Developmental causation and the problem of homology

Abstract

While it is generally agreed that the concept of homology refers to individuated traits that have been inherited from common ancestry, we still lack an adequate account of trait individuation or inheritance. Here I propose that we utilize a counterfactual criterion of causation to link each trait with a developmental-causal (DC) gene. A DC gene is made up of the genetic information (which might or might not be physically contiguous in the genome) that is needed for the production of the organismic attributes that comprise the trait. I argue that individuated traits-phenes-correspond to organismic features that are caused by DC genes. Using such an approach, we can define a DC map, which shows the relations between each pair of phenes and provides a succinct summary of genotype-phenotype relationships and phenotypic complexity. Phenes in parents and offspring are judged to be homologous if their DC genes are composed of orthologous genetic factors. When comparing more distantly related organisms, traits are homologous when linked by a chain of parent-offspring homologs along the path of ancestry that links the two organisms. There are three possible ways to deal with the potential for multiple equivalent DC genes: maximal, minimal, and consensus homology. Whereas maximal homology has limited utility, the other two approaches have value and can help to guide research at the intersection of evolution and development. IntroductionThe homology relation refers to the idea that different organisms of the same or different species share the same traits. For example, it is generally agreed that my middle finger nail and your middle finger nail are homologous with one other and with the hoof of a horse. As this example shows, homology does not require that the structures in question be identical in form or function. So what notion of "sameness" is connoted by homology? Darwin and subsequent biologists have generally agreed that the concept of homology relates in some way to descent from common ancestry (e.g., Lankaster 1870). A fingernail and a hoof are homologous because the common ancestor of a human and a horse had a structure that became modified to give rise to the human middle finger nail and the horse's hoof. Philos Theor Biol (2013) While the idea is simple, nailing down (no pun intended) the concept of homology has proved challenging, to say the least. While all agree that homology depends in some way on common ancestry, the manner of this dependence is far from clear. In particular, how can homology refer to the inheritance of traits from common ancestry when phenotypic traits are not passed on from generation to generation? Thankfully, we do not pass on our fingernails to our children by direct grafting! This paper is built on the premise that in order to get traction on homology, and put the concept to work in comparative biology, we first need to solve a much less studied conceptual problem: the nature of traits. When observing an organism we get the sense that it may be atomized into parts in some objecti...

Durianology, discovery, and saltation — the evolution of aroids

“…It is of course possible to vastly improve how characters are formulated, in particular using understanding of development and developmental genetics to arrive at characterisations that refer more adequately to the syntax of morphogenesis, and therefore to elements that perhaps can be said to evolve. Baum, for example, has proposed a concept of individuated 'phenes' corresponding to organismal features that are caused by DC (developmental-causal) genes "made up of the genetic information (which might or might not be physically contiguous in the genome) that is needed for the production of the organismic attributes that comprise the trait" (Baum, 2013; see also Baum, 2019 in this volume). I have no doubt that will be extremely informative, but it is still based on the premise that organisms are atomisable, despite the potential of the idea to exclude 'parts' that are morphogenetic-syntactical nonsense from a developmental genetic point of view.…”

Plant parts: processes, structures, or functions?

“…The problem of part existence is logically prior to homology (Baum, 2013;Olson, 2019). If, for example, parts were just subjective percepts without any existence outside of human perception then evaluating whether two 'leaves' are homologous would become a question of perceptual psychology rather than just natural science.…”

“…Here I will start by laying out a parts-as-structures approach, which is based on connecting aspects of the phenotype to their underlying genetic causes. Since I have previously explored this developmental-causal framework in some detail (Baum, 2013), I will only provide sufficient detail here to explain how it may be adapted into a parts-as-function version, which is to say one which looks not at developmental cause but at adaptive potential.…”

Evolutionary remnants as widely accessible evidence for evolution: the structure of the argument for application to evolution education

“…Unfortunately, in addition to the complexities with which the term "homology" is historically fraught (e.g., De Beer 1971;Hall 1994Hall , 2003Mindell and Meyer 2001;Wagner 2002;Brigandt and Griffiths 2007;Rieppel and Kearney 2007;McCune and Schimenti 2012;Baum, 2013;Minelli and Fusco 2013), this definition has the weakness of being tautological if we are seeking to use particular features as evidence for common ancestry (Gilbert 2003;Griffiths 2007). In this context, DWM is the explanation for homology, not its definition.…”

“…In this context, DWM is the explanation for homology, not its definition. A variety of other definitions of homology run aground on the increasingly common observations that many homologous features are derived from different genes and/or different embryological/developmental pathways (Hall 1994;Shubin et al 2009; but see Baum 2013). Thus, many modern evolutionists revert to a very simple definition of homology: "structural and positional similarity… the same organ in different animals under a variety of form and function" (Panchen 1994: 56).…”