Lecture Notes

We will post the slides from lecture as we go along in the course. Please note that these do not include the various goodies that we work out on the board in class, so don’t use this as an alternative to attending lecture! Please do not share these notes with anyone outside of the course.

Lecture 1 | We begin our discussion of the biogeography in the context of oceanic islands.

Lecture 2 | We finish up our puzzle of oceanic islands and examine biogeography in the context of microbial pathogens.

Lecture 3 | We conclude our discussion of biogeography by solving the puzzle of the 2010 Haitian cholera outbreak.

Lecture 4 | The concept of keystone species and trophic cascades are introduced, along with a brief description of the coming homework.

Lecture 5 | We give a brief history of dinosaurs and the fossil record and examine the limb-to-fin transition in the context of whales.

Lecture 6 | We conclude our discussion of the fossil record and examine the evolution of whales in the context of molecules and genes. We also briefly discuss the fin-to-limb transition and the transitional form Tiktaalik.

Lecture 7 | The facts of evolution.

Lecture 8 | We do a quick recap of the facts of evolution and discuss the mathematics behind the idea of genetic drift.

Lecture 9 | In this lecture, we examine of turning light into biological material beginning from the quantum mechanics of light absorption through the generation of ATP.

Lecture 10 | These slides are basically supporting material to complement class which was largely interactive and done on the board.

Lecture 11 & 12 | We derive quantitative models of gene expression using our knowledge of mRNA production and degradation rates as well as through a statistical mechanical approach. The bulk of these lectures were performed on the blackboard.

Lectures 13 & 14 | We look at organismal development using Drosophila melanogaster as our model organism. Here, we tie together much of our discussion on diffusion with the positioning of the cephalic furrow via the Bicoid morphogen.

Lecture 15 & 16 | We investigate how bacterial cells measure concentrations of molecules in their environment and control their directed motion. As with lectures 11 & 12, the bulk of this material was performed on the blackboard.

Recitation Notes

Materials relevant to the recitations will be posted here as the course carries onward.

Recitation 2 | This presentation has some interesting images to use for making estimates about the central dogma and we introduce the problem of the reintroduction of wolves to Yellowstone National Park. [PDF notes][data set] [paper]

Recitation 3 | This presentation has some details about deep time along with some fun order-of-magnitude estimates to understand how genetic information changes with time. [PDF notes]

Recitation 5 | These slides cover the principles of photosynthesis in a little more depth along with some fun estimates.

In-Class Readings

Readings mentioned specifically in class will be listed here as the course progresses.

Week 1 - Biogeography and Introduction

Freshwater paths across the ocean: Molecular Phylogeny of the frog Pychadena newtoni gives insights into amphibian colonization of oceanic islands by G. John Measey et al. Journal of Biogeography 34(1) 2007. This paper examines the biogeography and origins of the Pychadena newtoni frogs on São Tomé and Príncipe and their travel across Africa.

Nepalese origin of cholera epidemic in Haiti by R. R. Frerichs et al. Clinical Microbiology and Infection 18(6) 2012. This work determines the origin of the sudden Haitian Cholera outbreak in 2010 following the catastrophic magnitude 7 earthquake in January of that year. This study shows how sequencing can be used to track the geographic dispersal of life.

Floods, floodplains, delta plains - a satelite imaging approach by James P.M. Syvitski, Irina Overeem, G. Robert Brakenridge, and Mark Hannon. Sedimentary Geology 267 2012. This paper examines the geography of large floodplains all over the world and infers information regarding the frequency of large floods over time.

A First Exposure to Statistical Mechanics for Life Scientists: Applications to Binding by Hernan G. Garcia, Jané Kondev, Nigel Orme, Julie A. Theriot, and Rob Phillips. Self Published 2007. Statistical mechanics is a powerful tool for the quantitative analysis of the molecules of the cell that we will turn to repeatedly throughout the term. This article gives an introduction to the “statistical mechanics protocol” that can be used in problems ranging from the function of ion channels to how genes are regulated.

Cell Biology by the Numbers by Rob Phillips and Ron Milo. Garland Science 2015. This book gives a view of how biological numeracy can provide insights into a broad variety of topics in modern biology.

Week 2 - Trophic Cascades and Megafaunal Collapse

How should we be selecting our graduate students? by Orion Weiner. Molecular Biology of the Cell 25 2013. This paper gives an interesting perspective on what makes a”good” graduate student.

Some animals are more equal than others by Howard Hughes Medical Institute ** 2013. This fantastic video describes the experiment performed by Robert Paine that revealed the importance of keystone species.

Terror in Black and White by Robert L. Pittman and Susan J. Chivers. Natural History 12/1998 - 1/1999 . This magazine article describes the author’s observation of a coordinated killer whale attack on a pod of sperm whales off the coast of California.

Sequential megafaunal collapse in the North Pacific Ocean: An ongoing legacy of industrial whaling? by A. M. Springer et al.. PNAS 100(21) 2003. A sudden decline in the population of Stellar sea lions in the Northern Pacific Ocean and Bering during the 1980’s took the marine conservation community by surprise. While many hypothesized the cause was due to nutritional limitation, the authors of this work describe an alternative hypothesis in which the post-war whaling industry led to a sequential megafaunal collapse, upending the fragile marine ecosystem.

Mammal-eating killer whales, industrial whaling, and the sequential megaffaunal collapse in the North Pacific Ocean: A reply to critics of Springer et al. 2003 by A. M. Springer et al.. Marine Mammal Science 24(2) 2008. The author 2003 paper on the megafaunal collapse in the North Pacific Ocean was met with harsh criticism and dubious claims and suspect claims of probability. In this work, the authors respond to these criticisms in a detailed manner, strengthening their claims.

Killer appetites: assesing the role of predators in ecological communities by T. M. Williams et al.. Ecology 85(12) 2004. Building upon their previous work (Springer et al. 2003), the authors explore the influence large predators with high daily caloric requirements can exert on large, interconnected ecological communities.

Causes and consequences of marine mammal population declines in southwest Alaska: a food-web perspective by J. A. Estes, D. F. Doak, A. M. Springer, and T. M. Williams. Philosophical Transatctions of the Royal Society B 364 2009. The authors examine the megafaunal collapse of Orcas due to a decline in sea otter populations. This work emphasizes the interconnectedness of ecosystems and how small perturbations of one component can trigger large-scale changes.

Dangerous Migrations ( Part I and Part II) by David Attenborough. National Geographic Wild 2017. We discussed keystone species and tropic cascades with our final example being the plight of the wildebeests in the Serengeti. This two video series from legendary David Attenborough has the most stunning footage of the great migration I have ever seen. You are busy, but perhaps take 30 minutes to watch at least part of it.

Week 3 - The Fossil Record and Evolution

Annihilation of ecosystems by large asteroid impacts on the early Earth by Norman H. Sleep, Kevin J. Zahnle, James F. Kasting, and Harold J. Morowitz. Nature 342 1989. This paper is considers the ability of large asteroid impacts to sterilize ecosystems. This paper was the topic of our estimation regarding asteroid size and impact energy.

Whale Evolution by Philip Gingerich. PBS 2007. A very interesting brief video featuring Philip Gingerich and his work on whale evolution and the fossil record.

On the Secular Cooling of the Earth by Lord Kelvin (William Thomson). Transactions of the Royal Society of Edinburgh XXIII 1863. This fun paper by Lord Kelvin posits that the Earth is only about 20,000,000 to 400,000,000 years old due to the current temperature of the Earth. While we now know this is not correct (as he didn’t know about convection currents and nuclear reactions), it is still an interesting view into a once controversial topic and its implication for evolution.

A Devonian tetrapod-like fish and the evolution of the tetrapod body plan by Edward B. Daeschler, Neil H. Shubin, and Farish A. Jenkins Jr. Nature 440(6) 2006. While the relationship between fins and limbs has been well characterized, the origin of the major tetrapod features absent in finned aquatic organisms was a puzzle for decades. The authors discovered and described Tiktaalik roseae, a representative organism in the process of the fin-to-limb transition.

From Land to Water: the Origins of Whales, Dolphins, and Porpoises by J. G. M. Thewissen et al.. Evolution: Education and Outreach 2 2009. While land-dwelling tetrapods arose from aquatic life, several large aquatic mammals developed from land-dwelling tetrapods venturing into the water. This paper covers the origins of dolphins, whales, and porpoises and covers the evolution of the cetacean organ system in detail.

Molecular evolution tracks macroevolutionary transitions in Cetacea by Michael R. McGowen, John Gatesy, and Derek E. Wildman. Cell Press: Trends in Ecology and Evoltution 29(6) 2014. This paper gives a beautiful description of the way in which molecules have evolved in Cetaceans with respect to other mammals.

Week 4 - Population Genetics

Introduction to Biology by Eric Lander. MIT 2004. Prof. Lander between 10:00 and 16:00 gives an inspiring description of where Gregor Mendel’s work really came from.

Pigeon Breeding: Genetics at Work by The Genetic Science Center. Unversity of Utah . Our discussion of heritable transmission of traits was based in part in thinking about the head-crest in pigeons and this wonderful website is a great resource to learn more.

Gene Frequency in Small Populations of Mutant Drosophila by Peter Buri. Evolution 10(4) 1956. This seminal work performed a beautiful experiment measuring the effect of genetic drift on small populations using Drosophila.

From biophysics to evolutionary genetics: statistical aspects of gene regulation by Michael Lässig. BMC Bioinformatics 8(6) 2007. A wonderful review by statistical physicist Michael Lässig on the connection between biophysics and evolutionary fitness landscapes.

Predicting evolution by Michael Lässig, Ville Mustonen, and Aleksandra M. Walczak. Nature Ecology and Evolution 1 2017. A recent review and perspective on the changing face of evolution and how the use of concepts from physics can help build a predictive theory of evolution.

Week 5 - Photosynthesis

PDB Molecule of the Month series for Photosystem II and Photosystem I by David Goodsell. Protein Data Bank 2004 & 2001. These two brief entries from the molecule of the month series at the Protein Data Bank give a very nice description of the photosystem complexes, central to the process of photosynthesis.

Week 6 - Cell Biology & Gene Expression

Qunatitative dissection of the simple repression input-output function by Hernan G. Garcia and Rob Phillips PNAS 108(29) 2011. As is mentioned in the week one readings, statistical mechanics is a useful tool in a biologists toolbox. This paper shows the predictive power of a statistical mechanical description of genetic regulation via simple repression.

Week 7 - The Body Plan

Understanding morphogenetic growth control - lessons from flies by Ortud wartlick, Peer Mumcu, Frank Jülicher, and Marcos Gonzalez-Gaitan. Nature Reviews 12 2011. In class we discuss the idea of morphogens and how they might confer positional information in developing embryos. This paper gives a review of such ideas.

A Gradient of bicoid Protein in Drosophila Embryos by Wolfgang Driever and Christiane Nüsslein-Volhard. Cell 54 1988. This work first described the concentration profile of the morphogen protein bicoid in developing Drosophila embryos, suggesting that expression was under temporal control. They hypothesized that the graident was due to diffusion from the anterior pole of the embryo.

Dynamic interpretation of materinal inputs by the Drosophila segmentation gene network. by Feng Liu, Alexander H. Morrison, and Thomas Gregor. PNAS 110(17) 2013. In this work, the authors test the assertion in Deriever and Nüsslein-Volhard that the exponential distribution of the bicoid morphogen in Drosophila was due to diffusion of the protein from the anterior pole.

Week 8 - Chemotaxis and Vision

The Vertebrate Retina: Structure, Function, and Evolution by Jeremy Nathans. iBiology lectures 2010. These lectures from Jeremy Nathans are the best I know of for getting a sense of the science behind vision. Much of what I do in class is inspired by Nathans.

week 9 - Vision and Physical Limits

Old news and new news about single-photon visibility by Phil Nelson. ** . Phil Nelson has written a wonderful new book on vision as told from the point of view of someone that loves both the biology and physics of vision. This talk gives a preview of Phil’s deep understanding of the subject.

Deriving the Poisson distribution from the Binomial distribution by Rob Phillips, Jané Kondev, Julie Theriot, and Hernan Garcia. from Physical Biology of the Cell, 2nd edition 2012. This shows how the Poisson distribution emerges from the binomial distribution in the limit that the probability of a success becomes very small and λ = Np is constant.