Biological Theory

Across the world people in different societies structure their family relationships in many different ways. These relationships become encoded in their languages as kinship terminology, a word set that maps variably onto a vast genealogical grid of kinship categories, each of which could in principle vary independently. But the observed diversity of kinship terminology is considerably smaller than the enormous theoretical design space. For the past century anthropologists have captured this variation in typological schemes with only a small number of model system types. Whether those types exhibit the internal co-selection of parts implicit in their use is an outstanding question, as is the sufficiency of typologies in capturing variation as a whole. We interrogate the coherence of classic kinship typologies using modern statistical approaches and systematic data from a new database, Kinbank. We first survey the canonical types and their assumed patterns of internal and external co-...

Pathology investigations are outlined in Table 1; liver function results shown represent the worst, recorded several days after admission. Chest X-ray was unremarkable on presentation. Serology for hepatitis A, B, C, toxoplasmosis, and recent cytomegalovirus ...

The study of biomechanics most often takes a classic adaptationist approach, examining the functional abilities of organisms in relation to what is allowed by physical parameters. This approach generally assumes strong selection and is less concerned with evolutionary stochasticity in determining the presence of biological traits. It is equally important, however, to consider the importance of constraint in determining the form of organisms. If selection is relatively weak compared to stochastic events, then the observed forms in living systems can be taken not as those shapes that were strongly selected for, so much as those forms that do not violate physical rules and therefore persist. Using the problem of maximum animal size as a case study for this alternative biomechanical philosophy, I demonstrate one example of how biomechanical approaches can be used to study constraint and consider the concept of absent forms. This alternative mindset and approach produces a complementary system to the traditional form and function approach in biomechanics. The two philosophies can be used in conjunction to better understand biological systems. I focus particularly on the maximum size of flying animals, as they are a heavily constrained class of system that has also been shaped by substantial stochasticity.

Understanding religion requires explaining why supernatural beliefs, devotions, and rituals are both universal and variable across cultures, and why religion is so often associated with both large-scale cooperation and enduring group conflict. Emerging lines of research suggest that these oppositions result from the convergence of three processes. First, the interaction of certain reliably developing cognitive processes, such as our ability to infer the presence of intentional agents, favors-as an evolutionary by-product-the spread of certain kinds of counterintuitive concepts. Second, participation in rituals and devotions involving costly displays exploits various aspects of our evolved psychology to deepen people's commitment to both supernatural agents and religious communities. Third, competition among societies and organizations with different faith-based beliefs and practices has increasingly connected religion with both within-group prosociality and between-group enmity. This connection has strengthened dramatically in recent millennia, as part of the evolution of complex societies, and is important to understanding cooperation and conflict in today's world.

The phenomenon of altruism extends from the biological realm to the human sociocultural realm. This article sketches a coherent outline of multiple types of altruism of progressively increasing scope that span these two realms and are grounded in an ever-expanding sense of ''self.'' Discussion of this framework notes difficulties associated with altruism at different levels. It links scientific ideas about the evolution of cooperation and about hierarchical order to perennial philosophical and religious concerns. It offers a conceptual background for inquiry into societal challenges that call for altruistic behavior, especially the challenge of environmental and social sustainability.

Niche construction is the process whereby organisms, through their activities and choices, modify their own and each other's niches. By transforming naturalselection pressures, niche construction generates feedback in evolution at various different levels. Niche-constructing species play important ecological roles by creating habitats and resources used by other species and thereby affecting the flow of energy and matter through ecosystems-a process often referred to as ''ecosystem engineering.'' An important emphasis of niche construction theory (NCT) is that acquired characters play an evolutionary role through transforming selective environments. This is particularly relevant to human evolution, where our species has engaged in extensive environmental modification through cultural practices. Humans can construct developmental environments that feed back to affect how individuals learn and develop and the diseases to which they are exposed. Here we provide an introduction to NCT and illustrate some of its more important implications for the human sciences.

Recent advances in genetics and neurobiology have greatly increased the degree of variation that one finds in what is taken to provide the biological foundations of our species-specific linguistic capacities. In particular, this variation seems to cast doubt on the purportedly homogeneous nature of the language faculty traditionally captured by the concept of ''Universal Grammar.'' In this article we discuss what this new source of diversity reveals about the biological reality underlying Universal Grammar. Our discussion leads us to support (1) certain hypotheses advanced in evolutionary developmental biology that argue for the existence of robust biological mechanisms capable of canalizing variation at different levels, and (2) a bottom-up perspective on comparative cognition. We conclude by sketching future directions for what we call ''comparative biolinguistics,'' specifying which experimental directions may help us succeed in this new research avenue.

Regeneration capabilities are found in most or all animals. Whether regeneration is part of the development of an animal or a distinct phenomenon independent of development is a debatable question. If we consider regeneration as a process belonging to development, similarly to embryogenesis or metamorphosis, the existence of regenerative capabilities in adults can be seen as an argument in favor of the theory that development continues throughout the life of animals. Here I perform a comparative analysis of regeneration versus ''classical'' developmental processes in animals in order to determine to what extent these processes are inclusive or distinct. I identify the existence of regeneration-specific processes, i.e., processes that occur during the regeneration, but not the initial development, of a given structure. In addition, I find that seemingly similar processes acting during development and regeneration may have differential molecular and cellular bases. I thus conclude that there are significant differences between regeneration processes in adult animals and developmental processes occurring during earlier phases of the life cycle. The existence of regenerative capabilities in adult animals can therefore not be used as an argument in favor of the idea that development spans the whole life.

Using the context of controversies surrounding evolutionary developmental biology (EvoDevo) and the possibility of an Extended Evolutionary Synthesis, I provide an account of theory structure as idealized theory presentations that are always incomplete (partial) and shaped by their conceptual content (material rather than formal organization). These two characteristics are salient because the goals that organize and regulate scientific practice, including the activity of using a theory, are heterogeneous. This means that the same theory can be structured differently, in part because theory presentations (as idealizations) intentionally depart from different features known to be present in a theory. Since there are diverse and potentially Love, A.C. (in press) "Theory is as theory does: scientific practice and theory structure in biology", Biological Theory.

We discuss the evolutionary transition from animals with limited experiencing to animals with unlimited experiencing and basic consciousness. This transition was, we suggest, intimately linked with the evolution of associative learning and with flexible reward systems based on, and modifiable by, learning. During associative learning, new pathways relating stimuli and effects are formed within a highly integrated and continuously active nervous system. We argue that the memory traces left by such new stimulus-effect relations form dynamic, flexible, and varied global sensory states, which we call categorizing sensory states (CSSs). These CSSs acquired a function: they came to act as internal "evaluators" and led to positive and negative reinforcement of new behavior. They are therefore the simplest, distinct, first-person motivational states that an animal can have. They constitute what we call basic consciousness, and are the hallmark of animals that can experience. Since associative learning has been found in many invertebrate taxa that first appeared during the Cambrian era, we propose that the processes underlying basic consciousness are phylogenetically ancient, and that their emergence may have fueled the Cambrian explosion.

This is the first of two papers in which we propose an evolutionary route for the transition from sensory processing to unlimited experiencing, or basic consciousness. We argue that although an evolutionary analysis does not provide a formal definition and set of sufficient conditions for consciousness, it can identify crucial factors and suggest what evolutionary changes enabled the transition. We believe that the raw material from which feelings were molded by natural selection was a global sensory state that we call overall sensation, which is a by-product of the incessant activity of the highly interconnected nervous systems that characterize all neural animals. We argue that global sensory states generated limited experiencing once they became coupled to the simplest kinds of nervous-system-mediated learning, a coupling that occurred in the most ancient taxa of neural animals, which were similar to present-day cnidarians and ctenophores. In such animals, limited experiencing involves a small number of persistent global sensory states. These sensory states, however, do not have a function and do not act as motivational states. As we argue in the next paper, with the evolution of associative learning they evolved into systems that gave animals basic consciousness.

Efforts have been dedicated to the understanding of social-ecological systems, an important focus in ethnobiological studies. In particular, ethnobiological investigations have found evidence and tested hypotheses over the last 30 years on the interactions between human groups and their environments, generating the need to formulate a theory for such systems. In this article, we propose the social-ecological theory of maximization to explain the construction and functioning of these systems over time, encompassing hypotheses and evidence from previous ethnobiological studies. In proposing the theory, we present definitions and two conceptual models, an environmental maximization model and a redundancy generation model. The first model seeks to address biota selection and its use by human populations. The second emphasizes how the system organizes itself from the elements that were incorporated into it. Furthermore, we provide the theoretical scenario of plant selection and use from an evolutionary perspective, which explicitly integrates the phylogenetic relationships of plants (or other living resources) and human beings.

The general concept of information does not belong in the category of universal and inexorable physical laws but in the category of initial conditions and boundary conditions. Boundaryconditions formed by local structures are often called constraints. Informational structures suchas symbol vehicles are a special type of constraint. It should be clear that the concepts of initialconditions and constraints in physics make no sense outside the context of the law-based physical dynamics to which they apply. This is also the case for the concept of information

Darwin provided us with a powerful theoretical framework to explain the evolution of living systems. Natural selection alone, however, has sometimes been seen as insufficient to explain the emergence of new levels of selection. The problem is one of "circularity" for evolutionary explanations: how to explain the origins of Darwinian properties without already invoking their presence at the level they emerge. That is, how does evolution by natural selection commence in the first place? Recent results in experimental evolution suggest a way forward: Paul Rainey and his collaborators have shown that Darwinian properties could be exogenously imposed via what they call "ecological scaffolding." This could solve the "black box" dilemma faced by Darwinian explanations of new levels of organization. Yet, despite "scaffolding" recently becoming a popular term in the study of cognition, culture, and evolution, the concept has suffered from vagueness and ambiguity. This article aims to show that scaffolding can be turned into a proper scientific concept able to do explanatory work within the context of the major evolutionary transitions. Doing so will allow us to once again extend the scope of the Darwinian model of evolution by natural selection.

These three chapters from the "Tournament" Section of my book City, Marriage, Tournament outline a psychoanalytic/ phenomenological approach to historical narratives about tournaments, focusing on James IV of Scotland's display of sovereignty in his Tournament of the Wild Knight and the Black Lady (1507/1508).

E. O. Wilson (1974: 54) describes the problem that social organisms pose: “On what bases do we distinguish the extremely modified members of an invertebrate colony from the organs of a metazoan animal?” This framing of the issue has inspired many to look more closely at how groups of organisms form and behave as emergent individuals. The possible existence of “superorganisms” test our best intuitions about what can count and act as genuine biological individuals and how we should study them. As we will discuss, colonies of certain organisms display many of the properties that we usually reserve only to individual organisms. Although there is good reason to believe that many social insects form genuine emergent biological individuals, the conclusion offered here is of a slightly different sort. I will argue that to understand some social insects' interactions and the emergent traits they give rise to, it may be helpful to shift our understanding from a community-level approach to an ecosystem-level approach. I will argue that viewing certain insect colonies (termites) as parts of ecosystems allows us to better understand some of the adaptations that have emerged from their evolution.

We are grateful to the commentators for taking the time to respond to our article. Too many interesting and important points have been raised for us to tackle them all in this response, and so in the below we have sought to draw out the major themes. These include problems with both the term 'ultimate causation' and the proximate-ultimate causation dichotomy more generally, clarification of the meaning of reciprocal causation, discussion of issues related to the nature of development and phenotypic plasticity and their roles in evolution, and consideration of the need for an extended evolutionary synthesis.

Understanding how neurons represent, process, and manipulate information is one of the main goals of neuroscience. These issues are fundamentally abstract, and information theory plays a key role in formalizing and addressing them. However, application of information theory to experimental data is fraught with many challenges. Meeting these challenges has led to a variety of innovative analytical techniques, with complementary domains of applicability, assumptions, and goals.

What role does non-genetic inheritance play in evolution? In recent work we have independently and collectively argued that the existence and scope of non-genetic inheritance systems, including epigenetic inheritance, niche construction/ecological inheritance, and cultural inheritance-alongside certain other theory revisions-necessitates an extension to the neo-Darwinian Modern Synthesis (MS) in the form of an Extended Evolutionary Synthesis (EES). However, this argument has been challenged on the grounds that non-genetic inheritance systems are exclusively proximate mechanisms that serve the ultimate function of calibrating organisms to stochastic environments. In this paper we defend our claims, pointing out that critics of the EES (1) conflate non-genetic inheritance with early 20th-century notions of soft inheritance; (2) misunderstand the nature of the EES in relation to the MS; (3) confuse individual phenotypic plasticity with trans-generational non-genetic inheritance; (4) fail to address the extensive theoretical and empirical literature which shows that non-genetic inheritance can generate novel targets for selection, create new genetic equilibria that would not exist in the absence of nongenetic inheritance, and generate phenotypic variation that is independent of genetic variation; (5) artificially limit ultimate explanations for traits to gene-based selection, which is unsatisfactory for phenotypic traits that originate and spread via non-genetic inheritance systems; and (6) fail to provide an explanation for biological organization. We

In 1958, Francis Crick distinguished the flow of information from the flow of matter and the flow of energy in the mechanism of protein synthesis. Crick's claims about information flow and coding in molecular biology are viewed from the perspective of a new characterization of mechanisms (Machamer, Darden, and Craver 2000) and from the perspective of information as holding a key to distinguishing work in molecular biology from that of biochemistry in the 1950s-1970s (Darden and Craver 2002). Flow of matter from beginning to end does not occur in the protein synthesis mechanism; flow of information (from Crick's perspective) does. The flow of information and coding in molecular biological mechanisms are distinguished, on the one hand, from formal information theory, and, on the other, from information as used in cognitive neuroscience, where information and representation are often coupled.

A simple molecular system ("autocell") is described consisting of the reciprocal linkage between an autocatalytic cycle and a self-assembling encapsulation process where the molecular constituents for the capsule are products of the autocatalysis. In a molecular environment sufficiently rich in the substrates, capsule growth will also occur with high predictability. Growth to closure will be most probable in the vicinity of the most prolific autocatalysis and will thus tend to spontaneously enclose supportive catalysts within the capsule interior. If subsequently disrupted in the presence of new substrates, the released components will initiate production of additional catalytic and capsule components that will spontaneously re-assemble into one or more autocell replicas, thereby reconstituting and sometimes reproducing the original. In a diverse molecular environment, cycles of disruption and enclosure will cause autocells to incidentally encapsulate other molecules as well as reactive substrates. To the extent that any captured molecule can be incorporated into the autocatalytic process by virtue of structural degeneracy of the catalytic binding sites, the altered autocell will incorporate the new type of component into subsequent replications. Such altered autocells will be progenitors of "lineages" with variant characteristics that will differentially propagate with respect to the availability of commonly required substrates. Autocells are susceptible to a limited form of evolution, capable of leading to more efficient, more environmentally fitted, and more complex forms. This provides a simple demonstration of the plausibility of openended reproduction and evolvability without self-replicating template molecules (e.g., nucleic acids) or maintenance of persistent nonequilibrium chemistry. This model identifies an intermediate domain between prebiotic and biotic systems and bridges the gap from nonequilibrium thermodynamics to life.

The evolution and maintenance of cooperation in human and animal societies challenge various disciplines ranging from evolutionary biology to anthropology, social sciences, and economics. In social interactions, cooperators increase the welfare of the group at some cost to themselves whereas defectors attempt to free ride and neither provide benefits nor incur costs. The problem of cooperation becomes even more pronounced when increasing the number of interacting individuals. Punishment and voluntary participation have been identified as possible factors to support cooperation and prevent cheating. Typically, punishment behavior is unable to gain a foothold in a population, while volunteering alone can efficiently prevent deadlocks in states of mutual defection but is unable to stabilize cooperation. The combined effects of the two mechanisms have surprisingly different consequences in finite and infinite populations. Here we provide a detailed comparison of the two scenarios and demonstrate that driven by the inherent stochasticity of finite populations, the possibility to abstain from social interactions plays a pivotal role, which paves the way for the establishment of cooperation and punishment.

According to Varmuza (2003: 963), Classical neo-Darwinian theory is predicated on the notion that all heritable phenotypic change is mediated by alterations of the DNA sequence in genomes. However, evidence is accumulating that stably heritable phenotypes can also have an epigenetic basis, lending support to the long-discarded notion of inheritance of acquired traits.

A partial review of Thomas Nagel's book, Mind and Cosmos: Why the Materialist Neo-Darwinian Conception of Nature Is Almost Certainly False is used to articulate some systems-theoretic ideas about the challenge of understanding subjective experience. The article accepts Nagel's view that reductionist materialism fails as an approach to this challenge, but argues that seeking an explanation of mind based on emergence is more plausible than seeking one based on panpsychism, which Nagel favors. However, the article proposes something similar to Nagel's neutral monism by positing a hierarchy of information processes that spans the domains of matter, life, and mind. As depicted in this hierarchy, subjective experience is emergent, but also continuous with informational phenomena at lower levels.

We are grateful to the commentators for taking the time to respond to our article. Too many interesting and important points have been raised for us to tackle them all in this response, and so in the below we have sought to draw out the major themes. These include problems with both the term 'ultimate causation' and the proximate-ultimate causation dichotomy more generally, clarification of the meaning of reciprocal causation, discussion of issues related to the nature of development and phenotypic plasticity and their roles in evolution, and consideration of the need for an extended evolutionary synthesis.

Developmental Systems Theory (DST) is a theoretical reinterpretation of biological phenomena that challenges the conventional gene-centered account of development and evolution. In this article, I focus on Griffiths and Gray's version of DST and particularly analyze their reconceptualization of inheritance. First, I present their concept of expanded and diffused inheritance; then, I examine and criticize their rejection of the multiple inheritance system model; finally, I present and oppose Griffiths and Gray's extension of what they call the "causal parity thesis" from development to evolution. I argue that their proposal is an interesting and programmatic philosophical perspective on biological phenomena but fails to provide either additional heuristic tools for empirical investigation in biology or a more realistic representation of the biological world.

It is widely thought that causal cognition underpins technical reasoning. Here we suggest that understanding causal cognition as a thinking system that includes theory of mind (i.e., social cognition) can be a productive theoretical tool for the field of evolutionary cognitive archaeology. With this contribution, we expand on an earlier model that distinguishes seven grades of causal cognition, explicitly presenting it together with a new analysis of the theory of mind involved in the different grades. We then suggest how such thinking may manifest in the archaeological or stone tool record and techno-behaviors of the last three million years or so. Our thesis is threefold: (a) theory of mind is an integral element of causal cognition; (b) generally speaking, the more advanced causal cognition is, the more it is dependent on theory of mind; and (c) the evolution of causal cognition depends more and more on mental representations of hidden variables. Ultimately, the final or seventh ...

Current debates about "Darwinizing culture" have typically focused on the validity of memetics. In this paper we argue that meme-like inheritance is not a necessary requirement for descent with modification. We suggest that an alternative and more productive way of Darwinizing culture can be found in the application of phylogenetic methods. We review recent work on cultural phylogenetics and outline six fundamental questions that can be answered using the power and precision of quantitative phylogenetic methods. However, cultural evolution, like biological evolution, is often far from tree-like. We discuss the problems reticulate evolution can cause for phylogenetic analyses and suggest ways in which these problems can be overcome. Our solutions involve a combination of new methods for the study of cultural evolution (network construction, reconciliation analysis, and Bayesian mixture models), and the triangulation of different lines of historical evidence. Throughout we emphasize that most debates about cultural phylogenies can only be settled by empirical research rather than armchair speculation.

I present a general theory for the initial domestication of plants and animals that is based on niche construction theory and incorporates several behavioral ecological concepts, including central-place provisioning, resource catchment, resource ownership and defensibility, and traditional ecological knowledge. This theory provides an alternative to, and replacement for, current explanations, including diet breadth models of optimal foraging theory, that are based on an outmoded concept of asymmetrical adaptation and that attempt to explain domestication as an adaptive response to resource imbalance resulting from either environmental decline or human population growth. The small-scale human societies that first domesticated plants and animals share a number of basic interrelated attributes that when considered as an integrated and coherent set of behaviors provide the context for explaining initial domestication not as an adaptive response to an adverse environmental shift or to human population growth or packing but rather as the result of deliberate human enhancement of resource-rich environments in situations where evidence of resource imbalance is absent. Keywords Agriculture Á Domestication Á Ecosystem engineering Á Niche construction The initial domestication of plants and animals and the subsequent development of agricultural economies mark a major evolutionary transition in earth's history. Small-scale human societies in perhaps as many as a dozen separate world areas independently brought a wide variety of different species under domestication between about 11,000 and 5,000 years ago, and these domesticates provided the lever with which we have transformed much of the earth into agricultural landscapes that feed an ever increasing global population. Over the past several decades, biologists and archaeologists working with different data sets at different scales of analysis, and from a number of complementary perspectives, have employed a range of new techniques that have substantially improved our understanding of many different aspects of the initial domestication of plants and animals (e.g., Doebley et al. 2006; Zeder et al. 2006; Bar-Yosef and Price 2011; Gepts and Famula 2012). Although there is considerable variation in the quality and quantity of information that is currently available from the different independent centers of domestication, these regions provide an excellent opportunity for comparative analysis in terms of the sequence, timing, and rate of domestication of different species as well as the environmental and cultural contexts within which domestication occurred. It is also at the regional scale of analysis that the most interesting and challenging developmental questions can be most successfully addressed, and where most researchers focus their efforts (Zeder and Smith 2009). Along with rapid, if variable, advances in our understanding of the domestication process in different world areas at a regional scale of analysis, there is also a continuing strong interest in formulating and refining overarching models and theories that can help to illuminate the underlying similarities of the domestication process on a global scale. The vast majority of the universal explanations for initial domestication and agricultural origins that have been proposed over the past half century, however, including,

Radiation science is dominated by a paradigm based on an assumption without empirical foundation. Known as the linear no-threshold (LNT) hypothesis, it holds that all ionizing radiation is harmful no matter how low the dose or dose rate. Epidemiological studies that claim to confirm LNT either neglect experimental and/or observational discoveries at the cellular, tissue, and organismal levels, or mention them only to distort or dismiss them. The appearance of validity in these studies rests on circular reasoning, cherry picking, faulty experimental design, and/or misleading inferences from weak statistical evidence. In contrast, studies based on biological discoveries demonstrate the reality of hormesis: the stimulation of biological responses that defend the organism against damage from environmental agents. Normal metabolic processes are far more damaging than all but the most extreme exposures to radiation. However, evolution has provided all extant plants and animals with defenses that repair such damage or remove the damaged cells, conferring on the organism even greater ability to defend against subsequent damage. Editors of medical journals now admit that perhaps half of the scientific literature may be untrue. Radiation science falls into that category. Belief in LNT informs the practice of radiology, radiation regulatory policies, and popular culture through the media. The result is mass radiophobia and harmful outcomes, including forced relocations of populations near nuclear power plant accidents, reluctance to avail oneself of needed medical imaging studies, and aversion to nuclear energy-all unwarranted and all harmful to millions of people.

In the study reported here we examined the
impact of population size and two proxies of risk of
resource failure on the diversity and complexity of the
food-getting toolkits of hunter–gatherers and small-scale
food producers. We tested three hypotheses: the risk
hypothesis, the population-size hypothesis, and a hypothesis
derived from niche construction theory. Our analyses
indicated that the toolkits of hunter–gatherers are more
affected by risk than are the toolkits of food producers.
They also showed that the toolkits of food producers are
more affected by population size than are the toolkits of
hunter–gatherers. This pattern is inconsistent with the
predictions of both the risk hypothesis and the populationsize
hypothesis. In contrast, it is consistent with the predictions
of the niche construction hypothesis. Our results
indicate that niche construction has affected the evolution
of technology in small-scale societies and imply that niche
construction must be taken into account when seeking to
understand technological variation among food producers
and the technological changes that occurred in association
with the various transitions to farming that have occurred
over the last 10,000 years.