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.

The Palynological Databases workshop at the AASP meeting in San Francisco, October 19 – 20.

This year there is a mega-meeting (relatively) of paleo-societies in San Francisco.  This is the 46th annual meeting for the Palynological Society (AASP-TPS), but also the annual meeting for Dino10, the Canadian Association of Palynologists (CAP), the North American Micropaleontology Section of SEPM (NAMS), and Commission Internationale de la Microflore du Paléozoïque (CIMP).

At this meeting I’ll be working with Eric Grimm and Simon Brewer to help run a workshop on the use of paleoecological databases in quantitative research.  In particular we focus on the Neotoma Paleoecological Database, and the package neotoma for R.  I’ve been revising the package since I first publicized it here, and it does some really amazing things now , so it would be great to train people to use it (particularly early-career researchers!) and get feedback for improvement. Continue reading The Palynological Databases workshop at the AASP meeting in San Francisco, October 19 – 20.