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PubMed2006

Medical informatics and bioinformatics: integration or evolution through scientific crises?

OBJECTIVES: To contribute a new perspective on recent investigations into the scientific foundations of medical informatics (MI) and bioinformatics (BI). To support efforts that could generate synergies and new research directions. METHODS: MI and BI are compared and contrasted from a philosophy of science perspective. Historical examples from MI and BI are analyzed based on contrasting viewpoints about the evolution of scientific disciplines. RESULTS: Our analysis suggests that the scientific approaches of MI and BI involve different assumptions and foundations, which, together with largely non-overlapping communities of researchers for the two disciplines, have led to different courses of development. We indicate how their respective application domains, medicine, and biology may have contributed to these differences in development. CONCLUSIONS: An analysis from the point of view of the philosophy of science is characteristic of established scientific disciplines. From a Kuhnian perspective, both disciplines may be entering a period of scientific crisis, where their foundations are questioned and where new ideas (or paradigm shifts) and a progressive research programme are needed to advance them scientifically. We discuss research directions and trends both supporting and challenging integration of the subdisciplines of MI and BI into a unified field of biomedical informatics (BMI), centered around the evolution of information cybernetics.

Computational Biology↗
PubMedDate not supplied

Molecular mechanisms of human embryogenesis: developmental pathogenesis of renal tract malformations.

The focus of this review is the normal and abnormal development of the kidney and lower urinary tract; for convenience, we will refer to the whole system as the renal tract. The content represents a convergence among the clinical disciplines of histopathology, nephrology, and urology as well the basic sciences of developmental biology and molecular genetics. The story has considerable clinical relevance since diverse renal tract malformations are increasingly detected on fetal ultrasound screening and constitute major causes of chronic renal failure necessitating dialysis and kidney transplantation in children. Evidence is emerging that at least some of these disorders have a defined genetic basis; in others, an abnormal embryonic, or even maternal, environment may contribute to the pathogenesis. This field of study is frequently updated, with new discoveries being made almost every week. Hence this review can not be exhaustive or definitive, but instead highlights some specific areas of interest.

Animals↗
PubMed2004

A new biology for a new century.

Biology today is at a crossroads. The molecular paradigm, which so successfully guided the discipline throughout most of the 20th century, is no longer a reliable guide. Its vision of biology now realized, the molecular paradigm has run its course. Biology, therefore, has a choice to make, between the comfortable path of continuing to follow molecular biology's lead or the more invigorating one of seeking a new and inspiring vision of the living world, one that addresses the major problems in biology that 20th century biology, molecular biology, could not handle and, so, avoided. The former course, though highly productive, is certain to turn biology into an engineering discipline. The latter holds the promise of making biology an even more fundamental science, one that, along with physics, probes and defines the nature of reality. This is a choice between a biology that solely does society's bidding and a biology that is society's teacher.

Biology↗
PubMed2001

Sapir's vision of culture and personality.

For Edward Sapir the concept of culture was a reification of processes that were rooted in individuals' personality and psychology. Sapir suggested that psychiatry's focus on individual biography and pathology gives it unique relevance for social science efforts to understand the mechanisms of cultural transmission and transformation. As a discipline that must integrate culture and biology in theory and practice, psychiatry can provide a corrective to the extremes of biological or cultural reductionism. Although mainstream psychiatry has largely abdicated the role it once had in the social sciences, the interdisciplinary field of cultural psychiatry may meet some of Sapir's hopes. Recent work in cultural psychiatry is centrally concerned with illness narratives that arise from the interaction of personal and collective meaning. Illness narratives may serve individual defensive functions, position individuals in a social world, and help to maintain overarching cultural formations. They also may challenge or subvert existing cultural meanings and create new forms of discourse. The close analysis of how cultural and individual meanings interact that is provided by cultural psychiatry has much to offer the wider field of cultural anthropology.

Anthropology, Cultural↗
PubMed2002

APBioNet: the Asia-Pacific regional consortium for bioinformatics.

Bioinformatics and computational biology, along with the related fields of genomics, proteomics, functional genomics and systems biology are new wave scientific disciplines that harness composite computational power across networks to advance biological knowledge at the most basic level and to direct traditional laboratory-based research efforts in the biomedical sciences. 'Fostering the growth of bioinformatics and allied disciplines in the Asia-Pacific region' is the motto of the first regional bioinformatics society, the Asia-Pacific Bioinformatics Network (APBioNet). APBioNet addresses the issues of hardware, software, databases and networks pertaining to bioinformatics, with the additional layer of pertinent education, training and research. Recent milestones achieved include hosting an international bioinformatics symposium in Asia and setting up large-scale regional grid-computing projects.

Asia↗
PubMed2004

Introducing "Frontiers in Zoology"

As a biological discipline, zoology has one of the longest histories. Today it occasionally appears as though, due to the rapid expansion of life sciences, zoology has been replaced by more or less independent sub-disciplines amongst which exchange is often sparse. However, the recent advance of molecular methodology into "classical" fields of biology, and the development of theories that can explain phenomena on different levels of organisation, has led to a re-integration of zoological disciplines promoting a broader than usual approach to zoological questions. Zoology has re-emerged as an integrative discipline encompassing the most diverse aspects of animal life, from the level of the gene to the level of the ecosystem.The new journal Frontiers in Zoology is the first Open Access journal focussing on zoology as a whole. It aims to represent and re-unite the various disciplines that look at animal life from different perspectives and at providing the basis for a comprehensive understanding of zoological phenomena on all levels of analysis. Frontiers in Zoology provides a unique opportunity to publish high quality research and reviews on zoological issues that will be internationally accessible to any reader at no cost.

Journal Article↗
PubMed2006

Towards a unified science of cultural evolution.

We suggest that human culture exhibits key Darwinian evolutionary properties, and argue that the structure of a science of cultural evolution should share fundamental features with the structure of the science of biological evolution. This latter claim is tested by outlining the methods and approaches employed by the principal subdisciplines of evolutionary biology and assessing whether there is an existing or potential corresponding approach to the study of cultural evolution. Existing approaches within anthropology and archaeology demonstrate a good match with the macroevolutionary methods of systematics, paleobiology, and biogeography, whereas mathematical models derived from population genetics have been successfully developed to study cultural microevolution. Much potential exists for experimental simulations and field studies of cultural microevolution, where there are opportunities to borrow further methods and hypotheses from biology. Potential also exists for the cultural equivalent of molecular genetics in "social cognitive neuroscience," although many fundamental issues have yet to be resolved. It is argued that studying culture within a unifying evolutionary framework has the potential to integrate a number of separate disciplines within the social sciences.

Animals↗
PubMed2005

Paradigm change in evolutionary microbiology.

Thomas Kuhn had little to say about scientific change in biological science, and biologists are ambivalent about how applicable his framework is for their disciplines. We apply Kuhn's account of paradigm change to evolutionary microbiology, where key Darwinian tenets are being challenged by two decades of findings from molecular phylogenetics. The chief culprit is lateral gene transfer, which undermines the role of vertical descent and the representation of evolutionary history as a tree of life. To assess Kuhn's relevance to this controversy, we add a social analysis of the scientists involved to the historical and philosophical debates. We conclude that while Kuhn's account may capture aspects of the pattern (or outcome) of an episode of scientific change, he has little to say about how the process of generating new understandings is occurring in evolutionary microbiology. Once Kuhn's application is limited to that of an initial investigative probe into how scientific problem-solving occurs, his disciplinary scope becomes broader.

Biological Evolution↗
PubMed1995

Who wrote the book of life? Information and the transformation of molecular biology, 1945-55.

This paper focuses on the opening of a discursive space: the emergence of informational and scriptural representations of life and hereditiy and their self-negating consequences for the construction of biological meaning. It probes the notion of writing and the book of life and shows how molecular biology's claims to a status of language and texuality undermines its own objective of control. These textual significations were historically contingent. The informational representations of heredity and life were not an outcome of the internal cognitive momentum of molecular biology; they were not a logical necessity of the unravelling of the base-pairing of the DNA double-helix. They were transported into molecular biology still within the protein paradigm of the gene in the 1940s and permeated nearly every discipline in the life and social sciences. These information-based models, metaphors, linguistic, and semiotic tools which were central to the formulation of the genetic code were transported into molecular biology from cybernetics, information theory, electronic computing, and control and communication systems--technosciences that were deeply embedded with the military experiences of World War II and the Cold War. The information discourse thus became fixed in molecular biology not because it worked in the narrow epistemic sense (it did not), but because it positioned molecular biology within postwar discourse and culture, perhaps within the transition to a post-modern information-based society.

History, 20th Century↗
PubMed2005

Again, what the philosophy of biology is not.

There are many things that philosophy of biology might be. But, given the existence of a professional philosophy of biology that is arguably a progressive research program and, as such, unrivaled, it makes sense to define philosophy of biology more narrowly than the totality of intersecting concerns biologists and philosophers (let alone other scholars) might have. The reasons for the success of the "new" philosophy of biology remain poorly understood. I reflect on what Dutch and Flemish, and, more generally, European philosophers of biology could do to improve the situation of their discipline locally, regionally, and internationally, paying particular attention to the lessons to be learned from the "Science Wars."

Animals↗
PubMed2005

Digital biology: an emerging and promising discipline.

This article examines the role of computation and quantitative methods in modern biomedical research to identify emerging scientific, technical, policy and organizational trends. It identifies common concerns and practices in the emerging community of computationally-oriented bio-scientists by reviewing a national symposium, Digital Biology: the Emerging Paradigm, held at the National Institutes of Health in Bethesda, Maryland, November 6th and 7th 2003. This meeting showed how biomedical computing promises scientific breakthroughs that will yield significant health benefits. Three key areas that define the emerging discipline of digital biology are: scientific data integration, multi-scale modeling and networked science. Each area faces unique technical challenges and information policy issues that must be addressed as the field matures. Here we summarize the emergent challenges and offer suggestions to academia, industry and government on how best to expand the role of computation in their scientific activities.

Computational Biology↗
PubMed2001

Diet and cancer prevention.

Research from several sources provides strong evidence that vegetables, fruits, and whole grains, dietary fibre, certain micronutrients, some fatty acids and physical activity protect against some cancers. In contrast, other factors, such as obesity, alcohol, some fatty acids and food preparation methods may increase risks. Unravelling the multitude of plausible mechanisms for the effects of dietary factors on cancer risk will likely necessitate that nutrition research moves beyond traditional epidemiological and metabolic studies. Nutritional sciences must build on recent advances in molecular biology and genetics to move the discipline from being largely 'observational' to focusing on 'cause and effect'. Such basic research is fundamental to cancer prevention strategies that incorporate effective dietary interventions for target populations.

Alcohol Drinking↗
PubMed2006

Opportunities for chemical biologists: a view from the National Institutes of Health.

The most exciting and vibrant areas of research often lie at the interfaces between disciplines that have traditionally been separate. In the case of the chemical and biological sciences, such interfaces have been fruitfully explored for more than a century. The fields of pharmacology, biochemistry, and biophysical chemistry are relatively mature, yet they are still quite active and full of challenging problems and opportunities for new discoveries. These fields are integral to biomedical research and have had a tremendous impact on human health.

Biochemistry↗
PubMed2006

Back to the future: education for systems-level biologists.

We describe a graduate course in quantitative biology that is based on original path-breaking papers in diverse areas of biology; each of these papers depends on quantitative reasoning and theory as well as experiment. Close reading and discussion of these papers allows students with backgrounds in physics, computational sciences or biology to learn essential ideas and to communicate in the languages of disciplines other than their own.

Biology↗
PubMed2005

Dynamic multiphoton imaging: a live view from cells to systems.

Leaps in scientific technology often occur at the interface of seemingly disparate disciplines. This holds true with the recent application of multiphoton microscopy to the biological sciences, leading to a new generation of imaging-based studies extending from the tracking of individual molecules within living cells to the observation of whole organisms.

Animals↗
PubMed2004

Implications of systems dynamic models and control theory for environmental approaches to the prevention of alcohol- and other drug use-related problems.

The approach described in this article is premised on the idea that drug and alcohol use-related problems are heterogeneously distributed with respect to population and geography, and therefore, are essentially local problems. More specifically, it is argued that viewing a local community as an interacting set of systems that support or buffer the occurrence of specific substance misuse outcomes, opens up to research two important prospects. The first of these involves creating adequate systems models that can capture the primary community structures and relationships that support public health problems such as alcohol and drug misuse and related outcomes. The second entails rationally testing control strategies that have the potential to moderate or reduce these problems. Understanding and controlling complex dynamic systems models nowadays pervades all scientific disciplines, and it is to research in areas such as biology, ecology, engineering, computer sciences, and mathematics that researchers in the field of addictions must turn to in order to better study the complexity that confronts them as they try to understand and prevent problems resulting from alcohol and drug use and misuse. Here we set out what such a systems-based understanding of alcohol- and drug use-related problems will require and discuss its implications for public policy and prevention programming.

Humans↗
PubMed2006

Cell biology should be taught as science is practised.

Over the past 20 years, there has been a dramatic transformation in the goals of science teaching at all levels and within all disciplines. The emphasis has moved from students obtaining a base of scientific facts to students developing a deep understanding of important concepts. This transformation requires a significant shift in the approach and attitude of the instructors and students, as well as in the procedures and techniques that are required to teach cell biology.

Biology↗