A Brief History of Websites (part 1)

I sent my first email in about 1988.  In theory, I had an email address via my university before that date but so few people outside computer science departments used email that it was pointless sending an email unless you knew that the recipient was expecting it.   I got my first private email address in 1995 though, again, there were few people to whom I could actually correspond.   From that point on, things moved quickly.  My 1995 modem was a dial-up modem outside the computer though any attachments over a few hundred kilobytes would lead to me fretting over phone bills.   Broadband arrived in about 2002, I think, and from that point on things moved very quickly.

Our generations have lived through the greatest paradigm shift in communication since Gutenberg invented the printing press yet broadband internet has become so much part of our lives over the past decade that we are in danger of forgetting just how young the internet is.  I don’t mean the technology per se, but the human systems that contribute and manage the content.

We know about Google and Facebook, and recognise that these companies make their money not directly from us, but from selling information about us to advertisers.   We respect Wikipedia’s philosophy, but have all seen their frequent pleas for donations to support their advert-free pages.   It takes real time to manage a good website and, however much we like “open access” as a philosophy, there are unanswered questions about how the very real costs of contributing content and maintaining sites will be met in the long term.

A couple of weeks ago, I was in London to discuss a possible online diatom Flora for Britain and Ireland.   This is not the first project of this nature that I have been involved with.  I helped to develop a CD-ROM based Flora for the Environment Agency a few years ago.  We had started with grand ideas about the output not being static in the way that traditional printed Floras were, but would be constantly updated.  However, funding priorities changed within the Environment Agency and the CD-ROM never was upgraded.   It quickly fell behind the pace for both the software and computer operating systems and, at the end of last year, was quietly deleted from the Environment Agency’s publication catalogue.   Fortunately, all information except the keys is available at craticula.ncl.ac.uk/EADiatomKey/html/index.html but, to me, this was an opportunity wasted.

The big lesson that I learned from this exercise was that long-term success of web-based projects depends less on the technology than on the people and institutions responsible for managing and maintaining the sites.  You can have the best-written webpages and the most authoritative content but if the institution that hosts the site changes priorities, then all this effort could be lost or, at best, fossilised, very quickly.  In a fast-moving field, “fossilised” is little better than “lost”.

Why am I saying all this?  I am trying to keep all my posts to under 500 words so you’ll have to wait until next time to find out…

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Bollihope Common

I spent part of last weekend wandering in the vicinity of a small reservoir on Bollihope Common in Weardale.   It is one of many small manmade water bodies in this part of the northern Pennines constructed to power the mills that served the lead mines in the region.

Rocks on the northern shore of the reservoir had tufts of a dark green, almost black, moss inhabiting the splash zone.   Under the microscope, I saw the characteristic wavy-edged cells which indicated that this was a Racomitrium.   This is Racomitrium aciculare, a semi-aquatic cousin of the species we encountered on rocks in Teesdale last year (see “Upper Teesdale in March”).   The southern shore of the lake, by contrast, was not fringed with rocks, but with rushes and Sphagnum moss, along with some Polytrichum.   This side of the reservoir receives the drainage from the fells above and, I suspect, the constant supply of sediment has led to the gradual infilling of the original shoreline.   There were at least a couple of species of Sphagnum present here, but I was most interested in the submerged moss, S. cuspidatum.

Bollihope_140208

Looking north towards the unnamed reservoir on Bollihope Common (NY 989 348).   The road on the left hand side of the image leads to Stanhope.

Bollihope_mosses

Aquatic mosses from the unnamed reservoir on Bollihope Common.  The left hand image shows Racomitrium aciculare on the tops of boulders and the right hand image shows Sphagnum cuspidatum from the boggy areas on the southern shore.

I shook portions of both mosses vigorously in a small amount of water from the reservoir to dislodge the attached algae.   The clear water quickly turned brown and I sucked up a few drops of each with a pipette and dropped them onto a microscope slides.  First up was the sample from the Racomitrum.  This was dominated by the small diatom Achnanthidium minutissimum (a – e in the figure below).  When I had looked at the Racomitrium leaves under the microscope, I had seen many of these attached to the leaves by short stalks.   These comprised just over half of all the diatom cells that I counted.  Long needle-like cells of Fragilaria rumpens (or something similar) which attached to the leaf by their base formed another 27% and another genus, Gomphonema (one or more forms in the G. parvulum complex), formed about 16%.  Most interesting to me were a few gracefully-curved cells of Hannaea arcus, as these are good indicators of a relatively pristine habitat.

Next up was the sample I had obtained from the Sphagnum.   Sphagnum usually favours acid habitats so I was intrigued to see what diatoms would be associated with it, having seen that the diatoms associated with Racomitrium, a hundred metres or so away, mostly suggested neutral or slightly alkaline conditions.

Once again, it was Achnanthidium, Fragilaria and Gomphonema that comprised the majority of the diatom cells (54, 19 and 16% respectively) but this time, about 8% of the total belonged to at least three species of a different genus, Eunotia, which is often associated with acid habitats, and the curved cells of Hannaea were conspicuous by their absence.   Interestingly, Sphagnum does not only favour acid conditions, peculiar features of its cell wall chemistry also helps to create those acid conditions and the diatoms living in the microhabitats around the submerged Sphagnum were clearly indicating a slight change in conditions, compared to those I found on the Racomitrium.

Bollihope_diatoms

Diatoms growing on and around mosses in the unnamed reservoir at Bollihope Common; a – e: Achnanthidium minutissimum complex; f,g: Gomphonema parvulum complex; h. Eunotia spp (probably E. implicata); i. Navicula (probably N. cryptocephala); j. Fragilaria (probably F. gracilis); k. Hannaea arcus.  Scale bar: 10 micrometres (1/100th of a millimetre).   Note, particularly for h and k, healthier specimens were present in the samples but none presented in a manner amenable to photography.

There was much more Sphagnum underfoot as I walked over Bollihope Common.  Given time – a couple more centuries, maybe – and the gradual invasion of Sphagnum from the moorland around the reservoir might continue and, we can hypothesise, the acid-loving diatom species might become more abundant.  Indeed, we could even argue that this would simply be nature re-establishing its influence, the reservoir being an unnatural and – in the grand scheme of things – temporary intrusion into the landscape.

#ThunderbirdsAreGo

At midnight yesterday, I was somewhere between Northallerton and Darlington.  It was five and a half hours since I left King’s Cross and my train had been stuck here for about three hours after the pantograph was blown off by the high winds.  We had to wait for a rescue unit, called a “Thunderbird”, to come from Newcastle and tow us to the nearest station.  Fortunately, I had enough charge on my iPad to idle away the hours learning how the app ‘Brushes’ works.   The picture below – my first ever from Brushes – is of the German traveller who was sitting in the seat diagonally opposite me.  I make few claims for its quality except to remind you that it was done at midnight.  However, I can see how, with a little more practice, one could start producing some quite reasonable pictures in this way.  I think that this is the app that David Hockney used for his show at the Royal Academy in 2012, so I am in good company.

Painting 2

A student in the carriage tweeted about our plight, and her tweet was picked up by BBC News.  A few minutes later they called and not long after that she was interviewed live on air, during the course of which she mentioned that a Thunderbird was coming to rescue us.   A few minutes later tweets about Thunderbirds coming to the rescue were arriving.

It had been a long day.  I had caught the 0610 train to London this morning and had expected to be home at about 2130.   Instead, I was sitting in a train that was rocking in the wind with no power save for emergency lighting.  No power meant no heating and no hot drinks.  The train crew handed out refreshments including free beer, which was a kind gesture but it didn’t warm us up.  Eventually they started handing out silver space blankets too.   Not long after that, they coupled the Thunderbird to the front of our train and towed us slowly up the line to our destinations.  I eventually got home at 2 AM.

More about floods …

And no sooner than I had uploaded the previous post, lo, my prophecy was proved correct.  Eric Pickles’ rant about the Environment Agency at the weekend betrayed such fundamental ignorance that one commentator (a Professor of Water Engineering, no less) suggested that Pickles would be “more use as a sandbag”.

The words of Liddell-Grainger and Pickles lead me back to a book I read last year, called “Nudge”.  Nudge theory is the idea that people can be persuaded to make right decisions by simple changes in how choices are presented to them.  It was touted as a way of reconciling a libertarian political outlook with responsible government, by-passing the “Nanny State” in the process.   Interestingly, the authors of Nudge, Richard Thaler and Cass Sunstein, both economists from the University of Chicago, pick out the environment as one area of government where “nudge” may be able to play a significant role.

Part of the reason Thaler and Sunstein were looking at the environment in this book was their perception that much environmental management adopted a “command-and-control” approach to regulation that did not fit with their own libertarian outlook.  Were there, they wondered, opportunities to encourage people and businesses to make more enlightened choices?   They give some examples of where this might be the case.  However, Rabbi Julia Neuberger, who chaired a House of Lords inquiry into “nudge” was more pessimistic.  In many cases a “push” or a “shove” is needed, not just a gentle “nudge”.

Nudge may work where individual choice is significant but the issues underlying the current problems associated with flooding and severe weather will only be solved by collective action.  And this is the problem for Conservative politicians: they argue against big government and for reducing the government spending but flood defence requires massive investment and co-ordinated action across several branches of the public service.   It will also – whisper this quietly – require “red tape” if developers and businesses are to be warned off inappropriate use of flood plains.   The aftermath of Hurricane Katrina is a grim warning of the dangers of ideology overriding common sense in flood defence management (see “Black Swan #2: McEcology and Steve Earle”)

But there is a bright side: I recall my visit last year to a flood alleviation scheme in east London masquerading as a “country park” (see “Things we’ve forgotten to remember”).  This was not high grade habitat but it was a vital green lung for local inhabitants and, once or twice a year, it provided flood relief for the surrounding area.   Interventions to prevent flooding can have wider societal benefits, but it does need to take place in a planning framework where experts from different disciplines can work together and, in some cases, over-ride short term and purely financial interests.   That’s the challenge that the Conservatives have to face over the coming months as flood waters recede and the usual bickering about public spending takes centre stage again.

More about Rivularia

My post on Rivularia from softwater habitats (‘“Looking’ is not the same as seeing”’) prompted an email from Bryan Kennedy in Ireland with some pictures of Rivularia from a moorland stream in Co. Mayo in the west of Ireland, once again from a catchment completely lacking limestone.   Bryan estimates the calcium concentration in the water to be between 5 and 10 milligrams per litre, which means that the water here is very soft.  He also comments that it was recorded in the 1970s from the Caragh catchment in south-west Ireland (average calcium concentration: 2.15 milligrams per litre: see Heuff & Horkan, 1984).

Yellow_river_trib

A tributary of the Yellow River, Co. Mayo, Ireland (left) with dark brown / black colonies of Rivularia beccariana on a submerged stone (right).  Photos: Bryan Kennedy.

The photomicrographs show the colony structure very well with filaments radiating out from the centre.   The major difference between these and the Rivularia biasolettiana I photographed in Upper Teesdale (“Blue skies and blue flowers in Upper Teesdale”) is that colonies of the latter contain calcite crystals, though these were not visible in my images.  The right hand image shows the structure of Rivularia filaments very clearly; the tapering blue-green filament gradually narrowing to a colourless hair.   Note the colourless cell at the base of the filament.  This is the “heterocyst”, and is the location where nitrogen fixation takes place.  This is a very useful adaptation in the nutrient-poor habitats where Rivularia is found, as it means that, like peas and beans, it can capture nitrogen directly from the atmosphere, rather than relying upon dissolved minerals.

Nitrogen-fixation, however, needs a lot of energy and organisms do not fix nitrogen if there is a ready supply available from other sources.   Once nitrogen is abundant, species such as Riviularia are at a competitive disadvantage and it is no surprise that Rivularia and it’s close relatives are found only in remote parts of the country, given the extent to which nitrate fertiliser washes off the land and into streams and rivers.   Even in upland areas, there are often nitrogen compounds in rain water, much of it originating in the exhaust emissions from our cars.   One wonders if Rivularia might have been much more widespread a hundred years ago than is the case now.

Rivularia_beccariana_tribYe

A close-up of a Rivularia beccarina colony from the tributary of the Yellow River, Co. Mayo, Ireland.  Photos: Bryan Kennedy.  

Reference

Heuff, H. & Horkan, K. (1984).  Caragh.  Pp. 363-384.  In: Ecology of European Rivers (edited by B.A. Whitton).   Blackwell Scientific Publications, Oxford.

 

 

 

Reflections from the trailing edge of science

All this talk of algae life-cycles alternating between diploid and haploid stages takes me back to winter afternoons in undergraduate botany practical classes when the basics of plant life cycles were driven into us.   Roughly speaking, the principles of biology can be split into those that are common sense and those that need to be explained over and over again to overcome our natural preconceptions.   “Common sense”, in this instance, means that the principle in question roughly aligns to our own anthropogenic outlook.  And one thing that humans – along with all other animals – don’t have is alternating generations.

A step backwards: “diploid” means a cell with a full complement of chromosomes and “haploid” is a cell with half a set of chromosomes (see note).   In the human, the “haploid” phase is the short period of the life cycle between production of sperm and egg cells (collectively termed “gametes”) and the successful fertilisation of an egg by a sperm cell.   So the human life-cycle consists solely of the alteration between a multicellular diploid phase (that’s you) and a unicellular haploid phase.  In the case of all but the very simplest algae, there is a multicellular haploid phase (the “gametophyte”) which produces the gametes.  These then fuse to produce a multicellular diploid phase (the “sporophyte”), some cells of which undergo meiosis to produce haploid spores.  These spores germinate to form the next generation of gametophytes.

Got that?  Probably not.  It is not an easy concept to grasp partly because it does not accord with the human experience.  Moreover, in flowering plants, the sporophyte is dominant and the gametophyte stages are reduced to “parts” of the flower (the entire male gametophyte, for example, is contained within the pollen grain).   It does not help the cause that the most conspicuous group of plants have their alternation of generations largely hidden from view.   When I was an undergraduate, knowing about alternation of generations was regarded as necessary if we were to understand the evolution of plants.   Unfortunately, the experience of having plant life cycles drilled into them probably turned many undergraduates off botany forever.   I am fairly sure that few UK university departments teach these principles in anything like the detail that my generation had to endure.

Alternation of generations isn’t something that the average biologist needs to know in great detail and, to be honest, I forgot a lot of the details.  I had to refresh myself when I taught courses on algae and the lower plants to undergraduates in Nigeria and, once again, when I started boning up for the post about Audouinella.   As Bill Farnham pointed out, I may not have got all the details right.   No excuses for my own failings but this is yet another manifestation of a problem that I have mentioned before: that science has a “trailing edge” of knowledge as well as a “leading edge” (see “An inordinate fondness for … algae”).  There is an enormous amount of information on algal life cycles in the literature but it is not always easy to find, especially when accessing the literature via internet search engines.   We might not need the information very often but it is as easy to lose familiarity with the terminology as it is for an athlete to fall out of condition through lack of exercise.

Note: another way of looking at it is to say that the haploid phase has a full set of chromosomes whilst the diploid phase has two full sets.  I was being deliberately anthropocentric in describing the haploid phase in this way.  And, if we are going to be pedantic, every “multicellular diploid phase” necessarily starts out, albeit briefly, as a single celled diploid phase.

The schizophrenic life of red algae …

Back in October, I showed a photograph of red algae growing in the River Ehen, naming this as Audouinella (At last .. a red alga that is really red ...”).  A friend commented in an email that I was brave to have made this identification if there were no spores or reproductive organs and that, in Germany, these filaments would simply be referred to as “chantransia stage”.   Although I had seen reproductive organs earlier in the year, I worried afterwards, that maybe I had been rash, and was mightily relieved when, a couple of months later, filaments with reproductive organs re-appeared.

What you can see in the picture below is the vegetative filaments from which short branches bearing carposporangia (female reproductive organs) arise.   There are over 300 species of Audouinella, mostly found on sea coasts with just a few freshwater representatives.   The life cycle seems to vary considerably from species to species so it is hard to generalise but, like many algae, there are two distinct phases, a diploid phase, following fertilisation of the carpospores by a male sexual cell, and a haploid phase, which occurs after these diploid cells have undergone meiosis.   In this image, you can see filaments in the haploid phase with bundles of carpogosporangia on short side branches.   In Audouinella, the diploid phase looks very similar but – and here’s the problem – they also look similar to the diploid phases of many other species of red algae.   Indeed, for a long time, these diploid phases were regarded as distinct species.   My 1927 flora, by West and Fritsch, for example, includes these filamentous stages as a distinct genus, Chantransia, and it was only later that people realised that they were one part of a more complicated life cycle.

Audouinella_hermanii_Ehen_J

Filaments of Audouinella hermanii from the River Ehen, January 2014, with the carposporangia indicated by arrows.   Scale bar: 10 micrometres (= 1/100th of a millimetre).

At this particular site on the River Ehen I have also found another red alga, Lemanea (see “The River Ehen in April”).  Lemanea also has a chantransia stage, so it pays to be careful with my identifications.   Lemanea, in my experience, tends to be found in the fastest-flowing stretches of streams attached to stable boulders, whereas Audouinella is generally more widespread across the river bed.