arXiv subjects

Joanna Masel

Publications and source records attributed to Joanna Masel.

7 recordsLinked to original sources

arXiv2026

What good is modeling? Introducing ecology and evolution students to theory

Theory and empirical science should be in constant dialogue, but often find it hard to understand one another. Here we describe a graduate-level university course we developed to improve matters. The course was designed to help empirically focused biology graduate students read and understand theory papers, despite little prior mathematical training. It uses several evidence-based principles of modern teaching: backwards design, active learning, and just-in-time teaching. This curricular content, emphasizing the nature of evidence and the role of theory in science, aims to improve critical thinking as a means of accelerating scientific progress.

physics.ed-ph↗

arXiv2023

Digital contact tracing/notification for SARS-CoV-2: navigating six points of failure

Digital contact tracing/notification was initially hailed as a promising strategy to combat SARS-CoV-2, but in most jurisdictions it did not live up to its promise. To avert a given transmission event, both parties must have adopted the tech, it must detect the contact, the primary case must be promptly diagnosed, notifications must be triggered, and the secondary case must change their behavior to avoid the focal tertiary transmission event. If we approximate these as independent events, achieving a 26% reduction in R(t) would require 80% success rates at each of these six points of failure. Here we review the six failure rates experienced by a variety of digital contact tracing/notification schemes, including Singapore's TraceTogether, India's Aarogya Setu, and leading implementations of the Google Apple Exposure Notification system. This leads to a number of recommendations, e.g. that tracing/notification apps be multi-functional and integrated with testing, manual contact tracing, and the gathering of critical scientific data, and that the narrative be framed in terms of user autonomy rather than user privacy.

q-bio.PE↗

arXiv2016

Predicting patterns of long-term adaptation and extinction with population genetics

Population genetics struggles to model extinction; standard models track the relative rather than absolute fitness of genotypes, while the exceptions describe only the short-term transition from imminent doom to evolutionary rescue. But extinction can result from failure to adapt not only to catastrophes, but also to a backlog of environmental challenges. We model long-term evolution to long series of small challenges, where fitter populations reach higher population sizes. The population's long-term fitness dynamic is well approximated by a simple stochastic Markov chain model. Long-term persistence occurs when the rate of adaptation exceeds the rate of environmental deterioration for some genotypes. Long-term persistence times are consistent with typical fossil species persistence times of several million years. Immediately preceding extinction, fitness declines rapidly, appearing as though a catastrophe disrupted a stably established population, even though gradual evolutionary processes are responsible. New populations go through an establishment phase where, despite being demographically viable, their extinction risk is elevated. Should the population survive long enough, extinction risk later becomes constant over time.

q-bio.PE↗

arXiv2015

Outcome orientation - a misconception of probability that harms medical research and practice

Human understanding of randomness and variation is shaped by a number of cognitive biases. Here we relate a lesser-known cognitive bias, the "outcome orientation", to medical questions and describe the harm that the outcome orientation can do to medical research and practice. People who reason according to an outcome orientation interpret probability as a subjective degree of belief that is constrained to consider events one at a time, in a way that is incompatible with Bayesian reasoning. Instead of accepting that uncertainty is inevitable, and generalizing from the frequency of similar events, the outcome orientation prefers one-off causal narratives. In medicine, the outcome orientation therefore erodes support for randomized controlled trials in favor of reductionist approaches. The rhetoric of personalized medicine resonates with, and can promote, the outcome orientation, by emphasizing how the measurable attributes of individual patients, rather than chance or unknowable factors, causally produce each particular patient's outcome.

physics.ed-ph↗

arXiv2015

Eco-evolutionary "fitness" in 3 dimensions: absolute growth, absolute efficiency, and relative competitiveness

Competitions can occur on an absolute scale, to be faster or more efficient, or they can occur on a relative scale, to "beat" one's competitor in a zero-sum game. Ecological models have focused on absolute competitions, in which optima exist. Classic evolutionary models such as the Wright-Fisher model, as well as more recent models of travelling waves, have focused on purely relative competitions, in which fitness continues to increase indefinitely, without actually progressing anywhere. This manuscript proposes a new way to describe both at the same time. It begins with a revised version of r/K-selection theory. r continues to describe maximum reproductive speed, but the new version of K, with a different subscript, now describes parsimoniousness in territory use, a group-selected, anti-tragedy-of-the-commons trait. A third dimension c of fitness is then added to this novel system, one which is unitless and normalized, and hence capable of capturing the population genetics concept w of a strictly relative, genetically-limited competitive race. MacArthur's original version of r/K-selection theory is shown to confound parsimoniousness K with competitive ability c, despite the fact that available data suggests a negative correlation between the two; here they are disentangled. A rotation of the resulting three-dimensional system provides a population genetic underpinning for Grime's universal adaptive strategy theory of ruderals (selected for high r), stress tolerators (selected for a combination of high r and high K), and competitors (selected for a combination of high r and high c).

q-bio.PE↗

arXiv2013

Cryptic Genetic Variation Can Make Irreducible Complexity a Common Mode of Adaptation

The existence of complex (multiple-step) genetic adaptations that are "irreducible" (i.e., all partial combinations are less fit than the original genotype) is one of the longest standing problems in evolutionary biology. In standard genetics parlance, these adaptations require the crossing of a wide adaptive valley of deleterious intermediate stages. Here we demonstrate, using a simple model, that evolution can cross wide valleys to produce "irreducibly complex" adaptations by making use of previously cryptic mutations. When revealed by an evolutionary capacitor, previously cryptic mutants have higher initial frequencies than do new mutations, bringing them closer to a valley-crossing saddle in allele frequency space. Moreover, simple combinatorics imply an enormous number of candidate combinations exist within available cryptic genetic variation. We model the dynamics of crossing of a wide adaptive valley after a capacitance event using both numerical simulations and analytical approximations. Although individual valley crossing events become less likely as valleys widen, by taking the combinatorics of genotype space into account, we see that revealing cryptic variation can cause the frequent evolution of complex adaptations. This finding also effectively dismantles "irreducible complexity" as an argument against evolution by providing a general mechanism for crossing wide adaptive valleys.

q-bio.PE↗

arXiv2012

Compensatory evolution and the origins of innovations

Cryptic genetic sequences have attenuated effects on phenotypes. In the classic view, relaxed selection allows cryptic genetic diversity to build up across individuals in a population, providing alleles that may later contribute to adaptation when co-opted - e.g. following a mutation increasing expression from a low, attenuated baseline. This view is described, for example, by the metaphor of the spread of a population across a neutral network in genotype space. As an alternative view, consider the fact that most phenotypic traits are affected by multiple sequences, including cryptic ones. Even in a strictly clonal population, the co-option of cryptic sequences at different loci may have different phenotypic effects and offer the population multiple adaptive possibilities. Here, we model the evolution of quantitative phenotypic characters encoded by cryptic sequences, and compare the relative contributions of genetic diversity and of variation across sites to the phenotypic potential of a population. We show that most of the phenotypic variation accessible through co-option would exist even in populations with no polymorphism. This is made possible by a history of compensatory evolution, whereby the phenotypic effect of a cryptic mutation at one site was balanced by mutations elsewhere in the genome, leading to a diversity of cryptic effect sizes across sites rather than across individuals. Cryptic sequences might accelerate adaptation and facilitate large phenotypic changes even in the absence of genetic diversity, as traditionally defined in terms of alternative alleles.

q-bio.PE↗