Sea of puddles?

I took this photograph of the Aral Sea (“Sea of Islands”) from the cabin window of our flight from Tashkent to London back in April.   The atlases which fed my young mind back in the sixties and seventies have changed enormously, but it is mostly political boundaries that have shifted, particularly in this part of the world.   There are few instances where the physical landscape has changed on quite such a scale as the Aral Sea which has largely disappeared from our maps.  This photograph was remarkable because you can actually see water: most of the Aral Sea is now just desert.

The Aral Sea was fed by two rivers: the Amu Darya – the Oxus of antiquity – and the Syr Darya. The latter was fed by the streams that flow down from the Tien’shan mountains (see “Theme and Variations”); the former rises in the Pamirs in northern Pakistan and then forms the border between Afganistan and Tajikistan before flowing through Turkmenistan and Uzbekistan to the Aral Sea.

Or, at least, that is what used to happen.   The story of the decline of the Aral Sea is a tale that puts most of the concerns about loss of connectivity of western European rivers into the shade.   In the 1960s, Soviet planners decided to use water from the Syr Darya and Amu Darya (“darya” is the Persian word for “river”) to irrigate the semi-arid lands of central Asia in order to grow crops such as cotton.   Not only did this reduce the flow of the rivers substantially, but poor design of the irrigation channels meant that most of the water did not get to the crops that it was meant to sustain.   The reduced flow of fresh water into the Aral Sea caused it to both shrink and become more saline (it is now as salty as the Dead Sea, according to some accounts).   In 1987 the lake split into two separate bodies, and the dried-up area between became the Aralkum desert.

It is a salutary story that, according to the limited research that I have been able to do on the Internet, wholly avoidable.  The Russian attitude to central Asia in the 19th century mirrored that of European power’s approaches to their colonies in Africa and Asia, with a mixture of geo-political manoeuvring and economic motives.  These attitudes were inherited by the Soviets in the 20th century and, even though experts predicted the dire consequences for the Aral Sea, the irrigation scheme was fixed into the Soviet’s five year plans and no-one dared contradict the Politburo’s decisions.

What is the relevance of this to us?   Only that we have just seen the appointment of a Secretary of State for Farming, the Environment and Rural Affairs who said, not much more than a year ago: “people in this country have had enough of experts”.

Theme and variations

Following our visit to the cities of the Silk Road (see “Daniel and his den of diatoms …”) in April we turned our eyes in the opposite direction and, within an hour of leaving Tashkent, we had left the flat plains behind and climbing into the foothills of the Tien’shan mountains.   The intensive agriculture of the lowlands gave way to pine forests and, as the road started to twist and turn up the slopes, we started to get tantalising glimpses of the snow-capped mountains which straddle Uzbekistan’s eastern border with Krygyzstan.

As ever, I looked for opportunities to combine business and pleasure, collecting one sample from a small calcareous seepage in the hills near the village of So’qoq and another from a stream running through mixed geology near the village of Kumyshkang, where we were staying in a Soviet-era dacha.   Sampling the seepage drew some curious looks from two women who were collecting water mint from further downstream, and yielded an almost pure growth of a diatom that is either Achnanthidium pyrenaicum or a close relative.   This would have been, by the way, the diatom that I would have expected to find were I to sample a remote, unpolluted calcareous stream in the UK.

Achnanthidium cf pyrenaicum from a calcareous stream near So’qoq in eastern Uzbekistan (41°18’45.6” N 69 ° 51’40” E).  a. – d.: rapheless valves; e. – g.: raphe valves; h.: girdle view.  Scale bar: 10 micrometres (= 1/100th of a millimetre).

Later in the day, we explored a side valley of an unnamed river that flows through the village of Kumyshkang.  The steep landscape on the south side of the valley had a thin cover of scrubby vegetation (in contrast to the wooded slopes on the other side) and the stream tumbled off the hillside towards the river below.  The biofilm, partly as a result of this harsh environment and partly, I suspect, due to grazing by invertebrates, was very thin but, nonetheless, quite diverse, with Achnanthidium minutissimum predominating.  There were a lot of outcrops of pink granite in the hillsides around the stream, but there were other rocks too, including shales and slates.   The flora here, as a So’qoq, would not look out of place in samples I find in the UK although the mix of taxa is not what I would expect if granite was the predominant rock in the catchment.   I travel light, without meters to check the chemical composition of the water, so there is no way to confirm this.  Except by going back one day better prepared …

Diatoms from a stream near Kumyshkang, Uzbekistan (41°18’45.6” N 69 ° 51’40” E, approx. 1400 m above sea level).  .   i.: Ulnaria ulna; j. – l.: Achnanthidium minutissimum; m.: A. cf. pyrenaicum; n., o.: A. cf caledonicum; p.: Achnanthidium girdle view; q.: Navicula tripunctata; r. Navicula sp.; s. Gomphonema gracile; t. Gomphonema sp.; u. Surirella brebissonii var. kutzingii; v. Diatoma moniliformis; w. Nitzschia sp.; x. Planothidium lanceolatum; y. Reimeria sinuata; z.: Encyonema ventricosum; aa.: Encyonopsis sp.   Scale bar 10 micrometres (= 100th of a millimetre).

I should add a caution about names applied to Asian diatoms using identification literature written for European freshwaters, especially after my comments in “Back to the Himalayas …”.   Until the 1980s there was a widespread belief that diatom species were cosmopolitan and could be found all around the world.  This belief became self-fulfilling as, armed with this assumption, biologists set out with books written by and for Europeans and blithely applied the names to the diatoms that they found.  From the 1980s, however, papers started to appear in which people took a closer look at variation in some of these apparently cosmopolitan species and argued that there were, in fact, substantial differences between forms from different locations, and that there were, in fact, much greater numbers of diatoms than previously thought, and that many of these were restricted to particular geographic regions.   But then, in 2002 Bland Finlay and colleagues challenged this emerging view by arguing that it was not diatoms that were restricted in their distributions, it was the locations where these detailed studies had been performed that were rare.   In other words, given enough time and effort on the part of diatomists, we should expect to see these so-called endemic species cropping up in samples from all over the world.

This created a brouhaha within the diatom world which resulted in some further papers that questioned Finlay’s assertions and argued from theoretical grounds that there was no reason why diatoms should not be restricted to a limited geographical area.  As the new century progressed, diatomists added molecular barcoding to their armouries and this offered partial support for both positions: some diatoms – or at least some strains of some diatoms, Nitzschia palea and Gomphonema parvulum, for example – do appear to be genuinely cosmopolitan whilst others do not.  Of course, Finlay and colleagues always hold the trump card in this respect: it is not possible to disprove the existence of any so-called endemic species elsewhere in the biosphere until every conceivable habitat has been examined. But a truce, of sorts, does seem to be emerging.

Sampling the calcareous seepage near So’qoq, April 2017.  The picture at the top of the post shows the valley upstream of Kumyshkang.

The truth may well lie between the two extreme positions.  Maybe many diatoms really are widely distributed because random dispersal mechanisms for microscopic organisms are highly effective, as Finlay and colleagues argue.  But every time a few viable cells of a diatom species land on a suitable habitat, their small pool of genetic variability will either thrive or disappear.   When they thrive, the story of Darwin’s finches will be replayed and a combination of genetic drift and selective pressures will create variations on the original theme, just waiting for an observant biologist to come along and discover the new species.

The question that intrigues me is whether or not the bugs that crawl across the submerged stones in search of food ever notice the difference.   One of my perennial bugbears is that the careful taxonomic work that has resulted in the discovery of all this diversity within diatoms is rarely accompanied by ecological analyses of similar rigour.   In particular, do these different forms of what we once regarded as “cosmopolitan” species actually have any effect on how energy flows through the ecosystem?  Do they, in other words, taste different to the invertebrates that crawl across the stones in search of food?  Or, as Bland Finlay hinted in a subsequent review article, are these different genotypes, in effect, variations on the same basic “ecotype”?   In which case, a casual observer crouching beside a foreign stream may not know the precise name of every species he encounters but still may have a pretty good idea of how these fit into the bigger picture of aquatic diversity.


Finlay, B.J. (2002). Global Dispersal of Free-Living Microbial Eukaryote Species.  Science (New York) 296: 1061-1063.

Finlay, B.J. (2004). Protist taxonomy: an ecological perspective.  Philosophical Transactions of the Royal Society Series B 359: 599-610.

Finlay, B.J., Monaghan, E.B. & Maberly, S.C. (2002). Hypothesis: the rate and scale of dispersal of freshwater diatom species is a function of their global abundance. Protist 153: 261-273.

Kemmarec, L., Bouchez, A., Rimet, F. & Humbert, J.-F. (2013). First evidence of the Existence of Semi-Cryptic Species and of a phylogeographic structure in the Gomphonema parvulum (Kützing) Kützing complex (Bacillariophyta). Protist 164: 686-705.

Mann, D.G. & Droop, S.J.M. (1996).  Biodiversity, biogeography and conservation of diatoms.  Hydrobiologia 336: 19-32.

Telford, R.J., Vandvik, V. & Birks, H.J.B. (2006). Dispersal limitations matter for microbial morphospecies. Science (New York) 312: 1015.

Trobajo, R., Clavero, E., Chepurnov, V.A., Sabbe, K., Mann, D.G., Ishihara, S. & Cox, E.J. (2009). Morphological, genetic and mating diversity within the widespread bioindicator Nitzschia palea (Bacillariophyceae). Phycologia 48: 443-459

Vyverman, W., Verleyen, E., Sabbe, K., Vanhoutte, K., Sterken, M., Hodgson, D.A., Mann, D.G., Juggins, S., van de Vijver, B., Jones, V., Flower, R., Roberts, D., Chepurnov, V., Kilroy, C., Vanormelingen, P. & de Wever, A. (2002). Historical processes constrain patterns in global diatom diversity. Ecology 88: 1924-1931.

A view of the Tien’shan mountains from near So’qoq, Uzbekistan.

Daniel and his den of diatoms …

After contemplating astronomy-without-optics at Ulug Beg’s observatory (see previous post) we walked ten minutes down the road to another of Samarkand’s sights, the mausoleum of Daniyar (the Old Testament prophet Daniel, also venerated by Muslims).  This was a much plainer structure than the polychromatic wonders we had seen elsewhere in the city and, no doubt as a result, fewer visitors.  Daniel’s sarcophagus runs the entire length of the building: the legend is that his severed leg has continued to grow, necessitating an eighteen metre tomb.  The presence of a group of pilgrims, praying with an Iman, reminded me that our word “holiday” is a concatenation of “holy day”, and that pilgrims were the original tourists, both in this part of the world and in Europe.

Our guidebook mentioned an ancient spring on the site, offering me my first opportunity to mix business and pleasure. Unfortunately, the spring was dry but, following the valley up a steep hillside, we reached a graveyard, beside which there was a water trough whose bottom, when I peered inside, was covered with dark brown circular patches, up to about half a centimetre across.  I had not really come prepared for diatom sampling but managed to commandeer an empty water bottle into which I scraped some of these colonies using a piece of plastic that I found lying on the ground nearby.   The water bottle was then stuffed into my rucksack as we continued our explorations, cutting across country towards another set of monuments that we could see on the horizon (Colin Thurbron describes the same journey in reverse in his excellent book The Lost Heart of Central Asia).   Once we were back at our hotel, I let the sample settle overnight, poured off the supernatant and then added an equal volume of local vodka to the remaining suspension.  As in India last year, this is the quickest and least hazardous way of keeping diatoms in reasonable condition when on the road (see “Diatoms from the Valley of Flowers”).

Left: the water trough near Daniyar’s mausoleum, Samerkand from which my diatom sample was collected and, right, the circular colonies of diatoms on the bottom of the water trough.  The largest of these colonies is about half a centimetre across.

Several freshwater diatoms form conspicuous colonies but what intrigued me about these particular growths was that the colonies were disc-shaped, reflecting horizontal growth with little vertical development.  Once back from my travels, I had a look under the microscope and was surprised to see that they were composed of almost-pure growths of either Achnanthidium minutissimum or a very close relative (my observations were on the vodka-preserved specimens and I have not yet had a chance to look at cleaned valves).   This is an extremely common constituent of biofilms all over the world but I have never seen it forming discrete colonies in this way.  I suspect that, given time, all of these colonies would merge to form a continuous biofilm and that, in a natural ecosystem (rather than a water trough), grazing by invertebrates would then control the biomass so that they formed a subaquatic and microscopic “turf”.   Maybe what I am seeing is the early stage of colonisation in a situation where there are, as yet, no grazers?   It is very hard to tell an ecological story from a single, brief visit to any habitat but that would be my opening gambit.

Microscopic views of Achnanthidium minutissimum colonies from the water trough near Daniyar’s mausoleum, Samarkand, April 2017.  The left hand image was taken at x100 magnification and shows a colony (or fragment) that is about 650 micrometres across.  The right hand image was taken at x1000 magnification.   Scale bar: 10 micrometres (= 1/100th of a millimetre).

Achnanthidium minutissimum was not the only familiar plant (in the broadest sense) that we saw on our travels.   The grazed grassland between Daniyar’s mausoleum and Bibi Khanym mosque, our next objective, contained several flowers familiar from home (see Heather’s blog) and our trip to the Tien’shan mountains a few days later revealed many more, including a steep-sided valley full of hawthorn bushes.   It is a good reminder that, however far from home we are, and however exotic our surroundings, we are still in the broad temperate belt around the Eurasian continent that allows a measure of biogeographical continuity across this area.  Some of the plants we saw in the wild in Uzbekistan are garden plants in north-west Europe (the tulip is a good example) but several others thrive in the wild in both places.

Botanising in the grassland between Daniyar’s mausoleum and Bibi Khanym mosque, Samerkand, April 2017.

Decoration on mausoleums at the Shar-i-Zinda complex in Samerkand, near the Bibi Khanym mosque and Daniyar’s mausoleum.  The photograph at the top of this post shows the exterior of Daniyar’s mausoleum.

Reaching for the stars …

One of the more intriguing characters I discovered during our time in Uzbekistan was Ulug Beg (1394 – 1449), grandson of Timur and inheritor of his empire.   Timur consolidated and expanded the conquests of Ghengis Khan and established Samarkand as the capital for an empire that extended from Turkey to northern India.   Ulug Beg, by contrast, was a more peaceful and intellectual character, more interested in science than statesmanship.   He endowed three Madrassas and stipulated a curriculum that extended beyond studying the Koran and Islamic law to include mathematics and astronomy too.   This is reflected in the decoration of the Ulug Beg Madrassas in both Samarkand and Bukhara which include depictions of the night sky and inscriptions extorting the Muslim faithful to aspire to knowledge.

On a hill on the outskirts of Samarkand, the distant snow-clad peaks of the Pamirs serve as a backdrop to Ulug Beg’s observatory, although all that remains now is part of a huge quadrant arc now largely buried.   Using this, Ulug Beg’s astronomers were able to determine the position of celestial bodies with great accuracy, to work out the tilt of the earth’s axis (23.52 degrees) and calculate the length of a year to within a minute of the best modern estimates.   This was accomplished two centuries before Galileo first pointed his telescope to the heavens and, indeed, without any optics at all.

The quadrant arc at Ulug Beg’s observatory in Samarkand.

His is not the only observatory from the Medieval Islamic world that has survived and I was lucky enough to visit the Mughal observatory, the Jantar Mantar (c. 1724) in Delhi last year.  Unlike the Samarkand observatory this one is above ground and has been restored, giving the visitor a much better sense of the scale of the undertaking.  The observatory at Jaipur is also in good condition and was the subject of a fascinating episode of In Our Time, for those readers who are able to access the BBC’s archives.   These were the most sophisticated scientific instruments of their day; now they stand as monuments before which modern scientists should reflect that Western hegemony of science is a very recent phenomenon.   Ulug Beg’s observatory stands as a reminder of science’s deep foundations in ancient wisdom preserved or discovered on the plains of Central Asia.

The Misra Yantra, part of the Jantar Mantar complex of astronomical instruments in Delhi.

Western astronomy’s paradigm shift occurred when people who were trying to understand the cosmos came into contact with with people with practical skills such as glassmaking (a pre-requisite for optics) and metalworking.   The individual elements were all present in the medieval Arab world but the one-off spark of genius that brought them all together just did not happen.  Glass is the least conspicuous of these components in Bukhara and Samarkand until we looked closely at the tiles which decorate their ancient buildings.  The glazes which gives these tiles their lustrous appearance are made from natural pigments mixed with ground glass (“faïence”); however, there was little evidence of extensive working of glass, so an astronomer would have been highly unlikely to have that serendipitous encounter that would have opened new opportunities. Progress is, we have to remember, often a stuttering series of serendipitous events, very few of which have any lasting impact.

What became of Ulug Beg?  He was murdered by his own son and his observatory was destroyed by religious fanatics.   He was, by all accounts, a better scientist than statesman.   The attention to detail that a scientist needs means taking your eye off the big picture.   Reading between the lines, this was Ulug Beg’s undoing and within a generation Timur’s empire had collapsed into a number of independent Khanates.    Over time, Ulug Beg’s discoveries were assimilated into European astronomical thinking and he and his fellow Central Asian polymaths were gradually written out of Western histories of science.   I’m grateful to a new generation of historians such as Peter Francopan (“The Silk Roads: A New History of the World“, Bloomsbury, 2015) who are giving us a less Euro-centric account of progress.  Compare his approach to that of Kenneth Clark in Civilisation (1969), for whom the term “barbarian” seems almost synonymous with non-European, and then look up at the intricate decoration on Samerkand’s madrassas.   Barbarians?  I don’t think so.

A view of the courtyard of the Ulug Beg Madrassa in Bukhara.   The photograph at the top of the article shows the exterior of the Ulug Beg Madrassa in the Registan in Samarkand.

Synchronicity in Samarkand …

I had intended my next post to continue the story of inorganic carbon in freshwater but a holiday has intervened. However, as is often the way with my travel, I have found some unexpected associations with my professional life.

I had wanted to show, using a graph, how much influence inorganic carbon supply (which freshwater biologists refer to, confusingly, as “alkalinity”) had on the types of diatom that are found in rivers. But the simple act of plotting a graph with Excel had, I realised, some unexpected resonances with my current location in Central Asia. I am in Samarkand, in Uzbekistan, a city with a very long history and which numbers Omar Khayyam (1048 – 1141) amongst its previous inhabitants. Omar Khayyam is best known in the West as a poet but was also a noted mathematician and astronomer. Khiva, another ancient city in Uzbekistan, was the birthplace of Muhammad ibn Musa al-Khwarizmi (c.780 – 850) regarded as one of the founders of algebra. Both, in other words, laid the groundwork for the equation y = mx + c, the equation for a straight line that allows me to express the relationship between the diatom assemblage and alkalinity in quantitative terms.

The relationship between the Trophic Diatom Index and alkalinity in a dataset drawn from UK rivers. More about this will follow in a future post but, for now, it is presented as an example of how biological data often fit y = mx + c, the equation for a straight line (indicated by the red line on the graph)

The point of algebra is that you can work out general principles that apply to a situation regardless of the quantities involved. An equation is simply a means of replacing these quantities with letters or symbols so that you can work out the value of something that you don’t know in terms of things that you do know. One of these ancient mathematicians – we don’t know who, but I am giving Uzbekistan the benefit of the doubt – decided to use the Arabic word “shay” (which means “thing”) to represent the unknown in his equations. When the early algebraic treatises were translated to Spanish in medieval times, “shay” became “xay”, which eventually was shortened to “x”. That, at least, is the legend, and no-one seems to have a better explanation. Whenever we use “x” in an equation, in other words, we should reflect that we are part of a tradition that extends back over 1000 years to the plains of Central Asia.

The straight line equation, however, bucks this neat theory to some extent as, in this realm of algebra, “x” represents the known rather than the unknown entity. The unknown, by convention, is indicated by “y”. “Why “y”?” you might ask and, I am afraid, I cannot help. It may be that there is no sensible explanation (“quarks” are, after all, named after a nonsense word in Finnigan’s Wake) but the etymology of “x” is, you have to admit, too good to waste. Especially when writing from Samarkand.

Timurlane’s tomb (Gur-i-Amir) in Samarkand. The photograph at the top of the post shows part of the Registan madrasah complex.

And, finally, I could not resist including this image of decoration on the Sher Dor Madrassa at the Registan: evidence that Medieval Islamic scholars knew about centric diatoms?