From iPlant to iAnimal, iEcosystem, and iBiosphere...

Five years ago this month I wrote an editorial for The Plant Cell called 21st Century Plant Biology: Viva la Revolución?, in which the concept of the 'iPlant' was introduced - as a small, connected device like the iPhone but with vastly greater capabilities, such as to model the growth, development and evolution of a plant. The logical extension of this to any 'iOrganism' was noted, as well as the need for ultimately developing an 'iEcosystem'. The 'iBiosphere' Initiative that is the subject of this blog is merely derivative of the original iPlant/iEcosystem concept.

Now, The iPlant Collaborative has branched out to implement 'iAnimal', rooted in the same Cyberinfrastructure and Discovery Environment as iPlant. Thus, iPlant is now explicitly addressing all organisms, not only plants. Clearly, this path has the potential to lead to an even more complex cyberinfrastructure supporting the study of interactions between and among organisms - ultimately leading toward iEcosystem and iBiosphere. It will be very interesting to see how the process develops and progresses, including whether iBiosphere will arise from the original iPlant or whether it will form on its own and merge or integrate with the iPlant/ iAnimal/ iOrganism complex.

It may seem that a cyberinfrastructure supporting ecosystems studies will need to be built somewhat differently from one supporting the study of individual organisms. But not necessarily. iPlant already deals in relationships among thousands of organisms as well as thousands of genes in its true of life and genotype-phenotype projects, and it also has developed an innovative taxonomic resolution tool used by biodiversity scientists to resolve conflicts in taxonomic databases. Thus, it already deals with a multitude of complex interaction, and may be well positioned to take on higher levels of complexity than might at first be apparent.

Most likely, however, I suspect we will see a coalescence of projects - including the iPlant Collaborative, the National Center for Ecological Analysis and Study(NCEAS), the National Evolutionary Synthesis Center (NESCent), the National Ecological Observatory Network (NEON), the National Institute for Mathematical and Biological Synthesis (NIMBioS) and others - leading eventually to a higher order entity that comprises a large part of what iBiosphere is envisioned to be. However, iBiosphere also needs to be much more - it must incorporate the social sciences, the agricultural sciences, and the environmental sciences as equal partners in order to inform and facilitate the kinds of policy and management decisions that will permit humankind to create and maintain sustainable systems from agriculture to ecology to the biosphere. 

Bringing together all these existing, developing entities in a meaningful and functional manner to allow complex decision making may seem like a nearly impossible task. But importantly, it is unlikely to happen by 'top down' planning; rather, it is more likely to just 'come together', through many efforts of many groups of people, in ways that are difficult or impossible to envision today. We can facilitate this coming together, but my guess is that we shouldn't try too hard to predict how exactly it is going to happen, or exactly what it is going to look like in the end. Taking a page from iPlant's original playbook, we should let the community decide what is needed, what the challenges are, and what the priorities ought to be, and then we should facilitate those efforts by responding to needs as they arise, not by deciding in advance what those needs might be. 

Contributions and responsibilities of authors, publishers, funders, and institutions

Responsibility for the dissemination of publicly funded research results is surely shared by multiple parties. Here are some thoughts on relative contributions and responsibilities. Note that these are intended to apply to primary original research articles reporting novel results, not necessarily to other types of publications such as reviews, commentaries, etc. The latter can be discussed separately, and should be, in my view.

1) The public surely has a right to access articles for no or low cost if public funds have paid for the research. For a citizen to have to pay $30 for an article regarding a disease they or a family member has is rightly viewed as unreasonable by the public. Researchers may have access through the subscriptions of their institutions, but this is no help to the average citizen who surely has an equal right to access.

2) Authors should accept responsibility for their decisions and publish so that their work is widely accessible. Authors control submissions, not publishers. Publishers can only choose among the submissions they actually receive. Publicly funded researchers make a decision as to where they publish their results, and thus they need to accept responsibility for understanding what rights they are granting to the publisher when they choose to publish in a given journal. Authors have options. They can choose open access (OA) journals or journals whose publishers charge no or low fees for individual articles that are requested by the public. Or they can choose to publish in journals that charge $30 for a single article. The latter seems unethical to me. Does it seem ethical to you as an author? If you are a publicly funded author and believe it is ethical to publish in a journal with a high per-article paywall for citizens, please explain in a comment below.

3) A publisher does provide an online system for submission and review that has some value, but not a lot. Publishers do provide typesetting, but self-publishing is inexpensive now, so the value of this is limited. Also, some publishers do copy editing, but it is questionable how much that benefits authors, or even readers. Authors are responsible for their every word, and can hire their own editors if they need help expressing themselves in the lingua franca of science, English. If editors and publishers want to impose changes in text on authors, authors do have the option to publish elsewhere. This is known as "voting with your feet".

4) OA journals have fixed costs of at least $1000 and often $2000 or more per article. Usually authors pay only part of that, and the rest is subsidized in most cases. Long term sustainability of OA journals presumably requires that authors pay the full cost of publication. Publication is a reasonable cost of performing research and should be factored into funding of research. Research that is not published has effectively not been done, i.e., doesn't exist - so publication is a necessary part of doing publicly funded research. Authors should take responsibility for paying for the costs of publication to ensure their research is widely available.

5) It is reasonable for funders to require researchers to publish in a way that makes the work widely accessible at reasonable cost, including data mining. Guidelines or rules are justifiable. Legislation should not be needed to create access, and also should not be used to limit access (as in the case of the RWA). All that is needed is that funders make their expectations known to grant recipients and hold them to it. Also, research institutions can require their researchers to publish their work in a manner that makes it widely accessible at reasonable cost.

In sum, authors, funders and research institutions all share responsibility for ensuring access to research results. By working together they should be able to come up with practices and policies that ensure wide availability at reasonable cost of publicly funded research results. Publishers facilitate the process of disseminating research results, but with enough competition among publishers, including OA journals, sufficient pressure will be applied to ensure fair access, but ONLY if authors, funders and institutions who are the source of the research take responsibility for their publication decisions.

Ethical responsibilities of scientists: re proposed US federal legislation on open science

iBiosphere depends heavily on openness - open access, open source, and open science - so we feel obliged to weigh in on current events that have the potential to seriously affect open science. New legislation being considered in the US has been the subject of much discussion in the blogosphere and in social media, especially the Research Works Act (RWA) and the Stop Online Piracy Act (SOPA). You only have to google these to find lots of discussion about them, but I would particularly refer readers to Cameron Neylon's blog on RWA. RWA would essentially end the NIH's Public Access Policy. For instance, data mining could be prevented by publishers by requiring onerous fees, and this could deal a devastating blow to efforts like iBiosphere that seek to facilitate exchange of public data and conclusions. By placing publications between a paywall, publishers could effectively control interactions among scientists and citizens who seek to assess, mine, and enhance the value of published, publicly funded research.

Politicians will do what politicians will do, including sometimes bending to the influence of money and vested interests.  It seems to us that, irrespective of what happens in the political sphere, scientists have an obligation to make their research data, results and conclusions that have been funded by the public available to the public. This means taking responsibility for where our research is published. In light of political actions by publishers to constrain access to previously published research, it becomes our responsibility to publish only in journals that will NOT put our research behind paywalls - we need to publish ONLY in truly open access journals. This of course means that the author pays for publication costs. But to choose to avoid paying for publication costs when it means restriction of access to publicly funded research is beginning to appear unethical, to state it generously.

Yes, ethics in science now requires each of us to publish in a way that makes our publicly funded research truly accessible to all - it means paying for Open Access options, and using only those OA option journals that guarantee permanent accessibility to research results, data and interpretations. Furthermore, it means agreeing to review and edit only for such journals, and to be members of only those professional societies whose policies and practices permit and facilitate true OA options. To find such options, one only has to look to Biomed Central, Public Library of Science, Frontiers and similar OA publishing options, as well as to professional society journals and even commercially published journals that offer author-pays OA options. We should choose and be willing to pay for OA and we should make certain that the OA we are paying for is truly OA, without any paywalls that would limit public access, including data and text mining, now and forever.

The "taxi driver" challenge

Bryan Heidorn commented in his recent blog on the challenge of reaching average citizens ("metaphorical taxi drivers"). As Byran notes, "iBiosphere is not only about climate change or deciding the causes but rather about all aspects of the biosphere. iBiosphere can not be the realm of scholars alone but must include all of the biosphere and its inhabitants in a way no other initiative ever has. Taxi drivers do not need to run XSEDE computer grids but the problems of taxi drivers need to inform scientists for both the inputs and outputs of iBiosphere. Luckily, the digital world has permeated all aspects of the taxi driver’s life from his GPS, to his cell phone, to his gas station, to his talk radio station.  iBiosphere must connect to him through his social network. The taxi driver’s daughter may be more open to new ideas and solutions for sustainability and she connects to the driver through chat on his phone. His gas station is run by an the oil executive who may be interested in sustainable profits through alternative energy sources. His radio station hires talk show hosts who attract sponsors. iBiosphere needs to include teenagers, executives, and talk show hosts as well as scientists. We can do this with smart phones, tablet computers, social media, computational modeling, visualization, science television, high school curricula, university extension offices and Arduino boards because they are all part of iBiosphere."


Bryan's full blogpost is here.