Un-Natural Selection: Human Evolution's Next Steps
by Joe Palca
Human beings are defying nature. Or at least we’re trying to.
For billions of years, species have evolved by natural selection, the process by which genetic mutations that help an organism survive are passed on from one generation to the next and harmful ones are eliminated.
But natural selection takes time — sometimes millions or even hundreds of millions of years. Humans have only been around for tens of thousands of years, but we are changing the world so much that genetic evolution simply can't keep up.
Millions of years ago, the natural environment was shaping us into the species we are now. Today, we create our own environments, and that has its consequences.
John Hawks, an anthropologist and geneticist at the University of Wisconsin, Madison, says we've created a lifestyle that is at odds with the one natural selection provided us with. Consider, for example, what ate when we were hunter gatherers, long before we started farming.
"We adapted to a diet that was much more balanced in terms of lean meat, in terms of high fiber vegetables. And by de-accentuating those aspects of our former diet, we've created a new environment that humans aren't real suited to," Hawks says.
Sometimes, though, genetic adaptation can happen fairly quickly. Hawks says the classic example is a mutation in a gene that makes red blood cells. It's called the sickle-cell mutation and spread through Africa once malaria became a problem there.
“That's a highly adaptive mutation where it occurs when there's malaria around, because it's protective against malaria," says Hawks. If you inherit the mutation from just one parent, you don't get sick. You only get malaria protection. It's only when you inherit the mutation from both parents that you get sickle-cell anemia. So if you're not living in a malaria environment, the mutation is just bad.” And you don’t want that gene, Hawks says, because your offspring have a chance of having sickle-cell anemia.
Keeping Bad Mutations Around
Really bad mutations tend to disappear, because the people who have them frequently don't live long enough to pass them on. That's what natural selection is all about.
But now in some cases we choose to keep these bad mutations around. Take the gene mutation that causes phenylketonuria, or PKU. People with the disease can't break down the amino acid phenylalanine, a problem that can lead to severe cognitive damage.
"It's a devastating disease that you can completely eliminate if you pick it up early," says Matthew Hirschfeld, a pediatrician at Alaska Native Medical Center.
And it can be picked up very early — there's a genetic test for PKU that all babies in the U.S. get at birth. The treatment includes maintaining a diet with low levels of phenylalanine.
But curing the disease does not mean eliminating the mutation. Once upon a time, children born with PKU probably would never have offspring. Now they can, and that helps keep the mutation in circulation.
Choosing Our Genes
In fact, a large part of modern medicine is in the business of overcoming bad mutations.
“We want to have cures for things, we want to make things better," says Hawks. We do this with eye sight: Nearsightedness could have been fatal for people whose ability to survive depended on spotting dinner off in the distance. Now it doesn't matter if we inherited nearsightedness — we wear eyeglasses.
"We wear contact lenses," says Hawks."You get Lasik surgery. We can affect eye sight in many different ways. It's not perfect, but like many instances of technological development, we tinker at it and it changes and eventually we come to a point where we like it or keep changing.
We've turned the notion of natural selection on its head. Nature isn't the only force that picks the genes that stick around — we're doing it too. We're moving toward a time when we can routinely repair, remove or even insert genes in people.
The question is whether we can do as good a job as nature has done up until now.
Showing posts with label complexity. Show all posts
Showing posts with label complexity. Show all posts
Tuesday, September 07, 2010
Tuesday, May 25, 2010
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.
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.
Monday, August 31, 2009
robots learn to lie
granted, this probably didn't go beyond the scope of what they were programmed to do, but it's still freaky nonetheless.
10 robots were given points for how often they went for "food," a light-colored ring on the floor vs. "poison," a darker ring at the other end of the space. the robots had blue lights that went off randomly but gave away their position. there were only 8 spots near the food, so they had to compete for the spots. the robots who were the best at finding food went on to the next round. after 50 rounds, the robots started deceiving each other by not emitting their blue light so as not to give away their position when they were near food.
10 robots were given points for how often they went for "food," a light-colored ring on the floor vs. "poison," a darker ring at the other end of the space. the robots had blue lights that went off randomly but gave away their position. there were only 8 spots near the food, so they had to compete for the spots. the robots who were the best at finding food went on to the next round. after 50 rounds, the robots started deceiving each other by not emitting their blue light so as not to give away their position when they were near food.
Monday, July 20, 2009
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
Wednesday, June 24, 2009
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!
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!
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