Month: August 2020

Evolution of Cellular Differentiation: From Hypotheses to Models

Pedro Márquez-Zacarías, Rozenn M. Pineau, Marcella Gomez, Alan Veliz-Cuba, David Murrugarra, William C. Ratcliff, Karl J.Niklas

Trends in Ecology and Evolution


Cellular differentiation is one of the hallmarks of complex multicellularity, allowing individual organisms to capitalize on among-cell functional diversity. The evolution of multicellularity is a major evolutionary transition that allowed for the increase of organismal complexity in multiple lineages, a process that relies on the functional integration of cell-types within an individual. Multiple hypotheses have been proposed to explain the origins of cellular differentiation, but we lack a general understanding of what makes one cell-type distinct from others, and how such differentiation arises. Here, we describe how the use of Boolean networks (BNs) can aid in placing empirical findings into a coherent conceptual framework, and we emphasize some of the standing problems when interpreting data and model behaviors.


The origins of life and its continuing wonder

Scientist and MacArthur Fellow Stuart Kauffman explains how life evolved from its earlier origins some 3,700 million years ago through the story of four protocells – Patrick, Rupert, Sly and Gus. He explains why our knowledge of the origins and early evolution of life can greatly help us understand our true place in the world. Our human species is part of nature, not above it.


Managing News Overload (MNO): The COVID-19 Infodemic

Sameera Tahira Ahmed

Information 2020, 11(8), 375


A crucial area in which information overload is experienced is news consumption. Ever increasing sources and formats are becoming available through a combination of traditional and new (digital) media, including social media. In such an information and media rich environment, understanding how people access and manage news during a global health epidemic like COVID-19 becomes even more important. The designation of the current situation as an infodemic has raised concerns about the quality, accuracy and impact of information. Instances of misinformation are commonplace due, in part, to the speed and pervasive nature of social media and messaging applications in particular. This paper reports on data collected using media diaries from 15 university students in the United Arab Emirates documenting their news consumption in April 2020. Faced with a potentially infinite amount of information and news, participants demonstrate how they are managing news overload (MNO) using a number of complementary strategies. Results show that while consumption patterns vary, all diaries indicate that users’ ability to navigate the news landscape in a way that fulfils their needs is influenced by news sources; platform reliability and verification; sharing activity; and engagement with news.


The evolution of universal adaptations of life is driven by universal properties of matter: energy, entropy, and interaction

Irun R. Cohen, Assaf Marron


The evolution of multicellular eukaryotes expresses two sorts of adaptations: local adaptations like fur or feathers, which characterize species in particular environments, and universal adaptations like microbiomes or sexual reproduction, which characterize most multicellulars in any environment. We reason that the mechanisms driving the universal adaptations of multicellulars should themselves be universal, and propose a mechanism based on properties of matter and systems: energy, entropy, and interaction. Energy from the sun, earth and beyond creates new arrangements and interactions. Metabolic networks channel some of this energy to form cooperating, interactive arrangements. Entropy, used here as a term for all forces that dismantle ordered structures (rather than as a physical quantity), acts as a selective force. Entropy selects for arrangements that resist it long enough to replicate, and dismantles those that do not. Interactions, energy-charged and dynamic, restrain entropy and enable survival and propagation of integrated living systems. This fosters survival-of-the-fitted – those entities that resist entropic destruction – and not only of the fittest – the entities with the greatest reproductive success. The “unit” of evolution is not a discrete entity, such as a gene, individual, or species; what evolves are collections of related interactions at multiple scales. Survival-of-the-fitted explains universal adaptations, including resident microbiomes, sexual reproduction, continuous diversification, programmed turnover, seemingly wasteful phenotypes, altruism, co-evolving environmental niches, and advancing complexity. Indeed survival-of-the-fittest may be a particular case of the survival-of-the-fitted mechanism, promoting local adaptations that express reproductive advantages in addition to resisting entropy. Survival-of-the-fitted accounts for phenomena that have been attributed to neutral evolution: in the face of entropy, there is no neutrality; all variations are challenged by ubiquitous energy and entropy, retaining those that are “fit enough”. We propose experiments to test predictions of the survival-of-the-fitted theory, and discuss implications for the wellbeing of humans and the biosphere.


An Ansatz for undecidable computation in RNA-world automata

Adam J. Svahn, Mikhail Prokopenko


In this Ansatz we consider theoretical constructions of RNA polymers into automata, a form of computational structure. The basis for transitions in our automata are plausible RNA-world enzymes that may perform ligation or cleavage. Limited to these operations, we construct RNA automata of increasing complexity; from the Finite Automaton (RNA-FA) to the Turing Machine equivalent 2-stack PDA (RNA-2PDA) and the universal RNA-UPDA. For each automaton we show how the enzymatic reactions match the logical operations of the RNA automaton, and describe how biological exploration of the corresponding evolutionary space is facilitated by the efficient arrangement of RNA polymers into a computational structure. A critical theme of the Ansatz is the self-reference in RNA automata configurations which exploits the program-data duality but results in undecidable computation. We describe how undecidable computation is exemplified in the self-referential Liar paradox that places a boundary on a logical system, and by construction, any RNA automata. We argue that an expansion of the evolutionary space for RNA-2PDA automata can be interpreted as a hierarchical resolution of the undecidable computation by a meta-system (akin to Turing’s oracle), in a continual process analogous to Turing’s ordinal logics and Post’s extensible recursively generated logics. On this basis, we put forward the hypothesis that the resolution of undecidable configurations in RNA-world automata represents a mechanism for novelty generation in the evolutionary space, and propose avenues for future investigation of biological automata.