DNA sequence variation is abundant in wild populations. While molecular biologists use genetically homogeneous strains of model organisms to avoid this variation, evolutionary biologists embrace genetic variation as the material of evolution since heritable differences in fitness drive evolutionary change. Yet, the relationship between the phenotypic variation affecting fitness and the genotypic variation producing it is complex. Genetic buffering mechanisms modify this relationship by concealing the effects of genetic and environmental variation on phenotype. Genetic buffering allows the build-up and storage (...) of genetic variation in phenotypically normal populations. When buffering breaks down, thresholds governing the expression of previously silent variation are crossed. At these thresholds, phenotypic differences suddenly appear and are available for selection. Thus, buffering mechanisms modulate evolution and regulate a balance between evolutionary stasis and change. Recent work provides a glimpse of the molecular details governing some types of genetic buffering. BioEssays 22:1095–1105, 2000. © 2000 John Wiley & Sons, Inc. (shrink)

For many decades, access to human biological samples, such as cells, tissues, organs, blood, and sub-cellular materials such as DNA, for use in biomedical research, has been central in understanding the nature and transmission of diseases across the globe. However, the limitations of current ethical and regulatory frameworks in sub-Saharan Africa to govern the collection, export, storage and reuse of these samples have resulted in inconsistencies in practice and a number of ethical concerns for sample donors, researchers and research ethics (...) committees. This paper examines stakeholders’ perspectives of and responses to the ethical issues arising from these research practices. (shrink)

Cells are cognitive entities possessing great computational power. DNA serves as a multivalent information storage medium for these computations at various time scales. Information is stored in sequences, epigenetic modifications, and rapidly changing nucleoprotein complexes. Because DNA must operate through complexes formed with other molecules in the cell, genome functions are inherently interactive and involve two-way communication with various cellular compartments. Both coding sequences and repetitive sequences contribute to the hierarchical systemic organization of the genome. By virtue of nucleoprotein complexes, (...) epigenetic modifications, and natural genetic engineering activities, the genome can serve as a read-write storage system. An interactive informatic conceptualization of the genome allows us to understand the functional importance of DNA that does not code for protein or RNA structure, clarifies the essential multidirectional and systemic nature of genomic information transfer, and emphasizes the need to investigate how cellular computation operates in reproduction and evolution. (shrink)

Concern about the ethics of clinical drug trials research on patients and healthy volunteers has been the subject of significant ethical analysis and policy development—protocols are reviewed by Research Ethics Committees and subjects are protected by informed consent procedures. More recently attention has begun to be focused on DNA banking for clinical and pharmacogenetics research. It is, however, surprising how little attention has been paid to the commercial nature of such research, or the unique issues that present when subjects are (...) asked to consent to the storage of biological samples. Our contention is that in the context of pharmacogenetic add-on studies to clinical drug trials, the doctrine of informed consent fails to cover the broader range of social and ethical issues. Applying a sociological perspective, we foreground issues of patient/subject participation or ‘work’, the ambiguity of research subject altruism, and the divided loyalties facing many physicians conducting clinical research. By demonstrating the complexity of patient and physician involvement in clinical drug trials, we argue for more comprehensive ethical review and oversight that moves beyond reliance on informed consent to incorporate understandings of the social, political and cultural elements that underpin the diversity of ethical issues arising in the research context. (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)

This paper investigates which of the variouslegal notions proposed for human DNA is themost appropriate from an ontological viewpoint – unique legal status, private property, commonproperty, person, or information. The focus is onthe difficulties that private property, commonproperty and person present. By usingHarré''s notion of ``file-self'''' we arguethat, ontologically, the most appropriate legalnotion to be applied is information. This hasconsequences for storage, control and use ofgenetic information as well as identifiablehuman body material.

Mass surveillance involves the collection and storage of vast amounts of information, such as DNA samples from the general population, or location data from cell phones towers, aerial surveillance, and other sources, to then be used when a future crime occurs. For example, DNA from a crime scene could be checked against the database to identify a suspect; location data could identify suspects who were at the scene of a crime. Mass surveillance implicates important privacy interests, but it would surely (...) reduce crime and therefore has been defended by those who reject “privacy at all costs.” I also reject “privacy at all costs.” However, while agreeing that privacy is a value that must be balanced against competing values, I argue that requiring everyone to provide a sample of their DNA or keeping track of everyone’s movements would limit the autonomy of vast numbers of people who there is no reason to suspect will pose a threat, and though such policies would make society safer, that is not worth the cost to individual autonomy. After explaining why individuals can have a substantial interest in privacy even if they are not guilty of a crime, by linking that interest to the value of individual autonomy, and drawing on a political theory of liberal pluralism to restrict what counts as a legitimate public interest that might justify mass surveillance, I articulate a method of balancing these competing interests that is more feasible than a utilitarian approach. (shrink)

This article proposes a new bi-directional way of understanding the convergence of biology and computing. It argues for a reciprocal interaction in which biology and computing have shaped and are currently reshaping each other. In so doing, we qualify both the view of a natural marriage and of a digital shaping of biology, which are common in the literature written by scientists, STS, and communication scholars. The DNA database is at the center of this interaction. We argue that DNA databases (...) are spaces of convergence for computing and biology that change in form, meaning, and function from the 1960s to the 2000s. The first part of the article shows how, in the 1980s, DNA sequencing shifted from passively incorporating computers to be increasingly modeled in digital coding and decoding. Information retrieval algorithms, reciprocally, were altered according to the peculiarities of DNA in the first sequence-storage databases. The second part of the article investigates the impact of these reciprocal interactions and globalization on the organization of research centers, ways of conducting big science, and scientific values. Through convergence and new technologies such as data mining, biology and computing were transformed technologically, institutionally, and culturally into a new bio-data enterprise called genomics. (shrink)

Concern about the ethics of clinical drug trials research on patients and healthy volunteers has been the subject of significant ethical analysis and policy development—protocols are reviewed by Research Ethics Committees and subjects are protected by informed consent procedures. More recently attention has begun to be focused on DNA banking for clinical and pharmacogenetics research. It is, however, surprising how little attention has been paid to the commercial nature of such research, or the unique issues that present when subjects are (...) asked to consent to the storage of biological samples. Our contention is that in the context of pharmacogenetic add-on studies to clinical drug trials, the doctrine of informed consent fails to cover the broader range of social and ethical issues. Applying a sociological perspective, we foreground issues of patient/subject participation or ‘work’, the ambiguity of research subject altruism, and the divided loyalties facing many physicians conducting clinical research. By demonstrating the complexity of patient and physician involvement in clinical drug trials, we argue for more comprehensive ethical review and oversight that moves beyond reliance on informed consent to incorporate understandings of the social, political and cultural elements that underpin the diversity of ethical issues arising in the research context. (shrink)

Many ethical concerns surrounding human genetics studies remain unresolved. We report here the situation in Cameroon.Objectives: To describe the profile of human genetic studies that used Cameroonian DNA samples, with specific focus on i) the research centres that were involved, ii) authorship, iii) population studied, iv) research topics and v) ethics disclosure, with the aim of raising ethical issues that emerged from these studies.Method: Bibliometric Studies; we conducted a PubMed-based systematic review of all the studies on human genetics that used (...) Cameroonian DNA samples from 1989 to 2009.Results and Discussion: Fifty articles were identified, involving predominantly research centres from Europe (64%) and America (32%). Only 7 (14%) Cameroonian institutions and 14 (28%) Cameroonian authors were associated with these publications.At least 52% of publications were devoted to population genetics (variation/migration patterns) amongst 30 Cameroonian ethnic groups. Very few studies concerned public health related genetic issues and only 5 (10%) references were found for hemoglobinopathies like sickle cell anaemia. Almost all DNA samples are ‘banked’ outside of the African continent.Capacity building, rights to the genetic information and benefits to the individuals, communities and populations who contribute to these studies are addressed.Conclusions: 1) Our data suggests the need for a wider debate towards building capacity and addressing ethical issues related to human genomic research in sub-Saharan Africa and specifically in Cameroon; 2) National ethical guidelines and regulations concerning the collection, use and storage of human DNA are urgently needed in Cameroon. (shrink)

DNA and RNA are the only known natural genetic materials. Systematic modification of each of their chemical building blocks (nucleobase, sugar, and phosphate) has enabled the study of the key properties that make those nucleic acids genetic materials. All three moieties contribute to replication and, significantly, all three moieties can be replaced by synthetic analogs without loss of function. Synthetic nucleic acid polymers capable of storing and propagating information not only expand the central dogma, but also highlight that DNA and (...) RNA are not unique chemical solutions for genetic information storage. By considering replication as a question of information transfer, we propose that any polymer that can be replicated could serve as a genetic material.Editor's suggested further reading in BioEssays Xenobiology: A new form of life as the ultimate biosafety tool Abstract. (shrink)

Biomolecules and particularly proteins and DNA exhibit some mysterious features that cannot find satisfactory explanation by quantum mechanical modes of atoms. One of them, known as a Levinthal’s paradox, is the ability to preserve their complex three-dimensional structure in appropriate environments. Another one is that they possess some unknown energy mechanism. The Basic Structures of Matter Supergravitation Unified Theory (BSM-SG) allows uncovering the real physical structures of the elementary particles and their spatial arrangement in atomic nuclei. The resulting physical models (...) of the atoms are characterized by the same interaction energies as the quantum mechanical models, while the structure of the elementary particles influence their spatial arrangement in the nuclei. The resulting atomic models with fully identifiable parameters and angular positions of the quantum orbits permit studying the physical conditions behind the structural and bonding restrictions of the atoms connected in molecules. A new method for a theoretical analysis of biomolecules is proposed. The analysis of a DNA molecule leads to formulation of hypotheses about the energy storage mechanism in DNA and its role in the cell cycle synchronization. This permits shedding a light on the DNA feature known as a C-value paradox. The analysis of a tRNA molecule leads to formulation of a hypothesis about a binary decoding mechanism behind the 20 flavors of the complex aminoacyle-tRNA synthetases - tRNA, known as a paradox. (shrink)

An astonishingly diverse biomolecular circuitry orchestrates the functioning machinery underlying every living cell. These biomolecules and their circuits have been engineered not only for various industrial applications but also to perform other atypical functions that they were not evolved for—including computation. Various kinds of computational challenges, such as solving NP‐complete problems with many variables, logical computation, neural network operations, and cryptography, have all been attempted through this unconventional computing paradigm. In this review, we highlight key experiments across three different ‘‘eras’’ (...) of molecular computation, beginning with molecular solutions, transitioning to logic circuits and ultimately, more complex molecular networks. We also discuss a variety of applications of molecular computation, from solving NP‐hard problems to self‐assembled nanostructures for delivering molecules, and provide a glimpse into the exciting potential that molecular computing holds for the future. Also see the video abstract here: https://youtu.be/9Mw0K0vCSQw. (shrink)

One of the most influential physics books of the twentieth century was actually about biology. In a series of lectures, Erwin Schrödinger described how he believed that quantum mechanics, or some variant of it, would soon solve the riddle of life. These lectures were published in 1944 under the title What is life? and are credited by some as ushering in the age of molecular biology. In the nineteenth century, many scientists thought they knew the answer to Schrödinger’s rhetorical question. (...) Life, they maintained, was some sort of magic matter. The continued use of the term ‘organic chemistry’ is a hangover from that era. The belief that there is a chemical recipe for life led to the hope that, if only we knew what it was, we could mix up the right stuff in a test tube and make life in the lab. Most research on biogenesis has followed that tradition, by assuming that chemistry was a bridge — and a long one at that — linking matter with life. Elucidating this chemical pathway has been a tantalizing goal, spurred on by the famous Miller–Urey experiment of 1952, in which amino acids were made by sparking electricity through a mixture of water and common gases. But the concept has turned out to be something of a blind alley, and further progress with prebiotic chemical synthesis has been frustratingly slow. The origin of life remains one of the great outstanding mysteries of science. To take up Schrödinger’s suggestion, a radical solution to the problem, ‘What is life?’ could be that quantum mechanics enabled life to emerge directly from the atomic world, without the need for complex intermediate chemistry. Life must have a chemical basis: organic molecules provide the hardware for biology. But what about the software? When Schrödinger asked, ‘What is life?’ he could already glimpse the central significance of the cell’s information storage and replication processes, even though the role of DNA and the genetic code was yet to be discovered.. (shrink)

Biobanking activities for genetic research purposes have recently undergone nothing short of a small revolution. Many biobanks have left their traditional home of a small refrigerator in a laboratory to reach the unprecedented proportion of large, sophisticated storage centers containing DNA samples from whole populations. As we turn our attention to research on complex diseases and show great interest in human genetic variation and genetic epidemiology, we need to base our research not only on the DNA of small family cohorts, (...) but on larger sample collections, coupled with geographic location, genealogical information, and environmental and medical data. Population genetic research projects are underway around the world. Setting up such large-scale population biobanks is a challenge for any researcher. Population genetic research projects raise legal, ethical, and social issues that need to be addressed properly in order to maintain the trust of the population, an absolute requirement for the success of such research endeavour. (shrink)

Biobanking activities for genetic research purposes have recently undergone nothing short of a small revolution. Many biobanks have left their traditional home of a small refrigerator in a laboratory to reach the unprecedented proportion of large, sophisticated storage centers containing DNA samples from whole populations. As we turn our attention to research on complex diseases and show great interest in human genetic variation and genetic epidemiology, we need to base our research not only on the DNA of small family cohorts, (...) but on larger sample collections, coupled with geographic location, genealogical information, and environmental and medical data. Population genetic research projects are underway around the world. Setting up such large-scale population biobanks is a challenge for any researcher. Population genetic research projects raise legal, ethical, and social issues that need to be addressed properly in order to maintain the trust of the population, an absolute requirement for the success of such research endeavour. (shrink)

Over the last decade the modeling and the storage of biological data has been a topic of wide interest for scientists dealing with biological and biomedical research. Currently most data is still stored in text files which leads to data redundancies and file chaos.In this paper we show how to use relational modeling techniques and relational database technology for modeling and storing biological sequence data, i.e. for data maintained in collections like EMBL or SWISS-PROT to better serve the needs for (...) these application domains.For this reason we propose a two step approach. First, we model the structure (and therefore the meaning of the) data using an Entity-Relationship approach. The ER model leads to a clean design of a relational database schema for storing and retrieving the DNA and protein data extracted from various sources. Our approach provides the clean basis for building complex biological applications that are more amenable to changes and software ports than their file-base counterparts. (shrink)

The study of culture and cultural selection from a biological perspective has been hampered by the lack of any firm theoretical basis for how the information for cultural traits is stored and transmitted. In addition, the study of any living system with a decentralized or multi-level information structure has been somewhat restricted due to the focus in genetics on the gene and the particular hereditary structure of multicellular organisms. Here a different perspective is used, one which regards living systems as (...) self-constructing energy users that utilize their genome as a library of information, making the genetic system just another component that adds fitness to the overall integrated unit. In this framework, basic fitness is measured as the ability to gather energy for growth and reproduction, and the fitness of the genetic system is broken down into two aspects: first, the effectiveness in searching for new somatic functional information, and second, the effectiveness in searching for better structures to store and process information. With this more generalized perspective, major evolutionary transitions to higher levels of organization become competitions between different information structures; furthermore the functioning and fitness of cultural systems can be more easily described and compared with other modes of information storage within biological systems. Modern technological societies are self-constructing systems that rely on written (symbolic) information storage and very complex algorithms that effectively search for variation with a high probability of successful selection. These systems are currently competing with traditional organic systems, and this competition constitutes the latest major evolutionary transition. Upon comparison of the energy-gathering potential of symbolic-based systems with DNA-based life, it appears that symbolic systems have a tremendous fitness potential and the current shift to a higher level of selection may be as significant and far-reaching as any of the previous major evolutionary transitions. (shrink)

The Italian Twin Registry (ITR) has been carrying out several genetic-epidemiological studies. Collection and storage of biological material from study participants has recently increased in the light of biobanking development. Within this scenario, we aimed at investigating understanding, awareness and attitude towards blood/DNA donation of research participants. About these quite unknown dimensions more knowledge is needed from ethical and social perspectives.

Introduction: This article discusses ethical, legal and social issues raised by the collection, storage and use of DNA in forensic databases. Review: The largest and most inclusive forensic database in the world, the UK National DNA database, leads the worldwide trend towards greater inclusivity. The performance of the NDNAD, criteria for inclusion, legislative framework and plans for integrating forensic databases across Europe are discussed. Comparisons are drawn with UK biobank that has started collecting DNA samples linked to medical records and, (...) unlike the NDNAD, requires informed consent from volunteers, allows withdrawal of samples and only includes adults. The potential uses of research into genes associated with violent and ‘antisocial’ behaviour are discussed in the context of an increasing degree of surveillance in the UK. Conclusion: It should not be assumed that the benefits of forensic databases will necessarily override the social and ethical costs, regardless of changes to the criteria for inclusion or the permitted uses of samples and profiles. The expansion of forensic databases raises issues of relevance to the medical profession. (shrink)

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

Presymptomatic testing for Huntington's disease has given rise to several ethical problems relating to such issues as confidentiality, the privacy of the individual, the testing of minors and informed consent in connection with blood sample donation. A multidisciplinary conference of staff from genetic centres involved with presymptomatic testing was organised in Cardiff to discuss these and other problems. Recommendations on good practice are described under four headings: pre- and post-test counselling; confidentiality in relation to test results; collection and storage of (...) DNA, and criteria for testing. (shrink)

Obesity and type 2 diabetes arise from a set of complex gene–environment interactions. Explanations for the heritability of these syndromes and the environmental contribution to disease susceptibility are addressed by the “thrifty genotype” and the “thrifty phenotype” hypotheses. Here, the merits of both models are discussed and elements of them are used to synthesize a “thrifty epigenotype” hypothesis. I propose that: (1) metabolic thrift, the capacity for efficient acquisition, storage and use of energy, is an ancient, complex trait, (2) the (...) environmentally responsive gene network encoding this trait is subject to genetic canalization and thereby has become robust against mutational perturbations, (3) DNA sequence polymorphisms play a minor role in the aetiology of obesity and type 2 diabetes—instead, disease susceptibility is predominantly determined by epigenetic variations, (4) corresponding epigenotypes have the potential to be inherited across generations, and (5) Leptin is a candidate gene for the acquisition of a thrifty epigenotype. BioEssays 30:156–166, 2008. © 2008 Wiley Periodicals, Inc. (shrink)

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

The Human Tissue Act 2004 is designed to regulate the storage and use of organs and tissues from the living, and the removal, storage and use of the same material from the deceased. It repeals much criticized legislation, including the Human Tissue Act 1961, and establishes a Human Tissue Authority to ensure compliance with the Act via a licensing and monitoring regime. When the Act comes into force, probably in April 2006, it will be a criminal offence not to comply (...) with certain provisions of the Act, and a new offence of DNA 'theft' will be introduced. Importantly, the Act places consent at the centre of the system, both from the living and from or on behalf of the deceased. (shrink)

To understand the impacts of development on native peoples requires an understanding of how their genetic make-up is implicated in their relationship with their landscapes. This is an area ripe for more research. The ASLME project on DNA Fingerprinting and Civil Liberties proposed improvements to the ethical and legal safeguards for the collection and storage of DNA-derived genetic information. Native peoples have proposed a similar examination of the ethical and legal issues related to the collection and storage of their genetic (...) information obtained via family histories and genealogies. (shrink)

There is probably only one information system in living nature — the macromolecular system including DNA, RNA and protein. Its unity for the genetic and nervous activity can be followed in the storage of information (heredity, memory) and in its processing (recombination and selection of both genetic and mental information). According to the hypothesis of the code of nerve impulses, nucleotide triplets of the nucleus, or more likely amino acids of the surface protein of the impulse generating area of a (...) neuron, generate a limited variety of interspike intervals so that each amino acid corresponds to a certain interspike interval and this particular interval initiates by means of a specific neurotransmitter, the synthesis of the same amino acid (or nucleotide triplet) in the postsynaptic neuron. Thus, a series of impulses produces in the postsynaptic neuron a sequence of amino acids in a form of a polypeptide identical to the polypeptide of the presynaptic neuron. (shrink)

How can the forensic scientist rationally justify performing a sequence of tests and analyses in a particular case? When is it worth performing a test or analysis on an item? Currently, there is a large void in logical frameworks for making rational decisions in forensic science. The aim of this paper is to fill this void by presenting a step-by-step guide on how to apply Bayesian decision theory to routine decision problems encountered by forensic scientists on performing or not performing (...) a particular laboratory test or analysis. A decision-theoretic framework, composed of actions, states of nature, and utilities, models this problem, and an influence diagram translates its notions into a probabilistic graphical network. Within this framework, the expected value of information (EVOI) for the submission of an item to a particular test or analysis addresses the above questions. The development of a classical case example on whether to perform presumptive tests for blood before submitting the item for a DNA analysis illustrates the use of this model for source level questions in forensic biology (i.e., questions that ask whether a crime stain consisting of a particular body fluid comes from a particular person). We show how to construct an influence diagram for this example, and how sensitivity analyses lead to an optimal analytical sequence. The key idea is to show that such a Bayesian decisional approach provides a coherent framework for justifying the optimal analytical sequence for a particular case in forensic science. (shrink)

Studies of learning in marine invertebrates have yielded new information, implicating protein kinase C and calmodulin‐dependent protein kinase as critical components in pathways for learning and memory that are shared with higher vertebrates. Recent advances correlating in vitro biochemical and biophysical measurements with in vivo learning have begun to elaborate the roles in memory storage for these two kinases, their substrates, and signaling proteins such as calexcitin and calmodulin. Other studies have implicated transcription factors associated with kinases such as the (...) cyclic AMP response element binding protein (CREB). These experiments have resulted in a greater understanding of the role of second messengers, principally calcium and cyclic AMP (cAMP), as vehicles for transforming memory‐specific effects occurring at the membrane into permanent DNA‐mediated cellular and structural changes. (shrink)

Objective To determine the attitudes of Egyptian patients regarding their participation in research and with the collection, storage and future use of blood samples for research purposes. Design Cross-sectional survey. Study population Adult Egyptian patients (n=600) at rural and urban hospitals and clinics. Results Less than half of the study population (44.3%) felt that informed consent forms should provide research participants the option to have their blood samples stored for future research. Of these participants, 39.9% thought that consent forms should (...) include the option that future research be restricted to the illness being studied. A slight majority (66.2%) would donate their samples for future genetic research. Respondents were more favourable towards having their blood samples exported to other Arab countries (62.0%) compared with countries in Europe (41.8%, p<0.001) and to the USA (37.2%, p<0.001). Conclusions This study shows that many individuals do not favour the donation of a blood sample for future research. Of those who do approve of such future research, many favour a consent model that includes an option restricting the future research to the illness being studied. Also, many Egyptians were hesitant to have their blood samples donated for genetic research or exported out of the Arab region to the USA and European countries. Further qualitative research should be performed to determine the underlying reasons for many of our results. (shrink)

This Christian sermon uses a DNA lab experience as a basis for theological reflection on ourselves and our offering. Who are we to God? What determines the self that we offer? Can the alphabet of DNA shed light for us on the Word of God in our lives? This first attempt to introduce the language and laboratory environment of genetic testing (represented by DNA fingerprinting) within a parish preaching context juxtaposes liturgical, scientific, and biblical language and settings for fresh insights.

Storage operators have been introduced by J. L. Krivine in [5] they are closed λ-terms which, for a data type, allow one to simulate a "call by value" while using the "call by name" strategy. In this paper, we introduce the directed λ-calculus and show that it has the usual properties of the ordinary λ-calculus. With this calculus we get an equivalent--and simple--definition of the storage operators that allows to show some of their properties: $\bullet$ the stability of the set (...) of storage operators under the β-equivalence (Theorem 5.1.1); $\bullet$ the undecidability (and semidecidability) of the problem "is a closed λ-term t a storage operator for a finite set of closed normal λ-terms?" (Theorems 5.2.2 and 5.2.3); $\bullet$ the existence of storage operators for every finite set of closed normal λ-terms (Theorem 5.4.3); $\bullet$ the computation time of the "storage operation" (Theorem 5.5.2). (shrink)

DNA methylation can be considered a component of epigenetic memory with a critical role during embryo development, and which undergoes dramatic reprogramming after fertilization. Though it has been a focus of research for many years, the reprogramming mechanism is still not fully understood. Recent results suggest that absence of maintenance at DNA replication is a major factor, and that there is an unexpected role for TET3-mediated oxidation of 5mC to 5hmC in guarding against de novo methylation. Base-resolution and genome-wide profiling (...) methods are enabling more comprehensive assessments of the extent to which ART might impair DNA methylation reprogramming, and which sequence elements are most vulnerable. Indeed, as we also review here, studies showing the effect of culture media, ovarian stimulation or embryo transfer on the methylation pattern of embryos emphasize the need to face ART-associated defects and search for strategies to mitigate adverse effects on the health of ART-derived children. DNA methylation, critical for embryo development, suffers significant changes after fertilization, including demethylation, remethylation and TET3-mediated oxidation of 5 mC to 5 hmC. In addition to infertility and environmental insults, ART could impact DNA methylation and ART related consequences in the offspring have been reported. (shrink)

The pedagogical function of science teaching may benefit from an analysis of the historical-epistemic dimension, without neglecting the socio-political context in which a given research was carried out. In the case of DNA structure, the background of its discovery is particularly complex. Starting from the analysis of some papers, the view on the circumstances that led to their drafting broadens. We try to answer the fundamental question for any educator: why teach all that? Ethics issues are related to the general (...) organisation of research, increasingly focused on speed and competition. Even teaching is affected by these dynamics, not only in higher education, but also at secondary level; students should be made aware of this trend. The history of science could therefore favour a more general awareness. _SUNTO_ La funzione pedagogica dell’insegnamento scientifico può trarre vantaggio da un’analisi della dimensione storico-epistemica, senza trascurare il contesto socio-politico nel quale una determinata ricerca è stata condotta. Nel caso della struttura del DNA, i retroscena della sua scoperta sono particolarmente complessi. Dopo l’analisi di alcuni articoli, si allarga gradualmente la vista sulle circostanze che hanno condotto alla loro stesura. Si cerca di rispondere a una domanda fondamentale per ogni educatore: perché insegnare tutto ciò? Le questioni etiche riguardano l’organizzazione generale della ricerca, sempre più tesa alla velocità e alla competizione. Persino l’insegnamento è influenzato da dinamiche simili, non solo in ambito accademico, ma anche a livello secondario; gli studenti dovrebbero essere a conoscenza di questa tendenza. La storia della scienza può dunque favorire una maggiore consapevolezza. (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 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)

DNA topoisomerases, capable of manipulating DNA topology, are ubiquitous and indispensable for cellular survival due to the numerous roles they play during DNA metabolism. As we review here, current structural approaches have revealed unprecedented insights into the complex DNA‐topoisomerase interaction and strand passage mechanism, helping to advance our understanding of their activities in vivo. This has been complemented by single‐molecule techniques, which have facilitated the detailed dissection of the various topoisomerase reactions. Recent work has also revealed the importance of topoisomerase (...) interactions with accessory proteins and other DNA‐associated proteins, supporting the idea that they often function as part of multi‐enzyme assemblies in vivo. In addition, novel topoisomerases have been identified and explored, such as topo VIII and Mini‐A. These new findings are advancing our understanding of DNA‐related processes and the vital functions topos fulfil, demonstrating their indispensability in virtually every aspect of DNA metabolism. (shrink)

Why do some invertebrates store so much carotenoids in their tissues? Storage of carotenoids may not simply be passive and dependent on their environmental availability, as storage variation exists at various taxonomic scales, including among individuals within species. While the strong antioxidant and sometimes immune-stimulating properties of carotenoids may be beneficial enough to cause the evolution of features improving their assimilation and storage, they may also have fitness downsides explaining why massive carotenoid storage is not universal. Here, the functional and (...) ecological implications of carotenoid storage for the evolution of invertebrate innate immune defenses are examined, especially in crustaceans, which massively store carotenoids for unclear reasons. Three testable hypotheses about the role of carotenoid storage in immunological (resistance and tolerance) and life-history strategies (with a focus on aging) are proposed, which may ultimately explain the storage of large amounts of these pigments in a context of host–pathogen interactions. (shrink)

DNA methylation is a repressive epigenetic mark vital for normal development. Recent studies have uncovered an unexpected role for the DNA methylome in ensuring the correct targeting of the Polycomb repressive complexes throughout the genome. Here, we discuss the implications of these findings for cancer, where DNA methylation patterns are widely reprogrammed. We speculate that cancer‐associated reprogramming of the DNA methylome leads to an altered Polycomb binding landscape, influencing gene expression by multiple modes. As the Polycomb system is responsible for (...) the regulation of genes with key roles in cell fate decisions and cell cycle regulation, DNA methylation induced Polycomb mis‐targeting could directly drive carcinogenesis and disease progression.Editor's suggested further reading in BioEssays Unmasking risk loci: DNA methylation illuminates the biology of cancer predisposition Abstract. (shrink)

In 1990, J. L. Krivine introduced the notion of storage operator to simulate “call by value” in the “call by name” strategy. J. L. Krivine has showed that, using Gödel translation of classical into intuitionistic logic, one can find a simple type for the storage operators in AF2 type system. This paper studies the ∀-positive types and the Gödel transformations of TTR type system. We generalize by using syntactical methods Krivine's theorem about these types and for these transformations. We give (...) a proof of this result in the case of the type of recursive integers. (shrink)

Those objecting to human DNA patenting frequently do so on the grounds that the practice violates or threatens human dignity. For example, from 1993 to 1994, more than thirty organizations representing indigenous peoples approved formal declarations objecting to the National Institutes of Health's bid to patent viral DNA taken from subjects in Papua New Guinea and the Solomon Islands. Although these were not patents on human DNA, the organizations argued that the patents could harm and exploit indigenous peoples and violate (...) their cultural values. NIH eventually dropped one of its patent applications.On May 18, 1995, 180 religious leaders, led by biotechnology critic Jeremy Rifkin, held a press conference objecting to DNA patenting in Washington, D.C. In their “Joint Appeal against Human and Animal Patenting,” these leaders decried any attempt to patent nature. Some of the more outspoken members of the Joint Appeal likened DNA patenting to slavery, while others objected to treating human beings as marketable commodities. In his recent book, The Biotech Century, Rifkin rehashed the objections to DNA patenting voiced by members of the Joint Appeal. (shrink)

The regulation of DNA replication is a fascinating biological problem both from a mechanistic angle—How is replication timing regulated?—and from an evolutionary one—Why is replication timing regulated? Recent work has provided significant insight into the first question. Detailed biochemical understanding of the mechanism and regulation of replication initiation has made possible robust hypotheses for how replication timing is regulated. Moreover, technical progress, including high‐throughput, single‐molecule mapping of replication initiation and single‐cell assays of replication timing, has allowed for direct testing of (...) these hypotheses in mammalian cells. This work has consolidated the conclusion that differential replication timing is a consequence of the varying probability of replication origin initiation. The second question is more difficult to directly address experimentally. Nonetheless, plausible hypotheses can be made and one—that replication timing contributes to the regulation of chromatin structure—has received new experimental support. (shrink)

Type II DNA topoisomerase activity is required to change DNA topology. It is important in the relaxation of DNA supercoils generated by cellular processes, such as transcription and replication, and it is essential for the condensation of chromosomes and their segregation during mitosis. In mammals this activity is derived from at least two isoforms, termed DNA topoisomerase IIα and β. The α isoform is involved in chromosome condensation and segregation, whereas the role of the β isoform is not yet clear. (...) DNA topoisomerase IIβ was first reported in 1987. Here we review the research on DNA topoisomerase IIβ over the last 10 years. BioEssays 20:215–226, 1998.© 1998 John Wiley & Sons, Inc. (shrink)

In 1990, J. L. Krivine introduced the notion of storage operator to simulate, for Church integers, the “call by value” in a context of a “call by name” strategy. In the present paper we define for every λ-term S which realizes the successor function on Church integers the notion of S-storage operator. We prove that every storage operator is an S-storage operator. But the converse is not always true.

The nuclear pore complex (NPC) is emerging as a center for recruitment of a class of “difficult to repair” lesions such as double‐strand breaks without a repair template and eroded telomeres in telomerase‐deficient cells. In addition to such pathological situations, a recent study by Su and colleagues shows that also physiological threats to genome integrity such as DNA secondary structure‐forming triplet repeat sequences relocalize to the NPC during DNA replication. Mutants that fail to reposition the triplet repeat locus to the (...) NPC cause repeat instability. Here, we review the types of DNA lesions that relocalize to the NPC, the putative mechanisms of relocalization, and the types of recombinational repair that are stimulated by the NPC, and present a model for NPC‐facilitated repair. (shrink)

Over 30 million people worldwide have taken a commercial at-home DNA test, because they were interested in their genetic ancestry, disease predisposition or inherited traits. Yet, these consumer DNA data are also increasingly used for a very different purpose: to identify suspects in criminal investigations. By matching a suspect’s DNA with DNA from a suspect’s distant relatives who have taken a commercial at-home DNA test, law enforcement can zero in on a perpetrator. Such forensic use of consumer DNA data has (...) been performed in over 200 criminal investigations. However, this practice of so-called investigative genetic genealogy raises ethical concerns. In this paper, we aim to broaden the bioethical analysis on IGG by showing the limitations of an individual-based model. We discuss two concerns central in the debate: privacy and informed consent. However, we argue that IGG raises pressing ethical concerns that extend beyond these individual-focused issues. The very nature of the genetic information entails that relatives may also be affected by the individual customer’s choices. In this respect, we explore to what extent the ethical approach in the biomedical genetic context on consent and consequences for relatives can be helpful for the debate on IGG. We argue that an individual-based model has significant limitations in an IGG context. The ethical debate is further complicated by the international, transgenerational and commercial nature of IGG. We conclude that IGG should not only be approached as an individual but also—and perhaps primarily—as a collective issue. There are no data in this work. (shrink)

Through analysis of film sequences focusing on DNA in two British Broadcasting Corporation nonfiction science television programs, Wonders of Life and Bang! Goes the Theory, first broadcast in 2013, contrasting “religious” and “secular” representations of science are identified. In the “religious” portrayal, immutable scientific knowledge is revealed to humanity by nature with minimal human intervention. Science provides a creation story, “explanatory omnicompetence,” and makes life existentially meaningful. In the “secular” portrayal, scientific knowledge is changeable; is produced through technical skill in (...) expert communities; and is ambiguous, potentially positive and negative for society. Television representations of science affect audience understandings, and this is particularly the case for nonfiction representations of science, as they are likely to be “taken more seriously” than fictional representations. The consequences of the “religious” representation of science are discussed, and it is argued that a widespread understanding of science as presented in the religious portrayal would negatively impact democracy. (shrink)