Ecologists are challenged by the need to bridge and synthesize different approaches and theories to obtain a coherent understanding of ecosystems in a changing world. Both food web theory and regime shift theory shine light on mechanisms that confer stability to ecosystems, but from different angles. Empirical food web models are developed to analyze how equilibria in real multi-trophic ecosystems are shaped by species interactions, and often include linear functional response terms for simple estimation of interaction strengths from observations. Models (...) of regime shifts focus on qualitative changes of equilibrium points in a slowly changing environment, and typically include non-linear functional response terms. Currently, it is unclear how the stability of an empirical food web model, expressed as the rate of system recovery after a small perturbation, relates to the vulnerability of the ecosystem to collapse. Here, we conduct structural sensitivity analyses of classical consumer-resource models in equilibrium along an environmental gradient. Specifically, we change non-proportional interaction terms into proportional ones, while maintaining the equilibrium biomass densities and material flux rates, to analyze how alternative model formulations shape the stability properties of the equilibria. The results reveal no consistent relationship between the stability of the original models and the proportionalized versions, even though they describe the same biomass values and material flows. We use these findings to critically discuss whether stability analysis of observed equilibria by empirical food web models can provide insight into regime shift dynamics, and highlight the challenge of bridging alternative modelling approaches in ecology and beyond. (shrink)

To many who develop and use free software, the GNU General Public License represents an embodiment of the meaning of free software. In this paper we examine the definition and meaning of free software in the context of three events surrounding the GNU General Public License. We use a case involving the GPU software project to establish the importance of Freedom 0 in the meaning of free software. We analyze version 3 of the GNU General Public License and conclude that (...) although a credible case can be made that the added restrictions are consistent with the definition of free software, the case requires subtle arguments. Strong arguments against the added restrictions are less subtle, and may therefore be more convincing to many users and developers. We also analyze the Affero General Public License and conclude that it is inconsistent with the definition of free software. (shrink)

In this paper we examine the case of Tay, the Microsoft AI chatbot that was launched in March, 2016. After less than 24 hours, Microsoft shut down the experiment because the chatbot was generating tweets that were judged to be inappropriate since they included racist, sexist, and anti-Semitic language. We contend that the case of Tay illustrates a problem with the very nature of learning software that interacts directly with the public, and the developer's role and responsibility associated with it. (...) We make the case that when LS interacts directly with people or indirectly via social media, the developer has additional ethical responsibilities beyond those of standard software. There is an additional burden of care. (shrink)

The original, prescientific Western belief that the mantis is a pious, helpful creature became a widely held explanation for the mantid's unique resting posture, and for one of its cryptic displays. This belief was a characteristic part of a broader discourse about nature in which ancient authority, religious beliefs, and superstition, but few original observations, mixed freely. Gradually, the belief in mantid gentleness and piousness became a commonplace through the continual retelling of the myths and superstitions surrounding this fascinating insect.By (...) the seventeenth century, a growing interest in observation had begun to replace blind reliance on established wisdom and ancient authority. However, the various young sciences to which the period gave rise did not progress equally, and neither did the subdisciplines within each scientific field; biology, especially entomology, was particularly slow to free itself from past beliefs and contemporary superstitions. In the specific case of the praying mantis, the situation may have been at its worst.Early observers of nature found evidence that seemed, at first, to disconfirm the well-established belief that mantids are gentle creatures. These few observers, faced with startling firsthand information about mantid voraciousness, created a new characterization of mantids as merciless predators and then often juxtaposed the two images in their descriptions. However, it was not until the beginning of the nineteenth century that the two characterizations-gentleness versus cruelty— became reconciled.An amalgamation of these seemingly mutually exclusive characterizations was achieved by an interesting accommodation of each to the other. That is, while it could no longer be maintained that mantids are simply gentle insects, neither could it be accepted that they are all cruelty and viciousness. The melding of the two characterizations yielded a hybrid explanation which claimed that the praying mantis actually hastwo sides to its character! On the one hand, and like other creatures, mantids must nourish themselves, and do so quite reasonably by capturing small insects for food. However, even when “well nourished,” and without “the excuse of hunger,” their other, vicious side may surface; when this happens, the darkest of behaviours, cannibalism, is the result.To understand the remainder of the story one must pause to consider what had happened in the other sciences up to this point. In the mid-seventeenth century, professional scientific societies were established throughout Europe. The societies, and the various journals and periodicals that they produced or encouraged, represented an institutionalization of both science and its special, structured discourse. However, as we have stated, entomology lagged behind; and in the case of some insects, superstitions and anthropomorphisms did not fade from descriptions of their behavior for centuries to come.By the time the new scientific discourse was applied to mantids the creatures were already firmly shackled with a dual personality, and this assumption was never challenged. In fact, it was functionally impossible to disconfirm. Captures of small prey were considered part of the mantid's normal side; captures of large prey were considered part of the mantid's abnormal side. There was no alternative explanation.As luck would have it, by the time that the strictures of scientific discourse had tightened sufficiently to disallow the use of anthropomorphisms in the explanation of insect behavior, another acceptable explanation of mantid cannibalism became immediately available: cannibalism became part of mantid mating behavior. That is, the fundamental explanatory model remained unchanged; it was merely couched in more appropriate terms. The acceptance of this new explanation for cannibalism was virtually immediate and complete. For instance, no one ever asked the following questions: If the headless male remains able to mate as a putative precaution against female cannibalism, for what reason does the headless female remain able to fashion “a perfectly constructed ootheca”? Or: If female-on-male cannibalism plays a role in mating behavior, what role is played by genderindifferent cannibalism, especially that among immature mantids? The latter phenomena were simply ignored — they were just uninteresting artifacts of insect life. However, the grand logic of nature was immediately apparent in the headless male's ability to mate. The ruling theory, to use Chamberlin's term, had been able to accommodate itself to, and assimilate, the new scientific discourse. It remained unscathed.A persistent question posed by several historians of this particular topic has been, Why did not the results of Ken Roeder's experiments debunk the myth that males are regularly cannibalized by the females with which they mate? The reason, which we hope is now clear, is that there were two interdependent ruling theories operating here. If one accepts the argument that mantids' cannibalism is simply a normal part of their prey-catching behavior, then one attacks not only the theory that mantids have two separate predatory strategies, but also the more recent theory that mantids have evolved to be the ideal fly-catching machines. This second theory found its first confirming support in the centuries-old practice of feeding flies to captive mantids. Again, the disconfirming evidence of mantids eating prey of various sizes had no impact on the theory. Confirming observations were accepted: disconfirming observations were seen as anomalies.Additional confirmation of both ruling theories was garnered in experiments done in the mid-twentieth century. These experiments were based on the assumption that the original conceptualizations were correct, and consequently they did not test other hypotheses. The combined strength of the two theories is evidenced especially in the Raus' failure to account for the fact that their empirical observations were at odds with many of the conclusions that they drew, and in the fact that Roeder's work is still used to support the belief in the regularity of mating-related cannibalism despite the fact that Roeder, himself, argued the opposite. with both theories well entrenched, it is virtually impossible to promote an alternative theory of mantid behavior: namely, that mantids are generalized, opportunistic predators that manage to survivein spite of the fact that cannibalism sometimes occurs. (shrink)

We contend that software developers have an ethical responsibility to strive for reliable software. We base that obligation on long standing engineering traditions that place the public good as a central tenant and on the professional relationship between a software developer and the users of the software developed.

There is a growing literature on the concept of e-trust and on the feasibility and advisability of “trusting” artificial agents. In this paper we present an object-oriented model for thinking about trust in both face-to-face and digitally mediated environments. We review important recent contributions to this literature regarding e-trust in conjunction with presenting our model. We identify three important types of trust interactions and examine trust from the perspective of a software developer. Too often, the primary focus of research in (...) this area has been on the artificial agents and the humans they may encounter after they are deployed. We contend that the humans who design, implement, and deploy the artificial agents are crucial to any discussion of e-trust and to understanding the distinctions among the concepts of trust, e-trust and face-to-face trust. (shrink)

In this essay we argue that the current social and ethical structure in the Open Source Software Community stem from its roots in academia. The individual developers experience a level of autonomy similar to that of a faculty member. Furthermore, we assert that the Open Source Software Community’s social structure demands benevolent leadership. We argue that it is difficult to pass off low quality open source software as high quality software and that the Open Source development model offers strong accountability. (...) Finally, we argue that Open Source Software introduces ethical challenges for universities and the software development community. (shrink)

"The Rules" are found in a collaborative document that states principles for responsibility when a computer artifact is designed, developed and deployed into a sociotechnical system. At this writing, over 50 people from nine countries have signed onto The Rules. Unlike codes of ethics, The Rules are not tied to any organization, and computer users as well as computing professionals are invited to sign onto The Rules. The emphasis in The Rules is that both users and professionals have responsibilities in (...) the production and use of computing artifacts. In this paper, we use The Rules to examine issues of trust. (shrink)

Perfect adaptation in a dynamical system is the phenomenon that one or more variables have an initial transient response to a persistent change in an external stimulus but revert to their original value as the system converges to equilibrium. With the help of the causal ordering algorithm, one can construct graphical representations of dynamical systems that represent the causal relations between the variables and the conditional independences in the equilibrium distribution. We apply these tools to formulate sufficient graphical conditions for (...) identifying perfect adaptation from a set of first-order differential equations. Furthermore, we give sufficient conditions to test for the presence of perfect adaptation in experimental equilibrium data. We apply this method to a simple model for a protein signalling pathway and test its predictions in both simulations and using real-world protein expression data. We demonstrate that perfect adaptation can lead to misleading orientation of edges in the output of causal discovery algorithms. (shrink)

Health care reform proposals threaten to exacerbate tensions physicians already face in trying to balance traditional duties to individual patients against increasing pressure to serve broader societal and institutional goals. To cope with reform, medical ethics must clarify physicians' moral obligations, change existing ethical codes, and develop an ethics of institutions.

The myside bias in written argumentation entails excluding other side information from essays. To determine the locus of the bias, 86 Experiment 1 participants were assigned to argue either for or against their preferred side of a proposal. Participants were given either balanced or unrestricted research instructions. Balanced research instructions significantly increased the use of other side information. Participants' notes, rather than search patterns, predicted the myside bias. Participants who defined good arguments as those that can be “proved by facts” (...) were more prone towards the myside bias. In Experiment 2, 84 participants of high and low argumentation ability read a text called “More Than Just the Facts” designed to contradict this fact-based argumentation schema. For high argumentation ability participants, the intervention reduced the myside bias, but for low ability participants it increased. The roots of the myside bias are underdeveloped argumentation schemata leading to misconceptions about research and argumentation. (shrink)

Technology has outpaced the capacity of researchers performing research on human participants to interpret all data generated and handle those data responsibly. This poses a critical challenge to existing rules governing human subjects research. The technologies used in research to generate images, scans, and data can now produce so much information that there is significant potential for incidental findings, findings generated in the course of research but beyond the aims of the study. Neuroimaging scans may visualize the entire brain and (...) even the entire head; computed tomography colonography research may visualize the entire torso, from the base of the lungs to the pubis; genetics studies may reveal “extra” and sometimes unwanted information about the family, such as misattributed paternity and undisclosed adoption; and genomic microarray research increasingly involves whole-genome analysis revealing an individual’s complete genotype, with enormous potential for uncovering unexpected information about an individual’s genetics and risks of developing future conditions. (shrink)

This paper argues that we ought to conceive of the Dark Energy problem—the question of how to account for observational data, naturally interpreted as accelerated expansion of the universe—as a crisis of underdetermined pursuit-worthiness. Not only are the various approaches to the Dark Energy problem evidentially underdetermined; at present, no compelling reasons single out any of them as more likely to be true than the other. More vexingly for working scientists, none of the approaches stands out as uncontroversially preferable over (...) its rivals in terms of its rationally warranted promise, i.e. the reasons to further work on, explore, and develop it. We demonstrate this claim by applying a Peircean economic model of pursuit-worthiness in terms of a cognitive cost/benefit estimate—with the instantiation of theory virtues as key indicators of cognitive gains—to the four main Dark Energy proposals (the cosmological constant approach, modified gravity, quintessence, and inhomogeneous cosmologies). According to our analysis, these approaches do not admit of an unambiguous, or uncontroversial, ranking with respect to which ansatz deserves distinguished attention and research efforts. The overall methodological counsel that our analysis underwrites recommends a pragmatic double research strategy forward: to encourage and foster theory pluralism and the search for tests—with the goal of enhancing the testability of the \(\Lambda \) CDM model and “testing it to destruction". (shrink)

No consensus yet exists on how to handle incidental fnd-ings in human subjects research. Yet empirical studies document IFs in a wide range of research studies, where IFs are fndings beyond the aims of the study that are of potential health or reproductive importance to the individual research participant. This paper reports recommendations of a two-year project group funded by NIH to study how to manage IFs in genetic and genomic research, as well as imaging research. We conclude that researchers (...) have an obligation to address the possibility of discovering IFs in their protocol and communications with the IRB, and in their consent forms and communications with research participants. Researchers should establish a pathway for handling IFs and communicate that to the IRB and research participants. We recommend a pathway and categorize IFs into those that must be disclosed to research participants, those that may be disclosed, and those that should not be disclosed. (shrink)

Bioethics has paid surprisingly little attention to the special problems faced by women and to feminist analyses of current health care issues other than ...

The Covid‐19 pandemic has exposed four myths in bioethics. First, the flood of bioethics publications on how to allocate scarce resources in crisis conditions has assumed authorities would declare the onset of crisis standards of care, yet few have done so. This leaves guidelines in limbo and patients unprotected. Second, the pandemic's realities have exploded traditional boundaries between clinical, research, and public health ethics, requiring bioethics to face the interdigitation of learning, doing, and allocating. Third, without empirical research, the success (...) or failure of ethics guidelines remains unknown, demonstrating that crafting ethics guidance is only the start. And fourth, the pandemic's glaring health inequities require new commitment to learn from communities facing extraordinary challenges. Without that new learning, bioethics methods cannot succeed. The pandemic is a wake‐up call, and bioethics must rise to the challenge. (shrink)

Genomic research results and incidental findings with health implications for a research participant are of potential interest not only to the participant, but also to the participant's family. Yet investigators lack guidance on return of results to relatives, including after the participant's death. In this paper, a national working group offers consensus analysis and recommendations, including an ethical framework to guide investigators in managing this challenging issue, before and after the participant's death.

Participant-driven research is a burgeoning domain of research innovation, often facilitated by mobile technologies. Return of results and data are common hallmarks, grounded in transparency and data democracy. PDR has much to teach traditional research about these practices and successful engagement. Recommendations calling for new state laws governing research with mHealth modalities common in PDR and federal creation of review mechanisms, threaten to stifle valuable participant-driven innovation, including in return of results.

The current explosion of genetic knowledge and the rapid proliferation of genetic tests has rightly provoked concern that we are approaching a future in which people will be labeled and disadvantaged based on genetic information. Indeed, some have already suffered harm, including denial of health insurance. This concern has prompted an outpouring of analysis. Yet almost all of it approaches the problem of genetic disadvantage under the rubric of “genetic discrimination.”This rubric is woefully inadequate to the task at hand. It (...) ignores years of commentary on race and gender demonstrating the limits of antidiscrimination analysis as an analytic framework and corrective tool. Too much discussion of genetic disadvantage proceeds as if scholars of race and gender had not spent decades critiquing and developing antidiscrimination theory.Indeed, there are multiple links among race, gender, and genetics. Dorothy Roberts has discussed the historical links between racism and genetics, while she and others have begun to map connections between gender and genetics. (shrink)

Debate over the proper use of racial and ethnic categories in biomedical research has raged in recent years. With the Human Genome Project showing that human beings are overwhelmingly alike genetically, exhibiting more genetic variation within supposed “races” than between them, many have come to doubt the scientific utility of such categories. Yet federal authorities use Directive 15 from the Office of Management and Budget to mandate the continued use of such categories in research. Moreover, researchers studying health disparities argue (...) that data collection using racial and ethnic categories is necessary to determine whether conditions and care vary by race and ethnicity. Epidemiologists also defend the use of racial and ethnic categories to understand contributors to disease such as the stress of experiencing racial prejudice and reduced access to care because of bias. (shrink)

Human genomics is a translational field spanning research, clinical care, public health, and direct-to-consumer testing. However, law differs across these domains on issues including liability, consent, promoting quality of analysis and interpretation, and safeguarding privacy. Genomic activities crossing domains can thus encounter confusion and conflicts among these approaches. This paper suggests how to resolve these conflicts while protecting the rights and interests of individuals sequenced. Translational genomics requires this more translational approach to law.

A fundamental question in biology is whether phenotypes can be predicted by ecological or genomic rules. At least five cases of convergent evolution of the crab‐like body plan (with a wide and flattened shape, and a bent abdomen) are known in decapod crustaceans, and have, for over 140 years, been known as “carcinization.” The repeated loss of this body plan has been identified as “decarcinization.” In reviewing the field, we offer phylogenetic strategies to include poorly known groups, and direct evidence (...) from fossils, that will resolve the history of crab evolution and the degree of phenotypic variation within crabs. Proposed ecological advantages of the crab body are summarized into a hypothesis of phenotypic integration suggesting correlated evolution of the carapace shape and abdomen. Our premise provides fertile ground for future studies of the genomic and developmental basis, and the predictability, of the crab‐like body form. (shrink)

Oversight of human gene transfer research presents an important model with potential application to oversight of nanobiology research on human participants. Gene therapy oversight adds centralized federal review at the National Institutes of Health's Office of Biotechnology Activities and its Recombinant DNA Advisory Committee to standard oversight of human subjects research at the researcher's institution and at the federal level by the Office for Human Research Protections. The Food and Drug Administration's Center for Biologics Evaluation and Research oversees human gene (...) transfer research in parallel, including approval of protocols and regulation of products. This article traces the evolution of this dual oversight system; describes how the system is already addressing nanobiotechnology in gene transfer: evaluates gene therapy oversight based on public opinion, the literature, and preliminary expert elicitation; and offers lessons of the gene therapy oversight experience for oversight of nanobiotechnology. (shrink)

Developing ethical standards for clinical use of large-scale genome and exome sequencing has proven challenging, in part due to the inevitability of incidental or secondary findings. Policy of the American College of Medical Genetics and Genomics has evolved but remains problematic. In 2013, ACMG issued policy recommending mandatory analysis of 56 extra genes whenever sequencing was ordered for any indication, in order to ascertain positive findings in pathogenic and actionable genes. Widespread objection yielded a 2014 amendment allowing patients to opt-out (...) from analysis of the extra genes. In 2015, ACMG published the amended policy, providing that patients could opt out of the full set of extra genes, but not a subset. In 2016, ACMG enlarged the set and indicated planned expansion of the roster of extra genes to include pharmacogenetic findings. ACMG policy does not protect the respect for patient choice that prevails in other domains of clinical medicine, where informed consent allows patients to opt in to desired testing. By creating an expanding domain of genomic testing that will be routinely conducted unless patients reject the entire set of extra tests, ACMG creates an exceptional domain clinical practice that is not supported by ethics or science. (shrink)

Nanomedicine is yielding new and improved treatments and diagnostics for a range of diseases and disorders. Nanomedicine applications incorporate materials and components with nanoscale dimensions where novel physiochemical properties emerge as a result of size-dependent phenomena and high surface-to-mass ratio. Nanotherapeutics and in vivo nanodiagnostics are a subset of nanomedicine products that enter the human body. These include drugs, biological products, implantable medical devices, and combination products that are designed to function in the body in ways unachievable at larger scales. (...) Nanotherapeutics andin vivonanodiagnostics incorporate materials that are engineered at the nanoscale to express novel properties that are medicinally useful. These nanomedicine applications can also contain nanomaterials that are biologically active, producing interactions that depend on biological triggers. Examples include nanoscale formulations of insoluble drugs to improve bioavailability and pharmacokinetics, drugs encapsulated in hollow nanoparticles with the ability to target and cross cellular and tissue membranes and to release their payload at a specific time or location, imaging agents that demonstrate novel optical properties to aid in locating micrometastases, and antimicrobial and drug-eluting components or coatings of implantable medical devices such as stents. (shrink)

Answering important public health questions often requires collection of sensitive information about individuals. For example, our understanding of how HIV is transmitted and how to prevent it only came about with people's willingness to share information about their sexual and drug-using behaviors. Given the scientific need for sensitive, personal information, researchers have a corresponding ethical and legal obligation to maintain the confidentiality of data they collect and typically promise in consent forms to restrict access to it and not to publish (...) identifying data.The interests of others, however, can threaten researchers' promises of confidentiality when legal demands are made to access research data. In some cases, the subject of the litigation is tightly connected to the research questions, and litigants' interest in the data is not surprising. Researchers conducting studies on tobacco or occupational or other chemical exposures, for example, are relatively frequent targets of subpoenas. (shrink)