As biologists, we seek to understand life and living organisms. A quick look at the physical world of bees, trees, and other humans makes it seems like it could be straightforward to identify the individual. This class investigates how a core concept in Biology, that of the organism, is perhaps not so straightforward or even knowable. We will study examples like the Pando groves of Utah, which are either 50,000 trees or 1 tree with 50,000 trunks and colonial animals from bees to siphonophores, to ask if the colony itself is the organism. We investigate the messy, multicellular, and multispecies collaborations that are metazoa like humans. Through the course, we will collectively define life at the organismal level by collecting taxonomic examples from primary literature and excavating overarching principles. Along the way, we will encounter topics on apoptosis and the immune system, investigate what it means to be multicellular, and contend with the idea of biological altruism.
This course is part of the University Core and is a Writing Enriched Designation when this course is taken in addition to BIOL 205L. BIOL 205L and BIOL 399 are part of the Writing Enrichment Couplet for Biology Majors.
My goals are to:
Build an environment where you are comfortable and interested in exploring challenging concepts and developing new skills.
Introduce you to a framework for how knowledge is generated in the field of Biology.
Provide an overview of topics and techniques to inform and support your growth as a scientist.
Guide your trajectory in building skills to read, write, and communicate primary literature.
Your goals should be to:
Understand, critically evaluate, and communicate experimental evidence as applied to topics in Biology.
Focus on how a biological question can be formulated as an experimental question, investigate how data speak to this question, reason through the model’s strengths and possible shortcomings, and hopefully, broaden your appreciation for scientific experimentation.
Develop reading, writing, and discussion-based scientific communication skills: When you find it difficult to share in class, challenge yourself to do so. When you find it easy to speak up in class, challenge yourself to foster discussion with others.
Gain a more thorough understanding of the academic writing process including the incorporation of feedback received during revisions, integration of both primary and secondary literature in writing, and the use of a citation manager.
Goals of the Class: The goal of this class is to learn how to read, communicate results from primary literature, and synthesize an argument. I want to emphasize: Learning how to read and write in this style is a skill and this class is about developing that skill. You should not expect to comprehend everything! These papers require areas of expertise, which means lots of specific terminology. If there’s a term you don’t know, look it up. Write down your questions and bring them to class. The goal is not to come to class able to explain the paper as well as the authors, it’s to come to class prepared to discuss what you did and didn’t understand so that you can build these skills. This is both a discussion-based and writing-based class. Part of the skill building in this class is learning how to talk about scientific results and express your opinions. It is not to get everything right or be as knowledgeable as the authors.
*What to Bring to Class:
For each paper, the minimum is to be able to:
1. Locate the biological question the authors are trying to address.
2. Pick one of the figures from the text and be able to explain each of the panels, it can be any figure.
3. Write down 3 questions about the paper. It can be a question about a method, why the authors chose to do something, or something about the broader relevance. If you don’t understand an aspect of the paper, this is where you address your gap in understanding.
4. Generate your perspective on how this paper contributes to our ideas about “What is an organism?”
DATE ASSIGNMENT
Individuals or Communities?
W 9/2 Introduction to the Class
F 9/4 “Assignment #1 Due Before Class
Wilson, H.V., “On Some Phenomena of Coalescence and Regeneration In Sponges”, The Journal of Experimental Zoology, 1907”
W 9/9 Ramon Massana, The nitroplast: A nitrogen-fixing organelle, 2024
F 9/11 Manko et al., “The evolution of an individual-like dispersive stage in colonial siphonophores” Current Biology 35, 4946-4958, 2025
W 9/16 Herron and Michod, “Evolution of Complexity in the Volvocine Algae: Transitions in Individuality Through Darwin’s Eye”, Society for the Study of Evolution, 2007
Is Organism a Useful Concept?
F 9/18 Andersson, J.O. “Is Buchnera a bacterium or organelle?” Current Biology Vol 10: 23, 2000
W 9/23 “(1) Anderson et al. “Clonal evolution and genome stability in a 2500-year-old fungal individual” Proceedings of the Royal Society B, 2018
(2) Brasier, C., “A champion thallus” Nature Vol 356, 1992”
F 9/25 Pineau et al., “Mosaic of somatic mutations in one of Earth’s largest organisms, Pando” Biorxiv 2025
Biological Altruism
W 9/30 “Keller and Ross, “Selfish genes: a green beard in the red fire ant”, Nature, 1998
Papers Due for Presentation”
F 10/2 Katoh-Kurasawa et al., “The greenbeard gene tgrB1 regulates altruism and cheating in Dictyostelium discoideum” Nature Communications, 2024
Networks & Collaboration
W 10/7 Song et al. “Defoliation of interior Douglas-fir elicits carbon transfer and stress signalling to ponderosa pine neighbors through ectomycorrhizal networks” Scientific Reports, 5: 8495, 2015
F 10/9 Presentation #1
W 10/14 Prindle et al., “Ion channels enable electrical communication in bacterial communities” Nature, 2015
F 10/16 Presentation #2
W 10/21 Pfeffer et al., “Filamentous bacteria transport electrons over centimetre distances”, Nature, 2012
F 10/23 Presentation #3
Are We Individuals?
W 10/28 Amy Howlett, “Defining Multicellularity: Evolutionary Features of Biological Individuality and Potential Exceptions” Gonzaga University, BIOL 399 May 2026.
F 10/30 Presentation #4
W 11/4 “Tillisch et al., “Consumption of fermented milk product with probiotic modulates brain activity”, Gastroenterology, 2013
Review Article Topic Due ”