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.

Announcing Open Quaternary


Open Quaternary is a new, fully open access journal dedicated to the Quaternary Sciences, published by Ubiquity Press (the Call for Papers is below) with very low publishing costs (£250, about $425USD).  The journal will cover a number of related disciplines, focusing on the Quaternary, including almost anything you can put “paleo” in front of (climate, botany, ecology), geomorphology, palynology, vertebrate and invertebrate palaeontology, zooarchaeology, geoarchaeology, biological anthropology and Palaeolithic archaeology. All papers are licensed under Creative Commons CC by 3.0 license and Open Quaternary actively encourages pre-publication of submissions “as it can lead to productive exchanges, as well as earlier and greater citation of published work”.

I was lucky enough to be invited to join the Editorial Board by the excellent team of Editors in Chief, Matthew Law (Bath Spa University), Suzanne Pilaar Birch (Brown University), and Victoria Herridge (Natural History Museum, UK). The Editorial board looks great too. A very diverse group of researchers, with a broad range of expertise and career stages represented.

Another nice aspect of the journal is the institution of double blind review. Emily Darling recently published an article in Conservation Biology supporting double blind review. She shows that journals with double blind reviews appear to have higher rates of publication for female lead authors and leverages recent work by Moss-Racusin et al. (2012) showing subtle, but distinct bias by academics against “Jennifer”s in academia . Encouraging diversity is a worthwhile goal for those of us in academia, and since publications remain a key metric for advancement, changes that encourage equality across gender and background should be supported. Until broader metrics of academic advancement are accepted (Goring et al., 2014) we need to support efforts to reduce advantages gained solely on the basis of sex or background.

Open Quaternary Editorial Board
Geoff Bailey, University of York; Canan Cakirlar, Groningen University; Bethan Davies, University of Reading; Ben Gearey, University College, Cork; Tom Gilbert, University of Copenhagen; Jacquelyn Gill, University of Maine; Simon Goring, University of Wisonsin-Madison; Seren Griffiths, Freelance/ Cardiff University; Erika Guttmann-Bond, Trinity St David, University of Wales; Tom Hill, Natural History Museum; Anson Mackay, University College London; John Marston, Boston University; Kirsty Penkman, University of York; Matthew Pope, University College London; Teresa Steele, University of California, Davis.


We are now accepting submissions for the 2014 launch of our new journal, Open Quaternary.

Open Quaternary is a fully open access, double-blind peer-reviewed journal, publishing contributions that consider the changing environment of the Quaternary as well as the development of humanity.

The editors are welcoming articles from a range of disciplines relating to Quaternary science. The broad scope of the journal covers a range of specialisms such as geomorphology, palaeoclimatology, palaeobotany, palynology, vertebrate and invertebrate palaeontology, zooarchaeology, geoarchaeology, biological anthropology and Palaeolithic archaeology.

The editors welcome submissions of Research, Methods, Reviews, and Engagement papers, as well as encouraging Data publications. Data can also be deposited in the journal’s Dataverse repository, allowing data to accompany research in a fully open format. For more information on data papers, click here.

Open Quaternary publishes one issue per year, with rapid publication as soon as articles are ready, to ensure that research is available as soon as possible. All submissions are thoroughly peer-reviewed to ensure that the highest standards are met.

Article Processing Charges (APCs) have been kept to a minimum to ensure that the journal can operate whilst sustainably remaining low cost and fully open access. The £250 APC is just 10-20% that of some competitors. We never expect authors to pay the APC, but that institutions or funding bodies will cover these costs. Your institution may already have a membership with the publisher to guarantee that funds are available. Full waivers are available for those without such funds available. For further details of the APC, please click here.

We accept online submissions via our journal website. See Author Guidelines for further information. Alternatively, please contact the journal editors for more information.

A pollen short course. The best way to spend early June!

This summer I will be working with Jacquelyn Gill and Andrea Nurse in beautiful Orono, Maine to deliver a workshop for researchers interested in using both modern and fossil pollen as part of their research. Pollen has a long and fantastic history in the scientific literature. It is used in biomedical, paleoecological, forensic, evolutionary, agricultural and nutritional research, but as with any specialized tool, pollen requires training to learn how to collect, process and analyze it properly. The workshop is supported by the Climate Change Institute at the University of Maine, and by the PalEON Project.

We will be leading participants through collection, processing and analysis of pollen, using both fossil and modern samples. We will be using R and some specialized tools to do the statistical analysis, and I’ll walk people through some of the newer features of Neotoma as part of the course. This is also an opportunity for early career researchers to make connections outside their home institutions with others who are engaged in the incredibly exciting world of palynological analysis! (I’m allowed to talk up my field right?)

One feature of this workshop that I’m really excited about are the evening mini-courses. These are focused on providing an introduction to early career researchers about topics that relate more to the sociology of science. What is open science? How do scientists use social media to improve outreach? How do I make the most of interdisciplinary collaboration?

If you’re interested in the course please feel free to contact any of us, and be sure to get your application in by April 15, 2014. We’re looking forward to seeing you!


GSA Sessions and Scholarship Information

I’ve been a member of the Canadian Association of Palynologists for several years now, both as a student member and now as a member of the Executive. We are a small society but we have been very active over the past few years, hosting sessions at various conferences and producing a great (open access!) newsletter (back-issues here). Alwynne Beaudoin (who you may remember from an earlier post here) has also curated a fantastic website for CAP.

One recent initiative has been the creation of a graduate scholarship. The deadline is coming up, so please consider submitting an application:

The Canadian Association of Palynologists Annual Student Research Award was established in 2009 to recognize students’ contributions to palynological research. The award is open to any undergraduate or graduate student who is a member, in good standing, of CAP, regardless of their nationality or country of residence. The intent of the research award is to support student research with a strong palynological component. The award consists of a three-year membership in the Association and $300 CDN, to be put toward some aspect of the student’s research.
The application should consist of: 1) a one-page statement outlining the nature of the research project, its scientific importance, the approximate timeline to completion of the project, and the aspect of the research the funds would be directed toward; (2) a CV; and, (3) a letter of support from the student’s supervisor.

Applications may be submitted in French or English and should be submitted by email. Completed applications are due by March 1.

Applications or questions concerning the award should be sent to the CAP President, Dr. Francine McCarthy (fmccarthy[at]brocku[dot]ca), by March 1 2014.

From the CAP Website

In addition to the scholarship, CAP is also hosting a session at GSA 2014 in Vancouver, BC. The session, titled “Palynology in Geoarcheological and Environmental Studies” is one of the technical sessions that you will be able to submit to this year. Please consider it when you submit your abstract this year (deadline is July 29th!).

Vegetation-­climate relationships using historical climate data from the 19th Century Forts & Observer Database, expanding species realized niches

I’m presenting this week’s CPEP seminar at the Center for Climatic Research, UW-Madison (1:00pm, AOSS room 1039, 1225 W. Dayton St., Madison, WI).  As before, I’ll post the slides once I get them done.  Much of the material will be similar to work I’ve presented at the IBS and in my Yi-Fu seminar, but I’ve been working hard with the 19th Century Forts database over the past little while, and doing some fun things with some AWOS data that I’ll hopefully have time to present.  As with all things paleo and historical, you really need to understand how the modern system works to begin to make inferences about the past that are meaningful.

Here is the talk abstract:

Historical data sets for both vegetation and climate exist, covering a time period prior to major land use conversion in the upper Midwestern United States.  We aim to improve information about species fundamental niches in climate space by extending gridded climate data products to the early 1800s so that they are coincident with early estimates of pre-settlement vegetation in the American Midwest.  Here I present work detailling the creation of the gridded data sets and their application to species distribution modelling to show the sensitivity of future suitability maps to added data from historical records.

UPDATE:  This presentation is similar enough to my Yi-Fu and IBS talks that I’m not going to put it up on figshare.

#IBS13 Wrap-up, refelections from Miami

IBS Logo
Figure 1. The International Biogeography Society is worth joining, if you haven’t already. Membership information is here.

The International Biogeography Society held its 2013 meeting at Florida International University in Miami, Florida.  The plenary speaker, Jim Brown, wrapped up the meeting with a talk on the latitudinal gradient of diversity, and our apparent inability to answer the question “Why are there more species in the tropics”. He made a great point during his talk, that I think is applicable to a number of ideas: There are multiple hypotheses about the latitudinal gradient of diversity, they are not generally exclusive, and the fact that the gradient is so ubiquitous across taxa and geographic regions indicates the fact that answering the question “Why?” shouldn’t require an overly complex solution (although it remains unsolved). Continue reading #IBS13 Wrap-up, refelections from Miami

PalEON Berkeley Workshop 2012 – Update

This is the one year anniversary of the blog (give or take a week), so this post is going to be a bit of looking back, and looking forward. It’s also about AGU, but since it’s only in passing, here is a link to RealClimate with a list of good climate related sessions.

Network model of the PalEON team.
Figure 1. The network that makes PalEON work. Blue points represent the PIs, linking the vegetation modellers (at the top of the figure), to paleoecologists and statisticians that make up the rest of the team. This was the structure of the team about a year ago.

We had a great day in Berkeley today. Lots of work to get done, but it’s amazing how far we have come collectively since our meeting a year ago in Chicago. The PalEON team has enlarged again, and there’s lots of new faces at the workshop. New post-docs, new collaborators, and a few visitors, dipping their feet into the PalEON waters. Along with Jason McLachlan, Mike Dietze, Steve Jackson, Jack Williams and Chris Paciorek, we’ve added new PIs, Dave Moore, Mevin Hooten, Phil Higuera, Neil Pederson and Jenn Marlon.

Continue reading PalEON Berkeley Workshop 2012 – Update

Some Bacon and a brief comic interlude. . .

So, my last post was the all time highest post at downwithtime, with 3000-some hits and counting.  Most of that traffic came from, which is a sort of link aggregator with a social component.  While it gets some press for some unsavoury behaviour from participants, it also has some nice communities for people interested in geography, geology, statistics and paleo-everything.   Worth checking out, but be forewarned, there’s a lot of chaff. Continue reading Some Bacon and a brief comic interlude. . .

Making ridiculous graphs.

I make some pretty terrible graphs, especially when I’m working out ideas.  It’s a really bad habit of mine.  You’d think I’d have learned to label my axes, add legends and all that jazz by now, but lets face it, when you’re coding down to the wire in time for a meeting. . . well, the axes don’t just label themselves informatively on their own.  R does of course label the axes by default, but seriously, what does dry.test$zonestuff vs. dry.test$pca.attempt tell anyone?  Well, it tells people you need to learn how to make informative variable names, but, aside from that.

With this in mind, I’d like to present a graph I made a while back, just after I switched into my Ph.D that was recently sent back to me by Elizabeth Elle at Simon Fraser University.  Continue reading Making ridiculous graphs.

Criticism when warranted, praise when deserved.

Storm clouds developing over a small pond in the Chilcotin
Figure 1. Ecological systems depend on objects that manifest across multiple scales. Macrosystems Ecology seeks to understand ecology at regional to continental scales, which means understanding process at each of these scales.

A quick post today to keep the posting flowing.  I’m currently working on a number of papers that are really interesting and <sarcasm>sure to be the most highly cited papers ever in the history of science</sarcasm>.  In particular the group of authors who met at the NSF Macrosystems meeting in Boulder in March (Dave Schimel has some great thoughts here on the NEON website) have been working on a set of papers discussing what exactly ‘Macrosystems Ecology’ is, how it is undertaken and what it might tell us.  The collaborators include some great researchers at all stages of their careers including Pat Soranno, Andrew Finley, Jim Heffernan and others. Continue reading Criticism when warranted, praise when deserved.