Digest: Fossils,evolutionary models,and diatoms*

Adaptation to new environments by organisms has been and is of much interest in scientific research. Does the diatom lineage Stephanodiscus niagarae/yellowstonensis follow models compatible with adaptation to a new environment? Voje (2019) shows that in this lineage, none of the current models tested—decelerated evolution, Ornstein-Uhlenbeck, and random walk—fully explained how multiple traits—valve diameter, the number of costae, and spines per valve—evolved. More accurate models are needed to understand the evolutionary history of these diatoms.     

Biological design — a neglected art

I ought now, perhaps, to offer a summary of what I have been trying to convey in this lecture — but I am haunted by the failure which attended an effort, by an eminent scholar of this city, to do something of the same kind many years ago. Sir John Sheppard, Provost of King's, once gave a public lecture during one of the University's ceremonial gatherings. His subject was the Trojan War. The large audience sat spellbound in admiration of his depth of insight, breadth of knowledge and grasp of detail. As he was leaving after the meeting, a young man came up to him and explained that he was a graduate studuent engaged in research on the economic consequences of the Trojan War. He had, however, been spellbound by the lecture and had been too engrossed to write anything down. Would Sir John be so kind as to lend him his notes so that he could make a summary of the lecture? “My dear chap”, said Sheppard, “I'd be delighted; here are my notes — use them as you wish and let me have them back whenever they have served your purpose”. So saying he handed the young man a postcard on which was written: Agamemnon — Achilles — Agamemnon.I hope that members of the audience won't mind if I leave them to make their own summary of my remarks to which they have listened so patiently this evening.     

Beyond economic and ecological standardisation

Supply chain capitalism forages among the ruins of military and industrial landscapes—and so do real foragers, such as Southeast Asian refugees picking wild mushrooms in the US Pacific Northwest for commercial shipment to Japan. This essay explores how supply chain dynamics thrive on deregulation and diversity, encouraging cultural and ecological variety as a source of profit. Supply chain values are created through diversity—and sometimes, disaster. I aim to provoke anthropologists to revive ethnography for the challenge of studying supply chains, as these erupt like mushrooms after a rain in the cracks of economic and ecological standardisation.     

结构稳定性: 概念、方法和应用

群落内物种间相互作用的结构是高度组织化的。群落结构对多物种共存的影响机制是群落生态学的核心科学问题之一。目前生态学界在这一问题上存在多种不同的观点。一个可能的原因是, 由于环境因子的复杂性, 大部分研究忽略了环境因子对群落结构和物种共存的重要影响。在这一背景下, 近期发展起来的结构稳定性理论系统地联系了群落结构、环境因子和物种共存, 并在此基础上建立了一个和经验数据紧密结合的理论框架。本文首先简要回顾了当前关于群落结构研究的争鸣, 然后介绍了结构稳定性的理论框架和计算方法, 最后详细介绍了结构稳定性理论在不同生态群落和不同生态学问题中的应用。在全球气候变化的背景下, 结构稳定性理论提供了一种新的视角来理解群落层面的生物多样性维持机制。     

Are humans disturbing conditions in ecology?

In this paper I argue, first, that ecologists have routinely treated humans—or more specifically, anthropogenic causal factors—as disturbing conditions. I define disturbing conditions as exogenous variables, variables “outside” a model, that when present in a target system, inhibit the applicability or accuracy of the model. This treatment is surprising given that (1) humans play a dominant role in many ecosystems and (2) definitions of ecology contain no fundamental distinction between human and natural. Second, I argue that the treatment of humans as disturbing conditions is an idealization: since it is, and has long been, known that humans are pervasive, this treatment amounts to an intentionally introduced theoretical distortion. Finally, characterizing this treatment as idealization forces us to confront the question of its justification, and so, drawing on three different kinds of idealization, I evaluate how this treatment may be justified.     

Entropy increase and information loss in Markov models of evolution

Markov models of evolution describe changes in the probability distribution of the trait values a population might exhibit. In consequence, they also describe how entropy and conditional entropy values evolve, and how the mutual information that characterizes the relation between an earlier and a later moment in a lineage’s history depends on how much time separates them. These models therefore provide an interesting perspective on questions that usually are considered in the foundations of physics—when and why does entropy increase and at what rates do changes in entropy take place? They also throw light on an important epistemological question: are there limits on what your observations of the present can tell you about the evolutionary past?     

Plant Communities of Western Amazonia

In this review I focus on the socially and ecologically important western Amazon basin and its associated plant communities. I delineate this vast area as between the Andes to the west and the confluence of the Amazon and its first major black-water river, the Rio Negro, to the east. Although scientists have explored here, and local people have lived here for years, we still have—unfortunately—only a most basic understanding of its plant communities. This review is motivated by that lack of knowledge, and attempts both to add a level of organization to what we do know and to suggest future avenues of research. I do this by first realizing that plant communities here must be fundamentally differentiated by the degree of flooding they experience, the kind of water involved, and how regularly that flooding occurs. Within that context, plant communities can then be further defined by such characteristics as soil type, micro-topological relief, and human-induced disturbance regime. After completing the review, I suggest that the diversity of plant communities, not just the plants themselves, is large and likely to grow substantially as we sample more and more, that is to say the peak of the plant community-sampling area curve has not yet been reached. I close with basic questions to help guide future efforts, ideas on how plant communities could be defined quantitatively, and a call for more research funding of the Western Amazon.     

A Role for Bone Morphogenetic Protein-4 in Adipocyte Development

Obesity is characterized by increases in the number of mature adipocytes. Nascent adipocytes arise from mesenchymal stem cells (MSCs) by a multi-step process — MSCs are recruited to the adipocyte lineage forming determined preadipocytes, these committed progenitors proliferate, undergo growth arrest, and finally differentiate into mature adipocytes. Although the genetic mechanisms that control the differentiation of preadipocytes into mature adipocytes are understood to a large extent, the earliest events in adipogenesis — especially the commitment of MSCs into preadipocytes — are largely unknown. Recently, bone morphogenetic protein-4 (BMP-4) has been implicated in the commitment of pluripotent MSCs to the adipocyte lineage by two independent lines of investigation. First, growth-arrested 10T1/2 cells do not normally respond to a hormonal cocktail that causes various growth-arrested preadipocyte cell lines to differentiate into adipocytes, but if 10T1/2 cells are first treated with BMP-4 they will respond to these hormonal inducers by undergoing terminal adipocyte differentiation. Second, a preadipocyte cell line, A33 cells, derived from 10T1/2 cells after exposing the cells to the DNA methyltransferase inhibitor 5-azacytidine was shown to express BMP-4, and this endogenous BMP-4 expression is required for acquisition of the preadipocyte phenotype of these cells. A role for the BMP-4 signaling pathway in adipogenesis is discussed.     

CRANIAL SIZE VARIATION AND LINEAGE DIVERSITY IN EARLY PLEISTOCENE HOMO

A recent article in this journal concluded that a sample of early Pleistocene hominin crania assigned to genus Homo exhibits a pattern of size variation that is time dependent, with specimens from different time periods being more different from each other, on average, than are specimens from the same time period. The authors of this study argued that such a pattern is not consistent with the presence of multiple lineages within the sample, but rather supports the hypothesis that the fossils represent an anagenetically evolving lineage (i.e., an evolutionary species). However, the multiple‐lineage models considered in that study do not reflect the multiple‐species alternatives that have been proposed for early Pleistocene Homo. Using simulated data sets, I show that fossil assemblages that contain multiple lineages can exhibit the time‐dependent pattern of variation specified for the single‐lineage model under certain conditions, particularly when temporal overlap among fossil specimens attributed to the lineages is limited. These results do not reject the single‐lineage hypothesis, but they do indicate that rejection of multiple lineages in the early Pleistocene Homo fossil record is premature, and that other sources of variation, such as differences in cranial shape, should be considered.     

The Principle of Procreative Beneficence: Old Arguments and A New Challenge

In the last ten years, there have been a number of attempts to refute Julian Savulescu's Principle of Procreative Beneficence; a principle which claims that parents have a moral obligation to have the best child that they can possibly have. So far, no arguments against this principle have succeeded at refuting it. This paper tries to explain the shortcomings of some of the more notable arguments against this principle. I attempt to break down the argument for the principle and in doing so, I explain what is needed to properly refute it. This helps me show how and why the arguments of Rebecca Bennett, Sarah Stoller and others fail to refute the principle. Afterwards, I offer a new challenge to the principle. I attack what I understand to be a fundamental premise of the argument, a premise which has been overlooked in the literature written about this principle. I argue that there is no reason to suppose, as Savulescu does, that morality requires us to do what we have most reason to do. If we reject this premise, as I believe we have reason to do, the argument for Procreative Beneficence fails.     

Dr Jekyll and Mrs Hyde: Risky hybrid sex by amphibian‐parasitizing chytrids in the Brazilian Atlantic Forests

In their article in this issue of Molecular Ecology, Jenkinson et al. ( 2016 ) and colleagues address a worrying question—how could arguably the most dangerous pathogen known to science, Batrachochytrium dendrobatidis (Bd), become even more virulent? The answer: start having sex. Jenkinson et al. present a case for how the introduction into Brazil of the globally invasive lineage of Bd, BdGPL, has disrupted the relationship between native amphibians and an endemic Bd lineage, BdBrazil. BdBrazil is hypothesized to be native to the Atlantic Forest and so have a long co‐evolutionary history with biodiverse Atlantic Forest amphibian community. The authors suggest that this has resulted in a zone of hybrid Bd genotypes which are potentially more likely to cause fatal chytridiomycosis than either parent lineage. The endemic–nonendemic Bd hybrid genotypes described in this study, and the evidence for pathogen translocation via the global amphibian trade presented, highlights the danger of anthropogenic pathogen dispersal. This research emphasizes that biosecurity regulations may have to refocus on lineages within species if we are to mitigate against the danger of new, possibly hypervirulent genotypes of pathogens emerging as phylogeographic barriers are breached.     

Rethinking the role of theory in exploratory experimentation

To explain their role in discovery and contrast them with theory-driven research, philosophers of science have characterized exploratory experiments in terms of what they lack: namely, that they lack direction from what have been called “local theories” of the target system or object under investigation. I argue that this is incorrect: it’s not whether or not there is direction from a local theory that matters, but instead how such a theory is used to direct an experiment that matters. Appealing to contemporary exploratory experiments that involve the use of experimental techniques—specifically, examples where scientists explore the interaction of neural activity and human behavior by magnetically stimulating brains—I argue that local theories of a target system can inform auxiliary hypotheses in exploratory experiments, which direct these experiments. These examples illustrate how local theories can direct the exploration of target systems where researchers do not aim to evaluate these theories.     

Materiality and Global Spiritual Networks: Old and new sacred places and objects

In this article, I am interested in how belief and religious materiality—sacred objects, places, infrastructures and digital media—are entangled in globalisation processes. Drawing on a case study of the John of God spiritual movement, I analyse the ways in which places and objects that have recently acquired sacred status enter into older, more established global spiritual networks, and by doing so are able to travel and ‘settle’ elsewhere. I argue that if we want to make sense of the place of religion in the world today, we need to link two fields of research on religion which have mostly developed separately: the fields of Material Religion and Globalisation of Religion. Furthermore, I contend that it is precisely because of its (mostly mobile) materiality that the John of God movement was able to survive somewhat after its charismatic leader was sentenced and jailed for sexual crimes in 2019.     

A path to the powerhouse: systems‐to‐structure approaches for studying mitochondrial proteins

The young investigator award from the Protein Society was a special honor for me because, at its essence, the goal of my laboratory is to define what obscure proteins do. Years ago, I stumbled into mitochondria as a venue for this work, and these organelles continue to define the biological theme of my laboratory. Our approaches are fairly broad, reflecting my own somewhat unorthodox training among diverse scientific fields spanning organic synthesis, chemical biology, mechanistic biochemistry, signal transduction, and systems biology. Yet, whatever the theme or the discipline, we aim to understand how proteins work—especially those that hide in the dark corners of mitochondria. Below, I recount my own path into this arena of protein science, and describe how my experiences along the way have shaped our current multi‐disciplinary efforts to define the inner workings of this complex biological system.     

Trashing life’s tree

The Tree of Life has traditionally been understood to represent the history of species lineages. However, recently researchers have suggested that it might be better interpreted as representing the history of cellular lineages, sometimes called the Tree of Cells. This paper examines and evaluates reasons offered against this cellular interpretation of the Tree of Life. It argues that some such reasons are bad reasons, based either on a false attribution of essentialism, on a misunderstanding of the problem of lineage identity, or on a limited view of scientific representation. I suggest that debate about the Tree of Cells and other successors to the traditional Tree of Life should be formulated in terms of the purposes these representations may serve. In pursuing this strategy, we see that the Tree of Cells cannot serve one purpose suggested for it: as an explanation for the hierarchical nature of taxonomy. We then explore whether, instead, the tree may play an important role in the dynamic modeling of evolution. As highly-integrated complex systems, cells may influence which lineage components can successfully transfer into them and how they change once integrated. Only if they do in fact have a substantial role to play in this process might the Tree of Cells have some claim to be the Tree of Life.     

Darwinism after Mendelism: the case of Sewall Wright's intellectual synthesis in his shifting balance theory of evolution (1931)

Historians of science have long been agreeing: what many textbooks of evolutionary biology say, about the histories of Darwinism and the New Synthesis, is just too simple to do justice to the complexities revealed to critical scholarship and historiography. There is no current consensus, however, on what grand narratives should replace those textbook histories. The present paper does not offer to contribute directly to any grand, consensual, narrational goals; but it does seek to do so indirectly by showing how, in just one individual case, details of intellectual biography connect with big picture issues. To this end, I examine here how very diverse scientific and metaphysical commitments were integrated in Sewall Wright's own personal synthesis of biology and philosophy. Taking as the decisive text the short final section of Wright's long 1931 paper on 'Evolution in Mendelian populations,' I examine how his shifting balance theory (SBT) related to his optimum breeding strategy research, his physiological genetics, his general theory of homogenising and heterogenesing causation and his panpsychist view of mind and matter; and I discuss how understanding these relations can clarify Wright's place in the longue durée of evolutionary thought.     

Paradigms of expected failure

This study explores the outsourcing and offshoring of clinical trials and how they interconnect with the dynamics of drug development and regulation in the United States. I focus on the activities of United States-based contract research organizations, which make up a specialized global clinical trials industry focusing on the recruitment of human subjects and investigators. Tracking this industry’s activities in eastern Europe and Latin America, two clinical trial market ‘growth regions,’ I address the strategies of evidence-making that inform clinical trial offshoring. I also show how aspects of the clinical trial model—in which failures to predict safety outcomes or a paradigm of expected failure—are being exported along with the offshored trial. The clinical trials industry is a crucial, highly mobile, and profitable arm of the global pharmaceutical industry. Where state agencies furnish limited or no health care, drug developers claim that trial expansion and experiments have become social goods in themselves. But questions remain: How is drug value and research integrity maintained? And how do the results of clinical trials strengthen or undermine the delivery of affordable and effective interventions? As this essay shows, clinical trials are not only hypothesis-testing instruments; they are operative environments redistributing resources and occasioning tense medical and social fields. In highlighting the inefficiencies and uncertainties of global drug development, this study points to problems in the operational model of drug development and in systems of human protection. It also considers new forms of accountability at the nexus of private sector science and public health.     

Human Perceptual and Phobic Biases for Snakes: A Review of the Experimental Evidence

In this paper I review the literature on the evolutionary origins of phobias and describe the current state of research on the neurobiology and developmental origins of ophidiophobia—fear of snakes. In doing so I compare experimental evidence related to evolutionary explanations for snake fears and phobias which are outlined in Seligman’s Preparedness Theory and Isbell’s Snake Detection Theory. These theories have been tested extensively using a variety of experimental paradigms aimed at determining the “innateness” of snake fears, the neural pathways involved in fear responses to snakes, and the perceptual biases associated with snake stimuli. However, in the vast majority of these experiments, the stimuli presented are photographs of snakes rather than the real thing. I argue that this point of methodology, while ironically supportive of the findings, is based on some assumptions about cognition and consciousness which run counter to neuroscience. In understanding human responses to snakes, we need to understand better the interplay between cognition and consciousness and how these represent a pluralism of mind in which perception is much more than we think.     

The evolution of costly displays,cooperation and religion: credibility enhancing displays and their implications for cultural evolution

This paper lays out an evolutionary theory for the cognitive foundations and cultural emergence of the extravagant displays (e.g., ritual mutilation, animal sacrifice and martyrdom) that have so tantalized social scientists, as well as more mundane actions that influence cultural learning and historical processes. In Part I, I use the logic of natural selection to build a theory for how and why seemingly costly displays influence the cognitive processes associated with cultural learning — why do “actions speak louder than words?” The core idea is that cultural learners can both avoid being manipulated by their models (those they are inclined to learn from) and more accurately assess their belief commitment by attending to displays or actions by the model that would seem costly to the model if he held beliefs different from those he expresses verbally. Part II examines the implications for cultural evolution of this learning bias in a simple evolutionary model. The model reveals the conditions under which this evolved bias can create stable sets of interlocking beliefs and practices, including quite costly practices. Part III explores how cultural evolution, driven by competition among groups or institutions stabilized at alternative sets of these interlocking belief-practice combinations, has led to the association of costly acts, often in the form of rituals, with deeper commitments to group beneficial ideologies, higher levels of cooperation within groups, and greater success in competition with other groups or institutions. I close by discussing the broader implications of these ideas for understanding various aspects of religious phenomena.