Programming and Data Science for Biologists (PDSB) will introduce students to fundamental computational skills and concepts for working with large biological data sets. This will include an introduction to several programming languages (Python, R, Julia), and in-depth training in one language in particular (Python). We will cover tools for collaboration and version control (git, GitHub), and how these tools can be used to host and share code, data, and websites. A core focus throughout the course will be reproducibility and learning tools (jupyter) and practices for this purpose. We will learn to organize and structure data for statistical analyses (DataFrames, arrays, datatypes), and explore tools for scientific analyses (scipy, pymc3, scikit-learn, keras) and visualization (matplotlib, toyplot, bokeh). Exercises and assignments will introduce students to large empirical datasets used in the biological sciences, from studies of genomics to biodiversity. The latter half of the class is organized around individual projects, in which students will be guided to design a command-line program and/or API for performing a specific type of analysis. Computer programs are ubiquitous in biology, but few biologists receive formal training in designing and writing software. This course offers a deeper introduction to computational techniques and algorithms commonly applied to biological datasets.

Prerequisite(s): One year of introductory biology or permission from the instuctor

Prerequisite(s): Prerequisites: (EEEB UN1010) or (EEEB UN1011)

In this course we take an integrative and comparative approach to understanding the sexual lives of primates.  Focusing on mating and reproductive behavior with an explicitly evolutionary perspective, we will identify the fundamental principles of how and why selection has favored particular behaviors and morphologies in different primate species.

Genome sequencing, the technology used to translate DNA into data, is now a fundamental tool in biological and biomedical research, and is expected to revolutionize many related fields and industries in coming years as the technology becomes faster, smaller, and less expensive. Learning to use and interpret genomic information, however, remains challenging for many students, as it requires synthesizing knowledge from a range of disciplines, including genetics, molecular biology, and bioinformatics. Although genomics is of broad interest to many fields—such as ecology, evolutionary biology, genetics, medicine, and computer science—students in these areas often lack sufficient background training to take a genomics course. This course bridges this gap, by teaching skills in modern genomic technologies that will allow students to innovate and effectively apply these tools in novel applications across disciplines. To achieve this, we implement an active learning approach to emphasize genomics as a data science, and use this organizing principle to structure the course around computational exercises, lab-based activities using state-of-the-art sequencing instruments, case studies, and field work. Together, this approach will introduce students to the principles of genomics by allowing them to generate, analyze, and interpret data hands-on while using the most cutting-edge genomic technologies of today in a stimulating and engaging learning experience.

Enrollment limit 25

The Amazon Basin is one of the largest equatorial forests on earth.  Far from being an untouched bioma the Amazon has a rich and instigating sociobiodiversity that can be apprehended in its uniqueness since pre-colombian times.  History, culture, politics correlated with hydrology, climate and ecology are elements for the understanding of contemporary dynamics in the Amazon.  The course aims towards an interdisciplinary approach of the Amazon as a unique ecosystem in Latin America which reflects a myrad of questions crucial for the understanding not only of South America but of nature and society in modern times.

Controversial issues that exist in current biological/physical anthropology, and controversies surrounding the descriptions and theories about particular fossil hominin discoveries, such as the earliest australopithecines, the diversity of Home erectus, the extinction of the Neandertals, the evolution of culture, language, human cognition.

Enrollment limited to 15 students plus instructor approval.

Prerequisite(s): A course in evolutionary biology such as EEEB W1010 Human Species, W1011, Behavioral Biology of Living Primates or EEEB W2001 Environmental Biology 1 is highly recommended. Or instructor approval.

This course addresses the role of evolution in contemporary human social behavior including such topics as kind selection, sexual selection, parenting, altruism, and conflict. Populations explored will include both industrialized and traditional societies with an emphasis on the interaction between evolutionarily influenced behavior and the local ecological context.

Priority given to students with backgrounds in ecology or plant systematics. A survey of the relationships between people and plants in a variety of cultural settings. Sustainability of resource use, human nutrition, intellectual property rights, and field methodologies are investigated.

Prerequisite(s): One year of college Biology.

Forest Ecology focuses on interpreting and understanding pattern and process in forested ecosystems. These ecosystems include the assemblages of trees and the biological communities and environments in which they exist. The complex interactions among the organisms and the physical environment are a major focus of this course. The course involves lecture, literature discussion, and field laboratory components, with an emphasis on the analysis and interpretation of student-collected data.

Lab Required.

Discussion Section Required.

This course will provide an introduction to ecosystem ecology. Topics include primary production carbon storage, nutrient cycling, and ecosystem feedbacks to climate change. By the end of the course, students will be well versed in the basics of ecosystem ecology and have exposure to some current areas of research. Topics covered will include some aspects that are well established and others that are hotly debated among scientists. Throughout the course, students will be encouraged to think independently and act like research scientists.

Fish are an incredibly diverse group with upwards of 27,000 named species. They are important ecologically, represent one of the major vertebrate lineages and face numerous conservation threats. This course will provide students with the tools to understand how the evolution, systematics, anatomy, and diversity of fishes influence their conservation status.

Prerequisite(s): EEEB 2001 and 2002 or equivalent or instructor approval.

An advanced survey of the basic concepts and theories of ecology and evolution, with particular emphasis on topics relevant to conservation biology.

In this course, will we use evolutionary genetic principles and population genetic models to describe the extent and distribution of genetic variation in populations and species and determine ways to conserve it. A basic knowledge of genetics and mathematics is assumed.

The course will introduce students to wildlife diseases, disease ecology and conservation, ecosystem health, and conservation medicine.

Maximum: 25 students.

Prerequisite(s): EEEB 2001 and 2002 or equivalent.

The basic ornithology class lays the foundation for more in-depth study as it presents an overview of avian evolution, ecology, and current conservation issues.

Recommended for archaeology and physical anthropology students, pre-meds, and biology majors interested in the human skeletal system.

The course provides an intensive study of human skeletal materials using anatomical and anthropological landmarks to assess sex, age, and ethnicity of bones. Other primate skeletal materials and fossil casts are used for comparative study. G4147–skull, G4148–postcranial bones.

Prerequisite(s): Calculus, Introductory Biology

This course will provide an introduction to theoretical ecology. Topics will include population, community, ecosystem, disease, and evolutionary ecology. Lectures will cover classic and current concepts and mathematical approaches. The numerical analysis laboratory will cover computational tools for numerical and graphical analysis of the models we cover in lecture, using MATLAB. By the end of the course, students will be well versed in the basics of theoretical ecology and will be able to read theoretical ecology literature, analyze and simulate mathematical models, and construct and analyze their own simple models.

Lab Required.

Changes in land use and land cover underlie multiple environmental and sustainability concerns, including conservation of biodiversity, impacts of climate change, climate mitigation through terrestrial carbon storage, urbanization and watershed protection. This class provides basic theory in landscape analysis and training methods for analyzing landscapes, focusing on interpretation of satellite images.

Prerequisite(s): Environmental Biology 1 or equivalent; instructor approval.

Marine ecosystems are among the most threatened on the globe, and thus there is a pressing need to develop and implement effective conservation and management measures. Moreover, because marine environments differ in their physics, chemistry and biology, conservation in the marine realm is fundamentally different than in terrestrial habitats. This course is intended to educate students – as members of our global society – as to the basic principles of marine biology that are necessary to understand the most pressing environmental problems affecting the marine sphere. We will do this through providing overviews of physical and biological processes central to understanding marine ecology, examining the impacts of human activities on these processes and on marine environments and communities, and considering potential actions to mitigate or lessen the effects of these activities.

Prerequisite(s): Introductory course in Biology or Evolution

This taxon-based course provides students with a basic understanding of the diversity and natural history of the mammals. Broad coverage of mammalian biology includes: morphological adaptations, evolutionary history, ecology, social behavior, biogeography, and conservation.

Prerequisite(s): At least one course in Introductory Biology.

The course explores the science of herpetology in three parts: 1) the evolution and ecology of amphibians and reptiles; 2) their physiological adaptations; and 3) requirements for conservation, management, policy and monitoring.

This course presents an overview of migration, from the selective pressures animals face in migrating to the mechanisms of navigation and orientation. We will explore migration in a variety of animal taxa. Bird migration will be studied in-depth, as birds exhibit some of the most spectacular long distance migrations and are the most well-studied of animal migrators. The challenges of global climate change and changing land use patterns, and how species are coping with them, will also be explored.

Enrollment limit 25, field trips will be scheduled.

The course focuses on human identity, beginning with the individual and progressing to communal and global viewpoints using a framework of perspectives from biology, genetics, medicine, psychiatry, religion and the law. W4321 evolved from a Columbia College Core Capstone course developed initially from a Ford Foundation grant to the Center for the Study of Science and Religion, and is cross-listed as well with the Center for the Study of Ethnicity and Race. As a graduate level course, it is open to interested seniors and graduate students including those from the Medical Center campus.

This course explores human adaptation from a biological, ecological and evolutionary perspective. From our earliest hominin ancestors in Africa to our own species’ subsequent dispersal throughout the world, our lineage has encountered innumerable environmental pressures. Using morphological, physiological and behavioral/cultural evidence, we will examine the responses to these pressures that helped shape our unique lineage and allowed it to adapt to a diverse array of environments.

This class examines the social, ecological, and political-economic roles of what and how we eat from a global perspective. Discussion will include how people across cultures derive identity through food gathering, preparation, and eating systems, as well as the relationships between culture and diversity of food systems.

Enrollment Max 25

Prerequisite(s): Instructor approval.

Many areas of the world with high biological diversity also have high levels of linguistic diversity (a proxy for cultural diversity). These places are generally in parts of the world that have been, until quite recently, at the frontiers of resource extraction, human migration and resettlement, and capital expansion. Cultural, linguistic, and biological diversity are now imperiled by the same threats (including resource extraction, human migration and resettlement, and capital expansion). This course will explore how different fields have sought to understand and sustain the reciprocal, mutually influencing relationships between human societies and their environments. The term “biocultural diversity” – which denotes the truism that human societies influence and are influenced by the environments of which they are a part – is relatively new (although increasingly in use). Students will be able to differentiate how different scholars and academic traditions define and apply biocultural diversity and will explore its application in biodiversity conservation and cultural revitalization through case studies.

Prerequisite(s): E3B courses in Ecology, Evolution, and/or Biodiversity or instructor approval.

Survey of current advances in scientific research that focuses on the role biodiversity plays in governing ecological processes (e.g. biogeochemistry, resisting invasion by exotic species, or stabilizing communities) and ecosystem services (e.g. soil fertility, water quality, climate regulation).

Prerequisite(s): upper-division undergraduate or graduate status.

Introduction to phylogenetic relationships, evolution and ecology of the major groups of arthropods, with emphasis on insects. Lab: identification of common families of spiders and insects of the northeastern United States.

Undergraduate Environmental Biology majors have priority. Enrollment limited to 25.

From Aristotle to the Bell Curve, this course examines the history of race as a biological concept. We will explore the complex relationship between the scientific study of biological differences, real, imagined, or invented and the historical and cultural factors involved in the development and expression of “racial ideas.”

Enrollment limited to 15.

Incoming MA students aiming for the thesis-based program are guided through the process of defining a research question, finding an advisor and preparing a research proposal. By the end of the semester the students will have a written research proposal which will be submitted to potential advisors for revision. Subject to a positive review

Mandatory for all 1st year E3B MA students in thesis based program.

Incoming MA students aiming for the thesis-based program are guided through the process of defining a research question, finding an advisor, and preparing a research proposal. By the end of the semester the students will have a written research proposal to submit to potential advisors for revision. Subject to a positive review of the research proposal, students are allowed to continue with the thesis-based program and will start working with their advisor. The course will also provide an opportunity to develop basic skills that will facilitate the reminder of the student’s stay at E3B and will help in their future careers.

A survey of vascular plants with emphasis on features of greatest utility in identifying plants in the field to the family level. This will be coupled with a survey of the major plant communities of northeastern North America and the characteristic species found in each. The course will consist of one lecture and one laboratory per week with several lab sessions extended to accommodate field trips to local regional natural areas.

Prerequisite(s): Some background in Ecology, Evolutionary Biology, and/or Statistics is recommended.

An introduction to the theoretical principles and practical application of statistical methods in ecology and evolutionary biology. The course will cover the conceptual basis for a range of statistical techniques through a series of lectures using examples from the primary literature. The application of these techniques will be taught through the use of statistical software in computer-based laboratory sessions.

An exploration of data-based models as tools for inference in ecological research. Emphasis on the formulation and development of scientific models, modern statistical and computational methods for estimating model parameters, and evaluation of alternate models using strength of evidence. Laboratory exercises challenge students to apply these methods to real ecological data, including their own research. The course also explores the philosophical underpinnings of different statistical schools of thought including frequentist, likelihoodist, and Bayesian approaches.

Lecture course covering principal topics of evolutionary biology from genetics, genome organization, population and quantitative genetics, the history of evolutionary theory, systematics, speciation and species concepts, co-evolution, and biogeography.

Priority given to first-year students in EEB

Prerequisite(s): Required course for first year Ph.D. students and second year M.A. students on academic track

Covers foundational topics and developments in many branches of ecology, including population, community, and ecosystems ecology.

Broad coverage of the fundamentals and recent developments in the field of primate behavior. An evolutionary perspective in the study of behavior is stressed, but is not limited to questions of evolutionary function. Constraints on evolutionary design inherent in the causal mechanisms underlying behavior (e.g. limits on cognition).

This course will introduce the Coupled Natural and Human system framework to study socio-ecological systems and introduce active learning of Agent-based models (ABM) as one of the most common methods to study CNH systems.

Prerequisite(s): Degree in Biological Sciences.

Seminar series includes lectures on methods and case studies of specific biological research projects; emphasis on evolution, ecology, and conservation biology. Weekly lectures by Columbia faculty, researchers, students and guest speakers.

Graduate students in EEB program have priority.

Prerequisite(s): Preference given to graduate students in EEB or Anthropology.

The assumptions upon which community-based conservation and development projects are based, their successes and shortcomings within the context of history and the environment. Experienced guest lecturers.

How to formulate research hypotheses, choose a design, and collect, analyze and present data. Students undertake individual projects on zoo or park animals.

This course will help guide E3B Ph.D. students towards candidacy by teaching them the skills necessary to be effective and independent scientists. Students will conduct an extensive literature review, write a preliminary dissertation proposal, and present their research ideas to the group on multiple occasions. Students will learn how to give and receive constructive written and oral feedback on their work.

Prerequisite(s): Biology, Ecology, Genetics, and Evolution.

This course is an introduction to the applied science of maintaining the earth’s biological diversity, its landscapes, and wilderness. The course will focus on the biological principles relevant to biodiversity conservation at the genetic, population, and community and landscape levels.

Prerequisite(s): One graduate semester completed.

Research opportunities for graduate students: experimental design, development of tests for specific hypotheses, acquisition of new techniques, analysis of data, interpretation and discussion of results.

EEB graduate students only.

Supervised directed readings and literature review in areas relevant to a student’s research program.