Distant relatives …


The easing of lockdown means that fieldwork can resume (real fieldwork, that is, rather than virtual perambulations around the margins of Lough Down) and I was in the Lake District last week collecting samples for an ongoing project.  The New Normal means a rethink of logistics to account for social distancing which, in my case, meant Heather taking the place of Ben as BenthoTorch wielder so that we could safely share a single car.

Our travels took us to the River Calder, a short river that rises on the western fells of the Lake District, just south of Ennerdale Water, and flows about 12 kilometres to join the Irish Sea at Sellafield (it actually flows through the BNFL site and those with a long memory may remember that the first incarnation of the nuclear reprocessing site was known as “Calder Hall”).   This is one of a number of rivers of this name in the UK, with an ancient Celtic root referring either to the violence of the flow or the stony nature of the bed.   The two roots are linked: a harsh hydrology will flush away all but the largest and roughest stones and, as the photograph above shows, the bed of the Calder has plenty of these.

When not photographing me peering at stream beds through a bathyscope, Heather noticed some bright yellow growths on the floor of the forest surrounding the stream which she recognised as a slime mold with the rather unappetisiing name of dog’s vomit.  For once, the Latin name, Fuligo septica, sounds more appealing.   Under the microscope, all I saw were spherical spores but these will germinate and the cells will aggregate to form an amoeboid-like mass that moves around searching for nutrients.    YouTube has some fascinating videos that shows this happening.


Fuligo septica – dog’s vomit slime mold – photographed in woodland beside the River Calder, Cumbria, June 2020 (photograph: Heather Kelly)

Slime molds interest me for another reason today: they are a group that has bounced around the tree of life in the years since I started my career.  When I was at school, slime molds were dealt with cursorily as one group within the fungi which, in those far-off days, were considered to be part of the plant kingdom.  In the far past, algae and fungi were grouped together as the “Thallophyta”.   This particular slime mold still sits in a class called the Myxomycota (literally “slime fungi”) which alludes to this heritage.  Now, the idea of fungi being relatives of the plants is quite laughable: they differ in so many ways, not least the completely different form of the cell wall and the absence of photosynthesis.   The fungi are treated as a separate kingdom but the slime molds have undergone one further divorce. No longer are they considered to be a group within the fungi, rather they have all been shifted to the Protozoa, itself also a separate kingdom.  The slime molds do, superficially, resemble some fungi in some respects but, in others, they are completely different.  This fragmentation from the straightforward view of biological classification of the past, resembles that which has occurred in the algae: once considered primitive “plants” but now spread between four kingdoms.   The Euglenophyceae, which have appeared in this blog on a couple of occasions (see “A visit to Loughrigg Fell” and “Puzzling puddles on the Pennine Way”), are, in fact, more closely related to dog’s vomit slime mold than they are to any other group of algae.


Microscopic view of cells of Fuligo septica, dog’s vomit slime mold. Scale bar: 10 micrometres (= 100th of a millimetre).

The slime molds are not the only group that used to be classified as fungi but which are now more closely allied to algae.   Potato blight (Phytophora infestans) belongs to the Oomycota (or “egg-fungi”, due to their large oogonia).   This group is now classified in the same kingdom (Chromista) and phylum (Heterokontophyta) as several groups of algae including the diatoms and brown seaweeds.   It is a fairly distant relationship in the grand scheme of things (equivalent to comparing yourself to a sea squirt) but it still means that I make my living from relatives of the organism that drove my ancestors to leave Ireland.


Some other highlights from this week:

Wrote this whilst listening to: old Glastonbury sets on the BBC iPlayer, particularly from 2009 and 2010, when I was there.   Notably Blur’s headline set (watch out for the crowd surfer who disappears from view halfway through Song 2.  I was directly underneath.   Also Dizzee Rascal from 2010 and highlights from Bruce Springsteen’s 2009 set.   And Radiohead from 1997.

Cultural highlights:  The new interpretations of Alan Bennett’s Talking Heads, produced by Nicholas Hytner on BBC2.  ]

Currently reading:   Lethal White by Robert Galbraith (aka J.K. Rowling).

Culinary highlight:  French onion ramen, a French/Japanese fusion from Tim Anderson’s Vegan Japaneasy.

The search for the perfect river …


One of the ironies of studying the health of aquatic ecosystems is that, whilst it is easy to recognise a polluted river, it is much harder to define the opposite: a river in its pristine state.  Back in the 1970s you could argue that it was not a particularly pressing question: there was so much obvious pollution in our rivers, lowland ones in particular, that simply reducing that load was the immediate concern.

The Water Framework Directive (WFD) ushered in a paradigm shift: defining the health of a river not in terms of the presence of undesirable traits (such as pollutants) but by the presence of desirable ones.  Just as a healthy human is defined by more than the absence of illness, so a healthy ecosystem means more than just an absence of pollution.   However, moving from these vague assertions to workable measures of river “health” has proved to be a substantial challenge.  The presumption was that we can define the health of a river by comparing its ecological properties with those of rivers that we already know are healthy, just as a doctor has a pre-determined idea of what a healthy body should look like and how it should behave.  Or, to put it another way, whether dealing with the human body or a river ecosystem, we compare what we can see with what we would expect to see were that body or ecosystem in peak condition.   Yet, for ecologists that begged another question: these expectations should be based on our own experience yet are there enough rivers left on our small, crowded , busy island in this perfect state to provide us with the experience we need in order to judge the condition of every other river?

Our search for these “perfect rivers” took us to the remotest corners, where the human footprint is barely discernible.  Information we got from these rivers allowed us to form a view of the properties to which all rivers and lakes should aspire.  There was, however, a hitch: these remote, unpopulated regions are generally unpopulated for a reason: their geological foundations made them unsuitable for most forms of agriculture, for example, so using these as a basis for comparisons with rivers in regions where the geological foundations gave rise to flatter landscapes and richer soils was not ideal.

We’ve grappled with this problem over the years and, like Goldilocks, failed to achieve complete satisfaction on our first two attempts.   Our original effort was deemed, after testing, to be too stringent by Environment Agency.  Chalk streams, in particular, even when they supported rich invertebrate and plant communities failed to achieve the crucial “good status” criterion when their diatoms were assessed.  The second effort, however, swung too far the other way, which made it unusable in hard water areas.   We’ve been scratching our heads for a few years to find a way of defining the “expected” condition for the large number of rivers that flow across lowland areas of the UK, but for which there are no pristine examples against which their ecological properties can be compared.

Our third attempt (“just right”, to push the Goldilocks analogy) has just been published in Ecological Indicators.   What we have done differently this time is, rather than seek out perfect examples of lowland rivers, we have looked at a large dataset of TDI values calculated from diatom samples – irrespective of the level of pollution – and plotted that against alkalinity (which shows the influence of limestone in the catchment).   The bottom edge of this relationship, then, shows the best we can expect at any particular alkalinity.   There are bells and whistles that don’t really belong in a blog post, but that’s the essence of the new approach.


Modelled reference TDI values overlain on scatter plot of observed TDI. Blue line = original reference equation (“too stringent”: spring dashed, autumn solid); black line = current reference equation (“too lenient”); red line = new reference equation (“just right”: spring dashed, autumn solid).   Figure 2 from Kelly et al. (2020).

This immediately raises a question: how do we know that the best we’ve got is the best we can attain?  Suppose that all of our rivers are sufficiently altered by human actions that even the best we’ve got isn’t good enough?   There isn’t an easy way to answer this and, in fact, this approach was frowned upon for a long time because of the ambiguity in the outcomes.  However, having failed with all other approaches, and with so much more data available now, we felt that it was worth revisiting this approach.  Even so, the final step still needs to involve a scrutiny of the values produced in order to make a judgement about whether the best we’ve got equates to the elusive “reference state”.  The alternative is to use this value to define a different boundary (when I was involved in a similar exercise for Romanian lakes, for example, we decided that the best we had equated to the boundary between high and good status, rather than to the reference state).

The pure scientist may shudder at the thought that the final call is subjective rather than objective but a philosopher might understand us better. We have shifted our perspective from realism to idealism: the perfect stream, in other words, exists in our imaginations not in a real landscape (just as economists know that “perfect competition” is unattainable).   The early years of WFD implementation were dominated by this search for ideal “reference sites” but, apart from a few remote areas where population densities were low and wilderness still existed, the reality often proved elusive.  Over time, attention shifted to making sure that everyone agreed on a notion of “good enough” (the boundary between “good ecological status” and “moderate ecological status”).  Pragmatism won out over idealism and, more importantly, everyone recognised the dangers of basing a nation’s water management policy on extrapolation from the few plausible “reference sites”.    However, we’ve tried to keep alive the idea of a “guiding image”: a competent ecologist should be able to visualise the ecological condition to which s/he hopes that any individual stream or river could attain.    Nigel Willby wrote a thought-provoking editorial for Aquatic Conversation on this topic back in 2011 and this exercise of imagination, which seems at odds with the quantitative thrust of most modern ecology, is a valuable reality-check for the outcomes of high -powered statistical models.   Models are good friends, when it comes to addressing questions such as this, but poor masters.  At some point, some old-school boot-on-the-ground common sense is needed to spark their dry quantitative outputs into life.


Kelly, M.G., Phillips, G., Juggins, S. & Willby, N.J. (2020).  Re-evaluating expectations for river phytobenthos assessment and understanding the relationship with macrophytes.  Ecological Indicators 117: 106582

Willby, N.J. (2011).  From metrics to Monet: the need for an ecologically-meaningful guiding image.  Aquatic Conservation: Marine and Freshwater Ecosystems 21: 601-603.


Low Butterby pond, an ox-bow lake on the flood plain of the River Wear with flag iris and yellow water lily.  The photograph at the top of the post shows Lund Bridge over the River Irt in Cumbria. 

Some other highlights from this week:

Wrote this whilst listening to: I’ve taken a brief break from my Bob Dylan retrospective.  Enjoyed Phoebe Bridgers new album, Punisher, which led me back to Julien Baker’s album Turn out the Lights, as well as their joint EP as Boygenius.

Cultural highlights:  Days of the Bagnold Summer: lo-fi British comedy about a heavy-metal obsessed adolescent and his relationship with his mother.

Currently reading:   Peter Hessler’s Country Driving: A Chinese Road Trip.   Fascinating travel book that gets under the skin of modern China.

Culinary highlight:  a Victoria sponge with “peanut butter and jelly”-flavoured icing.  The search for a decent dairy-free icing/frosting continues with this is a strong contender.

More about Spirulina …


This post is a brief follow-up to my post “Twisted tales …” in which I wrote about the cyanobacterial genus Spirulina.   My interest piqued, I bought a packet of milled Spirulina from a local health food shop and added it to pasta dough to make a rather vivid green tagliatelle.   The photograph below shows the result of adding about a tablespoon of Spirulina powder to a dough made from 150 g of flour and two eggs.

The effect, I should add, was mostly to add colour rather than flavour.   However, it made a fine bed to a portion of salmon cooked in a brandy source to an Asturian recipe in Claudia Roden’s The Food of Spain.   I remain a sceptic about the claims for Spirulina as a “superfood” (is there any such thing?) but it is high in protein (67%) and low in fat (0.9%) so it is certainly healthier than many of the ingredients that pass through our kitchen.   I’m also expecting that it will add a umani “kick” to sauces, stews and soups, though we haven’t got around to trying this yet.


Spirulina powder and (right) home-made pasta dough with added Spirulina.  The photograph at the top of the post shows the fragments of Spirulina filaments in the powder (each about 10 micrometres – 100th of a millimetre – wide).

Some other highlights from this week:

Wrote this whilst listening to: Down in the Groove, Dylan and the Dead (a live album recorded in 1989 with the Grateful Dead) and Modern Times.  The latter is definitely a return to form after a few flat studio albums in the mid-1980s.

Cultural highlights:  Not sure that I can think of one this week.

Currently reading:   J.K. Rowling’s Harry Potter and the Chamber of Secrets: more nostalgia for the days when the children were young enough to want books read to them.

Culinary highlight:   Probably the salmon in a brandy sauce mentioned above served on home-made tagliatelle.


The strange case of the migrant diatom …


I’m taking time during lockdown to catch up on some papers that I had been meaning to write for some time.  One of these, for a special issue of the journal Ecological Indicators, is about the diatoms of Cyprus, a subject that I’ve touched upon in a few earlier posts (see “Diatoms from the Troodos Mountains”).  Writing about Cyprus, even via the dry prose of an academic paper, reminded me how much I had enjoyed earlier visits, and when I might be  able to return.

Most of the hard work to produce the data in this paper was, I have to admit, done by Marco Cantonati and, in the process, he has found several species that had not previously been described, which makes us wonder if the endemism for which the higher plant flora of Cyprus is well-known also extends to the diatoms.  There has been a vigorous debate about the extent to which diatoms are cosmopolitan rather than restricted to particular geographic areas in recent years, with evidence now to show that some species definitely seem to be cosmopolitan whereas others are much more localised in their distribution.  The diatom flora of an island such as Cyprus ought to be a valuable test case for this.

One species that we had not seen before but which, after searching the literature, Marco was able to match with a previously-described species was Achnanthidium tepidaricola – shown in the picture at the top of the post.  Achnanthidium is a large genus of small diatoms, and we have only really started to appreciate the diversity within the genus over the past 20 years or so (see “Quantifying our ignorance …”).  This particular species, however, has a story to tell.  It was first found growing on a wet stone wall in a greenhouse in the National Botanic Garden in Meise, Belgium by Bart van der Vijver a few months after the wall had been constructed.   Finding the same species in Belgium and Cyprus ought to be a hint that it is relatively cosmopolitan.  However, our story has an interesting twist …

The twist is that the wall that Bart sampled in the greenhouse in Meise was built with stones that had been imported from Turkey.  Suddenly, A. tepidaricola is looking less Flemish and more like a migrant.   Turkey is, of course, the nearest mainland country to Cyprus, and shares the same arid climate of the eastern Mediterranean.   Many of the streams in this part of the world will, naturally, dry out in the summer and the diatoms will have to be prepared to survive in these conditions.   Suddenly, A. tepidaricola growing both in Cyprus and on that one particular wall in Belgium is looking less like evidence of endemism and more like a hint that, even if not endemic to Cyprus, this species may be characteristic of the eastern Mediterranean.  It may be more widespread than that, but this is certainly where it is being recorded at the moment.

That’s the trouble with biogeography: the distribution of species is forever shifting, and our modern joined-up world only accelerates this process.  Dump a pile of stones from Turkey almost anywhere else in Meise and the Flemish climate would probably have sent Achnanthidium tepidarociola to the Great Biofilm in the Sky.  But these particular stones were put into a greenhouse where they were able to thrive and, eventually, to be noticed by Bart.   Humans helping previously unknown bugs to move across the world?  Where else have I heard about that before?

The photo at the top of this post was taken by Marco Cantonati and shows a population of Achnanthidium tepidarocola from Vyzakia, Cypris in March 2019.


Van der Vijver, B., Jarlman, A., Lange-Bertalot, H., Mertens, A., de Haan, M. & Ector, L. (2011).  Four new European Achnanthidium species (Bacillariophyceae).  Algological Studies 136/137: 193-210.


Some other highlights from this week:

Wrote this whilst listening to: 1980s Bob Dylan (probably not his greatest period): Empire Burlesque and Knocked Out Loaded.  Also an elderly, rather scratchy recording of Rachmaniov’s first two piano concertos with Rachmaniov himself on piano.   And Scottish singer-songwriter Siobhan Wilson’s There Are No Saints.  Well worth checking out, if you have never heard her before.

Cultural highlights:  Jojo Rabbit.   This one split the critics but was a box office hit.  There were too many negative reviews when it first came out for us to make the trip out to see it but our son persuaded us to give it a try.  Glad we did.   Very clever soundtrack.

Currently reading:   HG Well’s War of the Worlds.

Culinary highlight:   Caesar Salad, from a Felicity Cloake recipe in The Guardian.  We also found some pumpkin lurking in the depths of the freezer and turned it into a pie.   Ate both whilst sitting in the garden: a rare treat in our climate.