Paradigm shift …

When I’m teaching people to identify diatoms, I start by telling them that there are two groups: the centric diatoms, characterised by at least one plane of radial symmetry, and the pennate diatoms, which have only longitudinal symmetry.  This is a good place for a beginner to start but reality is, inevitably, more complicated.  The two diatoms I describe in the previous post are, for example, both centric diatoms but it is difficult to discern this from the photograph, because their side views do not suggest any radial symmetry.  But, as I’ve said many times before, taxonomy and identification require very different approaches.

The basic centric/pennate dichotomy, however, is not just about outline, however convenient this is as a teaching aid for beginners.  Centric diatoms have a different mode of reproduction (oogamous) compared to pennates (isogamous) and also typically have many discoid plastids rather than a few plate-like ones.   I’ve illustrated one of the diatoms we saw at Deptford – Hydrosera triquetra – in the illustration at the top of the post, in order to delve deeper into this topic of shape as an identification aid.

The first thing we notice is that the valve face is not circular.  The literature describes it as “triangular” but, in reality, the shape is closer in shape to a star-of-David.  You could, however, take a pair of compasses and draw a circle that connected all of the valve angles, so you can see how this may be related to the more obviously circular diatoms.  The valve face is covered with a seemingly random array of coarse pores apart from the ends of three of the valve angles (termed “pseudocelli”) which appear to be plain, but which are, in reality, a mesh of very fine pores through which mucilage is secreted. This allows the cells to join together to form chains, or to attach to surfaces.  

Hydrosera triquetra is related to the other diatom I illustrated in the previous post – Biddulphia pulchella but whilst I can just about persuade you that Hydrosera is related to centric diatoms, it is harder to do this for Biddulphia, which is more obviously lanceolate in outline.  It also has psedocelli, which hints at a relationship with Hydrosera, and also has many small discoid chloroplasts (hinting at a relationship with the wider centric diatoms) but it sure ain’t round, by anyone’s definition.

The efforts of many taxonomists to shoehorn Biddulphia into the centric diatoms recalls Thomas Kuhn’s observations in The Structure of Scientific Revolutions – scientists approach data with strong preconceptions and outliers to the prevailing wisdom require ever more elaborate justifications to fit the pattern, something Kuhn described as “puzzle solving”.  Eventually, someone recognises that “normal science” is no longer viable, and proposes a new theory – a so-called “paradigm shift” (a phrase first used by Kuhn). 

In the case of Biddulphia and Hydrosera, the paradigm shift came in a 2004 paper by Linda Medlin and Irena Kaczmarscka who proposed a new class, Mediophyceae, for these “multipolar centrics” based on molecular sequence data, and that has now become the established classification (see “Who do you think you are?”).  Or, to use the language of Kuhn, we have re-entered a phase of “normal science”, at least until the next revolutionary biologist comes along with a better idea …

My picture was supposed to show Hydrosera triquetra growing on a vertical wall in Deptford Creek (with the bridge carrying the Dockland Light Railway over the river just visible in the background).  There are eight orders of magnitude difference between the Hydrosera cells (which are relatively chunky by the standards of diatoms) and the DLR bridge – which is a depth of field way beyond any camera could achieve.  Less impressive, from my point of view, is the appearance of a few mutant Hydrosera cells with five, rather than six, poles.  I finished the picture in rather a hurry as I wanted to post this before we headed off on holiday.  Sorry.

References

Ashworth, M. P., Nakov, T., & Theriot, E. C. (2013). Revisiting Ross and Sims (1971): toward a molecular phylogeny of the Biddulphiaceae and Eupodiscaceae (Bacillariophyceae). Journal of Phycology 49: 1207-1222.

Kuhn, T. (1962).  The Structure of Scientific Revolutions.  University of Chicago Press.

Medlin, L. K., & Kaczmarska, I. (2004). Evolution of the diatoms: V. Morphological and cytological support for the major clades and a taxonomic revision. Phycologia 43: 245-270.

Some other highlights from this week:

Wrote this whilst listening to:  Marika Hackman, following her gig at the Cluny in Newcastle.

Currently reading:  The Story of Art Without Men by Katy Hessel.  My daughter thought I needed educating.

Cultural highlight:  Marika Hackman in a packed Cluny.  Can’t help wondering why she’s not better known.  

Culinary highlight:  immediately prior to the gig, we ate at the Ship Inn, just across the road, which has all the attributes of a traditional Newcastle pub with football on big screens and “pub grub” on the menu, only the whole menu is vegan.  We ate their take on fish and chips – tofu wrapped in seaweed and then battered and deep fried – which rather proved my point that fish is algae-flavoured protein.

Dispatches from the city of migrants …

The journey to the location for this post started at the foot of the first “s” in the East Enders title sequence and ended beside the little blue squiggle at the bottom of the television screen, directly under the “a”.  I got off the Elizabeth Line at Stratford with no other plan other than that I had some time on my hands and headed roughly south, triangulating on glimpses of the O2 Arena and Canary Wharf as best I could.  I passed the splendid Italian Gothic edifice at Abbey Mills that houses the pumping station built as part of Bazelgette’s great sewer, walked alongside the muddy lower reaches of the River Lea, skirted numerous industrial estates and finally arrived, some two hours and nine kilometres later, at Island Gardens, a small area of green amidst the docklands sprawl, with a splendid view across the Thames to Wren’s Royal Navel College.  After crossing the river via the Greenwich foot tunnel, I emerged beside the Cutty Sark from where a short walk brought me to the blue squiggle that was my destination. 

That blue squiggle is Deptford Creek, scene of some posts at the end of last year (see “Floundering around in Deptford Creek” and “Throwing shapes …”) and I had come back to see how the project was progressing as well as finding some time to poke and scrape at more patches whose golden-yellow hue promised interesting diatoms.  The mudflats themselves looked much greener than I remembered, but it is hard to know if this is a genuine biological phenomenon or is just the random chance of two observations being different.  Today, however, I was more interested in what was growing around on the training walls at the edge of the creek rather than on the mud itself.  

My eye was caught straight away by bright green growths on the shelf on the wall beside the slipway.  Their distinctly felty texture made it easy to recognise the genus as Vaucheria although naming the species is a more difficult job.  We’ve met Vaucheria several times in freshwater (see “the pros and cons of cell walls …”) but it is also commonly found in brackish habitats.  My interest today was not in what species was growing, but in the way that it was helping to build a habitat within which a clump of moss and the shoot of a flowering plant were able to grow.  We saw this with happening with Rhizoclonium riparian during my previous visit (see “If only we looked …”); this time it is an alga from a different phylum, but we are looking at essentially the same phenomenon.

A patch of Vaucheria growing on the wooden training wall beside Deptford Creek, March 2024.  Note the moss (back right) and the shoot that have established themselves in the algal patch.  The patch is about 30 cm across.   The photo at the top of the post shows the training wall beside the slipway at Deptford Creek. 

Underneath this shelf, there was a distinct yellow-brown patch on the wall whose dominant constituent was Hydrosera triquetra.  I commented on its absence in a previous post (see “Deptford’s Heart of Darkness …”) but, in truth, the mudflat is not where I would most expect to find it.  It is a chain-forming diatom that seems to be associated with vertical surfaces and which can tolerate exposure. When individual cells are seen end-on (“valve view”), they are very distinctive, resembling a Star of David, with two overlapping triangles; however, the cells attach at these faces and the characteristic shape is not immediately apparent when seen in fresh material.  You need to focus carefully to understand the third dimension (see “Seeing with my fingers …”).  

Hydrosera triequetra in Deptford Creek, March 2024.  The left-hand image shows a patch growing on a wooden support (the central one visible in the image at the top of the post). The right-hand image shows a magnified view. The scale bar is 20 micrometres (= 1/50^th of a millimetre) long.  

Hydrosera triquetra was first observed in the Thames in the early 1970s, and is widely-assumed to have been accidentally introduced, perhaps by a ship discharging ballast water.  Now it is widely-established.  I’m often sceptical of claims about “alien” species  but H. triquetra is sufficiently large and distinctive that it seems unlikely that it would not have been seen by earlier generations of microscopists at least occasionally.  Whether it justifies the term “invasive” is a moot point (see “Pens are too light …”).   That would require some evidence of wholesale changes in both the composition of the microscopic flora, and the way it functioned.  Personally, I love the diversity of modern London and am prepared to embrace a migrant diatom or two without feeling the need to apply pejorative adjectives.  

On the opposite side of the slipway, I noticed a seepage that, again, had a golden-brown hue suggestive of diatoms.  However, I could not see any Hydrosera growing amidst this assemblage, instead, there was a mix of Melosira varians and Biddulphia pulchella, a relative of Hydrosera, which lives in brackish water and forms zigzag colonies.  Motile diatoms such as Nitzschia sigma glided in and around these filaments.  The presence of Melosira varians is interesting.  I am fairly sure, based on examination of living cells, that these filaments are not one of the related species of Melosira that are more tolerant of salinity. That a freshwater species with only mild affinity for salt is thriving here supports some observations of higher plants on the slipway made by Nick and Andy from Creekside Discovery Centre. They noticed that these, too, are mostly not especially salt-tolerant plants, leading them to think that the upper slipway represents a freshwater tidal marsh, rather than a salt marsh, and that it is the result of fresh water from the Ravensbourne being lifted above the denser salt water that pushes into Deptford Creek on each tidal cycle.  A freshwater species tolerant of some salt rubbing along beside a brackish species that can cope with an occasional dose of freshwater seems like a good metaphor for this part of London where people from every part of the world live side-by-side.

Another seepage beside the slipway at Deptford Creek, this time with a mix of Melosira varians (right) and Biddulphia pulchella (left). The scale bar is 20 micrometres (= 1/50^th of a millimetre) long.

Some other highlights from this week:

Wrote this whilst listening to:  vintage Jefferson Airplane and, for contrast, Kendrick Lamar’s To Pimp A Butterfly.

Currently reading:  The Secret Diaries of Charles Ignatius Sancho by Patterson Joseph, a novel that is, by coincidence, about 18^th century migrants in London.

Cultural highlight:  Lines, a play at the Crucible in Sheffield exploring injustice in Palestine and Uganda.  Rather challenging.

Culinary highlight:  Seven course tasting menu at Prashad, an Indian vegetarian restaurant  in Drighlington, just south of Leeds

What lurks beneath The Skating Minister?

My reason for visiting Duddingston Loch (see “Paddling in January”) was to contrast the way that a location is perceived in an art gallery with the way that it is seen by a scientist.  Duddingston Loch is familiar as the location for Henry Raeburn’s The Skating Minister. A few years ago this was voted “Scotland’s favourite painting” and it is one of the biggest attractions at the National Gallery of Scotland.  But how many of the people who gaze at the image hanging on the gallery wall know that it represents a location within walking distance of the gallery itself, and how many of that subset know anything about this particular loch other than that it is the setting for this rather famous painting?  This is a theme I’ve circled around for most of the time I’ve been writing this blog.  We “see” a place differently, depending on what we are looking for.   For the casual visitor to the National Gallery of Scotland, Duddingston Loch is no more than a setting for a painting, and the character of the loch itself was never part of Raeburn’s vision for his painting.   For Edinburgh’s citizens, the loch is somewhere to enjoy fresh air and nice views without the need to travel beyond the city limits.  Keener naturalists might take binoculars and watch the waterfowl.  I’m pushing that “natural history” angle one stage further today by exploring the world that only becomes apparent when you peer through a microscope.  

Even then, there is not one single world that becomes apparent.  In my January post I wrote about the algae that I saw in the fresh sample that I had brought back.  Since then, I have prepared the sample for examination at high magnification, and the results of that are presented in this post.  I found a total of 37 different species of diatom in my examination, of which 17 are illustrated below.  Of particular note, given where the sample was collected, are the variety of species of Navicula and Nitzschia.   I referred to these in my earlier post as “gliding around” because, when you observe them on a microscope slide, they move as gracefully and serenely as the Reverend Robert Walker appears to do in Raeburn’s painting.  In Duddingston Loch, however, their habitat is not an ice-smooth microscope slide, but a tumble of tiny silt and sand particles. Their movement is more like that of the algae I described from Deptford Creek (see “Commuting to work …” and links) but without the strong tidal rhythms.  Just as the swans who glided across to me in the expectation that I was going to toss them some bread, so the diatoms here are savvy enough to adjust their position when they think that there is some benefit.  In their case, as “plants”, rather than “animals”, they are more interested in light than bread.   

Diatoms from Duddingston Loch I: Fragilariophyceae: a., b. Fragilaria radians; c.,d.,e.: Pseudostaurosira brevistriata; f.,g. Staurosira construens; h., i. Staurosira binodis; j. Staurosirella pinnata; k.,l. Pseudostaurosira elliptica.  Scale bar: 10 micrometres (= 1/100^th of a millimetre).  This post is about the range of encounters we have with nature.  Many people come to Duddingston Loch simply for the pleasure of being in a being in the countryside, albeit in the midst of a large city.  Many others experience it vicariously via Henry Raeburn’s picture, either in the National Gallery of Scotland or in reproduction.  But others encounter it as more active observers, whether of the birds and other wildlife or, in my case, looking at the microscopic life that inhabits the loch.  There is a direct pleasure that we obtain from this observation – another form of the type of encounter that casual visitors are experiencing.  However, we can take the observer’s experience one step further.  When we pass from purely observing to recording what we see, another opportunity arises.  We can look at Duddingston Loch not in isolation but as one of many small lochs in Scotland.  I can, for example, compare the records I have made at Duddingston with those myself and others have made at other lochs and ponds around the UK.  Is there anything unique about Duddingston Loch and, more importantly, is there anything that should concern those involved with its management?   

My day job involves performing “health checks” on lakes and rivers and I could not resist applying one of these tests to the data I collected from Duddingston Loch.  Unfortunately, the result was not encouraging: Duddingston Loch would not, I am afraid, meet the criteria for “good ecological status” based on the sample I collected.  The standard test is based on two, rather than a single sample so we should not leap to a hasty conclusion. However, to take a footballing analogy, Duddingston Loch is going into the second leg of this fixture at a distinct disadvantage.  

Diatoms from Duddingston Loch II: other groups.  a., b.,c.,d. Amphora pediculus; e. Rhoicosphenia abbreviata; f.,g. Navicula caterva; h., Platessa conspicua; i., Sellaphora atomoides; j. Encyonema leibleinii; k. Epithemia adnata; l. Nitzschia amphibia; m., Nitzschia fonticola; n. Nitzschia solgensis; o.,p.,q.,r. Nitzschia soratensis.  Scale bar: 10 micrometres (= 1/100^th of a millimetre).  

The most likely reason is, I suspect, the wildfowl themselves.  Duddingston Loch has a very small catchment area, mostly draining the south and west side of Arthur’s Seat, and unlikely to be a major source of nutrients.  As well as the ducks and swans greedily feeding on bread brought by visitors, there is also a heronry at the west end of the Loch.  Birds such as herons which scout around quite large areas but then return to the same location each night are going to transfer nutrients from other ponds and streams into Duddingston Loch via their faeces.  There is quite a large literature on the impact that birds can have on water quality in small shallow lochs.  Of course, birds also have a positive impact, drawing naturalists to locations such as this and it is also possible that it is the loss of good habitats more widely that ends up in birds congregating in numbers in the places where conditions are favourable.  I certainly don’t want to end this post by annoying the ornithological lobby.  Not least because if I want to play out the “second leg” of this particular fixture, then I will need to keep on the right side of the wardens!  

References

Gremillion, P. T., & Malone, R. F. (1986). Waterfowl waste as a source of nutrient enrichment in two urban hypereutrophic lakes. Lake and Reservoir Management 2: 319-322.

Scherer, N. M., Gibbons, H. L., Stoops, K. B., & Muller, M. (1995). Phosphorus loading of an urban lake by bird droppings. Lake and Reservoir Management 11: 317-327.

Tobiessen, P., & Wheat, E. (2000). Long and short term effects of waterfowl on Collins Lake, an urban lake in upstate New York. Lake and Reservoir Management 16: 340-344.

Some other highlights from this week:

Wrote this whilst listening to:  Laufrey, lush jazz-pop from Iceland.

Currently reading:  To the River, by Olivier Lang, a travel book following the Sussex Ouse from source to sea, with reflections on the life of Virginia Wolff.  And I have just finished The Fraud by Zadie Smith.

Cultural highlight:  Zone of Interest, a remarkable film about Auschwitz that perfectly captures the meaning of the phrase “banality of evil”.

Culinary highlight:  A home-cooked Ghormeh Sabzi (Iranian lamb, kidney bean and herb stew) wins over an enjoyable but somewhat lacklustre meal at The Ivy in York.