ANTH 488 A: Agroecology

Spring 2024
TTh 3:30pm - 5:20pm / * *
Section Type:
Syllabus Description (from Canvas):

Decolonizing the Soil Rhizosphere and Human Gut Microbiomes


Offered in Partnership with The Acequia Institute 

Instructor of Record: Professor Devon G. Peña

On Duwamish, Suquamish, Tulalip, and Muckleshoot lands and waters in Washington

On Nuchuu (Caputa Ute) - Dinè - Tewa - Genizarx lands in Colorado and New Mexico

Land and water acknowledgement without action on the ground is a cheap performative form of allyship.

What are you doing today to be a good ancestor?

The 2020 seed sanctuary milpa 2.jpg 

Note on Fig 1. (above). The 2020 Seed Sanctuary Milpa at The Acequia Institute, Rancho Chiquito.

San Francisco, CO. Elevation 8100 ft. (July 2020).

Class Meetings TTh 330-520 pm. Distance Learning via Zoom Live Streamed and Recorded Sessions.

Office Hours. Via  Zoom private meeting room; only by prior appointment. Message to Canvas my Inbox or email with Subj: 488 appt.

Zoom Virtual Office Link:

Contact info:

Remat milpa 1.jpgNote on Fig 2. (above). The 2020 Milpa at The Acequia Institute Almunyah.

Viejo San Acacio, CO. Elevation 7960 ft. (July 2020).

Catalog Course Description  Cross-cultural survey of agroecological research methods, theoretical problems, policy issues, and ethical debates. Local knowledge and ethnoscientific bases of alternative agriculture. Comparative political ecology of agroecosystems with a focus on indicators of social equity and ecological sustainability. (5 credits) NSc/SSc

Focus and Themes of the 2024 Seminar. Our focus this year takes us beyond the more typical "farm to table" discourse and instead pursues critical investigations on the connections between soil and gut health. More precisely we will examine the relationship between the ecology of the soil rhizosphere and a healthy human gut microbiome. We will begin by learning about methods, theories, and ethics in agroecology, the ethnoscientific basis of sustainable agriculture. We will then examine how this agroecological framework can inform critical review of a vast set of scientific discourses on the impact of modern agricultural technologies on the rhizosphere and the human gut microbiomes. Each student will address the dirt-to-gut connection by developing a design proposal for an agroecological restoration project that draws connections between cultural and ecological integrity in our relations to land, water, and the entire 'web of life.' 

My approach to the complex and challenging theme of "dirt-to-gut" is grounded in my own experiences as a decolonial biodynamic farmer with training in collaborative interdisciplinary research methods that allow me to integrate methods and materials from agroecology, ethnoedaphology and ethnopedology, and conservation biology with related studies in fields as diverse as risk science, epigenetics, foodways, nutrigenomics, diet and nutrition, and the study of Indigenous heritage cuisines.

Considering a wide range of risk science studies is an important part of this approach. This involves engaging the evidence offered by studies of the health of the rhizosphere and human gut microbiomes.  This year we will focus on the effects of ubiquitous use of the herbicide glyphosate and its adjuvants and contrast conventional, organic, and biodynamic farming systems and their effects on the nutrient density of food and forage crops. We will engage a wide variety of scholarly and scientific discourses many of which are unfamiliar to us in the social sciences and humanities.

This approach is based on the principle that we do not have to be scientists to become scientifically literate but this also involves recognizing there are many pathways to practicing science including those based on Indigenous epistemologies. My ultimate aim is to introduce these varied epistemes and discourses to a new audience while also constantly working to "decolonize" the course texts by identifying Indigenous analogs, challenging binary constructs, and addressing erasures of Indigenous knowledge domains and other instances of epistemic violence. 

Finally, given the $2.3 million in grants we are administering under the San Luis Food Sovereignty Initiative in the Culebra acequia watershed, we will be exploring one approach to addressing a community health crisis. Costilla County has a 15 percent rate of diabetes affecting near every family in this Spanish-Mexican-Genizaro community in south central Colorado. The initiative involves transforming the historic R&R Market (est. 1857) into a worker self-managed community food cooperative linked to local acequia farmers and youth apprentices. We will visit with the farmers, youth apprentices, community organizers, and Market staff over the entire three weeks of field-based instruction.

Diagram of Soil Health and how the health of our foods, farms, and ecosystems depend upon the health of our soils.

Note on Fig. 2 (above). Indigenous farmers have understood soil as a living organism for millennia and this knowledge is now confirmed by agroecological and related sciences. Evidence suggests soil health is the underpinning of environmental, community, and human health.

A decolonial approach to the dirt-gut problematic starts with the proposition that the land (soil) has suffered the same historical trauma and structural violence as Indigenous peoples displaced from ancestral homeland commons. Cultural genocide, soil erosion, and the decline of phyto-diversity are by-products of the same processes unleashed by settler colonialism. This violence is currently encapsulated in modernist corporate projects to patent life and control seeds resulting in certifiably catastrophic consequences for public health especially in the most vulnerable communities. How do we critically marshal these scientific discourses to ally with Indigenous perspectives on healing the colonial wounds affecting the health of the soil and our bodies?

RAFI food-variety-tree.gif


Note on Figure 3 (above). The decline of agro-biodiversity is a major threat to food sovereignty and global food security. The decimation of crop phytodiversity is associated with changes in the nutrient density of major  food crops. The decline is associated with settler colonial modernist projects involving agricultural biotechnologies and practices that degrade the rhizosphere (root zone) microbiome with possible effects on the human gut microbiome. Documented impacts of soil erosion, compaction, demineralization, and salinization as well as toxicity are affecting vital micro-organismic communities in the root zone. These changes also have profound and usually overlooked impacts on human health and wellbeing.

Course Assignments

    1. Agroecological design project. Each student will outline an agroecological restoration project that addresses the "dirt-to-gut" connection in a place-based manner. For details please consult Assignment Handout #1. For a sample design proposal, consult Assignment Handout #2 (Ten-Year Plan). For the Prospectus of our Food Sovereignty Project (Growing a Healthy Community Foodscape). Relevant appendices: Altieri et al on climate change farming. Companion Planting Chart.  
    2. Seminar participation. This includes contributions to seminar discussions during Zoom synchronous lectures or as posted to Canvas Discussion pages; participation includes summary statements on and questions to field-based co-teachers as arranged in the Course Field calendar below.

Assignment Grading (100 point scale; GPA rated)

    1. Agroecological design project.  Total of 80 points.
    2. Participation. Total of 20 points. 

Download and review GPA scale here. This scale describes the conversion from the 100 percent grading scale to the GPA (Grade Point Average) score of 4.0 to 0.0.

Course Texts There are no required textbooks to purchase and all Open-Access readings are embedded in the course calendar below and may also be downloaded from the Files Page.

Learning Goals

  1. Become well grounded in the scholarly and activist discourses framing the field of agroecology especially with a focus on the transformative impact of Indigenous and Native studies.
  2. Learn about the interdisciplinary range of methods and materials used in and produced for and by students of agroecology, permaculture, biodynamics, etc. but above all value the epistemic disobedience grounded in the knowledge, belief, practice ensembles of deeper Indigenous sources.
  3. Understand the variety of recent theoretical developments including: decolonial; feminist; queer; Marxist; social movement; indigeneity; and alterity.
  4. Develop critical awareness of the social, cultural, ecological, and political economic effects of white settler colonialism and capitalism.
  5. Develop your capacity to critique capitalism in a manner that empowers existing and emerging alterNative solidarity economies.
  6. Become literate in the perspectives and principles of Indigenous epistemology; embrace the practice of epistemic disobedience and delinking of your own work from institutions, norms, and relations of settler colonial and capitalist domination.
  7. One does not have to be a "scientist" to become scientifically literate: This means learning to decode and understand peer reviewed scientific discourses.
  8. We also must understand that "Western" science is only one among many paths/paradigms to the development of knowledge systems about the human relationship to the environment. Ethnoscience is a term that refers to the thousands of Indigenous knowledge systems that avoid the subject/object dichotomy and the positivist separation of "facts" from "values" resulting in knowledge and praxis ensembles that promote resilient co-habitation of Earth's ecosystems.

Policies and Expectations

Attendance.  Regular on-time attendance is encouraged. There is much that happens during class time that adds to your educational experience beyond what you can learn from just reading and writing. Students are to enter the classroom space with a positive mind and willingness to engage and be active participants with a community of learners. If an emergency arises which prevents you from attending, it is your responsibility to gather notes from your peers.

Assignments and late papers.  All assignments are to be turned in on time or penalties will be assessed.

Class behaviors and civility.  Any form of harassment against other students—including racist, sexist, homophobic/transphobic, or threatening comments and behaviors that create a hostile and unpleasant environment will not be tolerated and is a violation of university harassment guidelines and respectable human behavior. We will strive to create a classroom where respect for all people and diversity of opinion is the standard and desired. These rules apply to on-line sessions.

Academic honesty.  Please adhere to the university’s academic standards including those governing academic dishonesty, including cheating, plagiarism (submitting the language, ideas, thoughts or work of another as one’s own), or fraud. The university considers plagiarism a serious academic offense, which subjects those engaging in the practice to severe disciplinary and grading consequences.

Disability statement. Students with special needs who need assistance should contact the Disability Resource Center immediately ( (Links to an external site.)). Please meet with me early in the quarter if you require accommodations. I will make reasonable efforts to accommodate your special needs.

Religious accommodations. Washington state law requires that UW develop a policy for accommodation of student absences or significant hardship due to reasons of faith or conscience, or for organized religious activities. The UW’s policy, including more information about how to request an accommodation, is available at Religious Accommodations Policy ( (Links to an external site.). Accommodations must be requested within the first two weeks of this course using the Religious Accommodations Request form (


REQUIRED READING: Before our first seminar meeting on July 21, I am asking all students to read and reflect on the text by Linda T. Smith from her book, Decolonizing methodologies. Chapter 8 presents "25 Indigenous projects" that will guide our critical readings of the course texts and also provide a framework for the development of the students' agroecology restoration design projects. The PDF may be downloaded here: Linda T. Smith, 1999. 25 Indigenous projects.

NOTE: It is also recommended that each student take time to watch this video before we meet for the first session of the seminar on July 23. The World According to Monsanto is a 2004 documentary film which makes an in-depth investigation into unlabelled, patented, genetically engineered foods that have quietly made their way onto grocery stores in the United States for the past decade. It voices the opinions of farmers in disagreement with the food industry and details the impacts on their lives and livelihoods from this new technology, and shines a light on the market and political forces that are changing what we eat.

The World According To Monsanto (Full Length)



T-26 Introductions. Overview of seminar: Learning objectives; texts; requirements; logistics. Seminar topics and themes.

Two video clips to watch over before our first seminar session.

Recommended Video: Get to know our work at The Acequia Institute. 10 minute clip on the "Wildness" project.

Devon Pena - Wildness

Recommended Video: Prof. Peña Interviewed by host Alan Wartes of Think Radio. We spoke about advocacy of the “decolonization of identity” among Indigenous peoples and how everyone can benefit from this concept.   The title  was  fashioned  by  Mr.  Wartes." Decolonizing Everything.

Th-28 Agroecology: Indigenous knowledges and practices of sustainable/regenerative agriculture. Centers of origin and diversification of landraces. 


T-2 San Luis Concho and chicos del horno. Hopi agroecology of landrace maize.  Seed rematriation and food sovereignty. The seed rematriation campaign. Rowen White (Akwesasne).

Required Video: Rowen White, Seed Keeper from Akwesasne. In this 2018 NOFA Summer Conference keynote address Rowen shares stories of the rematriation of seeds, where seeds come back to their communities of origin, and encourages people of all backgrounds to reconnect with their ancient food ways.  Rowen White - Rematriation of Seeds

  • Recommended Video: Miguel Altieri. Earth Talk: Agroecology: Who will feed us in a planet in crisis? Lecture delivered to Schumacher College, UK. 

Earth Talk: Agroecology: Who will feed us in a planet in crisis with Miguel A. Altieri

Th-4 Traditional polycultures and sustainability. A close look at the landscape ecology of contemporary Mayan milpas: Shifting mosaics in long-duration rotation islands. Remaking the soils of culture: Indigenous ethnopedology and ethnoedaphology.

T-9 The environmental history of soil degradationMyths of modern agriculture

Today's highlighted music video clip. Loli Cosmica.  Version de cancion medicina de la comunidad Shuar de Ecuador. [Trans. Version of a medicine song from the Shuar Indigenous culture of Ecuador]. El autor es Nase Chiriap . En Shuar, "Tzen Tze Re Re" significa la flecha que avanza y abre las puertas .

Th-11 "A Seed Sanctuary and Regenerative Farming at The Acequia Institute."

Field Session and Farm Tour: Devon G. Peña. Viejo San Acacio & San Francisco, CO. Please view posted vignettes before class.

T-16 Rise of soil restorationist movements.  Settler colonial regenerative agriculture. Deep seeds and First foods: Indigenous food autonomy and self-determination(sovereignty).

Th-18 Indigenous knowledge, survivance, and the struggle against soil 'governmentalities.' 

T-23 Indigenous knowledge and soil biodynamics: The deeper Indigenous roots of permaculture, biodynamics, and regenerative agroecosystems. Decolonizing the science and politics of soil conservation. The gut/spirit/place connection: Decolonizing Indigenous cuisine and foodways. 

Farm Tour and Guests: Farm Tour: A visit to the Culebra Creek ecological restoration area at the Almunyah de las Dos Acequias. 

II. Into the Root Zone: Rhizosphere Ecology and Human Health

Th-25 Conceptualizing the rhizosphere 


Note on Figure 6 (above). A list of 30+ diseases that have dramatically increased in incidence since 1990 with the red line plotted and indicating increased use of the herbicide glyphosate in conjunction with GMO herbicide-resistant crops.

T-30  Microbiome Medicine: Challenging the genetic determinist paradigm?

This Chart shows a correlation between glyphosate Use and Super Weeds (1).jpg


Th-2  No class. Work and consultations on design projects.

 T-7 Nutrigenome and Gut Microbiome. Glyphosate as case study of adverse impacts on soil rhizosphere and human gut microbiomes. 

 III. Decolonizing and Re-Indigenizing the Rhizosphere and Human Gut Microbiomes

 Th-9 Guest lecture: Kris Barney (Navajo farmer) on Indigenous agroecology and food sovereignty. 

The science of the rhizosphere in Diné traditional knowledge. The "microbial sponge" as "biotic pump." The place of soil in reviving Indigenous place-based knowledge, belief and practice ensembles. 

  • Required Podcast (27 mins):  James Skeet (Diné, Naabeehó). Mr. Skeet discusses in English and Navajo languages the science of the rhizosphere as seen through Indigenous ways of knowing and being in the world.  Link here: scroll down to the podcast, NAVAJO FARMING: HEALING THE SOIL PODCAST.
  • Recommended podcast: YouTube clip (55 mins). Online gathering, convened by the NM Healthy Soil Working Group. Watch a short presentation by James Skeet, followed by conversation with participants. James Skeet (Navajo) and his wife Joyce founded the Native-led educational non-profit Covenant Pathways and established Spirit Farm on Navajo Nation as a demonstration farm focused on healing the high desert southwestern soil with the intentional use of microbiology and composting. Their goal is to reclaim traditional farming and spiritual practices and pair them with regenerative methods to achieve resiliency and food sovereignty in the local Navajo and Zuni communities. To learn more about Covenant Pathways and Sprit Farm visit

Diné Regenerating Soil and Soul. 


T-14 Seed rematriation as as pathway to food sovereignty.

Visit the Seed Sanctuary at Milpa Alta farm.

Th-16. Film Watch Session and Discussion. "Gather" (2020, 1:14). Director: Sanjay Rawal. An intimate portrait of the growing movement amongst Native Americans to reclaim their spiritual, political and cultural identities through food sovereignty, while battling the trauma of centuries of genocide. Gather follows Nephi Craig, a chef from the White Mountain Apache Nation (Arizona), opening an indigenous café as a nutritional recovery clinic; Elsie Dubray, a young scientist from the Cheyenne River Sioux Nation (South Dakota), conducting landmark studies on bison; and the Ancestral Guard, a group of environmental activists from the Yurok Nation (Northern California), trying to save the Klamath river.

Required Film Discussion. "Gather" (2020, 1 hr. 14 mins.). "Gather" is the definitive Indigenous film on Food Sovereignty. 

T-21 Project Protect Food Systems Workers. Farm Worker Bill of Rights (SB 21-087) and the creation of the Promotoras Network serving farm and other food chain workers during pandemic times across the state of Colorado.

Th-23 Rethinking agroecology beyond academia as a community-based asset building movement.

T-28 Presentation of student design projects.

Th-30 Presentation of student design projects.





Catalog Description:
Cross-cultural survey of agroecological research methods, theoretical problems, policy issues, and ethical debates. Local knowledge and ethnoscientific bases of alternative agriculture. Comparative political ecology of agroecosystems with a focus on indicators of social equity and ecological sustainability. Recommended: ANTH 210. Offered: Sp.
GE Requirements Met:
Social Sciences (SSc)
Natural Sciences (NSc)
Last updated:
May 23, 2024 - 6:36 pm