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"Names and attributes must be accommodated to the essence of things, and not the essence to the names, since things come first and names afterwards." – Galileo

Man Creates Life ?

First Self-Replicating, Synthetic Bacterial Cell Constructed by J. Craig Venter Institute Researchers

Man has Created the First Self-Replicating, Synthetic Bacterial Cell

Life re-created. Blue colonies (top) indicate a successfully transplanted genome, with self-replicating bacteria revealed in an electron micrograph.
CREDITS (TOP TO BOTTOM): J. CRAIG VENTER INSTITUTE; T. DEERINCK AND M. ELLISMAN/NCMIR, UNIVERSITY OF CALIFORNIA, SAN DIEGO

Read the Full Press Release below:

First Self-Replicating Synthetic Bacterial Cell

First Self-Replicating, Synthetic Bacterial Cell Constructed by J. Craig Venter Institute Researchers

ROCKVILLE, MD and San Diego, CA (May 20, 2010)— Researchers at the J. Craig Venter Institute (JCVI), a not-for-profit genomic research organization, published results today describing the successful construction of the first self-replicating, synthetic bacterial cell. The team synthesized the 1.08 million base pair chromosome of a modified Mycoplasma mycoides genome. The synthetic cell is called Mycoplasma mycoides JCVI-syn1.0 and is the proof of principle that genomes can be designed in the computer, chemically made in the laboratory and transplanted into a recipient cell to produce a new self-replicating cell controlled only by the synthetic genome.

This research will be published by Daniel Gibson et al in the May 20th edition of Science Express and will appear in an upcoming print issue of Science.

“For nearly 15 years Ham Smith, Clyde Hutchison and the rest of our team have been working toward this publication today–the successful completion of our work to construct a bacterial cell that is fully controlled by a synthetic genome,” said J. Craig Venter, Ph.D., founder and president, JCVI and senior author on the paper. “We have been consumed by this research, but we have also been equally focused on addressing the societal implications of what we believe will be one of the most powerful technologies and industrial drivers for societal good. We look forward to continued review and dialogue about the important applications of this work to ensure that it is used for the benefit of all.”

According to Dr. Smith, “With this first synthetic bacterial cell and the new tools and technologies we developed to successfully complete this project, we now have the means to dissect the genetic instruction set of a bacterial cell to see and understand how it really works.”

To complete this final stage in the nearly 15 year process to construct and boot up a synthetic cell, JCVI scientists began with the accurate, digitized genome of the bacterium, M. mycoides. The team designed 1,078 specific cassettes of DNA that were 1,080 base pairs long. These cassettes were designed so that the ends of each DNA cassette overlapped each of its neighbors by 80bp. The cassettes were made according to JCVI’s specifications by the DNA synthesis company, Blue Heron Biotechnology.

The JCVI team employed a three stage process using their previously described yeast assembly system to build the genome using the 1,078 cassettes. The first stage involved taking 10 cassettes of DNA at a time to build 110, 10,000 bp segments. In the second stage, these 10,000 bp segments are taken 10 at a time to produce eleven, 100,000 bp segments. In the final step, all 11, 100 kb segments were assembled into the complete synthetic genome in yeast cells and grown as a yeast artificial chromosome.

The complete synthetic M. mycoides genome was isolated from the yeast cell and transplanted into Mycoplasma capricolum recipient cells that have had the genes for its restriction enzyme removed. The synthetic genome DNA was transcribed into messenger RNA, which in turn was translated into new proteins. The M. capricolum genome was either destroyed by M. mycoides restriction enzymes or was lost during cell replication. After two days viable M. mycoides cells, which contained only synthetic DNA, were clearly visible on petri dishes containing bacterial growth medium.

The initial synthesis of the synthetic genome did not result in any viable cells so the JCVI team developed an error correction method to test that each cassette they constructed was biologically functional. They did this by using a combination of 100 kb natural and synthetic segments of DNA to produce semi-synthetic genomes. This approach allowed for the testing of each synthetic segment in combination with 10 natural segments for their capacity to be transplanted and form new cells. Ten out of 11 synthetic fragments resulted in viable cells; therefore the team narrowed the issue down to a single 100 kb cassette. DNA sequencing revealed that a single base pair deletion in an essential gene was responsible for the unsuccessful transplants. Once this one base pair error was corrected, the first viable synthetic cell was produced.

Dr. Gibson stated, “To produce a synthetic cell, our group had to learn how to sequence, synthesize, and transplant genomes. Many hurdles had to be overcome, but we are now able to combine all of these steps to produce synthetic cells in the laboratory.” He added, “We can now begin working on our ultimate objective of synthesizing a minimal cell containing only the genes necessary to sustain life in its simplest form. This will help us better understand how cells work.”

This publication represents the construction of the largest synthetic molecule of a defined structure; the genome is almost double the size of the previous Mycoplasma genitalium synthesis. With this successful proof of principle, the group will now work on creating a minimal genome, which has been a goal since 1995. They will do this by whittling away at the synthetic genome and repeating transplantation experiments until no more genes can be disrupted and the genome is as small as possible. This minimal cell will be a platform for analyzing the function of every essential gene in a cell.

According to Dr. Hutchison, “To me the most remarkable thing about our synthetic cell is that its genome was designed in the computer and brought to life through chemical synthesis, without using any pieces of natural DNA. This involved developing many new and useful methods along the way. We have assembled an amazing group of scientists that have made this possible.”

As in the team’s 2008 publication in which they described the successful synthesis of the M. genitalium genome, they designed and inserted into the genome what they called watermarks. These are specifically designed segments of DNA that use the “alphabet” of genes and proteins that enable the researcher to spell out words and phrases. The watermarks are an essential means to prove that the genome is synthetic and not native, and to identify the laboratory of origin. Encoded in the watermarks is a new DNA code for writing words, sentences and numbers. In addition to the new code there is a web address to send emails to if you can successfully decode the new code, the names of 46 authors and other key contributors and three quotations: “TO LIVE, TO ERR, TO FALL, TO TRIUMPH, TO RECREATE LIFE OUT OF LIFE.” – JAMES JOYCE; “SEE THINGS NOT AS THEY ARE, BUT AS THEY MIGHT BE.”-A quote from the book, “American Prometheus”; “WHAT I CANNOT BUILD, I CANNOT UNDERSTAND.” – RICHARD FEYNMAN.

The JCVI scientists envision that the knowledge gained by constructing this first self-replicating synthetic cell, coupled with decreasing costs for DNA synthesis, will give rise to wider use of this powerful technology. This will undoubtedly lead to the development of many important applications and products including biofuels, vaccines, pharmaceuticals, clean water and food products. The group continues to drive and support ethical discussion and review to ensure a positive outcome for society.

Funding for this research came from Synthetic Genomics Inc., a company co-founded by Drs. Venter and Smith.

Background

The research published today was made possible by previous breakthroughs at JCVI. In 2007 the team published results from the transplantation of the native M. mycoides genome into the M. capricolum cell which resulted in the M. capricolum cell being transformed into M. mycoides. This work established the notion that DNA is the software of life and that DNA dictates the cell phenotype.

In 2008 the same team reported on the construction of the first synthetic bacterial genome by assembling DNA fragments made from the four chemicals of life—ACGT. The final assembly of DNA fragments into the whole genome was performed in yeast by making use of the yeast genetic systems. However, when the team attempted to transplant the synthetic bacterial genome out of yeast and into a recipient bacterial cell, viable transplants could not be recovered.

Ethical Considerations: Since the beginning of the quest to understand and build a synthetic genome, Dr. Venter and his team have been concerned with the societal issues surrounding the work. In 1995 while the team was doing the research on the minimal genome, the work underwent significant ethical review by a panel of experts at the University of Pennsylvania (Cho et al, Science December 1999:Vol. 286. no. 5447, pp. 2087 – 2090). The bioethical group’s independent deliberations, published at the same time as the scientific minimal genome research, resulted in a unanimous decision that there were no strong ethical reasons why the work should not continue as long as the scientists involved continued to engage public discussion.

Dr. Venter and the team at JCVI continue to work with bioethicists, outside policy groups, legislative members and staff, and the public to encourage discussion and understanding about the societal implications of their work and the field of synthetic genomics generally. As such, the JCVI’s policy team, along with the Center for Strategic & International Studies (CSIS), and the Massachusetts Institute of Technology (MIT), were funded by a grant from the Alfred P. Sloan Foundation for a 20-month study that explored the risks and benefits of this emerging technology, as well as possible safeguards to prevent abuse, including bioterrorism. After several workshops and public sessions the group published a report in October 2007 outlining options for the field and its researchers.

Most recently in December of 2008, JCVI received funding from the Alfred P. Sloan Foundation to examine ethical and societal concerns that are associated with the developing science of synthetic genomics. The ongoing research is intended to inform the scientific community as well as educate our policymakers and journalists so that they may engage in informed discussions on the topic.

About the J. Craig Venter Institute

The JCVI is a not-for-profit research institute in Rockville, MD and La Jolla, CA dedicated to the advancement of the science of genomics; the understanding of its implications for society; and communication of those results to the scientific community, the public, and policymakers. Founded by J. Craig Venter, Ph.D., the JCVI is home to approximately 400 scientists and staff with expertise in human and evolutionary biology, genetics, bioinformatics/informatics, information technology, high-throughput DNA sequencing, genomic and environmental policy research, and public education in science and science policy. The legacy organizations of the JCVI are: The Institute for Genomic Research (TIGR), The Center for the Advancement of Genomics (TCAG), the Institute for Biological Energy Alternatives (IBEA), the Joint Technology Center (JTC), and the J. Craig Venter Science Foundation. The JCVI is a 501 (c) (3) organization. For additional information, please visit http://www.JCVI.org. Media Contact: Heather Kowalski, 301-943-8879, hkowalski(AT)jcvi.org

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Bobby Fischer is dead!

 Life Magazine cover photo of Bobby Fischer

Read the Reuters Report below:

Chess genius Bobby Fischer dies in Iceland

Fri Jan 18, 2008 8:53am EST

By Kristin Arna Bragadottir

REYKJAVIK (Reuters) – Bobby Fischer, America’s first and only world chess champion, who beat the Soviet Union’s Boris Spassky in a blaze of Cold War publicity in Reykjavik in 1972, has died in Iceland at the age of 64.

A spokesman for Fischer, who was feted as a national hero for beating Spassky but fell foul of U.S. authorities in his later years, confirmed that the eccentric chess genius had died but offered no further details.

Rumors that Fischer, once dubbed the “Mozart of Chess”, had been ill had circulated in recent weeks on chess-related Web sites. Iceland national radio reported he had died after a serious, but unspecified, illness.

Fischer, a child prodigy who once said he liked to watch his opponents squirm and who had become an Icelandic citizen, could have faced jail in the United States for violating sanctions on former Yugoslavia by playing a chess match there with Spassky.

Former world chess champion Garry Kasparov hailed Fischer as “the pioneer and the father of professional chess”.

Kasparov said he had followed the 1972 clash of the U.S. and Soviet titans closely. “Fischer’s chess was so fresh and so new and we all grew up under the strongest impression of Fischer’s victories,” he told Sky News television.

“From an ideological stance it was the fight of an individual against a totalitarian system. He had a lot of supporters even in the Soviet Union. No one viewed him as an American fighting Soviets, it was more a great man fighting the mighty machine,” Kasparov said.

Spassky, who now lives in Paris, was less eloquent on the subject of his old adversary. Asked by Reuters for his reaction, he replied: “It’s bad luck for you. Bobby Fischer is dead,” then hung up without further comment.

NO DEFENCE

The brilliant and unpredictable American abandoned his world title without moving a pawn by failing to defend his crown in Manila in 1975. World chess authorities reluctantly awarded it to challenger Anatoly Karpov of the Soviet Union, who was to hold it for the next decade.

Fischer withdrew into himself, not playing in public and living on little more than the magic of his name, although millions of enthusiasts regarded him as the king of chess.

He made headlines when he came out of seclusion to play Spassky in Yugoslavia in 1992, at a time when the country was the target of sanctions during Belgrade’s war with breakaway republics.

He vanished after the match, for which he won $3 million, and resurfaced after the September 11, 2001, attacks on America. In an interview with a Philippine radio station, Fischer praised the strikes and said he wanted to see America “wiped out”.

Fischer, who also stirred controversy with anti-Semitic remarks, was granted Icelandic citizenship in March 2005 after eight months in detention in Japan fighting a U.S. deportation order.

Fischer always had a high opinion of himself. Asked who was the greatest player in the world, he once replied:

“It’s nice to be modest, but it would be stupid if I did not tell the truth. It is Fischer.”

It was not an idle claim. Arguably the greatest natural chess genius the world has seen, he was called “the Mozart of chess” when he began winning at the age of six.

“SEE ‘EM SQUIRM”

Fischer gained a reputation for being cocky. He told interviewers his favorite moment was when opponents began to feel they would lose. “I like to see ’em squirm,” he said.

He was U.S. junior champion at 13 and U.S. Open champion at 14, retaining the title whenever he chose to defend it.

He became an international grandmaster at 15, gaining the rating at his first international tournament in Yugoslavia. He once defeated 21 grandmasters in succession — no U.S. player had beaten more than seven in a row.

As Fischer’s fame grew, his temperament became more unpredictable. He walked out of tournaments because of what he considered to be bad lighting or bad air conditioning. He refused to play matches on Saturday, the Jewish Sabbath.

In the mid-1960s, he opted out of two world championship qualifying series because he thought the tournament system favored the Russians. In 1967, when officials would not meet his demands for better conditions, Fischer angrily withdrew from international competition “for a period of introspection”.

He took his massive collection of chess books and moved to California, where he later said he had “plotted my revenge if I ever came back”.

When the rules were changed in 1972 to include an eight-player eliminator to find the challenger to world champion Spassky, Fischer had the chance to prove he was as good as he always said he was. He became a national hero; Americans who had never played chess followed the Fischer saga.

But by the 1990s, he was said to be living under assumed names in cheap hotels in Pasadena on the outskirts of Los Angeles, surviving on occasional royalties from his books.

Former friends painted a picture of a solitary man spending much of his day in rooms littered with chess books, oranges and jars of vitamins, playing chess by himself and reading magazines on chess to keep in touch.

One commentator said there was one constant through his life’s exceptional peaks and troughs — his “running battle with the rest of the human race”.

(Additional reporting from Paris bureau; Editing by Peter Millership)

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Mumbai City Snippet

“If you’re late for work…and you reach the station just as the train is leaving the platform, you …find many hands stretching out to grab you on board, unfolding outwards from the train like petals… at the moment of contact, they do not know if the hand that is reaching into theirs belongs to a Hindu or Muslim or Christian or Brahmin or untouchable, or whether you were born in this city or arrived only this morning…Come aboard they say, we’ll adjust…”

Suketu Mehta – “Maximum City”

Filed under: Travel, , , ,

Can Life exist without DNA?

Red rain could prove that aliens have landed

Amelia Gentleman and Robin McKie
Sunday March 5, 2006
The Observer

There is a small bottle containing a red fluid on a shelf in Sheffield University’s microbiology laboratory. The liquid looks cloudy and uninteresting. Yet, if one group of scientists is correct, the phial contains the first samples of extraterrestrial life isolated by researchers.
Inside the bottle are samples left over from one of the strangest incidents in recent meteorological history. On 25 July, 2001, blood-red rain fell over the Kerala district of western India. And these rain bursts continued for the next two months. All along the coast it rained crimson, turning local people’s clothes pink, burning leaves on trees and falling as scarlet sheets at some points.

Investigations suggested the rain was red because winds had swept up dust from Arabia and dumped it on Kerala. But Godfrey Louis, a physicist at Mahatma Gandhi University in Kottayam, after gathering samples left over from the rains, concluded this was nonsense. ‘If you look at these particles under a microscope, you can see they are not dust, they have a clear biological appearance.’ Instead Louis decided that the rain was made up of bacteria-like material that had been swept to Earth from a passing comet. In short, it rained aliens over India during the summer of 2001.

Not everyone is convinced by the idea, of course. Indeed most researchers think it is highly dubious. One scientist who posted a message on Louis’s website described it as ‘bullshit’.

But a few researchers believe Louis may be on to something and are following up his work. Milton Wainwright, a microbiologist at Sheffield, is now testing samples of Kerala’s red rain. ‘It is too early to say what’s in the phial,’ he said. ‘But it is certainly not dust. Nor is there any DNA there, but then alien bacteria would not necessarily contain DNA.’

Critical to Louis’s theory is the length of time the red rain fell on Kerala. Two months is too long for it to have been wind-borne dust, he says. In addition, one analysis showed the particles were 50 per cent carbon, 45 per cent oxygen with traces of sodium and iron: consistent with biological material. Louis also discovered that, hours before the first red rain fell, there was a loud sonic boom that shook houses in Kerala. Only an incoming meteorite could have triggered such a blast, he claims. This had broken from a passing comet and shot towards the coast, shedding microbes as it travelled. These then mixed with clouds and fell with the rain. Many scientists accept that comets may be rich in organic chemicals and a few, such as the late Fred Hoyle, the UK theorist, argued that life on Earth evolved from microbes that had been brought here on comets. But most researchers say that Louis is making too great a leap in connecting his rain with microbes from a comet.

For his part, Louis is unrepentant. ‘If anybody hears a theory like this, that it is from a comet, they dismiss it as an unbelievable kind of conclusion. Unless people understand our arguments – people will just rule it out as an impossible thing, that extra-terrestrial biology is responsible for this red rain.’

Source: The Guardian

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