Curious parallels and curious connections--phylogenetic thinking in biology and historical linguistics

In The Descent of Man (1871), Darwin observed "curious parallels" between the processes of biological and linguistic evolution. These parallels mean that evolutionary biologists and historical linguists seek answers to similar questions and face similar problems. As a result, the theory and methodology of the two disciplines have evolved in remarkably similar ways. In addition to Darwin's curious parallels of process, there are a number of equally curious parallels and connections between the development of methods in biology and historical linguistics. Here we briefly review the parallels between biological and linguistic evolution and contrast the historical development of phylogenetic methods in the two disciplines. We then look at a number of recent studies that have applied phylogenetic methods to language data and outline some current problems shared by the two fields.     

Making environmental DNA count

The arc of reception for a new technology or method – like the reception of new information itself – can pass through predictable stages, with audiences’ responses evolving from ‘I don't believe it’, through ‘well, maybe’ to ‘yes, everyone knows that’ to, finally, ‘old news’. The idea that one can sample a volume of water, sequence DNA out of it, and report what species are living nearby has experienced roughly this series of responses among biologists, beginning with the microbial biologists who developed genetic techniques to reveal the unseen microbiome. ‘Macrobial’ biologists and ecologists – those accustomed to dealing with species they can see and count – have been slower to adopt such molecular survey techniques, in part because of the uncertain relationship between the number of recovered DNA sequences and the abundance of whole organisms in the sampled environment. In this issue of Molecular Ecology Resources, Evans et al. ( 2015 ) quantify this relationship for a suite of nine vertebrate species consisting of eight fish and one amphibian. Having detected all of the species present with a molecular toolbox of six primer sets, they consistently find DNA abundances are associated with species’ biomasses. The strength and slope of this association vary for each species and each primer set – further evidence that there is no universal parameter linking recovered DNA to species abundance – but Evans and colleagues take a significant step towards being able to answer the next question audiences tend to ask: ‘Yes, but how many are there?’     

Situational Designations in "Glossoethnographic" Perspective

Soviet and foreign linguists and educators continually stress the importance of studying a foreign language within its cultural context. Accordingly, a new field of applied linguistics has emerged, at the borderline between linguistics and foreign language instruction, that we have termed "glossoethnography" [see 1, 2, 4, 61. This new area of linguistics has not yet sufficiently delimited i t s subject matter: it abuts on other areas that are also relatively new and as yet ill defined, such as sociolinguistics, ethnolinguistics, linguistic anthropology, linguistic typology (for the various definitions of these disciplines, see reference 7). The many interesting examples adduced in studies in this new area all deal with specific national features of linguistic means of expression (sometimes in combination with paralinguistic means). However, these specific features exist on different levels: there are the specific features of the real objects expressed in language, and then there are those of the linguistic forms themselves, which are independent of the properties of the real objects to which they refer.     

Mayan Language Revival and Revitalization Politics: Linguists and Linguistic Ideologies

Although spoken by a relatively large population, Mayan languages show signs of language shift and loss because the children in some of the speech communities are no longer learning the language. At the same time, Mayas are participating in a movement of cultural reaffirmation, a principle focus of which is language. Maya linguists are central in formulating and reshaping language ideologies to further the goals of revitalization, and they play a significant role in cultural/linguistic activism. This article shows the extent of the contribution of linguistics to Mayan language vitality through an analysis of language ideologies and how they have been reformulated by Maya linguists, and by a review of an apparently successful attempt at reversing language loss that has arisen through an integrated community-based program of cultural revitalization that centers, to a large extent, on language and makes specific use of linguistics. [Keywords: language shift, language ideologies, language revitalization, Mayan languages, Maya movement]     

Human cumulative culture: a comparative perspective

Many animals exhibit social learning and behavioural traditions, but human culture exhibits unparalleled complexity and diversity, and is unambiguously cumulative in character. These similarities and differences have spawned a debate over whether animal traditions and human culture are reliant on homologous or analogous psychological processes. Human cumulative culture combines high‐fidelity transmission of cultural knowledge with beneficial modifications to generate a ‘ratcheting’ in technological complexity, leading to the development of traits far more complex than one individual could invent alone. Claims have been made for cumulative culture in several species of animals, including chimpanzees, orangutans and New Caledonian crows, but these remain contentious. Whilst initial work on the topic of cumulative culture was largely theoretical, employing mathematical methods developed by population biologists, in recent years researchers from a wide range of disciplines, including psychology, biology, economics, biological anthropology, linguistics and archaeology, have turned their attention to the experimental investigation of cumulative culture. We review this literature, highlighting advances made in understanding the underlying processes of cumulative culture and emphasising areas of agreement and disagreement amongst investigators in separate fields.     

‘Arctic Crashes:’ Revisiting the Human-Animal Disequilibrium Model in a Time of Rapid Change

The paper introduces a new vision advanced by the recent project, Arctic People and Animal Crashes: Human, Climate and Habitat Agency in the Anthropocene (2014–2015) developed at the Smithsonian Institution. Unlike earlier top-down models of polar animal-climate-people connections that tied changes in Arctic species’ abundance and ranges to alternating warmer and cooler temperatures or high ice/low sea-ice regimes, rapid animal declines (‘crashes’) may be better approached at regional and local scales. This approach is close to Arctic peoples’ traditional vision that animals, like people, live in ‘tribes’ and that they ‘come and go’ according to their relations with the local human societies. As the Arctic changes rapidly and climate/sea-ice/ecotone boundaries shift, we see diverse responses by Arctic people and animals to environmental stressors. I examine recent data on the status of three northern mammal species – caribou/reindeer, Pacific walrus, and polar bear—during two decades of the ongoing Arctic warming. The emerging record may be best approached as a series of local human-animal disequilibria interpreted from different angles by population biologists, indigenous peoples, and anthropologists, rather than a top-down climate-induced ‘crash.’ Such new understanding implies the varying speed of change in the physical, animal, and human domains, which was not factored in the earlier models of climate–animal–people’s interactions.     

On the Concept of Code in Linguistics and Biosemiotics

Biosemioticians use language and linguistic concepts as a window onto phenomena and processes on all levels of life. Like most biologists, some biosemioticians use language and linguistic concepts as metaphors for phenomena and processes on the cellular level. Even mainstream biologists may be aware that with concepts like code, information or communication on the level of the cell, they are anthropomorphizing the living things they study. The paradox of linguistics is that the object of study is at the same time the cognitive tool for its analysis. Like everyone else, biologists depend on the species-specific cognitive tool of language to study the laws and phenomena of all kinds of living organisms. Biosemioticians face both paradoxes and the challenge of mediating between the terminologies of the disciplines they navigate. At the 11^th Gatherings in Biosemiotics in New York, several papers commented on inadequate concepts in the field of linguistics and the failure of the discipline of linguistics as a whole. In this paper, I comment on some of the claims that were made specifically about the distinctive feature and the notion of code in linguistics.     

Life With or Without Names

The terms ‘life’, ‘species’ and ‘individuals’ are key concepts in biology. However, theoretical and practical concerns are directly associated with definitions of these terms and their use in researchers’ work. Although the practical implications of employing definition of ‘species’ and ‘individuals’ are often clear, it is surprising how most biologists work in their field of study without adhering to a specific definition of life. In everyday scientific practice, biologists rarely define life. This is somewhat understandable: the majority of biologists accept the standard definition of life without exploring it, but this represents a bad attitude. In this essay, we update the concepts of life, species, and individuals in the light of the new techniques for massive DNA sequencing collectively known as high throughput DNA sequencing (HTS). A re-evaluation of the newest approaches and traditional concepts is required, because in many scientific publications, HTS users apply concepts ambiguously (in particular that of species). However, the absence of clarity is understandable. For most of the last 250 years, from Linnaeus to the most recent researches, identification and classification have been performed applying the same process. On the contrary, through HTS, biologists have become simply identifiers, who construct boundaries around the biological entities and do not examine the taxa at length, resulting in uncertainty in most readers and displeasure in traditional taxonomists. We organised our essay to answer a basic question: can we develop new means to observe living organisms?     

The annual Day of the Dead song contest: musical‐linguistic ideology and practice,piratability, and the challenge of scale

Building on research theorizing scale, this article proposes augmentations to existing frameworks that will help illuminate how localities are linked to ‘stranger collectives’ like nations, ethnicities, and global religious ‘communities’. In this case of ethnic revival from Mexico's Sierra Mazateca, people use new vernacular literacy practices tied to local musical performances as a way of ‘customizing’ modular forms deployed by national and global institutions to manage indigenous difference. People ‘re‐imagine’ locality through a localized indigenous literacy that takes templates provided by the Mexican state and the Catholic Church and places them in productive tension with local context: musical properties of the indigenous language Mazatec, locally valued performance practices, and local musical‐linguistic ideologies. While this revival movement draws on immanently modular forms, once locally embedded they become ‘unpiratable’, and constitute a new resource for inscribing local belonging. This case suggests the importance of considering linguistic and musical aspects of social context often taken for granted in anthropological investigations of scale.     

Aquarium und Museum für Fischzucht, 1906–1937 in Brüssel,Belgien

In the beginning of last century an aquarium opened in Brussels where besides fishes also a collection of amphibians and reptiles was shown to the public. A small museum was also included. This aquarium was started with the aim just to show freshwater fishes but shortly after the opening also marine species were part of the collection.Curious inhabitants of Brussels who wanted to get acquainted with the unknown animal world and people who were interested in the scientific aspects of fishes, pisciculture, marine life and freshwater world found what they were looking for in the small aquarium and museum. Shortly after the inauguration it was described as ‘…a useful aquarium not only for the scientist who looks for information about all facets of live in water but also for the average visitors who want to get new impressions and enjoys the silence but also want to learn something. Families and schools as well have the possibility to let children and students learn about animals in a total new way’. A few renowned specialists and hydro biologists gave support but the aquarium had to face different problems and the interest of the public dropped off. A short time before World War II the aquarium was closed.     

Revisiting the links between bone remodelling and osteocytes: insights from across phyla

We question two major tenets of bone biology: that the primary role of remodelling is to remove damage in the bone (so‐called damage‐driven remodelling) and that osteocytes are the only strain‐sensing orchestrators of this process. These concepts are distilled largely from research on model mammal species, but in fact, there are a number of features of various bones, from mammalian and non‐mammalian species, that do not accord with these ‘rules’. Here, we assemble a variety of examples, ranging from species that lack osteocytes but that still seem capable of remodelling their bones, to species with osteocytic bones that do not remodel, and to instances of inter‐species, inter‐bone and/or intra‐bone variation in bone remodelling that show that this purported repair process is not always where the ‘rules’ tell us it should be. This collection of points argues that our understanding of the advantages, roles and primary drivers of remodelling are inadequate and biased to quite a small phylogenetic cross section of the species that possess bone. We suggest a variety of new directions for bone research that would provide us with a better understanding of bone remodelling, tying together the interests of comparative biologists, palaeontologists and medical researchers.     

Bayesian approaches in evolutionary quantitative genetics

The study of evolutionary quantitative genetics has been advanced by the use of methods developed in animal and plant breeding. These methods have proved to be very useful, but they have some shortcomings when used in the study of wild populations and evolutionary questions. Problems arise from the small size of data sets typical of evolutionary studies, and the additional complexity of the questions asked by evolutionary biologists. Here, we advocate the use of Bayesian methods to overcome these and related problems. Bayesian methods naturally allow errors in parameter estimates to propagate through a model and can also be written as a graphical model, giving them an inherent flexibility. As packages for fitting Bayesian animal models are developed, we expect the application of Bayesian methods to evolutionary quantitative genetics to grow, particularly as genomic information becomes more and more associated with environmental data.     

Images as tools. On visual epistemic practices in the biological sciences

Contemporary visual epistemic practices in the biological sciences raise new questions of how to transform an iconic data measurements into images, and how the process of an imaging technique may change the material it is ‘depicting’. This case-oriented study investigates microscopic imagery, which is used by system and synthetic biologists alike. The core argument is developed around the analysis of two recent methods, developed between 2003 and 2006: localization microscopy and photo-induced cell death. Far from functioning merely as illustrations of work done by other means, images can be determined as tools for discovery in their own right and as objects of investigation. Both methods deploy different constellations of intended and unintended interactions between visual appearance and underlying biological materiality. To characterize these new ways of interaction, the article introduces the notions of ‘operational images’ and ‘operational agency’. Despite all their novelty, operational images are still subject to conventions of seeing and depicting: Phenomena emerging with the new method of localization microscopy have to be designed according to image traditions of older, conventional fluorescence microscopy to function properly as devices for communication between physicists and biologists. The article emerged from a laboratory study based on interviews conducted with researchers from the Kirchhoff-Institute for Physics and German Cancer Research Center (DKFZ) at Bioquant, Heidelberg, in 2011.     

The virtual ecologist approach: simulating data and observers

Ecologists carry a well‐stocked toolbox with a great variety of sampling methods, statistical analyses and modelling tools, and new methods are constantly appearing. Evaluation and optimisation of these methods is crucial to guide methodological choices. Simulating error‐free data or taking high‐quality data to qualify methods is common practice. Here, we emphasise the methodology of the ‘virtual ecologist’ (VE) approach where simulated data and observer models are used to mimic real species and how they are ‘virtually’ observed. This virtual data is then subjected to statistical analyses and modelling, and the results are evaluated against the ‘true’ simulated data. The VE approach is an intuitive and powerful evaluation framework that allows a quality assessment of sampling protocols, analyses and modelling tools. It works under controlled conditions as well as under consideration of confounding factors such as animal movement and biased observer behaviour. In this review, we promote the approach as a rigorous research tool, and demonstrate its capabilities and practical relevance. We explore past uses of VE in different ecological research fields, where it mainly has been used to test and improve sampling regimes as well as for testing and comparing models, for example species distribution models. We discuss its benefits as well as potential limitations, and provide some practical considerations for designing VE studies. Finally, research fields are identified for which the approach could be useful in the future. We conclude that VE could foster the integration of theoretical and empirical work and stimulate work that goes far beyond sampling methods, leading to new questions, theories, and better mechanistic understanding of ecological systems.     

Live-cell imaging in the era of too many microscopes

At the time of this writing, searching Google Scholar for ‘light-sheet microscopy’ returns almost 8500 results; over three-quarters of which were published in the last 5 years alone. Searching for other advanced imaging methods in the last 5 years yields similar results: ‘super-resolution microscopy’ (>16 000), ‘single-molecule imaging’ (almost 10 000), SPIM (Single Plane Illumination Microscopy, 5000), and ‘lattice light-sheet’ (1300). The explosion of new imaging methods has also produced a dizzying menagerie of acronyms, with over 100 different species of ‘light-sheet’ alone, from SPIM to UM (Ultra microscopy) to SiMView (Simultaneous MultiView) to iSPIM (inclined SPIM, not to be confused with iSPIM, inverted SPIM). How then is the average biologist, without an advanced degree in physics, optics, or computer science supposed to make heads or tails of which method is best suited for their needs? Let us also not forget the plight of the optical physicist, who at best might need help with obtaining healthy samples and keeping them that way, or at worst may not realize the impact their newest technique could have for biologists. This review will not attempt to solve all these problems, but instead highlight some of the most recent, successful mergers between biology and advanced imaging technologies, as well as hopefully provide some guidance for anyone interested in journeying into the world of live-cell imaging.     

Crowdsourcing Language Change with Smartphone Applications

Crowdsourcing linguistic phenomena with smartphone applications is relatively new. In linguistics, apps have predominantly been developed to create pronunciation dictionaries, to train acoustic models, and to archive endangered languages. This paper presents the first account of how apps can be used to collect data suitable for documenting language change: we created an app, Dialäkt Äpp (DÄ), which predicts users’ dialects. For 16 linguistic variables, users select a dialectal variant from a drop-down menu. DÄ then geographically locates the user’s dialect by suggesting a list of communes where dialect variants most similar to their choices are used. Underlying this prediction are 16 maps from the historical Linguistic Atlas of German-speaking Switzerland, which documents the linguistic situation around 1950. Where users disagree with the prediction, they can indicate what they consider to be their dialect’s location. With this information, the 16 variables can be assessed for language change. Thanks to the playfulness of its functionality, DÄ has reached many users; our linguistic analyses are based on data from nearly 60,000 speakers. Results reveal a relative stability for phonetic variables, while lexical and morphological variables seem more prone to change. Crowdsourcing large amounts of dialect data with smartphone apps has the potential to complement existing data collection techniques and to provide evidence that traditional methods cannot, with normal resources, hope to gather. Nonetheless, it is important to emphasize a range of methodological caveats, including sparse knowledge of users’ linguistic backgrounds (users only indicate age, sex) and users’ self-declaration of their dialect. These are discussed and evaluated in detail here. Findings remain intriguing nevertheless: as a means of quality control, we report that traditional dialectological methods have revealed trends similar to those found by the app. This underlines the validity of the crowdsourcing method. We are presently extending DÄ architecture to other languages.     

Life After Logging: Strategic Withdrawal from the Garden of Eden or Tactical Error for Wilderness Conservation?

Conservation management has undergone a dramatic paradigm shift from the strong ‘wilderness conservation’ ethos of the 1980s and 1990s to the ‘biodiversity on degraded lands’ ethos of recent years. Most conservation biologists now consider that wilderness conservation alone is no longer sufficient to conserve biodiversity, and conservation strategies must also demand more effective protection for biodiversity on degraded lands. Recognition of this shifting paradigm in biodiversity conservation has led to an overt change in tone of recent studies, emphasizing relatively modest effects of human disturbance, and high biodiversity values on some degraded lands. A case in point is a series of studies from Southeast Asia reporting relatively modest impacts of logging on biodiversity, with the majority of species (75%) persisting after repeated intensive logging. This is a marked shift in conservation message after >30 yrs of research showing substantial adverse effects of logging on biodiversity, and raises serious questions about the appropriate ways to qualify the conflicting messages that ‘human impact degrades biodiversity’ yet ‘degraded habitats have high biodiversity value.’ Clearly logging is the lesser of two land‐use evils compared with conversion to intensive cattle pastures, crop fields or oil palm plantations, but there is a real risk that overselling the ‘biodiversity on degraded lands’ paradigm might end up being a double‐edged sword for conservation management. After all, if >75 percent of species are resilient to repeated logging, why bother trying to preserve the few remaining wilderness areas from being logged themselves? It remains to be seen whether this new message of ‘weak’ effects of logging on biodiversity will serve its strategic purpose of conserving biodiversity on degraded lands, or simply devalue the last vestiges of wild nature.