All urchins, all the time

Science has placed a large number of resources regarding the urchin genome, including some free content and links to its subscriber only articles, on a single page. If you wish to follow up on any of this information, that's the place to start. In the mean time, we can dive right in. HangZhou Night Net

As I mentioned earlier, echinoderms such as the sea urchin are among the most distant members of the deuterostomes, a group that includes all vertebrates. How distant? The deuterstome common ancestor dates from the pre-Cambrian, and echinoderms with tube feet and a water-based vascular system appear in the early Cambrian, well over 500 million years ago. Echinoderms we can recognize as having modern features became the dominant group following the great Permian-Triassic extinction 250 million years ago. So, the genome, in some ways, provides a glimpse into the distant past, as it reveals what the ancestor to all vertebrates had in its genome half a billion years ago.

Read on for the full story.

The process of obtaining of the genome itself took advantage of a few interesting new ideas in genome sequencing. Much of the sequence was generated with what's called a "whole genome shotgun," a technique that frequently leaves questions regarding the order of sequences and gaps in the final product. In this case, these problems were corrected by the use of large fragments of the genome cloned into bacterial artificial chromosomes (BACs).

Normally, sequencing BACs is laborious, but the authors developed a technique that sequenced pools of BACs simultaneously, getting the process done in 1/5 the normal time, and at 10 percent of the usual cost. By arranging the BACs on a grid, they could pool DNA from the columns and rows and sequence it in batches; the source of specific sequences could be identified based on the intersection of the pools that shared the same sequences. The information generated by BAC sequencing was then integrated with the whole genome shotgun sequence by computer. The computer programs that assemble genome sequences had to be altered because the sea urchin population appears to be very diverse, with one base difference per every 50, a level that the assembly programs interpreted as sequencing errors. The authors suggest the diversity results from the urchin's reproductive strategy: they simply release eggs and sperm into the currents, limiting the probability of forming local, inbred populations.

Identifying the genes began before the BAC sequencing was complete. Four separate programs scanned the sequence for features typical of eukaryotic genes and similarity to genes in other organisms. Predicted genes were fed into a database that was accessible to a number of experts in sea urchin biology; they went through and evaluated and annotated the predictions, sharing their work on a listserve set up for the purpose. In the end, the sequence yielded a genome of 814 Megabases, carrying over 23,000 genes. The structure of many of these genes were refined by the use of a whole genome tiling array, which also revealed that nearly half of them are expressed during the first few stages of embryogenesis.

Well over 7,000 of the genes are shared with vertebrates, although a number that appear to be unique to the echinoderms were found. Many of these unique genes are involved in the production of the sea urchin's skeleton, which is composed of calcite, unlike the vertebrate skeleton. As none of other deuterostomes have skeletons, it appears that the formation of mineralized tissue has developed twice within the lineage.

Many classes of related proteins are encoded by multiple genes in vertebrates, in part because that lineage appears to have undergone two whole-genome duplications. Echinoderms seem to have kept a more ancestral genome (no duplications), and many of these proteins are present only as a single copy. In some cases, however, urchins have made up for this with smaller duplications of individual genes—one such case are the small GTPases (including Ras and RABs), which mediate many signaling processes and direct the motion of vesicles around the cell.

There's a few types of genes that sea urchins appear to lack entirely. These include part of the cell's skeleton called the intermediate filaments, as well as the integrins and cadherins which link these filaments to the cell's surface. They also lack the proteins that are needed to form gap junctions, the links between cells that allow electric currents to pass between them—this appears to limit the ways in which the nerves of urchins can propagate signals.

The nervous system in general had a few other surprises. It's been kown that each appendage in sea urchins has a local sensory-motor loop which manages its activities; overall coordination is handled by radial nerve bundles. There are no obvious sensory organs. But the genome reveals a huge number of receptors similar to the ones that mammals use to sense odors, balance, and noise, and there are six different light sensing proteins. Expression analysis shows that many of the sensory genes are expressed in the urchin's tube feet, suggesting a previously unrecognized sensory sophistication.

Some of the biggest differences are apparent in the immune system. The basic building blocks of the deuterostome immune system appear to be ancient: nearly all of the transcription factors and signaling molecules used by vertebrates are present in the urchin genome, including key signaling systems like the Interleukins and Tumor Necrosis Factor. But most of the urchin immune response appears to be based on what's called "innate immunity." Innate immunity typically uses a limited number of receptors that recognize a large number of pathogens. In the sea urchin, that limited number has been expanded to take up nearly three percent of its genes.

Sea urchins, like everything other than jawed vertebrates, don't appear to have the "adaptive immunity" arm of the immune system, which relies on antibodies and the T-cell receptor. Intriguingly, however, the raw material for antibodies may be present. The genes that catalyze the DNA rearrangements that produce unique antibodies, termed RAGs, are present in the urchin genome. Stretches of DNA resembling the raw materials of the variable regions in antibodies are there, too, although they lack the sequences that the RAGs need to generate mature antibody genes. These findings suggest that the production of antibodies isn't much of a vertebrate innovation, as was initially thought. The authors even raise the possibility that the RAGs are mediating the production of some other variable immune molecule—we just don't know how to recognize it yet.

It's hard to tell how to wrap a story like this up, because work like this is so far-reaching. It has answered some outstanding questions, it has removed questions that have lingered over the biology, and it has provided some answers about the genetic raw material that our ancestors had to work with over half a billion years ago. One other thing that's worth noting is that the money for this effort was almost certainly justified by suggesting we'd get exactly these sorts of answers. To me, at least, it appears that us taxpayers have had our money well-spent in this case.

CCP and…White Wolf? Okay, I didn’t see that one coming

CCP is a great company: from their customer service to their ability to stay focused on their one product (EVE Online) and really serve the community, I've always been impressed with them. Of course, they're a small company with a fanatical online following, so there isn't a lot of news about them that isn't EVE based. Until now. Did I really think I would wake up and find out that they merged with White Wolf? If I put on my analyst hat and sat down for a month or so to see what quirky mergers I could think of, that probably never would have made it on the table. I'm also going to have to admit in this post that in high school I used to play a lot of World of Darkness pen and paper games with my friends. There, my secret is out. I'm getting geekier by the day. I'm also excited about what this means: HangZhou Night Net

CCP is bringing a range of White Wolf's role-playing properties online, while the table-top publisher will develop card games, RPG systems, novels and more based on the EVE Online universe.

The EVE universe is ripe for this sort of thing, but CCP's access to the World of Darkness gets me all sweaty. The idea of online games with White Wolf's take on Vampires,Werewolves, Changelings, and all the other sundry monsters and backstories from the World of Darkness is enough to get any fan going. CCP's dedication in the online gaming world as well as their attention to detail make them a good match to see if any of this IP will work in the gaming world outside of RPG titles like Vampire: The Masquerade. I can't wait to see what these two companies come up with.

White Wolf and CCP…I just can't get over it. This makes me want to get out my old source books, order a large pizza or two, grab a bag of die, and spend a weekend giving those Sabbat punks a what for.

Online education continues to grow in higher-ed

According to a new report on the state of online learning in U.S. higher education, more students than ever before have been taking online courses. The full report, entitled "Making the Grade: Online Education in the United States 2006," estimates that nearly 3.2 million students took at least one online course during the fall 2005 term, an increase of nearly a million people from the previous year.HangZhou Night Net

Nearly three-quarters of those hopping online to learn are undergraduate students looking to complete either Bachelor’s or Associate’s degrees, while most of the rest are doing work towards a Master’s designation. Among undergrads, the majority of students are in Associate’s programs.

More than 96 percent of schools with more than 15,000 students offer some form of online courses. About two-thirds of the very largest organizations offer complete programs online which purport to allow students to complete nearly all of their degree work remotely. These figures, which have also increased from 2004, show that online education has definitely entered the mainstream as far as higher education is concerned. The overall percentage of schools who identified online education as a critical long-term strategy grew from 49 percent in 2003 to 56 percent in 2005.

Not all the news about online education is positive. Educators still have some concerns about the extra discipline required from online students compared to their in-class counterparts. In general, the report says, teachers believe that it takes more effort to teach a class online than face-to-face. However, the consensus among educators was that evaluation was no more difficult in online courses.

Just as important, the report says that college and university education leaders by and large believe that online education is as good as traditional face-to-face education, with nearly 17 percent saying that it’s actually better. Of course, those same leaders are in charge of developing and ultimately marketing their own online programs, which undoubtedly leads some of them to be bullish in their assessments.

Whatever the case, online education is indeed growing rapidly, but the overwhelming majority of students who use it are supplementing traditional face-to-face education, not replacing it. Will that change? According to the report, educators generally feel that it is the student themselves that are holding back online education, with nearly two-third suggesting that the biggest challenge facing students is their own discipline to complete an online course.

After all, at least with traditional face-to-face education, regular course meetings help to keep students on track, even if they show up to class only to hop on the Wi-Fi and surf the day away.

The study (PDF) was supported by the Alfred P. Sloan Foundation and conducted by the Babson Survey Research Group in partnership with the College Board.

Ken Fisher contributed to this report.

RIAA defendant argues damages are excessive

A defendant in one of the RIAA’s many file-sharing lawsuit will be able to argue that the damages sought by the RIAA are unconstitutionally excessive. The defendant in question, Marie Lindor, was sued by Universal Music Group in early 2006 as part of the RIAA’s legal campaign against file sharing. In all of the cases that have made it to court so far, the RIAA has sought statutory damages of $750 per song shared, an amount Lindor believes is excessive.HangZhou Night Net

In his ruling, Judge David Trager gave Lindor leave to argue the excessiveness of the RIAA’s $750 figure as part of her defense: "Lindor cites to case law and to law review articles suggesting that, in a proper case, a court may extend its current due process jurisprudence prohibiting grossly excessive punitive jury awards to prohibit the award of statutory damages mandated under the Copyright Act if they are grossly in excess of the actual damages suffered."

Lindor argues that the actual damages suffered by the RIAA are along the lines of 70 cents per song, not $750. The basis for her assertion is the 99¢ per track price for the majority of downloads and from that, the 70¢ the label receives. Even if the plaintiffs are able to prove infringement on the part of Lindor, she believes that the damages should be capped far below the record industry’s figure.

UMG v. Lindor has proven to be case worth watching because of the vigorousness of the defense. Lindor is defended by Ray Beckerman, the attorney who runs the Recording Industry vs The People blog, who is pulling out every stop as the case meanders towards a jury trial sometime in 2007. Beckerman has accused the recording industry of engaging in the use of file-sharing to distribute music to record stations, a charge which the RIAA denied after what appeared to be only a very cursory investigation. Lindor also raises antitrust and conspiracy questions in her defense, accusing the RIAA of engaging "in a conspiracy to defraud the Courts of the United States, by bringing lawsuits against persons who are not known to have infringed copyrights, and to make false and unsupported allegations that the defendants have infringed copyrights."

None of the file-sharing lawsuits brought by the RIAA is known to have gone all the way to trial. In the vast majority of cases, the defendants have either settled with the RIAA, or the RIAA has dropped the suit once it became apparent that the cartel had targeted the wrong person. Should the RIAA have to face off against a defendant in court, we will find out more about the soundness of its legal arguments.

An explosion that puts our sun to shame

A few months ago we at NI covered
the launch of a satellite that is designed to study solar flares and
coronal mass ejections. These are where a star releases an
unimaginable amount of energy and blows millions of tons of highly
energetic particles out into the space surrounding it. In the
previous article I tried to compare the energy we are talking about,
and related it to a human event. The largest man made
explosion ever was the Soviet Tsar Bomba test, which released about 5.3
yottawatts of energy, which is only about one millionth of the energy
imparted by a large meteor or asteroid impact. This type of extra-terrestrial based impact, in turn, pales in
comparison to the energy released by a solar flare. Now, a
flare was observed by the NASA Swift satellite mission on the star II Pegasi, in the constellation Pegasus,
that puts the average solar flare to shame. HangZhou Night Net

In December of 2005, a stellar flare was observed that was
approximately 100 million times more energetic than a typical solar
flare—that would be on the order of tens of millions of trillions
times more energetic than an atomic weapon blast. This flare
is thought to be the most energetic magnetic explosion ever witnessed
by man. Had a similar event occurred on our sun, there would
have been a mass extinction on Earth. Fortunately, we don't have to
worry about these from the sun or other stars. The sun is a stable star
and has stopped erupting
with these ultra-flares a long time ago, and II Pegasi is over 100
light-years from Earth and poses no real threat. What is
interesting about this—other than the über-explosion—is that
II Pegasi isolder
than the sun, but is still energetic due to being part of a binary star system whose rapid
rotation acts as a fountain of stellar youth. This event has
scientific importance in that is is the first time researchers have been
able to observe and monitor a stellar flare that did not originate from
the sun with such detail.

Since this explosion was so powerful, it was first believed to be caused by a
stellar explosion or merger, which result in gamma-ray bursts.
The energy released by the flare triggered a false alarm in Swift's
Burst Alert Telescope, which is used to quickly detect stellar
explosions. The satellite also detected high-energy "Hard"
X-rays, which accompany the initiation of the early stages of a
stellar flare. By detecting the emissions, the scientists
studying the phenomena were able to learn a good deal about the initial
stages of a flare formation. According to the authors of the
study, to be released later in an edition of Astrophysical Journal (arXiv pre-print here),
there is an irony to this. Had this event happened on
Earth (as mentioned above) it would have spelled doom for us,
yet the authors hypothesize that it is events exactly like this—those
that eject thousands of tons of stellar matter away from a star—that
allow enough dust and matter to exist in interstellar space for planets
to form in the first

Politics and tech companies: follow the money

The technology business is a right-leaning one, if judged by the candidates that tech companies funded in the most recent election cycle. In this special report, Ars totals the dollar amounts to show consumers what politicians tech companies support, and why. Let’s follow the money.HangZhou Night Net

Data compiled by the Center for Responsive Politics shows that computer- and Internet-focused firms gave just over $4 million to federal candidates in the 2006 election cycle. The money wasn’t doled out evenly, though; Republican candidates pulled in 67 percent of it.

The gap between the high end and the low end was significant. Microsoft took first place with $651,100 given out, while Hewlett-Packard gave only $185,550, and Gateway gave a paltry $2,000. Microsoft’s donations certainly illustrate well the true size of the company and the extent of its political concerns.

More surprising is that the number two position is held by Siebel, an unfamiliar name to many consumers. The business software vendor was swallowed up by Oracle earlier this year, but still managed to give $635,000 to candidates, 89 percent of it to Republicans. Intel holds the third spot ($339,197) with Cisco in number four ($209,500).

Apple and Google are not on the list (though Google has recently jumped into the lobbyist game, hiring firms like Podesta Mattoon and the notorious DCI).

PAC your bags, we’re going to Washington!

The numbers above don’t give the whole story. They reflect only the money that corporate political action committees (PACs) give to federal candidates, but the companies behind the PACs spend far more than this on nonfederal candidates and lobbying.

For instance, Microsoft’s PAC spent $1.7 million in the 2006 election cycle, but only a third of this went to federal candidates. What happened to the rest? It went to local campaigns, paid out a few thousand dollars at a time to groups like “Boal for Iowa House” in Ankeny, IA. It also funded other PACs like the “Associated Republicans of Texas” and the “Blue Dog Political Action Committee.” No race is apparently too small to be funded; even Indiana State Representative Terri Austin of Anderson, IN got $500.


But the real money isn’t even given to the candidates directly. It goes to lobbyists, which can be safer investments since they stand no chance of losing at the polls. The complete-year figures from 2005 show that Microsoft spent $8.7 million on lobbyist expenses. Almost a million dollars of that money went to Covington & Burling, a lobbying firm that also represents the National Football League and the Pharmaceutical Research & Manufacturers of America. Microsoft’s total spending on lobbying has risen substantially from the $4 million it spent in 1998.

It’s not just Microsoft that is spending these massive amounts. The computer/Internet industry as a whole dropped $84 million on lobbying in 2005—more even than the TV/movies/music groups. Although the firms at the end of the Internet “pipes” are spending money, it’s dwarfed by the expenditures of those firms that own the “pipes” themselves.

AT&T alone spent $60 million in lobbying in 2005, and Verizon spent another $11.7 million; Comcast paid $4 million. Together, the network operators formed one of the largest lobbying blocs in the country, which means that their concerns get plenty of attention in DC.

Network operators also give money directly to candidates, especially when they chair powerful committees. Ted Stevens, the Alaska Republican best known for his $250+ million “bridge to nowhere” and his opposition to network neutrality, is the (outgoing) chair of the Senate committee that is overhauling the 1996 Telecommunications Act. So it’s no surprise to find that he is well-supported by the TV/movies/music industry, the telephone utilities, telecom equipment makers, and computers/Internet firms.

Where does it come from?

Although some of this money comes from large employee donations, most of it does not. Take Microsoft, for instance; the Center for Responsive Politics says that the company received only $302,599 from individual donors who gave more than $200 in this election cycle, only a small fraction of the $1.7 million actually spent. As is typical, much of this money came from the company’s top brass, while the rest was made up of small contributions.

The maximum individual contribution to a PAC is $5,000 a year. Melinda, whose occupation is listed in Federal Election Commission records as “homemaker,” regularly contributes this amount, as does Bill. Steve Ballmer coughed up, too. Microsoft can use general company funds to support the PAC and its operations, but cannot give directly to candidates.

Although donations have gone mostly to Republicans in recent years, changes in the political makeup of Congress means that Democrats can probably expect more cash in the next cycle.

In fact, the pendulum has already begun to swing the other way. The New York Times reported that in the last days of the midterm campaign, corporate donations increased significantly to Democrats as it became clear that they might win control of Congress. The Times notes that “the shift in political giving, for the first 18 days of October, has not been this pronounced in the final stages of a campaign since 1994, when Republicans swept control of the House for the first time in four decades.”

This story has been updated to clarify the role of corporations in funding their PACs.

Game Review: Elite Beat Agents

Somewhere in Japan there is a room with a few devkits, stacks of CDs, and a lot of pot. It has to be true—there is no other reason for a game like Osu! Tatakae! Ouedan to come into existence. The game gained a large following in Japan as well as cult status among importers in the US. Now we finally have our own version: Elite Beat Agents. Just in case this game is new to you, let me break down what is going on here. HangZhou Night Net

We live in a world with many problems. Trying to hook up with that cheerleader, trying to get a pregnant lady to the hospital on time, trying to find treasure in the sea… we deal with these and other issues every day. What we don't realize is that for those of us who need a little more help, there is a group of brave men called the Elite Beat Agents who watch over the world and come to the aid of those who need them the most. With a little song, a little dance, and a lot of energy, they help regular people like you or me finish our daily tasks. Led by Commander Kahn, who sends them out with a cry of "Agents are go!", they make sure that the world is safe and happy.

It really is that crazy. They're basically male cheerleaders, and in fact the Japanese name translates into "All right! Fight! Cheer Squad." Where do you come in? Well, you help the Elite Beat Agents cheer on their clients by tapping the screen along to the music. Numbered dots pop up on screen, surrounded by a tightening circle. When the circle touches the outside of the dot, you tap it. There are some bits where you have to rub a line or curve in time with the music, but it's mostly tapping. This may sound easy, but let me assure you it gets very challenging, very quickly. This is one of those games you'll need to spend hours practicing before you achieve mastery.

Luckily the graphics are bright and attractive, and while the soundtrack is rather hit or miss, the routines you have to perform along with the songs are always fun. YMCA, in particular, is a blast. So is Walkie Talkie Man, although that song drives me up a wall. The ministories you find in each level are always insane and fun to watch.

Elite Beat Agents has a high level of goofiness to it, but that can be a good thing. It's impossible to take Elite Beat Agents seriously, and it'll always leave you smiling.

Some may be turned off by the difficulty, and you will have to practice a lot of these songs multiple times before you become skilled but for those of us who don't mind a good challenge there is a lot to like here. I'm hoping for a sequel with a slightly stronger tracklist. That said, this is a great portable rhythm game for fans looking for something new and different. Agents are go, indeed.

Status: Buy

Price: $34.99 (shop for this game)

System: DS

Publisher and Developer: Nintendo of America

ESRB Rating: Everyone (10)

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Yahoo to embed instant messaging into e-mail

E-mail was arguably the first killer application of the Internet, but recently it has become somewhat less useful as the war between spammers and antispammers has left some Internet users feeling like innocent victims in a battle between good and evil. The younger generation tends to eschew e-mail in favor of instant messaging. Now, Yahoo has decided to bring the two technologies together for a new version of Yahoo Mail.HangZhou Night Net

Brad Garlinghouse, vice president of communications at Yahoo, said that the reason for the move was to improve the overall user experience, something he claims is lacking from many “Web 2.0” applications. “I would argue that many Web 2.0 applications are already dead,” he said. “Web 2.0 as an application is leaving tremendous value on the table for consumers and for us as businesses.”

So is the new Yahoo Mail an example of Web 2.5? The company is not the first to have the idea of integrating e-mail and instant messaging. For almost as long as there has been MSN Messenger, Microsoft has enabled access to its contact list within Outlook Express. Google also recently added chat features to its Gmail application. However, the new Yahoo Mail is even more integrated with instant messaging. It does not require any separate instant message program, allowing direct chatting within its web-based interface.

Yahoo and Microsoft recently announced that they would be making their IM services interoperable, so MSN users will have a new method of keeping track of their friends while online. Will the IM integration and MSN compatibility help push Yahoo’s services over the top? The battle for instant messaging supremacy has not been a close one, at least in the United State, where AOL Instant Messenger continues to hold a strong lead. However, the web is increasingly international, and the race outside the US is much closer. What prizes await the victor? Untold riches in the form of ad revenues.

Disney nears half-million sales through iTunes

Disney CEO Bob Iger said during the company’s fourth quarter conference call that the movie studio has sold nearly a half million movies on the iTunes Store since they announced their partnership with Apple, signaling a strong presence for downloadable movies on iTunes despite having very limited content so far. Disney also says that it expects to generate $50 million in revenue during its first full year on iTunes.HangZhou Night Net

Within the first week of the partnership, which was announced during Apple’s "It’s Showtime" event on September 12, Disney announced that it had sold 125,000 movies and cleared $1 million in revenue. Since then, the numbers have continued to grow over the last eight weeks, averaging roughly 62,500 movies sold per week since the partnership’s inception.

Rumors claim that Apple had originally intended on launching with multiple movie studios on board, but that all but Disney backed out at the last minute due to threats from retail powerhouses such as Wal-Mart. Wal-Mart reportedly threatened to cut orders for certain movies during the holiday season if they did not receive the same deals from the studios as iTunes was getting, and the studios allegedly bowed to the pressure.

Disney has yet to see any pressure from Wal-Mart and it seems that other studios are close to signing on with the iTunes Store after seeing Disney’s success. There are now rumors that 20th Century Fox is about to become the second studio to sign on with Apple, which will be a welcome addition to iTunes for many potential buyers.

Microsoft surprised us this week with the announcement of their own movie download service through Xbox Live, and so far seems to have a decent collection of movie studios on board. The difference, however, is that the Xbox’s movie service is rental only and is expected to be somewhere between $3 an $7 per download with some downloads being available in HD.

As the movie download market matures, we’ll get a better idea of which model consumers prefer: $3-7 rentals or $13-15 sales.

Allchin says Vista doesn’t need antivirus? Nope.

Windows Vista doesn’t need antivirus! *snort* *snicker* HangZhou Night Net

This is the vibe that has been following a "report" that has been circulating over the last few days, dubiously headlined: "Allchin Suggests Vista Won’t Need Antivirus." The "cut-to-the-chase" version is this: Allchin says that his seven-year-old son uses Windows Vista, and that he is comfortable with what his son can and can’t do on his computer. Allchin says nothing about Vista not needing antivirus software. Here’s the quote:

"My son, seven years old, runs Windows Vista, and, honestly, he doesn’t have an antivirus system on his machine. His machine is locked down with parental controls, he can’t download things unless it’s to the places that I’ve said that he could do, and I’m feeling totally confident about that," he added. "That is quite a statement. I couldn’t say that in Windows XP SP2."

Notice what is lacking: any statement whatsoever to the effect that "Windows Vista doesn’t need antivirus." The point Allchin was trying to make was that he believes that Windows Vista is more secure than Windows XP SP2, and in particular he makes it clear that he believes Vista’s parental controls will prevent his son from downloading stuff he shouldn’t be downloading. If you’ve had a chance to play with Vista, you may know that the parental controls essentially remove almost all of a user’s rights. In Allchin’s case, his son can only visit websites that have been whitelisted. Does this sound like normal Windows usage to you? Would you infer that he’s talking about normal Windows usage here?

Allchin also mentions that his son doesn’t have an antivirus application, but he neither recommends this state of affairs or says that it is good thing per se. Obviously the key here is the parental controls, and Allchin’s hope that Vista is indeed more secure than XP SP2. How this was morphed into him boasting that Vista doesn’t need antivirus software is beyond us.

The story was subsequently picked up by a number of writers who neither looked at what Allchin said nor put it into context, so Allchin himself decided to post a rebuttal on his blog. Unsurprisingly, some authors are spinning this as Allchin "backing off" his claims, but a closer look shows that he’s no backing off of his claims, he’s saying that he was misrepresented by the stories in question.

Allchin explicitly denies having said anything along the lines of what was inferred from his comments, writing that "it is also clear from the transcript [of the chat] that I didn’t say that users shouldn’t run antivirus software with Windows Vista! In fact, later in the call, I explicitly made this point again, because I had realized I wasn’t as clear as I should have been." Ars Technica has seen a transcript of the call, and Allchin did in fact make his point suitably clear.

Now one may believe that Vista will indeed be more secure than Windows XP SP2, but Allchin did not say that regular Windows Vista users should go commando when it comes to anti-virus software. You have to infer that from his comments, and the context makes it quite clear that such an inference would be off base.

To be sure, Allchin has said things in the past that have made him look a bit silly, but this isn’t one of them. Even if we suspend reality and pretend that Vista will be so secure that it doesn’t need antivirus (yeah, right), are we supposed to believe that Microsoft’s big plan with Windows OneCare—the new software suite Microsoft is selling centered around antivirus protection—is that… no one needs it? That’ll be the day.

Pre-DOCSIS 3.0 rollout in South Korea hits 100Mbps

Those stuck with slow broadband connections have another reason to look across the Pacific with envy. Some South Korean cable Internet subscribers are now able to get 100Mbps connections thanks to deployment of pre-DOCSIS 3.0 hardware by cable operator ARRIS.HangZhou Night Net

"We are pleased to announce this very successful deployment proving the technical ability of the ARRIS Wideband solution to deliver 100Mbps of service over an HFC network," said HCN Operational Director Jong-Myung Joo. "This deployment represents a big step toward meeting the Korean Ministry of Information and Communications’ IT 839 strategy of building a converged network to deploy 100Mbps ubiquitous wideband service in Korea."

ARRIS has over 1.1 million video subscribers, many of whom also subscribe to the company’s broadband service.

DOCSIS 3.0 is the successor to DOCSIS 1.1, which is currently used by almost all cable ISPs in North America. DOCSIS 2.0b was ratified as a standard, but never deployed in the US as ISPs preferred to wait for version 3.0.

The latest version the DOCSIS standard offers full support for downstream data speeds of up to 160Mbps and 120Mbps upstream via channel bonding, which allows it to use more than a single 6MHz channel to transmit data. It also offers full support for the next-generation IPv6 addressing scheme, and enhanced network management and security features. DOCSIS 3.0 also offers enough bandwidth for IPTV and other high-def video services.

With pre-DOCSIS 3.0 hardware reliably delivering speeds in excess of 100Mbps, it bodes well for the introduction of fully-compliant hardware in the latter part of 2007. Once the hardware becomes widely available, US cable companies will begin upgrading their networks to support 3.0. ABI Research estimates that just shy of 40 percent of cable customers will have DOCSIS 3.0 equipment in their homes by 2011, which means that those 100Mbps connections are still a ways off in North America.

Further reading:US is a broadband laggard, according to FCC commissionerDOCSIS 3.0: coming, but not quickly

What’s the big deal with Sea Urchins?

With genomes being completed on a regular basis, the wrapping up of a new one is making less and less of a splash. An exception to this trend occurred yesterday with the completion of the sea urchin genome, specifically the one from the purple species Strongylocentrotus purpuratus. Not only did this rate six separate articles in the latest issue of Science, but a special issue of Developmental Biology will be devoted to it in December. This is far more attention than the dog genome got, and is probably on par with the excitement that greeted the chimp genome. HangZhou Night Net

Those of you familiar with sea urchins from tide pools, aquariums, or Japanese restaurants may be a bit shocked by this level of buzz. After all, what could a prickly sphere tell us about humans, with our asymmetrically placed limbs and sensory organs? At the risk of making two-part posts a habit, I'll spend today's post letting you know why there's so much excitement. A detailed analysis of the six papers will follow over the weekend.

Sea urchins actually have a long history in biology. They're easy to keep, thriving in a combination of sterilized tap water and a collection of salts sold under the trade name "Instant Ocean." They're also long lived—the source of the genome in question was estimated at 20 years old, based on its size— and can produce copious numbers of offspring. Critically, these offspring develop externally, and are transparent for their earliest stages, making them very amenable to development studies. In fact, one of the perspectives cites a century-old paper as using sea urchins to show that embryonic development is a fundamentally genetic process: deleting any of its chromosomes from any of its early cells was enough to bring development to a crashing halt.

Further analysis of urchin development has continued to this day. When I cloned a gene from mice that I was working on a couple of years back, I was surprised to find that an equivalent gene didn't exist in things like Drosophila and most other invertebrate model organisms. The only other organism where it had been described, in fact, was the sea urchin, where the transparent embryos had allowed researchers to visualize cells migrating along tracks composed of the urchin's equivalent of my gene.

The presence of this gene in the urchin genome was no fluke; despite their almost other-worldly appearance, sea urchins are family. They and humans belong to a group called the deuterostomes, identified by common processes we both undertake during early development. Some of the commonalities are a bit surprising. Even though they look like a sphere, sea urchins develop with clear "sides" internally, and these sides express the same genes that we vertebrates use to differentiate our left from our right.

Sea urchins represent the most distant members of the deuterostome family that we're likely to get a genome from any time soon, and the first one sequenced that doesn't form any sort of nerve cord. As such, they will be critical in identifying those genes that all deuterostomes have in common—the raw material that all of the species in this group inherited from a distant ancestor. It appears that that ancestor was more sophisticated than we might think. Despite their lack of an obvious sensory system, urchins have nearly as many genes involved in odorant receptors as we do, and six different light sensing pigments (compared to our four). It's also expected that an analysis of non-coding sequences may reveal the sites where regulatory factors bind to DNA to turn genes on and off, which will identify those regulatory circuits have been present since the first deuterostomes.

Identifying the similarities is also a key step in identifying the differences. Vertebrates have many novelties that aren't present in other deuterostomes, and the genome sequence will help answer one of the basic questions in evo-devo: how much of this novelty is the result of something truly new, and how much comes from using the same material in new ways? A quick skim of the articles reveals that the immune system of urchins appears radically different, which will not only help us understand our own better, but may point towards new directions to take in developing antibiotics.

So, if you were tempted to shrug your shoulders at what may have appeared to be hype, I hope this has convinced you that there are many reasons for the buzz surrounding this genome. If nothing else, I hope I've convinced you to check back when I go through the actual data.

NVIDIA announces move into integrated graphics for Intel

Fresh off their purchase of PortalPlayer and their launch of a next-generation GPU (the Geforce 8800), NVIDIA revealed yesterday in a conference call that they’re moving directly onto Intel’s turf with an integrated graphics processor (IGP) aimed at Intel platforms. This move is like their newly announced stream processing-oriented GPU in that it marks yet another way in which the company is trying to expand its graphics expertise beyond its core market of selling standalone graphics chips. HangZhou Night Net

Intel’s integrated graphics processors for both desktop and mobile segments make the processor giant the undisputed king of graphics chip makers, at least in terms of sheer sales volume. For the vast majority of consumers and business customers, integrated graphics processors, which sit on the motherboard as part of a core logic chipset and cannot be upgraded, are powerful enough to do regular Windows computing. More powerful discreet graphics products, like GPUs from ATI and NVIDIA, constitute a much smaller, more specialized market consisting of gamers and media professionals.

Both NVIDIA and ATI have had some success in filling the IGP hole in AMD’s chipset lineup, but neither have really had a presence in the IGP market for Intel platforms. ATI’s attempts at Intel-oriented IGP never took off, and NVIDIA hasn’t even tried, preferring to stick to offering IGPs for AMD products. But NVIDIA is clearly no longer content to be relegated to minority markets, like discreet graphics and IGP products for AMD, so they’re aiming to take a bite out of the larger piece of the graphics market pie that Intel has been hoarding for itself.

It also helps that ATI is now getting out of the Intel chipset business, subsequent to the company’s acquisition by AMD. This will leave NVIDIA to duke it out alone with Intel in the Intel IGP space. To have any hope of succeeding, NVIDIA is going to have to offer something quite compelling, which is why my guess is that the first NVIDIA IGP for Intel will be based on the newly unveiled G80 architecture. The very large, power-hungry design could be cut down for use in an IGP by removing some of the parallel execution hardware. In particular, the GeForce 8800GTX’s eight large thread processor groups (what I called “tiles” in my previous coverage) could probably be cut down to four or fewer and still offer enough horsepower to push pixels for a Vista display. A process shrink to 65nm would also help in getting a G80 derivative onto a motherboard.

Further readingNVIDIA rethinks the GPU with the new GeForce 8800Epic VP: Intel is killing PC gaming! Ars: Not really.Intel looks to make its 3D more Extreme