This post really is about Christmas turkeys

Back to the subject of turkeys: real turkeys, this time, rather than bad science.

In the days leading up to Christmas, as the country gradually shut down and real news dried up, so the newspapers filled their space with advice from celebrity chefs on how to roast the perfect turkey.   Strip away all the suggestions to brine, baste, cover with foil and more, and most can be reduced to the very simple formula that I learnt from my mother: 20 minutes per pound, plus 20 minutes.   Which, if you think about it, is basic algebra: y = mx + c, where y = cooking time, x = the weight of the bird and c, the constant = 20 minutes.   I spend much of my working life battering data into forms that can be expressed as lines on graphs and, it seems, I cannot switch off, even when I cook the Christmas dinner.

The relationship between cooking time and size of turkey, based on the formula 20 minutes per pound plus twenty minutes, but re-calibrated to a metric scale.  The line is the hypothetical relationship; the open circles indicate the reality – read on …

Any cook knows that this relationship is just a guideline, that the best way to determine when the bird is cooked is to pull it out of the oven and poke it with a fork or skewer.  Given the shortcomings of oven thermostats, constant opening and closing of the oven door to put in vegetables as well as variations in the birds themselves, we cannot reduce cooking a turkey to a reductionist formula.   That’s why I put the open circles onto my graph: to show that sometimes the bird is ready sooner, sometimes it takes much longer than we expect.   At some point, the scientist in me has to stand back and let the inner craftsman take over to decide when the turkey is ready to carve.

Back in June I talked about the philosopher William Wimsatt’s work to understand complex systems (“Ecology in an Age of Austerity“), suggesting that it was often better to collect several bit-size nuggets of information, rather than rely upon a single strand of evidence.  My point back then related to ecology, suggesting that the effort spent refining existing approaches to assessment might be better spent looking at alternative sources of evidence.   Cooking a turkey offers a fine example of just that: it may be possible to include more variables and produce a more precise formula for cooking a turkey.   But would it be worth the effort?   We can go only so far with predictive models before we will want to reach for a fork in search of corroboration.  .

The irony is that, pushing my analogy a little further, scientists make their reputations by innovation and a paper entitled A multivariate model for predicting temporal parameters in domestic poultry roasting  will probably be accepted and published by a journal somewhere .  Science will have advanced, albeit incrementally, even if no-one ever puts the elegant ideas developed in the paper into practice.  Lesson #1 from 2013: just because it is in a peer-reviewed journal doesn’t mean that the ideas are superior to the status quo, especially when that draws upon an individual’s experience and wisdom.

Happy New Year

First record of Achnanthidium catenatum for the UK?

I came across a few strangely-shaped diatoms whilst examining a sample from Llyn Padarn in Snowdonia a couple of weeks ago.   The girdle (side) view has a characteristic “spoon” shape whilst the outline in valve view (i.e. seen from above) is lanceolate with expanded (“capitate”) ends.   I had previously seen this only as illustrations in continental Floras and once in a sample from Corsica.

Valves of Achnanthidium catenatum from Llyn Padarn, Snowdonia, September 2013; left hand view: two girdle (side) views; right hand view: valve view.   Scale bar: 10 micrometres (= 1/100^th of a millimetre).

To the best of my knowledge, this is the first record of the species in the UK.  I helped to compile a checklist of freshwater algae about 10 years ago and found no records then.  A lot of samples have been analysed since this checklist was published, but I have seen no reports of this species being recorded.   There are, however, two problems with knowing that this really is the first record for the UK.  The first is that there are no formal structures for validating new records, such as exist for higher plants.  If a species is found in a part of the country where it had not previously been recorded, then there are specialists, appointed by the Botanical Society of the British Isles, and similar bodies, who can check the identity of the specimen.  The algal world still lacks this level of organisation.   I can send my images or slides to colleagues who can confirm my hunch, but this is all very informal.  More significantly, no single individual holds a truly definitive list of UK algal records.

The second problem with knowing that this is the first record of Achnanthidium catenatum is that I have not, actually, seen this species alive.  My sample from Llyn Padwan contains a few dead shells from which we can infer that there is probably a population of A. catenatum present.   However, as this lake lies in a popular tourist area, we cannot wholly exclude the possibility that these simply washed off the boot of a visitor from continental Europe.   This picks up the issue I discussed in A Christmas Turkey .. that reliance on the dead shells is dangerous.   A useful New Year’s resolution might be to visit Llyn Padwan, or find a colleague who can visit it for me, and see if I can find some living populations of A. catenatum.   Only then will we be sure that this really is a new addition to the UK algal flora.

… and a Christmas cracker:

What is the connection between a bar of Cadburys Dairy Milk chocolate …

and the diatom Asterionella formosa, which we met in the post of 7 July?

In that post back in July I also introduced you to Arthur Hill Hassall, a pioneer of algal studies in the middle of the nineteenth century.   Hassall’s interest in algae was motivated by the search for the cause (and, thereby, a cure) for the cholera epidemics that were sweeping through Europe at the time.   His interest in public health gradually overtook his interest in algae and, by the 1870s, he was focussing on the widespread problem of food adulteration.  Many food manufacturers of the time were using cheap fillers such as flour and even sawdust, to increase the apparent quantity of more expensive items.   In 1876 Hassall published an important book, Food. Its Adulterations and the Methods for their Detection.  The subject of food adulteration was widely discussed in the press of the time, with Hassall regarded as one of the leading experts in the field.  His work came to the attention of a Quaker family in Birmingham called Cadbury, who were trying to establish a business selling chocolate.  They had invested in new approach to manufacturing chocolate.  Previously, starch and other fillers had to be added to mask the flavour of the cocoa butter but their new press removed this cocoa butter, thus removing the need to add starch.   The widespread concern about food adulteration, spearheaded by Hassall’s investigations, meant that they could market their new Cocoa Essence as “Absolutely Pure.  Therefore Best.”   The success of the product, in turn, helped transform this small family business into a worldwide company.

Happy Christmas.

References

Deborah Cadbury (2010).  Chocolate Wars: From Cadbury to Kraft: 200 years of Sweet Success and Bitter Rivalry.  Harper Collins, London.

Gray, E.A. (1983).  By Candlelight.  The Life of Dr Arthur Hill Hassall 1817-94.   Robert Hale, London.

A Christmas turkey …

A few months ago, I was sent a paper to review for a journal (better not name authors or journal title … if you are that interested, you will probably be able to work these out from the information I am about to give you).   I read the paper, and sent back my recommendation: reject.   So, imagine my surprise when I saw the same paper appear, little-altered from the version I had refereed, in the very same journal.   Of course, a single peer reviewer does not have the ultimate say on whether or not a paper should be accepted but, in this case, I had queried both the experimental question and some aspects of data analysis, both of which seemed quite fundamental.  In the final version, the question is the same, the weaknesses in the dataset remain and the original analyses are now shored-up by some heavy-duty stats which go a small way to allaying some of my concerns.

The paper looks at how the diversity of diatom assemblages varies in different types of rivers, and suggests that this might be a useful property to include in ecological status assessments.   Most ecologists would probably agree that the diversity of organisms ought to be a property that we ought to consider when assessing the condition of a site but the use of diatom diversity has a troubled history.   For some types of pollution (heavy metals, for example), there is a clear relationship, with fewer species being recorded as the level of the pressure increases.  For other types of pollution (nutrient and organic pollution for example), results have been much more ambiguous.  This may be partly due to the measures of diversity that we use, but it also reflects a more fundamental problem: the focus on diatoms alone is very artificial.   We have had success when we use diatoms to indicate, indirectly, the level of chemical pressures but it is much harder to infer fundamental ecological processes when you have digested away all the algae that share the habitat with the diatoms.

My concerns about this paper were prompted in part by some analyses I had done with Dean DeNicola of Slippery Rock University, Pennsylvania, which had shown us that the diversity of diatoms alone had very little relationship to the diversity of all the algae present in a dataset of samples from the littoral zone of lakes.   The paper is currently in press in Freshwater Science, so I could not quote chapter and verse in my review.   As levels of pressure change, it is possible not just that interactions amongst the diatoms will change (and, thus, influence their diversity) but also that interactions between diatoms and other algae will change (which will not necessarily be reflected in a diversity measure based on diatoms alone).

This is a manifestation of a much broader problem: diatomists form a very insular and self-referential community.   Methods have evolved that focus on the (dead) diatom shell, not on the living organism, with a prevailing belief that the ability to recognise many species from the shapes and patterns of these shells trumps the insights that come from looking at the whole community of benthic algae.  Diatomists review each other’s papers and generally accept these assumptions wholesale.  As a result, the community, particularly in Europe, is drifting further and further away from mainstream functional ecology.  It is something that I have talked about before and will need to return to again if we are to start having any serious influence on the decision-making process.

References

DeNicola, D. & Kelly, M.G. (2014).  The role of benthic algal communities in ecological assessment of lakes.  Freshwater Science (in press).

Kelly, M.G. (2013). The semiotics of slime: visual representation of phytobenthos as an aid to understanding ecological status.  Freshwater Reviews 5: 105119.

Angus Smith: the “father of acid rain”

I spent yesterday running a workshop on the diatoms associated with soft waters and acidic habitats at the Scottish Environment Protection Agency’s brand new office at Holytown, just outside Glasgow.  By a happy coincidence, Roger Flower, my fellow tutor and I were teaching this workshop in a building named after Angus Smith, a pioneering environmental scientist who was the first person to use the term “acid rain” back in 1852.

Robert Angus Smith was born in Glasgow in 1817, trained to be a clergyman (as did his near-contemporary Charles Darwin) but left before being ordained.   He went to Germany a few years later and studied chemistry at the University of Giessen under the famous chemist Justus von Lieberg.

A bust of Angus Smith in the foyer of Angus Smith House, Holytown.

Smith was active during the middle of the nineteenth century, when the consequences of the Industrial Revolution and urbanisation on public health and the environment was just beginning to be understood (see posts of 22 June and 23 June).   Smith’s own interests as an analytical chemist led him to investigate the chemistry of rain water.  Although Smith himself acknowledged that other scientists had already noted that rainwater was often acidic, he was the first person to link this acidity to industrial activity.   Working from Manchester, he made the link between the low pH of rain water here and sulphates derived from the combustion of coal.   He then went on to link this “acid rain” to the dissolution of some types of building stone, bricks, mortar and metal in the areas, as well as effects on vegetation.

The subject of “acid rain” then received only scant attention for about 100 years, before becoming a major political issue during the 1980s due, in no small part, to the work of Roger Flower and Rick Batttarbee.   One further consequence is that I remember reading one of their early papers on the diatoms of a loch in Galloway as an undergraduate.   I was inspired by the way that they had used ecology to gain insights into weighty environmental issues to pursue a PhD in freshwater ecology myself.  Thirty years later, I found myself standing next to Roger as we both contemplated a bust of Angus Smith.

Roger Flower introducing SEPA biologists to the subtleties of Scotland’s softwater diatom flora at Angus Smith House, Holytown, December 2013.

References

Flower, R.J. & Battarbee, R.W. (1983).  Diatom evidence for recent acidification of two Scottish lochs.  Nature (London) 20: 130-133.

Gorham, E. (1982).  Robert Angus Smith , F.R.S., and ‘Chemical Climatology’.  Notes and Records of the Royal Society 36: 267-272.

Every (fifth) breath you take …

Ever on the hunt for a good ecological metaphor, I enjoyed David Mann’s suggestion that we should try missing out every fifth breath we take in order to appreciate the contribution that diatoms make to global productivity.   Approximately 20% of the oxygen that we breathe comes from diatoms, principally in the world’s oceans.   You can see the whole article here:  http://www.scotsman.com/news/little-word-about-the-mighty-diatom-1-3227674.

Paul Falkowski of Rutgers University, New Jersey makes an even greater claim for the impact of diatoms on humans: put simply, we would not be here without them.   His reasoning goes something like this: oxygen concentrations in the atmosphere have approximately doubled over the past 205 million years, a consequence, he argues, of the evolution of the diatoms and coccolithophorids. This increase in oxygen concentrations, in turn, facilitated the expansion and diversification of mammals, who depend upon the transfer of oxygen across the placenta.  Higher oxygen concentrations allows larger mammals to evolve and survive.  Ergo … no diatoms, no humans.

Reference

Falkowski, P.G., Katz, M.E., Milligan, A.J., Fennel, K., Cramer, B.S., Aubry, M.P., Berner, R.A., Novacek, M.J. & Zapol, W.M. (2005).  The rise of oxygen over the past 205 million years and the evolution of large placental mammals.   Science (New York) 309: 2202-2204.

Ecosystem services … again

Sorry to bang the same drum repeatedly, but I want to return to the theme I explored on 17 November, when I suggested that not all situations where man interacts with water will necessary benefit from “good ecological status”.   Last time, I used the example of angling, suggesting that, as fish yields were a consequence of productivity, there would be situations where anglers, an important stakeholder community, would prefer enriched ecosystem to the pristine ecosystems that us Fundamentalist Ecologists yearn for.

I also mentioned in my post on 9 November that other recreational users of water, rowers, for example, might not appreciate the removal of weirs, even if some conservationists regarded this as desirable.  Having written these words, I started to wonder if there were any situations where conservationists themselves might not regard good status to be a desirable outcome?

I think we can take as a general rule-of-thumb that protecting natural habitats and restoring degraded habitats to their “pristine” state is a general goal for conservation.   But maybe there are exceptions that go against this general dogma?   Perhaps, too, conservationists sometimes overstate the link between high quality habitat and naturalness?  One example that springs to mind is the recent spread of the otter.  For a long time, we regarded the spread of the otter as a sign of the gradually increasing health of our freshwaters.  Yet it is now so widely distributed, often in rivers that are not pristine, that we need to re-examine this assumption.   Evidence for the ink between otters and toxic pollutants that biomagnify along the food chain is quite good.  However, some other types of pollution, such as a moderate amount of enrichment by organic and inorganic nutrients might not be problematic and, indeed, by boosting overall productivity, might raise the carrying capacity of the habitat.  I have never seen this idea explored in detail but it would be worth a look.

Another example of an organism that might actually thrive from enrichment is an unprepossessing but rather rare aquatic plant called Najas marina which is found in only six locations in the UK.   One of these is Upton Great Broad, a habitat that is far from pristine.   Yet it appears that Najas marina is a relatively recent arrival to this lake, only being recorded after the onset of enrichment.   This, of course, creates a conundrum as restoring Upton Great Broad back to more “natural” conditions might bring other conservation benefits, but what would happen to the population of Najas marina if we did this?

I recall a situation that arose in the early 1990s when Northumbrian Water were required, by EU law, to build a sewage works at the mouth of the Tees, rather than discharge raw sewage as they had been doing.  The problem was that the sewage provided an excellent food supply for worms on the tidal mudflats which, in turn, sustained an internationally-important wading bird sanctuary.   This location was, indeed, protected by a different piece of EU legislation, the Birds Directive.   Work on the wading birds of the Tees Estuary was led by Professor Peter Evans of Durham University whilst I was still working there.  I have, however, not seen any of this published in a peer-reviewed journal, which is a shame as it would provide a thought-provoking case study of the trade-offs that many involved in applied ecology have to face.   Here, as in the other examples I’ve mentioned, it might well be the case that an ecosystem at less than good status is actually of greater conservation value than one that has been restored back to good status.

At this point I had better duck my head below the parapet and wait to see what kind of responses this generates.

A diagram illustrating the relationship between conservation and ecological status.  The EU’s Water Framework Directive expresses the quality of an ecosystem in terms of five classes, from “high” to “bad”, with good status being the theoretical target that all water bodies should achieve.

References

Ayres, K.R., Sayer, C.D., Skeate, E.R. & Perrow, M.R. (2008). Palaeolimnology as a tool to inform shallow lake management: an example from Upton Great Broad, Norfolk, UK.  Biodiversity and Conservation 17: 2153-2168

Mason, C.F. & MacDonald, S.M. (1990).  Impact of organochlorine pesticide residues and PCBs on otters (Lutra lutra) in eastern England.  Science of the Total Environment 138: 147-160.

“In Our Time” looks at the history of the microscope

Melvyn Bragg’s ever-fascinating series on Radio 4 looked at the history of the microscope this week, from the earliest days of Robert Hooke and Anton van Leuwenhoek right up to the Scanning Electron Microscopes of our modern age.   UK readers can access the program via this link:

http://downloads.bbc.co.uk/podcasts/radio4/iot/iot_20131128-1045a.mp3

There is a lot packed into this 45 minute discussion so it is churlish of me to pick up on omissions.  However, I am intrigued by the social history of the microscope, particularly during the 19^th century.   An earlier post talked about the contribution that Arthur Hill Hassall’s microscopy made to the public health debates of the 19^th century (and I will write more about him at some point soon).   He was just one of many Victorian gentlemen who peered down microscopes and made important discoveries.

This was the Age of Empire and a generation of European explorers, including Richard Burton and David Livingstone, were captivating audiences with tales of previously unknown regions of the world.   Yet, at the same time, amateur naturalists equipped with a microscope were able to find an equally exotic assortment of organisms from ponds and streams within walking distance of their own homes.   In 1865, for example, “some 60 persons” attended the first meeting of the Quekett Microscopical Club in London, attesting to the wide appeal of microscopy in an age where there were fewer distractions than in our modern age.