Thus, functional homology seems to be a category error because what a structure does should not enter into an evaluation of homologue correspondence and similarity of function is often the result of adaptation via natural selection to common environmental demands, not common ancestry. Swapping structurally homologous genes between species to rescue mutant or null phenotypes is not a genuine criterion of functional homology, especially when there is little or no attention to establishing a phylogenetic context.
This makes many claims of functional homology between model organisms suspect.
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Debate has raged about which of them if any is most appropriate for different aspects of biological and psychological reasoning or most general in scope i. If we are to avoid mixing homology and analogy, then the appropriate notion of function cannot be based on selection history, which is allied with the concept of analogy and concerns a particular variety of function. Similarly, viability interpretations concentrate on features where the variety of function is critical because of conferred survival advantages.
It too focuses on a particular variety of function, though in a way different from either selected effect or viability interpretations. An evaluation of sameness due to common ancestry is made separately from the role the function plays or its use , whether understood in terms of a causal role, a fitness advantage, or a history of selection. More precisely, homology of function can be defined as the same activity-function in different animals under every variety of form and use-function Love This unambiguously removes the tension that plagued functional homology.
Careful discussions of regulatory gene function in development and evolution recognize something akin to the distinction between activity- and use-function i. When studying the molecular evolution of regulatory genes, their biochemical and developmental function must be considered separately.
The biochemical function of PAX-6 and eyeless are as general transcription factors which bind and activate downstream genes , but their developmental function is their specific involvement in eye morphogenesis Abouheif The biochemical function is the activity-function and the developmental function is the use-function. This distinction helps to discriminate between divergent evolutionary trajectories.
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The developmental roles of Hox genes in axial patterning may be conserved by virtue of their biochemical activity-function homologies but Hox genes are not use-function homologues because of these developmental roles. Instead of focusing on the activity of a gene component and its causal role in axial patterning, we shift to the activity of axial patterning and its causal role elsewhere or elsewhen in embryonic development. Introducing a conceptually legitimate idea of homology of activity-function is not about keeping the ideas of developmental biology tidy.
It assists in the interpretation of evidence and circumscribes the inferences drawn. For example, NK-2 genes are involved in mesoderm specification, which underlies muscle morphogenesis. In Drosophila , the expression of a particular NK-2 gene tinman is critical for both cardiac and visceral mesoderm development.
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If tinman is knocked out and transgenically replaced with its vertebrate orthologue, Nkx , only visceral mesoderm specification is rescued; the regulation of cardiac mesoderm is not Ranganayakulu et al. The homeodomains stretches of sequence that confer DNA binding for vertebrate Nkx and Drosophila tinman are interchangeable.
The inability of Nkx to rescue cardiac mesoderm specification is not related to the activity-function of differential DNA binding. One component of the orthologous homologous proteins in both species retains an activity-function homology related to visceral mesoderm specification but another component not the homeodomain has diverged.
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This homeobox gene does not have a single use-function as expected , but it also does not have a single activity-function. Any adequate evaluation of these cases must recognize a more fine-grained decomposition of genes into working units to capture genuine activity-function conservation. We can link activity-function homologues directly to structural motifs within a gene but there is not necessarily a single activity-function for an entire open reading frame.
Defusing the conceptual tensions between developmental and evolutionary biology with respect to homology of function has a direct impact on the causal generalizations and inferences made from model organisms Section 4.
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Activity-function homology directs our attention to the stability or conservation of activities. This conservation is indicative of when the study of mechanisms in model organisms will produce robust and stable generalizations. The widespread use of functional homology in developmental biology is aimed at exactly this kind of question, which explains its persistence in experimental biology despite conceptual ambiguities. Generalizations concerning molecular signaling cascades are underwritten by the coordinated biochemical activities in view, not the developmental roles though sometimes they may coincide.
Thus, activity-function details about a signaling cascade gleaned from a model organism can be generalized via homology to other unstudied organisms even if the developmental role varies for the activity-function in other species. All reasoning strategies combine distinctive strengths alongside of latent weaknesses. For example, decomposing a system into its constituents to understand the features manifested by the system promotes a dissection of the causal interactions of the localized constituents, while downplaying interactions with elements external to the system Wimsatt ; Bechtel and Richardson Sometimes the descriptive and explanatory practices of the sciences are successful precisely because they intentionally ignore aspects of natural phenomena or use a variety of approximation techniques.
Idealization is one type of reasoning strategy that scientists use to describe, model, and explain that purposefully departs from features known to be present in nature. For example, the interior space of a cell is often depicted as relatively empty even though intracellular space is known to be crowded Ellis ; the variable of cellular volume takes on a value that is known to be false i.
Idealizations involve knowingly ignoring variations in properties or excluding particular values for variables, in a variety of different ways, for descriptive and explanatory purposes Jones ; Weisberg The study of ontogeny in model organisms Section 4 is usually executed by establishing a set of normal stages for embryonic development see Other Internet Resources. A developmental trajectory from fertilized zygote to fully-formed adult is broken down into distinct temporal periods by reference to the occurrence of major events, such as fertilization, gastrulation, or metamorphosis Minelli ch.
This enables researchers in different laboratory contexts to have standardized comparisons of experimental results Hopwood , They are critical to large communities of developmental biologists working on well-established models, such as chick Hamburger and Hamilton or zebrafish Kimmel et al. These normal stages are a form of idealization because they intentionally ignore kinds of variation in development, including variation associated with environmental variables.
While facilitating the study of particular causal relationships, this means that specific kinds of variation in developmental features that might be relevant to evolution are minimized in the process of rendering ontogeny experimentally tractable Love a. Phenotypic plasticity is a ubiquitous biological phenomenon. It involves the capacity of a particular genotype to generate phenotypic variation, often in the guise of qualitatively distinct phenotypes, in response to differential environmental cues Pigliucci ; DeWitt and Scheiner ; Kaplan ; Gilbert and Epel One familiar example is seasonal caterpillar morphs that depend on different nutritional sources Greene The reaction norm is a summary of the range of phenotypes, whether quantitatively or qualitatively varying, exhibited by organisms of a given genotype for different environmental conditions.
When the reaction norm exhibits discontinuous variation or bivalent phenotypes rather than quantitative, continuous variation , it is often labeled a polyphenism Figure 6.
Figure 6: A color polyphenism in American Peppered Moth caterpillars that represents an example of phenotypic plasticity. Phenotypic plasticity has been of recurring interest to biological researchers and controversial in evolutionary theory. Extensive study of phenotypic plasticity has occurred in the context of quantitative genetic methods and phenotypic selection analyses, where the extent of plasticity in natural populations has been demonstrated and operational measures delineated for its detection Scheiner ; Pigliucci Other aspects of plasticity require different investigative methods to ascertain the sources of plasticity during ontogeny, the molecular genetic mechanisms that encourage plasticity, and the kinds of mapping functions that exist between the genotype and phenotype Pigliucci ; Kirschner and Gerhart ch.
These latter aspects, the origin of phenotypic variation during and after ontogeny, are in view at the intersection of development and evolution: How do molecular genetic mechanisms produce or reduce plasticity? What genotype-phenotype mapping functions are prevalent or rare? Does plasticity contribute to the origination of evolutionary novelties West-Eberhard ? In order to evaluate these questions experimentally, we need to alter development through the manipulation of environmental variables and observe how a novel phenotype can be established within the existing plasticity of an organism Kirschner and Gerhart ch.
This manipulation could allow for the identification of patterns of variation through the reliable replication of particular experimental alterations within different environmental regimes. But without measuring variation across different environmental regimes, you cannot observe phenotypic plasticity. These measurements are required to document the degree of plasticity and its patterns for a particular trait, such as qualitatively distinct morphs. An evaluation of the significance of phenotypic plasticity for evolution requires answers to questions about where plasticity emerges, how molecular genetic mechanisms are involved in the plasticity, and what genotype-phenotype relations obtain.
Developmental stages intentionally ignore variation associated with phenotypic plasticity. Animals and plants are raised under stable environmental conditions so that stages can be reproduced in different laboratory settings and variation is often viewed as noise that must be reduced or eliminated if one is to understand how development works Frankino and Raff This practice also encourages the selection of model organisms that exhibit less plasticity Bolker The laboratory domestication of a model organism may also reduce the amount or type of observable phenotypic variation Gu et al.
Despite attempts to reduce variation by controlling environmental factors, some of it always remains and is displayed by the fact that absolute chronology is not a reliable measure of time in ontogeny, and neither is the initiation or completion of its different parts Mabee et al.
get link Developmental stages allow this recalcitrant variation to be effectively ignored by judgments of embryonic typicality. Normal stages also involve assumptions about the causal connections between different processes across sequences of stages Minelli ch. Once these stages have been constructed, it is possible to use them as a visual standard against which to recognize and describe variation as a deviation from the norm DiTeresi But, more typically, variation ignored in the construction of these stages is also ignored in the routine consultation of the stages in day-to-day research contexts Frankino and Raff Normal stages fulfill a number of goals related to descriptive and explanatory endeavors that developmental biologists engage in Kimmel et al.
They yield a way to measure experimental replication, enable consistent and unambiguous communication among researchers, especially if stages are founded on commonly observable morphological features, facilitate accurate predictions of developmental phenomena, and aid in making comparisons or generalizations across species. Idealizations also can facilitate abstraction and generalization, both of which are a part of extrapolating findings from the investigative context of a model organism to other domains Steel ; see Section 4 and 5. There are various weaknesses associated with normal stages that accompany the fulfillment of these investigative and explanatory goals.
Key morphological indicators sometimes overlap stages, terminology that is useful for one purpose may be misleading for another, particular terms can be misleading in cross-species comparisons, and manipulation of the embryo for continued observation can have a causal impact on ontogeny. Avoiding variability in stage indicators can encourage overlooking the significance of this variation, or at least provide a reason to favor its minimization. Thus, there are good reasons for adopting normal stages to periodize model organism ontogeny, and these help explain why their continued use yields empirical success.
At the same time, there are ways in which the practice of staging involves idealizations—decisions to intentionally misrepresent particular kinds of variation. Similar to other standard successful practices in science, normal stages are often taken for granted, which means their biasing effects are neglected Wimsatt , some of which are relevant to evolutionary questions e.
This is critical to recognize because the success of a periodization is not a function of the eventual ability to relax the idealizations; periodizations are not slowly corrected so that they become less idealized. Instead, new periodizations are constructed and used alongside the existing ones because different idealizations involve different judgments of typicality that serve diverse descriptive and explanatory aims.
In addition to the systematic biases involved in developmental staging, most model organisms are poorly suited to inform us about how environmental effects modulate or combine with genetic or other factors in development—they make it difficult to discover details about mechanisms underlying reaction norms.
Short generation times and rapid development are tightly correlated with insensitivity to environmental conditions through various mechanisms such as prepatterning Bolker The tension between the specific practice of developmental staging in model organisms and uncovering the relevance of variation due to phenotypic plasticity for evolution can be reconstructed as an argument. Although this tension obtains even if the focus is not on evolutionary questions, sometimes encouraging developmental biologists to interpret absence of evidence as evidence of the developmental insignificance of phenotypic plasticity, it is exacerbated for evolutionary researchers.
The documentation of patterns of variation is precisely what is required to gauge the evolutionary significance of phenotypic plasticity. Practices of developmental staging in model organisms can retard our ability to make either a positive or negative assessment.