Eyeball

Here come old flat top
He come groovin’ up slowly
He got joo joo eyeball
Come together
Lennon  & Mccartney

We have been working on the applications of random matrix theory to ecology for four years. By now, it is quite clear that the most important challenge ahead is to extend the theory to the case of structured networks (as described here). A new study we just published is a first step in this direction:

 Stefano Allesina, Jacopo Grilli, György Barabás, Si Tang, Johnatan Aljadeff & Amos Maritan
Predicting the stability of large structured food webs
Nature Communications, 2015

In this work, we studied community matrices produced according to the cascade model, in which “big fish eat little fish”. These matrices look like this:

eyeballmatwhere the red squares represent negative coefficients (effects of predators on prey), and the blue ones positive coefficients (effects of prey on predators). These matrices produce a peculiar spectrum, suggestive of an “eyeball”:

matA2

In the paper, we derive simple, analytical results that allow us to approximate the spectrum (and hence the stability) of the eyeball.

 I wrote an R package that performs the analysis described in the paper, and published it on github.

PS: Despite the quote from the Beatles above, all I could listen to while writing the paper was Pink Floyd. Maybe because I remember another eyeball I saw a long time ago

Metapop

In a new paper, Jacopo, Gyuri and I studied the persistence of metapopulations living in a landscape where patches of suitable habitat are scattered randomly.

We found strong connections between metapopulation theory, the mathematics of Random Geometric Graphs, and the physics of disordered systems. You can find the paper here:

Jacopo Grilli, György Barabás, Stefano Allesina
Metapopulation Persistence in Random Fragmented Landscapes
PLoS Computational Biology, 2015

A bit on the backstory: in December 2014, I gave a talk at UC Davis, and, at dinner, Sebastian Schreiber mentioned that if I liked problems involving eigenvalues I should have looked at the classic Hanski & Ovaskainen model. Back in Chicago, Gyuri (who had just started his postdoc) and Jacopo (who was visiting from Italy) thought it would be a good project to jumpstart our collaboration…

More is more (when it comes to abstracts)

In the summer of 2013, I was coordinating a class meant to prime incoming graduate students on what it takes to succeed in graduate school. One session dealt with writing good abstracts. You have heard the usual advice: keep it short and simple, avoid jargon, write it for a general reader, etc.

I thought that it would be fun to test whether following this type of advice increases readership (citations). After a few months, I pitched this idea to my friend James Evans, and we decided to try it out with the help of Cody Weinberger, an undergraduate student in my laboratory.

We collected about 1M abstracts from 8 disciplines, and we tested the impact of following the usual advice on citations, once accounted for obvious factors such as age of the article, journal where it was published, etc. To our surprise, we found that following some of the most common suggestions leads to a significant decrease in citations!

You can read the results here:
Cody J. Weinberger, James A. Evans, Stefano Allesina
Ten Simple (Empirical) Rules for Writing Science
PLoS Computational Biology, 2015

citations

The short article starts with a quote from Boyle’s “Proemial Essay”. Robert Boyle was one of the main proponents of the use of “modern” scientific articles to disseminate science (i.e., instead of books). Amusingly, while describing the advantages of this approach, Boyle already states some guidelines on how the essays should be written: we’ve been told how should we write our science for at least 350 years!

Update: The Chronicle of Higher Education features a Q&A with Cody.

Random matrices in ecology: the challenges ahead

RMT-ProductIn October 2013, I was a speaker at the 29th Annual Meeting of the Society of Population Ecology, held in Osaka, Japan. The invitation came with the possibility of writing an article for a special issue of the journal Population Ecology.

 

I thought that this would be a great occasion to review the progress my laboratory has made on the study of the stability of large ecological systems. Even better, this article could outline a research program on this topic, listing the main challenges that we are facing.

My former student Si Tang (now pursuing a second PhD in Statistics) and I set to work with this idea in mind. You can now read this hybrid between a review and a list of “grand challenges”:

Stefano Allesina & Si Tang
The stability–complexity relationship at age 40: a random matrix perspective
Population Ecology, 2015

Our hope is that all the challenges we list will be solved by the time May’s 1972 paper turns 50.

Traveling in Northern Europe

Just before the Winter break, I’ve been traveling in Sweden and the Netherlands. In Linköping, I gave a 3-hr lecture on the stability of large ecological systems for the 6th Swedish Meeting in Mathematics in Biology. It was a great experience, and it was so nice to get to see my former postdoc Anna Eklöf and spend some time with her and her family.

In the Netherlands, I was part of a workshop on Spatio-Temporal Dynamics in Ecology at the Lorentz Center in Leiden. This is a great place for workshops, and I think I will organize one in the near future!

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