The advantages of taking a chance with a new journal – OpenQuaternary

Full disclosure: I’m on the editorial board of Open Quaternary and also manage the blog, but I am not an Editor in Chief and have attempted to ensure that my role as an author and my role as an editor did not conflict.

Figure 1.  Neotoma and R together at last!
Figure 1. Neotoma and R together at last!

We (myself, Andria Dawson, Gavin L. SimpsonEric GrimmKarthik Ram, Russ Graham and Jack Williams) have a paper in press at a new journal called Open Quaternary.  The paper documents an R package that we developed in collaboration with rOpenSci to access and manipulate data from the Neotoma Paleoecological Database.  In part the project started because of the needs of the PalEON project.  We needed a dynamic way to access pollen data from Neotoma, so that analysis products could be updated as new data entered the database.  We also wanted to exploit the new API developed by Brian Bills and Michael Anderson at Penn State’s Center for Environmental Informatics.

There are lots of thoughts about where to submit journal articles.  Nature’s Research Highlights has a nice summary about a new article in PLoS One (Salinas and Munch, 2015) that looks to identify optimum journals for submission, and Dynamic Ecology discussed the point back in 2013, a post that drew considerable attention (here, here, and here, among others).  When we thought about where to submit I made the conscious choice to choose an Open Source journal. I chose Open Quaternary partly because I’m on the editorial board, but also because I believe that domain specific journals are still a critical part of the publishing landscape, and because I believe in Open Access publishing.

The downside of this decision was that (1) the journal is new, so there’s a risk that people don’t know about it, and it’s less ‘discoverable’; (2) even though it’s supported by an established publishing house (Ubiquity Press) it will not obtain an impact factor until it’s relatively well established.  Although it’s important to argue that impact factors should not make a difference, it’s hard not to believe that they do make a difference.

Figure 2.  When code looks crummy it's not usable.  This has since been fixed.
Figure 2. When code looks crummy it’s not usable. This has since been fixed.

That said, I’m willing to invest in my future and the future of the discipline (hopefully!), and we’ve already seen a clear advantage of investing in Open Quaternary.  During the revision of our proofs we noticed that the journal’s two column format wasn’t well suited the the blocks of code that we presented to illustrate examples in our paper.  We also lost the nice color syntax highlighting that pandoc offers when it renders RMarkdown documents (see examples in our paper’s markdown file).  With the help of the journal’s Publishing Assistant Paige MacKay, Editor in Chief Victoria Herridge and my co-authors we were able to get the journal to publish the article in a single column format, with syntax highlighting supported using highlight.js.

I may not have a paper in Nature, Science or Cell (the other obvious option for this paper /s) but by contributing to the early stages of a new open access publishing platform I was able to change the standards and make future contributions more readable and make sure that my own paper is accessible, readable and that the technical solution we present is easily implemented.

I think that’s a win.  The first issue of Open Quaternary should be out in March, until then you can check out our GitHub repository or the PDF as submitted (compleate with typoes).

Macrosystems Ecology: The more we know the less we know.

Dynamic Ecology had a post recently asking why there wasn’t an Ecology Blogosphere. One of the answers was simply that as ecologists we often recognize the depth of knowledge of our peers and as such, are unlikely (or are unwilling) to comment in an area that we have little expertise. This is an important point. I often feel like the longer I stay in academia the more I am surprised when I can explain a concept outside my (fairly broad) subject area clearly and concisely.  It surprises me that I have depth of knowledge in a subject that I don’t directly study.

Of course, it makes sense.  We are constantly exposed to ideas outside our disciplines in seminars, papers, on blogs & twitter, and in general discussions, but at the same time we are also exposed to people with years of intense disciplinary knowledge, who understand the subtleties and implications of their arguments.  This is exciting and frightening.  The more we know about a subject, the more we know what we don’t know.  Plus, we’re trained to listen to other people.  We ‘grew up’ academically under the guidance of others, who often had to correct us, so when we get corrected out of our disciplines we are often likely to defer, rather than fight.

This speaks to a broader issue though, and one that is addressed in the latest issue of Frontiers in Ecology and the Environment.  The challenges of global change require us to come out of our disciplinary shells and to address challenges with a new approach, defined here as Macrosystems Ecology.  At large spatial and temporal scales – the kinds of scales at which we experience life – ecosystems cease being disciplinary.  Jim Heffernan and Pat Soranno, in the lead paper (Heffernan et al., 2014) detail three ecological systems that can’t be understood without cross-scale synthesis using multi-disciplinary teams.

Figure 1.  From Heffernan et al. (2014), multiple scales and disciplines interact to explain patterns of change in the Amazon basin.
Figure 1. From Heffernan et al. (2014), multiple scales and disciplines interact to explain patterns of change in the Amazon basin.

The Amazonian rain forest is a perfect example of a region that is imperiled by global change, and can benefit from a Macrosystems approach.  Climate change and anthropogenic land use drives vegetation change, but vegetation change also drives climate (and, ultimately, land use decisions). This is further compounded by teleconnections related to societal demand for agricultural products around the world and the regional political climate.  To understand and address ecological problems in this region then, we need to understand cross-scale phenomena in ecology, climatology, physical geography, human geography, economics and political science.

Macrosystems proposes a cross-scale effort, linking disciplines through common questions to examine how systems operate at regional to continental scales, and at multiple temporal scales.  These problems are necessarily complex, but by bringing together researchers in multiple disciplines we can begin to develop a more complete understanding of broad-scale ecological systems.

Interdisciplinary research is not something that many of us have trained for as ecologists (or biogeographers, or paleoecologists, or physical geographers. . . but that’s another post).  It is a complex, inter-personal interaction that requires understanding of the cultural norms within other disciplines.  Cheruvelil et al. (2014) do a great job of describing how to achieve and maintain high-functioning teams in large interdisciplinary projects, and Kendra also discusses this further in a post on her own academic blog.

Figure 2.  Interdisciplinary research requires effort in a number of different areas, and these efforts are not recognized under traditional reward structures.
Figure 2. From Goring et al., (2014). Interdisciplinary research requires effort in a number of different areas, and these efforts are not recognized under traditional reward structures.

In Goring et al. (2014) we discuss a peculiar issue that is posed by interdisciplinary research.  The reward system in academia is largely structured to favor disciplinary research.  We refer to this in our paper as a disciplinary silo.  You are in a department of X, you publish in the Journal of X, you go to the International Congress of X and you submit grant requests to the X Program of your funding agency.  All of these pathways are rewarded, and even though we often claim that teaching and broader outreach are important, they are important inasmuch as you need to not screw them up completely (a generalization, but one I’ve heard often enough).

As we move towards greater interdisciplinarity we begin to recognize that simply superimposing the traditional rewards structure onto interdisciplinary projects (Figure 2) leaves a lot to be desired.  This is particularly critical for early-career researchers.  We are asking these researchers (people like me) to collaborate broadly with researchers around the globe, to tackle complex issues in global change ecology, but, when it comes time to assess their research productivity we don’t account for the added burden that interdisciplinary research can require of a researcher.

Now, I admit, this is self-serving.  As an early career researcher, and member of a large interdisciplinary team (PalEON), much of what we propose in Goring et al. (2014) strongly reflects on my own personal experience.  Outreach activities, the complexities of dealing with multiple data sources, large multi-authored papers, posters and talks, and the coordination of researchers across disciplines are all realities for me, and for others in the project, but ultimately, we get evaluated on grants and papers.  The interdisciplinary model of research requires effort that never gets valuated by hiring or tenure committees.

That’s not to say that hiring committees don’t consider this complexity, and I know they’re not just looking for Nature and Science papers, but at the same time, there is a new landscape for researchers out there, and we’re trying to evaluate them with an old map.

In Goring et al. (2014) we propose a broader set of metrics against which to evaluate members of large interdisciplinary teams (or small teams, there’s no reason to be picky).  This list of new metrics (here) includes traditional metrics (numbers of papers, size of grants), but expands the value of co-authorship, recognizing that only one person is first in the authorship list, even if people make critical contributions; provides support for non-disciplinary outputs, like policy reports, dataset generation, non-disciplinary research products (white papers, books) and the creation of tools and teaching materials; and adds value to qualitative contributions, such as facilitation roles, helping people communicate or interact across disciplinary divides.

This was an exciting set of papers to be involved with, all arising from two meetings associated with the NSF Macrosystems Biology program (part of NSF BIO’s Emerging Frontiers program).  I was lucky enough to attend both meetings, the first in Boulder CO, the second in Washington DC.  As a post-doctoral researcher these are the kinds of meetings that are formative for early-career researchers, and clearly, I got a lot out of it.  The Macrosystems Biology program is funding some very exciting programs, and this Frontiers issue attempts to get to the heart of the Macrosystems approach.  It is the result of many hours and days of discussion, and many of the projects are already coming to fruition.  It is an exciting time to be an early-career researcher, hopefully you agree!

“Pollen richness, a cautionary tale” is out in the Journal of Ecology

I have a new paper out in the Journal of Ecology here.  The article also contains a supplement with R Markdown code that will allow users to reproduce the analysis in the article nearly faithfully (here, and as a code repository on GitHub here if you want to fork it and modify the code).

Figure 5 from Goring et al., the relationships between plant richness and smoothed pollen richness and vice versa both show a slightly negative relationship (accounting for very little variability), meaning higher plant richness is associated with lower pollen richness.
Figure 5 from Goring et al., the relationships between plant richness and smoothed pollen richness and vice versa both show a slightly negative relationship (accounting for very little variability), meaning higher plant richness is associated with lower pollen richness.

The paper sets out to test whether pollen richness is truly a measure of plant richness in a modern context in British Columbia.  Using a network of 16,000 plant sample plots and 167 lake sediment records from across British Columbia we show that pollen cannot be counted on to faithfully reproduce plant richness in this region.  We show that rarefaction plays little role in the lack of a relationship between plant species richness and pollen taxonomic richness, and that the taxonomic smoothing between plant species and the representative pollen morphotypes does degrade the relationship, but that some signal still exists. Continue reading “Pollen richness, a cautionary tale” is out in the Journal of Ecology

Three new papers in various stages of publication.

I’ve just gone through and put some new papers into my Research page.  I’ve been busy over the past little while and it seems to be paying off.  Here are some of my latest papers, with brief summaries for your enjoyment:

Figure 5 from Goring et al., the relationships between plant richness and smoothed pollen richness and vice versa both show a slightly negative relationship (accounting for very little variability), meaning higher plant richness is associated with lower pollen richness.
Figure 5 from Goring et al., the relationships between plant richness and smoothed pollen richness and vice versa both show a slightly negative relationship (accounting for very little variability), meaning higher plant richness is associated with lower pollen richness.

Goring S, Lacourse T, Pellatt MG, Mathewes RW.  Pollen richness is not correlated to plant species richness in British Columbia, Canada.  Journal of Ecology,   Accepted. [Link][Supplement]

  • Although pollen richness has acted as a proxy for vegetation richness in the literature, our paper shows that this may not be the case.  Taphonomic processes, from release of the pollen to deposition and preservation in lake sediments, appear to degrade the signal of plant richness to the point that there is no significant relationship between plant species richness and pollen taxonomic richness.  The supplementary material includes all the R code and a sample of the raw data (we could not freely share some of the data) used to perform the analysis.

Combourieu-Nebout N, Peyron O, Bout-Roumazeilles V, Goring S, Dormoy I, Joannin S, Sadori L, Siani G, and Magny M. 2013. Holocene vegetation and climate changes in central Mediterranean inferred from a high-resolution marine pollen record (Adriatic Sea). Climate of the Past Discussions, 9:1969-2014. [Link]

  • Another great paper on Holocene and late-Glacial change in the Mediterranean, part of a Special Series in Climate of the Past.  This paper uses multiple proxies, including the use of clay mineral fractions to match climate signals from pollen to sediment transport into the Adriatic from the Po River watershed, sediment blown from the Sahara and sediment transported down the Apennines.  This paper further examines shifts in seasonal precipitation in the central Mediterranean associated with changes in insolation during the Holocene and broader scale shifts in the relative influences of major climate systems in the region.

Gill JL, McLauchlan KK, Skibbe AM, Goring S, Williams JW. Linking abundances of the dung fungus Sporormiella to the density of Plains bison: Implications for assessing grazing by megaherbivores in the paleorecord. Journal of Ecology. Early view: [Link]

  • Three great papers in a row!  This paper uses modern pollen traps in the Konza Prairie LTER to examine the relationship between Sporormiella pollen and bison grazing.  This is an important link to make because Sporormiella has been used to indicate the presence of megafauna such as mammoths and mastadons in the late-glacial.  The declining signal of Sporormiella at Appleman Lake, IN was a key feature in the onset of non-analogue vegetation at the site in the late-Glacial (Gill et al., 2009).  This paper provides an explicit link between the theoretical potential of the spore as an indicator of megafaunal presence and the degree of grazing at sites.

New Paper: Sedimentation rates across space and time in Eastern North America

We’ve got a new paper out in the August issue of Quaternary Science Reviews looking at sedimentation rates across the northeastern United States. The paper is co-authored with Jack Williams, Jessica Blois, Stephen Jackson, Jennifer Marlon, Chris Paciorek, Bob BoothMaarten Blaauw and Andrés Christen (incidentally, a really great group of co-authors, you should all write papers with them).  We were primarily interested in looking at sedimentation rates since Bayesian age-depth models such as Bacon require well informed priors to produce accurate estimates of deposition times.  I talked about this paper earlier on this blog in the context of providing open data along with attachments.  Having said that, the publication itself is not open. Continue reading New Paper: Sedimentation rates across space and time in Eastern North America

Choosing the right acronym for your project.

In my first thesis publication I propose a method for pollen-based climate reconstruction using non-metric multidimensional scaling and generalized additive models, called (clunkily) NMDS/GAM.  Follow this up with a talk by Jim Ramsay where he discussed the fact that Functional Data Analysis isn’t really an accurate title, but it’s catchy.  He (jokingly?) made the point that if you want people to use your method you need to come up with a good name for it. Continue reading Choosing the right acronym for your project.

It’s not the Rolling Stone, but it’s a cover nonetheless.

Our Garry oak paper made the cover of Environmental Management, although strangely the journal homepage still has last issues’ cover up, so just trust me on this one. Continue reading It’s not the Rolling Stone, but it’s a cover nonetheless.