Dieser Beitrag befasst sich mit der Befürchtung, dass eine Erweiterung der DNA-Analyse von Tatortspuren für Zwecke der Polizeiarbeit zu Diskriminierungen führen wird. Diese Erwartung bezieht sich insbesondere auf die Ermittlung der sogenannten biogeografischen Abstammung und der Hautschattierung. In dieser Untersuchung werden einige Stellen im Ermittlungsprozess, an denen auf Grundlage solcher Analysen Diskriminierungspotential auftreten könnte, zunächst gesammelt und dargelegt. Im zweiten Teil wird dann der Diskriminierungsbegriff genauer beleuchtet. Dabei wird sich zeigen, dass verschiedene Positionen zu der Frage, was genau eine Diskriminierung (...) moralisch problematisch macht, zu unterschiedlichen Einschätzungen der DNA-Phänotypisierung in der Polizeiarbeit führen. / There is a concern according to which analyzing crime scene DNA to determine biogeographic origin and skin color of suspects can lead to discrimination against minority populations. This article summarizes and explains some of those parts of the investigation process that can give rise to discrimination. The second part of the paper offers an analysis of the notion of discrimination and presents different accounts of the exact ground of its moral wrongness. As it will emerge, these different accounts lead to different assessments of the use of DNA phenotype analyses in police investigations. (shrink)

The metamorphosis from larvae to adult butterflies has represented the “mystery” of life since the ancient Greeks. How could we explain the various steps of development from caterpillars to the most beautiful butterflies? A mystery preva lent in the twentieth century concerned the storage of the complete genetic informa tion of an organism in the DNA of its every cell. How and why do so many different cell types develop throughout the lives of organisms at the right time and place? (...) With the rise of epigenetics, the “fog” of mystery is starting to clear. We now know that the genetic storage medium in every living cell acquires an incredible plasticity through certain markings on the genetic text, linking the inheritable information with the contextuality of the real lifeworld of each organism. This means that the concrete living organism influences during development the various stages of gene expression, transcription, translation, immunity, and DNA repair actively and leads to various phenotypic outcomes without altering the DNA storage medium. More surprisingly, such variations of developmental phenotypes were found capable of successfully adapting to changing environmental circumstances. Better adapted organisms may lead to reprogramming in the epigenetic states which may reach an inheritable status for many generations or even become a fixed part of the genetic identity of the species. This is how evolution learns. (shrink)

We provide a new perspective on the relation between the space of description of an object and the appearance of novelties. One of the aims of this perspective is to facilitate the interaction between mathematics and historical sciences. The definition of novelties is paradoxical: if one can define in advance the possibles, then they are not genuinely new. By analyzing the situation in set theory, we show that defining generic (i.e., shared) and specific (i.e., individual) properties of elements of a (...) set are radically different notions. As a result, generic and specific definitions of possibilities cannot be conflated. We argue that genuinely stating possibilities requires that their meaning has to be made explicit. For example, in physics, properties playing theoretical roles are generic; then, generic reasoning is sufficient to define possibilities. By contrast, in music, we argue that specific properties matter, and generic definitions become insufficient. Then, the notion of new possibilities becomes relevant and irreducible. In biology, among other examples, the generic definition of the space of DNA sequences is insufficient to state phenotypic possibilities even if we assume complete genetic determinism. The generic properties of this space are relevant for sequencing or DNA duplication, but they are inadequate to understand phenotypes. We develop a strong concept of biological novelties which justifies the notion of new possibilities and is more robust than the notion of changing description spaces. These biological novelties are not generic outcomes from an initial situation. They are specific and this specificity is associated with biological functions, that is to say, with a specific causal structure. Thus, we think that in contrast with physics, the concept of new possibilities is necessary for biology. (shrink)

Darwinian evolutionary theory has two key terms, variations and biological selection, which finally lead to survival of the fittest variant. With the rise of molecular genetics, variations were explained as results of error replications out of the genetic master templates. For more than half a century, it has been accepted that new genetic information is mostly derived from random error-based events. But the error replication narrative has problems explaining the sudden emergence of new species, new phenotypic traits, and genome innovations (...) as a sudden single event. Meanwhile, it is recognized that errors cannot explain the evolution of genetic information, genetic novelty, and complexity. Now, empirical evidence establishes the crucial role of non-random genetic content editors, such as viruses, diversity generating retroelements, and other RNA networks, to produce new genetic information, complex regulatory control, inheritance vectors, genetic identity, immunity, new sequence space, evolution of complex organisms, and evolutionary transitions. (shrink)

Somatic diversification of antigen receptor genes depends on the activity of enzymes whose homologs participate in a mutagenic DNA repair in unicellular species. Indeed, by engaging error-prone polymerases, gap filling molecules and altered mismatch repair pathways, lymphocytes utilize conserved components of genomic stress response systems, which can already be found in bacteria and archaea. These ancient systems of mutagenesis and repair act to increase phenotypic diversity of microbial cell populations and operate to enhance their ability to produce fit variants during (...) stress. Coopted by lymphocytes, the ancient mutagenic processing systems retained their diversification functions instilling the adaptive immune cells with enhanced evolvability and defensive capacity to resist infection and damage. As reviewed here, the ubiquity and conserved character of specialized variation-generating mechanisms from bacteria to lymphocytes highlight the importance of these mechanisms for evolution of life in general. (shrink)

Gregor Mendel (1822-1884) was the first to explain that certain 'traits' were inherited in plants from one generation to the next. These would later become known as genes. Frederich Miescher in 1869 analyzed a substance from the nucleus of cells, which he therefore called nuclein. Further study of nuclein revealed that it contained elements like hydrogen, oxygen, nitrogen and phosphorous, with a specific ratio of nitrogen to phosphorous. Then in 1878 Albrecht Kossel determined that nuclein contained nucleic acid, from which (...) he isolated five nucleobases (nitrogen compounds now referred to by the letters C, G, A, T, U representing cytosine, guanine, adenine, thymine, and uracil). It was also discovered that ribose, a sugar was present in the nuclein compound. What Miescher had isolated from the cell nucleus was actually what would latter be identified as DNA (Deoxyribonucleic acid). C. H. Waddington (1905 - 1975) first proposed the term “epigenetics” in 1942 to describe the region between the gene and the whole organism (phenotype) [3]. Today, what is called the epigenome refers to all the chromosomal modifications, DNA modifications, chromatin protein modifications and their complexes. It is the epigenome that determines both the expression of the genes and their inheritance. R. A. Jorgenson reports [4], "Many of these modifications appear to be “programmable” and to be “read out” to influence chromosomal functions." Nobel laureate Barbara McClintock stated this revolutionary proposal more clearly in her Nobel lecture [5], “to determine the extent of knowledge the cell has of itself, and how it utilizes this knowledge in a ‘thoughtful’ manner when challenged.” In 1960 R. A. Brinks suggested that chromosomes possess a paragenetic function in addition to their genetic function [7]. The physical nature of the paragenetic function is characterized by the variety of forms or states of chromatin that can reside at any genetic locus. While the genetic function is stable, the paragenetic function is labile and programmable in ontogeny. It is this latter function that allows organisms to transfer informational macromolecules (RNA and proteins) in a systematic and regulated manner over what is known as the “RNA information superhighway.” Given this capacity, organisms may be able to store information at numerous genetic loci in the form of paragenetic chromatin states, which can be reprogrammed during ontogeny or environmental stress [8]. This reprogrammable system could operate over the whole organism as a storage device, allowing it to make informed ‘decisions' during growth and development, or in response to the environment. Such processing capacity could be considered a form of ‘intelligence,' which also could be passed on to future generations. The study of the flow of information within and between cells and organisms represents the cutting edge of modern biological research. While physical correlates of cognitive behavior in living organisms are being discovered, it does not spell reduction to such correlates. The electronic activity within the physical components of a radio, for example, may be minutely determined, but ultimately it is not merely the electrical activity that produces the intelligent speech that is heard. Only the intelligent person whose voice is being broadcast through the radio can explain that. Without the broadcaster, the radio would sit silently even though fully functional. An organism without its living agency also appears to be devoid of metabolic activity although all the chemical components are fully present. How to connect life to matter will be the ultimate challenge that has to be met. This will prove to be a philosophical problem we hope to address in the near future. (shrink)

In a now classic paper published in 1991, Alberch introduced the concept of genotype–phenotype (G!P) mapping to provide a framework for a more sophisticated discussion of the integration between genetics and developmental biology that was then available. The advent of evo-devo first and of the genomic era later would seem to have superseded talk of transitions in phenotypic space and the like, central to Alberch’s approach. On the contrary, this paper shows that recent empirical and theoretical advances have only sharpened (...) the need for a different conceptual treat- ment of how phenotypes are produced. Old-fashioned metaphors like genetic blueprint and genetic programme are not only woefully inadequate but positively misleading about the nature of G!P, and are being replaced by an algorithmic approach emerging from the study of a variety of actual G!P maps. These include RNA folding, protein function and the study of evolvable soft- ware. Some generalities are emerging from these disparate fields of analysis, and I suggest that the concept of ‘developmental encoding’ (as opposed to the classical one of genetic encoding) provides a promising computational–theoretical underpinning to coherently integrate ideas on evolvability, modularity and robustness and foster a fruitful framing of the G!P mapping problem. (shrink)

Phenotypic integration refers to the study of complex patterns of covariation among functionally related traits in a given organism. It has been investigated throughout the 20th century, but has only recently risen to the forefront of evolutionary ecological research. In this essay, I identify the reasons for this late flourishing of studies on integration, and discuss some of the major areas of current endeavour: the interplay of adaptation and constraints, the genetic and molecular bases of integration, the role of phenotypic (...) plasticity, macroevolutionary studies of integration, and statistical and conceptual issues in the study of the evolution of complex phenotypes. I then conclude with a brief discussion of what I see as the major future directions of research on phenotypic integration and how they relate to our more general quest for the understanding of phenotypic evolution within the neo-Darwinian framework. I suggest that studying integration provides a particularly stimulating and truly interdisciplinary convergence of researchers from fields as disparate as molecular genetics, developmental biology, evolutionary ecology, palaeontology and even philosophy of science. (shrink)

The aim of this paper is to explain the emergence and use of DNA fingerprinting technology in India, noting the specific concerns faced by the Indian Legal System related to the use of this novel forensic technology in the justice process. Furthermore, the proposed construction of a National DNA Data Bank is discussed taking into consideration the challenges faced by the government in legislating the DNA Bill into law. A critical analysis of the DNA Technology (Use and Application) Regulation Bill, (...) 2019 is provided to throw light upon many ethical, social, and legal issues that need to be addressed before the operationalization of the Bill to ensure that this technology is governed democratically to protect the civil liberties of citizens. (shrink)

In this paper, we discuss the ethical concerns that may arise from the synthesis of human DNA. To date, only small stretches of DNA have been constructed, but the prospect of generating human genomes is becoming feasible. At the same time, the significance of genes for identity, health and reproduction is coming under increased scrutiny. We examine the implications of DNA synthesis and its impact on debates over the relationship with our DNA and the ownership of our genes, its potential (...) to disrupt common understandings of reproduction and privacy, and the way in which synthetic DNA challenges traditional associations between genes and identity. We explore the degree to which synthetic DNA may further undermine overgeneticised accounts of identity, health, reproduction, parenthood and privacy that are prevalent in the public domain and in some areas of policy-making. While avoiding making normative claims of our own, we conclude that there is a need for reflection on the ethical implications of these developing technologies before they are on us. (shrink)

An exploration of the nexus between ecology, evolutionary biology and molecular biology, via the concept of phenotypic plasticity.

In addition to considerable debate in the recent evolutionary literature about the limits of the Modern Synthesis of the 1930s and 1940s, there has also been theoretical and empirical interest in a variety of new and not so new concepts such as phenotypic plasticity, genetic assimilation and phenotypic accommodation. Here we consider examples of the arguments and counter- arguments that have shaped this discussion. We suggest that much of the controversy hinges on several misunderstandings, including unwarranted fears of a general (...) attempt at overthrowing the Modern Synthesis paradigm, and some fundamental conceptual confusion about the proper roles of phenotypic plasticity and natural selection within evolutionary theory. (shrink)

The study of phenotypic plasticity has progressed significantly over the past few decades. We have moved from variation for plasticity being considered as a nuisance in evolutionary studies to it being the primary target of investigations that use an array of methods, including quantitative and molecular genetics, as well as of several approaches that model the evolution of plastic responses. Here, I consider some of the major aspects of research on phenotypic plasticity, assessing where progress has been made and where (...) additional effort is required. I suggest that some areas of research, such the study of the quantitative genetic underpinning of plasticity, have been either settled in broad outline or superseded by new approaches and questions. Other issues, such as the costs of plasticity are currently at the forefront of research in this field, and are likely to be areas of major future development. (shrink)

Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that (...) has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today's data barriers and facilitate analytical reproducibility. (shrink)

Is integrative biology a good idea, or even possible? There has been much interest lately in the unifica- tion of biology and the integration of traditionally separate disciplines such as molecular and develop- mental biology on one hand, and ecology and evolutionary biology on the other. In this paper I ask if and under what circumstances such integration of efforts actually makes sense. I develop by example an analogy with Aristotle’s famous four “causes” that one can investigate concerning any object (...) or phenomenon: material (what something is made of), formal (what distinguishes that particular object from others), efficient (how was the object made) and final (why was the object made). The example is provided by ongoing research on different aspects of flowering time in the model system Arabidop- sis, a small weed belonging to the mustard family. I show that understanding how flowering time is controlled is an epistemologically different sort of question from why and how it evolved, and that the two research agendas can be pursued largely independently of each other. Toward the end, I propose that the real goal of integrative biology is to understand the boundary layers between levels of biologi- cal analysis, something to which modern philosophy of science can contribute significantly. (shrink)

DNA possesses a double nature: it is both an analog chemical compound and a digital carrier of information. By distinguishing these two aspects, this paper aims to reevaluate the legally and politically influential idea that the human genome forms part of the common heritage of mankind, an idea which is thought to conflict with the practice of patenting DNA. The paper explores the lines of reasoning that lead to the common heritage idea, articulates and motivates what emerges as the most (...) viable version of it, and assesses the extent to which this version conflicts with gene-patenting practices as exemplified by the U.S. regime. It concludes that the genome is best thought of as a repository of information to which humanity has a fiduciary relationship, and that on this view, the perceived conflict with gene-patenting largely dissolves. (shrink)

A phenome occurs through the many pathways of the complex net of interaction between the phenome and its environment; therefore researching and understanding how it arises requires investigation into many possible causes that are in constant interaction with each other. The most comprehensive investigations in biology are the ones in which many biologists from different sub-areas—evolutionary biology, developmental biology, molecular biology, physiology, genetics, epigenetics, ecology—have collaborated. Still, biologists do not always need to collaborate or look for the most comprehensive explanations. (...) A more standard investigation in biology occurs within a single subarea, and uses well-defined experiments with very specific conditions. This paper is about causation and related explanation in plant phenome research and its relevance to Aristotle’s Theory of Four Causes. I argue that there are causes which resemble Aristotle’s formal, material, and efficient causes in phenotype explanation and occurrence; but causes which resemble Aristotle’s final causes occur in phenotype explanation only, not in the occurrence. (shrink)

The short paper introduces the concept of possible branches of double-stranded DNA (later sometimes called palindromes): Certain sequences of nucleotides may be followed, after a short unpaired stretch, by a complementary sequence in reversed order, such that each DNA strand can fold back on itself, and the DNA assumes a cruciform or tree-like structure. This is postulated to interact with regulatory proteins. -/- .

Writers, philosophers, and theologians have oft made the comparison between being a mature human being and a masterpiece work of art or design. Employing the analogy between the creation of artistic value and the creation of full-fledged human value, this paper stakes out a middle ground between pro-choice and pro-life by considering a more general account of value and the relationship between being a potential X and a mature implementation of X's potential. I argue that the value of a potential (...) X is a function of a number of factors, most importantly, what I call the "accessibility relation" between a potential X and a full-fledged instantiation of this potential. The value is as much intrinsic to the “seed” as to some future implementation of the seed’s potential. This approach inclines even a secular humanist to reasonably confer a significant degree of moral value to a human conceptus, and even more to an early term fetus. (shrink)

Background: One of the all-time questions in evolutionary biology regards the evolution of organismal shapes, and in particular why certain forms appear repeatedly in the history of life, others only seldom and still others not at all. Recent research in this field has deployed the conceptual framework of constraints and natural selection as measured by quantitative genetic methods. Scope: In this paper I argue that quantitative genetics can by necessity only provide us with useful statistical sum- maries that may lead (...) researchers to formulate testable causal hypotheses, but that any inferential attempt beyond this is unreasonable. Instead, I suggest that thinking in terms of coordinates in phenotypic spaces, and approaching the problem using a variety of empirical methods (seeking a consilience of evidence), is more likely to lead to solid inferences regarding the causal basis of the historical patterns that make up most of the data available on phenotypic evolution. (shrink)

Developmental plasticity as the nexus between genetics and ecology.

I begin with a description of the benefits and limits of DNA barcoding as presented by its advocates not its critics. Next, I argue that due to the mutually dependent relationship between defining and delimiting species, all systems of classification are grounded in theory, even if only implicitly. I then proceed to evaluate DNA barcoding in that context. In particular, I focus on the barcoders’ use of a sharp boundary by which to delimit species, arguing that this boundary brings along (...) additional theoretical commitments inconsistent with the way taxonomists conceive of species, viz., as entities that have vague boundaries and that cannot be defined by any single attribute other than ancestry. Given these inconsistencies, I conclude that even if groupings based on DNA barcodes match those of an existing taxonomy, the two systems of classification are not necessarily tracking the same entities, i.e., species. (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)

How to use a model organism to study phenotypic integration and constraints on evolution.

We attempt to improve the understanding of the notion of agene being `for a phenotypic trait or traits. Considering theimplicit functional ascription of one thing being `for another,we submit a more restrictive version of `gene for talk.Accordingly, genes are only to be thought of as being forphenotypic traits when good evidence is available that thepresence or prevalence of the gene in a population is the resultof natural selection on that particular trait, and that theassociation between that trait and the gene (...) in question isdemonstrably causal. It is therefore necessary to gatherstatistical, biochemical, historical, as well as ecologicalinformation before properly claiming that a gene is for aphenotypic trait. Instead of hampering practical use of the `genefor talk, our approach aims at stimulating much needed researchinto the functional ecology and comparative evolutionary biologyof gene action. (shrink)

Most molecular biological concepts derive from physical chemical assumptions about the genetic code that are basically more than 40 years old. Additionally, systems biology, another quantitative approach, investigates the sum of interrelations to obtain a more holistic picture of nucleotide sequence order. Recent empirical data on genetic code compositions and rearrangements by mobile genetic elements and non-coding RNAs, together with results of virus research and their role in evolution, does not really fit into these concepts and compel a re-examination. In (...) this review we try to find an alternate hypothesis. It seems plausible now that if we look at the abundance of regulatory RNAs and persistent viruses in host genomes, we will find more and more evidence that the key players that edit the genetic codes of host genomes are consortia of RNA agents and viruses that drive evolutionary novelty and regulation of cellular processes in all steps of development. This agent-based approach may lead to a qualitative RNA sociology that investigates and identifies relevant behavioural motifs of cooperative RNA consortia. In addition to molecular biological perspectives this may lead to a better understanding of genetic code evolution and dynamics. (shrink)

The aim of this paper is to retrace the history of genetic patents, analyzing the metaphors used in the public debate, in patent offices, and in courtrooms. I have identified three frames with corresponding metaphor clusters: the first is the industrial frame, built around the idea that DNA is a chemical; the second is the informational frame, assembled around the concept of genetic information; last is the soul frame, based on the idea that DNA is or contains the essence of (...) the individual. (shrink)

Digital phenotyping will potentially enable earlier detection and prediction of mental illness by monitoring human interaction with and through digital devices. Notwithstanding its promises, it is certain that a person’s digital phenotype will at times be at odds with their first-person testimony of their psychological states. In this paper, we argue that there are features of digital phenotyping in the context of psychiatry which have the potential to exacerbate the tendency to dismiss patients’ testimony and treatment preferences, which (...) can be instances of epistemic injustice. We first explain what epistemic injustice is, and why it is argued to be an extensive problem in health and disability settings. We then explain why epistemic injustice is more likely to apply with even greater force in psychiatric contexts, and especially where digital phenotyping may be involved. Finally, we offer some tentative suggestions of how epistemic injustice can be minimised in digital psychiatry. (shrink)

A response to Via about the existence (or not) and role of plasticity genes in evolution.

The usage of Quantum Similarity through the equation Z = {∀Θ∈Z→∃s ∈ S ʌ ∃t ∈ T: Θ= (s,t)}., represents a way to analyze the way communication works in our DNA. Being able to create the object set reference for z being (s,t) in our DNA strands, we are able to set logical tags and representations of our DNA in a completely computational form. This will allow us to have a better understanding of the sequences that happen in our DNA. (...) With this approach, we can also utilize mathematical formulas such as the Euler–Mascheroni constant, regressional analysis, and computational proofs to answer important questions on Quantum biology, Quantum similarity, and Theoretical Physics. (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)

Psychiatry has witnessed a new wave of approaches to clinical phenotyping and the study of psychopathology, including the National Institute of Mental Health’s Research Domain Criteria, clinical staging, network approaches, the Hierarchical Taxonomy of Psychopathology, and the general psychopathology factor, as well as a revival of interest in phenomenological psychopathology. The question naturally emerges as to what the relationship between these new approaches is – are they mutually exclusive, competing approaches, or can they be integrated in some way and (...) used to enrich each other? In this opinion piece, we propose a possible integration between clinical staging and phenomenological psychopathology. Domains identified in phenomenological psychopathology, such as selfhood, embodiment, affectivity, etc., can be overlaid on clinical stages in order to enrich and deepen the phenotypes captured in clinical staging (‘high resolution’ clinical phenotypes). This approach may be useful both ideographically and nomothetically, in that it could complement diagnosis, enrich clinical formulation, and inform treatment of individual patients, as well as help guide aetiological, prediction, and treatment research. The overlaying of phenomenological domains on clinical stages may require that these domains are reformulated in dimensional rather than categorial terms. This integrative project requires assessment tools, some of which are already available, that are sensitive and thorough enough to pick up on the range of relevant psychopathology. The proposed approach offers opportunities for mutual enrichment: clinical staging may be enriched by introducing greater depth to phenotypes; phenomenological psychopathology may be enriched by introducing stages of severity and disorder progression to phenomenological analysis. (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)

How we ought to diagnose, categorise and respond to spectrum disabilities such as autism and Attention Deficit/Hyperactivity Disorder (ADHD) is a topic of lively debate. The heterogeneity associated with ADHD and autism is described as falling on various continua of behavioural, neural, and genetic difference. These continua are varyingly described either as extending into the general population, or as being continua within a given disorder demarcation. Moreover, the interrelationships of these continua are likewise often vague and subject to diverse interpretations. (...) -/- In this paper, I explore geneticists' and self-advocates’ perspectives concerning autism and ADHD as continua. These diagnoses are overwhelmingly analysed as falling on a continuum or continua of underlying traits, which supports the notion of “the neurodiversity spectrum”, i.e., a broader swath of human neural and behavioural diversity on which some concentrations of different functioning are diagnosed. I offer a taxonomy of conceptions of the genetic, phenotypic, and endophenotypic dimensionality within and beyond these diagnostic categories, and suggest that the spectrum of neurodiversity is characteristically endophenotypic. (shrink)

Mehlman and Li offer a framework for approaching the bioethical issues raised by the military use of genomics that is compellingly grounded in both the contemporary civilian and military ethics of medical research, arguing that military commanders must be bound by the two principles of paternal- ism and proportionality. I agree fully. But I argue here that this is a much higher bar than we may fully realize. Just as the principle of proportionality relies upon a thorough assessment of harms (...) caused and military advantage gained, the use of genomic research, on Mehlman and Li’s view, will require an accurate understanding of the connection between genotypes and phenotypes – accurate enough to ameliorate the risk undertaken by our armed forces in being subject to such research. Recent conceptual work in evolutionary theory and the philosophy of biology, however, renders it doubtful that such knowledge is forthcoming. The complexity of the relationship between genotypic factors and realized traits (the so-called ‘G→P map’) makes the estimation of potential military advantage, as well as potential harm to our troops, incredibly challenging. Such fundamental conceptual challenges call into question our ability to ever satisfactorily satisfy the demands of a sufficiently rigorous ethical standard. (shrink)

A number of debates in philosophy of biology and psychology, as well as in their respective sciences, hinge on particular views about the relationship between genotypes and phenotypes. One such view is that the genotype-phenotype relationship is relatively straightforward, in the sense that a genome contains the ?genes for? the various traits that an organism exhibits. This leads to the assumption that if a particular set of traits is posited to be present in an organism, there must be a corresponding (...) number of genes in that organism's genome to account for those traits. This assumption underlies what can be called the ?counting argument,? in which empirical estimates of the number of genes in a genome are used to support or refute particular hypotheses in philosophical debates about biology and psychology. In this paper, we assess the counting argument as it is used in discussions of the alleged massive modularity of the brain, and conclude that this argument cannot be upheld in light of recent philosophical work on gene concepts and empirical work on genome complexity. In doing so, we illustrate that there are those on both sides of the debate about massive modularity who rely on an incorrect view of gene concepts and the nature of the genotype-phenotype relationship. (shrink)

In his late years, Thomas Kuhn became interested in the process of scientific specialization, which does not seem to possess the destructive element that is characteristic of scientific revolutions. It therefore makes sense to investigate whether and how Kuhn’s insights about specialization are consistent with, and actually fit, his model of scientific progress through revolutions. In this paper, I argue that the transition toward a new specialty corresponds to a revolutionary change for the group of scientists involved in such a (...) transition. I will clarify the role of the scientific community in revolutionary changes and characterize the incommensurability across specialties as possessing both semantic and methodological aspects. The discussion of the discovery of the structure of DNA will serve both as an illustration of my main argument and as reply to one criticism raised against Kuhn—namely, that his model cannot capture cases of revolutionary yet non-disruptive episodes of scientific progress. Revisiting Kuhn’s ideas on specialization will shed new light on some often overlooked features of scientific change. (shrink)

Starting with the results of Li et al. in 1992 there is valuable interest in finding long range correlations in DNA sequences since it raises questions about the role of introns and intron-containing genes. In the present paper we studied two sequences that are the human T-cell receptor alpha/delta locus, Gen-Bank name HUMTCRADCV, a noncoding chromosomal fragment of M = 97630 bases (composed of less than 10% of coding regions), and the Escherichia Coli K12, Gen-Bank name ECO110K, a genomic fragment (...) with M = 111401 bases consisting of mostly coding regions and containing more that 80% of coding regions. We attributed the value (+1) to the purines and the value (-1) to the pirimidines and to such reconstructed random walk we applied the method of the Recurrence Quantification Analysis(RQA) that was introduced by Zbilut and Webber in 1994. By using dimension D=1 and Embedded Dimensions D=3 and D=5, we obtain some indicative results. Also by a simple eye examination of the reconstructed maps, the differences between coding and non coding regions are evident and impressive and consist in the presence in noncoding regions of long patches of the same colour that are absent in the coding sequence. At first sight this suggests a simple explanation to the concept of „long-range‟ correlation. On the quantitative plane, we used the %Rec., the %Det., the Ratio, the Entropy, the %Lam., and the Lmax that, as explained in detail in the text, represent the basic variables of RQA. The significant result that we have here is that both Lmax and Laminarity exhibit very large values in HUMTCRADCV and actually different in values respect to ECO110K where such variables assume more modest values. Therefore we suggest that there is the observed difference between HUMTCRADCV and ECO110K. The claimed higher long-range correlations of introns respect to exons from many authors may be explained here in reasonof such found higher values of Lmax and of Laminarity in HUMTCRADCV respect to ECO110K. (shrink)

Abstract: Lung cancer is the top reason of cancer-associated deaths globally. Surgery is the typical treatment for early-stage non-small cell lung cancer (NSCLC). Advancement in the knowledge of the biology of non-small cell lung cancer has shown molecular evidence used for systemic cancer therapy aiming metastatic disease, with a significant impact on patients’ overall survival (OS) and eminence of life. Though, a biopsy of overt metastases is an invasive technique restricted to assured positions and not effortlessly satisfactory in the clinic. (...) The examination of peripheral blood samples of cancer patients embodies a new basis of cancer-derived material, recognized as liquid biopsy, and its constituents (circulating tumour cells (CTCS), circulating free DNA (cfDNA), exosomes, and tumour-educated platelets (TEP)) may be gotten from nearly any body liquids. These constituents have shown to imitate features of the status of both the primary and metastatic diseases, aiding the clinicians to go towards a tailored medicine. In this paper, the reasons of lung cancer will be recognized and the risk elements that initiated the increase of infection, for instance Smoking, Disclosure to secondhand smoke, Disclosure to radon gas, Disclosure to asbestos and other compounds, Family past history of lung cancer, and decrease of the spread of disease and approaches of handling and prevention of lung cancer. (shrink)

During the last two decades the role of quantitative genetics in evolutionary theory has expanded considerably. Quantitative genetic-based models addressing long term phenotypic evolution, evolution in multiple environments (phenotypic plasticity) and evolution of ontogenies (developmental trajectories) have been proposed. Yet, the mathematical foundations of quantitative genetics were laid with a very different set of problems in mind (mostly the prediction of short term responses to artificial selection), and at a time in which any details of the genetic machinery were virtually (...) unknown. In this paper we discuss what a model is in population biology, and what kind of model we need in order to address the complexities of phenotypic evolution. We review the assumptions of quantitative genetics and its most recent accomplishments, together with the limitations that such assumptions impose on the modelling of some aspects of phenotypic evolution. We also discuss three alternative appr oaches to the theoretical description of evolutionary trajectories (nonlinear dynamics, complexity theory and optimization theory), and their respective advantages and limitations. We conclude by calling for a new theoretical synthesis, including quantitative genetics and not necessarily limited to the other approaches here discussed. (shrink)

Invasion biologists often suggest that phenotypic plasticity plays an important role in successful plant invasions. Assuming that plasticity enhances ecological niche breadth and therefore confers a fitness advantage, recent studies have posed two main hypotheses: (1) invasive species are more plastic than non-invasive or native ones; (2) populations in the introduced range of an invasive species have evolved greater plasticity than populations in the native range. These two hypotheses largely reflect the disparate interests of ecologists and evolutionary biologists. Because these (...) sciences are typically interested in different temporal and spatial scales, we describe what is required to assess phenotypic plasticity at different levels. We explore the inevitable tradeoffs of experiments conducted at the genotype vs. species level, outline components of experimental design required to identify plasticity at different levels, and review some examples from the recent literature. Moreover, we suggest that a successful invader may benefit from plasticity as either (1) a Jack-of-all-trades, better able to maintain fitness in unfavourable environments; (2) a Master-of-some, better able to increase fitness in favourable environments; or (3) a Jack-and-master that combines some level of both abilities. This new framework can be applied when testing both ecological or evolutionary oriented hypotheses, and therefore promises to bridge the gap between the two perspectives. (shrink)

Noting minimal philosophical attention to the shift of the meanings of “genotype” and “phenotype,” and their distinction, as well as to the variety of meanings that have co-existed over the last hundred years, this note invites readers to join in exploring the implications of shifts that have been left unexamined.

DNA evidence is one of the most significant modern advances in the search for truth since the cross examination, but its format as a random-match-probability makes it difficult for people to assign an appropriate probative value (Koehler, 2001). While Frequentist theories propose that the presentation of the match as a frequency rather than a probability facilitates more accurate assessment (e.g., Slovic et al., 2000), Exemplar-Cueing Theory predicts that the subjective weight assigned may be affected by the frequency or probability format, (...) and how easily examples of the event, i.e., ‘exemplars’, are generated from linguistic cues that frame the match in light of further evidence (Koehler & Macchi, 2004). This paper presents two juror research studies to examine the difficulties that jurors have in assigning appropriate probative value to DNA evidence when contradictory evidence is presented. Study 1 showed that refuting evidence significantly reduced guilt judgments when exemplars were linguistically cued, even when the probability match and the refuting evidence had the same objective probative value. Moreover, qualitative reason for judgment responses revealed that interpreting refuting evidence was found to be complex and not necessarily reductive; refutation was found indicative of innocence or guilt depending on whether exemplars have been cued or not. Study 2 showed that the introduction of judges’ directions to linguistically cue exemplars, did not increase the impact of refuting evidence beyond its objective probative value, but less guilty verdicts were returned when jurors were instructed to consider all possible explanations of the evidence. The results are discussed in light of contradictory frequentist and exemplar-cueing theoretical positions, and their real-world consequences. (shrink)

Francis Collins had an impressive track record as a gene hunter (cystic fibrosis, neurofibromatosis, Huntington’s disease) when he was appointed Director of the Human Genome Project (HGP) in 1993. In June 2000, together with Craig Venter and President Bill Clinton, he presented the draft version of the human genome sequence to a worldwide audience during a famous press conference. And in 2009, President Barack Obama nominated him as director of the National Institutes of Health (NIH), the largest Tfunding agency for (...) biomedical research in the world. s The In 2006, Collins published his book The Language of God,3 an autobiographical account of the HGP and its scientific, historical, and societal significance, with special attention paid to the impact of the human sequence on the way we see our world and ourselves.4 Now, by way of a sequel, he has written The Language of Life. Wherea Language of God focused on the genome sequence of mankind in general, and on the HGP as a “revolution” in biomedicine, the new book, as indicated by its subtitle, is oriented towards “the revolution in personalized medicine”, the impact of the genomics revolution on the personal lives of individuals. Before subjecting Collins’ book to a closer reading, I first of all would like to explain how I will read it and from what perspective. Why is genomics in general, and the HGP and its aftermath in particular, a subject of interest to a philosopher like me? Why did I become interested in assessing the HGP and in studying the work and views of some of its key contributors? (shrink)

After introducing the new field of cultural evolution, we review a growing body of empirical evidence suggesting that culture shapes what people attend to, perceive and remember as well as how they think, feel and reason. Focusing on perception, spatial navigation, mentalizing, thinking styles, reasoning (epistemic norms) and language, we discuss not only important variation in these domains, but emphasize that most researchers (including philosophers) and research participants are psychologically peculiar within a global and historical context. This rising tide of (...) evidence recommends caution in relying on one’s intuitions or even in generalizing from reliable psychological findings to the species, Homo sapiens. Our evolutionary approach suggests that humans have evolved a suite of reliably developing cognitive abilities that adapt our minds, information-processing abilities and emotions ontogenetically to the diverse culturally-constructed worlds we confront. (shrink)

Signal measurement Electrochemical methods are very suitable for detecting direct DNA oxidation because electrochemical reactions directly generate electronic signals and therefore do not require expensive converters. In addition, in this process, because the order of the immobilized game can be limited to onlya series of electrode substrates, the act of tracking is performed by a series of in expensive electrochemical analyzes. Electrochemical sensors are used to perform clinical or environmental tests; The basis of the sensitivity of electrochemical signals to direct (...) oxidation orinterval catalysis of DNA is also based on the reduction reactions of reporter molecules or enzymes. (shrink)

Metaphors play a crucial role in both science in particular and human discourse in gen- eral. Plato’s story of the cave—about people shackled to a wall and incapable of perceiv- ing the world as it really is—has stimulated thinking about epistemology and the nature of reality for more than two millennia. But metaphors can also be misleading: being too taken with Plato’s story has cost philosophers endless discussions about how to access the world “as it is,” until Kant showed us (...) that it is just not going to happen, ever. (shrink)

I reconstruct the background of ideas, concerns and intentions out of which Moore’s early essays, the preliminary version, and then the final version of Principia Ethica originated. I stress the role of religious concerns, as well as that of the Idealist legacy. I argue that PE is more a patchwork of rather diverging contributions than a unitary work, not to say the paradigm of a new school in Ethics. I add a comparison with Rashdall’s almost contemporary ethical work, suggesting that (...) the latter defends the same general claims in a different way, one that manages to pave decisive objections in a more plausible way. I end by suggesting that the emergence of Analytic Ethics was a more ambiguous phenomenon than the received view would make us believe, and that the wheat (or some other gluten-free grain) of this tradition, that is, what logic can do for philosophy, has to be separated from the chaff, that is, the confused and mutually incompatible legacies of Utilitarianism and Idealism. (shrink)