Understanding Evolutionary Trees

Charles Darwin sketched his first evolutionary tree in 1837, and trees have remained a central metaphor in evolutionary biology up to the present. Today, phylogenetics—the science of constructing and evaluating hypotheses about historical patterns of descent in the form of evolutionary trees—has become pervasive within and increasingly outside evolutionary biology. Fostering skills in “tree thinking” is therefore a critical component of biological education. Conversely, misconceptions about evolutionary trees can be very detrimental to one’s understanding of the patterns and processes that have occurred in the history of life. This paper provides a basic introduction to evolutionary trees, including some guidelines for how and how not to read them. Ten of the most common misconceptions about evolutionary trees and their implications for understanding evolution are addressed.

Amazon Forestry Tranformed: Integrating Knowledge for Smallholder Timber Managemet in Eastern Brazil

Recent discussions of local knowledge emphasize its dynamic nature invoking local peoples’ ability to effectively integrate traditional or local with science-based or “modern” knowledges. The smallholder timber industry of the Amazon’s estuarine floodplain provides an outstanding example of local patterns of resource management and economic activities transformed from within by smallholder farmers who participated in the industrial timber boom of the 1970s and 1980s. These farmers of eastern Amazonia have developed a vertically integrated local industry based on expertise reflecting profound locally developed knowledge of specific forests and management of ecological processes, individual observation and experimentation, as well as concepts and practices derived from temporary employment by large-scale industrial timber firms. At each stage of the smallholder forestry process—from managing natural regeneration to running small sawmills and marketing lumber—local managers apply an innovative set of practices reflecting their diverse experiences. This combination of technical, market, and ecological knowledge results in forests, timber markets, and economic patterns that do not correspond to many of the widely-held generalizations concerning either local or industrial tropical timber exploitation. This article uses data from 7 years of research in the Amazon floodplain.

Do Students See the “Selection” in Organic Evolution? A Critical Review of the Causal Structure of Student Explanations

This paper critically reviews and characterizes the student's causal-explanatory understanding; this is done as a step toward explicating the problematic of evolution education as it concerns the cognitive difficulties in understanding Darwin's theory of natural selection. The review concludes that the student's understanding is fundamentally different from Darwin's, for the student understands evolutionary change as necessary individual transformation caused by the transformative action of various physical and behavioral factors. This is in complete contrast to Darwin's (and even the Darwinian's, for that matter) understanding of evolutionary change as a change caused by accumulative selection. Hence, to understand natural selection, the student has to learn to “see” how the accumulative selection causes evolutionary change.

Assessing the fitness landscape revolution

According to Pigliucci and Kaplan, there is a revolution underway in how we understand fitness landscapes. Recent models suggest that a perennial problem in these landscapes—how to get from one peak across a fitness valley to another peak—is, in fact, non-existent. In this paper I assess the structure and the extent of Pigliucci and Kaplan’s proposed revolution and argue for two points. First, I provide an alternative interpretation of what underwrites this revolution, motivated by some recent work on model-based science. Second, I show that the implications of this revolution need to carefully assessed depending on question being asked, for peak-shifting is not central to all evolutionary questions that fitness landscapes have been used to explore.

Adaptationism and the adaptive landscape

Debates over adaptationism can be clarified and partially resolved by careful consideration of the ‘grain’ at which evolutionary processes are described. The framework of ‘adaptive landscapes’ can be used to illustrate and facilitate this investigation. We argue that natural selection may have special status at an intermediate grain of analysis of evolutionary processes. The cases of sickle-cell disease and genomic imprinting are used as case studies.

Teaching Evolution with Historical Narratives

This paper focuses on evolution as a unifying theme in biology education. Our aim is to argue that the different topics taught in secondary school biology classes should be enriched with and linked together by means of accounts of the history of life. We named this approach a “natural history perspective” on biology education. An essential aspect of the natural history perspective is the claim that evolutionary history forms the context for the development of an understanding of evolutionary processes. While there are some indications that a natural history perspective can function as a context for understanding micro-evolutionary processes, more research is called for.

Is it a revolution?

Jablonka and Lamb's claim that evolutionary biology is undergoing a ‘revolution’ is queried. But the very concept of revolutionary change has uncertain application to a field organized in the manner of contemporary biology. The explanatory primacy of sequence properties is also discussed.

Biological Levers and Extended Adaptationism

Two critiques of simple adaptationism are distinguished: anti-adaptationism and extended adaptationism. Adaptationists and anti-adaptationists share the presumption that an evolutionary explanation should identify the dominant simple cause of the evolutionary outcome to be explained. A consideration of extended-adaptationist models such as coevolution, niche construction and extended phenotypes reveals the inappropriateness of this presumption in explaining the evolution of certain important kinds of features—those that play particular roles in the regulation of organic processes, especially behavior. These biological or behavioral ‘levers’ are distinctively available for adaptation and exaptation by their possessors and for co-optation by other organisms. As a result they are likely to result from a distinctive and complex type of evolutionary process that conforms neither to simple adaptationist nor to anti-adaptationist styles of explanation. Many of the human features whose evolutionary explanation is most controversial belong to this category, including the female orgasm.

Hierarchies and the Sloshing Bucket: Toward the Unification of Evolutionary Biology

Evolutionary biology presents a bewildering array of phenomena to scientists and students alike—ranging from molecules to species and ecosystems; and embracing 3.8 billion years of life’s history on earth. Biological systems are arranged hierarchically, with smaller units forming the components of larger systems. The evolutionary hierarchy, based on replication of genetic information and reproduction, is a complex of genes/organisms/demes/species and higher taxa. The ecological hierarchy, based on patterns of matter–energy transfer, is a complex of proteins/organisms/avatars/local ecosystems/regional ecosystems. All organisms are simultaneously parts of both hierarchical systems. Darwin’s original formulation of natural selection maps smoothly onto a diagram where the two hierarchical systems are placed side-by-side. The “sloshing bucket” theory of evolution emerges from empirical cases in biological history mapped onto this dual hierarchy scheme: little phenotypically discernible evolution occurs with minor ecological disturbance; conversely, greatest concentrations of change in evolutionary history follow mass extinctions, themselves based on physical perturbations of global extent. Most evolution occurs in intermediate-level regional “turnovers,” when species extinction leads to rapid evolution of new species. Hierarchy theory provides a way of integrating all fields of evolutionary biology into an easily understood—and taught—rubric.

Objects limit human comprehension

This paper demonstrates that the human visual system, the primary sensory conduit for primates, processes ambient energy in a way that obligatorily constructs the objects that we ineluctably perceive. And since our perceptual apparatus processes information only in terms of objects (along with the properties and movements of objects), we are limited in our ability to comprehend ‘what is’ when we move beyond our ordinary world of midsize objects—as, for example, when we address the micro microworld of quantum physics.

Sexual selection and mate choice in evolutionary psychology

The importance of mate choice and sexual selection has been emphasized by the majority of evolutionary psychologists. This paper assesses three cases of work on mate choice and sexual selection in evolutionary psychology: David Buss on cross-cultural human mate preferences, Randy Thornhill and Steve Gangestad on the link between mate preferences and fluctuating asymmetry, and Geoffrey Miller on the role of Fisher’s runaway process in human evolution. A mixture of conceptual and empirical problems in each case highlights the general weakness of work in evolutionary psychology on these issues.

Understanding Natural Selection: Essential Concepts and Common Misconceptions

Natural selection is one of the central mechanisms of evolutionary change and is the process responsible for the evolution of adaptive features. Without a working knowledge of natural selection, it is impossible to understand how or why living things have come to exhibit their diversity and complexity. An understanding of natural selection also is becoming increasingly relevant in practical contexts, including medicine, agriculture, and resource management. Unfortunately, studies indicate that natural selection is generally very poorly understood, even among many individuals with postsecondary biological education. This paper provides an overview of the basic process of natural selection, discusses the extent and possible causes of misunderstandings of the process, and presents a review of the most common misconceptions that must be corrected before a functional understanding of natural selection and adaptive evolution can be achieved.

Embryos in evolution: evo-devo at the Naples Zoological Station in 1874

Eighteen seventy-four was a high point in evolutionary embryology. Thanks to Charles Darwin, the theory of evolution by natural selection provided a revolutionary new way of viewing the relationships and origins of organisms on Earth. Thanks to Ernst Haeckel, embryos were the way to study evolution (Haeckel in Generelle morphologie der organismen, vols 1, 2. Verlag Georg Reimer, Berlin, 1866)—it really was embryos in evolution—and recapitulation was in the air. Thanks to Anton Dohrn, a new research facility was on the ground, designed, located and structured to facilitate the study of embryos in evolution. Anton Dohrn devised, designed, financed, supervised the construction and then administered the Naples Zoological Station specifically so that researchers from all nations would have a facility where Darwin’s theory of evolution by natural selection could be tested. The zoologists who took advantage of the brand new facility within weeks of its opening late in 1873 established lines of research into evolutionary embryology, the field we now know as evolutionary developmental biology (evo-devo), the study of embryos in evolution. I examine the approach taken by Ambrosius Hubrecht, the first Dutch embryologist to undertake research at the station, and then evaluate the research of three British zoologists—E. Ray Lankester, Albert Dew-Smith, and Francis Maitland (Frank) Balfour. All four sought insights into origins, especially vertebrate origins that rested on comparative embryology, homology, germ layers, and a Darwinian approach to origins.

The rise and fall of the adaptive landscape?

The discussion of the adaptive landscape in the philosophical literature appears to be divided along the following lines. On the one hand, some claim that the adaptive landscape is either “uninterpretable” or incoherent. On the other hand, some argue that the adaptive landscape has been an important heuristic, or tool in the service of explaining, as well as proposing and testing hypotheses about evolutionary change. This paper attempts to reconcile these two views.

The Social Impacts of Nanotechnology: an Ethical and Political Analysis

This paper attempts some predictions about the social consequences of nanotechnology and the ethical issues they raise. I set out four features of nanotechnology that are likely to be important in determining its impact and argue that nanotechnology will have significant social impacts in—at least—the areas of health and medicine, the balance of power between citizens and governments, and the balance of power between citizens and corporations. More importantly, responding to the challenge of nanotechnology will require confronting “philosophical” questions about the sort of society we wish to create and the role that technology might play in creating it. This in turn will require developing institutions and processes that allow the public to wield real power in relation to technological trajectories. My ultimate contention is that the immediate task established by the likely social impacts of nanotechnology is not so much to develop an ethics of nanotechnology as to facilitate an ethical conversation about nanotechnology.

Contradictory results on the role of polarized light in compass calibration in migratory songbirds

Experiments with migrating birds on the interaction between magnetic and celestial cues have produced heterogeneous results. A recent study claimed that the magnetic compass in passerine migrants is calibrated by the pattern of polarized light at sunset and sunrise and that the area just above the horizon is crucial for this calibration. To test the latter hypothesis, we performed a similar experiment with Australian Silvereyes. It produced contrary results, however, the birds, in spite of observing the natural polarization pattern at sunrise and sunset down to the horizon in an altered magnetic field, continued in their normal southerly magnetic direction when subsequently tested in the local geomagnetic field—the conflict between magnetic and polarized light cues had not caused them to recalibrate their magnetic compass. This contradicts the assumption that skylight polarization patterns generally serve as a primary calibration reference for migratory songbirds.

Risk Management by Communal Decision in Trans-Himalayan Farming: Manang Valley in Central Nepal

It is generally assumed that peasants optimize security of food supply rather than maximize profit. One way of securing the survival of the household is to spread risk in farming by extending the planting and harvesting seasons in order to avoid all crops being damaged if unfavorable production conditions should occur. It thus seems peculiar that some Himalayan peasant communities act in the opposite manner by compressing peak agricultural activity into a minimum period, and furthermore that all cultivators simultaneously start planting and harvesting on dates fixed by the village headman in consultation with a lama (Buddhist priest). Rather than suggesting that any single explanation for this practice is the right one, however, this article contends that specific farming system cannot be understood properly unless a combination of subsystems — or facets — are included in the analyses.

Language processing with dynamic fields

We construct a mapping from complex recursive linguistic data structures to spherical wave functions using Smolensky’s filler/role bindings and tensor product representations. Syntactic language processing is then described by the transient evolution of these spherical patterns whose amplitudes are governed by nonlinear order parameter equations. Implications of the model in terms of brain wave dynamics are indicated. Electronic supplementary material  The online version of this article (doi: ) contains supplementary material, which is available to authorized users.