DNA evidence has rapidly become a significant and routine feature of modern criminal prosecutions. The first introduction of DNA evidence in a U.S. Court occurred in 1987. By 1994, 42 percent of local prosecutors reported that they had used DNA evidence in a felony case at least once. By 2001 that number had increased to 68 percent. Moreover, from a technical point of view, the potential benefits of DNA testing are substantial. Early hurdles to admissibility during trial (...) have been overcome by the adoption of rigorous standards for DNA analysis. Rapid development of identification technology, fueled in significant part by the Human Genome Project, and the resultant development and expansion of national forensic DNA databases, has increased the potential of DNA to play a major role in crime solving. Indeed, over three million offender profiles, collected by state and federal authorities, now reside in the National DNA Index System. This number is likely to increase as more states and the federal government are expanding compelled DNA collections to individuals arrested for certain crimes. (shrink)

DNA profiling is a well-established technology for use in the criminal justice system, both in courtrooms and elsewhere. The fact that DNA profiles are based on non-coding DNA and do not reveal details about the physical appearance of an individual has contributed to the acceptability of this type of evidence. Its success in criminal investigation, combined with major innovations in the field of genetics, have contributed to a change of role for this type of evidence. Nowadays DNA (...) class='Hi'>evidence is not merely about identification, where trace evidence is compared to a sample taken from a suspect. An ever-growing role is anticipated for DNA profiling as an investigative tool, a technique aimed at generating a suspect where there is none. One of these applications is the inference of visible traits. As this article will show, racial classifications are at the heart of this application. The Netherlands and its legal regulation of 'externally visible traits' will serve as an example. It will be shown that, to make this technology work, a large number of actors has to be enrolled and their articulations invited. This indicates that instead of a 'silent witness', a DNA profile should rather be seen as an 'articulate collective'. Based on two cases, I argue that the normativity of visible traits is context-dependent. Taking into account the practices in which technology is put to use alerts us to novel ethical questions raised by their application. (shrink)

This paper examines the English case, Regina v Adams in which the difference between "scientific reason" and "common sense" was explicitly at stake in the use of DNA evidence. In its decision the Appellate Court reinstated a boundary between "scientific" and "common sense" evidence, arguing that this boundary was necessary to preserve the jury's role as trier of fact. The paper's discussion of the court's work of demarcation addresses the unresolved problems with the place of probability estimates in (...) jury trials. (shrink)

Many epistemological terms, such as investigation, inquiry, argument, evidence, and fact were established in law well before being associated with science. However, while legal proof remained qualified by standards of ‘moral certainty’, scientific proof attained a reputation for objectivity. Although most forms of legal evidence continue to be treated as fallible ‘opinions’ rather than objective ‘facts’, forensic DNA evidence increasingly is being granted an exceptional factual status. It did not always enjoy such status. Two decades ago, the (...) scientific status of forensic DNA evidence was challenged in the scientific literature and in courts of law, but by the late 1990s it was being granted exceptional legal status. This paper reviews the ascendancy of DNA profiling, and argues that its widely-heralded objective status is bound up with systems of administrative accountability. The ‘administrative objectivity’ of DNA evidence rests upon observable and reportable bureaucratic rules, records, recording devices, protocols, and architectural arrangements. By highlighting administrative sources of objectivity, this paper suggests that DNA evidence remains bound within the context of ordinary organisational and practical routines, and is not a transcendent source of ‘truth’ in the criminal justice system. (shrink)

The paper uses insights from the so-called rape in disguise case study to describe forensic DNA practices in the Netherlands in late 1980s. It describes how "reliabilities" of forensic DNA practices were achieved. One such reliability - convincing evidence - proliferates body parts through time and space. Then, attention shifts to the individual who was suspected of having committed the rape. He was asked to deliver tissue for DNA typing, but refused to do so. Hence DNA typing could not (...) be used to connect the suspect to a cervical smear collected from the body of the victim. His refusal and the legal impossibility to use force to obtain his biological material led first to questions in the Dutch parliament and then to the Dutch forensic DNA law. Other legal measures enacted after this are also described. I argue that, by means of the various Dutch forensic DNA laws and new forensic genetic techniques, the application of forensic DNA practices have shifted from identification and evidence to a tool for criminal investigation and prevention of future crimes. In the final part of the paper, the right to inviolability of the body and its synonym bodily integrity are emphasised. I argue that despite the various forensic DNA laws, bodily integrity of obtained tissue for DNA typing is still at stake as the result of convincing evidence. (shrink)

사용-참신성 예측주의에 따르면, 가설 구성에 사용된 자료는 증거가 되기 어렵다. DNA 이중 나선 구조의 발견에 대한 사례 연구는 이에 대한 반례를 제공한다. 로잘린드 프랭클린의 DNA X선 회절 사진은 이중 나선 가설의 구성에 사용된 동시에 증거로도 사용되었다. 이 사례에서 증거는 제약에 의한 대안가설의 명시적 제거에 의존하는 증거와 제약들 사이의 정합성 확인에 의존하는 증거로 구분되며, 두 증거 모두 ‘사용-참신한 예측’이라는 조건에는 의존하지 않는다.

In this paper, I discuss the discovery of the DNA structure by Francis Crick and James Watson, which has provoked a large historical literature but has yet not found entry into philosophical debates. I want to redress this imbalance. In contrast to the available historical literature, a strong emphasis will be placed upon analysing the roles played by theory, model, and evidence and the relationship between them. In particular, I am going to discuss not only Crick and Watson's well-known (...) model and Franklin's x-ray diffraction pictures (the evidence) but also the less well known theory of helical diffraction, which was absolutely crucial to Crick and Watson's discovery. The insights into this groundbreaking historical episode will have consequences for the ‘new’ received view of scientific models and their function and relationship to theory and world. The received view, dominated by works by Cartwright and Morgan and Morrison ([1999]), rather than trying to put forth a ‘theory of models’, is interested in questions to do with (i) the function of models in scientific practice and (ii) the construction of models. In regard to (i), the received view locates the model (as an idealized, simplified version of the real system under investigation) between theory and the world and sees the model as allowing the application of the former to the latter. As to (ii) Cartwright has argued for a phenomenologically driven view and Morgan and Morrison ([1999]) for the ‘autonomy’ of models in the construction process: models are determined neither by theory nor by the world. The present case study of the discovery of the DNA structure strongly challenges both (i) and (ii). In contrast to claim (i) of the received view, it was not Crick and Watson's model but rather the helical diffraction theory which served a mediating purpose between the model and the x-ray diffraction pictures. In particular, Cartwright's take on (ii) is refuted by a comparison of Franklin's bottom-up approach with Crick and Watson's top-down approach in constructing the model. The former led to difficulties, which only a strong confidence in the structure incorporated in the model could circumvent. How to Get to the Structure 1.1 X-ray diffraction and its synthesis 1.2 Model building and Pauling's panache 1.3 The structure of proteins 1.3.1 A failed inference to the best explanation 1.3.2 The misleading 5.1 Å spot in proteins and how to get rid of it 1.3.3 Derived predictions from Pauling's alpha-helix of protein molecules The CCV Theory of Helical X-Ray Diffraction 2.1 The role of the CCV theory in the discovery of the DNA structure Killing the Helix 3.1 Appreciating all evidence—in vain Conclusion Epilogue: Chargaff's Ratios CiteULike Connotea Del.icio.us What's this? (shrink)

DNA supercoiling is one of the mechanisms that can help unlinking of newly replicated DNA molecules. Although DNA topoisomerases, which catalyze the strand passing of DNA segments through one another, make the unlinking problem solvable in principle, it remains difficult to complete the process that enables the separation of the sister duplexes. A few different mechanisms were developed by nature to solve the problem. Some of the mechanisms are very intuitive while the others, like topology simplification by type II DNA (...) topoisomerases and DNA supercoiling, are not so evident. A computer simulation and analysis of linked sister plasmids formed inEscherichia colicells with suppressed topoisomerase IV suggests an insight into the latter mechanism. (shrink)

DNA profiling and databasing are now commonplace. A body of state and federal legislation enables the establishment and operation of profile databases for law-enforcement purposes. Enabling legislation is usually specific about who, or what evidence, may be profiled for a database. It may be less specific or silent on the issue of specimen retention following profiling and databasing.

This article considers individual rights and fundamental tenets of the criminal justice system in the context of DNA evidence, in particular recent advancements in genomics that have significantly advanced law enforcement investigative capabilities in this area. It discusses a technique known as Investigative Genetic Genealogy (IGG) which utilizes genomic data held by commercial direct-to-consumer ancestry and health companies to investigate the identity of suspects linked to serious crimes. Using this technique, even if only a small proportion of the population (...) (e.g. 5%) has submitted genomic data to these companies, almost anyone in the population can be identified. We discuss this phenomenon in the context of the existing literature and arguments in relation to universal forensic DNA databases, as well as relevant recent developments in both liberal democracies and authoritarian states. We introduce the concept of a quasi-universal forensic DNA database and consider associated implications for the criminal justice system and society from the perspectives of privacy, the right not to self-incriminate, joint rights, and collective responsibility. (shrink)

Emerging evidence suggests that DNA topology plays an instructive role in cell fate control through regulation of gene expression. Transcription produces torsional stress, and the resultant supercoiling of the DNA molecule generates an array of secondary structures. In turn, local DNA architecture is harnessed by the cell, acting within sensory feedback mechanisms to mediate transcriptional output. MYC is a potent oncogene, which is upregulated in the majority of cancers; thus numerous studies have focused on detailed understanding of its regulation. (...) Dissection of regulatory regions within the MYC promoter provided the first hint that intimate feedback between DNA topology and associated DNA remodeling proteins is critical for moderating transcription. As evidence of such regulation is also found in the context of many other genes, here we expand on the prototypical example of the MYC promoter, and also explore DNA architecture in a genome-wide context as a global mechanism of transcriptional control. Torsional stress, and supercoiling generated by transcription, shape the topology of DNA. Furthermore, the resultant secondary DNA structures and their interacting partners provide feedback to regulate gene expression. Emerging evidence suggests these mechanisms, identified through analysis of the MYC promoter, are applicable genome-wide. (shrink)

Mouse embryo cells, primed to differentiate with the hypomethylating agent 5‐azacytidine (5‐aza‐CR), provide an excellent model system in which cellular differentiation can be studied at the molecular level. An inherent advantage of this system is the availability of clonal populations of cells representative of the non‐differentiated precursor, those whose determinative state is that of a specific lineage, and the end stage, phenotypically mature cell. Analysis of these cultures at the cellular and molecular level will advance our understanding of requirements for (...) and the mechanism of action of growth modulators as well as the necessity for controlled expression of certain proto‐oncogenes. At a more fundamental level, the system can be used to identify, isolate and characterize genes whose expression alters the phenotypic fate of cells. (shrink)

The DNA‐passage activity of topoisomerase II accidentally produces DNA knots and interlinks within and between chromatin fibers. Fortunately, these unwanted DNA entanglements are actively removed by some mechanism. Here we present an outline on DNA knot formation and discuss recent studies that have investigated how intracellular DNA knots are removed. First, although topoisomerase II is able to minimize DNA entanglements in vitro to below equilibrium values, it is unclear whether such capacity performs equally in vivo in chromatinized DNA. Second, DNA (...) supercoiling could bias topoisomerase II to untangle the DNA. However, experimental evidence indicates that transcriptional supercoiling of intracellular DNA boosts knot formation. Last, cohesin and condensin could tighten DNA entanglements via DNA loop extrusion (LE) and force their dissolution by topoisomerase II. Recent observations indicate that condensin activity promotes the removal of DNA knots during interphase and mitosis. This activity might facilitate the spatial organization and dynamics of chromatin. (shrink)

Recent evidence from studies on DNA repair systems that are implicated in accelerated aging syndromes, have revealed a mechanism through which low levels of persistent damage might exert beneficial effects for both cancer prevention and longevity assurance. Beneficial effects of adaptive responses to low doses of insults that in higher concentrations show adverse effects are generally referred to as hormesis. There are numerous examples of hormetic effects ranging from mild stresses of irradiation to heat stress, hypergravity, pro‐oxidants, or food (...) restriction. Although the notion of hormesis is supported by many observations in various organisms, at least two major caveats have thus far prevented the application of hormesis for disease prevention in humans. First, the very nature of hormesis using toxins as a treatment regimen harbors the inherent danger of detrimental consequences. Second, the molecular mechanisms through which insults might exert beneficial effects have thus far remained elusive. Here, I discuss a mechanistic basis for hormesis and its implications for cancer prevention and healthy aging. (shrink)

Although DNA microarrays are now widely used in research settings, they have been slow to penetrate clinical practice in spite of their apparent advantages. This is due to the very different requirements for a clinical test in contrast to a research tool, and to a strict necessity for demonstrated clinical utility. There is a clear differentiation between two types of DNA array tests: “genomic” diagnostics, developed to ascertain the presence or absence of mutations, deletions or duplications, and for which clinical (...) evidence is already established, and tests using expression profiling for prognosis or predictive purposes, in which case the clinical correlate must be proven. Most array diagnostics currently used belong, understandably, to the “genomic” variety. It is to be expected that future improvements in tailored technology, as well as a logical trend towards measuring an ever‐increasing number of parameters, will ensure an important diagnostic role for DNA arrays in the coming decade. BioEssays 29:699–705, 2007. © 2007 Wiley Periodicals, Inc. (shrink)

This paper focuses on the question of whether DNA patents help or hinder scientific discovery and innovation. While DNA patents create a wide variety of possible benefits and harms for science and technology, the evidence we have at this point in time supports the conclusion that they will probably promote rather than hamper scientific discovery and innovation. However, since DNA patenting is a relatively recent phenomena and the biotechnology industry is in its infancy, we should continue to gather (...) class='Hi'>evidence about the effects of DNA patenting on scientific innovation and discovery as well the economic, social, and legal conditions relating to intellectual property in biotechnology. We should give the free market, the courts, researchers, and patent offices a chance to settle issues related to innovation and discovery, before we seek legislative remedies, since new laws proposed at this point would lack adequate foresight and could do more harm than good. However, we should be open to new laws or regulations on DNA patents if they are required to in order to deal with some of the biases and limitations of the free market. (shrink)

Balanced pools of deoxyribonucleoside triphosphates (dNTPs) are essential for DNA replication to occur with maximum fidelity. Conditions that create biased dNTP pools stimulate mutagenesis, as well as other phenomena, such as recombination or cell death. In this essay we consider the effective dNTP concentrations at replication sites under normal conditions, and we ask how maintenance of these levels contributes toward the natural fidelity of DNA replication. We focus upon two questions. (1) In prokaryotic systems, evidence suggests that replication is (...) driven by small, localized, rapidly replenished dNTP pools that do not equilibrate with the bulk dNTP pools in the cell. Since these pools cannot be analyzed directly, what indirect approaches can illuminate the nature of these replication‐active pools? (2) In eukaryotic cells, the normal dNTP pools are highly asymmetric, with dGTP being the least abundant nucleotide. Moreover, the composition of the dNTP pools changes as cells progress through the cell cycle. To what extent might these natural asymmetries contribute toward a recently described phenomenon, the differential rate of evolution of different genes in the same genome? (shrink)

There is growing evidence that mutations can arise in non‐dividing cells (both bacterial and mammalian) in the absence of chromosomal replication. The processes that are involved are still largely unknown but may include two separate mechanisms. In the first, DNA lesions resulting from the action of endogenous mutagens may give rise to RNA transcripts with miscoded bases. If these confer the ability to initiate DNA replication, the DNA lesions may have an opportunity to miscode during replication and thus could (...) give rise to apparently ‘adaptive’ mutations. A second mechanism is suggested by recent work in starved bacteria, showing that there is much more turnover of chromosomal DNA than has been previously thought. This could permit polymerase errors to lead to mutations in non‐dividing cells. Such cryptic DNA synthesis, which may essentially replace existing DNA rather than duplicating it, could, in principle, act as an additional source of variability on which selection may act, initially in the absence of cell division. In mammals such processes would undoubtedly have implications for germ cell mutagenesis and carcinogenesis. (shrink)

Higher plant nuclear genomes contain many families of dispersed repeats that change during evolution. Recent evidence from studies on genetically defined transposable elements raises the possibility that many of the dispersed repeats are remnants of such elements. Transposition of DNA has also occurred between mitochondria, chloroplasts and nuclei, a fact that underlines the major role played by DNA transposition in determining the structure of plant genomes.

A number of public controversies have emerged around forensic DNA testing backlogs at crime laboratories in the United States. This study provides a first look at public responses to such backlogs, using a controversy in the state of Wisconsin as a case study. First, it builds on research about public understandings of DNA and the “CSI effect” to develop a theoretical framework. Next, it explores news coverage of the Wisconsin backlog. It then uses survey data to show that public understandings (...) of DNA, media use, and demographic factors were related to how closely respondents followed the story about the backlog and/or how much they supported increased spending on DNA testing at the crime lab. Self-reported understanding of DNA predicted following the backlog, whereas perceived reliability of DNA evidence predicted both following the backlog and support. Total television viewing was not related to either following the backlog or support, but watching crime television predicted following the backlog. Reading a newspaper and watching local TV news each predicted following the backlog; reading a newspaper also predicted support. These results suggest a number of theoretical insights into how members of the public may reason about and draw on media messages regarding DNA and DNA testing in responding to forensic DNA testing backlogs. (shrink)

Mild and massive DNA damage are differentially integrated into the cellular signaling networks and, in consequence, provoke different cell fate decisions. After mild damage, the tumor suppressor p53 directs the cellular response to cell cycle arrest, DNA repair, and cell survival, whereas upon severe damage, p53 drives the cell death response. One posttranslational modification of p53, phosphorylation at Serine 46, selectively occurs after severe DNA damage and is envisioned as a marker of the cell death response. However, the molecular mechanism (...) of action of the p53 Ser46 phospho‐isomer, the molecular timing of this phosphorylation event, and its activating effects on apoptosis and ferroptosis still await exploration. In this essay, the current body of evidence on the molecular function of this deadly p53 mark, its evolutionary conservation, and the regulation of the key players of this response, the p53 Serine 46 kinases, are reviewed and dissected. (shrink)

Based on an ethnographic study of fingerprint and DNA evidence practices in the Swedish judicial system, this article analyses the materialization of forensic evidence. It argues that forensic evidence, while popularly understood as firmly rooted in materiality, is inseparably technoscientific and cultural. Its roots in the material world are entangled threads of matter, technoscience and culture that produce particular bodily constellations within and together with a particular sociocultural context. Forensic evidence, it argues further, is co-materialized with (...) crimes as well as with particular bodily and social constellations. Consequently, the article suggests that an analysis of how forensic evidence is produced can contribute to feminist understandings of the inseparability of sex and gender: understanding bodies as ongoing technoscientific-material-cultural practices of materialization may be a fruitful approach to analysing their complexity, and the relationships in which they are placed, without surrendering to either cultural or biological determinism. Taking a theoretical point of departure not only in an STS-informed approach, but also in material feminist theorizations, the article also underlines that the suggested theoretical conversations across borders of feminist theory and STS should be understood as a two-way-communication where the two fields contribute mutually to each other. (shrink)

Law and Order: Special Victims Unit (SVU) (1999–present) is a popular primetime drama that spotlights the use of genetic information to solve crimes. Despite the show’s heavy reliance on the forensic use of DNA evidence, the role of genetics in defining family and identity arises in complex ways. Many episodes wrestle with social, ethical, and legal questions that reflect assumptions about genetic essentialism and genetic determinism, but counterarguments about the importance of non-biological relationships, social factors, and legal entitlements are (...) given equal or greater weight. For this study, we identified and viewed 38 episodes from SVU’s first twenty seasons centered on genetic themes in non-forensic contexts. Two recurring themes emerged: (1) that the role DNA plays is only one factor in a complex web of biological and social considerations that shape our understanding of kinship; and (2) that genetic predispositions to behavioral traits such as mental illness or violence should not be seen as obscuring the responsibility of personal choice. By treating genetics as a complex source of information requiring social context to be understood, SVU allows audiences to play an active role in interpreting its meaning. (shrink)

The prelims comprise: Introduction How it Works Sources of Error and Uncertainty DNA Typing Results as Legal Evidence The Legal Reception of DNA Typing DNA Typing and the Judicial Assessment of Scientific Evidence Social Impact: Criminal Investigation and Adjudication Conclusion Notes.

PurposeThe purpose of this paper is to discuss the UK National DNA Database and some of the controversies surrounding it with reference to legal and ethical issues, focusing particularly on privacy and human rights. Governance of this database involves specific exemptions from the Data Protection Act, and this gives a rise to concerns regarding both the extent of surveillance on the UK population and the possibility for harm to all citizens. This is of wider importance since every current citizen, and (...) everybody who visits the UK, could become a record in the DNA database. Principally, the paper seeks to explore whether these exemptions would also imply exemptions for software developers from codes of practice and ethics of their professional societies as relate to constructing or maintaining such data and the database.Design/methodology/approachThe paper makes a comparison between the principles of the DPA, as would need to be followed by all other organizations handling personal data, professional responsibilities‐based codes of ethics of professional societies, and the current reality as reported in relation to the NDNAD and the exemptions offered through the DPA.FindingsPrimarily, if NDNAD was not exempted from certain provisions in the DPA, the potential for the kinds of data leakages and other mishandlings could largely be avoided without the need for further considerations over so‐called “data minimization”. It can be seen how the lack of afforded protection allows for a wide range of issues as relate at least to privacy.Originality/valueThe paper provides the first evaluation of the combination of law, codes of ethics, and activities in the real world as related to NDNAD, with concomitant considerations for privacy, liberty, and human rights. Originality is demonstrated through consideration of the implications of certain exemptions in the DPA in relation to crime and taxation and national security and in relating the expected protections for personal data to widely reported evidence that such protections may be variously lacking. In addition, the paper provides a broad overview of controversies over certain newer kinds of DNA analysis, and other relatively recent findings, that seem generally absent from the vast majority of debates over this kind of analysis. (shrink)

Evidence for recombination suppression has been identified in linkage studies of several unstable DNA diseases. Also sex‐specific changes in recombination frequency have been detected at the loci of Huntington's disease and myotonic dystrophy. It can be hypothesized that meiotic recombination is regulated by genome‐wide genomic imprinting and that changes in meiotic recombination imply the presence of the genomic imprinting defect. If aberrant recombination at the locus of trinucleotide repeat expansion is verified, new theoretical and experimental opportunities will arise in (...) studies on the role of genomic imprinting in the unstable DNA diseases. (shrink)

DNA replication is both highly conserved and controlled. Problematic DNA replication can lead to genomic instability and therefore carcinogenesis. Numerous mechanisms work together to achieve this tight control and increasing evidence suggests that post‐translational modifications (phosphorylation, ubiquitination, SUMOylation) of DNA replication proteins play a pivotal role in this process. Here we discuss such modifications in the light of a recent article that describes a novel role for the deubiquitinase (DUB) USP7/HAUSP in the control of DNA replication. USP7 achieves this (...) function by an unusual and novel mechanism, namely deubiquitination of SUMOylated proteins at the replication fork, making USP7 also a SUMO DUB (SDUB). This work extends previous observations of increased levels of SUMO and low levels of ubiquitin at the on‐going replication fork. Here, we discuss this novel study, its contribution to the DNA replication and genomic stability field and what questions arise from this work. (shrink)

DNA helicases are a class of molecular motors that catalyze processive unwinding of double stranded DNA. In spite of much study, we know relatively little about the mechanisms by which these enzymes carry out the function for which they are named. Most current views are based on inferences from crystal structures. A prominent view is that the canonical ATPase motor exerts a force on the ssDNA resulting in “pulling” the duplex across a “pin” or “wedge” in the enzyme leading to (...) a mechanical separation of the two DNA strands. In such models, DNA base pair separation is tightly coupled to ssDNA translocation of the motors. However, recent studies of the Escherichia coli RecBCD helicase suggest an alternative model in which DNA base pair melting and ssDNA translocation occur separately. In this view, the enzyme‐DNA binding free energy is used to melt multiple DNA base pairs in an ATP‐independent manner, followed by ATP‐dependent translocation of the canonical motors along the newly formed ssDNA tracks. Repetition of these two steps results in processive DNA unwinding. We summarize recent evidence suggesting this mechanism for RecBCD helicase action. (shrink)

This paper assesses the effect of DNA barcoding—the use of informative genetic markers to identify and discriminate between species—on taxonomy. Throughout, we interpret this in terms of _varipraxis_, a concept we introduce to make sense of the treatment of biological variation by scientists and other practitioners. From its inception, DNA barcoding was criticised for being reductive, in attempting to replace multiple forms of taxonomic evidence with just one: DNA sequence variation in one or a few indicative genes. We show, (...) though, how DNA barcoding has not narrowed or reduced taxonomy in the way it was projected to. We examine the development and implementation of DNA barcoding across three kingdoms of life: animals, plants, and protists. Through this, we demonstrate that for DNA barcoding to work, the range of acceptable intra-specific variation needs to be demarcated from variation deemed to be characteristic of inter-specific differences. Consequently, biological processes responsible for particular patterns of variation need to be investigated and understood. This encourages an integrative disposition towards understanding and explaining the evolutionary processes affecting the rate and nature of change at the nucleotide level. We detail how the impact of DNA barcoding has manifested differently across the three kingdoms we examine, assessing this in terms of the ontological commitments that are held and instantiated in practice. Based on this evaluation, we consider the problem of studying multi-kingdom communities, and assess the consequences of our analysis for understanding classification and taxonomy. (shrink)

The great majority of phenotypic characteristics are complex traits, complicating the identification of the genes underlying their expression. However, both methodological and theoretical progress in genome‐wide association studies have resulted in a much better understanding of the underlying genetics of many phenotypic traits, including externally visible characteristics (EVCs) such as eye and hair color. Consequently, it has become possible to predict EVCs from human samples lacking phenotypic information. Predicting EVCs from genetic evidence is clearly appealing for forensic applications involving (...) the personal identification of human remains. Now, a recent paper has reported the genetic determination of eye and hair color in samples up to 800 years old. The ability to predict EVCs from ancient human remains opens up promising perspectives for ancient DNA research, as this could allow studies to directly address archaeological and evolutionary questions related to the temporal and geographical origins of the genetic variants underlying phenotypes. (shrink)

The exchange of forensic DNA data is seen as an increasingly important tool in criminal investigations into organised crime, control strategies and counter-terrorism measures. On the basis of a set of interviews with police professionals involved in the transnational exchange of DNA data between EU countries, this paper examines how forensic DNA evidence is given meaning within the various different ways of constructing a police epistemic culture, it is, a set of shared values concerning valid knowledge and practices normatively (...) considered adequate and legitimate. The police epistemic culture is fuelled by multiple dynamics of boundary work, revealing how police professionals involved in international cooperation (i) define their specific core activities and competencies; (ii) construct particular understandings of valid knowledge and how it should be produced; (iii) enact the police epistemic culture in contrast to the epistemic cultures of the judicial authorities and forensic scientists. (shrink)

According to Scheck, Newfeld, and Dwyer (2000), there have been innumerable individuals wrongly convicted of a crime and sentenced to life imprisonment or to death based upon faulty evidence. The historical development of DNA evidence as a tool in the investigative process during the past 25 years is explained/analyzed, and the role of eyewitness evidence in the wrongful conviction of innocent individuals. This paper culminates in the Anthony Capozzi case study where eyewitness testimony wrongfully imprisoned a man (...) before the advent of DNA technology and which ultimately freed him years after the crime. The methodology used is the examination of journal articles, books, and newspaper articles on the phenomenon of wrongful convictions. (shrink)

Extensive studies of DNA secondary structure during the past decade have shown that DNA is a dynamic molecule, whose structure depends on the underlying nucleotide sequence and is influenced by the environment and the overall DNA topology. Three major non‐B‐DNA structures have been described (Z‐DNA, triplex DNA and cruciform DNA) which are stabilized by unconstrained negative supercoiling and can be formed under physiological conditions. In this essay we summarize the DNA primary structure features that are pertinent to the formation of (...) these conformers and present data concerning the occurrence of these sequences in the eukaryotic genome. The evidence in favor of the existence of these unusual DNA structures in vivo is discussed. The effect of alternative non‐B‐DNA structures on the way DNA is organized in chromatin is considered, and this is followed by evaluation of the data relating these structures to eukaryotic transcription. Some possible mechanisms by which the effect of non‐B structures on transcription might be exerted are proposed. (shrink)

There is something puzzling about statistical evidence. One place this manifests is in the law, where courts are reluctant to base affirmative verdicts on evidence that is purely statistical, in spite of the fact that it is perfectly capable of meeting the standards of proof enshrined in legal doctrine. After surveying some proposed explanations for this, I shall outline a new approach – one that makes use of a notion of normalcy that is distinct from the idea of (...) statistical frequency. The puzzle is not, however, merely a legal one. Our unwillingness to base beliefs on statistical evidence is by no means limited to the courtroom, and is at odds with almost every general principle that epistemologists have proposed as to how we ought to manage our beliefs. (shrink)

There is growing evidence of evolutionary genome plasticity. The evolution of repetitive DNA elements, the major components of most eukaryotic genomes, involves the amplification of various classes of mobile genetic elements, the expansion of satellite DNA, the transfer of fragments or entire organellar genomes and may have connections with viruses. In addition to various repetitive DNA elements, a plethora of large and small RNAs migrate within and between cells during individual development as well as during evolution and contribute to (...) changes of genome structure and function. Such migration of DNA and RNA molecules often results in horizontal gene transfer, thus shaping the whole genomic network of interconnected species. Here, we propose that a high evolutionary dynamism of repetitive genome components is often related to the migration/movement of DNA or RNA molecules. We speculate that the cytoplasm is probably an ideal compartment for such evolutionary experiments. (shrink)

As nations strengthen borders and restrict refugee admissions, national security officials are screening for fraudulent nationality claims. One tool to investigate nationality claims is DNA testing, either for claimed relationships or for ancestral origins. At the same time, the plight of global statelessness leaves millions without documentation of their nationality, and DNA testing might be the only recourse to provide evidence of heritage or relationships. DNA testing has been used sparsely to date to determine ancestral origin as a proxy (...) for nationality but could increase as border controls tighten. Given the historic lessons in eugenics and the potential for misuse of personal genetic information, it is essential to consider the ethical parameters in order to guide the implementation of genetic data for such purposes. Here, we break down examples of the use of DNA testing for nationality, and the risks and benefits of genetic testing for this purpose. Important ethical considerations discussed include (1) empowerment of stateless individuals with evidence for citizenship proceedings; (2) imprecise correlation between genetic heritage and nationality; (3) effective protection of state interests; and (4) practicalities of DNA testing. (shrink)

Recent advances in population genetics have made it possible to infer an individual's ancestral origin with a high degree of reliability, giving rise to the new technology called ‘DNA Ancestry Profiling’. Bioethicists have raised concerns over using this technology within a forensic context, many of which stem from issues concerning race. In this article, I offer some reasons why we ought to allow forensic scientists to use DNA Ancestry Profiling to infer the race or ethnicity of perpetrators — on a (...) particular understanding of race or ethnicity — in at least some cases. First, there is reason to think the process will meet our evidential standards in many cases. Second, the technology has serious prospects for improving racial justice. Third, the ethical concerns that have been raised can be addressed. And last, using Forensic DNA Ancestry Profiling to infer race or ethnicity has many benefits over its successor technology known as Molecular Photofitting. I conclude the essay by sketching the empirical work that remains to be done. (shrink)

Oxidised bases, such as 8-oxo-guanine, occur in cellular DNA as a result of attack by oxygen free radicals. The cancer-protective effect of vegetables and fruit is attributed to the ability of antioxidants in them to scavenge free radicals, preventing DNA damage and subsequent mutation. Antioxidant supplements (e.g., β-carotene, vitamin C) increase the resistance of lymphocytes to oxidative damage, and a negative correlation is seen between antioxidant concentrations in tissues and oxidised bases in DNA. Large-scale intervention trials with β-carotene have, however, (...) led to increases in cancer. Recent measurements of the frequency of oxidised DNA bases indicate that earlier estimates were greatly exaggerated; there may be only a few thousand 8-oxo-guanines per cell. Convincing evidence for mutations resulting from oxidative damage, in tumours or cultured cells, is lacking. It seems that efficient antioxidant defences together with DNA repair maintain a steady-state level of damage representing minimal risk to cell or organism. BioEssays 21:238–246, 1999. © 1999 John Wiley & Sons, Inc. (shrink)

A widely accepted assumption in radiobiology is that ionizing radiation kills cells by inducing forms of damage in DNA structures that lead to the formation of lethal chromosome aberrations. One goal of radiation biology research is the identification of these forms of DNA damage, the characterization of the mechanisms involved in their repair and the elucidation of the processes involved in their transformation to chromosome damage, In recent years, evidence has accumulated implicating DNA double stranded breaks as lesions relevant (...) for cell killing. Here, the available information on this topic is reviewed together with the methods most commonly used to quantitate induction and repair of this type of lesion. The presentation concludes with an outline of present research directions and future goals. (shrink)

Oxidised bases, such as 8-oxo-guanine, occur in cellular DNA as a result of attack by oxygen free radicals. The cancer-protective effect of vegetables and fruit is attributed to the ability of antioxidants in them to scavenge free radicals, preventing DNA damage and subsequent mutation. Antioxidant supplements (e.g., β-carotene, vitamin C) increase the resistance of lymphocytes to oxidative damage, and a negative correlation is seen between antioxidant concentrations in tissues and oxidised bases in DNA. Large-scale intervention trials with β-carotene have, however, (...) led to increases in cancer. Recent measurements of the frequency of oxidised DNA bases indicate that earlier estimates were greatly exaggerated; there may be only a few thousand 8-oxo-guanines per cell. Convincing evidence for mutations resulting from oxidative damage, in tumours or cultured cells, is lacking. It seems that efficient antioxidant defences together with DNA repair maintain a steady-state level of damage representing minimal risk to cell or organism. BioEssays 21:238–246, 1999. © 1999 John Wiley & Sons, Inc. (shrink)

Both opponents and proponents of the death penalty express faith in science and in DNA evidence to justify their positions. This article examines the production of forensic evidence as a social activity and suggests that tendencies toward bias and error may not apply symmetrically in inculpation and exoneration contexts.

Throughout evolution, there has been interaction and exchange between RNA pools in the environment, and DNA and RNA pools of eukaryotic organisms. Metagenomic and metatranscriptomic sequencing of invertebrate hosts and their microbiota has revealed a rich evolutionary history of RNA virus shuttling between species. Horizontal transfer adapted the RNA pool for successful future interactions which lead to zoonotic transmission and detrimental RNA viral pandemics like SARS‐CoV2. In eukaryotes, noncoding RNA (ncRNA) is an established mechanism derived from prokaryotes to defend against (...) viral attack through innate immunity and regulation of host‐derived mRNA. Transgenerational inheritance of ncRNA is evidence for feedforward adaptive immunity and epigenetically encoded environmental change across generations, which may explain the ‘‘missing heritability’’ of common disease. Causal graph theory and the Price Equation can model epigenetic inheritance involving dynamic internal and external RNA pools. Experimental designs should include metatranscriptomic analyses to understand how ncRNA responds to rapidly changing environmental conditions, within and between organisms, and across generations. (shrink)

Methylation of cytosine DNA residues is a well‐studied epigenetic modification with important roles in formation of heterochromatic regions of the genome, and also in tissue‐specific repression of transcription. However, we recently found that the ciliate Oxytricha uses methylcytosine in a novel DNA elimination pathway important for programmed genome restructuring. Remarkably, mounting evidence suggests that methylcytosine can play a dual role in ciliates, repressing gene expression during some life‐stages and directing DNA elimination in others. In this essay, I describe these (...) recent advances in the DNA methylation field and discuss whether this unexpected novel role for methylcytosine in DNA elimination might be more widely conserved in eukaryotic biology, particularly in apoptotic pathways. (shrink)

The forensic use of DNA involves the public in a number of roles. The rapid adoption of DNA identification as a part of the legal system and continuing developments have afforded little opportunity to thoroughly interrogate public understandings of issues. This article reports on a survey that explores public understanding of the forensic use of DNA: sources of knowledge, understandings of processes, and attitudes toward DNA use. Overall, knowledge about DNA use was limited, particularly around means of taking samples and (...) storage, and two thirds stated that they did not have enough information about DNA use. While the majority agreed that such use of DNA is “a great step forward,” they “would be happy to give a DNA sample if requested,” and considered DNA evidence to be important, concern was indicated about some areas, such as possible mistakes. This was particularly the case for indigenous peoples. (shrink)