Serendipitous Lessons in Data Management

In a previous blog post I mentioned a document I’ve been spending a lot of time with, a technical manual for collecting and processing plankton samples, that was sent to me by our Russian colleagues. I was translating the manual searching for crucial information Derek needed to do some particular analyses. Unfortunately my Russian skills are not so advanced that I can easily skim a text and get the gist of it so I needed to translate the entire thing, and along the way I realized that I was engaged in a task that had much greater meaning that what I initially set out to do.

Part of my job as the information manager for this project is to ensure that anyone who might be interested in our data can access and understand them. This means keeping the data well organized, storing data in non-proprietary formats, and keeping exhaustive metadata (among other things). Effective data management is critical in any large collaborative project, and particularly one that has such a long history.

So, I started thinking of my work on this sampling protocol as an aspect of data management. The document was a wealth of information. I had received the document as a zipped folder of a bunch of low-resolution jpeg scans of the original document, and in the process of translating the whole thing I’d also first transcribed the Russian version. So in the end in addition to creating a version of the text that non Russian speakers can read I also produced two documents that are much more convenient to deal with than the original images (by having searchable text, for example). Our Russian colleagues will have both an English-language and a Russian-language version that they can use internally and share with new colleagues in the future. I have really enjoyed knowing that this work – so critical to us right now on the Dimensions project – also will have positive benefits for our Russian colleagues for years to come.

Ruminations on Time-Squared

Star Trek Guys by Matthew Sheean (CC-BY-NC 2.0)

No, not the Star Trek episode, sorry.

Apparently there is a Star Trek episode called “Time Squared” which I only know because I’ve been looking to see how other people explain why time series analysts sometimes use both “Time” and “Time Squared” to fit seasonal effects in their models. And most of the initial Google hits are for Star Trek.

(I’m not above placing a little Star Trek graphic here though, just to scratch that itch.)

Derek, Steve and I put a lot of effort into thinking about how to account for season in time series modeling, on the Baikal Dimensions project and many others.

Adding the variables Time (e.g., months 1, 2, 3 …) and Time Squared (e.g. months 1, 4, 9 …) to a linear model is one of the common ways that a seasonal pattern can be accounted for when you are trying to understand the drivers of some phenomenon that varies in at least a semi-predictable way annually. e.g., more bugs in the summer, more leaves falling in the autumn, or more crocuses blooming in the springtime. (Not the band Krokus, they are year-round.)

Useful resource for those who might speak about Baikalsk pulp mill

Bird’s eye 360°-view of Baikalsk pulp mill, clickable, with explanations (in Russian) of the technological cycle, pollution control devices, etc. Useful if you want to talk about the pulp mill in a lecture.

http://ria.ru/infografika/20130426/934048210.html

A reminder of the important contributions of history to ecological research

I was reminded this week of the importance considering historical events when trying to understand long-term ecological changes. One of the surprising results from our analysis of the amazing long-term Baikal data set has been that many zooplankton species are shifting to shallower positions in the water column through time (see my previous post). There could be many explanations for this, but we think that changes in fish predation could be particularly important. Zooplankton typically migrate to deeper water during the daylight hours to avoid predation by planktivorous (plankton-eating) fish. If fish populations have changed through time then perhaps zooplankton have altered their vertical migration behaviour? Although we do not have long-term data on fish populations in Lake Baikal, we might be able to gain some insight into changes in the abundance of fish by looking at the history of fishing and fisheries management in Lake Baikal. Over the past week we have contacted a historian that has worked on this issue (Dr. Nicholas Breyfogle) and have done some of our own reading on the subject.

In general, it seems that fish populations dropped dramatically in the 1940s with the demands of World War II and the rapidly expanding use of drift nets in the lake. The most precipitous decline occurred after the building of the Irkutsk Dam in the 1950s and the rise of the water levels in Baikal that reduced spawning grounds. Since the 1960s and 1970s there have been efforts to reduce the amount of fishing in the lake, with a ban being imposed on omul (Coregonus migratorius) fishing between 1969 and 1977. It also seems that most commercial fishing on Baikal was halted when the Soviet Union collapsed in 1991.

While we might not be able to directly link these events to changes in the plankton, it is important to consider them as we try to understand the long-term changes occurring in Baikal plankton communities. Over the last few decades historical ecology has grown into an exciting, dynamic field and our study of plankton depth changes in Baikal provides one more example of why ecologists should know their history!

Baikal is not the only cold and beautiful lake being invaded by Daphnia galeata

I just received a thank you letter from New Zealand’s Marsden fund (for reviewing) along with their Update brochure. Its cover is below:

According to a Marsden-funded study by Ian Duggan et al of Univ. of Waikato, invasion of non-native species in experimental mesocosms is facilitated by low native species diversity.  Perhaps those of us who are interested in the creeping invasion of Daphnia galeata into Baikal’s species poor zooplankton should keep an eye on Ian’s work.

Parkes, SM; Duggan, IC. 2012. Are zooplankton invasions in constructed waters facilitated by simple communities?  Diversity And Distributions 18: 1199-1210.

More outreach in East Tennessee

Gave a lecture on “Biodiversity hotspots” in my Ecology class today. In which of course an important component was a ~20-min feature about Baikal and about our grant. My students are by far less cute than Larry’s, but did enjoy the lecture. Sad observation: East Tennessee students were able to answer the question “What is the most famous species flock in Great African Rift Lakes?” (cichlids), but were unable to answer the questions “What area in North America is famous as a biodiversity hotspot?” and “What endemic species flocks is it famous for?” (East Tennessee; salamanders, darters and unionid mussels).  How unpatriotic.

We had plans (and I think I mentioned it in BI) to create an exhibit “Biodiversity hotspots” with Baikal and MidAppalachia as features at our Gray Fossil Site Natural History Museum,  but there was management change since and I have not discussed it with the new leadership yet. There are some cool connections, most obvious being of course the fact that North American sculpins, including the black sculpin common in our rivers are a close outgroup to the Baikal endemic species flock.

BBC Radio 4 Highlights Lake Baikal Research

“An enormous drill crushes its way through a meter of ice covering Lake Baikal in southern Siberia. It’s the deepest lake on earth and alone contains 20% of the world’s liquid fresh water.”

With these words, spoken over the sounds of the drill itself boring into the ice, BBC Radio 4′s Costing the Earth begins a thirty minute program that details the work of our friends across the pond as they conduct their winter field work at Lake Baikal. I mentioned their work in a previous post, and now you can hear all about it in much more detail (or read about it on their blog).

The radio program covers the team’s research goals, sampling methods, and living conditions at the lake, as well as information about Lake Baikal itself and its environmental influences. It is well worth a listen, and it’s currently available here.