Researchers Say They Created a ‘Synthetic Cell’

Researchers Say They Created a ‘Synthetic Cell’
By NICHOLAS WADE
May 20, 2010
New York Times
http://www.nytimes.com/2010/05/21/science/21cell.html?hpw

The genome pioneer J. Craig Venter has taken another step in his quest to create synthetic life, by synthesizing an entire bacterial genome and using it to take over a cell.

Dr. Venter calls the result a “synthetic cell” and is presenting the research as a landmark achievement that will open the way to creating useful microbes from scratch to make products like vaccines and biofuels. At a press conference Thursday, Dr. Venter described the converted cell as “the first self-replicating species we’ve had on the planet whose parent is a computer.”

“This is a philosophical advance as much as a technical advance,” he said, suggesting that the “synthetic cell” raised new questions about the nature of life.

Other scientists agree that he has achieved a technical feat in synthesizing the largest piece of DNA so far — a million units in length — and in making it accurate enough to substitute for the cell’s own DNA.

But some regard this approach as unpromising because it will take years to design new organisms, and meanwhile progress toward making biofuels is already being achieved with conventional genetic engineering approaches in which existing organisms are modified a few genes at a time.

Dr. Venter’s aim is to achieve total control over a bacterium’s genome, first by synthesizing its DNA in a laboratory and then by designing a new genome stripped of many natural functions and equipped with new genes that govern production of useful chemicals.

“It’s very powerful to be able to reconstruct and own every letter in a genome because that means you can put in different genes,” said Gerald Joyce, a biologist at the Scripps Research Institute in La Jolla, Calif.

In response to the scientific report, President Obama asked the White House bioethics commission on Thursday to complete a study of the issues raised by synthetic biology within six months and report back to him on its findings. He said the new development raised “genuine concerns,” though he did not specify them further.

Dr. Venter took a first step toward this goal three years ago, showing that the natural DNA from one bacterium could be inserted into another and that it would take over the host cell’s operation. Last year, his team synthesized a piece of DNA with 1,080,000 bases, the chemical units of which DNA is composed.

In a final step, a team led by Daniel G. Gibson, Hamilton O. Smith and Dr. Venter report in Thursday’s issue of the journal Science that the synthetic DNA takes over a bacterial cell just as the natural DNA did, making the cell generate the proteins specified by the new DNA’s genetic information in preference to those of its own genome.

The team ordered pieces of DNA 1,000 units in length from Blue Heron, a company that specializes in synthesizing DNA, and developed a technique for assembling the shorter lengths into a complete genome. The cost of the project was $40 million, most of it paid for by Synthetic Genomics, a company Dr. Venter founded.

But the bacterium used by the Venter group is unsuitable for biofuel production, and Dr. Venter said he would move to different organisms. Synthetic Genomics has a contract from Exxon to generate biofuels from algae. Exxon is prepared to spend up to $600 million if all its milestones are met. Dr. Venter said he would try to build “an entire algae genome so we can vary the 50 to 60 different parameters for algae growth to make superproductive organisms.”

On his yacht trips round the world, Dr. Venter has analyzed the DNA of the many microbes in seawater and now has a library of about 40 million genes, mostly from algae. These genes will be a resource to make captive algae produce useful chemicals, he said.

Some other scientists said that aside from assembling a large piece of DNA, Dr. Venter has not broken new ground. “To my mind Craig has somewhat overplayed the importance of this,” said David Baltimore, a geneticist at Caltech. He described the result as “a technical tour de force,” a matter of scale rather than a scientific breakthrough.

“He has not created life, only mimicked it,” Dr. Baltimore said.

Dr. Venter’s approach “is not necessarily on the path” to produce useful microorganisms, said George Church, a genome researcher at Harvard Medical School. Leroy Hood, of the Institute for Systems Biology in Seattle, described Dr. Venter’s report as “glitzy” but said lower-level genes and networks had to be understood first before it would be worth trying to design whole organisms from scratch.

In 2002 Eckard Wimmer, of the State University of New York at Stony Brook, synthesized the genome of the polio virus. The genome constructed a live polio virus that infected and killed mice. Dr. Venter’s work on the bacterium is similar in principle, except that the polio virus genome is only 7,500 units in length, and the bacteria’s genome is more than 100 times longer.

Friends of the Earth, an environmental group, denounced the synthetic genome as “dangerous new technology,” saying that “Mr. Venter should stop all further research until sufficient regulations are in place.”

The genome Dr. Venter synthesized is copied from a natural bacterium that infects goats. He said that before copying the DNA, he excised 14 genes likely to be pathogenic, so the new bacterium, even if it escaped, would be unlikely to cause goats harm.

Dr. Venter’s assertion that he has created a “synthetic cell” has alarmed people who think that means he has created a new life form or an artificial cell. “Of course that’s not right — its ancestor is a biological life form,” said Dr. Joyce of Scripps.

Dr. Venter copied the DNA from one species of bacteria and inserted it into another. The second bacteria made all the proteins and organelles in the so-called “synthetic cell,” by following the specifications implicit in the structure of the inserted DNA.

“My worry is that some people are going to draw the conclusion that they have created a new life form,” said Jim Collins, a bioengineer at Boston University. “What they have created is an organism with a synthesized natural genome. But it doesn’t represent the creation of life from scratch or the creation of a new life form,” he said.

stephen hawking: "humans have entered a new stage of evolution"

http://www.dailygalaxy.com/my_weblog/2009/07/stephen-hawking-the-planet-has-entered-a-new-phase-of-evolution.html

Although It has taken homo sapiens several million years to evolve from the apes, the useful information in our DNA, has probably changed by only a few million bits. So the rate of biological evolution in humans, Stephen Hawking points out in his Life in the Universe lecture, is about a bit a year.

"By contrast," Hawking says, "there are about 50,000 new books published in the English language each year, containing of the order of a hundred billion bits of information. Of course, the great majority of this information is garbage, and no use to any form of life. But, even so, the rate at which useful information can be added is millions, if not billions, higher than with DNA."

This means Hawking says that we have entered a new phase of evolution. "At first, evolution proceeded by natural selection, from random mutations. This Darwinian phase, lasted about three and a half billion years, and produced us, beings who developed language, to exchange information."

But what distinguishes us from our cave man ancestors is the knowledge that we have accumulated over the last ten thousand years, and particularly, Hawking points out, over the last three hundred.

"I think it is legitimate to take a broader view, and include externally transmitted information, as well as DNA, in the evolution of the human race," Hawking said.

In the last ten thousand years the human species has been in what Hawking calls, "an external transmission phase," where the internal record of information, handed down to succeeding generations in DNA, has not changed significantly. "But the external record, in books, and other long lasting forms of storage," Hawking says, "has grown enormously. Some people would use the term, evolution, only for the internally transmitted genetic material, and would object to it being applied to information handed down externally. But I think that is too narrow a view. We are more than just our genes."

The time scale for evolution, in the external transmission period, has collapsed to about 50 years, or less.

Meanwhile, Hawking observes, our human brains "with which we process this information have evolved only on the Darwinian time scale, of hundreds of thousands of years. This is beginning to cause problems. In the 18th century, there was said to be a man who had read every book written. But nowadays, if you read one book a day, it would take you about 15,000 years to read through the books in a national Library. By which time, many more books would have been written."

But we are now entering a new phase, of what Hawking calls "self designed evolution," in which we will be able to change and improve our DNA. "At first," he continues "these changes will be confined to the repair of genetic defects, like cystic fibrosis, and muscular dystrophy. These are controlled by single genes, and so are fairly easy to identify, and correct. Other qualities, such as intelligence, are probably controlled by a large number of genes. It will be much more difficult to find them, and work out the relations between them. Nevertheless, I am sure that during the next century, people will discover how to modify both intelligence, and instincts like aggression."

If the human race manages to redesign itself, to reduce or eliminate the risk of self-destruction, we will probably reach out to the stars and colonize other planets. But this will be done, Hawking believes, with intelligent machines based on mechanical and electronic components, rather than macromolecules, which could eventually replace DNA based life, just as DNA may have replaced an earlier form of life.

Casey Kazan

Source: http://www.rationalvedanta.net/node/131

Tendency Toward Complexity

i'm currently reading "shantaram," by gregory david roberts. it's a fascinating book about a fugitive's life in india, first living in a slum, then working with the mafia. however, there are many times in the book when he waxes philisophical and it just annoys me, usually because it's not quite how i view the world.

but in one conversation they discuss the meaning of the universe and how you define good and evil. i couldn't believe how much it seemed to sum up my thoughts these days about evolutionary extinction and how nothing in the universe is random. i will insert those passages here when i have time, but basically since the "big bang" the universe has been expanding and forming more complex, moving towards an order. it is the "tendency toward complexity," and maybe "god" is the ultimate complexity.

i haven't wrapped my mind yet around the good and evil aspect of it; that good is anything that helps the universe along toward the ultimate complexity, and evil is anything that holds it back.

i'm looking forward to exploring this further!

evoluntionary extinction revisited

Researchers were building robot nanoworms, designed to seek out and kill cancer cells, and swarms of robot dragonflies for the U.S. military. South Korean customs authorities began training seven clones of Chase, their preeminent sniffer dog, and Sri Lankan researchers announced success in teaching mongoose-robot teams to detect land mines.

- Harpers Magazine, July 2008, Findings pg. 96.

(also see my blog post from dec. 11, 2007, and all the comments for more on our shift toward nanotechnology, the merging of technology and humanity, and evolutionary extinction.)

artificial life

from "findings," harper's magazine, april 2008:

american scientists artificially reproduced the dna of a venereal-disease bacterium and expected to use the technique to create artificial life within ten years.

man clones himself

from harper's, march 2008, pg. 96 "findings":

japanese scientists unvelied a robot that plays the violin, a robot that solves rubik's cubes, a robot that recognizes itself in a mirror, a robot snoplow that eats snow and excretes ice bricks, a robot exoskeleton that can be worn be elderly farmers, and a robot that walks at the command of a monkey on a treadmill in north carolina.

a california scientist used skin cells to create embryonic clones of himself.

more on evolutionary extinction

from harper's (magazine), june 2007, pg. 96, "findings":

scientists in nevada created a sheep-human hybrid that is about 15 percent human; other researchers successfully grew sperm from human bone marrow, which could theoretically lead to a future in which pairs of lesbian mothers can produce their own daughters without the intervention of a male.

roboticists were working hard to create robots that will interact "rhythmically" with humans.

from harper's, april 2007, pg. 108, "findings":

a woman with a bionic arm can now sense her missing fingers in her chest.

new cloning techniques

"Skin cells bring cloning a step nearer to efficiency," Nicholas Wade, New York Times, Jan. 5, 2000The much-heralded era of animal cloning has moved closer to fruition with a new technique that seems far more efficient than earlier methods. With the new cloning technique, four calves, now 7 months to 9 months old, have been cloned from skin cells scraped from the ear of a prize Japanese bull.

god has been cloned

i read this in Harper's Magazine and it changed my life, giving me my new fascination with evolutionary extinction and cloning, and i further took it toward it's natural conclusion of robots, androids and nanotechnology.

GOD HAS BEEN CLONED..:
(From a book of interviews between Jean Baudrillard and Enrique Valiente Noailles, Exiles from Dialogue, to be published next month by Polity. Baudrillard, who died in March, was the author of more than fifty works of philosophy and criticism, including
Simulacra and Simulation. Noailles is a philosopher and journalist. Translated from the French by Chris Turner.)
ENRIQUE VALIENTE NOAILLES: You say there's sometimes a simultaneous upsurge of good and evil – that combating evil leads to reactivating it.
JEAN BAUDRILLARD: You've only to take the "zero deaths" formula, a basic concept of the security order. It's clear that this equates mathematically to "zero lives." By warding off death at all costs (burdensome medical treatment, genetics, cloning), we're being turned, through security, into living dead. On the pretext of immortality, we're moving toward extermination. It's the destiny of maximum good, of absolute happiness, to lead to a zero sum. Illusion – that is, evil – is vital. When you exchange this vital illusion for the unconditional promotion of good, then you're heading for a blowback from the accursed share. This is how things are getting better and better yet, at the same time, worse and worse.
NOAILLES: History might be an attempt to annihilate one part of the duality.
BAUDRILLARD: Human beings can't bear this duality either in the world or in themselves. They can't bear failing the world by their very existence, nor the world failing them. They've sown disorder everywhere, and in wishing to perfect the world, they end up failing themselves. Self-hatred fuels the whole technological effort to make the world over anew. It's on this failing of existence that all religions thrive. You have to pay. In the past, it was God who took the reprisals; now we do it. We have undertaken to inflict the worst on ourselves, and to engineer our disappearance in an extremely complex and sophisticated way, in order to restore the world to the pure state it was in before we were in it.
NOAILLES: Perhaps the Last Judgment has taken place, and we're carrying out the punishment.
BAUDRILLARD: A fine metaphysical hypothesis, except that this self-hatred is a turn taken by Western subjectivity, and also one it's currently imposing on the rest of the world. This nihilism begins with Romanticism, but it has now become a major undertaking, an enterprise of self-immolation by technology against a background of obscure resentment at the evil spirit that's dragging us into it. So depending on how you see it, it can be taken as a challenge in suicidal form or as the enactment, as you said, of God's judgment.
NOAlLLES: What makes it look more like a punishment being carried out than a suicide is that it's taking place in slow motion.
BAUDRILLARD: And cloning can be said to be a slow-motion suicide – not a sudden disappearance but an innovative form of extinction of the species by doubling. The obliteration of something by that selfsame thing is the definition of suicide.
NOAILLES: This could also be a repetition of the original act: in the same way as we received it, giving the world over to another species, handing on the torch. We can't do any more with it, so over to you!
BAUDRILLARD: It's a way of being rid of the problem, of relieving ourselves of the responsibility by devolving it to another – artificial species; a way of telling God, "Sort it out with them!" But that's just a dream. One question remains: Isn't the process of artificial perpetuation of the species – which runs counter to evolution – part of evolution? "Natural" evolution wants species to disappear. It isn't just a biological fact that every species and every individual wishes both to survive and at the same time to disappear. It isn't just that it's destined to disappear but that it wants to, by another kind of will, and does all it can to do so. Human beings are opting to break that rule today by aiming for immortality, through cloning and many other things. But aren't they actually obeying the same rule or even bringing about an accelerated disappearance? It might be an opportunity for the human race, by putting a world of clones into orbit, to recover its original form, but God will be forced to clone himself too! It would take a clone-God to manage a world of clones.
NOAILLES: Nietzsche's madman, who went looking for God with a lantern in the daytime, would run off horrified, shouting, "God has been cloned!" And if we've materialized the kingdom of God in this world, we've created an immanence with all the tools of transcendence, including salvation and damnation. If what Saint Thomas Aquinas cruelly points out is true-"So that the saints may enjoy their beatitude and the grace of God more abundantly, they are permitted to see the punishment of the damned in hell"-it is perhaps this deep delight in the misfortune of others that's the engine of the duplication.
BAUDRILLARD: But we're already in this artificial world. We've already become clones here and now. We've already exchanged transcendence for the law of DNA. The moral law, Kant's law, the one that was written in the starry sky and in man's inner world, is now inscribed in the genetic code. There's no ideal site of consciousness any longer. And if in the past we could symbolically exchange this world with God under the sign of a moral law we'd invented, we can't exchange it for anything any longer, except the spectral universe that awaits us. Even in the economic field, the field of exchange par excellence and of value, we're beginning to realize, as generalized speculation takes over, that it's the nothing that circulates. And this is why things are going faster and faster, no longer being hampered by either the moral law or the law of value. There's obviously an extraordinary fragility in this, which shows up in the perpetual crisis of the economic and political spheres. But there's a complicity in this exchange of the nothing, a deep complicity that has a bright future because it's a collusion between criminals, between accomplices in the perfect crime. There will no longer be anyone to say the emperor has no clothes, no longer anyone to betray the fact that all this generalized exchange is based on nothing and that it can generalize itself only on the basis of the nothing. If this were revealed, it would be the apocalypse in the literal sense, and we would stand before the nothing as a fait accompli.