Cloning

Cloning in biology is the process of producing populations of genetically-identical individuals that occurs in nature when organisms such as bacteria, insects or plants reproduce asexually. Cloning in biotechnology refers to processes used to create copies of DNA fragments (molecular cloning), cells (cell cloning), or organisms. More generally, the term refers to the production of multiple copies of a product such as digital media or software.

Contents 1 Etymology 2 Molecular cloning 3 Cellular cloning 4 Cloning in stem cell research 5 Organism cloning 5.1 Horticultural 5.2 Parthenogenesis 5.3 Reproductive cloning 5.3.1 Dolly the Sheep 5.3.2 Species cloned 5.3.3 Human cloning 5.3.4 Ethical issues of cloning 5.3.5 Cloning extinct and endangered species 6 References 7 External links and references

Etymology

The term clone is derived from κλών, the Greek word for "twig, branch", referring to the process whereby a new plant can be created from a twig. In horticulture, the spelling clon was used until the twentieth century; the final e came into use to indicate the vowel is a "long o" instead of a "short o"^{[citation needed]}. Since the term entered the popular lexicon in a more general context, the spelling clone has been used exclusively.

Molecular cloning

This section is missing citations or needs footnotes. Using inline citations helps guard against copyright violations and factual inaccuracies. (February 2008)

Molecular cloning refers to the process of making multiple copies of a defined DNA sequence. Cloning is frequently used to amplify DNA fragments containing whole genes, but it can also be used to amplify any DNA sequence such as promoters, non-coding sequences and randomly fragmented DNA. It is used in a wide array of biological experiments and practical applications ranging from genetic fingerprinting to large scale protein production. Occasionally, the term cloning is misleadingly used to refer to the identification of the chromosomal location of a gene associated with a particular phenotype of interest, such as in positional cloning. In practice, localization of the gene to a chromosome or genomic region does not necessarily enable one to isolate or amplify the relevant genomic sequence.

In practice, in order to amplify any DNA sequence in a living organism, that sequence must be linked to an origin of replication, which is a sequence of DNA capable of directing the propagation of itself and any linked sequence. However, a number of other features are needed and a variety of specialised cloning vectors (small piece of DNA into which a foreign DNA fragment can be inserted) exist that allow protein expression, tagging, single stranded RNA and DNA production and a host of other manipulations.

Cloning of any DNA fragment essentially involves four steps ^[1]

1. fragmentation - breaking apart a strand of DNA
2. ligation - gluing together pieces of DNA in a desired sequence
3. transfection - inserting the newly formed pieces of DNA into cells
4. screening/selection - selecting out the cells that were successfully transfected with the new DNA

Although these steps are invariable among cloning procedures a number of alternative routes can be selected, these are summarized as a cloning strategy’.

Initially, the DNA of interest needs to be isolated to provide a DNA segment of suitable size. Subsequently, a ligation procedure is used where the amplified fragment is inserted into a vector (piece of DNA). The vector (which is frequently circular) is linearised using restriction enzymes, and incubated with the fragment of interest under appropriate conditions with an enzyme called DNA ligase. Following ligation the vector with the insert of interest is transfected into cells. A number of alternative techniques are available, such as chemical sensitivation of cells, electroporation and biolistics. Finally, the transfected cells are cultured. As the aforementioned procedures are of particularly low efficiency, there is a need to identify the cells that have been successfully transfected with the vector construct containing the desired insertion sequence in the required orientation. Modern cloning vectors include selectable antibiotic resistance markers, which allow only cells in which the vector has been transfected, to grow. Additionally, the cloning vectors may contain colour selection markers which provide blue/white screening (α-factor complementation) on X-gal medium. Nevertheless, these selection steps do not absolutely guarantee that the DNA insert is present in the cells obtained. Further investigation of the resulting colonies is required to confirm that cloning was successful. This may be accomplished by means of PCR, restriction fragment analysis and/or DNA sequencing.

Cellular cloning

Cloning cell-line colonies using cloning rings

Cloning a cell means to derive a population of cells from a single cell. In the case of unicellular organisms such as bacteria and yeast, this process is remarkably simple and essentially only requires the inoculation of the appropriate medium. However, in the case of cell cultures from multi-cellular organisms, cell cloning is an arduous task as these cells will not readily grow in standard media.

A useful tissue culture technique used to clone distinct lineages of cell lines involves the use of cloning rings (cylinders)^[2]. According to this technique, a single-cell suspension of cells which have been exposed to a mutagenic agent or drug used to drive selection is plated at high dilution to create isolated colonies; each arising from a single and potentially clonally distinct cell. At an early growth stage when colonies consist of only a few of cells, sterile polystyrene rings (cloning rings), which have been dipped in grease are placed over an individual colony and a small amount of trypsin is added. Cloned cells are collected from inside the ring and transferred to a new vessel for further growth.

Cloning in stem cell research

Somatic cell nuclear transfer can also be used to create a clonal embryo. The most likely purpose for this is to produce embryos for use in research, particularly stem cell research. This process is also called "research cloning" or "therapeutic cloning." The goal is not to create cloned human beings, but rather to harvest stem cells that can be used to study human development and to potentially treat disease. While a clonal human blastocyst has been created, stem cell lines are yet to be isolated from a clonal source.^[3]

Organism cloning

Organism cloning refers to the procedure of creating a new multicellular organism, genetically identical to another. In essence this form of cloning is an asexual method of reproduction, where fertilization or inter-gamete contact does not take place. Asexual reproduction is a naturally occurring phenomenon in many species, including most plants (see vegetative reproduction) and some insects.

Parthenogenesis

Clonal derivation exists in nature in some animal species and is referred to as parthenogenesis (reproduction of an organism by itself without a mate). An example is the "Little Fire Ant" (Wasmannia auropunctata), which is native to Central and South America but has spread throughout many tropical environments.

Reproductive cloning

Reproductive cloning uses "somatic cell nuclear transfer" (SCNT) to create animals that are genetically identical. This process entails the transfer of a nucleus from a donor adult cell (somatic cell) to an egg which has no nucleus. If the egg begins to divide normally it is transferred into the uterus of the surrogate mother.

Such clones are not strictly identical since the somatic cells may contain mutations in their nuclear DNA. Additionally, the mitochondria in the cytoplasm also contains DNA and during SCNT this DNA is wholly from the donor egg, thus the mitochondrial genome is not the same as that of the nucleus donor cell from which it was produced. This may have important implications for cross-species nuclear transfer in which nuclear-mitochondrial incompatibilities may lead to death.

Dolly the Sheep

Dolly (1996-07-05 – 2003-02-14), a Finn Dorsett ewe, was the first mammal to have been successfully cloned from an adult cell, though the first actual thing to be cloned, was a tadpole in 1952[1]. She was cloned at the Roslin Institute in Scotland and lived there until her death when she was six. On 2003-04-09 her stuffed remains were placed at Edinburgh's Royal Museum, part of the National Museums of Scotland.

Dolly was publicly significant because the effort showed that the genetic material from a specific adult cell, programmed to express only a distinct subset of its genes, could be reprogrammed to grow an entire new organism. Before this demonstration, there was no proof for the widely spread hypothesis that differentiated animal cells can give rise to entire new organisms.

Cloning Dolly the sheep had a low success rate per fertilized egg; she was born after 277 eggs were used to create 29 embryos, which only produced three lambs at birth, only one of which lived. Seventy calves have been created from 9,000 attempts and one third of them died young; Prometea took 328 attempts. Notably, although the first clones were frogs, no adult cloned frog has yet been produced from a somatic adult nucleus donor cell.

There were early claims that Dolly the Sheep had pathologies resembling accelerated aging. Scientists speculated that Dolly's death in 2003 was related to the shortening of telomeres, DNA-protein complexes that protect the end of linear chromosomes. However, other researchers, including Ian Wilmut who led the team that successfully cloned Dolly, argue that Dolly's early death due to respiratory infection was unrelated to deficiencies with the cloning process.

Species cloned

The modern cloning techniques involving nuclear transfer have been successfully performed on several species. Landmark experiments^{[clarification needed]} in chronological order:

• Tadpole: (1952) Many scientists questioned whether cloning had actually occurred and unpublished experiments by other labs were not able to reproduce the reported results.^{[citation needed]}
• Carp: (1963) In China, embryologist Tong Dizhou cloned a fish. He published the findings in a Chinese science journal which was never translated into English.^[4]
• Mice: (1986) were the first successfully cloned mammal; Soviet scientists Chaylakhyan, Veprencev, Sviridova, and Nikitin had the mouse "Masha" cloned. Research was published in the magazine "Biofizika" volume ХХХII, issue 5 of 1987.^{[clarification needed][5]}
• Sheep: (1996) From early embryonic cells by Steen Willadsen. Megan and Morag^{[citation needed]} cloned from differentiated embryonic cells in June 1995 and Dolly the sheep from a somatic cell in 1997.^[6]
• Rhesus Monkey: Tetra (female, January 2000) from embryo splitting^{[7][clarification needed]}
• Gaur: (2001) was the first endangered species cloned.^[8]
• Cattle: Alpha and Beta (males, 2001) and (2005) Brazil^[9]
• Cat: CopyCat "CC" (female, late 2001), Little Nicky, 2004, was the first cat cloned for commercial reasons^{[citation needed]}
• Mule: Idaho Gem, a john mule born 4 May 2003, was the first horse-family clone.^{[citation needed]}
• Horse: Prometea, a Haflinger female born 28 May 2003, was the first horse clone.^{[citation needed]}

  Further information: List of animals that have been cloned

Human cloning

Human cloning is the creation of a genetically identical copy of an existing or previously existing human. The term is generally used to refer to artificial human cloning; human clones in the form of identical twins are commonplace, with their cloning occurring during the natural process of reproduction. There are two commonly discussed types of human cloning: therapeutic cloning and reproductive cloning. Therapeutic cloning involves cloning cells from an adult for use in medicine and is an active area of research: while reproductive cloning would involve making cloned human beings. Such reproductive cloning has not been performed and is illegal in many countries. A third type of cloning called replacement cloning is a theoretical possibility, and would be a combination of therapeutic and reproductive cloning. Replacement cloning would entail the replacement of an extensively damaged, failed, or failing body through cloning followed by whole or partial brain transplant.

The various forms of human cloning are controversial.^[10] There have been numerous demands for all progress in the human cloning field to be halted. Some people and groups oppose therapeutic cloning, but most scientific, governmental and religious organizations oppose reproductive cloning. The American Association for the Advancement of Science (AAAS) and other scientific organizations have made public statements suggesting that human reproductive cloning be banned until safety issues are resolved ^[11]. Serious ethical concerns have been raised by the idea that it might be possible in the future to harvest organs from clones. Some people have considered the idea of growing organs separately from a human organism - in doing this, a new organ supply could be established without the moral implications of harvesting them from humans. Research is also being done on the idea of growing organs that are biologically acceptable to the human body inside of other organisms, such as pigs or cows, then transplanting them to humans, a form of xenotransplantation.

The first human hybrid human clone was created in November 1998, by American Cell Technologies.^[12]. It was created from a man's leg cell, and a cow's egg whose DNA was removed. It was destroyed after 12 days. Since a normal embryo implants at 14 days, Dr Robert Lanza, ACT's director of tissue engineering, told the Daily Mail newspaper that the embryo could not be seen as a person before 14 days. While making an embryo, which may have resulted in complete human had it been allowed to come to term, according to ACT: "[ACT's] aim was 'therapeutic cloning' not 'reproductive cloning'"

On January, 2008, Wood and Andrew French, Stemagen's chief scientific officer in California, announced that they successfully created the first 5 mature human embryos using DNA from adult skin cells, aiming to provide a source of viable embryonic stem cells. Dr. Samuel Wood and a colleague donated skin cells, and DNA from those cells was transferred to human eggs. It is not clear if the embryos produced would have been capable of further development, but Dr. Wood stated that if that were possible, using the technology for reproductive cloning would be both unethical and illegal. The 5 cloned embryos, created in Stemagen Corporation lab, in La Jolla, were destroyed.

Cloning extinct and endangered species

Cloning, or more precisely, the reconstruction of functional DNA from extinct species has, for decades, been a dream of some scientists. The possible implications of this were dramatized in the best-selling novel by Michael Crichton and high budget Hollywood thriller Jurassic Park. In real life, one of the most anticipated targets for cloning was once the Woolly Mammoth, but attempts to extract DNA from frozen mammoths have been unsuccessful, though a joint Russo-Japanese team is currently working toward this goal.^[17]

In 2001, a cow named Bessie gave birth to a cloned Asian gaur, an endangered species, but the calf died after two days. In 2003, a banteng was successfully cloned, followed by three African wildcats from a thawed frozen embryo. These successes provided hope that similar techniques (using surrogate mothers of another species) might be used to clone extinct species. Anticipating this possibility, tissue samples from the last bucardo (Pyrenean Ibex) were frozen immediately after it died. Researchers are also considering cloning endangered species such as the giant panda, ocelot, and cheetah. The "Frozen Zoo" at the San Diego Zoo now stores frozen tissue from the world's rarest and most endangered species.^[18][19]

In 2002, geneticists at the Australian Museum announced that they had replicated DNA of the Thylacine (Tasmanian Tiger), extinct about 65 years previous, using polymerase chain reaction.^[20] However, on 2005-02-15 the museum announced that it was stopping the project after tests showed the specimens' DNA had been too badly degraded by the (ethanol) preservative. Most recently, on 2005-05-15, it was announced that the Thylacine project would be revived, with new participation from researchers in New South Wales and Victoria.

One of the continuing obstacles in the attempt to clone extinct species is the need for nearly perfect DNA. Cloning from a single specimen could not create a viable breeding population in sexually reproducing animals. Furthermore, even if males and females were to be cloned, the question would remain open whether they would be viable at all in the absence of parents that could teach or show them their natural behavior. Essentially, if cloning an extinct species were successful — it must be considered that cloning is still an experimental technology that succeeds only by chance. It is far more likely than not that any resulting animals, even if they were healthy, would be little more than curios or museum pieces.

Cloning endangered species is a highly ideological issue. Many conservation biologists and environmentalists vehemently oppose cloning endangered species — not because they think it won't work but because they think it may deter donations to help preserve natural habitat and wild animal populations. The "rule-of-thumb" in animal conservation is that, if it is still feasible to conserve habitat and viable wild populations, breeding in captivity should not be undertaken in isolation.

In a 2006 review, David Ehrenfeld concluded that cloning in animal conservation is an experimental technology that, at its state in 2006, could not be expected to work except by pure chance and utterly failed a cost-benefit analysis.^[21] Furthermore, he said, it is likely to siphon funds from established and working projects and does not address any of the issues underlying animal extinction (such as habitat destruction, hunting or other overexploitation, and an impoverished gene pool). While cloning technologies are well-established and used on a regular basis in plant conservation, care must be taken to ensure genetic diversity. He concluded:

“

Vertebrate cloning poses little risk to the environment, but it can consume scarce conservation resources, and its chances of success in preserving species seem poor. To date, the conservation benefits of transgenics and vertebrate cloning remain entirely theoretical, but many of the risks are known and documented. Conservation biologists should devote their research and energies to the established methods of conservation, none of which require transgenics or vertebrate cloning.[21]

”

Meson

The new meson was observed in electron-positron collisions by the international Belle collaboration at KEK and quickly decays into two well-known particles called the Omega and J/psi. The properties of the decay have led the Belle team to believe that it is not a standard quark-antiquark particle but may be a hybrid meson containing a charm quark, a charm antiquark and a gluon. The existence of such hybrid charm-anticharm-gluon particles was first predicted theoretically in 1978.

Although many of the properties of Y(3940) match those expected for a hybrid meson, its mass -- which is about the same as that of a single helium atom -- is much lower than theory predicts. The Belle collaboration now hopes to solve this enigma by further analysing its data.

The new meson is the latest in a list of recent surprising discoveries in particle physics. These include several particles called pentaquarks (which may or may not exist) that contain five quarks, a particle called the X(3872) that appears to be made of four quarks, and another meson called the Ds(2317) that does not behave as predicted.

The Fourth Dimension as Space

Sometimes, the fourth dimension is interpreted in the spatial sense: a space with literally 4 spatial dimensions, 4 mutually orthogonal directions of movement. This is the space used by mathematicians when studying geometric objects such as 4-dimensional polytopes. To avoid confusion with the more common Einsteinian notion of time being the fourth dimension, however, the use of this spatial interpretation should be stated at the outset.

Mathematically, the 4-dimensional spatial equivalent of conventional 3-dimensional geometry is the Euclidean 4-space, a 4-dimensional normed vector space with the Euclidean norm. The "length" of a vector

expressed in the standard basis is given by

which is the natural generalization of the Pythagorean Theorem to 4 dimensions. This allows for the definition of the angle between two vectors (see Euclidean space for more information).

TIME

Time is often referred to as the "fourth dimension". It is one way to measure physical change. It is perceived differently from the three spatial dimensions in that there is only one of it, and that we cannot move freely in time but subjectively move in one direction.

The equations used in physics to model reality do not treat time in the same way that humans perceive it. The equations of classical mechanics are symmetric with respect to time, and equations of quantum mechanics are typically symmetric if both time and other quantities (such as charge and parity) are reversed. In these models, the perception of time flowing in one direction is an artifact of the laws of thermodynamics (we perceive time as flowing in the direction of increasing entropy).

The best-known treatment of time as a dimension is Poincaré and Einstein's special relativity (and extended to general relativity), which treats perceived space and time as components of a four-dimensional manifold, known as spacetime, and in the special, flat case as Minkowski space.

An Artificial Brain with 20 Billion Neurons

A California-based company founded in 2003,Artificial Development, is developing neural network cognitive systems and wants to introduce "the first 5th Generation computer to the world." According to e4engineering.com, the company recently completed a representation of a functioning human brain. This project, named CCortex, has vast ambitions. The company hopes that their "software may have immediate applications for data mining, network security, search engine technologies and natural language processing." This software runs on a Linux cluster with 1,000 processors and the CCortex system has 20 billion neurons and 20 trillion connections. The company says this is "the first neural system to achieve a level of complexity rivaling that of the mammalian brain."

Here is a picture of the CCortex Linux cluster which has 500 nodes for 1,000 processors, 1 terabyte of RAM, and 200 terabytes of storage (Credit: Artificial Development). The company says that "CCortex is up to 10,000 times larger than any previous attempt to replicate, partially or completely, primary characteristics of human intelligence."

Here is the status of the project.

The first CCortex-based Autonomous Cognitive Model ('ACM') computer 'persona,' named 'Kjell' in homage to AI pioneer Alan Turing, was activated last month and is in early testing stages. CCortex, Artificial Development's high-performance, parallel supercomputer, runs the persona simulation.

The ACM is intended as a test-bed for future models and is still incomplete. While the Kjell persona uses a realistic frontal cortex, motor and somatosensory areas, it still lacks the visual and auditory cortex areas, two of the most important cortical structures. Other structures, such as the hippocampus, basal ganglia and thalamic systems, are still being developed and are unable to perform most normal functions.

How does this work?

The ACM interacts with trainers using a text console, reading trainer's input and writing answers back, similar to a conventional 'chat' program. The ACM is being trained with a stimulus-reward learning process, based on classical conditioning rules. It is encouraged to respond to simple text commands, associating previous input with rewarded responses.

The ACM uses the associative cortex to 'evolve' possible antagonistic responses. Large populations of neurons compete for their own associated response until the strongest group overcomes the others. The 'winner' response is then tested and rewarded or deterred, depending on its validity. The ACM takes into account new experiences and uses them to modify the equilibrium between the responses and the strength of the associate neural path. Thus it creates a new neural status quo with more chances to generate accurate responses.

So CCortex is intended to simulate our brains. Yet the company employs only programmers and mathematicians. It has no neuroscientists, even if it plans to recruit some. I wonder if the company can deliver interesting results without having any specialist of the brain on board.

It's also interesting to note that the company was founded -- and funded -- by a man who made money by managing some of the largest ISPs in Spain, an activity very different from studying the brain.

And a final remark: how did the company managed to get such a short domain name, ad.com? Any clues?

Sources: Artificial Development press release, via e4engineering.com, July 14, 2

Blue Brain

Blue Brain is a project, begun in May 2005, to create a computer simulation of the brain of mammals including the human brain, down to the molecular level.^[1] The aim is to study the brain's architectural and functional principles. The project was founded by Henry Markram from the Brain and Mind Institute at the École Polytechnique (EPFL) in Lausanne, Switzerland.^[1] and is based on 15 years of experimental data obtained from reverse engineering the microcircuitry of the neocortical column.

The project uses a Blue Gene supercomputer,^[1] running a simulation software, the MPI-based Neocortical Simulator (NCS) developed by Phil Goodman, to be combined with Michael Hines's NEURON software. The simulation will not consist of a mere artificial neural network, but will involve much more biologically realistic models of neurons.

The initial goal of the project, completed in December 2006^[2], was the simulation of a rat neocortical column, which can be considered the smallest functional unit of the neocortex (the part of the brain thought to be responsible for higher functions such as conscious thought). Such a column is about 2 mm tall, has a diameter of 0.5 mm and contains about 60,000 neurons in humans; rat neocortical columns are very similar in structure but contain only 10,000 neurons (and 10⁸ synapses). Between 1995 and 2005, Markram mapped the types of neurons and their connections in such a column.

In November 2007^[3], the project reported the end of the first phase, delivering a data-driven process for creating, validating, and researching the neocortical column.

Now that the column is finished, the project is pursuing two separate goals:

1. construction of a simulation on the molecular level,^[1] which is desirable since it allows to study effects of gene expression;
2. simplification of the column simulation to allow for parallel simulation of large numbers of connected columns, with the ultimate goal of simulating a whole neocortex (which in humans consists of about 1 million cortical columns.

004; Artificial

About the Blue Brain Project

The Blue Brain project is the first comprehensive attempt to reverse-engineer the mammalian brain, in order to understand brain function and dysfunction through detailed simulations.

In July 2005, EPFL and IBM announced an exciting new research initiative - a project to create a biologically accurate, functional model of the brain using IBM's Blue Gene supercomputer. Analogous in scope to the Genome Project, the Blue Brain will provide a huge leap in our understanding of brain function and dysfunction and help us explore solutions to intractable problems in mental health and neurological disease.

At the end of 2006, the Blue Brain project had created a model of the basic functional unit of the brain, the neocortical column. At the push of a button, the model could reconstruct biologically accurate neurons based on detailed experimental data, and automatically connect them in a biological manner, a task that involves positioning around 30 million synapses in precise 3D locations.

In November, 2007, the Blue Brain project reached an important milestone and the conclusion of its first Phase, with the announcement of an entirely new data-driven process for creating, validating, and researching the neocortical column.

Artificial intelligence

Garry Kasparov playing against Deep Blue, the first machine to win a chess match against a world champion.

Artificial intelligence (AI) is the intelligence of machines and the branch of computer science which aims to create it.

Major AI textbooks define the field as "the study and design of intelligent agents,"^[1] where an intelligent agent is a system that perceives its environment and takes actions which maximize its chances of success.^[2] John McCarthy, who coined the term in 1956,^[3] defines it as "the science and engineering of making intelligent machines."^[4]

Among the traits that researchers hope machines will exhibit are reasoning, knowledge, planning, learning, communication, perception and the ability to move and manipulate objects.^[5] General intelligence (or "strong AI") has not yet been achieved and is a long-term goal of some AI research.^[6]

AI research uses tools and insights from many fields, including computer science, psychology, philosophy, neuroscience, cognitive science, linguistics, ontology, operations research, economics, control theory, probability, optimization and logic.^[7] AI research also overlaps with tasks such as robotics, control systems, scheduling, data mining, logistics, speech recognition, facial recognition and many others.^[8]

Other names for the field have been proposed, such as computational intelligence,^[9] synthetic intelligence,^[9] intelligent systems,^[10] or computational rationality.^[11] These alternative names are sometimes used to set oneself apart from the part of AI dealing with symbols (considered outdated by many, see GOFAI) which is often associated with the term “AI” itself.

IBM AIMS TO STIMULATE ARTIFICIAL BRAIN

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NEW YORK - IBM has embarked on a quest for the holy grail of neuroscience--the far-off goal of creating a computer simulation of the human brain.

When the first mammals evolved from reptiles 200 million years ago, one of the biggest changes was inside their heads. Their brain cells were structured together into columns, an innovation that could be repeated like a computer chip to make larger and more powerful minds-- from mice to cats and dogs to humans.

"This was the jump from reptiles to mammals," says Henry Markram, founder of the Brain/Mind Institute at the Ecole Polytechnique Fédérale in Lausanne, Switzerland. "It was like discovering a G5 processor or Pentium 4 and just copying it."

Now, Markram is announcing a collaboration with IBM (nyse: IBM - news - people ) to create a computer simulation of these fundamental neurological units, called neocortical columns. The process will involve building a Blue Gene supercomputer with 8,000 processors that can roar along at 23 trillion operations per second. Each processor will be used to simulate one or two neurons. If finished immediately, the machine would be one of the five fastest supercomputers in the world.

A neurocortical column is a structure half a millimeter in diameter and 2 millimeters long that contains about 60,000 neurons. (The human brain is made of 10 billion neurons.) The columns were discovered by Nobel Prize-winner Torsten Wiesel of Rockefeller University. They remain similar in different mammals, but the human brain is crammed with more of them. It was the need to fit in more columns that forced the human brain into its crinkly, wrinkled shape.

In Switzerland, Markram has put together a large lab dedicated to studying neurocortical columns in animals. His first effort with IBM will be to simulate a single rat neurocortical column. That alone is likely to take several years, as the computer model is rigorously checked in experiments against neurocortical columns taken from rats.

Once it is clear that one column has been simulated, the project will move on to simulating several such columns, again verifying its results by experiments with real brain tissues. Then, it will be possible to create larger simulations. After a decade or more, it may even be possible to create a model of the human brain. Markram and IBM both emphasize that the project would not create artificial intelligence but a way to study how neurons in the brain interact with one another.

"We believe that we will be able to capture the heart of the information process," says Markram. "Not just the column but how the information was formed in memories and retrieved."

The project could lead to new understandings of various diseases such as schizophrenia, autism and attention deficit hyperactivity disorder. Degenerative diseases such as Alzheimer's may turn out to be more difficult to model because they involve the failure of more than just brain cells, Markram says.

For IBM, the project represents one of several initiatives in its Blue Gene program, which involves building supercomputers based on a powerful new computer architecture. The most powerful of these units, at Lawrence Livermore National Laboratory, is 16 times more powerful than the one Markram is using and will be used to simulate the intricate ways that proteins fold--one of biology's big mysteries. Other efforts exist in astrophysics, atmospheric modeling and financial modeling.

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BLACK HOLE

What is a black hole?

A black hole is a region of spacetime from which nothing can escape, even light.

To see why this happens, imagine throwing a tennis ball into the air. The harder you throw the tennis ball, the faster it is travelling when it leaves your hand and the higher the ball will go before turning back. If you throw it hard enough it will never return, the gravitational attraction will not be able to pull it back down. The velocity the ball must have to escape is known as the escape velocity and for the earth is about 7 miles a second.

As a body is crushed into a smaller and smaller volume, the gravitational attraction increases, and hence the escape velocity gets bigger. Things have to be thrown harder and harder to escape. Eventually a point is reached when even light, which travels at 186 thousand miles a second, is not travelling fast enough to escape. At this point, nothing can get out as nothing can travel faster than light. This is a black hole.

Do they really exist?

It is impossible to see a black hole directly because no light can escape from them; they are black. But there are good reasons to think they exist.

When a large star has burnt all its fuel it explodes into a supernova. The stuff that is left collapses down to an extremely dense object known as a neutron star. We know that these objects exist because several have been found using radio telescopes.

If the neutron star is too large, the gravitational forces overwhelm the pressure gradients and collapse cannot be halted. The neutron star continues to shrink until it finally becomes a black hole. This mass limit is only a couple of solar masses, that is about twice the mass of our sun, and so we should expect at least a few neutron stars to have this mass. (Our sun is not particularly large; in fact it is quite small.)

Stellar black holes, mid-mass black holes, and supermassive black holes.

18 Jun 08

M81

A spiral galaxy located about 12 million light years from Earth.

16 Apr 08

NGC 4374

A sample of nine galaxies each containing supermassive black holes in their centers.

NGC 4472

A sample of nine galaxies each containing supermassive black holes in their centers.

NGC 4552

A sample of nine galaxies each containing supermassive black holes in their centers.

NGC 5846

A sample of nine galaxies each containing supermassive black holes in their centers.

GOODS Chandra Deep Field-South

A compilation of long observations on the same patch of sky.

03 Jan 07

NGC 4472

Astronomers have found a black hole where few thought they could ever exist, inside a globular star cluster.

21 Jun 06

GRO J1655-40

A binary star system consisting of a black hole and a normal star, located about 11,000 light years from Earth.

24 Apr 06

13 Oct 05

Sagittarius A*

Chandra's image of the Galactic Center has provided evidence for a new and unexpected way for stars to form.

23 May 05

How the First Stars Were Born.

A new supercomputer simulation offers the most detailed view yet of how the first stars evolved after the Big Bang.

The model follows the simpler physics that ruled the early universe to see how cold clumps of gas eventually grew into giant star embryos.

"Until you put that physics in the code, you can't evaluate how the first protostars formed," said Lars Hernquist, an astrophysicist at Harvard University whose early-stars model is detailed in this week's issue of the journal Science. His remarks were made Wednesday during a press teleconference.

Mysterious "dark matter" provided the first gravitational impetus for hydrogen and helium gas to start clumping together, Hernquist said. The gas began releasing energy as it condensed, forming molecules from atoms, which further cooled the clump and allowed for even greater condensing.

Unlike previous models, the latest simulation takes this cooling process of "complex radiative transfer" into account, said Nagoya University astrophysicist Naoki Yoshida, who headed up the modeling project.

Eventually gravity could not condense the gas cloud any further, because the densely-packed gas exerted a pressure against further collapse. That equilibrium point marked the beginning of an embryonic star, called a protostar by astronomers.

Simulation runs show that the first protostar likely started with just 1 percent the mass of our sun, but would have swelled to more than 100 solar masses in 10,000 years.

"No simulation has ever gotten to the point of identifying this important stage in the birth of a star," Hernquist noted.

The first protostars reached such massive size because they consisted of mainly simple elements such as hydrogen and helium. That bloated existence means the stars which eventually form from such protostars could create heavier elements such as oxygen, carbon, nitrogen and iron in their fiery furnaces.

The researchers eventually hope to run the simulation all the way up through the point where protostars ignite into true stars.

WORLD

Our Solar System Born in Little Bang'

First there was the theoretical Big Bang that got the universe going. Several billion years passed. Then a Little Bang birthed our solar system.

At least scientists have long thought that's how it went, and now they have a computer model to back up the idea that our sun is the product of an explosive event. The new modeling finds that a supernova, or exploding star, could indeed have triggered birth of our sun in a dense cloud of gas and dust, the researchers say.

Stars are born when a cloud of material collapses. Exactly what triggers the collapse is not entirely known. One idea is that most stars, including perhaps our sun, were created in dense starbirth regions when another very massive star explodes, putting intense pressure on surrounding clouds.

"We've had chemical evidence from meteorites that points to a supernova triggering our solar system's formation since the 1970s," said theorist Alan Boss of the Carnegie Institution. "But the devil has been in the details. Until this study, scientists have not been able to work out a self-consistent scenario, where collapse is triggered at the same time that newly created isotopes from the supernova are injected into the collapsing cloud."

Short-lived radioactive isotopes -- versions of elements with the same number of protons, but a different number of neutrons -- found in very old meteorites decay on time scales of millions of years and turn into different (so-called daughter) elements. Finding the daughter elements in primitive meteorites implies that the parent short-lived radioisotopes must have been created only a million or so years before the meteorites themselves were formed.

"One of these parent isotopes, iron-60, can be made in significant amounts only in the potent nuclear furnaces of massive or evolved stars," Boss today. "Iron-60 decays into nickel-60, and nickel-60 has been found in primitive meteorites. So we've known where and when the parent isotope was made, but not how it got here."

Previous models by Boss and former DTM Fellow Prudence Foster showed that the isotopes could be deposited into a pre-solar cloud if a shock wave from a supernova explosion slowed to 6 to 25 miles per second and the wave and cloud had a constant temperature of -440 degrees Fahrenheit (10 K).

"Those models didn't work if the material was heated by compression and cooled by radiation, and this conundrum has left serious doubts in the community about whether a supernova shock started these events over four billion years ago or not," said Harri Vanhala, who found the negative result in his Ph.D. thesis work at the Harvard-Smithsonian Center for Astrophysics in 1997.

In several runs on the computer, the shock front was made to strike a pre-solar cloud of material with the mass of our sun, consisting of dust, water, carbon monoxide, and molecular hydrogen, reaching temperatures as high as 1,340°F (1000 K). In the absence of cooling, the cloud could not collapse.

However, with a newly crafted theoretically plausible cooling law, the researchers found that after 100,000 years the pre-solar cloud was 1,000 times denser than before, and that heat from the shock front was rapidly lost, resulting in only a thin layer with temperatures close to 1,340 degrees F (1000 K). After 160,000 years, the cloud center had collapsed to become a million times denser, forming the protosun. The researchers found that isotopes from the shock front were mixed into the protosun in a manner consistent with their origin in a supernova.

Other studies have suggested that our sun may have been born in a very crowded environment, near massive stars, but has since drifted to its relatively lonely position in space.

"This is the first time a detailed model for a supernova triggering the formation of our solar system has been shown to work," said Boss. "We started with a Little Bang 9 billion years after the Big Bang."

The results are detailed in the Oct. 20 issue of the Astrophysical Journal. Boss has previously shown that all this violent activity might have contributed to the makeup of our planetary system, too.