Monthly Archives: October 2011

Entrepenurial science

The grand vision:
Understand viral evolution, both inter and intra host, so we can stop the bastards.

How do I fill in the details?
What do I bring?
Napolean had the art of artillery, thomas had machine learning. And me?
What do I see, which is currently not in the world  yet should be?
Theory of contagion- done
Vaccines- done
Antibiotics- done
Vector control- done
Mathematical epidemiology- done
Emergence of resistance- done
Quasi species- done
Genetics (geno to pheno)- done


Resistance pathways

We know virus develop resistance to drugs. The interesting cases are when resistance depends on combinations of mutations; mutational pathways.

The concept pathway implies an order. Is there one?
fitness landscapse or seascape?
survival of the fittest or the flattest?
colonizer/competitor dynamics?

What is a reference sequence? Does this define the virus???

Possible titles “Tracing evolutionary pathways through seascapes and bottlenecks”

hmmm– ship in a bottle, early mariners, exploring, setting up trade outposts???

How to do high-impact work

What question do people want answered?

Need to be early or first, find/define an emerging subject.

HIV was a field before Thomas, but not statistical learning and HIV.

Protein docking was a field before Thomas, but not with flexible protein structures.

What is mine?

Thomas suggests integrative model stretching from cell to population

rates of HIV evolution

Prabhav suggested comparing rates of viral evolution within patients to those within a transmission cluster.

We could measure/compare rates of adoptation to treatment to rates of adoptation to a new host.

The confound is that we identify the transmission clusters via genetic distance. It would be easier if we had a known transmission chain.

Alternately, EuResist does have ~6000 cases with two samples taken under one treatment. We could compare rates here with rates after a treatment change.

Yang Lan: The generation that’s remaking China

Yang Lan

The Oprah of China.

This talk opened my eyes to the currents flowing in modern China. China faces the same social unrest as we see everywhere in the world today. Dissaffected youth, aware that the system is set up to exploit them, and angry about it.

Justin Hall-Tipping: Freeing energy from the grid

Justin Hall-Tipping

He presents some of the possibilities offered by carbon nanotubes.

A window which can lighten or darken, in response to a 2V current running for a few microseconds.

Solar power generation.

The idea that each house generates its own electricity this way, and can beam it to its neighbors (as light).

Infrared glasses

Richard Wilkinson: How economic inequality harms societies

Richard Wilkinson

Stuff we knew before, pulled together into a coherent presentation.

Differences in measures of social well-being (almost ALL such measures) in Western democracies show zero correlation with national GDP. Within each country, however, they show incredibly strong correlation with household income.

NGS review/ Beerenwinkel

Ultra-deep sequencing for the analysis of viral populations
Beerenwinkel and Zagordi,
Curr Opin Virol 2011:1

Very general. Presents the process and challenges. Lists major software for haplotype identificaiton, but does not provide a comprehensive review of their capacities and differences.

filed under beerenwinkel_cov_2011.pdf

competition-colonization dynamics

Competition-colonization dynamics
An ecology approach to quasispecies dynamics and virulence evolution in RNA viruses
Samuel Ojosnegros, Niko Beerenwinkel, and Esteban Domingo

Not the first or best paper on the subject, just the one I read today. A single viral clone, raised in a pure cell culture, evolved into two differnt subpopulations. The phenotypes of the two clades clearly displayed either the competitor (less fit, less virulent, but interfered with replication of the other type) or the colonization (more fit, more virulent) strategy.

stored as ojosnegros2011.pdf


We see things not as they are, but as we are