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:


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.

Reproducibility and R – Better results, better code, better science.

I made a short presentation for our most recent weekly lab meeting about best practices for reproducible research.  There are a few key points, the first is that the benefits of reproducible research are not just for the community.  Producing reproducible code helps you, both after publication (higher citation rates: Piwowar and Vision, 2013) but in the long run in terms of your ability to tackle bigger projects.

Lets face it, if you intend to pursue a career inside or outside of academia your success is going to depend on tackling progressively larger or more complex projects.  If programming is going to be a part of that then developing good coding practice should be a priority.  One way to get into the habit of developing good practice is to practice.  In the presentation (PDF, figShare) I point to a hierarchy (of sorts) of good scientific coding practice, reproducible programming helps support that practice:

  1. An integrated development environment (IDE) helps you organize your code in a logical manner, helps make some repeatable tasks easier and provides tools and views to make the flow of code easier to read (helping you keep track of what you’re doing)
  2. Version control helps you make incremental changes to your code, to comment the changes clearly, and helps you fix mistakes if you break something.  It also helps you learn from your old mistakes, you can go back through your commit history and see how you fixed problems in the past.
  3. Embedded code helps you produce clean and concise code with a specific purpose, and it help you in the long run by reducing the need to “find and replace” values throughout your manuscript.  It helps reviewers as well.  Your results are simply a summary of the analysis you perform, the code is the analysis.  If you can point readers and reviewers to the code you save everyone time.

So, take a look at the presentation, let me know what you think.  And, if you are an early-career researcher, make now the time to start good coding practice.

Guest post: What skills do you wish you learned? What skill should you impart?

Recently on CAGList, the mailing list for the Canadian Association of Geographers an early career researcher asked established researchers  what kind of training  they wish they had obtained as grad students and post-docs.  Alwynne Beaudoin, adjunct Professor at the University of Alberta, curator of Quaternary Environments at the Royal Alberta Museum and active member of the Canadian Association of Palynologists, posted an excellent reply.

I asked her if it would be okay to post it here (and she’s agreed), because I think it speaks to the heart of what many of us are beginning to realize:  Our ‘hard skills’ training is often excellent, but the soft skills that make our lives much more manageable and enjoyable, and can play a significant role in your career development both inside and outside academia.

Continue reading Guest post: What skills do you wish you learned? What skill should you impart?

Yi-Fu Tuan Lecture, February 15th.

UPDATE:  I have uploaded the slides of my Yi-Fu seminar to figshare, DOI: 10.6084/m9.figshare.157094.  If you have questions or comments about the presentation, please feel free to ask in the comments here or on figshare.  I’d be happy to discuss my work.

Once the presentation is done I’ll upload the slides here and to figshare so that people who aren’t able to attend can see the talk.  The talk will be at 3:30pm in Room 180 of Science Hall at the University of Wisconsin (550 N Park St).  This talk is part of the Yi-Fu Tuan (personal page here)  lecture series.

Using Historical Records to Help Predict the Future: The Public Land Survey, 19th Century Climate and the PalEON Project

Figure 1.  The shaded parts of Minnesota, Wisconsin and Michigan are my study region.  They will be the focus of my talk.
Figure 1. The shaded parts of Minnesota, Wisconsin and Michigan are my study region. They will be the focus of my talk.

Predicting the response of organisms to changing climates in the 21st century is a major conservation challenge.  Standard practice uses the relationship between modern species ranges and climate to predict future distributions under various future climate scenarios.  The widespread and significant land use conversion in North America, particularly in the upper Midwest, challenges the basic assumptions of this model.  I use historical records of vegetation and climate to build a better understanding of the state of forests in the upper Midwest prior to European settlement.  Pre-settlement forests show significantly different structure and composition than modern forests, and our interpretations of the kinds of climates that tree species can occupy is likely to be affected by the broad-scale changes brought about by agricultural conversion.  This analysis forms part of the broader PalEON project, and I will highlight how the information we gain from historical data can inform and improve our estimates of future climate change, species distributions and, ultimately help inform conservation planning in the 21st century.

My talk at the International Biogeography Society (January 12, 2012)

EDIT:  If you have any comments or questions about the presentation, I`d be happy to answer them in the comments below.

EDIT #2: Following the recommendations of several people on twitter I’ve also decided to upload my talk to Figshare, where it was assigned the DOI 10.6084/m9.figshare.106654 since uploading it yesterday it has had 218 views.  That’s more than the number of people who have viewed it on this blog, and far more than the number of people who saw it at IBS.  I’m a big fan of Figshare!

Figure 1. The kernel density of walnut species in the Upper Midwest shows clear shifts in July precipitation and temperature since settlement. These result from both land us change and shifts in the climate normals. The 95% CI are indicated by rectangles at the bottom of each plot.

I should be preparing my talk, but instead I’d like to attach my talk here just in case you can’t be there.  I’m presenting in the Biogeography of the Anthropocene session, which should be really great.  I’m looking forward to talks by Anthony Barnosky, Naia Morueta-Holme, Carolina Tovar, Kim Diver and Blaise Petitpierre all examining the changes in earth systems, biodiversity and species composition during the last 150 years and into the future, in an age that’s largely defined by the increasing fingerprint of human activity. Continue reading My talk at the International Biogeography Society (January 12, 2012)