Termite eusociality

Termites are eusocial by possessing two subfertile or sterile castes, the worker and the soldier. The consensus is that eusociality in termites is the result of a suite of factors (Thorne, 1997), though the relative importance accorded to each in the literature has shifted over time (Howard and Thorne, 2011). For the purpose of a quick review, I have not looked into mechanisms that appear … Continue reading Termite eusociality

Network structural uncertainty in Qualitative Modelling

Background Imagine a situation in which we want to model the behaviour of a food web, but we don’t know what the species interaction strengths are, and we’re not 100 percent sure what the structure of the food web is, either. For example, in the figure below, experts are are uncertain about whether or not there is a direct interaction between species 4 and 5, … Continue reading Network structural uncertainty in Qualitative Modelling

Some notes on the Principle of Indifference

A classical statement of the Principle of Indifference (PI) is as follows (p. 45 Keynes, 1921): if there is no known reason for predicating of our subject one rather than another of several alternatives, then relatively to such knowledge the assertions of each of these alternatives have an equal probability. Thus equal probabilities must be assigned to each of several arguments, if there is an … Continue reading Some notes on the Principle of Indifference

Fibonacci numbers and alternating signs in species responses to press perturbation in a food chain

In a paper from 2001, Dambacher and Rossignol made a curious observation: Fibonacci numbers appear in the adjoint and absolute feedback matrices that result from a weighted-predictions matrix type analysis (Dambacher et al. 2003) on food chains. The weighted-predictions matrix analysis is a way of predicting how species in a food web will respond to a the press perturbation of one of the species, so … Continue reading Fibonacci numbers and alternating signs in species responses to press perturbation in a food chain

The Principle of Indifference is actually two principles in one

In a previous post, I wrote about the philosophical problems caused by the Principle of Indifference. The problems are illustrated with a variety of thought-experiments that create paradoxes, such as Bertrand’s paradox. I also discussed how a problem in ecological modelling for conservation decision-making seems closely related to this philosophical problem. When I realised this connection, it seemed to me that, in order to solve … Continue reading The Principle of Indifference is actually two principles in one

Bad for birds, good for squirrels

Here’s a nice video I stumbled upon about Lisa Aubry’s group’s work at Utah State Uni. Climate change is having a positive effect on uinta ground squirrels, allowing them to fatten-up and attain weights higher than those recorded historically. This population is survival limited, and survival probability is higher the fatter the squirrels are, so abundance responds positively to this climate change. I can’t handle … Continue reading Bad for birds, good for squirrels

Import self-made Sage modules and functions into Sage script?

Let’s say that I have created a bunch of Sage code — Sage functions etc. — that I wish to reuse by importing into various Sage scripts. In straight Python, one would put these functions into their own separate file and import them using the usual from foo import funcname as localfuncname type procedure. It is unclear to me what the proper procedure for doing … Continue reading Import self-made Sage modules and functions into Sage script?

“ValueError: expected a DNF expression” when trying espresso_exprs example from pyeda docs

I’ve recently been working on a qualitative modelling project where I am trying to uncover “truths” about the response of species in an ecosystem to control of invasive species. Long story short, I’ve been looking into various boolean minimisation techniques. I’ve been playing with Python EDA, a Python library that I think provides a front-end to the Robert Brayton and Richard Rudell espresso heuristic logic … Continue reading “ValueError: expected a DNF expression” when trying espresso_exprs example from pyeda docs

The Principle of Indifference in ecological modelling

(Update April 2019: a paper on the topic below has now been published in MEE) Qualitative modelling Qualitative modelling (QM) holds the promise of obtaining predictions from dynamical models even when we don’t have all the data needed to parameterise them. How does QM achieve this? In short, the idea is to explore the range of possible parameter values to create an ensemble of possible … Continue reading The Principle of Indifference in ecological modelling