Wednesday, August 20, 2014

New project: Analysis of cyanobacteria sensor data

I am pleased to announce the start of a new project entitled “Robust Identification and Model Validation for a Class of Nonlinear Dynamic Systems and Applications”. This is a collaboration with Mario Sznaier and Octavia Camps from ECE, sponsored by NSF. In this project we will develop and apply data-driven models to high-volume environmental parameters (e.g. from cyanobacteria sensors) that hopefully will help us understand and manage water quality problems, including harmful algal blooms (HABs), in the Charles River and other water bodies. Here is a picture of a sensor buoy (courtesy GLEON) and a link to the project abstract.

Monday, July 28, 2014

2nd Public Swim in Charles River

On Saturday I jumped into the Charles River … again. This is a now annual event organized by the Charles River Conservancy. Last year there was one swim day. This year there were two scheduled, but the first one had to be cancelled because of a cyanobacteria bloom. Hopefully next year we will have even more and eventually a permanent beach or dock. Here is a link to CRCs web site:

Wednesday, July 2, 2014

Summer Sampling Under Way

Our summer sampling program has started. This year, PhD student Frank Schellenger and YSP students Mia Kobs and Mindy Wu are exploring the role of phosphorus loading from lakefront septic systems to lakes. An interesting aspect of this problem is the time dimension. Because phosphate sorbs strongly onto the solids in the ground a lot of it remains there and does not reach the lake. But P is conservative, so it will get there (“break through”) eventually. When do we expect this to happen? Here is a picture of Frank, Mia and Mindy at the lake and a link to more pictures.

Thursday, June 19, 2014

Tufts Conference Report

This week we have the UCOWR/NIWR/CUAHSI Conference at Tufts. The theme is “Water Systems, Science, and Society under Global Change”. We have two presentations: I will give a talk on Neil’s Lake Taihu model and Xiaodan will present her work on Lake Loading/Export modeling.

Here is a link to the conference: 

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: