Postgenomics function monism

Brzović, Zdenka; Šustar, Predrag

doi:10.1016/j.shpsc.2019.101243

Cited by 8 publications

(3 citation statements)

References 34 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The closest discussion is recent work on maintenance functions (Elliott et al 2014;Linquist et al 2020;Linquist 2022; but see also Brzović and Šustar 2020). As part of their discussion of the debate over ENCODE and human genome function, Brzović and Sustar (2020) provide a helpful definition of conserved sequence in a footnote: "Evolutionarily conserved regions are sequences which are similar or identical across different taxa.…”

Section: An Opportunity To Characterize a Concept Of Conserved Functionmentioning

confidence: 99%

“…There is broad consensus among philosophers of biology that multiple meanings of 'function' are valuable for science because they operate in different types of explanation (Godfrey-Smith 1994). Nonetheless, maintaining multiple meanings sometimes leads to miscommunications and flawed reasoning, such as when different studies of genome function in humans arrive at incompatible conclusions about the prevalence of "junk DNA" (Gerstein et al 2007;Graur et al 2013;Germain et al 2014;Brzović and Šustar 2020;Linquist et al 2020) or when the current benefits of a trait are a poor guide to its evolutionary origins (Autumn et al 2002;Brunet et al 2021). Most of the recent literature on function has focused on refining existing definitions and clarifying their relationships in order to illuminate and possibly avoid these problems, with some occasional novel views proposed (Saborido 2014;Garson 2016).…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

An account of conserved functions and how biologists use them to integrate cell and evolutionary biology

Sterner,

Elliott,

Wideman

2023

Biol Philos

View full text Add to dashboard Cite

We characterize a type of functional explanation that addresses why a homologous trait originating deep in the evolutionary history of a group remains widespread and largely unchanged across the group's lineages. We argue that biologists regularly provide this type of explanation when they attribute conserved functions to phenotypic and genetic traits. The concept of conserved function applies broadly to many biological domains, and we illustrate its importance using examples of molecular sequence alignments at the intersection of evolution and cell biology. We use these examples to show how the study of conserved functions can integrate knowledge of a trait's causal effects on fitness and its history of natural selection without invoking adaptation. We also show how conserved function provides a novel basis for addressing objections against evolutionary functions raised by Robert Cummins.

show abstract

Section: An Opportunity To Characterize a Concept Of Conserved Functionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

An account of conserved functions and how biologists use them to integrate cell and evolutionary biology

Sterner,

Elliott,

Wideman

2023

Biol Philos

View full text Add to dashboard Cite

show abstract

“…For example, Linquist et al (2020) proposed to distinguish between maintenance functions (if conditions 1 and 2 above are satisfied) and origin functions (if condition 3 is satisfied). A different view is held by Brzović and Šustar (2020) , who put the emphasis on the action of purifying selection (similar to the idea of maintenance functions ), calling it the “weak etiological monism” (WEM) principle, which would be more appropriate than SSE. More recently, Brunet et al (2021) , who favors the SSE definition for biological function but recognizes the role of exaptation and CNE in genome evolution, argued that the WEM suffers from two major drawbacks.…”

Section: Beyond Se and The Multiple Origins Of Functional Elementsmentioning

confidence: 99%

What We Talk About When We Talk About “Junk DNA”

Fagundes

Bisso‐Machado

Figueiredo

et al. 2022

Genome Biology and Evolution

View full text Add to dashboard Cite

“Junk DNA” is a popular yet controversial concept that states that organisms carry in their genomes DNA that has no positive impact on their fitness. Nonetheless, biochemical functions have been identified for an increasing fraction of DNA elements traditionally seen as “Junk DNA”. These findings have been interpreted as fundamentally undermining the “Junk DNA” concept. Here, we reinforce previous arguments that this interpretation relies on an inadequate concept of biological function that does not consider the selected effect of a given genomic structure, which is central to the “Junk DNA” concept. Next, we suggest that another (though ignored) confounding factor is that the discussion about biological functions includes two different dimensions: a horizontal, ecological dimension that reflects how a given genomic element affects fitness in a specific time, and a vertical, temporal dimension that reflects how a given genomic element persisted along time. We suggest that “Junk DNA” should be used exclusively relative to the horizontal dimension, while for the vertical dimension, we propose a new term, “Spam DNA”, that reflects the fact that a given genomic element may persist in the genome even if not selected for on their origin. Importantly, these concepts are complementary. An element can be both “Spam DNA” and “Junk DNA”, and “Spam DNA” can also be recruited to perform evolved biological functions, as illustrated in processes of exaptation or constructive neutral evolution.

show abstract

A relic of design: against proper functions in biology

Ratti

Germain

2022

Biol Philos

View full text Add to dashboard Cite

The notion of biological function is fraught with difficulties—intrinsically and irremediably so, we argue. The physiological practice of functional ascription originates from a time when organisms were thought to be designed and remained largely unchanged since. In a secularized worldview, this creates a paradox which accounts of functions as selected effect attempt to resolve. This attempt, we argue, misses its target in physiology and it brings problems of its own. Instead, we propose that a better solution to the conundrum of biological functions is to abandon the notion altogether, a prospect not only less daunting than it appears, but arguably the natural continuation of the naturalisation of biology.

show abstract

Postgenomics function monism

Cited by 8 publications

References 34 publications

An account of conserved functions and how biologists use them to integrate cell and evolutionary biology

An account of conserved functions and how biologists use them to integrate cell and evolutionary biology

What We Talk About When We Talk About “Junk DNA”

A relic of design: against proper functions in biology

Contact Info

Product

Resources

About