First functional synthetic bacterial genome announced
Craig Venter, who has been a prominent figure in genome research, has been using Science magazine as a host for updates on his latest project: building a bacteria that runs off a genome engineered for specific tasks. As of early 2008, his research group had managed to assemble the entire genome of a small bacteria in a yeast cell, starting with nothing but mail-order DNA. At the time, it seemed like just a short step from there to having that DNA running a cell. That short step took a year and a half, and there were some stumbles along the way.
For starters, the original bacterial genome that the team had assembled came from an extremely slow-growing strain, which complicated the process of growing out cells with the replacement genome. So they switched to a related species, Mycoplasma capricolum. M. capricolum turned out to have a defense system against foreign DNA based on a restriction enzyme that cut any DNA originating in yeast into small pieces; the researchers eventually found the gene responsible and deleted it from the genome of the bacteria.
There were also issues with contamination from the yeast's own linear chromosomes, which the authors found a clever solution for. Instead of trying to separate huge DNA molecules out on a gel, they simply formed the gel around the DNA. The fibers of the gel actually extended through the circular bacterial chromosome, trapping it in place so that when a current was applied, the yeast chromosomes flowed out of the gel, leaving purified bacterial DNA behind.
The last (and perhaps most annoying) problem they faced was an assembly error: their million-base artificial chromosome contained a single base deletion that just happened to reside in an essential gene called dnaA. By gradually transferring smaller pieces of chromosome, they narrowed the problematic region of the genome down until they identified and corrected this issue. With that fix, the authors were finally able to get the genome into a host cell, and have it replace the original one.
Ultimately, this is just another step on the way to a designer genome, one with a specific set of genes that rewire the bacteria's metabolism to produce a specific biomolecule, digest a toxin, or something of that nature. We're still not there yet, although it seems likely that some of the solutions developed during this work will speed the process in the future. Still, the number of things that went wrong here suggest that the synthetic genome approach won't necessarily be the quick-and-easy route to designer organisms that some have expected.
Science, 2010. DOI: 10.1126/science.1190719 (About DOIs).Read the comments on this post
Read More ...
Australia would like to see your porn collection
The Australian Sex Party is not a major player (no pun intended) on the political scene, with only 2,000 members and a couple of staffers. But the group made news across Australia this week when it highlighted a little-noticed change to the country's Incoming Passenger Cards—a new question about pornography.
Most people entering Australia must fill out the customs card, which asks whether they are carrying food items, wood products, steroids, illegal drugs, or huge quantities of cash. For the last few months, the card has also asked if they are carrying "pornography."
Read the comments on this post
Read More ...
Take the horse, leave the prince: the games to buy this week
This Tuesday saw a huge rush of game releases hit store shelves, and for those gamers with a limited gaming budget, picking the right ones can be a little bit of a challenge. That's why we're here! Let's run down this week's releases and give some recommendations on what you should buy, what you should rent, and what is safe to ignore.
Read the comments on this post
Read More ...
Google data collection eyed by Congress, class action lawsuit
The heat is being turned up on Google over its recent WiFi data collection incident. Two members of Congress have now sent a letter to the FTC asking a series of questions about how Google's actions might be covered by federal law and what actions the FTC might take. The letter is short and sweet, but it shows that there is growing concern in Congress over Google's "mistake."
The letter, signed by Rep. Joe Barton (R-TX) and Rep. Ed Markey (D-MA), first asks if the FTC has begun investigating the issue and what the Commission's understanding is of the type of data collected. Who had access to the data? Did Google collect people's passwords? Did the company violate the public's expectation of privacy? Were Google's actions illegal?
These are all questions that the two congressmen want the FTC to answer by June 2. Of course, they're not the only ones asking the FTC to take a look into Google's gaffe—earlier this week, public interest group Consumer Watchdog also called on the agency to investigate Google's "flagrant intrusion into consumers' privacy." German authorities have also demanded that Google hand over the hard drives it used to store the data.
Google's voluntary admission definitely touched a sensitive nerve with lawmakers and the public alike, and the company is now paying the price—at least in terms of increased scrutiny. The search giant has arguably been walking on thin ice when it comes to perceptions of how it protects its users' privacy, but in this case, it may have softened the blow (slightly) by coming out about the "mistake" before anyone else noticed.
Update: Google's data collection mistake is now also the subject of a class action lawsuit out of Oregon. The plaintiffs alleged that "hundreds if not thousands of Google employees throughout the United States and the world have access to data maintained on Google's servers." EU justice commissioner Viviane Reding has also accused the company of flouting EU privacy regulations.
Read the comments on this post
Read More ...
Figuring out how fast the ocean is warming
We recently described a proposal that would improve the tracking of global surface temperatures by generating a unified data set and providing validated methods to adjust for systemic errors in the data. A paper in Nature shows just how valuable that effort could be. By using a single data source and comparing different methods of calculating ocean temperatures, the work identifies why there are differences among the estimates, and comes up with a robust number for how quickly the ocean has been warming over the last decade and a half.
The oceans, because of water's high heat capacity, don't respond very quickly to changes in the climate. And, even as they do respond, they don't do so evenly; various currents and stratification between the surface and deep waters ensures that any mixing is fairly slow and complex. Nevertheless, it's important to find out what the ocean is up to, since better understanding how it exchanges heat with the atmosphere can inform both global and regional climate models.
Read the comments on this post
Read More ...
Hands on with the Kindle reader for Android
Amazon recently revealed plans to bring its Kindle e-book application to Google's Android mobile platform. I got a hands-on demo of the software prototype, which the book vendor brought to Google I/O. Much like the desktop and iPhone versions, it has support for synchronizing with Amazon's cloud. Page number, notes, and other information will transparently match up across all supported devices.
Screen readability is good and offers a solid reading experience. Users can select from several different font sizes and background colors. Options include a sepia mode and a white-on-black mode for night reading. The application user interface has a brightness adjustment slider, but it wasn't yet functional in the prototype that I tested.
The application lacks a built-in bookstore, but it can automatically sync content that the user has purchased. To add a book from the device itself, the user visits Amazon's website, purchases a book, and then uses the reader application's synchronization feature to pull it down onto the device. When the user deletes a book from the device in order to free up storage space, it is still accessible from an "archive" menu which can be used to re-download the content.
Amazon's application is not a general-purpose reader—it can only display books from Amazon's own bookstore. If you want to read other kinds of content, such as free e-books from Project Gutenberg, you will still need a separate third-party reader application like FBReader or Aldiko.
I often read e-books on my cell phone when I travel. I recently managed to get through two William Gibson novels during the flights to and from the Ubuntu Developer Summit that took place earlier this month in Brussels. Getting e-books on my phone today is often a bit of a chore. The ability to buy books over the air and have them available and fully synced on all of my devices will be a welcome addition to the Android platform.
Read the comments on this post
Read More ...
Social standards: understanding Google's new APIs for Buzz
Google unveiled new APIs for its Buzz social networking service on Wednesday during a presentation at the company's I/O developer conference. The new APIs will make it possible for third-party developers to write software—such as desktop and mobile client applications—that can read and post content on Buzz. The Buzz APIs are built on top of open standards to enable broad compatibility with other services.
Google's Chris Chabot started the session by describing Google's vision for social networking. The Web is becoming increasingly social, he explained, but social networking is heavily fragmented due to the multitude of disparate services that are popular among users. Google hopes to unify social networking and make it a pervasive part of the Internet experience, but not at the cost of diversity and rich competition in the marketplace. The solution, said Chabot, is to facilitate interoperability through open standards. He said that Google wants Buzz to be part of a bigger ecosystem, one that includes a healthy quantity of good third-party software.
Read the comments on this post
Read More ...
Should Uncle Sam save public media with huge cash infusion?
Say what you want about Free Press. The media reform group is not afraid to launch long shot crusades on a dime. What's the latest? Expanding the government's commitment to public broadcasting, or as Free Press wants us to call it, "public media," given the extension of television and radio to the Web.
"There is no longer enough private capital—in the form of advertising, subscriptions, philanthropy and other sources—to support the depth and breadth of quality local, national and international news reporting that our communities need to participate in a 21st-century democracy," the latest call to arms insists (we get about three a week from them).
"In sum, the need has never been greater for a world-class public media system in America."
Read the comments on this post
Read More ...
More carbon dioxide makes plants picky about their fertilizer
The concentration of carbon dioxide in the atmosphere continues to ramp up, but maybe that's not all bad—plants will love it, right? Not necessarily, according to a study published this week. Researchers have found that an increase in ambient carbon dioxide actually inhibits plants' assimilation of nitrate from the soil, meaning they can't process a larger carbon dioxide load when this is their primary source of nitrogen.
In the experiment, scientists tried five different soil and atmosphere combinations on wheat and Arabidopsis, a member of the mustard family. The plants were exposed to various combinations of plain and nitrate-enriched soil, and atmospheres with normal and elevated carbon dioxide levels.
The results showed that it didn't matter to the plants how much nitrogen or carbon dioxide they were exposed to, as they assimilated the same amount regardless of the environment. This is notably different from when the plants are supplied with nitrogen via ammonium, which, in combination with excess CO2, can stimulate growth. The authors speculate that this difference is due to the biochemical mechanisms that the plants use to incorporate nitrates into biomolecules.
Researchers point out that plants may yet adapt to increased carbon dioxide levels, but there would still be a drawback—once they can use all that carbon dioxide, they will need to pull more and more nitrate from the soil. We may be able to lean on ammonium- and nitrate-based fertilizers to restore the soil's balance, but that would increase our reliance on fertilizers, which have their own issues.
Science, 2010. DOI: 10.1126/science.1186440 (About DOIs).
Read the comments on this post
Read More ...
Mobile market up, smartphones up, Android and iPhone way up
The mobile phone market is up big for the first quarter of 2010 after sales declines during 2009, according to the latest sales figures released by market research firm Gartner. Smartphones are also growing faster each quarter as they continue to replace feature phones for many users. No surprise that the iPhone and Android-based phones saw the biggest gains, as the two platforms were the only two in the top five to gain market share year-over-year.
Worldwide, mobile phone vendors sold 314.7 million phones—smart and otherwise—in the first quarter, a 16.9 percent increase from the first quarter of 2009. Nokia, Samsung, and LG continue to grab most of the market with little year-over-year change, while numerous other vendors battle for small parts of the remainder. However, the importance of smartphones can be seen in the overall mobile market. Big market share drops for Sony Ericsson and Motorola allowed BlackBerry maker RIM to move into fourth place globally, making RIM the first smartphone-only vendor to crack the top five.
Read the comments on this post
Read More ...
Facebook privacy coming to a head, changes may be imminent
Facebook has found itself facing some tough choices when it comes to the direction of the company, specifically revolving around user privacy. As most Netizens know, Facebook has faced harsh criticism in recent months—which may be coming to a head after having built up slowly over the years—regarding how it handles user information. Now, the company is left deciding whether it wants to revert to its old principles and go against founder Mark Zuckerberg's policy of forging ahead, privacy be damned.
Facebook public policy head Tim Sparapani said in a radio interview Tuesday that the company was working on simplifying its privacy controls because of user complaints about their complexity. "I think we are going to work on that. We are going to be providing options for users who want simplistic bands of privacy that they can choose from and I think we will see that in the next couple of weeks," he said.
Read the comments on this post
Read More ...
Rogue ISP ordered to liquidate, pay FTC $1.08 million
A rogue Internet service provider that hosted and participated in the distribution of spam, malware, and porn has finally been shut down as a result of a request made by the FTC to a district court judge. The ISP, 3FN, has had its servers and assets seized and has been ordered to turn over $1.08 million of its proceeds to the FTC.
The FTC first charged 3FN in June 2009 with a number of… really bad things. These included active recruiting of and working with criminals to distribute content such as spyware, trojan horses, phishing schemes, and pornography—including child porn. The FTC says 3FN advertised its services to like-minded people in the "darkest corners" of the Internet, like chat rooms for spammers.
Read the comments on this post
Read More ...
US Deputy CTO gets reprimand for Google lobbying contacts
What happens when Google's former public policy director starts working in the White House—but continues to e-mail current Google lobbyists, and to take their e-mails? If you're Consumer Watchdog, the answer is simple: he "should resign his position."
But to the White House, the headhunting is ridiculous. US Deputy CTO Andrew McLaughlin has already been "reprimanded" over what it characterized as "incidental" communications with Google's current crop of lobbyists.
"Andrew regrets these violations," we were told.
Read the comments on this post
Read More ...
There are no truly good men, according to cooperation study
A new study indicates that human generosity may have a limit, even when being generous would fulfill our selfish tendencies too. In an economic game where investing all available resources in cooperation with others gave the largest possible reward, players would still hold back from contributing everything they had, and continued to view their collaborators as potential competitors. Our ability to cooperate appears to have definite limits, just as our selfishness does.
Many scientists have suggested that humans cooperate as well as we do because of natural selection. When a person could only do so much sabre-tooth-tiger killing or berry-gathering in a day, cooperating and exchanging goods gave groups of humans a competitive edge over other species. Observing this tendency in studies lead some researchers to conclude that we have a predilection for engaging in as much cooperation as we can get back in return. The new work suggests that those study designs may have been flawed.
Read the comments on this post
Read More ...
PixelJunk Shooter 2 announced, demo for original incoming
Q-Games' PixelJunk series of PlayStation Network games has constantly shifted genres, starting with a simple racer, then moving on to tower defense and platforming before finally landing on a shooter. Now the developer has announced that it will be developing the first direct sequel in the series: PixelJunk Shooter 2.
"For those that haven’t already heard, PixelJunk Shooter 2 is in full production, full steam ahead, anchors away and all that…commotion to that order," Q-Games president Dylan Cuthbert wrote on the PlayStation Blog. "I can’t say much about it now, but it will have some features that are new to the PixelJunk series in general and will be bigger than the first game! We’re busy implementing all the ideas that were left on the drawing board for the first game to make Shooter 2 as jam-packed full of crazy fun as possible...I’m pretty sure we won’t make a Shooter 3 because everything and the kitchen sink (probably quite literally) is going into Shooter 2."
Based on the first two images released, it looks like the sequel will be introducing new elements to interact with, such as light. It also looks like you may get the opportunity to explore more than just subterranean caves. One of the images looks almost biological, suggesting the possibility of exploring the inside of some giant creature.
No release date has been set yet, but if you haven't yet had the opportunity to try the first PixelJunk Shooter, Q-Games will be releasing a demo on May 25.
Read the comments on this post
Read More ...
Intel may open door for bigger netbooks
One of the ways that Intel has kept netbooks from cannibalizing notebook sales is by imposing a limitation on netbook screen sizes—netbooks that use the Atom N series have been restricted to screen sizes no bigger than 10.2 inches. But rumor has it that Intel will lift this restriction in the second half of the year, and allow larger screens on netbooks that use the dual-core N550.
This move isn't too surprising, given that netbook sales have started to level off as a percentage of mobile sales. Intel is probably looking for a way to keep netbooks interesting, and offering more form factors is one of them. It's also the case that Intel has been pitching the Pine Trail + Broadcom CrystalHD combo as a way to do 1080p video on a netbook—and 1080p certainly makes more sense for larger screens than it does on a sub-10" panel.
A final argument for the restriction's elimination is that it's quite likely that the coming wave of ARM-based "smartbooks" will include units with screen sizes above 10.2 inches. Intel won't want the Atom platform to be arbitrarily restricted in competing with ARM-based offerings, so now is as good a time as any to do away with the ban. That way, OEMs get the all-clear to work on larger Atom-based netbooks that will hit the shelves in the second half of the year, as ARM A8- and A9-based smartbooks start to trickle out onto the market from Lenovo and other vendors.
The increase in screen size raises one question: at what point is a netbook no longer a netbook? I don't have an answer to this, so I'd like to ask the readers to weigh in on the question. Is it a specific price point? A particular form factor or range of form factors? A combination of price, form factor, and flash memory for a main storage pool?
Read the comments on this post
Read More ...
Google opens VP8 codec, aims to nuke H.264 with WebM
Ever since Google announced its purchase of video codec company On2 in August 2009, there's been an expectation that On2's VP8 codec would someday be open-sourced and promoted as a new, open option for HTML5 video. An open VP8 would offer comparable quality to H.264, but without the patent and royalty encumbrances that codec suffers.
Last month, this speculation seemed confirmed, with inside sources claiming that Google would announce the open-sourcing of the VP8 codec this month at the company's I/O conference.
Today, Google, Mozilla, and Opera announced the launch of the WebM Project. The goal of the project is to develop a high-quality, open-source, royalty-free video format suitable for the Web. WebM video files do indeed use VP8 for their video compression, coupled with Vorbis audio compression. The video and audio data will be combined into container files that are based on the open-source Matroska container.
Read the comments on this post
Read More ...
Google pounds the open standards drum during I/O keynote
During the opening keynote at the Google I/O conference this morning in San Francisco, the search giant unveiled new Web technologies and reaffirmed its commitment to open standards.
Vic Gundotra, Google's VP of engineering, started the keynote by highlighting the waning relevance of desktop applications and discussing the significance of software's ascent into the cloud. The most important applications today are Web apps, he said. Although the Web has transformed the way that software is developed, deployed, and consumed, it has introduced new challenges that have to be overcome before it can fulfill its potential. The Web is growing up, Gundotra remarked, but the diverse ecosystem of Internet stakeholders must work together to ensure that it continues to advance.
Read the comments on this post
Read More ...
Google may be skewing how the public views nanotechnology
With the profusion of information available on the Web, search engines have become a key mediator by directing people to the information they're interested in. But that has also turned the search engines into gatekeepers; both by ranking the results and by offering suggested search terms, the sites can subtly (and, in some cases, not so subtly) influence the sorts of information that a significant fraction of the public will encounter. A new survey of Google search terms looks into how this is playing out when it comes to information on nanotechnology. The researchers found that both suggested queries and search results may be pushing that field down a path that is similar to the one that was traveled by genetically modified foods, where an initial focus on technology and applications has been replaced by worries about health and ethical issues.
Nanotechnology is a sprawling field that is based on a simple observation: the properties of many familiar materials are completely different when they are structured at the nanometer scale. So, for example, differences between bulk gold and gold nanoparticles include color, melting point, and electronic properties. Our ability to control the bulk production of nanostructured materials is a relatively recent development, and it holds both promises and risks.
Read the comments on this post
Read More ...
HP: introducing the webOS... printer?
We've been all over the ins and outs of HP's planned acquisition of Palm—the tablets, the phones, the bright promise of a cloud services company buying a cloud client, the grim prospect of one failed smartphone maker buying another—but for all that Palm will supposedly do for HP, the one thing I haven't seen mentioned is the idea that webOS will go into a printer. At least, not until HP's quarterly earnings call, where HP's Mark Hurd said:
I think in this case of Palm, and our planned acquisition of Palm, it really has more to do with the intellectual property and the fact that when you look across the HP ecosystem of interconnected devices, it is a large family of devices. When we think of printers, you’ve now got a whole series of web-connected printers that, as they connect to the web, need an OS. We prefer to have that OS in our case to be our IP, where we can control the customer experience as we always have in the printing business, and that’s a big deal to us.
In other words, webOS gives HP its own lightweight, Web-savvy client operating system for all of its consumer-facing gadgetry up through netbooks. For anything that cries out for a touch-based OS—as opposed to a stylus- or mouse-based OS—HP now has webOS as an in-house option. One wonders what's next: Calculators? Digital cameras? (Actually, a digital camera would certainly be a candidate for the webOS treatment.)
Hurd also reiterated the obvious point that HP is indeed planning a webOS-based tablet. Of course it is—the only question is whether said tablet will be based on ARM, x86, or both. And if it's based on x86, will it dual-boot Windows?
When discussing tablets, Hurd went out of his way to emphasize that HP isn't necessarily abandoning a Windows tablet. "Microsoft is probably one of the best relationships we’ve got in our company, and they’re still extremely important," Hurd said.
Read the comments on this post
Read More ...
Axis of P2P Evil? Congress, RIAA call out six worst websites in the world
This morning, the Congressional International Anti-Piracy Caucus held a press conference along with RIAA CEO Mitch Bainwol to call out the six worst websites in the world. Think of them as an "Axis of P2P Evil."
Who made the cut? The Pirate Bay, naturally. Canada's IsoHunt was no surprise. One-click download service RapidShare was less expected, as a German court ruled only two weeks ago that the site was not responsible for infringement by its users and that it had no duty to preemptively censor uploaded content.
Read the comments on this post
Read More ...
No comments:
Post a Comment