Quaternary Science . . . on Mars . . . three billion years ago.


Cross-posted from the Open Quaternary blog.

Originally posted on OpenQuaternary Discussions:

For a curious person, one of the great benefits of being a Quaternary researcher is the breadth of research that is relevant to your own research questions.  The recent publication of fifty key questions in paleoecology (Seddon et al., 2014) reflects this breadth, spanning a broad range questions that reflect human needs, biogeophysical processes, ecological processes and a broad range of other issues.  The editorial board of Open Quaternary also reflects this incredible disciplinary breadth.  To me it is clear that the Quaternary sciences is an amalgam of multiple disciplines, and, at the same time, a broadly interdisciplinary pursuit.  To be successful one must maintain deep disciplinary knowledge in a core topic, as well as disciplinary breadth across topics such as ecology, anthropology, geology (and specifically geochronology), and you need a good grounding in statistics and climatology.

One of the things that is not always quite as apparent is the breadth…

View original 700 more words

We’re reading the same paper, but we’re getting different messages.

Earlier I posted about an interesting paper by Jankó and colleagues in Geoforum about similarities and differences in citation patterns between the IPCC and the NIPCC.  It turns out I wasn’t the only one interested in it.

It was pointed out to me that Judith Curry, Watts Up With That and the Heartland Institute have all written posts about the paper.  Their key takeaway message seems to come from the fact that the citations between the two are similar, and that Jankó and co-authors include language that indicates that reflexively dismissing ‘skeptic’ arguments does a disservice to scientific advancement.  This does an injustice to Jankó and colleagues because it misrepresents what I believe is very interesting work into the underpinnings of scientific inquiry, particularly around climate change.  Much of the support Bast and Curry see in the paper comes from a single sentence, associated with a citation from a 2013 paper by Mayanna Lahsen.

My reading of the sentence:

But when we take the contrarian arguments seriously, there is a chance to bring together the differing views and knowledge claims of the disputing ‘interpretive communities’ (Lahsen, 2013b).

Is not to say that we need to accept their arguments as alternate fact, but to say that the reflexive dismissal of contrarian viewpoints limits our ability to engage and understand the contrarian viewpoint.  The paper itself “Anatomy of dissent: A cultural analysis of climate skepticism” certainly shows little support of skepticism. Mayanna Lahsen has done some excellent work understanding climate change denial (skepticism?) from a sociological/anthropological viewpoint.  Indeed, her arguments in the cited reference point more to the fact that scientists need to work harder to engage with skeptics in an effort to avoid cultural backlash.  She is not arguing that skeptics pose acceptable alternative models to anthropogenic climate change.  Take this sentence for “Anatomy of dissent” (the same paper cited by Jankó and colleagues):

To promote their agenda, powerful backlash actors have frequently adopted deceptive strategies to create the fictitious appearance of broad grassroots and scientific support.

Does this in any way suggest that we ought to be taking contrarian arguments seriously because they are valid?  No, we are being asked to take them seriously because by understanding their backgrounds and motivations we can begin to address the causes of backlash against climate science, and move forward toward solutions.

I argued in my last post that just because the IPCC and NIPCC use the same citations, they are not equally acceptable models for global climate and climate change.  Interestingly, just because Bast, Curry and I read the same paper doesn’t mean we came to the same conclusions either.

Working on the frozen finger!

This post also appears on the PalEON Blog.  There are some great posts there so check it out!

We’re at Camp PalEON this week.  It’s lots of fun and I think that the attendees get a lot out of it.  Effectively we’re trying to distill process associated with the entire seven year project into one week of intensive learning.  We teach probability theory, Bayesian methods, ecosystem modelling, dendrochronology, paleoecology and pollen analysis, age modelling and vegetation reconstruction to seventeen lucky early-career researchers in six intensive days (people were still plunking away at 11pm last night, our first day!).

We spend a lot of our time at the University of Notre Dame’s Environmental Research Center indoors looking at computers, but we had a very nice time yesterday afternoon.  I hung out on a raft with Jack Williams and Jason McLachlan, coring with a frozen finger.  The frozen finger is a special kind of corer, used to recover lake sediment that preserves the sediment stratigraphy in a much cleaner way than many other coring techniques.

Jack Williams and Jason McLachlan filling the core casing with ethanol so that the cold slurry conducts to the outer wall.

Jack Williams and Jason McLachlan filling the core casing with ethanol so that the cold slurry conducts to the outer wall. (photo credit: Jody Peters)

When using the frozen finger we fill the base of the corer with dry ice, and suspend the dry ice in ethanol to create an incredibly cold surface.  We then drop the casing into the lake sediment.  The sediment freezes to the surface of the core casing over the course of ten or fifteen minutes before we pull the corer back to the surface of the lake.  The freeze-corer (or frozen finger) is often used for ancient DNA studies (e.g., Anderson-Carpenter et al., 2011) since the freezing process helps stabilize DNA in the lake sediment until the core can be brought back to the lab and analyzed.

The sediment on the outside of the core casing  is peeled off carefully and wrapped before it is stored in a cooler of dry ice. (photo credit: Jody Peters)

The sediment on the outside of the core casing is peeled off carefully and wrapped before it is stored in a cooler of dry ice. (photo credit: Jody Peters)

Jason McLachlan and I are going to go sieve the sediment ourselves later this afternoon to give the workshop participants a chance to take a look at lake sediment, pick charcoal and find macrofossils later tonight.  Meanwhile everyone is hard-coding an MCMC model in R and, later today, learning about Midwestern Paleoecology.  All in all, it’s a great course and I’m happy to be involved with it for a second time.  Hopefully we’ll have some more posts, but in the meantime we’ve made the preliminary readings open to the public on our project wiki, and most of our R work is up and available on GitHub so that you can take a look and work along.

How do you edit someone else’s code?

As academics I like to think that we’ve become fairly used to editing text documents. Whether handwriting on printed documents (fairly old school, but cool), adding comments on PDFs, or using some form of “track changes” I think we’ve learned how to do the editing, and how to incorporate those edits into a finished draft. Large collaborative projects are still often a source of difficulty (how do you deal with ten simultaneous edits of the same draft?!) but we deal.

Figure 1. If your revisions look like this you should strongly question your choice of (code) reviewer.

Figure 1. If your revisions look like this you should strongly question your choice of (code) reviewer.

I’m working on several projects now that use R as a central component in analysis, and now we’re not just editing the text documents, we’re editing the code as well.

People are beginning to migrate to version control software and the literature is increasingly discussing the utility of software programming practices (e.g., Scheller et al., 2010), but given that scientific adoption of programming tools is still in its early stages, there’s no sense that we can expect people to immediately pick up all the associated tools that go along with them. Yes, it would be great if people would start using GitHub or BitBucket (or other version control tools) right away, but they’re still getting used to basic programming concepts (btw Tim Poisot has some great tips for Learning to Code in Ecology).

The other issue is that collaborating with graduate students is still a murky area. How much editing of code can you do before you’ve started doing their work for them? I think we generally have a sense of where the boundaries are for written work, but if code is part of ‘doing the experiment’, how much can you do? Editing is an opportunity to teach good coding practice, and to teach new tools to improve reproducibility and ease of use, but give the student too much and you’ve programmed everything for them.

I’m learning as I go here, and I’d appreciate tips from others (in the comments, or on twitter), but this is what I’ve started doing when working with graduate students:

  • Commenting using a ‘special’ tag:  Comments in R are just an octothorp (#), I use #* to differentiate what I’m saying from a collaborator’s comments.  This is fairly extensible, someone else could comment ‘#s’ or ‘#a’ if you have multiple collaborators.
  • Where there are major structural changes (sticking things in functions) I’ll comment heavily at the top, then build the function once.  Inside the function I’ll explain what else needs to be done so that I haven’t done it all for them.
  • If similar things need to be done further down the code I’ll comment “This needs to be done as above” in a bit more detail, so they have a template & the know where they’re going.

The tricky part about editing code is that it needs to work, so it can be frustratingly difficult to do half-edits without introducing all sorts of bugs or errors.  So if code review is part of your editing process, how do you accomplish it?

Don’t forget the Deevey Award!

NOTE:  ESA2014 is all wrapped up.  If you didn’t apply, you didn’t win!

If you are a graduate student, or have completed your Ph.D within the last 9 months, and you are attending this year’s ESA to present, don’t forget to apply for the Edward S. Deevey Award.  The Deevey Award is presented to the nominee with the best presentation in paleoecology at the annual ESA meeting (this year in Sacramento [thanks Hank]).

Edward Deevey was a major contributor to our understanding of lake systems through time and moved paleolimnology from a broadly qualitative to a quantitative science, contributing to the widespread use of 14C as a tool in modern paleoecological studies.  He was also the first to publish a pollen stratigraphy for northeastern North America (Deevey, 1939) as G. Evelyn Hutchinson‘s second Ph.D student.  From Yale, Deevey continued his distinguished career through multiple postings across the United States, at Yale, Rice, Woods Hole and elsewhere.

Figure 1.  The first pollen diagram for the northeastern United States, published by Edward Deevey in 1939.  It also looks like an early use of Comic Sans.

Figure 1. The first pollen diagram for the northeastern United States, from Connecticut.  Published by Edward Deevey in 1939. It also looks like some paleo-Comic Sans lettering

Deevey’s studies mark a major milestone in North American paleoecology, as they brought together both multi-proxy analysis and deep ecological understanding of lake systems, founded on a broad survey of both paleoecological and neoecological data.

More information on Deevey can be found from his National Academy of Sciences biography (here)

Past winners of the Deevey Award include PalEON members and contributors Jason McLachlan, Bob Booth (who has a great blog: Among the Stately Trees), and Sara Hotchkiss, and more recently Alex Ireland, Ryan Kelly and W. John Calder.

If you are a paleoecology grad student, or recent graduate and you will be attending ESA be sure to submit your application by August 1st.  You can email or send the completed application form (Word or PDF) and a copy of your abstract to the Deevey Award Committee Chair at Deeveyaward@gmail.com.

Good Luck!

What do citations tell us about the climate divide?

UPDATE:  An interesting turn of events has led me to write a follow-up to this post.

I came across an interesting article in Geoforum this past week:

Jankó, F., Móricz, N., & Papp Vancsó, J. (2014). Reviewing the climate change reviewers: Exploring controversy through report references and citations. Geoforum, 56, 17-34.

The authors are in the Faculty of Economics and the Faculty of Forestry at the University of West-Hungary, in Sopron, about an hour directly south of Vienna, Austria. They take an interesting quantitative and human geographic perspective of the use of citations in understanding the physical science basis of climate change from both scientific and skeptical perspectives. A number of bloggers have taken on the science in the NIPCC (Richard Telford has several posts on his blog), but this paper provides interesting insight into the human aspects of scientific report writing. As such the paper falls much more easily into human geography than it does the physical sciences it seeks to understand.

Figure 1.  Heartland's funders did not particularly like the comparison between climate science and the Unabomber. (image source: wikipedia)

Figure 1. Heartland’s funders did not particularly like the comparison between climate science and the Unabomber. (image source: wikipedia)

The issue of climate change is as much part of the domain of human geography as it is physical geography. In particular the dynamic of ‘skeptical’ backlash against the consensus of anthropogenic climate change is well worth studying.  Understanding resistance to scientific knowledge around climate change will be key to eventually moving forward with adaptation policies that can find broad acceptance.  The public self-reports as being less knowledgeable about climate change than it was in 2007 (Stoutenborough et al., 2014), and multiple, competing narratives are likely to play a role in that dynamic.

Lahsen (2013) points out that without examining the differences in perception between climate groups we risk making the science behind our current understanding of anthropogenic climate change more vulnerable to public backlash, and we frequently see interaction between place and social change within the organizations (Jankó et al. mention the impact of the grossly unpopular Unabomber billboard in Chicago on the Heartland Institute’s network of funders and climate change affiliates).

To study characteristics of resistance and acceptance of the science surrounding climate change, the authors review the citation lists of both the IPCC (AR4 – WG1, the Physical Science Basis) and the NIPCC ‘s Climate Change Reconsidered.  By examining similarities and differences in citations and the use of citations we can understand how the rhetoric around climate change science changes the interpretation of the published literature. Jankó et al. use a great quote from Bruno Latour to help guide the discussion:

Whatever the tactics, the general strategy is easy to grasp: do whatever you need to the former literature to render it as helpful as possible for the claims you are going to make. The rules are simple enough: weaken your enemies, paralyse those you cannot weaken […], help your allies if they are attacked, ensure safe communications with those who supply you with indisputable instruments […], oblige your enemies to fight one another […]; if you are not sure of winning, be humble and understated” (Latour, 1987, pp. 37–38).

Figure 2.  Citations are important, but they're rarely used in an impartial manner. (image source: wikipedia)

Figure 2. Citations are important, but they’re rarely used in an impartial manner. (image source: wikipedia)

I feel like this overstates the case for the IPCC a little bit (though I may be biased). The IPCC is not set up to directly combat ‘skeptical’ literature, as is the case of the NIPCC.  The NIPCC is explicitly structured to mirror and refute the IPCC.  Regardless, we often think that as researchers we use citations in a neutral manner, but I would argue that that’s rarely the case. Citations in the literature are selected to help bolster arguments, they’re selected because we know people, and they’re occasionally massaged to change the point of an argument in an effort to support our own.

So the question becomes, how is the literature used and modified in these summaries to help develop an agenda?

Interestingly Jankó et al. show that only 4.4% of total citations (IPCC + NIPCC) were used in both reports. This was surprising to me. I had expected that many of the primary sources to explain climate systems and their modern behaviour might have made up a much larger proportion of both reports. Jankó et al. include a table with analysis of many of the overlapping citations (Appendix B)and we see that most cases of duplicate citations show similar tone in the treatment of the citations. Differences do exist however.  Where there is extensive overlap in citations Jankó et al. have some very insightful points to make here.  One surprising point was that both reports use particular language around references they like (‘find’, ‘indicate’, ‘report’, ‘show’, ‘conclude’) and don’t like (‘claim’, and ‘contend’), although how the language is applied to individual citations varies between reports (the discussion of Tropical Cyclones is well worth a read).  The other main difference in these overlapping citations is that key NIPCC citations, challenging climate change are often found in the IPCC to support understanding of uncertainties.  Thus, what the IPCC sees as an uncertainty, the NIPCC sees as evidence against anthropogenic climate change.

The real issue that piqued my interest however was the much higher proportion of paleo-journals in the NIPCC literature.  The Holocene is cited 12 times more frequently in the NIPCC than in the IPCC,  Geology and Quaternary Research are both cited 10 times more often.  Why would skeptics cite paleoecological literature at higher rates than the IPCC?  In large part this is due to a key motivation for the NIPCC, and a particular focus in the paleoclimate sections.

The analytical goal of the NIPCC is to increase the perception of uncertainty, attempting to add more ‘non-supportive’ and ‘uncertain’ literature to the argument, and to use that increased uncertainty to take apart the arguments for anthropogenic climate change.  In this way the paleo-literature becomes a tool for skeptics with which to attack our understanding of climate change science.  Indeed, of the 18 references from the Holocene in the NIPCC, only one could be considered ‘Neutral’ while the other 17 were considered to be ‘Not Supporting’ of climate change science.  For Quaternary Research 2 citations were ‘Neutral’ and ’12 were ‘Not Supporting’.  Again, what might be considered uncertainty in the IPCC is considered evidence against in the NIPCC.

Figure 1.  Does showing climate has changed in the past prove that climate change is natural?

Figure 3. Does showing climate has changed in the past prove that climate change is natural?

Jankó et al. explain this trend by showing that the NIPCC uses the past to explain the present in such a way as to downplay the unprecendented nature of modern climate change, while the IPCC uses the past to search for analogues of modern climate change.  Effectively, the NIPCC view stops at the present:  The past was warmer, therefore change is not unprecedented.  The IPCC is searching for ways to explain the future: The past had warmer periods. What caused those changes, what happened  during those periods, and how can we use the past to constrain models for the future?

This, to my mind, is the difference between the camps.  The science marshaled in the IPCC is focused toward improving hypotheses and theoretical (and mechanistic) models.  It is prescriptive science in that uncertainties are identified, and used to improve our understanding of modern and future change.  In the ‘skeptical’ camp, science is marshaled to disprove anthropogenic causes, and when it does, the avenue of research is closed.  It is effectively a descriptive model without an overarching theoretical framework.  This allows it to attach the label ‘skeptical’ to disparate threads of knowledge across the literature, without having to concern itself with how those pieces join together.  Jankó et al. point out that the narrative style of the NIPCC report is structured around an anecdotal style, summarizing each paper individually and often adding textual quotes, while the IPCC synthesizes knowledge from multiple sources and provides block references for statements.  In one we see a descriptive format that highlights any contrary (or uncertain) position, in the other we see an effort to synthesize knowledge into a theoretical framework.

The scientific basis for anthropogenic climate change is strongly grounded in a fairly simple physical model that finds broad based theoretical support across a range of physical sciences.  The scientific community has shown that over time (since at least the 1970s), counter-examples and uncertainties found in the literature have been able to highlight weaknesses in our understanding, bu, rather than collapse the structure, these weaknesses have been marshaled to improve the science and to develop a much more robust scientific understanding of climate change.

Literature Cited

Idso, Craig Douglas, & Siegfried Fred Singer. 2009. Climate change reconsidered: 2009 report of the Nongovernmental International Panel on Climate Change (NIPCC). Nongovernmental International Panel on Climate Change.

Jankó, F., Móricz, N., & Papp Vancsó, J. (2014). Reviewing the climate change reviewers: Exploring controversy through report references and citations. Geoforum56, 17-34.

Jansen, E., J. Overpeck, K.R. Briffa, J.-C. Duplessy, F. Joos, V. Masson-Delmotte, D. Olago, B. Otto-Bliesner, W.R. Peltier, S. Rahmstorf, R. Ramesh, D. Raynaud, D. Rind, O. Solomina, R. Villalba and D. Zhang, 2007: Palaeoclimate. In: Climate Change 2007: The Physical Science Basis. Contribution of Working Group I to the Fourth Assessment Report of the Intergovernmental Panel on Climate Change [Solomon, S., D. Qin, M. Manning, Z. Chen, M. Marquis, K.B. Averyt, M. Tignor and H.L. Miller (eds.)]. Cambridge University Press, Cambridge, United Kingdom and New York, NY, USA.

Latour, B. (1987). Science in action: How to follow scientists and engineers through society. Harvard university press.

Lahsen, M. (2013). Climategate: the role of the social sciencesClimatic change119(3-4), 547-558.

Stoutenborough, J. W., Liu, X., & Vedlitz, A. (2014). Trends in Public Attitudes Toward Climate Change: The Influence of the Economy and Climategate on Risk, Information, and Public Policy. Risk, Hazards & Crisis in Public Policy,5(1), 22-37.