Team kicking off extreme ecology research in Tierra del Fuego

In collaboration with Professor Katie O’Meara, an architect, Professor Zaitchik, an Earth Scientist, and researcher Claire Moriarty, we are examining the use of drones to map keystone species in extreme environments such as cushion plants in Patagonia or shrubs in deserts. This is just a pilot experiment (haha, get it), and we need a graduate student for 2020 to dig in and ground-truth the metrics we will derive from imagery. The focus will be structure and architecture in natural systems.

Bromus ecotypic contrast experiment up and running in Israel for winter growing season 2020

York Science Fellow Dr. Jacob Lucero and international collaborator Dr Merav Seifan are launching into 2020 with an ambitious experiment in Israel and California. The purpose is to explore the relative importance of provenance of a highly invasive species of bromus in the deserts of California by comparing performance and key interactions in its home range, Israel, and in its introduced range, California. This is a new direction from previous work published in NeoBiota entitled ‘The dark side of facilitation: native shrubs facilitate exotic annuals more strongly than native annuals’ that demonstrated a very significant effect of bromus on local plant community dynamics.

Setup in Israel was a positive adventure!

steps to update a manuscript that was hung up in peer review forever then rejected (or just neglected for a long time)

Sometimes, peer review (and procrastination) help. Other times, the delays generate more net work. I was discussing this workflow with a colleague regarding a paper that was submitted two-years ago, rejected, then we both ran out of steam. This was the gold-standard workflow we proposed (versus reformat and submit to another journal immediately).

Workflow

  1. Hit web of science and check for new papers on topic.
  2. Download the pdfs.
  3. Read them.
  4. Think about what to cite or add.
  5. Add citations and rebuild biblio. 
  6. Update writing to mention new citations especially if they are really relevant (intro and discussion).
  7. Take whatever pearls of wisdom you can from rejection in first place and revise ideas, plots, or stats.
  8. Format for new journal.
  9. Check requirements for that journal.
  10. Search the table of contents for the journal and check your lit cited to ensure you cite a few papers from that journal – if not, assess whether that the right journal for this contribution.
  11. Download pdfs from new journal, read, cite, and interpret.
  12. Then, look up referees and emails.
  13. Write cover letter.
  14. Set up account for that new and different annoying journal system – register and wait.
  15. Fight with system to submit and complete all the little boxes/fields.

3D Printing: A hand guide for ecologists

3D printing may seem like a hyper-modern, futuristic tool from Star Trek or Doctor Who. But the first comprehensive outline for the technique was described in 1974 (by David E. Jones), and was in practice at some manufacturing companies all throughout the 80’s. Most popularly, it’s a great way to design prototypes of complex machine parts that have unusual shapes. But now it’s a common technique for most inventors, as well as hobbyists who have small, affordable 3D printers at home. And in many cases, it’s available for a small, small cost at your local library with the help of tech experts.

The Printing Process

The printer’s function is important for all aspects of the project, from design, to printer settings, to finish. The project doesn’t just magically appear, but (most commonly) is created using “fused deposition modeling” (FDM). Essentially, this means that the printer melts the material, and squirts it out on a the printer bed. But it doesn’t just squirt out a whole product. It lays out a thin layer of plastic on the printer bed’s plane. After that layer is done, the printer prints another layer on top of it, repeating the process until the project has taken shape.

There are lots of parts to a printer, but I’ll lay out a few that will make further explanations easier to understand.

http://blog.supermediastore.com/article/nitty-gritty-3d-printing
  • Print bed: the flat board that the material will land on. Think of as you bottom, or even x-axis and z-axis plane.
  • Hot end: the nozzle that the printing material will squirt out of once melted
  • Extruder: the chamber where the material is melted for printing
  • Filament: the plastic tube string that is the material for printing

Designing a Project

Designing your project is the most creative part of the process, and there are lots of platforms (free and not) to design on. I like to use TinkerCad, since it’s open source, online, and relatively user friendly. It’s great for hobbyists, or non professional designers, and it’s outputs are compatible with most printers we’ll run into. For a quick and comprehensive tutorial, check out this Tinkercad video.

Since the printing process is essentially layering plastic on itself, you can see why you can’t just print any sort of shape imaginable. The printing process relies on gravity, and each layer must print on something else. Sturdy, solid objects are generally easier to print than thin, flimsy ones. Sometimes this can be as easy as laying the object in a different way on your bed. For example, if I wanted to print something shaped like a pencil, it would be easier to lay the pencil on its side in the design than on it’s eraser. But that doesn’t mean we can’t get creative with our designs! I’ll explain how to get around the little problem of gravity later in the print prep section.

Here are some tips to keep in mind while designing that I came across.

  • Use the copy+paste option whenever there’s a repeating element. It saves so much time, and keeps things consistent.
  • When you use copy+paste, try and use the arrows on your computer to re-position the new element, especially if you want it to remain even to the original in at least 1 of the 3 planes (x, y, or z).
  • Group elements as you go, especially for repeated elements that might need a bit of adjusting as you go.
  • Keep gravity in mind! Floating objects will just fall to the ground in a clump when you actually try to print them.
  • Make sure different elements are securely connected. If elements are only barely touching, they’ll probably fall apart in real life.
  • You can only use one color when printing, but you can always paint your object afterwards if you like/have the time.
  • Think about material availability if you’re printing lots of copies. There won’t be endless filament, especially if you need them all to be the same color.
  • Export your project as .obj, and save onto a flash drive if you are going to print at the library.

Print Prep

Once you’ve designed your project in TinkerCad, you’ll take that file to the printer. For our group, we like to use the Toronto Public Library’s Fort York Branch. They have some great techs there that help with design, prep, and machine work, and the price is one 10 cents per gram (that is a steal). They have several brands of printers, and certain printers require certain software programs for you to prep your design in. All you need is a library card!

Prepping is the step when we make decisions about settings for the printing project. This includes things like layer size, supports, rafts, and other things specific to the printer in question. After you’ve personalized each setting, you’ll save that new file to an SD card, and insert that SD card into the machine itself. (At the library, the techs will help you with this part).

Basic settings will work for most projects, but as you get more advanced, it’s nice to have some options to optimize your printing. When changing settings, always take into account the print time (it can get very long if you’re not careful) and filament use (you don’t want to be wasting filament on extras you don’t really need).

When part of your design “overhangs” the previous layer, you can employs a printing strategy called supports. These are essentially buttresses that the program will insert for you once you are prepping your final print. These supports print underneath the project itself, and are removable (but be gentle when you snap them off!).

Rafts are another type of support, that are helpful when you have a project that needs a strong base. It prints a thin sheet of plastic that you’re design will be printed on. This makes your project a lot longer to print, but is necessary when the bottom of a project isn’t simple.

Layer size will determine the thickness of each printed layer. The thicker the layer, the coarser the design will be, so if you have a very detailed design, I would recommend making it a smaller layer size. However, smaller sizes take a lot longer to print, so if your design is a simple shape, keep if coarse.

3D Printing is Versatility

It’s not only printing objects themselves that 3D printing can be useful for. A common practice is printing molds of objects that you’d like to make copies of. This is a great option if you think you might need to make more in the field (when you don’t have access to a printer). Resin, plaster, rubber, and cement are all common mediums for mold making, and can be bought at most hardware stores.

3D printed objects are also great replacements for machine parts that have gone missing, or need customization. Need a new handle for your net? A back for your GPS unit? A special box for strangely shaped equipment? You can absolutely 3D print that! And on top of that, superglue works great with 3D printed materials, so you can print parts and combine later.

I got into 3D printing for creating mimics of cactus fruits, which are a strange shape that I can’t find in any shop (scientific or otherwise). So for experiments when you need a control for shapes (this is great for facilitation experiments), 3D printing your objects is an excellent option.

It may seem intimidating, but 3D printing is an accessible tool that can be learned in an afternoon. And you might even find yourself making some projects just for fun!

Gimme Shelter: How to Throw Shade the Cool Way.

Foundation plant species, such as some shrubs, are able to facilitate other taxa though the cooling effect provided by their canopy. Under the new paradigm of climate change, more and more animals are relying on these canopies during the peak heat hours of the day as a cool oasis. Unfortunately, new shrubs do not grow as fast the demand for their canopies, and this demand will only increase in the upcoming years as the impacts of climate change continue to accelerate.

This field season, my colleague Mario and I embarked on a journey of building man-made shelters that can withstand extreme weather, but also serve as a cooling canopy for animals. We deployed these shelters in Panoche Hills, California.

Designing these shelters was a long process (although they look quite simple), but all the back and forth with the design proved to be useful when the they assembled almost perfectly in the field. At the end the deign was narrowed down to two shapes: square and triangle.

The design consisted of PVC piping and the connector parts, metal stakes for sturdiness, as well UV resistant shades with different percentage of light permeability. We paired the shelters with temperature and light loggers to test how each shelter affects these parameters.

The aim is to provide a cheap and effective design, which can be used for animal conservation while more shrubs are grown.

The wrong kind of help…and an unexpected friend!

Facilitation is usually considered an ecosystem service — positive interactions between species can increase biodiversity and ecosystem function. But what happens when the beneficiary species is an exotic invader that degrades ecosystems?

This spring, I sampled the annual plant community using a paired shrub-open microsite contrast at six sites situated along an aridity gradient from Mesquite, NV to Panoche Hills, CA.

At each study site, I found that Bromus rubens, an annual grass species native to Eurasia and northern Africa but highly invasive across southwestern North America, associated strongly with native shrubs. Specifically, Bromus abundance, biomass, and fecundity were consistently greater under shrubs than in the open. Interestingly, the strength of facilitation did not depend on the size or species of foundation shrubs, but it did depend on aridity — Bromus-shrub associations were strongest in the most arid environments.

A halo of beefy Bromus rubens plants growing under an Ephedra shrub in the Cuyama Valley, CA. This pattern was typical at all study sites.
Bromus was facilitated in abundance at all sites, but Bromus-shrub associations were strongest in the most arid environments.

These findings suggest that invasive B. rubens can associate with native foundation shrubs across a large portion of the non-native range, and that positive interactions mediated by native shrubs can potentially exacerbate B. rubens invasion by increasing abundance, fitness (i.e., fecundity), and competitive ability (i.e., size). The positive relationship between aridity and facilitation strength suggests that the threat of facilitated invaders may be greatest in the most arid conditions.

Oh, and look what else I found:

An endangered desert tortoise chillin’ under a shrub…amongst the Bromus. Don’t see that every day!