A load of balls …

Lough_Cullin_BKennedy

This post is still mostly about the ecology of Lough Down, though it draws heavily upon photographs taken at Lough Cullin, in County Mayo, Ireland.   Lough Down shares some characteristics with Lough Cullin, but more with Lake Wobegon.   I suspect that the summers in Lough Down are not quite as long or as hot as those experienced around Lake Wobegon but, also, that a walker passing around the edge of Lake Wobegon would not see the round balls of algae that are a common sight along the shoreline of Lough Down.   Maybe I’m wrong: if anyone in Minnesota knows differently, please do let me know.

From a distance, these look like an unsightly mass of algae cast up on the foreshore; it is only when you get close that you see that this mass is, in fact, composed of a large number of discrete spherical growths.   You can see, in the photograph below, where Bryan Kennedy, my erstwhile Lough Down correspondent, has built a few of these into an Andy Goldsworthy-esque sculpture.   These are “Cladophora balls”, a phenomenon encountered in lakes around the northern hemisphere.  In Japan, they’ve even made their way onto postage stamps.

Aegagropila_Lough_Cullin

Aegagropila linnaei washed up on the shore of Lough Cullin, Co. Mayo, Ireland.  The photograph at the top of the post also shows Lough Cullin (photographs: Bryan Kennedy).

Until relatively recently, as their name suggests, the alga from which these balls are formed, belonged to the genus Cladophora, a frequent subject on this blog (see “The pros and cons of cell walls” for a recent example).   Like Cladophora, these are branched filaments composed of relatively large, multinucleate cells with a reticulate chloroplast.  This was, however, recognised as a different species to Cladophora glomerata, the common species of enriched lowland rivers: Cladophora aegagropila.  However, recent molecular studies have shown that it is not so closely related to Cladophora glomerata as its outward appearance suggests, leading to the resurrection of a very old name, Aegagropila linnaei.

In rivers, Aegagropila linnaei forms carpet-like growths of short filaments, not growing into the long wefts that we associate with Cladophora glomerata.  However, C. glomerata can sometimes be profusely branched as well, so telling these two species apart both in the field and under the microscope can be tricky.   One of the most useful characteristics is that the branches of Aegagropila are sub-terminal, meaning that they arise just below the end of the parent cell, rather than at the end, as is the case in Cladophora (see diagram below).   It is strange that two such similar species in appearance are, in fact, not particularly closely-related.  This is, however, an important distinction asA. linnaei prefers, as far as we can tell, less enriched conditions than C. glomerata.

Aegagropila

Left: a section through a ‘Cladophora’ ball from Lough Cullin and, right, profusely-branched filaments of Aegagropila linnaei.  Photographs: Bryan Kennedy.

Why does it form these distinctive spherical growths in lakes?   I have not managed to find a paper that gives an authoritative explanation so here are a few possibilities, none mutually exclusive.  First, filamentous algae that display apical growth and copious branching tend to form hemispherical growths if attached and spherical ones if not.  We’ve seen that for Cyanobacteria such as Rivularia (see “More about Rivularia”) and Gloeotrichia (see “Rewriting history at Talkin Tarn”).  Second, the constant ebb and flow in the lake littoral zone will create a physical stress on attached carpets of Aegagropila leading, eventually, to parts becoming detached.  Third, the profuse branching that is characteristic of Aegagropila will mean that adjacent filaments will become entangled around another, creating a Velcro-type effect.   Finally, the apices of the filaments will continue to grow towards the light, meaning that the free-floating balls gradually expand in size.

Aegagropila’s dislike of nutrient-rich conditions mean that the number of places where it is found has been decreasing over recent decades.   It was, for example, recorded from several locations in the Netherlands in the past but not since 1967.  There are records from in the UK, but mostly from the more remote regions.   There are also a number of records from loughs in Ireland, as is the case here  The river form is, in my opinion, hard to differentiate unequivocally from Cladophora glomerata without very careful examination and this raises the spectre of “identification by association”, particularly when it is recorded by macrophyte surveyors who often do not have time to check material under the microscope.   Christian Boedeker, who has done much of the recent work on Aegagropila, thinks that a limited dispersal capability will mean that it will be slow to re-colonise habitats once it has been lost.

So that’s another day over here at Lough Down, a quiet lake that no-one has visited but everyone has got to know very well.   It’s one of those places, I like to think, where naturalists notice all of nature, not just the pretty, cuddly and exciting things.  Everyone leaves a little wiser, even if only because they have noticed that something everyone else overlooks is, actually, a thing of great intrinsic beauty.  As Garrison Keillor himself once said: “Thank you, God, for this good life and forgive us if we do not love it enough”.

Aegagropila_v_Cladophora

Diagrams of branching patterns in Aegagropila linnaei (a.) and Cladophora glomerata (b.).   Note how the branches of A. linnaei arise just below the end of the cell (“sub-terminal”, indicated by arrows) whereas the branches of C. glomerata arise at the ends.

References

Boedeker, C., & Immers, A. (2009). No more lake balls (Aegagropila linnaei Kützing, Cladophorophyceae, Chlorophyta) in The Netherlands? Aquatic Ecology. https://doi.org/10.1007/s10452-009-9231-1

Boedeker, C., Eggert, A., Immers, A., & Wakana, I. (2010). Biogeography of Aegagropila linnaei (Cladophorophyceae, Chlorophyta): A widespread freshwater alga with low effective dispersal potential shows a glacial imprint in its distribution. Journal of Biogeography. https://doi.org/10.1111/j.1365-2699.2010.02309.x

Boedeker, C., Kelly, C. J., Star, W., & Leliaert, F. (2012). Molecular phylogeny and taxonomy of the Aegagropila clade (Cladophorales, Ulvophyceae), including the description of Aegagropilopsis gen. nov. and Pseudocladophora gen. nov. Journal of Phycology. https://doi.org/10.1111/j.1529-8817.2012.01145.x

 

Some other highlights from this week:

Wrote this whilst listening to: This post has been a long time in gestation, so ’ve listened to a lot.  These included Bob Dylan’s Shot of Love, Infidels and Real Live, as well as Courtney Barnett’s A Sea of Split Peas and Arvo Pärt’s Tabula Rasa.

Cultural highlights:  The National Theatre At Home’s Streetcar Named Desire, starring Gillian Anderson.

Currently reading:   JK Rowling’s Harry Potter and the Philosopher’s Stone.  Comfort reading.

Culinary highlight:   I have to admit that fish, chips and mushy peas from Bells in Gilesgate was hard to beat.

How not to win the Hilda Canter-Lund competition

HCL_winners_2009&2010

The 2020 Hilda Canter-Lund competition for the best photograph of an alga is underway again, with a closing date of Friday 5 June.  Over the years I’ve written a few posts to encourage entries, by focussing on what makes a good entry for the competition (listed at the end of this post).  This time, however, I’m coming at the problem from a different angle because, each year, as we make our first review of entries in order to prepare a shortlist, the judges always reluctantly leave one or two images out due to fairly basic flaws that could have been corrected prior to submission.   At least two of our winners have used smartphones for their photos and even these now have basic editing capabilities, so there really is no excuse for a little cropping or tonal adjustment prior to submission, if that is what it takes.

A photograph is a record of a unique event.   It is objective, up to a point, but it reflects a decision, made by the photographer, about when to release the shutter.   The microscopist scans a slide, and picks out particularly well-presented organisms or cells, not overlain by other cells or detritus in the sample, and also for pleasing juxtapositions of cells or filaments.   The same applies to those who photograph larger algae.  Tiff Stephens, the 2016 winner, could have waited a few moments longer, taken a step along the deck to her left or right, or held the camera at a slightly different angle.   Each would have given her a slightly different image of essentially the same phenomenon.  Whether photographing landscapes or using a microscope, there is nothing sacrosanct about the image beyond it being a record of the photographer’s decision to press a button.  Indeed, I suspect that most of our shortlisted entries are not unique records of the phenomena they record, but one of a number of images, and that a second stage of decision-making is needed to select the image that will be used.

Tiff_Stephens_Swell_Life

Tiffany Stephen’s Swell Life: winner of the 2016 Hilda Canter-Lund prize.   The images at the top of the post show the 2009 and 2010 winners of the Hilda Canter-Lund competition, by Mariano Sirioni and Ernesto Macayo respectively. 

Having challenged the idea that the image, itself, is sacrosanct, there is no particular reason why you should not apply a third stage of decision-making and edit the image to enhance the story that you want to tell.   The field of view that is recorded when you press the shutter release is somewhat arbitrary.  You may be able to modify this, in a generic sense, in your camera’s settings but we usually adjust these only rarely and it is easier to adjust the pictorial space post hoc, using crop and rotate commands in a photo editing package.  The microscopist is further limited because most microscope stages do not rotate so the orientation of an organism can only be adjusted after the image itself has been collected.  Similarly, those of us who are photographing larger algae have only the small screens on our cameras with which to check images in the field, possibly in the face of inclement weather.  There is no disgrace in some judicious imaging editing once we can examine the image on a large screen, and the rules allow for this, along with focus stacking and stitching, essential tools in the microscopist’s armoury.

What about adjustment of colour and tone?   Bear in mind that colour, in the macro world with which we are most familar is reflected and objects can only reflect those wavelengths that reach them.  That means that colour and tone, in underwater photography especially, is not really a fundamental property of the organism you are photographing.   Move the same alga from a deep location to a shallow one, and it will look different for no other reason than the amount and quality of light transmitted through the water will change.   The microscopist is less likely to deal with reflected light, as the camera will be recording light that has passed through a specimen but, here too, the light is far from natural.  It will depend on the type of bulb, the intensity of light that you are using and the set-up of the microscope itself.  Once again, the colour and tones recorded are not fundamental properties of the specimen.   Under such circumstances, there seems to be no particular reason not to use the “levels” and “curves” options in editing packages to produce an image that is visually pleasing.  The judges are looking for basic authenticity and honesty in the image, so as not to deceive or misrepresent the natural world to the viewer, but there is a wide tolerance around this criterion because, frankly, natural light is, itself, so changeable.

The pair of photographs below illustrate this point well.  I was walking through local woodlands as I was thinking about this post.  May in the UK is the time when woodland floors turn a spectacular violet-blue due to the flowers of the bluebell (Hyacinthoides non-scripta).   I took the upper photograph on my iPhone then walked a few steps into the woodland to remove the dead tree that runs diagonally across the foreground.  I went back to my original position and took another photograph.   No more than 30 seconds elapsed between the two pictures, but the colour balance is completely different.   It may be a product of the metering in the camera itself (I’ve cropped both to show the same scene but the upper image had more bluebells and less woodland than the lower one) and this introduces another source of variation: the oh-so-clever electronics inside even fairly basic cameras that are making decisions on your behalf.

Shincliffe_bluebells_May20

Two images taken within 30 seconds of each other from the same spot in woodland near Shincliffe, Co. Durham, May 2020.  The images at the top of the post show the 2009 and 2010 winners of the Hilda Canter-Lund competition, by Mariano Sirioni and Ernesto Macayo respectively. 

Most scientists assume that photography offers a “truthful” account of the objects that they are recording.   That’s at odds with the approach of critical theorists in the arts and humanities who recognise how many interventions lie between any object and the final image that is presented to third party viewers.   Susan Sontag, for example, challenges the “presumption of veracity” – less of an issue, perhaps, for fine artists but almost everything we think of as “documentary photography” or “photojournalism” is loaded with presumptions by both photographer and viewer, and it is a small step from those disciplines to scientist’s efforts to use photographs as objective evidence in their research.

The Hilda Canter-Lund competition is, however, not about photography as a scientific tool, but as a means of communication.  Appreciating the artificial nature of photography should be a liberation not a constraint: you, as photographer, probably have as accurate a memory of the image you have captured as the jpeg or tiff file that represents the digital record of the moment you released the shutter.   So feel free to open up the file in an editing package and use your discretion to adjust all the factors that were either in-built constraints or impulsive spur-of-the-moment decisions.   And send the final image to us for consideration for the 2020 Hilda Canter-Lund prize.

You can find the rules of the competition at https://brphycsoc.org/hilda-canter-lund-prize/ along with examples of recent shortlists to inspire you.

Reference

Sontag, Susan (1977).  On Photography.  Penguin Books, Hamondsworth.

Other posts on photographing algae

How to win the Hilda Canter-Lund prize

How to win the Hilda Canter-Lund prize (2)

How to win the Hilda Canter-Lund prize (3)(guest post by Chris Carter, twice winner of the competition)

How to win the Hilda Canter-Lund prize (4)

 

Some other highlights from this week:

Wrote this whilst listening to: still working through my resolution to listen to all Bob Dyla’s albums in sequence.   This week I listened to The Basement Tapes, Desire, Hard Rain (much underrated in my opinion) and Street Legal.  Also enjoyed Jagged Little Pill by Alanis Morissette.

Cultural highlights:  The Assistant is an excellent but gruelling film that references the predatory behaviour of Harvey Weinstein but manages to do this almost entirely by inference and implication.

Currently reading:  Tamed by Alice Roberts, about the domestication of plants and animals, is interesting but rather turgid so I’m alternating chapters with Slaves of New York, a 1986 short story collection by Tama Janowitz which I borrowed from my son’s bookshelf.

Culinary highlight:   Baked cod topped with a pesto made from garlic mustard (Alliaria petiolata) foraged from the garden and allotment.

The dark side of the leaf …

Whites_Level_lower_epiphytes

Having mentioned in my previous post that the epiphytes on the top and bottom surfaces of a Potamogeton polygonifolius leaf were different, I have produced a companion piece to the painting I showed in that post.   The new painting is of the lower surface, and shows a greater number of diatoms than are present on the upper surface.  In order to explain why this is the case, it is helpful to look at the structure of the Potamogeton leaves.  The first image, therefore, shows a section through a leaf. It is quite a thick section but we can see the upper epidermis, the palisade mesophyll cells below this, which have plenty of chloroplasts in order to capture the sunlight that the plant needs for photosynthesis.  Below this, we can see parenchymous tissue arranged to create some large internal air spaces which contribute to the leaves buoyancy. Finally, at the bottom, there is a single layer of epidermal cells.   All this is crammed into a thickness of about half a millimetre.

Potamogeton_polygonifolius_leaf_section

Part of a section of a leaf of Potamogeton polygonifolius.  The leaf vein is on the left, thinning to the leaf blade on the right.  The leaf blade is about half a millimetre thick.   The picture at the top of the post shows an artist’s impression of diatoms and Chamaesiphon cf. confervicolus on the lower surface of a Potamogeton polygonifolius leaf. 

 Viewed from the underside, these parenchymous tissues create polyhedronal chambers, ranging from about 100 to 200 micrometres (a tenth to a fifth of a millimetre) along the longest axis.  There are also a few stomata scattered across the leaf surfaces (see the right hand image below).

With this in mind, take a look at my impression of the epiphytes growing on the lower surface of a Potamotgen polygonifolius leaf.   There are a number of cells of Chamaesiphon cf confervicolius, as seen on the upper surface, but there are several cells of the diatom Achnanthidium minutissimum, growing on short stalks, plus a few long, thin cells of Ulnaria ulna, growing in small clusters on the leaf surface (there were a few other species present, but such low numbers that I have not included them here).    It might seem strange to think of two surfaces of a leaf having such different communities of epiphytes but that’s because we’re thinking like large land-dwelling organisms, not like algae.   The longest alga visible in the image of the leaf underside is Ulnaria ulna, at about a 10th of a millimetre in length.  Therefore, to get a realistic impression of the two images, we really need to put a distance of five of these between them, and then pack the gap with chloroplast-rich mesophyll cells inside the Potamogeton leaf.   Allowing for foreshortening, this distance is about five times the height of the image.

Pot_polygonifolius_leaf

The structure of a Potamogeton polygonifolius leaf viewed from the underside.  The left hand image (100x magnification) shows a leaf vein running diagonally across the lower right hand side along with the polyhedron-shaped chambers; the right hand image (400x magnification) shows the outline of one of these chambers superimposed behind the epidermal cells with a stomata with two guard cells visible just above the centre.   Scale bar: 20 micrometres (= 1/50th of a millimetre). 

The epiphytes on the upper surface of the leaf get first dibs at the meagre Pennine sunlight, which then has to pass through the upper layers of the Potamogeton leaf, where the mesophyll cells will continue to feast on the tastiest wavelengths, leaving relatively meagre pickings for the epiphytes that hang around on the underside of the leaf.

Chlorophyll, the molecule that makes plants green, absorbs light over a relatively narrow range of wavelengths – predominately red and blue – and this means that there are plenty of other wavelengths awaiting an organism with different pigments.   Diatoms have chlorophyll, but they also have some carotenoids (principally fucoxanthin) that grabs energy from the green part of the visible light spectrum (which is reflected, rather than absorbed by chlorophyll) and passes it to the cell’s photosynthetic engine.  Having this capability means that they can survive in relatively low light, which is why we see more diatoms on the underside of the Potamogeton leaf than on the top.

And that, best beloved, is the story of how Potamogeton got its epiphytes …

 

Some other highlights from this week:

Wrote this whilst listening to: more Bob Dylan.   I’ve got to the mid-70s, which means the live version of Like a Rolling Stone on Before the Flood plus the great Blood on the Tracks.  Also, as I was reading Ian Rankin, I listened to John Martyn’s Solid Air.

Cultural highlights:  we’re watching the BBC adaptation of Sally Rooney’s Normal People

Currently reading:  Ian Rankin’s Rather be the Devil.

Culinary highlight:   A rather fine vegetarian chilli, from Felicity Cloake’s column in The Guardian last week.   Served with corn bread, using a recipe we got from a hand-me-down American housekeeping magazine during our time in Nigeria.

 

Whatever doesn’t kill you …

Potamogeton_epiphytes_April20

The previous post focussed mostly on the higher plants that I found in the short stream that connects White’s Level with Middlehope Burn.  I mentioned the mass growths of algae that I found growing immediately below the entrance to the adit, but I did not talk about them in any detail, instead spinning off on a tangent while I mused on why the water cress had a purplish tinge.

When I did find time to examine the algal floc, I found it to consist of a mix of three different algae, the most abundant of which was Tribonema viride, but there were also populations of a thin Microspora (not illustrated) and Klebsormidium subtile.   I talked about Tribonema in the drainage from the Hadjipavlou chromite mine in Cyprus last year (see “Survival of the fittest (1)”) and both Microspora and Klebsormidium are also genera that are known to frequent these habitats.  Indeed, there is evidence that the populations that grow in these extreme habitats have physiological adaptations that help them to cope with the conditions.  Brian Whitton, my PhD mentor, led several studies on these adaptations in the streams of the northern Pennines in the 1970s, and Patricia Foster did similar studies in Cornwall at about the same time.   There is probably a mixture of physiological strategies involved, including the production of low-molecular weight proteins, which bind the toxic metals, and the production of extracellular mucilage.  Most of the populations I find in such habitats have a distinctly slimy feel due to the production of extracellular polysaccharides, and it is possible that these play a role in trapping the metal ions before they can get into the cell and cause damage.

Tribonema_viride_WhitesLevel_Apr20

Filamentous algae from the drainage channel below White’s Level, upper Weardale, April 2020.  a., b. & c.: Tribonema cf. viride, showing the characteristic H-shaped cell ends.   d.  Klebsormidium cf. subtile.  Scale bar: 10 micrometres (= 100th of a millimetre).   The picture at the top of the post shows an artist’s impression of Chamaesiphon cf. confervicolus on the upper surface of a Potamogeton polygonifolius leaf. 

I also had a look at the algae growing on the submerged leaves of Potamogeton pergonifolius in the channel between the adit and Middlehope Burn.   One easy way of examining them is to add a small amount of stream water then shake the leaves vigorously in a plastic bag.  The result is a brownish suspension of algae that can be sucked up with a Pasteur pipette and placed on a microscope slide.  When I did this, I found a community that was dominated by a short cyanobacterium, closest in form to Chamaesiphon cf. confervicolus.  The other abundant alga in the sample was Achnanthidium minutissimum, which is often common in minewaters, along with smaller numbers of a few other species.  The total number of species in the sample was just 12, which is low by the standards of streams without metal pollution, but such suppression of all but the hardiest species is another characteristic effect of heavy metal pollution.

I’ve added a “cf” (from the Latin conferre, meaning “compare to”) to my identification of Chamaesiphon confervicolus because this is the closest name, based on a comparison with images in the Freshwater Algal Flora of Britain and Ireland.  However, it is not an exact match.  Whether this is because the metals have strange effects on Chamaesiphon (as we saw for diatoms in “A twist in the tale …”) or whether our knowledge of the species within this genus is imperfect is not clear.  But discretion is the better part of valour in this instance.  Chamaesiphon species fall into two groups: those that live on stone surfaces (see “Survival of the fittest (2)”) and those that live on algae and plants, such as the one we see today (another is illustrated in “More from the River Ehen”).   They consist of a single, elongate but gently tapering cell, attached at one end to the plant and enclosed in a sheath.   The upper end of the filament forms small spherical buds (technically “exospores”).  One reason that I am wary of calling this population C. confervicolus is that most illustrations of this species show a stack of exospores in the sheath, whereas the White’s Level population all had just a single exospore.

Chamaesiphon_confervicolus

Chamaesiphon confervicolus, growing on Potamogeton polygonifolius in White’s Level outflow, April 2020.   Note the exospores at the end of the cell.  f. and g. show the sheath very clearly.  Scale bar: 10 micrometres (= 100th of a millimetre). 

The picture at the top of this post shows an artist’s impression of the Chamaesiphon cf confervicolus on the upper surface of the Potamogeton leaf.   I wanted to get some idea of the size, shape and arrangement of the epidermal and stomatal cells on the Potamogeton leaves and resorted to the tried and tested technique of painting a layer of clear nail varnish onto the leaf surface, then peeling this off when it had dried.  This had the added (and unexpected) benefit of also pulling of the epiphytes, giving some idea of their arrangement on the leaf surface at the same time.   One extra observation that this yielded was that upper surface was dominated by Chamaesiphon, growing in clusters, whilst the lower surface had greater representation of diatoms.   I’ve also tried to portray the chloroplasts in the stomata guard cells.  Plant epidermal cells generally do not contain chloroplasts, as their purpose is to protect the mesophyll cells that are the main centres of photosynthesis.  Guard cells of stomata, however, need energy to open and close the stomata so these are the exception to this rule.  I had not even been sure that I would see stomata on the upper surface of the cell, as these are mostly found on the underside of leaves; however, Potamogeton appears to have stomata on both surfaces.  As ever, there is a certain amount of evidence along with a dose of extrapolation.   Imagined, but not imaginary …

You can find a description of the terrestrial plant life of Slitt Mine and its environs in this post on Heather’s blog.

References

Foster, P.L. (1982).  Metal resistances of Chlorophyta from rivers polluted by heavy metals. Freshwater Biology 12: 41-61.

Harding, J.P.C. & Whitton, B.A. (1976).  Resistance to zinc of Stigeoclonium tenue in the field and the laboratory. British Phycological Journal 11: 417-426.

Robinson, N.J. (1989).  Algal metallothioneins: secondary metabolites and proteins.  Journal of Applied Phycology 1: 5-18.

Say, P.J., Diaz, B.M. & Whiton, B.A. (1977).  Influence of zinc on lotic plants. I. tolerance of Hormidium species to zinc.  Freshwater Biology 7: 357-376.

Sorentino, C. (1985).  Copper resistance in Hormidium fluitans (Gay) Heering (Ulotrichaceae, Chlorophyceae).  Phycologia 24: 366-368.

(Note that Hormidium is the old name for the genus Klebsormidium.  There is an orchid genus called Hormdium and, as this was described first, it takes priority.)

 

Some other highlights from this week:

Wrote this whilst listening to: Bob Dylan’s New Morning and Pat Garrett and Billy the Kid.   Also, Samuel Barber’s Prayers of Kirkegaard.

Cultural highlights:  The Netflix series Unorthodox, about a young woman fleeing a Hassidic community in New York.

Currently reading:  Agatha Christie’s A.B.C. Murders.

Culinary highlight:   Arroz con leche (Spanish rice pudding) served with peaches poached in madeira.

A reasonable excuse for exercise ..

High_Mill_falls_Apr2020A redefinition of the travel restrictions hereabouts means that “driving to the countryside and walking (where far more time is spent walking than driving)” it is now “likely to be reasonable” within the terms of Regulation 6 of the The Health Protection (Coronavirus, Restrictions) (England) Regulations 2020. That means that, rather than plan another post about the fascinating ecology of Lough Down, I can look a little further afield.   As both Heather and I are writing chapters for a forthcoming book on the Natural History of Weardale, we turned our eyes to the hills, largely for exercise and a change of scenery, but also as part of our background research for these chapters.

We parked the car at Westgate and followed a path alongside Middlehope Burn, a tributary of the Wear with a long history of lead mining and, as such, a case study in how man has shaped the ecology of Weardale, both terrestrial (Heather’s domain) and aquatic.  The first part of the walk is through Slitt Wood, where the stream cascades over a series of low step-like waterfalls, alternately sandstone and limestone, illustrating the bedrock geology of the area.   The air is full of birdsong and there are patches of primroses feasting greedily on the light that is still plentiful on the forest floor at this time of year.   However, this idyll is short-lived as, passing through a gate we emerge into a grassed area surrounded by derelict mine buildings.  Early on a Saturday morning in the midst of the pandemic, we have the place to ourselves and it is a struggle to imagine this place as a busy industrial site.   Similar sites are scattered throughout Weardale and the surrounding dales; all are now closed but once they would have employed large numbers of people.  There would have been the miners, working underground, of course, but also gangs of people (including women and children) breaking down and sorting the ore as it was brought to the surface, plus ancillary workers involved in construction, both above and below ground.

A couple of hundred metres beyond the site of the main shaft at Slitt Mine, I spot an adit (a shaft driven horizontally into a hillside) and make my way towards it.  These are intriguing habitats for ecologists interested in the interactions between man and nature and I was intrigued to see what was growing in this one, White’s Level.  The mine’s levels and shafts act as natural drainage channels, collecting water that has percolated through the rocks but, because the miners have driven the levels along the mineral veins, the water comes into contact with lead, zinc and cadmium during the course of its underground journeys, emerging with concentrations far in excess of those deemed safe by toxicologists.  However, the channel immediately downstream of the entrance of White’s Level was lush with vegetation.   I could see thick wefts of filamentous algae giving way to beds of water-cress (Rorippa nasturtium-aquaticum) and bog pondweed (Potamogeton polygonifolius).  The latter two were surprising as, in my experience, most of the streams draining north Pennine adits are dominated by algae rather than by higher plants.

Whites_Level_April20

The stream flowing from White’s Level to Middlehope Burn, April 2020.  The left-hand image shows the beds of water-cress very clearly whilst the right hand image shows the filamentous algae growths immediately below the entrance.   The picture at the top of the post shows Middlehope Burn at High Mill Falls, just upstream from Westgate.

The water cress had a distinctive purplish tinge which is probably a response to stress.  We’ve encountered this type of colour-change in response to stress elsewhere (see “Escape to Southwold”).   In this post, and in “Good vibrations under the Suffolk sun …” I talked about how plants have to regulate the amount of energy from sunlight in order that their internal photosynthetic machinery is not overwhelmed.  Those posts were both written after a hot weekend in July, but this was a chilly and overcast April morning in the Pennines where the prospect of plant cells being overcome by heat seems faintly ludicrous.   Here, instead, is my alternative hypothesis.

Although White’s Level and the other mines in the northern Pennines were driven by the demand for lead, lead is a relatively insoluble element and zinc, which is found alongside the lead in the metal-rich veins of the northern Pennines, is more soluble and, therefore, has a greater toxic influence on the plants and animals in these streams.  Zinc affects the metabolism of plants in several ways, one of the most important of which is to reduce the effectiveness of the chlorophyll molecules which are responsible for photosynthesis.  It does this by nudging the magnesium atom, which lies at the heart of every chlorophyll molecule, out of place.

Whites_Level_macrophytes_Apr20

Macrophytes in the stream flowing from White’s Level to Middlehope Burn, April 2020.   Left: Potamogeton polygonifolius; right: Rorippa nasturtium-aquaticum.

What this does, then, is alter the balance of the equation that tries to balance energy inputs and photosynthesis.   If your chlorophyll molecules are hobbling along, then the point at which they are overwhelmed by even the meagre Pennine sunlight shifts so that  the need for the plants to manufacture their on-board sunscreen kicks in sooner.   Just a hypothesis, as I said: if you have a better explanation, please let me know.

A few hundred metres further on, there is another lush growth of water cress in the stream flowing out of another adit, Governor and Company Level, this time even extending beyond the metal grille designed to keep the curious from harm.  I most associate watercress farms with the headwaters of chalk stream, which are characteristically spring-fed and, therefore, have very stable conditions.   The adits of the northern Pennines are, this respect, very similar to springs insofar as their flow, temperature and chemical conditions vary little over the course of a year.   In that respect, it is perhaps less of a surprise that we find water cress growing so prolifically here.   The zinc, admittedly, is a complication we don’t find in most springs but, that apart, the adits could be thought of as man-made springs, creating a series of almost unique, but largely overlooked habitats.

In the next post, I’ll talk about the algae that I found in the White’s Level channel.

Governor_Company_Level_Apr20

A prolific growth of water cress in the drainage channel below Governor and Company Level, April 2020. 

Some other highlights from this week:

Wrote this whilst listening to: Still working through Dylan’s back catalogue: John Wesley Harding, , Nashville Skyline and Self-Portrait, the latter a blip in an otherwise superb run of albums.   Next up is New Morning but I want to re-read the chapter in Dylan’s Chronicles Volume One where he describes the genesis of this album before listening.

Cultural highlights:  My book group looked at Pride and Prejudice but, being deep into The Mirror and The Light, I did not had time to read this.   We watched the 2005 film version starring Kiera Knightly instead.   Turned out that three of the six participants in the book group had also watched the film the night before our Zoom meeting, rather than (re-)reading the book itself.

Currently reading:  Finally finished The Mirror and The Light which was, definitely, worth the effort.  Started Kate Atkinson’s Big Sky.

Culinary highlight:   Home-made tortellini filled with mushroom paté, served with a consommé made from turkey stock from the freezer.  Culinary ambition hereabouts always goes sky high in the week of the MasterChef finals.

The littoral ecology of Lough Down

BotrydiumA-5_CRCarter

My recent overviews of the major groups of algae have been useful as a way of highlighting which families and orders I’ve neglected.  That’s mostly because my posts are largely reactions to the circumstances I find myself in, rather than as a comprehensive overview of the world of freshwater algae.  My travels, this week, have brought me to Lough Down, a little-known Irish lake to which many of us have journeyed over the past few weeks.   Today, I thought I would peer at the littoral zone in the hope that I might find an alga from an order I have not previously written about.

I seem to be in luck: there has not been much rain recently and there is recently-exposed mud.  When I look closely, I see tiny green spheres, each the size of a pin head, dotted across the mud surface.   These are vesicles of the alga Botrydium and, despite their bright green colour, they actually belong to the Xanthophyceae (see “When a green alga is not necessarily a Green Alga …”).   Below this pear-shaped vesicle there is a system of branched rhizoids which anchor the plant to the surface (see lowermost photograph).  Surprisingly, the whole plant is a single cell, a similar situation to the one we encountered in Vaucheria, another representative of the Xanthophyceae (see “The pros and cons of cell walls”).

The vesicle itself is green, and a close look reveals the presence of many chloroplasts and also (less easy to see without special stains) nuclei.   You can also see, on the image below, crystals of calcium carbonate which are deposited on the vesicle.   However, if the marginal mud where Botrydium thrives is flooded again, the cell contents divide into a large number of spores, each with a single nucleus and two flagellae, which are liberated.  On the other hand, if the pond continues to dry, then a different type of spore is produced, as the cell contents retracts into the rhizoids where it forms thick-walled spores, which can survive long periods of desiccation.   Once the mud is dampened again, these spores germinate into motile spores.

BotrydiumD-5_CRCarter

A vesicle of Botrydium granulatum spotted with crystals of calcium carbonate.  The photograph at the top of the post shows vesicles on the bed of a pond (both photos: Chris Carter).

Botrydium is a small genus, with just eleven species listed on AlgaeBase, of which just one, B. granulatum, is recorded from the UK and Ireland.  It fills in one glaring gap in my coverage of the Xanthophyceae, leaving just two Orders still to feature.  These are the ones containing the awkward little single cells and colonies that are difficult to identify and easy to confuse with similar-shaped forms in the Chlorophyta.   I’ll get around to writing about these one day.   Maybe I’ll find representatives from them on a future visit to Lough Down.  Who knows how much time I will have to become acquainted with this fascinating lake?

BotrydiumE-5_CRCarter

A complete Botrydium granulatum plant, showing the vesicle on the left with a series of rhizoids extending out below.  The lowermost rhizoids are obscured by soil particles (photo: Chris Carter).  All images in this post are from material collected from Pitsford Water, Northamptonshire.

 Some other highlights from this week:

Wrote this whilst listening to: J.S. Bach’s St Matthew’s Passion and Laura Marling’s new album, Song for Our Daughter.  My systematic review of Dylan’s back catalogue has reached the incomparable Blonde on Blonde.

Cultural highlights:  Portrait of a Lady on Fire.   French arthouse film.  I know, I know …

Currently reading:  Drawing to the close of The Mirror and The Light .

Culinary highlight:   Buying a bag of strong white flour after many abortive attempts.   And a Simnel Cake, in celebration of Easter.

 

Blessed are you that hunger …

Mackay_et_al_2020_graphical_abstract

At the time of writing, four of my five working days are given over to ecology whilst the fifth is spent volunteering for the local Foodbank, which is gearing itself for a huge run on the stocks built up from generous donations over the Christmas period.   It occurred to me last week that I spend four days extolling hunger in an ecological context whilst spending the fifth trying to alleviate it in a human one.

“Hunger” in an ecological context is a them to which I have returned several times over the years.   We set the threshold for “good ecological status” for attached algae at a point that we thought coincided with the algal community switching from species that were adapted to “stressed” (i.e. nutrient-poor) conditions to those adapted to compete when nutrients were not in short supply (see “What does it all mean?” and references therein).   I’ve also talked, in some of my posts, about the adaptations some algae have to scavenge scarce nutrients (“A day out in Weardale”).   We’ve then gone on to try to work out what that means in terms of nutrient concentrations in UK and European rivers (references at the end of the post).

So I was pleased to see a paper appear last week that confirms some of these hunches.   Broadly speaking, Eleanor Mackay and colleagues have shown, using in situ bioassays, that as the concentration of inorganic nutrients decreases so the algae make more use of phosphorus and nitrogen bound into organic complexes.  As the algae get more “hungry”, in other words, they become more adept at scavenging for the resources that they need.

The graph at the top of this post is the graphical abstract from the paper which summarises this, whilst the one below shows the response to organic sources of phosphorus as a function of the concentration of “soluble reactive phosphorus” (the standard measure of “inorganic” phosphorus).  I’ve added an arrow to the right-hand side of this which shows roughly the current UK threshold, based on the work mentioned above.   Ellie’s graph seems to be confirming that, once that limit is exceeded, the algae are no longer “hungry”, meaning that they no longer need the nutrients bound into organic complexes.  Because organic phosphorus utilisation depends upon production of phosphatase enzymes to break down the organic complexes to releasee the phosphorus, there must be a greater energetic cost to the organism than if there was a ready supply of inorganic phosphorus that they can access.  I have, I must admit, never seen any figures that quantify this cost.

Mackay_et_al_2020_Fig5c

Fig. 5c from Mackay et al. (2020):  The relationship between “soluble reactive phosphorus” and dissolved organic phosphorus use by algae in in situ bioassays.  The “response ratio” is the natural logarithm of the ratio between the chlorophyll concentration of the treatment and the chlorophyll concentration of the corresponding control.  The arrow on the right-hand side indicates the approximate position of the regulatory threshold for phosphorus (see note at end of post).  The figure at the top of the post is the graphical abstract from Mackay et al. (2020). 

Part of me, then, is reassured that the regulatory threshold for phosphorus is roughly in the right place.  The Environment Agency’s reliance on a single measure of inorganic phosphorus, measured infrequently, is often criticised by hydrochemists but we can take some comfort from knowing that other forms of phosphorus (more difficult to analyse and quantify) only become important at concentrations lower than the current UK targets.   There is still part of me, however, that sees room for improvement.  That there are relationships between algae and other plants and phosphorus is not in doubt, and I am sure that a shift in strategies for nutrient acquisition help to define this relationship, particularly at low concentrations.  However, the relationships are not very strong and predictions about the ecological benefits of lowering phosphorus concentrations are imprecise.

Adding another strand of evidence to the current decision-making process makes scientific sense, and looking at how organisms respond to nutrients, rather than just measuring chemistry and describing community structure, seems like a sensible way of doing this.   In situ bioassays clearly have potential, as this paper shows; however, they are time consuming.   An alternative would be to measure phosphatase activity directly.  The Environment Agency did, in fact, fund research on this in the late 1990s and David Harper used these assays in a DEFRA-funded project in the early 2000s, but they have never become routine.  That’s a shame because, particularly for catchment-level investigations, they could add a useful additional insight.

The downfall of all these methods is not science, but the “more-with-less” ethos that has prevailed in the UK public sector for the past decade.  Everyone recognises that diffuse nutrient pollution offers a challenge that current monitoring and decision-making processes struggle to address.  However, most of the serious research effectively concludes with “if you spend a lot more money, you’ll discover that the problem is more complicated than you initially thought”.   That’s a difficult message to pass up through managerial hierarchies trying to keep a cash-starved regulatory agency moving forward.

Reference

Mackay, E. B., Feuchtmayr, H., De Ville, M. M., Thackeray, S. J., Callaghan, N., Marshall, M., Rhodes, G., Yates, C.A., Johnes, P.J. & Maberly, S. C. (2020). Dissolved organic nutrient uptake by riverine phytoplankton varies along a gradient of nutrient enrichment. Science of the Total Environment 722: 137837.   https://doi.org/10.1016/j.scitotenv.2020.137837

Poikane, S., Kelly, M. G., Salas Herrero, F., Pitt, J. A., Jarvie, H. P., Claussen, U., Leujak, W., Solheim, A.S., Teixeira, H. & Phillips, G. (2019). Nutrient criteria for surface waters under the European Water Framework Directive: Current state-of-the-art, challenges and future outlook. Science of the Total Environment 695: 133888. https://doi.org/10.1016/j.scitotenv.2019.133888

 

Note: regulatory threshold for inorganic phosphorus

The arrow indicating the approximate position of the regulatory threshold for phosphorus uses the current UK TAG phosphorus standard.   This is site specific, using altitude and alkalinity as predictor variables.  This means that a range of thresholds is possible and the position of the arrow reflects the average alkalinity (50 mg L-1 CaCO3) and altitude (75 m) in a database of river samples collected as part of DARES project. Note, too, that P standards are based on the Environment Agency’s standard measure, which is unfiltered molybdate reactive P.  This approximates to “soluble reactive P” or “orthophosphate-P” in most circumstances but the reagents will react with phosphorus attached to particles that would have been removed by membrane filtration.

 

Some other highlights from this week:

Wrote this whilst listening to: My lockdown project of listening to all Bob Dylan’s albums in sequence has brought me up to Bringing It All Back Home and Highway 61 Revisited.

Cultural highlights:  Bait, a low-key black and white British film from 2019.  Definitely sits in the “sub hero” genre that I much prefer to the crash, bang, wallop of most Hollywood blockbusters.

Currently reading:  About three-quarters of the way through Hilary Mantel’s The Mirror and The Light now.  Jane Seymour is gone; Anne of Cleeves coming up next.

Culinary highlight:   Grilled mackerel with sautéed potatoes, probably.  A close second was home-made tortellini filled with mushroom paté and served with garlic mustard (Alliaria petiola) butter.   Mrs K is forager-in-chief hereabouts.

grilled_mackerel

Not quite a coral reef …

Fold_Sike_March2020

Working on the principle that we usually pass only a handful of people during our walks in Upper Teesdale we decided that this counted as “social distancing” and headed off to the hills.  Whether this is still deemed to be acceptable behaviour this week is another matter, but I can report that Teesdale in midweek was certainly far less crowded than the tourist honey-pots that were the focus of so much bad press over the weekend.   But I digress.

Our regular beat follows the Pennine Way for a long stretch with the River Tees on our left and the looming cliffs of Falcon Clints on our right.   Just before the Pennine Way gets to this section, however, the valley is broader, with a flat floor that is used as grazing land by Widdybank Farm.  A small stream, Fold Sike, flows off Widdybank Fell and crosses the Pennine Way at an oblique angle before joining the River Tees.   I’ve walked past it many times, mentally noting prolific growths of a broad leafed Potamogeton as I press on, but little else.  Today, however, my eyes were caught by light-coloured crusts on many of the basalt stones just below the surface of this shallow stream.   If you look closely at these crusts you’ll see that they are not homogeneous: there are distinct nodules on their surfaces and they are more prominent on the edges, rather than the tops, of the stones.  You’ll also see a distinct green tinge in some areas.

Fold_Sike_with_Potamogeton

Potamogeton and Homoeothrix crustacea growing in Fold Sike, Upper Teesdale (NY 834 292) in March 2020.   The photograph at the top of the post shows the view looking back down the valley from Fold Sike with Widdybank Farm in the distance.

Homoeothrix_crustacea_Fold_Sike_March20

A basalt cobble from the bed of Fold Sike showing the surface nodules and the greenish tinge to the crust.  

This crust is distinctive: I know from previous encounters that it is formed, primarily, of the cyanobacerium Homoeothrix crustacea, a member of the Oscillatoriales (see “Shuffling the pack”).  I also know that it is a beast to photograph, having very narrow filaments and, in this case, also is extensively calcified.  I describe the process of calcification of Chara in “Everything is connected” and the same principles are likely to apply here too.   the I did try to dissolve away the calcite with some vinegar, but without much success in this case.  I’ve included some photographs of another species below, and you can see yet another species of Homoeothrix in “Algae from the Alto Duoro”.   The microscopic image shows the characteristic tapering filament combined with the absence of a heterocyst.  In the far past, Homoeothrix was thought to be a heterocyst-free relative of Calothrix, rather than a tapering relative of Oscillatoria and Phormidium.

Homoeothrix_images

Some images of Homoeothrix: a. Homoeothrix crustacea encrusting a boulder (approximately 40 cm across) from a calcareous stream in Cumbria, UK; b. filaments of H. fusca from a crust on Whitbarrow tufa stream, Cumbria (scale bar: 100 micrometres, 0.1 millimetre); c: close-up of a single trichome from the same stream. Note the distinctive tapering and absence of a heterocyst (scale bar: 10 micrometres, one hundredth of a millimetre).

The greenish patches on the surface of the crust were mostly composed of the green alga Bulbochaete (discussed in more detail in other posts – see “A winter wonderland in the River Ehen“) and I also saw a number of diatoms, principally Achnanathidium minutissimum and Delicata delicatula.  The latter, formerly included in Cymbella, is a common species in streams hereabouts, though relatively uncommon in the UK as a whole.  I also saw a few trichomes of a member of the Rivulariaceae, though did not find any intact colonies.  Were this a warm, shallow maritime environment a few dominant calcifying algae that create a habitat for a range of other species would be called a “reef”.  That word stretches the imagination when applied to a small windswept sike in upland County Durham, but the processes are the same even if scale and context are very different.   However, what with all the travel restrictions and closed borders at the moment, this might be the closest any of us will get to a coral reef for quite some time …

Delicata_delicatula_FoldSike

Delicata delicatula (?) from Fold Sike, March 2020.   Scale bar: 10 micrometres (= 1/100th of a millimetre).

Some other highlights from this week:

Wrote this whilst listening to: Bob Dylan’s first two albums.  One of my projects for the next weeks is to listen to all Bob Dylan’s albums sequentially.  Tony Allen and Hugh Masekela’s latest album, Rejoice, is also well worth a listen.

Cultural highlights:  The Perfect Candidate.  A Saudi film about a female doctor battling misogyny to get elected to the local council.   Under normal circumstances we would probably have ventured up to the Tyneside Cinema in Newcastle to see this.  Instead, we streamed it via Curzon Home Cinema.

Currently reading:  Still ploughing through Hilary Mantel’s The Mirror and The Light.  Oddly, despite the enforced isolation, I don’t seem to be finding much time to read at the moment.

Culinary highlight:   The bad news is that Durham Indoor Market has finally succumbed to the inevitable and closed its doors, taking with it most of our opportunities to buy non-supermarket food.   That means that the risotto we cooked with a stock made from the leftovers from last weekend’s prawns probably wins the “culinary highlight” this week, if only because it may be some time before we can make another.

 

 

How to be an anchorite (1)

Ankers_Museum

Having worked from home for almost 25 years, I feel that I ought to have some wisdom to impart as the whole country is encouraged to minimise unnecessary contact with others.  The truth is that I am so normalised to an eremitical working life that it is hard to compare and contrast my experiences with life in an office.   That means that the addition of a “(1)” to the title of this post may be optimistic and I will get back to the core business of this blog next week.

My period of freelance home working has straddled the digital revolution so that, in 1995, almost nobody in ecology communicated by email whilst today, obviously, email is ubiquitous.  In 1995 I often walked to the Post Office twice a day; now, it Is more like once a fortnight.   I regularly travelled up and down the country by train whereas now, I am more likely to join meetings by Skype, Zoom or Teams.   A wise person wrote on Twitter last week “I think what we’ll discover over the coming weeks is both the undiscovered potential of digital tools, and their limitations in the long term as a replacement for literally being physically in the proximity of other human beings”.  I agree totally except that, I think we know enough already to draw some general conclusions.

Online meetings work really well when all involved have stable internet connections and plenty of bandwidth, when the video displays are large enough to detect body language (never the case when many people are involved), when the participents know each other and when all are working to a common goal.   However, much we try to reduce our carbon footprints, I think there are benefits associated with meeting in person at least once a year, and in including some downtime to enable us to get to know each other better.  Working remotely through digital tools proceeds much better when there are also periodic face-to-face interactions..

I wrote about the opposite situation recently in an opinion paper for Metabarcoding and Metagenomics.   There were several layers to the situation I describe but over-reliance on digital communication rather than face-to-face gatherings played a contributory factor, particularly in the latter stages.   Several of the rules I outlined in the previous paragraph were flouted, but most important from this perspective, we were not working to a common goal.  The project we were discussing had several controversial elements and not everyone agreed that the time was right to push ahead.  Additionally, not everyone understood the nuts and bolts of the technical issues that needed to be addressed and the meetings were structured for “deciding”, not “learning”.

Despite this, I’m largely optimistic about the prospects of working with digital tools such as Skype, Zoom and Teams.  The problems lie, as ever, not with the tools themselves but with how they are used.   The problem I discussed in my Metabarcoding and Metagenomics essay was primarily about the management of change which is never easy, even when you are given plenty of time.   The shift to working from home has happened so quickly that mistakes are bound to be made.   However, one easy lesson is that, even with perfect digital set-ups and plenty of bandwidth, now is probably not the time to push ahead with new, contentious or divisive projects.  Put them on hold or, if that is not possible, adjust your deadlines to allow plenty of time for learning and consensus-building.

 

The picture at the top of the post shows the west end of St Mary and St Cuthbert’s church, Chester-le-Street, County Durham.   A medieval anchorite’s cell (now a museum) can be seen on the right-hand side of this image. [http://www.maryandcuthbert.org.uk/parish-church-/ankers-house/]

 

Some other highlights from this week:

Wrote this whilst listening to: the news.  Isn’t everyone?

Cultural highlights:  The Florida Project, a 2017 film by Sean Baker.  Opinion hereabouts is divided about whether this is as dark as or somewhat lighter than Ken Loach’s recent films.   The underlying story is very dark but there is a vein of humour running through it and it set in the bright Florida sunlight.

Currently reading:  Still reading Hilary Mantel’s The Mirror and The Light

Culinary highlight:   A combination of limited availability of pasta in the supermarkets and abundant time on my hands seems like a good reason to make my own tagliatelle.   Combined it with prawns and rocket (and chilli) following a recipe in a Jamie Oliver cookbook.   The prawn trimmings made a rich stock which we’ll use next week.  Hooray for “slow food”!

Disagreeable distinctions …

When you look at an organism, how do you know what it is?   That’s a big question that hovers over many of the posts that I write.   I tell you the names of organisms and you believe me. Sometimes I do too.   The truth is that we take the way that our brains process the constant stream of signals that our eyes send us as we observe the natural world without a second thought.   The subject intrigues me, but I only manage to scratch the surface in the posts that I write (see “Abstracting from reality …” and “Do we see through a microscope?” for some of these speculations).

The plate below offers a case study in this process.  It shows a diatom we encountered in a recent ring test, and which most us agreed was either Fragilaria austriaca or something quite similar.   In binary terms, though, we have to be blunt: either it is Fragilaria austriaca or it is not which may have implications for subsequent recording and interpretation (see “All exact science is dominated by the idea of approximation”).   How come a group of experienced analysts can look at the same population of diatoms and reach different conclusions?   I’ve got two suggestions: the first is that we differ in how we process the images, and the second is that there are sources of systematic error which confound our attempts to seek the right answer.

Fragilaria_austriaca_Foreshield

Fragilaria austriaca” from Foreshield Burn, Cumbria, May 2019.

There are three basic strategies that we use to name an organism:

  • Probabilistic reasoning, through the use of keys which, in theory at least, have a logical structure that guides a user to the correct identity of an unknown specimen. In practice, this is not quite as straightforward as it sounds (see “Empathy with the ignorant …”) and, at some point, many of us will abandon the formal structure of a key and switch to …
  • Pattern recognition, which amounts to flicking through images until we find one that matches our specimen. We can then corroborate this preliminary match by checking the written description.  In practice, we will probably switch from probabilistic reasoning to pattern recognition and back again as we home in on the identity of an unknown specimen. Repeating this process several times will lodge a schemata of this species in our memories, leading to a third strategy:
  • Recall. In practice, most of us probably have seen many of the common and even less-common species so often that we can by-pass these first two steps completely because we recognise the species without recourse to any books.

Disagreements, then, arise partly because we use different books as part of our naming process, our prior experiences differ and because our discipline in checking measurements of our own specimens against descriptions is not always as good as it should be.   In many cases, especially with modern understanding of diatom species, boundaries between species are frequently being redrawn and descriptions of newer species can only be found in obscure journal articles, often behind paywalls, and knowledge of these often diffuses through the community of diatomists more slowly than it should.   However, our discussions about the identity of the mystery Fragilaria also revealed a further issue, which I’ve illustrated in the graph below.

When we switch from “pattern recognition” to “probabilistic reasoning” we often base decisions on categoric distinctions of continuous variables such as length and width.  In this case, the literature quotes a maximum width of four micrometres for F. austriaca, and this was an important factor contributing to decisions about the correct identity.  However, there were differences in our measurements which means that some decided that the population was too broad to qualify as F. austriaca whilst others decided that it fell within the correct range.   The likelihood, based on these graphs, is that at least some of us were making incorrect measurements but, at this stage, we don’t know who they are.

FAUS_measurements

Measurements of width, stria density and length of the population of “Fragilaria austriaca”.  Six analysts were involved in total, using either the eyepiece (“E”), an image projected onto a screen (“S”) or a measuring program (“P”) to make measurements (some used more than one approach). The dashed lines show the upper and lower limits for each parameter.

But that, itself, brings me to another point: do we know the correct size range of Fragilaria austriaca?  In order to be sure, we would need measurements of both initial cells (the largest in a cell cycle) and cells at the point where they are about to undergo sexual reproduction (the smallest in the cell cycle), ideally from several populations.  As this is rarely the case, we actually have three problems: first, is the description reliable? Second, are your measurements accurate? Third, we are using a point on a continuous scale as a criterion for a categorical judgement which implies perfect knowledge of the size range of the target population.  Even if you are sure of your microscope’s calibration, the best you can say is that the largest valve that you saw in the sub-sub-sub-sub-sub-sub sample of the population that lived in the stream you sampled exceeds (or not) the largest valve that the original author measured in the sub-sub-sub-sub-sample that s/he examined.   Several of our measurements just tip over four micrometres, the maximum width quoted in the literature for Fragilaria austriaca but, given these other factors, is that enough to drive a decision?   Statisticians are more comfortable predicting means, modes and medians than predicting extreme values.   Taxonomists, by contrast, seem to have undue reverence for maxima and minima.

Molecular biologists are approaching similar questions with considerable vigour.   The arrival of metabarcoding and high throughput sequencing means that they have had to write complicated computer code (“bioinformatics pipelines”) to sort the millions of sequences that emerge from sequencers, matching as many as possible to sequences from organisms whose names we already know, in order to turn those sequences into data that biologists can use (see “When a picture is worth a thousand base pairs …”).   We are conscious that decisions about software and settings within packages contribute to variations in the final output for reasons that we cannot always answer to our satisfaction.  But, whilst engaged in these discussions about cutting-edge technology, I’m conscious that old-school biologists such as myself each perform our own private “bioinformatics” every time we try to name an organism and we don’t always agree on the outputs from these thought processes.   Molecular biology, in a roundabout way, holds up a mirror to the way that we’ve been used to operating and should make us ask hard questions.

Some other highlights from this week:

Wrote this whilst listening to: my elderly vinyl copy of Mike Oldfield’s Tubular Bells

Cultural highlights:  Milton Jones at Newcastle City Hall

Currently reading:  Hilary Mantel’s The Mirror and The Light

Culinary highlight: polenta served with a mushroom and cheese sauce.

Finally, breaking news: I’m going to be live at the Green Man festival this August.  More details of our event “Slime Time”, and all the other performers at Einstein’s Garden can be found here

GM2020_EINSTEINS GARDEN (1)