Nonhuman primates don’t have formal kinship systems, but genetic relatedness shapes patterns of residence, behavior, mating preferences, and cognition in the primate order. The goal of this article is to provide insight about the ancestral foundations on which the first human kinship systems were built. In order for evolution to favor nepotistic biases in behavior, individuals need to have opportunities to interact with their relatives and to be able to identify them. Both these requirements impose constraints on the evolution (...) of kinship bonds in primate species. For nonhuman primates and many other mammals, maternal care generates close ties between mothers and offspring and among littermates. For species in which mother–offspring bonds extend beyond weaning, associations with the mother also generate familiarity among siblings of different ages. For species with female philopatry, mother–offspring ties provide the foundation for lifelong relationships between mothers and daughters, and dense matrilineal kin networks. However, several factors constrain the development of kinship bonds in nonhuman primates. First, dispersal strategies, which are designed to reduce inbreeding, bias kinship networks in favor of the philopatric sex. Second, hostile relationships between groups mean that kin ties are usually severed when individuals move from one group to another. Third, in species with polygynandrous mating systems, uncertainty about paternity and restricted periods of male reproductive monopoly limit the scope for development of ties among fathers and offspring, paternal siblings, or extended paternal kin networks. In this article, I explore the impact of these factors on the evolution of ancestral human kinship systems. (shrink)

The concept of individuality as applied to species, an important advance in the philosophy of evolutionary biology, is nevertheless in need of refinement. Four important subparts of this concept must be recognized: spatial boundaries, temporal boundaries, integration, and cohesion. Not all species necessarily meet all of these. Two very different types of pluralism have been advocated with respect to species, only one of which is satisfactory. An often unrecognized distinction between grouping and ranking components of any species concept is necessary. (...) A phylogenetic species concept is advocated that uses a grouping criterion of monophyly in a cladistic sense, and a ranking criterion based on those causal processes that are most important in producing and maintaining lineages in a particular case. Such causal processes can include actual interbreeding, selective constraints, and developmental canalization. The widespread use of the biological species concept is flawed for two reasons: because of a failure to distinguish grouping from ranking criteria and because of an unwarranted emphasis on the importance of interbreeding as a universal causal factor controlling evolutionary diversification. The potential to interbreed is not in itself a process; it is instead a result of a diversity of processes which result in shared selective environments and common developmental programs. These types of processes act in both sexual and asexual organisms, thus the phylogenetic species concept can reflect an underlying unity that the biological species concept can not. (shrink)

The concept of a temporal phylogenetic network is a mathematical model of evolution of a family of natural languages. It takes into account the fact that languages can trade their characteristics with each other when linguistic communities are in contact, and also that a contact is only possible when the languages are spoken at the same time. We show how computational methods of answer set programming and constraint logic programming can be used to generate plausible conjectures about contacts between (...) prehistoric linguistic communities, and illustrate our approach by applying it to the evolutionary history of Indo-European languages. (shrink)

Three-legged animals do not exist today and such an animal is not found in the fossil record. Which constraints operate to result in the lack of a triped phenotype? Consideration of animal locomotion and robotic studies suggests that physical constraints would not prevent a triped from being functional or advantageous. As is reviewed here, the strongest constraint on the evolution of a triped is phylogenetic: namely, the early genetic adoption of a bilaterally symmetrical body plan occurring before (...) the advent of limbs. Presumably, this would greatly constrain any three-legged animal from ever evolving. Tripedalism is employed only by a few animals, but many use a tripod stance while engaged in a variety of activities. Because terms are often used interchangeably in the literature, a standardization of locomotion terminology is proposed. Understanding the constraints behind “forbidden” phenotypes forces us to confront gaps in our evolutionary understanding of which we may be unaware. (shrink)

By linking the concepts of homology and morphological organization to evolvability, this paper attempts to (1) bridge the gap between developmental and phylogenetic approaches to homology and to (2) show that developmental constraints and natural selection are compatible and in fact complementary. I conceive of a homologue as a unit of morphological evolvability, i.e., as a part of an organism that can exhibit heritable phenotypic variation independently of the organism’s other homologues. An account of homology therefore consists in (...) explaining how an organism’s developmental constitution results in different homologues/characters as units that can evolve independently of each other. The explanans of an account of homology is developmental, yet the very explanandum is an evolutionary phenomenon: evolvability in a character-by-character fashion, which manifests itself in phylogenetic patterns as recognized by phylogenetic approaches to homology. While developmental constraints and selection have often been viewed as antagonistic forces, I argue that both are complementary as they concern different parts of the evolutionary process. Developmental constraints, conceived of as the presence of the same set of homologues across phenotypic change, pertain to how heritable variation can be generated in the first place (evolvability), while natural selection operates subsequently on the produced variation. (shrink)

Evolutionary change is opportunistic, but its course is strongly constrained in several fundamental ways. These constraints (historical/phylogenetic, functional/adaptive, constructional/morphogenetic) and their dynamic relationships are discussed here and shown to constitute the conceptual framework of Constructional Morphology. Notwithstanding recent published opinions which claim that the discovery of constraints renders Neodarwinian selection theory obsolete, we regard the insights of Constructional Morphology as being entirely consistent with this theory. As is shown here in the case of the Hyracoidea, formal analysis (...) of the constraints which have framed the evolution of various characters extends our understanding of the evolution of a taxon. (shrink)

In an influential paper, Stephen Jay Gould and Richard Lewontin contrasted selection-driven adaptation with phylogenetic, architectural, and developmental constraints as distinct causes of phenotypic evolution. In subsequent publications Gould has elaborated this distinction into one between a narrow “Darwinian Fundamentalist” emphasis on “external functionalist” processes, and a more inclusive “pluralist” emphasis on “internal structuralist” principles. Although theoretical integration of functionalist and structuralist explanations is the ultimate aim, natural selection and internal constraints are treated as distinct causes of (...) evolutionary change. This distinction is now routinely taken for granted in the literature in evolutionary biology. I argue that this distinction is problematic because the effects attributed to non-selective constraints are more parsimoniously explained as the ordinary effects of selection itself. Although it may still be a useful shorthand to speak of phylogenetic, architectural, and developmental constraints on phenotypic evolution, it is important to understand that such “constraints” do not constitute an alternative set of causes of evolutionary change. The result of this analysis is a clearer understanding of the relationship between adaptation, selection and constraints as explanatory concepts in evolutionary theory. (shrink)

A fundamental question in biology is whether phenotypes can be predicted by ecological or genomic rules. At least five cases of convergent evolution of the crab‐like body plan (with a wide and flattened shape, and a bent abdomen) are known in decapod crustaceans, and have, for over 140 years, been known as “carcinization.” The repeated loss of this body plan has been identified as “decarcinization.” In reviewing the field, we offer phylogenetic strategies to include poorly known groups, and direct (...) evidence from fossils, that will resolve the history of crab evolution and the degree of phenotypic variation within crabs. Proposed ecological advantages of the crab body are summarized into a hypothesis of phenotypic integration suggesting correlated evolution of the carapace shape and abdomen. Our premise provides fertile ground for future studies of the genomic and developmental basis, and the predictability, of the crab‐like body form. (shrink)

This volume presents a collection of refereed papers reflecting the state of the art in the area of over-constrained systems. Besides 11 revised full papers, selected from the 24 submissions to the OCS workshop held in conjunction with the First International Conference on Principles and Practice of Constraint Programming, CP '95, held in Marseilles in September 1995, the book includes three comprehensive background papers of central importance for the workshop papers and the whole field. Also included is an introduction by (...) one of the volume editors together with a bibliography listing 243 entries. All in all this is a very useful reference book relevant for all researchers and practitioners interested in hierarchical, partial, and over-constrained systems. (shrink)

Despite thermodynamic, bioenergetic and phylogenetic failings, the 81‐year‐old concept of primordial soup remains central to mainstream thinking on the origin of life. But soup is homogeneous in pH and redox potential, and so has no capacity for energy coupling by chemiosmosis. Thermodynamic constraints make chemiosmosis strictly necessary for carbon and energy metabolism in all free‐living chemotrophs, and presumably the first free‐living cells too. Proton gradients form naturally at alkaline hydrothermal vents and are viewed as central to the origin (...) of life. Here we consider how the earliest cells might have harnessed a geochemically created proton‐motive force and then learned to make their own, a transition that was necessary for their escape from the vents. Synthesis of ATP by chemiosmosis today involves generation of an ion gradient by means of vectorial electron transfer from a donor to an acceptor. We argue that the first donor was hydrogen and the first acceptor CO2. (shrink)

Despite thermodynamic, bioenergetic and phylogenetic failings, the 81‐year‐old concept of primordial soup remains central to mainstream thinking on the origin of life. But soup is homogeneous in pH and redox potential, and so has no capacity for energy coupling by chemiosmosis. Thermodynamic constraints make chemiosmosis strictly necessary for carbon and energy metabolism in all free‐living chemotrophs, and presumably the first free‐living cells too. Proton gradients form naturally at alkaline hydrothermal vents and are viewed as central to the origin (...) of life. Here we consider how the earliest cells might have harnessed a geochemically created proton‐motive force and then learned to make their own, a transition that was necessary for their escape from the vents. Synthesis of ATP by chemiosmosis today involves generation of an ion gradient by means of vectorial electron transfer from a donor to an acceptor. We argue that the first donor was hydrogen and the first acceptor CO2. (shrink)

I develop an account of homology and homoplasy drawing on their use in biological inference and explanation. Biologists call on homology and homoplasy to infer character states, support adaptationist explanations, identify evolutionary novelties and hypothesize phylogenetic relationships. In these contexts, the concepts must be understood phylogenetically and kept separate: as they play divergent roles, overlap between the two ought to be avoided. I use these considerations to criticize an otherwise attractive view defended by Gould, Hall, and Ramsey & Peterson. (...) By this view, homology and homoplasy can only be delineated qua some level of description, and some homoplasies (parallelisms) are counted as homologous. I develop an account which retains the first, but rejects the second, aspect of that view. I then characterize parallelisms and convergences in terms of their causal role. By the Strict Continuity account, homology and homoplasy are defined phylogenetically and without overlaps, meeting my restriction. Convergence and parallelisms are defined as two types of homoplasy: convergent homoplasies are largely constrained by external factors, while parallelisms are due to internal constraints. (shrink)

Stephen Jay Gould argued that replaying the “tape of life” would result in a radically different evolutionary outcome. Some biologists and philosophers, however, have pointed to convergent evolution as evidence for robust replicability in macroevolution. These authors interpret homoplasy, or the independent origination of similar biological forms, as evidence for the power of natural selection to guide form toward certain morphological attractors, notwithstanding the diversionary tendencies of drift and the constraints of phylogenetic inertia. In this paper, I consider (...) the implications of homoplasy for the debate over the nature of macroevolution. I argue that once the concepts of contingency and convergence are fleshed out, it becomes clear that many instances of homoplasy fail to negate Gould’s overarching thesis, and may in fact support a Gouldian view of life. My argument rests on the distinction between parallelism and convergence, which I defend against a recent challenge from developmental biology. I conclude that despite the difficulties in defining and identifying parallelism, the concept remains useful and relevant to the contingency controversy insofar as it underscores the common developmental origins of iterated evolution. (shrink)

In identifying intrinsic molecular chance and extrinsic adaptive pressures as the only causally relevant factors in the process of evolution, the theoretical perspective of the Modern Synthesis had a major impact on the perceived tenability of an ontology of dispositional properties. However, since the late 1970s, an increasing number of evolutionary biologists have challenged the descriptive and explanatory adequacy of this “chance alone, extrinsic only” understanding of evolutionary change. Because morphological studies of homology, convergence, and teratology have revealed a space (...) of possible forms and phylogenetic trajectories that is considerably more restricted than expected, evo-devo has focused on the causal contribution of intrinsic developmental processes to the course of evolution. Evo-devo’s investigation into the developmental structure of the modality of morphology – including both the possibility and impossibility of organismal form – has led to the utilisation of a number of dispositional concepts that emphasise the tendency of the evolutionary process to change along certain routes. In this sense, and in contrast to the perspective of the Modern Synthesis, evo-devo can be described as a “science of dispositions.” This chapter discusses the recent philosophical literature on dispositional properties in evo-devo, exploring debates about both the metaphysical and epistemological aspects of the central dispositional concepts utilised in contemporary evo-devo and addressing the epistemological question of how dispositional properties challenge existing explanatory models in evolutionary biology. (shrink)

Darwinists classify biological traits either by their ancestry (homology) or by their adaptive role. Only the latter can provide traditional natural kinds, but only the former is practicable. Process structuralists exploit this embarrassment to argue for non-Darwinian classifications in terms of underlying developmental mechanisms. This new taxonomy will also explain phylogenetic inertia and developmental constraint. I argue that Darwinian homologies are natural kinds despite having historical essences and being spatio-temporally restricted. Furthermore, process structuralist explanations of biological form require an (...) unwarranted assumption about the space of developmental possibility. (shrink)

Evolutionary epistemology has experienced a continuous rise over the last decades. Important new theoretical considerations and novel empirical findings have been integrated into the existing framework. In this paper, I would like to suggest three lines of research that I believe will significantly contribute to further advance EE: ontogenetic considerations, key ideas from cognitive biology, and the framework of the Extended Evolutionary Synthesis. EE, in particular the program of the evolution of epistemological mechanisms, seeks to provide a phylogenetic account (...) of the generation of cognitive processes underlying knowledge creation. Traditionally, EE and EEM have been oriented towards an account of evolutionary theory that mainly drew from the tenets of the Modern Synthesis. The Modern Synthesis largely dismisses ontogenetic processes and considers them irrelevant for evolutionary explanations. If anything, the role of development in evolution is believed to be that of a constraint. There is, however, ample evidence for a tight intertwinement of developmental and evolutionary processes. Organisms employ their cognitive apparatus to interact with the environment in order to achieve a fully functioning perceptual and cognitive nervous system. Also, ontogeny provides generative potentials to enable variations that natural selection can act upon. EEM’s agenda may, therefore, strongly benefit from bringing together ontogenetic and phylogenetic approaches. To grapple with this challenge, an alternative vision of the evolutionary theory termed Extended Evolutionary Synthesis could be used. This extended evolutionary theory explores relationships between the processes of individual development and phenotypic change during evolution and can provide a more suitable framework for EEM to draw from. In recent years, cognitive biology has gained momentum as an independent research field. Cognitive biology builds on the concepts of EEM and understands knowledge as a biogenic phenomenon. Its main objective is also the formulation of substantiated interrelations between cognition and evolution but it focuses on cognitive functionality at all levels of biological organization. It thus employs a “vertical” approach that encompasses nested hierarchies which span from single molecules, cells, and tissues to the organismal level, communities, and societies. In contrast to cognitive biology, EEM is here understood to adopt a “horizontal” approach that focuses on phylogenetic explanations of cognition and knowledge acquisition. Linking EEM with the key ideas of cognitive biology could make EEM’s research program stronger as it can more easily accommodate phylogenetic and ontogenetic questions within a hierarchical, multilevel perspective. This is of particular importance for a more comprehensive account of cognition since living systems are subject to context-dependent causal influences from different organizational levels. In addition to EEM, there is a second program of EE. This program has been labeled evolutionary epistemology of theories and understands the increase in human knowledge, such as scientific theories, as naturalistic accounts of evolution. Both, EEM and EET initially drew from the core concepts of the Modern Synthesis. Several scholars have severely criticized the analogies made between EET and the Neo-Darwinian key processes of evolution. In particular processes of random mutation, the rate of variation, natural selection as the unique driving force, and the adaptationist agenda are believed to reveal disanalogies. In contrast to the Modern Synthesis, the Extended Evolutionary Synthesis not only recognizes developmental processes but also ecological interactions and systems dynamics as well as social and cultural evolutionary reciprocity as important evolutionary processes. Concepts of the Extended Evolutionary Synthesis are therefore expected to be more fruitful for re-conceptualizing parallels between scientific theorizing and biological evolution. (shrink)

Cultural forms are constrained by cognitive biases, and writing is thought to have evolved to fit basic visual preferences, but little is known about the history and mechanisms of that evolution. Cognitive constraints have been documented for the topology of script features, but not for their orientation. Orientation anisotropy in human vision, as revealed by the oblique effect, suggests that cardinal orientations, being easier to process, should be overrepresented in letters. As this study of 116 scripts shows, the orientation (...) of strokes inside written characters massively favors cardinal directions, and it is organized in such a way as to make letter recognition easier: Cardinal and oblique strokes tend not to mix, and mirror symmetry is anisotropic, favoring vertical over horizontal symmetry. Phylogenetic analyses and recently invented scripts show that cultural evolution over the last three millennia cannot be the sole cause of these effects. (shrink)

In our target article, we discussed the standards of evidence that could be used to identify adaptations, and argued that building an empirical case that certain features of a trait are best explained by exaptation, spandrel, or constraint requires the consideration, testing, and rejection of adaptationist hypotheses. We are grateful to the 31 commentators for their thoughtful insights. They raised important issues, including the meaning of “exaptation”; whether Gould and Lewontin's critique of adaptationism was primarily epistemological or ontological; the necessity, (...) sufficiency, or utility of design evidence, phylogenetic analyses, homology, and molecular genetics in distinguishing exaptations from adaptations; whether adaptationists accept adaptationist hypotheses too quickly; and the real utility of adaptationism to human behavioral science. We organize our response along the major points of the target article, in some situations defending our original claims and in others modifying them. While debate on these issues will undoubtedly continue, we are cautiously optimistic that the main points of the target article (as modified by our response) will help move the debate in a positive direction. (shrink)

There is, of course, The Given: what is given in experience. The ‘Myth Of The Given’ is just a wrong answer to the question ‘What is given?’ This paper offers a brief sketch of three possible right answers. It examines an early account by Charles Augustus Strong of why The Myth is a myth. It maintains that a natural and naturalistic version of empiricism is compatible with the fact that the Myth is a myth. It gives proper place to enactivist (...) considerations. It is ) broadly in line with the Sellarsian view as refined by John McDowell. It meets an important constraint: acknowledging the reality of something that seems at first to lend support to The Myth—i.e. the fact that we can engage in ‘non-inferential self-attribution of … sensations’ —without in any way succumbing to the Myth. (shrink)

This book is divided in two parts, the first of which shows how, beyond paleontology and systematics, macroevolutionary theories apply key insights from ecology and biogeography, developmental biology, biophysics, molecular phylogenetics, and even the sociocultural sciences to explain evolution in deep time. In the second part, the phenomenon of macroevolution is examined with the help of real life-history case studies on the evolution of eukaryotic sex, the formation of anatomical form and body-plans, extinction and speciation events of marine invertebrates, hominin (...) evolution and species conservation ethics. The book brings together leading experts, who explain pivotal concepts such as Punctuated Equilibria, Stasis, Developmental Constraints, Adaptive Radiations, Habitat Tracking, Turnovers, (Mass) Extinctions, Species Sorting, Major Transitions, Trends, and Hierarchies – key premises that allow macroevolutionary epistemic frameworks to transcend microevolutionary theories that focus on genetic variation, selection, migration and fitness. Along the way, the contributing authors review ongoing debates and current scientific challenges; detail new and fascinating scientific tools and techniques that allow us to cross the classic borders between disciplines; demonstrate how their theories make it possible to extend the Modern Synthesis; present guidelines on how the macroevolutionary field could be further developed; and provide a rich view of just how it was that life evolved across time and space. In short, this book is a must-read for active scholars and, because the technical aspects are fully explained, it is also accessible for non-specialists. Understanding evolution requires a solid grasp of above-population phenomena. Species are real biological individuals, and abiotic factors impact the future course of evolution. Beyond observation, when the explanation of macroevolution is the goal, we need both evidence and theory that enable us to explain and interpret how life evolves at the grand scale. (shrink)

Complex vocal learning, the capacity to imitate new sounds, underpins the evolution of animal vocal cultures and song dialects and is a key prerequisite for human speech and song. Due to its relevance for the understanding of cultural evolution and the biology and evolution of language and music, the trait has gained much scholarly attention. However, while we have seen tremendous progress with respect to our understanding of its morphological, neurological and genetic aspects, its peculiar phylogenetic distribution has remained (...) elusive. Intriguingly, animals as distinct as hummingbirds and humpback whales share well-developed vocal learning capacity in common with humans, while this ability is quite limited in nonhuman primates. Yet, solving this ‘vocal learning conundrum’ may shed light on the constraints ancestral humans overcame to unleash their vocal capacities. To this end I consider major constraints and functions that have been proposed. I highlight an especially promising ecological constraint, namely the spatial dimensionality of the environment. Based on an informal comparative review, I suggest that complex vocal learning is associated with three-dimensional habitats such as air and water. I argue that this is consistent with recent theoretical advances—i.e., the coercion-avoidance and dimensionality hypotheses—and with the long-standing hypothesis that mate choice is a major driver of the evolution and origin of complex vocal learning. However, I stress that multiple functions may apply and that quantitative phylogenetic comparative methods should be employed to finally resolve the issue. (shrink)

Speech sounds are an essential vehicle of information exchange and meaning expression in approximately 7,000 spoken languages in the world. What functional constraints and evolutionary mechanisms lie behind linguistic diversity of sound systems is under ongoing debate; in particular, it remains conflicting whether there exists any universal relationship between these constraints despite of diverse sounds systems cross-linguistically. Here, we conducted cross-linguistic typological and phylogenetic analyses to address the characteristics of constraints on linguistic diversity of vowel systems. (...) First, the typological analysis revealed a power-law based dependence between the global structural dispersion and the local focalization of vowel systems and validated that such dependence was independent of geographic region, language family, and linguistic affiliation. Second, the phylogenetic analysis further illustrated that the observed dependence resulted from correlated evolutions of these two structural properties, which proceeded in an adaptive process. These results provide empirical evidence that self-organization mechanisms helped shape vowel systems and common functional constraints took effect on the evolution of vowel systems in the world’s languages. (shrink)

The present paper offers an approach to anticipation and meaning, based on Wild Systems Theory, which begins by describing organisms as self-sustaining energy transformation systems that constitute embodiments of context. This idea leads to the assertion that anticipation refers to a self-sustaining system’s ability to prespecify and constrain the dynamic possibilities of its nested transformation systems. The paper describes how anticipation, defined as the prospective constraint of context, evolved from the small-scale contexts constrained by a single cell to the full-blown, (...) self-aware prespecification and constraint of contexts exhibited in human anticipation. Specifically, anticipation scaled up because the systems that phylogenetically entailed it were simultaneous energy transformation systems whose status as such rendered them a possible energy source for potentially emergent energy transformation systems and as self-sustaining embodiments of context, such systems are naturally and necessarily “about” the contexts they embody. As a result, they are inherently meaningful, and the phenomenon we refer to as consciousness, or self-awareness, is a phylogenetically scaled-up recursion of the self-sustaining prespecification and constraint of nested, dynamic possibilities we see in single-cell organisms. (shrink)

In the genomics era, bioinformatic analysis, especially in non‐model species, facilitates the identification and naming of numerous new proteins, the function of which is then inferred through homology searches. Here, we question certain aspects of these approaches. What are the criteria that permit such a determination? What are their limits? Naming is classifying. We review the different criteria that are used to name a protein and discuss their constraints. We observe that the name given to a protein often introduces (...) a bias for further functional analyses, a bias that is not often taken into account when analysing results. Last but not least, the heterogeneity of criteria used for naming proteins leads to self‐inconsistent or contradictory protein classification that is potentially misleading. Finally, we recommend a wider use of phylogenetic criteria in protein naming. BioEssays 30:349–357, 2008. © 2008 Wiley Periodicals, Inc. (shrink)

The paper argues that the rich cognitive abilities of humans are the result of a unique functional system in the human brain which is absent in the nonhuman brain. This "frontal feedback system" is suggested to have evolved in the transition from the great apes to humans and is a product of a reversal in the preferred direction of information flow in the human cortex due to the phylogenetic enlargement of the human frontal lobe. The frontal feedback system forms (...) an autonomous functional unit in the cortex whereby action-schemes in frontal cortices continually create fictitious sensory scenarios in posterior sensory cortices by manipulating the release of sensory representations there. These internal scenarios are created free of environmental constraints and reflect the human's internal cognitive and language processes. Nonhumans do not have a frontal feedback system and their internal cognitive processes are stimulus-bound. Evidence in support of the proposal is presented and some implications of the frontal feedback model for human experience are discussed. (shrink)

In the eukaryotic cell, DNA compaction is achieved through its interaction with histones, constituting a nucleoprotein complex called chromatin. During metazoan evolution, the different structural and functional constraints imposed on the somatic and germinal cell lines led to a unique process of specialization of the sperm nuclear basic proteins (SNBPs) associated with chromatin in male germ cells. SNBPs encompass a heterogeneous group of proteins which, since their discovery in the nineteenth century, have been studied extensively in different organisms. However, (...) the origin and controversial mechanisms driving the evolution of this group of proteins has only recently started to be understood. Here, we analyze in detail the histone hypothesis for the vertical parallel evolution of SNBPs, involving a “vertical” transition from a histone to a protamine‐like and finally protamine types (H → PL → P), the last one of which is present in the sperm of organisms at the uppermost tips of the phylogenetic tree. In particular, the common ancestry shared by the protamine‐like (PL)‐ and protamine (P)‐types with histone H1 is discussed within the context of the diverse structural and functional constraints acting upon these proteins during bilaterian evolution. (shrink)

This book aims to "develop the idea that evolution is an axiomatic consequence of organismic information and cohesion systems obeying the second law of thermodynamics in a manner analogous to, but not identical with, the second law's usual application in physical and chemical systems." The authors "adhere to a particular methodological approach called phylogenetic systematics." They have "devoted most of their primary research efforts to discovering historical effects in developmental patterns." Finding that "such historical effects seem ubiquitous," they "began (...) to believe that these historical effects were constraints on the evolutionary process, suggesting the influence of a natural law of history.". (shrink)

Argues for the primacy of the phylogenetic system as the general reference system in biology. This book, first published in 1966, generated significant controversy and opened possibilities for evolutionary biology.

I respond to the bad lot argument in the context of biological systematics. The response relies on the historical nature of biological systematics and on the availability of pattern explanations. The basic assumption of common descent enables systematic methodology to naturally generate candidate explanatory hypotheses. However, systematists face a related challenge in the issue of character analysis. Character analysis is the central problem for contemporary systematics, yet the general problem of which it is a case—what counts as evidence?—has not been (...) adequately discussed by proponents of inference to the best explanation. Facing this problem is the price of adopting abductive methods. I sketch an account of how systematists approach the problem of evidence. (shrink)

An examination of the post-Darwinian history of biological taxonomy reveals an implicit assumption that the definitions of taxon names consist of lists of organismal traits. That assumption represents a failure to grant the concept of evolution a central role in taxonomy, and it causes conflicts between traditional methods of defining taxon names and evolutionary concepts of taxa. Phylogenetic definitions of taxon names (de Queiroz and Gauthier 1990) grant the concept of common ancestry a central role in the definitions of (...) taxon names and thus constitute an important step in the development of phylogenetic taxonomy. By treating phylogenetic relationships rather than organismal traits as necessary and sufficient properties, phylogenetic definitions remove conflicts between the definitions of taxon names and evolutionary concepts of taxa. The general method of definition represented by phylogenetic definitions of clade names can be applied to the names of other kinds of composite wholes, including populations and biological species. That the names of individuals (composite wholes) can be defined in terms of necessary and sufficient properties provides the foundation for a synthesis of seemingly incompatible positions held by contemporary individualists and essentialists concerning the nature of taxa and the definitions of taxon names. (shrink)

It is widely accepted that pictures can only depict visible things. The paper criticises this ‘visibility constraint’ on the objects of depiction. The constraint is shown to imply that the range of visibilia is settled prior to an investigation of what can be seen in pictures. By contrast to this, I suggest that settling what can be seen in pictures is relevant to settling the range of visibilia. It is what we experience in pictures, and not the objects of depiction, (...) that is subject to a visibility constraint, I propose. After criticising the widely accepted visibility constraint in the first half of the paper, I outline an account of what we experience in pictures in the second half of the paper. (shrink)

The long-awaited revision of the industry standard on phylogenetics Since the publication of the first edition of this landmark volume more than twenty-five years ago, phylogenetic systematics has taken its place as the dominant paradigm of systematic biology. It has profoundly influenced the way scientists study evolution, and has seen many theoretical and technical advances as the field has continued to grow. It goes almost without saying that the next twenty-five years of phylogenetic research will prove as fascinating (...) as the first, with many exciting developments yet to come. This new edition of Phylogenetics captures the very essence of this rapidly evolving discipline. Written for the practicing systematist and phylogeneticist, it addresses both the philosophical and technical issues of the field, as well as surveys general practices in taxonomy. Major sections of the book deal with the nature of species and higher taxa, homology and characters, trees and tree graphs, and biogeography—the purpose being to develop biologically relevant species, character, tree, and biogeographic concepts that can be applied fruitfully to phylogenetics. The book then turns its focus to phylogenetic trees, including an in-depth guide to tree-building algorithms. Additional coverage includes: Parsimony and parsimony analysis Parametric phylogenetics including maximum likelihood and Bayesian approaches Phylogenetic classification Critiques of evolutionary taxonomy, phenetics, and transformed cladistics Specimen selection, field collecting, and curating Systematic publication and the rules of nomenclature Providing a thorough synthesis of the field, this important update to Phylogenetics is essential for students and researchers in the areas of evolutionary biology, molecular evolution, genetics and evolutionary genetics, paleontology, physical anthropology, and zoology. (shrink)

An examination of the post-Darwinian history of biological taxonomy reveals an implicit assumption that the definitions of taxon names consist of lists of organismal traits. That assumption represents a failure to grant the concept of evolution a central role in taxonomy, and it causes conflicts between traditional methods of defining taxon names and evolutionary concepts of taxa. Phylogenetic definitions of taxon names (de Queiroz and Gauthier 1990) grant the concept of common ancestry a central role in the definitions of (...) taxon names and thus constitute an important step in the development of phylogenetic taxonomy. By treating phylogenetic relationships rather than organismal traits as necessary and sufficient properties, phylogenetic definitions remove conflicts between the definitions of taxon names and evolutionary concepts of taxa. The general method of definition represented by phylogenetic definitions of clade names can be applied to the names of other kinds of composite wholes, including populations and biological species. That the names of individuals (composite wholes) can be defined in terms of necessary and sufficient properties provides the foundation for a synthesis of seemingly incompatible positions held by contemporary individualists and essentialists concerning the nature of taxa and the definitions of taxon names. (shrink)

Our aim in this paper is to present the distinct ways in which Wolff, Baumgarten, and Kant understand the relationship between necessitation, constraint, and reluctant action in an effort to illustrate the subtle ways in which their conceptions of obligation differ from each another. Whereas Wolff conceives of natural or moral obligation as incompatible with constraint, Baumgarten holds that constraint and reluctant action are, in some instances, compatible with natural obligation. Kant departs from Baumgarten by conceiving of obligation as necessarily (...) involving constraint: as Kant’s reply to Schiller’s famous objection reveals, obligation must take on the character of constraint to reluctant action on account of the fact that human beings possess inclinations that always threaten to impel them in directions that oppose morality. (shrink)

According to the Generality Constraint, mental states with conceptual content must be capable of recombining in certain systematic ways. Drawing on empirical evidence from cognitive science, I argue that so-called analogue magnitude states violate this recombinability condition and thus have nonconceptual content. I further argue that this result has two significant consequences: it demonstrates that nonconceptual content seeps beyond perception and infiltrates cognition; and it shows that whether mental states have nonconceptual content is largely an empirical matter determined by the (...) structure of the neural representations underlying them. (shrink)

The concept of ‘phylogenetic inertia’ is routinely deployed in evolutionary biology as an alternative to natural selection for explaining the persistence of characteristics that appear sub-optimal from an adaptationist perspective. However, in many of these contexts the precise meaning of ‘phylogenetic inertia’ and its relationship to selection are far from clear. After tracing the history of the concept of ‘inertia’ in evolutionary biology, I argue that treating phylogenetic inertia and natural selection as alternative explanations is mistaken because (...) phylogenetic inertia is, from a Darwinian point of view, simply an expected effect of selection. Although Darwin did not discuss ‘phylogenetic inertia,’ he did assert the explanatory priority of selection over descent. An analysis of ‘phylogenetic inertia’ provides a perspective from which to assess Darwin’s view. (shrink)

Feinberg and Mallatt, in their presentation of neurobiological naturalism, have suggested that visual consciousness was acquired by early vertebrates and inherited by a wide range of descendants, and that its neural basis has shifted to nonhomologous nervous structures during evolution. However, their evolutionary scenario of visual consciousness relies on the assumption that visual consciousness is closely linked with survival, which is not commonly accepted in current consciousness research. We suggest an alternative idea that visual consciousness is linked to a specific (...) class of agency, consequently justifying their phylogenetic claim. We also examine the implication of their phylogenetic claim: visual consciousness is homologous across vertebrates, but its neural basis is not. This apparent incongruence illustrates a general phenomenon of homology, and that the resulting hierarchical view of visual consciousness and its neural basis can be straightforwardly accommodated by neurobiological naturalism. Throughout these discussions, we aim to address the potential theoretical issues in neurobiological naturalism and refine the picture illustrated by Feinberg and Mallatt regarding phylogenetic distribution and trajectories of visual consciousness. (shrink)

In this paper we propose a pragmatic approach to the evolution of language based on analysis of a particular element of human communication: discourse coherence. We show that coherence is essential for effective communication. Through analysis of a collection of neuropsychological and neurolinguistic studies, we maintain that the proper functioning of executive processes responsible for planning and executing actions plays a key role in the construction of coherent discourses. Studies that tested the discursive and conversational abilities of bonobos have showed (...) that apes are unable to construct a flow of discourse governed by coherence, and therefore, apes’ conversational interactions are quite different from those of humans. We then propose that the emergence of coherence in communication occurred after the split between great apes’ and humans’ lines of descendants and that this emergence might have been the result of a specific gradual development in the course of hominin evolution of the executive functions. (shrink)

This chapter contains sections titled: Introduction From Art to Science: An Introduction to Schools of Thought How to Infer Phylogeny, Or, Why Some Cladists Aren't “Cladists” Summary and Synthesis Acknowledgment References.

Phylogenetics has inherent utility in evolutionary developmental biology (EDB) as it is an established methodology for estimating evolutionary relationships and for making comparisons between levels of biological organization. However, explicit phylogenetic methods generally have been limited to two levels of organization in EDB—the species and the gene. We demonstrate that phylogenetic methods can be applied broadly to other organizational levels, such as morphological structures or cell types, to identify evolutionary patterns. We present examples at and between different hierarchical (...) levels of organization to address questions central to EDB. We argue that this application of “hierarchical phylogenetics” can be a unifying analytical approach to the field of EDB. BioEssays 27:1158–1166, 2005. © 2005 Wiley Periodicals, Inc. (shrink)

This chapter develops a subtle model that integrates environmental and internal factors. It describes the phylogenetic distribution of multicellular organisms in general and complex multicellular life in particular, clarifying the important distinction between the two. This chapter shows that the long apparent lag between the appearance of simple multicellularity in eukaryotes and the radiation of groups with complex multicellular organization has an environmental component that can be associated back to the consequences of life with interior and exterior cells. It (...) suggests that the evolutionary transition from unicells to complex multicellular organisms has several steps. (shrink)

The aptationist program includes attempts at sorting adaptations from exaptations, and therefore requires knowledge of historical changes in biological character states (traits) and their effects or functions, particularly for nonoptimal aptations. Phylogenetic inference is a key approach for historical aspects of evolutionary hypotheses, particularly testing evolutionary scenarios, and such “tree-thinking” investigation is directly relevant to the aptationist program.

Philosophers examining mechanistic explanations in biology have identified heuristic strategies scientists use in discovering mechanisms. This paper examines the heuristic strategy of investigating phylogenetically distant model organisms, using research on sleep in fruit flies as an example. At the time sleep was discovered in flies in 2000 next to nothing was known about mechanisms regulating sleep in flies and what they could reveal about those in us. One relatively straightforward line of research focused on homologous genes in flies and humans, (...) using those in flies to understand what roles their homologs played in controlling sleep in us. But other research focused on a higher level of organization—the neural networks involved in homeostatic and circadian control of sleep. This raises a puzzle—given that fly and vertebrate brains are organized very differently, how could sleep regulation in flies serve as an informative model of vertebrate sleep? I argue that the basic design of mechanisms such as those regulating sleep can be conserved even as the composition of the mechanism changes and that researchers can hope to use the designs deciphered in flies as heuristic models for understanding sleep in humans. (shrink)

The concept of ‘phylogenetic inertia’ is routinely deployed in evolutionary biology as an alternative to natural selection for explaining the persistence of characteristics that appear sub-optimal from an adaptationist perspective. However, in many of these contexts the precise meaning of ‘phylogenetic inertia’ and its relationship to selection are far from clear. After tracing the history of the concept of ‘inertia’ in evolutionary biology, I argue that treating phylogenetic inertia and natural selection as alternative explanations is mistaken because (...) phylogenetic inertia is, from a Darwinian point of view, simply an expected effect of selection. Although Darwin did not discuss ‘phylogenetic inertia,’ he did assert the explanatory priority of selection over descent. An analysis of ‘phylogenetic inertia’ provides a perspective from which to assess Darwin’s view. (shrink)

Cadherins are a multigene family of proteins which mediate homophilic calcium‐dependent cell adhesion and are thought to play an important role in morphogenesis by mediating specific intercellular adhesion. Different lines of experimental evidence have recently indicated that the site responsible for mediating adhesive interactions is localized to the first extracellular domain of cadherin. Based upon an analysis of the sequence of this domain, I show that cadherins can be classified into three groups with distinct structural features. Furthermore, using this sequence (...) information a phylogenetic tree relating the known cadherins was assembled. This is the first such tree to be published for the cadherins. One cadherin subtype, neural cadherin (N‐cadherin), shows very little sequence divergence between species, whereas all other cadherin subtypes show more substantial divergence, suggesting that selective pressure upon this domain may be greater for N‐cadherin than for other cadherins. Phylogenetic analysis also suggests that the gene duplications which established the main branches leading to the different cadherin subtypes occurred very early in their history. These duplications set the stage for the diversified superfamily we now observe. (shrink)