Cloning,stem cells,and the current national debate: incorporating ethics into a large introductory biology course

Discussing the ethical issues involved in topics such as cloning and stem cell research in a large introductory biology course is often difficult. Teachers may be wary of presenting material biased by personal beliefs, and students often feel inhibited speaking about moral issues in a large group. Yet, to ignore what is happening "out there" beyond the textbooks and lab work is to do a disservice to students. This essay describes a semester-long project in which upperclass students presented some of the most complex and controversial ideas imaginable to introductory students by staging a mock debate and acting as members of the then newly appointed President's Council on Bioethics. Because the upperclass students were presenting the ideas of real people who play an important role in shaping national policy, no student's personal beliefs were put on the line, and many ideas were articulated. The introductory audience could accept or reject what they were hearing and learn information important for making up their own minds on these issues. This project is presented as an example of how current events can be used to put basic cell biology into context and of how exciting it can be when students teach students.     

A Conceptual Framework for Biology Part II

This essay is part of the seventh yearly presentation of aneducational project of the American Society of Zoologists, Scienceas a Way of Knowing. It is also the second part of a "ConceptualFramework for Biology." Part II begins a discussion of evolutionand deals with an overview of living metazoans and then discussestheir history during the Phanerozoic Eon. Part III will completethe discussion of evolution and then consider "Classification,"Ecology," "Geographic Distribution," "Methods of Science,"and "Science and Human Welfare." The intended readers are thosewho teach the first-year biology courses in colleges and universitiesas well as teachers of the precollege grades.     

Science as a Way of Knowing--Evolutionary Biology

This essay is part of an educational project of the AmericanSociety of Zoologists that will make proposals for improvingthe first-year biology course inthe universities. The detailedsuggestions emphasize the importance of the conceptual frameworkof the biological sciences. The topic for this year is EvolutionaryBiology and it is developed largely by the hypothetico-deductivemethod emphasizing that science, in addition to its store ofinformation, is a way of knowing. Other topics will be consideredin future years in the ongoing project.     

Musicality in human evolution,archaeology and ethnography

This essay reviews Iain Morley’s The Prehistory of Music, an up-to-date and authoritative overview of recent research on evolution and cognition of musicality from an interdisciplinary viewpoint. Given the diversity of the project explored, integration of evidence from multiple fields is particularly pressing, required for any novel evolutionary account to be persuasive, and for the project’s continued progress. Moreover, Morley convincingly demonstrates that there is much more to understanding musicality than is supposed by some theorists. I outline Morley’s review of the archaeological and ethnographic literature, and then go on to critique his assessment of philosophical and evolutionary theories, offering some alternative perspectives that might better benefit his project.     

Hybrids, pure cultures, and pure lines: from nineteenth-century biology to twentieth-century genetics

Prompted by recent recognitions of the omnipresence of horizontal gene transfer among microbial species and the associated emphasis on exchange, rather than isolation, as the driving force of evolution, this essay will reflect on hybridization as one of the central concerns of nineteenth-century biology. I will argue that an emphasis on horizontal exchange was already endorsed by 'biology' when it came into being around 1800 and was brought to full fruition with the emergence of genetics in 1900. The true revolution in nineteenth-century life sciences, I maintain, consisted in a fundamental shift in ontology, which eroded the boundaries between individual and species, and allowed biologists to move up and down the scale of organic complexity. Life became a property extending both 'downwards', to the parts that organisms were composed of, as well as 'upwards', to the collective entities constituted by the relations of exchange and interaction that organisms engage in to reproduce. This mode of thinking was crystallized by Gregor Mendel and consolidated in the late nineteenth-century conjunction of biochemistry, microbiology and breeding in agro-industrial settings. This conjunction and its implications are especially exemplified by Wilhelm Johannsen's and Martinus Beijerinck's work on pure lines and cultures. An understanding of the subsequent constraints imposed by the evolutionary synthesis of the twentieth century on models of genetic systems may require us to rethink the history of biology and displace Darwin's theory of natural selection from that history's centre.     

'Like all that lives': biology,medicine and bacteria in the age of Pasteur and Koch

This essay draws a new picture of the science of bacteria in its 'golden age', circa 1880-1900: the organization of its knowledge and practice, its germ theory of disease, the difference between its two major research traditions, and, above all, its place in life science in this period that bristled with theories and debates over inheritance, variation, selection, evolution and that witnessed the transition from natural history to laboratory biology. Pasteur and Koch's science acquired this biological dimension not despite being outside academic biology, nor despite the limitations of its applied, medical matrix, but rather because of that framework. The very practices of vaccine development constituted, at the same time, a new biological model of bacterial species and variation, which aligned them with other living things. Finally, the new picture reveals unsuspected continuity to later microbiology and molecular biology. In illuminating the self-perceptions of these sciences in relation to the past, it situates and opens a critical perspective on writings by bacteriologists such as Ludwik Fleck, Fran?ois Jacob and René Dubos, which have widely informed how we understand science.     

The Hydra genome: insights, puzzles and opportunities for developmental biologists

The sequencing of a Hydra genome marked the beginning of a new era in the use of Hydra as a developmental model. Analysis of the genome sequence has led to a number of interesting findings, has required revisiting of previous work, and most importantly presents new opportunities for understanding the developmental biology of Hydra. This review will de-scribe the history of the Hydra genome project, a selection of results from it that are relevant to developmental biologists, and some future research opportunities provided by Hydra genomics.     

Bioactive peptides,networks and systems biology

Bioactive peptides are a group of diverse intercellular signalling molecules. Almost half a century of research on this topic has resulted in an enormous amount of data. In this essay, a general perspective to interpret all these data will be given. In classical endocrinology, neuropeptides were thought of as simple signalling molecules that each elicit one response. However, the fact that the total bioactive peptide signal is far from simple puts this view under pressure. Cells and tissues express many different bioactive peptides and they are also able to respond to many different bioactive peptides, indicating that multiple receptors and signal transduction pathways are present in a single cell. Therefore, the authors suggest that the bioactive peptide signalling system should be regarded in the context of network and systems biology. Bioactive peptides can best be viewed as an extension of the protein interaction network that allows regulating and fine‐tuning the metabolism of the different cells and tissues in the body. The cell thus responds to the ‘peptidome’ instead of to a single peptide. The intracellular part of this signalling network consists of the various signalling transduction cascades. Recently, new systems biology approaches have emerged for the modelling of cell signalling. The network and systems biology approach is also able to shed new light on the evolution of intercellular signalling.     

Reductionism Redux: Computing the Embryo

This paper argues that the consensus physicalist antireductionism in the philosophy of biology cannot accommodate the research strategy or indeed the recent findings of molecular developmental biology. After describing Wolperts programmatic claims on its behalf, and recent work by Gehring and others to identify the molecular determinants of development, the paper attempts to identify the relationship between evolutionary and developmental biology by reconciling two apparently conflicting accounts of bio-function – Wrights and Nagels (as elaborated by Cummins). Finally, the paper seeks a way of defending the two central theses of physicalist antireductionism in the light of the research program of molecular developmental biology, by sharply reducing their metaphysical force.     

The Reconfiguring Self

This essay presents a theory about cultural systems of self. It counters disclaimers as to the possibility of building cross-culturally valid theory, often taken to be the intellectual outcome of postmodernism. Nonetheless, such theory is a logical descendant of the postmodern project, predicating multiple selves and multiple constructions of social reality. It offers an explanatory framework for conceptions of personhood that are loosely interconnected and only partially and problematically shared between culture members.     

Interview with Sydney Brenner

The following text is an edited version of a recent interview with Sydney Brenner who has been at the forefront of many developments in molecular biology since the 1950s. It provides a participant’s view on current issues in the history and epistemology of molecular biology. The main issue raised by Brenner regards the relation of molecular biology to the new field of systems biology. Brenner defends the original programme of molecular biology—the molecular explanation of living processes—that in his view has yet to be completed. The programme of systems biology in contrast he views as either trivial or as not achievable since it purports to deal with inverse problems that are impossible to solve in complex living systems. Other issues covered in the conversation concern the impact of the human genome sequencing project, the commercial turn in molecular biology and the contested disciplinary status of the science.     

An expanded view of the eukaryotic cytoskeleton

A rich and ongoing history of cell biology research has defined the major polymer systems of the eukaryotic cytoskeleton. Recent studies have identified additional proteins that form filamentous structures in cells and can self-assemble into linear polymers when purified. This suggests that the eukaryotic cytoskeleton is an even more complex system than previously considered. In this essay, I examine the case for an expanded definition of the eukaryotic cytoskeleton and present a series of challenges for future work in this area.     

Membranes,viruses, detergents,and endosomes

The fluid mosaic model for biological membranes was formulated 40 years ago. Ten years later endosomes were discovered as important prelysosomal organelles. At the outset of my research career, I was fortunate to witness both these turning points in biochemistry and cell biology from close up, and to participate in some of the studies. In this short essay, I will describe how this came about, and also try to provide some background as to the general starting situation in those not so distant pioneering years of membrane biology.     

Selection within organisms in the nineteenth century: Wilhelm Roux's complex legacy

Selectionism, or the extension of darwinian chance/selection dynamics beyond the individual level, has a long history in biological thought. It has generated important theories in immunology or neurology, and turns out to be a convincing framework to account for the intrinsic stochastic nature of core events in cellular biology. When looking back at the intellectual origins of selectionism, the essay by the German embryologist Wilhelm Roux, Der Kampf der Theile im Organismus (The Struggle of the Parts in the Organism - 1881) might be one, if not the earliest reference after the darwinian revolution. It describes the individual as a multilevel structure, where each level results from a 'darwinian' struggle of its parts (molecules, cells, tissues, organs). But Roux's theory, far from being a simple extension of natural selection, has complex and even conflictual relationships with darwinism. This essay is worth rediscovering as a subtle historical testimony of the evolutionary and developmental life sciences debates of its time. Moreover, some of its theses may also enrich some current debates among evolutionary biologists over levels of selection, and among cellular and molecular biologists over the status of determinism in biology today.     

The complementary roles of observation and experiment: Theodosius Dobzhansky's Genetics of Natural Populations IX and XII

Theodosius Dobzhansky has long been recognized by historians as a pioneer in the combining of the 'field natural history' and 'laboratory experimentalist' traditions in biology (Allen 1994). The following essay analyzes two papers in his well-known Genetics of Natural Populations series, GNP IX and GNP XII, which demonstrate how Dobzhansky combined field and laboratory work in the pursuit of an evolutionary question. The analysis reveals the multiple and complementary roles field observations and experiments played in his investigations. But it also identifies several interpretive problems associated with the use of intervention that limited the effectiveness of his approach. The essay argues that these problems reflect a fundamental tension between the amount of control Dobzhansky had over the circumstances of his experiments and the applicability of his results to natural populations. It concludes that this trade-off represents an important distinction between experiments in biology and most other sciences.     

The Concept of Monophyly: A Speculative Essay

The concept of monophyly is central to much of modern biology. Despite many efforts over many years, important questions remain unanswered that relate both to the concept itself and to its various applications. This essay focuses primarily on four of these: i) Is it possible to define monophyly operationally, specifically with respect to both the structures of genomes and at the levels of the highest phylogenetic categories (kingdoms, phyla, classes)? ii) May the mosaic and chimeric structures of genomes be sufficiently important factors in phylogeny that situations exist in which the concept may not be applicable? iii) In the history of life on earth were there important groups of organisms that probably had polyphyletic, rather than monophyletic, origins? iv) Does the near universal search for monophyletic origins of clades lead, on occasion, to both undesirable narrowing of acceptable options for development of evolutionary scenarios and sometimes actual omission from consideration of less conventional types of both data and modes of thought, possibly at the expense of biological understanding? Three sections in the essay consider possible answers to these questions: i) A reassessment is made of major features of both the concept and some of its applications. Recent research results make it seem improbable that there could have been single basal forms for many of the highest categories of evolutionary differentiation (kingdoms, phyla, classes). The universal tree of life probably had many roots. Facts contributing to this perception include the phylogenetically widespread occurrences of: horizontal transfers of plasmids, viral genomes, and transposons; multiple genomic duplications; the existence and properties of large numbers of gene families and protein families; multiple symbioses; broad-scale hybridizations; and multiple homoplasys. Next, justifications are reassessed for the application of monophyletic frameworks to two major evolutionary developments usually interpreted as having been monophyletic: ii) the origins of life; and iii) the origins of the vertebrate tetrapods. For both cases polyphyletic hypotheses are suggested as more probable than monophyletic hypotheses. Major conclusions are, as answers to the four questions posed above: probably not, yes, yes, and yes.     

Thought in a vat: thinking through Annie Cattrell

This essay reflects on some aspects of the brain in a vat problem through a consideration of the work of the sculptor Annie Cattrell. Cattrell’s series of sculptures ‘Sense’ render in three dimensions MRI scans of different sensory functions in the human brain. These objects—which could be said to represent thought itself stilled and suspended in a transparent medium—make dramatically visible the doctrine of the localization of brain function. The essay argues that the brain in a vat problem in philosophy is an outcome of the same neural ‘mapping’ project as made Cattrell’s ‘thought in a vat’ possible. An interview with the artist reveals a moral dimension to her preoccupation with the localization of function. The article therefore goes on to consider the brain in a vat in the context of some of the history and ethics of the localizationist paradigm.     

The human genome project: Towards an analysis of the empirical,ethical, and conceptual issues involved

In this paper I claim that the goal of mapping and sequencing the human genome is not wholly new, but rather is an extension of an older project to map genes, a central aim of genetics since its birth. Thus, the discussion about the value of the HGP should not be posed in global terms of acceptance or rejection, but in terms of how it should be developed. The first section of this paper presents a brief history of the project. The second section distinguishes among four kinds of issues relevant to an evaluation of the HGP: those economic and organizational issues related to the feasibility of the project; the ethical questions arising in the development of the project and the application of the data gathered; the empirical issues relevant to the scientific value of the project; and conceptual issues like reductionism and determinism relevant to understand the nature and scope of the project. In a third section, I analyze in detail whether the HGP and, more generally, molecular biology is reductionistic.     

The legacy of Hans Molisch (1856–1937), photosynthesis savant

Hans Molisch (1856–1937) was an exceptionally gifted and productive researcher who had broad interests in plant biology, physiology and biochemistry. In addition, he pioneered in isolating a number of species of purple photosynthetic bacteria in pure culture (including Rhodobacter capsulatus), which facilitated his discovery of basic aspects of bacterial photosynthesis. Molisch demonstrated conclusively that molecular oxygen is not produced by photosynthetic bacteria, and discovered the photoheterotrophic growth mode. The range of Molisch's research accomplishments was impressive, and he emerges as a major figure in the history of photosynthesis research. This essay reviews the numerous research contributions made by Molisch, particularly in regard to advancing knowledge of the several forms of photosynthetic metabolism. An English translation of his 1914 paper on the photosynthetic creation of visual images on leaves is included as an Appendix.