Open source hardware for conservation

Last week I was happy to find several papers in Methods in Ecology and Evolution (one of my favourite journals) that presented open-source tools. Two of these present open-source software (the ViXeN stand-alone package for camera trap picture management, by Ramachandran & Devarajan; and the R package ‘BIEN’ to access the Botanical Information and Ecology Network database, by Maitner et al.). These follow the increasingly established culture of sharing software tools in an open way, often linking to data access.

But the prompt for this blog entry is actually the third paper, by Shipley et al., who present an open-source sensor-logger for recording vertical movement in free-living organisms. Not very often one finds the concept of open-source applied to hardware, the physical part of a device (including the electronics and mechanical parts; although often intrinsically linked to some piece of software that controls its functionality). Some other recent papers that present open source hardware include (Whytock & Christie 2016) and (Prinz et al. 2016).

Interestingly, a new journal called HardwareX (Elsevier; 1st issue April 2017) is entirely dedicated to “promoting free and open source designing, building and customizing of scientific infrastructure (hardware)”. It is not specific to the study of biodiversity, but I expect to see a growing number of relevant papers; check for example the “time-sorting pitfall trap and temperature datalogger for the sampling of surface-active arthropods” (McMunn 2017).

fig1sm

Pitfall trap and datalogger from McMunn (2017). Left: trap layout. Right: wiring diagram for the Arduino-controlled system.

Open source hardware (or open hardware) is a growing and maturing movement worldwide with a fascinating history (which deserves its own blog entry!). I’ll just say here that the basic philosophy is simple and will be familiar to anyone doing any coding: if we all shared our hardware designs, and let others modify them and re-distribute their derived designs (as we already do with code and programs), the whole community would end up benefitting of an increased diversity of products, knowledge and support (as we already experience with code, e.g. the R community).

There is a growing open source hardware community in other scientific disciplines, particularly wet labs (Pearce 2012) and it is now slowly getting into ecology and conservation too. As an engineer, I am really fascinated by this topic! And as an applied ecologist and conservation scientist, I believe open source hardware has an important role to play in the developing ‘conservation technology revolution’.

At the last International Congress for Conservation Biology (ICCB 2017, Cartagena, Colombia), we discussed a fair bit about conservation technology. And there was a very clear excitement about the open source way and its potential for conservation. As chair of the Conservation Technology Working Group (CTWG) of the Society for Conservation Biology, I can say we will do our best to promote the agenda of open source hardware in our discipline!

Stay tuned…

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The University of Melbourne supports drone-based research

MUASIP
The end of February saw the launch of the new Melbourne Unmanned Aircraft Systems Integration Platform (MUASIP). Unmanned aerial vehicles (UAVs) – often simply known as drones – offer great opportunities for remotely imagingVinyard-Arial-Imaging-3-310x232 or sensing the natural and build environments. The MUASIP is born with the aim to provide “academic and professional services and training to internal University users and external partners, to facilitate collaborations and trigger innovations in UAV development and its applications.” It will provide support and know-how related to the use of drones, integration of sensors, remote sensing and data acquisition, as well as assistance in flying drones through an agreement with the commercial operator XM2.

The platform is a collaboration between several Schools and Centres, including the School of BioSciences. As contributing member, researchers from the School have access to these services at competitive rates.

If you want more details about what MUASIP can do for your project, please contact me (as the BioSciences representative in the MUASIP platform), or Rodger Young (riy[at]unimelb.edu.au), the platform manager.

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Conservation 3.0?

I have just returned from ICCB2015, the bi-annual International Congress for Conservation Biology, which gathered over 2000 people in the beautiful city of Montpellier (southern France) around a common interest in biodiversity conservation. I really enjoyed it, and as usual from such a forum, it was the place to meet old friends, forge new alliances and spark fresh ideas.

This year, I was positively surprised by the amount of attention given to the use of technology in conservation, which is a topic of direct relevance for me. This included several symposia, for example on the applications of new technologies to the study of primates, on satellite remote sensing for conservation, and an aspirational one suggestively named “Conservation 3.0”. Speakers talked about a variety of technological innovations, including nano-satellites, Implanted Radio Telemetry, automated passive acoustic monitoring, apps to unleash the power of citizen science… and of course, drones!

I left with two clear ideas in mind. The first one reinforces my impression that we really are on the brink of a technological revolution, with great potential to become a game-changer in conservation (and I’d extend this to ecology too!). The second idea is a sobering reminder that it’s all too easy to get over-excited by gadgets and technology, and as an engineer, I certain do! (Is this a male trait, given the line-out of speakers? *).

But not all conservation problems will benefit from technology –after all we’ll still rely on brave people patrolling national parks, or on providing alternative likelihoods to populations that would otherwise rely on threatened species and habitats. The classic narratives of conservation will not magically vanish with the technology wand. Technology shouldn’t be the reason itself, but the means to an end, an enabler of conservation science and action.

Furthermore, nor all emerging technological promises will deliver in practice. Two speakers showed the terribly interesting “hype cycle” curve of technology, a graphic representation of maturity and adoption of technologies and applications. Experience says that every technological development skyrockets through a phase of over-excitement and media visibility (peak of inflated expectations), followed by a crash when it fails to fulfil overinflated expectations (trough of disillusionment). After that, some technologies will become obsolete while others will mature through a slope of enlightenment to their full potential in a plateau of productivity– this is where we can reap the full benefits of a well-understood technology, while pioneers will have benefited from early (and more risky) opportunity gaps. This plot, produced annually by analysts in Gartner, shows the phase at which different emerging and novel technologies are.

The plot is not specific to conservation and not all technologies assessed will be relevant for us. Nevertheless, a couple of points deserve a quick note. Drones are reaching the peak of inflated expectations (as discussed in this article from 2013). For the last years, everyone and its dog got excited by drones. It was supercool to fly one and record video footage from the sky. But it is now that we’re starting to get realistic with this technology as more and more programs use them, comment on their limitations and usefulness. Drones can be fantastic tools for wildlife monitoring and vigilance, but we should better understand their limitations and have a clear idea of what a program will do with the data collected from drones, otherwise we’re just wasting money in expensive toys.

Two other emerging technologies are sliding towards “disillusionment”. I’ll talk about “Big Data” in Ecology in more detail in a future blog post, because I’ve got a strong interest in this topic. You may or may not have heard about the other one, the “Internet of Things” (IoT), the connection of objects and electronic devices through the internet. That is, you could tweet your coffee machine to have your coffee ready when you get home, get an email from your fridge warning you’re running low on milk, or you could command your washing machine from your phone to start a cycle (alas, clothes still won’t get marchin’ into the machine yet…). Technologists and society got really excited about IoT a few years back but it may not be terribly useful for conservation problems, which commonly happen away from internet connectivity. Although you never know, we’re already hearing about bringing internet connectivity to remote areas from the sky using drones! In any case, we are definitely going to witness the creation of local networks of environmental sensors that “talk” to each other.

I leave you with a (popular?) quote, which is very fitting here: it’s not about the technology, but what you do with it.

(*) I got the impression (and this is just an impression, not a statistic!) that there were more men than women hyper-excited by technology … the boy’s toys?? Is this another area to target to improve gender bias? Women out there developing or using novel technologies for conservation: shout out, make your voice heard!!

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Is your SDM fit for purpose?

For an answer to that important question, check out Gurutzeta’s blog post about our recent paper (Guillera-Arroita et al. 2015 GEB)!

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Technology in Ecology

The last decade has witnessed tremendous advances in technology. Electronics and manufacturing have reduced prices to the point that many devices, whose use was historically limited to businesses or large institutions, are now available at a consumer and hobbyist level. Ecology research has benefited from this hardware revolution already to some extent (e.g. camera traps are cheaper than ever and miniature radio transmitters have been fitted to insects), but there is still a massive opportunity gap. Reaping the full benefits of this hardware revolution has the potential to transform expensive or anecdotal data collection into an affordable and powerful source of ecological data. From drones to tiny radiotransmitters, technology could soon be changing the way we sample our environment!

The biggest opportunity gap is in the possibility to affordably design and manufacture project-specific devices, or customise off-the-shelf commercial products to suit specific needs, in order to facilitate basic and applied ecological research, as well as conservation in practice. The possibilities are endless! Some examples include:

  • remotely-controlled, pre-programmed or autonomous vehicles (land, water or aerial unmanned vehicles) for collecting samples, patrolling or tracking individuals, or access and monitoring in remote areas;
  • data logging from networks of sensors, either static (e.g. environmental measurements like CO2 concentration or water flow) or dynamic (e.g. located on animals, to study social interactions within a group);
  • adding non-standard functionalities or intelligent behaviour to camera traps or arrays of microphones by customising off-the-shelf devices;
  • cheap measuring devices and data-loggers to facilitate large-scale citizen science;
  • prototyping and manufacturing of field equipment using 3-D printers…

With a background in Engineering and Statistics, I am interested in exploring how emerging technologies can be integrated with good survey design and sound statistical analysis to improve the way we survey the natural world and open new possibilities. The last years have already witnessed some creative applications being published. I will be blogging about interesting applications of technology to enhance ecological research as I read about them, particularly when these applications have been developed specifically for ecology.

temperature logger

… and in the meantime,  I’m enjoying a bit of tinkering with the Arduino platform! A simple temperature logger, acting as a web server (connected to the internet using an Ethernet shield), it measures temperature at home and displays it in a website.

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Fox baiting experiment workshops

As part of our Adaptive Management project for malleefowl conservation (see my previous blog post), we are planning a large-scale experiment to test whether baiting for foxes (and other predators) has a beneficial effect on malleefowl populations.

We want this experiment to have paired ‘treatment’ (baited) and ‘control’ (unbaited) sites, and have spatial replication across the range of the species… that is, from Western Australia all the way to New South Wales! To achieve this, we need many ‘sites’ to participate. These sites need to have malleefowl breeding in them, and some of these must have (or plan to have) baiting as a management action. Malleefowl breeding activity monitoring (following the standard procedures used country-wide) will be our means to observe potential differences in the response between baited and unbaited sites.

In order to find suitable sites we recently held two workshops, in Perth and Mildura, with land managers across Australia. Cindy has just posted an excellent blog entry with more details on these workshops, check it out here!

And of course a big thank you to all the participants from Western Australia, South Australia, Victoria and New South Wales!

Perth workshop

Describing site characteristics in our workshop in Perth

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Experimental learning: fox baiting for malleefowl conservation

[This post is an expanded version of the article in the latest edition of ‘Around the Mounds‘, the newsletter of the National Malleefowl Recovery Team]

It is not every day that one adds a new megapode species to the life list! I’m spending a few days on Tetepare Island, a great conservation initiative to preserve the largest uninhabited island in the Solomons, and it has Melanesian megapodes (Megapodius eremita). Brownish, inconspicuous and rather small, they roam around the traditional palm leaf house that serves as lodge. The species resorts to external sources of heat to incubate the eggs, but unlike its cousin the malleefowl it tends to use piles of decomposing vegetation or volcanically-heated sandy soils.

Melanesian megapode

Clockwise from upper left: a) A shy Melanesian megapode (Megapodius eremita), a relative to the orange-footed scrubfowl (Megapodius reinwardt) that inhabits Australia. b) Mangrove monitor (Varanus indicus) digging eggs from a mound in Tetepare island. c) Megapode eggs on sale at Gizo market (S$7 = A$1). d) Man-made megapode hatcheries in volcanic soil on Simbo island, used to stimulate egg production for harvesting.

This morning, I found a monitor lizard digging megapode eggs from a mound. This reminded me of foxes and malleefowl, and I started reflecting on the progress that the Adaptive Management team has made over this year. Like the monitor lizard I was observing, we know for a fact that foxes prey on malleefowl. There is even very graphic evidence from camera traps of foxes digging eggs from mounds. From the conservation management point of view, however, the real question is whether such predation compromises the long term survival of malleefowl, and whether fox baiting – one of the main conservation actions currently undertaken – actually contributes to the recovery of the species. The evidence in the scientific literature regarding these questions is rather mixed.

Adaptive management is about using management actions to learn how we can improve future management decisions. In the case of foxes and malleefowl, a carefully planned “experiment” that compares malleefowl breeding activity at sites where baiting is carried out with similar sites where it isn’t, could help settle whether fox baiting is an effective way of protecting malleefowl. Indeed, the ideal way of conducting such an experiment would be to find pairs of sites where: a) one site can be baited and the other left unbaited as a reference; b) malleefowl mound activity (the ‘response’ of the species) is being monitored or monitoring can be started; and c) paired sites are close enough to share the same environmental variability (such as how much rain falls in a given year), but not so close that baiting can affect what happens at the non-baited site.

The adaptive management team set out to plan and organize such an experiment across the species’ range, with the help and support of Tim Burnard and Joe Benshemesh. Finding pairs of sites that fulfil these four conditions is a real challenge. Tim initially gathered information and contacts of potential malleefowl monitoring sites. They then both travelled across the country gathering support from land managers.

One of the keys to a successful statistical experiment is “replication”: if the same reaction to baiting is observed again and again at many experimental sites, we can draw conclusions with more confidence. So, how many pairs of sites are needed to be able to make some useful inference about fox baiting? The adaptive management team conducted a “power analysis” to help answer that question. This statistical procedure requires lengthy computer simulations and analyses, but the basic principle behind it is quite simple. If the increase in malleefowl breeding activity due to fox baiting is very large, then observing it at a few sites would be enough. At the other end of the spectrum, if the effect of baiting is very small, it would take many sites to detect it in a statistical analysis, but then again it wouldn’t matter because a small effect would mean that fox baiting would not be an efficient way of increasing malleefowl breeding activity. Our power analysis indicated that about 20 pairs of sites monitored for at least 5 years could be needed to have a reasonable chance to detect an effect of fox baiting that we believe would have a real impact at a population level.

The devil is in the details though, and conducting experiments with natural systems is often trickier that in a laboratory. Ecosystems are always messier and more nuanced than the simplified model used in our power analysis. We also know that we will never get pairs of treatment and reference sites that experience exactly the same environmental conditions over time. Furthermore baiting can be conducted at different regimes of intensity and timing, and the experimental sites will be located within a broader geographic landscape in which other landowners may conduct baiting. As we begin incorporating real sites into this plan, we can collect this more detailed information and account for at least some of it in our analysis.

Despite these challenges, the experiment approach we propose is still our best shot to obtain a robust answer to the question of fox baiting as a management tool for malleefowl conservation. A growing network of experimental sites will establish a solid base to provide the learning we need to improve management practices. And the methodology can be used more broadly, as it will serve as a blueprint to tackle other management uncertainties in malleefowl conservation, such as the effect of fire regimes on malleefowl populations.

It will take several years to gather enough data, so the sooner we start the better. In the adaptive management team, we are really excited to see the progress so far, with several potential sites in WA and SA already under consideration. Stayed tuned!

 

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