I disagree. Distractions provide insight, illuminate errors, and highlight the importance of effective methods in detecting and reporting false positives.

2. Red herring as Bayesian calibration tool.


Our capacity to assess relative frequency, importance, and experience from a procedural/effective experimental design paradigm is enhanced and accelerated by a clear sense of the red-herring effect within sets of factors or within the manifestations of ecological processes of interest.

3. Red herring as a source of creative inquiry.


Ecology is both science and art. Explicitly seeking the red herring can provide information on processes that are difficult to measure directly, and in imagining and designing experiments wherein a factor does not apply, we better understand the context when it does. The red herring moments are also often synonymous with eureka moments – perhaps not even for you but for the reader in enjoying your narrative of how you solved the ecological mystery at hand.

Failure in science is not a crime, and false leads provide necessary scientific truths.



What are the grand challenges for restoration ecology?

I am a destruction ecologist not restoration ecologist.




In most of my primary ecological fieldwork, we take things apart. We clear plots, remove individuals and sometimes immediate neighborhoods, or clip plants. This is not entirely without its merits. In some happy instances, the interactions we detected in the absence of others can inform restoration albeit indirectly. For instance, in an alpine-neighbourhood-removal experiment, plants near targets facilitate these individuals at higher elevations (Callaway et al 2002).



In some of my dissertation research, I explored whether the loss of even tiny little desert annuals (but the relatively ‘larger’ ones) could influence patch dynamics.  We did selective removals of the subdominant annuals and demonstrated some positive not always negative effects of larger congeneric species as typically assumed for these systems (Lortie & Turkington 2008).



I also like the much larger-scale ideas of biodiversity knockout experiments (http://www.zoology.ubc.ca/person/sinclair) as a means to explore the implications of loss of entire functional groups (or see metabolics/genomics approaches or the work of Diaz & others on different types of ecological removals).  Collectively, I suspect there is a nice opportunity for restoration to address some of the challenges it faces using experimental designs predicated upon removal.  Also, I suspect that anthropogenic effects can also remove players from ecosystems relatively regularly and that experiments emulating some of these perturbations can be informative.  This got me thinking that like most ecology, restoration ecology could be very plug and play.



We add, we remove, and/or we observe. However, there is a fourth approach available to restoration ecology in the form of needs-driven research and perhaps in particular syntheses.  For instance, the work of Science for Nature and People exploring the importance of evidence in shaping human dynamics and management.



Inspired by these initiative, I want to do a synthesis.  I do not want to do it alone. Help me! I love the idea of ‘grand challenges’ for a discipline.  If Obama can do it, we can do it too!  See the #wethegeeks series mostly for engineering. There is also a Grand Challenges in Global Health Program that is a really amazing.

I am very keen to become a restoration ecologist in some form maybe when I grow up. A synthesis of the challenges faced by the discipline, formally, would be a fantastic exercise in determining how an individual new to the field could contribute.  I imagine that some of the challenges that restoration ecology faces are not unique to it relative to other ecological disciplines such as access to open data, divergent semantics and non-standard vocabularies, funding, relevancy, and partnership expectation challenges.  However, I would love to know what challenges are unique to restoration ecology and how challenges faced in other disciplines also speak to this field. There have been some nice discussions of challenges in general for restoration (practice, paradigms, policy, & principles for specific systems), but to the best of my knowledge, there has been no formal and global synthesis as a primer to facilitate getting started and in avoiding/addressing some of the common pitfalls.  There has been many formal syntheses in the form of meta-analyses (see Gomez-Aparacio for instance on plant interactions for restoration or socioeconomic benefits of restoration by Aronson et al) but none at the global-thematic scale. I envisage the first steps to this process as a brainstorming of questions that need to be addressed for the discipline and a long list of challenges. Then, a matching exercise to explore whether there is correspondence between the questions being actively pursued and the challenges that restoration ecologists face.


Final step, solutions – perhaps even a general blueprint.





The synthesis could take many forms but a great step would be the big picture summarized.

General questions
1. How well does conservation biology and restoration ecology support and enable one another?
2. Does fundamental ecological theory significantly contribute to restoration ecology or does most restoration begin with a ‘problem’ that needs a solution?
3. Is most restoration ecology manipulative? How are mensurative experiments and observation leveraged in restoration ecology?
4. How inter-related are management and restoration in their alignment of needs and research agendas?
5. Are there syntheses of the local-versus-regional drivers that influence the outcome restoration efforts?
6. How commonly are the human factors included in restoration efforts or in experiments?
7. Does social science regularly contribute and support restoration efforts?
8. Does socioeconomic research support restoration? When it does, how it is used?
9. Is an effective restoration plan similar to a conservation blueprint?
10. What are main primary research topics that restoration ecologists examine?  Are there taxa and/or ecosystem specific biases and how general are the lessons?
11. What is the most common scale of restoration?
12. Are there themes that transcend restoration and speak to a wider audience?
13. Is restoration ecology increasing collaborative similar to other disciplines?
14. Are restoration ecology experiments often interdisciplinary?
15. What are the main challenges that most restoration ecologists would list in either doing research or in implementing a restoration effort?

I hope this set of questions is a good start in getting the ball rolling. I suspect a survey of experts in the field, a formal systematic review, and maybe a workshop and we would be up and running towards a nice list of grand challenges!



The revolution will not be televised: the end of papers & the rise of data.







I had the good fortune to attend the Datacite Annual Conference this year about giving value to data. Thomson Reuters presented their new Data Citation Index that I had previously explored only cursorily for my ESA annual meeting ignite presentation on data citations. However, after the presentation by Thomson Reuters and the Q&A, I realized that a truly profound moment is upon us – the opportunity to FULLY & independently give value to data within the current framework of merit recognition (i.e. I love altmetrics and we need them too, but we can make a huge change right now with a few simple steps).

The following attributes of the process are what you need to know to fully appreciate the value of the new index: the data citation index is partnering with Datacite to ensure that they capture citations to datasets in repositories with doi’s, citations from papers to datasets are weighted equally to paper-paper citations, and (in the partnership with Datacite) citations from one dataset to another dataset will also be captured and weighted equally. Unless I misunderstood the answers provided by Thomson Reuters, this is absolutely amazing.

Disclaimer: As I mentioned in my ignite presentation, citations are not everything and only one of many estimates of use/reuse. However, we can leverage and link citations to other measures and products to make a change now.

The revolution

data to data citation impact white.001

data to data citation impact white.002

data to data citation impact white.003

If we publish our data in repositories, with or without them being linked to papers, we can now provide the recognition needed to data as independent evidence products. Importantly, if you use other datasets to build your dataset such as a derived dataset for a synthesis activity such as a meta-analysis or if you aggregate data from other datasets, cite those data sources in your meta-data. The data citation index will capture these citations too. This will profoundly reshape the publication pipeline we are now stuck in and further fuel the open science movement.

Consequently, publish your datasets now (no excuses) and cite the data sources you used to build both your papers and your datasets. Open science and discovery await.