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Posts Tagged ‘Artificial Life’

I am late with my echo statement on this.

Over the past few days, the internet is abuzz with news of Craig Venter and his team for creating the first fully functional cell, controlled by synthetic DNA and discussions on what might be the ethical consequences of future work in this area.

The fact that this has happened is not surprising at all. Dr Venter has been very open about his work and has been promoting it for some years now.  For instance, a couple of years ago there was a wonderful TED talk in which Venter talks about his team being close to creating synthetic life. The latest news is ofcourse not of synthetic life, but a step closer to that grand aim.

Another Instance : Two years there was a brainstorming session whose transcript was converted by EDGE into a book available for free download too.

Dimitar Sasselov, Max Brockman, Seth Lloyd, George Church, J. Craig Venter, Freeman Dyson, Image Courtesy - EDGE

The BOOK can be downloaded from here.

So from such updates, it did not surprise me much when Venter made the announcement.

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Ethics : There have been frenzied debates on what this might lead us to on the internet, on television and elsewhere. These discussions on ethics appear to me to be inevitable and I find it most appropriate to quote the legendary Freeman Dyson on it.

“Two Hundred years ago, William Blake engraved The Gates of Paradise, a little book of drawings and verses. One of the drawings, with the title “Aged Ignorance”, shows an old man wearing professional eyeglasses and holding a large pair of scissors. In front of him, a winged child running naked in the light from a rising sun. The old man sits with his back to the sun. With a self satisfied smile he opens his scissors and chips the child’s wings. With the picture goes a little poem :

“In Time’s Ocean falled drown’d,
In aged ignorance profound,
Holy and cold, I clip’d the Wings
Of all Sublunary Things.”

This picture is an image of the human condition in the era that is now beginning. The rising sun is biological science, throwing light of every increasing intensity onto the processes by which we live and feel and think. The winged child is human life, becoming for the first time aware of itself and its potentialities in the light of science. The old man is our existing human society, shaped by ages of past ignorance. Our laws, our loyalities, our fears and hatreds, our economic and social injustices, all grew slowly and are deeply rooted in the past. Inevitably the advance of biological knowledge will bring clashes between the old institutions and new desires for human improvement. Old institutions will clip the wings of human desire. Up to a point, caution is justified and social constraints are necessary. The new technologies will be dangerous as well as liberating. But in the long run, social constraints must bend to new realities. Humanity can not live forever with clipped wings. The vision of self-improvement which William Blake and Samuel Gompers in their different ways proclaimed, will not vanish from the Earth.”

(The above is an excerpt from a lecture given by Freeman Dyson at the Hebrew University of Jerusalem in 1995. The lecture was pulished by the New York Review of Books in 1997 and later as a chapter in Scientist as Rebel. )

Artificial Life Beyond the Wet Medium :

Life is a process which can be abstracted away from any particular mediumJohn Von Neumann

Wet Artificial-Life is what is basically synthetic life (in synthetic life you don’t really abstract the life process into another medium, but you digitize it and recreate it instead as per your requirement).

I do believe abstracting and digitizing life from a “wet chemical medium” to a computer is not very far off either i.e. a software that not only would imitate “life” but also synthesize it. And coupled with something like Koza’s Genetic Programming scheme embedded in it, develop something that possesses some intelligence other than producing more useful programs.

Coded Messages :

This is the fun part from the news about Venter and his team’s groundbreaking work. The synthetic DNA of the bacteria has a few messages coded into it.

1. “To live, to err, to fall, to triumph, to create life out of life.” – from James Joyce’s A Portrait of the Artist as a Young Man.

James Joyce is one of my favourite writers*, so I was glad that this was encoded too. But I find it funny that what this quote says can also be the undoing of synthetic life or rather a difficult problem to solve. The biggest enemy of synthetic life is evolution (creating life out of life :), evolution would ensure that control of the synthetic bacteria is lost soon enough. I believe that countering this would be the single biggest challenge in synthetic biology.

*When I tried reading Ulysses, I kept giving up. But had this compulsive need to finish it anyway. I had to join an Orkut community called “Who is afraid of James Joyce” and after some motivation could read it! ;-)

2. What I can not build, I can not understand – Richard P. Feynman

This is what Dr Venter announced, isn’t “What I can not create, I do not understand” the correct version?

Feynman's Blackboard at the time of his death: Copyright - Caltech

3. “See things not as they are, but as they might be” – J. Robert Oppenheimer from American Prometheus

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Recommendations :

1. What is Life – Erwin Schrodinger (PDF)

2. Life – What A Concept! – EDGE (PDF)

3. A Life Decoded : My Genome, My Life – C. J. Venter (Google Books)

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Before I make a start I would want to make it very clear that inspite of what that the title may suggest, this is not a “sensational” post. It is just something that really intrigued me. It basically falls under the domain of image segmentation and pattern recognition, however it is something that can intrigue a person with a non-scientific background with a like (or dislike) for Franz Kafka’s work equally. I keep the title because it is the title of an original work by Dr Vitorino Ramos and hence making changes to it is not a good thing.

Note: For people who are  not interested in technical details can skip those parts and only read the stuff in bold there.

Franz Kafka is one writer whose works have had a profound impact on me in terms that they disturbed me each time I thought about them. No, not because of his writings per se ONLY but for a greater part because i had read a lot on his rather tragic life and i saw a heart breaking reflection in his works of what happened in his life (i see a lot of similarities between Kafka’s life and that of Premchand albeit that Premchand’s work got published in his lifetime mostly, though he got true critical acclaim after his death). Yes i do think that his writings give a good picture of Europe at that time, on human needs and behavior, but the prior reason outweighs all these. Kafka remains one of my favorite writers, though his works are basically short stories. He mostly wrote on a theme that emphasized the alienation of man and the indifferent society. Kafka’s tormenting thoughts on dehumanization, the cruel world, bureaucratic labyrinths which he experienced as being part of the not so liked Jewish minority in Prague, his experiences in jobs he did, his love life and affairs, on a constant fear of mental and physical collapse as a result of clinical depression and the ill health that he suffered from, reflected in a lot of his works. Including in his novella The Metamorphosis.

W. H Auden rightly wrote about Kafka:

“Kafka is important to us because his predicament is the predicament of the modern man”

In metamorphosis the protagonist Gregor Samsa turns into a giant insect when he wakes up one morning. It is kind of apparent that the “transformation” was meant in a metaphorical sense by Kafka and not in a literal one, mostly based on his fears and his own life experiences. The Novella starts like this. . .

As Gregor Samsa awoke one morning from uneasy dreams he found himself transformed in his bed into a monstrous vermin.

While rummaging through a few scientific papers that explored the problem of pattern recognition using a distributed approach i came across a few by Dr Ramos et al, which dealt with the issue using the artificial colonies approach.

In the previous post i had mentioned that the self organization of neurons into a brain like structure and the self organization of an ant colony were similar in more than a few ways. If it may be implemented then it could have implications in pattern recognition problems, where the perceptive abilities emerge from the local and simple interactions of simple agents. Such decentralized systems, a part of the swarm intelligence paradigm look very promising in applying to pattern recognition and the specific case of image segmentation as basically these may be considered a clustering and combinatorial problem taking the image itself as an ant colony habit.

The basis for this post was laid down in the previous post on colony cognitive maps. We observed the evolution of a pheromonal field there and a simple model for the same:

[Evolution of a distribution of (artificial) ants over time: Image Source]

Click to Enlarge

The above is the evolution of the distribution of artificial ants in a square lattice, this work has been extended to digital image lattices by Ramos et al. Image segmentation is an image processing problem wherein the regions of the image under consideration may be partitioned into different regions. Like into areas of low contrast and areas of high contrast, on basis of texture and grey level and so on. Image segmentation is very important as the output of an image segmentation process may be used as an input in object recognition based scenarios. The work of Ramos et al (In references below) and some of the papers cited in his works have really intrigued me and i would strongly suggest readers to have a look at them if at all they are interested in image segmentation, pattern recognition and self organization in general, some might also be interested in implementing something similar too!

In one of the papers a swarm of artificial ants was thrown on a digital habitat (an image of Albert Einstein) to explore it for 1000 iterations. The Einstein image is replaced by a map image. The evolution of the colony cognitive maps for the Einstein image habitat is shown below for various iterations.

[Evolution of a pheromonal field on an Einstein image habitat for t= 0, 1, 100, 110, 120, 130, 150, 200, 300, 400, 500, 800, 900, 1000: Image Source]

The above is represented most aptly in a .gif image.

[Evolution of a pheromonal field on an Einstein habitat: Image Source]

Now instead of Einstein a Kafka image was taken and was subject to the same. Image Source

The Kafka image habitat is replaced by a red ant in the second row. The abstract of the paper by the same name goes as.

Created with an Artificial Ant Colony, that uses images as Habitats, being sensible to their gray levels. At the second row,  Kafka is replaced as a substrate, by Red Ant. In black, the higher levels of pheromone (a chemical evaporative sugar substance used by swarms on their orientation trough out the trails). It’s exactly this artificial evaporation and the computational ant collective group synergy reallocating their upgrades of pheromone at interesting places, that allows for the emergence of adaptation and “perception” of new images. Only some of the 6000 iterations processed are represented. The system does not have any type of hierarchy, and ants communicate only in indirect forms, through out the successive alteration that they found on the Habitat.

Now what intrigues me is that the transition is extremely rapid. Such perceptive ability with change in the image habitat could have massive implications at how we look at pattern recognition for such cases.

Extremely intriguing!

Resources on Franz Kafka:

1. A Brief Biography

2. The Metamorphosis At Project Gutenberg. Click here >>

3. The Kafka Project

References and STRONGLY recommended papers:

1. Artificial Ant Colonies in Digital Image Habitats – A Mass behavior Effect Study on Pattern Recognition. Vitorino Ramos and Filipe Almeida. Click Here >>

2. Social Cognitive Maps, Swarms Collective Perception and Distributed Search on Dynamic Landscapes. Vitorino Ramos, Carlos Fernandes, Agostinho C. Rosa. Click Here >>

3. Self-Regulated Artificial Ant Colonies on Digital Image Habitats. Carlos Fernandes, Vitorino Ramos, Agostinho C. Rosa. Click Here >>

4. On the Implicit and the Artificial – Morphogenesis and Emergent Aesthetics in Autonomous Collective Systems. Vitorino Ramos. Click Here >>

5. A Strange Metamorphosis [Kafka to Red Ant], Vitorino Ramos.

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General Background: Since childhood i have enjoyed sketching and painting, and very much at that! Sometimes i found myself copying an existing image or painting, making small changes here and there in it. Yes, the paintings came out beautiful (or so i think!), but one thing always made me unhappy, i thought that the creativity needed to make original stuff was missing at times (not always). It was not there all the time. It came in bursts and went away.

I agree with Leonel Moura (from his article) that creativity is basically produced due to different experiences and interactions. Absence or lack of which could make art lose novelty.

Talking of novelty, how about looking at art in nature? Richard Dawkins states that the difference between human art or design and the amazingly “ingenious” forms that we encounter in nature, is due tho the fact that Human art originates in the mind , while the natural designs result from natural selection. Which is very true. However it is another matter that natural selection and cultural selection, that will ultimately decide on the “popularity” of an art don’t function in the same way. Anyhow How can we remove the cultural bias or the human bias that we have in our art forms?
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Answers in Artificial Life: Artificial life may be defined as “A field of study devoted to understanding life by attempting to derive general theories underlying biological phenomena, and recreating these dynamics in other physical media – such as computers – making them accessible to new kinds of experimental manipulation and testing. This scientific research links biology and computer science.”
Most of the A-Life simulations today can not be considered truly alive, as they still can not show some properties of truly alive systems and also that they have considerable human bias in design. However there are two views that have existed on the whole idea of Artificial Life and the extent it can go.
Weak A-Life is the idea that the “living process” can not be achieved beyond a chemical domain. Weak A-life researchers concentrate on simulating life processes with an underlying aim to understand the biological processes.
Strong A-Life is exactly the reverse. John Von Neumann once remarked life is a process which can be abstracted away from any particular medium. In recent times Ecologist Tom Ray declared that his computer simulation Tierra was not a simulation of life but a synthesis of life. In Tierra, computer programmes compete for CPU time and access to the main memory. These programs are also evolvable, can replicate, mutate and recombine.
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Relating A-Life to Art: While researching on these ideas and the fact that these could be used to generate the art forms that i talked about in the first paragraph i came across a few papers by Swarm Intelligence Guru Vitorino Ramos and a couple of articles by Leonel Moura who had worked in collaboration with Dr Ramos on precisly this theme.
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Swarm Paintings: Thus the idea as i had mentioned in my very first paragraph is to create an organism ideally with minimum pre-commitment to any representational art scheme or human style or taste. Sounds simple but is not so simple to implement!
There are a number of projects that have dealt with creating art, but these mostly have been evolutionary algorithms that learn from human behavior, and learn about human mannerisms and try to create art according to that. The idea here is to create art with a minimum of human intervention.
I came across a project by Dr Vitorino Ramos to which i had pointed out implicitly in the last paragraph. This project called ARTSBOT (ARTistic Swarm roBOTs) project. This project tries to address this issue of minimizing the human intervention in aesthetics , ethnicity, taste,style etc. In short their idea was to remove or to minimize the anthropocentric bias that pervades all our art forms. Obviously all this can have massive implications in our understanding of the biological processes also, however here we’ll talk of only art.
Two of the first paintings that emerged were:
(Source: Here)
(Source: Here)
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These paintings were among the first swarm paintings by Leonel Moura and Vitorino Ramos. Now we see that these seem detached from a functional human pre-commitment. They don’t seem to represent any emotion or style or taste. However they still look very pleasant!
However the point to be understood and to be noted is that these are NOT random pictures created either by a programme or by a swarm of robots moving “randomly”. These pictures were generated by a horde of artificial ants and also by robots. They are not random, but they EMERGE from a process of pheromone deposition and evaporation as was simulated in this system from ants. Thus the result that we have above is a Colony Cognitive Map. The colony cognitive map is analogous to a cognitive map in the brain. I will cover the idea of a colony cognitive map in the next post.
A couple of more beautiful paintings can be seen below!
(Source for both images : Here>>)
Though i have already mentioned how these art forms emerge, i would still like to quote a paragraph from here:

The painting robots are artificial ‘organisms’ able to create their own art forms. They are equipped with environmental awareness and a small brain that runs algorithms based on simple rules. The resulting paintings are not predetermined, emerging rather from the combined effects of randomness and stigmergy, that is, indirect communication trough the environment.
Although the robots are autonomous they depend on a symbiotic relationship with human partners Not only in terms of starting and ending the procedure, but also and more deeply in the fact that the final configuration of each painting is the result of a certain gestalt fired in the brain of the human viewer. Therefore what we can consider ‘art’ here, is the result of multiple agents, some human, some artificial, immerged in a chaotic process where no one is in control and whose output is impossible to determine.
Hence, a ‘new kind of art’ represents the introduction of the complexity paradigm in the cultural and artistic realm.’

A Painting bot is something like in the picture shown below:

A swarm of robots at work:

The final art generated by the swarm of these robots is beautiful!

(Photo Credit for the three pictures above: Here>>

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Conclusions:

The work of Dr Ramos and Leonel Maura can be summed up as:
1. The human is only the “art-architect”, the “swarm” is the artist.
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2. The “life” of Artificial Life shows characteristics like natural life itself namely Morphogenesis, ability to adapt to changing environments, evolution etc.
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Leonel Moura’s wonderful article states that the final aim is to create an “Artificial Autopoietic System”, intriguing indeed and eagerly awaited!!
Such simulations could change the way we understand the biological processes and life.
Also i am now thinking how could music be produced based on the same or similar ideas. I wonder if Swarm music could be available. It would be most interesting and i can’t wait to listen to it already!
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Have a look at this video by Leonel Moura, having some time lapse footage of robots painting.
References:
1. Ant- Swarm Morphogenese By Leonel Moura
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2. On the Implicit and on the Artificial – Morphogenesis and Emergent Aesthetics in Autonomous Collective Systems, in ARCHITOPIA Book, Art, Architecture and Science, INSTITUT D’ART CONTEMPORAIN, J.L. Maubant et al. (Eds.), pp. 25-57, Chapter 2, Vitorino Ramos.
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3. A Strange Metamorphosis [From Kafka to Red Ant], Vitorino Ramos
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Links:
Follow the following links to follow on more exciting papers and paintings.

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