Scale-invariant topology and bursty branching of evolutionary trees emerge from niche construction

Xue, Chi; Liu, Zhiru; Goldenfeld, Nigel

doi:10.1073/pnas.1915088117

Cited by 24 publications

(14 citation statements)

References 67 publications

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“…8-10, it is clear that the trees produced by the optimal protocol exhibit a vastly different topology from those constructed by sub-optimal protocols. A scaling analysis could reveal that optimal and sub-optimal protocols lead to different asymptotic behaviors with respect to phylogeny, a result that could reflect a complex interplay between ecological and evolutionary processes during AM [49].…”

Section: Discussionmentioning

confidence: 99%

Mechanisms underlying vaccination protocols that may optimally elicit broadly neutralizing antibodies against highly mutable pathogens

Ganti

Chakraborty

2020

Preprint

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Effective prophylactic vaccines usually induce the immune system to generate potent antibodies that can bind to an antigen and thus prevent it from infecting host cells. B cells produce antibodies by a Darwinian evolutionary process called affinity maturation (AM). During AM, the B cell population evolves in response to the antigen. Antibodies that bind specifically and strongly to the antigen are thus produced. Highly mutable pathogens pose a major challenge to the development of effective vaccines because antibodies that are effective against one strain of the virus may not protect against a mutant strain. Antibodies that can protect against diverse strains of a mutable pathogen are called broadly neutralizing antibodies (bnAbs). In spite of extensive experimental and computational studies that have led to important advances, an effective vaccination strategy that can generate bnAbs does not exist for any highly mutable pathogen. Here we study a minimal model of AM in different time-varying antigenic environments to explore the mechanisms underlying optimal vaccination protocols that maximize the production of bnAbs. We find that the characteristics of the time-varying Kullback-Leibler distance (KLD) between the B cell population distribution and the fitness landscape imposed by antigens is a key determinant of bnAb evolution. The optimal vaccination protocol requires a relatively low KLD in the beginning in order to increase the entropy (diversity) of the B cell population so that the surviving B cells have a high chance of evolving into bnAbs upon subsequently increasing the KLD. For a discretized two-step variation in antigenic environment, there are optimal values of the KLDs for the first and second steps. Phylogenetic tree analysis further reveals the evolutionary pathways that lead to bnAbs. The connections between our results and recent simulation studies of bnAb evolution and the general problem of evolution of generalists versus specialists are discussed.

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Section: Discussionmentioning

confidence: 99%

Mechanisms underlying vaccination protocols that may optimally elicit broadly neutralizing antibodies against highly mutable pathogens

Ganti

Chakraborty

2020

Preprint

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“…Species and niche are causal factors in the evolution of each other (circular causation). As an example, environmental conditions can affect rates of genetic evolution [116,117].…”

Section: Species-niche Co-evolution and Self-identitymentioning

confidence: 99%

Science-Driven Societal Transformation, Part I: Worldview

Boik

2020

Sustainability

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Humanity faces serious social and environmental problems, including climate change and biodiversity loss. Increasingly, scientists, global policy experts, and the general public conclude that incremental approaches to reduce risk are insufficient and transformative change is needed across all sectors of society. However, the meaning of transformation is still unsettled in the literature, as is the proper role of science in fostering it. This paper is the first in a three-part series that adds to the discussion by proposing a novel science-driven research-and-development program aimed at societal transformation. More than a proposal, it offers a perspective and conceptual framework from which societal transformation might be approached. As part of this, it advances a formal mechanics with which to model and understand self-organizing societies of individuals. While acknowledging the necessity of reform to existing societal systems (e.g., governance, economic, and financial systems), the focus of the series is on transformation understood as systems change or systems migration—the de novo development of and migration to new societal systems. The series provides definitions, aims, reasoning, worldview, and a theory of change, and discusses fitness metrics and design principles for new systems. This first paper proposes a worldview, built using ideas from evolutionary biology, complex systems science, cognitive sciences, and information theory, which is intended to serve as the foundation for the R&D program. Subsequent papers in the series build on the worldview to address fitness metrics, system design, and other topics.

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“…Species and niche are causal factors in the evolution of each other (circular causation). As an example, environmental conditions can affect rates of genetic evolution [118,119].…”

Section: Species-niche Co-evolution and Self-identitymentioning

confidence: 99%

Science-Driven Societal Transformation, Part I: Worldview

Boik¹

2020

Preprint

View full text Add to dashboard Cite

Humanity faces serious social and environmental problems, including climate change and biodiversity loss. Risks are increasing and conditions deteriorating. Increasingly, scientists, global policy experts, and the general public conclude that incremental approaches are insufficient and transformative change is needed across all sectors of society. However, the meaning of transformation is still unsettled in the literature, as is the proper role of science in fostering it. This paper is the first in a three-part series that adds to the discussion by proposing a novel science-driven research-and-development program aimed at societal transformation. More than a proposal, it offers a perspective and conceptual framework from which societal transformation might be approached and understood. While acknowledging the necessity of reform to existing societal systems (e.g., governance, economic, and financial systems), the focus of the series is on transformation understood as systems change or systems migration—the de novo development of and migration to new societal systems. The series provides definitions, aims, reasoning, worldview, and a theory of change, and discusses fitness metrics and design principles for new systems. This first paper proposes a worldview built using ideas from evolutionary biology, complex systems science, cognitive sciences, and information theory that is intended to serve as the foundation for the R&amp;D program.

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Scale-invariant topology and bursty branching of evolutionary trees emerge from niche construction

Cited by 24 publications

References 67 publications

Mechanisms underlying vaccination protocols that may optimally elicit broadly neutralizing antibodies against highly mutable pathogens

Mechanisms underlying vaccination protocols that may optimally elicit broadly neutralizing antibodies against highly mutable pathogens

Science-Driven Societal Transformation, Part I: Worldview

Science-Driven Societal Transformation, Part I: Worldview

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