Epigenetics bilbiography

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Epigenetics bilbiography

Postby ShawnMiller » Wed Sep 09, 2015 1:54 pm

Download this bibliography and all PDFs in a compressed file (http://filos.io/docs/ep.d.zip)

Baedke, Jan. "Causal explanation beyond the gene." THEORIA. Revista de Teoría, Historia y Fundamentos de la Ciencia 27, no. 2 (2012): 153-174. (http://filos.io/docs/ep.d/baedke-2012.pdf)

Abstract: This paper deals with the interrelationship between causal explanation and methodology in a relatively Keywords: young discipline in biology: epigenetics. Based on cases from molecular and ecological epigenetics, I show that James Woodward's interventionist account of causation captures essential features about how epigeneticists using highly diverse methods, i.e. laboratory experiments and purely observational studies, think about causal explanation. I argue that interventionism thus qualifies as a useful unifying explanatory approach when it comes to cross-methodological research efforts. It can act as a guiding rationale (i) to link causal models in molecular biology with statistical models derived from observational data analysis and (ii) to identify test-criteria for reciprocal transparent studies in different fields of research, which is a shared is sue across the sciences.

Baedke, Jan. "The epigenetic landscape in the course of time: Conrad Hal Waddington’s methodological impact on the life sciences." Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 44, no. 4 (2013): 756-773. (http://filos.io/docs/ep.d/baedke-2013.pdf)

Abstract: It seems that the reception of Conrad Hal Waddington’s work never really gathered speed in mainstream biology. This paper, offering a transdisciplinary survey of approaches using his epigenetic landscape images, argues that (i) Waddington’s legacy is much broader than is usually recognized—it is widespread across the life sciences (e.g. stem cell biology, developmental psychology and cultural anthropology). In addition, I will show that (ii) there exist as yet unrecognized heuristic roles, especially in model building and theory formation, which Waddington’s images play within his work. These different methodological facets envisioned by Waddington are used as a natural framework to analyze and classify the manners of usage of epigenetic landscape images in post-Waddingtonian ‘landscape approaches’. This evaluation of Waddington’s pictorial legacy reveals that there are highly diverse lines of traditions in the life sciences, which are deeply rooted in Waddington’s methodological work.

Boniolo, Giovanni, and Giuseppe Testa. "The identity of living beings, epigenetics, and the modesty of philosophy." Erkenntnis 76, no. 2 (2012): 279-298. (http://filos.io/docs/ep.d/boniolo-2012.pdf)

Abstract: Two problems related to the biological identity of living beings are faced: the who-problem (which are the biological properties making that living being unique and different from the others?); the persistence-problem (what does it take for a living being to persist from a time to another?). They are discussed inside a molecular biology framework, which shows how epigenetics can be a good ground to provide plausible answers. That is, we propose an empirical solution to the who- problem and to the persistence-problem on the basis of the new perspectives opened by a molecular understanding of epigenetic processes. In particular, concerning the former, we argue that any living being is the result of the epigenetic processes that have regulated the expression of its genome; concerning the latter, we defend the idea that the criterion for the persistence of its identity is to be indicated in the continuity of those epigenetic processes. We also counteract possible objections, in particular (1) whether our approach has something to say at a metaphysical level; (2) how it could account for the passage from the two phenotypes of the parental gametes to the single phenotype of the zygote; (3) how it could account for the identity of derivatives of one living being that continue to live disjoined from that original living being; (4) how it could account for higher mental functions.

Buchman, Daniel Z. "Neglecting the social system: Clinical neuroimaging and the biological reductionism of addiction." Journal of Ethics in Mental Health 2, no. 2 (2007): 1-5. (http://filos.io/docs/ep.d/buchman-2007.pdf)

Abstract: A main strength of neuroimaging and neuroscience is its reductionist focus on the brain. A limitation is that it runs the possibility of ignoring larger social factors. The brain image may not necessarily indicate the brain’s neuroplastic ‘rewiring’ over time from genomic, epigenetic, environmental and social conditions. These factors are all necessary to understand the diverse nature of our brains, especially complex concerns such as addiction. For addiction to emerge it requires an intersection of genetic, environmental and social influences. It is foreseeable to ignore this multi-factorial interaction in the clinical setting when interpreting predictive brain imaging scans. This paper argues that relying too heavily on clinical neuroimaging in the treatment of patients who present a vulnerability to addiction can lead to cases of biological reductionism ignoring the influence social systems have on brain responses.

Burian, Richard M. "On microRNA and the need for exploratory experimentation in post-genomic molecular biology." History and Philosophy of the Life Sciences (2007): 285-311. (http://filos.io/docs/ep.d/burian-2007.pdf)

ABSTRACT - This paper is devoted to an examination of the discovery, characterization, analysis of the functions of microRNAs, which also serves as a vehicle for demonstrating importance of exploratory experimentation in current (post-genomic) molecular biology. material on microRNAs is important in its own right: it provides important insight into and the The the extreme complexity of regulatory networks involving components made of DNA, RNA, and protein. These networks play a central role in regulating development of multicellular organisms and illustrate the importance of epigenetic as well as genetic systems in evolution and development. The examination of these matters yields principled arguments for the historicity of the functions of key biological molecules and for the indispensability of exploratory experimentation in contemporary molecular biology as well as some insight into the complex interplay between exploratory experimentation and hypothesis-driven science. This latter result is not only important for philosophy of science, but also of practical importance for the evaluation of grant proposals, latter claim must be left for another occasion.

De Tiège, Alexis, Koen Tanghe, Johan Braeckman, and Yves Van de Peer. "From DNA-to NA-centrism and the conditions for gene-centrism revisited." Biology & Philosophy 29, no. 1 (2014): 55-69. (http://filos.io/docs/ep.d/deTiege-2014.pdf)

Abstract: First the ‘Weismann barrier’ and later on Francis Crick’s ‘central dogma’ of molecular biology nourished the gene-centric paradigm of life, i.e., the conception of the gene/genome as a ‘central source’ from which hereditary specificity unidirectionally flows or radiates into cellular biochemistry and development. Today, due to advances in molecular genetics and epigenetics, such as the discovery of complex post-genomic and epigenetic processes in which genes are causally integrated, many theorists argue that a gene-centric conception of the organism has become problematic. Here, we first explore the causal implications of the following two central dogma-related issues: (1) widespread reverse transcription—arguing for an extension from ‘DNA-genome’ to RNA-encompassing ‘NA-genome’ and, thus, from tradi- tional DNA-centrism to a broader ‘NA-centrism’; and (2) the absence of a mechanism of reverse translation—arguing for the ‘structural primacy’ of NA-sequence over protein in cellular biochemistry. Secondly, we explore whether this latter conclusion can be extended to a ‘functional primacy’ of NA-sequence over protein in cellular biochemistry, which would imply a limited kind of ‘gene/NA-centrism’ confined to the subcellular level of NA/protein-based biochemistry. Finally, we explore the conditions—and their (non)fulfilment—for a more generalised form of gene-centrism extendable to higher levels of biological organisation. We conclude that the higher we go in the biological hierarchy, the more dubious gene-centric claims become.

Huneman, Philippe. "Assessing the prospects for a return of organisms in evolutionary biology." History and philosophy of the life sciences (2010): 341-371. (http://filos.io/docs/ep.d/huneman-2010.pdf)

ABSTRACT - An argument has been raised from various perspectives against the Modern Synthesis (MS) in the past two decades: it has forgotten organisms. Niche construction theorists (Odling-Smee et al. 2003), developmental biologists like West-Eberhard (2003) and Evo-Devo elaborated various views which concur on a rehabilitation of the explanatory role of organisms, formerly neglected by an evolutionary science mostly centered on genes. This paper aims at assessing such criticisms by unraveling the specific arguments they use and evaluating how empirical findings may support them. In the first section, I review the usual critiques about the way MS treats organisms and show that the organisms-concerned critique is multifaceted, and I use the controversy about units of selection in order to show that purely conceptual and empirical arguments have been mixed up when organisms were concerned. In the second section, I consider successively the challenges raised to evolutionary MS by structuralist biologists and then the developmentalist challenge mostly raised by Evo-Devo. I distinguish what is purely conceptual among those criticisms and what mostly relies on recent empirical findings about genome and epigenetics. The last section discusses another program in transitions" research, as enquiry into the emergence of organisms.

Jablonka, Eva, and Marion J. Lamb. "Bridges between development and evolution." Biology and Philosophy 13, no. 1 (1998): 119-124. (http://filos.io/docs/ep.d/jablonka-lamb-2008.pdf)

Abstract: Adaptive evolution is usually assumed to be directed by selective processes, devel- opment by instructive processes; evolution involves random genetic changes, development involves induced epigenetic changes. However, these distinctions are no longer unequivocal. Selection of genetic changes is a normal part of development in some organisms, and through the epigenetic system external factors can induce selectable heritable variations. Incorporating the effects of instructive processes into evolutionary thinking alters ideas about the way environmental changes lead to evolutionary change, and about the interplay between genetic and epigenetic systems.

Jablonka, Eva, and Marion J. Lamb. "The expanded evolutionary synthesis—a response to Godfrey-Smith, Haig, and West-Eberhard." Biology & Philosophy 22, no. 3 (2007): 453-472. (http://filos.io/docs/ep.d/jablonka-lamb-2007.pdf)

Abstract: In responding to three reviews of Evolution in Four Dimensions (Jablonka and Lamb, 2005, MIT Press), we briefly consider the historical background to the present genecentred view of evolution, especially the way in which Weismann’s theories have influenced it, and discuss the origins of the notion of epigenetic inheritance. We reaffirm our belief that all types of hereditary information—genetic, epigenetic, behavioural and cultural—have contributed to evolutionary change, and outline recent evidence, mainly from epigenetic studies, that suggests that non-DNA heritable variations are not rare and can be quite stable. We describe ways in which such variations may have influenced evolution. The approach we take leads to broader definitions of terms such as ‘units of heredity’, ‘units of evolution’, and ‘units of selection’, and we maintain that ‘information’ can be a useful concept if it is defined in terms of its effects on the receiver. Although we agree that evolutionary theory is not undergoing a Kuhnian revolution, the incorporation of new data and ideas about hereditary variation, and about the role of development in generating it, is leading to a version of Darwinism that is very different from the gene-centred one that dominated evolutionary thinking in the second half of the twentieth century.

Jablonka, Eva. "Information: its interpretation, its inheritance, and its sharing." Philosophy of Science 69, no. 4 (2002): 578-605. (http://filos.io/docs/ep.d/jablonka-2002.pdf)

Abstract: The semantic concept of information is one of the most important, and one of the most problematical concepts in biology. I suggest a broad definition of biological information: a source becomes an informational input when an interpreting receiver can react to the form of the source (and variations in this form) in a functional manner. The definition accommodates information stemming from environmental cues as well as from evolved signals, and calls for a comparison between information-transmission in different types of inheritance systems—the genetic, the epigenetic, the behavioral, and the cultural-symbolic. This comparative perspective highlights the different ways in which information is acquired and transmitted, and the role that such information plays in heredity and evolution. Focusing on the special properties of the transfer of information, which are very different from those associated with the transfer of materials or energy, also helps to uncover interesting evolutionary effects and suggests better explanations for some aspects of the evolution of communication.

Lamm, Ehud, and Eva Jablonka. "The nurture of nature: hereditary plasticity in evolution." Philosophical Psychology 21, no. 3 (2008): 305-319. (http://filos.io/docs/ep.d/lamm-jablonka-2008.pdf)

Abstract: The dichotomy between Nature and Nurture, which has been dismantled within the framework of development, remains embodied in the notions of plasticity and evolvability. We argue that plasticity and evolvability, like development and heredity, are neither dichotomous nor distinct: the very same mechanisms may be involved in both, and the research perspective chosen depends to a large extent on the type of problem being explored and the kinds of questions being asked. Epigenetic inheritance leads to transgenerationally extended plasticity, and developmentally-induced heritable epigenetic variations provide additional foci for selection that can lead to evolutionary change. Moreover, hereditary innovations may result from developmentally induced large-scale genomic repatterning events, which are akin to Goldschmidtian ‘‘systemic mutations’’. The epigenetic mechanisms involved in repatterning can be activated by both environmental and genomic stress, and lead to phylogenetic as well as ontogenetic changes. Hence, the effects and the mechanisms of plasticity directly contribute to evolvability.

Loi, Michele, Lorenzo Del Savio, and Elia Stupka. "Social epigenetics and equality of opportunity." Public health ethics 6, no. 2 (2013): 142-153. (http://filos.io/docs/ep.d/loi-2013.pdf)

Abstract: Recent epidemiological reports of associations between socioeconomic status and epigenetic markers that predict vulnerability to diseases are bringing to light substantial biological effects of social inequalities. Here, we start the discussion of the moral consequences of these findings. We firstly highlight their explanatory importance in the context of the research program on the Developmental Origins of Health and Disease (DOHaD) and the social determinants of health. In the second section, we review some theories of the moral status of health inequalities. Rather than a complete outline of the debate, we single out those theories that rest on the principle of equality of opportunity and analyze the consequences of DOHaD and epigenetics for these particular conceptions of justice. We argue that DOHaD and epigenetics reshape the conceptual distinction between natural and acquired traits on which these theories rely and might provide important policy tools to tackle unjust distributions of health.

Lorusso, Ludovica. "The Epigenetic Hypothesis and the New Biological Role of Self-Identified Racial Categories." Critical Philosophy of Race 2, no. 2 (2014): 183-203. (http://filos.io/docs/ep.d/lorusso-2014.pdf)

Abstract: In biomedicine self-identified racial classifications of humans are used to infer genetic differences causally responsible for different susceptibilities to complex diseases between racial categories. In this paper I analyze the epistemological status of these classifications within the three main types of hypotheses that explain the epidemiological differences between racial categories: the genetic, the epigenetic, and the environmental hypothesis. These hypotheses differ in the use of self-identified racial classifications as proxies respectively for genetic, epigenetic, and environmental differences causally responsible for differences in the risk of complex diseases between racial categories. I show that the use of self- identified racial classifications under the genetic hypothesis is not justifiable from an epistemological point of view, and recent biological evidence rather highlights the relevance of different kinds of nongenetic factors in the causation of specific susceptibilities to complex diseases, therefore supporting both the environmental and the epigenetic hypotheses. My conclusion is that the use of self-identified racial classifications may be justifiable only under either the environmental or the epigenetic hypothesis. In particular, the biological role of self-identified racial categories as models of an epigenetic kind of variation within the whole human population may be relevant in the investigation of epigenetic mechanisms causally responsible for susceptibilities to complex diseases.

Manicas, Peter T. "Reduction, epigenesis and explanation." Journal for the Theory of Social Behaviour 13, no. 3 (1983): 331-354. (http://filos.io/docs/ep.d/manicas-1983.pdf)

Abstract: Few problems linger as maliciously as the relation of the biological and cultural sciences to the explanation of behavior. The problems of “nature versus nurture,” of Naturw‘ssenschaften versus Geistew’ssenschaften, indeed, of “freedom versus determinism” seem at once embroiled and perhaps for that reason, ultimately irresolvable. No one denies, of course, that humans are bio- social “products” and that both biology and culture are “relevant” to understanding what we are and what we do, both as a species and as individual persons. Unfortunately, such concessions are most often uninteresting.’ No one, e.g., will deny that human brains have something to do with cognition and that human brains are the products of a long evolutionary history. Nor will it be denied that cognition is language-dependent and that language is, of all things, quintessentially cultural. The problem is to say exactly how this bears on our understanding of human cognition.

Morange, Michel. "Post-genomics, between reduction and emergence." Synthese 151, no. 3 (2006): 355-360. (http://filos.io/docs/ep.d/morange-2006.pdf)

Abstract: It is frequently said that biology is emerging from a long phase of reductionism. It would be certainly more correct to say that biologists are abandoning a certain form of reductionism. We describe this part form, and the experiments which challenged the previous vision. To face the difficulties which were met, biologists use a series of concepts and metaphors -- pleiotropy, tinkering, epigenetics -- the ambiguity of which masks the difficulties, instead of solving them. In a similar way, the word "postgenomics" has different meanings, depending upon who uses it. Which of these meanings will become dominant in the future is an open question.

Rosenberg, Alex. "Is epigenetic inheritance a counterexample to the central dogma?." History and philosophy of the life sciences (2006): 549-565. (http://filos.io/docs/ep.d/rosenberg-2006.pdf)

Abstract: This paper argues that nothing that has been discovered in the increasingly complex details of gene regulation has provided any grounds to retract or qualify Crick's version of the central dogma. In particular it defends the role of the genes as the sole bearers of information, and argues that the mechanism of epigenetic modification of the DNA is but another vindication of Crick's version of the central dogma. The paper shows that arguments of C.K. Waters for the distinctive causal role of the genes are equivalent in important respects to the present ones and concludes with a defense of the informational role of the genes against an argument from trans-acting genetic regulation due to Stotz.

Rothstein, Mark, A. "Epigenetic Exceptionalism." Journal of Law, Medicine & Ethics 41, no. 3 (September 2013): 733-736. (http://filos.io/docs/ep.d/rothstein-2013.pdf)


Shanks, Niall, Ray Greek, and Jean Greek. "Are animal models predictive for humans?." Philosophy, Ethics, and Humanities in Medicine 4, no. 1 (2009): 2. (http://filos.io/docs/ep.d/shanks-2009.pdf)

Abstract: It is one of the central aims of the philosophy of science to elucidate the meanings of scientific terms and also to think critically about their application. The focus of this essay is the scientific term predict and whether there is credible evidence that animal models, especially in toxicology and pathophysiology, can be used to predict human outcomes. Whether animals can be used to predict human response to drugs and other chemicals is apparently a contentious issue. However, when one empirically analyzes animal models using scientific tools they fall far short of being able to predict human responses. This is not surprising considering what we have learned from fields such evolutionary and developmental biology, gene regulation and expression, epigenetics, complexity theory, and comparative genomics.

Stotz, Karola. "The ingredients for a postgenomic synthesis of nature and nurture." Philosophical Psychology 21, no. 3 (2008): 359-381. (http://filos.io/docs/ep.d/stotz-2008.pdf)

Abstract: This paper serves as an introduction to the special issue on ‘‘Reconciling Nature and Nurture in Behavior and Cognition Research’’ and sets its agenda to resolve the ‘interactionist’ dichotomy of nature as the genetic, and stable, factors of development, and nurture as the environmental, and plastic influences. In contrast to this received view it promotes the idea that all traits, no matter how developmentally fixed or universal they seem, contingently develop out of a single-cell state through the interaction of a multitude of developmental resources that defies any easy, dichotomous separation. It goes on to analyze the necessary ingredients for such a radical, epigenetic account of development, heredity and evolution: 1. A detailed understanding of the epigenetic nature of the regulatory mechanisms of gene expression; 2. The systematical questioning of preconceptions of ‘explanatory’ categories of behavior, such as ‘innate’ or ‘programmed’; 3. Especially in psychological research the integration of the concepts of ‘development’ and ‘learning’, and a richer classification of the concept of ‘environment’ in the production of behavior; 4. A fuller understanding of the nature of inheritance that transcends the restriction to the genetic material as the sole hereditary unit, and the study of the process of developmental niche construction; and last 5. Taking serious the role of ecology in development and evolution. I hope that an accomplishment of the above task will then lead to a ‘postgenomic’ synthesis of nature and nurture that conceptualizes ‘nature’ as the natural phenotypic outcome ‘nurtured’ by the natural developmental process leading to it.

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