Homology and the hierarchy of biological systems

Homology is the similarity between organisms due to common ancestry. Introduced by Richard Owen in 1843 in a paper entitled "Lectures on comparative anatomy and physiology of the invertebrate animals", the concept of homology predates Darwin's "Origin of Species" and has been very influential throughout the history of evolutionary biology. Although homology is the central concept of all comparative biology and provides a logical basis for it, the definition of the term and the criteria of its application remain controversial. Here, I will discuss homology in the context of the hierarchy of biological organization. I will provide insights gained from an exemplary case study in evolutionary developmental biology that indicates the uncoupling of homology at different levels of biological organization. I argue that continuity and hierarchy are separate but equally important issues of homology.     

Phylogeny and evo-devo: characters, homology, and the historical analysis of the evolution of development

The concept of homology continues to attract more and more commentary. In systematic and evolutionary biology the meaning of homology as synapomorphic similarity inherited from a common ancestor has gained wide acceptance over the last three or four decades. In recent years, however, developmental biologists, in particular, have argued for a new approach to, and new definition for, homology that revolves around the desire to make it more process-oriented and more mechanistic. These efforts raise questions about the relationship between developmental and evolutionary biology as well as how the evolution of development is to be studied. It is argued in this paper that this new approach to homology seemingly decouples developmental biology from the study of the evolution of development rather than to facilitate that study. In contrast, applying the notion of historical, phylogenetic homology to developmental data is inherently comparative and therefore evolutionary.     

Field homology: a meaningless concept.

Most biological homologues involve comparison of single characters in two or more taxa. It is possible, however, to recognize homologous characters between two or more taxa that involve the transformation of one character into many characters or many characters into one character. This type of homology is recognized as field homology and it has been widely used in comparative neuroanatomy. The emergence of the cladistic analysis of embryonic stages in the development of neural characters, however, strongly suggests that field homology is a meaningless concept. When it appears necessary to recognize field homologues, it is because comparisons are being made at an inappropriate level within a given biological hierarchy. Furthermore, recognition of field homologues restricts evolutionary mechanisms to a single mechanism of parcellation as defined by Ebbesson.     

Evolutionary Novelty and the Evo-Devo Synthesis: Field Notes

Accounting for the evolutionary origins of morphological novelty is one of the core challenges of contemporary evolutionary biology. A successful explanatory framework requires the integration of different biological disciplines, but the relationships between developmental biology and standard evolutionary biology remain contested. There is also disagreement about how to define the concept of evolutionary novelty. These issues were the subjects of a workshop held in November 2009 at the University of Alberta. We report on the discussion and results of this workshop, addressing questions about (i) how to define evolutionary novelty and understand its significance, (ii) how to interpret evolutionary developmental biology as a synthesis and its relation to neo-Darwinian evolutionary theory, and (iii) how to integrate disparate biological approaches in general.     

Biodiversity Realism: Preserving the tree of life

Biodiversity is a key concept in the biological sciences. While it has its origin in conservation biology, it has become useful across multiple biological disciplines as a means to describe biological variation. It remains, however, unclear what particular biological units the concept refers to. There are currently multiple accounts of which biological features constitute biodiversity and how these are to be measured. In this paper, I draw from the species concept debate to argue for a set of desiderata for the concept of “biodiversity” that is both principled and coheres with the concept’s use. Given these desiderata, this concept should be understood as referring to difference quantified in terms of the phylogenetic structure of lineages, also known as the ‘tree of life’.     

Evo-devo and the search for homology (“sameness”) in biological systems

Developmental biology and evolutionary studies have merged into evolutionary developmental biology (“evo-devo”). This synthesis already influenced and still continues to change the conceptual framework of structural biology. One of the cornerstones of structural biology is the concept of homology. But the search for homology (“sameness”) of biological structures depends on our favourite perspectives (axioms, paradigms). Five levels of homology (“sameness”) can be identified in the literature, although they overlap to some degree: (i) serial homology (homonomy) within modular organisms, (ii) historical homology (synapomorphy), which is taken as the only acceptable homology by many biologists, (iii) underlying homology (i.e., parallelism) in closely related taxa, (iv) deep evolutionary homology due to the “same” master genes in distantly related phyla, and (v) molecular homology exclusively at gene level. The following essay gives emphasis on the heuristic advantages of seemingly opposing perspectives in structural biology, with examples mainly from comparative plant morphology. The organization of the plant body in the majority of angiosperms led to the recognition of the classical root–shoot model. In some lineages bauplan rules were transcended during evolution and development. This resulted in morphological misfits such as the Podostemaceae, peculiar eudicots adapted to submerged river rocks. Their transformed “roots” and “shoots” fit only to a limited degree into the classical model which is based on either–or thinking. It has to be widened into a continuum model by taking over elements of fuzzy logic and fractal geometry to accommodate for lineages such as the Podostemaceae.     

A Particular Synthesis: Aleksandr Promptov and Speciation in Birds

During the 1930s, Aleksandr Promptov—a student of the founder of Russian population genetics Sergei Chetverikov—developed an elaborate concept of speciation in birds. He conducted field investigations aimed at giving a naturalistic content to the theoretical formulations and laboratory models of evolutionary processes advanced within the framework of population genetics, placing particular emphasis on the evolutionary role of bird behavior. Yet, although highly synthetic in combining biogeographical, taxonomic, genetic, ecological, and behavioral studies, Promptov’s speciation concept was ignored by the architects of the 1930s and 1940s evolutionary synthesis, including Theodosius Dobzhnasky, Ernst Mayr, and Julian Huxley. In this article, I argue that the story of Promptov’s concept and its reception by other evolutionists challenges the traditional presentation of the synthesis as a singular, international process of the unification of biology, which led to the creation of a universal synthetic theory of evolution. It suggests that during the same time period, within largely the same theoretical framework, there were multiple, intrinsically local, attempts at creating synthetic evolutionary concepts. These concepts were often quite particular—in their taxonomic applicability, in their explanations of various evolutionary factors, and in the range of disciplines unified in the synthesis. Apparently, these concepts ran contrary to the universal aspirations of the synthesis architects, and as a result, they were disregarded, first by the architects and later by historians of the evolutionary synthesis.     

Homology: Why We Know a Whale Is Not a Fish

Homology is a fundamental concept in comparative and evolutionary biology and yet often the focus of antievolution challenges. In describing structural similarity that is the result of common ancestry, hypotheses about homology require rigorous testing and form the basis for making predictions about anatomy and physiology as well as the fossil record. Communicating the basics of homology to students is essential for a high school biology curriculum.     

Evolution and development: Past, present, and future

The paper tries to set right certain ideas about the history of evolutionary developmental biology. The main point is, that we had to enface the dominance of a comparative approach towards evolutionary developmental biology before 1900, which even later on was effective in Russia, for example, till the 1930s. The problem of the experimentalist approach set against this tradition was and is that there is no concept of gestalt that may allow to integrate the former comparative views and the modern mechanistic interpretations. We argue, that it would be wrong just to describe the comparative tradition as being outdated, as it may allow to get the framework for a dynamical concept of Gestalt that may integrate the ideas of morphogenesis and pattern formation worked out in evo-devo recently.     

Popper, falsifiability, and evolutionary biology

First, a brief history is provided of Popper's views on the status of evolutionary biology as a science. The views of some prominent biologists are then canvassed on the matter of falsifiability and its relation to evolutionary biology. Following that, I argue that Popper's programme of falsifiability does indeed exclude evolutionary biology from within the circumference of genuine science, that Popper's programme is fundamentally incoherent, and that the correction of this incoherence results in a greatly expanded and much more realistic concept of what is empirical, resulting in the inclusion of evolutionary biology. Finally, this expanded concept of empirical is applied to two particular problems in evolutionary biology — viz., the species problem and the debate over the theory of punctuated equilibria — and it is argued that both of them are still mainly metaphysical.     

Molecular evolution: concepts and the origin of disciplines

This paper focuses on the consolidation of Molecular Evolution, a field originating in the 1960s at the interface of molecular biology, biochemistry, evolutionary biology, biophysics and studies on the origin of life and exobiology. The claim is made that Molecular Evolution became a discipline by integrating different sorts of scientific traditions: experimental, theoretical and comparative. The author critically incorporates Timothy Lenoir’s treatment of disciplines (1997), as well as ideas developed by Stephen Toulmin (1962) on the same subject. On their account disciplines are spaces where the social and epistemic dimensions of science are deeply and complexly interwoven. However, a more detailed account of discipline formation and the dynamics of an emerging disciplinary field is lacking in their analysis. The present essay suggests focusing on the role of scientific concepts in the double configuration of disciplines: the social/political and the epistemic order. In the case of Molecular Evolution the concepts of molecular clock and informational molecules played a central role, both in differentiating molecular from classical evolutionists, and in promoting communication between the different sorts of traditions integrated in Molecular Evolution. The paper finishes with a reflection on the historicity of disciplines, and the historicity of our concepts of disciplines.     

Assessing similarity: on homology,characters and the need for a semantic approach to non‐evolutionary comparative homology

The problem of homology has been a consistent source of controversy at the heart of systematic biology, as has the step of morphological character analysis in phylogenetics. Based on a clear epistemic framework and a characterization of “characters” as diagnostic evidence units for the recognition of not directly identifiable entities, I discuss the ontological definition and empirical recognition criteria of phylogenetic, developmental and comparative homology, and how these three accounts of homology each contribute to an understanding of the overall phenomenon of homology. I argue that phylogenetic homologies are individuals or historical kinds that require comparative homology for identification. Developmental homologies are natural kinds that ultimately rest on phylogenetic homologies and also require comparative homology for identification. Comparative homologies on the other hand are anatomical structural kinds that are directly identifiable. I discuss pre‐Darwinian comparative homology concepts and their problem of invoking non‐material forces and involving the a priori assumption of a stable positional reference system. Based on Young's concept of comparative homology, I suggest a procedure for recognizing comparative homologues that lacks these problems and that utilizes a semantic framework. This formal conceptual framework provides the much needed semantic transparency and computer‐parsability for documenting, communicating and analysing similarity propositions. It provides an essential methodological framework for generalizing over individual organisms and identifying and demarcating anatomical structural kinds, and it provides the missing link to the logical chain of identifying phylogenetic homology. The approach substantially increases the analytical accessibility of comparative research and thus represents an important contribution to the theoretical and methodological foundation of morphology and comparative biology.     

The female orgasm and the homology concept in evolutionary biology

The definition of homology and its application to reproductive structures, external genitalia, and the physiology of sexual pleasure has a tortuous history. While nowadays there is a consensus on the developmental homology of genital and reproductive systems, there is no agreement on the physiological translation, or the evolutionary origination and roles, of these structural correspondences and their divergent histories. This paper analyzes the impact of evolutionary perspectives on the homology concept as applied to the female orgasm, and their consequences for the biological and social understanding of female sexuality and reproduction. After a survey of the history of pre-evolutionary biomedical views on sexual difference and sexual pleasure, we examine how the concept of sexual homology was shaped in the new phylogenetic framework of the late 19th century. We then analyse the debates on the anatomical locus of female pleasure at the crossroads of theories of sexual evolution and new scientific discourses in psychoanalysis and sex studies. Moving back to evolutionary biology, we explore the consequences of neglecting homology in adaptive explanations of the female orgasm. The last two sections investigate the role played by different articulations of the homology concept in evolutionary developmental explanations of the origin and evolution of the female orgasm. These include the role of sexual, developmental homology in the byproduct hypothesis, and a more recent hypothesis where a phylogenetic, physiological concept of homology is used to account for the origination of the female orgasm. We conclude with a brief discussion on the social implications for the understanding of female pleasure derived from these different homology frameworks.     

THE APPLIED BIOLOGIST, THE CHILD, AND SOCIETY

Consideration of the characteristics of past and current applied biology reveals its fundamentally ecological nature, and also indicates the potent influence of the applied biologist upon society. It is urged that in order to impress influence upon pupils biological education should be based mainly upon field studies, rather than upon predominantly evolutionary, morphological and physiological studies. The nature of past and existing school biology strongly reinforces the abovel conclusion.
The results of attempts to find and evaluate evidence of the social influences of past and present biological education are presented, both in relation to the whole population, as well as to particular aspects, like food poisoning, the press, and the education of Civil Servants and Members of Parliment.
The potentialities of a Sixth Form biology resting chiefly upon field study are discussed not only as a means of developing an outlook valuable to-day, but also of treating suitably the pre-university education of future applied biologists.     

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.     

From Types to Populations: A Century of Race, Physical Anthropology, and the American Anthropological Association

In the 1960s, U.S. physical anthropology underwent a period of introspection that marked a change from the old physical anthropology that was largely race based to the new physical anthropology, espoused by Washburn and others for over a decade, which incorporated the evolutionary biology of the modern synthesis. What actually changed? What elements of the race concept have been rejected, and what elements have persisted, influencing physical anthropology today? In this article, I examine both the scientific and social influences on physical anthropology that caused changes in the race concept, in particular the influence of the American Anthropological Association. The race concept is complicated but entails three attributes: essentialism, cladistic thinking, and biological determinism. These attributes have not all been discarded; while biological determinism and its social implications have been questioned since the inception of the field, essentialism and the concomitant rendering of populations as clades persists as a legacy of the race concept. [Keywords: race, essentialism, physical anthropology]     

Ontogeny, anatomy, and the problem of homology: Carl Gegenbaur and the American tradition of cell lineage studies

Summary In this paper we analyze Carl Gegenbaur’s conception of the relationship between embryology (“Ontogenie”) and comparative anatomy and his related ideas about homology. We argue that Gegenbaur’s conviction of the primacy of comparative anatomy and his careful consideration of caenogenesis led him to a more balanced view about the relationship between ontogeny and phylogeny than his good friend Ernst Haeckel. We also argue that Gegenbaur’s ideas about the centrality of comparative anatomy and his definitions of homology actually laid the conceptual foundations for Hans Spemann’s (1915) later analysis of homology. We also analyze Gegenbaur’s reception in the United States and how the discussions between E.B. Wilson and Edwin Conklin about the role of the “embryological criterion of homology” and the latter’s argument for an even earlier concept of cellular homology reflect the recurring theme of preformism in ontogeny, a theme that finds its modern equivalent in various genetic definitions of homology, only recently challenged by the emerging synthesis of evolutionary developmental biology. Finally, we conclude that Gegenbaur’s own careful methodological principles can serve as an important model for proponents of present day “evo-devo”, especially with respect to the integration of ontogeny with phylogeny embedded in comparative anatomy.     

Environmental stress and adaptational responses: consequences for human health outcomes

With the dramatic pace of modernization of the world's population, human adaptation as a theoretical construct and paradigm will likely become a focal scientific issue involving scientists from many disciplinary areas during the 21st Century. Macro and micro environments are in rapid flux and human populations are exposed to rapid change. The concept of adaptation, at least in the field of biological anthropology and human biology, will likely remain tied to evolutionary processes and concepts of selection and fitness. In this paper, we discuss the theoretical constructs of adaptation and adaptability and select three current examples from our ongoing research that involve studies of adaptation and evolutionary processes in modernizing populations in different locations worldwide.     

扩散生态学及其意义

扩散研究是生态学研究中的一个热点领域 ,而扩散生态学则是生物学领域一门新的分支学科。本文综述了扩散生态学研究的一些基本理论问题 ,包括扩散的定义、扩散生态学的研究内容及其与生物学其它分支学科的关系 ,并阐述了研究扩散的重要意义。扩散生态学的研究内容十分广泛 ,既涉及所有生物 (从微生物到脊椎动物 )的生态学 (如复合种群、群落、生态系统多样性、复杂性和稳定性 )和进化 (如种化 )等理论问题 ,又涉及物种保护、生物多样性保育、有害生物 (包括外来物种 )的控制、流行病防范、环境保护和人口管理等应用问题。因此 ,研究生物的扩散具有十分重要的理论和实践意义。