Monthly Archives: August 2011

Bj\ornstad 2005, Evolution and Emergence of Bordetella in Humans

Bordetella is the bacteria responsible for whooping cough, one of the most contagious directly transmitted human pathogens (according to IDH:DC). Whooping cough is causes by one of two sub-species, B. pertussis or B. parapertussis

The original bacteria, B. bronchiseptica infects a wide range of mamals, and can persist for life in the nasal cavity of its host. It is not particularily virulent nor pathenogetic. The whooping cough species, however, are both 1) strongly pathenogetic, and 2) only infect transiently (latent 7-10 days, active ~3 weeks).

The authors posit this as an example of Grenfell’s (2001) hypothesis on the invasion/persistence tradeoff.

Grenfell, B. T. (2001) Dynamics and epidemiological impact of microparasites. In New challenges to health: the threat of virus infection (ed. G. l. Smith, W. L. Irving, J. W. McCauley & D. J. Rowlands), pp. 33-52. Cambridge: Cambridge University Press.

Note that Grenfell and Bj\ornstad are collaborators


Prabhakaran (2011) HIV haplotype inference using a constraint-based DPM

This paper extends SHORAH to better infer global haplotypes.

The work is a collaboration between Niko Beerenwinkel’s group and Volker Roth’s group. Roth is at the the U Basel computer science department. Other authors are Melanie Rey, Osvaldo Zagordi, Huldrych Günthard, and Karin Metzner.

the paper really isn’t clear on how they move from local to global reconstruction.

They introduce the following soft constraint. If two reads are assigned to different local haplotypes (i.e. differ in their local window) then they must be assinged to different haplotypes at the global level. Such do-not-link constraints are incorporated into the prior distribution of the subequent class assignments

Sugihara: Nonlinear forecasting as a way of distinguishing chaos from measurement error in time series

Heard about this paper from a short bio of the author, Sugihara

He, along with Robert May, coauthored several papers on chaos theory and financial markets. This lead to him being given a huge pile of money by Deutsche Bank.

Robert May ended up as Baron of Oxford, among other honors. Baron May also wrote the landmark Infectious Diseases of Humans: Dynamics and Control (Oxford Press, 1992).

This paper presents an approach for making short-term predictions about the trajectories of chaotic dynamical systems. The method is applied to data on measles, chickenpox, and marine phytoplankton populations, to show how apparent noise associated with deterministic chaos can be distinguished from sampling error and other sources of externally induced environmental noise.

Two sources of uncertainty in forecasting natural systems: additive noise (ie measurement error) and complex dynamics. The prediction error for additive noise should be constant regardless of how many time steps ahead one is predicting. Prediction error for chaotic dynamics should increase sharply the more timesteps ahead one looks.

To create the C.D. predictor:
Lag series by E steps
To predict outcome of sample t,
find t’s E+1 nearest neighbors in the lagged data
predicted outcome is exponetially weighted mean of n.neighbor’s outcomes, with
weight == distance between t and the neighbor
E is related to the number of attractor by E_min < 2D +1. You can (given enough data) estimate D using i.e. the Grassberer-Procaccia algorithm.

One can also test for changes in system dynamics by comparing accuracy of
1) predict second half using first half
2) randomly select training data over entire series

Possible follow-ups:
Can we describe the E-dimensional space? Do the points cluster, or are they diffuse?

Given that we can test for changes in the system dynamics, can we detect these change-points?

How does this relate to the resilience of cities paper, and its concept of slow trends pushing the city off a cliff; leading to sudden and drastic state changes

How does this relate to the nature and structure of human dynamics (thinking of the insurgency paper, which I will post soon).

Samantha Power on a complicated hero (2008)

Samantha Power‘s talk.

Starts out discussing the birth in the 21st century of the “save the people” movement, like early environmentalism but dedicated to ending genocide. This movement is mostly US-based, and largely on college campuses. She then segues into a hero of hers,
Sergio Vieira de Mello.

Sergio worked tirelessly to confront evildoeers.

Samantha Power started (?) as a journalist covering the Yugoslav Wars. She then attended Harvard Law School, where a paper she wrote on genocide turned into the book The Problem from Hell, is a survey of genocide. This got her named by Time Magazine as a top thinker. She then took a position working with Senator Obama on foreign policy. She continues to be active in his administration as the Senior Director for Multilateral Affairs, as well as holding a professorship.


For movies. Requires a special plug-in. Not sure if I trust the plug-in

Immorality of debt

More inspiration for the paper I wish I had time to write on this!!

David Graeber interview

First comes gift-giving (which creates reciprical obligation). This becomes encoded in debt, which leads to money. Barter only comes later.

The old myth is that barter came first, then money. Rebuttal: “Think about what they’re saying here – basically: that a bunch of Neolithic farmers in a village somewhere will be engaging in transactions only through the spot trade.”

Sean Gourley on the mathematics of war

Sean Gourley

Dr. Gourley’s team wrote a Nature paper defining how to measure an insurgency.
“Common Ecology Quantifies Human Insurgency“
The size distributions of casualties both in whole wars from 1816 to 1980 and terrorist attacks have separately been shown to follow approximate power-law distributions6, 7, 9, 10. However, the possibility of universal patterns ranging across wars in the size distribution or timing of within-conflict events has barely been explored. Here we show that the sizes and timing of violent events within different insurgent conflicts exhibit remarkable similarities. We propose a unified model of human insurgency that reproduces these commonalities, and explains conflict-specific variations quantitatively in terms of underlying rules of engagement. Our model treats each insurgent population as an ecology of dynamically evolving, self-organized groups following common decision-making processes

See also

I want to link his evolution of insurgency models to my own viral evolution work. He specifically discusses that when an insurgent group breaks up, the parts don’t dissapear, they re-associate with remaining groups– showing preferential attachment. Also, strongest groups grow fastest.

Bruce Bueno de Mesquita predicts Iran’s future

Bruce Bueno

Dr. de Mequita uses game theory to model all the parties in a negotiation and finds equilibrium points. He can thus predict, with high accuracy, what the eventual settlement will be based on known data at the start.

PW Singer on military robots and the future of war

PW Singer

Robots are transforming war.

The US has a lead, but not a strong one. Robot building is still a DIY art with low barriers to entry.

Parag Khanna maps the future of countries

Parag Khanna

Damn, TED is frustrating. Not easy to find the dates/conferences for talks. Just the title.

Parag draws maps which focus on infrastructure, not boundaries. Good infrastructure determines the balance of power and makes for good neighbors.

Example: Kurds would need good relations with their neighbors to be able to get their oil to a port so they could sell it.

Example: China is conquering the world. They have “invaded” Russia– by moving farmers into Siberia, leasing the land. Etc. Chinese is becoming a language of power brokers.