So that was 2015 …


It seems like just a few weeks ago that I was writing “122 days to go” in anticipation of the UK General Election. That, however, is now 243 days in the past. Nonetheless, the first question that I asked in that post (“What will happen to the UK environment if we vote in parties that want to leave the EU?”) is still as pertinent as ever, and the referendum on UK’s membership of the EU will probably be the defining political issue here during 2016.   I am sure that I will be returning to this topic over the next few months.

My word map for 2016 is similar to that for 2015 (see “And finally …”) although I am intrigued to see that “see” is larger this year than “algae”.   Seeing the world from unexpected perspectives is a large part of what my blog is about. The impetus for my intellectual journey over the past three years or so has been a reaction to what I saw as complacency on the part of my fellow algal scientists, many of whom collect samples and processing data with too little consideration for how those samples related to the natural state of the communities from which they were taken. That, in turn, had prompted my depictions of the underwater world.   That journey now describes a wider arc – travelling on from reflecting first on how our observations and measurements relate to the natural state, to think about how those same observations translate into policy and decisions.   A series of posts in June (starting with “the human ecosystem of environmental management”) as I was making my way towards a scientific meeting in Trento unwrap the issues around this.

Finally, thanks for bearing with me in 2015. WordPress tell me that my blog has been read by people in 128 different countries (up from 110 last year) and that the 13,000 views equate to filling the Sydney Opera House five times.   Anyone who has heard me sing will marvel that a single sentence can reference both me and the Sydney Opera House …

An Ocean Garden


If you write a blog about algae you shouldn’t be surprised if people give you books about algae as Christmas presents (maybe I should start writing a blog about single malt whisky or fine wine and see what that yields?).   This year, it was a book on seaweeds, called “An Ocean Garden: The Secret Life of Seaweed” by Josie Iselin, a rather beautiful little volume that straddles the boundary between fine art and natural history.   The book is structured as a series of diary entries, each detailing a visit to her local coast (Maine and California at different times), accompanied by a beautiful image of the seaweeds that she collected on that visit.   The images were produced by arranging the fronds on the glass of a flatbed scanner, and then generating a computer image file.   The results are intriguing, perhaps because the translucence of the thin tissues of seaweed fronds creates a fascinating balance between reflected and transmitted light. The artist’s sensibility comes to the fore as she arranges the fronds on the plate; the scientist in the naming of each species and the comments on their natural history; the writer in her weaves the strands of anecdote and fact into the notes that accompany each image.

I’d like to think that I had infected people around me with a little of my enthusiasm for algae. I fear that the truth is that I have inoculated them, and that they have developed a tolerance that means that they can zone out whenever I start to ramble on about algae yet again. However, I think that I could probably leave Josie Iselin’s book lying around, and that those same people might well pick it up and start to marvel yet again.   Well worth investigating.


Josie Iselin (2014). An Ocean Garden: The Secret Life of Seaweed. Abrams Books, New York.

Do we see through a microscope?

I would have considered this to be a question that barely needs an answer. That, however, was before I read an essay by philosopher Ian Hacking who brings the spirit of logical positivism to the question. When we look through a microscope we see objects that are not “… physical things in a literal sense,”, he writes, “but merely by courtesy of language and pictorial imagination.” Confused? Read on.

First of all, “seeing” is not the same as “looking”.   “Seeing” implies a higher level activity than mere “looking”.   Both involve the reaction of light on the retina, leading to stimulation of the optical nerve.   However, what we see when we look down a microscope differs from what we see when we look at a view out of a window in two important ways. The first is that most of the time our eyes are analysing reflected light, whereas the microscopist mostly (though not always) is looking at transmitted light, light that has passed through the object we are looking at.   The tones we see are a consequence of variations in the proportions of light that are transmitted or absorbed rather than in the proportions that are reflected or absorbed.

The second difference is that a consequence of magnification using an optical microscope is a very shallow depth of field (i.e. the space within which objects are in acceptable focus).   The picture below shows the view down my microscope as I was examining the specimens that I wrote about in my previous post.   In practice, I never actually “saw” this image, and I certainly could not have photographed it, due to the limitations of depth of field. In practice, I was constantly adjusting the focus with my right hand, whilst drawing with my left.   This is a point that Hacking makes: you have to learn to “see” through a microscope. As children we learn to judge distance by correlating visual information with tactile experiences, so microscopists learn to infer three dimensions in their worlds by gentle manipulation of the fine focus mechanism on their microscopes.   “Seeing”, in other words, is far more than just the consequence of light hitting the retina.


River Ehen, near the outflow from Ennerdale Water, December 2015. Drawn at x400 magnification.   See images in previous post for indications of scale.

More broadly, we could argue that “seeing” in the microscopic world requires interventions.   The lenses in our microscopes are one type of intervention, of course and without these we would not be able to see tiny objects with clarity.   But this is just the start: we often use stains to adjust the optical properties of certain parts of cells, making it both easier to see these and, in many cases, to infer their composition (iodine binding to starch is a good example).   These stains are often highly toxic so one unwelcome “intervention” is that we necessarily study dead or dying tissues.   The study of diatoms depends upon high resolution mountants, which make the task of viewing structural details of objects that are, essentially, microsocopic lumps of glass mounted between a glass slide and a glass cover slip much easier. This follows a stage in which the cellular contents are dissolved away by the action of strong oxidising agents.   So routine is this stage that many diatomists are in danger of forgetting that the empty glass shell is not really the reality that they seek.

We could argue that microscopic observations approach truth only when they can be validated by an independent means. At low magnifications, the difference between the raw and magnified images are small and individuals can easily validate what they see through a lens.   I know that there are words on a page of writing because I can see them crisply through my reading glasses but I could also, if necessary, hand the page to my son who will be able to confirm that the fuzzy blur that my unaided eyes discern is, indeed, writing.   However, there is a threshold in magnification beyond which this form of validation will not work.   We rely on a network of theoretical “proofs” to confirm the truth in a microscopic image. At one end of the scale this may involve a continuum of consistent observations from the hand lens to medium or high power optical microscope.   At the other end of the scale, it may involve a completely different approach to visualisation (the electron microscope, for example) to corroborate an observation. During my postgraduate days, a fellow student defined the cellular organelles he saw in his electron micrographs as “reproducible artefacts”.   His flippancy, in fact, contains a deep truth: we make our observations on highly manipulated specimens and need to be rigorous in our efforts to confirm their validity.

Hacking’s conclusion was that we see with a microscope, but it is naïve to suggest that we see through a microscope. We may look through a microscope but the images make sense only because of interactions that go beyond patterns of light hitting the retina.   “Seeing”, in other words, is a higher-level process that involves interactions with the brain and with the specimen itself.   Hacking calls on a lot of high power philosophy to make his point; all we need to do is to take care before equating the images we create with the truth.

Happy Christmas.


River Wear, Wolsingham: four views down the microscope: top left: January 2009; top right: March 2009; bottom left: June 2009; bottom right: September 2009.  


Ian Hacking (1981). Do we see through a microscope? Pacific Philosophical Quarterly 62: 305-322.

The water had receded from the earth …

Having used Biblical language to encapsulate the floods that immersed much of northern England a week or so ago (see “And the waters prevailed upon the earth …”) I feel I must turn back to Genesis in order to find a title for this follow-up piece (chapter 8 verse 11, if you are interested).   My regular fieldwork haunts on the River Ehen in western Cumbria experienced such high flows that at one point they went off the top of the scale, meaning more than 3000 MLD (mega litres per day).   To put this in perspective, we regard 500 MLD as the absolute limit for safe field work at this particular location.   An additional problem was that our route to the River Ehen passed three of the most flood-affected parts of Cumbria, complicating our travel plans. But that was then, and by Monday morning the hydrograph was indicating flows of about 300 MLD, and I lost no time in heading off down the long and lonesome highway. I get my kicks at the far end of Route 66 …

The differences were apparent as soon as we peered into the river: at this time of the year the Ehen typically supports lush growths of algae (see “How green is my river?”) but today the stones were missing their usual green clothing.   This is what the bed of the river usually looks like in the summer, when grazing invertebrates keep the quantities of algae low.   It was a surprise to see the river bed looking like this in December.


Cobbles and pebbles on the bed of the River Ehen, Cumbria, just below the outflow of Ennerdale Water, 16 December 2016.   The larger stones are about 10 cm across.

A kilometre or so downstream, the bed consists of a greater proportion of boulders and many of the cobbles are more deeply embedded into the river bed.   Here, the stones again had lost their usual covering of green algae but, this time, some of the larger stones had conspicuous brown patches, where the diatoms were thriving in the absence of competition from other algae.


A boulder (about 25 cm across) on the bed of the River Ehen, about a kilometre below the outfall from Ennerdale Water. Note the brown growths of diatoms on the upper surface.

The diatoms that I saw when I looked at a sample under the microscope were much the same as those that I had been seeing for much of the time that I have been looking at the River Ehen. I don’t get a sense that this is a community of distinctive “pioneer” species colonising a bare surface, rather that this is an inoculum formed from the scattered remnants of the usual rich community.   There were a lot of Achnanthidium minutissimum (which many regard as a typical “pioneer” species) but also long-stalked Gomphonema sp. which we would expect to thrive in thicker biofilms plus two or three species of needle-like Fragilaria species (which are hard to identify with certainty in the live state).   One of the Gomphonema sp. is the form that I wrote about in Diatoms and Dinosaurs and which is, again, hard to identify with certainty.


Diatoms in the River Ehen, December 2016: a. Tabellaria flocculosa; b. Gomphonema acuminatum; c. Gomphonema sp. (see note in text); d. and e.: Fragilaria species; g. – i.: Achnanthidium minutissimum.   Scale bar: 10 micrometres (= 1/100th of a millimetre).  

There were other types of algae in the samples; again, these were the species that I have seen at other times from the River Ehen but this time they were present only in very small quantities.   In particular, I noted a few isolated filaments of the cyanobacterium Calothrix sp, one of which had a number of Achnanthidium minutissimum valves growing directly on the sheath.


Achnanthidium minutissimum (and one cell of Gomphonema) growing on Calothrix in the upper River Ehen, December 2016. Scale bar: 10 micrometres (= 1/100th of a millimetre).

I can’t wait now for our next trip to the River Ehen, in the middle of January, in order to see how the river has changed in the month following the floods.   Many algae are adapted to growing in winter so it is possible that there will be lush growths again, so long as there are no more big floods. But large climate-driven events can have consequences for rivers that are measured in months (see “How green is my river?”) or years (see “And the waters prevailed on the earth”).   We are close to the end of our third year of intensive studies on the River Ehen and there is a pleasure in knowing that there is still more to learn. That said, fieldwork in January does involve plunging your hands into a freezing cold river …

A stamp of approval …


A small parcel arrived from Germany last week bearing, in addition to a seasonal offering of Lebkuchen, two stamps featuring diatoms, part of a series of stamps termed “Microworld”.   A little detective work has revealed this picture to be the work of KAGE Institute of Scientific Photography, based in an impressive castle in Baden-Württemberg, about 60 km to the east of Stuttgart. Their website modestly includes Spiegel Online’s description of them as “Prominentester Mikrofotograf der Welt” (“most famous microphotographer in the world”).

Of course, after all I have written about the poor perception of algae in the wider world, it is good to see diatoms being honoured with their own stamp, even though false-coloured scanning electron micrographs (SEMs) rank low in my estimate of ways to depict the microscopic world.   This relates to a deeper concern about the way in which we see the world through microscopes.   It is a theme that I want to develop in a post in the near future; but it also overlaps with a broader concern about the reality of microscopic images more generally

SEMs beguile us with three-dimensional impressions of the microscopic world but they also present the transparent as opaque and everything is monochrome. The latter is a temptation to anyone with rudimentary knowledge of Photoshop to show off their skills although, in the process, they remove the image a little further away from “reality” and towards “abstraction”.   Is that a problem?   In artistic terms, the answer must be “no”, so long as we are honest about what is happening. Having abstracted the image (i.e. removed it from … ) its context, we are free to evaluate it purely in terms of artistic merit. We have had SEMs on the Hilda Canter-Lund shortlist that work as abstract images; however, one of the critera that the judges look for when drawing up the short list is to find basic authenticity and honesty in the images. That raises a whole lot of questions when dealing with the microscopic world, but does suggest a limit to the amount of image manipulation that is acceptable.   The key point, in my opinion, is to ensure that the viewer never forgets that these organisms are part of the natural world and not products of the imagination of an inferior Salvador Dali clone.

And the waters prevailed on the earth …

Conscious that this blog, which purports to be about natural history, has not actually had any posts reporting my own observations for some time, I had tentative plans to go out and collect some samples this weekend.   Storm Desmond, however, had other plans for me: high winds and heavy rain from Friday evening onwards pushed local river levels up to dangerously high levels, and I was left to contemplate the capricious nature of the British climate from a largely sedentary perspective.

A screenshot of the Environment Agency’s river level gauge shows how the spate developed. We had high winds in Durham, but not excessive amounts of rain, and the steep rise in levels during Saturday reflects the time-lag between rain falling on the Pennines and arriving in the Wear at Durham.   The peak in level occurred early on Sunday morning, and the subsequent pictures show the river in Durham at about 10:30 on Sunday morning. Though high, this is not the highest I can remember: that was in 2009 when the road into Durham was impassable at Shincliffe as the river had broken its banks.


A screenshot from the Environment Agency’s river level website, showing the passage of Storm Desmond through Sunderland Bridge, a few kilometres upstream of Durham City, from midday on Friday 4 December to midday on Sunday 6 December.


The River Wear in spate on 6 December 2015: the view downstream from Elvet road bridge.


The River Wear in spate on 6 December 2015: the view upstream from close to the Count’s House, showing the same clump of Japanese Knotweed that featured in my post “In praise of Japanese Knotweed” in early November. You can see how the river has risen up and covered the bankside footpath.

As I have some old-fashioned ideas about fieldworkers being part of the benthos not the plankton, I am watching river levels with interest. I have fieldwork planned in Cumbria at the end of the week and am intrigued to see what Storm Desmond has done to the algal communities. The irony being that to study the effect of spates on ecology, one has to first get into the river… or even get close to the river. This may be an issue as my route to the River Ehen passes some of the most affected parts of Cumbria.

However, questions about the effect of a spate on a river can be generalised into a broader question of how occasional catastrophic events alter ecosystems which, in turn, makes us think about problems that may arise from simplistic interpretations of the relationship between explanatory variables and response variables, discussed in the previous post.   The temptation is always to interpret ecology in terms of the variables that are easiest to collect and measure when you are collecting your samples whereas, looking back at “How green is my river?” we see how late summer conditions in the River Atna are at least partly the consequence of high flows in the Spring.

Biologists have suspected this for a long time, and there is anecdotal evidence of changes wrought by individual events. I was pleased, therefore, to see that a whole issue of Freshwater Biology had been devoted to this topic.   With the effects of flooding uppermost in our minds this weekend, the introduction to this issue, by Mark Ledger and Alexander Milner, reminds us that “catastrophic events” can also extend to droughts and heatwaves. One point that emerges, even from a quick scan through the contents of this issue, is the importance of long-term datasets – revisiting, again, topics that wrote about in “How green is my river?” It is more pertinent than ever because of the fiscal squeeze on our environment agencies and, ironically, the flooding that results from Storm Desmond is going to lead to calls for yet more DEFRA money to be diverted to flood defence, which can only mean less money for environmental regulation.   Therein lies the biggest irony of all: a government department that trumpets the virtues of “evidence-based policy” is planning to collect less evidence. Work that one out, if you can.


Ledger, M.E. & Milner, A.M. (2015). Extreme events in running waters. Freshwater Biology 60: 2455-2460.

The politics of complexity (and the complexity of politics)

As there are globally-significant discussions this week on both climate (in Paris) and the civil war in Syria, I thought that I would prepare a cut-out-and-keep guide to guide all of you to the correct decision in each case.

For those of you on the political Right: cutting global carbon dioxide emissions is a ludicrous suggestion as there are far too many uncertainties associated with climate science, and the risk to global economic growth is too great. At the same time, bombing Syria is necessary as ISIS is an evil force that needs to be curtailed. Moreover, we have the military capability to target the ISIS leadership and this will, in turn, reduce the threat of terrorism in western cities.

For those of you on the political Left: cutting global carbon dioxide emissions is an urgent and necessary step but bombing ISIS is a potentially disastrous as there are far too many uncertainties and it is not a foregone conclusion that removing the ISIS leadership in Syria will curtail Islamic extremists elsewhere in the world. It may even encourage them.

Stand back from the details and both climate change and the situation in the Middle East resolve into the same problem: highly complex situations that are either reduced to simple cause-effect relationships by politicians with a point to make, or unpacked to reveal the huge uncertainties that would accompany any plan of action, should you want to block that path.   Left and Right simply swop sides when the discussion switches from climate to Syria (see “Is our world too complex to be trusted to politicians?“)

In both cases, the protagonists are telling us that there is a cause-effect relationship that means that a particular course of action (bombing ISIS strongholds, cutting carbon dioxide emissions) will have a predictable outcome. This is illustrated in graphical terms below. The “explanatory variable” is the action you think should be taken; the “response variable” shows the outcome.   The dots show the evidence on which this is based and indicate that in all circumstances for which you have evidence, increasing the value of the explanatory variable (e.g. by permitting UK bombers to target ISIS in Syria), will automatically have an effect on the response variable (e.g. reduced capability of ISIS).


Political rhetoric, expressed graphically: an adjustment in the value of the “explanatory variable” (increasing the quantity of bombs dropped on Syria, for example) will lead to a corresponding change in the response variable (reduced capability of ISIS).

The graph also summarises, very neatly, the plot of most action films .. James Bond, Superman, Misson Impossible … the list is endless. The hero is faced with an improbable situation and the climax invariably involves a rapid adjustment to a single explanatory variable that causes an immediate and dramatic change in the response variable such that the Evil Genius is thwarted. The problem is that this type of thinking then rolls over into real life: I’ve lost count of the number of times that a “security analyst” has come on the radio and explained how western bombs will disable ISIS capabilities and, by implication, eliminate the threat of Islamic extremism in Europe.

These highly predictable cause-effect relationships may be observed in controlled conditions in laboratories, where you are able to hold every other variable constant during an experiment. Out here, in the real world, however, we have to accept that many other variables will be changing at the same time as the two that we considering. In the sense that philosophers and mathematicians now understand “complexity”, we also need to recognise that  some of these other variables may behave unpredictably as the explanatory variable changes, with the potential for positive feedback loops to accentuate some outcomes, and dampen others. The best we can hope for is illustrated in the second graph.


Political reality expressed graphically: the situation is rarely so neat that a tweak to a single explanatory variable will automatically lead to a change in the response variable. Whatever the politicians tell you.

This is the type of situation we encounter very frequently in ecology: there is weak relationship between the explanatory variable and the response variable, but it is not possible to say with certainty how much effect a change in the explanatory variable will have.  The state of the response variable is influenced by many factors, not just the explanatory variable.    Indeed, it is possible that a small change in the explanatory variable will have no effect on the response variable at all and even that the system will behave completely unpredictably.   It is tempting to make the leap from using evidence to describe the state of the world, to making predictions; of confusing “correlation” and “causation”.   The risk is heightened if you look at data such as these through the lens of your chosen political ideology.   We also need to remember that, in the case of rapidly-evolving situations, the evidence base on which actions should be determined often does not exist (or is not in the public domain).

In the case of Syria, in the aftermath of events in Paris last month, the sense that Something Must Be Done seems to have overruled the lessons learned painfully and bloodily in Afghanistan, Iraq and, more recently, Libya.   All were sold to us as neat, surgical exercises to excise a tyrannical leader; none turned out that way.   Donald Rumsfeld, bless him, got it right with his oft-mocked quote about the Iraq war: “There are known knowns. These are things we know that we know. There are known unknowns. That is to say, there are things that we know we don’t know. But there are also unknown unknowns. There are things we don’t know we don’t know.”   And then, of course, there are things that we’ve decided to forget and things that only happen in action films.

(Note to Right-leaning friends: replace “climate change” with “Syrian civil war” as you read the article, if you wish. The details may differ but the principles are pretty much the same)