Tuesday, September 18, 2012

Feather patterns

A rather old publication caught my attention today. The patterns of feathers are something that can perhaps be better understood by simulating their formation. The feather is born from a circular set of germ cells and it grows out of the follicle just as hairs and nails do. The colours on feathers arise from pigment and micro-structure. This 1901 publication by J. L. Bonhote "On the Evolution of Pattern in Feathers" examines the change in feather pattern from the bold streaks on a young sparrowhawk to the bars found in adults.

Pattern variations in the feathers of a sparrowhawk

Bonhote goes on to speculate on what patterns are more primitive and what are more derived. He expresses surprise at how such a regular pattern appears on the bird with bits of the pattern being present on separate feathers. 

More complex patterns with colours

It is quite surprising that not much work has actually gone into this in the years since. A 2004 study examines the developmental biology of feather follicles and briefly mentions colour patterns and the signalling that might be involved. I have always thought that a good approach to study them would be to build a simulation. Perhaps a Java applet that allows different types of signals and their diffusion in different ways along the ring of cells. Parameters like direction and rate of movement or diffusion should be controllable. A little animation (Note: Animated PNG that may or may not work on your browser) is given below to give the idea for a high-school programming project.
A rough indication for a feather simulation applet. Here two signals diffuse inwars to create a U pattern on a feather.
It would be great if an applet that has different kinds of diffusion patterns along the germ cells in the feather follicle could simulate the whole gamut of patterns one sees in nature and perhaps find some that are as yet unknown.

Further reading

Thursday, September 13, 2012

A little-known bird artist

One of the hazards of contributing to Wikipedia is that one does not read enough of what is on it. Bumping into a series of interesting paintings of South African birds I looked up the artist marked as Sergeant C. G. Davies. Turns out that he was Claude Gibney Finch-Davies, a somewhat lesser known artist. Born in Delhi in 1875 he went to England and joined the army in South Africa. Somewhere along the line he picked up an interest in birds and art. A couple of biographies have been written about him by A C Kemp, but it would seem like he has largely been unknown, partly due to something he did that blemished his career and led perhaps to his death/suicide. His keen interest in illustration led him to remove plates from books in the museums and libraries that he referred to. Today there are probably art collectors who must be eager to steal this man's paintings.

The Natural History Museum at London holds some of his unpublished notebooks and paintings. Fortunately for us his paintings are out of copyright since 70 years have passed since his untimely death. Some of his paintings can be found here on Wikimedia Commons

His biography on Wikipedia is interesting but some of the details seem to be untraceable - it says [emphasis mine]:
He was born in Delhi, India, the third child and eldest son of Major-General Sir William and Lady Elizabeth B. Davies née Field. His father later became Governor of Delhi and was awarded the Order of the Star of India, while his mother was said to be an expert on Indian snakes.
The names of the mother and father are confirmed elsewhere as well. But it is odd that no further information is found on his father in the ODNB. Does anyone know further details and sources?

Sunday, September 9, 2012

Quirky Quinarians

My last post on the Digital Library of India was mainly incidental but an interesting find there was two volumes (missing one though) of William Swainson's book on the natural history and classification of the birds. It is a remarkable book, outdated for uses than historical, but still worth examining.

It is remarkable for giving a first hand account on how ornithologists saw patterns in the world around them in that period well before Darwin. One of these was the Quinarian classification. The quinarians believed that nature had been designed and that the Creator had chosen the magic number 5 in the grand plan. After all why else did most of us have five fingers on each hand or most flowers (at least the dicots) have 5 petals. By finding this order in nature, you were not just an ornithologist, but a devoted natural theologist who could see the signature of the Creator. Swainson's begins :
IF elegance of form, beauty of colouring, or sweetness of voice, were peculiarities which constituted the superiority of one class of beings over another, we should unquestionably assign to birds the highest station in the scale of the animal creation. No shadow of fear mixes with those pleasurable sensations with which they are viewed; and those feelings, moreover, are heightened by the ethereal nature of the creatures themselves. In a moment they may spread their wings, launch into boundless air, and be seen no more. We almost view them as beings of a happier world, alighting upon this "dim spot called earth," more as a place of temporary rest, in their voyage through the regions of space, than as their permanent abode. They remind us of those invisible spirits of the unseen world, which, we are taught to believe, traverse the air on the wings of the wind ; who alight, but for a moment, among the sons of men, and then depart to breath a purer atmosphere. Of all unintelligent beings, they alone are gifted with a musical voice, possessing both sweetness and varied expression. Their language, in some measure, is thus intelligible even to man, inspiring him with cheerfulness or melancholy. Hence it is, that from among birds the poets have selected their sweetest themes. They are, both poetically and literally, the butterflies of vertebrated animals;
We will come back to what he means in the last bit. The philosophical foundations of quinarianism were introduced by W S MacLeay. His book can be found on the Internet Archive and remarkably, the copy that has been scanned belonged to Thomas Horsfield and was bequeathed to Frederic Moore then presumably to the East India Museum and on to the British Museum. In one place Moore notes that the margin notes in the book are by Horsfield. 

Horae entomologicae : or, Essays on the annulose animals (1819)

MacLeay is very interesting in that he tries to support the entire structure by reconstructing them from more basic principles. Now this was a time when life forms were arranged in a linear scale with man at the "upper" end. MacLeay suggested that this line had to be turned to a circle. So all animals to him were made up by a circle composed of five groups - Acrita, Mollusca, Vertebrata, Annulosa, Radiata - in that order. MacLeay's saw the top level plan of life forms (which he saw merely as matter that had been organized by a vital princple) made up of two circles touching each other and indicating similarities. The stars are placeholders for groups that according to him had not yet been found !
Organized matter organized into circles (Acrita ~ lower animals, Annulosa ~ arthropods, Radiata ~ echinoderms)
Each group then was divided again into smaller circles each again with five groups. Working on in this way and dealing with exceptions and so on he finally reaches on page 318 with this.
 He then goes on to show how his view of the world can be shown to be geometrically isomorphic with Lamarck's branching diagram of groups - " Now this tabic of affinities which is given in page 457, vol. i. of the Histoire Nat. des Animaux sans Vertebres, however confused it may appear, or subramose, as it is termed by Lamarck, coincides with the tabular view which I have laid before the public in the preceding part of this chapter." and further goes on to say that "a progression of some sort does exist, neither believer nor atheist will deny ..."

MacLeay's "province" being in entomology, he then gives the plan of arthropods as :

And to further prove his point he comes up with the idea of analogies (similarities between groups at common positions on contiguous circles) - noting for instance that the Araneidea and the Lepidoptera were similar in the ability to spin silk ! 
Whatever it was, his work was to have a considerable influence on people in other "provinces" such as Swainson with his birds. He finds the analogy that was waiting to be found - "The feathers of birds, soft and imbricate, are perfectly analogous to the down upon the wings of butterflies, and both are disposed in the same manner." Swainson created five groups within the birds which he called the "Orders".
  • The Raptorial (The birds of prey - with retractile claws like that of the cats !)
  • The Incessorial (most passeriformes)
  • The Natatorial (swimmers)
  • The Grallatorial / Tenuirostral (Waders)
  • The Rasorial / Scansorial (fowl)
 Like a good quinarian he gets around breaking each of his orders into 5 sub groups. The raptors he breaks into vultures, falcons and owls. Of the two he is unable to find, one he assigns to - wait a minute - the dodo ! Anyway he is convinced for he can further find those perfect analogies that ought to exist.

The Avocet compared to a racoon Nasua !
The influence of quinarianism was great, with T.C.Jerdon following it in his Birds of India (1862) in spite of Darwin's publication. He was however following a list by George Gray. A reviewer (unidentifiable) in the 1864 Quarterly Journal of Science noted that: 
Dr. Jerdon, however, seems to take a very candid view of Mr. Darwin's theory on other points, though he is of opinion that that distinguished naturalist, "perhaps, lays too much stress on external and fortuitous circumstances as producing varieties, and not enough on the inherent power of change." 
and finally concludes that 
In thus following the phantasies of Kaup, and the mad vagaries of Bonaparte (in his latest writings), we cannot believe that Dr. Jerdon has acted well for his own reputation, nor wisely as regards the class of readers for whom his volumes are specially intended.

Old books, even those that are demonstrably inaccurate, are still worth examining. In going through Swainson's work I found a statement that the only bird with a true "horn" was Palamedea. A little searching identified the bird as the Horned Screamer. It turns out, interestingly, that this horn is not a feather quill but a peculiar cornified structure arising from the skull, which, unlike a feather grows continuously.

PS: For a more sympathetic reading and view of Quinarianism - see:
Novick, Aaron (2016) On the Origins of the Quinarian System of Classification. Journal of the History of Biology 49(1):95-133.

Further reading

Saturday, September 8, 2012

Digital Library of India

 IMPORTANT NOTE (3 May 2015) - The Digital Library of India has a new interface, one that works!

This post is about the Digital Library of India, a rather poorly designed website born from excellent intention but languishing in an unusable state in spite of being associated with one of the most enlightened of Indian educational institutions. Attempts to contact them through email seem to produce no response so here goes one more attempt at communication.

The sad thing about this site is that there is actually good material underneath, some of which is not even available on the Internet Archive (although in some cases I have been copying content to that site, reasons for which will become apparent below).

Reactions to the home page, easily improved with a bit of thinking (aloud perhaps and the public can help)
The first page itself appears rather poorly designed, although this is in the same style as some of the NIC designed government sites from northern India. This is rather unfortunate given that this is hosted from perhaps one of India's best educational institutions (IISc). If the first page is a let down (several of the links from the first page including to partner sites in Hyderabad and Noida are dead), the results from a search can be even more annoying. I have no idea how it searches for Indic text but in the case of English it is marginally functional for words in the title but that cannot be said about searches by author. The metadata on the site is often incorrectly spelt making search quite useless. When you do find material, it is a good idea to check on the Internet Archive, the scans made there from American libraries are of a much better quality not to mention with better presentation.

The metadata can often be incorrect in spelling or missing
The results of a search lead to two links - BookReader-1 and BookReader-2 and taking one of these two routes will take you to the point where 99% of the audience will exit the website. Here is what clicking BookReader-1 on my Mozilla Firefox browser does. It tries to download a TIF file (the first page, which is often a blank white page) and it tells me that I need to install certain additional software.

BookReader-1 a deadend for most lay-users
Book reader 2 seems to show a rather promising layout in a new window but that says you need to install Apple Quicktime. I do not think most people will make any headway with this interface.

Exit point 2

Now all this is a terrible pity because it can be easily improved. There are books here that are really rare and worthy of readership. A bit of ingenuity is needed to extract the material. I sometimes take material out and reupload them to the Internet Archive where the website runs an OCR (at least for English or other Latin scripts) to make the text searchable. The Internet Archive does not require any plugins to be installed but it needs JavaScript for the online-reader.

Here are a few tips to getting material from the Digital Library of India.

You need to generate a list of links to the pages for a book. You can easily figure out the format, but for Windows users who do not have the time or ingenuity for it - here is a little utility to help you. In case it does not run, you might need to install the VB runtime which you can get on the Microsoft website. If you see errors about comdlg32.ocx missing, follow instructions here. Now run this application. Right click and copy the link indicate in front of BookReader-1 above (it says "click here" - but do not).

Copy the BookReader-1 link into this and create a list of links into a text file
Now click "Make Download list" to generate a list of links in a text file. You then give this list to a download manager - I use Free Download Manager

Provide the list of downloads to Free Download Manager

Ensure that you download all the files to a directory of your choice. Once you are done downloading the files, which might take time, you can see the TIF image files of each page. You could use any image viewer to go through them and IrfanView is a good option. If you are more savvy, you can convert all the page files into a single PDF or other favourite file format.

If you make a PDF out of it you can upload them to the Internet Archive as I sometimes do. Examples include a translation of the Gajasasthra or a work on the Sanksrit names of Indian birds by Raghuvira. These are little-known pamphlets published on a small scale in India and therefore not easily available. They are what scholars in the western world would call grey literature, but it does not have to be that. The quality of the scans on the site is poor. Indeed the Digital Library of India could well do a good job of scanning material in colour and use more modern loss-less formats like JPEG2000 which allow for streaming at variable levels of detail. According to a 2006 paper describing the project - getting books to scan is hard. Now it makes all the more sense to make a good copy. The project people only need to learn from the incredibly well-done and large scale Biodiversity Heritage Library. The cost of doing all this scanning is ultimately far less than actually trying to acquire printed material in the public libraries across India. If one argues that the site is indeed a library, one could even surmount certain problems with the copyright act. After all libraries are allowed to loan books to their customers without paying extra royalty to the authors. The principle of first sale could then perhaps be applied. Learning about the current amounts spent by government public libraries, the kind of books purchased and the quality of service provided will only serve to pain any citizen with a conscience.

The Digital Library of India is thus an amazing resource but it can easily be run in a way that could be of use. The site could use some expertise on copyrights - a lot of material may not technically be copyright free but it would seem like they are using the principle that orphaned works are ok to copy. Now that is indeed a very good idea but it would be even better if they legitimized it by working with the lawyers who amend the Copyright Laws. The Indian Copyright Law stands in contravention of the spirit of the RTI Act. The RTI Acts says that all information generated by public bodies be made available through the cheapest medium while the Copyright Act happily goes on to state that all Government works will remain copyrighted for 70 years. Personal attempts to point this out to a law-related organization in Bangalore that proposed amendments to the Copyright Act failed and comments on an NIC website seeking feedback on the proposed Copyright Act amendments also reached nowhere. If ever the government can clean up its act (or Acts), it should scan up all the material in its public libraries, state archives and government bodies and put them all in a digital library apart from being a storehouse of born-digital documents and other material produced as it functions. I am sure they can easily work at the same scale as the Internet Archive. Attempts to communicate with even enlightened organizations like the IISc that host the Digitial Library of India seem to be useless. So perhaps we just have to trudge along and make improvements the hard way by fixing things as mere individuals.

Some other digital libraries