28 papers · ranked by Valyu relevance
Michael Yarus
Favored characteristics evolve at two roughly-defined rates: selection of fitness < truncation ≈ truncation with fitness. The fastest route is also the most probable path; the path of least selection. When possible, truncations, requiring x ≥ threshold x_t_, implement least selection for x. Least selection is also…
A Gardner
The theory of multilevel selection (MLS) is beset with conceptual difficulties. Although it is widely agreed that covariance between group trait and group fitness may arise in the natural world and drive a response to ‘group selection’, ambiguity exists over the precise meaning of group trait and group fitness and as…
George Ellis
A conflict exists between field biologists and physiologists ("functional biologists" or "evolutionary ecologists") on the one hand and those working in molecular evolution ("evolutionary biologists" or "population geneticists") on the other concerns the relative importance of natural selection and genetic drift. This…
Bastien Mallein, Francesco Paparella, Emmanuel Schertzer, Zsófia Talyigás
'Zsófia Talyigás'] Biological evolution depends on the passing down to subsequent generations of genetic information encoding beneficial traits, and on the removal of unfit individuals by a selection mechanism. However, selection acts on phenotypes, and is affected by random contingencies. Thus, a combination of…
Michael E. Palmer, Marcus W. Feldman, Chrisantha Thomas Fernando
For a lineage to survive over long time periods, it must sometimes change. This has given rise to the term evolvability, meaning the tendency to produce adaptive variation. One lineage may be superior to another in terms of its current standing variation, or it may tend to produce more adaptive variation. However…
Riccardo Rao, Stanislas Leibler
Any realistic evolutionary theory has to consider: (i) the dynamics of organisms that reproduce and possess heritable traits; (ii) the appearance of stochastic variations in these traits; and (iii) the selection of those organisms that better survive and reproduce. These elements shape the “evolutionary forces” that…
Steven A. Frank
The theory of natural selection has two forms. Deductive theory describes how populations change over time. One starts with an initial population and some rules for change. From those assumptions, one calculates the future state of the population. Deductive theory predicts how populations adapt to environmental…
A. Carvajal-Rodríguez
Sexual selection plays a crucial role in modern evolutionary theory, offering valuable insight into evolutionary patterns and species diversity. Recently, a comprehensive definition of sexual selection has been proposed, defining it as any selection that arises from fitness differences associated with nonrandom success…
W. A. Tiefenbrunner
Although according to the second law of thermodynamics the world tends toward maximum disorder, over millions of years evolution has given rise to an enormous variety of complex organisms. To explain this, one must assume that natural selection is a process of information acquisition. Since some years an information…
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…
Luca Peliti
Life forms exhibit such a degree of exquisite organization that it seems impossible that they could have developed out of a process of trial and error, as intimated by the theory of Darwinian evolution. In this general public paper I discuss how differential reproduction rates work in producing an exceedingly high…
Dinkar Wadhwa
There is no satisfactory explanation for why peacock possesses a tail, presence and especially courtship display of which makes the organism vulnerable to predation. Here, I present a model according to which in a polygynous mating system a mechanism which increases vulnerability to predation, a Zahavian handicap…
Allen J. Moore, Joel W. McGlothlin, Jason B. Wolf
Strikingly elaborate weapons and displays are widespread features of male contests for mates across the animal kingdom. Male combat is familiar to students of behavior, and yet while we understand how female mate choice results in a runaway process, how such evolutionary extremes arise from male-male competition is…
Joshua Meyers, Nathan Brown
De novo molecular design is effective for optimizing compounds with desirable properties in drug discovery. In the realm of chemoinformatics, population-based evolutionary approaches have been known for over a decade including those that use retrosynthetically inspired fragment-based workflows to to balance the…
Steven A. Frank
Natural selection acts on traits at different scales, often with opposing consequences. This article identifies the particular forces that act at each scale and how those forces combine to determine the overall evolutionary outcome. A series of extended models derive from the tragedy of the commons, illustrating…
Michael Doebeli, Yaroslav Ispolatov, Burt Simon, Wenying Shou
Most evolutionary thinking is based on the notion of fitness and related ideas such as fitness landscapes and evolutionary optima. Nevertheless, it is often unclear what fitness actually is, and its meaning often depends on the context. Here we argue that fitness should not be a basal ingredient in verbal or…
Raymond Noble, Denis Noble, Edward L. Braun, Jukka Finne
The question whether evolution is blind is usually presented as a choice between no goals at all (‘the blind watchmaker’) and long-term goals which would be external to the organism, for example in the form of special creation or intelligent design. The arguments either way do not address the question whether there are…
Alexander Hendricks, Rachel Cohen, Gavin McEwen, Tony Tien + 4 more
: Glutathione Reductase-Like Metalloid Reductase (GRLMR) is an enzyme that reduces selenodiglutathione (GS-Se-SG), forming zerovalent Se nanoparticles (SeNPs). Error prone polymerase chain reaction was used to create a library of ~10,000 GRLMR variants. The library was expressed in BL21 Escherichia coli in liquid…
Joachim Krug
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Brianna Greenstein, Danielle Elsey, Geoffrey Hutchison
Genetic algorithms (GAs) are a powerful tool to search large chemical spaces for inverse molecular design. However, GAs have multiple hyperparameters that have not been thoroughly investigated for chemical space searches. In this work, we examine the general effects of a number of hyperparameters, such as population…
Irun R. Cohen
The evolution of species, according to Darwin, is driven by struggle - by competition between variant autonomous individuals for survival of the fittest and reproductive advantage; the outcome of this struggle for survival is natural selection. The Neo-Darwinians reframed natural selection in terms of DNA: inherited…
Authors not listed
Organic molecular crystals offer a broad spectrum of potential applications. The vast number of possible molecules is both an opportunity and a challenge, because of the prohibitive expense of exhaustively searching chemical space to find novel molecules with promising solid-state properties. Computational methods can…
Adi Livnat
The theory of interaction-based evolution argues that, at the most basic level of analysis, there is a third alternative for how adaptive evolution works besides a) accidental mutation and natural selection and b) Lamarckism, namely, c) information provided by natural selection on the fit between the organism and its…
Adi Livnat
How does new genetic information arise? Traditional thinking holds that mutation happens by accident and then spreads in the population by either natural selection or random genetic drift. There have been at least two fundamental conceptual problems with imagining an alternative. First, it seemed that the only…
Gerd B. Müller
Since the last major theoretical integration in evolutionary biology-the modern synthesis (MS) of the 1940s-the biosciences have made significant advances. The rise of molecular biology and evolutionary developmental biology, the recognition of ecological development, niche construction and multiple inheritance…
Jonas Verhellen
Computer-assisted design of small molecules has experienced a resurgence in academic and indus- trial interest due to the widespread use of data-driven techniques such as deep generative models. While the ability to generate molecules that fulfill required chemical properties is encouraging, the use of deep learning…
Authors not listed
RNA droplets assembled from co-transcriptionally folded nanostructures have recently emerged as a promising platform for constructing protocells and minimal synthetic cell models. In these systems, a custom-designed DNA template encodes an RNA nanostar, which is produced by transcription and self-assembles into…
Authors not listed
The identification of kinetically feasible reaction pathways that connect a reactant to its product, including numerous intermediates and transition states, is crucial for predicting chemical reactions and elucidating reaction mechanisms. However, as molecular systems become increasingly complex or larger, the number…