Wednesday, June 8, 2016

The many shades of citizen science

Everyone is a citizen but not all have the same kind of grounding in the methods of science. Someone with a training in science should find it especially easy to separate pomp from substance. The phrase "citizen science" is a fairly recent one which has been pompously marketed without enough clarity.

In India, the label of a "scientist" is a status symbol, indeed many actually proceed on paths just to earn status. In many of the key professions (example: medicine, law) authority is gained mainly by guarded membership, initiation rituals, symbolism and hierarchies. At its roots, science differs in being egalitarian but the profession is at odds and its institutions are replete with tribal ritual and power hierarchies.

Long before the creation of the profession of science, "Victorian scientists" (who of course never called themselves that) pursued the quest for knowledge (i.e. science) and were for the most part quite good as citizens. In the field of taxonomy, specimens came to be the reliable carriers of information and they became a key aspect of most of zoology and botany. After all what could you write about or talk about if you did not have a name for the subjects under study. Specimens became currency. Victorian scientists collaborated in various ways that involved sharing information, sharing /exchanging specimens, debating ideas, and tapping a network of friends and relatives for more. Learned societies and their journals helped the participants meet and share knowledge across time and geographic boundaries.  Specimens, the key carriers of unquestionable information, were acquired for a price and there was a niche economy created with wealthy collectors, not-so-wealthy field collectors and various agencies bridging them. That economy also included the publishers of monographs, field guides and catalogues who grew in power along with organizations such as  museums and later universities. Along with political changes, there was also a move of power from private wealthy citizens to state-supported organizations. Power brings disparity and the Victorian brand of science had its share of issues but has there been progress in the way of doing science?

Looking at the natural world can be completely absorbing. The kinds of sights, sounds, textures, smells and maybe tastes can keep one completely occupied. The need to communicate our observations and reactions almost immediately makes one need to look for existing structure and framework and that is where organized knowledge a.k.a. science comes in. While the pursuit of science might seem be seen by individuals as being value neutral and objective, the settings of organized and professional science are decidedly not. There are political and social aspects to science and at least in India the tendency is to view them as undesirable and not be talked about so as to appear "professional".  

Being silent so as to appear diplomatic probably adds to the the problem. Not engaging in conversation or debate with "outsiders" (a.k.a. mere citizens) probably fuels the growing label of "arrogance" applied to scientists. Once the egalitarian ideal of science is tossed out of the window, you can be sure that "citizen science" moves from useful and harmless territory to a region of conflict and potential danger. Many years ago I saw a bit of this  tone in a publication boasting the virtues of Cornell's ebird and commented on it. Ebird was not particularly novel to me (especially as it was not the first either by idea or implementation, lots of us would have tinkered with such ideas, even I did with - BirdSpot - aimed to be federated and peer-to-peer - ideally something like torrent) but Cornell obviously is well-funded. I commented in 2007 that the wording used sounded like "scientists using citizens rather than looking upon citizens as scientists", the latter being in my view the nobler aim to achieve. Over time ebird has gained global coverage, but has remained "closed" not opening its code or discussions on software construction and by not engaging with its stakeholders. It has on the other hand upheld traditional political hierarchies and processes that ensure low-quality in parts of the world where political and cultural systems are particularly based on hierarchies of users. As someone who has watched and appreciated the growth of systems like Wikipedia it is hard not to see the philosophical differences - almost as stark as right-wing versus left-wing politics.

Do projects like ebird see the politics in "citizen-science"?
Arnstein's ladder is a nice guide to judge
the philosophy behind a project.
I write this while noting that criticisms of ebird as it currently works are slowly beginning to come out (despite glowing accounts in the past). There are comments on how it is reviewed by self-appointed police  (it seems that the problem seems to be not just in the appointment - indeed why could not have the software designers allowed anyone to question any record and put in methods to suggest alternative identifications - gather measures of confidence based on community queries and opinions on confidence measures), there are supposedly a class of user who manages something called "filters" (the problem here is not just with the idea of creating user classes but also with the idea of using manually-defined "filters", to an outsider like me who has some insight in software engineering poor-software construction is symptomatic of poor vision, guiding philosophy and probably issues in project governance ), there are issues with taxonomic changes (I heard someone complain about a user being asked to verify identification - because of a taxonomic split - that too a split that allows one to unambiguously relabel older records based on geography - these could have been automatically resolved but the lazy developers obviously prefer to get users to manage it), and there are now dangers to birds themselves. There are also issues and conflicts associated with licensing, intellectual property and so on. Now it is easy to fix all these problems piecemeal but that does not make the system better, fixing the underlying processes and philosophies is the big thing to aim for. So how do you go from a system designed for gathering data to one where you want the stakeholders to be enlightened. Well, a start could be made by first discussing in the open.

I guess many of us who have seen and discussed ebird privately could have just said I told you so, but it is not just a few nor is it new. Many of the problems were and are easily foreseeable. One merely needs to read the history of ornithology to see how conflicts worked out between the center and the periphery (conflicts between museum workers and collectors); the troubles of peer-review and open-ness; the conflicts between the rich and the poor (not just measured by wealth); or perhaps the haves and the have-nots. And then of course there are scientific issues - the conflicts between species concepts not to mention conservation issues - local versus global thinking. Conflicting aims may not be entirely solved but you cannot have an isolated software development team, a bunch of "scientists" and citizens at large expected merely to key in data and be gone. There is perhaps a lot to learn from other open-source projects and I think the lessons in the culture, politics of Wikipedia are especially interesting for citizen science projects like ebird. I am yet to hear of an organization where the head is forced to resign by the long tail that has traditionally been powerless in decision making and allowing for that is where a brighter future lies. Even better would be where the head and tail cannot be told apart.

Saturday, June 4, 2016

Ordering chicken

A few weeks ago, I was asked a few questions by a couple of friends relating to why the bird-groups in bird-books are ordered the way they are. The groupings themselves were not so much in question, it was only the sequence. Why do the larger birds come before the smaller birds? It then led to further questions on why the Galliformes (for example chicken or junglefowl) are considered representatives of an older branch of birds (simply sometimes stated as "primitive", and termed "basal" by cladists) compared to say crows. Part of the question was also the understanding that the sequence to a large extent has been around since the first bird-guides for the Indian region. It was hard to make a clean, coherent, non-anachronistic reconstruction particularly since the sequence has to a large extent been followed long before molecular biology took root. In trying to clarify this, at least for myself, I have been forced to look at some historic literature that few read in modern times. [Needless to say my research also led me to improve some Wikipedia biographies.]

Max Fürbringer (1846-1920)
We can skip the pre-Darwinian state largely because the birds were then put in groups whose order was largely decided by tradition and never questioned (at least not within birds which were themselves placed in the scala naturae / "ladder") - and in this we have already seen ideas such as Quinarianism that were followed by Jerdon in India. But why order birds? It appears that everyone wants some order when listing out all the birds of the world and like dictionaries they initially followed some kind of convention that did not need to be questioned. These lists beginning with that of Linnaeus include those of G.R. Gray and R.B.Sharpe. The sequence that Gray and Sharpe followed was based on one established by N.A.Vigors - again a quinarian. Whether the desire to get away from this sequence was related to the unpopularity of quinarianism, I do not know but the sequence followed in  modern bird books has its roots in a system that was established by two ornithologists who are sadly somewhat lesser known perhaps because their writings were in German. (Interestingly Jerdon's contemporary, Edward Blyth, taught himself German and had little tolerance for Jerdon's scheme that followed Swainson). The two Germans who matter for our analysis are Max Fürbringer (1846-1920) and Hans Gadow (1855–1928) [and they had a counterpart in botany Adolf Engler (1844-1930)]. Gadow by virtue of moving to Britain and writing in English is somewhat better known but his work draws greatly on a lot of hard work and thinking on the part of Fürbringer. 

Pierre Belon's comparative anatomy (1555)
After Darwin, the idea of genealogical trees was well adopted and it was also quite clear that evolutionary processes decidedly lacked order and the ragged bush representing the birds of the world had some bushy branches while others were skeletal and many where difficult to place. Now flattening out this bush (or at least the leaves on a 2-dimensional representation of the bush) and reducing it to a linear list can be done in many ways (computer literates will recognize only two - a breadth-first and a depth-first approach!). There were numerous ways in which the tree itself was being re-arranged (phylogenetics) starting with methods that went from the use of intelligent guesswork on the basis of morphological and anatomical characters to methods that reduced guesswork and attempted to reconstruct evolutionary history on the basis of DNA sequences. Ernst Mayr and Walter Bock referred to the "standard sequence" as one based on Gadow-Wetmore-Peters. Mayr and Bock also went to the extent of suggesting that the sequence be maintained independent of matters of phylogeny (then already showing signs of fluidity) so as to make communication easier. Modern bird-guidebook authors and publishers have obviously given that suggestion a pass. Mayr and Greenway in 1956 set three principles for the taxonomic sequence to be followed - (A) To follow as closely as possiblethe traditional arrangements, except where subsequent work has shown conclusively that a change is advisable (B) To place familes near each other whichare presumably closely related (C) To place the more primitive families near the beginning and the more advanced families near the end.

Back to Max Fürbringer who was a student of  Carl Gegenbaur and a great comparative anatomist. Comparative anatomy at this point had evolved from its early origins as an area of amateur investigation in medical studies. It was not just about looking at gross skeletal similarities but looked at minutiae such as the twisting of the tendons of the foot and the bones of the skull. Fürbringer made use of 51 characters, mostly internal anatomy but also some that included whether the state in which the young are born. He had worked earlier on reptiles and their musculature and was an expert on fossils and osteology as well. He gives special importance to the muscules and tendons on the shoulder. It is quite mind boggling to think of the time and effort it would take to dissect and examine the shoulders of so many kinds of birds, leave alone obtaining the specimens needed for it. Given that it has to be done over a significant length of time, it involves meticulous note making and sketching. Fürbringer identified the key characters for each of the bird groups and then he compared every pair of bird group noting the number of common characteristics and the number of differing characters. He used this pair of numbers (matches and mismatches) to put in a measure of distance between the groups (what we would now call as phenetics - but all this was done before Hennig and the birth of cladistics). Gadow would, four years later in 1892, comment that Fürbringer was being a bit too precise (read "German"!) in doing this pair-wise distance computation and decided that it this was overkill that was not quite needed. Gadow also made some alterations, he noted that not all characters were equal and that the equal weightage for characters was perhaps inappropriate. So he decided based on his expertise that some relationships that Fürbringer saw were spurious. It is worth reading his original text:

The anatomical portion has been written with the view of abstracting there from a classification. In the meantime (after Huxley, Garrod, Forbes, Sclater, and Reichenow's systems) have appeared several other classifications: one each by Prof. Newton, Dr. Elliott Coues, Dr. Stejneger, Prof. Fuerbringer, Dr. R. B. Sharpe, and two or three by Mr. Seebohm. Some of these systems or classifications give no reasoning, and seem to be based upon either ornithological matters or upon inclination—in other words, upon personal convictions. Fuerbringer5s volumes of ponderous size have ushered in a new epoch of scientific ornithology. No praise can be high enough for this work, and no blame can be greater than that it is too long and far too cautiously expressed. For instance, the introduction of " intermediate " groups (be they suborders or gentes) cannot be accepted in a system which, if it is to be a working one, must appear in a fixed form.     In several important points I do not agree with my friend ; moreover, I was naturally anxious to see what my own resources would enable me to find out. This is my apology for the new classification which I propose in the following pages.

The author of a new classification ought to state the reasons which have led him to the separation and grouping together of the birds known to him. This means not simply to enumerate the characters which he has employed, but also to say why and how he has used them. Of course there are characters and characters. Some are probably of little value, and others are equivalent to half a dozen of them. Some are sure to break down unexpectedly somewhere, others run through many families and even orders;  but the former characters are not necessarily bad and the latter are not necessarily good. The objection has frequently been made that we have no criterion to determine the value of characters in any given group, and that therefore any classification based upon any number of characters however large (but always arbitrary, since composed of non-equivalent units) must necessarily be artificial and therefore be probably a failure. This is quite true if we take all these characters, treat them as all alike, and by a simple process of plus or minus, i. e. present or absent, large or small, 1, 2, 3, 4, &c, produce a "Key," but certainly not a natural classification.

To avoid this evil, we have to sift or weigh  the same characters every time anew and in different ways, whenever we inquire into the degree of affinity between two or more species, genera, families, or larger groups of creatures.

Of my 40 characters about half occur also in Fuerbringer's table, which contains 51 characters. A number of skeletal characters I have adopted from Mr. Lydekker's 'Catalogue of Fossil Birds' after having convinced myself, from a study of that excellent book, of their taxonomic value. Certain others referring to the formation of the rhamphotheca, the structure and distribution of the down in the young and in the adult, the syringeal muscles, the intestinal convolutions, and the nares, have not hitherto been employed in the Class of Birds.
Of course this merely mathematical principle is scientifically faulty, because the characters are decidedly not all equivalent. It may happen that a great numerical agreement between two families rests upon unimportant characters only, and a small number of coincidences may be due to fundamentally valuable structures, and in either case the  true affinities would  be obscured.

Of the 26 positive points not less than 19 are common to Falconidae, Psittaci, and Coccyges. In the remaining 7 points Psittaci and Falconidae agree together against Coccyges, namely nestlings, downs of young and adult, fifth cubital, temporal fossa, fleshy tongue, convolutions of intestines. Most of these characters seem important, especially the woolly nestlings, considering that Psittaci breed in holes, and agree in the convolutions in spite of the totally different food.
On the other hand, the sifting of the 14 negative characters shows On the other hand, the sifting of the 14 negative characters shows that in 13 of them the Parrots agree with Cuculidae or with Musophagidae, or with both, and differ along with the Coccyges from the Falconidae. The syrinx is an absolute specialization. Fuerbringer remarks that powder-downs, ceroma, and beak speak for Falconidae against Coccyges. Again, Psittaci and Falconidae differ greatly in the formation of the furcula, in nearly the whole of the muscular system, and in the bones of the wings and legs.
Conclusion.—The Psittaci are much more nearly allied to the Coccyges than to the Falconidae, and of the Coccyges the Musophagidae are nearer than the  Cuculidae because of the vegetable food, ventral pterylosis, presence of aftershaft, tufted oil-gland, absence of vomer, truncated mandible and absence of caeca.

Gadow's weighing and sifting probably went wrong there as a 2011 study re-established the closeness between the parrots and falcons. (Fürbringer had carefully compared them but he too had them branching apart widely).
Suh A, Paus M, Kiefmann M, et al. Mesozoic retroposons reveal parrots as the closest living relatives of passerine birds. Nature Communications. 2011;2:443-. doi:10.1038/ncomms1448.
It is somewhat sad that Fürbringer is still hardly known in ornithological circles. Mayr and Bock call the bird-sequence used for so many years as the Gadow-Wetmore-Peter's sequence. I saw with delight however that Tim Birkhead in his Ten Thousand Birds (2014) puts 1888 on the ornithological timeline to mark this landmark work.

Fürbringer's work is also remarkable because he finally produced a graphical summary of his entire work. An evolutionary tree and wait, it was a three-dimensional tree! He tried to represent it with side views from two opposite points and horizontal cross-sections at three levels. The cross-sections indicate phenetic distances between the groups. He seems to have hit upon some kind of manual equivalent of what we might produce today using canonical correspondence analysis. (It would be amazing if someone-who-knows-German could recreate his three-dimensional rendition and compare his own distance matrix which what a CCA algorithm would produce - Heidelberg University would do well to make a three-dimensional tree model as a tribute)


Front views of the avian tree.
Rear view of tree

Okay, so we now hopefully have a historical view of how the bird relationships were established. We still have a part of the original question hanging, why are chicken considered "primitive" or "basal" to use the more accurate phylogenetic term. The answer again lies in Fürbringer's scientific past- he had worked extensively on reptilian anatomy and he saw more of the older traits in parts of his bird-tree. Remember also that he tried to place extinct birds into the tree. Today, the way a tree is rooted or oriented is by comparing with an outgroup - a specimen that you know from prior knowledge to be distant enough to have a common shared ancestor with all the others that are in focus.

The specific characters that Gadow listed for the Galliformes (in which he also included the hoatzin) while he placed them as the 14th group (after the ratites, herons, seabirds and falcons but before the cranes) are :
  • Galliformes- Phytophagous. Nares impervious. Furcula with hypocleidium. Plagiocoelous type V. Caeca large. Crop globular. 10 primaries. 
    • Galli -  16 or more cervical vertebrae. Holorhinal. Coracoids touching each other. Flexors of type I. Hallux large. Neck without lateral apteria.
      • Gallidae -16 cervical vertebrae. Nidifugous. Spina communis sterni. Sternum with long posterior later processs and with obliue processes. Hypotarsus complex.
      • Opisthocomidae - 18 or 19 cervical vertebrae. Nidicolous. Spina externa only present. Sternum with small notches or fenestra only; no oblique process. Oil-gland tufted.
The Hoatzin has since been moved elsewhere but interestingly the claws on the hand used for clambering up vegetation are not even used.

That leaves one other question which is on whether the sizes matters in this sequence. It appears that the Galloanserae which appear early in the sequence are in general somewhat large sized, the ratites and flightless birds also tend to be large. At the other end of the spectrum the passerines tend to be small but it appears that there is no strong evolutionary trend in size.

Note: Thanks to Emmanuel Theophilus and Ashish Kothari for the original questions and discussions.
Postscript: Note that there were many other comparative anatomists in the period and many pieces of bird and reptile evolution had been figured out by several others including Archibald Garrod (1873-74 on muscles part 1 part 2 and W.H. Flower.
I have also found this very nice interactive site on comparative anatomy of birds that uses chicken as a model. 
Note that I had mistakenly attributed the parrot-falcon affinity to Fürbringer, turns out that he did not think much about it.
9 June 2016 - I have also found an interesting review by R.W. Shufeldt (that infamous racist!) which also summarizes the work of Professor William Kitchen Parker. Parker (1862) is quoted "I will first show, in two parallel columns, how both the Fowls and the Rails run insensibly through certain leading genera into the lowest (reptilian) types of diving-birds" 1862, William Kitchen Parker "On the Osteology of Gallinaceous Birds and Tinamous" in Shufeldt, R.W. (1904) An Arrangement of the Families and the Higher Groups of Birds. The American Naturalist 38(455/456):833-857.
Appendix - a list of the characters used by Gadow.

A.   Development.
Condition of young when hatched: whether uidifugous ur nidi-colous; whether naked or downy, or whether passing through a downy stage.
B.  Integument.
Structure and distribution of the first downs, and where distributed.
Structure and distribution of the downs in the adult: whether absent, or present on pteryls or on apteria or on both.
Lateral cervical pterylosis : whether solid or with apteria.
Dorso-spinal pterylosis : whether solid or with apterium, and whether forked or not.
Ventral pterylosis: extent of the median apterium.
Aftershaft:  whether present, rudimentary, or absent.
Number of primary remiges.
Cubital or secondary remiges: whether quinto-or aquinto-cubital.
Oil-gland: present or absent, nude or tufted.
Rhamphotheca: whether simple or compound, i. e. consisting of more than two pieces on the upper bill.
C. Skeleton.
Palate: Schizo-desmognathous.   Nares, whether pervious or impervious, i. e. with or without a complete solid naso-ethmoidal septum.
Basipterygoid processes: whether preseut, rudimentary, or absent: and their position.
Temporal fossa, whether deep or shallow.
Mandible: os angulare, whether truncated or produced ; long and straight or recurved.
Number of cervical vertebra;.
Haemapophyses of cervical and of thoracic vertebra;: occurrence and shape.
Spina externa and spina interna sterui: occurrence, size, and shape.
Posterior margin of the sternum, shape of.
Position of the basal ends  of the  coracoids: whether separate, touching, or overlapping.
Procuracoid process: its size and the mode of its combination with acrocoraeoid.
Furcula: shape; presence or absence of hypocleidium and of interclavicular process.
Groove on the humerus for the humero-coracoidal ligament: its occurrence and depth.
Humerus, with or without ectepicondj lar process.
Tibia: with bony or only with ligamentous bridge, near its distal tibio-tarsal end, for the long extensor tendons of the toes : occurrence and position of an intercondylar tubercle, in vicinity of the bridge.
Hypotarsus : formation with reference to the tendons of the long toe-muscles:—(1) simple, if having only one broad groove; (2) complex, if grooved and perforated ; (3) deeply grooved and to what extent, although not perforated.
Toes :   number and position, and connexions
D.  Muscles.
Garrod's symbols of thigh-muscles A B X Y,—used, however, in the negative sense.
Formation of the tendons of the m. flexor perforans digitorum : the number of modifications of which is 8 (I.-VIII.) according to the numbering in Bronn's Vogel, p. 195, and Fuerbringer, p. 1587.
E.   Syrinx.
Tracheal, broncho-tracheal, or bronchial.
Number and mode of insertion of syringeal muscles.
F.   Carotids.
If both right and left present, typical: or whether only left present, and the range of the modifications.
G.   Digestive Organs
Convolutions of the intestinal canal. Eight types, numbered L-VIIL, according to Bronn's Vogel, p. 708, and P. Z.S. 1889, pp. 303-
Caeca: whether functional or not.
Tongue: its shape.
Food.—Two principal divisions, i. e. Phytophagous or Zoophagous, with occasional subdivisions such as Herbivorous, Frugivorous, Piscivorous, Insectivorous, etc.

List of Characters employed occasionally.
Shape of bill.
Pattern of colour. Number of rectrices ; and mode of overlapping of wing-coverts, according to Goodchild (P.Z.S. 1886, pp. 184-203).
Vomer.    Pneumatic foramen of humerus.
Supraorbital glands.
Certain wing-muscles according to Fuerbringer.
Mode of life: Aquatic, Terrestrial, Aerial, Diurnal, Nocturnal, Rapacious, etc.
Mode of nesting: breeding in holes.
Structure of eggs.
Geographical distribution.

Tuesday, March 1, 2016

Some unsung Lepcha collectors

Photo from Bruce, C.G. (1923) The Assault on Mount Everest 1922. New York: Longmans, Green & Co.
A chance enquiry by Richard Conniff on some Lepcha collectors for his website for fallen naturalists led me to some very interesting tit-bits and as usual, I was surprised by the paucity of local interest and research. Not having had the good fortune of exploring the richness of north-eastern India (except for a short trip in Bhutan) it was hard to feel grounded with sufficient local context but reading through some of the available bits makes it clear that that so much local knowledge has been squandered in recent times. Hopefully someone based in Sikkim or nearby can make amends with a more detailed study.

The Gazetteer of Sikhim (1894) has an excellent introduction to ethnic and biological diversity. It includes a list of birds along with Lepcha names. It also has bits of local bio-lore such as notes on birds of good and ill omen. The sections on butterflies was written by J. Gammie and Lionel de Niceville while the one on birds was by L.A.Waddell. Wadell writes while dealing with the birds:
The Pahariyas, speaking a Sanskritic dialect- the Parbatiya, and the Bhotiyas, including the Tibetans are much less discriminating in their bird-names than the Lepchas, who are "born naturalists";  - [1894. The Gazetteer of Sikhim. p. 202.]
The butterfly section by Niceville makes a tantalizing statement but sadly, he does not actually list the Lepcha names for butterflies:
It might be noted that the Lepcha collectors of Sikhim are most skilful, and would compare favourably with those of any country in the world: they are the only race in Hindostan who have names for the different species of butterflies. - [1894. The Gazetteer of Sikhim. p. 115.]
Mycalesis (Pachama) mestra, Hewitson. Has frequently been brought into Darjeeling from the neighbourhood of Buxa in Bhutan by the Lepcha collectors employed by Messrs. Otto and F.A. Moller, A.V.Knygett and G.C.Dudgeon. -[1894. The Gazetteer of Sikhim. p. 121.]
It turns out that Lepcha butterfly collectors went far from their traditional grounds.  
In 1893 and 1894 Mr de Niceville induced three amateur collectors in British India to send down to Sumatra some of the well-known Lepcha collectors from Darjiling to Dr Martin's care. These men met with very good success, though at first they were afraid to mix with the cannibal Battaks, and refused to go to the mountains. However, after giving them a Battak guide and interpreter, they went off to the hills regularly, and did very well there. - [Anon. (1896) Reviews and notices of book. The Butterflies of Sumatra. The Entomologist's Record and Journal of Variation 8(1):22-24.]
And some of them perished in their travels (the original enquiry) and the only person to have taken some trouble to document the Lepcha collectors has been C.F.Cowan. In his 1967 note in the Journal of the Bombay Natural History Society he finds some information on the collectors of William Doherty, the famous butterfly collector. When Doherty fell ill in Africa, his Lepcha assistants carried him to the hospital in Nairobi. Doherty wrote to Elwes: "I had to go to Darjeeling for my Lepchas and got two fairly good men: I have also two other men... and hope to keep them permanently." He had his Lepchas climb hills, "Each of my men used to take a peak and stay there all day". One collector, Pambu, made treetop platforms and stayed on them all day. Doherty took some of his collectors to Java and in his letters to Ernst Hartert mentions Chedi and Tungkyitbo (who died at sea). It seems that some of the collectors stayed on in the Malay peninsula and worked for other collectors like Oberthur. These include Lakatt and Pamboo. Lakatt returned to Calcutta in 1895. Pambu unfortunately did not make it and was "murdered by savages" on Japen Island, Geelving Bay, West Irian in 1898. Cowan notes: 
So passed Pambu, working some 5000 miles from home. We can picture him a dedicated and enterprising naturalist, a faithful and cheerful companion and a staunch and steady friend. 
Lakatt's name has been commemorated in butterfly nomenclature by the Lycaenid Jamides zebra lakatti Corbet, 1940 (Proc. R. ent. Soc. London (B) 9:2). It is hoped shortly to give Pambu similar recognition.

Lepcha bird trappers find a mention in Mackintosh's  Birds of Darjeeling (1915) - with a comment on Lepchas imitating the call of Glaucidium brodiei to lure small passerines.

Lepcha collectors were in demand among the botanists as well. They not only found the plants but processed them into herbarium sheets (Lepcha boxes of butterfly specimens are also mentioned).
Mr Cave of the Loyd Botanic Gardent at Darjiling, who provided an admirable Lepcha collector always active and good-tempered, and helped me to find my way among so many genera that were strange.  [Lacaita, C.C. (1916) Plants collected in Sikkim, including the Kalimpong District, April 8th to May 9th, 1913. Botanical Journal of the Linnean Society 43:457-492.]
Portrait of Dr Hooker with his Lepcha collectors -
original painting by Frank Stone mezzotint by William Walker

Hooker, in his introduction to the work of J.F.Cathcart, an amateur botanist notes:
He had already established a corps of Lepcha collectors, who scoured the neighbouring forests, descending to 2000 feet, and ascending to 8000 bringing every plant that was to be found in flower; and in his house were two artists busily at work. He told me his plans, and invited my co-operation ; he intended to procure more artists, the best that could be obtained, from Calcutta, especially those skilled ones, who had been trained under Wallich and Griffith in the Botanic Garden, and to draw every plant of interest that he or I could procure. Knowing that a Flora of the Himalaya was a work which I contemplated, he most liberally offered me the use of all the drawings on my return to England, and expressed a wish that I should direct his artists to the plants best worth figuring, and instruct them in perspective, and in drawing the microscopic details, the points in which native artists are mainly deficient. -[J. D. Hooker in his introduction to J.F. Cathcart's - Illustrations of Himalayan Plants (1855) ]
Hooker's collectors maintained careful accounts written in the Lepcha script of which there is an interesting description from the Kew archives. [Sprigg, R.K. (1983) Hooker's Expenses in Sikkim: An Early Lepcha Text. Bulletin of the School of Oriental and African Studies. 46(2):305-325.]

George King of the Calcutta botanical garden also used Lepcha collectors and we find mention of the names of Dungboo  and Dotho.

The tradition seems to have continued at least till the late 1920s for we find mention of Rohmoo pictured at the head of this article. Rohmoo worked along with another collector Ribu for several botanists in the Botanical Survey of India and the Lloyd Botanical Garden at Darjeeling. He collected for several botanical expeditions in Sikkim including those of William Wright Smith, George H. Cave and Roland Edgar Cooper. Poa rohmooana was named after him by Henry Noltie in his Flora of Bhutan.

A statement by H.H.Risley (the physical anthropologist) in the introduction to the Gazetteer is particularly striking:
The Lepchas alone seem to doubt whether life is worth living under the shadow of advancing civilisation, and there can, we fear, be little question that this interesting and attractive race will soon go the way of the forest which they believe to be their original home. 

A similar pessimistic outlook is expressed by Florence Donaldson in her book Lepcha land, or Six weeks in the Sikhim Himalayas (1900).
Current events... are likely to open the flood-gates of Western civilization. But when this comes to pass, "Lepcha Land" will be a misnomer, and another primitive, patriarchal and peace-loving people will have died out.
PS: It turns out that some researchers have tried some very interesting experiments, using Lepchas to monitor bird species.

Further reading

Tuesday, February 16, 2016

Moving Plants

All humans move plants, most often by accident and sometimes with intent. Humans, unfortunately, are only rarely moved by plants. 

The history of plant movements have often been difficult to establish. In the past the only way to tell a plant's homeland was to look for the number of related species in a region to provide clues on origin. This idea was firmly established by Nikolai Vavilov before being sent off to his unfortunate death in Siberia. Today, genetic relatedness of plants can be examined by comparing the similarity of chosen DNA sequences and among individuals of a species those sequence locations that are most variable. Some recent studies on individual plants and their relatedness have provided some very interesting glimpses into human history. A study on baobabs in India and their geographical origins in East Africa established by a study in 2015 and that of coconuts in 2011 are hopefully just the beginnings. These demonstrate ancient human movements which have never received much attention in story-tellings of history. 

Unfortunately there are a lot of older crank ideas that can be difficult for untrained readers to separate. I recently stumbled on a book by Grafton Elliot Smith, a Fullerian professor who succeeded J.B.S.Haldane but descended into crankdom. The book "Elephants and Ethnologists" (1924) can be found online and it is just one among several similar works by Smith. It appears that Smith used a skewed and misapplied cousin of Dollo's Law. According to him, cultural innovation tended to occur only once and that they were then carried on with human migrations. Smith was subsequently labelled a "hyperdiffusionist", a disparaging term used by ethnologists. When he saw illustrations of Mayan sculpture he envisioned an elephant where others saw at best a stylized tapir. Not only were they elephants, they were Asian elephants, complete with mahouts and Indian-style goads and he saw this as definite evidence for an ancient connection between India and the Americas! An idea that would please some modern-day cranks and zealots.

Smith's idea of the elephant as emphasised by him.
The actual Stela in question
 "Fanciful" is the current consensus view on most of Smith's ideas, but let's get back to plants. 

I happened to visit Chikmagalur recently and revisited the beautiful temples of Belur on the way. The "Archaeological Survey of India-approved" guide at the temple did not flinch when he described an object in one of the hands of a carving as being maize. He said maize was a symbol of prosperity. Now maize is a crop that was imported to India and by most accounts only after the Portuguese sea incursions into India in 1492. In the late 1990s, a Swedish researcher identified similar  carvings (actually another one at Somnathpur) from 12th century temples in Karnataka as being maize cobs. It was subsequently debunked by several Indian researchers from IARI and from the University of Agricultural Sciences where I was then studying. An alternate view is that the object is a mukthaphala, an imaginary fruit made up of pearls.
Somnathpur carvings. The figures to the
left and right hold the puported cobs.
(Photo: G41rn8)

The pre-Columbian oceanic trade ideas however do not end with these two cases from India. The third story (and historically the first, from 1879) is that of the sitaphal or custard apple. The founder of the Archaeological Survey of India, Alexander Cunningham, described a fruit in one of the carvings from Bharhut, a fruit that he identified as custard-apple. The custard-apple and its relatives are all from the New World. The Bharhut Stupa is dated to 200 BC and the custard-apple, as quickly pointed out by others, could only have been in India post-1492. The Hobson-Jobson has a long entry on the custard apple that covers the situation well. In 2009, a study raised the possibility of custard apples in ancient India. The ancient carbonized evidence is hard to evaluate unless one has examined all the possible plant seeds and what remains of their microstructure. The researchers however establish a date of about 2000 B.C. for the carbonized remains and attempt to demonstrate that it looks like the seeds of sitaphal. The jury is still out.
I was quite surprised that there are not many writings that synthesize and comment on the history of these ideas on the Internet and somewhat oddly I found no mention of these three cases in the relevant Wikipedia article (naturally, fixed now with an entire new section) - pre-Columbian trans-oceanic contact theories

There seems to be value for someone to put together a collation of plant introductions to India along with sources, dates and locations of introduction. Some of the old specimens of introduced plants may well be worthy of further study.

Introduction dates
  • Pithecollobium dulce - Portuguese introduction from Mexico to Philippines and India on the way in the 15th or 16th century. The species was described from specimens taken from the Coromandel region (ie type locality outside native range) by William Roxburgh.
  • Eucalyptus globulus? - There are some claims that Tipu planted the first of these (See my post on this topic).  It appears that the first person to move eucalyptus plants (probably E. globulosum) out of Australia was  Jacques Labillardière. Labillardiere was surprized by the size of the trees in Tasmania. The lowest branches were 60 m above the ground and the trunks were 9 m in diameter (27 m circumference). He saw flowers through a telescope and had some flowering branches shot down with guns! (original source in French) His ship was seized by the British in Java and that was around 1795 or so and released in 1796. All subsequent movements seem to have been post 1800 (ie after Tipu's death). If Tipu Sultan did indeed plant the Eucalyptus here he must have got it via the French through the Labillardière shipment. 
  • Muntingia calabura
  • Delonix regia 

Further reading
  • Johannessen, Carl L.; Parker, Anne Z. (1989). "Maize ears sculptured in 12th and 13th century A.D. India as indicators of pre-columbian diffusion". Economic Botany 43 (2): 164–180.
  • Payak, M.M.; Sachan, J.K.S (1993). "Maize ears not sculpted in 13th century Somnathpur temple in India". Economic Botany 47 (2): 202–205. 
  • Pokharia, Anil Kumar; Sekar, B.; Pal, Jagannath; Srivastava, Alka (2009). "Possible evidence of pre-Columbian transoceaic voyages based on conventional LSC and AMS 14C dating of associated charcoal and a carbonized seed of custard apple (Annona squamosa L.)" Radiocarbon 51 (3): 923–930.
  • Veena, T.; Sigamani, N. (1991). "Do objects in friezes of Somnathpur temple (1286 AD) in South India represent maize ears?". Current Science 61 (6): 395–397.

Saturday, January 30, 2016

The value of outsiders - a bit of big-data

There are many examples from the past where  recruiting someone from an entirely different specialization into an organization pushed the envelope of knowledge. It is quite remarkable to see how organizations rapidly turn dull when narrow policies are in place. Too many establishments languish because of inbreeding and the lack of a broad vision. Outsider perspectives are passively discouraged or even actively blocked out.

I have written in the past on Reginald Moreau and his contribution to ornithology thanks to being imported from accounting by C. B. Williams. Here are a couple of other stories from closer home.

A recent buzzword is "big-data". Like other fashionable words in business, this too will pass. But I like to extoll some of the great ideas related to data analysis that took root in India and became less important in later times. One of these was the Baconian ideal of evidence-based reasoning. It is interesting how India became a place where the idea of "facts" (an older word for data) and their collection grew in importance rather early. One of the early forces was W. H. Sykes, the man who brought the "Dukhun" (Deccan) into worldview, was perhaps the earliest data fancier. Sykes was a "statistical reporter" and founding member of the Statistical Society of London and when he returned to England he became an MP and a director of the East India Company where he championed methods of data collection for decision making. Sykes was amazingly interdisciplinary in his early data-collection work. Zoologists know him for the birds and fish that he collected but he was also a great collector of other kinds of data and a bit of an analyst. He calculated the efficiency of the E.I.C. and its army - comparing costs with those of the French. He looked at life expectancy, insurance and a number of ideas that were still unknown.

Sir Gilbert "Boomerang" Walker
Another place where data gathering became quite important was in the study of weather. The Indian Meteorological Department as we have seen earlier was established by an order signed by A. O. Hume (there are claims that Hume "established" the IMD but this is probably incorrect and it seems like more credit might be due to someone Hume did not like - Sir Richard Strachey) and was headed by a geologist Henry Francis Blanford (whose brother, another geologist, would plunge into zoology and be the founding editor of the Fauna of British India series).  One of the things that Blanford unearthed was a link between the amount of snow falling in the Himalayas and the monsoon in the subsequent season. Large scale patterns like the depression in barometric pressure across the country had already been detected before this. It soon became clear that someone with skills beyond traditional meteorology was needed and that was when Gilbert T. Walker known for his mathematical gifts left a teaching position at Cambridge to join the Indian Meteorological Department. He had already become a Fellow of the Royal Society thanks to his contributions to the mathematics of electromagnetism. Early in his career he worked on so much mathematics that he fell ill and needed to take breaks in Switzerland, a period in which he became an expert ice skater! Walker had other interests including boomerangs and had earned himself the nickname of Boomerang Walker. Walker like E.H. Hankin, the microbiologist, took an interest in the soaring of birds in India. When in India, he was frequently seen throwing boomerangs on the grounds of Annandale in Shimla. Here he worked on the physics of boomerangs and the mathematics behind the paths taken and examined parameters such as the twist and angle of the surfaces. Walker also began to examine weather data and developed methods to deal with time-series. Autoregression models today use what are called the Yule-Walker equations. The other contributor was Udny Yule who worked on sunspot patterns. (Interestingly it turns out that Walker's contributions were overlooked for years and one reviewer who had dismissed him was Herman Wold who helped developed the multivariate technique of PLS!) Using these methods Walker found large scale weather patterns across the southern hemisphere - what is now referred to as the ENSO (El Nino Southern Oscillation).

Thomas Nelson Annandale, a director of the Zoological Survey of India, was broad-minded enough to get someone with a statistical and mathematical perspective to examine data collected by physical anthropologists (the main collector was a Herbert Risley who has also been called a "scientific racist"). Annandale chose to hand out the dataset to P.C. Mahalanobis and that led to a major leap in multivariate analysis. The eponymous measure of distance (i.e. the opposite of similarity), Mahalanobis distance, is today one of the most widely used ways to examine the similarity of an object to a predefined group of objects and examine the likelihood of its membership to the group on the basis of a set of variables measured on a continuous scale.

Know an organization that needs to changes its valuation of specialists from other fields?