Form Follows Function

Natural history. Teaching. Writing. All have form, all have function. But just as no architecture is risk-free, no architecture is neutral. In this personal essay, I explore the surprising connections that develop when university students engage with natural history as way of knowing the ground underfoot

Form Follows Function

Natural history. Teaching. Writing. All have form, all have function. But just as no architecture is risk-free, no architecture is neutral. In this personal essay, I explore the surprising connections that develop when university students engage with natural history as way of knowing the ground underfoot

An Invitation for Engagement: Assigning and Assessing Field Notes to Promote Deeper Levels of Observation

This paper explores current practices for teaching the discipline of keeping field notes within academic natural history courses. We investigate how journal projects can be structured to promote engagement with the natural world while emphasizing the importance of recording accurate and honest observations. Particular attention is paid herein to the assignment of field notes, and to the process of assessing the results of these assignments. Our discussion includes results from an informal survey of best practices among colleagues representing numerous natural history disciplines

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Multiorgan MRI findings after hospitalisation with COVID-19 in the UK (C-MORE): a prospective, multicentre, observational cohort study

Introduction: The multiorgan impact of moderate to severe coronavirus infections in the post-acute phase is still poorly understood. We aimed to evaluate the excess burden of multiorgan abnormalities after hospitalisation with COVID-19, evaluate their determinants, and explore associations with patient-related outcome measures. Methods: In a prospective, UK-wide, multicentre MRI follow-up study (C-MORE), adults (aged ≥18 years) discharged from hospital following COVID-19 who were included in Tier 2 of the Post-hospitalisation COVID-19 study (PHOSP-COVID) and contemporary controls with no evidence of previous COVID-19 (SARS-CoV-2 nucleocapsid antibody negative) underwent multiorgan MRI (lungs, heart, brain, liver, and kidneys) with quantitative and qualitative assessment of images and clinical adjudication when relevant. Individuals with end-stage renal failure or contraindications to MRI were excluded. Participants also underwent detailed recording of symptoms, and physiological and biochemical tests. The primary outcome was the excess burden of multiorgan abnormalities (two or more organs) relative to controls, with further adjustments for potential confounders. The C-MORE study is ongoing and is registered with ClinicalTrials.gov, NCT04510025. Findings: Of 2710 participants in Tier 2 of PHOSP-COVID, 531 were recruited across 13 UK-wide C-MORE sites. After exclusions, 259 C-MORE patients (mean age 57 years [SD 12]; 158 [61%] male and 101 [39%] female) who were discharged from hospital with PCR-confirmed or clinically diagnosed COVID-19 between March 1, 2020, and Nov 1, 2021, and 52 non-COVID-19 controls from the community (mean age 49 years [SD 14]; 30 [58%] male and 22 [42%] female) were included in the analysis. Patients were assessed at a median of 5·0 months (IQR 4·2–6·3) after hospital discharge. Compared with non-COVID-19 controls, patients were older, living with more obesity, and had more comorbidities. Multiorgan abnormalities on MRI were more frequent in patients than in controls (157 [61%] of 259 vs 14 [27%] of 52; p<0·0001) and independently associated with COVID-19 status (odds ratio [OR] 2·9 [95% CI 1·5–5·8]; padjusted=0·0023) after adjusting for relevant confounders. Compared with controls, patients were more likely to have MRI evidence of lung abnormalities (p=0·0001; parenchymal abnormalities), brain abnormalities (p<0·0001; more white matter hyperintensities and regional brain volume reduction), and kidney abnormalities (p=0·014; lower medullary T1 and loss of corticomedullary differentiation), whereas cardiac and liver MRI abnormalities were similar between patients and controls. Patients with multiorgan abnormalities were older (difference in mean age 7 years [95% CI 4–10]; mean age of 59·8 years [SD 11·7] with multiorgan abnormalities vs mean age of 52·8 years [11·9] without multiorgan abnormalities; p<0·0001), more likely to have three or more comorbidities (OR 2·47 [1·32–4·82]; padjusted=0·0059), and more likely to have a more severe acute infection (acute CRP >5mg/L, OR 3·55 [1·23–11·88]; padjusted=0·025) than those without multiorgan abnormalities. Presence of lung MRI abnormalities was associated with a two-fold higher risk of chest tightness, and multiorgan MRI abnormalities were associated with severe and very severe persistent physical and mental health impairment (PHOSP-COVID symptom clusters) after hospitalisation. Interpretation: After hospitalisation for COVID-19, people are at risk of multiorgan abnormalities in the medium term. Our findings emphasise the need for proactive multidisciplinary care pathways, with the potential for imaging to guide surveillance frequency and therapeutic stratification

Seeing the forest for the bryophytes : the effects of forest fragmentation on the bryophyte community in coastal temperate rainforests of British Columbia

In the coastal temperate rainforests of British Columbia, forest fragmentation from logging has created three different landscape elements that vary in habitat quality for bryophytes: unlogged old-growth remnant forest patches, edge habitats and younger-aged forest stands. Bryophytes are an important component of these forest ecosystems, yet little is known about the impact of habitat fragmentation on bryophyte patterns of richness and abundance. In this thesis I examined the effects of three separate components of fragmentation on patterns of bryophyte species richness, abundance and community composition: (1) effects of proximity to the edge within remaining forest patches, (2) effects of stand age in younger-aged forests adjacent to oldgrowth patches and (3) effects of remnant patch size. To achieve greater generality in my conclusions, I examine each of these issues through comparative analysis using different sampling scales and both taxonomic and ecological functional groupings of bryophytes. Edge effects: Edge habitats (sampled from 0-45 m from the patch edge) showed an increase in the richness of clearing-affiliated bryophytes without a loss of old-growth associated bryophytes. In contrast, interior habitats (sampled primarily >100 m from the forest edge) had a greater abundance of old-growth associated bryophyte functional groups (as measured by finescale sampling and percent cover estimates). Old-growth associated species exhibited no consistent changes with increasing distance up to 45 m from the edge, implying that the influence of the forest edge on these species extends at least this far into unlogged remnants. Effect of stand age: Bryophyte species richness peaked in regeneration stands (stand ages 5-30 years), declined to its lowest levels in immature stands (stand ages 25-49 years) and increased in old-growth stands (stand ages >300 years). In comparison with old-growth, both regenerating clear-cuts and immature forests had a greater richness of clearing affiliated bryophytes. There was no loss of old-growth associated species in regeneration plots; however, old-growth associated species in immature plots showed significant declines in richness which suggests that immature forests represent a propagation bottleneck for bryophytes in harvested landscapes. The pattern of bryophyte species occurrence in younger-aged stands supports an initial floristics model of succession. Effects of patch size: The richness and abundance of dispersal-limited and microclimate sensistive groups showed significant declines as patch size decreased. In contrast, groups expected to increase in richness or abundance as patch size decreased (colonist and open canopy species) showed little association with patch size indicating that center of small remnant patches had no greater richness of clearing affiliated species than large remnant patches. The absence of clearing affiliated species in the center of small remnant patches may well reflect the lack of available microhabitats. The results of this thesis imply that the bryophyte community in the study area has been impacted by human disturbance caused by large-scale forest fragmentation. The bryophyte community in disturbed habitats (i.e., edge and younger-aged stands) showed an increase in the number of clearing affiliated species and a decreased abundance of old-growth associated species. This has important management implications. Although variable retention will introduce greater structural heterogeneity into regenerating forests, it will do little to alleviate the effects of fragmentation on bryophytes. The maintenance of bryophyte diversity in coastal temperate rainforests will depend not only on adequate old-growth reserves but also on longer forestry rotations that will help mitigate the adverse environmental effects associated with introduced edges, younger-aged forests and decreasing patch size.Science, Faculty ofBotany, Department ofGraduat

SESSION 1.2: Mapping Moss: Crossidium seriatum

On a Sunday morning in May, I’m on my hands and knees, loaded with collecting gear, searching for an endangered moss, Crossidium seriatum, that can’t be seen—or at least not with the naked eye. Instead, perched on the silt cliffs above Okanagan Lake in southern BC, I scan for tiny microsites where it might live—what biologists call its “potential habitat.” In ecology, mapping other species dates back to Alexander von Humboldt, but as the sun looms higher I worry about its implicit limitations. All plants—but especially tiny mosses and liverworts—test our imagination. What does it mean to live anchored in place by tiny threads of cellulose? What’s touch for organisms that live with no epidermis? How does time beat when you curl dormant for decades, before the gift of water plumps you awake again? By the time I’m back at my car, I understand that if describing the habitats of others is a mountain to be climbed, the real goal lies not in the summit but the maps we make enroute. For in the Anthropocene, it is in the moment of uncertainty, of figuring—here, not there; on this slope, not that one—that we come to know the world, to taste its blood and silt. This creative reading will use my experience hunting for an endangered moss to argue that, today, our greatest challenge lies less in what we can measure and more in how we allow ourselves to be shaped by the more-than-human world