Related papers: What Omicron Does, and How It Does It
CRISPR is a newly discovered prokaryotic immune system. Bacteria and archaea with this system incorporate genetic material from invading viruses into their genomes, providing protection against future infection by similar viruses. The…
Although several synonymous codons can encode the same aminoacid, this symmetry is generally broken in natural genetic systems. In this article, we show that the symmetry breaking can result from selective pressures due to the violation of…
Current-day genomes bear the mark of the evolutionary processes. One of the strongest indications is the sequence homology among families of proteins that perform similar biological functions in different species. The number of proteins in…
Evolutionary complexity is here measured by the number of trials/evaluations needed for evolving a logical gate in a non-linear medium. Behavioural complexity of the gates evolved is characterised in terms of cellular automata behaviour. We…
We introduce a two-strain model with asymmetric temporary immunity periods and partial cross-immunity. We derive explicit conditions for competitive exclusion and coexistence of the strains depending on the strain-specific basic…
High-throughput molecular screening is required to investigate the origin and diffusion of antimicrobial resistance in pathogen outbreaks. The most frequent cause of human infection is Escherichia coli, which is dominated by sequence type…
Empirical evidence reveals that contagion processes often occur with competition of simple and complex contagion, meaning that while some agents follow simple contagion, others follow complex contagion. Simple contagion refers to spreading…
Detections of mutations of the SARS-CoV-2 virus gave rise to new packages of interventions. Among them, international travel restrictions have been one of the fastest and most visible responses to limit the spread of the variants. While…
The evolution of multicellularity was a major transition in the history of life on earth. Conditions under which multicellularity is favored have been studied theoretically and experimentally. But since the construction of a multicellular…
What is motivation and how does it work? Where do goals come from and how do they vary within and between species and individuals? Why do we prefer some things over others? MEDO is a theoretical framework for understanding these questions…
Organisms result from adaptive processes interacting across different time scales. One such interaction is that between development and evolution. Models have shown that development sweeps over several traits in a single agent, sometimes…
Motivated by epidemics such as COVID-19, we study the spread of a contagious disease when behavior responds to the disease's prevalence. We extend the SIR epidemiological model to include endogenous meeting rates. Individuals benefit from…
Nature features a plethora of extraordinary photonic architectures that have been optimized through natural evolution. While numerical optimization is increasingly and successfully used in photonics, it has yet to replicate any of these…
The mutual influence of dynamics and structure is a central issue in complex systems. In this paper we study by simulation slow evolution of network under the feedback of a local-majority-rule opinion process. If performance-enhancing local…
The problem of evolutionary complexification of life is considered one of the fundamental aspects in contemporary evolutionary theory. Parasitism is ubiquitous, inevitable, and arises as soon as the first replicators appear, even during the…
Preventing infectious disease like flu from spreading to large communities is one of the most important issues for humans. One effective strategy is voluntary vaccination, however, there is always the temptation for people refusing to be…
Based on a recent model of evolving viruses competing with an adapting immune system [1], we study the conditions under which a viral quasispecies can maximize its growth rate. The range of mutation rates that allows viruses to thrive is…
Bacteria, in contrast to eukaryotic cells contain two types of genes: chromosomal genes that are fixed to the cell, and plasmids that are mobile genes, easily shared to other cells. The sharing of plasmid genes between individual bacteria…
I reflect on the statistical methods of the Christakis-Fowler studies on network-based contagion of traits by checking the sensitivity of these kinds of results to various alternate specifications and generative mechanisms. Despite the…
Jim Shapiro synthesizes a great many observations about the mechanisms of evolution to reach the remarkable conclusion that large-scale modification, exchange, and rearrangement of the genome are common and should be viewed as fundamental…