A Critique of Gender Ideology

It is common nowadays to meet young people who are confusedabout their gender identity. To feel like the other gender is verymuch in fashion; it is the new trending topic. In the UnitedKingdom, for instance, the Gender Identity Development Servicereported that it received 1,986 referrals of children in 2016/2017, upfrom 94 referrals in 2009/2010, making for a relative increase of2,000%. In Canada, a parent was allowed to register her/his child’ssex as “U” (probably for unspecified) so that the child will have thefreedom to choose its own gender later on. And in the Philippines,10% of males aged 18–25 years old now identify with the oppositegender. How are we to react to this? How are we to discern the “signsof the times” (see Mt. 16:3) here

Learning to live with novelty: Implications of exotic earthworms and their interactions with seeds, mulch, and wood ash for ecological restoration

A major challenge in restoration ecology is the biological invasion of ‘exotic’ species, some of which may spread widely and have undesirable impacts as ‘invasive’ species. Ongoing debates and changing perspectives suggest we may be overlooking opportunities to consider exotic species more broadly, not only as adversaries but also as potential null players or even allies in restoration. This may be exemplified by the invasion of exotic earthworms in North America, a long-term and widespread invasion of ecologically-influential organisms without practical ways to control it. The purpose of this dissertation is to consider the integration of exotic earthworms into restoration by exploring how they interact with three restoration interventions: seeds, mulch, and wood ash. I used laboratory microcosms and field-based experiments with a focus on the ecosystem engineering nightcrawler earthworm (Lumbricus terrestris L.). Overall, earthworms had effects that might be contextually beneficial or detrimental to ecological restoration: earthworms selectively consumed and buried seeds which could reduce recruitment from seed mixes or contribute to seed bank formation (Chapter 2); earthworms collected and buried mulch which exposed the soil underneath but could help mix organic matter into degraded soils (Chapter 3); and earthworms responded behaviourally and in population density to different wood ashes and helped mix surface-applied wood ash into the soil (Chapter 4). I propose that by recognizing exotic earthworms as a novel and increasingly common ecosystem feature in North America and by learning how to mitigate their undesirable impacts and take advantage of their benefits, we could more efficiently and effectively restore these changing ecosystems. This dissertation contributes to our expanding knowledge of earthworm ecology, facilitates increased integration of earthworm interactions into restoration, and offers insights into the broader implications of biological invasion for conservation. Studying the case of exotic earthworms in North America raises important questions about why we restore and conserve, the value of case-by-case management of invasions based on impact, the importance of considering the longer-term outcomes of invasion and naturalization, and – in some cases – the merit in learning to live with novelty

Nonlinear sound propagation in 2D curved ducts : a multimodal approach

A method for studying weakly nonlinear acoustic propagation in 2D ducts of general shape - including curvature and variable width - is presented. The method is based on a local modal decomposition of the pressure and velocity in the duct. A pair of nonlinear ODEs for the modal amplitudes of the pressure and velocity modes is derived. To overcome the inherent instability of these equations, a nonlinear admittance relation between the pressure and velocity modes is presented, introducing a novel `nonlinear admittance' term. Appropriate equations for the admittance are derived which are to be solved through the duct, with a radiation condition applied at the duct exit. The pressure and velocity are subsequently found by integrating an equation involving the admittance through the duct. The method is compared, both analytically and numerically, against published results and the importance of nonlinearity is demonstrated in ducts of complex geometry. Comparisons between ducts of differing geometry are also performed to illustrate the effect of geometry on nonlinear sound propagation. A new 'nonlinear reflectance' term is introduced, providing a more complete description of acoustic reflection that also takes into account the amplitude of the incident wave

“Brother, Father, Mister, Doctor!” - From a Missionary Surgeon in the Philippines

The children’s faces lit up the darkness of the night. I had come with Bong, a Filipino, to treat a young child with a cough and high fever. The girl was sat with her 3 young sisters on a bench outside their ‘house’, aflimsy wooden shack which was their home. “Brother James”, “Father James”, “Mister James”, “Doctor James” they chimed simultaneously jumping up and down with excitement. “Just call me James" I responded in the local dialect, “much easier". After speaking to the mother and examining the child we prescribed the  appropriate antibiotics. “Keep it in the fridge" I advised the mother. Bong coughed, trying to give me a subtle hint. I looked at Bong and he smiled at me through the candlelight. The light bulb came on in my mind “of course, the candles...these houses d o n 't have electricity never mind a fridge”, I spoke to the mother once more “OK, we will come back every day to administer the medicine". As we snaked our way back home through the coconut trees, tired but content, my steps made lighter by the gleeful voices of the children ringing in my ears, the days of ward rounds, white cell counts and chest x rays seemed but a distant memory..

TreeToReads - a pipeline for simulating raw reads from phylogenies.

BackgroundUsing phylogenomic analysis tools for tracking pathogens has become standard practice in academia, public health agencies, and large industries. Using the same raw read genomic data as input, there are several different approaches being used to infer phylogenetic tree. These include many different SNP pipelines, wgMLST approaches, k-mer algorithms, whole genome alignment and others; each of these has advantages and disadvantages, some have been extensively validated, some are faster, some have higher resolution. A few of these analysis approaches are well-integrated into the regulatory process of US Federal agencies (e.g. the FDA's SNP pipeline for tracking foodborne pathogens). However, despite extensive validation on benchmark datasets and comparison with other pipelines, we lack methods for fully exploring the effects of multiple parameter values in each pipeline that can potentially have an effect on whether the correct phylogenetic tree is recovered.ResultsTo resolve this problem, we offer a program, TreeToReads, which can generate raw read data from mutated genomes simulated under a known phylogeny. This simulation pipeline allows direct comparisons of simulated and observed data in a controlled environment. At each step of these simulations, researchers can vary parameters of interest (e.g., input tree topology, amount of sequence divergence, rate of indels, read coverage, distance of reference genome, etc) to assess the effects of various parameter values on correctly calling SNPs and reconstructing an accurate tree.ConclusionsSuch critical assessments of the accuracy and robustness of analytical pipelines are essential to progress in both research and applied settings

The individuality of shape asymmetries of the human cerebral cortex

Asymmetries of the cerebral cortex are found across diverse phyla and are particularly pronounced in humans, with important implications for brain function and disease. However, many prior studies have confounded asymmetries due to size with those due to shape. Here, we introduce a novel approach to characterize asymmetries of the whole cortical shape, independent of size, across different spatial frequencies using magnetic resonance imaging data in three independent datasets. We find that cortical shape asymmetry is highly individualized and robust, akin to a cortical fingerprint, and identifies individuals more accurately than size-based descriptors, such as cortical thickness and surface area, or measures of inter-regional functional coupling of brain activity. Individual identifiability is optimal at coarse spatial scales (~37 mm wavelength), and shape asymmetries show scale-specific associations with sex and cognition, but not handedness. While unihemispheric cortical shape shows significant heritability at coarse scales (~65 mm wavelength), shape asymmetries are determined primarily by subject-specific environmental effects. Thus, coarse-scale shape asymmetries are highly personalized, sexually dimorphic, linked to individual differences in cognition, and are primarily driven by stochastic environmental influences

Phylesystem: a git-based data store for community-curated phylogenetic estimates

Motivation: Phylogenetic estimates from published studies can be archived using general platforms like Dryad (Vision, 2010) or TreeBASE (Sanderson et al., 1994). Such services fulfill a crucial role in ensuring transparency and reproducibility in phylogenetic research. However, digital tree data files often require some editing (e.g. rerooting) to improve the accuracy and reusability of the phylogenetic statements. Furthermore, establishing the mapping between tip labels used in a tree and taxa in a single common taxonomy dramatically improves the ability of other researchers to reuse phylogenetic estimates. As the process of curating a published phylogenetic estimate is not error-free, retaining a full record of the provenance of edits to a tree is crucial for openness, allowing editors to receive credit for their work and making errors introduced during curation easier to correct. Results: Here, we report the development of software infrastructure to support the open curation of phylogenetic data by the community of biologists. The backend of the system provides an interface for the standard database operations of creating, reading, updating and deleting records by making commits to a git repository. The record of the history of edits to a tree is preserved by git’s version control features. Hosting this data store on GitHub (http://github.com/) provides open access to the data store using tools familiar to many developers. We have deployed a server running the ‘phylesystem-api’, which wraps the interactions with git and GitHub. The Open Tree of Life project has also developed and deployed a JavaScript application that uses the phylesystem-api and other web services to enable input and curation of published phylogenetic statements