Mare Island/USGS NatureNerdFest Report

[Reblogged from Nerds For Nature]

Here’s the complete report on last December’s fantastic NatureNerdFest field event with the US Geological Survey. You can see even more photos on the N4N Flickr stream.

Thanks to Isa and Susan and William and the other WERC researchers who gave us such a warm welcome, and a special thanks to Dan Rademacher for helping pull the carpool effort together under quickly-changing circumstances. And thanks as well to our drivers, you all saved the day for us carless Nerds!


USGS Overview

Wildlife biologists Isa Woo and Dr. Susan De La Cruz gave us a fascinating overview of their work, which generally focuses on the impact of climate change on coastal estuaries and the crucial habitat they provide for many struggling and/or protected species. Several detailed slides showed us helpful cross-sections of the types of areas that they monitor, but perhaps the most striking part of the presentation was a video of the tide coming in at China Camp State Park in the not-too-distant future, if current projections for sea level rise hold true.

The USGS info page for this video explains further:

This time-lapse video shows the dramatic natural tidal cycles of a salt marsh in San Francisco Bay — daily rhythms to which animals take refuge in high ground, and the marsh receives sediment and nutrients from the estuary. But what will happen to these marsh ecosystems under sea level rise scenarios? Will we see shifts in vegetation and animal species, or lose some marsh ecosystems altogether? Learn more at the San Francisco Bay Sea Level Rise Project website.

This video really captures the urgency of the work that the Western Ecological Research Center and other climate change researchers are facing, and why we are so enthused to be talking with them about possible collaborations. For much more information on their mission and ongoing projects, check out their website.

Flight For Nature – Drones and eco-research

Several drone experts had to back out for the day due to various schedule conflicts, so the UAV activity was not quite as organized as we had hoped. But several other DIY flight enthusiasts jumped in to provide us with some definite thrills.


Quadcopter getting a good look at Mare Island — photo by Ed Brownson


Reiner’s quadcopter with GoPro camera attached was the star of the show. He showed the gawking crowd some impressive low-level maneuvers, a nice vertical lift with some fun spins and twirls, and generally gave us eco-drone newbies an idea of the possibilities. Brain-gears were almost audibly grinding through exciting new things to do with autonomous flying platforms.

Ragi Burhum (GIS/Geo programmer/entrepreneur and organizer of GeoMeetup) summarizes the discussion around the “drone table” and throws out some ideas for the next gathering:

This meeting was about exploration. Initially, people were interested in what we could do with drones. The concerns about resolution, precision and such went away after we explained that these little guys can take whatever you are willing to lose in a crash!

I think it would be interesting to set some fun, useful, and doable goals for the next event. This will definitely gather interest from a larger pool of drone enthusiasts.

  • Take ortho-photos of a particular area.
  • Overlay drone photos on a map.
  • Do manual reconnaissance of a stationary target.
  • Do automatic reconnaissance/image acquisition of a stationary target at a particular latitude/longitude.
  • Do manual/automatic reconnaissance of a moving object tagged with a GPS and wireless/radio connectivity.
We’ve also heard from other biologists and eco-researchers just in the past few days about using hyper-spectral imaging from low-flying drone platforms to image underwater vegetation in a local lake — and also from researchers studying the regrowth of habitat in a Bay Area natural area recently ravaged by a fierce forest fire, they are hoping to use drones to gather high-quality vegetation coverage data over large swaths of land.
We’re just getting started here, folks, so strap on your Nerd hats, spin up your Nerd propellers, and buzz on over to the Flight For Nature Google discussion group!
Crowdsourcing Nature — Bioblitzing and DNA Barcoding (and Spiders)
Damon shows Dan how to use an iPhone-mounted microscope to take a picture of an unidentified little hopper — photo by Ken-ichi Ueda
We took about a one-hour out-and-back hike on an old roadbed trail and found plenty of birds, some interesting plants, and even some curious bits of a skull that several Nerds pieced together into an official iNat observation. This “microblitz” was big fun, not for racking up huge numbers (64 observations at latest count) but for the chance to introduce new Nature Nerds to the practice, and to explore new technologies like a smartphone-mounted microscope. The Mare Island microblitz page features several cute little critters taken with this device and other close-up techniques, so go take a look!
imageUnidentified lichen at 50x — photo by Damien Tighe
Ken-ichi Ueda, developer of iNaturalist and inveterate species-hound, spent much of the day looking for spiders in mundane places like inside building roof vents and under moldy old mattresses. And what do you know (to no one’s surprise) he uncovered some real beauties.
imageFlatmesh Weaver found on Mare Island — photo by Ken-ichi Ueda
So what’s the focus on creepy-crawlies all about? Ken-ichi and a few other Nature Nerds are developing a standard protocol to help citizen scientists add DNA barcoding to their biodiversity-exploring repertoire. Ken-ichi explains what he and his fellow bug-hunters were up to:
Kaldari, Damon, and I successfully collected a bunch of spiders and we will be sending parts of them to Quintara Biosciences in Albany later this week for sequencing. In January we hope to do the same work ourselves at the Cal Academy to see how hard it is and what the cost difference is.

Join us on the N4N Bioblitzing Google Group to explore these ideas further.
Networking Nature — Remote yet connected environmental and ecological sensors
For those of you who saw the NerdBuoy demo at Mare Island, thanks for all of your encouragement and feedback! And for those of you who didn’t, read on…
So what’s a NerdBuoy? Well, it might or might not float, but we’ve borrowed the idea of a “buoy” being a general source of crucial information from a remote, possibly environmentally hostile location. We could have called it a “probe” or a “beacon” or a “Remote Telemetry Unit (RTU)” but general consensus among the designers has denied the acronym trend for something more inspirational.
imageNerdBuoy poses in front of the infamous Building 505 (previously a Navy communications complex where some of the first signals from the Pearl Harbor attack were received) — photo by Ed Brownson


The NerdBuoy, then, is primarily a technology exploration platform for open-source citizen science types like us Nature Nerds to take our sensors out in the field and provide enough information to design more targeted systems that solve real problems in ecological research. It was inspired by USGS requirements to monitor water depth, temperature, and salinity in many of the tidal marshes that they monitor, but we think there are many more eco-research applications for this sort of open-source ruggedized electronic outpost.
NerdBuoy sensor and geolocation data is saved to a local memory card and also uploaded to the ManyLabs data server via cell phone and/or wifi link when within range, and mapped using a beta version of ManyLabs data mapping software. Over time other methods and services can be explored. For more details please review the preliminary google doc description, and to see some of the sensor data we collected as we carried the NerdBuoy along on our short bioblitz out-and-back hike, look at the map and data set.


Map view of some NerdBuoy windspeed data collected at the NerdFest, as viewed on the ManyLabs Data Hub.


This design is the first proof-of-concept prototype for a versatile technology exploration platform.  It will serve as an environmental sensor, attitude and position, and wireless signal telemetry unit, and can be placed in various spots around pilot test areas to gather data on a regular schedule for a few days or weeks at a time. It can also be carried by hand, bicycle, vehicle (or possibly even by drone in a stripped-down version) to profile a given area’s suitability for various technologies and protocols.


The NerdBuoy electronics module gets passed around for inspection — photo by Ed Brownson


For example, a major issue for most remote sensor projects is figuring out what wireless methods should be used for reliable yet cost-effective communication. Cell phone modems might provide adequate coverage, but ongoing service and data charges are likely to be expensive for even a moderate number of locations. Experimentation with various wavelengths and protocols might indicate that a local mesh or other dedicated RF link system would provide comparable bandwidth for a much cheaper ongoing cost.

In other words, this platform will allow variations on many technology themes to be developed quickly to explore the general problem space, then more refined design work can commence. The first version is built with circuit modules available off the shelf — Arduino boards and shields, Grove sensor boards. A mounting scheme using laser-cut plastic sheets as a “skeleton” to hold these various modules together has been customized by Peter Sand to make efficient use of this cylindrical instrumentation housing.


Once the NerdBuoy acquires data, the ManyLabs Data Hub provides lots of ways to look at it — composite screen capture by Ken McGary


This project is also an exercise in imagining the data structures and network software that will be required to accommodate a variety of envisioned smart buoys/remote environmental sensor platforms in the future. Multimedia features beyond GSM cellphone audio and perhaps very low-res video or still jpeg photos are not generally envisioned for this particular platform, but we expect these options will be explored in related projects soon.

We’ll have more information here on the NerdBuoy project as it develops, but for now join us on the Networking Nature Google Group to explore these ideas further.

What’s Next?

Now it’s time to start thinking about our next NerdFest! We’ll no doubt be back to Mare Island soon, but maybe there are other possibilities, too. Do you have connections at an outdoor venue that might be perfect for field-testing drone ideas or for exploring NerdBuoy operation, like one of the relatively abandoned air bases scattered around the Bay Area? Do you know of other research groups or agencies that we might collaborate with on similar problems? Throw out your ideas on our Google Groups or Meetup page and we’ll see what happens!

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