Looking back on 2019

wordle_2019

So at least we now know what will happen next: the UK is set to leave the European Union at the end of January 2020.  Then the hard work of deciding on the shape of a future relationship begins.  The Prime Minister has already announced that the transition period will not be extended beyond the end of 2020 which gives a ridiculously short period in which to reach a trade deal.  Whether he takes up the EU’s offer to extend this remains to be seen.  I suspect that, once the bluster dies down and the magnitude of the task ahead is clear, then common sense may prevail.   If we look for some positives amidst the wreckage of progressive politics after the election, then it is that the Prime Minister can no longer be dictated to by the toxic European Research Group.

What are the prospects for the UK environment in 2020?   I wrote about this in the run-up to the election and there is no need to repeat myself.   The Environment Bill will be re-introduced and, with the Conservative majority, I guess there is little prospect of significant change during the Committee stages, despite the reservations that the environment lobby have about some aspects of this.   The bigger question will be how agricultural support is re-organised once the UK is no longer part of the Common Agricultural Policy.   If there is a greater focus on “public money for public goods”, then this can only be good for the environment.  The question that I still cannot answer, after reading the manifesto before the election, is how a re-organised and more environment-friendly agricultural subsidy scheme can be managed and enforced without more skilled people working on the ground.

I also foresee a weaker focus on the UK’s aquatic resources over the next few years.   First, though the Water Framework Directive has been transposed into UK legislation, few believe that the proposed Office for Environmental Protection will have as many teeth as the European Court of Justice.  Second, the focus on the climate emergency will, without specific funding for a larger workforce in DEFRA and associated agencies, will weaken the capability to respond to the challenges that the aquatic environment still poses.   Third, two of the most obvious consequences of climate change at the moment are flooding and drought, so we can expect more of the Environment Agency’s time and resources to be focussed on these issues.  Finally, the state of the UK’s freshwaters is, to be frank, not that high on anyone’s agenda just at the moment.

There is one other trend, independent from Brexit and populism, that we need to resist.   That is the increasing reliance on the media as an intermediary between us and the environment.   On the one hand, we know about the global climate emergency because of pictures piped onto our homes via television and the internet.  On the other hand, we are not noticing the changes that happen in our own back gardens.   This disconnect makes us, I fear, more susceptible to political hype (left and right) and feeds into the issues I wrote about in the previous paragraph.  I started this blog in 2013 mostly as a way of making me look more closely at my own local environment, and I will continue in 2020, because I regard this self-discipline as a necessary corrective to the modern ecologist who spends more time indoors staring at spreadsheets than outside interacting with nature.  If a few of you want to join me on this journey, then I will be delighted to have some company …

20:20 hindsight …

Last week saw the publication of a paper that has undergone a slow gestation through the year.   It’s an opinion piece published in the new open access journal Metabarcoding and Metagenomics and describes some of the lessons I learned during the development of a new diatom metric based on metabarcoding data.   The science behind these projects is written up in reports and papers, but that only tells part of the story.  Applied science needs a context, and my paper is more about how the new science fits into a wider process of managing change in large and ponderous government agencies.

That’s where my title comes from: “Adapting the (fast-moving) world of molecular ecology to the (slow-moving) world of environmental regulation”.   The new science of metabarcoding is developing fast and some of the assumptions that we made at the start of the project have now been overtaken by developments in methods.  Yet the regulatory systems into which these methods will be integrated need to be stable and continual “tweaks” to optimise the system would not be welcome.   “Ponderous”, in this context, is not necessarily a bad thing.  Imagine driving in your local area and finding all the speed limits had changed at the whim of an official and without any consultation or advance warning.  Finding a balance between these two needs: for the best possible methods and a stable basis for regulation seems to be one of the biggest challenges those of us with an interest in molecular ecology face over the next few years.

My own view, reflecting back over the discussions I’ve had over the past few years, is that this is possible, but that the UK’s environment agencies will need some major structural changes for this to come about.   As I was reviewing the proofs of the paper, I came across Tim Harford’s fascinating podcast Cautionary Tales and, in particular, an episode called “How Britain Invented, then Ignored, Blitzkrieg”.  The point he made in this episode was that improvements to individual components of a system (tanks, in his example) have little value if the overall architecture within which those components operate are not also regularly updated.   He cited a paper by Rebecca Henderson and Kim Clark which, had I seen it sooner, would have strengthened the principal argument in my paper.

Henderson and Clark’s examples were drawn from manufacturing industry, but we can use the same kind of language to make their framework relevant to ecological assessment.   Broadly speaking, an ecological assessment method (using diatoms, in this case, but it could also be invertebrates, macrophytes or fish) is one component in a larger decision-making “machine”.  Replacing the existing methods, based on specialist biologists painstakingly analysing samples to identify and enumerate the taxa present by one based on metabarcoding technology constitutes a “modular innovation”, using the terminology in the table below.   That might well work in some cases (replacing an analogue by a digital telephone, for example, doesn’t fundamentally affect the way we communicate with one another).  However, the question that Henderson and Clark were asking was what happens when an innovation interacts differently with other components, in which case a shift in the entire product design might be necessary.

A framework for defining innovation (after Henderson and Clark, 1990)

  Core concepts
Reinforced Overturned
Linkages between core concepts and components

Unchanged

 

Incremental innovation

 

Modular innovation

Changed

 

Architectural innovation

Radical innovation

Harford used the comparative fortunes of IBM and Apple in his podcast (Henderson and Clark’s paper was written before the tech revolutions, otherwise I’m sure they would have done so too).  Apple did not invent the mouse or the graphical user interface, but they were able to fit these into a radical new architecture of components, opening up an enormous market for consumer-friendly gadgets.  IBM, by contrast, was the market leader for mainframe computers, but its thinking and organisational structures were so focussed on these that they were not nimble enough to adapt to this new world.

The question that arises when using metabarcoding in a regulatory capacity is whether this technology just constitutes a “modular innovation” or whether a broader refit of the organisations that use the technology is necessary in order to maximise their benefits. My argument is that metabarcoding constitutes a “radical innovation” partly because the way that individuals interpret  metabarcoding data is different to the way that they would traditional data, which means that the value that a biologist can add to evidence for a regulatory decision on his/her locale will change, and because the gathering of evidence by traditional means constituted an “unstructured training program” for freshwater biologists that gave them a broad awareness of freshwater ecology in their region.

Furthermore, the rate of development of these new technologies is such that a better way needs to be find of balancing innovation and regulatory stability beyond the very ponderous approach in force in the UK at the moment.  There are ways of doing this, but the mindset in the administrations needs to change before these can be implemented and there would also need to be more administrators to oversee this process, a big ask in a public sector still limping along on much reduced budgets.

One of the biggest lessons we learned was, in fact, that if you want to learn lessons you need to get stuck in and have a go.  There are plenty of review papers in the academic literature now saying how metabarcoding might be used for ecological assessment, and plenty of discussion about these new technologies within the hierarchies of the government agencies. But you can only go so far with theory: not all of the challenges we encountered were anticipated and, certainly, not all the assumptions that drove the original commissioning of the project turned out to be correct.   The only way of testing these was to take a step into the unknown.  We learned the hard way, but maybe future projects will benefit.

Reference

Henderson, R.M. & Clark, K.B. (1990).  Architectural innovation: the reconfiguration of existing product technologies and the failure of existing firms.  Administrative Science Quarterly 35: 9-30.

 

Reflections from Castle Eden Burn

As 2019 draws to a close, I have looked back at all the data I have collected from Castle Eden Burn over the past twelve months.   I chose this location precisely because it was different to my usual haunts and, despite having visited this Dene and others along the Durham coast for over thirty years, I realised that I had never had a look at the algae.  Dry river beds are not the most obvious hunting grounds for aquatic biologists, after all.   This year, I put that right over the course of a number of visits between January and November and in this post I am summarising what I found.

I found a total of 77 different diatoms in the six samples that I collected, not to mention green and yellow-green algae (see “When the going gets tough …”) and mosses (see “A thousand little mosses …”).   Of these diatoms, 48 were rare and infrequent, only found in one or two samples, and never forming more than one percent of the total number of diatoms present.   Of the remainder, only two were found in every sample (Humidophila contenta-type and Achnanthidium minutissimum) whilst another eight formed at least ten percent of the total on one occasion.  Numbers of each species waxed and waned over the year: Humidophila contenta-type was abundant in the sample from my first visit in January 2019 but relatively scarce thereafter.  In comparison, Luticola frequentissima was very abundant on two occasions (more than 80% of individuals), quite abundant on three other occasions but absent from the sample from my final visit in November.

Some of these differences are due to the variable flow regime: the stream was dry on three occasions, ponded on one and flowing on just two occasions.  Those occasions when there was no running water were those when the proportions of diatoms that are tolerant to desiccation (see “Life out of water …”) were most abundant, forming from 20 to 97 percent of all individuals.  When there was running water, it was motile Nitzschia  species that dominated.    In fact, there was a strong negative correlation between proportions of desiccation-tolerant and motile taxa in the samples, indicating that the diatoms responded rapidly to the changing pressures experienced in the stream.  There was also a relationship between the proportions of desiccation-tolerant diatoms and the number of taxa recorded – the latter is a good measure of the level of physiological stress experienced in a stream.

What of the diatoms themselves?  Humidophila contenta-type was one of the two ever-presents.  It is, however, very small (few of those in our samples were more than a 100th of a millimetre long), making it difficult to photograph and, indeed, to discern many of the features of the valve.   This species sometimes forms short chains though I did not see any in the Castle Eden Burn samples.  It is strange to think that, when I first started to identify diatoms, this was considered to be part of the genus Navicula.   Since then, it has moved into the genus Diadesmis before finally being transferred to the new genus Humidophila by Rex Lowe and colleagues in 2014.    Some recently-described Humidophila species cannot be differentiated from H. contenta without a scanning electron microscope, so I have referred to this as “Humidophila contenta-type”. Humidophila_contenta

Humidophila contenta ag. from Castle Eden Burn, Co. Durham, January 2019.  Scale bar: 10 micrometres.   Photograph: Lydia King. 

The most abundant diatom in samples collected during the dry periods was Luticola frequentissima.  I started the year referring to this as “Luticola mutica” but was gently corrected by colleagues more au fait with recent literature than me.   Luticola mutica is larger (length: 11-28 µm; breadth: 6-9.5 µm) and has more widely-spaced striae (16-18 / 10 µm) than L. frequentissima (length: 7 – 13.8 µm breadth: 4.8 – 6.8 µm; striae: 20 -24 / 10 µm).  The specimens in the plate below all fit the description for L. frequentissima.  Some of the large specimens have size ranges that overlap with L. mutica (though even the largest specimen as a striae density consistent with L. frequentissima).   L. mutica is associated with more brackish habitats whilst L. frequentissima prefers freshwaters.

Luticola_frequentissima

Luticola frequentissima from Castle Eden Burn, Co. Durham, January 2019. Scale bar: 10 micrometres (= 1/100th of a. millimetre).  Photographs: Lydia King.

Simonsenia delognei is another characteristic species of habitats that dry out periodically.   This species, which is in the same family as Nitzschia, is quite small and only lightly silicified so easily overlooked.  It was common early in the year, but rare thereafter.  Whether this is a real characteristic of the species or an artefact of the conditions in Castle Eden Burn this year is difficult to tell as it is not a particularly common species so there are few other records against which this trend can be compared.

Simonsenia_delognei_CEB

Simonsenia delognei from Castle Eden Burn, Co. Durham, January 2019.  Scale bar: 10 micrometres (= 1/100thof a millimetre). Photographs: Lydia King.

Two other species of Nitzschia were common: I illustrated N. clausii in “Out of my depth …” and have included photographs of N. sigma here.   I’m intrigued that two of the most conspicuous Nitzschia in this sample are sigmoid in outline.  I’ve visited the question of sigmoid diatoms before, and still don’t have any good explanation why a few diatoms have this outline (see “Nitzschia and a friend …”).  Note, too, that Nitzschia species can be sigmoid in valve view (i.e. looking down from above) or girdle view (i.e. looking from the side), although the great majority of species are straight in both planes.

Nitzschia_sigma

Nitzschia sigma from Castle Eden Burn, Co. Durham, January 2019.  Scale bar: 10 micrometres (= 1/100th of a millimetre).   Photographs: Lydia King.

Finally, one more relative of Nitzschia that was found in a couple of samples, but never in large numbers, was Tryblionella debilis.  The genus Tryblionella was treated as part of Nitzschia for much of the 20th century.   As it appears to form a natural group with some distinctive characteristics, it is now generally treated as a distinct genus, although the molecular evidence indicates a complicated evolutionary history.   The principle characteristic of the genus is a longitudinal undulation on the valve face that is most clearly manifest on those species in the genus which have visible striae.   T. debilis is a small species with striae that are not resolvable with the light microscope; however, the undulations are just apparent as faint longitudinal lines running along the valve face.

Tryblionella_debilis

Tryblionella debilis from Castle Eden Burn, Co. Durham, January 2019.  Scale bar: 10 micrometres (= 1/100th of a. millimetre).  Photographs: Lydia King.

That’s a lot of diatoms from a stream that is not always a stream.   I am sure that someone with interests in other groups of algae could probably make similarly long lists for some of those, and a more thorough exploration of habitats within the stream could add to the number of diatoms.  That’s before suggesting a molecular study, which might well reveal cryptic diversity (i.e. significant taxonomic variation that is impossible to discern with a light microscope) within the species I have already described.   The greater our capacity to unravel the mysteries of the microscopic world, the more, it seems, we discover we don’t know.

Reference

Lowe, R.L., Kociolek, P., Johansen, J.R., Van de Vijver, B., Lange-Bertalot, H. & Kopalová, K. (2014).  Humidophilagen. nov., a new genus for a group of diatoms (Bacillariophyta) formerly within the genus Diadesmis: species from Hawai’i, including one new species.  Diatom Research 29: 351-360.

Too much hot air?

Shetland_mist_rolling_in_May19

One day to go before polling day and I make no excuses for letting politics intrude into a blog that is primarily about natural history.  I try to explain, in my posts, how the algae that I see in the streams and lakes that I visit are affected by their environment, whether this be a stream in north-east England that periodically dries out, the drainage from a metal mine in Cyprus or a lake downstream of a major city in China (to take just three examples from my 2019 posts).   Those local effects are, however, always set within a broader context, part of which pertains to legal and regulatory frameworks and, via these, to the political process.  I cannot, in other words, extol the beauty of a desmid but ignore what the party manifestos say about policies that may enhance or degrade the habitats where desmids live.

Having said that, the film director Ken Loach, commented that the social problems he portrays in “Sorry I Missed You” were “beyond politics” during a Q&A in Durham last week.   That is much how I feel about the environmental problems we face: the structural changes required are addressed by the political parties in their manifestos but, at their root, they also need individuals to change.   Traditional economic systems are driven by demand, which equates to consumers wanting things.  Leaning to live well with less seems to be a prerequisite for moving forward, and that is an unpalatable message for politicians to sell to a fickle electorate.  More practically, such demand drives the economic growth, the tax revenues from which pay for government spending.

That means that a manifesto that pledges economic growth and a serious response to the climate emergency needs to be treated with a degree of scepticism.  How do the major party manifestos add up in this respect?    The Conservative manifesto is, unsurprisingly, the one most wedded to economic growth, using this phrase in a positive way 17 times, followed by the Liberal Democrats (5) and Labour (2).  The Green party refer to growth four times but three of these are negative and the fourth is neutral.

All Conservative and Liberal claims about the environment, therefore, need to be set in a broader context whereby their ambitions are dependent upon continued exploitation of the earth’s resources.   Granted, we can find references to “clean growth” in both manifestos and whilst it is possible for growth in the tech and service sectors to be “clean” we need to take care that a shift in emphasis in the UK economy does not simply mean the environmental costs of producing the goods that we need are not exported.   The UK has set itself challenging targets for becoming carbon neutral, but achieving these would be meaningless if it involved outsourcing our emissions to countries with weaker regulatory regimes.

The Labour manifesto, by contrast, is largely quiet on the subject of growth, albeit with some reference to promoting more sustainable design and manufacturing.  Their broader vision of creating equality within society does, at least, mean that they want to create opportunities for employment in this country which would mean that carbon emission targets would have to be met by reductions in the UK.  They also recognise that growth, alone, will not pay for increased government spending though their plans to underwrite their manifesto promises by borrowing alarms many people.   Both Labour and the Green Party promise overhauls of the tax system as one means of paying for extra expenditure on public service, but both are vague on the impact on individual taxpayers.   This is, unfortunately, the product of the previous decade of austerity, when the Tories ploughed ahead with cuts to public services whilst making tax raises a toxic issue.   Despite bolder promises from all parties on public spending than we’ve seen for some time, none seem to want to tackle head-on the possibility that this might necessitate income tax rises.

This suggests to me that, once the fine words in the manifesto are stripped away, the policy wonks in the major parties are not convinced that the electorate is ready for the scale of change that scientists believe to be necessary to tackle the climate emergency.   Scratch the surface of the green rhetoric and, as far as politicians are concerned, I suspect it is it is going to be business as usual once the dust from the election has settled.  This means that, as 2020 dawns, the environment will, once again, be competing with the health service and education for its share of the public purse.   That’s a miserable point on which to end but this has been a miserable election campaign.  At a time when we desperately need statesmen and visionary leaders, we have a sorry pair of contenders for the highest office in the land, neither of whom seems to command much respect beyond their hardcore support.