Two new papers

Two papers I am very fond of just came out.

The first one deals with competition: for decades, we’ve been teaching undergraduate students about the principle of competitive exclusion, showing the simple and appealing notion that intra-specific competition has to exceed inter-specific competition for two species to coexist. Often, however, we fail to mention that this simple rule does not extend to more than two species (guilty as charged).

Can we say anything interesting about the role of intra- and inter-competition in determining the stability of large systems? Turns out that some fairly old results in linear algebra, mixed with more recent advances in random matrix theory,  can be used to write simple conditions for the stability of large competitive communities.

György Barabás, Matthew J. Michalska-Smith & Stefano Allesina
The effect of intra- and interspecific competition on coexistence in multispecies communities
The American Naturalist, 2016

Interestingly, when we have more than two species we can think of how interaction strengths should be arranged to maximize (minimize) stability. Thanks to some very intensive numerical searches, we were able to show that these cases correspond to visually beautiful and ecologically reasonable patterns of interaction strengths:

The second paper takes a new angle to study a very old problem: are modular structures more conducive to stability than random ones? This idea was already put forward by Robert May at the end of his celebrated 1972 paper—yet, a good method to settle this question once and for all was lacking.

We have found a new way to calculate the stability of large random matrices with block structure, showing that rarely modularity has a positive effect on stability:

Jacopo Grilli, Tim Rogers & Stefano Allesina
Modularity and stability in ecological communities
Nature Communications, 2016

One interesting anecdote about this paper: Jacopo and I had been working on it for a while, and had received positive reviews from Nature Communications. However, we didn’t have a way to show that our conjectures were right. At the end of Dec 2015, I was at the Santa Fe Institute for a workshop. I gave a talk on this topic, and Charles Bordenave told me that a friend of his, Tim Rogers, had developed a method that could be used to perform this type of calculation. On Christmas day—thinking that at Christmas everybody’s good—I emailed Tim, asking whether he’d be able to help us out. Come New Year’s Eve and I receive an email from Tim: he had done the calculation, confirming our conjectures exactly!

The method Tim developed is based on quaternionic functions—I believe this is the first paper in ecology to ever mention quaternions in the abstract…

The Little Black Book

In Italy in the 1970s, youth belonging to counterculture movements would march in the streets, parading a copy of the Little Red Book  containing quotations from the writings of Chairman Mao Tse-tung.

Yesterday I turned 40, and to celebrate this very round anniversary, Gyuri, Jacopo, Liz and Matt presented me with a Little Black Book containing many of the things I often repeat, or particularly memorable utterances.


This was a truly moving gift, which made me laugh out loud — my labmates know me too well! (It also made me think that I am slowly becoming a grumpy old professor, always repeating the same Mantras)

I will keep the notebook in the lab, so that whenever someone feels the urge to record memorable quotations, they can be saved for posterity.

Joining NICO and PLoS Computational Biology

With the new year, I’ve been invited to join the Northwestern Institute on Complex Systems as an External Faculty, and the Editorial Board of PLoS Computational Biology.

nico-logoNICO is an institute dedicated to the study of complex systems, and is part of Northwestern University, in Evanston (a short train ride from Chicago). It is directed by Luis Amaral and Brian Uzzi, two of the best researchers working at the interface of networks and complex systems. I am very much looking forward to work with the faculty there, and I am very interested in the courses and conferences organized by the Center.

ploscb-logoPLoS Computational Biology is one of my favorite journals. I’ve published seven papers in the journal so far (three last year: 1, 2, 3), and I often reviewed and guest-edited for the journal. I am very happy to join the board as an Associate Editor, and I hope this will help increase the number of submissions from ecologists, as well as foster a dialogue between quantitative ecologists and other biologists interested in the computational, statistical, and mathematical aspects of the discipline.

Richard Levins 1930-2016

Sad news for theoretical ecology: on Jan 19th, Richard Levins died in Cambridge, MA. He was 85 years old.

His work has always been my main source of inspiration. I got to read some of his articles in college, when Antonio Bodini—who was then to become my PhD avisor—introduced Loop Analysis in a class on Environmental Impact Assessment. I immediately loved the simplicity, elegance, and power of this method, and I worked on it for my honors thesis (with Alessandro Zaccagnini and Antonio Bodini).

During my PhD years, I’ve read more of his work, including the wonderful (yet almost impossible to find) book with Charles Puccia, and the celebrated articles “The strategy of model building in population biology” and “Evolution in communities near equilibrium”.

All my work on stability, random matrices, and population dynamics has been inspired by Loop Analysis, and even today when I see a matrix, I actually see a composition of loops and paths.

Even the fact I am now in Chicago is somewhat influenced by Levins: he and Lewontin were professors here in the 1970s, and that’s why when I saw the ad for the position in Ecology & Evolution, I immediately felt I had to apply—this is my kind of Department!

There’s a nice picture of Levins in the Lillie Room downstairs: you can see him in his prime, explaining Loop Analysis on the board. That’s the way I want to remember him.


Beautiful places

Traveling is quite disruptive, especially when you have a family at home, and a lab to run. However, having to travel to incredibly beautiful destinations to meet old friends makes the whole ordeal much more pleasant.

I have just returned to Chicago after a week in Monterey, CA, where I taught a short course on computing at the Hopkins Marine Station of Stanford University. The class was great, and the organizer was my friend Giulio De Leo. I got to spend some time with Giulio and Fiorenza, as well as to interact with an incredibly motivated group of students. I also gave a talk at Hopkins and one at the main campus in Palo Alto. This is what I would see when I went for a run:

Monterey at 6:30AM
Monterey at 6:30AM

Just before heading to Stanford, I have been in Venezia, Italy, for a school on complex systems, organized by Antonio Trovato, Samir Suweis and our very own Jacopo Grilli. Again, the school was great, and the location—in San Servolo island—unbeatable:

Sunset in Venezia seen from San Servolo
Sunset in Venezia seen from San Servolo

These trips energized me a lot, but I am really happy to be home for a good stretch of time!