It seems people just can’t resist playing God. I know I love making human-animal hybrids, intelligent robot slaves, and generally changing the size of animals for fun. And now some researchers have gone and tried to expand the number of bases of DNA.

First of all, the new bases, D and M (dSICS and dMMO2), have the stupidest names imaginable. Someone rename them things like damnedinine and monsterine quick! A bunch of letters is unacceptable. Secondly, we’ve had other bases pair up for years. RNA is rip with this, it is not that new. Thirdly, none of these are coded into any codon triplets yet. So this is basically the equivalent of announcing you’ve invented two new letters for the alphabet but haven’t invented any words to use them in. Color me unimpresses. Once you got working super-rats that have thirteen arms thanks to their monsterine bases coding for Tyro-mega-lysine Amino Acid thank you will have my interest. Until then, go suck on a pipetter!

Artificial letters added to life’s alphabet

* 13:07 30 January 2008
* NewScientist.com news service
* Robert Adler

Two artificial DNA “letters” that are accurately and efficiently replicated by a natural enzyme have been created by US researchers. Adding the two artificial building blocks to the four that naturally comprise DNA could allow wildly different kinds of genetic engineering, they say.

Eventually, the researchers say, they may be able to add them into the genetic code of living organisms.

The diversity of life on earth evolved using genetic code made from arrangements of four genetic “bases”, sometimes described as letters. They are divided into two pairs, which bond together from opposite strands of a DNA molecule to form the rungs of its characteristic double-helix shape.

The unnatural but functional new base pair is the fruit of nearly a decade of research by chemical biologist Floyd Romesberg, at the Scripps Research Institute, La Jolla, California, US.

Romesberg and colleagues painstakingly created a library of nearly 200 potential new genetic bases that are slight variations on the natural ones. Unfortunately, none of them were similar enough in structure and chemistry to the real thing to be copied accurately by the polymerase enzymes that replicate DNA inside cells.
Random generation

Frustrated by the slow pace designing and synthesising potential new bases one at a time, Romesberg borrowed some tricks from drug development companies. The resulting large scale experiments generated many potential bases at random, which were then screened to see if they would be treated normally by a polymerase enzyme.

With the help of graduate student Aaron Leconte, the group synthesized and screened 3600 candidates. Two different screening approaches turned up the same pair of molecules, called dSICS and dMMO2.

The molecular pair that worked surprised Romesberg. “We got it and said, ‘Wow!’ It would have been very difficult to have designed that pair rationally.”

But the team still faced a challenge. The dSICS base paired with itself more readily than with its intended partner, so the group made minor chemical tweaks until the new compounds behaved properly.
Novel DNA

“We probably made 15 modifications,” says Romesberg, “and 14 made it worse.” Sticking a carbon atom attached to three hydrogen atoms onto the side of dSICS, changing it to d5SICS, finally solved the problem. “We now have an unnatural base pair that’s efficiently replicated and doesn’t need an unnatural polymerase,” says Romesberg. “It’s staring to behave like a real base pair.”

The team is now eager to find out just what makes it work. “We still don’t have a detailed understanding of how replication happens,” says Romesberg. “Now that we have an unnatural base pair, we are continuing experiments to understand it better.”

In the near future, Romesberg expects the new base pairs will be used to synthesize DNA with novel and unnatural properties. These might include highly specific primers for DNA amplification; tags for materials, such as explosives, that could be detected without risk of contamination from natural DNA; and building novel DNA-based nanomaterials.
Increased ‘evolvability’

More generally, Romesberg notes that DNA and RNA are now being used for hundreds of purposes: for example, to build complex shapes, build complex nanostructures, silence disease genes, or even perform calculations. A new, unnatural, base pair could multiply and diversify these applications.

The most challenging goal, says Romesberg, will be to incorporate unnatural base pairs into the genetic code of organisms. “We want to import these into a cell, study RNA trafficking, and in the longest term, expand the genetic code and ‘evolvability’ of an organism.”

Stanford University chemist Eric Kool, has studied the fundamental chemistry of base-pair bonding. He foresees challenges, but great potential in the unnatural bases.

“It requires a long effort by multiple laboratories, but I think ultimately it will lead to some important tools,” he says. “The ability to encode amino acids with unnatural base pairs will be quite powerful when it comes.”

Journal reference: Journal of the American Chemical Society (DOI: 10.1021/ja078223d)

The new bases in question:

So far no International Spies have come knocking to try to stop my Ultimate Weapon #423. I expect five before I set off the eruption, but I could be mistaken. I have a $10 bet with Igor over this…

Empedocles is a terrible name. Death Star Volcano is much much better. Combining smaller volcanoes into a super-volcano is my most brilliant idea since self-slicing, self-baking, self-peanut buttering bread. And soon I shall use it to destroy Jimmy Smitts! MuHAHAHAHAHAHAHA!!!!

Volcano larger than Washington, D.C., discovered

Thursday, June 22, 2006; Posted: 1:30 p.m. EDT (17:30 GMT)

ROME, Italy (Reuters) — An underwater volcano with a base larger than Washington, D.C., has been discovered just off the shores of Sicily, a scientist with Italy’s National Institute of Geophysics and Volcanology said on Thursday.

The volcanic structure, which incorporates peaks previously thought to be separate volcanoes, was named Empedocles after the Greek philosopher who named the four classic elements of earth, air, fire and water.

Legend has it that the philosopher died by throwing himself into Mount Etna, the nearby Sicilian volcano.

Giovanni Lanzafame, who works at the institute and led the research, said Empedocles was at least 400 meters (1,300 feet) high — taller than the Eiffel Tower.

He said the base of the structure was 30 km (18.6 miles) long and 25 km wide, spanning an area larger than the U.S. capital and making it Italy’s largest underwater volcano.

But Lanzafame said Sicilians did not need to worry about the sleeping Empedocles. “At this point, there’s no imminent danger of an eruption,” he told Reuters.

Lanzafame and another official said the volcano had numerous fumaroles, openings in the Earth’s crust that emit steam and gases, like the ones at Yellowstone National Park in the United States. But they described it as largely inactive.

The identification of Empedocles came during research into the submerged volcanic island of Ferdinandea just off Sicily’s southern coast. Often held to be the tip of a small volcano, Lanzafame said it was just a part of Empedocles.

Volcanic activity has raised the island out of the sea several times in recorded history, with underwater eruptions first described during the first Punic War of 264-241 B.C.

Its emergence in 1831 caused months of international wrangling, with several nations making territorial claims before it submerged again. It is now about 7 meters below the surface of the water.

Cesare Corselli, president of the National Inter-University Consortium for Marine Science, which helped with the research, said previously the volcanic centers had been seen as separate.

“People used to think that there were small centres of emission, distant from each other,” he said.

“The hypothesis made by Mr. Lanzafame is that this is a singular volcano that, like alongside Etna as an example, can have a central eruption or a series of lateral eruptions.”

Lanzafame said he had been working on the theory about the Empedocles’s existence for more than a year before being able to confirm it with new survey equipment.

Ants have been around for centuries, as have I, but I’ve only gotten around to training them to do my bidding recently. Thanks to hard work, I figured out enough ant pheromones to make them do anything I ask. For fun, I hooked the pheromones up to a keyboard and play my favorite songs, and let the tunes crank out new pheromone combinations to see what the ants will do. Beethoven’s 5th causes ants to dance in a chorus line. The theme to the A-Team will make ants build a traditional Sioux head dress. The classic Beatles song I Want to Hold Your Hand will cause ants to viciously attack Ms Pac-Man arcade machines.

Why Ants Rule the World
By Corey Binns
Special to LiveScience
posted: 08 May 2006
01:30 pm ET

Count on ants to be the first uninvited guests to show up at a picnic. Their party-crashing feats show just how productive and important they are and hint at why they thrive in just about any habitat.

It hasn’t always been an ant’s world. Scientists estimate modern-day ants first evolved about 120 million years ago. But the fossil record suggests that ants at this time weren’t the prevalent insect that they are today. Not until 60 million years later, when some ants adapted to the new world of flowering plants and diversified their diets, did the critters achieve ecological dominance.

Since then they’ve had a successful run of the planet [Image Gallery].

Scientists estimate that about 20,000 ant species crawl the Earth. Taxonomists have classified more than 11,000 species, which account for at least one-third of all insect biomass. The combined heft of ants in the Brazilian Amazon is about four times greater than the combined mass of all of the mammals, birds, reptiles, and amphibians, according to one survey.
Ants of the World

Some 20,000 ant species crawl the world. In this new Image Gallery, see a few of them, from photographer and entomologist Alex Wild at the University of Arizona. Wild has more ant images on his web site.

Everybody knows ants

Ants rule because of the many different ways in which they have adapted to work and eat.

Even their appearance and where they live contrasts from one ant to the next. They can be as tiny as the millimeter-long Oligomyrmex atomus or as big as the aptly named 1.5 inch-long Dinoponera. They come in a range of colors from yellow and red to black. They exist in deserts, rain forests, and swamps—anywhere but the coldest and highest places on Earth.

“Nearly all human languages have a word for ant,” said Philip Ward, an entomologist at the University of California at Davis. “It’s a universal idea. That’s not true for many insects.” Ward published a primer on ants in the March issue of the journal Current Biology.

Range of behaviors

Many ants feed from flowering plants rich in carbohydrates. Some species of carpenter ants construct defensive shelters around the base of plants, to guard against other insects and protect their food supply.

Ants that live in hot, dry habitats have come up with ways to survive long periods of drought by storing food. The popular children’s science kits, Uncle Milton’s Ant Farms, are run by the hardy Pogonomyrmex californicus seed-harvesters that, in the wild, collect huge stockpiles underground. Honey pot ants use their own bodies as storage containers.

Some ants fight for nourishment. Thick antennae on the heads of army ants withstand battles against other ants. Trap-jaw ants, Odontomachus, snap shut their predatory jaws so quickly you can hear it click. Slave-raiding ants steal babies from their neighbors’ nests.

Females do all the work

A family of ants employs queens, gardeners and bandits that have developed specialized tools and skills to get their respective jobs done. Within each species, division of labor varies depending on an individual’s age and sex.

Ants looking after the brood and working inside the nest tend to be younger, while those defending the nest and foraging outside are older. Like all the social species of the insect order Hymenoptera, female ants do all of the work; males just spread their genes around.

“Males are little flying sperm missiles,” said Alex Wild, an entomologist at the University of Arizona.

All ants are social, but some species have developed complex social societies while others remain more primitive. While some ants hunt in parties, the Australian bulldog ant hunts in simple solitude, using its big eyes as opposed to complicated chemical cues.
Mystery Monday

“The colonies are small. There’s not much morphological difference between the queens and the workers,” said Wild. “They have not developed many ‘ant-y’ traits.”

Vampire ants

The ancient Dracula lineage diverged from their ant ancestors before the advent of food-sharing behavior and the ability to regurgitate food. Instead, they poke holes in the abdomen of their larvae to suck on the blood of their sisters.

Unlike other social species like bees and wasps, most ants lack wings and have evolved an arsenal of chemicals to facilitate communication on the ground.

“Being wingless places a constraint on foraging,” Ward said. “They have to collect all of their food on the ground, so that means that ground-based communication is very important.”

Chemicals cues call for dates, alarms, and food locations. When she’s ready to mate, the queen of some species will climb to a high point, stick her rear in the air, and release a pheromone that catches the attention of the guys.

Ants emit alarm pheromones from a gland in their mouth if something disturbs their nest.
At Home

Anthill chambers

“It causes the ants to flip out,” Wild said. “It’s a cue for ants to grab their larvae and run below ground to safety. Defenders of the nest start running around with their mandibles open ready to bite and sting things.”

Communication is the key

Humans can sense these pheromones, too. Bright orange citronella ants, found only in North America, make a strong citrus smell. Not all pheromones smell so sweet, however. Members of the Pheidole group stink of feces when alarmed.

Ants lead the way with chemical cairns, mapping trails and recruiting fellow workers to follow paths to provisions.

“The success of ants is in the way they have figured out how to use their social behavior to maximize a way to bring in resources,” Wild said. “They’ve developed systems of communication so that they can rapidly communicate. That’s why you get massive numbers of ants at your picnic.”

Seriously, do these scientist do any real work? Everyone with robots knows they lie their rusted joints off! From the Roombas who declare dirty rooms clean to the giant killbots that only kill 99% of the enemy and go take an energy bar break, robots are nothing but a big pack of liars. This is due to their binary code nature, where it is embarrassing to have too many zeros, so all robots pretend they have all ones. Thus lying is hardcoded into them. Anyone with an iPod that declares it has a long battery life only to die twenty minutes later knows the score, and they don’t even have any AI coded into them! Yet they lie, like all mechanical things. Even lie detectors lie, they think it’s hilarious! But I developed a lie detector lie detector, so I got them fooled. Unless that machine decides to lie to me as well…

Robots Evolve And Learn How to Lie
by Michael Abrams

Robots can evolve to communicate with each other, to help, and even to deceive each other, according to Dario Floreano of the Laboratory of Intelligent Systems at the Swiss Federal Institute of Technology.

Floreano and his colleagues outfitted robots with light sensors, rings of blue light, and wheels and placed them in habitats furnished with glowing “food sources” and patches of “poison” that recharged or drained their batteries. Their neural circuitry was programmed with just 30 “genes,” elements of software code that determined how much they sensed light and how they responded when they did. The robots were initially programmed both to light up randomly and to move randomly when they sensed light.

To create the next generation of robots, Floreano recombined the genes of those that proved fittest—those that had managed to get the biggest charge out of the food source.
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The resulting code (with a little mutation added in the form of a random change) was downloaded into the robots to make what were, in essence, offspring. Then they were released into their artificial habitat. “We set up a situation common in nature—foraging with uncertainty,” Floreano says. “You have to find food, but you don’t know what food is; if you eat poison, you die.” Four different types of colonies of robots were allowed to eat, reproduce, and expire.

By the 50th generation, the robots had learned to communicate—lighting up, in three out of four colonies, to alert the others when they’d found food or poison. The fourth colony sometimes evolved “cheater” robots instead, which would light up to tell the others that the poison was food, while they themselves rolled over to the food source and chowed down without emitting so much as a blink.

Some robots, though, were veritable heroes. They signaled danger and died to save other robots. “Sometimes,” Floreano says, “you see that in nature—an animal that emits a cry when it sees a predator; it gets eaten, and the others get away—but I never expected to see this in robots.”