A brief return to Malham …

My speculations about the origin of lichens (“It takes two to tango …”) has led me to one final post about Malham’s lichens. Tucked into a shady cranny at the base of the trunk of a large tree was grey-green powdery lichen called Lepraria which represents one of the most primitive types of lichen: little more than some algae amongst a tangle of fungal hyphae.


Lepraria sp at the base of a beech tree in the grounds of Malham Tarn field centre, April 2014. Inset left: fungal hyphae and inset top right, algal cells. Scale bar: 10 micrometres (1/100th of a millimetre)

It was not easy to get an image showing both fungi and algae at the same time. Scraping the lichen off the bark and onto a microscope slide resulted in small pieces of bark and soil being mixed in with the lichen itself. Some could be teased apart but many clumps were too dense to photograph. You can see some of these dense particles in the background of the image of hyphae. However, looking at these primitive lichens does give you some idea of the starting point in the gradual evolution of the complex structures that we saw in “More about Malham’s lichens”.

The paradox that is Bacillaria

Having struggled to find words to describe the movement of Bacillaria paxillifer in last week’s post (“In the shadow of the Venerable Bede”), I have now uploaded a video, taken by Chris Carter, to YouTube showing a Bacillaria colony in action. In my photograph in last week’s post you will see the colony fully extended. Think of each cell as if it were one section of an extendable ladder. Chris’ video starts with the “ladder” fully retracted.

Imagine a single cell of Bacillaria in isolation. This will, in time, divide but the structure of Bacillaria’s silica cell wall (“frustule”) is such that the two cells remain intact via a “tongue and groove” structure associated with the raphe. The raphe is the part of the diatom cell responsible for movement but the tongue-and-groove structure means that the two cells can only move in relation to one another: sliding along the “track” along the centre of the valve (see lower photograph). Now imagine each of these cells dividing again, to give four cells joined in this way. Another division will produce eight cells, and so on.


A cleaned valve of Bacillaria paxillifer, an image from the ADIAC database [http://rbg-web2.rbge.org.uk/ADIAC/db/adiacdb.htm]. Note the central “ladder” (a “fibulate raphe system”) which forms the “tracks” along which adjacent cells move. The scale bar is 10 micrometres (= 1/100th of a millimetre). Photo: Micha Bayer.

Bacillaria paxillifer was one of the first diatoms to be described, being relatively large and distinctive. It was originally classified as Vibrio paxillifer in 1786, which is intriguing as Vibrio is now understood as a genus of bacteria (including V. cholerae, the organism responsible for cholera). In 1788, however, a German naturalist, Johann Friedrich Gmelin decided that Bacillaria was sufficiently distinctive that it deserved its own genus. And so it was that Bacillaria was the first genus of diatoms to be formally described. In the process, it lent it’s name to the class into which all other diatoms were eventually placed. And that, Best Beloved, is the reason why, in the formal taxonomic literature, diatoms are referred to as Bacillariophyceae or Bacillariophyta.


Schmid, A.-M. M. (2007). The “paradox” diatom Bacillaria paxillifer(Bacillariophyta) revisited. Journal of Phycology 43: 139-155.

Slow science and streamcraft

My recent post about natural history (“A paper you should all read …”) prompted a colleague to send me a link to an article on a related theme: “slow science”: a movement inspired by the thinking behind “slow food” that acts as an antidote to the pressures to publish and win grants and contract income that dominates Western universities. The outcome is, inevitably, over-specialisation at an early stage in a career, with an unhealthy focus on a few areas of science at the expense of others. The author uses the term “McUniversity” to encapsulate the over-managed institutions that subject their staff to constant appraisal. Having used the term “McEcology” myself to describe similar phenomena (see “Black Swan #2: McEcology and Steve Earle” and “Simplicity is the ultimate sophistication: McEcology and the dangers of call centre ecology”), I have complete sympathy and was gratified to see others thinking along similar lines.

I had continued to think about the issues raised by the Bioscience article natural history after I wrote my post and it was the problem of over-specialisation that had particularly bothered me. I believe that a combination of the failings of most degree courses to give a thorough grounding in practical skills and the very narrow focus of most PhDs means that many of us are in danger of missing important signs about the ecosystems that we study. Casting around for a term to encapsulate what I was trying to convey, I settled on “streamcraft”, based on deeply-lodged memories of reading Baden-Powell’s Scouting for Boys when I was younger. He was very keen to promote “woodcraft” which he defined as “…the knowledge of animals and nature”. He went on: “Woodcraft includes, besides being able to see the tracks and other small signs, the power to read their meaning … It teaches … which are the best wild fruits and roots for his own food, or which are favourite food for animals, and therefore likely to attract them.”

Taking Baden-Powell’s idea of woodcraft as a starting point, “streamcraft” becomes the ability to “read” the messages in the stream that enable us to understand the processes that are taking place and, in turn, the extent to which man’s activities have altered these. The trend that I see is for everyone to spend less time beside streams, except to collect a sample which will be examined in detail back in the laboratory. However, I can show instances where a few observations made in the field can provide most of the information gained from detailed analysis of a single group of organisms back in the laboratory. The problem is that we are rapidly losing the ability to think across several groups of organisms because the structures of science push us towards specialism. Specialisms, obviously, have their place but they should not usurp a broad awareness of natural history.

There is, however, one final argument for “streamcraft”: any interpretation based on visually-obvious properties will, in turn, produce information that can be more readily shared with stakeholders than any number of reports filled with highly-analysed data. It is easy, when talking to fellow ecologists, to forget that we have to function in a democracy where stakeholders have a right to know what we are doing and why.

All things bright and beautiful?


Jarrow Bridge, looking downstream from near St Paul’s church, 18 April 2014.

Walking up from the site where I collected the diatoms I wrote about in the previous post, I passed St Paul’s church, dating back to Saxon times. However, as it was Good Friday, the church was busy with worshippers, so I could not go in to look at the ancient stained glass. Just beyond the church is a bridge over the muddy creek that is the mouth of the River Don. The stones in the bed of the creek just upstream of the bridge had a whitish coating of sewage fungus which is, in my experience, never a healthy sign in a stream, tidal or not. Sewage fungus is much less common now in Britain than it was in the past, which is an indication of the gradually improving state of our rivers. The term “sewage fungus” is, in fact, a misnomer as the organisms that are lumped under this term include both fungi and bacteria. The important point is that they are not photosynthetic and so rely upon complex organic compounds in the water in order to obtain the energy that they need to grow. “Complex organic compounds”? Go figure.


Sewage fungus (probably Beggiatoa) smothering stones in the tidal creek just upstream of Jarrow Bridge.

Mixed in amidst the sewage fungus and green algae (Ulva sp.) on the rock there were lots of diatoms. The one that caught my eye was a large sigmoid Nitzschia gliding amidst the Beggiatoa filaments. There were several of these moving around the slide but what was most interesting to me was that each had at least one, and in some cases half a dozen, much smaller diatoms sitting on them as they moved around. Being a relative novice to brackish and marine habitats, I do not know what species these epiphytes were, though I suspect that they were Amphora, possibly A. exigua. The constant motion of the Nitzschia made it impossible to capture this crisply with my stacking software and I lack the hard heart necessary to kill diatoms purely to obtain a better photograph.


A sigmoid Nitzschia with a payload of Amphora spp. collected from the tidal creek near Jarrow Bridge, 18 April 2014.

I wrote “possibly Amphora exigua” based on the flimsiest of evidence. The latest monograph on Amphora, a massive tome, describes the details of the silica frustule in minute of detail but the ecological comments are vague. I should, it tells me, now call this diatom “Halamphora exigua” but, under “Distribution and ecology” all it can tell me is “not precisely known”. It is a sad reflection on the strange world of diatoms where, it seems, we know the shape of everything yet the meaning of nothing.


Levkov, Z. (2009). Amphora sensu lato. In: Diatoms of Europe, Volume 5. (H. Lange-Bertalot, ed). A.R.G. Gantner Verlag K.G. 916pp.

In the shadow of the Venerable Bede …

When I was at the Royal Botanic Gardens in Edinburgh last week, I was shown a microscope slide collected in the 19th century from a location recorded as ‘Jarrow Slake’. As Jarrow is just a few miles from where I live, my interest was piqued (which was probably why I was shown the slide in the first place).

Jarrow is a place name that resonates through the history of north-east England for over a thousand years, famous for its links with the Venerable Bede, the Saxon monk who wrote the first history of England. In the twentieth century, it is remembered as the starting point for the Jarrow March, a pivotal moment in the history of the Labour movement. It is located on the south side of the River Tyne, between Gateshead and South Shields and ‘Jarrow Slakes’ was the name for the expanse of intertidal mud to the east of the monastery. Actually, the name ‘Jarrow’ is, itself, derived from the Old English word for mud or marsh, though there is far less mud now as the historical Slake was reclaimed in 1972 and is now part of the Tyne Dock complex (more at “King Ecgfrith’s Port”) . One of the Slakes most gruesome claims to fame is that in 1832 it was the location for the last public gibbeting in England.


Jarrow Slakes, photographed from close to Bede’s World (NZ 338 657) in April 2014.

The Slakes had a local reputation as an area of quicksands which, after a couple of exploratory forays onto the soft mud at low tide, seemed very plausible. As a result, I confined my explorations to the upper part of the remaining mudflats in the area at the mouth of the River Don between St Paul’s church and the Slakes. I soon found what I was looking for: patches on the mud which had a distinct chocolate-brown hue, which I knew from previous experience to be teeming with diatoms.


A patch of diatoms on the upper intertidal mud at Jarrow Slakes, close to the position from which the earlier photograph was taken.

I don’t know enough about brackish and marine diatoms to be able to put names on all the diatoms that I saw in this sample. Many I recognised as species of Navicula, a large genus which is also common in freshwaters but some were less familiar to me. One that particularly entranced me was Bacillaria paxillifer although it’s rapid yet graceful movements were impossible to capture with my camera. The cells are all attached to one another by the raphe and slide along the length of each other in a manner similar to the movement of a slide rule. At one extreme, they form long chains, the cells attached only by the tips (the moment I caught with my photograph). The next moment, they all slide in unison to compress the chain into a ribbon of almost parallel cells. But this happens so quickly that there was no time to refocus and take a photograph before they are sliding along each other again back into an extended chain.


Diatoms from the upper intertidal mud at Jarrow Slakes, April 2014. A., b. and c. are species of Navicula (c. is probably N. phyllepta); d. is Amphora, possibly A. hyalina; e. is a Diploneis sp.; f. is Bacillaria paxillifer and g. is probably Paralia sulcata.

These diatoms are more than just a curiosity. Many of these diatoms produce extracellular polysaccharides for various purposes, including movement. These, in turn, create a sticky matrix which helps to bind the mud and sand together to create a more stable substratum into which other plants can colonise. These plants further consolidate the sediments, making them more resistant to erosion. Slowly, over time, the entire shape of estuaries can change. And all because of these small chocolate-brown patches on the mud.

Lichen on the menu?

An interesting article in yesterday’s Independent, following my recent posts about lichens, describes their culinary uses. The very best lichen comes, apparently, from the stomach of a freshly-killed reindeer though there are options for the more squeamish amongst us too. The very wonderful L’Enclume restaurant in Cumbria has experimented with deep-fried lichen though not, unfortunately, on the evening we were there in January

A paper you should all read …

I have tried to use this blog to promote the benefits of a broad interest in natural history over the narrow specialisms encouraged by modern academia. Consequently, I was delighted to see this issue receiving serious consideration in an essay in the latest issue of Bioscience: Natural History’s Place in Science and Society. It is open access, so you can read it even if you don’t have a subscription to Bioscience. No excuses, then. I’ve even given you the link.

The authors start with a definition of natural history as “the observation and description of the natural world, with the study of organisms and their linkages to the environment being central.” Natural history, in other words, is inherently cross-disciplinary and multiscaled. Implied, but never actually stated, is that the decline in natural history is a direct consequence of the growth of biochemical and molecular technologies. The latter may be excellent for answering questions about single organisms (and no-one would dispute the benefits for human health) but one cannot avoid knowing more and more about less and less. We need observation-based approaches if we are to ask the right questions in the first place, especially where more than one organism is involved.

I made my own case for this in a paper in Ecological Indicators last year. I was not arguing that there was no place for specialists, only that the day-to-day management of ecosystems needed people who were familiar with a wide range of organisms and who could make high-level decisions drawing on several complementary strands of evidence. The problem is more acute for the lower organisms, the focus of this blog, which lack the charismatic qualities of larger organisms such as birds.

By noting the decline in ‘natural history’ teaching in universities, the authors of the Bioscience essay are locating the cause of the problem in the supply-side of the equation (to use the language of economists). I have also wondered if there is not an issue in the demand for such courses. With the possible exception of bird watching, there has been a general decline in active participation in natural history in favour of ‘consuming’ nature via the television screen. Students come to university enthusiastic about the idea of natural history but find the opportunities for fieldwork to be limited and the reality of fieldwork less appealing. More so, perhaps, if struggling to name unfamiliar organisms (because of their lack of previous experience) in the vagaries of our climate. And, let us not forget, our flora and fauna are so much drabber than at the exotic locations that David Attenborough’s budget lets him visit.

The beauty of the Bioscience essay is that it not only laments the decline in ‘natural history’, it also presents examples of where broad cross-discipline thinking has led to insights that reductionist approaches alone could never have reached. And it has reclaimed the term ‘natural history’ for serious scientists. This, in my opinion, is more than just a matter of semantics. Anyone who uses science to argue for change needs to make the fullest possible use of the grey area between the jargon-filled papers of academic specialists and the non-technical beneficiaries of their endeavour. I’m proud to be a natural historian.


Kelly, M.G. (2013). Simplicity is the ultimate sophistication: building capacity to meet the challenges of the Water Framework Directive. Ecological Indicators 36: 519-523.

Tewksbury, J.J,, Anderson, J.G.T., Bakker, J.D., Billo, T.J., Dunwiddie, P.W., Groom, M.J. Hampton, Herman, S.G, Levey, D.J., Machnicki, N.J., Martinez del Rio, C., Power, M.E., Rowell, K., Salomon, A.K., Stacey, L., Trombulak, S.C. & Wheeler, T.A. (2014). Natural history’s place in science and society. Bioscience 64: 300-310.