Privacy Risks from Genomic Data-Sharing Beacons

The human genetics community needs robust protocols that enable secure sharing of genomic data from participants in genetic research. Beacons are web servers that answer allele-presence queries—such as “Do you have a genome that has a specific nucleotide (e.g., A) at a specific genomic position (e.g., position 11,272 on chromosome 1)?”—with either “yes” or “no.” Here, we show that individuals in a beacon are susceptible to re-identification even if the only data shared include presence or absence information about alleles in a beacon. Specifically, we propose a likelihood-ratio test of whether a given individual is present in a given genetic beacon. Our test is not dependent on allele frequencies and is the most powerful test for a specified false-positive rate. Through simulations, we showed that in a beacon with 1,000 individuals, re-identification is possible with just 5,000 queries. Relatives can also be identified in the beacon. Re-identification is possible even in the presence of sequencing errors and variant-calling differences. In a beacon constructed with 65 European individuals from the 1000 Genomes Project, we demonstrated that it is possible to detect membership in the beacon with just 250 SNPs. With just 1,000 SNP queries, we were able to detect the presence of an individual genome from the Personal Genome Project in an existing beacon. Our results show that beacons can disclose membership and implied phenotypic information about participants and do not protect privacy a priori. We discuss risk mitigation through policies and standards such as not allowing anonymous pings of genetic beacons and requiring minimum beacon sizes.     

Redefining viruses: lessons from Mimivirus

Viruses are the most abundant living entities and probably had a major role in the evolution of life, but are still defined using negative criteria. Here, we propose to divide biological entities into two groups of organisms: ribosome-encoding organisms, which include eukaryotic, archaeal and bacterial organisms, and capsid-encoding organisms, which include viruses. Other replicons (for example, plasmids and viroids) can be termed 'orphan replicons'. Based on this suggested classification system, we propose a new definition for a virus--a capsid-encoding organism that is composed of proteins and nucleic acids, self-assembles in a nucleocapsid and uses a ribosome-encoding organism for the completion of its life cycle.     

Redefining Nature: Ecology, Culture and Domestication

Redefining Nature: Ecology, Culture and Domestication. Roy Ellen and Katsuyoshi Fukui. eds. Oxford: Oxford International Publishers Ltd., 1996.664 pp.     

Redefining community: towards an ecological republicanism

This paper makes some suggestions for a concept of community which arguably satisfies the most important criteria for both human communities, as defined in the social sciences and humanities, and natural communities, as defined in ecology and biology. Beginning with the former, I arrive at two such criteria: (1) a material and social connection among members, and (2) some kind and degree of awareness of other members. These are then supplemented with a third drawn from civic republicanism, with its focus on citizenship and the common good: communities (3) enable and require certain practices for their maintainence. Turning to ecological definitions of community, I find the dominant (reductionist) one seriously deficient as compared with a more holist and ecosystemic approach. However, I invoke a nonreductive holism to defend the idea of community, and go on to argue that each of the three above-mentioned criteria can be fruitfully extended to include both social and ecological communities in a nonreductionist way – that is, in a way that neither reduces ecosystemic properties to individual organisms nor the reverse. This culminates in a discussion of what I call ecological republicanism, which I suggest could have powerfully positive effects on the contemporary crisis of undue human impact on the natural world.     

Meeting report: the Institute for Genomic Research/Wellcome Trust Conference: Genomes 2004 14-17 April 2004, the Wellcome Trust Conference Centre, the Wellcome Trust Genome Campus, Hinxton, Cambridge, UK

This conference brought the microbial genomics community together to share their most up-to-the-minute achievements, so much so that several talks cannot be covered here, as the work discussed has not yet been published. This meeting report has details of a cross-section of the talks from the sessions on 'Genome analysis and comparative genomics', 'Computational genomics' and 'Functional genomics', ranging from studies on complex environmental samples, to specific pathogenic bacteria, to yeasts.     

Advances in the Conceptualization and Measurement of Health Care Empowerment: Development and Validation of the Health Care Empowerment Inventory

The Health Care Empowerment Model offers direction for the investigation of patient-controlled engagement and involvement in health care. At the core of the model is the construct of Health Care Empowerment (HCE), for which there exist no validated measures. A set of 27 candidate self-report survey items was constructed to capture five hypothesized inter-related facets of HCE (informed, engaged, committed, collaborative, and tolerant of uncertainty). The full item set was administered to 644 HIV-infected persons enrolled in three ongoing research studies. Exploratory and confirmatory factor analyses resulted in a two factor solution comprising four items each on two subscales: (1) HCE: Informed, Committed, Collaborative, and Engaged HCE ICCE) and (2) HCE Tolerance of Uncertainty (HCE TU). Subscale scores were evaluated for relationships with relevant constructs measured in the three studies, including depression, provider relationships, medication adherence, and HIV-1 viral load. Findings suggest the utility of this 8-item Health Care Empowerment Inventory (HCEI) in efforts to measure, understand, and track changes in the ways in which individuals engage in health care.     

Privacy and environment

Orientations toward privacy were identified and individual differences in orientation assessed by means of the newly developed Privacy Preference Scale. Principal components analysis of the PPS revealed six major factors from which subscales were constructed, their content centering on orientations toward noninvolvement with neighbors, seclusion of the home, solitude, privacy with intimates, anonymity, and reserve. In a suburban adult sample (n = 101), these orientations toward privacy were related by means of correlation, multivariate analysis of variance, and canonical correlation to density of past and present environments and to features of the physical environment affecting potential privacy.This article is based in part on a doctoral dissertation submitted to the Department of Psychology at the University of California, Berkeley, and financed by Public Health Service Predoctoral Fellowship 4 F1 MH33979-04 from the National Institute of Mental Health.     

Redefining Rationality: Paranormal Investigators' Humour in England

In contemporary England, amateur paranormal investigators are actively engaged in attempts to produce objective knowledge about the ghostly and paranormal. Their project requires them to balance subjective, personal encounters with objective, technologically mediated ones. In doing so, they struggle to align their project with dominant understandings of rationality. Drawing on an ethnographic study of knowledge production among paranormal investigators, I explore paranormal investigators' use of humour and argue that they rely on humorous performances to align themselves with a powerful, hegemonic notion of rationality. Through their humour, they do not contest the scope of rationality; rather, they locate themselves as central to it.     

Beyond Trust: Plagiarism and Truth

Academic misconduct distorts the relationship between scientific practice and the knowledge it produces. The relationship between science and the knowledge it produces is, however, not something universally agreed upon. In this paper I will critically discuss the moral status of an act of research misconduct, namely plagiarism, in the context of different epistemological positions. While from a positivist view of science, plagiarism only influences trust in science but not the content of the scientific corpus, from a constructivist point of view both are at stake. Consequently, I argue that discussions of research misconduct and responsible research ought to be explicitly informed by the authors’ views on the relationship between science and the knowledge it produces.     

Redefining clinical trials: the age of personalized medicine

The triumph of personalized cancer therapeutics in recent years is prompting some oncologists to rethink clinical trial design; other researchers have different priorities for trial reform.     

Redefining animal signaling: influence versus information in communication

Researchers typically define animal signaling as morphology or behavior specialized for transmitting encoded information from a signaler to a perceiver. Although intuitively appealing, this conception is inherently metaphorical and leaves concepts of both information and encoding undefined. To justify relying on the information construct, theorists often appeal to Shannon and Weaver’s quantitative definition. The two approaches are, however, fundamentally at odds. The predominant definition of animal signaling is thus untenable, which has a number of undesirable consequences for both theory and practice in the field. Theoretical problems include conceptual circularity and running afoul of fundamental evolutionary principles. Problems in empirical work include that research is often grounded in abstractions such as signal honesty and semanticity, and thereby distracted from more basic and concrete factors shaping communication. A revised definition is therefore proposed, making influence rather than transmission of encoded information the central function of animal signaling. This definition is conceptually sound, empirically testable, and inclusive, yet bounded. Implications are considered in both theoretical and empirical domains.