Explanationism, Super-Explanationism, Ecclectic Explanationism: Persistent Problems on Both Sides

We argue that explanationist views in epistemology continue to face persistent challenges to both their necessity and their sufficiency. This is so despite arguments offered by Kevin McCain in a paper recently published in this journal which attempt to show otherwise. We highlight ways in which McCain’s attempted solutions to problems we had previously raised go awry, while also presenting a novel challenge for all contemporary explanationist views

Epigenetic Characterization of the FMR1 Gene and Aberrant Neurodevelopment in Human Induced Pluripotent Stem Cell Models of Fragile X Syndrome

Fragile X syndrome (FXS) is the most common inherited cause of intellectual disability. In addition to cognitive deficits, FXS patients exhibit hyperactivity, attention deficits, social difficulties, anxiety, and other autistic-like behaviors. FXS is caused by an expanded CGG trinucleotide repeat in the 5′ untranslated region of the Fragile X Mental Retardation (FMR1) gene leading to epigenetic silencing and loss of expression of the Fragile X Mental Retardation protein (FMRP). Despite the known relationship between FMR1 CGG repeat expansion and FMR1 silencing, the epigenetic modifications observed at the FMR1 locus, and the consequences of the loss of FMRP on human neurodevelopment and neuronal function remain poorly understood. To address these limitations, we report on the generation of induced pluripotent stem cell (iPSC) lines from multiple patients with FXS and the characterization of their differentiation into post-mitotic neurons and glia. We show that clones from reprogrammed FXS patient fibroblast lines exhibit variation with respect to the predominant CGG-repeat length in the FMR1 gene. In two cases, iPSC clones contained predominant CGG-repeat lengths shorter than measured in corresponding input population of fibroblasts. In another instance, reprogramming a mosaic patient having both normal and pre-mutation length CGG repeats resulted in genetically matched iPSC clonal lines differing in FMR1 promoter CpG methylation and FMRP expression. Using this panel of patient-specific, FXS iPSC models, we demonstrate aberrant neuronal differentiation from FXS iPSCs that is directly correlated with epigenetic modification of the FMR1 gene and a loss of FMRP expression. Overall, these findings provide evidence for a key role for FMRP early in human neurodevelopment prior to synaptogenesis and have implications for modeling of FXS using iPSC technology. By revealing disease-associated cellular phenotypes in human neurons, these iPSC models will aid in the discovery of novel therapeutics for FXS and other autism-spectrum disorders sharing common pathophysiology.FRAXA Research FoundationHarvard Stem Cell Institute (seed grant)Stanley Medical Research InstituteNational Institute of Mental Health (U.S.) (grant #R33MH087896

Treating age-related multimorbidity:the drug discovery challenge

Patients with multimorbidities have shorter life expectancy and their clinical management is more complex and expensive for healthcare systems currently focused on treating single diseases. Given that age is the major risk factor for multimorbidity, the challenge of treating these patients will only increase in coming years. Here, we review the case for targeting the core processes that drive the ageing phenotype as a novel pharmaceutical approach to multimorbidity. There is growing evidence that targeting ageing mechanisms can reduce or delay age-related diseases in animal models, and the first reports of clinical trials are now appearing. Although these trials currently focus on repurposed drugs, we propose several novel targets that would more specifically target ageing processes and thereby reduce multimorbidity and polypharmacy in future generations

Carbon-sensitive pedotransfer functions for plant available water

Currently accepted pedotransfer functions show negligible effect of management-induced changes to soil organic carbon (SOC) on plant available water holding capacity (θAWHC), while some studies show the ability to substantially increase θAWHC through management. The Soil Health Institute\u27s North America Project to Evaluate Soil Health Measurements measured water content at field capacity using intact soil cores across 124 long-term research sites that contained increases in SOC as a result of management treatments such as reduced tillage and cover cropping. Pedotransfer functions were created for volumetric water content at field capacity (θFC) and permanent wilting point (θPWP). New pedotransfer functions had predictions of θAWHC that were similarly accurate compared with Saxton and Rawls when tested on samples from the National Soil Characterization database. Further, the new pedotransfer functions showed substantial effects of soil calcareousness and SOC on θAWHC. For an increase in SOC of 10 g kg–1 (1%) in noncalcareous soils, an average increase in θAWHC of 3.0 mm 100 mm–1 soil (0.03 m3 m–3) on average across all soil texture classes was found. This SOC related increase in θAWHC is about double previous estimates. Calcareous soils had an increase in θAWHC of 1.2 mm 100 mm–1 soil associated with a 10 g kg–1 increase in SOC, across all soil texture classes. New equations can aid in quantifying benefits of soil management practices that increase SOC and can be used to model the effect of changes in management on drought resilience

Photography-based taxonomy is inadequate, unnecessary, and potentially harmful for biological sciences

The question whether taxonomic descriptions naming new animal species without type specimen(s) deposited in collections should be accepted for publication by scientific journals and allowed by the Code has already been discussed in Zootaxa (Dubois & Nemésio 2007; Donegan 2008, 2009; Nemésio 2009a–b; Dubois 2009; Gentile & Snell 2009; Minelli 2009; Cianferoni & Bartolozzi 2016; Amorim et al. 2016). This question was again raised in a letter supported by 35 signatories published in the journal Nature (Pape et al. 2016) on 15 September 2016. On 25 September 2016, the following rebuttal (strictly limited to 300 words as per the editorial rules of Nature) was submitted to Nature, which on 18 October 2016 refused to publish it. As we think this problem is a very important one for zoological taxonomy, this text is published here exactly as submitted to Nature, followed by the list of the 493 taxonomists and collection-based researchers who signed it in the short time span from 20 September to 6 October 2016

Reasons for Our Hope: Plain Talk About Hard Questions, - I have questions - Don’t some things about Christianity just not make sense?, Part 3

Why is there evil in the world? Why does God hide? Are we Christian just because of where and when we were born? We consider these and other obstacles to faith and suggest ways to help unwilling doubters come free of these obstacles and step into a rich experience of God

Knowing Jesus, Loving Truth: A Gentle Offer in a Skeptical Age, Part 2

We learn from scripture that eternal life is knowing the Father and the Son, and we learn that people perish for “refusing to love the truth.” In this age of a million voices, one can easily feel defeated by the prospect of a search for knowledge or truth. How should the church respond to this present skepticism

Knowing Jesus, Loving Truth: A Gentle Offer in a Skeptical Age, Part 1

We learn from scripture that eternal life is knowing the Father and the Son, and we learn that people perish for “refusing to love the truth.” In this age of a million voices, one can easily feel defeated by the prospect of a search for knowledge or truth. How should the church respond to this present skepticism

Reasons For Our Hope: Plain Talk About Hard Questions - I\u27m Not Sure About Jesus - Why Should I Trust In Him?, Part 2

In this lecture I say why I trust in Jesus, and why I think it makes sense to do so. My reasoning follows a moral argument for Christianity given by C.S. Lewis in “Mere Christianity,” and then I briefly recount the major philosophical reasons to think that God exists