A day out in Wasdale

Irt_LundBridge_Nov18

A few days after my trip to Weardale I found myself beside the River Irt, a few hundred metres below the point where it flows out of Wastwater, in the western part of the Lake District.   Whereas the River Wear drains a catchment underlain by Carboniferous rocks, including a high proportion of limestone (see “Co. Durham’s secret Karst landscape”), the Irt’s catchment is largely underlain by ancient volcanic rocks, resulting in much softer water.   I was curious to see how different the algae were here compared to those in the Wear.

The river bed at this point is dominated by boulders of granite, which host a patchwork of mosses, filamentous algae and discrete growths of diatoms (visible on the right-hand side of the figure below).  Between these there were areas of pebbles and gravels, suggesting good habitat for freshwater mussels.   The patches of filamentous algae (mostly no more than a couple of centimetres in length) were a mixture of Mougeotiaand Zygnema, similar to the forms that I find in the River Ehen, a 30 minute drive to the north.   These two species differ in the form of their chloroplasts (Mougeotiahas a flat plate whilst Zygnemahas two star-shaped chloroplasts, attached by thin cytoplasmic strands to resemble an animal skin stretched on a frame) but are closely-related, both belonging to the family Zygnemtaceae.

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An underwater photograph of the substratum of the River Irt in November 2018 showing patches of filamentous green algae, mosses and (on the right-hand side) diatoms growing on granite boulders.

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Filamentous green algae from the River Irt, November 2018.   The upper photograph shows cells from a filament of Mougeotiawhilst the lower image shows two filaments of Zygnema. Scale bar: 20 micrometres (= 1/50thof a millimetre).

In between the tufts of filamentous algae were apparently bare patches of rock (they almost certainly had a very thin biofilm that would be hard to sample in isolation from the lusher algal growths that shared their habitat) and some conspicuous orange-brown growths of colonial diatoms.  These turned out to be almost pure growths ofGomphonema hebridense, or a close relative (I can’t give a definitive answer until I have examined cleaned material), growing on long mucilaginous, sometimes branched, stalks to create a veritable “bush” of diatoms.  There were a few other species of diatom growing within this bush, most notably some cells of Achnanthidium (cf.) caledonicumthat seemed to be growing on short stalks attached to the Gomphonemastalks, but also a few cells of Gomphonema capitatum(which also grows on long stalks) and some chains of Tabellaria flocculosa.

Gomphonema hebridenseis a diatom that I have written about several times before, as it is also common in the River Ehen, and also presents a number of interesting challenges to taxonomists (see “Diatoms and dinosaurs”). Whatever future studies reveal, however, the presence of colonies of this (or these) species that are visible with the naked eye is something I associate with only the cleanest rivers in the country during the cooler times of year.  It should not have been a great surprise to me to find it flowing out of one of the most pristine lakes in England (see “The Power of Rock …”).

Gomphonema_Irt_x1000_Nov18

A close up of cells within a colony of Gomphonemacf hebridense.  Several mucilaginous stalks are also visible as well as (top left) a cell of Achnanthidiumcf caledonicum.   Scale bar: 10 micrometres (= 100th of a millimetre).

The predominance of boulders over smaller, more easily moved stones, suggests a river that has more energy than the River Ehen, one of my regular Lake District haunts.   Both flow out of lakes whose catchments include some of the wildest and most mountainous terrain in the country.   Lakes tend to act as shock absorbers in catchments, slowing down the water that pours off the fells after heavy rain.   Streams in this part of the world that have no such impediments to flow tend to have rocky, mobile beds and relatively sparse algal communities.   By contrast, the Irt and Ehen just below their respective lakes have relatively lush growths of algae.   The substrates of the two rivers, however, are very different: the Ehen having very few boulders in comparison to the Irt, due to the presence of a weir at the outfall. This allows Ennerdale Water to be used as a water supply for the towns of north west Cumbria but, at the same time, turns the lake into an even more effective hydrological shock absorber.  Yet more of the energy that should be washing smaller stones down the river is no longer available except after the most exceptional storms.

That’s my working hypothesis, then: the Irt is a river that is subject to just enough high energy events to move the rocky substrates around yet no so many that rich algal communities cannot develop between these.  The Ehen, by contrast, has fewer events, leading to fewer opportunities for the algae to be scoured away, whilst unregulated streams such as Croasdale Beck (see “What a difference a storm makes …”) have such regular scouring spates that the algal communities are usually sparse.   I might be wrong, of course and I might be back in a years time with a better hypothesis.  Until then …

 

 

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The River Wear in November

Wear_Wolsingham_181119

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.

Wear_Wolsingham_bed_Nov18

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.

Wolsingham_181119_#1

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 …

upper_Teesdale_Nov18

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.

Learning_from_Mum_HKelly

“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.

C Entomoneis alcohol mount.jpg

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.

D Entomoneis semicell in apical view in alcohol.jpg

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).

Ntaxa_v_pH_FORWATER

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.

The Imitation Game

About a year ago, I made a dire prediction about the future of diatom taxonomy in the new molecular age (see “Murder on the barcode express …“).   A year on, I thought I would return to this topic from a different angle, using the “Turing Test” in Artificial Intelligence as a metaphor.   The Turing Test (or “Imitation Game”) was derived by Alan Turing in 1950 as a test of a machine’s ability to exhibit intelligent behaviour, indistinguishable from that of a human (encapsulated as “can machines do what we [as thinking entities] can do?”).

My primary focus over the past few years has not been the role of molecular biology in taxonomy, but rather the application of taxonomic information to decision-making by catchment managers.   So my own Imitation Game is not going to ask whether computers will ever identify microscopic algae as well as humans, but rather can they give the catchment manager the information they need to make a rational judgement about the condition of a river and the steps needed to improve or maintain that condition as well as a human biologist?

One of the points that I made in the earlier post is that current approaches based on light microscopy are already highly reductionist: a human analyst makes a list of species and their relative abundances which are processed using standardised metrics to assign a site to a status class. In theory, there is the potential for the human analysts to then add value to that assignment through their interpretations.  The extent to which that happens will vary from country to country but there two big limitations: first, our knowledge of the ecology of diatoms is meagre (see earlier post) and, in any case, diatoms represent only a small part of the total diversity of microscopic algae and protists present in any river.   That latter point, in particular, is spurring some of us to start exploring the potential of molecular methods to capture this lost information but, at the same time, we expect to encounter even larger gaps in existing taxonomic knowledge than is the case for diatoms.

One very relevant question is whether this will even be perceived as a problem by the high-ups.  There is a very steep fall-off in technical understanding as one moves up through the management tiers of environmental regulators.   That’s inevitable (see “The human ecosystem of environmental management…“) but a consequence is that their version of the Imitation Game will be played to different rules to that of the Environment Agency’s Poor Bloody Infantry whose game, in turn, will not be the same as that of academic taxonomists and ecologists.  So we’ll have to consider each of these versions separately.

Let’s start with the two extreme positions: the traditional biologist’s desire to retain a firm grip on Linnaean taxonomy versus the regulator’s desire for molecular methods to imitate (if not better) the condensed nuggets of information that are the stock-in-trade of ecological assessment.   If the former’s Imitation Game consists of using molecular methods to capture the diversity of microalgae at least as well as human specialists, then we run immediately into a new conundrum: humans are, actually, not very good at doing this, and molecular taxonomy is one of the reasons we know this to be true.  Paper after paper has shown us the limitations of taxonomic concepts developed during the era of morphology-based taxonomy.  In the case of diatoms we are now in the relatively healthy position of a synergy between molecular and morphological taxonomy but the outcomes usually indicate far more diversity than we are likely to be able to catalogue using formal Linnaean taxonomy to make this a plausible option in the short to medium-term.

If we play to a set of views that is interested primarily in the end-product, and is less interested in how this is achieved, then it is possible that taxonomy-free approaches such as those advocated by Jan Pawlowski and colleagues, would be as effective as methods that use traditional taxonomy.   As no particular expertise is required to collect a phytobenthos sample, and the molecular and computing skills required are generic rather than specific to microalgae, the entire process could by-pass anyone with specialist understanding altogether.  The big advantages are that it overcomes the limitations of a dependence on libraries of barcodes of known species and, as a result, that it does not need to be limited to particular algal groups.  It also has the greatest potential to be streamlined and, so, is likely to be the cheapest way to generate usable information.   However, two big assumptions are built into this version of the Imitation Game: first, there is absolutely no added value from knowing what species are present in a sample and, second, that it is, actually, legal. The second point relates to the requirement in the Water Framework Directive to assess “taxonomic composition” so we also need to ask whether a list of “operational taxonomic units” (OTUs) meets this requirement.

In between these two extremes, we have a range of options whereby there is some attempt to align molecular barcode data with taxonomy, but stopping short of trying to catalogue every species present.  Maybe the OTUs are aggregated to division, class, order or family rather than to genus or species?   That should be enough to give some insights into the structure of the microbial world (and be enough to stay legal!) and would also bring some advantages. Several of my posts from this summer have been about the strange behavior of rivers during a heatwave and, having commented on the prominence and diversity of green algae during this period, it would be foolish to ignore a method that would pick up fluctuations between algal groups better than our present methods.   On the other hand, I’m concerned that an approach that only requires a match to a high-level taxonomic group will enable bioinformaticians and statisticians to go fishing for correlations with environmental variables without needing a strong conceptual behind their explorations.

My final version of the Imitation Game is the one played by the biologists in the laboratories around the country who are simultaneously generating the data used for national assessments and providing guidance on specific problems in their own local areas.   Molecular techniques may be able to generate the data but can it explain the consequences?  Let’s assume that method in the near future aggregates algal barcodes into broad groups – greens, blue-greens, diatoms and so on, and that some metrics derived from these offer correlations with environmental pressures as strong or stronger than those that are currently obtained.   The green algae are instructive in this regard: they encompass an enormous range of diversity from microscopic single cells such as Chlamydomonas and Ankistrodesmus through colonial forms (Pediastrum) and filaments, up to large thalli such as Ulva.   Even amongst the filamentous forms, some are signs of a healthy river whilst others can be a nuisance, smothering the stream bed with knock-on consequences for other organisms.   A biologist, surely, wants to know whether the OTUs represent single cells or filaments, and that will require discrimination of orders at least but in some cases this level of taxonomic detail will not be enough.   The net alga, Hydrodictyon(discussed in my previous post) is in the same family as Pediastrumso we will need to be able to discriminate separate genera in this case to offer the same level of insight as a traditional biologist can provide.   We’ll also need to discriminate blue-green algae (Cyanobacteria) at least to order if we want to know whether we are dealing with forms that are capable of nitrogen fixation – a key attribute for anyone offering guidance on their management.

The primary practical role of Linnaean taxonomy, for an ecologist, is to organize data about the organisms present at a site and to create links to accumulated knowledge about the taxa present.    For many species of microscopic algae, as I stressed in “Murder on the barcode express …”, that accumulated knowledge does not amount to very much; but there are exceptions.  There are 8790 records on Google Scholar for Cladophora glomerata, for example, and 2160 for Hydrodictyon reticulatum.  That’s a lot of wisdom to ignore, especially for someone who has to answer the “so what” questions that follow any preliminary assessment of the taxa present at a site.  But, equally, there is a lot that we don’t know and molecular methods might well help us to understand this.   There will be both gains and losses as we move into this new era but, somehow, blithely casting aside hard-won knowledge seems to be a retrograde step.

Let’s end on a subversive note: I started out by asking whether “machines” (as a shorthand for molecular technology) can do the same as humans but the drive for efficiency over the last decade has seen a “production line” ethos creeping into ecological assessment.   In the UK this has been particularly noticeable since about 2010, when public sector finances were squeezed.   From that point on, the “value added” elements of informed biologists interpreting data from catchments they knew intimately started to be eroded away.   I’ve described three versions of the Imitation Game and suggested three different outcomes.  The reality is that the winners and losers will depend upon who makes the rules.  It brings me back to another point that I have made before (see “Ecology’s Brave New World …”): that problems will arise not because molecular technologies are being used in ecology, but due to how they are used.   It is, in the final analysis, a question about the structure and values of the organisations involved.

References

Apothéloz-Perret-Gentil, L., Cordonier, A., Straub, F., Iseili, J., Esling, P. & Pawlowksi, J. (2017).  Taxonomy-free molecular diatom index for high-throughput eDNA monitoring.   Molecular Ecology Resources17: 1231-1242.

Turing, A. (1950).  Computing machinery and intelligence.  Mind59: 433-460.