Some links: 102

  • People movers (mobile lounges) at IAD are sticking around for at least 20 more years. I like ’em. Remember to hold on for when the lounge starts to move! (Eurgkkh, lots of clickbaity slop on this local TV news channel page.)
  • Why did Tom Lehrer give up writing, recording, and performing? Francis Beckett doesn’t really answer this question, but he does offer a nice recap of Lehrer’s oeuvre for the younger folks.
  • Jason Kottke reprises this lovely post about flying in a small plane with his father in the upper Midwest. Low on fuel. With a thunderstorm approaching.

    But the thing was, I was never scared. I should have been probably…it was an alarming situation. I’d been flying with my dad my whole life and he’d kept me safe that whole time, so why should I start worrying now? That’s what fathers are supposed to do, right? Protect their children from harm while revealing the limits of the world?

  • When I visited the Westmoreland Museum of American Art last month, I noticed that several works were labelled “artist once known.” Here’s an explainer from the Hood Museum of Art for that new convention.

I haven’t really decided whether I will continue posting at IEFBR14. In the meantime, here are two computing/math links:

Some links: 81

Some links, Coffee and Birds Edition:

  • Jodi Helmer reports on the nascent coffee industry in California. Even in this non-tropical climate, at least one farmer is going the shade-grown route:

    Andy Mullins of Mullins Family Farm in Temecula… planted 1,000 coffee trees under the canopies of the avocado trees on his 4-acre farm.

  • A study from India by Charlotte H. Chang et al. indicates that coffee plantations given over to robusta supported nearly the same level of biodiversity as arabica farms, as summarized by the Wildlife Conservation Society.

Gut check

Javier A. Ceja-Navarro et al. suggest a novel means of controlling the coffee berry borer (Hypothenemus hampei), as summarized by The Economist. The authors provide evidence that one of the species of bacteria that reside in the beetle’s digestive system, Pseudomonas fulva, detoxifies the caffeine that the coffee plant produces as a natural herbivore deterrent. Knock out the bacterium, perhaps with a targeted bacteriophage, and you knock out the pest.

Works in the Old World, too

In the past, when I’ve posted about shade-grown, bird-friendly coffee (for instance, here, here, and here), the research focus (by scientists like Ivette Perfecto and Russell Greenberg) has been on Central American farms and neotropical migrants. New research indicates that birds in Africa and Eurasia also benefit from shade cultivation in Ethiopia (the cradle of all domesticated coffee), as Brian Clark Howard reports. Ethiopian coffee farmers are under the same pressures to convert to intensive “sun coffee” production that their New World counterparts face.

“Importance of Ethiopian shade coffee farms for forest bird conservation” is now in press. Co-author Cagan H. Şekercioğlu

suggests that the Smithsonian Migratory Bird Center or the Rainforest Alliance, which certify bird-friendly coffee from other countries, should consider extending their programs to Ethiopia. Certification allows farmers to recoup a price premium, which can help deter the impulse to convert farms to full sun or otherwise develop their land.

Some links: 71

Catching up on a lot of bookmarks, so this will be a bit of a link dump.

  • Reduced-meat or meatless diets (Mediterranean, pescetarian, vegetarian) are both better for your health and more sustainable for the environment, as David Tilman and Michael Clark find in a recent paper, and as Elke Stehfest summarizes.
  • I am loving Nature‘s new sharing tools. Susannah Locke explains the journal’s move toward more open access.
  • Emily Dreyfuss signed up to give Wikipedia six bucks a month.

    …Wikipedia is the best approximation of a complete account of knowledge we’ve ever seen.

    It’s also the most robust. The most easily accessed. And the safest. It exists on servers around the world so, unlike the library at Alexandria, it can’t be burned down.

    You should chip in, too.

  • The Biodiversity Heritage Library has opened an online exhibit dedicated to women in science who began working before 1922. Some of my recent subjects are there, including Florence Merriam Bailey and Mabel Osgood Wright.

Mixed effects

A recent paper by Jason M. Gleditsch and Tomás A. Carlo explores the impact on nesting success of Gray Catbirds (Dumetella carolinensis) breeding in Pennsylvania landscapes dominated by invasive Asian honeysuckles (Lonicera sp.). It turns out that they found little evidence to support the claim that honeysuckle represents an “ecological trap” of increased predation risk and poor nutritive value from fruits, contrary to the results of other researchers. Adult birds may have made more trips to the nest, bearing what some have called “junk food,” but body mass measurements of the nestlings, in this study, show that they grow up just fine.

Our results show that relationships between introduced fleshy-fruited plants and native birds are complex and not easily characterized as purely harmful or beneficial because they can include negative, neutral, or positive outcomes.

Sometimes, in the authors’ view, using an alien species is the best the birds can do, under the circumstances.

… the traditional and widespread categorical approach to invasive species management should be revised to prevent harming certain communities and ecosystems, especially areas in a process of self-recovery from heavy human disturbances.

Into the spotlight

Citizen science has an important role to play in research in a wide range of biological disciplines, as Caren B. Cooper et al. write in a recently-published paper in PLOS ONE:

… the quality of data collected by volunteers, on a project-by-project basis, has generally been found as reliable as the data collected by professionals in community-based research and contributory projects across a wide variety of subjects, including lady beetles, moths, wolves, trees, air pollution, light pollution, plants, pikas, invasive plants, and bees.

However, volunteer data collection is largely “invisible:” in the reports that Cooper et al. examined, citizen science participation was recognized in a paper’s acknowledgements section, if at all. The authors make the case that volunteer data collection should be more widely appreciated for its scientific value. Furthermore, as Cooper says in a supporting blog post by Hugh Powell, participants should self-identify as citizen scientists, not merely as, say, birders or volunteer water quality monitors.

“…people who have been doing a hobby for years have tons of expertise, and they can make a very real contribution.”

The research paper also reinforces the point that volunteer data collection can go where full-time professionals can’t, into spatiotemporal domains spanning decades and land masses. And often, data collected for one area of study can be repurposed to examine some other phenomenon, as we see with various phenology datasets being used to understand climate change.

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Snow days are good for cleaning up the inbox of bookmarks.

  • Jeff Kelly shows how to build your own RFID data logger for $40 or less. It’s suitable for tracking birds at feeders, nest boxes, anywhere they hang out. The system works with any animal species large enough to carry an RFID tag; a battery at the logging station provides the power.
  • A new paper by G. Bohrer et al. describes an “exclusion zone” approach to siting wind turbines in an urban environment, as Roberta Kwok explains. The approach manages the tradeoff between maximizing the power produced by an array of turbines and minimizing its adverse effects on wildlife.

More than smooches

David M. Watson and Matthew Herring present an intriguing open-access paper: it presents the results of a removal experiment, quantifying the striking effect to which mistletoes serve as a keystone resource in Australian forests. The contribution of these parasitic species to leaf litter and the nutrient cycle is one of the factors favoring bird diversity, the authors report.

The Economist

More conservation tradeoffs

Emma Marris reviews the range of schemes for making choices in conservation biology and even uses the charged word “triage” for Nature‘s 8 November 2007 issue (paywall-protected link).

The EDGE program (Evolutionarily Distinct and Globally Endangered) of the Zoological Society of London gives priority to species that are taxonomically distinct, “far out on their own on the tree of life,” if you will. The reasoning is that a distinct taxon, now endangered, one that branched tens of millions of years ago from the tree, represents a unique chapter of evolutionary history that can’t be rewritten once lost. Priority amphibians include Chinese Giant Salamander (Andrias davidianus) (up to 1.8 meters long!), Sagalla Caecilian (Boulengerula niedeni), a worm-like burrower with an extremely restricted range in Kenya, and Purple Frog (Nasikabatrachus sahyadrensis), only described in 2003; top mammals are Yangtze River dolphin (Lipotes vexillifer) (perhaps already extinct), Long-beaked Echidna (Zaglossus bruijni), and Riverine Rabbit (Bunolagus monticularis) of South Africa. The system doesn’t appear to have been applied to other orders. A paper by Isaac et al., “Mammals on the EDGE: Conservation Priorities Based on Threat and Phylogeny” documents the EDGE metrics as applied to mammals.

The majority opinion among conservation biologists today is that they still understand too little about ecosystem functions to say for sure which species are the ‘load-bearing’ ones whose presence keeps a complex, multi-tiered ecosystem from collapsing into some worst case dull scenario of rats, roaches and invasive grass. “We are so fundamentally ignorant,” says Norman Myers, a fellow of the University of Oxford, UK, and adjunct professor at Duke University in Durham, North Carolina. “We cannot afford, by a long, long way, to say which species are dispensable.”

Thus Myers pioneered the concept of habitat hotspots, and a number of overlapping hotspot maps have proliferated. Birders may be familiar with catalogues of Important Bird Areas, Birdlife International’s Endemic Bird Areas, or Conservation International’s biodiversity hotspots. The problem for conservation biology is that each hotspot schema starts with different assumptions, chief among them the metric that is to be optimized. Do we seek to minimize extinctions of species or taxa, maximize land area preserved, maximize taxonomic diversity, or optimize some other measure? Marris writes that the work of Hugh Possingham of the University of Queensland in this area is getting a lot of attention: Possingham seeks to maximize the number of species conserved (vascular plants and vertebrates, in the paper cited below), trading off against the real-world costs of conservation efforts—land acquisition, invasive predator extirpation on islands, fire management, replanting, what have you. A paper by Kerrie A. Wilson et al., “Conserving Biodiversity Efficiently: What to Do, Where, and When,” explains the methodology and applies it as an example to 17 of the world’s 39 Mediterranean ecoregions.

What I find notable about the paper’s approach are the tools of economic analysis that are brought to bear on the problem. An expenditure in conservation activity is modelled as a financial investment. Different activities (“ecoactions”) show different expenditure streams: compare the one-time cost of land acquisition, for example, to the ongoing cost of fire management. The paper uses standard discounting methods and Net Present Value calculations to make investment choices comparable. The model reflects that the impact on species preservation will show diminishing marginal returns as investment is increased. The investment allocation algorithm is dynamic over time: it accounts for positive effects in the ecosystem as investments are made, and adjusts allocations year by year in response.

Wilson et al. acknowledge that the methodology does not yet account for uncertainty, a keystone of modern financial analysis. Also, it would be fruitful—albeit computationally more complicated—to consider the interaction effects of various conservation activities, rather than assuming that each activity acts independently of others.

A worked example chooses between three ecoactions in the Swan Coastal Plain region of Australia: revegetation to counteract habitat fragmentation, invasive predator control, and management of a soil-borne pseudo-fungus, Phytophthora cinnamomi). Even though Phytophthora management is the most expensive per square kilometer ($514K versus $301K for replanting and $7K for predator control), it is nevertheless the most cost-effective: a marginal $2 million spent controlling the pseudo-fungus, in this computation, will protect 49 species, versus 4 for predator management and effectively zero for revegetation.