Friday, May 30, 2014

Bigelow OCB Meeting Report

I am at Bigelow Lab in Boothbay Harbor, Maine for a workshop on single cell analysis for marine plankton. This is a very exciting area where novel observational technologies are rapidly growing the gap between observations and modeling. There simply is no correlation between our conventional/operational models and modern data. Today I learned something new. I was already aware of the high phenotypic heterogeneity we see in clonal cultures, but single cell genomics are now revealing a high degree of genomic heterogeneity in clonal populations as well! Is this variability neutral? What is the ecological role? How do we model it? Workshop link:

… and now my wife is coming up and we will go on to Acadia National Park for some hiking and camping. Visiting this park has been a goal of mine since 2004, and now we are finally doing it. This blog is for professional topics only, so this trip must therefore be hereby marked "sampling" solely to indicate this fact.

Friday, May 23, 2014

Portland JASM Meeting Report

I am in Portland (OR) for the JASM meeting. We have two presentations. I am giving a talk on our global ocean simulation and Neil is talking about our Taihu model. Yesterday I was at a session on “molecular ecology” and (as usual) I was struck by how disconnected the conventional phytoplankton/biogeochemical modeling approach is from the types of observations that are being generated. This session may be an extreme example of this, but people are presenting DNA, RNA, etc. data. Whatever happened to chlorophyll a? We really need to change our models to keep up with the changes in observational technology.

Here are links to our abstracts:

Monday, May 19, 2014

Boston ASM Meeting Report

This week I am at the general meeting of the American Society of Microbiology (ASM) here in Boston. We are presenting two posters: One is about evolution of ocean microbes at the global scale (“Exploring the Contribution of Neutral Evolution to Biogeography in Global Surface Ocean Microbes Using Agent-Based Modeling”) and another is about aging in bacteria (“From Protein Damage to Cell Aging to Population Fitness in E. coli: Insights from a Multi-level Agent-based Model”). Today I was at a session on "bacterial quiescence", where people talk about phenotypic differentiation of a small fraction of the population, including dormancy, sporulation, lag phase, viable but not culturable (VBNC), not growing metabolically active (NGMA), constant activity stationary phase (CASP), etc. One thing that strikes me is that its all about the heterogeneity. Biology no longer assumes that bacterial populations are homogeneous. This is in stark contrast to our mathematical models, which still treat bacteria as if they were homogenous populations. We are going to need agent-/individual-based models to analyze these data.

Here are links to our abstracts:

Tuesday, May 6, 2014

Vienna Stochastic Biology Workshop Report

I am at IST Austria for a workshop on Stochastic Biology. This is really a nice place to be and I enjoy listening to science during the day and then going for a run and dinner in Vienna in the evening. Today I gave a presentation on Kami’s model of aging in E. coli, which (I think) was well-received. This workshop focuses on how stochastic intracellular mechanisms (e.g. gene expression) give rise to cellular behavior. I am interested in incorporating these mechanisms into my microbe models and then modeling populations of these to see how they affect population and ecosystem behavior. However, right now I am sitting here in the audience with mixed emotions. On the one hand, I feel like a kid in a candy store. All these novel observational and experimental techniques are producing very exciting data and I want to model it all. On the other hand, these tools are now so good that it sometimes is difficult to see what modeling can still contribute. If we can observe everything, why do we need models? Here is a link to the workshop:

Friday, May 2, 2014

On N loading and export from lakes

I am pleased to announce that Xiaodan Ruan’s paper (co-authored by Frank Schellenger and myself) has been published in ES&T. This paper is concerned with nitrogen export from watersheds, which is a worldwide problem (e.g. the Mississippi River “dead zone”, see picture below). Our findings have important implications for watershed management. Specifically, we present a model that suggests a certain reduction (e.g. 50%) in N loading (i.e. from fertilizer or other sources) will not translate into the same amount of reduction at the watershed outlet, because N fixation by cyanobacteria in lakes and reservoirs may counteract the reduction. We are presently running whole-watershed models for a number of systems to develop a quantitative estimate of this problem.
Here is a link to the paper: