Who is a Scientist – Reflections on #AAG2016

This is the first time I’ve really been to the American Association of Geographers meeting. Last year it was held in Chicago, which is really close to Madison, and I was invited to speak at a session called “The View from the Anthropocene” organized by two great Geographers from the University of Connecticut, Kate Johnson and Megan Hill, but I had the kids & really only spent the morning there.  I’m pretty sure there was another reason as well, but I can’t remember what it was.

It was great to see Kate & Megan again this year, both of them are doing really cool stuff (check out their web pages), and it was really great to see that the momentum behind the original idea was enough to re-tool the session into the Symposium on Physical Geography at this year’s AAG meeting in San Francisco, with Anne Chin of UC-Denver on the organizing committee, and a host of fantastic speakers.

My own presentation in the session focused on the Anthropocene, and its role as both a boundary (whether you want to define it as an Epoch sensu stricto or as a philosophical concept – I think that Stanley Finney & Lucy Edward’s article in GSA Today nicely lays out the arguments) and a lens.  The second part of that equation (the lens) is a more diffuse point, but my argument is that the major changes we see in the earth system can impact our ability to build models of the past using modern analogues, whether those be climatic, or biological.  I show this using pollen and vegetation records from the Midwest, and make the connection to future projections with the example laid out in Matthes et al. (2015), where we show that the pre-industrial climate niche of plant functional types used in GCMs as part of the CMIP5 intercomparison are not better than random when compared to actual “pre-settlement” vegetation in the northeastern United States.

But I really want to talk about a single slide in my talk.  In the early part of my talk I use this slide:

MGDavisSlide

This is Margaret Davis, one of the most important paleoecologists in North America, past-president of the ESA [PDF], and, importantly, a scientists who thought deeply about our past, our present and our future.  There’s no doubt she should be on the slide.  She is a critical piece of our cultural heritage as scientists, an because of her research, is uniquely well suited to show up in a slide focusing on the Anthropocene.

But it’s political too.  I put Margaret Davis up there because she’s an important scientist, but I also chose her because she’s an important female scientist. People specifically commented on the fact that I chose a female scientist, because it’s political.  It shouldn’t be.  There should be no need for me to pick someone because of their gender, and there should be no reason to comment on the fact that she was a female scientist.  It should just “be”.

Personal actions should be the manifestation of one’s political beliefs, but so much of our day to day life passes by without contemplation.  Susanne Moser, later in my session, talked about the psychological change necessary to bring society  around to the task of reducing CO2, of turning around the Anthropocene, or surviving it, and I think that the un-examined life is a critical part of the problem.  If we fail to take account of how our choices affect others, or affect society then we are going to confront an ugly future.

Everything is a choice, and the choices we make should reflect the world we want for ourselves and for the next generations. If our choices go un-examined then we wind up with the status quo.  We wind up with unbalanced panels, continued declines in under-represented minority participation in the physical sciences, and an erosion of our public institutions.

This post is maybe self-serving, but it shouldn’t have to be.  We shouldn’t have to look to people like DN Lee, the authors of Tenure She Wrote, Chanda Prescod-WeinsteinTerry McGlynn, Margaret Kosmala, Oliver Keyes, Jacquelyn Gill and so many others who advocate for change within the academic system, often penalizing themselves in the process.  We should be able to look to ourselves.

Okay, enough soap-boxing. Change yourselves.

Semantics Shememantics

In science we work, more often than not, in teams.  Whether we work with one other individual, five individuals, or interact at workshops with hundreds of strangers, it’s important that we are clearly understood.  Clarity is critical, especially when explaining complex concepts.  KISS is my second favorite acronym, even if I can’t keep to the principle (NEFLIS, a camping acronym, is my favorite – No Excuse for Living in Squalor just because you’re out in the woods).

A recently funded project I’m working on, under the aegis of EarthCube, is the harmonization of the Neotoma Paleoecological Database and the Paleobiology Database. Neotoma is a database of Quaternary fossils (mammals and microfossils such as pollen and ostracodes), and the Paleobiology Database is a database of every other kind of fossil. Both are incredible repositories for their respective communities, and powerful research tools in their own right.  My Distinguished Lecture talk at the University of Wisconsin’s Rebecca J. Holz Research Data Symposium was about the role of Community Databases in connecting researchers to Big Data tools, while getting their data into a curated form so that others could easily access and transform their data to undertake innovative research projects.

Superman Card Game by Whitman (1978) - G by andertoons, on Flickr
Figure 1. Semantic differences can be kryptonite for a project.  Especially a project that has very short arms relative to the rest of its body like Superman does in this picture. [ credit: andertoons ]
Our recent joint Neotoma-PBDB workshop, in Madison WI, showed me that, even with such closely allied data and disciplinary backgrounds, semantics matter.  We spent the first morning of the meeting having a back and forth discussion, where it kept seeming like we agreed on core concepts, but then, as the conversations progressed, we’d fall back into some sort of confusion.  As it began to seem unproductive we stepped back and checked in to see if we really were agreeing on core concepts.

While both databases contain fossil data, there is a fundamental difference in how the data are collected.  Typically Paleobiology DB data is collected in isolation, a fossil whale, discovered & reported is more common than a vertical stratigraphic survey on a single outcrop at a specific Latitude and Longitude.  In Neotoma, so much of our data comes from lake sediment cores that it makes sense that much of our data (and data collection) is described from stratigraphic sequences.

This difference may not seem like much, especially when the Holocene (the last 11,700 years) is basically an error term in much of the Paleobiology Database, but it’s enough of a difference that we were apparently agreeing on much, but then, inexplicably, disagreeing on followup discussions.

This is one of the fundamental problems in interdisciplinary research. Interdisciplinarity is as much understanding the terms another discipline uses as it is understanding the underlying philosophy and application of those terms in scientific discourse.  Learning to navigate these differences is time consuming, and requires a skill set that many of us don’t have.  At the very least, recognizing this is a problem, and learning to address this issue is a skill that is difficult to master.  It took us a morning of somewhat productive discussion before we really looked at the problem.  Once addressed we kept going back to our draft semantic outline to make sure we knew what we were talking about when discussing each other’s data.

This is all to say, we had a great workshop and I’m really looking forward to the developments on the horizon.  The PBDB development team is great (and so is the Neotoma team) and I think it’s going to be a very fruitful collaboration.

See you at #AGU2015

I’m heading to AGU early this year, part of the Neotoma Annual Meeting at Berkeley.  We’ve recently been awarded an NSF EarthCube Integrated Activities award to harmonize Neotoma and the Paleobiology Database (and other allied paleobiological archives), but we’ve also made some big gains in working with allied Plio-Pleistocene databases and researchers across the globe in adding to Neotoma’s already considerable data holdings.

I’m looking forward to the upcoming Neotoma meeting. One very exciting development is our partnership with the University of Wisconsin’s Library System.  We’ve been working toward providing data contributors with persistent Digital Object Identifiers (DOIs) for their contributions.  Our work with the UW Library System has seen a new contract established between the UW Libraries and DataCite, which gives us access not only to DOI minting, but also new connections to a set of established metadata standards and a robust API for minting DOIs, editing metadata and searching for contributions.

My own poster [GC11E-1065] goes up on Monday Morning (so get registered early!) as part of the Dating the Anthropocene session.  There was a great paper in Eos in the last issue (What is the Anthropocene? by L. Edwards) that lays out some options for ways in which geoscientists might treat the Anthropocene.  My work in the Upper Midwestern United States leads me to believe that there is a clear and persistent signal of human agency on the landscape, but it’s time transgressive, and it varies.  It was nice to see Edwards point to some of the pioneering work by the great Canadian palynologist Jock McAndrews, but the signal of EuroAmerican settlement is so broad it clearly represents a state change (see our pre-print here, now in review), as opposed to the signal of earlier human land use, nicely reviewed in Munoz et al (2014).  If you want to talk about it, come find me on Monday!

Jack Williams will be presenting some of the work we’ve been doing with Neotoma with his poster on Tuesday afternoon in the poster session [IN23B-1731] for Facilitating Open Science and Data through Scientist Engagement and Evolving Technology.

WilliamsPoster

Alan Ashworth is also talking about Neotoma in another presentation on Tuesday from 9:15 – 9:30 in the Agile Curation, Data Access and Infrastructure, and Data Layers session.  This, incidentally, is a session that I am convening, along with Denise Hills of the Alabama Geological Survey and Marjorie Chan of the University of Utah, the two chairs of the EarthCube Engagement Team.  I am also convening the Facilitating Open Science through Engagement and Evolving Technology poster session on Tuesday afternoon.  Some great opportunities to find out about both EarthCube sponsored open data initiatives & the broad range of data and science platforms that are being developed.

So, once again, a very busy AGU for me, and I haven’t even mentioned Kevin Burke’s great poster on Monday morning.  Having finished his M.Sc Kevin is on to more great work modeling the influence of changing wind fields on our ability to reconstruct past vegetation from pollen data.

Hope to see you at AGU, I’ll be there from Friday to Wednesday, so if you’d like to get in touch, let me know!

The interdisciplinary study of organic walled microfossils: A ramble.

Figure 1.  That's really a lot of pollen.  A lot of pollen.  Image by Brooke Novak
Figure 1. That’s really a lot of pollen. A lot of pollen. Image by Brooke Novak

It’s no secret to members of the Canadian Association of Palynologists (join now!) that the study of organic-walled microfossils is the most interesting branch of science, but it may come as a surprise to some of our colleagues. The thing is, our colleagues all have their own opinions. If they’re in biology departments they probably like bears; geology, they probably like different kinds of gravel; geography, obviously they like the names of rivers and knowing where towns and cities are.  The reality of being a palynologist is that you’re often working in a department that specializes in something that isn’t palynology. From time to time this can be a curse, but it’s also a very exciting opportunity.

This year I had the pleasure of attending both the Ecological Society of America meeting and the Geological Society Meeting, both of which were held in Baltimore, Maryland (39.2833° N, 76.6167°W for the Geographers).  At both meetings I co-chaired a session titled “Paleoecological patterns, ecological processes, modeled scenarios: crossing temporal scales to understand an uncertain future”. The sessions highlighted the applications of paleoecology to understanding the processes of ecological and geophysical change across decadal to millennial time scales.

It really is a testament to palynologists (and paleoecologists more broadly) that neither session felt out of place in either ESA or GSA. The nature of the problems we address through our research rely on the integration of ecological knowledge and geophysical process.  Both sessions had impressive contributions from early-career researchers and established researchers, and both sessions pointed to new and unexplored avenues of research. Both sessions also showcased a bit of the flavor of the meetings themselves.  The ESA talks focused more on ecological processes, the accumulation of carbon in ecosystems, forest cover change and regional dynamics, and change within ecological systems.  At the GSA meeting there was a much heavier imprint of climate and deeper time scales.

In recent years paleoecology has become more visible to ecologists as they have begun to tackle the complex problems of predicting community change under various climate change scenarios.  At the same time, questions of carbon dynamics, vegetation-atmosphere feedbacks, and other large scale questions of relevance to geoscientists have increasingly drawn from the knowledge of paleoecologists and palynologists.  Of course, there is a long tradition of paleoecologists contributing significantly to interdisciplinary sciences. Palynologists have been using their unique view of the earth system over long time scales to help frame our understanding of the Earth’s past as far back as von Post (see Conway’s overview of von Post’s work in the New Phytologist).

Figure 2. Group photo from the First International Conference on Palynology. Palynologists have made great strides in improving gender parity since this time, but Margaret Davis is visible front center. [link from PALYNOS]
Palynology is great precisely because the people studying it continue to pursue innovative and exciting research that borrows strongly from our history as a deeply interdisciplinary discipline.  It is this interdisciplinary history that allows us to present our work to Foresters, Ecologists, Geologists, Climatologists, or Oceanographers. We have to be a little bit of all of these in order to make sense of the microscopic organic-walled microfossils that we see dancing under the microscope. [note: if they really are dancing you should cut down on the silicone oil]

Helping to fill the cloud from the bottom up.

Open data in the sciences is an aspirational goal, and one that I wholeheartedly agree with. The efforts of EarthCube (among others) to build an infrastructure of tools to help facilitate data curation and discovery in the Earth Sciences have been fundamental in moving this discussion forward in the geosciences, and at the most recent ESA meeting saw the development of a new section of the society dedicated to Open Science.

One of the big challenges to open science is that making data easily accessible and easily discoverable can be at odds with one another.  Making data “open” is as easy as posting it on a website, but making it discoverable is much more complex.  Borgman and colleagues (2007) very clearly lay out a critical barrier to data sharing in an excellent paper examining practices in “habitat ecology” (emphasis mine):

Also paradoxical is researchers’ awareness of extant metadata standards for reconciling, managing, and sharing their data, but their lack of use of such standards. The present dilemma is that few of the participating scientists see a need or ability to use others’ data, so they do not request data, they have no need to share their own data, they have no need for data standards, and no standardized data are available. . .

The issue, as laid out here, is that people know that metadata standards exist, but they’re not using them from the ground up because they’re not using other people’s data.  Granted this paper is now eight years old, but, for the vast majority of disciplinary researchers in the geosciences and biological sciences the extent of data re-use is most likely limited to using data tables from publications, if that. [a quick plug, if you’re in the geosciences, please take a few minutes to complete this survey on data sharing and infrastructure as part of the EarthCube Initiative]

So, for many people who are working with self-styled data formats, and metadata that is largely implicit (they’re the only ones who really understand their multi-sheet excel file), getting data into a new format (one that conforms to explicit metadata standards) can be formidable, especially if they’re dealing with a large number of data products coming out of their research.

Right now, for just a single paper I have ten different data products that need to have annotated metadata.  I’m fully aware that I need to do it, I know it’s important, but I’ve also got papers to review and write, analysis to finish, job applications to write, emails to send, etc., etc., etc., and while I understand that I can now get DOIs for my data products, it’s still not clear to me that it really means anything concrete in terms of advancement.

Don’t get me wrong, I am totally for open science, all my research is on GitHub, even partial papers, and I’m on board with data sharing.  My point here is that even for people who are interested in open science, correctly annotating data is still a barrier.

How do we address this problem? We have lots of tools that can help generate metadata, but many, if not all, of these are post hoc tools. We talk extensively, if colloquially, about the need to start metadata creation at the same time as we collect the data, but we don’t incentivise this process.  The only time people realize that metdata is important is at the end of their project, and by then they’ve got a new job to start, a new project to undertake, or they’ve left academia.

Making metadata creation a part of the research workflow is something I am working toward as part of the Neotoma project. Where metadata is a necessary component of the actual data analysis.   The Neotoma Paleoecological Database is a community curated database that contains sixteen different paleoecological proxies, ranging from water chemistry to pollen to diatoms to stable isotope data (see Pilaar Birch and Graham 2015). Neotoma has been used to study everything from modern patterns of plant diversity, rates of migration for plant and mammals, rates of change in community turnover through time, and species relationships to climate.  It acts as both a data repository and a research tool in and of itself.  A quick plug as well, the completion of a workshop this past week with the Science Education Resource Center at Carleton College in Minnesota has resulted in the development of teaching tools to help bring paleoecology into the classroom (more are on their way).

Neotoma has a database structure that includes a large amount of metadata.  Due in no small part to the activities of Eric Grimm, the metadata is highly curated, and, Tilia, a GUI tool for producing stratigraphic diagrams and age models from paleoecological data, is designed to store data in a format that is largely aligned with the Neotoma database structure.

In designing the neotoma package for R I’ve largely focused on its use as a tool to get data out of Neotoma, but the devastating closure of the Illinois State Museum by the Illinois Governor (link) has hastened the devolution of data curation for the database. The expansion of the database to include a greater number of paleoecological proxies has meant that a number of researchers have already become data stewards, checking to ensure completeness and accuracy before data is uploaded into the database.

Having the R package (and the Tilia GUI) act as a tool to get data in as well as out serves an important function, it acts as a step to enhance the benefits of proper data curation immediately after (or even during) data generation because the data structures in the applications are so closely aligned with the actual database structure.

We are improving this data/metadata synergy in two ways:

  1. Data structures: The data structures within the R package (detailed in our Open Quaternary paper) remain parallel to the database.  We’re also working with Mark Uhen, Shanan Peters and others at the Paleobiology Database (as part of this funded NSF EarthCube project) and, elsewhere, for example, the LiPD Project, which is itself proposing community data standards for paleoclimatic data (McKay and Emile-Geay, 2015).
  2. Workflow: Making paleoecological analysis easier through the use of the R package has the benefit of reducing the ultimate barrier to data upload.  This work is ongoing, but the goal is to ensure that by creating data objects in neotoma, data is already formatted correctly for upload to Neotoma, reducing the burden on Data Stewards and on the data generators themselves.

This is a community led initiative, although development is centralized (but open, anyone can contribute to the R package for example), the user base of Neotoma is broad, it contains data from over 6500 researchers, and data is contributed at a rate that continues to increase.  By working directly with the data generators we can help build a direct pipeline into “big data” tools for researchers that have traditionally been somewhere out on the long tail.

Jack Williams will be talking a bit more about our activities in this Middle Tail, and why it’s critical for the development of truly integrated cyberinfrastructure in the geosciences (the lessons are applicable to ecoinformatics as well) at GSA this year (I’ll be there too, so come by and check out our session: Paleoecological Patterns, Ecological Processes and Modeled Scenarios, where we’re putting the ecology back in ge(c)ology!).

People, climate, fire. The Future meets the Past, and decides it wants to do its own thing.

I’ve been very lucky to work with great co-authors over the past few years, and this year is no exception. Along with a raft of papers we are about to submit I just got notified that a paper we submitted a few months ago is now online in the Annals of the Association of American Geographers (journal title chosen in the pre-Twitter age, obv.).

This paper, with Megan Walsh, Jenn Marlon, Dan Gavin and Kendrick Brown (and also me!) is a great look at fire records from the Pacific Northwest (PNW) over the last 5000 years. This time period is particularly critical to understanding human-climate-fire relationships. Human populations over the last 5000 years were increasing in the region, and climate was shifting, gradually cooling and becoming more moist following the early Holocene xerothermic period.

Figure 1. Wildfires burn in the Pacific Northwest, even with its reputation as a wet region. In the past, as today, humans likely played a role, along with climate. Image from Wikimedia Commons.
Figure 1. Wildfires burn in the Pacific Northwest, even with its reputation as a wet region. In the past, as today, humans likely played a role, along with climate. Image from Wikimedia Commons.

The challenge is that the PNW is an incredibly heterogeneous region. You can hike nine kilometers and shift from dry valley bottom to an alpine peak. Most of the climatic gradients are more homogeneous on the NS axis than they are on the EW axis.  The more critical problem is that, in a more general sense, human activity, on a landscape scale, is very difficult to detect or attribute prior to widespread EuroAmerican colonization (see Sam Munoz‘s excellent paper here).

Our paper comes out at a particularly important time.  We’ve seen an incredible fire season in the Pacific Northwest this year, driven in part by very dry conditions, both during the summer, but, more importantly by low snow packs in the winter.  Knowing that past fire regimes in the region increased, even as temperatures cooled through the late Holocene, has serious implications for the future.  Biomass stocks in the PNW remain high (even following widespread logging), and the open fire-dominated forests that were adapted to warmer drier conditions of the early Holocene (mostly Douglas fir-dominated) are no longer established in the region.

We may be burning ourselves to a new ecological baseline.

Amy Hessl, who was a co-convener on our fantastic ESA session this year (link), has a nice paper in Ecological Applications from 2004 linking the Pacific Decadal Oscillation to fire activity in the PNW interior (here) based on a set of fire scar data, so changing the intensity and frequency of these climatic systems is certainly going to shift our frequency and intensity.  Wimberly and Liu (2014) support the idea that management focused on reducing biomass on the landscape (prescribed burning and thinning) will help counter increasing fire severity and frequency, suggesting that management may be the key in transitioning to a warmer, drier future, and the key to understanding what these future forests might look like.

Fire in the early Holocene resulted in forests on the north shore of Vancouver with much higher proportions of Douglas fir pollen than are found in many modern day sites (see Marion Lake on the Neotoma Explorer – here, and check out the “Diagram” tab).  Douglas fir is not a heavy pollen producer, and yet it reached almost 20% of the pollen sum, along with higher proportions of Alder and Bracken fern, a fire-adapted fern.  Currently these taxa are found in low proportions throughout the PNW, except in regions with very low rainfall, and historically low fire return intervals, and proportions of Douglas fir over 20% are almost entirely restricted to southern Vancouver Island in British Columbia, although there may be higher proportions in the US.

Are we heading to a new, old baseline?  

Figure 2. You don't like prescribed burns? Why not? Image from Wikimedia commons.
Figure 2. You don’t like prescribed burns? Why not? Image from Wikimedia Commons.

It’s unlikely that we’ll see fire return intervals as high as we’ve seen in the past.  Active fire management will certainly keep fire activity lower than in the Holocene record because we put so much effort into countering large-scale fire.  The interesting thing to me is the idea that we’ll be managing these landscapes for fire, so we’ll have aspects of forest structure that map onto historical forests well: more open canopies, lower biomass, fire tolerant species, but, because of political volatility of prescribed burning, we are likely to see some fire tolerant species absent from the landscape, particularly understory species that we are unlikely to manage.  This might lead to novel species assemblages, with fire tolerant canopy species, and less tolerant understory species.  The result of a “fire adapted” landscape that has arisen as the result of active management in the absence of fire.  Planting, thinning, and continued management, without the presence of fire.

This maps well to what we’ve seen in the Georgia Basin, the encroachment of Scotch Broom into what has historically been Garry Oak Savanna.  We have open canopies, a shrub layer of highly flammable, introduced and invasive species, but still the structural attributes of a savanna landscape, minus grasses, so, uh, well, not exactly savanna.  But that’s fine, because I said there was no real analogue, so QED.  This post is too long anyway🙂

ESA 2015 – On the way to a new century!

I’m involved in a Plenary Workshop this year, organized by some great folks at UNC-Chapel Hill.  I’m privileged to have been asked by these students, al of whom are currently Ph.D candidates.  They’ve taken a great idea and turned it into something that will be an excellent Plenary Session, with some (hopefully) long lasting impact.  Given the subject (the future of interdisciplinary ecology) it’s also perfectly well suited to the centennial ESA meeting.  They’ve just posted this to ECOLOG so I wanted to share it here, since many of my readers are likely involved in interdisciplinary research themselves.

Dear members and friends of the Ecological Society of America (ESA): This survey is relevant to all ecologists, especially those engaged in interdisciplinary research. In celebration of the Centennial of ESA, a team of doctoral students at UNC Chapel Hill are conducting a study to assess the state of interdisciplinary research and scholarship inside and outside of the academy (IRB #15-0821). The results of this study will be shared at an upcoming workshop convened as part of the 100th Meeting of the Ecological Society of America. Results are intended to help workshop organizers identify the challenges and rewards that interdisciplinary ecologists encounter. Click here for more information about this ESA Plenary Workshop and how you can still register (Aug 8th @ 306 Baltimore Convention Center). We welcome participation from ecological researchers at all career levels.

This online survey will take 15 minutes to complete. The survey link will remain active until July 15, 2015. Your participation is completely voluntary and confidential. Keep in mind that no compensation is provided. Your confidential feedback will be used for a peer-reviewed publication and shared widely with the global community of ecologists. Research methods are in full compliance with IRB policies regarding confidentiality and research ethics of the University of North Carolina at Chapel Hill. Please contact Principal Investigator Clare Fieseler for further questions or comments about the survey (link to Ecolog post with contact information)

ANONYNMOUS LINK TO SURVEY

Clare Fieseler PhD Candidate & Principal Investigator
Sierra Woodruff CEE PhD Candidate & Co-Investigator
Dennis Tarasi PhD Candidate & Co-Investigator