Recent work on the quality assurance of the Gene Ontology (GO, Gene Ontology Consortium 2004) from the perspective of both linguistic and ontological organization has made it clear that GO lacks the kind of formalism needed to support logic-based reasoning. At the same time it is no less clear that GO has proven itself to be an excellent terminological resource that can serve to combine together a variety of biomedical database and information systems. Given the strengths of GO, it is (...) worth investigating whether, by overcoming some of its weaknesses from the point of view of formal-ontological principles, we might not be able to enhance a version of GO which can come even closer to serving the needs of the various communities of biomedical researchers and practitioners. It is accepted that clinical and bioinformatics need to find common ground if the results of data-intensive biomedical research are to be harvested to the full. It is also widely accepted that no single method will be sufficient to create the needed common framework. We believe that the principles-based approach to life-science data integration and knowledge representation must be one of the methods applied. Indeed in dealing with the ontological representation of carcinomas, and specifically of colon carcinomas, we have established that, had GO (and related biomedical ontologies) followed some of the basic formal-ontological principles we have identified (Smith et al. 2004, Ceusters et al. 2004), then the effort required to navigate successfully between clinical and bioinformatics systems would have been reduced. We point here to the sources of ontologically-related errors in GO, and also provide arguments as to why and how such errors need to be resolved. (shrink)

There are a number of existing classifications and staging schemes for carcinomas, one of the most frequently used being the TNM classification. Such classifications represent classes of entities which exist at various anatomical levels of granularity. We argue that in order to apply such representations to the Electronic Health Records one needs sound ontologies which take into consideration the diversity of the domains which are involved in clinical bioinformatics. Here we outline a formal theory for addressing these issues (...) in a way that the ontologies can be used to support inferences relating to entities which exist at different anatomical levels of granularity. Our case study is the colon carcinoma, one of the most common carcinomas prevalent within the European population. (shrink)

There is a need recognized by the National Institute of Dental & Craniofacial Research and the National Cancer Institute to advance basic, translational and clinical saliva research. The goal of the Salivaomics Knowledge Base (SKB) is to create a data management system and web resource constructed to support human salivaomics research. To maximize the utility of the SKB for retrieval, integration and analysis of data, we have developed the Saliva Ontology and SDxMart. This article reviews the informatics advances in (...) saliva diagnostics made possible by the Saliva Ontology and SDxMart. (shrink)

BackgroundSystems medicine is the name for an assemblage of scientific strategies and practices that include bioinformatics approaches to human biology ; “big data” statistical analysis; and medical informatics tools. Whereas personalized and precision medicine involve similar analytical methods applied to genomic and medical record data, systems medicine draws on these as well as other sources of data. Given this distinction, the clinical translation of systems medicine poses a number of important ethical and epistemological challenges for researchers working to (...) generate systems medicine knowledge and clinicians working to apply it.DiscussionThis article focuses on three key challenges: First, we will discuss the conflicts in decision-making that can arise when healthcare providers committed to principles of experimental medicine or evidence-based medicine encounter individualized recommendations derived from computer algorithms. We will explore in particular whether controlled experiments, such as comparative effectiveness trials, should mediate the translation of systems medicine, or if instead individualized findings generated through “big data” approaches can be applied directly in clinical decision-making. Second, we will examine the case of the Riyadh Intensive Care Program Mortality Prediction Algorithm, pejoratively referred to as the “death computer,” to demonstrate the ethical challenges that can arise when big-data-driven scoring systems are applied in clinical contexts. We argue that the uncritical use of predictive clinical algorithms, including those envisioned for systems medicine, challenge basic understandings of the doctor-patient relationship. Third, we will build on the recent discourse on secondary findings in genomics and imaging to draw attention to the important implications of secondary findings derived from the joint analysis of data from diverse sources, including data recorded by patients in an attempt to realize their “quantified self.”SummaryThis paper examines possible ethical challenges that are likely to be raised as systems medicine to be translated into clinical medicine. These include the epistemological challenges for clinical decision-making, the use of scoring systems optimized by big data techniques and the risk that incidental and secondary findings will significantly increase. While some ethical implications remain still hypothetical we should use the opportunity to prospectively identify challenges to avoid making foreseeable mistakes when systems medicine inevitably arrives in routine care. (shrink)

The intersection of ethics, computing, and genetics plots a space not yet adequately mapped, despite its importance, indeed, its rapidly growing importance. Its subdomains are well-enough known: or the study of ethical issues in genetics and genomics, is part of core curricula everywhere. Ethics and computing is an established subfield. Computing and geneticshas in little more than a decade progressed from subsubspecialty to the sine qua non of contemporary biomedical research, and it bids fair to transform clinical practice. We (...) must prepare for the complete digitization of the genomes of individual patients and the storage of millions of these genomes in very large databases. (shrink)

American Academy of Pediatrics (AAP) and American College of Medical Genetics (ACMG) recently provided two recommendations about predictive genetic testing of children. The Clinical Sequencing Exploratory Research Consortium's Pediatrics Working Group compared these recommendations, focusing on operational and ethical issues specific to decision making for children. Content analysis of the statements addresses two issues: (1) how these recommendations characterize and analyze locus of decision making, as well as the risks and benefits of testing, and (2) whether the guidelines conflict (...) or come to different but compatible conclusions because they consider different testing scenarios. These statements differ in ethically significant ways. AAP/ACMG analyzes risks and benefits using best interests of the child and recommends that, absent ameliorative interventions available during childhood, clinicians should generally decline to order testing. Parents authorize focused tests. ACMG analyzes risks and benefits using the interests of the child and other family members and recommends that sequencing results be examined for additional variants that can lead to ameliorative interventions, regardless of age, which laboratories should report to clinicians who should contextualize the results. Parents must accept additional analysis. The ethical arguments in these statements appear to be in tension with each other. (shrink)

Research question and aimClinical Ethics Committees (CECs) aim to support healthcare professionals (HPs) and healthcare organizations to deal with the ethical issues of clinical practice. In 2020,...

For decades a debate has played out in the literature about who bioethicists are, what they do, whether they can be considered professionals qua bioethicists, and, if so, what professional responsibilities they are called to uphold. Health care ethics consultants are bioethicists who work in health care settings. They have been seeking guidance documents that speak to their special relationships/duties toward those they serve. By approving a Code of Ethics and Professional Responsibilities for Health Care Ethics Consultants, the American Society (...) for Bioethics and Humanities (ASBH) has moved the professionalization debate forward in a significant way. This first code of ethics focuses on individuals who provide health care ethics consultation (HCEC) in clinical settings. The evolution of the code's development, implications for the field of HCEC and bioethics, and considerations for future directions are presented here. (shrink)

Almost all biomedical research to date has relied upon mean measurements from cell populations, however it is well established that what it is observed at this macroscopic level can be the result of many interactions of several different single cells. Thus, the observable macroscopic ‘average’ cannot outright be used as representative of the ‘average cell’. Rather, it is the resulting emerging behaviour of the actions and interactions of many different cells. Single‐cell RNA sequencing (scRNA‐Seq) enables the comparison of the transcriptomes (...) of individual cells. This provides high‐resolution maps of the dynamic cellular programmes allowing us to answer fundamental biological questions on their function and evolution. It also allows to address medical questions such as the role of rare cell populations contributing to disease progression and therapeutic resistance. Furthermore, it provides an understanding of context‐specific dependencies, namely the behaviour and function that a cell has in a specific context, which can be crucial to understand some complex diseases, such as diabetes, cardiovascular disease and cancer. Here, we provide an overview of scRNA‐Seq, including a comparative review of emerging technologies and computational pipelines. We discuss the current and emerging applications and focus on tumour heterogeneity a clear example of how scRNA‐Seq can provide new understanding of a complex disease. Additionally, we review the limitations and highlight the need of powerful computational pipelines and reproducible protocols for the broader acceptance of this technique in basic and clinical research. (shrink)

The practice and development of modern medicine requires large amounts of data, particularly in the domain of cancer. The future of personalized medicine lies neither with “genomic medicine” nor with “precision medicine”, but with “data medicine”. The establishment of this DM has required far-reaching changes, to establish four essential elements connecting patients and doctors: biobanks, databases, bioinformatic platforms and genomic platforms. The “transformation” of scientific research areas, such as genetics, bioinformatics and biostatistics, into clinical specialties has generated a (...) new vision of care. Molecular tumor boards are one response to these changes and are now providing better access to next-generation sequencing and new cancer treatments to patients with inoperable or metastatic cancers, and those for whom the usual treatment has failed. However, MTB face a crucial ethical challenge: maintaining and improving the trust of patients, clinicians, researchers and industry in academic medical centers supported by private or public funding rather than providing genetic data directly to private companies. We believe that, in this era of DM, appropriate modern digital communication networks will be required to maintain this trust and to improve the organization and effectiveness of the system. There is, therefore, a need to reconsider the form and content of informed consent documents at all academic medical centers and to introduce dynamic and electronic informed consent. (shrink)

This book is the first systematic, detailed treatment of the approaches to ethical issues taken by biotech and pharmaceutical companies. The application of genetic/genomic technologies raises a whole spectrum of ethical questions affecting global health that must be addressed. Topics covered in this comprehensive survey include considerations for bioprospecting in transgenics, genomics, drug discovery, and nutrigenomics, as well as how to improve stakeholder relations, design ethical clinical trials, avoid conflicts of interest, and establish ethics advisory boards. The expert authors (...) represent multiple disciplines including law, medicine, bioinformatics, pharmaceutics, business, and ethics. (shrink)

Photo ID 72893750 © Rawpixelimages|Dreamstime.com ABSTRACT Solidarity is a concept increasingly employed in bioethics whose application merits further clarity and explanation. Given how vital cooperation and community-level care are to mitigating communicable disease transmission, we use lessons from the COVID-19 pandemic to reveal how solidarity is a useful descriptive and analytical tool for public health scholars, practitioners, and policymakers. Drawing upon an influential framework of solidarity that highlights how solidarity arises from the ground up, we reveal how structural forces can (...) impact the cultivation of solidarity from the top down, particularly through ensuring robust access to important social determinants of health. Public health institutions can support solidarity movements among individuals and communities by adopting a lens of social justice when considering public health priorities and, in turn, promote health equity. INTRODUCTION Over the past two decades, scholars have invoked the concept of solidarity when assessing a wide range of topics in bioethics, from CRISPR-Cas9 technology to organ donation to structural racism.[1] However, the growing literature on solidarity has not fully examined the roles and responsibilities of institutions and governments in fostering solidarity, especially regarding public health measures that implicate entire populations. We argue that it remains unclear how public health institutions should engage with solidarity and how their engagement will affect public health and its ethics. We first take Prainsack and Buyx’ three-tiered framework as an analytical starting point.[2] We then explore how public health institutions can foster solidarity by carefully considering factors that may bolster it on an interpersonal, community, and national scale. We conclude that public health institutions should adopt a lens of social justice to promote solidarity at the interpersonal and community levels, thereby promoting equity in future public health efforts. BACKGROUND Calls for solidarity in bioethics raise longstanding normative questions about the nature and limits of our duties to one another and how to weigh autonomy over considerations of justice.[3] Though the term is diversely applied, Prainsack and Buyx propose a potentially unifying definition in the 2011 Nuffield Council report, “Solidarity: Reflections On An Emerging Concept in Bioethics.” The report defines solidarity as an activity involving “shared practices reflecting a collective commitment to carry financial, social, emotional, and or other ‘costs’ to assist others.” Their conceptualization also includes important features that distinguish solidarity from other values like empathy or altruism: solidarity emphasizes action rather than mere internal feeling and recognition of connection as motivation.[4] Bioethicists have since applied this conceptualization when analyzing issues in public and global health, given that population-level efforts need cooperation from individuals and communities. Prainsack and Buyx further note that solidarity is relevant in bioethics discourses about justice and equity, in support of providing aid to low- and middle-income countries, and as a value exemplified by European welfare states.[5] Other bioethicists have argued that promoting solidarity can contribute to community engagement, partnership with Tribal communities, and global health equity.[6] Most recently, scholars have applied solidarity as a lens to assess the COVID-19 pandemic, highlighting the pitfalls of national mitigation efforts and global disparities in disease outcomes.[7] I. Solidarity at Three Levels It seems impossible to foster solidarity in public health if we cannot identify it in general contexts. Prainsack and Buyx articulate three levels of solidarity: interpersonal solidarity, group solidarity, and legal or contractual codifications of solidarity.[8] They argue that each level inherently informs the one ‘above’ it in a unilateral direction. In other words, solidarity is fundamentally a bottom-up phenomenon. Solidarity among individuals influences group norms, which then have the potential to shape policy and institutional practice.[9] Within the Prainsack and Buyx framework, it would seem nonsensical to posit how solidarity might be expressed vertically or from the “top down.” It appears intuitively odd to imagine how a government entity might ‘be’ in solidarity with a person or group if solidarity requires some cognition about their condition per Prainsack and Buyx’ definition. Some have argued that solidarity does not seem like something that one can impose, as instances of it arise from agents recognizing and acting upon some bond rather than in response to a command. Indeed, people may be rightfully hesitant to engage in solidarity if the official messaging is overly paternalistic or coercive.[10] However, some authors have countered that governments can express solidarity through enacting structural and policy changes, though it is ambiguous how these actions are distinct from a justice-driven approach.[11] If a bottom-up approach is thus the most practical means of achieving policy that reflects solidarity, then it does not add much to public health. Institutions would be ineffective without the population’s initiation of the corresponding social norms. However, we find this conclusion overly pessimistic. Fostering a culture of solidarity to improve public health has potential merit. Prainsack and Buyx’ framework overlooks how public health actors can influence solidarity between individuals and across communities. To clarify, we agree with the view that solidarity is a bottom-up phenomenon. Solidarity may not be able to originate in a top-down fashion, but we suggest that public health institutions can take a more active role in providing the public with accurate information, promoting social justice, and intervening in the social determinants of health. II. The COVID-19 Pandemic as a Case Study Lessons learned from the ongoing COVID-19 pandemic support our argument. The pandemic deepened socioeconomic disparities in the US and hindered access to vital resources such as food, housing, and healthcare.[12] Prainsack recently noted: “[n]ext to the immediate health effects of the virus, poverty and grave inequalities have been the root causes of human suffering during the pandemic.”[13] Prior to the pandemic, many rural and low-income populations lacked reliable access to the internet and devices like laptops or smartphones. This continued lack of access restricts the flow of information and prevents people from accessing telemedicine services.[14] Preexisting social, political, and health inequities worsened health outcomes among many marginalized racial and ethnic groups. It is well-documented that communities of color, including Black, American Indian or Alaska Native, and Latinx populations, had greater COVID-related mortality and morbidity due to the effects of structural racism.[15] Although federal US agencies such as the Centers for Disease Control and Prevention enacted laws that provided safety nets (e.g., the Federal Eviction Moratorium), the majority of such programs have ended, leaving many with little assistance and the threat of further hardship.[16] These disparities are relevant because Prainsack, Buyx, and others note that solidarity arises from agents recognizing and acting on some perceived attainable collective goal(s). Income inequality and disparate access to food, education, and health care may lead people to consider public health goals unattainable. This could limit the desire to work toward those goals collectively.[17] The existing literature on collective action theory supports this intuition. It emphasizes that structural conditions, such as an absence of perceived hope for social change among a group, can lead to low ‘group efficacy’ and little willingness to cooperate, both within and across socioeconomic strata.[18] The pandemic spurred countless messages from public health agencies. The messaging did not recognize or attend to the different material realities and circumstances of the US population. How can people feel comfortable getting vaccinated if they deeply distrust the government, including public health institutions? How can people remain motivated to wear masks and distance themselves if they cannot afford basic necessities and work jobs without adequate pay and leave policies? We ask these questions to illustrate how socioeconomic disparities can marginalize people if they feel ignored, apathetic, or resentful of those better off or those in power whom they perceive to “not be doing enough.” This marginalization precludes the formation of solidarity. There are instances when a population has disparate access to resources and social capital, but solidarity may still emerge from a shared goal or vision for the future. For example, a heterogeneous population living in the same town may come together to protest an environmental injustice that impacts their water supply with the common goal of securing access to safe drinking water. However, many populations in the US failed to recognize shared goals of this kind during the COVID-19 pandemic. A significant minority of the US population was reluctant to acknowledge the severity of COVID-19 infection and thus refused to participate in efforts to mitigate its spread. Even between groups who shared the goal of slowing COVID-19 transmission, the methods were widely debated. Approximately 20 percent of the adult population eligible for vaccination remains unvaccinated.[19] Governmental bodies responsible for disseminating information, coordinating the allocation of resources, and establishing guidelines have a large role in mediating these disagreements and intervening in socioeconomic conditions that impact people's ability and willingness to engage in solidarity. III. Solidarity, Social Justice, and the Role of Public Health Institutions Adopting a lens of social justice provides further insights into how public health actors impact solidarity. Powers and Faden argue that the “foundational moral justification for the social institution of public health is social justice.”[20] Their theory of social justice has two aims. First, it ensures that everyone has a sufficient amount of the six core elements of well-being and that public health institutions are responsible for “adopting policies and creating environments” where all can flourish.[21] Second, public health institutions should distribute resources meant to promote well-being and focus on the “needs of those who are the most disadvantaged.”[22] Public health institutions should enact policies that address injustice. In doing so, public health institutions can seed the opportunity to build solidarity from the bottom up. Equipping individuals and communities with resources will foster cooperation and adherence to policies that require solidarity, such as masking and vaccination. This is consistent with arguments illustrating how institutions such as Tribal governments promote the conditions needed for their group, and especially its most vulnerable members, to flourish.[23] Addressing social determinants of health with a social justice lens will create the circumstances under which more individuals and groups can find common causes and foster solidarity. In the long run, such efforts may result in the establishment of values and practices from the bottom up. There are societal and public health preconditions required before institutions can expect their audience to act in solidarity with one another. Through their great influence over information and resources, public institutions do have the power to impact what values are most widespread. Furthermore, public health may foster trust and hope, which are important psychosocial factors that influence collective action,[24] if policies increase access to resources that promote well-being. Messaging efficacy also depends on the context of public trust, education, and whether the institutions meet one’s basic needs. Disparate messaging across different public institutions may confuse or disillusion individuals. To apply our theory of solidarity to the decision to vaccinate, a policy would be to foster conditions that facilitate access to vaccines and information about vaccine efficacy instead of imposing a top-down mandate without first eliciting public trust. IV. Counterargument Some argue that discordant public health messaging, ineffective government, and inadequate social programs can also bring people together under pressure and foster solidarity. One may argue that the most powerful motivators towards solidarity are strife and disparity, as evidenced throughout history. During the pandemic alone, political struggle and personal hardship inspired solidarity in the US, from individual neighbors helping each other to mutual aid groups forming across communities. We thus do not claim that solidarity is possible only when our government programs and public health institutions are most effective. We instead point out that solidarity can be further hindered when people feel alienated, hopeless, and pitted against each other. CONCLUSION Many competing conceptualizations of solidarity persist in the bioethics literature, and Prainsack and Buyx offer one compelling framework that public health ethicists continue to draw upon.[25] However, their framework fails to acknowledge how public health institutions impact interpersonal and group solidarity. Public health institutions can foster solidarity through actions other than mere messaging, invoking catchphrases like “we are all in this together.” Efforts to address socioeconomic preconditions and alleviate health disparities can cultivate group solidarity. As we saw during the pandemic, cooperation and solidarity go hand-in-hand with disease mitigation efforts; solidarity has clear intrinsic value.[26] As this relationship becomes more apparent, we will continue to see attempts from public health institutions to foster or invoke solidarity. Therefore, public health institutions would be remiss to ignore their role in addressing the social determinants of health. Adopting a social justice lens when planning public health interventions will clarify and strengthen their role in facilitating solidarity. Ultimately, if health disparities continue to persist or widen, it is very hard to imagine how group solidarity can ever be achieved. The widescale adoption of many public health measures needed to promote health and well-being would be conducive to solidarity. - Disclaimer: The opinions expressed are the authors’ and do not represent the views of the NIH, DHHS, or the U.S. government. Funding Disclosure: This work was supported in part by the Intramural Program of the National Institutes of Health Clinical Center. - [1] John J Mulvihill et al., “Ethical Issues of CRISPR Technology and Gene Editing through the Lens of Solidarity,” British Medical Bulletin 122 (2017): 17–29, https://doi.org/10.1093/bmb/ldx002; Ben Saunders, “Altruism or Solidarity? The Motives for Organ Donation and Two Proposals,” Bioethics 26, no. 7 (September 2012): 376–81, https://doi.org/10.1111/j.1467-8519.2012.01989.x; -Vanessa Y Hiratsuka, “SPECIAL REPORT: A Critical Moment in Bioethics: Reckoning with Anti-Black Racism through Intergenerational Dialogue A Call for Solidarity in Bioethics: Confronting Anti-Black Racism Together,” 2022, https://doi.org/10.1002/hast.1380. [2] Prainsack and Buyx, Solidarity: Reflections on an Emerging Concept in Bioethics London: Nuffield Council on Bioethics, 2011; Prainsack and Buyx, “Solidarity in Contemporary Bioethics--towards a New Approach.” Bioethics 26, no. 7 (September 2012): 343–50. https://doi.org/10.1111/J.1467-8519.2012.01987.X. [3] Bob Simpson, “A ‘We’ Problem for Bioethics and the Social Sciences: A Response to Barbara Prainsack,” Science, Technology, & Human Values 43, no. 1 (January 12, 2018): 45–55, https://doi.org/10.1177/0162243917735899. [4] Barbara Prainsack and Alena Buyx, Solidarity: Reflections on an Emerging Concept in Bioethics (London: Nuffield Council on Bioethics, 2011). [5] Barbara Prainsack and Alena Buyx, “Solidarity in Contemporary Bioethics--towards a New Approach,” Bioethics 26, no. 7 (September 2012): 343–50, https://doi.org/10.1111/J.1467-8519.2012.01987.X. [6] Bridget Pratt, Phaik Yeong Cheah, and Vicki Marsh, “Solidarity and Community Engagement in Global Health Research,” The American Journal of Bioethics : AJOB 20, no. 5 (May 3, 2020): 43–56, https://doi.org/10.1080/15265161.2020.1745930; Sara Chandros Hull, F. Leah Nez (Diné), and Juliana M. Blome, “Solidarity as an Aspirational Basis for Partnership with Tribal Communities,” The American Journal of Bioethics 21, no. 10 (October 3, 2021): 14–17, https://doi.org/10.1080/15265161.2021.1965258; Mbih J. Tosam et al., “Global Health Inequalities and the Need for Solidarity: A View from the Global South,” Developing World Bioethics 18, no. 3 (September 1, 2018): 241–49, https://doi.org/10.1111/DEWB.12182. [7] Peter West-Oram, “Solidarity Is for Other People: Identifying Derelictions of Solidarity in Responses to COVID-19,” Journal of Medical Ethics 47, no. 2 (February 1, 2021): 65–68, https://doi.org/10.1136/MEDETHICS-2020-106522; Barbara Prainsack, “Solidarity in Times of Pandemics,” Democratic Theory 7, no. 2 (December 1, 2020): 124–33, https://doi.org/10.3167/DT.2020.070215; F. Marijn Stok et al., “Social Inequality and Solidarity in Times of COVID-19,” International Journal of Environmental Research and Public Health 18, no. 12 (June 2, 2021), https://doi.org/10.3390/IJERPH18126339; Ming Jui Yeh, “Solidarity in Pandemics, Mandatory Vaccination, and Public Health Ethics,” American Journal of Public Health 112, no. 2 (February 1, 2022): 255–61, https://doi.org/10.2105/AJPH.2021.306578; Barbara Prainsack, “Beyond Vaccination Mandates: Solidarity and Freedom During COVID-19.,” Am J Public Health 112, no. 2 (February 1, 2022): 232–33, https://doi.org/10.2105/AJPH.2021.306619. [8] Prainsack and Buyx, Solidarity: Reflections on an Emerging Concept in Bioethics London: Nuffield Council on Bioethics, 2011; Prainsack and Buyx, “Solidarity in Contemporary Bioethics--towards a New Approach.” Bioethics 26, no. 7 (September 2012): 343–50. https://doi.org/10.1111/J.1467-8519.2012.01987.X. [9] Prainsack and Buyx, Solidarity: Reflections on an Emerging Concept in Bioethics London: Nuffield Council on Bioethics, 2011; Prainsack and Buyx, “Solidarity in Contemporary Bioethics--towards a New Approach.” Bioethics 26, no. 7 (September 2012): 343–50. https://doi.org/10.1111/J.1467-8519.2012.01987.X. [10] Yeh, “Solidarity in Pandemics, Mandatory Vaccination, and Public Health Ethics”; Prainsack, “Beyond Vaccination Mandates: Solidarity and Freedom During COVID-19.” [11] Ho, Anita, and Iulia Dascalu. "Relational solidarity and COVID-19: an ethical approach to disrupt the global health disparity pathway." Global Bioethics 32, no. 1 (2021): 34-50; West-Oram, Peter. "Solidarity is for other people: identifying derelictions of solidarity in responses to COVID-19." Journal of Medical Ethics 47, no. 2 (2021): 65-68. [12] Monica Webb Hooper, Anna María Nápoles, and Eliseo J. Pérez-Stable, “COVID-19 and Racial/Ethnic Disparities,” JAMA 323, no. 24 (June 23, 2020): 2466, https://doi.org/10.1001/jama.2020.8598. [13] Prainsack, Barbara. “Beyond Vaccination Mandates: Solidarity and Freedom During COVID-19.” Am J Public Health 112, no. 2 (February 1, 2022): 232–33. https://doi.org/10.2105/AJPH.2021.306619. [14] Camille A Clare, “Telehealth and the Digital Divide as a Social Determinant of Health during the COVID-19 Pandemic,” Network Modeling Analysis in Health Informatics and Bioinformatics 10 (2021): 26, https://doi.org/10.1007/s13721-021-00300-y. [15] Patrick Nana-Sinkam et al., “Health Disparities and Equity in the Era of COVID-19,” Journal of Clinical and Translational Science 5, no. 1 (March 16, 2021): e99, https://doi.org/10.1017/cts.2021.23. [16] Kathryn M Leifheit et al., “Expiring Eviction Moratoriums and COVID-19 Incidence and Mortality,” American Journal of Epidemiology 190, no. 12 (December 1, 2021): 2503–10, https://doi.org/10.1093/aje/kwab196. [17] Barbara Prainsack, “Solidarity in Times of Pandemics,” Democratic Theory 7, no. 2 (December 1, 2020): 124–33, https://doi.org/10.3167/DT.2020.070215 [18] Maximilian Agostini and Martijn van Zomeren, “Toward a Comprehensive and Potentially Cross-Cultural Model of Why People Engage in Collective Action: A Quantitative Research Synthesis of Four Motivations and Structural Constraints.,” Psychological Bulletin 147, no. 7 (July 2021): 667–700, https://doi.org/10.1037/bul0000256. [19] Department of Health and Human Services (HHS) Centers for Disease Control and Prevention (HHS/CDC), “COVID Data Tracker,” 2023, https://covid.cdc.gov/covid-data-tracker. [20] Powers, Madison, and Ruth Faden. Social Justice: The Moral Foundation of Public Health and Health Policy. 1st editio. New York: Oxford Press, 2006, p. 9 and Chapter 4 [21] Powers and Faden, Social Justice: The Moral Foundation of Public Health and Health Policy; Madison Powers and Ruth Faden, Structural Injustice: Power, Advantage, and Human Rights (New York: Oxford University Press, 2019). [22] Powers, Madison, and Ruth Faden. Social Justice: The Moral Foundation of Public Health and Health Policy. 1st editio. New York: Oxford Press, 2006, p. 10 [23] Bobby Saunkeah et al., “Extending Research Protections to Tribal Communities,” The American Journal of Bioethics 21, no. 10 (October 3, 2021): 5–12, https://doi.org/10.1080/15265161.2020.1865477. [24] Agostini and van Zomeren, “Toward a Comprehensive and Potentially Cross-Cultural Model of Why People Engage in Collective Action: A Quantitative Research Synthesis of Four Motivations and Structural Constraints.” [25] Prainsack and Buyx, Solidarity: Reflections on an Emerging Concept in Bioethics. [26] Ruth Chadwick, “COVID‐19 and the Possibility of Solidarity,” Bioethics 34, no. 7 (September 8, 2020): 637–637, https://doi.org/10.1111/bioe.12813. (shrink)

This article explores the ways in which predictive information technologies are used in the field of personalized medicine and the relations between this use and how patients and disease are perceived. This is examined in a qualitative case study of a personalized cancer clinical trial, where oncologists made clinical decisions for each patient based on drug matchings and efficacy predictions produced by bioinformatic technologies and algorithms. I focus on personalized practice itself, as a postgenomic phenomenon, rather than on (...) epistemic, ethical and institutional critiques. Personalized medicine aims to process molecular, clinical, environmental and social data into individually tailored decisions. In this case, however, the engagement of clinicians with data and digital artefacts that processed multiple information sources resulted in treatment choices that were paradoxically both immutable and uncertain. In contrast to the situatedness of the body in postgenomics, this practice subverted the personalized medical approach while decontextualizing both cancer and patients. (shrink)

The practice and development of modern medicine requires large amounts of data, particularly in the domain of cancer. The future of personalized medicine lies neither with “genomic medicine” nor with “precision medicine”, but with “data medicine”. The establishment of this DM has required far-reaching changes, to establish four essential elements connecting patients and doctors: biobanks, databases, bioinformatic platforms and genomic platforms. The “transformation” of scientific research areas, such as genetics, bioinformatics and biostatistics, into clinical specialties has generated a (...) new vision of care. Molecular tumor boards are one response to these changes and are now providing better access to next-generation sequencing and new cancer treatments to patients with inoperable or metastatic cancers, and those for whom the usual treatment has failed. However, MTB face a crucial ethical challenge: maintaining and improving the trust of patients, clinicians, researchers and industry in academic medical centers supported by private or public funding rather than providing genetic data directly to private companies. We believe that, in this era of DM, appropriate modern digital communication networks will be required to maintain this trust and to improve the organization and effectiveness of the system. There is, therefore, a need to reconsider the form and content of informed consent documents at all academic medical centers and to introduce dynamic and electronic informed consent. (shrink)

Due to modern biochemistry and, in particular, recent developments in genomics, proteomics, and bioinformatics, human samples have become the most important raw materials for advancement in the health sciences. Such material has been at the center of fundamental biomedical research for a long time. What is new is its increased usefulness in research with direct clinical relevance, such as the development of drugs. Because of the larger commercial involvement in such research, this has also led to greater economic (...) interests in human biological material and in the information that can be extracted from it. (shrink)

This article provides an ethnographic account of how Big Data biology is produced, interpreted, debated, and translated in a Big Data-driven cancer clinical trial, entitled “Personalized OncoGenomics,” in Vancouver, Canada. We delve into epistemological differences between clinical judgment, pathological assessment, and bioinformatic analysis of cancer. To unpack these epistemological differences, we analyze a set of gazes required to produce Big Data biology in cancer care: clinical gaze, molecular gaze, and informational gaze. We are concerned with the interactions (...) of these bodily gazes and their interdependence on each other to produce Big Data biology and translate it into clinical knowledge. To that end, our central research questions ask: How do medical practitioners and data scientists interact, contest, and collaborate to produce and translate Big Data into clinical knowledge? What counts as actionable and reliable data in cancer decision-making? How does the explicability or translatability of genomic Big Data come to redefine or contradict medical practice? The article contributes to current debates on whether Big Data engenders new questions and approaches to biology, or Big Data biology is merely an extension of early modern natural history and biology. This ethnographic account will highlight how genomic Big Data, which underpins the mechanism of personalized medicine, allows oncologists to understand and diagnose cancer in a different light, but it does not revolutionize or disrupt medical oncology on an institutional level. Rather, personalized medicine is interdependent on different styles of thought, gaze, and practice to be produced and made intelligible. (shrink)

Though in existence for over thirty-five years, due to the increasing panoply of possible tests. Newborn screening programs are drawing public attention. Many jurisdictions have mandatory newborn screening programs for treatable disorders. Disorders are detected through tests on blood spots drawn from a newborn’s heel soon after birth and verified through a diagnostic test with follow-up. Unbeknownst to most parents, these blood spot cards are also stored thereafter. Indeed, while dried blood spots are primarily used for screening for health problems, (...) experience demonstrates that they can be made useful in various contexts unrelated to screening.Newborn dried blood spots have taken on a new life as a result of developments in genetics and the increasing ability of bioinformatics to link DNA information with clinical data. Additionally, storage and secondary uses have been documented to occur without parental consent. (shrink)

Though in existence for over thirty-five years, due to the increasing panoply of possible tests. Newborn screening programs are drawing public attention. Many jurisdictions have mandatory newborn screening programs for treatable disorders. Disorders are detected through tests on blood spots drawn from a newborn’s heel soon after birth and verified through a diagnostic test with follow-up. Unbeknownst to most parents, these blood spot cards are also stored thereafter. Indeed, while dried blood spots are primarily used for screening for health problems, (...) experience demonstrates that they can be made useful in various contexts unrelated to screening.Newborn dried blood spots have taken on a new life as a result of developments in genetics and the increasing ability of bioinformatics to link DNA information with clinical data. Additionally, storage and secondary uses have been documented to occur without parental consent. (shrink)

The Diagnostic and Statistical Manual of Mental Disorders (DSM) is universally acknowledged as the prominent reference textbook for the diagnosis and assessment of psychiatric diseases. However, since the publication of its first version in 1952, controversies have been raised concerning its reliability and validity and the need for other novel clinical tools has emerged. Currently the DSM is in its fourth edition and a new fifth edition is expected for release in 2013, in an intense intellectual debate and in (...) a call for new proposals. (shrink)

The genomics “revolution” is spreading. Originating in the molecular life sciences, it initially affected a number of biomedical research fields such as cancer genomics and clinical genetics. Now, however, a new “wave” of genomic bioinformation is transforming a widening array of disciplines, including those that address the social, historical and cultural dimensions of human life. Increasingly, bioinformation is affecting “human sciences” such as psychiatry, psychology, brain research, behavioural research (“behavioural genomics”), but also anthropology and archaeology (“bioarchaeology”). Thus, bioinformatics (...) is having an impact on how we define and understand ourselves, how identities are formed and constituted, and, finally, on how we (on the basis of these redefined identities) assess and address some of the more concrete societal issues involved in genomics governance in various settings. This article explores how genomics and bioinformation, by influencing research agendas in the human sciences and the humanities, are affecting our self-image, our identity, the way we see ourselves. The impact of bioinformation on self-understanding will be assessed on three levels: (1) the collective level (the impact of comparative genomics on our understanding of human beings as a species), (2) the individual level (the impact of behavioural genomics on our understanding of ourselves as individuals), and (3) the genealogical level (the impact of population genomics on our understanding of human history, notably early human history). This threefold impact will be assessed from two seemingly incompatible philosophical perspectives, namely a “humanistic” perspective (represented in this article by Francis Fukuyama) and a “post-humanistic” one (represented by Peter Sloterdijk). On the basis of this analysis it will be concluded that, rather than focussing on human “enhancement” by adding or deleting genes, genome-oriented practices of the Self will focus on using genomics information in the context of identity-formation. Genomic bioinformation will increasingly be built into our self-images and used in order to tailor and adapt our practices of Self to our “personalised” genome. We will keep working on ourselves, no doubt, not by modifying our genomes, but rather by fine-tuning our behaviour. What we are experiencing is a bioinformatisation of the life-world. Genomics-based technologies will increasingly pervade our daily lives, our autobiographies and narratives, as well as our anthropologies, rather than our genomes as such. (shrink)

The governments of China, India, and the United Kingdom are unanimous in their belief that bioinformatics should supply the link between basic life sciences research and its translation into health benefits for the population and the economy. Yet at the same time, as ambitious states vying for position in the future global bioeconomy they differ considerably in the strategies adopted in pursuit of this goal. At the heart of these differences lies the interaction between epistemic change within the scientific (...) community itself and the apparatus of the state. Drawing on desk-based research and thirty-two interviews with scientists and policy makers in the three countries, this article analyzes the politics that shape this interaction. From this analysis emerges an understanding of the variable capacities of different kinds of states and political systems to work with science in harnessing the potential of new epistemic territories in global life sciences innovation. (shrink)

"Databases containing the accumulated genomic data of the research community are growing exponentially. This book contains cutting-edge insights from scholars, bioethicists and legal practitioners who work at the ever-changing intersection of law and bioinformatics"--Page 4 of cover.

The principle of clinical equipoise has been variously characterized by ethicists and clinicians as fundamentally flawed, a myth, and even a moral balm. Yet, the principle continues to be treated as the de facto gold standard for conducting randomized control trials in an ethical manner. Why do we hold on to clinical equipoise, despite its shortcomings being widely known and well-advertised? This paper reviews the most important arguments criticizing clinical equipoise as well as what the most prominent (...) proposed alternatives are. In the process, it evaluates the justification for continuing to use clinical equipoise as the gold standard for randomized control trials. (shrink)

Motivation: One approach to inferring genetic regulatory structure from microarray measurements of mRNA transcript hybridization is to estimate the associations of gene expression levels measured in repeated samples. The associations may be estimated by correlation coefficients or by conditional frequencies or by some other statistic. Although these procedures have been successfully applied to other areas, their validity when applied to microarray measurements has yet to be tested. Results: This paper describes an elementary statistical difficulty for all such procedures, no matter (...) whether based on Bayesian updating, conditional independence testing, or other machine learning procedures such as simulated annealing or neural net pruning. The difficulty obtains if a number of cells from a common population are aggregated in a measurement of expression levels. Although there are special cases where the conditional associations are preserved under aggregation, in general inference of genetic regulatory structure based on conditional association is unwarranted. Contact: tchu@ andrew.cmu.edu. (shrink)

This article deals with the integration of ethical reflection into the research practices of the project at the Lille Nord-Pas-de-Calais genopole: “Multifactorial genetic pathologies and therapeutic innovations”. The general hypothesis of this text is that changes in research practices in biology (mainly through the use of bioinformatics) imply changes in medical practices, which require critical reflection. This hypothesis could be broken down into three sub-hypotheses: (1) Research in biology is undergoing a complete transformation; (2) Research in biology is a (...) cultural practice, which cannot be reduced to a simple cognitive action; (3) Research in biology is a techno-scientific practice. As for the method, the aim of our research at the Medical Ethics Centre is to elucidate the philosophical and ethical range of biomedical practices. This work entails a double task for reflection. On the one hand, from the revelation of ethical tensions present in these practices, we have to think about what is at stake in these practices, and more broadly in society. On the other hand, we have to analyse the conditions enabling the actors to assume the significance of ethical reflection in their practices. The method set up to undertake this double task could be qualified as “narrative hermeneutics”, as its aim is to attempt to interpret the stakes in practices from proximity with these practices and from what their actors have to say about them. The text then goes on to analyse more specifically the emergence and place of bioinformatics in present-day biomedical research. (shrink)

This book is about the ethical issues that clinicians encounter as they care for patients and is written to assist those who serve on hospital ethics committees as they deliberate about appropriate action in difficult ethical cases.

Reading, writing, publishing, and publicly presenting scientific works are vital for a young researcher's profile building and career development. Generally, the traditional educational curricula do not offer training possibilities to learn and practice how to prepare, write, and present scientific works. These are rather a part of lab meeting activities in research groups. The lack of such training is more critical in some developing countries because this adds to the rare opportunities to discuss and become involved in the exchanges on (...) state of the art scientific literature. Here the authors relate their experience in introducing a weekly 1‐day lab meeting in the framework of two previously organized 3‐month courses on “Bioinformatics and Genome Analyses”. The main activities which are developed during these lab meetings include scientific literature follow up as well as preparing and presenting oral and written scientific reviews. These activities prove to be useful for a student's self‐confidence building, for enhancing their active participation during the lectures and practical sessions, as well as for the positive impact on running the whole course program. Incorporation of such lab meeting activities in the course program significantly improves the capacity building of the participants, their analytical and critical reading of scientific literature, as well as communication skills. In this work it is shown how to proceed with the different steps involved in the implementation of lab meeting activities, and to recommend their regular institution in similar courses. (shrink)

In the life sciences, where large data sets are increasingly setting the stage for research, the role of bioinformatics is expanding. This has far-reaching consequences, not only for the way research is done, but also for the way this research affects our understanding of human identity. Using two case studies of practices involving bioinformatics, the software program Structure and the Genome of the Netherlands project, I will argue that bioinformatics and its tools can be understood as ‘infrastructure’ (...) as described by Bowker and Star. A number of value decisions are involved in the development of such tools. However, once the tools are ready for use, these values tend to blend into the background of the research. This may lead to the ‘naturalisation’ and ‘essentialisation’ of value-imbued aspects of population identities such as nationality, ethnicity and race. (shrink)

It is probable that, increasingly, genome investigations are going to be based on statistical formalization. This review summarizes the state of art and potentiality of using statistics in microbial genome analysis. First, I focus on recent advances in functional genomics, such as finding genes and operons, identifying gene conversion events, detecting DNA replication origins and analysing regulatory sites. Then I describe how to use phylogenetic methods in genome analysis and methods for genome‐wide scanning for positively selected amino acids. I conclude (...) with speculations on the future course of genome statistical modeling. BioEssays 25:266–273, 2003. © 2003 Wiley Periodicals, Inc. (shrink)

ABSTRACT In this paper I analyse the ethical implications of the two main competing methodologies in genomic research. I do not aim to provide another contribution from the mainstream legal and public policy perspective; rather I offer a novel approach in which I analyse and describe the patent‐and‐publish regime (the proprietary regime) led by biologist J. Craig Venter and the ‘open‐source’ methodologies led by biotechnology Nobel laureate John Sulston. The ‘open‐source methodologies’ arose in biotechnology as an alternative to the patent‐and‐publish (...) regime in the wake of the explosion in computer technology. Indeed, the tremendous increase in computer technology has generated a corresponding increase in the pace of genomics research. I conclude this paper by arguing that while the patent‐and‐publish method is a transactional method based on the exchange of extrinsic goods (patents in exchange for research funds), the free and open‐source methodology (FLOSS)1 is a transformational method based on a visionary ideal of science, which leads to prioritizing intrinsic goods in scientific research over extrinsic goods. (shrink)

This book is about the ethical issues that clinicians encounter as they care for patients and is written to assist those who serve on hospital ethics committees as they deliberate about appropriate action in difficult ethical cases.

What is life and what does it mean to be in the living political universe of entitiness without rhyme or reason? Flappy exudate, a bag in a bag, corpuscles of corporeality, worms (or flesh tubes) with appendages, even the cult of first involution – these are our body pods and the hunger and thirst of being-in. How can the situation of anatomical form be analysed without the illusion of instrumentalized reflection? Perhaps by amalgamating the categories and their issues. The issuance (...) of taxonomy is the actual fine muck of excrement, which every brick of ordered life leaks as exudence and decay. Deep thoughts leave a mucal snail trail of what was tabular-seeming about our bodily situation, our environs, our friends, our experiments and our nourishment. Especially in this current age of 露 露 and 娜娜 (Lulu and Nana), our first officially public transgenic kindred, the question becomes, ‘who are these free-living divergences and what does it mean to be the uber-ding beyond geoengineering’s capabilities?’. (shrink)

Two senses of ‘ontology’ can be distinguished in the current literature. First is the sense favored by information scientists, who view ontologies as software implementations designed to capture in some formal way the consensus conceptualization shared by those working on information systems or databases in a given domain. [Gruber 1993] Second is the sense favored by philosophers, who regard ontologies as theories of different types of entities (objects, processes, relations, functions) [Smith 2003]. Where information systems ontologists seek to maximize reasoning (...) efficiency even at the price of simplifications on the side of representation, philosophical ontologists argue that representational adequacy can bring benefits for the stability and resistance to error of an ontological framework and also for its extendibility in the future. In bioinformatics, however, a third sense of ‘ontology’ has established itself, above all as a result of the successes of the Gene Ontology (hereafter: GO), which is a tool for the representation and processing of information about gene products and their biological functions [Gene Ontology Consortium 2000]. We show how Basic Formal Ontology (BFO) has established itself as an overarching ontology drawing on all three of the strands distinguished above, and describe applications of BFO especially in the treatment of biological granularity. (shrink)

This book offers a philosophically-based, yet clinically-oriented perspective on current medical reasoning aiming at 1) identifying important forms of uncertainty permeating current clinical reasoning and practice 2) promoting the application of an abductive methodology in the health context in order to deal with those clinical uncertainties 3) bridging the gap between biomedical knowledge, clinical practice, and research and values in both clinical and philosophical literature. With a clear philosophical emphasis, the book investigates themes lying at the (...) border between several disciplines, such as medicine, nursing, logic, epistemology, and philosophy of science; but also ethics, epidemiology, and statistics. At the same time, it critically discusses and compares several professional approaches to clinical practice such as the one of medical doctors, nurses and other clinical practitioners, showing the need for developing a unified framework of reasoning, which merges methods and resources from many different clinical but also non-clinical disciplines. In particular, this book shows how to leverage nursing knowledge and practice, which has been considerably neglected so far, to further shape the interdisciplinary nature of clinical reasoning. Furthermore, a thorough philosophical investigation on the values involved in health care is provided, based on both the clinical and philosophical literature. The book concludes by proposing an integrative approach to health and disease going beyond the so-called “classical biomedical model of care”. (shrink)

In this paper I attempt to address what appears to be a novel theoretical and practical problem concerning physician-assisted suicide (PAS). This problem arises out of a newly created set of circumstances in which persons are hospitalized in jurisdictions where PAS, though now legally available to patients, remains morally contentious. When moral disagreements over PAS come to divide physicians, patients, and family members, it is quite likely they will today find their way to the hospital’s consulting ethicist, a member of (...) an emerging group of professionals charged with the responsibility (so we are told) of resolving moral conflict in the clinic. What can or should an ethics consultant do to fulfill this mandate in such circumstances? I argue that the now predominant conception of clinical ethics consultation is importantly deficient in that it provides no final guidance to ethicists on how they should respond in such cases. The ethicist may only recommend—or assist others to reach—solutions to moral disagreements falling within the limits of established norms. Since the normative landscape of PAS appears to be changing, whether it falls within these limits is unsettled. I conclude that the accepted goals of ethics consultation require a revised and expanded conception of the ethicist's role in cases involving PAS. I close by outlining what that revised understanding would look like and the further questions it raises. (shrink)

Discovering Spinoza's early modern psychology some 35 years into his own clinical practice, Ian Miller now gives shape to this connection through a close reading of Spinoza's key philosophical ideas. With a rigorous and expansive analysis of Spinoza's Ethics in particular, Miller explores how Spinozan thought simultaneously empowered the original conceptual direction of psychoanalytic thinking, and anticipated the field's contemporary theoretical dimensions. Miller offers a detailed overview of the philosopher's psychoanalytic reception from the early work of German-language psychoanalytic thinkers, (...) such as Freud and Andreas Lou-Salome, forward into its Anglophone reception, influencing both mid-century humanistic American psychoanalysis as well as anticipating thinkers such as Bion and Winnicott. Covering key concepts in psychoanalytic theory and clinical practice, this book demonstrates how knowledge of Spinoza's philosophical work can help to both illuminate and improve modern psychoanalytic therapies. (shrink)

Clinical trials and other forms of evaluation of medical treatment are held to give an objective assessment of the 'clinical effectiveness' of the medical treatments under evaluation. This kind of evaluation is central to the evidence-based medicine movement, as it provides a basis for the rational selection of treatment. The ethical status of randomised clinical trials is widely agreed to depend crucially upon the state of equipoise regarding which of two treatments is more effective in a defined (...) population. However, the meaning and nature of 'clinical effectiveness' are unclear. in this paper, I discuss the proposals to define clinical effectiveness as a relational property and as an intrinsic property, and the way effectiveness may supervene upon more fundamental physical properties of treatments. I discuss whether effectiveness is a single property or a family of properties; the types of outcome which can be explained by effectiveness properties; and the relationship between 'objective' and 'preference' outcomes. This paper suggests that while it may be possible to put clinical effectiveness on a proper metaphysical footing, in practice the language of clinical effectiveness is more properly a topic of the human sciences than of the natural sciences. (shrink)

Bioinformatics – the so-called shotgun marriage between biology and computer science – is an interdiscipline. Despite interdisciplinarity being seen as a virtue, for having the capacity to solve complex problems and foster innovation, it has the potential to place projects and people in anomalous categories. For example, valorised ‘outputs’ in academia are often defined and rewarded by discipline. Bioinformatics, as an interdisciplinary bricolage, incorporates experts from various disciplinary cultures with their own distinct ways of working. Perceived problems of (...) interdisciplinarity include difficulties of making explicit knowledge that is practical, theoretical, or cognitive. But successful interdisciplinary research also depends on an understanding of disciplinary cultures and value systems, often only tacitly understood by members of the communities in question. In bioinformatics, the ‘parent’ disciplines have different value systems; for example, what is considered worthwhile research by computer scientists can be thought of as trivial by biologists, and vice versa. This paper concentrates on the problems of reward and recognition described by scientists working in academic bioinformatics in the United Kingdom. We highlight problems that are a consequence of its cross-cultural make-up, recognising that the mismatches in knowledge in this borderland take place not just at the level of the practical, theoretical, or epistemological, but also at the cultural level too. The trend in big, interdisciplinary science is towards multiple authors on a single paper; in bioinformatics this has created hybrid or fractional scientists who find they are being positioned not just in-between established disciplines but also in-between as middle authors or, worse still, left off papers altogether. (shrink)

How Doctors Think defines the nature and importance of clinical judgment. Although physicians make use of science, this book argues that medicine is not itself a science but rather an interpretive practice that relies on clinical reasoning. A physician looks at the patient's history along with the presenting physical signs and symptoms and juxtaposes these with clinical experience and empirical studies to construct a tentative account of the illness. How Doctors Think is divided into four parts. Part (...) one introduces the concept of medicine as a practice rather than a science; part two discusses the idea of causation; part three delves into the process of forming clinical judgment; and part four considers clinical judgment within the uncertain nature of medicine itself. In How Doctors Think, Montgomery contends that assuming medicine is strictly a science can have adverse side effects, and suggests reducing these by recognizing the vital role of clinical judgment. (shrink)

The automatic integration of information resources in the life sciences is one of the most challenging goals facing biomedical informatics today. Controlled vocabularies have played an important role in realizing this goal, by making it possible to draw together information from heterogeneous sources secure in the knowledge that the same terms will also represent the same entities on all occasions of use. One of the most impressive achievements in this regard is the Gene Ontology (GO), which is rapidly acquiring the (...) status of a de facto standard in the field of gene and gene product annotations, and whose methodology has been much intimated in attempts to develop controlled vocabularies for shared use in different domains of biology. The GO Consortium has recognized, however, that its controlled vocabulary as currently constituted is marked by several problematic features - features which are characteristic of much recent work in bioinformatics and which are destined to raise increasingly serious obstacles to the automatic integration of biomedical information in the future. Here, we survey some of these problematic features, focusing especially on issues of compositionality and syntactic regimentation. (shrink)