Kemp, C. | bioRxiv Science

bioRxiv2021

The evolution of color naming reflects pressure for efficiency: Evidence from the recent past

It has been proposed that semantic systems evolve under pressure for efficiency. This hypothesis has so far been supported largely indirectly, by synchronic cross-language comparison, rather than directly by diachronic data. Here, we directly test this hypothesis in the domain of color naming, by analyzing recent diachronic data from Nafaanra, a language of Ghana and Cote dIvoire, and comparing it with quantitative predictions derived from the mathematical theory of efficient data compression. We show that color naming in Nafaanra has changed over the past four decades while remaining near-optimally efficient, and that this outcome would be unlikely under a random drift process that maintains structured color categories without pressure for efficiency. To our knowledge, this finding provides the first direct evidence that color naming evolves under pressure for efficiency, supporting the hypothesis that efficiency shapes the evolution of the lexicon.

animal behavior and cognition↗

bioRxiv2020

A functional module states framework reveals cell states for drug and target prediction

Cells are complex systems in which many functions are performed by different genetically-defined and encoded functional modules. To systematically understand how these modules respond to drug or genetic perturbations, we developed a Functional Module States framework. Using this framework, we 1) defined the drug induced transcriptional state space for breast cancer cell lines using large public gene expression datasets, and revealed that the transcriptional states are associated with drug concentration and drug targets; 2) identified potential targetable vulnerabilities through integrative analysis of transcriptional states after drug treatment and gene knockdown associated cancer dependency; and 3) used functional module states to predict transcriptional state-dependent drug sensitivity and built prediction models using the functional module states for drug response. This approach demonstrates a similar prediction performance as do approaches using high dimensional gene expression values, with the added advantage of more clearly revealing biologically relevant transcriptional states and key regulators.

systems biology↗