Category Archives: Papers

3 ≫ 2

In a new paper published today in Nature, we show that Higher-Order Interactions (HOIs) can have dramatic effects on the dynamics of ecological systems.

Jacopo Grilli, György Barabás, Matthew J. Michalska-Smith & Stefano Allesina
Higher-order interactions stabilize dynamics in competitive network models
Nature, 2017

I have written a short “Behind the paper” post for the Nature Ecology & Evolution Community, which you can find here.

James O’Dwyer has written a News & Views commentary.

Rob Mitchum has covered this work for the Computation Institute‘s website.

I have presented this work at several conferences. Here’s a video of my talk at the BES annual meeting in Liverpool (Dec 2016, ~30 mins):

What’s in a last name?

In a new paper published today in PNAS, Jacopo and I try to extract as much information as possible from an ostensibly meager source of data: a list of the names of all the researchers working in Italy, at the Centre National de la Recherche Scientifique in France, and at public universities in the US.

We show that by using simple randomizations, one can highlight several interesting facts about these different academic systems.

Queneau
In how many ways can you randomize a list of last names?

The work is a bona fide exercise in style: by introducing subtle variations of the randomization algorithm, we show that in Italy researchers work in the region where they were born and raised, while in the US geography does not influence the distribution of researchers; in France, we can detect academic couples working in the same unit; we demonstrate that academic nepotism in Italy (the focus of a previous paper of mine) is declining; finally, we show that in the US immigration is field-specific.

Jacopo Grilli & Stefano Allesina
Last name analysis of mobility, gender imbalance, and nepotism across academic systems
PNAS, 2017

Because the article is paywalled for 6 months, I have stored a personal copy here.
The data and code are available on GitHub.

The article is being covered by the popular press. Here below we link some of the coverage:
In English: EurekAlert; Science Life; U Chicago News; Nature;
In Italian: Corriere della Sera; adnkronos; La Repubblica; Lettera43; Il Giornale; Wired; Wired (again); Corriere della Sera 1 and 2; Il Messaggero; Il TempoSole 24 ore; Rai TV TG 1; TGCOM 24; Il Foglio (genius! …not really); Il Fatto Quotidiano; Il Foglio (again); La Stampa;
Other languages: Naked science (Russian); Science Times (Korean); polit.ru (Russian); Xataka Ciencia (Spanish);

Update: the study was mentioned on 9/25/2017 in the TG3 news, in relation to a new scandal in which professors allegedly conspired to have their pupils hired irrespective of merit:

The edition of the evening contains a brief interview with Jacopo:

On October 12th, TG3 broadcast a discussion on this theme (with Francesco Sylos Labini and Vincenzo Barone), which includes an interview with yours truly:

Quality vs Quantity…. or not?

It is not unusual to read the tirade of a senior scientist complaining that science was better back then, when papers were fewer, and ideas better (a perfect example of this genre is here). Usually, the conclusion is that we should publish less, lest producing lower-quality science.
These considerations are based on a quite precise hypothesis—that a scientist can either produce many papers, or produce fewer good ones. Detecting such a trade-off in actual data is quite difficult, though, as scientists vary dramatically in productivity, as well as field of study.
Matt and I tried a different route, and compared scientists with themselves: does a scientist produce better papers in the years when she’s most productive? For testing our method, we took the members of the National Academy of Sciences, and reconstructed their publication history. (The rationale being that their best papers must be of high quality).
We found that these scientists tend to produce their most recognized work in years when they’re most productive. However, they also tend to produce their least impactful articles during the same productive years. This is consistent with the “random impact” hypothesis: by publishing many papers, scientists sample their distribution of good ideas more thoroughly, leading to higher maxima and lower minima.
You can read the paper here:

Matthew J. Michalska-Smith & Stefano Allesina
And, not or: Quality, quantity in scientific publishing
PLoS One, 2017

Coexistence for more than two species

One of the main obsessions in the laboratory is to build robust ecological theories for communities composed of many species.
This is especially important in competitive systems—much of our  understanding in this area descends from the analysis of the dynamics of two competitors.
In a new review published this week in Nature, Jonathan Levine, Jordi Bascompte, Peter Adler, and yours truly provide a roadmap for extending these considerations to systems with more than two species.
Interestingly, certain mechanisms, such as higher-order interactions and intransitive competition, can only be studied in high-dimensional systems.
You can read the paper here:

Jonathan M. Levine, Jordi Bascompte, Peter B. Adler & Stefano Allesina
Beyond pairwise mechanisms of species coexistence in complex communities
Nature, 2017

Here’s the “Outlook”:

In this Review, we suggest that coexistence mechanisms that emerge only in systems with more than two competitors exert a largely unexplored control over the maintenance of diversity in species-rich communities. We also highlight that when studying more than two competitors, ecologists necessarily confront an ecological network. However, it remains largely unknown how the structure of the network influences coexistence. The sparseness of evidence results from the intractability of empirically evaluating competition between many species and the technical difficulties that are inherent in tightly coupling theory to data. Despite these challenges, there are compelling reasons to deepen our understanding of these more complex mechanisms of coexistence. Armed with advances in data-driven modelling and network analyses that have been developed for multitrophic systems, ecologists are well-positioned to determine, for at least some species-rich communities, how much of the coexistence results from mechanisms that emerge only in diverse systems. Few other questions in ecology have such great potential to radically shift how we think about the maintenance and fragility of biodiversity.

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…