Monthly Archives: August 2011
George Monbiot has just published a piece in The Telegraph berating for-profit academic publishers that will surely be castigated by some as over the top hyperbole and praised by others as a trenchant criticism of the state of academic publishing*. Starting off with the, perhaps, ever so slightly, contentious title of Academic publishers make Murdoch look like a socialist Monbiot proceeds to fire zingers like
Murdoch pays his journalists and editors, and his companies generate much of the content they use. But the academic publishers get their articles, their peer reviewing (vetting by other researchers) and even much of their editing for free. The material they publish was commissioned and funded not by them but by us, through government research grants and academic stipends. But to see it, we must pay again, and through the nose.
and backs up his position with a recent analysis by Deutsche Bank
The publishers claim that they have to charge these fees as a result of the costs of production and distribution, and that they add value (in Springer’s words) because they “develop journal brands and maintain and improve the digital infrastructure which has revolutionised scientific communication in the past 15 years”. But an analysis by Deutsche Bank reaches different conclusions. “We believe the publisher adds relatively little value to the publishing process … if the process really were as complex, costly and value-added as the publishers protest that it is, 40% margins wouldn’t be available.”
finally ending with a call to arms that even your, never shying away from a good fight, narrator would have toned down a bit**
The knowledge monopoly is as unwarranted and anachronistic as the corn laws. Let’s throw off these parasitic overlords and liberate the research that belongs to us.
Go read the whole thing. This is something that folks are going to be talking about, and I think it’s another good opportunity to ask ourselves whether the the group that contributes the least to the overall scientific process should the one that benefits the most financially. I take it as yet another sign that 2011 is the year that the war over academic publishing officially began.
*Yes, once I used the word “excoriation” in the title I got a little carried away with the big words.
**Though not for lack of agreement with the general sentiment; clearly.
As some of you may have heard, the BIO directorate at NSF has implemented some sweeping changes to the proposal process. Some of you youngsters may be unaware what the ‘old’ system was, but it involved two submission deadlines per year. At these deadlines, scientists would submit to a panel** one or more full proposals*** which were then reviewed by external reviewers and deliberated on by the panel the proposal was submitted to. Starting in January, this is changing. Some of the important highlights include:
1) Preproposals: we will now need to submit a preproposal before we can submit a full proposal. Preproposals will be 5 pages, 4 of which are for the science/broader impacts. These preproposals will be considered by a panel and full proposals will be solicited for a subset of those preproposals. No full proposals can be submitted unless solicited by NSF****.
2) fewer full proposal deadlines: The early year proposal deadline has been converted to a preproposal deadline so there is now a deadline for preproposals (January) and one later in the year for the solicited full proposals (August).
3) limits on submissions: the NSF info says, “In a given year, an individual may participate as a PI, co-PI, or lead senior investigator of a subaward on no more than two preliminary proposals submitted per Division solicitation (DEB or IOS).” I suspect from the wording that it is 2 total – regardless of how many different panels you want to submit to. Does anyone have more info on this?
NSF has highlighted the following as part of their motivation:
1) focus on transformative science. In their FAQ, NSF specifically highlights that they expect that the Preproposals panel will focus on how interesting and important the research is since obviously preproposal methods will be limited.
2) higher funding rate for full proposals. Also in the FAQ, NSF is aiming at a 25-35% funding rate for full proposals. For the youngsters, funding rates at least for the panel I tend to submit to have been in the range of 8-10%, so this will be a substantial improvement. However, this means that the rejection rates for the preproposals will be high.
The next year or two as we transition to the new process are going to be rocky. Some of my colleagues think these changes are akin to the 4 horsemen of the apocalypse running across the scientific landscape. I think there are some critical issues with respect to currently untenured faculty, and funding gaps for projects that were planning on having 2 submissions before funding runs out. But, assuming that we are able to get feedback on rejected full proposals in time to write revised preproposals for the next round, I’m actually cautiously optimistic that there will eventually be some benefits to this system. I’ve read some of the concerns on other blogs and I would recommend that our readers go check them out. One of the reasons I am cautiously optimistic is that the old system was broken and some of those concerns were unofficially being built into the old system anyway*****. The truth is that our funding world has changed and we all (NSF, scientists, and university tenure committees) need to figure out how to make our current reality work. NSF is trying to adjust, scientists are being forced to adjust, and I think those of us with tenure need to make sure our universities are also adjusting so that the young people coming up through the new reality don’t get screwed****** because the system has changed on them and we haven’t adjusted our expectations*******.
* DEB (Division of Environmental Biology) and IOS (Division of Integrated Organismal Systems) are divisions at NSF and cover pretty much everything from organismal physiology to ecosystem ecology. Incidentally, MCB (Division of Molecular and Cellular Biosciences) is/has also adopted the new system.
**Panel, n. 1) a program (in the generic sense, not the computer sense) to which unsolicited proposals on a certain research area (e.g., Population and Community Ecology, Ecosystems, etc) could be submitted twice a year. 2) a group of scientists invited to NSF to provide funding recommendations on proposals submitted to that panel.
***Full proposal: This involves a 1 page Project Summary, 15 page Project Description, Budget and Budget Justification, 2-page CV for each PI and co-PI, Lists of current and pending funding for each PI and co-PI, Data Management Plan, Cited Literature, and Postdoc mentoring plan (if you are going to fund a postdoc).
**** There are exceptions to this: CAREER, OPUS, RCN, LTER (i.e., pretty much anything with its own acronym except LTREB).
***** For example, proposals were being held by NSF until after the next deadline unless you specifically bugged your program director for it and then sometimes is was released with very little time before the deadline. I suspect it was only a matter of time before they refused to release them at all before the next deadline. The fact that it’s a deadline (i.e., late submissions rejected) and not a target date (i.e., acceptance or rejection of late submissions at the discretion of the program director) was also a relative recent change and indicative of where things were heading.
****** New system or old system, the fact is that 8% (or whatever the new number will be – though it’s hard to imagine it’ll be a LOT better) is horrid and frankly a lack of successful NSF funding is NOT indicative of quality or long-term prospects when percentages are that low. We need to make sure that productive people who have not landed the ‘gold standard’ grant are not being flushed out of the system.
******* This one’s just because I find the long string of astrixes (astrices?) funny.
If folks are interested in seeing what Weecology has been up to lately we have a bunch of posters and talks at ESA this year. In order of appearance:
- Tuesday at 2:30 pm in Room 9AB our new postdoctoral researcher Dan McGlinn will be giving a talk on looking at community assembly using patterns of with- and between-species spatial variation.
- Tuesday afternoon at poster #28 Morgan will be presenting research on how the long-term community dynamics of the plant and rodent communities near Portal, AZ are related to decadal scale climate cycles. She’ll be there from 4:30 to 6:30 to chat, or stop by any time and take a look.
- Wednesday at 1:50 pm in Room 19A one of our new members, Elita Baldridge, will be giving a talk on her masters research on nested subsets.
- Wednesday at poster #139 Ethan will be presenting on our two attempts to make it easier to find and use ecological data. He’ll be there from 4:30 to 6:30 to chat, or stop by any time and take a look (or grab a computer and check out EcologicalData and the EcoData Retriever).
- Thursday at 1:50 pm in Room 10A another of our new members, Zack Brym, will be giving a talk on his masters research on controls on the invasion of an exotic shrub.
- Thursday at 4 pm in Room 8 Sarah Supp will give a talk on her work looking at the impacts of experimental manipulations on macroecological patterns (highlighted as a talk to see by Oiko’s blog)
- And last, but certainly not least, bright and early Friday morning at 8 am in Room 8 Kate Thibault (who has now moved on to fame and fortune at NEON) will be presenting on our work using maximum entropy models to predict the species abundance distributions of 16,000 communities.
Very cool. I’m curious, how do you think this will compare/contrast/fight with the Data One project – https://www.dataone.org/ – or is this a different beast altogether?
As I started to answer it I realized that my thoughts on the matter were better served by a full post, both because they are a bit lengthy and because I don’t actually know much about DataONE and would love to have some of their folks come by, correct my mistaken impressions, and just chat about this stuff in general.
To begin with I should say that I’m still trying to figure this out myself, both because I’m still figuring out exactly what DataONE is going to be, and because EcologicalData is still evolving. I think that both projects goals could be largely defined as “Organizing Ecology’s Data,” but that’s a pretty difficult task, involving a lot of components and a lot of different ways to tackle them. So, my general perspective is that the more folks we have trying the merrier. I suspect there will be plenty of room for multiple related projects, but I’d be just as happy (even happier probably) if we could eventually find a single centralized location for handling all of this. All I want is solution to the challenge.
But, to get to the question at hand, here are the differences I see based on my current understanding of DataONE:
1. Approach. There are currently two major paradigms for organizing large amounts of information. The first is to figure out a way to tell computers how to do it for us (e.g., Google), the second is to crowdsource it’s development and curation (e.g., Wikipedia). DataONE is taking the computer based approach. It’s heavy on metadata, ontologies, etc. The goal is to manage the complexities of ecological data by providing the computer with very detailed descriptions of the data that it can understand. We’re taking the human approach, keeping things simple and trying to leverage the collective knowledge and effort of the field. As part of this difference in approach I suspect that EcologicalData will be much more interactive and community driven (the goal is for the community to actually run the site, just like Wikipedia) whereas DataONE will tend to be more centralized and hierarchical. I honestly couldn’t tell you which will turn out better (perhaps the two approaches will each turn out to be better for different things) but I’m really glad that we’re trying both at the same time to figure out what will work and where their relative strengths might be.
2. Actually serving data. DataONE will do this; we won’t. This is part of the difference in approach. If the computer can handle all of the thinking with respect to the data then you want it to do that and just spit out what you want. Centralizing the distribution of heterogeneous data is a really complicated task and I’m excited the folks at DataONE are tackling the challenge.
a. One of the other challenges for serving data is that is that you have to get all of the folks who “own” the data to let you provide it. This is one of the reasons I came up with the Data Wiki idea. By serving as a portal it helps circumvent the challenges of getting all of the individual stake holders to agree to participate.
b. We do provide a tool for data acquisition, the EcoData Retriever, that likewise focuses on circumventing the need to negotiate with data providers by allowing each individual investigator to automatically download the data from the source. But, this just sets up each dataset independently, whereas I’m presuming that DataONE will let you just run one big query of all the data (which I’m totally looking forward to by the way) .
3. Focus. The primary motivation behind the Data Wiki goes beyond identifying datasets and really focuses on how you should use them. Having worked with other folks’ data for a number of years I can say that the biggest challenging (for me anyway) is actually figuring out all of the details of when and how the dataset should be used. This isn’t just a question of reading metadata either. It’s a question of integrating thoughts and approaches from across the literature. What I would like to see develop on the Data Wiki pages is the development of concise descriptions for how to go about using these datasets in the best way possible. This is a very difficult task to automate and one where I think a crowdsourced solution is likely the most effective. We haven’t done a great job of this yet, but Allen Hurlbert and I have some plans to develop a couple of good examples early in the fall to help demonstrate the idea.
4. We’re open for business. Ha ha, eat our dust DataONE. But seriously, we’ve taken a super simple approach which means we can get up and running quickly. DataONE is doing something much more complicated and so things may take some time to roll out. I’m hoping to get a better idea of what their time lines look like at ESA. I’m sure their tools will be well worth the wait.
5. Oh, and their budget is a little over $2,000,000/year, which is just slightly larger than our budget of around $5,000/year.
So, there is my lengthy and meandering response to Jarrett’s question. I’m looking forward to chatting with DataONE folks at ESA to find out more about what they are up to, and I’d love to have them stop by here to chat and clear up my presumably numerous misconceptions.
 Though we do have some ideas for managing something somewhat similar, so stay tuned for EcoData Retriever 2.0. Hopefully coming to an internet near you sometime this spring.
Next week is the annual meeting of the Ecological Society of America. If you’ve ever been to ESA, then you know it’s….big, often between 3000-5000 ecologists (which I thought was big until I heard about some of the biomedical conferences which have the attendance of a small city). It seems like most of those people are giving talks or posters. Obviously it’s impossible to see everything, and frankly with talks spread out across 20-odd different rooms which are usually spread out across the far corners of the convention center plus various hotels, it’s probably not possible to see even a fraction of the things you’re interested in. If you try to do the ESA blitzkrieg (and most young graduate students will try at least once), you are guaranteeing an overwhelming, lonely, and futile experience. So, how do you navigate this beast and keep your sanity? I have two recommendations:
1) Pick a strategy. Some years I choose to focus on a specific concept or research area to learn a lot about a breaking area of ecology in a short period of time (like the year a majority of what I saw had the word ‘metacommunity’ in the title). Some years I choose breadth because I want to have a better feeling for where the field in general is going or to look for interesting new ideas (one year I saw talks that spanned from theory to empirical and from physiology to ecosystems – ah that was a fun year). The point is, decide what you want to get out of ESA before you go because once you get there, there’s a lot going on.
2) Find a conference buddy (or buddies). You can’t see everything, but if you coordinate with a friend then you can hear about twice as much as you can see. It helps with processing talks and keeping them from just blending together. It also has the added benefit of giving you someone to talk to regularly and keeping you from feeling like just another faceless cog in the giant ESA machine. Ethan and I often use this strategy, especially when there is more than one really interesting talk at the same time. Then we get together afterwards and swap stories. Just a piece of advice: make sure your conference buddy either has a good memory or takes good notes. I’m not pointing fingers or anything, but there’s nothing more frustrating than giving a detailed rendition of the talk you saw, asking about the talk they saw that you really want to know about, and getting, “It was really good. Uh, my notes here say they did something with a neutral model and the results were really compelling. The paper’s coming out soon. “
I’ve been waiting for a while now for Ted Hart’s blog to get up enough steam to send folks over there, and since in the last two weeks he’s had three posts, revamped the mission of the blog, and engaged in the ongoing conversation about Lindenmayer & Likens, it seems like that time has arrived.
I chose distributed ecology as a title because I like the idea of ecological thought like distributed computing. Lots of us scientists like little nodes around the web thinking and processing ideas into something great.
Sounds like what I’m hoping to see (and am increasingly witnessing) from the ecology blogs. So, head on over, check it out, click on the RSS button, and welcome Ted to the ecology blogging community.