Selfish Gene Research Articles

The Real Selfish Gene: Impact of Repetitive Elements on Read Mapping Accuracy, a Simulation Study

Repetitive elements, often referred to as selfish genes, pose significant challenges to genome assembly and read mapping in bioinformatics. These elements can replicate within the genome without providing functional benefits to the host organism, leading to complexities in accurate genome analysis. This study presents a simulation-based approach to illustrate the impact of repetitive elements on read mapping accuracy. By comparing genome sequences with and without repetitive elements, we demonstrate how these selfish genes create ambiguities and errors in read alignment. The findings underscore the importance of developing advanced bioinformatics tools aligned with artificial intelligence to mitigate the effects of repetitive sequences and improve the reliability of genomic analyses.

‘A movie about flowers?’ Notes on the ecological turn in adaptation studies

Abstract This article takes up and responds to the recent ecological turn in adaptation studies, exploring the discipline’s widespread interest in the overlap between the notion of adaptation in evolutionary biology and the notion of adaptation in literature, film, and media studies. It argues that in order to develop a historically and ecocritically alert approach to adaptation studies, it is necessary to unpack what is at stake in using biological terms and paradigms to study adaptation in art. Firstly, it offers a survey of several studies that have explored the overlap between adaptation in nature and adaptation in culture, arguing that these have been overly influenced by the notions of neo-Darwinism that were popularized by Richard Dawkins in The Selfish Gene (1976). Secondly, it offers a rereading of the film that has become a primary case study among theorists who have reached for biological metaphors to explain cultural change: Adaptation (2002). It argues that whereas scholars have often tended to use Adaptation as a springboard from which to launch an exploration of the purported homology between adaptation in nature and adaptation in art, in fact, the film’s evolutionary themes are clearly historicizable, tied to a set of values coordinated around ideas of heteronormative reproductivity, dissemination, and growth. Examining those values helps to demonstrate how the film’s evolutionary themes are deployed as part of its representational strategies, thereby challenging the idea that they might be unproblematically used to describe the overlap between adaptation in biology and adaptation in art.

The Self-ish Gene: Retroactive Tropes in Richard Dawkins’s Evolutionary Logic

ABSTRACT Building on recent developments in Lacanian rhetorical criticism, this essay demonstrates how contemporary evolutionary theory posits genetic determinism without a clear definition of the gene. It makes this case through close readings of Richard Dawkins’s The Selfish Gene, the landmark text of neo-Darwinian genetics. It demonstrates how Dawkins uses metaphors to substitute a single determinate agent in place of the genome’s essential complexity. Despite Dawkins’s admission that he could not define the gene, his metaphors give his “self-ish gene” a sense of unity and coherence that allows him to describe all other levels of life (organisms, species, ecosystems) as reducible to it. Dawkins’s use of metaphor leverages a broader reductionist logos, one that operates in discourses far beyond the biological. Methodologically, the essay advances the study of scientific metaphor by focusing on the formal properties of metaphor and the ways they afford logical closure.

Escalation of genome defense capacity enables control of an expanding meiotic driver.

From RNA interference to chromatin silencing, diverse genome defense pathways silence selfish genetic elements to safeguard genome integrity 1,2 . Despite their diversity, different defense pathways share a modular organization, where numerous specificity factors identify diverse targets and common effectors silence them. In the PIWI-interacting RNA (piRNA) pathway, which controls selfish elements in the metazoan germline, diverse target RNAs are first identified by complementary base pairing with piRNAs and then silenced by PIWI-clade nucleases via enzymatic cleavage 1,3 . Such a binary architecture allows the defense systems to be readily adaptable, where new targets can be captured via the innovation of new specificity factors 4,5 . Thus, our current understanding of genome defense against lineage-specific selfish genes has been largely limited to the evolution of specificity factors, while it remains poorly understood whether other types of innovations are required. Here, we describe a new type of innovation, which escalates the defense capacity of the piRNA pathway to control a recently expanded selfish gene in Drosophila melanogaster . Through an in vivo RNAi screen for repressors of Stellate -a recently evolved and expanded selfish meiotic driver 6-8 -we discovered a novel defense factor, Trailblazer. Trailblazer is a transcription factor that promotes the expression of two PIWI-clade nucleases, Aub and AGO3, to match Stellate in abundance. Recent innovation in the DNA-binding domain of Trailblazer enabled it to drastically elevate Aub and AGO3 expression in the D. melanogaster lineage, thereby escalating the silencing capacity of the piRNA pathway to control expanded Stellate and safeguard fertility. As copy-number expansion is a recurrent feature of diverse selfish genes across the tree of life 9-12 , we envision that augmenting the defense capacity to quantitatively match selfish genes is likely a repeatedly employed defense strategy in evolution.

Cooperative genes in smart systems: Toward an inclusive new synthesis in evolution

For more than half a century, biologist Julian Huxley's term, the “Modern Synthesis”, has been used as a label for a model of biological evolution where genetic influences are viewed as a principal source of creativity and change. Over the years, as evidence has accumulated that there are many other, far more important factors at work in evolution, theoretical “compromises,” such as the so-called “Extended Synthesis”, have been proposed. This is no longer tenable. It is time to abandon the Modern Synthesis, and its doppelganger “The Selfish Gene”. Here is the case for a new, multi-faceted, open-ended, “inclusive” evolutionary synthesis, where living systems themselves are recognized as purposeful (teleonomic) “agents” and cooperative effects (synergies) of various kinds are seen as all-important influences.

Did dawkins recant his selfish gene argument against group selection?

In 2007, David S. Wilson and Edward O. Wilson (27) pointed out that, Richard Dawkins had admitted that, contrary to what he had claimed in his book The Selfish Gene (1976) (7), the idea that only the gene is a fundamental unit of selection cannot be used as an argument against the notion of group selection. This elicited a sharp denial from Dawkins (30), which was followed by an explanatory reply by Wilson and Wilson (33) and another vehement denial by Dawkins (34). I analyse the prehistory of this surprisingly complex and convoluted dispute and subsequently disentangle it. My conclusion is that much of it is based on a series of misunderstandings. First, Wilson's and Wilson's (27) original interpretation of Dawkins' selfish gene argument was incorrect. Second, in their explanatory reply (33), they distinguished between two kinds of group selection: the idea that groups can be units of selection (theoretical group selection) and the idea that group selection plays a functional role in evolution (functional group selection). They clarified that their claim concerned theoretical group selection, not functional group selection. Third, that clarified claim was correct and not correct. It was incorrect because Dawkins has never explicitly acknowledged that he had erred by developing his selfish gene theory as an implicit argument against this kind of group selection. However, the distinction that he made, by 1978, between two kinds of unit of selection, replicators (genes) and vehicles (somas), does imply such an acknowledgment since it holds that groups can be units of selection (vehicles). In this important sense, Wilson's and Wilson's clarified claim (33) was correct. Fourth, Dawkins' second denial (34) concerned functional group selection, not theoretical group selection.

Mutual Aid: The Other Law of the Jungle. Gauthier Chapelle and Pablo Servigne. Cambridge, Polity Press. 2022. 310 pp

In 1902, the anarchist Peter Kropotkin published Mutual Aid in which he promoted a radical perspective on evolution in which cooperation, as well as selfishness, drive the form, diversification and organization of life on earth. Despite initial recognition, Kropotkin's contributions have been largely forgotten, even as modern evolutionary theory has recognized the central role of cooperation. In Mutual Aid: the other law of the jungle, Pablo Servigne and Gauthier Chappelle restore Kropotkin's insights to their rightful place as foundational for our understanding of evolution. They further seek to overturn the pernicious misconception of the 20th century, that nature is only selfish, and highlight how understanding the mechanisms that have evolved to drive cooperation in non-human organisms are also manifest in humans, our society and political institutions. Building forward, they present models of societies that generate, or atrophy, cooperation and consider how our current state will consequently affect our ability to respond to global crises. Through their emphasis on cooperation and its ubiquity in life, Servigne and Chappelle end by broadening their argument to suggest that we question the very nature of the self and reinterpret our existence as a component of a broader cooperative environment. Yet despite the compelling empirical evidence presented, one wonders whether skepticism has been neglected as the authors follow a single cooperative narrative. Does modern evolutionary theory reject the selfish gene in entirety, does selfishness acquiesce to the good of the group within our societies always, and is the centrality of cooperation grounds for the dissolution of the self? While recognizing the exceptional contribution Mutual Aid: the other law of the jungle makes to, it is also necessary to rebalance the vivacity of their cooperative narrative.

The Selfish Gene as a Possible Driving Force Behind HIIT

Purpose: High-Intensity Interval Training (HIIT) is a training method aimed at increasing the fitness of individuals. It is based on a combination of periods in which high-intensity alternate with low-intensity exercise or passive rest. The topic of this paper is a reflection on the benefits and risks of HIIT health use in recreational athletes. We investigate humans' conscious and unconscious motivations for choosing this specific method in the philosophical discourse. Problem: HIIT is a method that, in some ways and with particular approaches, strongly reflects the imperative of the postmodern age - to get as much as possible, as quickly as possible. Martin Heidegger perceives three fundamental existentials in the context of temporality – historicity, everydayness, and within-time-ness. Here conscious motivation may be linked to the temporal characteristic of human being. As Richard Dawkins presents, unconscious motivation may be related to the application of the selfish gene theory. The philosophical approach to the problem: The Heideggerian concept of temporality leads us to research the authenticity and inauthenticity of the Dasein phenomenon. Some features of motivation for applying HIIT can be examined as inauthentic forms of being. In focusing on possible elements of unconscious motivation, the concept of evolutionary biology, namely Dawkins's theory of the selfish gene, provides a unique platform. It is primarily (a human) effort to spread genes. Here, in connection with HIIT, we build on the concepts of replicator and vehicle and deal with the basic selection unit of evolution and its form. Conclusions: HIIT presents an exciting training method that is examined in the context of effectivity of sports training, social benefits, or health aspects. Here we would like to offer the HIIT concept as the reflection of philosophical (mainly ontological, partly ethical) discourse.

Hannah and Joe: Interspecies Art between Bird and Man

(This is a shortened version of a longer review at Leonardo Reviews: leonardo.info/review/2022/07/hannah-and-joe-interspecies-art-between-bird-and-man)Hannah is an African grey parrot. She is 24 years old and, based on other African greys that have lived in captivity, she could live double that or more. Her feathers are grisaille in tone, with the ones on her belly darker than those on her crown. In all the photos I’ve seen, her face is alert and attentive. Her bright small eyes contrast with her large dark beak, the two anatomies constituting perhaps the most prized tools of her trade— an aesthetic and artistic collaboration with the artist Joe Havel. While I’ve never met her in person, I’ve come to know her well over the last few years through images and conversations with Joe, an internationally acclaimed sculptor. Friends recognize his many gifts, identifying him also as an animal whisperer. In addition to sculpting and whispering, Joe has been the Director of the Glassell School of Art at the Museum of Fine Arts, Houston, Texas, since 1993, a post from which he would retire in June 2022. Then Joe would move to France with his partner, taking Hannah and Pixel, their teacup Yorkie. For the time of writing, Hannah and Joe’s collaboration continues and is the subject of two exhibitions in Dallas, Texas: a large overview of their work called Parrot Architecture at the Dallas Contemporary (16 April–21 August 2022) and a more intimate show with drawings and smaller works, Joseph Havel: Flight Paths and Floor Plans, at Talley Dunn Gallery (14 May–25 June 2022), also in Dallas.The art collaboration between Hannah and Joe began during COVID-19 quarantining. For fear of contagion, like so many people around the planet, Joe stayed home for months and had life’s necessities delivered. Cardboard boxes piled up and became the stuff of art. In playful and repetitive actions, Hannah created the whittled boxes that are the basic forms of their collaboration. Joe then cast or poured resin atop them in either single or stacked forms, creating the sparse forest of bronze and resin totems standing in the large industrial space of the Dallas Contemporary. Joe worked closely with Ken King’s foundry in Houston to distill in these pieces a striking verisimilitude of form [1]. The tactility of Hannah’s tiny chew marks rendered in bronze invite human touch, forever forbidden in the gallery setting. The burnished bronze of certain columnar forms and tan cardboard of others are, in certain instances, difficult to distinguish. Bronze here mimics cardboard. The vertical bronze cartons of Highrises create a counterpoint to the single-story coffers of Neighborhood. Joe calls the large works on the walls, the flattened boxes with Hannah’s bite marks and his own gestural brushstrokes of paint, “constructed paintings.” A similar type of work, though smaller and sketch-like, hangs on the walls of Talley Dunn Gallery in Joseph Havel: Flight Plans and Floor Plans. Like bird and man, nature and architecture work in tandem throughout. The names of the works—tumble towers, penthouses, high rises, neighborhoods, flight paths, and floor plans—bear out an expansion and layering of systematic complexities. Architecture, infrastructure, bird, and human synchronize and collectively become a network of networks. Empathy is the glue that binds, functioning as a formative material force in the creation of this avian-cum-primate city.The creative partnership of Hannah and Joe is a striking example of interspecies communication within art, a category in which works of art result from the interactions and meaningful connections between two different species. Some time ago, Charles Darwin identified the penchant for cross-communication among different kinds of animals, contending that, “With social animals, the power of intercommunication between the members of the same community— and with other species, between the opposite sexes, as well as between the young and the old—is of highest importance among them” [2]. Interspecies art brings home a pluralist evolutionary theory that includes sexual selection, aesthetic agency, symbiosis, cooperation, and female choice. Reading evolution with these vectors, in addition to natural selection, offers a more replete sense of Darwin the thinker and writer that should be set against the more parsimonious Darwinism, a language that includes scientific reductionisms like fitness, competition, freeloaders, survival, the selfish gene, procreation, and binary sex. For further elaboration, please see the longer version of this essay online.

Memeplex Mechanism in Consummating English Vocabulary Teaching

The memeplex is a form of memetics, which is formed by the combination of memes and gets to a close mode of collection. Memes comes from The Selfish Gene, a famous work of the famous British scientist Richard Dawkins. Imitation is the main transmission of the meme. English vocabulary learning is essentially the process of imitation, reproduction and transmission. Through analyzing the formation of the Memeplex Mechanism to resolve the lexical memes, the thesis discusses the positive driving effects of Memeplex Mechanism in English Vocabulary Teaching. It mainly discusses the following questions: First, the deconstruction of the Memeplex Forming Process; Second, the construction of the new vocabulary meme in the Memeplex Mechanism; Third, the positive transfer of Memeplex Mechanism in developing English Vocabulary Teaching. The study shows that the Memeplex Mechanism is of great significance in in perfecting English Vocabulary Teaching, which can not only improve the English Vocabulary Teaching methods, but also provide more effective learning methods for English vocabulary acquisition.

Walter Bruno Gratzer (1932–2021): In his own words, as far as possible

Miranda Robertson commemorates the life, remarkable times and witty and erudite writing of protein chemist and biophysicist Walter Gratzer.

Psychological Selfishness

Selfishness is central to many theories of human morality, yet its psychological nature remains largely overlooked. Psychologists often draw on classical conceptions of selfishness from evolutionary biology (i.e., selfish gene theory), economics (i.e., rational self-interest), and philosophy (i.e., psychological egoism), but such characterizations offer limited insight into the psychology of selfishness. To address this gap, we propose a novel framework in which selfishness is recast as a psychological construction. From this view, selfishness is perceived in ourselves and others when we detect a situation-specific desire to benefit the self that disregards others’ desires and prevailing social expectations for the situation. We argue that detecting and deterring such psychological selfishness in both oneself and others is crucial in social life—facilitating the maintenance of social cohesion and close relationships. In addition, we show how using this psychological framework offers a richer understanding of the nature of human social behavior. Delineating a psychological construct of selfishness can promote coherence in interdisciplinary research on selfishness and provide insights for interventions to prevent or remediate the negative effects of selfishness.

Godman‐Salvin Prize

Godman‐Salvin Prize

The Biological Robots Are Coming! But Note They Have Been Here for ∼3.5 Billion Years

The Biological Robots Are Coming! But Note They Have Been Here for ∼3.5 Billion Years

The selfish environment meets the selfish gene: Coevolution and inheritance of RNA and DNA pools: A model for organismal life incorporating coevolution, horizontal transfer, and inheritance of internal and external RNA and DNA pools.: A model for organismal life incorporating coevolution, horizontal transfer, and inheritance of internal and external RNA and DNA pools.

Throughout evolution, there has been interaction and exchange between RNA pools in the environment, and DNA and RNA pools of eukaryotic organisms. Metagenomic and metatranscriptomic sequencing of invertebrate hosts and their microbiota has revealed a rich evolutionary history of RNA virus shuttling between species. Horizontal transfer adapted the RNA pool for successful future interactions which lead to zoonotic transmission and detrimental RNA viral pandemics like SARS-CoV2. In eukaryotes, noncoding RNA (ncRNA) is an established mechanism derived from prokaryotes to defend against viral attack through innate immunity and regulation of host-derived mRNA. Transgenerational inheritance of ncRNA is evidence for feedforward adaptive immunity and epigenetically encoded environmental change across generations, which may explain the ''missing heritability'' of common disease. Causal graph theory and the Price Equation can model epigenetic inheritance involving dynamic internal and external RNA pools. Experimental designs should include metatranscriptomic analyses to understand how ncRNA responds to rapidly changing environmental conditions, within and between organisms, and across generations.

Origins and demise of selfish gene theory.

The idea of The Selfish Gene, first published in 1976, grew out of the Modern Synthesis of evolutionary biology formulated by Julian Huxley in 1942, and more specifically from George Williams' Adaptation and Natu - ral Selection in 1966. It presents a severely narrowed down version of Huxley's synthesis, which developed in the 1960s following the formulation of the Cen tral Dogma of molecular biology by Francis Crick. The idea rests on three assumptions: the isolation of the genome from any influences by the soma and its development in interaction with the environment (the Weis - mann Barrier), one-way causation from DNA to proteins (The Central Dogma), and the autoreplication of DNA (Schrödinger's aperiodic crystal). All three of these assumptions have now been shown to be incorrect. The 'replicator' (DNA) is not independent of the 'vehicle', the organism itself, so that The Selfish Gene can no longer be regarded as a valid scientific hypothesis.

Co-Designing Change

Co-Designing Change

Darwinian Dogma, the Selfish Gene, and thoughts on Post-Genetic Evolutionary Theory

Darwinian Dogma, the Selfish Gene, and thoughts on Post-Genetic Evolutionary Theory

Космический и молекулярный человек в процессе цифровой трансформации социальных систем Беларуси и России

To develop a strategy for building the Union State of Russia and Belarus’ better future, it is necessary to understand the mechanisms and identify the main causes that govern the dynamics of this complex and specifi c social system. As the main factor determining the social dynamics of a given civilization cluster, we consider the competition of two basic sociotypes. They are conditionally designated as a molecular man and a space man. A molecular person is a consumer whose social behavior is based on the power of the selfi sh gene and consumer society’s ideals. A space person is passionate, driven by the creative imperative of cognition and synthesis of culture. In our opinion, it is this fundamental confl ict that forms the social dynamics of the civilization cluster of the Union State. The scenario of its future development will depend on the resolution of this confl ict. In order to better understand this process, we have developed a cellular-automate computer model of competition between the two sociotypes in the framework of a unifi ed social system. This computer model can be considered as a simplifi ed cognitive proto-construct of the social system dynamics. By examining it, one can transfer the properties and features of its behavior to an unknown object under study - a society.

Selfish gene leaves bacteria behind.

This study identified a functional restriction modification system in the mitochondrial genome of a marine protist that originated in bacteria.