Math 151 - Fall 2007
References Cited for Lectures
August 22, 2007 lecture: Intro to Statistics
Ground squirrels use an infrared signal to deter rattlesnake predation
by Aaron S. Rundus, Donald H. Owings, Sanjay S. Joshi, Erin Chinn, and Nicolas Giannini
Full paper as a PDF file - Proc. Natl. Acad. Sci. 10.1073/pnas.0702599104. (Aug. 17, 2007)
Comments: This paper illustrates the impact of behavioral signaling using a previously unobserved method - heat radiation - in ground squirrels. They observe that ground squirrels, when faced by a potential predator (a rattlesnake) which has sensors that detect infra-red radiation from potential prey, heat up their tails much more than when they are faced by a predatory snake (gopher snake) which does not sense heat from potential prey. A hotter squirrel tail when the squirrels wave (flag) their tail, seems to deter rattlesnakes from attacking. These conclusions result from both observations of squirrels and snakes placed in cages, and from "robosquirrels" they built that have variably heated "tails". Thhey argue that this is an example of how the sensory mechanisms of predators have affected the evolution of behavioral and physiological defense mechanisms in squirrels.
Containing Pandemic Influenza at the Source
by Ira M. Longini, Jr., Azhar Nizam, Shufu Xu, Kumnuan Ungchusak, Wanna Hanshaoworakul, Derek A. T. Cummings, and M. Elizabeth Halloran
Full paper as a PDF file - Science 309: 1083-1087 (12 Aug 2005)
Comments: This paper uses a probability model to analyze the potential spread of "bird flu" among humans. The objective is to compare the potential effectiveness of alternative control methods to limit the spread of the pandemic at its initial source, using targeted drugs (antivirals), quarantine, and early vaccination. The resulting effectiveness depends upon the underlying reproductive number (how many secondary infections would arise from a single infected individual if no control were applied). They show that a mixture of these possible control methods could control the spread of the disease up to a reproductive number of 2.1 and they obtain results as to how much of a stockpile of antiviral drugs would be needed.
August 28, 2007 lecture: Bar Charts and categorical data
Evolution and Development of Sex Differences in Cooperative Behavior in Meerkats
by T. H. Clutton-Brock, A. F. Russell, L. L. Sharpe, A. J. Young, Z. Balmforth,3 G. M. McIlrath
Full paper as a PDF file - Science July 12 2002 297: 253-256
Comments: This article focuses on the issue of whether males or females devote more effort to caring for young, contrasting cooperatively breeding birds with meerkats. Female meerkats are more likley to breed and remain in their natal group than males, and the authors found that female meerkat helpers were more likely to contribute to rearing than males. They argue this is because females are more likely to derive genetic benefits (through helping more closely related individuals rear their young) than males in meerkat groups. The authors make use of extensive histograms, arranged by gender or experimental regime, to illustrate their points.
August 28, 2007 lecture: Bar Charts
An Experimental Study of Search in Global Social Networks
by Peter Sheridan Dodds, Roby Muhamad, Duncan J. Watts
Full paper as a PDF file - Science Aug 8 2003 301: 827-829
Comments: Experiment to determine how many contacts are necessary, using email, to reach a specific target individual about which the location, name and occupation are provided to the initial email sender. Bar charts show the length of an email chain necessary to reach the target.
August 28, 2007 lecture: Histograms
Extraordinary Flux in Sex Ratio
by Sylvain Charlat, Emily A. Hornett, James H. Fullard, Neil Davies, George K. Roderick, Nina Wedell, and Gregory D. D. Hurst
Full paper as a PDF file - Science July 13 2007 317: 214
Comments: Observations of the sex ratios in a butterfly species on the Samoan islands found populations with 99% females in 2001. This arose from a bacteria inherited from mothers that selectively kills male embryos. Sampling populations in 2006 found that within very few generations, the sex ratio had shifted to near 1:1 males to females. They used histograms to illustrate egg hatch rate as proportion of males varies for several different sites. Change in sex ratio arose due to the loss of male-killing efficiency in the bacterium, which they show is due to the evolution of genes in the butterfly which suppressed the effect of the bacterium.
September 5, 2007 lecture: Scatter plots, regressions and correlations
The Neural Basis of Economic Decision-Making in the Ultimatum Game
by Alan G. Sanfey, James K. Rilling, Jessica A. Aronson, Leigh E. Nystrom, Jonathan D. Cohen
Full paper as a PDF file - Science June 13 2002 300: 1755-1758
Comments: Individuals were observed using functional magnetic resonance imaging (fMRI) while playing an economic game with other humans, and with a computer. The intent was to determine if the "non-rational" response of humans to this game was reflected in the activity of certain areas of the brain, as measurable using the fMRI. The results indicate there is a correlation between activity in one area (anterior insula) and the acceptance of what could be perceived as an unfair offer in the game. This is an example of the work in the new area of neuroeconomics, which attempts to ascertain a biological basis for human economic decisionmaking.
September 5, 2007 lecture: Scatter plots, regressions and correlations
Reduced Egg Investment Can Conceal Helper Effects in Cooperatively Breeding Birds
by A. F. Russell, N. E. Langmore, A. Cockburn, L. B. Astheimer, and R. M. Kilner
Full paper as a PDF file - Science August 17 2007 317: 941-944
Comments: The authors investigate how the size of eggs laid by mothers of superb fairy-wrens are affected by the availability of "helpers" who can assist in feeding young birds. The question they address is, for cooperatively breeding organisms, in which offspring receive food from individuals other than their parents, why have there not been found any significant enhanced effects on offspring growth and survival when helpers are assisting in feeding the offspring. They suggest that this is because the mother invests less (in terms of the size of the eggs) when helpers are present than when helpers are not present. They provide evidence to support this claim.
September 10, 2007 lecture: Allometry
Global Allocation Rules for Patterns of Biomass Partitioning in Seed Plants
by Brian J. Enquist and Karl J. Niklas
Full paper as a PDF file - Science February 22 2002 295: 1517-1520
Comments: This paper shows numerous allometric relationships that arise both within and between species for plant parts.
September 12, 2007 lecture: Semi-log graphs
Immunization by Avian H5 Influenza Hemagglutinin Mutants with Altered Receptor Binding Specificity
by Zhi-Yong Yang, Chih-Jen Wei, Wing-Pui Kong, Lan Wu, Ling Xu, David F. Smith, and Gary J. Nabel
Full paper as a PDF file - Science August 10 2007 317: 825-828
Comments: This paper analyzes the impact of antibodies to bind to receptors in the avian flu virus strain. These antibodies bind to a receptor binding domwin within viral hemagglutinin. The results illustrate how the concentration of antibody affects the neutralization of the binding sites on the virus, thus rendering the virus incabaple of transmission at 100% neutralization. A semi-log graphing method is used to illustrate antibody binding often showing a two-phase response with different concentrations of different monoclonal antibodies.
September 24, 2007 lecture: Land Use Change and Markov Chains
Developing a science of land change: Challenges and methodological issues
by Ronald R. Rindfuss, Stephen J. Walsh, B. L. Turner II, Jefferson Fox, and Vinod Mishra
Full paper as a PDF file - PNAS Sept. 28, 2004, 101:13976-13981
Comments: This paper presents a summary of the modern science of land-use change and focuses on how this involves an integration of information science, geography and economics. They also discuss the basic techniques in geographic information systems appropriate to land use change analysis.
September 26, 2007 lecture: Matrix algebra
Mathematical models of RNA silencing: Unidirectional amplification limits accidental self-directed reactions
by Carl T. Bergstrom, Erin McKittrick, and Rustom Antia
Full paper as a PDF file - PNAS September 12, 2003, 100:11511- 11516
Comments: This paper presents a mathematical model to anaylze the "silencing" of genes in which aberrent genes are not expressed - this essentially is a method by which a mutant is suppressed by a rapid response of RNA transcription. It is a form of gene repair. They argue that current models do not explain how silencing doesn't also impact "good" genes which are not damaged, and produce two new mathematical models for silencing. One of these models uses a matrix formulation in which the components of the matrix symbolically represent the rates at which different types of silencing RNAs change from one type to another.
September 26, 2007 lecture: Matrix Algebra
Recovery and Management Options for Spring/Summer Chinook Salmon in the Columbia River Basin
by Peter Kareiva, Michelle Marvier, and Michelle McClure
Full paper as a PDF file - Science November 3, 2000, 290:977-979
Comments: This paper applies a matrix model for the demographics of salmon to issues associated with the effects of dams on the Snake river. One focus is on how the population might respond given different dam mitigation scenarios. They point out that the limitations on population growth and recovery of the salmon may not be related to further improvements in the ability of salmon to negotiate around the dams, but rather to mortality in other life stages.
October 3, 2007 lecture: Leslie Matrices and Population Projection
Human Population: The Next Half Century
by Joel E. Cohen
Full paper as a PDF file - 14 Nov 2003 Science 302:1172-1175
Comments: This paper reviews the history of human population on our planet focusing on the dynamics of the size of the population as well as its growth rates. The author points out how rapidly the human population has been growing, at an increasing rate. Thus the doubling time of the population has changed from 50 years in 1927 to 25 years in 1974. What is greatly significant is that the yearly population growth rate has declined over the past 3 decades from 2.1% to 1.2%, associated with a large reduction in the fertility rate (from over 5 to less than 3 children per woman per lifespan). The author uses mathematical models to project the changes in population structure (age) through the next 50 years.
October 8, 2007 lecture: Transfer matrices and compartment models
Human evolution: Pedigrees for all humanity
by JOTUN HEIN
News article as a PDF file - Nature September 30, 2004, 431:518-519
Comments: This is a news and views article that summarizes the below paper by Rohde et al. on the time to the common ancestor of all living humans.
see also
Modelling the recent common ancestry of all living humans
by DOUGLAS L. T. ROHDE, STEVE OLSON & JOSEPH T. CHANG
Full paper as a PDF file - Nature September 30, 2004, 431:562-566
Comments: This paper uses a mathematical model and a simulation model to estimate how many generations in the past you would have to go to find an individual who was an ancestor to all human beings currently alive (the most recent common ancestor - MRCA). They compare results from a simple model that assumes random mating between all humans to a model that assumes the world is broken down into sub-regions with transfers of humans regularly occuring between these regions, in the same way a transfer matrix describes the movement of something between various components. Their results indicate that the MRCA lived in the relatively recent past (a few thousand years ago), and going back a few thousand more years (to about 7,000 years ago) we would get to the IA point where each present-day human has exactly the same set of ancestors.
October 22, 2006 lecture: Chance and Biology
Monkeys reject unequal pay
by SARAH F. BROSNAN AND FRANS B. M. DE WAAL
Full paper as a PDF file - Nature September 18, 2003, 425:297-299
Comments: This paper describes experiments in which capuchin monkeys interacted with human experimenters who offered them a more valuable food (grapes) or a less favored one (cucumber) when they returned an item to the human. The monkeys generally, but not always, refused to participate in an exchange of items for food when they saw that other monkeys got a better food item and they did not. The monkeys thus had a tendency to refuse to participate if they saw another monkey get a better reward for no effort, but there was a random component to this - it did not happen all the time and the sample size of monkeys used was very small - only 5 monkeys. It was therefore not possible to predict exactly what any particular monkey would do.
October 22, 2006 lecture: Chance and Biology
Chimpanzees are indifferent to the welfare of unrelated group members
by Joan B. Silk, Sarah F. Brosnan, Jennifer Vonk, Joseph Henrich, Daniel J. Povinelli, Amanda S. Richardson, Susan P. Lambeth, Jenny Mascaro and Steven J. Schapiro
Full paper as a PDF file - Nature October 27, 2005, 437:1357-1359
Comments: This paper describes experiments in which chimpanzees were offered the opportunity to give a food reward (treat) to another chimp or not, with no cost to themselves. The chimp controlling the food reward always received a reward, whether the other chimp was given a reward or not. The experiments compared the actions of a chimp when no other chimp was present and when one was present. If the responses were different when another chimp was present from when another chimp wasn't present, there would be evidence that chimps display empathy or concern for the welfare of others. No such evidence was found. The chimps gave food equally likely when another chimp was present as when it wasn't. Responses of any particular chimp wre like a coin toss with about an equal chance of giving food reward to other chimp or not.
October 29, 2007 lecture: Probabilities and epidemics
Forecast and control of epidemics in a globalized world
by L. Hufnagel, D. Brockmann, and T. Geisel
Full paper as a PDF file - Proc. Natl. Acad. Sci. October 19, 2004, 101: 15148-15153
Comments: This paper describes, using SARS (severe acute respiratory syndrome) as an example, how to model the global spread of an epidemic. In addition to using the standard epidemiological model (susceptibles who become infected and then can infect others) in a local region served by an airport, they analyze global spread using data on movements of aircraft between airports. The probability of movement of individuals between airports is obtained from looking at the number of air passengers between different cities. This gives them a Markov chain (it is large - they used 500 airports giving a 500x500 matrix) to characterize movements between airports. They link this with local epidemic models to indicate how one infected individual can lead to a global epidemic and compare it to data from SARS.
November 5, 2007 lecture: Conditional probabilities
Modelling an outbreak of an emerging pathogen
by Emily Kajita1, Justin T. Okano1, Erin N. Bodine, Scott P. Layne & Sally Blower
Full paper as a PDF file - Nature Reviews Microbiology, September, 2007, 5:700-709
Comments: This paper shows how to use mathematical models to analyze the spread of an outbreak in a prison of a strain of Staphylococcus aureus which is resistant to a major antibiotic and is acquired through interactions in a community (so it is called CA for Community acquired MRSA for meticillin-resistant Staphylococcus aureus). The objective is in part to evaluate methods to control such outbreaks since this can cause otherwise healthy individuals to quickly die. This model includes stochasticity in several components. Among other outcomes, it allows one to calculate, given a certain average time that a prisoner is incarcerated, the probability an outbreak of CA_MRSA will occur.
November 7, 2007 lecture: Bayes Theorem and epidemics
Bayesian analysis of botanical epidemics using stochastic compartmental models
by G. J. Gibson, A. Kleczkowski, and C. A. Gilligan
Full paper as a PDF file - Proc. Natl. Acad. Sci. August 17, 2004, 101: 12120-12124
Comments: This paper combines several aspects of the material we have covered in this course: compartment models similar to matrix models with susceptible, exposed (or latent), and infected infected individuals; a probability framework built around an extension of the Markov chain type of models we have seen; and they use a Bayesian method to analyze experimental data and make inferences about the impact of the experiments. In this case, they analyze data on a fungal disease of radish plants in the presence and absence of another fungal species which is used to biologically control the harmful fungus. They conclude from their analysis that the biological control fungus is effective at reducing the rate of infection from the soil of the radish by the harmful fungus (primary infection) but not at limiting the spread of the disease from secondary (e.g. from other infected plants) infection.
November 12, 2007 lecture: Population genetics models
Genetic diversity and reproductive success in mandrills (Mandrillus sphinx)
by M. Charpentier, J. M. Setchell, F. Prugnolle, L. A. Knapp, E. J. Wickings, P. Peignot and M. Hossaert-McKey
Full paper as a PDF file - Proc. Natl. Acad. Sci. November 7, 2005, 102: 16723-16728
Comments: This paper analyzes the effects of heterozygosity on a variety of measures of individual fitness for a population of mandrills. They found that for both males and females higher heterozygosity was correlated with higher numbers of offspring, but this correlation in males only held for the alpha males. Achieving alpha status for males was not correlated with heterozygosity though the length of tenure as an alpha male was correlated with heterozygosity. They also found that the effects of heterozygosity on reproductive success was multi-locus, not due to a small number of loci with strong effects.
November 12, 2007 lecture: Population genetics models
Genetic Structure of Human Populations
by Noah A. Rosenberg, Jonathan K. Pritchard, James L. Weber, Howard M. Cann, Kenneth K. Kidd, Lev A. Zhivotovsky, and Marcus W. Feldman
Full paper as a PDF file - Science December 20, 2002, 298:2381-2385
Comments: This paper analyzes data on the genetic structure of human populations by analyzing information from over 1000 individuals in more than 50 locations. They looked at more than 300 genetic loci and found that the vast majority of genetic variation in humans is accounted for by variation within populations, and only a small amount (3-5%) is due to genetic differences between populations. Nevertheless, the data do indicate that there are distinct human populations, defined by the genetics, but correlating with geographically separate populations as well.
November 28, 2007 lecture: Difference Equation Models
Lattice Effects Observed in Chaotic Dynamics of Experimental Populations
by Shandelle M. Henson, R. F. Costantino, J. M. Cushing, Robert A. Desharnais, Brian Dennis, and Aaron A. King
Full paper as a PDF file - Science October 19, 2001, 294: 602-605
Comments: This paper analyzes both a discrete model in which organisms are counted as integers, and a continuous model in which the population size can take on non-integer values. Both of these models are discrete in time - that is they are difference equations. They apply their results to data from an experimental organism, the flour beetle Tribolium, and point out how chaotic dynamics can arise.
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