The Iron Lady II: the Agar Years

A word of explanation: for nine years until 2012 I wrote a regular column for the Institute of Ecology and Environmental Management’s magazine In Practice, based on the exploits of Basil O’Saurus, self-styled Professor of Tauro-Scatology.  As this is a quarterly publication, some of the seams that I mined for inspiration had lost topicality by the time I had to submit my copy, and a few articles have sat on my laptop unpublished.   One of these unpublished pieces was written when the film The Iron Lady was released.  The recent death of Margaret Thatcher gives me a chance to resurrect this piece so we catch up with Basil O’Saurus as he heads to a meeting in Soho, in London’s media heartland. 

Where are you heading today, Prof?

I’m pitching my latest film idea to a production company.  The film industry loves to cash in on a successful film, so I’m proposing a prequel to one of the biggest box office successes of the past year.   You’ve heard of “The Iron Lady”?

Of course, Famed for Meryl Streep’s Oscar-winning depiction of Margaret Thatcher

So now prepare yourself for: “The Iron Lady: The Agar Years”.  Ninety minutes of tense drama based on the true story of Margaret Thatcher’s time in a laboratory using algal by-products to improve the quality of ice cream.  Just think how different history might have been had she stayed.  Just think how different ice cream might have been if her talents had not been distracted by politics?

But surely you cannot base an entire movie on her one year in an industrial chemistry laboratory?

Of course not: The Iron Lady: the Agar Years will be searching for the dramatic untold stories in Margaret Thatcher’s early life and linking these to later events.

By “dramatic untold stories” do you mean “complete and utter fiction”?

Maybe, but a whole feature film devoted to algal by-products might tax even Meryl Streep’s acting so we need to dig deep.   And, just like in the original film, we’ll be telling the story through flashbacks.

Give us an example.

Picture the scene: Prime Minister Margaret Thatcher is planning the Falklands campaign, senior advisors are describing the terrible risks of sending a task force so far, Alexander Haig, the US Secretary of State is trying to broker a compromise and ….

Cut to a flash back?

Exactly.  Imagine the scene: the young, idealistic Margaret Thatcher poring over obscure phycological texts late into the evening, trying to find seaweeds that will yield newer and better polysaccharides … she finds a paper by H.J. Humon on agar resources of the South Atlantic published in Science in 1944 … it leads her to dig yet deeper into the subject ..

Cut back to 1982: Alexander Haig’s voice can be heard trying to persuade her that an unelected but pro-US right wing military junta has every right to invade an archipelago which, let’s face it, few British people had even heard about back in 1982 …

And, back to 1955 … she is reading the reports of the Discovery expedition from the early years of the twentieth century, as it investigates the marine resources in the southern Ocean …

1982, again, and her face has a steely resolve: to Alexander Haig these may be just a pile of rocks in the South Atlantic barely worth squabbling over, but they are British rocks and that is British seaweed fringing the littoral …

Maybe someone reminded her that the Falkland Islanders known as “kelpies”?   That must have meant something to her?

So The Iron Lady: The Agar Years is going to put a phycological spin on Margaret Thatcher’s entire premiership?   Surely you can’t explain her confrontation with the miners using algae?

Oh yes I can: coal industry waste was dumped into the sea at several points along the County Durham coast with devastating effects on marine life ….

So Margaret Thatcher engineers a confrontation with the miners ….

…. the entire social fabric of parts of north-east England come close to unravelling ….the mines close, the coal dumping ceases and, scrolling forwards thirty years, the coastline now has a healthy seaweed covered littoral.

And all because of Margaret Thatcher’s brief professional interest in ice cream?   Nice theory, but will it pass peer review?   Thanks for your insights, Prof.

 

Note #1: Fact or fiction?  Margaret Thatcher certainly worked for a time as a food research chemist for J. Lyons & co in London.  The precise nature of her work there is not clear; stories that she was involved in the invention of soft ice cream are anecdotal.  But it is too good a story to ignore completely.   A good account of her scientific career is by Jon Agar (I kid not): Thatcher: Scientist in the Notes and Records of the Royal Society 65: 215-232 (2011).

Note #2: Basil O’Saurus derives his name from the Basilosaurus, an extinct whale-like mammal that lived about 40 million years ago.

Note #3: Tauro-Scatology? Go away and think about it.

More reflections from the dawn of time …

It was only when a horse damp to its flanks passed us that I looked again at the map and realised that our circular walk included a ford.   And that, despite the dry weather over the past few weeks, it was far too deep to contemplate attempting fully clothed.  So our walk was aborted and, instead, we scrabbled along the banks of the Coquet (encountering my first nettles of the year in the process) in search of the cup and ring marks that our Ordnance Survey map told us were nearby.

Coquet_Morwick

The lower River Coquet near Morwick.  The sandstone cliff with the cup and ring marks is on the left.

Even though we had a map reference and some field notes from The Modern Antiquarian website we still ended up staring at a nondescript sandstone cliff for some time before our eyes adjusted and we started to pick out the patterns on the rock.   In particular, there was one set of three very clear marks – each a central depression surrounded by three concentric rings etched into the rock.   They were just a few centimetres across but they contain all the mystery of Stonehenge: who carved them? When? And what for?  You can find similar marks on rocks all over northern Britain, elsewhere along Europe’s Atlantic fringes and into the Mediterranean.  Others in Northumberland have been dated to the early Neolithic (4000 years ago) but the reason why someone without metal tools put in the effort to create these marks remains elusive.

Morwick_cupandring

Left hand image: the cup and ring marks on the cliffs overhanging the Coquet at Morwick; right hand image: the dark brown patch is the seepage on the cliffs dominated by blue-green algae.

We were contemplating these questions as we sat on rocks beside the river eating sandwiches when I noticed the seepage running down the cliff a few metres away from these marks.   Once again, an apparently bare (albeit damp) sandstone cliff revealed itself to the prepared mind.   Close up, the damp surface is pockmarked with tiny hummocks, just a few millimetres across and, when you look closely, with a distinct green tinge.  The prepared mind, however, had forgotten to bring any forceps or bottles, so I had to scrape off some of this film with a fingernail and wrap them in the clingfilm that had held my sandwich.

Morwick_Gloeocapsa

Upper image: a close-up of the seepage from the cliff at Morwick; lower image: cells of the blue-green alga Gloeocapsa from the seepage.  The scale bar represents approximately one centimetre in the upper image and ten micrometres (1/100th of a millimetre) in the lower image.

Under the microscope this film turned out to be a mass of blue-green cells, each encased in a colourless sheath.   The cells belong to a genus called Gloeocapsa and the thick sheath presumably offers some protection on those occasions when the seepage dries out.  Like Phormidium we met in the previous post, Gloeocapsa is a blue-green alga, one of the most primitive types of organism.  Though early microscopists classified them as part of the plant kingdom, we now know that they are actually bacteria, reflected by the formal name Cyanobacteria.

It is likely that Gloeocapsa, or organisms very similar to this, have inhabited damp habitats like these cliffs since the Precambrian.   Indeed, they might have been here as the Neolithic craftsmen painstakingly carved the cup and ring marks which lets us put them into context.   It is about 400 years since Shakespeare wrote Hamlet.   We have to multiply this time span by 10 to get to the Neolithic period, about 4000 years ago.  However, we then need to multiply this figure by 16250 to get to the Cretaceous period, when dinosaurs were common (65 million years ago) and then multiply this final figure by eight to take us into the Precambrian.   In other words, the 400 years between the Elizabethan period and today needs to be repeated one million three hundred thousand times to take us to the dawn of biological time.   And, for this entire period, organisms very similar to Gloeocapsa and Phormidium have been here.

Time, which antiquates antiquities, and hath an art to make dust of all things, hath yet spared these minor monuments …
(
Thomas Browne, 1605-1682)

in which the spirit of Jeremy Clarkson is evoked ….

The larger stones at one of the sites on the River Ehen I visited last week had curious leathery mats on their upper surface that I could peel away intact with my fingers.   They are dark-brown, almost black in appearance but, if you look closely, there is a distinct greenish tinge to the upper surface.   It is not easy to get a clear view of these under the microscope but, after gently teasing out the mat with a dissecting needle, the composition becomes clear.  The mats are composed of a dense network of intertwined blue-green filaments, belonging to a species called Phormidium autumnale.   Mats of this species are often found on the upper surfaces of rocks, where they are likely to dry out from time to time.  When this happens, the mat dries down to paper-like fragments that can blow in the wind.

Ehen_Phormidium

Leathery mats of Phormidium autumnale on a boulder removed from the River Ehen in April 2013.

Ehen_130419_7

A microscopic view of filaments of Phormidium autumnale from the mats in the photograph above.   The filaments are approximately 5 micrometres (1/200th of a millimetre) in diameter.

These filaments are almost identical in appearance to some of the oldest fossils ever recorded – from the Gunflint chert of Australia, estimated to be about 2000 million years old.   This nondescript mat in a northern English stream offers us a glimpse into a world some ten times older than that of the dinosaurs yet, somehow, these organisms have survived all the vicissitudes that led to the extinctions of so many other forms.

Naming these organisms is a challenge; more so, in some ways, than for the diatoms (see Berlin and barcodes).   There is little more for the eye to grasp than a filament divided into cells by simple cross-walls.  Consequently, those who study the blue-green algae have the same struggles as I described in my earlier post and, again, molecular approaches are coming to our aid.   If anything, the outcomes are more unsettling for the blue-green algae than was the case for diatoms, with some of the evidence (see below) suggesting that the taxonomy based on the optical microscope may need a complete rethink.  As ever, we are too easily deflected by our anthropocentric view that evolution results in ever more complicated and sophisticated organisms.  Look at how all three-door hatchback cars are broadly similar, regardless of the manufacturer.  They all inhabit a similar environment and, consequently, the models have evolved to the most efficient form to thrive there.   The same is true for these filamentous blue-green algae, only it has taken place over a much, much longer period.   And now, unless you are to blue-green algae what Jeremy Clarkson is to cars, frankly, they all look pretty much the same.

References

Marquardt, J. & Palinska, K.A. (2007).  Genotypic and phenotypic diversity of cyanobacteria assigned to the genus Phormidium (Oscillatoriales) from different habitats and geographical sites. Archives of Microbiology 187: 397-413.

Teneva, I.,  Dzhambazov, B.,  Mladenov, R. & Schirmer, K. (2005).  Molecular and phylogenetic characterization of Phormidium species (cyanoprokaryota) using the cpcB-IGS-cpcA locus.  Journal of Phycology 41: 188-194.

The River Ehen in April

There was blue sky over the fells this week when we visited the River Ehen for another of our monthly visits.  The first impression today was that the riverbed was much less green.  The cobbles still had a thick, slimy film but there was less of the Spirogyra and Draparnaldia that characterised the samples from January and February.   Another absentee was the thick growths of the red alga Audouinella hermanii although another red alga was very abundant at the same site: this was Lemanea, which forms wiry filamentous growths on stones submerged in the fastest-flowing parts of the stream.   Once again, however, this so-called red alga is actually olive-green in colour.  At some point in the near future, I must post some pictures of a red alga that really is red.

Ehen_Lemanea

Lemanea fluviatlis attached to a boulder from the River Ehen, April 2013.

In close up, Lemanea does not form the flaccid limp filaments of Spirogyra and other green algae that are just a single cell thick.  These are multicellular, a couple of millmetres thick at the base and tapering gradually to a point.   Many years ago, I cut a thin section from a filament of Lemanea and stained it with the fluourescent dye Calcofluor-white, which binds to the cell walls.  This photograph shows very clearly how the cells form a tube around a hollow core to give a streamlined form that can thrive in those parts of the stream where the physical stresses are greatest.

Lemanea_calcofluor

A section through a filament of Lemanea from the River Wear, stained with the fluorescent dye Calcofluor-white.

I was surprised to read that this unprepossessing plant was eaten in some parts of eastern India although, as Lemanea is a distant relative of Porphyra umbilicaris, the alga from which lava bread is made, perhaps I should not have been.   The first paper I read on this topic  contained few details and my own experiments, washing the filaments and chopping them over a salad met with less-than-ecstatic responses from friends and family.   However, I subsequently found another paper which gave more details.   As the alga is only abundant for a few months in the year, it is harvested and air-dried so that it can be stored.  Then it is cooked with vegetables to impart a fishy flavour.  This description gives the impression that it is used like a herb, adding flavour to the dish, rather than as a significant source of nutrition itself.  Time, perhaps, to think up some new recipes?  In the same way that samphire complements seafood dishes perhaps Lemanea would raise the flavour of trout or other delicately-flavoured freshwater fish?    My main problem may be persuading people that the dish I have served them really is a gastronomic treat and not just a pile of algae I pulled out of a local stream …

Colourless green ideas sleep furiously …

So wrote Noem Chomsky in 1957 to demonstrate that a sentence may be grammatically correct whilst still being semantically meaningless.   It is a phrase that bounces through my mind when I read some of the so-called applied science literature.   A scientist has a bright idea, writes it up, making careful use of statistics and a thorough literature review to support his case, but … ignores the context within which that science will be applied.  Good science but … meaningless.   In my case, the context is often that for a piece of science to be useful, it has to dovetail with the legislation and the needs of the organisations responsible for managing the environment.  The latter, perhaps, less than the former, but it is good sense not to push a large public sector organisations too far out of its comfort zone without a really strong case.

The article that prompted these thoughts today is a short opinion piece in a journal called Molecular Ecology with the modest title Biomonitoring 2.0: a new paradigm in ecosystem assessment …. by Donald Baird and Mehrdad Hajibabaei.   My previous post extolled the potential of DNA barcoding but Baird and Hajibabaei go much further … almost suggesting that a Cambodian-style “Year Zero” beckons for those of us involved in environmental monitoring.  In particular, they pick on another review which (rightly) highlights the current lack of knowledge of the response of individual species to stressors.  This, in turn, limits our ability to predict the outcome of expensive remediation efforts.  Yet the solution is not, as Baird and Hajibabaei imply, to bypass traditional taxonomy altogether, because the legislation that underpins our work in Europe refers to the composition of the biota of river, lakes and coastal waters and the regulators who are responsible for this will be reluctant to change without very good reason.  Another reason is that the “biomonitoring” that Baird and Hajibabaei refer to is the ecological equivalent of a doctor taking your blood pressure.  No more than that.  It is what we do with this information that is important, and improving our knowledge of distinct plant and animal species will help us devise strategies to bring rivers and lakes back to a healthy condition.   There is a future for DNA barcoding within ecosystem assessment (see my previous post) but we will need a synergy with the conceptual foundations that have been developed over the past decades if we are to make progress.

Just after I wrote these paragraphs, I heard the geneticist Steve Jones talking on the radio about the gulf between the claims for molecular biology and the reality that scientists had actually delivered.  He suggested, mischievously, that the four letter code for DNA, A (adenosine), G (guanine), T (thymine) and C (cytosine) should be changed to H, Y, P and E.   I’ve read many excellent studies that use molecular biology to further our understanding.   These generally fulfil Newton’s aphorism: “if I have seen further it is by standing on the shoulders of giants.”   I’ve also heard several preposterous suggestions that betray ignorance or just superficial understandings of complicated systems.  We may well be on the edge of a paradigm shift in the way we collect data for ecological assessment but if we ignore the broader context, we’ll end up with flashy papers in high impact scientific journals and little tangible progress towards our bigger goals.

Berlin and barcodes

Aristotle has been on my mind this week. I was at a workshop at the Botanischer Garten und Botanischen Museum in Berlin talking about topics far removed from Ancient Greek philosophers but, somehow, Aristotle kept intruding. The chain of thought went something like this: we were discussing a relatively new technique for identifying organisms called DNA barcoding. This is a technique similar to the genetic fingerprinting that is used to catch criminals (or, to use a topical example, to find horse meat in lasagne).  Instead of differentiating between humans, this variant allows us to distinguish different species of plant, animal or micro-organism. For those of us who deal with the microscopic world, putting a name on an organism is a time-consuming task for a highly-experienced individual and the possibility of doing this faster, and with a lower risk of mistakes, has huge potential.

Image

The tropical greenhouse at the Botanischen Garten in Berlin on a chilly April morning.

But why Aristotle? I wrote about beavers in a post a couple of weeks ago and, I’m guessing, the word ‘beaver’ conjured up an image of a medium-sized aquatic rodent with big teeth and a large flat tail. We tend to use the shape and physical properties of plants and animals as a mental shorthand to summarise the species. Strictly speaking, beavers are defined by a much wider set of properties, key amongst which is the ability of Mr and Mrs Beaver to produce healthy, fertile offspring. We can reduce “beaver” to a set of descriptive phrases but, in reality, a beaver is, well, beaverish. And this is where Aristotle comes in to the story. He looked at common objects such as tables and realised that these had properties that were more than just five pieces of wood. There was, in other words, a quintessence to a table that was irreducible.

The problem that those of us who study algae face is that their size means that there are relatively few features visible under the light microscope with which we can elucidate this quintessence (as the images in some previous posts will testify).  Until recently, the response was to wait for improvements in optical technology and the arrival of electron microscopy to give greater resolution and, therefore, more characteristics on which to base descriptions.  However, this still means that, unless you have a very expensive microscope and a highly-trained analyst, you can’t name many algae accurately.

What if we had access to a completely different set of characteristics?  There have been several attempts over the years to use biochemical characteristics to differentiate algae but none have the precision to compete with identification based on size and shape.   But the recent advances in molecular biology do seem to offer real possibilities.  More so now because the latest equipment can process samples at such a rate that the cost per sample is likely to be considerably lower than that for a conventional analysis.  You can forget the brilliance of the science, it is this that is making hard-nosed managers in the commercial and government sectors look hard at DNA barcoding.

All the characteristics of any living organism are controlled by its genes so DNA barcoding is not so very different to identification based on size and shape except that size and shape are, themselves, variable.   Grow a houseplant in a shaded corner of a room and it may look quite different to the same plant grown in full sunlight even though their genes are more-or-less identical.  On the other hand, identification based on size and shape gives you information from many genes simultaneously whereas a DNA barcode is one tiny fragment of one gene.

All is shaping up nicely for a vigorous debate.  In one camp, there is a large group of individuals who have spent years acquiring skills they are not going to relinquish to a technician with an expensive machine without a fuss.  In the other camp, a group who see potentials for overcoming the limitations of our traditional approaches, albeit recognising that some sacred cows may get damaged in the process.

This brings me back to the meeting in the Botanischen Museum.  The medium-term plan is to make sure that all the groups around Europe who work on these methods have broad agreement on the methods that are being used.   Because the EU frames our environmental legislation, there are many benefits if countries are using similar methods to assess the state of their environments.  Within this broad objective, however, there is also a hope that we can strengthen the links between the traditional and modern approaches to identifying organisms.  Ensuring that every barcode is linked to a photograph of the organism from which it was extracted would seem to be an obvious  check yet this is not a requirement of Genbank, the world’s major DNA depositary. As I have worked with CEN, the European Standards Organisation in the past, I gave a short Powerpoint presentation.  The irony struck me as I talked: I had to bring a special adaptor so that my iPad could plug into the data projector along with a second adaptor so that my three-pin plug could fit the European two-pin power sockets.  Yet I was the one extolling the benefits of standardisation…

Old Man’s Beard

Many of the trees in the Kilmartin and Knapdale areas were bedecked with grey-green growths of lichen – probably Usnea florideana (there a number of closely-related species in this genus so I cannot be more specific).  The sight of Usnea hanging from a tee always brings a smile to my face as it is a species that is very sensitive to air pollution.  Consequently, it is only in remote places such as this that I tend to find it.  I would be interested to see how much it’s distribution has changed over the past 20 years or so.   From a distance, it bears a faint resemble to the Spanish moss that hangs from trees in the Deep South of the USA, although Spanish moss is, actually, a flowering plant, Tilandsia usneoides.  The species name even acknowledges this resemblance.

Kilmartin_Usnea

Interestingly, Usnea has a long history of medicinal use, and contains a potent antibiotic.  The Wikipedia entry on Usnea is quite informative on medicinal uses and, more importantly, is, well-supported with citations, so I don’t have any hesitations about directing you towards this.

There is one more post on Kilmartin to follow shortly.  I made a start on a painting at the end of last week based on the diatoms and Myriophyllum in Kilmartin Glen; however, I was laid low at the weekend by a bug and did not make as much progress as planned.  Next stop for me is a workshop in Berlin, so maybe there will be a post from there before I get this Kilmartin picture finished?