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IPAK EDU

BIOB - Spring 2025

TUES 11AM ET, Start date TBA

Instructor: James Lyons-Weiler

Topic 1. Reading Gene Sequences: PCR and DNA Variation Analysis
We and other organisms employ polymerase to make copies of DNA. Humans have managed to reproduce this process in the test tube to produce millions of copies of specific, targeted DNA sequences. This process is essential for understanding the genetic basis of disease, how genomes work, and how species are related to each other. In this section, we’ll review how PCR works; how we sequence RNA viral genomes and look at some fascinating aspects of microbial biology revealed by sequence analysis. We’ll analyze a few sequences ourselves using some of the tools of Bioinformatics.

Concepts: Polymerase Chain Reaction; Reverse Transcript PCR; Microbial Point of Origin; GC-Skew, Intro to Bioinformatics

Concepts: Biotechnology, PCR, RT-PCR, Bioinformatics (DNA Sequence Analysis), BLAST Algorithm

Topic 2. Gas and Fluid Transport
Oxygen and carbon dioxide transport across membranes and throughout the circulatory systems and organs. Other dissolved gases. Oxygen and wellness. Carbon dioxide toxicity. Carbon monoxide poisoning. Dissolved nutrients.
Concepts: Circulation, transport, gas exchange.

The fluids in our body transport gases and our circulatory system transports fluids, cells and signaling molecules.

What happens when things go wrong. Relevance to society today.
Coagulopathy

Topic 3. Neurobiology
Simple nervous systems exist that pulse information across a simple net. More complex nervous systems result from diversification of nerve cells and their relatives and specialization of function. Some spectacular feats of development place the parts of the developing nervous system in the right place - at the right time. We’ll explore the central nervous system (CNS) and the autonomous nervous system (ANS). How do nerve cells communicate? What is a thought? What is a memory?
Concepts: The biological and electrochemical basis of nerve transmission, general human nervous system anatomy, memories, thoughts, knowledge, consciousness.

Ok, so we might not define once and for all consciousness.Or thoughts.Or memories.But we’ll have a look at the Central Nervous System and the Autonomic Nervous System.

What happens when things go wrong. Relevance to society today.

Topic 4. Hormones: The Symphony of the Glands
Our bodies speak to themselves, with one part telling another part “it’s time to wake up”; “it’s time to go to sleep”; “it’s time to make sperm”; “it’s time to make milk”. These signals are part of our endocrine system - and we hardly realize when these signals get passed and are received. Scare someone, they will feel an adrenaline rush. Love someone, they feel endorphins. As organisms, we respond to these signals most naturally. Making sense of us requires more than understanding anatomy, where organs are located, and how neurons work. It requires an appreciation for the waves of states of being that pass through us, and make us and other animals (we presume) feel a certain way. Hormones are essential for brain function, sexual development, falling in love, and of course human reproduction cycles. What happens when things go wrong. Relevance to society today.

Concepts: Hormones. Cell-to-cell signaling. Receptors.

Topic 5. The Human Immune System
The mammalian innate and adaptive immune systems are remarkable feats of evolutionary engineering. We’ll learn how the body reacts to initial infections, and how it learns to produce antibodies that can match just about any foreign antigen. Innate immunity. The immune system of the brain. We’ll look at common types of autoimmunity and study specific mechanisms of how and why an immune system can even turn on itself.

What happens when things go wrong. Relevance to society today.
Topic 6.Principals of Evolution

Given a set of conditions, evolution will happen.Genetic variation.Heritability.Relevance to survival and reproduction. Limits of evolution.The role of population size on drift.Natural selection.

I’ll give a special presentation on the Realms of Evolution and how human cognitive plasticity is about the generate two new realms of evolution The future of humans and our planet may ultimately depend on whether we choose to create these two new realms.

Topic 7 Modeling Evolution

Students sometimes perceive evolutionary processes better using simulations to show the effects of mutation, drift and selection.

Topic 8 Protists

They are small- but they are everywhere and vastly outnumber all other Eukaryotes.We’ll focus on types, yes, but also on how these organisms make a living.Origins and diversification of Eukaryotes.

Topic 9 Plants

Understanding life on earth is impossible without understanding the history of the evolution of plants.How did they invade land?How did they effect earth’s atmosphere and the evolution of animals?How have they diversified? When did the first flower bloom?How do they reproduce? How do plants evade predation? Symbioses.

Topic 10 Fungi

The cellular biology and reproduction cycles of fungi are unusual.They may be the largest organisms to ever have lived.How do they make their living? How have they diversified? How do they reproduce?Symbioses.

Topic 11 Animals (Invertebrates)

The Invertebrates are tough crowd – they are among the oldest surviving lineages of animals on the planet.How have they diversified?How do they make their living?How do they reproduce?Some are essential to the survival of humans.Their history is the history of the Animal kingdom.

Topic 12 Animals (Vertebrates)

Evolutionary newcomers, the vertebrates are invertebrates with a few add-ons.How did they diversify?How to they make their living? How do they reproduce?Symbioses.

Topic 13 Ecological Processes

Competition or collaboration? Each species has a niche.It is role to play, or an occupation?Or neither?Principal of competitive exclusion. Predator/Prey relationships.Patterns of diversity.

Topic 14 Modeling Ecological Processes

Simulations sometimes help students understand ecological dynamics.Systems dynamics, chaos theory, fractal processes like risk recombination and disturbance all play an underappreciated roles in the outcome of ecological processes.

Topic 15 Humans in Their Environment

Can you think of your own species as a species in its environment?What characteristics make humans successful?Are we too successful?What attributes do we seem to lack that might help make us better stewards of Planet Earth?

Recommended Books
Campbell Biology Ed 11 (or earlier)

Recommended Readings/Videos
You will receive recommended readings associated with each lecture. Please try to read these before the lecture.