Artificial life, thy name is AEGIS

dustindriver | Categroies: Biology, Genetics | Tags: , , , , , | Monday, March 2nd, 2009

“It’s evolving. It’s doing what we designed it to do.” That sentence isn’t from the chilling trailer for the next Michael Chrichton adaptation. It’s the words of an honest-to-goodness biochemist describing his creation, a synthetic self-replicating jumble of chemicals called AEGIS—Artificially Expanded Genetic Information System. 

AEGIS is an experiment devised by biochemist Steve Benner at the Foundation for Applied Molecular Evolution that aims to get at the roots of life itself by creating artificial self-replicating chemicals that are capable of evolution. And it works. Benner has AEGIS happily replicating and evolving in a beaker in his Florida lab. What makes AEGIS different than everyday life? For starters, it has 12 base pairs instead of four. Beyond that, information is sketchy, but Benner assured Discover News that AEGIS is thriving. In fact, it’s the first synthetic genetic system capable of Darwinian evolution.

Now all we have to do is wait for it to escape and consume us all.

I plan to contact Benner in the coming weeks to get more info about AGIS—how it was created, what he’s learned. Look for an update.

And thanks to Matt Chisholm for the tip!

Link to MSNBC article

MIT chemists hack plant to make drugs

dustindriver | Categroies: Biology, Engineering, Green Tech | Tags: , , , , | Wednesday, January 28th, 2009

Chemists at MIT have hacked a periwinkle plant to produce anti-cancer and hypertension-fighting drugs. The chemical engineers modified the plant’s existing chemical assembly line, tweaking genes to create chemical components of the medicines. The researchers engineered mutant forms of a gene and inserted them into plant cell cultures, causing the plant to produce chemical compounds it would never produce in nature.

Plants are essentially chemical factories, capable of fusing molecules to form virtually any compound. With enough tweaking, we could coax them to build everything from medicines to fuels to super-strong building materials to revolutionary soda pop. If we can control how plants grow, we can do almost anything.

Link to MIT story

Bad boys get the girls

dustindriver | Categroies: Biology, Environment | Tags: , , , , | Wednesday, June 18th, 2008

We’ve all seen how dames are drawn to bad dudes like iron filings to electro-magnets. Now scientists have confirmed the anecdotal evidence: Bad guys really do get the girls. Peter Jonason at New Mexico State University in Las Cruces found that guys who harbor three antisocial personality traits, dubbed the “Dark Triad,” had far more sexual partners than nice guys.

What’s the Dark Triad? A nasty, prickly trident forged from narcissism, psychopathy and Machiavellianism. Members of the Dark Triad aren’t antisocial like chain-smoking basement shut-ins huddling in the warmth of their Xbox 360s. They’re charismatic, outgoing and popular. They just don’t give a flying squirrel about other people’s feelings and will do pretty much anything to get what they want. Which, in this case, is lots of sex with multiple partners.

Jonason tested 200 college guys for the telltale signs of Dark Triadism. Those who racked up the highest evil scores had far more sexual partners than goody-two-shoes. The scientist theorizes that there must be some sort of evolutionary advantage to being just a little evil, otherwise the Dark Triad of personality traits would’ve been bred out of the population ages ago. He believes that it simply comes down to bad guys being able to spread their seed more effectively than good guys. They may not stick around to raise psychologically healthy kids, but they produce a lot of them.

If being a card-carrying member of the Triad is so good, from an evolutionary standpoint, then everybody should be a certified psychopath, right? That’s obviously not the case and researchers have yet to discover why. There must be negative aspects of membership in Club Evil (like incarceration, getting gunned-down by other psychopaths in Old-West style shootouts, contracting STDs). 

Another possibility, and I’m just talking off the cuff now, is that these personality traits aren’t actually inborn. They’re learned. It may explain why the kids of Dark Triad dads don’t all turn out to be bad apples.

Research is still being carried out to answer these questions. In the meantime, it may payoff to flip up your collar and adopt a wicked scowl.

Link to NewScientist article. 

U.C. Berkeley bioengineers discover possible youth serum

dustindriver | Categroies: Biology, Genetics, Medicine | Tags: , , , | Tuesday, June 17th, 2008

A U.C. Berkeley team has rejuvenated geriatric stem cells, restoring their youthful vigor and ability to rebuild damaged muscle tissue. With a simple injection of bioengineered antibodies, crotchety mice were able to recover from strenuous exercise and injury as well as spry young mice. The trick? The antibodies modified how adult stem cells respond to natural chemical signals that trigger aging.

 Irina Conboy, assistant professor of bioengineering and an investigator at the Berkeley Stem Cell Center and at the California Institute for Quantitative Biosciences (QB3), led the research team. She noticed that adult mice stem cells, when placed in “young” blood, behaved like young stem cells. They kicked into overdrive, dividing and repairing. Conversely, young stem cells slowed to a crawl when placed in “old” blood.

The researcher discovered that the cells were responding to two natural chemical signals via a set of receptors. The first receptor, called Notch, activates elated cell replication. The second, a receptor for the protein TGF-beta, sets off a chain reaction that slows cell division. Too much Notch and cells can divide too quickly, hastening tumor and cancer growth. Too much TGF-beta and adult stem cells slow down; cells succumb to the ravages of aging.

Conboy and her team knocked out the “aging pathway” that halts cell replication using a method of RNA interference and a custom antibody. The result: Old mice with the stem cells of young mice.

More research needs to be carried out before any such methods can be used on humans. Conboy fears that interrupting the aging pathway could lead to hyperactive cell division and increased rates of cancer. 

Link to U.C. Berkeley article.

Venter vows to vanquish oil industry

Craig Venter etched his name into the annals of history by decoding the human genome (his own genome, in fact) in less time than it takes the ebola virus to replicate. Now he has his sights set on oil. In a recent Newsweek interview with Fareed Zakaria, Venter outlines his plans to genetically engineer bacteria that will suck up C02 and spit out ethanol or biodiesel. The bug could solve two of humanity’s biggest problems—global warming and a dwindling supply of fossil fuels. From the interview:

Zakaria: How are you going to create the fuel of the future? 
Venter: We think multiple fuels of the future are going to come out of biology, by manipulating the genetic code of simple organisms to convert things like sugar or sunlight or carbon dioxide into fuels that people are very familiar with, like diesel fuel and gasoline.

What would a “refinery” that uses microorganisms to create fuel look like? 

They’re just large, bacteria-processing fermenters. People are familiar with this: that’s how wine and beer are made. We’re using similar processes, but ones that are designed to produce much more complex molecules than ethanol, and therefore fuels that will be much higher in energy content, and will work well with the existing energy infrastructure.

How close are you to creating an organism that can produce fuels in this way? 
We think the first fuels are maybe one to two years away. We’re definitely thinking in terms of years, not decades.

It’s a must-read interview that’ll fill even the most pessimistic doomsday prognosticators with warm fuzzy optimism. Kinda like wine and beer. All hail our genetically modified bacterial overlords!

Link to Newsweek article. 

Building blocks of life may have come from space

dustindriver | Categroies: Astronomy, Biology, Environment, Physics | Tags: , , , | Saturday, June 14th, 2008

Scientists have discovered new evidence that the basic building blocks of life were sprinkled across the solar system like the spores of a great intergalactic mushroom. The joint team of U.S. and U.K. scientists uncovered nucleobases—the bits that make up DNA and RNA—within fragments of the Murchishon meteorite, which plowed into the Australian desert in 1969. 

The two nucleobases, racil and xanthine (which, incidentally would be fantastic names for fraternal twins), were analyzed to ensure that they weren’t created when the meteorite crashed to earth. Both compounds contained heavy carbon atoms which can only be formed in space.

Lead researcher Dr Zita Martins, of the Department of Earth Science and Engineering at Imperial College London, told ScienceDaily that primeval life on earth could have incorporated nucleobases from meteorites about 3.8 to 4.5 billion years ago, when meteor showers were common. 

The discovery gives hope that life could flourish across the universe. Co-researcher Professor Mark Sephton, in a ScienceDaily article:

 

“Because meteorites represent left over materials from the formation of the solar system, the key components for life — including nucleobases — could be widespread in the cosmos. As more and more of life’s raw materials are discovered in objects from space, the possibility of life springing forth wherever the right chemistry is present becomes more likely.”

Link to ScienceDaily article.

 

Clone your dog

dustindriver | Categroies: Biology, Genetics | Tags: , , , , , | Tuesday, June 10th, 2008

One of the first dog clones, made by BioArts International.

Why settle for one lovable pooch when you could have two genetically identical lovable pooches? U.S. biotech firm BioArts International is auctioning off its recently perfected dog cloning service to five lucky pet owners on June 18th. The company has been working since 1998 to make dog clones a reality and has, to date, xeroxed at least four pups. 

The company uses somatic cell nuclear transfer (SCNT) to spawn the canines, the same procedure that scientists used to create Dolly, the first sheep clone, at the Roslin Institute in Scotland. The process involves swapping the nucleus (and thus, DNA) of an animal’s cell with the nucleus of an unfertilized egg cell. If the switcheroo works, the clone will grow. Clones begotten by SCNT aren’t genetically identical to their parents, however. SCNT does not clone mitochondrial DNA, so the dopplegangers are actually genetic chimeras, borrowing mitochondrial DNA from the donor egg cell.

BioArts International is an offshoot of Genetic Savings & Clone, a company known for its cat duping service. The company grew the world’s first cat clone in 2001 and began replicating felines for customers in 2004. Lou Hawthorne, CEO of Genetic Savings & Clone, founded BioArts International in 2006 to research companion animal cloning, livestock cloning and human genomics. The company has been granted the only worldwide license for cloning cats, dogs and endangered species.

Link to gizmag article.

Link to BioArts site about the first dog clones.

Cuttlefish learn to kill before they hatch

dustindriver | Categroies: Biology, Genetics | Tags: , , , | Friday, June 6th, 2008

Fetal cuttlefish peers through the shell of its egg.

Either it’ll give you the screaming heebeegeebees or fill you with a rapturous awe of nature: Fetal cuttlefish can identify and remember prey through the gelatinous, translucent shells of their eggs. That’s right, everyone’s favorite tentacle-mustachioed mollusk is a dyed-in-the-wool killer before birth.

It’s the first known instance of a fetus learning visual cues and scientists are wondrously confounded. So how does one teach a fetal cuttlefish? Ludovic Dickel and a team of scientists at the University of Caen Basse-Normandy, France, simply placed crabs alongside cuttlefish eggs. These cuttlefish preferred to dine on crab when they grew up. Cuttlefish who aren’t exposed to crab before they hatch prefer shrimp.

Dickel believes the fetal cuttlefish can see through their shells and make mental menus of their future prey.

Add this feat to the cuttlefish’s already impressive list of talents: dextrous tentacles, ink cloud, hydro-jet propulsion and color-changing dermis.

Link to BBC article.

Scientists find, eliminate your one true weakness

dustindriver | Categroies: Biology, Genetics, Medicine | Tags: , , , , | Tuesday, June 3rd, 2008

Researchers at UC Berkeley are working with the Defense Advanced Research Projects Agency (DARPA) to target and eliminate (with extreme prejudice) genetic weaknesses that can cause general performance deficits in otherwise healthy people.

The team of scientists, led by researcher Nicholas Marini and molecular and cell biology prof Jasper Rine, hope to pinpoint small genetic defects that can affect the efficiency of common enzymes. These enzyme deficiencies don’t express themselves as full-blown illness, but can cause fatigue, general malaise and other mild symptoms that can really screw up your day. Once the weaknesses are identified, doctors should be able to brew customized vitamin concoctions to counteract them.

ScienceDaily recently spoke with Marini. From the interview:

“Our studies have convinced us that there is a lot of variation in the population in these enzymes, and a lot of it affects function, and a lot of it is responsive to vitamins,” Marini said. “I wouldn’t be surprised if everybody is going to require a different optimal dose of vitamins based on their genetic makeup, based upon the kind of variance they are harboring in vitamin-dependent enzymes.”

No news on whether these super serums would turn the average cubicle jockey into a superstar, but the research looks promising so far. The team injected a sampling of human genes that code for an enzyme called methylenetetrahydrofolate reductase (MTHFR) into yeast cells. The enzyme uses the B vitamin folate to build DNA nucleotides. The researchers found that some variations of the gene were better at synthesizing MTHFR than others. They were then able to add supplements to the yeast diet to make up for the differences.

Marini and Rine guess that most people have about five rare mutant enzymes that could be counteracted with proper supplementation. 

From the ScienceDaily interview:

“There are over 600 human enzymes that use vitamins or minerals as cofactors, and this study reports just what we found by studying one of them,” Rine said. “What this means is that, even if the odds of an individual having a defect in one gene is low, with 600 genes, we are all likely to have some mutations that limit one or more of our enzymes.”

With the price of genetic testing approaching an all-time low (some estimate that it’ll soon cost about 100 bucks for a full sequence), the findings seem promising.

So what’s the DARPA connection? Again, from the ScienceDaily interview:

“Our soldiers, like top athletes, operate under extreme conditions that may well be limited by their physiology,” Rine said. “We’re now working with the defense department to identify variants of enzymes that are remediable, and ultimately hope to identify troops that have these variants and test whether performance can be enhanced by appropriate supplementation.”

Link to the ScienceDaily article.

 

 

Take your vitamins, live forever.

dustindriver | Categroies: Biology, Medicine | Tags: , , , , | Saturday, May 31st, 2008

In the future, legions of centenarians will romp through fields of flowers like spry teenagers, unimpeded by the ravages of old age. Or at least that’s what pharmaceutical juggernaut GlaxoSmithKline is betting on. The drug company recently spent $720 million on Sirtris Pharmaceuticals, a young upstart in the field of anti-aging research. The burgeoning company’s premiere drug is called “resveratrol” and it mimics the preserving effects of severe calorie restriction.

Cutting back on calories has been shown to extend life spans in everything from yeast to humans. Resveratrol targets a gene that becomes active during such sparse times, reenergizing fatigued mitochondria. The cell powerhouses are susceptible to corrosive oxidation by free radicals, the destructive byproducts of burning chemical energy in our bodies. This corrosion is thought to be at the feebly beating heart of all aging-related ailments, from heart disease to dementia. Repair mitochondria and reverse aging—or so the theory goes.

Brandon Keim of Wired News spoke to David Sinclair, cofounder of  Sirtris, at the World Science Festival Monday. Sinclair said resveratrol is in phase two of clinical trials and should hit the market within four or five years. The price for virtual immortality? $4 to $5 a pill, said Sinclair.

Link to Wired Science article

Link to Sirtris Pharmaceuticals

 

 

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