The Formation of the Theory of Homology in Biological Sciences

Homology is among the most important comparative concepts in biology. Today, the evolutionary reinterpretation of homology is usually conceived of as the most important event in the development of the concept. This paradigmatic turning point, however important for the historical explanation of life, is not of crucial importance for the development of the concept of homology itself. In the broadest sense, homology can be understood as sameness in reference to the universal guarantor so that in this sense the different concepts of homology show a certain kind of "metahomology". This holds in the old morphological conception, as well as in the evolutionary usage of homology. Depending on what is (or was) taken as a guarantor, different types of homology may be distinguished (as idealistic, historical, developmental etc.). This study represents a historical overview of the development of the homology concept followed by some clues on how to navigate the pluralistic terminology of modern approaches to homology.     

Convergent exaptation and adaptation in solitary island lizards

Independent evolutionary lineages often display similar characteristics in comparable environments. Three kinds of historical hypotheses could explain this convergence. The first is adaptive and evolutionary: nonrandom patterns may result from analogous evolutionary responses to shared conditions. The second explanation is exaptive and ecological: species may be filtered by their suitability for a particular type of environment. The third potential explanation is a null hypothesis of random colonization from a historically nonrandom source pool. Here we demonstrate that both exaptation and adaptation have produced convergent similarity in different size-related characters of solitary island lizards. Large sexual size dimorphism results from adaptive response to solitary existence; uniform, intermediate size results from ecological filtering of potential colonizers. These results demonstrate the existence of deterministic exaptive convergence and suggest that convergent phenomena may require historical explanations that are ecological as well as evolutionary.     

Constraining the adaptationism debate

This contribution to the adaptationism debate elaborates the nature of constraints and their importance in evolutionary explanation and argues that the adaptationism debate should be limited to the issue of how to privilege causes in evolutionary explanation. I argue that adaptationist explanations are deeply conceptually dependent on developmental constraints, and explanations that appeal to constraints are dependant on the results of natural selection. I suggest these explanations should be integrated into the framework of historical causal explanation. Each strategy explicitly appeals to some aspect of the evolutionary process, while implicitly appealing to others. Thus, adaptationists and anti-adaptationists can offer complementary causal explanations of the same explanandum. This eliminates much of the adaptationism debate and explains why its adversaries regularly agree with each other more than they would like. The adaptationism issue that remains is a species of the general issue of how to privilege causes in explanation. I show how a proposed solution to this general problem might be brought to bear on evolutionary explanations, and investigate some difficulties that might arise due to the nature of the evolutionary process.     

Thinking Temporally or Modernizing Anthropology

Recent changes within social and cultural anthropology have made history a key issue, but in this essay I argue that the field has yet to develop the resources that are required to deal with temporality. This point is made through an extended examination of Jean and John Comaroffs work on Christianity and colonialism in southern Africa. Arguably, the Comaroffs read history backward and then present its unfolding as a kind of inexorable logic. In doing so, they homogenize missionary and Tswana "cultures" and attribute agency to abstractions rather than to people acting in particular material contexts. In contrast, I argue for a narrative approach to historical anthropological explanation. The emergent qualities of events—and the variable ways in which capitalism, hegemony, Protestantism, and vernacular modernisms relate—require narrative for explanation, narrative that encompasses within itself the narratives of social actors themselves, [historical anthropology, narrative, the modern, South Africa]     

Between history and physics

Biology has traditionally occupied a middle ground between the determinism of classical physics and the uncertainties of history. These issues are analyzed with respect to statistical laws which are applied to the prebiotic domain and strategy laws which characterize evolutionary biology. The differences in approach between biology and physics are discussed in detail. The origin of life is discussed in the context of physical chemical laws. A scenario for biogenesis is presented in terms of known molecular hardware. Evolutionary biology is then examined with respect to the kinds of laws that are possible in a domain where thermal fluctuations (mutations) have macroscopic effects. Game theory is employed to demonstrate the kinds of theory appropriate to this historical domain. The transition point between physics and history is the origin and development of the code. This is discussed and it is concluded that we are not yet able to assign the code to either the deterministic domain or to the arena of history.     

What’s wrong with the modern evolutionary synthesis? A critical reply to Welch (2017)

Welch (Biol Philos 32(2):263–279, 2017) has recently proposed two possible explanations for why the field of evolutionary biology is plagued by a steady stream of claims that it needs urgent reform. It is either seriously deficient and incapable of incorporating ideas that are new, relevant and plausible or it is not seriously deficient at all but is prone to attracting discontent and to the championing of ideas that are not very relevant, plausible and/or not really new. He argues for the second explanation. This paper presents a twofold critique of his analysis: firstly, the main calls for reform do not concern the field of evolutionary biology in general but rather, or more specifically, the modern evolutionary synthesis. Secondly, and most importantly, these calls are not only inspired by the factors, enumerated by Welch, but are also, and even primarily, motivated by four problematic characteristics of the modern synthesis. This point is illustrated through a short analysis of the latest reform challenge to the modern synthesis, the so-called extended evolutionary synthesis. We conclude with the suggestion that the modern synthesis should be amended, rather than replaced.     

HISTORICAL VERSUS SELECTIONIST EXPLANATIONS IN EVOLUTIONARY BIOLOGY

Abstract— Evolutionary changes require historical explanations, yet these are limited by the evolutionary processes we entertain and investigate. Using phylogenetic analysis, adaptation and natural selection can be tested as historical claims, but this is appropriate only in those special cases where change follows the scheme of one character-one function, singled out in new environmental circumstances. Systematic treatment of the evolutionary origin of characters (in particular, origin through ecological and developmental flexibility) lies outside the scope of selectionist explanations. Structural hypotheses about regularities in the directions of change, also analyzed phylogenetically, expand the scope of historical explanation to include the origin of characters, yet retain the view of organisms as passive and constrained objects of evolutionary change. Historical biology needs to encompass both the active responses of organisms and the construction by organisms of their own environments. For this to be realized will require changes in the concepts and practices of evolutionary biology, including a re-examination of the Lamarckian theme that the active responses of organisms have evolutionary significance—the rarity of individual-to-individual transmission of "acquired" characters does not disprove the possibility of their frequency increasing in a population.     

Editorial policy and Notes for authors

Modern accounts of evolutionary mechanism pay little attention to the pattern and logic of Darwin's explanation, but recognition of the logic of Darwin's explanation has significance for our understanding of evolution and for our appreciation of the extent to which Darwin's concept of evolutionary mechanism accords with modern evolutionary thought. Also, Darwin's explanation exemplifies the concept of a scientific ‘law’ and thus is of considerable value in helping learners to understand the nature of scientific explanation.     

L'adaptation evolutive

Evolutionary adaptation. An essay on the concept of adaptation, seen from an evolutionary point of view. The conclusion is that adaptation in this sense is the historical narrative of evolution. The mechanism of the process is selection, the scientific argumentation of the explanation is based on a phylogenetic analysis.      

Can social and sexual selection explain the bizarre snout of proterosuchid archosauriforms?

Proterosuchids are a clade of quadrupedal, carnivorous Permo-Triassic diapsids crucial to understand the successful evolutionary radiation of archosaurs during the Mesozoic. The importance and good fossil record of proterosuchids nourished a renewed interest in recent years, but no function has been proposed for their bizarre snouts. An oversized and downturned premaxilla with up to nine teeth with continuous replacement is present in all proterosuchid species and seems to have represented a physiologically costly phenotype that increased towards adulthood. A non-functional or a species recognition hypothesis are not supported as evolutionary mechanisms that drove this phenotype because features expected for these explanations tend to have a very low or zero physiological cost. There is no evidence favouring – but neither rejecting ? that this morphology can be explained by non-sexual and non-social natural selection alone. Mutual social and/or sexual selection is favoured here as the most unambiguously supported explanation for the function and origin of the bizarre snout of proterosuchids based on several lines of evidence, including costliness, positive allometry, positive changes in growth rates and modern analogues. Social and/or sexual selection may have been important evolutionary mechanism in the dawn of the lineage that gave rise to crocodiles and dinosaurs.     

Testing the rare-alleles model of quantitative variation by artificial selection

The rare-alleles model of quantitative variation posits that a common allele (the ‘wild-type’) and one or more rare alleles segregate at each locus affecting a quantitative trait; a scenario predicted by several distinct evolutionary hypotheses. Single locus arguments suggest that artificial selection should substantially increase the genetic variance (Vg) if the rare-alleles model is accurate. This paper tests the ‘ΔVg prediction’ using a large artificial selection experiment on flower size of Mimulus guttatus. Vg for flower size does evolve, increasing with selection for larger flower while decreasing in the other direction. These data are consistent with a model in which flower size variation is caused by rare, partially dominant alleles. However, this explanation becomes increasingly tenuous when considered with other data (correlated responses to selection and the effects of inbreeding). A combination of modern (marker-based mapping) and classical (biometric) techniques will likely to be required to determine the distribution of allele frequencies at loci influencing quantitative traits.     

Childlessness drives the sex difference in the association between income and reproductive success of modern Europeans

The association between reproductive success and income in economically developed societies remains a controversial and understudied topic. The commonly made statement that individuals with a higher income have fewer children defies evolutionary explanation. Here we present results from an analyses of the association between lifetime reproductive success (LRS) and income for modern Europeans from 13 countries. We examine the relationships among income, partner income, sex and LRS, and the role of childlessness in driving the relationships. For women, we find a negative association between LRS and income, while for men, we find a flat or slightly positive one. The sex difference in the association appears to be driven by income's sex-specific association with childlessness; men with a low income have a relatively high risk of childlessness, while women with a low income have a low risk of childlessness. Consequently, once childless people are excluded from the analysis, LRS is negatively associated with income for both sexes. We argue that the observed LRS–income associations may be an outcome of evolved behavioural predispositions operating in modern environments and conclude that, even though humans fail to maximise LRS at all income levels in modern settings, evolutionary theory can still help to explain sex differences in LRS.     

Adaptive and Genomic Explanations of Human Behaviour: Might Evolutionary Psychology Contribute to Behavioural Genomics?

Evolutionary psychology and behavioural genomics are both approaches to explain human behaviour from a genetic point of view. Nonetheless, thus far the development of these disciplines is anything but interdependent. This paper examines the question whether evolutionary psychology can contribute to behavioural genomics. Firstly, a possible inconsistency between the two approaches is reviewed, viz. that evolutionary psychology focuses on the universal human nature and disregards the genetic variation studied by behavioural genomics. Secondly, we will discuss the structure of biological explanations. Some philosophers rightly acknowledge that explanations do not involve laws which are exceptionless and universal. Instead, generalisations that are invariant suffice for successful explanation as long as two other stipulations are recognised: the domain within which the generalisation has no exceptions as well as the distribution of the mechanism described by the generalisation should both be specified. It is argued that evolutionary psychology can contribute to behavioural genomic explanations by accounting for these two specifications.     

The Experimental Study of Bacterial Evolution and Its Implications for the Modern Synthesis of Evolutionary Biology

Since the 1940s, microbiologists, biochemists and population geneticists have experimented with the genetic mechanisms of microorganisms in order to investigate evolutionary processes. These evolutionary studies of bacteria and other microorganisms gained some recognition from the standard-bearers of the modern synthesis of evolutionary biology, especially Theodosius Dobzhansky and Ledyard Stebbins. A further period of post-synthesis bacterial evolutionary research occurred between the 1950s and 1980s. These experimental analyses focused on the evolution of population and genetic structure, the adaptive gain of new functions, and the evolutionary consequences of competition dynamics. This large body of research aimed to make evolutionary theory testable and predictive, by giving it mechanistic underpinnings. Although evolutionary microbiologists promoted bacterial experiments as methodologically advantageous and a source of general insight into evolution, they also acknowledged the biological differences of bacteria. My historical overview concludes with reflections on what bacterial evolutionary research achieved in this period, and its implications for the still-developing modern synthesis.     

The birth of an endemic species flock: demographic history of the Bellamya group (Gastropoda,Viviparidae) in Lake Malawi

Changes in habitat stability may significantly shape evolutionary patterns and processes in ancient lakes. In the present study, we use a hierarchical combination of molecular phylogenetic and coalescent approaches to investigate the evolutionary history of the endemic species of the gastropod genus Bellamya in the African rift‐lake Malawi. By integrating our findings with reported palaeontological and palaeolimnological data, we demonstrate that all but one evolutionary lineage of the Pliocene Bellamya fauna in Lake Malawi became extinct. Coalescent analyses indicate that the modern radiation underwent both a sudden demographic and a spatial expansion after a genetic bottleneck. We argue that a reflooding of the lake after severe Pleistocene low stands offers a straightforward explanation for this pattern and may have triggered speciation processes in the modern endemic Bellamya radiation in Lake Malawi. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 102 , 130–143.     

Buffon, Darwin, and the Non-Individuality of Species – A Reply to Jean Gayon

Gayon's recent claim that Buffon developed a concept of species as physical individuals is critically examined and rejected. Also critically examined and rejected is Gayon's more central thesis that as a consequence of his analysis of Buffon's species concept, and also of Darwin's species concept, it is clear that modern evolutionary theory does not require species to be physical individuals. While I agree with Gayon's conclusion that modern evolutionary theory does not require species to be physical individuals, I disagree with his reasons and instead provide logical rather than historical reasons for the same conclusion.     

Optimization, constraint, and history in the evolution of eyes

Several features of the evolution of eyes and photoreceptors are examined in an effort to explore the relative roles of adaptation and historical and developmental constraints. Optical design shows clear evidence of adaptation, which in some respects approaches optima predictable from physics. The primate fovea, on the other hand, illustrates how adaptation can be channeled by developmental heritage. The primary structures of opsins reveal multiple evolutionary lineages within both Drosophila and humans. The pigments of vertebrae rods comprise a subset of opsins whose evolutionary relationships map onto the phylogeny of the parent species. The evolutionary reasons for why most rod pigments absorb maximally at 500 +/- 10 nm are obscure, as there is no convincing explanation based on adaptation alone. Rods are appropriately distinguished from cones on the basis of which opsin gene is expressed. This criterion is likely to be in conflict with other definitions in phyletic lines (e.g., geckos, snakes) that have long diurnal or nocturnal histories accompanied by loss of one or more opsin genes, followed by a secondary adaptation to life in a different photic environment. Color vision--a generalizable perception associated with the spectral composition of light--is usefully distinguished from wavelength-specific behaviors. The latter are also based on multiple visual pigments and more than one spectral class of receptors but cannot be altered by learning. The distinction is particularly forceful in bees, which exhibit both kinds of behavior. The evolution of primate color vision has been shaped by historical factors involving an extensive period of early mammalian nocturnality. Birds, by contrast, have more elaborate cones and a richer set of visual pigments. Avian color space can be represented in a tetrahedron.     

The problem of similarity: analysis of repeated patterns of microsculpture on gastropod larval shells

Abstract. The problem of similarity is one of explaining the causes of striking resemblances between patterns and architectural themes that recur in organisms at various scales of biological organization. Classical explanations that have considered only the alternatives of homology and analogy overlook similarities of form that are primarily a consequence of fabrication, conveying little information about evolutionary relationships or functional role. When viewed at successively higher magnifications and when mapped onto a phylogeny, patterns of delicate cancellate microsculpture and granular microprotuberances on the surfaces of larval shells of marine gastropods fail to meet the predictions of exclusively historical or exclusively functional explanations, but are shown to be rich in fabricational information. Similar patterns suggest that early biomineralization of the initial organic shell is under weaker biological control than the processes that modulate assembly of the multi-layered, hierarchically-organized composite materials of the adult shell. Some patterns suggest remote biomineralization, without direct influence of living tissue. Scanning electron microscopy of larval shell features reveals previously undetected variation on basic themes that may have implications for the traditional disciplines of systematics, functional morphology, and fabricational morphology. The integration of the approaches of the traditional divisions of biology is required for full explanation of similarity and to generate a unified set of principles for the analysis of form in living and fossil organisms.     

Neandertals...150 years later

The place of Neandertals in modern human emergence has been a subject of debate since the first recognized Neandertal skeleton was discovered in 1856. This paper presents an overview of morphological, archaeological, and genetic evidence commonly used in discussions of Neandertals and their evolutionary significance. A brief historical sketch of the argument provides insight into the changing views on these interesting people. The major models proposed to explain modern human origins are also discussed.     

Evolutionary Contributions to Solving the ��Matrilineal Puzzle��

Matriliny has long been debated by anthropologists positing either its primitive or its puzzling nature. More recently, evolutionary anthropologists have attempted to recast matriliny as an adaptive solution to modern social and ecological environments, tying together much of what was known to be associated with matriliny. This paper briefly reviews the major anthropological currents in studies of matriliny and discusses the contribution of evolutionary anthropology to this body of literature. It discusses the utility of an evolutionary framework in the context of the first independent test of Holden et al.'s 2003 model of matriliny as daughter-biased investment. It finds that historical daughter-biased transmission of land among the Mosuo is consistent with the model, whereas current income transmission is not. In both cases, resources had equivalent impacts on male and female reproduction, a result which predicts daughter-biased resource transmission given any nonzero level of paternity uncertainty. However, whereas land was transmitted traditionally to daughters, income today is invested in both sexes. Possible reasons for this discrepancy are discussed.