Related papers: The Reconstruction of Science Phylogeny
We briefly review some of the scientific challenges and epistemological issues related to climate science. We discuss the formulation and testing of theories and numerical models, which, given the presence of unavoidable uncertainties in…
We introduce the Webworld model, which links together the ecological modelling of food web structure with the evolutionary modelling of speciation and extinction events. The model describes dynamics of ecological communities on an…
Clusters of genes that have evolved by repeated segmental duplication present difficult challenges throughout genomic analysis, from sequence assembly to functional analysis. Improved understanding of these clusters is of utmost importance,…
We define a novel quantitative strategy inspired by the ecological notion of nestedness to single out the scale at which innovation complexity emerges from the aggregation of specialized building blocks. Our analysis not only suggests that…
Scientific research is a major driving force in a knowledge based economy. Income, health and wellbeing depend on scientific progress. The better we understand the inner workings of the scientific enterprise, the better we can prompt,…
The algebraic properties of flattenings and subflattenings provide direct methods for identifying edges in the true phylogeny -- and by extension the complete tree -- using pattern counts from a sequence alignment. The relatively small…
Biomolecular communication demands that interactions between parts of a molecular system act as scaffolds for message transmission. It also requires an evolving and organized system of signs - a communicative agency - for creating and…
Genetic and comparative genomic studies indicate that extant genomes are more properly considered to be a fusion product of random mutations over generations and genomic material transfers between individuals of different lineages. This has…
Phylogenetics uses alignments of molecular sequence data to learn about evolutionary trees relating species. Along branches, sequence evolution is modelled using a continuous-time Markov process characterised by an instantaneous rate…
We show that the space in which scientific, technological and economic developments interplay with each other can be mathematically shaped using pioneering multilayer network and complexity techniques. We build the tri-layered network of…
In recent years, with the increase of social investment in scientific research, the number of research results in various fields has increased significantly. Cross-disciplinary research results have gradually become an emerging frontier…
We explore local vs. global evolution of knowledge systems through the framework of socio-epistemic networks (SEN), applying two complementary methods to a corpus of scientific texts. The framework comprises three interconnected…
The Science of Science (SoS) explores the mechanisms underlying scientific discovery, and offers valuable insights for enhancing scientific efficiency and fostering innovation. Traditional approaches often rely on simplistic assumptions and…
Phylogeny can be inferred using two sources of data from an organism: morphological data and molecular data. Historically, phylogenies were usually inferred using morphological characters, but some morphological features may not necessarily…
When dealing with evolving or multi-dimensional complex systems, network theory provides with elegant ways of describing their constituting components, through respectively time-varying and multi-layer complex networks. Nevertheless, the…
A fundamental question in the field of social studies of science is how research fields emerge, grow and decline over time and space. This study confronts this question here by developing an inductive analysis of emerging research fields…
Phylogenetic diversity is a measure for describing how much of an evolutionary tree is spanned by a subset of species. If one applies this to the (unknown) subset of current species that will still be present at some future time, then this…
Phylogenetic networks generalise phylogenetic trees and allow for the accurate representation of the evolutionary history of a set of present-day species whose past includes reticulate events such as hybridisation and lateral gene transfer.…
Humans are increasingly stressing ecosystems via habitat destruction, climate change and global population movements leading to the widespread loss of biodiversity and the disruption of key ecological services. Ecosystems characterized…
Cities are characterized by the presence of a dense population with a high potential for interactions between individuals of diverse backgrounds. They appear in parallel to the Neolithic revolution a few millennia ago. The advantages…