Titles and abstracts
Tuesday September 13th at 1:30pm
Automating theoretical biology: emergent collective behavior from statistical physics
The stochastic methods of statistical physics provide tools to derive the emergent macroscopic behaviour of a complex system from a microscopic description. These techniques may be used to analyse collective behaviour across a broad range of biological complexity: from the social behaviour of animals and insects, to neuronal populations in the brain, to cellular biochemical signalling and pattern formation.
Such an "agent-based mathematics" approach allows us to derive analytically the collective behaviour of finite-sized systems from an individual-level model. This contrasts both with top-down approaches in which a differential equation model, with or without arbitrary noise terms, is assumed; and agent-based simulations, which do not allow for analytical solutions.
We demonstrate this approach with an automated tool that allows the user to intuitively specify only the biologically tangible, individual-level interactions, from which it will automatically derive and graphically present both the collective, macroscopic behaviour and the emergent noise.
Wednesday September 14th at 12:30pm
Four fates of populations in a changing environment
One major concern of global warming is that the rate of climate change may be too rapid to allow populations to adapt, causing higher rates of extinction. In this talk, I modify a pre-existing mathematical model to examine how the rate of environmental change can affect the dynamics of local adaptation and extirpation. The model, first introduced by Heinz et al. (2009), assumes that an environmental gradient exists which interacts with sessile individuals in a population, where mortality rates determined by both the gradient and local population densities. Heinz et al. showed that the gradient allows the population to adapt locally, resulting in polymorphism in the population due to evolutionary branching. In this talk, I explore how environmental change affects the population through habitat shift and local adaptation. I assumed that the environmental gradient keeps a constant slope but shifts in a parallel fashion at a specified, constant rate. I find that the population-level responses to the speed of environmental change can be classified into four types (extinction, habitat shift & extinction, habitat shift & multiple branching, and viable). This result promotes a better understanding of ecological and evolutionary responses to climate change.
Wednesday September 21st at 12:30pm
Island biogeography of gut bacteria
Recent experiments on the human microbiome reveal that a surprising amount of a human’s physiology and pathophysiology can be conferred through the person’s gut bacteria. As such, researchers and private companies are looking to develop probiotics, motivating a need to understand the pharmacokinetics of bacterial supplements. To better understand the pharmacokinetics of probiotics, I consider one deceptively simple question: What happens to a pill of N bacteria after it is swallowed? To answer this question, I have translated Hubbell’s neutral theory into a proper hypothesis-testing framework for time-course data, and in the future I will be creating a similar framework for niche-based models. Next, I will use data from metagenomic studies on the microbiomes of germ-free (gnotobiotic) mice to classify the biogeographic processes at work in the gut. In this talk, I will present the hypothesis-testing framework for Hubbell’s neutral theory for use with time-course data I will also discuss simulations of invasive species intended to test the validity of the hypothesis-testing framework, and I will close with a discussion on the implications, applications, and caveats of using the human gut as a model system for studying principles of island biogeography.
Wednesday September 28th at 12:30pm
Plans for 1) modeling migration in the ocean and 2) managing predatory packs in social-ecological systems
I am going to present some thoughts and ideas about two future projects. First, I will talk about my plans to develop models of oceanic migration. Many marine species travel large distances, sometimes 1000s of kilometers. While here at Princeton, I intend to develop an evolving agent-based model of oceanic migration. The goal is to 1) identify the forces that create migratory behavior in marine megafauna and 2) predict how migratory routes wil change under different future climate and anthropogenic scenarios. Second, I will talk about some long-term plans to understand how we can manage packs. There have been great developments in our understanding of why certain species form herds, flocks, and schools. However, there is another level of aggregation that deserves attention- the formation of predatory packs. A long term goal of mine is to investigate how packs form, how signaling between predatory individuals (truthfully or not) changes outcomes, and finally how we can manage packs. Surprisingly, this work is aimed at us. For example, fishermen sometimes exhibit pack behavior. The specific goal of this work is to improve our understanding and ability to manage marine social-ecological systems.
Wednesday October 5th at 12:30pm
The mixotroph: a template for adapting plankton communities in the world
Marine phytoplankton influence our climate by performing up to 50 % of
global primary production. The strength of this influence is dependent on
the species composition of plankton communities, which varies profoundly in
time and space. This suggests that to quantify the interplay between
plankton and climate, one requires detailed knowledge on the physiology and
life history of hundreds of plankton species - knowledge that will remain
beyond our reach for many years. Fortunately, much of the functional
diversity in plankton is captured by variation in a small number of
principal traits, e.g., the chosen metabolic strategy (autotrophy and/or
heterotrophy). By representing key statistics of these traits, community
models acquire rich, adaptive behaviour without having to resolve large
numbers of species. This is not just a modeller's fancy: when embedded in
detailed physical models of a water column (1D) and the world ocean (3D),
these adaptive community models reproduce a wealth of features that are
commonly observed in natural marine systems. In line with complex adaptive
systems theory, a concise representation of species diversity in combination
with a detailed, variable environment allows plankton models to display a
surprisingly comprehensive range of realistic adaptive behaviours.
Wednesday October 12th at 12:30pm
Non-equilibrium field theory as a unifying framework in theoretical biology: from individuals to communities
Population genetics and community ecology have a long history of shared tools and concepts. One of the most recent, successful and controversial overlaps has been the application of the mathematics of neutral molecular evolution to derive predictions for community level ecological patterns. This approach is focused on the impact of stochastic `drift' of species abundances in a community, and despite ignoring much ecological detail produces surprisingly realistic predictions. In this talk we will explore an application of field theory methods to spatial processes in ecology, and a second application to the dynamics of population adaptation.
Wednesday October 19th at 12:30pm
Where's the beef? Nutrient location and colony morphology in microbes
Microbial colonies have traditionally been studied either in liquid
nutrient suspensions or on surface-bound nutrient plates, resulting in
artificial constraints on microbial ecology. By using a porous
membrane to deliver solutes through either a surface or a liquid
medium, one can create a far more flexible and realistic environment.
I will present progress toward the construction of such a device, and
explore some of the implications for the study of microbial ecology.
Wednesday October 26th at 12:30pm (Guyot 100)
Mechanism design in fur and feather: how to cooperate when you don't know your partner
Many organisms cooperate with each other despite -at first blush- facing conflicts of interests, which represents an evolutionary "puzzle". Especially puzzling are cases where one or more of the parties have private information about themselves or the state of the world. In such cases, individuals might benefit from misrepresenting their true information, which precludes mutually beneficial outcomes. Hence, stable cooperation in these situations requires special incentive structures. Mechanism design theory in economics deals with how such incentives can be constructed. I will talk about recent and ongoing work adopting to biology the methods of mechanism design, focusing specifically on how offspring can communicate to parents their needs, and how the distribution of reproductive output among group members is determined in group-living organisms
Wednesday November 9th at 12:30pm
Adaptive strategies of resource acquisition in nitrogen fixing plants
Despite the importance of nitrogen (N) fixation for bringing new nitrogen into systems at the scales of ecosystems and individual plants, we are only beginning to understand how soil nutrients such as N and phosphorus (P) constrain fixation. Recent work has suggested that resource acquisition strategies-- fixation for N and phosphatase activity and mycorrhizal colonization for P-- may allow plants to acquire nutrients that they could not otherwise obtain directly from the soil, thereby overcoming nutrient limitation. Here we develop a model of an individual plant that includes biomass, available nitrogen and available phosphorus pools, various forms of nutrient inputs and losses, N fixation, and a term that allows for P acquisition from an infinite pool via phosphatases and mycorrhizae. We evaluate the model to determine the P acquisition and fixation strategies plants should use under different N and P conditions. We compare model results to findings from an experiment and discuss mechanisms that could be included to improve model predictions. This work is very much in progress, and I would greatly appreciate feedback and advice on ways to move forward.
Wednesday November 16th at 12:30pm
Learning and collective intelligence in groups
Despite advances in our understanding of collective intelligence in animal groups in the past decade, it is not known how individuals in a group learn about their environment in a way that can result in the emergence of collective intelligence. I will present a model of group learning, compare its behavior to the optimal behavior, and discuss other experimental predictions from the model. Finally, I'll demonstrate a preliminary version of a game using Netlogo that will allow me to test the model using human subjects.
Wednesday November 23rd at 12:30pm
A family of formalisms for computing power on social networks
Consensus is important in many social systems. In particular, in primate social systems, an individual's power is defined by the consensus in the population about that individual's ability to use force. In the pigtailed macaque, one individual's perception of another's fighting ability is communicated through a subordination signal. The signaling network can therefore be used to infer the power structure of the population. Rather than looking at the mechanisms by which consensus is reached, I will present a class of formalisms used to measure the degree of consensus present. The computational and cognitive complexity of these formalisms, as well as the degree to which they can be manipulated by individuals in the population, will also be discussed.
Wednesday November 30th at 12:30pm
Competition for water down-regulates plant responses to CO2 fertilization: lack of cooperation in plants significantly decreases the potential for the biosphere to buffer increasing atmospheric CO2.
The amount of carbon in tree biomass is approximately equivalent to total carbon in the atmosphere. Thus, changes in the standing biomass of forests can have dramatic effects on CO2 concentrations of the atmosphere. As CO2 is a resource to plants, it has been proposed that with increased concentrations, plants will be more productive, store more carbon, and act as an effective buffer to increases from fossil fuel emissions. One of the proposed mechanisms of this increase in productivity is increased water-use-efficiency in plants. That is, with increased CO2 concentrations in the atmosphere, plants should be able to obtain more carbon for a given amount of water. However, recent reviews of experimental work and observational patterns show results which conflict with this notion. In this week's lab tea, I will investigate how shifting competitiveness of plant allocation strategies following increases in CO2 may negate much of the predicted increases in forest carbon storage. As these results depend critically on the timing of rainfall, I also hope to discuss current progress on extending this model to include treatments of more realistic rainfall regimes.
Wednesday December 7th at 12:30pm
Attached bacteria flux as a mechanistic control on mesopelagic particle remineralization
Sinking organic particles are a rich food source for heterotrophic bacteria living in the mesopelagic zone of the ocean environment. Bacteria can only transport bits of organic molecules into the cell, and have adapted to overcome this constriction by producing extracellular enzymes to cleave bits of organic matter from larger molecules, effectively transferring an essential function to the external environment. As bacteria metabolize, organic matter is converted back into inorganic nutrients. In order to assess the mechanisms of remineralization, I have developed a model to look at production and activity of particle attached bacteria and extracellular enzymes in the context of marine ecosystems. The model includes six state variables: dissolved organic matter, particulate organic matter, free-living bacteria, particle-attached bacteria, extracellular enzyme, and hydrolysate. Results from the numerical simulation indicate that bacterial populations, both free-living and attached, are not self-sustaining when constrained by measurements unless there is a flux of attached bacteria into the mesopelagic zone. The analytical solution to the model will also be presented.
Wednesday December 14th at 12:30pm
Fire spread as percolation in savanna landscapes
Fire spread modeling is an undertaking that has been tackled in a diversity of ways. However, it has historically been difficult to theoretically abstract in ways that are meaningful in the applied context for real landscapes. One of the primary challenges is that a theoretical approach to fire spread, based on percolation, is hard to generalize for heterogeneous landscapes, which are not easily reduced to simple and straightforward indices of heterogeneity. Kruger National Park provides an ideal context in which to test ideas about how to generalize fire spread theory. Heterogeneity takes a variety of forms, including that induced by herbivores, rivers and topography, and that arising from fire feedbacks itself. Here, we present a perspective on fire spread that is grounded in percolation theory and validated using Carnegie LIDAR vegetation structure data from a variety of landscapes around the park. We provide novel insights into the types of heterogeneity that are particularly meaningful in affecting fire spread and its ecosystem-level feedbacks on vegetation structure. These depend on the underlying shape of the landscape (topography), hard barriers to spread (like rivers and roads), and degree and type of vegetation patchiness, all of which interact both with geology and climate, as well as dynamic drivers such as fire and herbivory.
Monday December 19th at 11:00am
The Spread of Epidemics on the US Transportation Network: The Role of Air and Long Distance Auto Travel
SARS and the swine flu have rekindled interest in the spread of epidemics. Beginning with Colizza, V., A. Barrat, M. Barthélemy, and A. Vespignani, “The role of the airline transportation network in the prediction and predictability of global epidemics,” Proceedings of the National Academy of Sciences 103, 2015-2020 (2006), a series of important papers by Vittoria Colizza and her coauthors examined the implications for the spread of epidemics of data on a 3100 airport network across 220 countries. A disproportionate amount of air traffic flows through large hub airports near large population centers in their data and so it is unsurprising that such airports prove to be preferred pathways in the inter-ocean and intra-continental spread of epidemics in their simulations. Infected dispersion on the air travel network, not local growth based on local infection rates, is the main source of exponential growth. This study reexamines these issues on a different transportation network: a model of air and long distance automobile trips to and from all 3076 counties in the continental US. Airports close to large populations are not disproportionately more important in contrast to Colizza et al., and long-distance auto travel, a previously unstudied travel mode, is more important than air travel in these simulations. Exponential infected growth results primarily from the local county infection process after initial seeding by infected travelers.
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