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.

Vista, Office 2007 cracked. Kind of.

Microsoft has had a long history of battling against piracy, ever since Bill Gates’ Open Letter to Hobbyists in 1976, long before there was even a personal computer software industry to speak of. Now, Microsoft finds itself in its latest piratical engagement, with the recent cracks of Windows Vista and Office 2007, both of which just hit gold release status. Torrents of the cracks are already finding their way around pirate sites. HangZhou Night Net

The crack for Windows Vista (which is called “Vista BillGates”) is not a true crack, as it replaces components from the final version of the operating system with those from earlier betas. This allows the would-be pirate to use a product key that worked with Beta 1, Beta 2, RC1, or RC2, with the Gold release of the operating system. This allows the OS to be activated normally over the Internet, but does not bypass the activation system itself. Microsoft had made these earlier betas available to the public on a limited basis.

The other piratical news today is that a copy of the Enterprise edition of Office 2007 was also made available on the ‘Net. This version, like other “Corporate” editions of Microsoft products, uses a volume license key (in this case, Volume Activation 1.0) and does not require activation over the Internet.

Of course, Microsoft has methods of fighting back against these latest leaks. The company can push updates through Windows and Office Update that deactivate the pirated copies. As the company did with Windows XP Corporate Editions, Microsoft can invalidate corporate volume license keys that have leaked out at a later date. This latter strategy worked moderately well for Microsoft—at least a few people whose pirated copy of XP had its VLK invalidated did bite the bullet and replace it with a legitimate version. Also, Microsoft can continue their strategy of using Windows Genuine Advantage (WGA) to restrict access to certain non-essential updates. Internet Explorer 7 was an example of a product offered only to users who passed WGA.

Microsoft’s aim is to make piracy annoying enough that casual users will stop bothering with it, despite the fact that dedicated pirates will still manage to break it again and again. Still, it’s clear that the battle between pirates and those who would wish to stop them is far from over.

Microsoft celebrates Emergence Day with some online giveaways and events

Happy Emergence Day! Judging by my friends list, many of you already have the game. In fact you could have purchased it as early as last Tuesday, so this is kind of a late release celebration. Still, I'm not one to pass up free stuff. Here are some of the events Microsoft has planned for today. From the press release: HangZhou Night Net

Xbox Live® celebrates Emergence Day with 24 hours of special events beginning at 12:01 A.M. on Sunday, November 12 on Xbox Live. Gold members in North America can join online tournaments, download exclusive videos, win cool prizes, and participate in variety of other activities:

Leaderboard tournament: The 24-hour leaderboard tournament winner receives a one-of-a-kind Gears of War branded guitar as well as an automatic bye to the finals of a global Gears of War tournament planned for 2007. Hourly sweepstakes drawings: Prize giveaways mean you could win one of several Samsung HT-P29 Dolby 5.1 Surround Sound Systems. Gamer pic and theme: Score the exclusive free Gears of War gamer pic and theme, only available on Emergence Day. Game with Fame: Play with legendary heavy metal band and Gears of War fans Megadeth, the game's lead designer Cliff Bleszinski, and other members of the Epic Games team.New videos: Check out the never-before-seen videos including a special Emergence Day transmission from Cliff Bleszinski.MTV Special: Watch the MTV "Gears of War: The Road to Launch" sneak preview.

I have to remember to go online and grab that theme and gamerpic. I'm not sure if I'll even ever use them, but digital collectibles? C'mon, it woud be silly not to get excited! Sounds like today is the day to go online and chainsaw your friends.

Sun opens Java under the GPL

"The Java is free! The Java is free!"HangZhou Night Net

After years of speculation followed by years of waiting, Java has finally, truly been opened. Sun announced today that Java has made the jump to "open source," as Sun says that parts of the Java platform it owns are being licensed under the GPL open source license (version 2). The use of the GPL is surprising, because it puts any and all modifications back into the public source code, and not all software developers are eager to share their contributions. Nevertheless, in adopting the GPL, Sun is being aggressive in its move into open source. Solaris, for instance, is distributed under the far more restrictive Common Development and Distribution License (CDDL), which is mostly based on the Mozilla Public License (MPL).

"Everyone has been expecting that one day Sun would open source Java technology, but no one expected just how far they’d go—GPL. A bold move, and a great opportunity both for Sun and for free and open source software, " said Tim O’Reilly, founder and CEO of O’Reilly Media.

The upshot is this: not only has Sun open-sourced Java, but they’ve adopted a license that they hope will please the "free software" folks along with the hordes of commercial software developers that have been using Java for almost a decade. Java will be distributed with what is known as a "Class path exception" which will allow Java libraries to link to non-GPLed code, making it possible to continue to use Java with closed-source commercial development projects. Sun hopes it’s a win-win situation. Only time will tell.

Looking forward

Sun calls the move "one of the largest source code contributions under the GPL license," but the company is also quick to point out that this is big is another way, too. With 3.8 billion devices using Java, it’s the single largest platform for unifying software development for devices.

"By open sourcing Sun’s implementation of Java technology, we will inspire a new phase of developer collaboration and innovation using the NetBeans Integrated Development Environment (IDE) and expect the Java platform to be the foundation infrastructure for next generation Internet, desktop, mobile and enterprise applications," said Rich Green, executive VP of Software at Sun. "With the Java Development Kit (JDK) released as free software under the GPL, Sun will be working closely with distributors of the GNU/Linux operating system, who will soon be able to include the JDK as part of the open source repositories that are commonly included with GNU/Linux distributions."

Sun will also continue to sell Java-based software packages despite the licensing change.

All of the source code relating to Java is expected to be opened by the end of March 2007. For now, Sun has made available the first pieces of source code for Sun’s implementation of Java Platform Standard Edition (Java SE) and a buildable implementation of Java Platform Micro Edition (Java ME). More details are available at Sun’s new open source Java landing.

More coverage of interest to developers can be grokked at InfoQ, which has a great run-down on the licensing ramifications.

Google sees a future with free, ad-supported cellphones

In Google’s perfect world, cellphones would be free for those users who would be willing to watch ads on their devices. In an interview with Reuters, Google CEO Eric Schmidt said that cell phone price subsidies should increase in tandem with the amount of advertising delivered over cellular networks. "Your mobile phone should be free," Schmidt said to Reuters. "It just makes sense that subsidies should increase."HangZhou Night Net

Google has begn moving into cellphone advertising with experiemental ads consisting of brief video clips, images, and text ads underway in Japan.

Whether Google’s cellphone advertising plans succeed depends on how users interact with their cellphones. Schmidt sees a time when consumers spend up to 10 hours a day not only talking, but texting, surfing the ‘Net, and watching video. If you’re using your cellphone that much, Google’s hope is that you wouldn’t mind an ad or two, especially if it subsidized the price of the phone.

The advertising experiments in Japan are reportedly going well for Google, which bodes well for the company’s intention of delving deeply into advertising on mobile devices. Google has big plans for the market and is on record as predicting that revenues from cellphone advertising will eventually will eventually match those from its core, web-based ads.

Mobile phones are not the only place you will be seeing—and hearing—ads from Google in the future. The company recently entered the radio advertising market, acquiring dMarc Broadcasting for $102 million in January. dMark’s core product was an automated radio advertising system, which was integrated into Google’s AdSense for radio after the purchase. Google has also tried moving into print advertising, but the results haven’t been as impressive. A print ad auction earlier this year ended badly for Google as interest from potential bidders was lukewarm.

Will Google’s plans for the cellphone market pan out? It depends on how accepting consumers are of the concept. If the advertising is unobtrusive, perhaps with the cellphone display showing an advertiser’s logo while a call is being connected, consumers will likely go along—especially if the phone is free or subsidized. But if Google and cellular providers go overboard, consumers may stay away in droves.

Further readingCNN Money: Google CEO: Free cellphones for all, if…

AMD pulls plug on Personal Internet Communicator

AMD has stopped its work on the Personal Internet Communicator project after nearly two years of planning and development. The PIC was announced in late 2004 as a $250 headless computer, sporting a Geode x86 processor, 128MB of RAM and a 10GB hard drive. PIC was designed for "emerging markets" where the cost of computer hardware is seen as prohibitively high. HangZhou Night Net

In its third quarter filing with the Securities and Exchange Commission, AMD reported that "revenue from sales of PIC products has not been material and in the third quarter of 2006, we decided to stop manufacturing PIC products." AMD’s filing indicates that the company took a loss on unsold PIC inventory.

The death of PIC can almost certainly be attributed to the momentum of the much-hyped One Laptop Per Child (OLPC) program, which has announced that its first product will cost only $140 per unit. Executives at AMD aren’t shaking their fists at the OLPC, however. The Linux-based laptop is a remarkable achievement in low-cost design, and it just so happens to incorporate AMD technology. Manufactured by Chinese hardware company Quanta, the portable computer features a 400mhz AMD Geode processor, as well as 128MB of DRAM, built-in wireless support, and 512MB of flash memory for internal storage. More details of the project’s first laptop were covered by Ryan back in August.

Not everyone loves OLPC, however. OpenBSD founder Theo de Raadt had harsh words for the program, accusing the OLPC project of "work[ing] against the open source community" and engaging in "commercially expedient" activity that is "hurtful" to the open source community. Raadt’s objections stem primarily from OLPC’s willingness to enter into Non Disclosure Agreements.

AMD’s PIC now passes into the world of shadows, as have many "cheap PC" projects before it. It did enjoy brief success in countries such as Mexico, Brazil and China, where telecommunications companies sometimes leased the devices to subscribers. Attempts to market the device as a cheap Internet access solution ultimately failed to gain traction in the US and elsewhere, however.

Fox to sell low-cost DVDs in China to combat piracy

Twentieth Century Fox plans to be the second movie studio to start selling cheap DVDs in an attempt to beat piracy to the punch in China. Piracy in China, which has a long and sordid history, is costing movie studios an estimated $244 million a year in lost DVD and ticket sales, according to the MPAA. HangZhou Night Net

The first studio to announce such a strategy was Time Warner, which said in August that it planned to start releasing cheap DVDs in China in an attempt to fight piracy. The movies were to be released on DVD soon after their theatrical release for about 10 yuan (approximately $1.25) apiece. 10 yuan is close to the typical price for a pirated movie in China. Time Warner hoped that the move would lure customers to buy their DVDs instead of illegal alternatives. The short amount of time between theatrical and DVD release in China was also meant to try to beat pirates in getting the DVDs out as quickly as possible.

Fox’s strategy mirrors Time Warner’s, but they plan to offer DVDs at a slightly higher price of 20 to 25 yuan (about $3 per disc). This is, of course, about twice as much as the average street price of a pirated DVD in China, but Fox hopes that the premium isn’t so much that it deters customers from buying their discs. Fox’s international home-entertainment manager Keith Feldman told the Wall Street Journal that "it comes down to our ability as marketers to convince the Chinese consumer it’s worth spending the money."

In addition to offering low-priced DVDs, Fox also plans on aggressively improving its marketing and distribution in China. Feldman said that while the Chinese consumer is eager to buy foreign films, it’s often difficult to even find legal copies of them. Guo Zilong, president of Fox’s new distribution partner Zoke Culture Group, said that Zoke’s nationwide network of agents should help movie studios such as Fox improve their retail presence in China.

Studios such as Time Warner and Fox have come to the realization that if they don’t make such low-priced offerings to the people of China, they won’t make any sales at all. Charging $1.25 to $3.00 per disc and selling a few thousand movies is certainly better than (nearly) nothing, which is what they were making before. Plus, it gives them a chance to get legal copies of movies into Chinese homes and be able to legitimately bolster their sales numbers—an important strategy in an age where DVD sales in the US are beginning to plateau.

AMD 4×4 will set you back about a grand

All the cool kids are doing quad core. At least that’s what AMD and Intel want us to believe, as quad-core solutions have become the centerpiece of the their product lineups. Intel’s Kentsfield is expected to arrive shortly, and AMD’s 4×4 may be set for lift-off this week.HangZhou Night Net

At a briefing in Munich late last week, AMD revealed that the 4×4 will start around $1,000 and will run on an NVIDIA chipset. A cool grand will get you two dual-core FX-70 processors, with the FX-72 and FX-74 costing a bit more. A fourth CPU, the FX-76, will appear during the second quarter of 2007. German site golem.de reports All four CPUs are 90nm parts with 2MB of L2 cache. The clock speed on the new CPUs will range from 2.6GHz on the FX-70 up to 3.2GHz on the FX-76.

In the second half of 2007, AMD is expected to launch "true" quad-core CPUs which will be socket-compatible with the 4×4. As a result, deep-pocketed enthusiasts will be able to enjoy eight cores of computing goodness within a year. Unfortunately, there are not very many applications that can take advantage of multiple cores, but that will change as developers (like Valve) tweak their applications to take advantage of multicore systems.

Unlike Intel’s Kentsfield CPUs, which is two Core 2 Duo dies in a single package, AMD’s 4×4 platform consists of two dual-core Socket AM2 CPUs, with each socket connected to one another via a HyperTransport bus. The use of HyperTransport will result in a high aggregate bandwidth among the sockets and memory along with a level of coprocessor integration that Intel’s Core systems have yet to achieve. AMD’s high level of die- and system-level integration will likely result in a solution that should be very competitive with Intel’s offerings.

AMD has been under the gun lately for processor shortages and there are some concerns that the new 4×4 systems will exacerbate the problems. Two dual-CPUs can take up a lot of silicon, and with only one of AMD’s fabs (Fab 36) churning out 300mm wafers yet, the situation may not improve too much in the short term. When asked about the launch of the 4×4 CPUs, AMD corporate vice president of marketing Stephen DiFranco told Ars that it "won’t have any dramatic effect. People interested in 4×4 are primarily gamers and the high-end desktop market—a special part of the marketplace. It’s high-profile, but not high-volume."

Further reading:golem.de: AMDs 4×4: Zwei Dual-Core-CPUs schon ab 1.000,- US-DollarAMD hitches wagon to a HyperTransport-powered 4×4 and K8L