Structure of this Book

Motivation

Bioengineering has an unusually wide purview. All engineering disciplines can overlap with biology, which makes the topics we work on some of the most diverse of any field.

Bioengineering departments, however, face the near-impossible task of preparing students to be every kind of engineer at once (while also being a biologist). The effect, especially at the start, is that the curriculum can feel less cohesive, and sometimes less rigorous, than a single-discipline major. That’s a reflection of bioengineering sitting at the confluence of several major disciplines. Berkeley’s own bioengineering major reflects this - we hope to give you both a core engineering education, and allow you to specialize in an area that you are most excited about.

This course leads with applications, while still trying to respect the first-principles physics, chemistry, and math you’re learning in your other courses. We could instead teach this class by starting with engineering fundamentals and providing applications second, for example by having modules on mass transfer, fluids, and so on, with biological examples tacked on at the end. We don’t, for two reasons. First, bioengineers won’t encounter problems structured that way in practice. You won’t set out to work on a mass transfer project. You’ll set out to build a diagnostic for a disease, but of course you’ll need to know how fluid moves. Second, a major goal of this course is to help you decide what you’re most interested in — maybe it’s genetically engineering plants, building the next generation of non-invasive imaging techniques, or designing at-home infectious-disease diagnostics. We hope that leading with broader examples, and pulling in engineering concepts as you need them, gives you a sense of which subfield you’ll want to specialize in later.

Modules

The class is organized into small modules that loosely align with our core tracks. For deep treatment of the material, you will need to align your coursework with one of our tracks. You may want to also consider a double major. In this class, we will cover:

  • Medical Devices — This module introduces a major organ (the heart) and discusses how we can measure its function. The heart is a pump that works through the coordinated activity of electrically conductive cells. We will learn about pressure waves and electrical activity, and how to measure these signals using an echocardiogram and EKG.
  • Engineering Biomaterials — Tissues are complex, and when they become diseased, often the only solution is a replacement organ from another person. A major goal of tissue engineering is to build artificial tissue to promote healing or restore function. We will use a mass balance to understand how to grow an artificial layer of skin (dermagraft) in a dish.
  • Statistical Inference — How do we know if our dermagraft improves healing? In general, how do we know if a treatment, drug, or intervention is actually effective? If we observe a difference in outcomes, how do we know if that was due to noise? To answer these questions, we will think about data distributions, sampling, and hypothesis testing. Although statistics may feel out of place, it permeates all of science.
  • Pharmacokinetics — The effect of a drug is heavily dependent on how it spreads in the body, and how fast it is degraded or excreted. We will use a type of mass-balance called a compartment model to understand how the drug changes in concentration over time.
  • Molecular Diagnostics — How can we measure a biomolecule? Life has already made a large number of biosensors! We discuss how antibodies have been co-opted as sensors and assembled into a working diagnostic test.
  • Cells and Biomolecules — The unit of life is a single cell. Although cells are very diverse, they share a common language - they are made of biomolecules (DNA, RNA, protein, lipids, carbohydrates). Understanding the molecular biology of the cell is a foundation for cell engineering, and synthetic biology.
  • Synthetic Biology — Reading and writing DNA is now easy, but how can engineers design new function from sequences? In this module, we will discuss how to assemble simple DNA circuits for expressing proteins. We will gain fluency in both the terminology of synthetic biology as well as the steps needed to cut and paste DNA.