On the Artchitecture of Life

December 6, 2014

A conversation on the architecture of life has been recorded and released as an audio podcast at Syntalk.  The speakers are: Dr. Pushpa M. Bhargava (molecular biology, CCMB, Hyderabad), Prof. Nagarjuna G. (philosophy of science, HBCSE, Mumbai).  The following description is the text copied from the Syntalk link.

SynTalk thinks about the key conditions that characterize and create ‘biological’ life while constantly wondering whether life is a random accident, and if we are alone in the universe (because of a singularity?). What is the future of life? How aliens (if any) are also likely to be carbon and water based, but could be completely different morphologically and functionally. How was the first cell formed, and is this one of the biggest open questions today? The continuing journey after the big bang from the physical to astrophysical to chemical to biological to social evolution (across all species via, say, pollination) way into the distant future. The concepts are derived off / from Darwin, Crick, Watson, Hoyle, Prigogine, Manfred Eigen, Delbruck, Maturana, & Stuart Kauffman, among others. Is it possible to create synthetic life in a laboratory, and does the clue to this possibility lie in the (chemical?) nature of a virus? How does speciation happen? The core significance of the cell being a ‘phase separated structure’ with organizational closure. Is the cell the unity of life? How we do ‘not’ really know where biology ends and chemistry begins. Is life a physical state (just as liquid is a state of water)? The definition of life via replication (DNA, tRNA), metabolism (metabolic charts, glucose) and energy transduction. We discuss the role of glucose as a key molecule for all life, and wonder what it is like for glucose (& other bio molecules) to be ‘outside’ life. How does self organization arise in both physical and biological systems, and how (for example) phospholipids (with hydrophobic tails and hydrophilic heads) organize itself in water? How affinities can emerge between two DNA strands. How life is a dialogical state, and neither the physical equilibrium (oxidized state like carbon dioxide) nor the state of chemical death (‘petroleum state’). How virus ‘lives’ on the border of life and non-life. How all living stems can be characterized using unique chemistry, biochemistry, structure, & function. Why life originated from water? What is the role of weak bonds (in, say, the colloidal state of protoplasm)? How does ‘conscious cognition’ arise in living systems, & what are the links with ‘emancipated reflexive motor actions’, microtubules, dance, lizard, play, & consciousness (Mind from Matter). How does a living system talk to itself (why does a child suck its thumb)? How the feeling of ‘free will’ gives an (illusory) advantage. How life has multiple answers, and an inherent capability to change. How life is an expression of abundance. How a bio molecule is not like a sphere. The future with artificial life, cognitive robotics, & ‘languages in nature’ (of animals & languages). Why we can’t wear a full body armour anymore?


metaStudio and loom

February 19, 2013

This is the third post on metaStudio featuring the special features of gnowsys-studio

This post features a space for creating an online threaded discussion forum.  There are a number of threaded discussion forums, and  this one adds to that family of web apps that facilitate communication among a group of people.  Here is a link to one of the threads Leviathan and the air pump, where we use this feature for running a small graduate course.

The loom of gnowsys-studio is designed to do the following things:

  • Create a thread on a broad topic
  • Under each thread create twists.  A twist is a discussion trigger, it can be question, it can be a sub-topic of the thread.  It can be anything about which you want to seek responses from the community. If you use it to understand a topic, clear doubt, ask for help or offer help etc.
  • Under each twist, members can submit replies. 
  • Each respondent can choose a color of their choice for the text as well as the background. This will help to recognize the person’s messages easily in a long discussion thread.
  • The threads and twists can be classified using tags. Users can also rate them. The responses can be rates as well. The average score will be computed based on the ratings.

Thread’s description can be edited collaboratively.  twist can be edited, but messages once posted cannot be edited.  You can delete a message though. Whereever you can edit, the editor we provide is the same.  See the post on orgmode editor.

We have been using loom for discussions for undergraduate and graduate classes. The picture below gives you a glimpse of how a thread constructed in the loom looks like:

Image

While sending the responses you can add a picture, use hyperlinks, write mathematical equations, embed a video, SVG images, animation etc.  Therefore, it can used for a very rich technical dialogue in a community as well. 

We will be extending the loom architecture for comprehensive continuous assessment

 

 


metaStudio for semantic networks and concept maps

February 18, 2013

Image

This is the second post on metaStudio featuring the special features of gnowsys-studio.

The site allows collaborative construction of semantic networks between the wiki pages.  Users can define and use the relations between pages.  The graph produced is published in SVG which allows navigation of the graph by mouse click.  When Control + Click is used the graph reloads on the same page showing the additional nodes in the neighbourhood of the selected node. This way, a merged graph can be created.   Explore more pages at the site.

 


metaStudio, Emacs and orgmode

February 18, 2013

metaStudio, Emacs and orgmode

We have been developing a semantic platform for collaborative construction of knowledge networks of open educational resources.  We have reached some level of stability and so would invite members of the community to visit and explore the site.  The link to the site is: beta.metastudio.org

Here I will keep publishing a series of posts featuring some special features and a link to where the feature can be seen or a screenshot of the feature. In this post we feature a simple online orgmode editor implemented for collaborative editing of text.

Online Emacs Orgmode Editor

The site uses a very simple wiki style text editor that uses orgmode style markup (actually markDown).  The typed text is processed directly by orgmode vida emacs on the server side script.  The orgmode text as well as the automatically exported html are stored in the database.   This editor is limited only by the knowledge of the user about orgmode use and the html export limitations of orgmode.  It can have images, embedded videos, embedded java applets, or just about anything that we need to publish on the web.

The main highlight is the easy of use and very low learning curve.  Students and teachers who have never been exposed to any wiki or web authoring have picked up the editing methods with least training.

metastudio orgmode editor

metastudio orgmode editor

embedding video and orgmode

metastudio embedding video using orgmode


February 17, 2013

gnowgi:

Sameer Verma from SFSU visited Khairat School where we do field work and help the first OLPC project in India. The blog posted by Monsoon Grey.

Originally posted on Monsoon Grey:

M1130003_2

At Khairat near Mumbai, Sameer demonsrates the School Server installation to Rafikh and Sandeep Surve as kids look on.

In January 2013, Sameer Verma from SFSU, during a trip to India, visited Goa – a detour that happened mostly because of Harriet Vidyasagar’s efforts to keep all the working OLPC projects in India visible to the outside world, while simultaneously ensuring that we got the best minds to get a firsthand look at the projects here and to provide us inputs that would enable us to run these projects better. The previous such visit was by Walter Bender himself; this time it was Sameer from San Francisco. I’d been in touch with him over the email requesting very specific help about the School Server setup and administration, and that’s exactly what he and I focused on while he was here in Goa. Of course we had to make time between…

View original 401 more words


February 17, 2013

gnowgi:

A post on a new project of OLPC started in Goa by Monsoon Grey

Originally posted on Monsoon Grey:

Kids are delighted to have the XOs - personalised with their names stuck on them.

Kids are delighted to have the XOs – personalised with their names stuck on them.

The second Sugar-OLPC project in Goa went live today – Feb 5th, 2013 – at Nirmala Kindergarten. The first one at Merces has been running for close to 3 years now. For Nirmala KG, the planning had started a few months ago in August of 2012 (see previous post ‘Second Sugar-OLPC Project in Goa‘). We had visited the school to explore the possibility of doing an OLPC project there. Nirmala Institute of Education (NIE) is our partner for the Sugar-OLPC work that we do here in Goa, as well as the parent institute in whose premises the school is located.

After the initial discussions, we had conducted a Sugar Training Workshop at NIE in November 2012 for the teachers of Nirmala-KG (see post ‘Sugar Training for Nirmala-KG Teachers‘), and decided to…

View original 510 more words


my work in ten hundred words of science

January 24, 2013

I have recently posted what my job is without using any jargon.

http://tenhundredwordsofscience.tumblr.com/post/41307339297/our-job-is-to-help-make-children-learn-and-to

  • Our job is to help make children learn. And to picture what they learn. We make children learn about the world around us. Explain what happens in the world around us. Find out the reasons for each happening around us.

    Children know something. When they learn new things, the old things they know find a friend with the new things. Old ideas join with new ideas. But, the new thing does change the old thing as well. We want to picture this change when children learn. In other words, the form of what children know changes when new things get into their heads. Making the picture of these changes is our job. We want to show this changing picture to the children, so that they get to know what they have learnt. This will help them know what they know. This will help us to know what they know. This will help parents to know what they know.

    We use computers for this work. We make the computers make the pictures for everyone to see the learning. We tell computers how to make pictures, so that computers will tell us when there is a change in what we know.

    We help children work with other children. We work with them as one of us.

    When this becomes possible we will call a party and tell everyone. We are looking for friends who could work with us. Tell everyone of what we are doing. Join us.

    — Nagarjuna. This is to describe the work of http://lab.gnowledge.org/ and its collaborative platform http://beta.metastudio.org/
© 2013 Ten Hundred Words of Science

Interpreting Aaron Swartz’s actions by the media moghuls!

January 22, 2013

After the tragic death of Aaron Swartz, whom I consider a freedom fighter of the digital society, the media reported stories all around the world. Today’s Indian Express (http://www.indianexpress.com/news/in-swartz-s-wake/1062880/0) carried an editorial piece on the subject. The article ends with the following statements:

“It cannot be given away for free, as Swartz would have wanted, since the development of learning is expensive. But business models could be created to widen access while remaining fiscally prudent. ”

The editor is either utterly ignorant of the open access as a way out, or deliberately does not want to bring to the notice of the readers of the alternatives. The editor says “it cannot be given away for free”, but we ask, why not. They all must be given away for free. Scientific communications are not to be owned by anyone other than the citizens, since they have already paid for the development of learning in the form of tax. Looking for an alternate business model or more liberal business model misses the whole point. The scientist’s have foolishly given away their copyright to the Journal publishers. For this act of passing the copyright, no compensation was given to the author or the institution the author was affiliated to. The work was not commissioned or financially supported by the publishers, but mostly by the tax payers money almost anywhere in the world. Why should the citizens pay again for the work they have funded? This is the question to be answered.


cycling in Mumbai

June 23, 2011

I used to commute daily to my office near Anushakti Nagar from my home, TIFR colony at Navy Nagar, Colaba, by local train using the harbour line (from CST to Mankhurd and return). This happened for the last 15 years. One day, on May 2nd 2011, I went to a cycle shop and purchased a hybrid citi cycle (Trek 7100). From that day till today, except when I wasn’t in the city, commuting daily to my office. The track is about 26km or 23km depending on which route I take. I am covering this distance within 1:15min with an average speed of 19km/hour without much effort.

Cycling track TIFR colaba to Homi Bhabha Centre Mankhurd

Cycling track TIFR colaba to Homi Bhabha Centre Mankhurd

The picture is one of the routes I use for my commute.

What I realised from this experience is that Mumbai is a flat city. The change in altitude in my entire stretch of 26km is only 60meters. This makes the city an eminent place to commute by cycles. I did it in the hottest month of May, and also during the rains. Cycling in the rains is certainly less tiring than the humid and hot weather of Mumbai. Having tested my endurance in both the hottest and wettest weathers, I am hoping to continue to the rest of my life cycling.

I will write once in a while my experiences.  Happy cycling!


Have faith in your own reason! Be your own god!! Aham Brahmasmi!!!

April 25, 2011

While the nation is in grief about Sathya Sai Baba’s death, I wondered about his prediction that he would live till 96, and he will determine when he will die.  I would consider him a successful mask to see the truth, a curtain that withheld a large followers  to reason and their ability to see the truth.  All his miracles that made him famous were performed repeatedly by several rationalists around the world.

On this occasion  I cannot but use this space to spread the article written by Sanal Edamaruku here, which landed in my mailbox forwarded by a friend.

India would have been a better place without Sathya Sai Baba

Sanal Edamaruku
President
Indian Rationalist Association & Rationalist International

When Sathya Sai Baba died this morning (24 April 2011) at the age of 85 years, he proved once again that miracles and predictions fail. He had predicted at a public gathering at his head quarters in Puttaparthy, in 2000, and repeatedly many times, that he would die at the age of 96 only. And till the last moment, many of his devotees clung to his word and waited for a miracle. May it be an eye opener for the millions of gullible people whom he misguided and deluded.

De mortuis nihil nisi bene, they say, say nothing but good of the dead. But I think Sathya Sai Baba’s case qualifies for an exception. Too great is the damage that he did to India. His devastating influence on reason and scientific temper caused huge setback to the country. At a time, when scientific progress led to great social and economic leaps and scientific awakening started spreading all over India, Sathya Sai Baba launched a “counter revolution” of superstition, supported by irresponsible politicians and other public figures who should have known better. In my judgment, this is his greatest crime. I have succeeded again and again to expose him publicly as a fraud, so did some other rationalists. But due to his political protectors he was never held responsible for his crimes against public reason. Nor was he ever booked for any other crime he was accused of. Numerous cases of alleged sexual abuse and murder are yet to be investigated, not to mention the financial secrets of his empire.

Sathya Sai Baba insisted in all seriousness that he was god, the creator of the universe, and “proved” his divinity with a couple of small “miracles”. As son of a village tantric he was familiar with the hand sleights and tricks of the trade. However, he did not only fascinate poor and uneducated villagers with his fraudulent performances. Over the years, he managed to attract a galaxy of India’s rich and powerful, among them ministers, prime ministers, presidents, chief justices, top industrialists and superstars.

Sathya Sai Baba had a special modus operandi that was the key for his astonishing success and the root of his enormous clout. Many of his high society devotees came to serve their own vested interests. Some came to rub shoulders with the prominent. Many joined the club because it was working as a powerful syndicate spreading its tentacles all over the political system. It was a way to the top jobs and a way to get things done. Others were seeking financial support or wanted to get rid of ill-gotten black money: The empire, it is alleged, was based on money laundering, using foreign devotees and branches. In fact, the huge foreign donations to Sai Baba stood in contrast to the comparatively modest number of active foreign devotees and the sometimes quite weak foreign branches, some of them residing in private homes. That is no great surprise, when one considers that Sai Baba did not speak any other language than Telugu and traveled only once in his whole life abroad – to visit his friend Idi Amin in Uganda.

On his 80th birthday, Sai Baba’s supporters announced that he would turn from a miracle man to a philanthropist. That was, after I had demonstrated his miracles so often in TV shows that many kids in the streets could imitate them. That he since spent a part of the great fortunes, swindled out of the gullible, for social development around his ancestral village, is highlighted now to present him as a saint. But as useful and welcome hospitals, schools and drinking water projects for the poor always may be: this kind of alibi-philanthropy is well known even from mafia-bosses. It cannot be weighed against his crimes and the damage he has done to the Indian society.

In December 2005, I wrote a letter to then President Dr. Abdul Kalam, one of Sai Baba’s ardent supporters, which was never answered. I demanded criminal investigations against Sai Baba. If his social development projects are meant to be indulgence to nullify his crimes, this procedure is unprecedented and unacceptable, I wrote. It is a shame for India that well-founded accusations and numerous reputed witnesses against Sai Baba are ignored without any investigation. Do saffron clothes make an offender untouchable for the law? Do we have to tolerate that political protectionism raises its head so boldly, mocking India’s democracy?

Sathya Sai Baba caused great damage to India. His irresponsible political patrons corrupted the political culture of India. Encouraged by the clout of Sathya sai Baba, a new clan of miracle mongers imitated him. India would have been a better place without Sathya Sai Baba.

(This or other articles from the  Rationalist International Bulletin may be reproduced by journals, blogs or web sites without change or alteration in its content, and with due acknowledgment.)

Rationalist International: rationalistinternational@gmail.com


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