Archive for the ‘open science’ category

The most important Indian ornithology paper recently written!

2 February 2011

“Which is the most important Indian ornithology paper recently written?”

I was asked this by a young M.Sc. guy recently. I was taken aback because I had never encountered such an intelligent question from a young post-graduate before. But there he was – and they all looked at me for an answer. So, after a little thought, without going through hundreds of articles on Indian natural history that I should have before answering, anyway answered “In my opinion, Taking Indian Ornithology into the Information Age By L. Shyamal.”

 

An image from "Opinion: Taking Indian ornithology into the Information Age"

Now, Shyamal, no matter how militant he may be in his opinions, shuns the limelight and will undoubtedly disagree with me and be displeased by my actions.

At this stage, I will also disclose to you that he is a close friend of some years, a collaborator with me on Wikipedia and that I have met him a number of times.

But that is besides the point. Shyamal, putting it plainly and simply, is both a theorist and practitioner of open science. Read Shyamal’s views on Open science here on this very blog. And the article I have named above.

As far as practicing Open Science is concerned,  he is the single most prolific editor to Wikipedia on Indian natural history and biodiversity. He has an edit count of 34,176 edits to Wikipedia which is quite fantastic. His edit contributions can be found here.   Besides this, to date, Shyamal has donated, improved and uploaded 5200 free images to Wikimedia Commons which can be seen here 250 images at a time..

Shyamal is creative. He uses Inkscape and makes small, simple, easily printed scalable drawings of birds : cheap to print & places them under a free license on Wikimedia Commons. Find svg birds by Shyamal and many others over here. Use them as you wish – even commercially.

 

Free bird svg images by Shyamal

Shyamal spends a lot of time finding obscure details about Indian natural history and adding them to Wikipedia. He finds old material and loads them to http://www.archive.org. He has uploaded a large number of the iconic Newsletter of Birdwatchers of Dodda Gubbi post days on that site.

Shyamal created BirdSpot and provided that data and that dataset under a free license. This was the first common man’s implementation of a GIS in India.

But none of that matters. No matter how good or bad he is, it still wouldn’t matter.

Because, in this paper Shyamal has objectively analysed for us where we are, what needs to be done and what is the way to go ahead. The quality of science displayed in articles and actions of our birding community increases in bits and spurts and then takes a step back in time before returning to its jerky progress. We need to face the demon and berate it soundly. Then alone can we make it cower. And this we can do only if we are brutally honest with ourselves. Shyamal’s paper is honest in this manner. I’m deliberately not commenting more on the paper. It is for you to read and see where both Shyamal and I am coming from.

Now, doling paeans of praise on a friend is no longer politically correct. But faujis are not politicians. We call a spade a spade.

So, don’t believe me, abhor my parochial actions, disdain the personal depths I have probed but read for yourself and see!

 

The Onlooker

Images: All freely licensed. Click image to reach source.

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What is Wikimedia Commons all about?

18 January 2011

Most of us do not know enough about the free resources of the digital world available to us,  such as Wikimedia Commons!  This article, originally written to expound the philosophy of WikiPuneri, a Facebook group of people wanting to make a difference, has been added here for the greater public to read.

…starts…

Before I explain what WikiPuneri group does, I would like to explain in short about Wikimedia Commons. Wikimedia Commons is not an encyclopaedia, it is a media repository. Wikipedia, as you all know, is the free online encyclopaedia which anyone can edit. There are a total of 278 Wikipedias in the world, each in a different language. The English Wikipedia is the largest with 3,528,428 articles. As of now there are twenty wikipedias in Indian languages – including in Hindi, Bengali, Tamil, Malayalam, Marathi, blah, blah and blah. Of these Marathi Wikipedia is the third in size with over 30,000 articles. In addition there are twenty more wikipedias in other Indian languages in the process of being developed.

Now why I have mentioned this is because all of these use photographs, video clips and sound files. Now, it is a waste of space for each Wikipedia to load its images exclusively for itself. Hence the Wikimedia Foundation has created another project called as Wikimedia Commons or in short just Commons. Commons is the media repository. All photos, video clips and sound files are uploaded here just once and they immediately become available to all wikipedias.

The number of images on Wikimedia Commons about an important subject say Pune city is important. That is because all the images on Commons are free. When I say free, I mean free as in free speech as well as in free beer. You are free to use them as you wish, even commercially, as long as you attribute whose image you have used and as long as you make the material available under a free license. These images on Commons are placed under one of a variety of licenses that give you these rights and permissions – this kind of license is called a free license, which allows you to use the images as you wish, as long as you attribute and give free license to people to use your work in turn. The most common free license used around the world is the Creative Commons Attribution Sharealike license.

The full text of Creative Commons Attribution-ShareAlike 3.0 Unported License is given here.

But to explain it here is a more easily understood diagrammatic version of the same below :

 

The crux of the Creative Commons 3.0 Unported License

Why? Why this talk about free licenses?

Because images are usually copyrighted with all rights reserved by the creator. Because a person who is going to break the law and steal or illegally use your image will not bother about whether image is copyrighted or free to use. But the law abiding person can neither use a copyrighted image whose creator has kept all rights for himself without breaking the law nor can he afford it.

Usually you have to pay a fee ranging from a hundred to tens of thousands of rupees to use a photograph commercially per image. Poor people cant afford that, even if the cause is noble or good for society. Many people agree to permit use of their photos free for a good cause, but it is difficult or sometimes impossible to contact people who have good images on Flickr, Picassa or web ste. So a repository of free images is required. Wikimedia Commons is exactly that – it not only stores images for Wikipedias but also makes them available for everyone in society to use, even commercially.

Imagine a person, Mr Patil, who has knowledge which he wants to share with the world. Suppose he wants to write a very economically priced book on Butterflies Of Maharashtra in Marathi for all the children of Maharashtra to read. To illustrate it he will need over three hundred images. If he buys the images, the book will be extremely costly and not free or cheap. But he can take the images from Commons and use them to illustrate his book. He will have to do only two things – acknowledge the person whose photos he has used and publish it not under copyright with all rights reserved but with free Creative Commons license I mentioned to you. Mr Patil can use these images, print the book cheaply and even make a small honest profit.

The free license allows people to use Mr Patil’s book in a constructive manner. They can make derivatives. A biology teacher takes material from his book and makes a chart of common butterflies for display in class rooms. He acknowledges at the bottom of the chart that the information is taken from Patil’s book, mentions the authors of images used and publishes the chart under a free lisense. Another person thinks that the book and chart are valuable educational resources and translates it into English, Hindi, and other Indian Languages. The free license permits them to do so. And so on. The information and images get re-used freely, the contributions of all people are acknowledged and same freedoms are passed on by means of the license.

In such a context, it is important that enough free images are available on Commons to empower our people. If you check Wikimedia Commons today, you will find very few images of Pune. For example, there are more than 500 historial places such as temples, wadas, buidings etc in Pune city alone but only five such places are covered in Commons. There are images of front gate of Shaniwarwada but none of the many wonders inside.

So some photographers of Pune have decided to remedy this by starting a programme to add images of historical monuments of our city onto Commons. We have formed a group of like-minded people on Facebook and Flickr who are keen to further this noble cause to help society. We call this group “WikiPuneri”. We have already started with our first focus being Shaniwarwada the landmark symbol of Pune city which we photographed last Sunday. In coming weeks we will add many more images of Pune and Maharashtra so that hopefully by the time Wikipedia becomes 11 years of age, all of Pune’s monuments are photographed.

 

One of the images uploaded. - the Shaniwarwada gate - (Image:Ashok Bagade)

The other thing we will do is that we will ensure that both Marathi and English Wikipedias have articles on all these monuments and landmarks. In this way, our exposure of our beloved Pune will increase. People can get all the important information about Pune that they need from Wikipedia and images from Wikimedia Commons.

On the function on 15th January 2011, as a symbolic gesture, we will be have uploadinged in front of everyone for the first time an image which we have taken and contributed to Wikimedia Commons. Hopefully that will be followed by many, many more!

…ends…

THIS TEXT LICENSED UNDER CREATIVE COMMONS 3.0 UNPORTED (See link in main article)

On why FOSS is vital for science…

26 November 2009

From this article on Journal on Science and World Affairs, Vol. 3, No. 1, 2007

An Africa institution of higher learning has ‘got’ FOSS exactly right. Any hope for Indian centres of learning?

So why is open source software so vital for science? In the introduction to Voices from the Open Source Revolution, Chris DiBona, Sam Ockman, and Mark Stone point out:

Science is ultimately an Open Source enterprise.

The scientific method rests on a process of discovery, and a process of justification. or scientific results to be justified, they must be replicable. Replication is not possible unless the source is shared: the hypothesis, the test conditions, and the results. The process of discovery can follow many paths, and at times scientific discoveries do occur in isolation.

But ultimately the process of discovery must be served by sharing information: enabling other scientists to go forward where one cannot; pollinating the ideas of others so that something new may grow that otherwise would not have been born .

Where scientists talk of replication, Open Source programmers talk of debugging.

Where scientists talk of discovering, Open Source programmers talk of creating.

Ultimately, the Open Source movement is an extension of the scientific method, because at the heart of the computer industry lies computer science.

This shared method benefits both the industrial and scientific communities. Science gains a ready platform for distributing its ideas, and industry gains a wellspring of freely available ideas and innovations from which to construct new products and services. Ultimately, the free availability of information will help Africa to become competitive in the global economy, as well as turn the focus of technological innovation towards the real problems of the continent.


The only reasons I can think why Indian institutions aren’t already doing something like this en masse, in what appears to be a no-brainer as far as the nation’s best interests are concerned, are mediocrity, ignorance, carelessness, incompetence, laziness and greed!

Read more about this issue on this blog here:

Image credits – Tux (authors Larry Ewing, Simon Budig and Anja Gerwinski) & Gnu (Aurelio A. Heckert) from Wikimedia Commons. Free Software Foundation’s ‘join us’ tag from their web site, under fair use!

Freedom? Still awaited!

15 August 2009

Yesterday we celebrated the freedom of our nation. That was freedom  from dominion by an alien race. We wanted to be free – to prosper, to further ourselves, to contribute to our nations and mankind, to become better people.

the first stamp of independent India, released on 21 Nov 1947

The first stamp of independent India, released on 21 Nov 1947

We did not become free to serve new overlords – in any field, whether it was public life or in private life; definitely not in our love for learning, discovery and engagement with the world around us. In 62 years, more than a lifetime for many of us, we continue to be restrained. Simple things like Knowledge, which should be free, continue to elude us; nay to be denied us by artificial constructs such as copyright, by bureaucracies, by small, selfish people who are blind to the larger picture, the enormous latent possibilities in the hearts and minds of the common Indians and who do not consider the common man to be a stakeholder in anything which affects him.

“Satyameva jayate”

may be interpreted as

“The truth shall set you free.”

So on this day, I celebrate freedom. Free practices, free knowledge, free thinking.

I have placed this blog under free licenses explicitly.

The content on this blog is free!

Free to be used by you, quoted, modified, transformed and even used commercially.

But with the proviso that the freedom which I give you has to be passed on to your stakeholders and you cannot take that freedom away as they can’t  in their turn. And my copyright (or more accurately, my copyleft) needs to be acknowledged by attribution.

Wikipedia - free content in the real world!

Wikipedia - free content in the real world!

The exact terms can be seen from the links on the two licenses (take your pick of one) in the license widget in the right panel on the blog main page.

This blog already has an impassioned plea for Open science by Shyamal.

‘Open science’ is actually a weasel word, mistakenly used by me to title his op-ed; he had not given one to his piece.

We actually need ‘Free science’.

Just as Free software is a more powerful concept than Open source software, so is ‘Free Science’ more ‘free’ than ‘Open Science’.

Richard Stallman - The Prophet for Freedom in content!

Richard Stallman - The Prophet for Freedom in content!

“Value your freedom or you will lose it, teaches history. “Don’t bother us with politics,” respond those who don’t want to learn.”

Richard Stallman, circa 2000.

Just as open source is a compromise between the commercial world of big business and the FLOSS community, ‘Open Science’ envisages an avatar of traditional science where you and I are valued stakeholders.

But my wish is the same that Capt Vikram Batra, Param Vir Chakra (posthumous) paraphrased after the capture of  Pt 5140 p –

Yeh dil mange more!

Yeh dil mange more!

Science should not be just ‘open’ but also should be ‘free’

It should be free to all stakeholders to better their lives and their heritage. Clean green technology freely available to all for saving our planet. Technology to better our lives also free, if not to all concerned, but definitely to those who can’t feed their bellies every day. Science free from the top to the bottom – from academia to the hoi-polloi, from the technocrat to the consumer, from the practioner to the enthusiast.

Maybe, its a pipe dream, but I wish…..

If you find this rant mis-placed in the context of India’s freedom, I allow Stallman to reply for me once again. Only replace the word ‘software’ with the word ‘science’…

“It’s clear that other problems such as religious fundamentalism, overpopulation, damage to the environment, and the domination of business over government, science, thought, and society, are much bigger than non-free software. But many other people are already working on them, and I don’t have any great aptitude or ideas for how to address them. So it seems best for me to keep working on the issue of free software. Besides, free software does counter one aspect of business domination of society.”

—–

God bless all who gave their tomorrow for our today!

Credits – Wikipedia, Wiktionary, Wikiquote.

Open science! by L. Shyamal

9 August 2009

Introduction to today’s Guest Opinion Piece

The primary problem Indian naturalists face is lack of access to suitable information and knowledge about their own biodiversity.

Very often, this knowledge exists but is locked up in the minds and notes of experts. The common man is denied access to the fruits of  research, very often most of which has been funded by public money. Among the many inequalities in India, a de facto caste  system separates those involved in science from those interested in science.

Since this blog has by its licensing voted clearly and categorically for open science, I had the privilege of requesting Shyamal, a practitioner of making science open and accessible to all, to comment on this. Being a friend, he has obliged.

Open science!

by

L.Shyamal

Ashwin asked me to write about my rationale in contributing to science articles on Wikipedia and with some reluctance I have decided to try and articulate some of my reasons and it turns out that the linking ideas are more tortuous than I had first imagined.

Trying to think about how one acts requires an “out of one’s mind” experience! Probably the reason for the craziness of philosophers and the unreadability of their writings.

Bruno Latour

Bruno Latour

In the genre of unreadable French philosophy  are ideas from a French scholar named Bruno Latour, whose obfuscated writings have even prompted academic practical jokes (see Sokal affair), but some secondary interpretations of whose work are enlightening. Latour is a philosopher who has looked at science critically, a discipline that many would imagine is well-defined and not in need of any further thought.

Having been on several Indian campuses that ostensibly deal with science, I have often wondered if there was something completely faulty in the foundations.

India is perhaps unique in having a constitution that prescribes a “scientifc temper” as the duty of every citizen. This is dangerous country to tread on, especially when one does not have the required “clout”, academic or otherwise and even more so when most professional Indian scientists lead double lives, with even biologists (who in some other countries top in atheism) holding strong religious views, believing in miracles and praying that their papers get published. It would seem as if religious hierarchies are reflected in the hierarchies of science.

Indeed, questioning scientists is often made to look like blasphemy. When a scientist/ex-president touts the idea of linking rivers, it has be a “scientifically sound” idea right? Wrong, scientific ideas are always open to question and the scientific legitimacy/authority of an idea does not automatically transfer to all ideas produced by the same person.

Linus Pauling, one of the rare individuals to have received two Nobel prizes, had ideas on prolonging life that are today considered cranky. It is worth examining some ideas on science and breaking some myths. Latour suggests that real progress in science can only be made by breaking hierarchies and boundaries.

Thor Heyerdahl on 'borders'

Thor Heyerdahl on 'boundaries'..

Samuel Johnson - oet, essayist, moralist, novelist, literary critic, biographer, editor and lexicographer...

Samuel Johnson - poet, essayist, moralist, biographer, editor and lexicographer...

A famous quotation by Samuel Johnson, best known for his pioneering work in creating a dictionary of the English language, says –

“Knowledge is of two kinds. We know a subject ourselves, or we know where we can find information upon it. When we enquire into any subject, the first thing we have to do is to know what books have treated of it. This leads us to look at catalogues, and at the backs of books in libraries”.

While Isaac Newton said (supposedly during one of his rare moments of modesty, but also disputed by some scholars who claimed he was mocking Hooke) that

“If I have seen further it is by standing on ye shoulders of Giants”

Latour essentially clubs the ideas in these two quotes into what he terms as black-boxes, ideas that are used as founding principles to develop other ideas and the networks of links between ideas and their authors. He suggests that scientists gain legitimacy in their writings in journals by providing these linking ideas by citing other sources and stating in effect that-

“if you find me wrong, you are probably finding something wrong in all these others that I quote”.

This kind of legitimacy gain by garnering support is seen in many areas of scientific research. In others, one needs merely to be be descriptive, placing the facts and assuring the reader that the way the facts were gathered is “verifiable” and “repeatable“. Verifiability and repeatability are key to making scientific facts what they are.

Suppose, one heard that “Cherrapunji has the highest rainfall in India” – how does one determine if it was correct ? To determine if that claim was correct, one would actually have to measure rainfall in a uniform way in all parts of the country, but we do not measure the rainfall at every point and secondly we do not know if the man who makes the measurement in Cherrapunji is actually doing it right. (If I remember right, Alexander Frater found the local government guest-house cook in charge of taking the rain measurements and noted that he used used kitchen utensils to transfer water from the rain gauge into a measuring cylinder).

And yet despite the lack of “accuracy” it seems like the readings are “verifiable” in that if one took the water out of the rain gauge and poured it into a measuring cylinder onself, it would probably be the same as what our “cook” produces.

To a large extent, a lot of research data that is “verifiable” or “repeatable” is not actually verified or repeated as it is beyond the needs or means of most.

Now our governments tell us that they spent X million on developing Y which is supposedly good for all the people concerned. All of a sudden we have the Right to Information Act and we expect our government to tell us how they are spending the X million. None of this information is probably “verifiable” but the provision of that information gives us some “faith” in the path taken.

Scientific research takes the same route. Bruno Latour takes a huge step and brings in the thesis that politics and science are indistinguishable and suggests that there is convergent path. A guiding implicit principle in both politics and science is an inherent “equality” in the abilities of individuals.

What does any of this mean for people who are interested in biodiversity?

Most of us look at our natural world, but as “non-experts” we take it for granted that

(1) “experts” know everything

or

(2) as a “non-expert” one cannot contribute much to “expert” knowledge.

There are the fortunate few who are in a good position, for instance, to identify species based on their experience, access to collections, literature and other knowledgeable people. Some of these people have made that knowledge more widely accessible by digesting it into guide books. Field guides and other such literature enable further knowledge gathering by recruiting new observers who aid in refining information on distribution, knowledge on life-history and so on.

This kind of “democratization” of knowledge however can be seen by some “professionals” as undermining their expertise or monopoly.

Knowledge monopolies have been and will continue to be destroyed; Google Earth lets me find my way around, search for addresses of shops. At one level, there is nothing new in Google Earth, the underlying data is merely held locked up by the Survey of India, ISRO and the local telephone directories. Put them all together, make it cheaply accessible, leaving people to help themselves and the results are incredible.

Governments on the other hand are not even able to share information between their departments, a recent road underpass construction in Bangalore which was supposed to be done in a record 48 hours ended up taking two months because nobody could warn the roads departments of the water pipes and telephone wires that stood in their way!

While Governments often complain of the ways that such information can be misused, museum experts tend to point out that the lay public are unqualified to use knowledge.

This kind of circular reasoning has helped knowledge hierarchies sustain themselves and it seems that the flattening trend that has been introduced by Internet based ideas such as Google Earth, Wikipedia and The Internet Archive will have increasingly greater effects on the daily life of individuals and if Governments allow it, greater efficiency in governance.

Someone recently posted a photograph of a moth from Texas and based on a minimal education in entomology and access to information on websites I was able to identify it to down to the species level,   something that one simply cannot do for an Indian species because our experts (Where are they? Where does one find one?) probably expect formal letters requesting identification or perhaps even payments.

A lack of pro-activeness, plain laziness or wilful refusal to divulge information? Hard to tell, but “good science” is not just about a publication record but about making the path to knowledge more accessible and open to all and nothing is gained by obfuscating the path or by sanctimonious claims to knowledge that has been “revealed” to a select few.

Indeed it is hard to understand why the Zoological Survey of India, the Botanical Survey of India, and the Bombay Natural History Society, all of which receive public funds from the Ministry of Environment and Forests should not scan and make its library and specimen collections publicly available. In the meantime, as individuals, one can do their bit by sharing their daily learning and adding a drop of knowledge into the ocean.

Last week I happened on a beautiful and common cockroach. My one-time advisor Professor C A Viraktamath kindly identified it as a ”Therea petiveriana” and a little bit of browsing allowed me to put together whatever little appeared to be known about it on

http://en.wikipedia.org/wiki/Therea_petiveriana

Now you should not trust any bit of information on that page, but the bits of information on that page can be followed up to the original sources and maybe some of the information that has been published in the cited journals will be found to be incorrect. These corrections should be published in a suitable journal and that Wikipedia page should then be corrected by providing a citation to the newly published research.

That to me is the process of making science visible.

Are Indian scientists interested?

Further Reading

* Pearson, D. L. and J. A. Shetterly. 2006. How do published field guides influence interactions between amateurs and professionals in entomology? American Entomologist 52: 246-2.

* Pearson, D. L. and Cassola, Fabio. 2007. Are we doomed to repeat history? A model of the past using tiger beetles (Coleoptera: Cicindelidae) and conservation biology to anticipate the future.
Journal of Insect Conservation, Volume 11, Number 1 / March, 2007  (Copy available on request from the butterflydiaries).

* Kristine  L. Callis, Lindsey R. Christ, Julian Resasco, David W. Armitage, Jeremy D. Ash,  Timothy T. Caughlin, Sharon F. Clemmensen, Stella M. Copeland, Timothy J.  Fullman, Ryan L. Lynch, Charley Olson, Raya A. Pruner, Ernane H.M.  Vieira-Neto, Raneve West-Singh, Emilio M. Bruna (2009) Improving  Wikipedia: educational opportunity and professional responsibility. Trends  in Ecology & Evolution 24(4):177-179.

* http://www.csicop.org/circumnavigations/rockets/

* http://www.worldviewsofscientists.org/IndiaReport.pdf

* http://www.outlookindia.com/article.aspx?237780

* http://amasci.com/weird/sciattid.html

The End

Walk the talk! Some of the images Shyamal made for use freely by anyone! (Free license - CC SA 3.0 ).

Walk the talk! Some of the images by Shyamal made for use freely by anyone! (Free license - CC SA 3.0 ).

Find a list of images already made and to be  made by Shyamal here. His contributions to Wikipedia? Here!