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.     

Yahtzee: An Anonymized Group Level Matching Procedure

Researchers often face the problem of needing to protect the privacy of subjects while also needing to integrate data that contains personal information from diverse data sources. The advent of computational social science and the enormous amount of data about people that is being collected makes protecting the privacy of research subjects ever more important. However, strict privacy procedures can hinder the process of joining diverse sources of data that contain information about specific individual behaviors. In this paper we present a procedure to keep information about specific individuals from being “leaked” or shared in either direction between two sources of data without need of a trusted third party. To achieve this goal, we randomly assign individuals to anonymous groups before combining the anonymized information between the two sources of data. We refer to this method as the Yahtzee procedure, and show that it performs as predicted by theoretical analysis when we apply it to data from Facebook and public voter records.     

Anonymity versus Privacy in the Dictator Game: Revealing Donor Decisions to Recipients Does Not Substantially Impact Donor Behavior

Anonymity is often offered in economic experiments in order to eliminate observer effects and induce behavior that would be exhibited under private circumstances. However, anonymity differs from privacy in that interactants are only unaware of each others'' identities, while having full knowledge of each others'' actions. Such situations are rare outside the laboratory and anonymity might not meet the requirements of some participants to psychologically engage as if their actions were private. In order to explore the impact of a lack of privacy on prosocial behaviors, I expand on a study reported in Dana et al. (2006) in which recipients were left unaware of the Dictator Game and given donations as “bonuses” to their show-up fees for other tasks. In the current study, I explore whether differences between a private Dictator Game (sensu Dana et al. (2006)) and a standard anonymous one are due to a desire by dictators to avoid shame or to pursue prestige. Participants of a Dictator Game were randomly assigned to one of four categories—one in which the recipient knew of (1) any donation by an anonymous donor (including zero donations), (2) nothing at all, (3) only zero donations, and (4) and only non-zero donations. The results suggest that a lack of privacy increases the shame that selfish-acting participants experience, but that removing such a cost has only minimal effects on actual behavior.     

Reading the Mind in the Eyes or Reading between the Lines? Theory of Mind Predicts Collective Intelligence Equally Well Online and Face-To-Face

Recent research with face-to-face groups found that a measure of general group effectiveness (called “collective intelligence”) predicted a group’s performance on a wide range of different tasks. The same research also found that collective intelligence was correlated with the individual group members’ ability to reason about the mental states of others (an ability called “Theory of Mind” or “ToM”). Since ToM was measured in this work by a test that requires participants to “read” the mental states of others from looking at their eyes (the “Reading the Mind in the Eyes” test), it is uncertain whether the same results would emerge in online groups where these visual cues are not available. Here we find that: (1) a collective intelligence factor characterizes group performance approximately as well for online groups as for face-to-face groups; and (2) surprisingly, the ToM measure is equally predictive of collective intelligence in both face-to-face and online groups, even though the online groups communicate only via text and never see each other at all. This provides strong evidence that ToM abilities are just as important to group performance in online environments with limited nonverbal cues as they are face-to-face. It also suggests that the Reading the Mind in the Eyes test measures a deeper, domain-independent aspect of social reasoning, not merely the ability to recognize facial expressions of mental states.     

Certifying achievement in the control of Chagas disease native vectors: what is a viable scenario?

As an evaluation scheme, we propose certifying for “control”, as alternative to “interruption”, of Chagas disease transmission by native vectors, to project a more achievable and measurable goal and sharing good practices through an “open online platform” rather than “formal certification” to make the key knowledge more accumulable and accessible.     

Categorical Biases in Perceiving Spatial Relations

We investigate the effect of spatial categories on visual perception. In three experiments, participants made same/different judgments on pairs of simultaneously presented dot-cross configurations. For different trials, the position of the dot within each cross could differ with respect to either categorical spatial relations (the dots occupied different quadrants) or coordinate spatial relations (the dots occupied different positions within the same quadrant). The dot-cross configurations also varied in how readily the dot position could be lexicalized. In harder-to-name trials, crosses formed a “+” shape such that each quadrant was associated with two discrete lexicalized spatial categories (e.g., “above” and “left”). In easier-to-name trials, both crosses were rotated 45° to form an “×” shape such that quadrants were unambiguously associated with a single lexicalized spatial category (e.g., “above” or “left”). In Experiment 1, participants were more accurate when discriminating categorical information between easier-to-name categories and more accurate at discriminating coordinate spatial information within harder-to-name categories. Subsequent experiments attempted to down-regulate or up-regulate the involvement of language in task performance. Results from Experiment 2 (verbal interference) and Experiment 3 (verbal training) suggest that the observed spatial relation type-by-nameability interaction is resistant to online language manipulations previously shown to affect color and object-based perceptual processing. The results across all three experiments suggest that robust biases in the visual perception of spatial relations correlate with patterns of lexicalization, but do not appear to be modulated by language online.     

Consent to ‘personal’ genomics and privacy

Direct-to-consumer genetic tests and population genome research challenge traditional notions of privacy and consentThe concerns about genetic privacy in the 1990s were largely triggered by the Human Genome Project (HGP) and the establishment of population biobanks in the following decade. Citizens and lawmakers were worried that genetic information on people, or even subpopulations, could be used to discriminate or stigmatize. The ensuing debates led to legislation both in Europe and the USA to protect the privacy of genetic information and prohibit genetic discrimination.Notions of genetic determinism have also been eroded as population genomics research has discovered a plethora of risk factors that offer only probabilistic value…Times have changed. The cost of DNA sequencing has decreased markedly, which means it will soon be possible to sequence individual human genomes for a few thousand dollars. Notions of genetic determinism have also been eroded as population genomics research has discovered a plethora of risk factors that offer only probabilistic value for predicting disease. Nevertheless, there are several increasingly popular internet genetic testing services that do offer predictions to consumers of their health risks on the basis of genetic factors, medical history and lifestyle. Also, not to be underestimated is the growing popularity of social networks on the internet that expose the decline in traditional notions of the privacy of personal information. It was only a matter of time until all these developments began to challenge the notion of genetic privacy.For instance, the internet-based Personal Genome Project asks volunteers to make their personal, medical and genetic information publicly available so as, “to advance our understanding of genetic and environmental contributions to human traits and to improve our ability to diagnose, treat, and prevent illness” (www.personalgenomes.org). The Project, which was founded by George Church at Harvard University, has enrolled its first 10 volunteers and plans to expand to 100,000. Its proponents have proclaimed the limitations, if not the death, of privacy (Lunshof et al, 2008) and maintain that, under the principle of veracity, their own personal genomes will be made public. Moreover, they have argued that in a socially networked world there can be no total guarantee of confidentiality. Indeed, total protection of privacy is increasingly unrealistic in an era in which direct-to-consumer (DTC) genetic testing is offered on the internet (Lee & Crawley, 2009) and forensic technologies can potentially ‘identify'' individuals in aggregated data sets, even if their identity has been anonymized (Homer et al, 2008).Since the start of the HGP in the 1990s, personal privacy and the confidentiality of genetic information have been important ethical and legal issues. Their ‘regulatory'' expression in policies and legislation has been influenced by both genetic determinism and exceptionalism. Paradoxically, there has been a concomitant emergence of collaborative and international consortia conducting genomics research on populations. These consortia openly share data, on the premise that it is for public benefit. These developments require a re-examination of an ‘ethics of scientific research'' that is founded solely on the protection and rights of the individual.… total protection of privacy is increasingly unrealistic in an era in which direct-to-consumer (DTC) genetic testing is offered on the internetAlthough personalized medicine empowers consumers and democratizes the sharing of ‘information'' beyond the data sharing that characterizes population genomics research (Kaye et al, 2009), it also creates new social groups based on beliefs of common genetic susceptibility and risk (Lee & Crawley, 2009). The increasing allure of DTC genetic tests and the growth of online communities based on these services also challenges research in population genomics to provide the necessary scientific knowledge (Yang et al, 2009). The scientific data from population studies might therefore lend some useful validation to the results from DTC, as opposed to the probabilistic ‘harmful'' information that is now provided to consumers (Ransohoff & Khoury, 2010; Action Group on Erosion, Technology and Concentration, 2008). Population data clearly erodes the linear, deterministic model of Mendelian inheritance, in addition to providing information on inherited risk factors. The socio-demographic data provided puts personal genetic risk factors in a ‘real environmental'' context (Knoppers, 2009).Thus, beginning with a brief overview of the principles of data sharing and privacy under both population and consumer testing, we will see that the notion of identifiability is closely linked to the definition of what constitutes ‘personal'' information. It is against this background that we need to examine the issue of consumer consent to online offers of genetic tests that promise whole-genome sequencing and analysis. Moreover, we also demonstrate the need to restructure ethical reviews of genetic research that are not part of classical clinical trials and that are non-interventionist, such as population studies.The HGP heralded a new open access approach under the Bermuda Principles of 1996: “It was agreed that all human genomic sequence information, generated by centres funded for large-scale human sequencing, should be freely available and in the public domain in order to encourage research and development and to maximise its benefit to society” (HUGO, 1996). Reaffirmed in 2003 under the Fort Lauderdale Rules, the premise was that, “the scientific community will best be served if the results of community resource projects are made immediately available for free and unrestricted use by the scientific community to engage in the full range of opportunities for creative science” (HUGO, 2003). The international Human Genome Organization (HUGO) played an important role in achieving this consensus. Its Ethics Committee considered genomic databases as “global public goods” (HUGO Ethics Committee, 2003). The value of this information—based on the donation of biological samples and health information—to realize the benefits of personal genomics is maximized through collaborative, high-quality research. Indeed, it could be argued that, “there is an ethical imperative to promote access and exchange of information, provided confidentiality is protected” (European Society of Human Genetics, 2003). This promotion of data sharing culminated in a recent policy on releasing research data, including pre-publication data (Toronto International Data Release Workshop, 2009).There is room for improvement in both the personal genome and the population genome endeavoursIn its 2009 Guidelines for Human Biobanks and Genetic Research Databases, the Organization for Economic Cooperation and Development (OECD) states that the “operators of the HBGRD [Human Biobanks and Genetic Research Databases] should strive to make data and materials widely available to researchers so as to advance knowledge and understanding.” More specifically, the Guidelines propose mechanisms to ensure the validity of access procedures and applications for access. In fact, they insist that access to human biological materials and data should be based on “objective and clearly articulated criteria [...] consistent with the participants'' informed consent”. Access policies should be fair, transparent and not inhibit research (OECD, 2009).In parallel to such open and public science was the rise of privacy protection, particularly when it concerns genetic information. The United Nations Educational, Scientific and Cultural Organization''s (UNESCO) 2003 International Declaration on Human Genetic Data (UNESCO, 2003) epitomizes this approach. Setting genetic information apart from other sensitive medical or personal information, it mandated an “express” consent for each research use of human genetic data or samples in the absence of domestic law, or, when such use “corresponds to an important public interest reason”. Currently, however, large population genomics infrastructures use a broad consent as befits both their longitudinal nature as well as their goal of serving future unspecified scientific research. The risk is that ethics review committees that require such continuous “express” consents will thereby foreclose efficient access to data in such population resources for disease-specific research. It is difficult for researchers to provide proof of such “important public interest[s]” in order to avoid reconsents.Personal information itself refers to identifying and identifiable information. Logically, a researcher who receives a coded data set but who does not have access to the linking keys, would not have access to ‘identifiable'' information and so the rules governing access to personal data would not apply (Interagency Advisory Panel on Research Ethics, 2009; OHRP, 2008). In fact, in the USA, such research is considered to be on ‘non-humans'' and, in the absence of institutional rules to the contrary, it would theoretically not require research ethics approval (www.vanderbilthealth.com/main/25443).… the ethics norms that govern clinical research are not suited for the wide range of data privacy and consent issues in today''s social networks and bioinformatics systemsNevertheless, if the samples or data of an individual are accessible in more than one repository or on DTC internet sites, a remote possibility remains that any given individual could be re-identified (Homer et al, 2008). To prevent the restriction of open access to public databases, owing to the fear of re-identifiability, a more reasonable approach is necessary; “[t]his means that a mere hypothetical possibility to single out the individual is not enough to consider the persons as ‘identifiable''” (Data Protection Working Party, 2007). This is a proportionate and important approach because fundamental genomic ‘maps'' such as the International HapMap Project (www.hapmap.org) and the 1000 Genomes project (www.1000genomes.org) have stated as their goal “to make data as widely available as possible to further scientific progress” (Kaye et al, 2009). What then of the nature of the consent and privacy protections in DTC genetic testing?The Personal Genome Project makes the genetic and medical data of its volunteers publicly available. Indeed, there is a marked absence of the traditional confidentiality and other protections of the physician–patient relationship across such sites; overall, the degree of privacy protection by commercial DTC and other sequencing enterprises varies. The company 23andMe allows consumers to choose whether they wish to disclose personal information, but warns that disclosure of personal information is also possible “through other means not associated with 23andMe, […] to friends and/or family members […] and other individuals”. 23andMe also announces that it might enter into commercial or other partnerships for access to its databases (www.23andme.com). deCODEme offers tiered levels of visibility, but does not grant access to third parties in the absence of explicit consumer authorization (www.decodeme.com). GeneEssence will share coded DNA samples with other parties and can transfer or sell personal information or samples with an opt-out option according to their Privacy Policy, though the terms of the latter can be changed at any time (www.geneessence.com). Navigenics is transparent: “If you elect to contribute your genetic information to science through the Navigenics service, you allow us to share Your Genetic Data and Your Phenotype Information with not-for-profit organizations who perform genetic or medical research” (www.navigenics.com). Finally, SeqWright separates the personal information of its clients from their genetic information so as to avoid access to the latter in the case of a security breach (www.seqwright.com).Much has been said about the lack of clinical utility and validity of DTC genetic testing services (Howard & Borry, 2009), to say nothing of the absence of genetic counsellors or physicians to interpret the resulting probabilistic information (Knoppers & Avard, 2009; Wright & Kroese, 2010). But what are the implications for consent and privacy considering the seemingly divergent needs of ensuring data sharing in population projects and ‘protecting'' consumer-citizens in the marketplace?At first glance, the same accusations of paternalism levelled at ethics review committees who hesitate to respect the broad consent of participants in population databases could be applied to restraining the very same citizens from genetic ‘info-voyeurism'' on the internet. But, it should be remembered that citizen empowerment, which enables their participation both in population projects and in DTC, is expressed within very different contexts. Population biobanks, by the very fact of their broad consent and long-term nature, have complex security systems and are subject to governance and ongoing ethical monitoring and review. In addition, independent committees evaluate requests for access (Knoppers & Abdul-Rahman, 2010). The same cannot be said for the governance of the DTC companies just presented.There is room for improvement in both the personal genome and the population genome endeavours. The former require regulatory approaches to ensure the quality, safety, security and utility of their services. The latter require further clarification of their ongoing funding and operations and more transparency to the public as researchers begin to access these resources for disease-specific studies (Institute of Medicine, 2009). Public genomic databases should be interoperable and grant access to authenticated researchers internationally in order to be of utility and statistical significance (Burton et al, 2009). Moreover, to enable international access to such databases for disease-specific research means that the interests of publicly funded research and privacy protection must be weighed against each other, rather than imposing a requirement that research has to demonstrate that the public interest substantially outweighs privacy protection (Weisbrot, 2009). Collaboration through interoperability has been one of the goals of the Public Population Project in Genomics (P³G; www.p3g.org) and, more recently, of the Biobanking and Biomolecular Resources Research Infrastructure (www.bbmri.eu).Even if the tools for harmonization and standardization are built and used, will trans-border data flow still be stymied by privacy concerns? The mutual recognition between countries of privacy equivalent approaches—that is, safe harbour—the limiting of access to approved researchers and the development of international best practices in privacy, security and transparency through a Code of Conduct along with a system for penalizing those who fail to respect such norms, would go some way towards maintaining public trust in genomic and genetic research (P3G Consortium et al, 2009). Finally, consumer protection agencies should monitor DTC sites under a regulatory regime, to ensure that these companies adhere to their own privacy policies.… genetic information is probabilistic and participating in population or on-line studies may not create the fatalistic and harmful discriminatory scenarios originally perceived or imaginedMore importantly in both contexts, the ethics norms that govern clinical research are not suited for the wide range of data privacy and consent issues in today''s social networks and bioinformatics systems. One could go further and ask whether the current biomedical ethics review system is inadequate—if not inappropriate—in these ‘data-driven research'' contexts. Perhaps it is time to create ethics review and oversight systems that are particularly adapted for those citizens who seek either to participate through online services or to contribute to population research resources. Both are contexts of minimal risk and require structural governance reforms rather than the application of traditional ethics consent and privacy review processes that are more suited to clinical research involving drugs or devices. In this information age, genetic information is probabilistic, and participating in population or online studies might not create the fatalistic and harmful discriminatory scenarios originally perceived or imagined. The time is ripe for a change in governance and regulatory approaches, a reform that is consistent with what citizens seem to have already understood and acted on.? Open in a separate windowBartha Maria Knoppers     

Model-Based Control of Observer Bias for the Analysis of Presence-Only Data in Ecology

Presence-only data, where information is available concerning species presence but not species absence, are subject to bias due to observers being more likely to visit and record sightings at some locations than others (hereafter “observer bias”). In this paper, we describe and evaluate a model-based approach to accounting for observer bias directly – by modelling presence locations as a function of known observer bias variables (such as accessibility variables) in addition to environmental variables, then conditioning on a common level of bias to make predictions of species occurrence free of such observer bias. We implement this idea using point process models with a LASSO penalty, a new presence-only method related to maximum entropy modelling, that implicitly addresses the “pseudo-absence problem” of where to locate pseudo-absences (and how many). The proposed method of bias-correction is evaluated using systematically collected presence/absence data for 62 plant species endemic to the Blue Mountains near Sydney, Australia. It is shown that modelling and controlling for observer bias significantly improves the accuracy of predictions made using presence-only data, and usually improves predictions as compared to pseudo-absence or “inventory” methods of bias correction based on absences from non-target species. Future research will consider the potential for improving the proposed bias-correction approach by estimating the observer bias simultaneously across multiple species.     

Evolution of polygenic traits under global vs local adaptation

Observations about the number, frequency, effect size, and genomic distribution of alleles associated with complex traits must be interpreted in light of evolutionary process. These characteristics, which constitute a trait’s genetic architecture, can dramatically affect evolutionary outcomes in applications from agriculture to medicine, and can provide a window into how evolution works. Here, I review theoretical predictions about the evolution of genetic architecture under spatially homogeneous, global adaptation as compared with spatially heterogeneous, local adaptation. Due to the tension between divergent selection and migration, local adaptation can favor “concentrated” genetic architectures that are enriched for alleles of larger effect, clustered in a smaller number of genomic regions, relative to expectations under global adaptation. However, the evolution of such architectures may be limited by many factors, including the genotypic redundancy of the trait, mutation rate, and temporal variability of environment. I review the circumstances in which predictions differ for global vs local adaptation and discuss where progress can be made in testing hypotheses using data from natural populations and lab experiments. As the field of comparative population genomics expands in scope, differences in architecture among traits and species will provide insights into how evolution works, and such differences must be interpreted in light of which kind of selection has been operating.     

Redefining Genomic Privacy: Trust and Empowerment

Fulfilling the promise of the genetic revolution requires the analysis of large datasets containing information from thousands to millions of participants. However, sharing human genomic data requires protecting subjects from potential harm. Current models rely on de-identification techniques in which privacy versus data utility becomes a zero-sum game. Instead, we propose the use of trust-enabling techniques to create a solution in which researchers and participants both win. To do so we introduce three principles that facilitate trust in genetic research and outline one possible framework built upon those principles. Our hope is that such trust-centric frameworks provide a sustainable solution that reconciles genetic privacy with data sharing and facilitates genetic research.     

Social Identity Threat Motivates Science-Discrediting Online Comments

Experiencing social identity threat from scientific findings can lead people to cognitively devalue the respective findings. Three studies examined whether potentially threatening scientific findings motivate group members to take action against the respective findings by publicly discrediting them on the Web. Results show that strongly (vs. weakly) identified group members (i.e., people who identified as “gamers”) were particularly likely to discredit social identity threatening findings publicly (i.e., studies that found an effect of playing violent video games on aggression). A content analytical evaluation of online comments revealed that social identification specifically predicted critiques of the methodology employed in potentially threatening, but not in non-threatening research (Study 2). Furthermore, when participants were collectively (vs. self-) affirmed, identification did no longer predict discrediting posting behavior (Study 3). These findings contribute to the understanding of the formation of online collective action and add to the burgeoning literature on the question why certain scientific findings sometimes face a broad public opposition.     

The “Genetic Program”: Behind the Genesis of an Influential Metaphor

The metaphor of the “genetic program,” indicating the genome as a set of instructions required to build a phenotype, has been very influential in biology despite various criticisms over the years. This metaphor, first published in 1961, is thought to have been invented independently in two different articles, one by Ernst Mayr and the other by François Jacob and Jacques Monod. Here, after a detailed analysis of what both parties meant by “genetic program,” I show, using unpublished archives, the strong resemblance between the ideas of Mayr and Monod and suggest that their idea of genetic program probably shares a common origin. I explore the possibility that the two men met before 1961 and also exchanged their ideas through common friends and colleagues in the field of molecular biology. Based on unpublished correspondence of Jacob and Monod, I highlight the important events that influenced the preparation of their influential paper, which introduced the concept of the genetic program. Finally, I suggest that the genetic program metaphor may have preceded both papers and that it was probably used informally before 1961.     

Map of open and closed chromatin domains in Drosophila genome

Background

Chromatin compactness has been considered a major determinant of gene activity and has been associated with specific chromatin modifications in studies on a few individual genetic loci. At the same time, genome-wide patterns of open and closed chromatin have been understudied, and are at present largely predicted from chromatin modification and gene expression data. However the universal applicability of such predictions is not self-evident, and requires experimental verification.

Results

We developed and implemented a high-throughput analysis for general chromatin sensitivity to DNase I which provides a comprehensive epigenomic assessment in a single assay. Contiguous domains of open and closed chromatin were identified by computational analysis of the data, and correlated to other genome annotations including predicted chromatin “states”, individual chromatin modifications, nuclear lamina interactions, and gene expression. While showing that the widely trusted predictions of chromatin structure are correct in the majority of cases, we detected diverse “exceptions” from the conventional rules. We found a profound paucity of chromatin modifications in a major fraction of closed chromatin, and identified a number of loci where chromatin configuration is opposite to that expected from modification and gene expression patterns. Further, we observed that chromatin of large introns tends to be closed even when the genes are expressed, and that a significant proportion of active genes including their promoters are located in closed chromatin.

Conclusions

These findings reveal limitations of the existing predictive models, indicate novel mechanisms of epigenetic regulation, and provide important insights into genome organization and function.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-988) contains supplementary material, which is available to authorized users.     

Genome Wide Association for Addiction: Replicated Results and Comparisons of Two Analytic Approaches

Background

Vulnerabilities to dependence on addictive substances are substantially heritable complex disorders whose underlying genetic architecture is likely to be polygenic, with modest contributions from variants in many individual genes. “Nontemplate” genome wide association (GWA) approaches can identity groups of chromosomal regions and genes that, taken together, are much more likely to contain allelic variants that alter vulnerability to substance dependence than expected by chance.

Methodology/Principal Findings

We report pooled “nontemplate” genome-wide association studies of two independent samples of substance dependent vs control research volunteers (n = 1620), one European-American and the other African-American using 1 million SNP (single nucleotide polymorphism) Affymetrix genotyping arrays. We assess convergence between results from these two samples using two related methods that seek clustering of nominally-positive results and assess significance levels with Monte Carlo and permutation approaches. Both “converge then cluster” and “cluster then converge” analyses document convergence between the results obtained from these two independent datasets in ways that are virtually never found by chance. The genes identified in this fashion are also identified by individually-genotyped dbGAP data that compare allele frequencies in cocaine dependent vs control individuals.

Conclusions/Significance

These overlapping results identify small chromosomal regions that are also identified by genome wide data from studies of other relevant samples to extents much greater than chance. These chromosomal regions contain more genes related to “cell adhesion” processes than expected by chance. They also contain a number of genes that encode potential targets for anti-addiction pharmacotherapeutics. “Nontemplate” GWA approaches that seek chromosomal regions in which nominally-positive associations are found in multiple independent samples are likely to complement classical, “template” GWA approaches in which “genome wide” levels of significance are sought for SNP data from single case vs control comparisons.     

University campuses need people in them

As COVID‐19 has turned universities into ghost towns, David Smith cannot wait for the day when his campus fills with life again.

In the novel Fool’s Fate, Robin Hobb writes: “Home is people. Not a place. If you go back there after the people are gone, then all you can see is what is not there anymore.” I feel the same about university campuses.In late August 2020, after months of working from home, I returned to the campus of Western University where I am an associate professor of biology. It was supposed to be a short visit, in and out to grab some notebooks and an external monitor. But when I unlocked the office door and sat in that old wooden desk chair amongst the calm clutter of my workspace, I did not get up for a good two hours. I was comforted by the familiarity of my bookshelves, photographs, and professorial memorabilia, including a large bust of Darwin and a giant whale’s tooth. How I missed this place. And apart from two dead plants and a generous layer of dust, everything was as it should be.Outside my office was a different story. The water fountains were covered up with caution tape. Bright purple floor markings indicated the correct side of the hallway to walk down. Main offices, libraries, and canteens were closed. Large signs on all major doorways reiterated the social distancing policies. And apart from the odd security officer or grounds person, the campus was eerily empty. Nevertheless, I decided that for as long as the university remained open, I would keep coming to my office for a few hours a day, mainly to read and write without the cacophonic company of a toddler, but also to bring back some semblance of normalcy to my work life.The plan started off well. Each morning I would pack a large lunch, walk to campus and enjoy a few uninterrupted hours of academic productivity. But the stillness and emptiness of the university began to weigh on me. I could swear the fluorescent lights in my office were buzzing more loudly than before. Was the central air system always this rickety? After an hour of writing, I would take a quick walk around the department to clear my mind and see if anyone else was in. On my fifth day, I finally found someone: Vera’s office door was propped open! I quickly checked that my mask was on correctly and poked my head around. Small talk—glorious small talk—ensued for at least fifteen minutes. I had forgotten how nice it was to chat with a colleague in person. I went back to my office refreshed and put in another hour of good work. The next day, the building was deserted again. Not a sliver of light beneath Vera’s or any other door.I hoped that maybe once classes resumed in mid‐September, some vitality would return to campus. But, of course, nearly all of the classes were online and students and staff stayed home. Sometimes on my departmental wanderings, I would go into one of the large lecture halls and just stand at the podium. Once I even plugged my laptop into the AV system and practiced a presentation that I was preparing for an upcoming Zoom talk. As strange as it sounds, speaking to hundreds of lifeless seats in that old, stuffy hall felt more natural than talking to a grid of black boxes with nametags on my computer screen.As the weeks wore on and my visits to campus continued, a deep melancholy slowly took hold of me. I would spend hours on seemingly simple tasks, like tidying my office or answering emails. Harder tasks, such as writing a paper or developing a new lecture, felt insurmountable. I started leaving everything to the last minute or missing deadlines completely, which is unlike me. It felt as if my mood was somehow mirroring that of the vacant classrooms and buildings surrounding me. They, too, were paying the price of the pandemic.I have spent most of my life on college campuses. My father was a chemistry professor and often took me to work with him when I was a small child. My first daycare was at a university. As an adolescent and teenager, I would go to the local college most days for after‐school clubs. I learnt to swim at a university pool, became a senior boys 1500 m running champion on a university track, and discovered my love of mountain biking and cross‐country skiing on university trails. I met my closest friends in university residences. And my passion for science and writing was fostered in university classrooms. I love universities. I love what they represent: places of learning, scholarship, and development. I love the palpable emotions that they emit, from the endless possibilities of the first week of classes to the anxieties and sense of completion during final examinations. Most of all, I love the people that make up universities, their eclectic mix of personalities, backgrounds, ages, and beliefs. This might sound strange, but when I go on vacation, I visit universities elsewhere. I will spend an entire afternoon roaming around a campus, reading in the library, or sitting on a bench watching people come and go. This may be why I am so sad that my current institute sits unoccupied, at least in the physical sense. Ironically, enrollment is up. My department has more new undergraduate students than it has had in years.The other day on my walk home from work I ran into a colleague. He described to me how he has been working hard to get the upcoming introductory genetics course online, especially given the increase in students (there are more than 1200 currently enrolled in the course). I said, “You must be looking forward to the end of this crisis when we can start teaching in‐person again.” His response has had a lasting effect on me. “I’m not so sure things will go back to the way they were,” he said. “A lot of students are enjoying online learning—or are at least finding it convenient and cost‐effective. Many are saving money by living at home and by not having to bus into campus every day and buy overpriced food. They like being able to watch the recorded lectures on their own schedule and at their own speed. Even after the current crisis ends, I think there be will be a strong push for continued online learning.” “You might be right,” I said, “but I sure hope not.”When we parted ways, I felt even more downtrodden. I reminded myself that I was lucky to have a great job and that I needed to be adaptable. If the future is online learning, so be it. I can become a connoisseur of Camtasia. I can learn to be creative and engaging over Zoom. I can master those microphone and camera settings. But I could not help thinking this is not what I signed up for. When the pandemic is over, I do not want to exist in a cyber campus with online students and online colleagues. I do not want my home to be a lecture hall. I want brick and mortar and real bums in real seats. I want to stand in line for 20 minutes outside the student union building for lukewarm coffee. I want to waste precious time walking to meetings and making small talk in the corridors. I want the thing that I fell in love with. Until COVID‐19 is defeated, we need to stay vigilant. But when the war is won, will university campuses return to being physical gathering points for learning, engagement and community building or virtual concepts in an online learning space? Whatever the answer, I know that if you are looking for Associate Professor David R. Smith, you will find him holding out in the Biological and Geological Sciences Building, room 3028. The hand‐written sign on the door will say, “Going down with the ship.”     

The amplifying role of need in giving decisions

Hamilton's rule predicts that altruism should depend on costs incurred and benefits provided, but these depend on the relative needs of the donor and recipient. Rewriting Hamilton's rule to account for relative need suggests an amplifying effect of need on relatedness, but not necessarily other relationship qualities. In a reanalysis of three studies of social discounting and a new replication, we find that relative need amplifies the effects of relatedness on giving in two samples of U.S. adults recruited online, but not U.S. undergraduates or Indian adults recruited online. Among U.S. online participants, the effect of genetic kinship was greater when the partner was perceived to be in higher need than when in lower need. In the other samples, relatedness and greater partner need were associated with greater giving, but the effect of relatedness on giving was not significantly amplified by need. Need never amplified the effect of social closeness on giving, although it did diminish the effect of closeness in U.S. undergraduates, likely reflecting a ceiling effect. These results confirm predictions from a modification of Hamilton's rule in a sample of U.S. adults, but raise important questions about why they hold in some samples but not others. They also illustrate the importance of understanding how contextual factors, such as relative need, can moderate the importance of common variables used in evolutionary cost-benefit analyses.