Friday, January 6, 2017

THE THINGS WE THINK AND DO NOT SAY

I am pleased to announce the publication of “75 years since Monod: It is time to increase the complexity of our predictive ecosystem models”. This opinion paper contributes to the debate about the level of complexity in ecological modeling. I have been developing relatively complex models for some time now and often the complexity is the subject of criticism (as part of the Q&A part of talks and seminars and the journal and proposal peer review process). Over time I have come to develop counterarguments and I am now at a point where I feel it would be useful to share these with a larger audience. This paper is my attempt to deliver a broadside salvo at the critics of complex ecological models.

A bit of a personal perspective: With this paper I am questioning some of the long-standing principles of ecological modeling, i.e. that models should be as simple as possible. Writing this paper made me think of the movie “Jerry McGuire”, where he writes an assay “The Things we Think but Do Not Say” criticising how things are done in his business. He ends up getting fired…


Paper link:


Saturday, December 17, 2016

Saturday, December 3, 2016

Ocean currents and temperature selection

I am pleased to announce our latest paper on agent-based modeling of ocean microbes. Microbe biogeography studies typically assume that the microbes are affected only by local conditions. However, in areas with substantial advection (e.g. ocean currents), upstream conditions may play a stronger role in shaping the local community. Here we explore this effect for temperature selection in surface ocean microbes. We develop a novel agent-based model and perform simulations to quantify the effect of advection at the global scale. Our results show that advection by currents can change the effective selection temperature of microbes by several degrees Celsius, and therefore should be considered in microbe biogeography studies. We then apply our results to three global datasets and for all we can better explain observations when currents are considered. We make our results accessible to the broader community by providing an atlas of temperature corrections.

I think this is an interesting study with some important conclusions. In terms of my research program, this model also represents a stepping stone for a more complex global microbe agent-based model. Specifically, we are now working on integrating a gene-level model of Synechococcus I developed previously (see link below) into this model. We will then make predictions of gene, transcript and protein levels at the global scale. Pretty exciting!




PAPER

YOUTUBE MOVIE

CODE AT GITHUB

SYNCHOCOCCUS MODEL PAPER


Tuesday, August 23, 2016

ISME Conference Report

I am in Montreal at ISME16 (16th International Symposium on Microbial Ecology). Yesterday I presented a poster on our Anabaena - nitrogen interaction model. This is a very exciting meeting with many presentations that are very close to my research area. I listened to talks about the role of uncultured bacteria that live in symbiosis with eukaryotes and fix N in the ocean and “cable bacteria" that move electrons over distances of centimeters in sediments. There are so many interesting ecological problems where our modeling approach can make a contribution. The list of “future projects” continues to grow... 


http://www.isme-microbes.org/isme16

Wednesday, August 17, 2016

Special Issue in Frontiers in Microbiology

In collaboration with Frontiers in Microbiology, section Systems Microbiology, we are organizing a Research Topic titled "The Individual Microbe: Single-Cell Analysis and Agent-Based Modelling", hosted by Weiwen Zhang, Johan Leveau, Clara Prats, Jan-Ulrich Kreft, Ferdi L Hellweger. We would like to encourage you to contribute to this topic. Please find more information at the homepage we have created on the Frontiers website, which defines the focus of the topic, and where all published articles will appear.

http://frontiersin.org/Systems_Microbiology/researchtopics/The_Individual_Microbe_Single-Cell_Analysis_and_Agent-Based_Modelling/5193

Please note the submission deadline for this Research Topic: Apr 30, 2017


Wednesday, July 13, 2016

SIAM Conference Report

I am at the SIAM (Society of Industrial and Applied Mathematics) Life Sciences conference here in Boston. This morning I made a presentation about our Anabaena model and listened to many interesting talks about modeling microbes.

Here is a link to the program and abstract:
http://www.siam.org/meetings/ls16/
http://meetings.siam.org/sess/dsp_talk.cfm?p=78264



Monday, June 27, 2016

Gordon Research Conference Report

I am at the Gordon Research Conference on Environmental Sciences - Water in New Hampshire. Today I gave a talk about our research. In some ways this conference marks a 10 year anniversary for me. In 2006 I was here and presented my first poster on agent-based modeling (ABM) of phytoplankton. That was a real milestone, because since then this has been the defining theme of my research. In fact, that poster is still prominently displayed in my office :) 

A main goal of my presentation was to start a discussion about updating the biology in our water quality models. One reason for doing this is to bring models up to the level of modern observations (see figure below). When we first developed water quality models in the 1970s, people were measuring total phosphorus and chlorophyll a, and those were adopted as state variables in our model. Since then, observations have evolved and now observations include DNA, RNA, etc. However, our models have not kept up. This disconnect really limits the utility of our models, and I think it is leading to the extinction of a specialty: water quality modelers. A big problem, because most of our waterbodies are polluted and models are important tools for management and research in this area :(




Here is a link to the program:
https://www.grc.org/programs.aspx?id=11255