The River Wear in November

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I was back at the River Wear last week for my final visit of the year.   The heatwave that dominated the summer seems like an aeon ago as I plunged my arm into the cold water to find some stones and take some photographs.  I’m curious to see what is here, though.   The river has surprised me several times already this year.  Has it reverted to type as the British climate has regained a semblance of normality, or will the changes that we saw in the summer (see “Summertime blues …” and “Talking about the weather …”) still have consequences for the algae growing on the river bed?

The river bed itself had many patches of green filamentous algae which, on closer examination, turned out to be my old friend Ulothrix zonata, an alga that is common in these parts and which has a distinct preference for early spring conditions (see “Bollihope Bavakakra” and references therein).   A closer look showed two types of filament present: the normal vegetative ones with a single chloroplast encircling the cell but also some where the cell contents have divided to produce zoospores which are released and which, if they land on a suitable surface, will produce new vegetative filaments.   The “parent” filaments, themselves, are produced as zygotes, produced back in the spring, germinate.  The zygotes are the product of sexual reproduction, triggered by lengthening days (see reference in earlier post) and are dormant through the summer, only germinating once day length shortens and temperatures start falling.

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The river bed of the River Wear at Wolsingham, November 2018, showing conspicuous growths of Ulothrix zonata.

Ulothrix_zonata_Nov18

Magnified views of Ulothrix zonatafilaments from the River Wear at Wolsingham.  The upper image shows a vegetative filament and the lower image shows filaments where the cell contents have divided up prior to the release of zoospores.  Scale bar: 20 micrometres (= 1/50thof a millimetre).

The areas between the patches of Ulothrix zonatawere covered with a thick film, composed primarily of diatoms, in contrast to the situation on my last two visits when non-filamentous green algae predominated.  This time, it was Achnanthidium minutissimumdominated my count (about 70% of cells) although, because they are relatively small, they comprised just under half of the total volume of algae present.   Other diatoms bumped this up to about 70 per cent of the total volume, with motile cells of Navicula and Nitzschia, which were so abundant at the start of the year, beginning to appear in numbers again.   The green cells that dominated my counts in July and September now only constitute about five per cent of the total.   The River Wear, in other words, has shaken off the effects of the summer, just as a healthy human gets over a winter cold, and is now back to its old self.

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A view down my microscope whilst examining samples from the River Wear at Wolsingham showing the predominance of Achnanthidium minutissimum with (on the right-hand side) a filament of a narrow Ulothrix (not U. zonata).  

Unorthodox icons …

Towards the end of my most recent trip to Bucharest I came across, almost by chance, the Art Collections Museum, located on Calea Victoriei about 10 minute walk north from the National Museum of Art.  It brings together a number of collections that have been acquired by the state over the years, keeping each intact so that they reflect the taste of the original owners rather than reassembling them into broader thematic groupings.  On the day of my visit it was almost deserted, with attendants outnumbering visitors, despite this being the first Wednesday of the month, meaning that admission was free.   Their eyes followed me as I browsed, and their footsteps tracked mine through the empty rooms.

A museum such as this inevitably has some parts that enthral whilst other parts that fail to enthuse me. Highlights for me were the expressionist art of Alexandru Phoebus and the odalisques of Iosef Iser, both artists I had not previously encountered who had brought emerging ideas back from Paris and Berlin.   Then I walked into a room with a wall closely-hung with some very striking icons.  Two aspects struck me: their luminosity and the almost cartoon-nature of the scenes.  Imagine what Roy Lichtenstein might have produced were he to have brought his Pop Art sensibilities to religious subject matter.   The luminosity, I discovered, was because they had been painted on glass – a practice that arrived in the largely Catholic area of Transylvania from Hungary in the late 18thcentury.  This period coincided with the destruction of Orthodox monasteries and, with this, the loss of traditional icon painting skills.   Glass painting was, initially, a secular art form but, over time, it became a medium for religious imagery, initially drawing on Catholic representations of religious themes but gradually returning to Orthodox themes.

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Three glass icons from the Art Collections Museum in Bucharest.

The Catholic influence is apparent in the narrative content of some of the images that I’ve included here (see the Lamentation over the Dead Christ on the right-hand side of the top row and the centre of the bottom row, and the Last Supper on the left-hand side of the bottom row). Compare these with more traditional icons (see, for example, “The art of icons …”).   The middle image on the upper row is the Mystical Winepress, drawing on the metaphor of Christ as the true vine (Isaiah 27:2-5, John 15:1).  At the bottom right there is a rather strange-looking image of a figure with three faces but just four eyes).  This is a depiction of the Holy Trinity: God being simultaneously three persons and one.  It is also the image, of those I have chosen to depict, closest in style to traditional Orthodox icons.

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More icons on glass from the Art Collections Museum in Bucharest.

It is hard for a modern viewer, steeped in the visual culture of the 20thand 21stcenturies, to appreciate the impact of these images.  These were produced at a time when painters in western Europe were preoccupied with realism and capturing the dynamism of the world around them.   These are pared-back, almost cartoon-like depictions.  On the one hand, they are folk art, produced by artists without formal training; yet, at the same time, they are depicting such familiar subjects (for the audiences) that a suggestion of the subject matter is all that is needed.  Icons on the wall of a gallery are divorced from their context and analysing them in terms of visual representation does not do them justice. Icons in a church or in the home of an Orthodox believer are catalysts to deep spiritual experiences and can achieve this without sophisticated painting techniques.   Jesus, in Matthew’s Gospel, says we have to “become like children” (18:3) and, remembering how cartoons were able to draw me into imaginative worlds when I was young, perhaps it should not be a surprise that such apparently simple images make effective icons.

 

Terms and conditions apply …

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The draft withdrawal agreement, setting out how the UK leaves the European Union was published earlier this week, and has dominated domestic news coverage ever since.   Theresa May’s government seems to have weathered the storm – just – but the likelihood of the agreement surviving a vote in the House of Commons seems small, meaning that political uncertainty is set to continue for some time.

The agreement’s provisions for environment have received relatively little attention in the media during this period.  This is surprising, given the importance of this topic generally, and the central role that European legislation plays in our domestic environment policy.   As I have tried to offer a commentary on the Brexit process as it has unfolded (see “Environmental governance post Brexit” for the latest of these posts), I now need to steel myself for a scrutiny of the 585 page document (without even a contents page) to see what provisions have been made.

The political brouhaha has focussed around the problems surrounding the land border between the Republic of Ireland and Northern Ireland, and the proposal that the UK and the EU remain as a single customs territory, run according to existing EU rules, for as long as it takes to achieve a satisfactory long-term solution.   The prospect of being bound into EU legislation indefinitely is what has provoked the wrath of the hard Brexiteers; however, the rest of us need to bear in mind that the proposals set out in the withdrawal agreement are not indefinite.   Once a long-term solution is agreed, then UK administrations will be free to modify legislation unless a future trade deal specifically incorporates provisions for the environment.

The European Research Group’s argument that the UK will become a “rule taker” is disingenuous because the subsidiarity principle that was introduced as part of the Maastricht Agreement means that Member States always have had considerable liberty to implement EU legislation as they see fit.   The EU legislation tends to outline the ambition and principles rather than prescribe how these are achieved.  We already have strong domestic legislation that enforces environmental policy.  I have not heard the Brexit camp offering credible alternatives to the ambition set by the EU that might suggest that the UK will be constrained in this respect.

The key passages relevant to the environment are found in Annex 4, some 356 pages into the agreement.  These commit the UK to “non-regression in the level of environmental protection” which means that environmental standards in force at the end of the transition agreement (including, importantly, “access to environmental information”) should not be diluted during the period that the UK is part of the single customs territory.  The UK is also bound to adhere to the precautionary principle, the principle that preventative action should be taken, the principle that environmental damage should as a priority be rectified at source; and the “polluter pays” principle. We are also required to have “a transparent system for the effective domestic monitoring, reporting, oversight and enforcement of its [environmental] obligations … by an independent and adequately resourced body or bodies” (p. 359).  This is, in effect, the new watchdog that Michael Gove has already proposed but with greater independence as it needs to have power “to conduct inquiries on its own initiative” and the right to “bring a legal action before a competent court or tribunal in the United Kingdom in an appropriate judicial procedure, with a view to seeking an adequate remedy.”  Gove’s proposals put the new environmental watchdog under the control of DEFRA, which was widely regarded as compromising its independence.

The question that remains is how much latitude a future UK government will have to deviate from the principles of EU environment legislation.   The implication is that the UK and EU will move towards a long-term trade deal and my suspicion is that a level playing field for the environment will be a pre-condition from the EU for this to happen.  This would mean that the principles set out in the withdrawal agreement would apply in the long-term (though the UK would not necessarily be bound to comply with any new EU environment legislation).  What is also not clear is whether the UK would be expected to comply with collective decisions on implementation of existing Directives (and, indeed, to participate in reaching these) in the future.  The Water Framework Directive, for example, is 18 years old, but there are still aspects of implementation that are being discussed. The EU will want the UK to stay in line with new developments; the UK should regard participation in the debates around these to be a quid pro quo.

Almost every environment professional and academic I have met feels that leaving the EU to be a colossal mistake.  However, if we accept that leaving the EU is now inevitable (I still need to be convinced that a second referendum would offer a more decisive outcome than the first), then I think the provisions for the environment set out in the withdrawal agreement are good.   Even Michael Gove, an ardent Brexiteer, has acknowledged that the EU offers strong protection for the environment, and this agreement ensures that we go forward with as strong a foundation as we have at present.   However, the prospect of this agreement passing the various hurdles in front of it are slim, so a more likely scenario at present is that the UK crashes out of the EU in March 2019 with no transition arrangement and no trade deal in place.  That would leave UK environment legislation in a far more precarious position than is the case at present.

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“Learning from mum”: Heather’s prize-winning photograph in the 2018 BSBI photography competition shows her friend Priscilla botanising in Hannah’s Meadow, Upper Teesdale.  The photograph at the top of this post shows Upper Teesdale near Widdybank Farm, earlier this week.

Entomoneis in three dimensions

I’ve written about the genus Entomoneison a few occasions in the past (see “A typical Geordie alga …”).   It is a challenging species to understand partly because the cells often do not survive digestion in the strong oxidizing agents that we routinely use to understand the structure of diatom cell walls, and partly because of its unusual three-dimensional architecture.   I’ve commented on this before, using some of Chris Carter’s photos to illustrate this (see “The really rare diatom show”).  Now, thanks to yet more careful work from Chris, we have a new set of photos with which to understand this species.

The underlying problem of a complicated geometry (the frustule [cell wall] is actually twisted in two planes) is compounded by the shallow depth of field that is available when viewing organisms at high magnifications. The first of Chris’ images shows how most diatomists will encounter Entomoneis: as a cleaned cell mounted on a slide and shows how the girdle bands bands (the silica “spacers” between the two valves) seem to present a particular problem.  Look, in particular, at the arrangement of these in the left-hand image, focused on the top of the cell, and note how they appear to cross over one another.  Compare this to image that is focused on the bottom of the cell.  By contrast, a cell that has not been subjected to the strong oxidising agents that we use to “clean” diatoms prior to observation presents quite a different view, as seen in the second set of three photographs.   The contrast is poorer here, as the cell is not mounted in a high-resolution mountant (the reason diatomists “clean” their samples in the first place) but we can, nonetheless, see the girdle bands.   When Chris focuses on the top of the cell. the girdle bands are clearly visible, not criss-crossed, and diagonal across the cell. At the other extreme (focus on bottom of cell) the bands are still just visible, sloped the other way somewhat obscured by the cell contents but, most importantly, not presenting a gaping hole.

B Entomoneis naphrax mount.jpg

A cell of Entomoneisthat has been cleaned and mounted in Naphrax before being photographed at three focus levels using simple brightfield microscopy.  The left-hand image is focussed on the top of the cell and shows how the girdle bands appear to cross one another whilst the right hand image is focussed on the bottom of the cell and shows a chasm in the centre of the cell where the girdle bands have collapsed. The middle image shows an intermediate focal plane where the apices are in focus: this is where the girdle bands are attached.

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A cell of Entomoneisthat has been mounted in alcohol before being photographed at three focus levels. The contrast is much poorer here but at one extreme (focus on top of cell ie towards observer) the bands are clearly visible, not criss-crossed, and diagonal across the cell. At the other extreme (focus on bottom of cell) the bands are still just visible, sloped the other way but somewhat obscured by the cell contents.

What we think is happening is that the girdle bands are so weak that they collapse as soon as the frustule is dried or hits hot Naphrax; this collapse can be either towards the observer or away from the observer, creating a slightly different optical effect in each case.   Most of the time, however, the bands detach completely leaving isolated valves – sometimes with some straggly bits attached.  Chris thinks that almost all the published images of this taxon are misleading: usually flattened either optically or by software in order to give a sharp image for presentation and, in the process, disguising this detail.

These images all show us what Entomoneis looks like in girdle-view, the way we are most likely to encounter an intact cell when looking down a light microscope.  The next two plates show it from above (“valve view”) and in apical view (i.e. looking at the cell from one end), both of which are not often seen during routine observation.    The pair of valve views show the outline at different focal levels, and we can see how the thin wing (keel) is twisted towards the viewer; this twist is also present in the main (cylindrical) part of the cell but is not visible in these photographs.   The series of photographs in the next plate takes this further: the sequence along the top shows an apical view at several points of focus.  Some particulate matter is caught within the open structure of the frustule and acts as a reference point when comparing the two views. The thin keel with its thickened edge (containing the raphe) shows clearly. The body of the cell is not symmetrical because of the twist; the girdle band section is at the bottom of the inverted U section and is demarcated by ridges associated with each band: the number of bands can be estimated as shown on the enlarged fourth section. The other valve must have detached without holding onto any girdle bands.

A Entomoneis valve view in alcohol.jpg

Valve view of an alcohol mounted celul of Entomoneisat two focus levels.

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An alcohol mounted semicell of Entomoneis caught in both apical (top row, showing several points of focus) and girdle views (bottom right).  The image at the bottom left shows a slightly magnified version of the fourth apical view indicating the location of the girdle bands on the opposite sides of the valve (indicated by the vertical red lines).

Entomoneis highlights the limitations of using two-dimensions to portray algae.  The answer, Chris and I agree, would be a three-dimensional model (see “Taking desmids to the next dimension …”) that we could pick up and view from all angles.  Another option is to use a scanning electron micrograph (SEM), and the two references at the end of this article contain several useful images.   However, most of us are still going to encounter Entomoneisprimarily via the light microscope.  Having a sense of the three-dimensional form of an alga lodged in your mind makes it much easier to interpret the flattened two-dimensional images that we routinely encounter.  Prior to the era of SEMs, the three-dimensional form of Entomoneis, and, indeed, its true taxonomic position, was very difficult to appreciate.   Both the 1930 and 1990s editions of the Süsswassflora von Mitteleuropaplaced it with Naviculawhereas we now understand enough about the form of the raphe to know that Entomoneis is more closely related to Surirella(see Round et al.,referenced below).  It is a good reminder that the study of diatoms has always been limited by the technology available.   Our toys may have changed enormously over the past hundred years but the gaps in our understanding remain …

References

Round, F.E., Crawford, R.M. & Mann, D.G. (1990).  The Diatoms: Biology and Morphology of the Genera.  Cambridge University Press, Cambridge.

Dalu, T., Taylor, J.C., Richoux, N.B. & Froneman, P.W. (2015).  A re–examination of the type material of Entomoneis paludosa(W Smith) Reimer and its morphology and distribution in African waters.  Fottea15: 11-25.

The natural history of numbers

I have made a few facetious comments in this blog about the tendency for ecologists to spend more time staring at spreadsheets than engaging directly with the organisms and habitats they are trying to understand.   There is, of course, a balance that needs to be struck.   We can learn a lot from analysing big datasets that would not have occurred to a biologist who spent all his or her time in the field.  And, I have to admit, somewhat grudgingly, there is a beauty to the numerical landscapes that becomes apparent when a trained eye is brought to bear on data.

I’ve been involved in a project for the European Commission which has been trying to find good ways of converting the ecological objectives that we’ve established for the Water Framework Directive into targets for the pressures that lead to ecosystem degradation.   The key principle behind this work is summarised in the graph below: if the relationship between the biology (expressed as an Ecological Quality Ratio, EQR) and a pressure (in this case, the phosphorus concentration in a river or lake) can be expressed as a regression line then we can read off the phosphorus concentration that relates to any point on the biological scale.   (Note that there are many other ways of deriving a threshold phosphorus concentration, but this simple approach will suffice for now.)

PvEQR_1pressure

Relationship between biology (expressed as an Ecological Quality Ratio, EQR) and phosphorus concentration for a hypothetical dataset.  The blue line indicates the least squares regression line, the horizontal green line is the position of the putative good/moderate status boundary and the vertical green line is the phosphorus concentration at this boundary position.  Coefficient of determination, r2= 0.89 (rarely achieved in real datasets!)

This is fine if you have a strong relationship between your explanatory and response variables and you are confident that there is a causal relationship between them.  Unfortunately, neither of these criteria are fulfilled in most of the datasets we’ve looked at; in particular, it is rare for the biota in rivers to be so strongly controlled by a single pressure.  This means that, when trying to establish thresholds, we also need to think about how a second pressure might interact with the factor we’re trying to control.   If this second pressure has an independent effect on the biota then we might expect some sites that would have had high EQRs if we just considered phosphorus might now be influenced by this second pressure, so the EQR at these sites will fall below the regression line we’ve just established.   When we plot the relationship between EQR and phosphorus taking this second pressure into account, our data no longer fits a neat straight line, but now has a “wedge” shape, due to the many sites where the second pressure overrules the effect of phosphorus.   If you were tempted to put a simple regression line through this new cloud of data, you would see the coefficient of determination, r2, drop from 0.89 to 0.35.  Note, too, how the change in slope means that the position of the phosphorus boundary also falls.   More worryingly, we know that, for this hypothetical dataset, the new line does not represent a causal relationship between biology and phosphorus.  That’s no good if you want to use the relationship to set phosphorus targets and, indeed, you now also need to think about how to manage this second pressure.

PvEQR_2pressures

The same relationship as that shown in the previous graph, but this time with an interaction from a second pressure.  The blue line is the regression line established when phosphorus alone was considered, and the red line is the regression between EQR and phosphorus in the presence of this second pressure.

My purpose in this post is not to talk about the dark arts of setting targets for nutrient concentrations that will support healthy ecosystems but, rather, to talk about data landscapes.  Once we saw and started to understand the meaning of “wedge”-shaped data, we started to see similar patterns occurring in all sorts of other situations.   The previous paragraph and graph, for example, assumed that the factor that confounded the biology-phosphorus relationship was detrimental to the biology, but some factors can mitigate the effect of phosphorus, giving an inverted wedge, as in the next diagram.  Once again, the blue line shows the regression line that would have been fitted if this was a pure biology versus phosphorus relationship.

PvEQR_2pressures_#2

The same relationship, but this time with a second factor that mitigates against the effect of phosphorus.  Note how the original relationship now defines the lower, rather than the upper, edge of the wedge. 

Wedge-shaped data crop up in other situations as well.  The next graph shows the number of diatoms I recorded in a study of Irish streams and there is a distinct “edge” to the cloud of data points.   At low pH (acid conditions), I rarely found more than 10-15 species of diatom whereas, at circumneutral conditions, I sometimes found 10-15 species but I could find 30 or more.   Once again, we are probably looking at a situation where, although pH does exert a pressure on the diatom assemblage, lots of other factors do too, so we only see the effect of pH when its influence is strong (< pH 5).

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The number of diatom species recorded across a pH gradient in Irish streams.  Unpublished data.

In this case, the practical problem is that the link between species number and pH is weak so it is hard to derive useful information from the number of species alone.   It would be dangerous to conclude, for example, that the ecology at a site was impacted by acidification on the strength of a single sample.  On the other hand, if you visited the site several times and always recorded low species numbers, then you have a pretty good indication that there was a problem (not necessarily low pH; toxic metals would have a similar effect).   Whether such a pattern would be spotted will depend on how often a site is visited and the sad reality is that sampling frequencies in the UK are now much lower than in the past.

However, this post is not supposed to be about the politics of monitoring (evidence-based policy is so much easier when you don’t collect enough uncomfortable evidence) but about the landscapes that we see in our data, and what these can tell us about the processes at work.   Just as a field biologist can look up from the stream they are sampling and gain a sense of perspective by contemplating the topography of the surrounding land, so we should also be aware of the topography of our data before blithely ploughing ahead with statistical analyses.

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With Geoff Phillips and Heliana Teixaira – fellow-explorers of data landscapes in our project to encourage consistent nutrient boundaries across the European Union.