26 papers · ranked by Valyu relevance
Vitaly Vanchurin, Yuri I. Wolf, Mikhail I. Katsnelson, Eugene V. Koonin
We apply the theory of learning to physically renormalizable systems in an attempt to develop a theory of biological evolution, including the origin of life, as multilevel learning. We formulate seven fundamental principles of evolution that appear to be necessary and sufficient to render a universe observable and show…
Vitaly Vanchurin, Yuri I. Wolf, Mikhail I. Katsnelson, Eugene V. Koonin
'Eugene V. Koonin'] Title: Significance Modern evolutionary theory gives a detailed quantitative description of microevolutionary processes that occur within evolving populations of organisms, but evolutionary transitions and emergence of multiple levels of complexity remain poorly understood. Here, we establish the…
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…
Bernadette Mathew, Abhishek Halder, Nancy Jaiswal, Smruti Panda + 8 more
DNA is essentially a collection of short nucleotide sequences with a myriad of functionalities. These oligonucleotides are often studied for their function as molecular binding sites, regulatory motifs or sequence probes. The field of Bioinformatics uses a similar concept under the term “k-mers,” which is central to…
Ádám Kun
It is often claimed that humanity has stopped evolving because modern medicine erased all selection on survival. Even if that would be true, and it is not, there would be other mechanisms of evolution which could still led to changes in allelic frequencies. Here I show, by applying basic evolutionary genetics…
Hiroyuki Iizuka
This study introduces a novel theoretical framework, the Stacked Autoencoder Evolution Hypothesis, which proposes that biological evolutionary systems operate through multi-layered self-encoding and decoding processes, analogous to stacked autoencoders in deep learning. Rather than viewing evolution solely as gradual…
Robert Worden
In 1995 I wrote a paper 'A Speed Limit for Evolution' – whose main result was that evolution must proceed rather slowly, in accordance with the earlier views and intuitions of many authors. The abstract of the paper said: 'An upper bound on the speed of evolution is derived. The bound concerns the amount of genetic…
Franco Bagnoli, Tommaso Matteuzzi
Using as a narrative theme the example of Darwin's finches, a microscopic agent-based model is introduces to study sympatric speciation as a result of competition for resources in the same ecological niche. Varying competition among individuals and resource distribution, the model exhibits some of the main features of…
Julian Z. Xue, Leonid Chindelevich, Frédéric Guichard
Many well-documented macro-evolutionary phenomena, such as increases in organization hierarchy, or sudden and episodic creation of new taxa, still challenge current evolutionary theories. Here we show a new mechanism that can explain them. We begin by showing how the order of mutations can alter evolutionary…
Thomas Guillerme, Jen A. Bright, Christopher R. Cooney, Emma C. Hughes + 4 more
Widely documented, megaevolutionary jumps in phenotypic diversity continue to perplex researchers because it remains unclear whether these dramatic changes can emerge from microevolutionary processes. Here we tackle this question using new approaches for modeling multivariate traits to evaluate the magnitude and…
Kimberly L. Cooper
Humans are curious to understand the causes of traits that distinguish us from other animals and that distinguish vastly different species from one another. We also have a proclivity for simple stories and sometimes tend toward seeking and accepting simple genetic explanations for large evolutionary shifts, even to a…
Michael Yarus
Evolutionary theorizing resembles building an aircraft while also piloting it; new results change the scaffold for older ideas, requiring revised strategy to remain airborne. A calculated kinetic pathway exists (1) that, under explicit quantitative assumptions, delivers the SGC (Standard Genetic Code). The pathway and…
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…
Ben Bradley
In the 1940s, the ‘modern synthesis’ (MS) of Darwinism and genetics cast genetic mutation and recombination as the source of variability from which environmental events naturally select the fittest, such ‘natural selection’ constituting the cause of evolution. Recent biology increasingly challenges this view by casting…
Pim Edelaar, Jun Otsuka, Victor J. Luque
Evolutionary theory has made large impacts on our understanding and management of the world, in part because it has been able to incorporate new data and new insights successfully. Nonetheless, there is currently a tension between certain biological phenomena and mainstream evolutionary theory. For example, how does…
Denis Noble
Charles Darwin spent the last decade of his life collaborating with physiologists in search of the biological processes of evolution. He viewed physiology as the way forward in answering fundamental questions about inheritance, acquired characteristics, and the mechanisms by which organisms could achieve their ends and…
Patrick T. Rohner, David Berger
Evolutionary change necessitates genetic variation, and a reigning paradigm in biology is that rates of microevolution can be predicted from estimates of available genetic variation within populations. However, the accuracy of such predictions should decay on longer evolutionary timescales, as the influence of genetic…
Kristoffer Reinholt Thomsen, Steen Rasmussen
| 1 | Background | | 1 | | --- | --- | --- | --- | | | 1.1 | A Brief Historical Review of Lamarck's, Darwin's, and Baldwin's fundamental | | | | ideas | | 2 | | | 1.1.1 | Lamarck | 2 | | | 1.1.2 | Darwin | 3 | | | 1.1.3 | Baldwin | 4 | | | 1.2 | A Brief Summary of Modern Evolutionary and Learning Studies | 5 | | |…
Liudmyla Vasylenko, Adi Livnat
At the fundamental conceptual level, two alternatives have traditionally been considered for how mutations arise and how evolution happens: 1) random mutation and natural selection, and 2) Lamarckism. Recently, the theory of Interaction-based Evolution (IBE) has been proposed, according to which mutations are neither…
Mateusz Krukowski
The paper is devoted to the study of Darwinian evolution in two mathematical models. The first one is a variation on the Malthusian population growth model with Verhulst's environmental capacity. The second model is grounded in the theory of Markov chains and their stationary distributions. We prove preliminary results…
Yoshiharu Mukouyama, Kenya Tanaka, Shuji Nakanishi, Yoshihiro Nakato
The present work reveals that a prebiotic chemical system can generate self-organizing ability that leads to highly ordered structures and an active character such as free independent harmonious behavior. This result is the properties of natural things that have long been overlooked since Darwin’s theory of evolution…
Juan C. Castro-Alonso, Alejandro A. Hidalgo, John Sweller
The mechanisms that govern biological evolution and human cognition are analogous, as both follow the same principles of natural information processing systems. In this article, we describe the following five principles that provide an analogy between biological evolution and human cognition: (a) Randomness as Genesis…
Amit Kahana, Lior Segev, Doron Lancet
The origin of life must have involved an unlikely transition from chaotic chemistry to reproducing supramolecular structures. Previous quantitative analyses of reproducing mutually catalytic networks made of simple molecules have led to increasing popularity of this pre-RNA scenario for life’s origin. Here, we…
Authors not listed
Genetic Algorithms are a powerful method to solve optimization problems with complex cost functions over vast search spaces that rely in particular on recombining parts of previous solutions. Crossover operators play a crucial role in this context. Here, we describe a large class of these operators designed for…
Authors not listed
The GENERIC framework provides a robust structure for nonequilibrium dynamics but lacks a principled method to select reversible ($L$) and irreversible ($M$) brackets. Similarly, finite-time optimizations minimizing path-averaged reciprocal temperature exist but remain isolated. Here, we introduce the \textbf{Entropy…
Benjamin King, Max Winokan, Paul Stevenson, Jim Al-Khalili + 2 more
The adenine-thymine tautomer (A-T) has previously been discounted as a spontaneous mutagenesis mechanism due to the energetic instability of the tautomeric configuration. We study the stability of A-T while the nucleobases undergo DNA strand separation. Our calculations indicate an increase in the stability of A-T as…