ABI 198 Section 2 - Day 1!

We had a successful first day of class! Today was mostly spent discussing course logistics and planning for the quarter. The presentation slides from today's class are in the Miscellaneous folder in the Google Drive. Here were our meeting minutes: 

     

Time	Activity	Key Takeaway(s)
10:00	Class intro	Student-driven novel research
10:20	Blogger and MC signup	Check google drive schedule
10:25	Field safety briefing	Stay with a buddy! If you feel unsafe you can stop
10:30	Expectations	Be involved, volunteer, think, be creative
10:35	Constraints	Only 10 weeks. Limited vertebrate manipulation
10:40	Name game	If (when) you forget, ask!
10:50	Project	We need a site, a reasonable study subject, question
10:55	Organization	Rely on google drive. Need R, Discord, Zotero, Blogger
11:00	Lab spaces	Two, not large, spaces. Various equipment available
11:10	Our Question	Read, think, go outside, discuss, repeat
11:20	Grading	Set class to 5 units. Check syllabus for % breakdown
11:30	To do before next class	Ch. 1 and 2, get digitial infrastructure, read this blog
11:40	Friday Class	We will be meeting at the Mann Lab parking lot!

 

Everyone in the class should be signed up and able to access the course's digital infrastructure which includes:

• The class Google Drive
• Discord server (installing Discord on your phone and turning on notifications is highly recommended)
• Blogger website 
• Zotero shared folder

Please ask Crystal or Marshall if you need any help!

Course Goals

The goal of this class is to complete an original research project with you, the students, in the driver's seat! The world is your oyster, and myself and Marshall will do our best to facilitate any project of your choosing in animal field ecology. This project will serve as your practicum project. However, there are few constraints:

1.  Time (the quarter is only 10 weeks!)
2. $1000 to purchase supplies we are not able to obtain from Marshall's equipment collection or from (nicely) asking others on campus
3. Location must be near Davis
4. Complying with IACUC for vertebrate manipulations 
5. Must be a collaborative ecological experiment

If you have any project ideas, please write them in your notebook!

Course Outline

Goals

The central goal of this class is to conceptualize, develop, and perform a novel, innovative research project focused on the field ecology of animals. 

Structure

Each day, there will be an MC (Marshall this class day) and a blogger (Crystal this class day). 

The MC will direct everyone's efforts throughout the day, give an initial safety briefing in the field, and delegate tasks/ask for volunteers. 

The blogger will take notes on the day's activities and plan for the next class. They are responsible for the blog you are reading right now. The blogger takes over after each class and sends a debrief and action item message in Discord. 

Each student will be a blogger and an MC once. You will be an MC the class immediately following being the blogger. 

 

ABI 198 Field Notes (this blog)

We will rely on this course blog to both remember what we have done, and plan what we will do. Each meeting, two class members will sign up for roles 1) The MC – runs the meeting, keeps the class on task 2) The Blogger – write down what has been done during a meeting, and write the agenda for the next meeting. The blogger will implement their agenda as the MC in the next meeting. Please refer to the sign-up sheet in the Drive to see what dates you are signed up for.

On notebooks: almost all scientists have one, and keep them on their person. Most importantly the notebooks serve as a repository for ideas. They don’t need to be neat, but knowing where you wrote down an idea can be invaluable weeks or months later.

The often messy process of science

We all spent some time today discussing the traditional scientific method and how the reality of science is often much more messy.

 

Credit: https://undsci.berkeley.edu/science-flowchart/

 

The scientific method is rarely as linear as we learn in our intro science courses, instead the process looks like the flow chart above.

Moving into the quarter, we should be prepared to be creative! The best ecological questions often come from embracing a child-like wonder about the natural world. 

But where are the ants going? Why are trees green? Do ladybugs have friends? Why do spiders have to eat other animals and not plants?

I definitely asked my mom variations of all of these questions as a kid! We should embrace these sorts of simple questions throughout the quarter, they could be the basis for our research project. While publication, peer review, experimental design, and statistics are important; creative thinking must happen first! The rest will follow.

 

Science can be a daunting and frustrating process, but all scientists have bad days, even Charles Darwin. He wrote this quote in a letter:

"But I am very poorly today & very stupid & hate everybody & everything. One lives only to make blunders."

Developing a Research Question 

In the context of this course, a good research question (RQ) will be feasible, interesting, novel, ethical, manageable, and systematic (adapted from Ratan et al. 2019)

Asking a research question can be very intimidating, but it's helpful to think of it as a top-down process. First, you must select a topic you are interested in. For this class, anything within the realm of field ecology that can be studied in the Davis area is possible, which is overwhelming! Hopefully, after we spend some time outside and familiarize ourselves with the local ecosystems, you will discover certain organisms or systems you are interested in! You can formulate a question about anything in nature that is observable.

After finding a topic you are interested in, you can start reading about the subject. When first starting, it's okay to read some broad articles for the general public (Wikipedia, newspapers, etc.), but eventually you should read the primary scientific literature. Once you are reading the primary literature, you should be able to identify knowledge gaps in your topic area. It is especially useful to find previous research with methods you can borrow (with proper citation of course)! 

Look at the following figure for an example of formulating a question using COVID-19. 

 

 

The table below describes some problems you may approach and solutions when formulating a question: 

 

Figure from Ratan et al. 2019.

 

Over the next couple of weeks, we will identify a topic and formulate a research question as a class. Everyone will have an opportunity to pitch their ideas, so start thinking! 

This process can feel scary, but you will get through it! You have the support of your classmates, along with Crystal and Marshall to help you. Don't hesitate to rely on your scientific community for support. Ideally, this course should be a fun experience where you learn important skills.

How to Do Ecology (the book for this class):

The first six chapters of this book are available in the shared Zotero library. We will discuss the first two chapters on Thursday. They have great advice on how to develop and pose hypotheses so that they are feasible, novel, and interesting. Later chapters of the book will help with testing those hypotheses and analyzing data. 

Our next class meeting

For our next meeting, we will be visiting the Putah Creek Riparian Reserve and Stebbins Cold Canyon near Lake Berryessa! Please be prepared to spend six hours outside. We will do some light hiking.

 

Bring a notebook and pen, close-toed shoes, at least 2L of water, lunch/snacks, sunscreen, a hat, and a backpack. 

Please download the Seek and Merlin apps to your phone as well.

We will meet at the Mann Lab Parking Lot across Kleiber Hall Drive from Briggs and Storer at 10:00am. Please be on time!

 

We will spend our next class period making observations of the different types of organisms and their behaviors. After completing the observation activities, we will spend time discussing our observations as a class and finding common threads. We will then brainstorm any potential hypotheses or project ideas that come to mind.

 

We will also discuss this week's readings from How to Do Ecology (Ch. 1 and 2, available in the Zotero). You should also choose a reading (besides the book chapters) from the shared Zotero folder and read that before class.

Make sure to complete the readings before class!  

Our first R homework is due this Friday (4/4) after class. Please submit your R homework in the Google Drive.

Update with agenda (subject to change):

10:25 - Arrive at Putah Creek, explain activities and riparian area, repeat name game 

10:40 - self-guided observations; plants, inverts and vertebrates. General observations and exploration remaining time.

11:30 - reconvene and group discussion

 
How do the readings impact your observations? Do any potential study questions come to mind? How are these different organismal groups interconnected?

12:00 - Depart Putah Creek

 

12:30 - Arrive at Stebbins Cold Canyon and eat lunch

 

1:00- Begin hiking

 

3:10 - Return to vehicles and short discussion

 

4:00 - Arrive at Mann Lab 

Observation Activities and Questions (Putah Creek)

Plant community observations (Putah Creek):

How many tree and shrub species do you count? Collect a leaf from each species that has leafed out. Do you think any of these species are invasive?

How do you think seasonality is affecting plants right now? What life stage are they in? How might this change over the quarter?

Invertebrate community observations

Spend 10 minutes observing the invert community. Either choose a group/individual to observe or see how many different types of inverts you can spot. Where did you see the most inverts, the fewest?

Vertebrate community observations

Lastly, observe the vertebrate community. Which types of vertebrate groups did you observe? What are some challenges with observing vertebrates?

Discussion Questions

How did the readings impact your observations? How are these different groups of organisms interconnected?

 
What general patterns did you observe in the riparian area? Do any potential study questions come to mind? What was your favorite type of organism to observe?

Stebbins Cold Canyon activity

Using Seek and Merlin, how many organisms can you identify? What was the most interesting to you? 

Notebook 

Throughout class and afterward, please document observations in your notebook. Don't forget that we will read through your notebook at the end of the quarter, so make sure to use it. The formatting of your notebook is completely up to you! You should also document anything you do outside of class in the notebook as well. I recommend taking reading notes especially! 

Whew, that was a long one! I'm excited for our day out on Friday!! See you all then :)

 

References:

Ratan SK, Anand T, Ratan J. Formulation of Research Question - Stepwise Approach. J Indian Assoc Pediatr Surg. 2019 Jan-Mar;24(1):15-20. doi: 10.4103/jiaps.JIAPS_76_18. PMID: 30686882; PMCID: PMC6322175.