Friday, September 12, 2014

Non-Darwinian evolution produces biogeography in model ocean microbe population

I am very happy that our paper on agent-based modeling of global ocean microbe evolution is now published. This study shows that neutral evolution and dispersal limitation can lead to substantial biogeography in ocean microbe populations. In a nutshell: Microbes evolve faster than the ocean circulation can mix them. I expect these results will receive a lot of attention, and I look forward to the discussion. In this post I want to highlight another aspect of the paper I am excited about, focused more on modeling technology.

You know, when I start my research program here at Northeastern about 10 years ago, I set out to develop models that are consistent with the quantity and types of observations we generate today. So I went to the literature and started looking at what people are measuring. I ran across papers by Ed DeLong and Craig Venter that presented metagenomics observations. My initial reaction of excitement quickly turned to despair when I realized that the quantity of information generated by modern observational tools now greatly surpasses what we can get out of models. In this model we simulate individual microbes, each with a full 1 Mbp genome. That approach constitutes one possible direction towards closing this gap. In some ways, our model application turns the table again, at least in terms of information quantity. For example, one of our simulations (Fig. 1B in the paper, “start uniform” simulation) includes 2.9e8 mutations and thus unique genomes, for a total of 290 Tbp, which is far larger than metagenomics datasets (e.g. GOS has 6.3 Gbp) or what is currently in GenBank (160 Gbp, Feb. 2014). I have an opening for an undergraduate research assistant to upload this data to GenBank (joke).

Here are links to the paper, a perspective article, some news features and an animation (which has been approved for going viral).

Thursday, September 4, 2014

Here we go …

Our fall semester is starting this week. This semester I am teaching my graduate Surface Water Quality Modeling course. I always enjoy this class, because the topic is very close to my research. The nature of graduate education is changing: For the first time I have more “online” than “inclass” students. Here is a link to the syllabus.

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.