dunnettreader + genetics   40

Bruce Campbell: The Great Transition, Lecture 1 of 4 - Ellen McArthur Lectures 2013, Faculty of History, University of Cambridge
See his 2016 book with CUP - The Great Transition: Climate, Disease and Society in the Medieval World - kindle-available
Lecture schedule
Lecture 1 - The 14th century as tipping point: From one socio-ecological status quo to another
Lecture 2 - The enabling environment: The Medieval Solar Maximum and Latin Christendom's high-medieval efflorescence
Lecture 3 - A precarious balance: Mounting economic vulnerability in an era of increasing climatic instability
Lecture 4 - Disease intervenes: The Black Death and the 'Great Transition' to an alternative socio-ecological equilibrium
video  lecture  economic_history  social_history  environmental_history  disease  Black_Death  medieval_history  12thC  13thC  14thC  15thC  Italy  urbanization  foreign_trade  Mongols  Mamluks  spice_trade  Central_Asia  genetics  weather  agriculture  demography  economic_growth  climate-history  climate_change  Little_Ice_Age  Italy-cities  international_finance 
november 2017 by dunnettreader
Trade Agreements as Vectors for the Nagoya Protocol's Implementation | Centre for International Governance Innovation - 2017
A growing number of trade agreements include provisions related to access to genetic resources and the sharing of the benefits that arise out of their utilization. This paper maps the distribution and the diversity of these provisions. It identifies
 a great variety of provisions regarding sovereignty over genetic resources, the protection of traditional knowledge, prior informed consent, the disclosure of origin in patent applications and conditions for bioprospecting activities. It also finds that some recent trade agreements provide specific measures designed to facilitate the implementation of access and benefit-sharing (ABS) provisions, including measures related to technical assistance, transparency and dispute settlements. Thus,
 it appears that trade negotiations can become
 vectors for the implementation of ABS obligations stemming from the Convention on Biological Diversity and the Nagoya Protocol on Access
 to Genetic Resources and the Fair and Equitable Sharing of Benefits Arising from their Utilization.
 The integration of ABS commitments into trade agreements, however, varies greatly, depending
 on the countries involved. While Latin American countries have played a pioneering role, Canada and the United States still lag behind. The most exemplary ABS standards are not yet widely used, perhaps because they remain little known. These provisions deserve greater attention and should be integrated more widely into international trade agreements.
trade-agreements  genetic_resources  bioprospecting  genetics  IP  paper  Evernote  downloaded  sovereignty  biodiversity  biology  pharma 
july 2017 by dunnettreader
Peter Taylor - A Short Response to Lynch’s Counter-Criticisms| Social Epistemology Review and Reply Collective (2016)
Last in series of Lynch paper, Taylor comment, Lynch response and Taylor counter comment Taylor (U Mass Boston) is apparently even more disdainful than Lynch of Fuller, but he's sceptical of the Darwinian "selection" model (not the "natural' part apparently) and would go after Fuller without being completely wedded to Darwin, whereas Lynch sees questioning Darwinian basis of emerging multilevel evolutionary process as just begging for the sort of unholy alliance between fundies and "prigressive" apocalyptic types like Fuller. Downloaded the 4 pieces. (1) Lynch, William T. “Darwinian Social Epistemology: Science and Religion as Evolutionary Byproducts Subject to Cultural Evolution.” Social Epistemology Review and Reply Collective 5, no. 2 (2016): 26-68. (2) Taylor, Peter J. “Questioning the Darwinism that Lynch Presents as a Viable Basis for Humans to Pursue Science.” Social Epistemology Review and Reply Collective 5, no. 2 (2016): 85-87. (3) Lynch, William T. “Complexity, Natural Selection, and Cultural Evolution.” Social Epistemology Review and Reply Collective 5, no. 3 (2016): 64-72.
evolution  sociology_of_knowledge  forum  Darwinism  intelligent_design  epigenetics  downloaded  gene-culture_coevolution  complexity  sociology_of_religion  genetics  emergence  sociology_of_science_ 
may 2016 by dunnettreader
On human races | Plato's Footnote - March 2016
Why then is the concept of race so widespread? The idea that races are a natural feature of human diversity has long been the standard for anthropological…
Instapaper  biology  genetics  biodiversity  race  constructivism  nature-nurture  from instapaper
march 2016 by dunnettreader
Weibel P, Sloterdijk P, Finkielkraut A, Houellebecq M - La nouvelle conception de l'homme. La construction de l'être humain (2004) - Cairn.info
Weibel Peter, Sloterdijk Peter, Finkielkraut Alain, Houellebecq Michel, « La nouvelle conception de l'homme. La construction de l'être humain. », Le Philosophoire 2/2004 (n° 23) , p. 32-55
URL : www.cairn.info/revue-le-philosophoire-2004-2-page-32.htm.
DOI : 10.3917/phoir.023.0032.
Transcript from 2001 conference
Downloaded via iPhone to DBOX
21stC  evolution-social  biocultural_evolution  Modernism  humanism  downloaded  posthumanism  human_nature  change-social  conference  genetics  anti-humanism  neuroscience  social_theory  postmodern 
february 2016 by dunnettreader
Jonathan Kaplan - The end of the Adaptive Landscape metaphor?, Biology and Philosophy (2008) | via Researchgate
Biology and Philosophy (Impact Factor: 1.19). 11/2008; 23(5):625-638. DOI: 10.1007/s10539-008-9116-z -- ABSTRACT -- The concepts of adaptive/fitness landscapes and adaptive peaks are a central part of much of contemporary evolutionary biology;the concepts are introduced in introductory texts, developed in more detail in graduate-level treatments, and are used extensively in papers published in the major journals in the field. The appeal of visualizing the process of evolution in terms of the movement of populations on such landscapes is very strong; as one becomes familiar with the metaphor, one often develops the feeling that it is possible to gain deep insights into evolution by thinking about the movement of populations on landscapes consisting of adaptive valleys and peaks. But, since Wright first introduced the metaphor in 1932, the metaphor has been the subject of persistent confusion, from equivocation over just what the features of the landscape are meant to represent to how we ought to expect the landscapes to look. Recent advances—conceptual, empirical, and computational—have pointed towards the inadequacy and indeed incoherence of the landscapes as usually pictured. I argue that attempts to reform the metaphor are misguided; it is time to give up the pictorial metaphor of the landscape entirely and rely instead on the results of formal modeling, however difficult such results are to understand in ‘intuitive’ terms. -- downloaded pdf to Note
article  philosophy_of_science  biology  genetics  evolutionary_biology  natural_selection  evolution  scientific_method  modelling  levels_of_analyis  causation-evolutionary  downloaded 
january 2016 by dunnettreader
Jonathan Kaplan and Rasmus Grønfeldt Winther - Realism, Antirealism, and Conventionalism about Race , Philosophy of Science, Dec 2014 | via Researchgate
Philosophy of Science (Impact Factor: 0.83). 12/2014; 81(5):1039-1052. DOI: 10.1086/678314 -- ABSTRACT -- This paper distinguishes three concepts of " race " : bio-genomic cluster/race, biological race, and social race. We map out realism, antirealism, and conventionalism about each of these, in three important historical episodes: Frank Livingstone and Theodosius Dobzhansky in 1962, A. W. F. Edwards's 2003 response to Lewontin's 1972 paper, and contemporary discourse. Semantics is especially crucial to the first episode, while normativity is central to the second. Upon inspection, each episode also reveals a variety of commitments to the metaphysics of race. We conclude by interrogating the relevance of these scientific discussions for political positions and a post-racial future. -- downloaded pdf to Note
article  philosophy_of_science  biology  genetics  race  anthropology  kinds  ontology-social  racism  racialism  sociobiology  sociology_of_knowledge  sociology_of_science  sociology_of_science_&_technology  constructivism  politics-and-science  downloaded 
january 2016 by dunnettreader
Paul Newall interview with John Dupré: The Disunity of Science (2006) - The Galilean Library
John Dupré is a professor of philosophy of science in the Department of Sociology and Philosophy at Exeter University in the UK, and also the director of Egenis, the ESRC Centre for Genomics in Society. I was able to ask him about several keys areas of his work and relate it to contemporary issues in both science and the philosophy of science. -- Hits all my hot buttons. Anti mathematization of economics and its divorce from empiricism, disdainful of evo-devo psych, the Centre is part of a larger program looking at impacts of genetics and biology, from philosophy through sociology, economics, politics, art and humanities. Pal of Nancy Cartwright, Philip Kitcher and part of the "Stanford School". Author of Darwin's Legacy on Kindle -- downloaded page as pdf to Note
interview  philosophy_of_science  scientific_method  scientific_culture  scientism  methodology  laws_of_nature  empiricism  pragmatism  genetics  evolutionary_biology  molecular_biology  epigenetics  evo_psych  economic_models  mathematization  kindle  downloaded 
july 2015 by dunnettreader
Herbert Gintis - Gene–culture coevolution and the nature of human sociality | Royal Society - Issue Theme "Human Niche Construction" - Phil. Trans. R. Soc. B, 27 March 2011, vol. 366, no. 1566, 878-888
Human characteristics are the product of gene–culture coevolution, which is an evolutionary dynamic involving the interaction of genes and culture over long time periods. Gene–culture coevolution is a special case of niche construction. Gene–culture coevolution is responsible for human other-regarding preferences, a taste for fairness, the capacity to empathize and salience of morality and character virtues. -- Keywords: gene–culture coevolution, sociobiology, epistatic information transfer -- Published 14 February 2011 doi: 10.1098/rstb.2010.0310 -- downloaded pdf to Note
article  gene-culture_coevolution  sociobiology  social_theory  genetics  cultural_change  social_process  niche_construction  evolution  evolution-social  evolutionary_biology  human_nature  character  preferences  altruism  fairness  empathy  moral_sentiments  moral_psychology  morality-innate  morality-conventional  virtue  tradition  cultural_transmission  evolution-group_selection  downloaded  EF-add 
february 2015 by dunnettreader
Kim Sterelny - From hominins to humans: how sapiens became behaviourally modern | Royal Society - Issue Theme " Human Niche Construction " - Phil. Trans. R. Soc. B, 27 March 2011, vol. 366, no. 1566, 809-822
Philosophy Program and Tempo and Mode, Australian National University and Philosophy Program, Victoria University of Wellington -- This paper contributes to a debate in the palaeoarchaeological community about the major time-lag between the origin of anatomically modern humans and the appearance of typically human cultural behaviour. Why did humans take so long—at least 100,000 years—to become ‘behaviourally modern’? The transition is often explained as a change in the intrinsic cognitive competence of modern humans: often in terms of a new capacity for symbolic thought, or the final perfection of language. These cognitive breakthrough models are not satisfactory, for they fail to explain the uneven palaeoanthropological record of human competence. Many supposed signature capacities appear (and then disappear) before the supposed cognitive breakthrough; many of the signature capacities disappear again after the breakthrough. So, instead of seeing behavioural modernity as a simple reflection of a new kind of mind, this paper presents a niche construction conceptual model of behavioural modernity. Humans became behaviourally modern when they could reliably transmit accumulated informational capital to the next generation, and transmit it with sufficient precision for innovations to be preserved and accumulated. In turn, the reliable accumulation of culture depends on the construction of learning environments, not just intrinsic cognitive machinery. I argue that the model is (i) evolutionarily plausible: the elements of the model can be assembled incrementally, without implausible selective scenarios; (ii) the model coheres with the broad palaeoarchaeological record; (iii) the model is anthropologically and ethnographically plausible; and (iv) the model is testable, though only in coarse, preliminary ways. - Keywords : niche construction, behavioural modernity, hominins -- doi: 10.1098/rstb.2010.0301 -- downloaded pdf to Note
article  sociobiology  anthropology  paleontology  prehistoric  evolution  evolution-social  evolutionary_biology  genetics  gene-culture_coevolution  niche_construction  brain  social_process  cultural_change  learning  cognition  cognition-social  cultural_transmission  downloaded  EF-add 
february 2015 by dunnettreader
Luke Rendell, Laurel Fogarty and Kevin N. Laland - Runaway cultural niche construction | Royal Society Issue Theme " Human Niche Construction " - Phil. Trans. R. Soc. B, 27 March 2011 vol. 366 no. 1566, 823-835
School of Biology, University of St Andrews, -- Cultural niche construction is a uniquely potent source of selection on human populations, and a major cause of recent human evolution. Previous theoretical analyses have not, however, explored the local effects of cultural niche construction. Here, we use spatially explicit coevolutionary models to investigate how cultural processes could drive selection on human genes by modifying local resources. We show that cultural learning, expressed in local niche construction, can trigger a process with dynamics that resemble runaway sexual selection. Under a broad range of conditions, cultural niche-constructing practices generate selection for gene-based traits and hitchhike to fixation through the build up of statistical associations between practice and trait. This process can occur even when the cultural practice is costly, or is subject to counteracting transmission biases, or the genetic trait is selected against. Under some conditions a secondary hitchhiking occurs, through which genetic variants that enhance the capability for cultural learning are also favoured by similar dynamics. We suggest that runaway cultural niche construction could have played an important role in human evolution, helping to explain why humans are simultaneously the species with the largest relative brain size, the most potent capacity for niche construction and the greatest reliance on culture. Keywords: niche construction, cultural transmission, gene–culture coevolution, human evolution, spatially explicit models -- doi: 10.1098/rstb.2010.0256 -- didn't download
article  sociobiology  anthropology  genetics  gene-culture_coevolution  niche_construction  social_theory  social_process  change-social  cultural_transmission  evolution  evolution-social  evolutionary_biology  human_nature  evolution-group_selection  EF-add 
february 2015 by dunnettreader
Jeremy Kendal, Jamshid J. Tehrani and John Odling-Smee - Human niche construction in interdisciplinary focus | Royal Society - Theme Issue "Human Niche Construction" Phil. Trans. R. Soc. B, 27 March 2011, vol. 366, no. 1566, 785-792
doi: 10.1098/rstb.2010.0306 Jeremy Kendal1 and Jamshid J. Tehrani - Centre for the Coevolution of Biology and Culture, Department of Anthropology, University of Durham -- John Odling-Smee - School of Anthropology, University of Oxford -- Issue introduction -- Niche construction is an endogenous causal process in evolution, reciprocal to the causal process of natural selection. It works by adding ecological inheritance, comprising the inheritance of natural selection pressures previously modified by niche construction, to genetic inheritance in evolution. Human niche construction modifies selection pressures in environments in ways that affect both human evolution, and the evolution of other species. Human ecological inheritance is exceptionally potent because it includes the social transmission and inheritance of cultural knowledge, and material culture. Human genetic inheritance in combination with human cultural inheritance thus provides a basis for gene–culture coevolution, and multivariate dynamics in cultural evolution. Niche construction theory potentially integrates the biological and social aspects of the human sciences. We elaborate on these processes, and provide brief introductions to each of the papers published in this theme issue. -- downloaded pdf to Note
article  evolution  evolution-social  evolutionary_biology  sociobiology  human_nature  genetics  gene-culture_coevolution  niche_construction  ecology  species  environment  social_theory  social_process  change-social  cultural_change  cultural_transmission  downloaded  EF-add 
february 2015 by dunnettreader
Ashraf & Galor - The 'Out of Africa' Hypothesis, Human Genetic Diversity, and Comparative Economic Development | from American Economic Review 2013
This research advances and empirically establishes the hypothesis that, in the course of the prehistoric exodus of Homo sapiens out of Africa, variation in migratory distance to various settlements across the globe affected genetic diversity and has had a persistent hump-shaped effect on comparative economic development, reflecting the trade-off between the beneficial and the detrimental effects of diversity on productivity. While the diversity of Native American populations and the high diversity of African populations have been detrimental for the development of these regions, the intermediate levels of diversity associated with European and Asian populations have been conducive for development. - dowmloaded to iPhone zip file
economic_culture  development  economic_growth  demography  genetics  diversity-genetic  migration  deep_history  downloaded 
january 2015 by dunnettreader
Dawn Field - The practical genomics revolution | OUPblog Jan 2015
The post privides thumbnail descriptions of a host of Big Data research projects with links as well as some commercial services sprouting up - indirectly promoting her new book --Dawn Field, PhD, is the author of Biocode: The New Age of Genomics. She is a Senior Research Fellow at the NERC Centre for Ecology and Hydrology, a Research Associate of the Biodiversity Institute of Oxford at Oxford University and a Research Associate of the Smithsonian Institution. She is a founder of the Genomic Standards Consortium, the Genomic Observatories Network and Ocean Sampling Day. Follow her on Twitter @fiedawn.
books  genetics  molecular_biology  public_health  medicine 
january 2015 by dunnettreader
Marta Florio and Wieland B. Huttner - Neural progenitors, neurogenesis and the evolution of the neocortex (2014) | Development - online Journal of development biology
REVIEW - Abstract - The neocortex is the seat of higher cognitive functions and, in evolutionary terms, is the youngest part of the mammalian brain. Since its origin, the neocortex has expanded in several mammalian lineages, and this is particularly notable in humans. This expansion reflects an increase in the number of neocortical neurons, which is determined during development and primarily reflects the number of neurogenic divisions of distinct classes of neural progenitor cells. Consequently, the evolutionary expansion of the neocortex and the concomitant increase in the numbers of neurons produced during development entail interspecies differences in neural progenitor biology. Here, we review the diversity of neocortical neural progenitors, their interspecies variations and their roles in determining the evolutionary increase in neuron numbers and neocortex size. -- downloaded pdf to Note
article  neuroscience  evolutionary_biology  evolution  brain  brain-development  primates  human_nature  genetics  molecular_biology  downloaded  EF-add 
november 2014 by dunnettreader
Simon M. G. Braun and Sebastian Jessberger - Adult neurogenesis: mechanisms and functional significance (2014) | Development - online Journal of development biology
DEVELOPMENT AT A GLANCE -- Abstract - New neurons are generated throughout life in distinct regions of the mammalian brain. This process, called adult neurogenesis, has been implicated in physiological brain function, and failing or altered neurogenesis has been associated with a number of neuropsychiatric diseases. Here, we provide an overview of the mechanisms governing the neurogenic process in the adult brain and describe how new neurons may contribute to brain function in health and disease.
article  neuroscience  brain-development  brain  genetics  epigenetics  physiology  psychology  plasticity  neurogenesis  primates  molecular_biology  downloaded  EF-add 
november 2014 by dunnettreader
Jens Rister, Claude Desplan, and Daniel Vasiliauskas - Primer Series: Establishing and maintaining gene expression patterns: insights from sensory receptor patterning (2013)
Development. Feb 1, 2013; 140(3): 493–503. - doi: 10.1242/dev.079095 - PMCID: PMC3561783 - Primer Series - In this Primer, we summarize our current understanding of the mechanisms governing SR patterning in the fly retina, one of the best-understood systems for SR gene choice. We then compare these regulatory mechanisms with those used in the mouse retina and in the fly and mouse olfactory systems. -- Abstract - In visual and olfactory sensory systems with high discriminatory power, each sensory neuron typically expresses one, or very few, sensory receptor genes, excluding all others. Recent studies have provided insights into the mechanisms that generate and maintain sensory receptor expression patterns. Here, we review how this is achieved in the fly retina and compare it with the mechanisms controlling sensory receptor expression patterns in the mouse retina and in the mouse and fly olfactory systems. -- Introduction - Multicellular organisms are able to perceive and discriminate a broad range of environmental stimuli within a number of sensory modalities. To achieve this, the visual and olfactory systems deploy large numbers of sensory receptors (SRs). For example, five Rhodopsin genes are differentially expressed in the fly retina while over 1200 olfactory receptor genes are expressed in the nose of the mouse . In sensory systems of high discriminatory power, each sensory neuron generally expresses only one or very few SR gene(s), excluding all others . Importantly, the choice of expressing a particular SR determines the identity and response spectrum of the sensory neuron. Thus, each sensory neuron faces two regulatory challenges during its terminal differentiation: it first has to make an unambiguous choice of SR expression, and it must then maintain this decision throughout its lifespan. Failure in either case would compromise the ability of the sensory system to discriminate between stimuli. -- downloaded pdf to Note Keywords: Hippo pathway, Cell identity maintenance, Olfactory receptor, Opsin, Photoreceptor, Sensory --
article  neuroscience  brain  perception  sensation  brain-development  vision  molecular_biology  genetics  epigenetics  downloaded  EF-add 
november 2014 by dunnettreader
Kevin T. Eade, et al - Developmental Transcriptional Networks Are Required to Maintain Neuronal Subtype Identity in the Mature Nervous System (2012)
PLoS Genet. Feb 2012; 8(2): e1002501.-- doi: 10.1371/journal.pgen.1002501
PMCID: PMC3285578 -- Kevin T. Eade, Hailey A. Fancher, Marc S. Ridyard, and Douglas W. Allan* - William A. Harris, Editor -- Abstract - During neurogenesis, transcription factors combinatorially specify neuronal fates and then differentiate subtype identities by inducing subtype-specific gene expression profiles. But how is neuronal subtype identity maintained in mature neurons? Modeling this question in two Drosophila neuronal subtypes (Tv1 and Tv4), we test whether the subtype transcription factor networks that direct differentiation during development are required persistently for long-term maintenance of subtype identity. By conditional transcription factor knockdown in adult Tv neurons after normal development, we find that most transcription factors within the Tv1/Tv4 subtype transcription networks are indeed required to maintain Tv1/Tv4 subtype-specific gene expression in adults. Thus, gene expression profiles are not simply “locked-in,” but must be actively maintained by persistent developmental transcription factor networks. We also examined the cross-regulatory relationships between all transcription factors that persisted in adult Tv1/Tv4 neurons. We show that certain critical cross-regulatory relationships that had existed between these transcription factors during development were no longer present in the mature adult neuron. This points to key differences between developmental and maintenance transcriptional regulatory networks in individual neurons. Together, our results provide novel insight showing that the maintenance of subtype identity is an active process underpinned by persistently active, combinatorially-acting, developmental transcription factors. These findings have implications for understanding the maintenance of all long-lived cell types and the functional degeneration of neurons in the aging brain. -- downloaded pdf to Note
article  neuroscience  brain-development  brain-aging  genetics  epigenetics  molecular_biology  plasticity  downloaded  EF-add 
november 2014 by dunnettreader
Verena Wolfram and Richard A. Baines - Blurring the boundaries: developmental and activity-dependent determinants of neural circuits (2013
Trends in Neuroscience. Oct 2013; 36(10): 610–619. - doi: 10.1016/j.tins.2013.06.006
PMCID: PMC3794160 -- Abstract - The human brain comprises approximately 100 billion neurons that express a diverse, and often subtype-specific, set of neurotransmitters and voltage-gated ion channels. Given this enormous complexity, a fundamental question is how is this achieved? The acquisition of neurotransmitter phenotype was viewed as being set by developmental programs ‘hard wired’ into the genome. By contrast, the expression of neuron-specific ion channels was considered to be highly dynamic (i.e., ‘soft wired’) and shaped largely by activity-dependent mechanisms. Recent evidence blurs this distinction by showing that neurotransmitter phenotype can be altered by activity and that neuron type-specific ion channel expression can be set, and perhaps limited by, developmental programs. Better understanding of these early regulatory mechanisms may offer new avenues to avert the behavioral changes that are characteristic of many mental illnesses. -- downloaded pdf to Note
article  neuroscience  neuro-endocrine_system  brain  plasticity  psychology  genetics  epigenetics  downloaded  EF-add 
november 2014 by dunnettreader
Francisco J. Novo - Habit acquisition in the context of neuronal genomic and epigenomic mosaicism (2014)
Frontiers of Human Neuroscience. 2014; 8: 255. - doi: 10.3389/fnhum.2014.00255
PMCID: PMC4007014 -- See the article "Epigenetic Priming of Memory Updating during Reconsolidation to Attenuate Remote Fear Memories" in Cell, volume 156 on page 261. -- A recent paper (Gräff et al., 2014) shows that remote fear memories in mice can be stably attenuated with the administration of histone de-acetylase (HDAC) inhibitors during reconsolidation. This achieved persistent attenuation of remote memories, even though it is well established that the brief period of hippocampal neuroplasticity induced by recent memory recall is absent for remote memories. Apparently, such epigenetic intervention primed the expression of neuroplasticity-related genes. This work comes shortly after the finding (McConnell et al., 2013) that individual neurons show an extraordinary degree of genomic mosaicism. Sequencing the genomes of single human frontal cortex neurons, these authors found that up to 41% of neurons contain at least one de novo copy-number variant (CNV) of at least one megabase in size. Segmental duplications have greatly expanded in African great apes (Marques-Bonet et al., 2009), and it is possible that increased retrotransposon activity during human neurogenesis also contributes to this striking diversity in CNV numbers in neuronal genomes (Singer et al., 2010). Taken together, both studies support the notion that genomic and epigenomic mosaicism allows for the introduction of heritable changes at the single-cell level that promote neuronal plasticity, and thus help to explain how human actions can modify neural circuits involved in memory and learning. -- downloaded pdf to Note
article  genetics  epigenetics  primates  human_nature  brain  neuroscience  memory  learning  plasticity  downloaded  EF-add 
november 2014 by dunnettreader
David L. Molfese - Advancing Neuroscience through Epigenetics: Molecular Mechanisms of Learning and Memory (2011)
Dev Neuropsychol. Oct 2011; 36(7): 810–827. - doi: 10.1080/87565641.2011.606395 PMCID: PMC3191880 - NIHMSID: NIHMS325838 -- Abstract - Humans share 96% of our 30,000 genes with Chimpanzees. The 1,200 genes that differ appear at first glance insufficient to describe what makes us human and them apes. However, we are now discovering that the mechanisms that regulate how genes are expressed tell a much richer story than our DNA alone. Sections of our DNA are constantly being turned on or off, marked for easy access, or secluded and hidden away, all in response to on-going cellular activity. In the brain, neurons encode information – in effect memories – at the cellular level. Yet while memories may last a lifetime, neurons are dynamic structures. Every protein in the synapse undergoes some form of turnover, some with half-lives of only hours. How can a memory persist beyond the lifetimes of its constitutive molecular building blocks? Epigenetics – changes in gene expression that do not alter the underlying DNA sequence – may be the answer. In this article, epigenetic mechanisms including DNA methylation and acetylation or methylation of the histone proteins that package DNA are described in the context of animal learning. Through the interaction of these modifications a “histone code” is emerging wherein individual memories leave unique memory traces at the molecular level with distinct time courses. A better understanding of these mechanisms has implications for treatment of memory disorders caused by normal aging or diseases including schizophrenia, Alzheimer’s, depression, and drug addiction. -- downloaded pdf to Note - Keywords: epigenetics, genes, memory, learning, histone, hippocampus, behavior
article  genetics  epigenetics  memory  learning  brain  neuroscience  molecular_biology  primates  psychology  human_nature  downloaded  EF-add 
november 2014 by dunnettreader
Victoria Menzies, et al - Epigenetic Alterations and an Increased Frequency of Micronuclei in Women with Fibromyalgia (2013)
Nursing Research and Practice. 2013; doi: 10.1155/2013/795784 -- PMCID: PMC3766610 -- Victoria Menzies, 1 ,* Debra E. Lyon, 1 , 2 Kellie J. Archer, 3 Qing Zhou, 3 Jenni Brumelle, 4 Kimberly H. Jones, 4 , 5 G. Gao, 3 Timothy P. York, 6 and Colleen Jackson-Cook -- Abstract - Fibromyalgia (FM), characterized by chronic widespread pain, fatigue, and cognitive/mood disturbances, leads to reduced workplace productivity and increased healthcare expenses. To determine if acquired epigenetic/genetic changes are associated with FM, we compared the frequency of spontaneously occurring micronuclei (MN) and genome-wide methylation patterns in women with FM (n = 10) to those seen in comparably aged healthy controls (n = 42 (MN); n = 8 (methylation)). The mean (sd) MN frequency of women with FM (51.4 (21.9)) was significantly higher than that of controls (15.8 (8.5)) (χ2 = 45.552; df = 1; P = 1.49 × 10−11). Significant differences (n = 69 sites) in methylation patterns were observed between cases and controls considering a 5% false discovery rate. The majority of differentially methylated (DM) sites (91%) were attributable to increased values in the women with FM. The DM sites included significant biological clusters involved in neuron differentiation/nervous system development, skeletal/organ system development, and chromatin compaction. Genes associated with DM sites whose function has particular relevance to FM included BDNF, NAT15, HDAC4, PRKCA, RTN1, and PRKG1. Results support the need for future research to further examine the potential role of epigenetic and acquired chromosomal alterations as a possible biological mechanism underlying FM. -- downloaded pdf to Note
article  health  genetics  epigenetics  neuroscience  downloaded 
november 2014 by dunnettreader
Nassim Nicholas Taleb, et al - The Precautionary Principle (with Application to the Genetic Modification of Organisms) | arxiv.org - Oct 2014 [1410.5787]
Nassim Nicholas Taleb, Rupert Read, Raphael Douady, Joseph Norman, Yaneer Bar-Yam -- Abstract -- We present a non-naive version of the Precautionary (PP) that allows us to avoid paranoia and paralysis by confining precaution to specific domains and problems. PP is intended to deal with uncertainty and risk in cases where the absence of evidence and the incompleteness of scientific knowledge carries profound implications and in the presence of risks of "black swans", unforeseen and unforeseable events of extreme consequence. We formalize PP, placing it within the statistical and probabilistic structure of ruin problems, in which a system is at risk of total failure, and in place of risk we use a formal fragility based approach. We make a central distinction between 1) thin and fat tails, 2) Local and systemic risks and place PP in the joint Fat Tails and systemic cases. We discuss the implications for GMOs (compared to Nuclear energy) and show that GMOs represent a public risk of global harm (while harm from nuclear energy is comparatively limited and better characterized). PP should be used to prescribe severe limits on GMOs. -- see summary from arxiv Medium blog, saved via Instapaper
paper  risk  uncertainty  risk-systemic  biology  genetics  agriculture  GMOs  probability  precautionary_principle  risk-mitigation  global_system  EF-add 
october 2014 by dunnettreader
Oren Harman review - Sean B. Carroll, Brave Genius : A Scientist, a Philosopher, and Their Daring Adventures from the French Resistance to the Nobel Prize - "Chance and Necessity" Revisited | The Los Angeles Review of Books - July 2014
IN THE FALL of 1970, Éditions du Seuil published Le hasard et la nécessité, a monograph by the French molecular biologist Jacques Monod,. Chance and Necessity was a slim book laden with technical details of oligomeric proteins, teleonomic structures, and microscopic perturbations. Despite the technical jargon, the book sold over 200,000 copies in its first year and became a best seller in Germany and Japan. It was bested in France only by Erich Segal’s Love Story. What explains its popularity? Monod was an eminent scientist, to be sure: he’d received the 1965 Nobel Prize with André Lwoff and François Jacob for “discoveries concerning genetic control of enzyme and virus synthesis.” But the resonance of Chance and Necessity is best explained by two epigraphs that adorned its opening page, stoic reminders that this was an affair well beyond the confines of mere science. The first is a dramatic statement by the Greek philosopher Democritus: “Everything existing in the Universe is the fruit of chance and necessity.” The second epigram, more than anything, best explains the book’s salience: a lengthy quotation from Albert Camus’s essay The Myth of Sisyphus. “The struggle itself towards the heights is enough to fill a man’s heart”; it ends, “One must imagine Sisyphus happy.” Sean B. Carroll, the American developmental molecular geneticist, reveals the deep friendship between Camus and Monod in Brave Genius. Their relationship, Carroll finds, not only illuminates the work of both men, but also unlocks the political and philosophical contingencies of a key moment in 20th-century thought.
books  reviews  intellectual_history  political_history  history_of_science  existentialism  20thC  France  WWII  French_Resistance  biography  Camus  evolutionary_biology  genetics  biology  cosmology  nihilism  chance  determinism  necessity 
august 2014 by dunnettreader
Kevin Mitchell -- Wiring the Brain: Exciting findings in schizophrenia genetics – but what do they mean? - July 2014
Study of genome in huge number of people (with the disease and controls) doesn't solve the question of the architecture, but locates lots of areas to look at for not just mutations but interactions
genetics  neuroscience  psychology 
july 2014 by dunnettreader
Kevin Mitchell - Wiring the Brain: "Common disorders" are really collections of rare genetic conditions - July 2014
Disorders such as autism, schizophrenia and epilepsy each affect about 1% of the population and are therefore defined as “common disorders”. But are they really? I mean, they are clearly really that common, but are they really “disorders”? Are they natural categories that reflect some shared underlying etiology or are they simply groupings based on sets of shared symptoms? Genetics is providing an answer to that question and demonstrating that so-called “common disorders” are really collections of rare disorders with similar symptoms. This represents a complete paradigm shift in psychiatry, the full ramifications of which have yet to be appreciated. -- fascinating -- lots of links
health  medicine  genetics  psychiatry  neuroscience  links 
july 2014 by dunnettreader
The Gene Is Obsolete - Pacific Standard: The Science of Society - May 2014
One major challenge to the concept of a gene is the growing evidence that many genes are shapeshifters. Instead of a well-defined segment of DNA that encodes a single protein with a clear function, we should view a gene as “a polyfunctional entity that assumes different forms under different cellular states,” according to University of Washington biologist John Stamatoyannopoulos. While researchers have long known that genes are made up of discrete subunits called “exons,” they hadn’t realized until recently the degree to which exons are assembled—like Legos—into sometimes thousands of different combinations. -- Our concept of a gene is also challenged by the fact that much of the function in our DNA is located outside of conventionally defined genes. These “non-coding” functional DNA segments regulate when and where conventional protein-coding genes operate.
genetics 
may 2014 by dunnettreader
Kevin Mitchell - Wiring the Brain: The genetics of emergent phenotypes - March 2013
Nifty discussion of emergence in dynamic systems - he claims the higher level phenomena are reducible to lower level factors (post hoc explanation) but not deducible from the lower level. However the dynamic elements that change relations at or among higher level elements (which will change relations at lower levels) seem to be doing most of the explanatory work -- Why are some brain disorders so common? Schizophrenia, autism and epilepsy each affect about 1% of the world’s population, over their lifetimes. Why are the specific phenotypes associated with those conditions so frequent? More generally, why do particular phenotypes exist at all? What constrains or determines the types of phenotypes we observe, out of all the variations we could conceive of? Why does a system like the brain fail in particular ways when the genetic program is messed with? Here, I consider how the difference between “concrete” and “emergent” properties of the brain may provide an explanation, or at least a useful conceptual framework. --
genetics  medicine  psychology  physiology  neuroscience  mind  materialism  emergence  systems-complex_adaptive  EF-add 
march 2014 by dunnettreader
Kevin Mitchell - Wiring the Brain: No gene is an island - July 2013
What is the effect on the trait of each of the individual loci in isolation? Well, here’s the surprise. In many cases, the phenotypic effects of these single loci are much bigger than you would expect – often explaining 50% or more of the difference between the two strains. This means that if you simply added up their effects you would get much more than the 100% of the difference you started with. In fact, the range for behavioural traits averages at ~800%, if you simply add up the effects of the decomposed individual loci. Even more remarkably, some of the individual chromosome substitution strains show a phenotypic level that is outside the range of either of the initial parents, sometimes even moving the trait distribution in the opposite direction to the “donor” parent strain. These results clearly show that non-additive interactions for variants affecting quantitative traits are common, large and unpredictable. They are a ubiquitous feature of the genetic architecture of quantitative traits, whether morphological, physiological or behavioural and are seen across many different species, including worms, flies, chickens, yeast. Even if such interactions average out across all the combinations encountered in the population, so that they appear additive, statistically, this biological reality places a severe limit on our ability to predict any individual’s phenotype based purely on additive calculations. -- sum up, we're each remarkably unique
genetics  biology 
march 2014 by dunnettreader
Kevin Mitchell - Wiring the Brain: Reductionism! Determinism! Straw-man-ism! - Feb 2014
Good post and comments -- cmnt 1 - I like your juxtaposition of "the system is complex" and "single variants can influence a complex system". One variant at a time studies aren't inherently reductionist. We all want to know what the effects of any variant are independent of genomic background and ecology. This is an important part of genetic architecture and should not be ignored. From my point of view the problem is with the *assumptions* made when investigating the single variant effect on interindividual variation in a biological trait. One assumption (1) is that the system is complex and the single variant analysis will reveal only a piece of that complexity. Another assumption (2) is that the system is complex but can be teased apart as a sum of independent effects. Yet another assumption (3) is that the system appears complex but is really simple and can be explained by a sum of variants. The human genetics and genetic epidemiology disciplines span all of these assumptions in a non-uniform manner. I am old enough to have been a graduate student and beginning assistant professor during the linkage era that began with assumption 3 coming off the successes of Mendelian genetics and positional cloning. This off course shifted to assumption 2 during the GWAS era. I think we are now in the process of shifting toward assumption 1 as digest the largely negative results of using single variant analyses to predict disease susceptibility. I believe this shift in assumptions will continue over the next year as WGS plays out. Thanks for the post! - Jason Moore (Dartmouth)
scientific_method  genetics  biology  science-public  evolutionary_biology  materialism  reductionism  EF-add 
march 2014 by dunnettreader
Tim Lewens - What Is Wrong with Typological Thinking? | JSTOR: Philosophy of Science, Vol. 76, No. 3 (July 2009), pp. 355-371
What, if anything, is wrong with typological thinking? The question is important, for some evolutionary developmental biologists appear to espouse a form of typology. I isolate four allegations that have been brought against it. They include the claim that typological thinking is mystical; the claim that typological thinking is at odds with the fact of evolution; the claim that typological thinking is committed to an objectionable metaphysical view, which Elliott Sober calls the ‘natural state model’; and finally the view (endorsed by Ron Amundson and Günter Wagner) that typological thinking—and specifically evolutionary developmental biology’s typological thinking—is committed to a peculiar form of causation that does not fit neatly into the causal models endorsed by population genetics. I argue that, properly understood, the typological thinking of evolutionary developmental biology does not run into any of these problems. -- paywall Chicago
article  jstor  paywall  philosophy_of_science  genetics  evolutionary_biology  evo_psych  causation-evolutionary  kinds  EF-add 
february 2014 by dunnettreader
Olivier Rieppel - New Essentialism in Biology | JSTOR: Philosophy of Science, Vol. 77, No. 5 (December 2010), pp. 662-673
The architects of the modern synthesis banned essentialism from evolutionary theory. This rejection of essentialism was motivated by Darwin’s theory of natural selection, and the continuity of evolutionary transformation. Contemporary evolutionary biology witnesses a renaissance of essentialism in three contexts: “origin essentialism” with respect to species and supraspecific taxa, the bar coding of species on the basis of discontinuities of DNA variation between populations, and the search for laws of evolutionary developmental biology. Such “new essentialism” in contemporary biology must be of a new kind that accommodates relational (extrinsic) properties as historical essences and cluster concepts of natural kinds.
article  jstor  paywall  evolution  evolutionary_biology  species  genetics  natural_kinds  essentialism  EF-add 
january 2014 by dunnettreader
Herb Gintis - Gene–culture coevolution and the nature of human sociality | Royal Society | Phil Trans B 2011
Published 14 February 2011 doi: 10.1098/rstb.2010.0310 Phil. Trans. R. Soc. B 27 March 2011 vol. 366 no. 1566 878-888 -- downloaded pdf to Note Abstract --
Human characteristics are the product of gene–culture coevolution, which is an evolutionary dynamic involving the interaction of genes and culture over long time periods. Gene–culture coevolution is a special case of niche construction. Gene–culture coevolution is responsible for human other-regarding preferences, a taste for fairness, the capacity to empathize and salience of morality and character virtues.
article  genetics  biocultural_evolution  epigenetics  human_nature  moral_psychology  moral_sentiments  character  downloaded  EF-add 
january 2014 by dunnettreader
Genes Aren’t Just Architects; They’re Actors | David Dobbs's NEURON CULTURE -Aug 2013
On bad or incomplete science reporting -- Robinson and others have for years been waving their hands, pointing at results like this, and arguing that the endgame in genetics is not in differences in what genes we carry, but — especially when most of our genes our shared — in differences in how and when the shared genes express themselves. This is important in understanding differences within a species, whether it be honey bees or humans.

This has been accepted for a while now about development — that is, in how we develop from zygotes to infants (and beyond); we share 99% of our genome with chimpanzees, but we are built differently because so many of the shared genes act differently during development. Robinson — and this paper — are saying that the same goes for behavior: Our differences and individuality arise not just partly but mainly because our shared genes behave differently. Figuring out why they do so is at least as important as figuring out what our genetic differences are.
genetics  epigenetics 
january 2014 by dunnettreader
John Mikhail - Review of Patricia S. Churchland, 'Braintrust: What Neuroscience Tells Us About Morality':: SSRN
The treatment of these subjects is generally informative and often quite illuminating, albeit occasionally superficial. Churchland writes elegantly and presents a clear, distinctive, and forceful viewpoint on the science of morality, which draws inspiration from Aristotle, Hume, and Darwin. Her principal thesis, that moral and social values are rooted in the neurobiology of care, trust, and cooperation, deserves to be taken seriously by scientists and philosophers alike. In this review, I focus on three perceived weaknesses of Churchland’s stimulating book that likely will be of particular interest to philosophers: her interpretation of Hume, her skepticism toward innate moral principles, and her treatment of moral rules. I then conclude by making a few brief observations about the general significance of Braintrust. Keywords: Churchland, Darwin, Hume, Aristotle, Plato, morality, nativism, epistemology, computation, rules, neurobiology, care, attachment, norms, genes, evolution -- downloaded pdf to Note
books  kindle  reviews  moral_philosophy  cognition  neuroscience  Hume  naturalism  evolutionary_biology  evo_psych  epistemology  genetics  downloaded  EF-add 
september 2013 by dunnettreader
Selected sources for “The Social Life of Genes” | David Dobbs's NEURON CULTURE
Finally made time to create a list of selected reading/sources for my Pacific Standard article “The Social Life of Genes.” (A few of you had asked.)

The list is below, and also at http://daviddobbs.net/smoothpebbles/selected-references-for-social-life-of-genes/
bibliography  genetics  evolution  biocultural_evolution 
september 2013 by dunnettreader

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