Stuff(t)�(or the Protocol of Biological Dynamics)

Skills Week

MBL Physiology Course

Summer 2024

Adventure Map

a physical view

of biological phenomena

(for your rotations

and “real life”)

physical

models

order-of-magnitude

estimates

pen-and-paper

calculations

numerical

simulations

in Python

theory —

experiment

dialogue

Math and

computation

as biology’s

next microscope

the power

of abstraction

biological

numeracy

statistical

analysis

The Incredible Diversity of Time Scales in Biological Processes

Stuff(t) Pervades All of Science�Galileo and Falling Bodies

Stuff(x,t) Pervades All of Science�The Belousov–Zhabotinsky Reaction

Stuff(t) Pervades All of Science�Human Impacts and the Keeling Curve

Stuff(t) Pervades All of Science�Dynamics of the Immune System

The Step-In-Time Protocol

Stuff(t) Pervades All of Science�Dynamics of Bacterial Growth

• Your turn: Estimate the division time in this movie
• What sets the time scale for bacterial division?
• Let’s answer this question by developing a feeling for the organism!

​

Neidhardt and His Lifelong Love for dN/dt

Measuring Growth Dynamics in Bulk

Bacterial Growth Dynamics Revealed the Great Insight from Monod and Jacob: Genes That Control Other Genes

Monod (1949)

Single-Cell Bacterial Growth in High Throughput: The Mother Machine

Suckjoon Jun @ UCSD

The Mathematics of Change

A Model of Bacterial Growth

A Recurring Theme: Divide and Conquer�The Example of Riemann Integrals

Divide and Conquer in Time to Integrate Differential Equations Using the Euler Method

A Chat with ChatGPT

…

Our First Key Equation: Exponential Growth

A Feeling for Exponential Growth

• Your turn: How long would it take for E. coli doubling every 30 minutes to cover the whole surface of the Earth?

Logistic Growth Accounts for the Carrying Capacity of a Cell Culture

Logistic Growth

Measuring Colony Growth and Fitting for the Growth Rate

Stuff(t) Leads Us to “Dynamical Systems”�Differential Equations as Update Rules

Adventure Map

a physical view

of biological phenomena

(for your rotations

and “real life”)

physical

models

order-of-magnitude

estimates

pen-and-paper

calculations

numerical

simulations

in Python

theory —

experiment

dialogue

Math and

computation

as biology’s

next microscope

the power

of abstraction

biological

numeracy

statistical

analysis

Our First Exercise In Mathematicizing�Our Pathetic Thinking