DNA is a great way to store information—just ask your cells. Its molecules are stable, and billions of base pairs coil neatly into a few microns in a cell nucleus. While it’s easy for a cell to read information from DNA, a cell can’t rewrite new data into its DNA sequence.
But now synthetic biologists at Stanford have managed to pull off that very trick. To do so, they had to abandon the genetic code of ATCG and get a DNA sequence to act like bits—pieces of binary information—in a computer. The memory system uses two enzymes that can cut out and reintegrate a sequence of DNA in a live cell. Crucially, the attachment sites are designed so that the DNA sequence can be flipped every time it is put back in. The sequence oriented one way would represent 1, and its inversion is 0.
Early Earth’s chemical seas are presumed to have given rise to the first life, but how could anything so complex have come from such a disorganized stew of molecules? That’s the question Gerald Joyce of the Scripps Research Institute is exploring with his swarms of self-replicating RNA, which can evolve over time. Along with Steve Benner, Craig Venter, Jack Szostak, and others, he is on the road to creating life in the lab, thus giving us insight into both our origins and what, exactly, “life” is. As Dennis Overbye writes in a look at the field in the New York Times:
The possibilities of a second example of life are as deep as the imagination. It could be based on DNA that uses a different genetic code, with perhaps more or fewer than four letters; it could be based on some complex molecule other than DNA, or more than the 20 amino acids from which our own proteins are made, or even some kind of chemistry based on something other than carbon and the other elements that we take for granted, like phosphorous or iron. Others wonder whether chemistry is necessary at all. Could life manifest itself, for example, in the pattern of electrically charged dust grains in a giant interstellar cloud, as the British astronomer and author Fred Hoyle imagined in his novel “The Black Cloud”?
What’s the News: Several days ago, a tasty tidbit hit the science blogosphere: writing in a journal of the American Chemical Society, scientists reported the successful production of gelatin from human proteins.
Understandably, the verdict of the crowd was, “Groooooosss!” The details of the experiment were dutifully reported—the human gene for collagen, the protein in skin and bones that makes up gelatin, was inserted into a yeast, which then cranked it out, along with the help of certain enzymes—but its purpose was sometimes glossed over in favor of giant images of quivering dessert. Like the one above. Yum.
So why use human genes to make gelatin?
Diagram of the new DNA circuit
What’s the News: Researchers have built the most complex DNA-based computer yet, a circuit of 130 strands of DNA that can compute the square root of numbers up to 15. The system, reported today in Science, is made of biological logic gates, which do computations using DNA strands’ natural propensity to zip and unzip. This new method is easily adapted for different calculations and can be automated, meaning it could be used to build much larger circuits.
Research teams around the world are attempting to develop new tiny synthetic particles that will enter your bloodstream to act as red blood cells, to play the part of platelets and stop the bleeding, to latch onto damaged areas and deliver drugs there, and more. And to make these lab-created particles as effective as possible, they need to stay in one’s system and not get stuck. In this week’s Proceedings of the National Academy of Sciences, Joseph DiSimone and colleagues say they have figured out a way to mimic the twistable, turnable, bendable, foldable nature of red bloods cells to make long-lasting synthetic particles, and that they’ve tested those particles on a living system, a first.
Previous studies had focused on how size, shape and surface characteristics of particles affected their movement through the bloodstream, the team wrote, but flexibility’s role is less well understood. To test it out, the researchers built artificial cells out of a gel material with “tunable elasticity” — that is, the team could control how deformable the cells were. [Los Angeles Times]
Maximizing that elasticity could allow for particles that can wiggle through tiny blood vessels:
It has long been speculated that the deformability of particles influences how long they circulate and where they are distributed in the body. Red blood cells are equipped for longevity and have an average lifespan of 120 days. As they age, they become stiffer and less capable of passing through the tiny vascular structures in the spleen, where they’re ultimately removed. [Nature]
In its first official report, the Presidential Commission for the Study of Bioethical Issues recommended that the budding field of synthetic biology remain unregulated.
In the report‘s (pdf) 18 recommendations, the commission does suggest that synthetic biologists should self-regulate their work and be required to take ethics training. It also recommends that the president’s office better coordinate government agencies to oversee the work. But it stopped short of calling for a halt on research that creates organisms not found in nature.
“The commission thinks it imprudent either to declare a moratorium on synthetic biology until all risks can be determined and mitigated, or to simply ‘let science rip,’ regardless of the likely risks,” the report says. “The Commission instead proposes a middle ground — an ongoing system of prudent vigilance that carefully monitors, identifies and mitigates potential and realized harms over time.” [The New York Times]
Here in the United States, people are all atwitter about Craig Venter’s announcement last week of a new “synthetic cell,” and whether it constitutes creating life or simply a nifty new step in genetic engineering. Across the pond in the U.K., however, there are increasing rumblings of a more practical matter: Whether the patents that Venter is seeking to protect his work will bring a chill to genetic engineering research elsewhere.
Dr Venter’s [team] has applied for patents on the methods it used to create the new organism, nicknamed Synthia, by transferring a bacterial genome built from scratch into the shell of another bacterium. Synthia’s genetic code contains four DNA “watermarks”, including famous quotations and the names of the scientists behind the research, that could be used to detect cases of unauthorised copying [The Times].
Nobel winner John Sulston is the main man sounding the alarm (pdf); he argues that Venter is trying to obtain a “monopoly” on a range of genetic engineering techniques, which would prevent other researchers from freely experimenting with those methods. He’s also a familiar adversary to Venter. The two butted heads a decade ago when scientists were rushing to sequence the human genome.
Craig Venter led a private sector effort which was to have seen charges for access to the information. John Sulston was part of a government and charity-backed effort to make the genome freely available to all scientists [BBC News].
In another step forward in the quest to create artificial life in a test tube, a team of genetic engineers led by Craig Venter has built a synthetic genome and proved that it can power up when placed inside an existing 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.” [The New York Times]
The technical achievement is worth crowing about. The researchers built on Venter’s trick from last year, in which he took the genome from one bacterium, transferred it the hollowed-out shell of a different bacterial species, and watched as the new cell “booted up” successfully. In this new step, the researchers built a genome from scratch, copying the genetic code from a bacterium that infects goats and introducing just a few changes as a “watermark”; then they transferred that synthetic genome to a cell. As the researchers report in Science, the cell functioned and replicated, creating more copies of the slightly altered goat-infecting bacterium–now nicknamed Synthia.
But the reactions to Venter’s accomplishment have been mixed–while some celebratory headlines trumpeted the creation of artificial life, many scientists said the reaction was overblown, and took issue with Venter’s claim of having created a truly synthetic cell. Here, we round up a selection of responses from all corners of the science world.
One small step for flashing bacteria, one giant leap for synthetic biology. In a new Nature study, molecular biologist Jeff Hasty and his team say they have created a line of E. coli bacteria that flash in fluorescent light and keep time like a clock.
Previously, scientists had engineered only single cells to become oscillators — devices that could count time by performing a particular activity on a cyclical schedule [Nature News]. Back in 2008, Hasty and his team created an oscillator for single cells that could be set to temperature or chemical triggers. But now the researchers have induced a whole host of bacteria to work together to keep time by taking advantage of the way they collaborate naturally: quorom sensing.
Although scientists may not have come close to cataloging all the different kinds of life on the planet, genetics pioneer Craig Venter is pressing ahead with his plans to create biology version 2.0. Venter is at the forefront of the new field of synthetic biology, in which scientists try to create all new organisms out of their component genetic parts: “We’re moving from reading the genetic code to writing it” [Pittsburgh Post-Gazette], Venter has said. Now, he and his colleagues have taken the next step towards synthetic life.
In a study published in Science, the researchers explain how they took the genome from the bacterium Mycoplasma mycoides and transferred it to a yeast cell, where established genetic engineering techniques allow for easier tinkering. After altering the genome in several key ways, they transplanted it into the hollowed out shell of a different bacterial species, Mycoplasma capricolum. The breakthrough came when the altered genome “booted up” and began instructing its host bacterium to produce colonies of M. mycoides.
That success will help researchers overcome a stubborn obstacle that has prevented the creation of a made-from-scratch life form. Last year, Venter’s team created a synthetic bacterial genome by stitching together pieces of synthesized DNA. To build a synthetic organism, however, researchers will have to transplant that synthetic genome into a cell and have it successfully reboot the cell. But that last step has proved problematic. The synthetic genome was assembled in yeast, which means it lacked some of the molecular markings characteristic of bacteria. Researchers discovered that without those markings, the host bacterium viewed the transplanted genome as a foreign invader and destroyed it [Technology Review]. In the new study, the researchers added chemical markings called methyl tags to the M. mycoides genome while it was in the yeast cell, permitting the genome to sneak past the host bacterium’s defenses.