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)

When a green alga is not necessarily a Green Alga…

Tribonema_Norfolk_pond_GPhillips

I will end this short series of posts on the organisation of the major groups of algae with a look at the Xanthophyceae, or yellow-green algae.   My old copy of West and Fritsch’s Treatise on British Freshwater Algae from 1927 includes this group of algae with the green algae, although we now know that, apart from a generally green appearance, these two groups of algae have very little in common.  The big differences lie, however, in the types of details that are beyond the purview of the casual natural historian, so you may well find yourself flicking back and forth between “green algae” and “yellow-green algae” as you try to put a name on a specimen.  The definitive test is to add some iodine to your sample, as the Xanthophyceae do not produce starch as a storage product, and so do not produce the characteristic blue-black colour in the cells.  However, iodine is messy stuff and most of us will struggle along without for as long as possible.

The five orders of Xanthophyceae are shown in the table below.   In contrast to the case for most algal groups where molecular studies have led to many revisions of traditional classifications, the Orders of the Xanthophyceae have proved to be quite robust when subjected to this type of scrutiny.   Two of the Orders have siphonous organisation, though the form that this takes is very different in each (see “The pros and cons of cell walls” for more about siphonous lifestyles).  Tribonematales is an Order of filamentous algae that can be difficult to differentiate from filamentous green algae, whilst the Mischococcales are easily confused with small Chlorophyceae.

Xanthophyceae_organisation

The organisation of the Xanthophyceae into five orders.  Organisation follows Algaebase.   The image at the top of this post shows Tribonema smothering the surface of a pond in Norfolk (photo: Geoff Phillips).

That’s one of the mysteries of freshwater algae: to the lay observer, an organism such as Vaucheria looks very similar to Cladophora or another green alga.  Yet they are distant relatives, belonging to different Kingdoms (Chromista and Plantae respectively).  That means that they share the same genetic affinity to one another as they do to us, which is a staggering thought (see “Who do you think you are?”).   What we are seeing is two organisms supremely well adapted to living in similar habitats, which means that natural selection has, gradually, shaped two quite distinct gene pools in quite different ways to arrive at the same end-point.   Just as motor manufacturers have, in the hatchback, found a style of car that is well-adapted to urban living, so the rival algae manufacturing corporations (“Plantae Inc” and “Chromista plc”) have come up with two broadly similar models that are both well-adapted to life in lowland streams.  Just as, in the case of hatchbacks, you can lift up the bonnet and see differences in the engine (petrol, diesel, hybrid, electric) but within the same basic shape, so many of the big differences in algal groups concern their internal machinery not outward appearances.

Vaucheria-frigida_ChrisCarter

Reproductive structures growing from a filament of Vaucheria frigida (photo: Chris Carter)

References

Maistro, S., Broady, P.A., Andreoli, C. & Negrisolo, S. (2009).  Phylogeny and taxonomy of Xanthophyceae (Stramenopiles, Chromalveolata).  Protist 160: 412-426.

Appendix

Links to posts describing representatives of the major groups of Xanthophyceae found in freshwaters.  Only the most recent posts are included, but these should contain links to older posts (you can also use the WordPress search engine to find older posts).

Group Link
Botrydiales Botryidium: The littoral ecology of Lough Down
Mischococcales Watch this space …
Rhizochloridales Watch this space …
Tribonemetales Tribonema: Survival of the fittest (1)
Vaucheriales Vaucheria: When the going gets tough …

Some other highlights from this week:

Wrote this whilst listening to: Two Hands, by Big Thief

Cultural highlights:  Jon Hopkins at the Sage.  What Radio 3’s Ibiza night might sound like.

Currently reading: the last few pages of Bill Bryson’s The Body: A Guide for Occupants (454 pages) prior to starting Hilary Mantel’s The Mirror and The Light (904 pages)

Culinary highlight: fish pie.  Spécialitié de la maison.