Saturday, June 11, 2005
This Day:

The fundamental carrier of life on Earth is a Cell. Cells are the structural and functional unit of all living organisms. The organisms range from single celled bacteria, to trillions of cells in large animals such as whales (humans consist of about 50 trillion cells, give or take a few billion ;)). Therefore, any new technique that enables us to understand how individual cells behave, or how they interact with their neighbors or the surroundings, has a lot of practical applications.
Now scientists at the University of Chicago and Argonne National Laboratory have constructed a computer simulation that allows them to study the relationship between biochemical fluctuations within a single cell and the cell's behavior as it interacts with other cells and its environment.

Simulation (Courtesy: University of Chicago)
The simulation is called AgentCell. It is a model based on agents, which are semi-autonomous program modules that interact with other agents. For example, in a bacterial study, there will be hundreds of bacteria modeled, with each having it own chemotaxis network (phenomenon in which cells direct their movements according to certain chemicals in their environment), motors and flagella. If the cell behavior could be accurately modeled at the chemical level, then the aggregate network can be used to simulate large collections of cells, including bacterial swamps, diseases, and even population growths. Not surprisingly, this technique has possible applications in cancer research, drug development and combating bioterrorism.
A major goal in single-cell biology today is to document the connection between internal biochemical fluctuations and cellular behavior. AgentCell should be able to help in this research. It has already simulated some actual bacterial behavior: for example, In the bacteria E. Coli, one type of protein controlled the sensitivity of its chemotaxis system, which helps the bacteria find food. In the simulation, when the level of that protein was changed, it would change the sensitivity of the cell. The actual real-life cell behaved exactly in the same way:):).
The end goal of this research is focussed on solving problems involving bio-terrorism and disease spread. But another interesting by-product could be understanding how macro-processes (such as life) evolve from micro-processes (such as chemistry and fluid/energy transport systems):):).

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6 Comments:

At June 13, 2005 7:16 PM, Blogger Sray said...
Hmmm... it is possible! But the goal of this project is to simulate small sets of cells to start with. Perhaps then will treat a clump of cells as a single unit (at least at the first approximation), and proceed from there.
 
At June 14, 2005 9:08 PM, Blogger Unknown said...
Hmmmm. Now I wonder what is life! If life is just a lump of chemicals reacting in a particular sequence.... these digital bacteria, that behave according to sequences of electronic signals.... are also living!
 
At June 14, 2005 10:29 PM, Blogger Sray said...
I am inclined to say that anything that can be simulated programmatically (hence is deterministic) is not life. After all, if it is deterministic, then it is nothing but an automaton.
 
At June 17, 2005 9:44 PM, Blogger Unknown said...
That's an interesting view.... A world similar to ours should be uncertain(in the quantum mechanical sense).
 
At June 20, 2005 6:55 AM, Blogger Sray said...
But non-determinism can arise from deterministic components, e.g. weather, turbulence etc.. so perhaps it is not that impossible after all!
 
At October 01, 2005 4:36 PM, Blogger UpNDown said...
Hi, what a great page! Really enjoyed it, keep up the great work!
how to make spy gadget
 

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Friday, June 10, 2005
This Day:

Genes control the growth and development of our body. From the conception till death, the genes encode and regulate protein development, and also make sure that a eye grows in the eye socket and not a nose:)). There is considerable interest in the medical community about how the genes manage to make sure that the body develops as it does, since technically, all the cells in our body carry the same genetic material. It is the way the genes switch on and off that gives our body the final shape and form.

Fruit Fly compound eye, and its micrograph image (Courtesy: Wash. University)
One interesting find is how physics influences the growth of organs. For example, the laws of physics combine with the mutual attraction of two proteins to create the honeycomb pattern of fruit fly eyes, say molecular biologists at Washington University School of Medicine in St. Louis. This same combination of forces forms the delicate filtering structures of the mammalian kidney.
The findings are reported in the June issue of Developmental Cell, and provides a new understanding of how individual cells find their niche during organ developments. This means that the fruit fly eye can serve as a model for similar complex organs in higher animals.
Just as molecules of oil floating in water will gather together to exclude water molecules, cells with "sticky" molecules on their surface will gather together in clumps to exclude "non-sticky" cells during organ development. This property of cell adhesion has been previously proposed as a key to moving different cell types into the right positions as developing organs change from an immature, disorganized state to a mature, functional state.
Interestingly, the proteins that govern the growth of fruit fly eyes, are similar to those that contribute in the growth of mammalian kidneys! According to Professor Ross Cagan, The evolution of these similar proteins in two very distantly related groups of organisms and for these similar purposes suggests that the two systems, the developing kidney and the developing fly eye, used these proteins to solve the same problem—the problem of how to build intricate, fine-structured, tissues from a loose collection of cells:):).

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8 Comments:

At June 11, 2005 10:07 PM, Blogger Unknown said...
Wow! Now thats something!
 
At June 11, 2005 10:07 PM, Blogger Unknown said...
And yea! I'm back to the blogosphere
 
At June 11, 2005 10:40 PM, Blogger Sray said...
Welcome back! I was wondering what happened to you all of a sudden :).
 
At June 12, 2005 5:23 PM, Blogger Sray said...
Yes and no. This will help us understand how our kidneys and other complicated organs are easily formed from a very small set of genes. One fundamental aspect of physical laws is that systems tend to minimize the total energy as they evolve. So a droplet of water is always spherical, as that is the minimum energy structure. Once we understand how physical laws affect the growth of organs, we might be able to use them to grow artificial organs. Then we might be able to control aging as well, as aging might be the body trying to gracefully get rid of old cells, and thus minimizing the energy required to keep up the maintenance.
 
At June 14, 2005 9:13 PM, Blogger Unknown said...
Hmmmm..... So.... we are not entirely controlled by our genes..... that means, clones shouldnt be alike!
 
At June 14, 2005 10:30 PM, Blogger Sray said...
Clones are never alike :)). There are differences that accumulate when the brain develops, similar to why clones do not have same fingerprints!
 
At June 15, 2005 7:15 AM, Blogger Wayne Smallman said...
It's interesting to note that in a lot of instances, there's simply no background intelligence behind the design of things.

In this case, simple dumb mechanical principles are the mechanism...
 
At June 15, 2005 7:28 AM, Blogger Sray said...
Trial and error... thats the key in evolution...
 

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Thursday, June 09, 2005
This Day:

Hominids are the members of the biological family Hominidae (the great apes), which includes the extant species of humans, chimpanzees, gorillas, and orangutans, as well as many extinct species. Very close members of the human subfamily, which would include Australopithecus (4.2 million years ago), Homo Habilis (2 - 1.5 million years ago), Home Erectus (1.2 - 0.5 million years ago) etc., are classified as Homininae.
Among these, the Homo Erectus lived in Asia and Europe, had a brain 74% as large as ours, and were on average 1.79m (5 feet, 10 inches) tall. Recent discoveries by a team of archaeologists indicate that the coast of the Caspian Sea in Mazandaran Province, Iran was home to the earliest such hominid habitation in that region:):).

Hominid skull (Courtesy: Wikipedia)
Archaeologist Ali Mahforuzi said on Wednesday that 400,000-year-old stone tools discovered in the valleys of Shuresh near the Rostam Kola, Huto, and Kamarband caves are the oldest ever found in the area. Previous studies had indicated a human presence from about 50,000 years ago.
The studies were conducted by a joint team of archaeologists from the Mazandaran Cultural Heritage and Tourism Department and archaeologists from the Mazandaran National Museum. The stone tools that were discovered were firmly dated to about 400,000 years old by Professor Marcel Otte of the University of Liege in Belgium.
More studies are currently being planned and conducted to find more about these ancient people:).

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7 Comments:

At June 11, 2005 4:26 AM, Blogger LEMNA said...
You seem to have a great interest to the apes family:D:DMy deareee friend,y i cann see ur first page at it is???
 
At June 11, 2005 4:27 AM, Blogger LEMNA said...
This wasnn meeee:D:D:D
 
At June 11, 2005 4:28 AM, Blogger LEMNA said...
Good news i had,wake uppp...Tagh toogh tagh tooooogh not Tip toe Tip toe... this time:D:D
 
At June 11, 2005 4:32 AM, Blogger LEMNA said...
By the way havenn they arrived at a clear inf about our beginnin'??:D
 
At June 11, 2005 6:56 AM, Blogger Sray said...
Oyeee!!! You know my face... dont you see a similarity with the apes?! :D:D:D:D... I got your good newss... but I wasnt sure :).
 
At June 11, 2005 6:57 AM, Blogger Sray said...
Many small details about our beginnings are still in question... especially about how some cousins of ours lived, and why and how they got extinct (e.g. Neanderthals, Homo Erectus, etc.) :). The broad picture is quite clear.. the details are still being worked out.

By the way, this current find in Mazandaran must be one of your ancestors :D:D:D... as it is in Iran :)).
 
At June 12, 2005 5:25 PM, Blogger Sray said...
Really nice, isnt it? But we see tool-use among non-human primates today, e.g. chimps and bonobos. These primates are thinking beings too, for example, if you read about Kanzi the Bonobo, or Koko the gorilla, you will find that they have a mind of their own, they can communicate with us humans, and have emotions and feelings too. It is just that it is sometimes hard for us to understand their language, and very few of us take the effort to try to understand.
 

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Wednesday, June 08, 2005
This Day:

The electronic revolution started with the invention of the Vacuum Tubes in the late 1800s. Soon, the inventions of Tesla, Marconi, Hertz and others, ushered in a revolution. Long distance communication through radio waves became a reality, and we were launched into the modern age. The pace of progress has only accelerated ever since, and with the invention of the (solid-state) transistor (semi-conductor based device which replaced the tube-based valves) by Shockley, Bardeen and Brattain around 1950, we step into the world of micro-electronics:):). Since then, the ubiquitous transistor has shrunk to a few microns inside a modern microprocessor chip.

Single Molecule Transistor (Courtesy: National Research Council, Canada)
However, to keep pace with our insatiable requirements for faster and smaller processors, the size of the transistor must be reduced further. It seems that scientists from University of Liverpool may have finally achieved the ultimate goal: creation of a molecular transistor:):).
Dr. Werner Hofer, from the University's Surface Science Research Centre, is one of an international team of scientists who have created a prototype that demonstrates a single charged atom on a silicon surface can regulate the conductivity of a nearby molecule. Computers and other technology based on this concept would require much less energy to power, would produce much less heat, and run much faster.
The team tested the transistor potential of a molecule by using the electrostatic field emanating from a single atom to regulate the conductivity of a molecule, allowing an electric current to flow through the molecule.
Modern transistors are a few microns (1/1000th of a millimeter) in size. In contrast, the molecular transistor are a 1000 fold smaller (1/1000th of a micron), and if it is possible to integrate millions of such transistors on a chip, it should usher in a nano-electronic revolution. From Desktop, to Laptop, to Palmtop, we might have ThumbTop and PinheadTop computers in this century:D:D.

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4 Comments:

At June 09, 2005 2:12 PM, Blogger Sray said...
That is always the problem. But hopefully, we will also have some really good anti-spy gadgets:):).
 
At June 10, 2005 8:00 AM, Blogger Sray said...
Dear Lucretia, you are welcome any time :). But I must say this, I am missing your wonderful blog.. hope you start one again :):).
 
At June 11, 2005 10:02 PM, Blogger Unknown said...
Thumbtop??? Where do I give the input? Where do i see the output? (Palms are disgustingly small enough)
 
At June 11, 2005 10:42 PM, Blogger Sray said...
Well, by the time we have thumbtops, we should have a) Projectable monitors/views/keyboards, b) True Voice recognition softwares, c) Sub-compact solar-cells :).
 

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Tuesday, June 07, 2005
This Day:

In physics, acceleration is defined as the rate of change of velocity (or speed). For example, if we drop a ball from our hand, it has an acceleration of about 9.81m/s2 (also known as 1-g), which means it will have a speed of 9.81 m/s after the first second, 2x9.81=19.62 m/s after two seconds, and so on. We humans can endure accelerations of upto 5-10g.

Z Machine (Courtesy: LiveScience)
Scientists at the Sandia National Labs in Albuquerque, New Mexico have accelerated a small plate from zero to 76,000 mph (34 km per second) in less than a second, which is equivalent to 1010g!! In contrast, the Earth travels at a speed of 30 km per second around the Sun. This is 50 times faster than the fastest bullet, and 10 times faster than the International Space Station:):).
The ultra-tiny aluminum plates are just 850 microns (1 micron = 1/1000th of a millimeter) thick. Z’s hurled plates strike a target after traveling only five millimeters, or less than a quarter-inch. The impact generates a shock wave - in some cases, reaching 15 million times atmospheric pressure - that passes through the target material. The waves are so powerful that they turn solids into liquids, liquids into gases, and gases into plasmas in the same way that heat melts ice to water or boils water into steam.
One purpose of these very rapid flights is to help understand the extreme conditions found within the interiors of giant planets in our solar system. By creating states of matter extremely difficult to achieve on Earth, the flyer plates provide hard data to astrophysicists speculating on the structure and even the formation of planets like Jupiter and Saturn.
Later this year and next, more experiments are planned, that will push towards higher and higher velocities:):).

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6 Comments:

At June 08, 2005 4:39 AM, Blogger Wayne Smallman said...
I've always been fascinated with science, but my main fascination is that of the planets and the stars.

Specifically, what conditions are they expecting to see inside the likes of Saturn and Jupiter? Two planets that are vastly different.

It's been my understanding that the core of Jupiter is a seething sphere of hydrogen that has been put under such enormous pressures that it's been turned into a metal...
 
At June 08, 2005 7:07 AM, Blogger The Lil fairy & her angel friends said...
wats teh pik about:S didnt get it
 
At June 08, 2005 7:45 PM, Blogger Sray said...
Wayne: The core of Jupiter is a hydrogen metal, possibly surrounding a (very small) rocky core. Saturn is similar. Scientists are trying to simulate the pressures that exist inside these planets; more specifically, the impact of shock waves that ripple through their bodies. By simulating similar conditions (even for a brief microsecond) on Earth, they should be able to estimate the composition of the interior of these planets, and from that, clues to the creation of the Solar System might be found.
 
At June 08, 2005 7:49 PM, Blogger Sray said...
Unaiza, the Z machine implodes a small amount of ionized gas, and makes it travel millions of miles per hour. It is this gas that then punches the plate in my post to such high accelerations. The gas is accelerated by huge electric and magnetic fields, which accelerate the ionized particles. The light that you see in the picture are the sparks in that surrounding electromagnetic field (almost like in a Tesla coil, or Van De Graff lightning generators.
 
At June 14, 2005 3:31 AM, Blogger ESIH said...
Veyr informative posts...nice blog too..
 
At June 14, 2005 6:35 AM, Blogger Sray said...
Thanks Susmita! Please come again :).
 

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Monday, June 06, 2005
This Day:

Other than humans, many other animals have been observed to use tools in the wild. Chimpanzees use straws to dig out termites, and have been observed to break hard-to-crack nuts using a stone. Eagles have been known to throw turtles from great heights to crack open their shells. These animals even teach their young how to use the tools, thus hinting at a generation to generation transfer of knowledge hitherto believed to be employed only by humans. Now scientists in Australia have observed a community of dolphins to use sponges to protect their sensitive snout, and suspect that they teach the technique to their young too:):).

Poor Spongebob :D (Courtesy: NewScientist)
Lacking hands, dolphins are limited in what they can do with a tool, but some bottlenose dolphins in Shark Bay, Western Australia, have devised a way to break marine sponges off the seafloor and wear them over their snouts when foraging. Most sponges are flat, but tool-using dolphins select conical ones that will not fall off their snouts. The majority of dolphin spongers are females.
A comparison of their nuclear DNA showed that the spongers were closely related, suggesting that spongers are descendants of a recent Sponging Eve. From the usage pattern among the different dolphins, the researchers conclude that the behaviour is culturally transmitted, presumably by mothers teaching the skills to their sons and daughters, although they have not actually observed this feat in action.
As we look more into the animal world, we find intelligent creatures employing creative ideas to make their lives a little better than usual. Our ancestors started the same way, hundreds of thousands of years ago. Who is to say the dolphins wont inherit the Earth, millions of years hence?

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11 Comments:

At June 07, 2005 6:16 AM, Blogger LEMNA said...
Poor Spongebob:D:D:D This is not me sneakin' here haaaaaaa!This is sb else:DShhhhhh....
 
At June 07, 2005 6:17 AM, Blogger LEMNA said...
Tipilyyyy Toeeeeee....Tipily Toeeeeee....Tipilyyyy Toe:D:D:D
 
At June 07, 2005 6:21 AM, Blogger Sray said...
Welcome back :):). Heyyy you are the top commenter again!!
 
At June 07, 2005 6:42 AM, Blogger LEMNA said...
ME?!??!?!Where?!Whom?!Lemna or the one who did sneak?:DIt's totally different haa:DThose special faces u know which one:D
 
At June 07, 2005 6:46 AM, Blogger Sray said...
Sneakk in all you want, but I still know when it is youuu... I have my tricks :D:D:D.
 
At June 07, 2005 7:00 AM, Blogger LEMNA said...
You cannnn:D:D:D:D:DHeh,I run away:D
 
At June 07, 2005 7:06 AM, Blogger Sray said...
But you will come back, again and again :D:D.
 
At June 07, 2005 11:15 AM, Blogger Sray said...
Ghalib Saahaab... you are good in what you do, and not everyone is good in everything :). Thanks for visiting, and leave comments whenever you feel like it. Thanks, and please come again :).
 
At June 07, 2005 1:36 PM, Blogger Akruti said...
Dolphin,the moment i saw the word i read it all,and laughing out so loudly,hahaha,they r so sweet:) oneday i will sure see them live in action,abhi thak tho nahi dekha:) but they r cho chweet:)
 
At June 07, 2005 2:41 PM, Blogger Sray said...
Gindy: They tear the sponges with their teeth, and then push against them in the sand to fit them on their snout :).
 
At June 07, 2005 2:42 PM, Blogger Sray said...
Neelima: You must see them! And they are also very lovely to touch and run your hand over :):). Very friendly, and you can see the intelligence in their eyes :):).
 

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Sunday, June 05, 2005
This Day:

Our brain is the most complex piece of machinery on the planet. Now scientists at IBM and Brain and Mind Institute at the Ecole Polytecnique Fédérale de Lausanne (EPFL), Switzerland have launched an effort to create the first computer simulation of the entire human brain, right down to the molecular level.
Termed the Blue Brain Project, the project will involve building a custom-made supercomputer based on IBM’s Blue Gene design. The hope is that the virtual brain will help shed light on some aspects of human cognition, such as perception, memory and perhaps even consciousness.

The Brain (Courtesy: University of Wisconsin, Madison)
Over the next two years scientists from both organizations will work together using the huge computational capacity of IBM’s eServer Blue Gene supercomputer to create a detailed model of the circuitry in the neocortex – the largest and most complex part of the human brain. By expanding the project to model other areas of the brain, scientists hope to eventually build an accurate, computer-based model of the entire brain.
The system that will be installed at EPFL will occupy the floor space of about four refrigerators, and will have a peak processing speed of at least 22.8 trillion floating-point operations per second (22.8 teraflops), making it one of the most powerful supercomputers in the world.
The first phase of the project will be to make a software replica of a column of the neocortex. The neocortex constitutes about 85% of the human brain’s total mass and is thought to be responsible for the cognitive functions of language, learning, memory and complex thought. An accurate replica of the neocortical column is the essential first step to simulating the whole brain and also will provide the link between genetic, molecular and cognitive levels of brain function. The second and subsequent phases will be to expand the simulation to include circuitry from other brain regions and eventually the whole brain.
Hopefully, in our lifetime, we will solve the ultimate mystery... What makes us human?:):)

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7 Comments:

At June 06, 2005 9:51 AM, Blogger Tupinambah said...
then, everything that will be revealed had been obvious...
 
At June 06, 2005 5:53 PM, Blogger Sray said...
Lots of interesting things might come out of this project.. this will go on for generations I assume:):).
 
At June 11, 2005 9:52 PM, Blogger Unknown said...
Will that computational power suffice? i.e. Is our brain simulatable by a mere supercomputer?
 
At June 11, 2005 9:55 PM, Blogger Unknown said...
Is it only the circuitry that matters? Wont some stuff done chemically? (I remember having heard long ago, about info stored using Nissl granules in neurons, but the theory may be outdated as of now)
 
At June 11, 2005 10:39 PM, Blogger Sray said...
I dont think the brain can be simulated by a computer, at least, not yet. But certain brain circuits can definitely be transcribed. Also, there is possibly a lot of field effects in the brain (circuits affecting neighboring circuits), and that is quite hard to do in a (non-quantum) computer!
 
At June 14, 2005 9:28 PM, Blogger Unknown said...
The post on Slashdot and new Scientist said "simulation of the brain.... right down to the molecular level". That was the thing that psyched me out.

ok.... so if its just circuitry of some part of the brain.... definitely do-able
 
At June 14, 2005 10:32 PM, Blogger Sray said...
Well, I dont think the brain can be simulated just like that. But it is possible that some probabilistic model can be developed, by which one could predict the most likely way a particular person would react to a particular stimuli. This is frightening too, in its own way!
 

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