Sandbox Germination Livestream

The COVID-19 Pandemic has created worldwide restrictions, one of which is the ability to easily cross borders. This is not a huge issue if you can easily work virtually but as a field ecologist whose field sites are in a different country, you have to come with creative ways to conduct experiments here at home. Our lab room was not getting much use since classes went virtual, so we decided to transform it into a sandbox germination experiment and livestream it so we can view the experiment any time, from anywhere. We used cotton fabrics and burlap in a half tent design and placed trays of Phacelia tanacetifolia (desert fiddlenck), an annual species native to the Southwestern region of the U.S.A, and Cylindropuntia acanthocarpa (buckhorn cholla), a native cactus, in the open and underneath tents. We also used temperature, light, and humidity loggers to monitor how microclimatic parameters are affected underneath the shelters and in the open. Additionally, we set up LED lights for UV and heat lamps to replicate the desert heat. You can say things are heating up in the lab!

A view of the entire setup with LED and heat lamps.
Phaclia and buckhorn underneath tent canopy with loggers.
seed trays in the open with loggers.

Returning to the Greenhouse

After unceremoniously abandoning my pots back in March of 2020 when the Virus that Must Not Be Named struck with force, I’ve finally been given special permission to return to campus and start again. I will eventually be examining the effects of different types of damage to plants on flower production, but for now I’m just hoping these seeds I purchased back in April 2020 will actually germinate. I planted 200 pots worth of desert dandelion (Malacothrix glabrata) seeds a week ago and I am already starting to see some germination!

All 200 pots in the greenhouse
A seedling!
A seedling that has started to branch

Land Acknowledgments

Recent talks I have attended mentioned indigenous histories at their research sites. This is a positive form of provenance not just of the site or place but of the sense of its ecology. Nonetheless, it has been proposed that talk is cheap. There at least five major implications of this premise.

  1. Acknowledge but propose a solution for those lands to better recognize the diversity of peoples associated with its present and past.
  2. Similar to prepping a data management plan, prepare a land and research provenance management plan that includes sharing and communicating results to current and past stakeholders within the region.
  3. Provide the audience or readers with an opportunity to contribute to this recognition process. This can include mechanisms such as an NPO or charity to support associated with the land use culture and peoples, a mailing address or contact details for more information, a link to additional resources or the site for deeper reflection, and finally lead by example and mention how your research process incorporated provenance.
  4. Revisit the culture, history, and ecology at the end of the talk by reconnecting with its peoples. In many of the systems we work in as a team in Central California, Ephedra californica is a foundation plant species. This plant has a long history of use and management by many. Mention this as a key connector to the ecology that we now study. These ephedra parklands reflect many processes of change including active management.
  5. The written word is powerful. In the standard ‘study site’ description included in the Methods section of field ecology papers, consider a statement describing and citing work on the indigenous people and culture that supported your study site.

Campus tree project 2020

Two super experiments.

  1. Exotic animal responses to trees and disturbance.
  2. Individual tree and patch-level dynamic responses to disturbance.
  3. Post hoc synthesis and contrast of interaction pathways.

Sample academic plans

Table, list, freeform, calendar, all good. Match your modality or even use more than one mechanism to support your journey this Fall and beyond.

Journey rabbit


Read Spatio-temporal statistics with R

Read Advanced R (skim some bits, functions)


Rangeland brome papers x2

Scientific synthesis paper

Editorial on distributed learning

Dream on – notes on how to do experiments into paper

Magic paper with Mario

Synthesis papers with Mario, Nargol, and Malory


Teach BIOl3250

Review apps for Diol grad committee

Support team in papers and planning


Seminars on experimental science

Connect with USAID folks



YUFA to write a book

Journey army ants

1) Apply for NSERC and other grants

2) Readings list for PhD project

3) Select committee Members 

4) Come up with a few thesis questions

a. Possibly run a meta/Systematic review (Would need to make a super clear one though)

b. Continue with density? Maybe make areas with a bunch of replicate shrubs and see what happens. Or cut some shrubs down and see what happens

c. Maybe look at how density of shrubs has an impact on invasive grasses?

d. Maybe look at one specific animal species and compare density of that specific species to density of shrubs?

e. Or maybe take a completely new route on thing.

5) Brainstorm possible field projects for PhD (When we are going, manipulative for experiments, timeframes, etc.)

6) Work on posters and other outside projects/research papers

Journey salamander

Read “Fundamentals of Statistics” Aug 2020

Research possible committee members and reach out Oct 2020

Select a committee member Dec 2020

Come up with a thesis question Dec 2020

Field Work/Data Collection Apr 2020 – Aug 2020

Data Analysis Fall 2021

Reading list for research Winter 2020

Take remote sensing course? Winter 2020

Thesis Writing Winter 2022

Hugh C. Morris Experiential Learning Fellowship application February 15, 2021

Scholarship/fellowship research Oct 1, 2020

Ontario Graduate Scholarships (OGS) application Dec 1, 2020

Journey chipmunk

Not including how ongoing work is structured.. mostly deadlines, hopeful progress and some milestones


Decide on topic

Find committee

Submit NSERC/OGS application

Transfer final insect survey specimens to ethanol

Some progress on synthesis


Come up with a review/meta

Come up with 1or 2 new chapters on top of lizard diet

Progress report

Mail first run of samples to Mark


Field planning

Resurrect and write-up spatial veg finally

Apply for permits if needed

Work through a review

Compile taxonomist list


Family level data input

Second round of specimens sent to Mark

Review data extracted – what is the story?

Do I need to get additional data?

Get into grad level GIS course


Learn simulations 


Research evaluation meeting

Submit thesis proposal to FGS


Submit interim report to BLM

My Q: 

How focused does a topic need to be? How related are chapters?

How do expectations differ for phd from msc

Journey hellgrammite

1) Apply for NSERC and other grants

2) Readings list for PhD project

3) Select committee Members 

4) Come up with a few thesis questions

a. Possibly run a meta/Systematic review (Would need to make a super clear one though)

b. Continue with density? Maybe make areas with a bunch of replicate shrubs and see what happens. Or cut some shrubs down and see what happens

c. Maybe look at how density of shrubs has an impact on invasive grasses?

d. Maybe look at one specific animal species and compare density of that specific species to density of shrubs?

e. e. Or maybe take a completely new route on thing.

5) Brainstorm possible field projects for PhD (When we are going, manipulative for experiments, timeframes, etc.)

6) Work on posters and other outside projects/research papers

Journey capybara

Largest focus on teaching for the fall term. Followed by restarting the greenhouse experiment and finishing seeds in October. Two papers are currently submitted and going through review, with another manuscript in preparation.

Journey kangaroo

-September’s end: finalize rough research questions and ideas to explore for PhD (human-wildlife conflict, trampling, and facilitation)-October 20th: confirm committee members-October: Collect reading list, get seeds and scale from lab to continue seed allocation side project-October 15th: Confirm all AIF Climate Activist Videos online-November: Work through reading list & submit grants (National Geogrpahic Explorer Grant, MITACS?, other small grants). Seed allocation data analyses-December 1st: first progress report-December: Continue working through reading lists, add to lists as necessary. -December’s end: Finish full draft of seed allocation paper-January: Determine 2 cognates and begin drafting cognate literature reviews-March: Finish up first full draft of proposal (due beginning of May)

Using Magic the Gathering to Teach Experimental Design

With the current circumstances in today’s world, we have all been forced to adjust to a new method of learning. With classes moving online, one of the major challenges that has arisen is keeping students interested and engaged in their studies. Online classes extremely limit student-student and student-faculty interactions, making these courses feel almost impersonal. That being said, finding a way to make these online lessons fun and engaging could both help students enhance their overall understanding of basic academic concepts (such as experimental design, report writing, and figure generation) while also allowing them to work with novel information.

This semester I am one of the TAs for Biol 3250, a course dedicated to teaching students in varying academic disciplines how to plan, conduct, and analyze scientific data collected through experimentation. Many of the labs we have designed focus on proper planning and execution of these scientific experiments, but there is one section of the course that is a bit different. For this section, students are presented with several large datasets and are tasked with designing a hypothesis, predictions, and/or predict the patterns presented in the pre-collected data. From there, students are asked to create a figure and run a statistical test to support their ideas. To keep the students engaged and interested, one of these datasets used data collected from something outside the scientific field. This data was collected from opening packs of a popular tabletop card game titled “Magic the Gathering”.

What is Magic the Gathering

Magic the Gathering is a popular tabletop card game that uses a combination of strategy and chance to win. The game, designed first in 1993, has since expanded in both size and popularity with over 35 million players worldwide. The game puts players against each other with their pre-constructed decks, where the goal is to get their opponent’s life points from 20 to 0. Packs of these cards can be purchased containing 1 Rare/Mythic, 3 Uncommon, and 9 Common cards. To see how these packs are opened and what a booster box looks like check out the Youtube channel Mario MTG. Each set released is thematically unique from the previous, taking players to worlds (known as planes) that push the bounds of one’s imagination. Players get to choose from a variety of color themes and combinations for their decks with each color representing something different.

  • White: The color of order, community, and peace.
  • Blue: The color representing knowledge, perfection, and control.
  • Black: The color of resurrection, opportunity, success, and satisfaction
  • Red: The color of freedom, strength, and destruction
  • Green: The color of nature, growth, beauty, and harmony

So How Does This Tie Into Learning?

So I bet you are wondering now, “How could a fun tabletop card game possibly have any connection to an experimental design course?” The best answer to that is that it teaches students to work with large amounts of data while also showing that experimental designing can be fun! Boxes of these Magic the Gathering sets were opened with each individual card inputted into the data as a datapoint. Each pack ranged from 14-15 datapoints and after opening several boxes, well over 6000 data points (and soon more) have been collected. Each individual data point in itself looked at various aspects of each card such as name, color, ability, etc.

With this large dataset now compiled, students are free to generate any possible questions or hypotheses they could think of. “What is the probability of getting a mythic card”, “On average how many foil (shiny) cards can you get in a box”, “which set has a larger number of higher value cards.” These are just some small questions that could be addressed by analyzing this dataset. We want to show students that you can run an experiment on anything, even a fun game, and we want them to have a fun and unique way of working with big datasets. Being able to find new and inventive ways to keep students engaged in their studies is quite a task. Since everything is now done virtually online, it is important to try and new and fun ways of both engaging and teaching students.

For those who want to see how these data points were collected the Youtube channel Mario MTG goes through a bunch of box openings (Shameless plugin haha). On this channel, I go through opening boxes of the newest sets of magic the Gathering and also provide some commentary on the cards, prices, news, formats, and the overall future of the game.

The link to the channel can also be found below!!!

Fall 2020 goals


  1. Stay healthy.
  2. Be safe.
  3. Connect with team.
  4. Learn something new.


  1. Academic plan.
  2. MSc and PhD committees built and summoned.
  3. Read a pile of papers on existing focus and begin a new direction too.
  4. Proposal.
  5. Complete and submit outstanding synthesis papers.
  6. Book and schedule progress reports.
  7. Prep deck and present at report meeting.


  1. Set hard and soft deadlines.
  2. Populate google calendar.
  3. Identify stepping stones to larger goals and make lists breaking each deliverable down.
  4. Select someone to be accountable to.
  5. Identify collaborations and update them on stepping stones.
  6. Keep track of progress (Gantt charts, notes, meetings, GitHub repos with issues to track).
  7. Plan breaks from the screen.
get the lands out so you have the mana to spend


This Fall will be remote for the majority of academic activities. The 8.0 credit honours thesis program is approximately 8mos in duration. The student leads an independent research project. As a team, we would like to work with two individuals on one of the following projects. Each student will work with a graduate student or postdoc and Chris Lortie.

a. Each project is individually implemented by the student safely.
b. Zoom calls with Chris and the co-mentor to ideate, solve, and plan will be used to collaborate in addition to editing datasheets and docs.
c. It will be beneficial for the student to have experience in R and be able to work independently.
d. The pre-reqs are listed online for BIOL4000 are here and currently include students their final year with a BIOL GPA of at least 6.0.

Tree forest dynamics at YorkU

(1) Subway effects on trees and woodlots. A census of tree forest dynamics and individual tree changes on YorkU campus. Jenna Braun, Mike Belanger, and I dug through census records compiled by the YorkU master gardener in 2012 and 2013. Over 5000 trees were tagged on campus and their size and health were recorded. The data are here. This is a fantastic project and opportunity to revisit a superb dataset in R and also resample some or many of the trees. We now have a subway rumbling away underneath campus, and we can check trees near and far from the line and test the hypothesis that disturbance belowground influences tree growth and health.

(2) Other ecological hypotheses relevant to urban forest dynamics (disturbance, new buildings, edge or center of campus etc). There are at least two projects here. The students can work independently and still split up the work of testing more than question or hypothesis. One individual can (re)sample trees from 2012 and 2013 near/far subway lines, and a second student can examine any other ecological question with disturbance, new buildings, or how sets of trees are doing in different ecological contexts on a university campus.

Desert ecology data analyses

We have many open datasets ready to go for deep analysis work if you are competent in R (or Python but we work in R in the lab). Many spatial questions, niche questions, or use or plant and animal survey data and join them to new data on climate or downscaled remote data if you are game for that adventure. Here are a few examples.

Vegetation under shrubs and in the open in the Central California Deserts.

Desert arthropod diversity patterns in California.

Camera traps and birds of the deserts.

In each instance, the workflow will include a few Zooms to plan analyses and additional data lookups, then the student researcher digs in!

To apply

If you meet the pre-reqs and are in your final year in YorkU Biology, please email lortieatyorkudotca, and we will set up an interview with you for the team!