text:
Huw J. Griffiths
British Antarctic Survey (BAS), United Kingdom
Ulrich V. Bathmann
Leibniz Institute for Baltic Sea Research (LG), Germany
Thomas Saucede
Université Bourgogne Franche-Comté, France
Front. Ecol. Evol., 06 July 2018
Sec. Biogeography and Macroecology
Volume 6 - 2018 | https://doi.org/10.3389/fevo.2018.00094
Mapping Antarctic Suspension Feeder Abundances and Seafloor Food-Availability, and Modeling Their Change After a Major Glacier Calving
Jan Jansen1,2*, Nicole A. Hill1, Piers K. Dunstan3, Eva A. Cougnon1,4, Benjamin K. Galton-Fenzi2,4 and Craig R. Johnson1†
1Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, Australia
2Australian Antarctic Division, Kingston, TAS, Australia
3CSIRO Oceans and Atmosphere, Hobart, TAS, Australia
4Antarctic Climate & Ecosystem Cooperative Research Centre, University of Tasmania, Hobart, TAS, Australia
Seafloor communities are a critical part of the unique and diverse Antarctic marine life. Processes at the ocean-surface can strongly influence the diversity and abundance of these communities, even when they live at hundreds of meters water depth. However, even though we understand the importance of this link, there are so far no quantitative spatial predictions on how seafloor communities will respond to changing conditions at the ocean surface. Here, we map patterns in abundance of important habitat-forming suspension feeders on the seafloor in East Antarctica, and predict how these patterns change after a major disturbance in the icescape, caused by the calving of the Mertz Glacier Tongue. We use a purpose-built ocean model for the time-period before and after the calving of the Mertz-Glacier Tongue in 2010, data from satellites and a validated food-availability model to estimate changes in horizontal flux of food since the glacier calving. We then predict the post-calving distribution of suspension feeder abundances using the established relationships with the environmental variables, and changes in horizontal flux of food. Our resulting maps indicate strong increases in suspension feeder abundances close to the glacier calving site, fueled by increased food supply, while the remainder of the region maintains similar suspension feeder abundances despite a slight decrease in total food supply. The oceanographic setting of the entire region changes, with a shorter ice-free season, altered seafloor currents and changes in food-availability. Our study provides important insight into the flow-on effects of a changing icescape on seafloor habitat and fauna in polar environments. Understanding these connections is important in the context of current and future effects of climate change, and the mapped predictions of the seafloor fauna as presented for the study region can be used as a decision-tool for planning potential marine protected areas, and for focusing future sampling and monitoring initiatives.
Primary productivity is at the base of most marine ecosystems. In Antarctica, primary production is highly seasonal and intricately tied to the location, timing and duration of sea-ice and ice-free areas such as polynyas (Arrigo and Van Dijken, 2003). The collapse of large ice-shelves or calving of massive icebergs, and the retreat of sea-ice that is mainly observed around the Western Antarctic Peninsula in recent years (Parkinson and Cavalieri, 2012), can dramatically alter the oceanographic setting with down-stream effects on the pattern of primary production hotspots and on Southern Ocean ecosystems (Arrigo et al., 2002; Gutt et al., 2011). Resulting changes in the location, timing and intensity of phytoplankton blooms (Cape et al., 2014) can influence the distribution of krill and predator aggregations (Gutt et al., 2011), the abundances of benthic suspension feeders (Fillinger et al., 2013; Gutt et al., 2013) and can affect carbon storage (Peck et al., 2010).
For most seafloor communities living below the photic zone (~200 m), surface-derived primary production represents their main food source (Dayton and Oliver, 1977; Duineveld et al., 2004; Ruhl et al., 2014), and is therefore critical for their survival. Seafloor communities represent the richest component of Antarctic biodiversity (Griffiths, 2010), are highly endemic (Griffiths et al., 2009), and play an important role in the marine ecosystem (Thurber et al., 2014). However, despite evidence that a changing environment influences the distribution of these communities (Gutt et al., 2011, 2013; Fillinger et al., 2013; Griffiths et al., 2017), no study has so far quantified and mapped how their distribution might change due to a changing icescape at the ocean surface. One of the reasons for the lack of quantitative studies is that although surface-derived food is one of the main drivers, it is only recently that the nature and strength of this relationship has been quantified on the Antarctic shelf using a so-called Food-Availability-Model (FAM) (Jansen et al., 2018). Combining surface-productivity and ocean currents with particle-tracking, FAMs estimate the distribution of surface-derived food at the seafloor, and evaluate the estimates against data from sediment cores. Jansen et al. (2018) demonstrated a strong link between modeled flux of suspended food along the seafloor and abundances of sessile suspension feeders, providing a framework that allows to estimate the distribution of key elements of the seafloor community and to predict how they may change with changing ocean productivity and currents.
One Antarctic region that has recently undergone drastic environmental changes is the George V shelf in East Antarctica. The calving of the Mertz Glacier Tongue (MGT) in 2010 (Young et al., 2010) has resulted in profound environmental changes in the region, such as increased sea-ice concentrations (Campagne et al., 2015), and changes in ocean currents along the shelf as suggested by observations (Aoki et al., 2017) and modeling studies (Cougnon et al., 2017; Kusahara et al., 2017). These environmental changes have consequences for the dynamics and distribution of primary production (Shadwick et al., 2013), the abundance of top-predators (Wilson et al., 2016), and has been observed to influence the community structure of shallow-water benthos (Clark et al., 2015). However, the effect of the MGT-calving on the seafloor across the region has so far neither been assessed nor observed, and so its impact on benthic communities across the continental shelf is still unknown. Obtaining this knowledge, however, is crucial for meaningful assessment of the comprehensiveness, effectiveness and representativeness of the proposed marine protected areas in this region.
Here, we (i) quantify differences in the environmental setting on the George V shelf that will affect the supply of food to the benthos. In our modeling, we apply a recently developed FAM (Jansen et al., 2018) on two 5-year climatologies of remotely sensed surface chlorophyll-a for the period before and after the glacier calving, and use ocean current velocities from a purpose-built oceanographic model (Cougnon et al., 2017) (more details can be found in the section Materials and Methods). We then (ii) map the distribution of benthic suspension feeder abundances before the glacier calving, using faunal abundances derived from underwater camera images and environmental predictor variables. Using the pre-calving statistical model for the suspension feeder abundances and the change in environmental conditions after the glacier calving, we then (iii) predict changes in suspension feeder abundances across the region, revealing the strong impact of the changing icescape on the seafloor ecosystem (Figure 1 for general results, and Figure 2 for an overview of the study-region).
Figure 1. Graphic summarizing observed and predicted changes in environmental conditions (sea-ice, surface-chl-a, ocean current speeds, food-export) and seafloor fauna due to the calving of the Mertz Glacier Tongue (MGT) in 2010. The graphics shows a cross-section of the George V continental shelf ~80 km off the coast, looking South toward the Antarctic continent. The top graphic shows pre-calving environmental conditions and displays abundances of suspension feeders as observed from towed camera images. The bottom graphic shows observed changes in sea-ice, surface-chl-a and the position of the grounded iceberg B09B, as well as modeled changes in ocean current speeds, food-availability and suspension feeder abundances. Simplified food-availability-model (FAM) results are indicated for (1) Mertz Bank, (2) Adélie Sill, (3) Adélie Bank, and (4) Adélie Basin. Additional indicators are included in the bottom graphic to highlight important changes.
Figure 2. Bathymetry (Beaman et al., 2011) with selected contour lines (in gray), coastline and sample locations in the study area. Major glacial features such as the Iceberg B09B in the center (location in 2016) and the Mertz Glacier Tongue (MGT) on the Eastern margin of the map are included. The dashed line shows the extent of the MGT prior to the calving in 2010. The inset map shows the location of the study area as highlighted by the red box.
Changes in Environmental Conditions
Our results reveal that several aspects of the observed and the modeled marine environment have changed since the calving of the MGT (Figure 3). Average sea-ice concentrations increased in the study region by 50–80%, particularly in the spring season, except over the Mertz Bank and where the calved MGT was located (Supplementary Figure 1). Near the Mertz Bank, average surface-chlorophyll-a (chl-a) concentrations increase by a factor of two or more (Figure 3C). The area of highest average surface-chl-a concentration also shows an eastward extension into areas previously covered by sea-ice. West of the Mertz Bank, the George V Basin and the Adélie Bank show decreasing values for surface-chl-a (Figure 3C). In this area, the breakup of the sea-ice post-calving occurs much later in the year (Supplementary Figure 1), shortening the time-period where surface phytoplankton is observed by satellites from around 4.5 to 3 months. At the South-East tip of the Adélie Bank, north of the grounded giant iceberg B09B, the outline of a newly formed polynya (Tamura et al., 2012; Fogwill et al., 2016) can be observed, marked by lower spring-time sea-ice concentrations and higher surface-chl-a relative to the surrounding area. Modeled seafloor current speeds (Supplementary Figure 2) increase by about 5 cm/s on the shallower sections of the shelf down to around 500 m depth, and decrease by almost 50% at the shelf break and slope, as well as in the area previously occupied by the MGT. Changing bottom tidal current speeds account for almost all the increase in current speed on the South-Western flanks of the Adélie and Mertz Bank, in the deep George V Basin and below the iceberg B09B at the North-Western edge of Commonwealth Bay (Figure 3F).
Figure 3. Comparison of mean values for selected biologically relevant environmental variables before and after the calving of the Mertz Glacier Tongue (MGT) in 2010. The first row shows environmental conditions in the 5 years leading up to the calving, the second row in the 5 years after, and the bottom row shows the magnitude of the change. Panels (A–C) are satellite-derived (MODIS-A) estimates of surface-chl-a corrected for Southern Ocean application (Johnson et al., 2013). The missing data at the previous location of the MGT stems from a landmask-artifact in the NASA-data. Panels (D–F) represent the speed of fluctuating currents (tidal currents) at the bottom layer of the regional ocean model used for this study (Cougnon et al., 2017). Panels (G–I) show the number of particles moving horizontally along the seafloor before their permanent sedimentation (on log-scale). In all maps the strongest changes can be observed in the Eastern section of the region, close to the location of the MGT. In the post-calving maps, the outline of the newly grounded iceberg B09B is added for reference while dotted lines indicate the original position of the glacier tongue before it broke off.
The FAM tracks and quantifies three components of surface-derived food particles: the sinking component captures the advection of phytodetrital matter by currents as it sinks through the water column until it reaches the seafloor; the flux component represents the horizontal flux of food particles along the seafloor before sedimentation; the settling component represents the final location of advected particles after taking into account the redistribution by seafloor currents. Sinking and settling particles follow similar patterns to the other environmental variables mentioned before, with an eastward shift for the peak number of sinking and settling particles. The model-output shows an absence of sedimentation on large parts of the Mertz Bank (closest to the former tip of the MGT) due to increased current speeds (Supplementary Figure 3). Horizontal food flux along the seafloor, which is dependent mainly on the interaction between the distribution of surface productivity and seafloor current speeds, increases 20- to 50-fold on wide sections of the Mertz Bank (Figure 3I). In contrast, changes are more patchy on the Adélie Bank, where increases in flux are mostly restricted to the inner section of the bank and the shelf break, while the edges of the bank experience decrease in flux. Further, most of the deeper sections of the shelf experience lower flux than before the calving.
Predicted Changes in Suspension Feeder Abundances
Mapped predictions of suspension feeder (SF) cover are based on the statistical relationship between pre-calving cover estimated from still-images, and the environmental covariates depth and log (horizontal flux) (Supplementary Table 1, deviance-explained = 44%), which are selected as the best predictor variables by the stepwise regression process (Supplementary Table 2). There is a good fit between the predicted values from the statistical model and the observed values at the sampling sites, with a slight underestimation of high cover values (Figure 4). SF-cover before the calving is high on most of the shallower sections of the shelf (<500 m depth) (Figure 5A), with values estimated between 60 and 100% cover. The two shallow banks in the study area, the Mertz Bank closest to the MGT in the East and Adélie Bank in the West, show relatively similar patterns of SF-cover, with average values of around 60% except for on the edges of the banks, where cover of suspension feeders may reach up to 100%. In contrast, post-calving predictions show a clear difference between the two banks (Figure 5B) in that SF-cover is predicted to increase by 20–40% (Figure 5C) on large parts of the Mertz Bank, while the Adélie Bank and other areas retain similar SF-cover as previously. The strong predicted increase in SF-abundance on the Mertz Bank in the east stems directly from the 20- to 50-fold increase in predicted particle flux that is a direct result of both increased surface production and stronger tidal currents.
Figure 4. Diagnostic plot showing the fit between predicted values from the pre-calving statistical model and the observed %-cover estimates from benthic still images at the sample sites. The red dotted line indicates a perfect fit.
Figure 5. Spatial predictions of percentage cover of suspension feeders on the seafloor before and after the glacier calving. The cover of each species is estimated separately, thus overlapping cover can result in total coverage exceeding 100%. Panels (A–C) show the predicted mean, and (D–F) the standard deviation of the predictions. Note that changes are most pronounced on the Mertz bank close to where the glacier calving happened. The high predicted cover pre-calving under the glacier tip is driven by high current speeds, but samples have so far not been taken in this location.
We predict that the calving of massive icebergs will have far-reaching effects on benthic communities mediated through the mechanism of pelagic-benthic coupling, and that changes occur even hundreds of kilometers away from the glacier tongue. While previous studies have shown that calving events can have localized negative impacts on the benthos through iceberg scouring (Gutt et al., 1996), here we predict that the combination of changes in local oceanography and surface production influences patterns of seafloor food-availability at much larger scales. Particularly strong changes are predicted in the horizontal flux of food particles post-calving, which is important in determining the distribution of suspension feeders (Jansen et al., 2018). Similar to other Antarctic regions that have recently become ice-free (e.g., Fillinger et al., 2013), our results suggest environmental conditions on the Mertz Bank now are much more favorable for suspension feeders (SFs) than before the calving. Our modeling suggests that there will be a strong, but locally confined increase in SF-abundance on the Mertz Bank of up to 40%. Further away, near the Adélie Bank, increases in bottom current speeds seem to compensate for the overall decrease in food supply, resulting in a prediction of only marginal changes in SF-abundance. The distribution of surface production around the newly formed polynya on the leeward side of the grounded iceberg B09B (Fogwill et al., 2016) seems to slightly influence SF-abundances with relatively stable cover predicted beneath the polynya in contrast to decreasing cover in the ice-covered area directly north of the iceberg B09B. Close to and below the position of the tip of the MGT before it broke away, where Beaman and Harris (2005) have previously found a high number of macrobenthic species, including many sponges and bryozoans, our model predicts a substantial decrease in SF-abundance, due to a decrease in floor current speed affecting the horizontal food-flux. However, we caution that little confidence should be placed in this result; the environmental conditions in this area might be unique due to the glacier tongue and we lack biological samples for this area. Further, we also lack confidence in the food-availability-data because of missing data in the remotely sensed surface chl-a dataset (see section Surface Productivity and Sea-Ice). Unfortunately, the shallower sections of the Mertz Bank and the western part of the Adélie Bank, which we show here are particularly interesting areas, have not been physically sampled as part of the survey (see Figure 2). However, because the survey was designed to cover a wide range of depths and geomorphologies (Hosie et al., 2011), because of the high confidence in the predicted values from the statistical model (Figure 4), and because of the similarity in environmental conditions between the shallow banks prior to the glacier calving, we are confident the relationship between environmental variables and distributional patterns of suspension feeder abundances is consistent across the region.
Regions around ice-shelves and glacier tongues provide valuable insight into the dynamic environment of the Antarctic shelf. When an ice-shelf calves a massive iceberg or collapses entirely, the marine environment, to which species might have acclimated to for many years, can transition quickly between a food-poor and a food-rich system (Gutt et al., 2011). The MGT is thought to calve massive icebergs in a ~70 year cycle (Campagne et al., 2015; Giles, 2017), meaning that there are likely also differences in the long-term stability of environmental conditions, and in the frequency of iceberg-scour between the Mertz Bank near the MGT and the Adélie Bank in the West of the George V shelf. Studies on the West Antarctic Peninsula suggest that at least some components of Antarctic benthic communities on the shelf, such as glass sponges and pioneering species, can increase rapidly in areas that are newly ice-free, fueled by higher export of surface production (Gutt et al., 2011; Fillinger et al., 2013). Conversely, slower-growing deep-sea corals and bryozoans may respond more slowly to changing environmental conditions. Whether any species or communities have adapted to these long-term cyclic events in the George V region is unknown, because a comparative study between the Mertz and Adélie Bank has so far not been conducted due to a lack of biological data. Further, it is currently also not possible to validate our predictions with independent data, because there have been no comprehensive observations of the deep seafloor since the glacier calving. However, if the benthic community response in East Antarctica is similar to that of the West Antarctic Peninsula, the community composition on the Mertz Bank can be expected to change rapidly in the more favorable environment after the glacier calving, or will have undergone changes already, given that 8 years have passed since the calving event. The postulated more favorable environment on the Mertz Bank might continue to persist for some time until the MGT regrows the ice tongue. Further, oceanographic models from after the calving indicate an increase in basal melting of the MGT due to warmer, faster moving waters from the east after grounded tabular iceberg relocation and the MGT calving (Cougnon et al., 2017) which may slow the regrowth of the MGT.
Food-availability is a key factor influencing species distributions. Here, we map predicted changes in relevant seafloor-food-availability caused by the calving of a major glacier tongue, and predict change in distributional patterns of benthic suspension feeders, a key element of Antarctic biodiversity. The study area on the George V shelf lies within the recently proposed East Antarctic MPA (AAD, 2017), and we suggest the Mertz Bank and Adélie Bank should be considered as distinct areas for future sampling of the benthic community. The predicted distribution of suspension feeders after the glacier-calving provides an up to date picture of a key part of seafloor biodiversity, from which the representativeness of the proposed MPA can be assessed. Until regular monitoring programs are established, modeling studies such as ours give important information and context for future monitoring and assessment. Our study provides insight into temporal change and into the mechanisms that drive changes at the seafloor. This is important for a holistic understanding of the Antarctic marine ecosystem, and helps us to understand how climate change can affect the seafloor in the future.
The study area is located on the relatively deep (500–700 m) East Antarctic continental shelf and slope between latitudes 139 and 147°E (Figure 2). The depth of the shelf ranges between 200 m on the banks to 1,300 m in the basins. The most prominent feature in this region is the Mertz Glacier Tongue (MGT) in the east which has strong influences on both oceanography (Barber and Massom, 2007) and biology (Arrigo and Van Dijken, 2003; Sambrotto et al., 2003; Beans et al., 2008; Jansen et al., 2018). Strong katabatic winds in the region drive sea-ice production (Massom et al., 2001), convection of dense water that contributes to overturning circulation (e.g., Williams et al., 2008), and importantly also form ice-free surface areas on the westward sides of the MGT and the grounded icebergs. These permanent ice-free areas support a long growing season for phytoplankton resulting in high phytoplankton productivity (Arrigo and Van Dijken, 2003; Sambrotto et al., 2003; Beans et al., 2008). Abundant and diverse benthic suspension feeder communities have been found primarily on the shallower section of the shelf between 200 and 600 m (Post et al., 2011). Further, tidal currents on the seafloor redistribute surface derived production, with flux rates of organic particles directly related to the abundance and species richness of the benthic community (Jansen et al., 2018).
The MGT calves off massive icebergs in an estimated 70-year cycle (Campagne et al., 2015), the last event happening in 2010 after a collision between the massive iceberg B09B and the MGT. Since the calving of the MGT, the Mertz Polynya has decreased significantly in size (Tamura et al., 2016), changing ocean circulation (Aoki et al., 2017; Cougnon et al., 2017; Kusahara et al., 2017) and increasing sea-ice concentrations (Tamura et al., 2012). The iceberg B09B grounded on the South-Eastern flank of the Adélie Bank shortly after the collision, and a new polynya has formed on its leeward side (Fogwill et al., 2016). For more details on the study area and the oceanography we refer to numerous papers on the region (e.g. Beaman and Harris, 2005; Cougnon et al., 2013, 2017; Shadwick et al., 2013; Kusahara et al., 2017; Jansen et al., 2018).
Environmental Data and Numerical Modeling
Ocean Model and Bathymetry
Ocean current speeds and directions before and after the glacier calving are derived from a tide-simulating oceanographic model for the George V shelf developed by Cougnon et al. (2017) based on the Regional Ocean Modeling System (ROMS) (Shchepetkin and McWilliams, 2005). The model setup used here is similar to that described by Cougnon et al. (2013), using the same horizontal and vertical grid. The horizontal grid has a resolution of 2.16 km near the southern boundary and 2.88 km near the northern boundary. The vertical grid is arranged to give higher resolution at the top and bottom of the water column. The model domain encompassed the area from the Antarctic coastline to the deep ocean at 62.72°S, and from 135.77°E to the west of the French base, Dumont D'Urville, to 158.08°E to the east of George V Land (Cougnon et al., 2013).
The model includes ocean-ice shelf thermodynamics described by three equations following Holland and Jenkins (1999), frazil ice thermodynamics following Galton-Fenzi et al. (2012), as used in previous studies (e.g., Cougnon et al., 2013; Gwyther et al., 2014) and a simplified analytic tidal forcing at the lateral boundaries (Cougnon et al., 2017 for details). The bathymetry in both simulations is based on RTopo-1 (Timmermann et al., 2010), and modified to include local high-resolution bathymetry (Beaman et al., 2011) as described in Mayet et al. (2013). Ice draft of the MGT and B09B, along with the underlying bathymetry, is based on an early version of the most up-to-date product by Mayet et al. (2013).
The total run time of the model for each simulation(before and after calving) is 33 years, using an annually repeating loop of the same lateral forcing for both simulations and an annually repeating loop of the surface forcing corresponding to each icescape. This 33 year run includes a spin-up phase of 30 years to reach equilibrium. The spin-up phase of the model has no relevance for the seafloor communities, but is a procedure to ensure the ocean model reaches equilibrium (so that the ocean heat content and the ocean currents are relatively stable under the applied forcing, allowing to analyze the output). The iceberg B09B is at equilibrium in the model. In the model, icebergs and ice-shelves are steady and do not move or change shape. However, they are thermodynamically active, which means that heat and salt fluxes due to ocean-driven melting/refreezing are taken in consideration.
Surface Productivity and Sea-Ice
We estimated spatial patterns of surface productivity from measures of ocean color derived from NASA's Moderate Resolution Imaging Spectroradiometer (MODIS-Aqua) (NASA Goddard Space Flight Center, Ocean Ecology Laboratory, Ocean Biology Processing Group, 2014). We used Level-3 binned daily remote sensing reflectance, provided at a resolution of 4 km equal-area bins, and corrected the values for Southern Ocean application using the algorithm in Johnson et al. (2013). Daily measures of chlorophyll-a concentrations were averaged for southern hemisphere spring and summer in each year for a 5-year period before (2005–2009) and after (2011–2016) the calving of the MGT. There are no data available from NASA for the area previously covered by the MGT, presumably due to a landmark artifact.
We estimated seasonal patterns of sea-ice concentrations from satellite-measures of Nimbus-7 SMMR and DMSP SSM/I-SSMIS Passive Microwave Data (Cavalieri et al., 1996, updated yearly). Daily measures of sea-ice concentrations were averaged for southern hemisphere spring and summer in each year for a 5-year period both before (2005–2009) and after (2011–2016) the calving of the MGT.
Food Availability Model (FAM)
We mapped the availability of surface-derived food at the seafloor before and after the calving event using a validated food-availability model (FAM) as described in Jansen et al. (2018). The FAM uses a distribution of particles that is based on multi-year averages of satellite derived chlorophyll-a (section Surface Productivity and Sea-Ice), and tracks individual particles from the surface to the seafloor while accounting for their sinking speed, the speed and direction of currents (section Ocean Model and Bathymetry) in 3D, and the sedimentation-rate of particles on the seafloor based on particle sizes (Jansen et al., 2018). The model generates three maps of food availability, namely a sinking-map (showing the number of particles arriving/temporarily settling on the seafloor), a map of horizontal flux (showing where particles move along the seafloor before their sedimentation), and a settling-map (showing where particles permanently settle on the seafloor). While the objectives in our study differ strongly from the Jansen et al. (2018)-study (Jansen et al. described & validated a new method, while we apply the method to map the distribution of suspension feeders and their changes through time), the only difference in the food-availability model is using a different ocean model and a different surface-chl-a climatology. Current speeds on the shelf seem to be slightly lower in the pre-calving part of the model developed by Cougnon et al. (2017) compared to that of Cougnon et al. (2013), but are within the seasonal variation of the Cougnon et al. (2013) model.
For the particle tracking, we used four consecutive time-slices of the ocean-model for the summer season before and after the calving respectively. We used the four consecutive time slices with the strongest differences in current direction and speed, to ensure that each time slice adequately captures one full tidal movement (a 6 h time-slice with 3 h of incoming tide and 3 h of outgoing tide would show very little current speed). The maximum number of seed particles was ~4.5 million for the pre-calving model and the particles were tracked in 30 min time-steps. At each time-step the location of each particle with respect to the ROMS-cells was calculated, and water current speed and direction at that location updates for advection of the particles during the next time-step. Particles were stopped when they either moved out of the study area or matched the stopping criteria for the respective model, as described in Jansen et al. (2018). The resulting particle distributions from each model-run were back-transformed into a regular grid with a resolution of 1/15 degrees.
We use the FAM-parameters previously defined for this region (Jansen et al., 2018), namely a sinking speed of 300 m/day, a particle radius of 0.24 mm, the density of seawater at 1,030 kg/m3, the density of settling particles at 1,100 kg/m3 and an aspect ratio of 1 representing idealized spherical particles in our modeling.
For the particle tracking, we used R Version 3.3.1 (R Core Team, 2016) with the packages "ptrackr" (Jansen and Sumner, 2017), "raster" (Hijmans, 2015), "ncdf4" (Pierce, 2014), "nabor" (Elseberg et al., 2012), "geostatspat" (Brown, 2015) and "spatstat" (Baddeley and Turner, 2005).
Biological Data Collection
We use the same dataset of benthic images as used by Jansen et al. (2018), which is available through the Australian Antarctic Division Data Centre (Jansen et al., 2017). It comprises detailed underwater still images collected during the Collaborative East Antarctic Marine Census (CEAMARC) for the Census of Antarctic Marine Life in December 2007 to February 2008 (Hosie et al., 2011). Transects during the CEAMARC were designed to cover a wide range of depths and geomorphologies in the region and therefore can be considered representative of the area modeled. A forward facing 8 megapixel Canon EOS 20D SLR with two speedlight strobes was mounted on a beam trawl and pictures were taken every 10 s. 32 sites were sampled with transect length mostly between 4 and 6 km, with exceptions ranging between 3 and 16 km. The trawl was controlled using a deck winch. Benthic fauna were identified to the lowest taxonomic resolution possible and, where species identification was not possible, specimens with similar overall appearance were grouped into morphotypes. The bottom third of each image was scored. For each image, the abundance of each species/morphotype was estimated within 5% bins from 0 to 50% and 10% bins from 50 to 100%. Using taxonomy and body-type along with expert knowledge, the abundance of the suspension feeding fauna in each picture was calculated.
We use the image data and the maps of environmental data for 2005–2009 to generate a pre-calving statistical model, aiming at producing the statistical model that best explains the abundance of suspension feeders (SF). Each transect was split at the boundaries of the environmental grid cells to ensure all pictures lay within the same value for the environmental covariates. We multiplied %-cover estimates in each image by 100 and rounded up to generate integer values that better suit a statistical analysis using a multiple linear regression with a negative binomial GLM (assuming the values would then represent the number of pixels covered by the fauna). We backwards selected variables from a full model using AIC. The full model contained the important environmental variables identified by Jansen et al. (2018), namely depth, tidal-current speed and the horizontal flux of particles along the seafloor. The final model contained only depth and log(horizontal-flux) as predictor variables. We found that using a negative binomial generalized linear model (compared to a linear model in the previous study) did not affect the selection of model terms. Therefore, the change in selected model terms is likely to come from the difference in the ocean model or the surface productivity. The pre-calving statistical model showed a good fit between the predicted and the observed values at the sample sites, with possibly a slight underestimation of suspension feeders at high abundances (Figure 5). Due to the limited amount of biological data available, we were not able to use separate datasets for training and testing the statistical model.
We then used the pre-calving statistical model to predict the spatial distribution of SF-cover in both the pre-calving and the post-calving environment. The difference between the resulting maps was used to make inferences about areas with expected increases and decreases in the abundance of suspension feeders. Further, we bootstrapped the parameters of the pre-calving statistical model to obtain estimates for the standard-deviation of the predictions.
For the statistical analysis, we used R Version 3.3.1 (R Core Team, 2016) and the packages "raster" (Hijmans, 2015), "MASS" (Venables and Ripley, 2002), "maptools," and "modEvA."
Estimates of suspension feeder abundances from benthic images are available through the Australian Antarctic Division Data Centre (Jansen et al., 2017). Raster files containing mapped predictions of food-availability and suspension feeder abundances presented in this study, from before and after the glacier calving are available through the Australian Antarctic Data Centre (Jansen, 2018).
JJ, NH, CJ, PD, and EC conceived and designed the study. JJ, NH, CJ, and PD analyzed the data. EC and BG-F did the numerical modeling. JJ prepared all figures and wrote the paper with contributions from all authors.
We thank Marc Eléaume for useful discussions and for making the original biological data available to us, and the reviewers of the paper for their comments. Biological samples were collected during the CEAMARC program as part of the IPY #53 Census of Antarctic Marine Life program. Coastline and glacial features for the figures are taken from the Antarctic Digital Database version 5. JJ is supported by a Tasmanian Graduate Research Scholarship and a QAS Top-Up scholarship. This work was completed as part of Australian Antarctic Science project 4124.
The Supplementary Material for this article can be found online at: https://www.frontiersin.org/articles/10.3389/fevo.2018.00094/full#supplementary-material
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Keywords: food availability, Antarctic marine biodiversity, pelagic-benthic-coupling, sea-ice, climate change, surface productivity, Mertz Glacier Tongue
Citation: Jansen J, Hill NA, Dunstan PK, Cougnon EA, Galton-Fenzi BK and Johnson CR (2018) Mapping Antarctic Suspension Feeder Abundances and Seafloor Food-Availability, and Modeling Their Change After a Major Glacier Calving. Front. Ecol. Evol. 6:94. doi: 10.3389/fevo.2018.00094
Received: 22 February 2018; Accepted: 19 June 2018;
Huw James Griffiths, British Antarctic Survey (BAS), United Kingdom
Ulrich Volkmar Bathmann, Leibniz Institute for Baltic Sea Research (LG), Germany
Thomas Saucede, Université Bourgogne Franche-Comté, France
Copyright © 2018 Jansen, Hill, Dunstan, Cougnon, Galton-Fenzi and Johnson. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
*Correspondence: Jan Jansen, jan.jansen@utas.edu.au
†Craig R. Johnson orcid.org/0000-0002-9511-905X
Antarctic Biology: Scale Matters


text:
Q: Improving frequency time normalization/hilbert transfer runtimes So this is a bit of a nitty gritty question...
I have a time-series signal that has a non-uniform response spectrum that I need to whiten. I do this whitening using a frequency time normalization method, where I incrementally filter my signal between two frequency endpoints, using a constant narrow frequency band (~1/4 the lowest frequency end-member). I then find the envelope that characterizes each one of these narrow bands, and normalize that frequency component. I then rebuild my signal using these normalized signals... all done in python (sorry, has to be a python solution)...
Here is the raw data:

and here is its spectrum:

and here is the spectrum of the whitened data:

The problem is, that I have to do this for maybe ~500,000 signals like this, and it takes a while (~a minute each)... With almost the entirety of the time being spend doing the actual (multiple) Hilbert transforms
I have it running on a small cluster already. I don't want to parallelize the loop the Hilbert is in.
I'm looking for alternative envelope routines/functions (non Hilbert), or alternative ways to calculate the entire narrowband response function without doing a loop.
The other option is to make the frequency bands adaptive to the center frequency over which its filtering, so they get progressively larger as we march through the routines; which would just decrease the number of times I have to go through the loop.
Any and all suggestions welcome!!!
example code/dataset:
https://github.com/ashtonflinders/FTN_Example

A: Here is a faster method to calculate the enveloop by local max:
def calc_envelope(x, ind):
    x_abs = np.abs(x)
    loc = np.where(np.diff(np.sign(np.diff(x_abs))) < 0)[0] + 1
    peak = x_abs[loc]
    envelope = np.interp(ind, loc, peak)
    return envelope

Here is an example output:

It's about 6x faster than hilbert. To speedup even more, you can write a cython function that find next local max point and does normalization up to the local max point iteratively.

redpajama_set_name: RedPajamaStackExchange


text:
Hanging Flags
Keywords: inglefield clips | grommets | rope and toggle |
There are three means to attach a flag to the rope to hoist it up the pole.
Rope & toggle (with variations on the hardware used)
Cloth tabs on the flag to tie to the rope or pole.
From my observation it seems that rope & toggle is the most used worldwide. I have only seen grommets on American-made flags, or for flags used in America. Are these observations correct? Do other countries use grommets as the normal method of attachment?
Nathan Bliss, 9 October 1996
I collect flags made in the country they represent. Rope and toggle or sleeved/tabbed headings are found on the following flags: Australia, Belgium, Canada, Peoples Republic of China, Costa Rica, Czechoslovakia, East Germany, Finland, France, Germany, India, Lithuania, Malaysia, Netherlands, New Zealand, Nigeria, Norway, Poland, Russia, Singapore, Sierra Leone, Solomon Is (these last two are probably UK made), South Africa, South Vietnam, Sri Lanka, Sweden, Switzerland (metal clips attached to each end of rope), Turkey, Turkmenistan, USSR, Zimbabwe.
Grommets are found on the following: USA, Israel, Jordan (and I suspect the grommets on the latter two may have been added by the person who owned both of them before me, though I cannot confirm that.) It looks like grommets are definitely a US idea. I'm not sure why. With this system, the halyard is a closed loop and the snaps are tied at the correct interval(s). This means you cannot easily use flags of different sizes without rearranging the clips. With the systems using Inglefield clips or beckets and toggle, the halyard is cut at the point where the flag(s) is (are) attached. Any size flag is easy to accommodate. Perhaps we are afraid of letting go of the halyard and having the loose end run up to the truck! That is impossible with a closed loop halyard.
US Government specification flags for the Navy, among others, call for a roped heading with brass snaps at either end.
Nick Artimovich, 9 October 1996
New Zealand flag makers offer a choice of either rope and toggle or ovoid plastic split rings which engage with similar split rings on the halyard. If these split rings are grommets, then we use them (though less commonly than the toggle method).
Stuart Park, 10 October 1996
Only US flags have grommets (usually brass flat rings which are smashed together, one on top of the hoist canvas, the other directly underneath on the other side of the canvas). Israel and Jordan have also been mentioned. A friend of mine brought me back 3 Chinese flags from various points he visited in China. One flag is about 3x4 ft. It has a canvas heading and brass-looking grommets.
I have long wonder why the US does it differently. It really doesn't look as good, because no matter what color on the flag is next to the hoist, we always have this natural canvas heading as the last color we see when these flags are draped on walls, for instance.
Canadian and others make the header as a continuation of the color from the flag by the hoist, if possible, or make it white. But, it is of the same fabric (usually) and does not have two holes at either end with shiny brass rings around them, as we see on US flags even of other countries but made in the US.
Steve Stringfellow, 10 October 1996
-When brass grommets are used, what attaches them to the halyard?
-With toggles, is there a gap in the halyard? That is, do you disconnect the two halves and fit the flag into the space? Are there versions where they are simply attached to a rope which runs along outside the hoist?
-Is there always a rope inside the hoist when there are toggles?
Nathan Lamm, 27 July 2004
Sometimes, or sometimes the kind with a spring-loaded catch, like you use to fasten a dog's leash to its collar, if you have a dog. Probably lots of other designs as well.
In the US, at least, the clips are usually--or perhaps I should say "correctly"--tied to the halyard with the distance between them approximately equal to the hoist of the flag to be hoisted. If more than one flag is flown, then more than two clips are attached; if different sizes of flag are flown at different times, then additional clips are attached to match the hoists of the different flags.
(I say "in the US" because American flagpoles are the only ones I'm familiar with; other arrangements may well be used elsewhere.)
Another way of doing it, common in maritime applications and possibly elsewhere, is for the flag itself to have a length of rope, called a distance line, stitched into the heading (i.e., the heavy fabric at the hoist). At one end of this rope is a clip, at the other a ring. The halyard is equipped with a ring at one end and a clip at the other; the flag is attached by fastening the clip on the distance line to the ring on the halyard and vice versa. Multiple flags can be hoisted by fastening the clip of the lower to the ring of the higher.
The Royal Navy, its offspring, and perhaps others (not the USN) use something called an Inglefield clip, which I believe doesn't have any moving parts and is held by its supporters to be more efficient than the kind used by the USN. I couldn't hope to describe them. However, the Inglefield also presupposes the use of a distance line.
Joe McMillan, 28 July 2004

redpajama_set_name: RedPajamaCommonCrawl


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Many years ago I was sitting at Caribou Pass on the Kongukut River, in the Northeast corner of Alaska, hoping that I might see some caribou. I was not alone. along with the guests that I had on my trip there was a professional photographer Gary Braasch, who was also there waiting. I understand waiting is one of the great skills that a photographer must posess. I had not met him before but two days and about 20,000 caribou later we had struck up a bit of a friendship.
Shortly after his time photographing in the Arctic Refuge, Gary launched an incredibly ambitious project to capture images of global warming that would inspire people to take action. This is no easy task, with 24 hour news stations and the internet constantly bombarding us with images it is very difficult to produce something that is iconic. And global warming is such "big" issue that just deciding where to point your camera could keep an average guy up at night. But Gary has held true to his vision and has been working on this project ever since. Our paths have crossed on and off over the years as I have continued in my conservation advocacy work and Gary continues to take pictures that matter.
Just this past week Gary published pictures of Shell's drill rig the Kulluk anchored just 12 miles offshore of the coast of the Arctic National Wildlife Refuge. These pictures bring home the impact that Arctic drilling will have on the landscape and the wildlife in this treasured area. These pictures are especially motivating to me beacuse this past summer I floated the Canning River all the way from the heart of the Brooks Range mountains across the coastal plain and right up to the edge of the Arctic Ocean. On that trip I saw moose, river otters, wolves, Gyr and Perigrine falcons, and tens of thousands of caribou. If I were to do that trip today, for the last half of the trip, every time I looked North, down river, I would have seen the drill rig looming out in the ocean. This is unacceptable and why I'm doing everything I can to convince the Obama Administration not to allow drilling in our Arctic Ocean and to permanently protect the treasured landscapes of America's Arctic. You can join me in these efforts by "liking" the Sierra Club's Chill The Drills Campaign on facebook or by signing the petition urging the Obama administration to stop the drilling.
If you just look at the top half of Gary's image you can see the beauty of the Arctic Refuge, but when you look at the whole picture you can clearly see why we need to make a stand and take action.


Brandon Anderson shares his first hand insights to update this blog post.
You can create custom property definitions for catalog part families using the Spec Editor, but these properties are not visible at the part size level within those families.
For example a part family for pipe may contain sizes from 1-12", but the Spec Editor interface will not display these custom properties in the sizes tab of the catalog editor.
** It is possible with the following workflow to populate unique property values to the part sizes at the catalog level.
When adding a custom property definition select "All Part Groups' for the add property to: option and you must fill in the default value field. Click the add button below the added properties column to include the property in all of the part families (groups) in the catalog. Click the OK button to apply the changes and then save the change to the catalog.
Here I have created a custom property "Custom1" with a default value of "Null" and a field size of 20.
Editing property definition fields after a property has been created does not save over the original rather it creates a duplicate. If changes to a current attribute is needed remove and recreate it.
Also keep in mind that removing and recreating a custom property removes any data you had populated under that definition.
Back in the Spec Editor tab we can then add part families to the specification that we are defining or add our custom property to an out of the box spec.
Double click the Long Description of the family name in the top half of the dialog and you will see the Edit Parts box pop up. Switch to the Edit Properties tab in the top left corner of the Edit Parts box to show the same Property Definition fields that we populated on the catalog side. Here we want to recreate the definition making sure that ALL name fields match what we put in before. Now if we switch over to the Parts List tab and scroll to the right we will see that the custom property "Custom1" has been added to each part size in the specification.
In the Catalog Editor tab we can import/export the catalog family and/or size data to an Excel file.
This is extremely helpful in populating information for the catalog part sizes once they have been created in the Spec Editor, but it also enables us to re-populate the default entries for the custom parameter "Custom1" for each size in the catalog.
Select the Full catalog data export option or the resulting Excel file will only contain a list of the defined families and not their individual sizes.
In the Excel file you will have to unprotect the sheet before you can make any changes.
It is important to remember that you cannot add columns (Parameters) or rows (Sizes) into the Excel file...this data will not import back into the catalog if you do.
Note: You can safely edit most of the field in the Excel file, but you should never edit the SIZERECORDID. You will also notice that you are not allowed the edit any of the Piping Component Properties that you see in the Catalog Editor.
When importing the modified data back into the catalog the Spec Editor it will identify and highlight those changes as seen here. This allows the user to accept or reject the changes individually or globally with the tool buttons located at the top left corner of the tabular list of properties and their values.
Once they have been accepted or rejected you can click OK to apply the changes and then save the catalog. If you Accept the changes but do not Apply the changes they will not be added to your catalog.
Note: If you Apply the changes means that the exported Excel file will always win. So if someone is making changes to your catalog in the Spec Editor application while someone is making changes in the exported Excel file it is possible to overwrite the exported changes if you are not managing this properly.
Back on the Spec Editor tab you can "Check for Catalog Updates".
Choose to update or discard the changes as required and then save the changes to the specification before closing the Spec Editor.
You will then need to add the custom property "Custom1" to the appropriate Plant 3D Class definition.
Right click on the project name to access its properties.
This parameter will cascade down through the tree to all sub-branches...so be sure to place the custom property at the highest level of the required class.
In a 3D drawing in the plant project you can now route pipe using the specification that you just created/updated.
The properties palette will show the part size values for "Custom1" under the section titled General.


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Media Releases >
NSW Government Announces $127,000 For Mulgoa's Heritage
The heritage of Mulgoa will benefit from a grant of $127,000 awarded through the NSW Government's Heritage Grants program, Heritage Minister Robyn Parker and Mulgoa MP Tanya Davies announced today.
Ms Parker said the grant is just one of 40 being awarded to new heritage projects today by the NSW Government, totalling more than $2 million.
"The NSW Government recognises the important role that our State's diverse heritage plays in creating a shared understanding of our cultural history and providing interesting and unique drawcards to our towns and cities," Ms Parker said.
These grants will allow communities to take a hands-on approach to conserving important heritage places as an investment for future generations.
Today's grants are expected to lead to tourism and employment opportunities, particularly in rural and regional communities.
Tanya Davies welcomed the $127,000 grant which has been awarded through the Major Works Program to the Sydney Anglican Schools Corporation to undertake essential conservation works to the sandstone exterior of the State Heritage Register-listed St Thomas Anglican Church, Mulgoa.
"The Major Works Program is the flagship program for NSW Heritage Grants; it assists owners and managers of State Heritage Register-listed items to conserve, restore and reuse their heritage properties," Tanya Davies said.
The St. Thomas' site was originally granted to the Anglican Church in 1831 by William Cox for use as a church and school.
"It is one of the most beautiful rural church settings in NSW, and has significance both for its superb landscape value and for the intactness of the church." Tanya Davies said
The surrounding church yard has a picturesque graveyard of clustered headstones and notable classical sandstone monuments, predominantly of the pastoralist Cox family.
The NSW Heritage Grants program is designed to provide direct financial assistance to private owners, councils and community based organisations to maintain and improve their heritage assets.
The NSW Government is committed to conserving, revitalising and caring for places of heritage significance.
Tanya Davies MP
Member for Mulgoa
Phone: (02) 9834 2966. Electorate Office: Shop 43, St Clair Shopping Centre, 155 Bennett Road, St Clair NSW 2759.
Authorised by Tanya Davies MP, Shop 43, St Clair Shopping Centre, 155 Bennett Rd, St Clair NSW 2759. Funded using Parliamentary entitlements.


What are the key metrics for your service? Think about all the metrics that will help you determine whether or not your MVP is delivered.
Write all of 1-10 key metrics, each on their own line.
These key metrics are the main metrics you need to measure and optimize for your business to grow. These metrics will also tell you whether or not your MVP works.
Twitter found out that when a new user follows at least 30 users on their first visit, then the user is a lot more likely to become a permanent user. So, one of twitter's main key metrics is actually the number of followers/new user. They make it as easy as possible for you to follow 30 users upon your first login.


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Thor & Friends
By Bob Gourley | Published on October 22, 2016
Having spent five years as the touring percussionist for Swans, Thor Harris has launched a new, very different project called Thor & Friends. Heavily influenced by minimalist composers, the rhythmic instrumental songs are built around such instruments as marimba and xylophone. Other instruments and sounds come into play, often bringing an experimental edge to the music, but the compositions are never allowed to get too cluttered. The result is a catchy, whimsical sound that would appeal equally to those seeking out avant-garde music and those who are afraid of it. Thor & Friends recently released a self-titled debut album and are currently out on tour. In a phone interview, Thor discussed the project.
How did you come to start up Thor & Friends?
"I listened to a lot of electronic music, and I also listened to a lot of those mid-20th century composers like Philip Glass, Steve Reich, Terry Riley. That music, the 20th century minimalist, is so beloved by almost everyone that I know, certainly the musicians. I wanted to do something like that, something hyponic. I wanted it to be instrumental. I was coming off of 6 years on the road with Swans, so I didn't want to hear drums, bass, or distorted guitars anymore. I just wanted to hear clear sounds. I'd been playing vibes and woodwinds a lot. And so, I was attempting to put together either a solo show or a really small group.
"But as soon as my friends in Austin saw this group play, a lot of them wanted to be in it. Who was I to tell them no? I started saying yes, if someone wanted to come play with us. So now, if we play in Austin or New York City, the two places where I have a lot of friends who play music, the group is usually at least 10 people. But I don't have to do much in the way on reigning people in; I'm really not a control freak. I'm kind of open to seeing what happens if you let people do what they want to do, as long as you pick the people somewhat carefully. So far it's been really great. There's no lead instrument in this group; it's layer upon layer of simply melodies. With some of those melodies, we have people double on whatever instrument they're playing. So often we're just teaching the pieces to people hours before we play a show.
"That's basically how this band started. And then [I worked with] Heather and Jeremy, from the Hawk and the Hacksaw; they are dear old friends. Jeremy Barnes is the drummer from Neutral Milk Hotel, and Heather Troost is a violin player in Hawk and the Hacksaw. They live in Albuquerque, and an excuse to drive up to New Mexico from Austin is always welcome. John Dieterich of Deerhoof was also available. He mostly engineered, but also played guitar and bass on the record. [Otherwise] it was really just me, Peggy Ghorbani, and Sarah Gautier, and we recorded it in about 3 days. These were songs that we had been working on live for just a couple of months, so this band has only existed for about a year. It was thanks to Jeremy Barnes, and they put out the record on their label which is called LM Dupli-cation."
Had you considered doing this type of music previously?
"I hadn't thought much about doing it, and I certainly hadn't thought about touring with a group like this, something so non-vocal rock or pop. I'd been making these ambient records for a long, long time. The first one I made was called 'Fields of Innards.' I made that one around 1999. I had done shows around Austin with a group of instrumental improvisers, where it's not jazz because there's no solos but it is kind of slow moving, somewhat improvised music. But I think it was just sort of restless, nervous energy and my inability to sit still that led to it becoming a full-blown record with a tour to follow."
As you're always working with different people live, do you feel that this album represents the definitive versions of the songs?
"No, I don't think there will be definitive versions. And with this band, I would like to release multiple records every year. We're going to start recording our live shows more, and I think that different versions of the same songs may appear on future records, just because they are going to be so different, depending on the personnel. It is a compromise, because I can't take everyone that I love playing with in Austin on tour. It's just too expensive. And I can't take everyone I love playing with in New York on tour either. But I think some of them are going to do several shows.
"Everything is based on marimba and xylophone parts. Although those will be the same as a live version of those pieces, we did utilize a lot of cool things in the studio. We won't have a melotron live, and for most shows we won't have John Dieterich or Jeremy Barnes. John Dieterich makes a lot of strange prepared guitar sounds. It will be a trade-off. We'll have different people doing those kind of strange drones that John did on the record. I really look forward to it being pretty different every night. We will have at least 6 or 7 people on stage at any given show, because we're touring with this great young singer called Adam Torres. I played on a record that he made last winter that just came out. So all of those guys from his band will be playing in Thor & Friends and then I'll play drums in his band."
I've heard that you also make your own instruments?
"I do, yeah. I've built a lot of percussion instruments. I've built some electric string instruments. I'll have an electric hammer dulcimer with me that I built. In Swans, I played an electric viola that I built. I started building instruments when I was around 14 years old. I grew up in a house with a lot of tools, and there was a metal shop next to the dining room because my dad was such a tinkerer. He was always working on something."
Are you generally looking to create a specific sound or just experimenting?
"People have been making instruments for tens of thousands of years, at least. So I'm usually looking to make a bigger or a lower sound; it's based on some instrument that already exists, but I want a louder one, or I want bass one of those. Something like that. But they do not always turn out how you want, and some of them are just total garbage. There's a lot of failure involved. When I was a kid, and well into my 30's, I didn't use any kind of guide; I sort of built these things by instinct. Now I have this great book by this guy called Bart Hopkin [Musical Instrument Design: Practical Information for Instrument Making]. There are a lot of tables and things in it that are pretty helpful. I built a marimba and for tuning the resonator tubes, there was a helpful table for determining the lengths of those tubes."
Do you see Thor & Friends as your primary focus going forward?
"I am open to other collaborations for sure. Like Swans, I love those guys and would happily work with them again. I just wanted to do a lot of different things. People were asking me to record and there just wasn't time when I was on the road with Swans half of the days every year. They're doing a tour cycle right now that started a few months ago and will go for at least another year. So I didn't know I was going to make Thor & Friends and that it would even tour. I do plan to keep it alive for a long time, and I want to keep it going. But there may be breaks from it where I tour with other groups. I never know what will come up, and I don't have a clear plan for the next 5 or 10 years. But when there's time, I'd like to keep this thing going and keep making records."
Do you have any concrete plans for the additional releases you mentioned earlier?
"I'm not sure exactly how we're going to do it. They may just be available on Bandcamp, but I would like them to be released. We also did a version of the Terry Riley piece 'In C' and we're going to release that. I'm not sure how yet. It's so strange, because getting music to people is in such flux right now. We have some demos from before we made the record with Jeremy and Heather; some of those are good enough to release. We might just start packaging some of those up. I would like a limited run of some kind of physical copy of these things. We might release them in different ways, and some things might not ever make their way to physical copies."
"I'm really excited to play this music for people. We've played quite a few live shows already, and it's' pretty different from playing a rock concert. That can be terrifying, but it's kind of gone from terror to actual excitement now. We had this one show in Toronto where we set up in front of the stage because we quickly ascertained that with the sound system and the soundmen we had available, it was not going to work out for us and the PA. So we all set up in front on the stage, kind of right in the audience. That show was such an experience for everybody. It was really intimate, the audience was 2 feet from us and we had to walk through them as we switched instruments. That's when I knew that this wasn't a rock concert; this isn't what I'd been doing for a long time. But this was something different that I really thought could work, even in these rock and roll venues."
For more info, visit thorharris.org. If you're interested in buying the album, please support Chaos Control by following this link and purchasing from Amazon.
VIEW CHAOS CONTROL INTERVIEWS ARCHIVE
I also currently contribute to the Please Kill Me website (based on the book of the same name.) Below are some of my recent interviews from there.
Anni Hogan
Jah Wobble interviewed about Invaders of the Heart, PiL and his long career
Limahl talks about his career and new Christmas single
Vonavi interviewed about "Reflection"
Archive Highlights
Jay Aston's Gene Loves Jezebel return with "Dance Underwater"
Skye & Ross
Pop Will Eat Itself
Get alerted when new interviews and other features are added to the site! Join our email list, or Like our Facebook page!
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Unless otherwise noted, all content ©1992 - 2019 Bob Gourley
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Hearing the story of Christmas you can always expect a twist to it, but seeing and hearing it through the eyes of a child is extra special. Merry Christmas!
Thank you to all the help we had producing this, especially Carrie Hood, Leigh Halsema, Abby Parker and Davis Harwell.


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From toxins to t-cells, in evolution existence precedes essence
"Existence precedes essence", the credo of Existentialist philosophy, is also a central tenet of evolutionary thinking.
The French philosopher Jean-Paul Sartre coined the phrase "existence precedes essence" to describe the core proposition of a strain of philosophy (Existentialism) that preceded his own existence by centuries, if not millennia. What does this deceptively simple assertion actually mean? No more (or less) than that humans do not come into being with a ready-made purpose or meaning (an "essence") but have to create their own reason for being through their actions and their understanding of those actions. We tell our own stories; justify our own existence. For Sartre, this was a criticism of religious views in which the meaning of life is imposed on us from outside – by God or gods. He rejected this notion, insisting that we must create our own unique meaning of life, formulated within ourselves and then enacted in the world. This meant that humans were radically free, but with this freedom came a great deal of responsibility – time to grow up and make our own beds. Whilst this view is very popular today it's also not beyond reproach, and it would be quite possible (and fun) to spend several paragraphs criticising it. On the other hand, this is not a philosophy blog – it's a venom biology blog – so the onus is now on me to justify bringing it up at all. What exactly does "existence precedes essence" have to do with biology?!
Jean-Paul Sartre (1905-1980) was one of the 20th Century's most popular and influential writers and philosophers. He is pictured here with his life companion and fellow philosophical luminary, author of The Second Sex, Simone de Beauvoir (1908-1986). Sartre coined the term "existence precedes essence" in his essay "Existentialism is a Humanism" which was aimed at dispelling the notion that Existentialism was a gloomy or pessimistic philosophy. Photo: Getty Images.
Exaptation
It turns out that this notion that things (all kinds of things) first emerge for no particular reason, and then "discover" their reason for being retroactively, is a core part of the view of the world provided by the lens of contemporary evolutionary biology. I've discussed the phenomenon of "exaptation" in a few blog posts already (e.g. here) – it's what we call the process in which a property (something that merely exists) becomes a function (something that has a reason for existing – a purpose). The term was coined in 1982 by the palaeontologists Stephen Jay Gould and Elisabeth Vrba. Gould was an extremely famous and influential evolutionary biologist and in science fame and influence are almost invariably accompanied by controversy. Gould had numerous intellectual feuds with other influential biologists, such as Richard Dawkins and Simon Conway Morris, and most ideas associated with him have been extensively criticised. Many of them have become canonical, however, including exaptation. It's not that Gould and Vrba were the first to realise that properties become functions, but they were the first to give the process a name. The philosopher Daniel Dennett once observed that exaptation was a "trivial" (obvious, barely worth drawing attention to) process, since all adaptations begin as exaptations. Although I greatly admire Dennett, he misses the point here – it's precisely because exaptation is trivial and ubiquitous that people completely overlook it, and thus why it required a catchy name. We mustn't forget that evolution itself is equally trivial – it's just future states of systems being descended from past states – and that Thomas Huxley, speaking of Darwin's monumental "discovery" of natural selection, remarked that it was "extremely stupid not to have thought of that!". The best ideas are often those that seem most obvious as soon as someone else has identified them.
Stephen Jay Gould (1941-2002) was a palaeontologist and one of the most influential evolutionary biologists of the 20th Century. Whilst many of his ideas remain controversial within the field, his impact upon it is unquestionable. Some of his most famous contributions include the idea of "punctuated equilibrium" - the assertion that evolution typically proceeds slowly but occasionally leaps forward; his cautions against "adaptationism" - the notion that all of an organism's features are adapted and functional (rather than some being simply "properties"); and exaptation. Image: Newsweek.
Order from randomness
It's also the case that the simplest and most ubiquitous of processes can have the most counter-intuitive of consequences. One of the most difficult things to understand about evolution is the way in which apparently "random" change ends up creating all the wondrous order and complexity of the natural world. This has long been one of the most powerful arguments in support of creationism – "surely you don't believe that all this beauty, all this structure, could be the result of a random process? In order for complex structure to emerge, it takes an even more complex process to design it!". Well, sure – I don't believe it's the result of a random process, I believe it's the result of a process that turns more or less random change into absolutely non-random structure. The change isn't "absolutely" random, either, it's just undirected – change simply happens and changes become purposeful (or not) after they emerge. Existence precedes essence – that's exaptation. I also agree with the second point – evolution is a highly complex process, more complex than any of its products, but that complexity is the result of iterated (repeated) feedback cycles, it's not all there "in the beginning". Complexity accumulates as the result of the repetition of an extraordinarily simple process of change and constraint – change occurs (more or less randomly) and that change is constrained by what already exists (the past constrains the future). As complex structure forms, the potential emerges for more complexity to be built atop what is already present. It's important to note here that "evolution" is the whole process – the random change and the constraint. Exaptation is part of that process – the conversion of random change into purposeful product via the mechanism of selection (there's more to the concept than this, but I've discussed that in other AVRU blogs). Selection is one form of constraint on change – it's the kind that Darwin identified and it's extremely important for the evolution of biological organisms.
William Paley (1743-1805) was an English clergyman and philosopher. He is most famous for his use of the "watchmaker analogy" in the book Natural Theology, or Evidences of the Existence and Attributes of the Deity collected from the Appearances of Nature. The gist of the analogy is that if one were to stumble across a watch - an intricately designed artefact - just lying about, one would automatically assume that something so complex must have been created by an intelligent designer. Following the same intuition, Paley says that we should assume the same conclusion when we observe the complexity of nature. The book was published in 1802, 57 years before Darwin published On the Origin of Species - arguments between proponents of an intelligent designer and those of an impersonal evolutionary process are ancient, and did not begin (or end) in the Victorian Era. Richard Dawkins referenced Paley's argument in his book The Blind Watchmaker. Painting by George Romney.
Innate and adaptive immunity
OK, that's more than enough theory for now, how about some examples? It's probably safe to say that immunity has been on a lot of people's minds lately. We'd all like to be immune to the coronavirus responsible for Covid-19. But how does immunity work? There are two basic kinds of immunity – innate and adaptive (acquired). Innate immunity is something organisms are born with – it's conferred by their genes. As AVRU blog readers know, organisms are fantastically elaborate chemistry sets – we produce a huge variety of functional molecules, like proteins, that are responsible for all sorts of activities within our bodies. A subset of these molecules was designed (by natural selection!) to protect us from invaders. For example, we produce enzymes that are great at killing bacteria. Since we produce these innately, they are ready to go at any time and are thus our first line of defence against invaders. They're quite relevant to toxin evolution, because some enzymes that have been recruited for use as toxins are ancestrally antibacterial. You may recognise this as an example of exaptation – the molecules had one function, which made them good at killing cells (e.g. bacteria) and this function made them potentially useful for injecting into other organisms in order to subdue them. Thus, phospholipases, which are ancestrally antibacterial and part of our innate immune response, have been recruited as toxins by a number of venomous lineages (e.g. snakes and bees).
Phospholipases, which ancestrally functioned as components of the innate immune response, are important toxins in the venom of the Mojave rattlesnake (Crotalus scutulatus) and other vipers. The Mojave rattlesnake is considered one of the most dangerous of all rattlesnakes, due to the presence of a neurotoxin in its venom, formed from two phospholipase enzymes stuck together to form a complex toxin. Photo: BLM Nevada, Wiki Commons.
Unfortunately, we don't have innate immunity against coronaviruses. So how does adaptive immunity work? Not only is the process of acquiring immunity to unique pathogens extremely important to our survival, it's exceptionally cool and is a beautiful microcosm of the evolutionary process in which undirected change is converted into functional products. B-cells are a type of white blood cell that secretes antibodies. When a B-cell comes in contact with an "antigen" (something that stimulates an immune response) it begins to multiply by dividing itself over and over again, and this is where the fun begins. During this process of proliferation, "somatic hypermutation" occurs in the aptly named "hypervariable" regions of the antibodies that the B-cell produces. These are the regions of the antibodies that detect and bind to antigens. As you know, "hyper" means "a lot", so what this means is that a great deal of mutation is occurring in these regions – the mutation rate may be 1 million times higher than normal – resulting in, well, a lot of variation! Now, you've probably guessed the punchline here – all this variation is undirected. It's essentially random (although of course where it occurs is not random at all). Most of this variation is completely meaningless and doesn't result in an increased affinity (ability to bind) for the antigen. It's a bit like scrolling randomly through channels on the radio (if anyone remembers radio) until you hit upon something you like. By chance, some small subset of all that change in the binding regions of the antibodies increases their affinity for the antigen, and when that happens, that undirected change has found its calling – it now has a purpose. Note that the same variations may have come up many times before and remained meaningless – meaning (function) only emerges when the right change occurs at the right time. Meaning is dependent on the relationship between the change in the variable region and the structure of the antibody. When a match occurs by chance, selection occurs – the B-cells with the right antibodies start to proliferate preferentially and we're on our way to an adaptive immune response. This is exactly what happens in evolution in general – undirected mutations largely have meaningless (typically neutral) or occasionally deleterious results. On occasion, the right mutation occurs at the right time and positive selection occurs – a novel function is born. Most change has results that are "epiphenomenal" (another way of saying it "just is"), but when a change encounters the right context, it is exapted and becomes functional.
The hypervariable regions of the B cell receptor - which is a transmembrane antibody that functions as an antigen receptor - undergo somatic hypermutation. The mutation rate of these regions may be as much as 1 million times greater than the background rate, and they continue changing until they hit upon the solution to a problem - effective binding of a pathogenic invader. Image: Wikipedia.
Memory T-cells and Covid-19
OK, now I have to justify the alliteration in the title – it mentions T-cells, not B-cells. Well, T-cells are another kind of white blood cell, and one of the things they do is kill infected cells directly. For a long time it was thought that somatic hypermutation only occurred in B-cells, but more recently evidence has emerged to suggest that it occurs in T-cells too (at least in camels and sharks). This is obviously cool from an evolutionary perspective, but T-cells have also been in the news recently for slightly different reasons. T-cells multiply in response to the detection of a pathogen, but after the infection is dealt with most of the T-cells specific to that pathogen die. A small subset – the "memory T-cells" – remains, however, as part of a persistent acquired immune response to a particular pathogen. Next time you encounter that "bug", you're able to respond to it more rapidly. Remember SARS (severe acute respiratory syndrome) from back in 2003? It was caused by a coronavirus. Turns out that the memory T-cells of patients that recovered from SARS infection also recognise the coronavirus that causes Covid-19 (check out the study here). In fact, it looks like a surprisingly high percentage of the population, with no exposure to the SARS or Covid-19 viruses, might already have memory T-cells that recognise these potential invaders (see additional studies here and here). This could be part of the reason why some people have relatively mild reactions to the virus. From the perspective of this article, it's another incredible example of exaptation. These memory T-cells that recognise the Covid-19 virus did not evolve for that purpose. In fact, they evolved (or were developed, if you prefer) before the virus itself even existed! This means that the particular variants of the surface proteins of the T-cells were meaningless (epiphenomenal) until they met the surface proteins of the virus. Many years after they came into existence, these T-cells discovered their essence.
Evolution is just so cool
Since this kind of thing is ubiquitous in evolution, it probably goes without saying that similar things happen with toxins. Sometimes the possibility of a molecule becoming a toxin doesn't exist until it is accidentally injected into another organism. For example, antibacterial molecules in lizard saliva – they weren't designed to weaken prey animals, they just got injected into those prey animals as part of a typical predatory interaction in which the lizard was trying to subdue its meal by biting it. Sometimes those molecules have properties that have no function whatsoever, but those properties suddenly become functional when they are introduced to a new context – like the insides of another animal. That's existence preceding essence. Exaptation.
In a future article, we're going to explore the ways in which toxins become toxins – "how the toxin got its toxicity" – in more depth. There's also another exciting (I mean, really really exceptionally fantastically cool) thing to talk about in relation to adaptive immunity. Remember I said that the process of somatic hypermutation was like a microcosm of the evolutionary process? The thing is, in the case of adaptive immunity, the mechanics of evolution have themselves been selected for – it's a functional exploitation of the process of evolution itself! Not sure why that's mind-bogglingly cool? Tune in to future AVRU blog posts in which I'll try to convince you that your jaw should be on the floor…..
Dr Timothy Jackson
timothy.jackson@unimelb.edu.au


The Boston University cross country team captured individual first place honors in both the men's and women's races with standout performances by junior Eric Ashe and graduate student Andrea Walkonen in the Vermont Invitational on Sunday.
Walkonen's performance carried the women's team to victory, while the men finished third.' Walkonen finished the 5,000-meter run with a time of 17 minutes, 50.68 seconds '- Ashe completed his 8,000-meter run with a time of 25:24.16.
The women won thanks to great depth. Walkonen had help in the form of sophomore Katie Matthews and senior Sarah Mosser, who both finished in the top 10. Junior Kathleen Davies and freshman Marita Stressenger slipped into the top 20 to piece together a 49-point place total.
'Although it's early, it's always nice to get the win,' Johnson said.
Sophomores Craig MacPherson and Peter Gilmore joined Ashe in the top 10 for the men, who were hurt by their final two scorers. Sophomore Joe Greenspun and senior David Polgar couldn't stay with the pack in finishing 22nd and 31st.
The University of New Hampshire won the men's overall meet with 39 points. The University of Vermont took second place with 63 points. New Hampshire put just four runners in the top 10-one more than BU. Vermont had just one top-10 finisher.
But by eliminating stragglers, each team was able to come up with the most efficient overall score.
The women won because their back-end scorers stayed competitive, not hurting the efforts of the top three by putting up crooked numbers.
Walkonen, who was a 2008 All-American, used four years of experience to avoid this pitfall.
To say Walkonen pressed hard is an understatement. She routed the entire field, beating second place finisher, University of Maine sophomore Corey Conner, by 35 seconds. Ashe faced a tougher path to the win, edging University of Vermont senior Doug Maisey by seven seconds.
The Terriers run in Boston next weekend in their host meet, the BU Invitational. The meet will be held at Franklin Park and both the men's and women's teams will be in action.