Monday, September 15, 2014

Links: Reanalyzing R-squares, NSF pre-proposals, and the difficulties of academia for parents

First, Will Pearse has done a great job of looking at the data behind the recent paper looking at declining R and p-values in ecology, and his reanalysis suggests that there is a much weaker relationship between r2 values and time (only 4% rather than 62% as reported). Because the variance is both very large within-years and also not equal through time, a linear model may not be ideal for capturing this relationship.
Thanks @prairiestopatchreefs for linking this.

From the Sociobiology blog, something that most US ecologists would probably agree on: the NSF pre-proposal program has been around long enough (~3 years) to judge on its merits, and it has not been an improvement. In short, pre-proposals are supposed to use a 5 page proposal to allow NSF to identify the best ideas and then invite those researchers to submit a full proposal similar to the traditional application. Joan Strassman argues that not only is this program more work for applicants (you must write two very different proposals in short order if you are lucky to advance), it offers very few benefits for them.

The reasons for the gender gap in STEM academic careers gets a lot of attention, and rightly so given the continuing underrepresentation of women. The demands of parenthood often receive some of the blame. The Washington Post is reporting on a study that considers parenthood from the perspective of male academics. The study took an interview-based, sociological approach, and found that the "majority of tenured full professors [interviewed] ... have either a full-time spouse at home who handles all caregiving and home duties, or a spouse with a part-time or secondary career who takes primary responsibility for the home." But the majority of these men also said they wanted to be more involved at home. As one author said, “Academic science doesn’t just have a gender problem, but a family or women, if they want to have families, are likely to face significant challenges.”

On a lighter note, if you've ever joked about PNAS' name, a "satirical journal" has taken that joke and run with it. PNIS (Proceedings of the Natural Institute of Science) looks like the work of bored post-docs, which isn't necessarily a bad thing. The journal has immediately split into two subjournals: PNIS-HARD (Honest and Real Data) and PNIS-SOFD (Satirical or Fake Data), which have rather interesting readership projections:

Friday, September 12, 2014

Do green roofs enhance urban conservation?

ResearchBlogging.orgGreen roofs are now commonly included in the design of new public and private infrastructure, bolstered by energy savings, environmental recognition and certification, bylaw compliance, and in some cases tax or other direct monetary incentives (e.g., here).  While green roofs clearly provide local environmental benefits, such as reduced albedo (sunlight reflectance), storm water retention, CO2 sequestration, etc., green roof proponents also frequently cite biodiversity and conservation enhancement as a benefit. This last claim has not been broadly tested, but existing data was assessed by Nicholas Williams and colleagues in a recent article published in the Journal of Applied Ecology.

Williams and colleagues compiled all available literature on biodiversity and conservation value of green roofs and they explicitly tested six hypotheses: 1) Green roofs support higher diversity and abundance compared to traditional roofs; 2) Green roofs support comparable diversity and composition to ground habitat; 3) Green roofs using native species support greater diversity than traditional green roofs; 4) Green roofs aid in rare species conservation; 5) Green roofs replicate natural communities; and 6) Green roofs facilitate organism movement through urban areas.

Photo by: Marc Cadotte

What is surprising is that given the abundance of papers on green roofs in ecology and environmental journals, very few quantitatively assessed some of these hypotheses. What is clear is that green roofs support greater diversity and abundance compared to non-green roofs, but we know very little about how green roofs compare to other remnant urban habitats in terms of species diversity, ecological processes, or rare species. Further, while some regions are starting to require that green roofs try to maximize native biodiversity, there are relatively few comparisons, but those that exist reveal substantial benefits for biodiverse green roofs.

How well green roofs replicate ground or natural communities is an important question, with insufficient evidence. It is important because, according to the authors, there is some movement to use green roofs to offset lost habitat elsewhere. This could represent an important policy shift, and one that may ultimately lead to lost habitats being replaced with lower quality ones. This is a policy direction that simply requires more science.

There is some evidence that green roofs, if designed correctly, could aid in rare species conservation. However, green roofs, which by definition are small patches in an inhospitable environment, may assist rare species management in only a few cases. The authors caution that enthusiasm for using green roofs to assist with rare species management needs to be tempered by designs that are biologically and ecologically meaningful to target species. They cite an example where green roofs in San Francisco were designed with a plant that is an important food source for an endangered butterfly, Bay Checkerspot, which currently persists in a few fragmented populations. The problem was that the maximum dispersal distance of the butterfly is about 5 km, and there are no populations within 15 km of the city. These green roofs have the potential to aid in rare species conservation, but it needs to be coupled with additional management activities, such as physically introducing the butterfly to the green roofs.

Overall, green do provide important environmental and ecological benefits in urban settings. Currently, very few studies document the ways in which green roofs provide ecological processes and services, enhance biodiversity, replicate other ground level habitats, or aid in biodiversity conservation. As the prevalence of green roofs increases, we will need scientifically valid ecological understanding of green roof benefits to better engage with municipal managers and affect policy.

Williams, N., Lundholm, J., & MacIvor, J. (2014). Do green roofs help urban biodiversity conservation? Journal of Applied Ecology DOI: 10.1111/1365-2664.12333

Monday, September 8, 2014

Edicts for peer reviewing

Reviewing is a right of passage for many academics. But for most graduate students or postdocs, it is also a bit of a trial by fire, since reviewing skills are usually assumed to be gained osmotically, rather than through any specific training. Unfortunately, the reviewing system seems ever more complicated for reviewers and authors alike (slow, poor quality, unpredictable). Concerns about modern reviewing pop up every few months, and different solutions to the difficulties of finding qualified reviewers and the quality of modern reviews (including publishing an instructional guide, taking alternative approaches (PeerJ, etc), or skipping peer review altogether (arXiv)). Still, in the absence of a systematic overhaul of the peer review system, an opinion piece in The Scientist by Matthew A. Mulvey and Dean Tantin provides a rather useful guide for new reviewers and a useful reminder for experienced reviewers. If you are going to do a review (and you should, if you are publishing papers), you should do it well. 
From "An Ecclesiastical Approach to Peer Review" 
"The Golden Rule
Be civil and polite in all your dealings with authors, other reviewers, editors, and so on, even if it is never reciprocated.
As a publishing scientist, you will note that most reviewers break at least a few of the rules that follow. Sometimes that is OK—as reviewers often fail to note, there is more than one way to skin a cat. As an author you will at times feel frustrated by reviews that come across as unnecessarily harsh, nitpicky, or flat-out wrong. Despite the temptation, as a reviewer, never take your frustrations out on others. We call it the “scientific community” for a reason. There is always a chance that you will be rewarded in the long run. 
The Cardinal Rule
If you had to publish your review, would you be comfortable doing so? What if you had to sign it? If the answer to either question is no, start over. (That said, do not make editorial decisions in the written comments to the authors. The decision on suitability is the editors’, not yours. Your task is to provide a balanced assessment of the work in question.) 
The Seven Deadly Sins of sub-par reviews
  1. Laundry lists of things the reviewer would have liked to see, but have little bearing on the conclusions.
  2. Itemizations of styles or approaches the reviewer would have used if they were the author.
  3. Direct statements of suitability for publication in Journal X (leave that to the editor).
  4. Vague criticism without specifics as to what, exactly, is being recommended. Specific points are important—especially if the manuscript is rejected.
  5. Unclear recommendations, with little sense of priority (what must be done, what would be nice to have but is not required, and what is just a matter of curiosity).
  6. Haphazard, grammatically poor writing. This suggests that the reviewer hasn’t bothered to put in much effort.
  7. Belligerent or dismissive language. This suggests a hidden agenda. (Back to The Golden Rule: do not abuse the single-blind peer review system in order to exact revenge or waylay a competitor.) 
Vow silence
The information you read is confidential. Don’t mention it in public forums. The consequences to the authors are dire if someone you inform uses the information to gain a competitive advantage in their research. Obviously, don’t use the findings to further your own work (once published, however, they are fair game). Never contact the authors directly.
Be timely
Unless otherwise stated, provide a review within three weeks of receiving a manuscript. This old standard has been eroded in recent years, but nevertheless you should try to stick to this deadline if possible. 
Be thorough
Read the manuscript thoroughly. Conduct any necessary background research. Remember that you have someone’s fate in your hands, so it is not OK to skip over something without attempting to understand it completely. Even if the paper is terrible and in your view has no hope of acceptance, it is your professional duty to develop a complete and constructive review.
Be honest
If there is a technique employed that is beyond your area of expertise, do the best you can, and state to the editor (or in some cases, in your review) that although outside your area, the data look convincing (or if not, explain why). The editor will know to rely more on the other reviewers for this specific item. If the editor has done his or her job correctly, at least one of the other reviewers will have the needed expertise.
Most manuscript reviews cover about a page or two. Begin writing by briefly summarizing the state of the field and the intended contribution of the study. Outline any major deficits, but refrain from indicating if you think they preclude publication. Keep in mind that most journals employ copy editors, so unless the language completely obstructs understanding, don’t bother criticizing the English. Go on to itemize any additional defects in the manuscript. Don’t just criticize: saying that X is a weakness is not the same as saying the authors should address weakness X by providing additional supporting data. Be clear and provide no loopholes. Keep in mind that you are not an author. No one should care how you would have done things differently in a perfect world. If you think it helpful, provide additional suggestions as minor comments—the editor will understand that the authors are not bound to them.
Judgment Day
Make a decision as to the suitability of the manuscript for the specific journal in question, keeping in mind their expectations. Is it acceptable in its current state? Would a reasonable number of experiments performed in a reasonable amount of time make it so, or not? Answering these questions will allow you to recommend acceptance, rejection, or major/minor revision. 
If the journal allows separate comments to the editor, here is the place to state that in your opinion they should accept and publish the paper as quickly as possible, or that the manuscript falls far below what would be expected for Journal X, or that Y must absolutely be completed to make the manuscript publishable, or that if Z is done you are willing to have it accepted without seeing it again. Good comments here can make the editor’s job easier. The availability of separate comments to the editor does not mean that you should provide only positive comments in the written review and reserve the negative ones for the editor. This approach can result in a rejected manuscript being returned to the authors with glowing reviewer comments. 
A second review is not the same as an initial review. There is rarely any good reason why you should not be able to turn it around in a few days—you are already familiar with the manuscript. Add no new issues—doing so would be the equivalent of tripping someone in a race during the home stretch. Determine whether the authors have adequately addressed your criticisms (and those of the other reviewers, if there was something you missed in the initial review that you think is vital). In some cases, data added to a revised manuscript may raise new questions or concerns, but ask yourself if they really matter before bringing them up in your review. Be willing to give a little if the authors have made reasonable accommodation. Make a decision: up or down. Relay it to the editor. 
Congratulations. You’ve now been baptized, confirmed, and anointed a professional manuscript reviewer."