Although completing a genome provides science with lots of information, the completion of several genomes provides us with far more than the individual genomes do. Comparisons between the genomes of related organisms can provide us with information about the changes in gene content that accompany major evolutionary transitions. A great example of this is how the sequencing of the Chlamydomonas genome shed light on the origin of plants. Today, Science will be offering up an advanced publication that describes the sequencing of a moss, a relative of Chlamydomonas and descendant of the world's first land plants.
The organism in question is a Bryophyte called Physcomitrella patens. The genome itself is an unassuming 480 Megabases and contains about 36,000 genes. Its significance resides primarily in the fact that Bryophytes are the modern descendants of the first muticellular plants that made their way onto land. If you view Chlamy as lying on the border between algae and animals, you can view Bryophytes as on the border between Chlamy and trees. They are clearly adapted to life on land, but they still need a fairly wet environment, lacking as they do adaptations such as a complex root system and the vascular transport of water.
Physcomitrella itself appears to have only undergone a single whole-genome duplication, in contrast to the multiple rounds of duplications that characterize many of the flowering plants. As a result, there are far fewer duplicated genes and most gene families have fewer members.
Based on its capacity for sending signals between cells, the organism appears partly adapted to the muticellular lifestyle. It contains everything needed to make and use cytokinins, which regulate plant morphology. But it seems to lack other intercellular signaling molecules, such as auxins. It may be able to use ethylene, which flowering plants use to regulate fruit ripening, but the evidence is somewhat sketchy.
It appears to be partly adapted for surviving freezing and desiccation. Like flowering plants, it has a large number of ABC transporters, which reside on cell membranes and help control the flow of material into and out of the cell. It also has enhanced DNA repair capabilities compared to Chlamy, suggesting it can cope with higher exposure to sunlight. In fact, it appears to be well equipped for benefitting from a range of light conditions; the authors say it, "has increased the genetic playground for photosynthesis and connected carbon-based metabolism."
One of the best features of the new genome is that many of the predictions that come out of the genome analysis will be testable. Physcomitrella handles DNA repair in the same way that Yeast does, by homologous recombination. As such, it should be easy to knock out the genes we have now identified and examine the impact that has on its ability to survive in a terrestrial environment.
Science, 2007. DOI: 10.1126/science.1150646
Google boosted its army in the social networking battle last month by announcing OpenSocial, a platform for providing applications and widgets that any site or social network can adopt. This concept of "write once, run anywhere" is certainly an appealing one for third parties looking to get their products in front of lucrative social networking eyeballs. It was clearly also a response to Facebook's open API initiative that it launched back in May, which almost instantly opened the floodgates to a new rush of users and developers that has only increased in size. Though Google and Facebook have been scoring their respective social networking partnerships over the last few months, two separate announcements this week from major web players Bebo and Meebo are the latest to help tip the scales in Facebook's favor.
MySpace and Facebook may dominate social networking traffic in the US, but Bebo holds strong at third place. The company's visibility is likely to increase as well with its new implementation of the Facebook Platform. This will allow developers to build their apps simultaneously for Bebo and Facebook with a minimal amount of fuss—perhaps none at all. Considering that Facebook reportedly had over 32 million unique visitors in October 2007 and Bebo had almost 4.5 million, this new application compatibility can only be a boost to the traffic of both companies. Interestingly though, Bebo also announced its plans to eventually support Google's OpenSocial sometime in 2008, making it (potentially) the first social networking site to embrace both platforms. Still, Facebook's obvious place at the top of Bebo's list will only be a boon to their offerings—while sticking a thorn in OpenSocial's side.
The second pro-Facebook announcement comes from Meebo, the reigning king of web-based chat which now claims over 20 million unique monthly users. Offering a range of products, advertising opportunities, and unique features like co-op games with chat buddies, its announcement of meebo rooms, a Partner Edition custom-tailored for the Facebook Platform will be another major symbiotic win. As a social site, Facebook's integration of a web-based chat leader that allows users to easily share links and play embedded videos will undoubtedly be a boost to traffic and the amount of time users spend at the site. Meebo can even bring its other major partnerships to the chat rooms it enables Facebook with, like the one it made with Rock-A-Fella Records in September to allow users in a room to preview Kanye West's new album in a social atmosphere.
Likely to Google's dismay, Meebo did not mirror Bebo's intentions to also support OpenSocial at a future date.
While third parties and independent developers have been quick to hop on both Facebook's and Google's platforms, these announcements from significant players in other social corners of the web are a major win for Facebook. The social network is also at an advantage due to its being a visible destination with an established user base for developers. Google, by contrast, could see more difficulties in snagging partners due to its OpenSocial platform feeling more like an ambiguous middleman with no major faces to match with its name.
Ultimately though, the battle for the social networking space is just getting started. Google has notoriously deep pockets and a broader grasp on the web, while Facebook valuations are still at an amazing $15 billion. Grab some popcorn; this should be a good show.
A pair of paleontological finds are reported in the literature this week. The first is a newfound genus and species of one of the massive sauropodomorphs that was discovered in Antarctica—only the second Jurassic dinosaur ever found there. The second discovery comes from Africa and represents one of the largest carnivorous dinosaurs ever found.
The latest issue of Acta Palaeontologica Polonica contains an article (open access) that describes the discovery of a massivesauropodomorph. The fossils, which consisted of partial foot, leg, and ankle bones, were foundon Mt. Kirkpatrick near the Beardmore Glacier in Antarctica at an elevation of more than 13,000 feet. Sauropodomorph dinosaurs were gigantic herbivores, and were the predecessors of the more well known Sauropods. They are also closely related to—in evolutionary terms—theropods, which include Tyrannosaurus, Velociraptor, and modern birds.
Currently in paleontology there is open debate about the evolutionary relationship and development of sauropodomorph. This find establishes that the sauropodomorph dinosaurs were more widely spread, existing in the Americas, China, South Africa, and now Antarctica. Secondly, in conjunction with a prior Antarctic find of an early sauropod, it suggests thatGlacialisaurus hammeri—the new species—coexisted with true sauropods during the late Triassic and early Jurassic.
The second bit of dino-related news comes from a find not near a pole, but from just above the equator in the African nation of Niger. The fossils of interest here are not new—not that any fossil really is—they were discovered during an expedition in 1997 by University of Chicago paleontologist Paul Sereno. These fossils were identified as belonging to a new species, Carcharodontosaurus iguidensis, by a University of Bristol graduate student. This species would have been one of the largest carnivorous dinosaurs to have ever walked the earth—measuring in at 13-14 meters long, it would have been taller then a double decker bus.
Fossils of this species have an interesting history. The first known fossils of Carcharodontosaurus were found in the 1920s and consisted of two teeth—each the size of bananas. However, in the intervening decades, these relics have been lost. Other remains were found in Egypt in the 1930s, but were destroyed in the bombing of Munich in 1944. A skull of the dinosaur was found about a decade ago in the Moroccan Sahara. This leaves little evidence for scientists to go with, but it does illustrate that a number of species of theropods were living simultaneously in Africa around 95 million years ago. The current set of fossils consists ofseveral pieces of the skull—parts of the snout, lower jaw, and braincase—as well as part of the neck. The findings are reported in this week's edition of theJournal of Vertebrate Paleontology.
 Acta Palaeontologica Polonica, 2007. 52 (4): 657-674
 Journal of Vertebrate Paleontology, 2007.
The House today held a hearing on the new PRO-IP Act that beefs up intellectual property enforcement. Rick Cotton, a top NBC lawyer and representative for the Coalition Against Counterfeiting and Piracy (CACP), called counterfeiting and piracy "a global pandemic" and "a dagger into the heart of America's future economic security." What the US needs, he said, is a "declaration of war." But not even the Department of Justice is convinced that PRO-IP, in its current form, is that sort of declaration.
Counterfeit goods are certainly a problem, and no one at the hearing stands opposed to crafting good intellectual property law to protect creative work and new products (even Public Knowledge's Gigi Sohn proclaimed her support for IP law and enforcement).
Rep. Darrell Issa (R-CA), who made money in the car alarm business and was the voice of the "Viper" system, used his opening statement to tell his fellow representatives about how other companies ripped off his products, including his voice, and sold them in the US market. Defective products would arrive at Issa's company that he had not even manufactured, though in the minds of customers, his company was to blame. Will PRO-IP help to fix such problems?
Concerns from Justice
The PRO-IP Act seeks to stem the "tsunami" (as one representative put it) of counterfeitingand piracy by making a pair of changes to the structure of the federal government. First, a new executive branch office devoted to intellectual property enforcement would be created in the White House, and it would be modeled on the office of the US Trade Representative. The Department of Justice would also get a new IP enforcement division that would consolidate work currently done in several other divisions.
Sigal Mandelker, a Deputy Assistant Attorney General at the DOJ, told the subcommittee that this plan raised some concerns at Justice. For one thing, having a White House office that can direct the priorities and investigations at Justice could undermine the independence of the department, she said.In addition, the current arrangement at Justice is "actually quite effective."
Public Knowledge weighs in
Other concerns came from Gigi Sohn, president of Public Knowledge, who attacked the PRO-IP Act's increase to the statutory damages that can be leveled for copyright infringement.Referencing the Jammie Thomas case in Minnesota, Sohn noted that statutory damages are already "disproportionate penalties for infringement," and called on Congress to move them in the other direction.
Despite several significant criticisms of the bill, Sohn said that she was pleased with how subcommittee chair Howard Berman (D-CA)listened to many different stakeholders and had already removed the most egregious provisions from the bill.
"Unslakable lust for more"
Google's senior copyright counsel, William Patry, wasn't at the hearing, but he had a far less charitable take on the legislation. Calling it the most "outrageously gluttonous IP bill ever introduced in the US," Patry made clear that he was appalled by the "unslakable lust for more and more rights, longer terms of protection, draconian criminal provisions, and civil damages that bear no resemblance to the damages suffered."
One might expect that coming from a Google lawyer (the blog is written in his private capacity), since the company is a voracious consumer of copyrighted work, but Patry has himself served in the Copyright Office and has written perhaps the definitive seven-volume tome on the subject of US copyright law. Instead, he says, he is "pro-IP in this most important of senses. But an excessive amount of something that is beneficial in measured doses can become fatal in overdoses, and copyright is already at fatal strength."
The PRO-IP Act, with its attempt to increase statutory damages andincrease forfeiture penaltiesfor equipment used for copyright infringement, clearly moves in a way that Patry dislikes. Fortunately, when it comes to criminal matters, Justice remains steadfastly unconcerned with prosecuting minor infringement cases, as Mandelker again made clear in response to a question.
Still, with even harsher laws on the books, there's always a chance that thepenalties won't hit only those who import ripped-off car alarms, but a huge array of ordinary Americans. Where penalties are needed, they should fit the crime. Ruining someone's financial lifeover the equivalent of a box of CDs or DVDs hardly seems to meet that standard.
AMD held its annual Financial Analyst Day this morning. This time around, there was no glitter, no flash, and no rosy pep talks about the current (or future) dominance of AMD products in the marketplace. The various corporate executives who spoke, including Hector Ruiz (CEO), Mario Rivas (executive vice president, Computing Products Group), and Dirk Meyer (president, chief operating officer), acknowledged the difficulties AMD is currently experiencing, admitted that the company's execution had slipped badly over 2007, and pledged that 2008 would be different. AMD's word of the day was "apologize," and multiple executives expounded on the theme. Future-casting was kept to a bare minimum, and most of the information discussed is already common knowledge in technical circles.
That's not necessarily a bad thing given AMD's current financial position and the company's desire to strike a different tone with the financial industry. Admitting the truth of where it stands and the need for change paints the company as an honest one that's willing to give real information on its operations, even when that information isn't good. The best way to follow up on such statements, however, is to deliver realistic good news about what's expected in 2008. Unfortunately, that didn't really happen, and the statements and projections AMD didn't make resonate more strongly than those it did.
According to AMD, platform-based solutions will remain a major focus for the company thanks to strong demand for them from its customers. Sunnyvale also gave some hard numbers on current quad-core shipments, stating that it shipped 34,000 Barcelona cores in the third quarter, expected to ship "hundreds of thousands" by the end of the fourth quarter, and would double Q4 shipments in the first quarter of 2008. The company also clarified what the exact state of Barcelona shipments is at the moment. Barcelona parts are shipping, but only to specific customers, and only in situations where AMD is able to work with the company to ensure that the TLB erratum will never be encountered. Phenom shipments will continue, but major OEMs aren't expected to offer complete systems based around the part until the end of the first quarter or the beginning of the second. This implies that most manufacturers are largely passing on Phenom until its TLB erratum is completely resolved, though AMD did not make that particular correlation.
AMD projects that it will ship Phenom and Barcelona parts in a 3:1 ratio through the first quarter of the year. Around the end of Q1/beginning of Q2, the new "B3" stepping of the K10 core should be available in volume. Once this occurs, Barcelona production and availability will be ramped, and the processor will be made available in volume to Fortune 500 companies.
That's basically all AMD had to say about Barcelona and K10. While the tone of the meeting would've made aggressive rose-colored predictions unpalatable, AMD's decision to say so little about what we can expect from K10 in 2008 was surprising. The company did discuss its transition to 45nm process technology, stating that samples were set to be delivered in January, with volume ramp beginning in the second half of 2008, but that projection is short enough to raise some eyebrows; it'll be surprising if AMD can switch to 45nm that quickly. AMD is working on a 45nm, octal-core K10.5 with 6MB of L3 per cache and an MCM approach (two quad-cores per die), but the die itself has not been produced on actual silicon—at least not yet.
Good vibes on ATI
ATI was the only real bright spot of the day. That particular segment of AMD is downright bullish in its expectations for 2008, and intends to challenge NVIDIA in the mid-range and high-performance desktop segments while simultaneously retaking market share in the notebook segment. New midrange and budget GPUs based on the RV620 and RV635 will be available in the first quarter of next year, and the company's RV680 (dual X3870 GPUs on one PCB) should debut relatively early in the year as well.
ATI also announced two new capabilities that will come with next-generation video cards and integrated chipsets. Going forward, integrated chipsets built on the 780G platform will be able to increase overall video performance by plugging in a budget or midrange GPU that will work in concert with the already integrated GPU to boost performance. Think of the combination as a weak Crossfire solution, but one that actually makes some sense; integrated users who upgrade to even a budget GPU will see a greater performance boost than they previously would've. ATI hasn't revealed much about this technology yet, but the company claims that it will function best with lower-end cards. As performance becomes increasingly asymmetric between the integrated GPU and the discrete part, the overhead created by enabling Crossfire inevitably overwhelms the advantage of using it.
The other announcement from ATI today is that it will begin shipping DisplayPort capable cards this year. DisplayPort is designed as an alternative to HDMI, and uses fiber optic cable rather than twisted copper. This allows a display to use a much longer signal cable before image quality begins to degrade. There are no DisplayPort-capable monitors shipping at this time, but various companies including Dell, Samsung, IBM, and Lenovo have all said that they will be adopting the standard in the future.
If not for ATI's recent resurgence, AMD's event today would've come across as downright depressing. AMD's presentations and speeches were meant to demonstrate both an acceptance of the company's current position as well as a determination to turn things around and put the CPU manufacturer back on track. Unfortunately, neither determination nor admission of accountability are easily converted into cash. Today's event didn't seem to be the work of a company that's expecting much good news in the fourth quarter, and the lack of information on upcoming K10 improvements cast doubt on that processor's ability to carry the company financially.