Bridging the gap between developmental systems theory and evolutionary developmental biology

Many scientists and philosophers of science are troubled by the relative isolation of developmental from evolutionary biology. Reconciling the science of development with the science of heredity preoccupied a minority of biologists for much of the twentieth century, but these efforts were not corporately successful. Mainly in the past fifteen years, however, these previously dispersed integrating programmes have been themselves synthesized and so reinvigorated. Two of these more recent synthesizing endeavours are evolutionary developmental biology (EDB, or "evo-devo") and developmental systems theory (DST). While the former is a bourgeoning and scientifically well-respected biological discipline, the same cannot be said of DST, which is virtually unknown among biologists. In this review, we provide overviews of DST and EDB, summarize their key tenets, examine how they relate to one another and to the study of epigenetics, and survey the impact that DST and EDB have had (and in future should have) on biological theory and practice.     

An objective view of biological diversity: how history and epistemology shaped current treatment

The concept of biological diversity has inspired important discussions throughout the history of ecology. Although its meaning and usefulness have been questioned, it is currently one of the key artifacts of ecology. One way to try to understand why such a concept has undergone so many discussions is to examine its emergence and history from the epistemology perspective. In the present work, we investigated how the emergence of mechanical objectivity (as an epistemic virtue) and trained judgment affected how ecologists address the concept of biological diversity. Thus, we employed the theoretical framework of objectivity (provided by Daston and Galison in Objectivity. Zone Books, New York, 2007) to analyze different periods of scientific literature in ecology (“initial period”: end of the nineteenth century and beginning of the twentieth century; “intermediate period”: mid-twentieth century; “contemporary period”: from the second half of the 1980s). Our results showed that the emergence of mechanical objectivity and trained judgment affected biological diversity research. In particular, the ideal of objectivity behind the way in which the concept of biological diversity is addressed in different fields of contemporary ecology could not be the same.     

Milestones and rates of growth in the development of biology.

An attempt has been made to examine the exponetial rate of increase of the great discoveries, the "milestones," in the rise of biology from the beginning of the seventeenth century, and particularly in the rise of genetics from the beginning of the twentieth century. The biological sciences in general, during the three centuries named, exhibit a doubling of the number of great discoveries in each fifty years. Genetics, in the twentieth century, has risen much faster. Its doubling time for the most significant discoveries has been about twenty-two and a half years. Either of these rates is of course far slower than the exponential rise in the total output of biological science, the number of scientists, or the cost of science, which have been generally reported to double about every ten years or less. It follows that, as time passes, and until these exponetial rates become considerably altered, a relationship of diminishing returns is quite evident. As time passes, even though the most significant discoveries continue to increase exponetially, it takes a greater total output, a greater number of (assisting?) scientists, and greater amounts of money to yield a set quantity of major new findings. The rapid rise of the life sciences cannot continue its present course into the twenty-first century without meeting ineluctable limits to expansion. It may be argued that as in other human spheres of activity, so too in natural science there are limits to growth which we are rapidly approaching. From the predictable asymptote only unpredictable breakthroughs might deliver us.     

Uexküllian <Emphasis Type="Italic">Umwelt</Emphasis> as science and as ideology: the light and the dark side of a concept

The concept of Umwelt, in particular the interpretation originally developed by Jakob von Uexküll, played an important role in the development of biological thought of the first half of the twentieth century. The theory of Umwelt (Umweltlehre) was one of the most original ideas that appeared in German biology at that time. It was the first attempt to introduce subjectivity into a science about organisms; it laid down the foundations of behavioural research and inspired the development of ethology. However, the theory of Umwelt has also been used to support more sinister activities and even some dangerous ideologies. The concept of Umwelt is of interest not only to historians: within some intellectual circles, it is still broadly used today. Our aim was to analyse the notion’s historic development within the context of biological thought of the first half of the 20th century. In particular, we focus (1) on how the concept was adopted and adapted for various, often widely diverging purposes; (2) on interactions between the Umweltlehre and other contemporary worldviews. We argue that in order to understand the developments that occurred in twentieth century biology, one needs to properly appreciate the role which Umweltlehre played in these. Even more importantly, the Umweltlehre is a worldview that influenced not only science but also politics and social affairs. In this respect it functioned rather like a number of other scientific and ideological frameworks of that time, such as Synthetic Darwinism.     

Cancer,Conflict, and the Development of Nuclear Transplantation Techniques

The technique of nuclear transplantation – popularly known as cloning – has been integrated into several different histories of twentieth century biology. Historians and science scholars have situated nuclear transplantation within narratives of scientific practice, biotechnology, bioethics, biomedicine, and changing views of life. However, nuclear transplantation has never been the focus of analysis. In this article, I examine the development of nuclear transplantation techniques, focusing on the people, motivations, and institutions associated with the first successful nuclear transfer in metazoans in 1952. The conflict between embryologists and geneticists over the mechanisms of differentiation motivated Robert Briggs to pursue nuclear transplantation experiments as a way to resolve the debate. Briggs worked at the Lankenau Hospital Research Institute, a research facility devoted to the study of cancer. The goal of understanding cancer would play a role in the development of the technique, and the story of nuclear transplantation sheds light on the role that biomedical contexts play in biological research in the second half of the twentieth century.     

Genomics for the ecological toolbox

Genomics technologies have expanded the types of question that can be addressed in human genetics and health and in fields such as ecology. Genome-scale approaches provide ways to examine physiological changes that occur when a pathogen invades a host, the response of an organism to a change in its environment, and the way in which changes in the microbial community affect ecosystem function. Here, we examine successful applications of genomics to ecological science to date and describe ways that classic ecological research disciplines might benefit from genomic approaches. We also address some of the challenges of using this methodology, and discuss how ecological researchers embracing these approaches enhance its effectiveness in applications such as gene hunting and gene expression analysis.     

In pursuit of a science of agriculture: the role of statistics in field experiments

Since the beginning of the twentieth century statistics has reshaped the experimental cultures of agricultural research taking part in the subtle dialectic between the epistemic and the material that is proper to experimental systems. This transformation has become especially relevant in field trials and the paper will examine the British agricultural institution, Rothamsted Experimental Station, where statistical methods nowadays popular in the planning and analysis of field experiments were developed in the 1920s. At Rothamsted statistics promoted randomisation over systematic arrangements, factorisation over one-question trials, and emphasised the importance of the experimental error in assessing field trials. These changes in methodology transformed also the material culture of agricultural science, and a new body, the Field Plots Committee, was created to manage the field research of the agricultural institution. Although successful, the vision of field experimentation proposed by the Rothamsted statisticians was not unproblematic. Experimental scientists closely linked to the farming community questioned it in favour of a field research that could be more easily understood by farmers. The clash between the two agendas reveals how the role attributed to statistics in field experimentation defined different pursuits of agricultural research, alternately conceived of as a scientists’ science or as a farmers’ science.

     

Collecting,Comparing, and Computing Sequences: The Making of Margaret O. Dayhoff’s <Emphasis Type="Italic">Atlas of Protein Sequence and Structure</Emphasis>, 1954–1965

Collecting, comparing, and computing molecular sequences are among the most prevalent practices in contemporary biological research. They represent a specific way of producing knowledge. This paper explores the historical development of these practices, focusing on the work of Margaret O. Dayhoff, Richard V. Eck, and Robert S. Ledley, who produced the first computer-based collection of protein sequences, published in book format in 1965 as the Atlas of Protein Sequence and Structure. While these practices are generally associated with the rise of molecular evolution in the 1960s, this paper shows that they grew out of research agendas from the previous decade, including the biochemical investigation of the relations between the structures and function of proteins and the theoretical attempt to decipher the genetic code. It also shows how computers became essential for the handling and analysis of sequence data. Finally, this paper reflects on the relationships between experimenting and collecting as two distinct “ways of knowing” that were essential for the transformation of the life sciences in the twentieth century.     

Toward an integration of evolutionary biology and ecosystem science

At present, the disciplines of evolutionary biology and ecosystem science are weakly integrated. As a result, we have a poor understanding of how the ecological and evolutionary processes that create, maintain, and change biological diversity affect the flux of energy and materials in global biogeochemical cycles. The goal of this article was to review several research fields at the interfaces between ecosystem science, community ecology and evolutionary biology, and suggest new ways to integrate evolutionary biology and ecosystem science. In particular, we focus on how phenotypic evolution by natural selection can influence ecosystem functions by affecting processes at the environmental, population and community scale of ecosystem organization. We develop an eco-evolutionary model to illustrate linkages between evolutionary change (e.g. phenotypic evolution of producer), ecological interactions (e.g. consumer grazing) and ecosystem processes (e.g. nutrient cycling). We conclude by proposing experiments to test the ecosystem consequences of evolutionary changes.     

Purple Matter, Membranes and ‘Molecular Pumps’ in Rhodopsin Research (1960s–1980s)

In the context of 1960s research on biological membranes, scientists stumbled upon a curiously coloured material substance, which became called the “purple membrane.” Interactions with the material as well as chemical analyses led to the conclusion that the microbial membrane contained a photoactive molecule similar to rhodopsin, the light receptor of animals’ retinae. Until 1975, the find led to the formation of novel objects in science, and subsequently to the development of a field in the molecular life sciences that comprised biophysics, bioenergetics as well as membrane and structural biology. Furthermore, the purple membrane and bacteriorhodopsin, as the photoactive membrane transport protein was baptized, inspired attempts at hybrid bio-optical engineering throughout the 1980s. A central motif of the research field was the identification of a functional biological structure, such as a membrane, with a reactive material substance that could be easily prepared and manipulated. Building on this premise, early purple membrane research will be taken as a case in point to understand the appearance and transformation of objects in science through work with material substances. Here, the role played by a perceptible material and its spontaneous change of colour, or reactivity, casts a different light on objects and experimental practices in the late twentieth century molecular life sciences. With respect to the impact of chemical working and thinking, the purple membrane and rhodopsins represent an influential domain straddling the life and chemical sciences as well as bio- and material technologies, which has received only little historical and philosophical attention. Re-drawing the boundary between the living and the non-enlivened, these researches explain and model organismic activity through the reactivity of macromolecular structures, and thus palpable material substances.     

Cells as irreducible wholes: the failure of mechanism and the possibility of an organicist revival

According to vitalism, living organisms differ from machines and all other inanimate objects by being endowed with an indwelling immaterial directive agency, ‘vital force,’ or entelechy. While support for vitalism fell away in the late nineteenth century many biologists in the early twentieth century embraced a non vitalist philosophy variously termed organicism/holism/emergentism which aimed at replacing the actions of an immaterial spirit with what was seen as an equivalent but perfectly natural agency—the emergent autonomous activity of the whole organism. Organicists hold that organisms unlike machines are ‘more than the sum of their parts’ and predict that the vital properties of living things can never be explained in terms of mechanical analogies and that the reductionist agenda is doomed to failure. Here we review the current status of the mechanist and organicist conceptions of life particularly as they apply to the cell. We argue that despite the advances in biological knowledge over the past six decades since the molecular biological revolution, especially in the fields of genetics and cell biology the unique properties of living cells have still not been simulated in mechanical systems nor yielded to reductionist—analytical explanations. And we conclude that despite the dominance of the mechanistic–reductionist paradigm through most of the past century the possibility of a twentyfirst century organicist revival cannot be easily discounted.     

Variations on a Chip: Technologies of Difference in Human Genetics Research

In this article we examine the history of the production of microarray technologies and their role in constructing and operationalizing views of human genetic difference in contemporary genomics. Rather than the “turn to difference” emerging as a post-Human Genome Project (HGP) phenomenon, interest in individual and group differences was a central, motivating concept in human genetics throughout the twentieth century. This interest was entwined with efforts to develop polymorphic “genetic markers” for studying human traits and diseases. We trace the technological, methodological and conceptual strategies in the late twentieth century that established single nucleotide polymorphisms (SNPs) as key focal points for locating difference in the genome. By embedding SNPs in microarrays, researchers created a technology that they used to catalog and assess human genetic variation. In the process of making genetic markers and array-based technologies to track variation, scientists also made commitments to ways of describing, cataloging and “knowing” human genetic differences that refracted difference through a continental geographic lens. We show how difference came to matter in both senses of the term: difference was made salient to, and inscribed on, genetic matter(s), as a result of the decisions, assessments and choices of collaborative and hybrid research collectives in medical genomics research.     

Diffusion theory in biology: a relic of mechanistic materialism

Diffusion theory explains in physical terms how materials move through a medium, e.g. water or a biological fluid. There are strong and widely acknowledged grounds for doubting the applicability of this theory in biology, although it continues to be accepted almost uncritically and taught as a basis of both biology and medicine. Our principal aim is to explore how this situation arose and has been allowed to continue seemingly unchallenged for more than 150 years. The main shortcomings of diffusion theory will be briefly reviewed to show that the entrenchment of this theory in the corpus of biological knowledge needs to be explained, especially as there are equally valid historical grounds for presuming that bulk fluid movement powered by the energy of cell metabolism plays a prominent note in the transport of molecules in the living body. First, the theory's evolution, notably from its origins in connection with the mechanistic materialist philosophy of mid nineteenth century physiology, is discussed. Following this, the entrenchment of the theory in twentieth century biology is analyzed in relation to three situations: the mechanism of oxygen transport between air and mammalian tissues; the structure and function of cell membranes; and the nature of the intermediary metabolism, with its implicit presumptions about the intracellular organization and the movement of molecules within it. In our final section, we consider several historically based alternatives to diffusion theory, all of which have their precursors in nineteenth and twentieth century philosophy of science. This revised version was published online in July 2006 with corrections to the Cover Date.     

Has psychology “found its true path”? Methods,objectivity, and cries of “crisis” in early twentieth-century French psychology

This article explores how French psychologists understood the state of their field during the first quarter of the twentieth century, and whether they thought it was in crisis. The article begins with the Russian-born psychologist Nicolas Kostyleff and his announcement in 1911 that experimental psychology was facing a crisis. After briefly situating Kostyleff, the article examines his analysis of the troubles facing experimental psychology and his proposed solution, as well as the rather muted response his diagnosis received from the French psychological community. The optimism about the field evident in many of the accounts surveying French psychology during the early twentieth century notwithstanding, a few others did join Kostyleff in declaring that all was not well with experimental psychology. Together their pronouncements suggest that under the surface, important unresolved issues faced the French psychological community. Two are singled out: What was the proper methodology for psychology as a positive science? And what kinds of practices could claim to be objective, and in what sense? The article concludes by examining what these anxieties reveal about the type of science that French psychologists hoped to pursue.     

Science and Sentiment: Grinnell’s Fact-Based Philosophy of Biodiversity Conservation

At the beginning of the twentieth century, the biologist Joseph Grinnell made a distinction between science and sentiment for producing fact-based generalizations on how to conserve biodiversity. We are inspired by Grinnellian science, which successfully produced a century-long impact on studying and conserving biodiversity that runs orthogonal to some familiar philosophical distinctions such as fact versus value, emotion versus reason and basic versus applied science. According to Grinnell, unlike sentiment-based generalizations, a fact-based generalization traces its diverse commitments and thus becomes tractable for its audience. We argue that foregrounding tractability better explains Grinnell’s practice in the context of his time as well as in the context of current discourse among scientists over the political “biases” of biodiversity research and its problem of “reproducibility.”     

Maximizing farm-level uptake and diffusion of biological control innovations in today’s digital era

When anthropologists interviewed Honduran and Nepali smallholders in the mid-1990s, they were told that “Insects are a terrible mistake in God’s creation” and “There’s nothing that kills them, except for insecticides”. Even growers who maintained a close bond with nature were either entirely unaware of natural pest control, or expressed doubt about the actual value of these services on their farm. Farmers’ knowledge, beliefs and attitudes towards pests and natural enemies are of paramount importance to the practice of biological control, but are all too often disregarded. In this study, we conduct a retrospective analysis of the extent to which social science facets have been incorporated into biological control research over the past 25 years. Next, we critically examine various biological control forms, concepts and technologies using a ‘diffusion of innovations’ framework, and identify elements that hamper their diffusion and farm-level uptake. Lastly, we introduce effective observation-based learning strategies, such as farmer field schools to promote biological control, and list how those participatory approaches can be further enriched with information and communication technologies (ICT). Although biological control scientists have made substantial technological progress and generate nearly 1000 papers annually, only a fraction (1.4%) of those address social science or technology transfer aspects. To ease obstacles to enhanced farmer learning about biological control, we describe ways to communicate biological control concepts and technologies for four divergent agricultural knowledge systems (as identified within a matrix built around ‘cultural importance’ and ‘ease of observation’). Furthermore, we describe how biological control innovations suffer a number of notable shortcomings that hamper their farm-level adoption and subsequent diffusion, and point at ways to remediate those by tactical communication campaigns or customized, (ICT-based) adult education programs. Amongst others, we outline how video, smart phones, or tablets can be used to convey key ecological concepts and biocontrol technologies, and facilitate social learning. In today’s digital era, cross-disciplinary science and deliberate multi-stakeholder engagement will provide biocontrol advocates the necessary means to bolster farmer adoption rates, counter-act surging insecticide use, and restore public trust in one of nature’s prime services.     

Advancing ecological understandings through technological transformations in noninvasive genetics

Noninvasive genetic approaches continue to improve studies in molecular ecology, conservation genetics and related disciplines such as forensics and epidemiology. Noninvasive sampling allows genetic studies without disturbing or even seeing the target individuals. Although noninvasive genetic sampling has been used for wildlife studies since the 1990s, technological advances continue to make noninvasive approaches among the most used and rapidly advancing areas in genetics. Here, we review recent advances in noninvasive genetics and how they allow us to address important research and management questions thanks to improved techniques for DNA extraction, preservation, amplification and data analysis. We show that many advances come from the fields of forensics, human health and domestic animal health science, and suggest that molecular ecologists explore literature from these fields. Finally, we discuss how the combination of advances in each step of a noninvasive genetics study, along with fruitful areas for future research, will continually increase the power and role of noninvasive genetics in molecular ecology and conservation genetics.     

Enlightening the life sciences: the history of halobacterial and microbial rhodopsin research

The history of research on microbial rhodopsins offers a novel perspective on the history of the molecular life sciences. Events in this history play important roles in the development of fields such as general microbiology, membrane research, bioenergetics, metagenomics and, very recently, neurobiology. New concepts, techniques, methods and fields have arisen as a result of microbial rhodopsin investigations. In addition, the history of microbial rhodopsins sheds light on the dynamic connections between basic and applied science, and hypothesis-driven and data-driven approaches. The story begins with the late nineteenth century discovery of microorganisms on salted fish and leads into ecological and taxonomical studies of halobacteria in hypersaline environments. These programmes were built on by the discovery of bacteriorhodopsin in organisms that are part of what is now known as the archaeal genus Halobacterium. The transfer of techniques from bacteriorhodopsin studies to the metagenomic discovery of proteorhodopsin in 2000 further extended the field. Microbial rhodopsins have also been used as model systems to understand membrane protein structure and function, and they have become the target of technological applications such as optogenetics and nanotechnology. Analysing the connections between these historical episodes provides a rich example of how science works over longer time periods, especially with regard to the transfer of materials, methods and concepts between different research fields.     

Advanced microscopic and histochemical techniques: diagnostic tools in the molecular era of myology

Over the past two centuries, myology (i.e. the basic and clinical science of muscle and muscle disease) has passed through 3 stages of development: the classical period, the modern stage and the molecular era. The classical period spans the last part of nineteenth century and the earlier part of the twentieth century. During this time, several major muscle diseases were clinically and pathologically characterized, including Duchenne muscular dystrophy (DMD), myotonic dystrophy (DM) and facioscapulohumeral dystrophy (FSHD). The modern stage in the second half of the twentieth century is characterized by the adaptation of histo and cytochemical techniques to the study of muscle biopsies. These tools improved the diagnostic accuracy and made possible the identification of new changes and structures (Engel and Cunningham, 1963; Scarlato, 1975).     

Palaeontology and Evolutionary Developmental Biology: A Science of the Nineteenth and Twenty–first Centuries

A wind of change has swept through palaeontology in the past few decades. Contrast Sir Peter Medawar’s dismissive: ‘palaeontology is a particularly undemanding branch of science’ (as recalled by John Maynard Smith in Sabbagh 1999, p. 158) with ‘Palaeontology: grasping the opportunities in the science of the twenty–first century’, the title of a contribution to a special issue of Geobios by the Cambridge palaeontologist, Simon Conway Morris (1998a). The winds of change have come partly from palaeontologists seeking to broaden the impact of their studies and partly from biologists (neontologists) realizing the contributions that palaeontology can make to their disciplines. Consequently, impressions of past life preserved in stone are coming alive. Fossils are being described and analyzed using new tools and languages as the static fossil record becomes a record of transitions in patterns that can be explained and related to biological, ecological, climatic and tectonic changes. The latest addition is evolutionary developmental biology, or ‘evo–devo’, whose language provides a new basis upon which to interpret anatomical change, both materially and mechanistically. In this review I examine the major contributions made by palaeontology, how palaeontology has been linked to evolution and to embryology in the past, and how links with evo–devo have enlivened and will continue to enliven both palaeontology and evo–devo. Closer links between the two fields should illuminate important unresolved issues related to the origin of the metazoans (e.g. Why is there a conflict between molecular clocks and the fossil record in timing the metazoan radiation; were Precambrian metazoan ancestors similar to extant larvae or to miniature adults?) and to diversification of the metazoans (e.g. How do developmental constraints bias the direction of evolution; how do microevolutionary developmental processes relate to macroevolutionary changes?).