Defining vision: what homology thinking contributes

The specialization of visual function within biological function is reason for introducing “homology thinking” into explanations of the visual system. It is argued that such specialization arises when organisms evolve by differentiation from their predecessors. Thus, it is essentially historical, and visual function should be regarded as a lineage property. The colour vision of birds and mammals do not function the same way as one another, on this account, because each is an adaptation to special needs of the visual functions of predecessors—very different kinds of predecessors in each case. Thus, history underlies function. We also see how homology thinking figures in the hierarchical classification of visual systems, and how it supports the explanation of visual function by functional role analysis.

The notion of homology in current comparative biology

Current notions on homology, and its recognition, causation, and explanation are reviewed in this report. The focus is primarily on concepts because the formulation of precise definitions of homology has contributed little to our understanding of the issue. Different aspects or concepts of homology have been contrasted, currently the most important ones being the distinction between systematic and biological concepts. The systematic concept of homology focuses on common ancestry and on taxa; the biological concept tries to explain patterns of conservatism in evolution by shared developmental constraints. Similarity or correspondence is generally accepted as a primary criterion in the delimitation of homologues, albeit that this criterion is not without practical and theoretical problems. Apart from similarity, the biological concept of homology also stresses developmental individuality of putative homologous structures. Structural and positional aspects of homology can be separated, with positional homology acquiring an independent status. Similarity, topographic relationships, and ontogenetic development cannot be tests of homology. Within the cladistic paradigm, the most decisive test of homology is that of congruence; proponents of the biological-homology concept have been less concerned with test implications. Adopting a hierarchical view of nature suggests that characters have to be homologized at their appropriate level of organization. A taxic or systematic approach to homology has precedence over a transformational or biological approach. Nevertheless, pattern analysis and process explanations are not independent of each other.     

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.     

Gene note. Isolation of an Arabidopsis thaliana cDNA encoding a pleckstrin homology domain protein, a putative homologue of human pleckstrin

Screening of an Arabidopsis cDNA library allowed the isolation of a cDNA encoding a pleckstrin homology (PH) domain protein, AtPH1, which consists of one PH domain with a short N-terminal extension. According to its structural features, AtPH1 is proposed to be a plant homologue of human pleckstrin. Northern blot analysis indicated that the AtPH1 gene was expressed constitutively in all tissues examined, with variation in the levels. The presence of a plant pleckstrin homologue offers new insights into the biological function of the PH domain in plant signalling.     

Functional homology and homology of function: biological concepts and philosophical consequences

“Functional homology” appears regularly in different areas of biological research and yet it is apparently a contradiction in terms—homology concerns identity of structure regardless of form and function. I argue that despite this conceptual tension there is a legitimate conception of ‘homology of function’, which can be recovered by utilizing a distinction from pre-Darwinian physiology (use versus activity) to identify an appropriate meaning of ‘function’. This account is directly applicable to molecular developmental biology and shares a connection to the theme of hierarchy in homology. I situate ‘homology of function’ within existing definitions and criteria for structural assessments of homology, and introduce a criterion of ‘organization’ for judging function homologues, which focuses on hierarchically interconnected interdependencies (similar to relative position and connection for skeletal elements in structural homology). This analysis of biological concepts has at least three broad philosophical consequences: (1) it provides the grounds for the study of behavior and psychological categories as homologues; (2) it demonstrates that philosophers who take selected effect function as primary effectively ignore large portions of comparative, structural, and experimental research, thereby misconstruing biological reasoning and knowledge; and, (3) it underwrites causal generalizations, which illuminates inferences made from model organisms in experimental biology.

Molecular analysis of the QM gene from <Emphasis Type="Italic">Penaeus monodon</Emphasis> and its expression on the different ovarian stages of development

In present study, a QM gene was obtained from the ovary and neurosecretory organ in eyestalk cDNA library of black tiger prawn (Penaeus monodon). The full-length black tiger prawn QM (PmQM) cDNA contained a 5′-UTR of 41 bp, an ORF of 663 bp encoding a polypeptide of 220 amino acids with molecular weight 25.5 kDa, and a 3′-UTR of 54 bp. Homology analysis of the deduced amino acid sequence of the PmQM with other known QM sequences by MatGAT software revealed that the PmQM was high homology with other invertebrates. A conserved signature sequence of the QM family was found in the PmQM deduced amino acid sequence. Analysis of the tissue expression pattern of the PmQM gene showed that the PmQM mRNA was expressed in all tissues tested, with highest levels in ovary. Furthermore, the PmQM expression was found to be different in three important ovarian stages of development. The results indicated PmQM might play an important role in ovarian development.     

Molecular cloning and expression analysis of an HINT1 homologue from maize (Zea mays L.)

Histidine triad nucleotide binding protein (HINT1) belongs to a histidine triad (HIT) superfamily, which contains a highly conserved His-X-His-X-His-XX motif (X is a hydrophobic amino acid) and plays an important role in many biological processes. In this study, we have isolated the full-length cDNA of an HINT1 homologue from maize (Zea mays L.), designated as Zm-HINT1. The full-length cDNA of Zm-HINT1 consists of 729 bp with an ORF encoding a 138-amino acid protein. The deduced amino acid sequence of Zm-HINT1 shows high sequence homology to the mammalian HINT1 and contains conserved domains including the HIT motif, helical regions and β-strands, which are the characteristics of HINT1 proteins. The phylogenetic analysis has revealed that Zm-HINT1 is branched along with Caenorhabditis elegans HINT1. RT-PCR analysis has revealed that Zm-HINT1 is ubiquitously expressed in maize tissues but not in the pericarp, thus suggesting that Zm-HINT1 may not be related to the production of fibrin. Furthermore, expression levels of Zm-HINT1 have increased rapidly following treatment with salicylic acid. Taken together, these results indicate that Zm-HINT1 is a mammalian HINT1 homologue and may be involved in the immune response of maize.     

On homology

Homology in cladistics is reviewed. The definition of important terms is explicated in historical context. Homology is not synonymous with synapomorphy: it includes symplesiomorphy, and Hennig clearly included both plesiomorphy and synapomorphy as types of homology. Homoplasy is error, in coding, and is analogous to residual error in simple regression. If parallelism and convergence are to be distinguished, homoplasy would be evidence of the former and analogy evidence of the latter. We discuss whether there is a difference between molecular homology and morphological homology, character state homology, nested homology (additive characters), and serial homology. We conclude by proposing a global definition of homology. ©The Will Henning Society 2011.     

Homology as a relation of correspondence between parts of individuals

The recognition of correspondences has long been a fundamental activity among systematists. Advocates ofNaturphilosophie, such as Lorenz Oken, drew far-fetched analogies between taxonomic groups and all sorts of other things, including the Persons of the Trinity. They treated change through time either as analogous to an ontogeny or as the product of divinely instituted laws of nature. Darwin changed things by making the taxonomic units strictly historical, implying that they are not classes but rather individuals in a broad metaphysical sense. That means that taxa are concrete, particular things, or wholes made up of parts which are themselves individuals, and that there are no laws of nature for them. Homology is a relationship of correspondence between parts of organisms that are also parts of populations and lineages. It is not a relationship of similarity, and unlike similarity it is transitive. Analogy is a relationship of correspondence between parts of organisms that are members of classes, and is not necessarily due to function. Taxa, like other individuals, can change indefinitely, and the only thing that they must share is a common ancestor. They do not share an essence, Platonic Idea orBauplan, although “conservative characters” may be widespread in them. Iterative homology likewise is a relationship of correspondence, but the nature of that correspondence remains unclear. The difficulties of the homology concept can be overcome by treating phylogenetics and comparative biology in general as historical narrative. From the 46th “Phylogenetisches Symposium”, Jena, Germany, November 20–21, 2004. Theme of the symposium: “Evolutionary developmental biology—new challenges to the homology concept”.     

The history of the homology concept and the “Phylogenetisches Symposium”

The homology concept has had a long and varied history, starting out as a geometrical term in ancient Greece. Here we describe briefly how a typological use of homology to designate organs and body parts in the same position anatomically in different organisms was changed by Darwin’s theory of evolution into a phylogenetic concept. We try to indicate the diversity of opinions on how to define and test for homology that has prevailed historically, before the important books by Hennig (1950. Grundzüge einer Theorie der Phylogenetischen Systematik. Deutscher Zentralverlag, Berlin) and Remane (1952. Die Grundlagen des Natürlichen Systems, der Vergleichenden Anatomie und der Phylogenetik. Geest & Portig, Leipzig) brought more rigor into both the debate on homology and into the usage of the term homology among systematists. Homology as a theme has recurred repeatedly throughout the history of the “Phylogenetisches Symposium” and we give a very brief overview of the different aspects of homology that have been discussed at specific symposia over the last 48 years. We also honour the fact that the 2004 symposium was held in Jena by pointing to the roles played by biologists active in Jena, such as Ernst Haeckel and Carl Gegenbaur, in starting the development towards a homology concept concordant with an evolutionary world view. As historians of biology, we emphasize the importance of major treatises on homology and its history that may be little read by systematists active today, and have sometimes also received less attention by historians of biology than they deserve. Prominent among these are the works of Dietrich Starck, who also happened to be both a student, and later a benefactor, of systematics at Jena University.     

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.     

Homology in Development and the Development of the Homology Concept

Homology is a central concept for Developmental Evolution. HereI argue that homology should be explained within the referenceprocesses of development and evolution; development becauseit is the proximate cause of morphological characters and evolutionbecause it deals with organic transformations and stability.This was already recognized by Hans Spemann in 1915. In a seminalessay "A history and critique of the homology concept" Spemannanalyzed the history and present problems of the homology concept.Here I will continue Spemann's project and analyze some of the20th century contributions to homology. I will end with a fewreflections about the connections between developmental processesand homology and conclude that developmental processes are inherentin (i) the assessment of homology, (ii) the explanation of homology,(iii) the origin of evolutionary innovations (incipient homologues),and (iv) can be considered homologous themselves.     

Homology-Modelling Protein-Ligand Interactions: Allowing for Ligand-Induced Conformational Change

Current homology-modelling methods do not consider small molecules in their automated processes. Therefore, the development of a reliable tool for protein-ligand homology modelling is an important next step in generating plausible models for molecular interactions. Two automated protein-ligand homology-modelling strategies, requiring no expert knowledge from the user, are investigated here. Both employ the “induced fit” concept with flexibility in side chains and ligand. The most successful strategy superimposes the new ligand over the original ligand before homology modelling, allowing the new ligand to be taken into consideration during protein modelling (rather than after), facilitating conformational change in the local backbone if necessary. We show that this approach results in successful modelling of the ligand and key binding-site residues of angiotensin-converting enzyme 2 (ACE2) from its homologue ACE, which is not possible via conventional homology modelling or by homology modelling followed by docking. Several other difficult target complexes are also successfully modelled, reproducing native protein-ligand contacts with significantly different biological substrates and different binding-site conformations. These include the modelling of Cdk5 (cyclin-dependent kinase 5) from Cdk2, thymidine phosphorylase from a bacterial homologue, and dihydrofolate reductase from a recombinant variant with a markedly different inhibitor. In terms of average modelling quality across 82 targets, the ligand RMSD with respect to the experimental structure is 1.4 Å (and 2.0 Å for the protein binding site) for “easy” cases and 2.9 Å for the ligand (and 2.7 Å for the protein binding site) in “hard” cases. This demonstrates the importance of selecting an optimal template. Ligand-modelling accuracy is strongly dependent on target-template ligand structural similarity, rather than target-template sequence identity. However, protein-modelling accuracy is dependent on both. Our automated protein-ligand homology-modelling strategy generates a higher degree of accuracy than homology modelling followed by docking, generating an average ligand RMSD that is 1-2 Å better than docking with homology models.     

Molecular cloning,expression, and cytokinin (6-benzylaminopurine) antagonist activity of peanut (<Emphasis Type="Italic">Arachis hypogaea</Emphasis>) lectin SL-I

Isolation and purification of a α-methyl-mannoside specific lectin (SL-I) of peanut was reported earlier [Singh and Das (1994) Glycoconj J 11:282–285]. Native SL-I is a glycoprotein having ∼31 kDa subunit molecular mass and forms dimer. The gene encoding this lectin is identified from a 6-day old peanut root cDNA library by anti-SL-I antibody and N-terminal amino acid sequence homology to the native lectin. Nucleotide sequence derived amino acid sequence of the re-SL-I shows amino acid sequence homology with the N-terminal and tryptic digests’ amino acid sequence of the native SL-I (nSL-I). Presence of a putative glycosylation (QNPS) site and a hydrophobic adenine-binding (VLVSYDANS) site is also identified in SL-I. Homology modeling of the lectin suggests it to be an archetype of legume lectins. It is expressed as a ~30 kDa apoprotein in E. coli and has the carbohydrate specificity and secondary structure identical to its natural counterpart. The lectin SL-I inhibits cytokinin 6-benzylaminopurine (BA)-induced “delayed leaf senescence” and “cotyledon expansion”. Equilibrium dialysis revealed a single high-affinity binding site for adenine (7.6 × 10⁻⁶ M) and BA (1.09 × 10⁻⁵ M) in the SL-I dimer and thus suggesting that the cytokinin antagonist effect of SL-I is mediated by the direct interaction of SL-I with BA.The nucleotide sequence data reported here are available in the DDBJ/EMBL/GenBank databases under the Accession No. AJ585523     

Culture,biology, and human behavior

Social scientists have not integrated relevant knowledge from the biological sciences into their explanations of human behavior. This failure is due to a longstanding antireductionistic bias against the natural sciences, which follows on a commitment to the view that social facts must be explained by social laws. This belief has led many social scientists into the error of reifying abstract analytical constructs into entities that possess powers of agency. It has also led to a false nature-culture dichotomy that effectively undermines the place of biology in social scientific explanation. Following the principles of methodological individualism, we show how behavioral explanations supported by data and theory from the neurosciences can be used to correct the errors of reificationist thinking in the social sciences. We outline a mechanistic approach to the explanation of human behavior with the hope that the biological sciences will begin to find greater acceptance among social scientists.     

Molecular cloning and analysis of the mouse homologue of the tumor-associated mucin, MUC1, reveals conservation of potential O-glycosylation sites, transmembrane, and cytoplasmic domains and a loss of minisatellite-like polymorphism.

We present here the full-length cDNA sequence and genomic structure of the mouse homologue of the tumor-associated mucin, MUC1. This mucin (previously called polymorphic epithelial mucin) is present at the apical surface of most glandular epithelial cells. The mouse gene, Muc-1, encodes an integral membrane protein with 40% of its coding capacity made up of serine, threonine, and proline, a composition typical of a highly O-glycosylated protein. The mucin core protein consists of an amino-terminal signal sequence, a tandem repeat domain encoding 16 repeats of 20-21 amino acids, and unique sequence containing transmembrane and cytoplasmic domains. Homology with the human protein is only 34% in the tandem repeat domain, mainly showing conservation of serines and threonines, presumed sites of O-linked carbohydrate attachment. Homology rises to 87% in the transmembrane and cytoplasmic domains, suggesting that these regions may be functionally important. The pattern of expression of the mouse mucin is very similar to that of its human counterpart and accordingly the two promoter regions share high homology, 74%, although previously identified potential hormone-responsive elements are not conserved. Interestingly, the mouse homologue, unlike its human counterpart does not exhibit a variable number tandem repeat polymorphism. We present evidence that suggests that the mouse gene was at one time polymorphic but has mutated away from this state.     

Homology and errors

A recent review of the homology concept in cladistics is critiqued in light of the historical literature. Homology as a notion relevant to the recognition of clades remains equivalent to synapomorphy. Some symplesiomorphies are “homologies” inasmuch as they represent synapomorphies of more inclusive taxa; others are complementary character states that do not imply any shared evolutionary history among the taxa that exhibit the state. Undirected character‐state change (as characters optimized on an unrooted tree) is a necessary but not sufficient test of homology, because the addition of a root may alter parsimonious reconstructions. Primary and secondary homology are defended as realistic representations of discovery procedures in comparative biology, recognizable even in Direct Optimization. The epistemological relationship between homology as evidence and common ancestry as explanation is again emphasized. An alternative definition of homology is proposed. © The Willi Hennig Society 2012.     

Traumatic Amputation: A Case of Laotian Indignation and Injustice

Culture is an essential variable of diagnosis and treatment. A cultural perspective draws attention to the social context within which symptoms arise, are given meaning, and are managed. Ethno-cultural work on illness narratives suggests that most people can provide culturally-based explanations for their symptoms. While these explanations are inconsistent with biomedical theory, they relieve patient distress by allowing the patient to create meaning for symptoms. Exploring the characteristics, context, and antecedents of the symptoms enables the patient to convey them to the clinician who may have a divergent explanation of sickness. This case study uses the Outline for Cultural Formulation of the DSM-IV created for clinicians to elicit a narrative account of the illness experience from the patient. Our study examines how the patient, a Laotian used social indignation (“Kwam khem keuang”) as an explanatory model for his ailment. He was diagnosed with post-traumatic stress disorder after having undergone a traumatic amputation. In the process of explaining his illness through a cultural idiom, the patient was able to reveal both personal and collective meaning of repressed anger and frustration, expressing them in a context that was acceptable to him. This cultural idiom allowed the patient to reflect upon the structure of the health care system and the specific context in which symptoms and their possible origins are recounted and explored. It also clarified to the treating clinicians some categories of experience and causal explanations that did not fit easily with western biomedical and psychiatric understanding. The case study illustrates how a cultural approach to illness from the patient’s perspective offers a reflexive stance on the clinician–patient interaction that allows for better patient care.     

Phyletic size change and brain/body allometry: A consideration based on the African pongids and other primates

A problematic aspect of brain/body allometry is the frequency of interspecific series which exhibit allometry coefficients of approximately 0.33. This coefficient is significantly lower than the 0.66 value which is usually taken to be the interspecific norm. A number of explanations have been forwarded to account for this finding. These include (1) intraspecificallometry explanations, (2) nonallometric explanations, and (3) Jerison’s “extraneurons” hypothesis, among others. The African apes, which exhibit a lowered interspecific allometry coefficient, are used here to consider previous explanations. These are found to be inadequate in a number of ways, and an alternative explanation is proposed. This explanation is based on patterns of brain and body size change during ontogeny and phytogeny. It is argued that the interspecific allometry coefficient in African apes parallels the intraspecific one because similar ontogenetic modifications of body growth separate large and small forms along each curve. In both cases, body size differences are produced primarily by growth in later postnatal periods, during which little brain growth occurs. Data on body growth, neonatal scaling, and various lifehistory traits support this explanation. This work extends previous warnings that sizecorrected estimates of relative brain size may not correspond very closely to our understanding of the behavioral capacities of certain species in lineages characterized by rapid change in body size.