Back in the middle of June, Mike Pinkerton checked multi-line textarea spell-checking into the Camino trunk and branch nightly builds.iWebUserSites is a website directory of pages made with Apple's iWebPeople have long pined for a text editor that hides all distractions and let them get down to work. Since a manual typewriter just isn't practical these days, Hog Bay Software has created WriteRoom : "For Mac users who enjoy the simplicity of a typewriter, but
live in the digital world. WriteRoom is a full screen, distraction
free, writing environment. Unlike standard word processors that focus
on features, WriteRoom is just about you and your text. Requires Mac OS
X 10.4 or later."
Speaking of cool and innovative applications, Liquifile is a file browser for OS X that has a unique visual representation of your documents: "An alternative Finder, if you will. It is designed for visual thinkers
who want to get a bigger picture of their files and feel them more
directly. But not only for them ;-). Did you ever wonder why searching
and browsing is so separated in today's interfaces? Ever wished you had
a bigger screen when finding or organizing your files? Ever lost files
in deep hierachical structures? Ever wondered what the next big thing
in file browsing might be…?"
If you doubted Apple was working on a resolution independent UI before, you might be a little more likely to believe it with Apple's HIGeometry API that popped up on June 28th: "HIGeometry is a Quartz-compatible API for describing and manipulating
basic geometric objects such as points, rectangles, and sizes.
HIGeometry expresses all coordinates using floating-point numbers. This
API provides functions to convert an object’s coordinates into a
different coordinate space. These functions support resolution
independence mode drawing by taking into account the scale factor of
your application’s user interface."
Bleep's Buildfactory makes the process of managing, checking-out, and compiling multiple Xcode projects super-easy. BF seems as if it picks up where Xcode and Apple left off: "BuildFactory is a tool aimed at helping developers do what they do
best, develop. With BuildFactory you can run automated builds, build
refreshed sources from Subversion, open errors and warnings in your
external editor of choice (even Xcode), and build multiple projects
with the click of a button." Bleep recently donated a bunch of licenses to the Adium crew!
Since it's an extended holiday weekend here in the US, science news has slowed down considerably, allowing me the time to write up a post I hope will bring some clarity an issue that's popped up more than once, including just last week. The topic is junk DNA, namely does it exist, and if so, how do we identify it? I'm going to go over a few of the types of potential junk DNA and then wrap up with a my own conclusions on the topic, just so I can refer to this in the future without re-starting the debate over whether junk DNA really is junk.
Read more …
The concept of junk DNA arose when researchers started sequencing large pieces of the genome, and found that very little of it coded for proteins. With the completion of the human genome, we can give a more precise figure on that: only 1.4 percent of the genome is likely to code for an actual protein. But other genomes tell a very different story. For example, the pufferfish (Fugu rubripes) has a genome that's 1/8 the size of humans, but has roughly the same number of genes. The difference, it appears, is largely in the junk: Fugu doesn't have much of it, and so serves as a useful point of comparison. Comparing the two genomes can help us identify how junky all the bits of non-coding DNA are. There are a few classes of DNA sequences that appear to have a substantial junk content:
Inter-regulatory sequences: before a protein gets produced, you have to copy the DNA that encodes it into an RNA message, a process that is regulated by the DNA surrounding the message. The DNA sequences that regulate a gene's expression can reside up to hundreds of kilobases away from the actual gene. But does the DNA in between the regulatory sequences matter? In some cases yes, but Fugu suggests that those are the exceptions. Many of the same regulatory DNA sequences are used in both humans and fish, but in Fugu those sequences are often much closer together, with the intervening sequences eliminated. This suggests that much of the sequence near genes is junk.
Introns: In eukaryotes (all multicellular animals), the protein coding portion of a gene is split up into exons. The intervening DNA (termed introns) is eliminated from the final RNA message. All told, the DNA sequence of introns accounts for about 24 percent of the human genome. These introns contain regulatory sequences that signal for the elimination of the intron from the final message, and can contain sequences that regulate gene expression as well. But these account for a small fraction of the total intron sequence. Many organisms (such as flies and Fugu) have much smaller introns than humans, and small, rapidly dividing eukaryotes such as yeast have gotten rid of the majority of their introns.
Pseudogenes: Large duplications of genetic material go on all the time. Some of the duplicated genes (and their accompanying introns and regulatory regions) develop new functions, but others don't get used, and mutations eventually silence them. The human genome is littered with dead copies of genes, called pseudogenes. It's always possible that further mutation will do something useful with these genes, but in many cases, it's highly unlikely. In the case of odorant receptors, over half the nearly 1,000 present in the human genome are now pseudogenes; it's hard to imagine all of them being put to use in the future.
Disabled retroviruses and transposons: Many viruses reproduce by inserting a copy of themselves into the genome. When this process goes badly, an inactive virus is left behind; this process accounts for approximately 2 percent of the human genome. More significant are the transposons, mobile genetic elements that have hopped around the genome and now account for nearly half of it. Most of these transposon copies are non-functional, and will never hop again. Combined, these disabled parasites account for a significant fraction of what is commonly considered junk.
Other stuff: There are other regions of the genome that appear to simply not contain genes. Those regions are largely absent in the Fugu genome, and do not have any obvious function.
People tend to refer to all of these classes of DNA elements collectively as junk, which is where much of the problem arises. Although the junk is probably useless on average, there are clear exceptions. I've covered at least three cases where transposons or pieces of them have been used to form a functional gene product. These cases are often announced with press releases proclaiming something along the lines of "a new use for junk DNA is found." This tends to obscure the fact that these transposons are only useful within the context of a normal gene. Even in cases where the actual transposons may be doing something useful, it's far from clear whether any individual element or the huge number of transposons present are actually required for the useful activity.
So, when I refer to junk DNA, I'm not referring to any specific DNA sequence (which may or may not be useful), but to the collective populations of several types of DNA sequences that, on average, appear to be junk. By extension, I'd say that a lot of the genome appears to be junk. Fortunately, we've reached the point where we can begin to test this experimentally; if I'm wrong about much of the genome being junk, you may see a mea culpa here in the future.
An article appeared yesterday at Space.com that discusses some of the odd things that pass for normal on a brown dwarf, the class of body that resides between "super Jupiter" type planets and stars. The article doesn't appear to be based on new research but it fascinated me, so I thought it was worth a mention. The article focuses on the work of two researchers who have published extensively on brown dwarves, and much of it appears to be based on a paper they published together back in 2002.
There are noticeable differences between Jupiter and the Sun. Of the two, brown dwarves seem to be a bit closer to Jupiter in terms of behavior, as there are observational indications that they have weather and storms driven by convection (on the sun, magnetism is a major driving force). Temperature wise, brown dwarves start out much hotter than Jupiter. Without a star's fusion output, however, they gradually cool over time. This cooling has some bizarre implications: early in their history, brown dwarves have temperatures which are sufficient to not only melt metal, but evaporate it. Once the cooling kicks in, that metal will return to the dwarf's surface in a rain of liquid iron.
Part of this view into the world of brown dwarves is based on theoretical modelling, but direct observation has made some contributions as well. These dim objects are extremely difficult to observe, but inferences regarding their temperatures can be made. The researchers were somewhat surprised to find that older dwarves, which should be the coolest, actually appeared hotter and brighter than young ones. It seems that the clouds of hot metal initially act as an insulator, retaining heat for much longer than might be predicted. As these clouds fall to the surface as rain, more heat is able to radiate from the dwarf, making it appear to get hotter as it ages.
Overall, the article points out that, despite often being labeled "failed stars," brown dwarves are interesting objects with a distinct set of features.
Google has strong words for legislators who are currently mulling over net neutrality issues: the company will take any perceived abuse to the US Department of Justice. Speaking at a news conference in Bulgaria, Internet pioneer and now Google VP Vint Cerf said that the company will be "happy" if legislators ultimately opt to support net neutrality principles, but in the absence of such support, the company will take a wait-and-see approach.
"If we are not successful in our arguments… then we will simply have to wait until something bad happens and then we will make known our case to the Department of Justice’s anti-trust division," he said.
Cerf’s comments recognize one of the most heated debates within the net neutrality fight: whether or not this could become an antitrust issue. Some opponents of net neutrality argue that legislation is not needed because the market will sort it out—a notion founded on the belief that there is more than adequate competition in broadband across the country to prevent monopolistic behavior. Net neutrality advocates often argue the opposite, namely that there is not sufficient competition throughout the country to prevent monopolistic abuses. Without such competition, service providers could punish their competition with impunity, advocates say. "We are worried that some of the broadband service providers will interfere with that principle and will attempt to use their control over broadband transport facilities to interfere with services of competitors," Cerf said.
Recently Senator Ron Wyden (D-OR) announced that he will place a "hold" on any legislation addressing the telecommunications industry that lacks "effective policy" on net neutrality. "The days of unfettered, unlimited and free access to any site on the world wide web, what I call net neutrality, are being threatened," said Sen. Wyden. "Those who own the pipes, the giant cable and phone companies, want to discriminate on which sites you can access."
The war between the two opposing sides is filled with accusations and light on actual facts. Net neutrality opponents have said time and time again that premature action could lead to the stifling of innovation. Telecom lobbyist Mike McCurry recently warned that net neutrality laws "will dampen investor interest in building bigger, faster, smarter pipes," which he argues will ultimately lead to an Internet slowdown. Nevertheless, advocates of net neutrality continue to charge the telecommunications industry with ulterior motives, a charge which they believe "sticks" on account of now infamous comments made by several telecommunications executives over recent years, including AT&T CEO Ed Whiteacre’s claim that Internet companies were using "[his] pipes" for free, and that they should not be "allowed" to do that.
Nanotubes. Lately, it seems like the solution to any problem we can think of lies in harnessing the capabilities of nanotubes—super-strong molecule-sized carbon pipes, which are believed to have potential uses in everything from transistors to tissue growth to infinitely rechargeable batteries. Yet even though commercial applications for nanotube technology have proven somewhat elusive, researchers are continuing to find more applications for the tiny things, and the latest mouthwatering tidbit comes from hard drive manufacturer Seagate.
Seagate has filed a patent application for a design which would use lubricant stored in carbon nanotubes. As the drive spins, the lubricant slowly leaks out of the nanotubes as a vapor, keeping the drive running smoothly and happily for its intended lifespan.
The next question, no doubt, is why would Seagate want to create a hard drive that leaks lubricant?
Hard drive platters coated with a conventional recording medium are capable of recording data to a certain, relatively low density. Greater density is important because it not only allows more data to be stored in a given space, but data can be searched and read more quickly from a higher density platter. Unfortunately, increasing the density—outside of using techniques like perpendicular recording—also increases the instability of the data. In other words, placing ones and zeros too close together increases the likelihood that one bit may "flip" its neighbor.
One solution to this problem is to use a recording medium with a high magnetic anisotropy—which is much harder to alter magnetically, but would allow data to be packed more tightly with less risk of instability. The other side of the coin is that conventional hard drive heads are incapable of generating a magnetic field strong enough to write to such materials.
Heating high anisotropy materials makes them easier to record upon, however, and techniques exist for doing just that by aiming a tiny laser beam at the area under the hard drive head. In this way, the recording medium maintains its stability and greater data density, without requiring an exotic and expensive recording head.
The flip side to heating the platter surface, however, is that the all-important lubricant film is either evaporated or decomposed by the heat, which can severely limit the life span of a drive. Replenishing that lubricant is a tricky thing, and that’s where the carbon nanotubes come in handy. Like a high-tech sponge, the nanotubes can be made to hold a supply of the lubricant, which is then emitted as a vapor around the platter to keep things running smoothly for a very long time.
Researchers are continually discovering ways to keep the storage limits of conventional hard drives several steps ahead of the flash-based memory that is predicted to eventually replace them. Nanotube-stored lubricant is one more step toward keeping hard drives around for a long time. Before you head to the store to seek out one of these new drives, however, keep in mind that they probably won’t be on the market for a some time—if ever.
Speculation time: while the basic concept seems sound, the concern that comes to my mind has to do with the practical longevity of such drives. Focusing enough heat on the platter to cause changes in the lubricant makes one wonder what the long-term stability of that lubricant will turn out to be. Decomposed lubricant sounds suspiciously like dirt to me, and I have to wonder if, while replenishing lubricant in vapor form might be helpful in the short-term, there may be performance tradeoffs down the road.
The SCO Group’s lawsuit against Linux distributors IBM, Red Hat, and Novell hit a major snag yesterday as Magistrate Brooke C. Wells of the US District Court in Salt Lake City dismissed 182 of SCO’s 294 claims. The dismissal is part of a 39-page ruling that comes down hard on SCO for continually refusing to provide specific details about which lines of code in SCO’s products were stolen by Linux programmers.
“SCO’s arguments are akin to SCO telling IBM, ‘Sorry we are not going to tell you what you did wrong because you already know,'” Wells wrote in the ruling. “Given the amount of code that SCO has received in discovery, the court finds it inexcusable that SCO is, in essence, still not placing all the details on the table.”
SCO’s reaction to the news was predictably unrevealing. “Our legal team is reviewing the judge’s ruling and will determine our next steps in the near future,” said SCO spokesperson Blake Stowell.
The painfully long and drawn-out saga of the SCO lawsuit started in March 2003, when SCO sued IBM for allegedly “devaluing” their version of the Unix operating system. The lawsuit was extended to include Novell later that year. SCO claimed that both companies had taken code from Unix and put it into Linux. The company was ordered in 2004 to hand over examples of the infringing code in no less than 45 days, but SCO has managed to dither and delay without producing any hard evidence. Clearly, the judges are losing patience.
So will SCO decide to reveal their trump card after all? It seems highly unlikely. In a memo that was leaked last year, SCO’s internal code audit from 2002 found no infringing code in Linux. SCO’s response at the time was to reveal an 1999 e-mail from an outside consultant that allegedly found “troubling similarities” between Linux and Unix code. However, similarities do not equal stolen code. SCO has even backtracked from their initial assessment, stating that the problem may lie in “methods and concepts” rather than stolen lines of code.
SCO may have known for a while that their case was hopeless, and are simply deciding to see the case through in hopes that they may at least recover a small amount of money through technicalities. The company stated in 2004 that they wanted to concentrate more on new products than on lawsuits. This latest news may force them to do just that.
SCO’s stock fell from US$4 to below US$3 on the news, and currently sits at US$3.25.
Antitrust regulators from the European Union’s 25 member nations have voted unanimously against Microsoft, finding the software giant guilty of non-compliance with the EU’s 2004 ruling. The decision opens the door for the EU to levy daily fines of up to €2 million (US$2.5 million) on Microsoft. The exact amount of the fine will be decided at another meeting to be held next week.
The debate centers on the EU’s interpretation of Microsoft’s compliance with an earlier judgement handed down in 2004. In that hearing, Microsoft was charged with unfair bundling and anticompetitive behavior, and was told to do three things: pay a fine, release a version of Windows without Media Player bundled, and disclose information about their server products to enable competitors to more easily write software that can interact with them. Microsoft paid the fine, delivered Windows XP N—with the N apparently standing for the version of Windows Nobody wanted to buy—and delivered large stacks of technical documents covering Windows Server protocols.
It was this last deliverable that the EU had problems with. A monitoring trustee, British professor Neil Barrett, was appointed to judge the information released by Microsoft, and his initial response was that the documentation was inadequate. Microsoft replied by offering to license parts of the source code itself, but that effort was dismissed by the EU regulators.
For its part, Microsoft claims to be working hard to deliver the information the EU desires. “Microsoft is dedicating massive resources to meet the aggressive schedule and high-quality standards set by the trustee and the commission in this process,” a Microsoft employee said in a statement. “Our engineers are working around the clock to meet the seventh and final delivery date for this project scheduled for July 18.”
Clearly the prospect of more fines and continued antitrust action is a concern for Microsoft, as much for their public image as for their bank balance. Given this, one wonders what the exact reasons are for the EU’s dissatisfaction with Microsoft’s documentation. A cynical answer might be that the EU simply wants to keep the Microsoft money train flowing. Looking at things from a different angle, perhaps Microsoft wants to make sure that while it may become possible for third parties to build replacements for Microsoft’s server software, the documentation should not make it easy. The issue is made more difficult by the EU’s failure to make it clear exactly what type of information they are looking for.
The EU is not the only governing body to issue fines and judgements against Microsoft. South Korea fined the software giant US$35 million for similar antitrust issues, although without the request to provide additional documentation. Microsoft has agreed to pay this fine. Back in the US, Microsoft recently agreed to extend federal oversight over their 2002 antitrust ruling until at least 2009, and the company has decided to “rewrite significant portions of the documentation in an effort to substantially improve the overall quality of the documentation.”
Whenever you interview Tomonubo Itagaki, the glasses wearing head of Team Ninja, you're sure to get him to say something outrageous. From bashing Tekken to calling the girls in Dead or Alive his daughters, he's always entertaining. It seems now he has two projects he's working on,the next Dead or Alive Xtreme Beach Volleyball and Ninja Gaiden 2. When trying to design jet ski levels and new bikinis for his volleyball title, where do the ideas come from? Drinking!
Kikizo: So, how many drinks does it take for ideas to stop being feasible, good ideas, and start being just complete nonsense?
Itagaki: Haha! It's hard to say, because I am drinking pretty much full-time. Of course, there are ups and downs, waves, of how I drink in terms of the amount, but it's a long period of time. In the last ten years – not that you asked this question – I think I had better ideas when I was drinking whisky. When I am drinking shochu, that's a conservative drink, so the ideas are not that great. Beer is just like water to me, so it just helps me and everyone else loosen up a little bit, it doesn't really contribute to coming up with ideas.
So there you have it. If you want good ideas, drink whisky. Not that we at Opposable Thumbs would ever advocate drinking, but Itagaki seems to think it's a big part of his creative process. You have to admit, the idea of him stumbling around Team Ninja's headquarters, yelling at everyone to make the bikinis smaller, is pretty funny. When the interviewer says he's not at Itagaki's level yet, the famed developer had a few choice words of wisdom:
It just means that you haven't been drinking enough. Haha! Not often enough. This afternoon, keep drinking more.
Who are we to argue with genius?
A new study from marketing research company Ipsos Insight indicates that while file sharing may be down, it still constitutes a significant percentage of the music found on today’s portable digital music players. Yet music downloads from legal services have eclipsed those stemming from P2P and other unauthorized sources. In fact, the study indicated that more than 70 percent of such music stems from legal sources, and that music download services are on the rise. The numbers show how far the industry has come from the days when CEOs would argue that "the most common format of music on an iPod is ‘stolen’." If that view was dubious before, it’s now outright ridiculous.
According to the study of more than 1,100 people, existing CD collections still provide the lion’s share of music on portable players, accounting for 44 percent of such content. Download-to-own sales accounted for 25 percent of music on portable devices, while unauthorized file sharing accounted for 19 percent. While the music industry may be pleased, the study also indicated that 6 percent of music stemmed from users "ripping" CDs owned by others—something the industry considers akin to raw piracy. With an average of 700 songs per player according to the study, approximately 175 songs per player have not been properly licensed or purchased in the eyes of the recording industry. (Of course, that number would be significantly higher if the RIAA’s views on ripping legally acquired CDs were ever enforced.)
Portable music players are quite popular, too. The study indicates that one in five people over the age of 12 have a portable music player, and one in twenty actually have more than one. The study suggests that the percentage of portable player ownership is increasing at a rate of roughly five percent a year, as 2003 and 2004 saw 11 and 15 percent penetration, respectively.
The strong sales are good news for the music industry, which has seen aggressive growth in digital sales in recent years. Sales tripled in 2005 according to the International Federation of the Phonographic Industry (IFPI), climbing up to represent 6 percent of global music receipts that year. And while younger people generally dominate the uptake of new electronics, persons aged 35 to 54 are getting in on the action as well, with one in ten sporting a portable music player last year.
Radio star need not fear video?
There are signs that the music video revolution won’t be portable, however. Approximately one in three people aged 12 to 24 said that they are interested in portable video, including music videos, TV shows, and movies. By way of comparison, almost 1 in 2 were interested in FM radio capabilities being integrated into players, while nearly 2 in 5 expressed interested in satellite music support. For persons ages 24 to 54, interest in video content was only 1 in 6.
Nevertheless, Matt Kleinschmit, a Vice President with Ipsos Insight and author of the study, interpreted the findings as being bullish for video sales.
"These recent findings showing the desire for broader multimedia content on a portable device could suggest we are reaching a turning point in which consumers are truly recognizing the value of anytime, anywhere multimedia content on-the-go," Kleinschmit said in a statement. "While this phenomenon may have initially centered on music, younger MP3 player owners are clearly interested in a wide variety of broader content options for their devices."
The study (PR) was based off of responses from 1,112 Americans aged 12 and over. It carries a 95 percent certainty that the results are accurate to within +/- 2.94 percent.
The debacle surrounding Windows Genuine Advantage just won’t go away. Late last month Microsoft found itself the target of a complaint seeking class action status over WGA’s behavior, and now we have learned that a second related suit has been filed.
Brought by Engineered Process Controls, LLC, Univex, Inc., Edward Mifsud, David DiDomizio, and Martin Sifuentes, the suit charges that WGA is essentially spyware, inasmuch as users are deceived to install it by being led to believe that it is a security update. The suit was filed in the US District Court for the Western District of Washington.
"WGA is ‘spyware’ that transmits data to Microsoft’s central computer ("phones home") every time a PC is booted up and every 24 hour thereafter," the suit alleges. The accusations are in response to the revelation that beta versions of Windows Genuine Advantage did "phone home" once every day, but the company recently confirmed that more recent versions communicate with the company approximately once every 90 days. Microsoft maintains that the daily checks were there because the software was in beta, not because the company intended to test daily checkups.
Daily or not, privacy advocates are outraged. The suit complains that "Microsoft does not advise users of these phone home capabilities. WGA gathers data that can easily identify individual PCs and WGA can be modified remotely to collect additional information at Microsoft initiation." The complaint continues, "software hackers can exploit WGA to not only collect data but also to modify users’ computers." The suit contends that Microsoft and WGA violate Federal and Washington State law and "public policy on privacy, security, consumer deception, notice and consent."
The suit seeks compensatory damages, injunctive relief and a requirement for Microsoft to fully disclose WGA’s "potential security and other risks" to the public. The suit also asks that Microsoft be made to produce a tool that can easily remove WGA from any Windows system. Should the plaintiffs prevail, Microsoft would have to scrap WGA and would be subject to treble damages. Among the damage claims is a request seeking "either actual damages or one hundred thousand dollars per violation, whichever is greater."
For both cases, the debate is expected to center around the definition of spyware. The suit itself uses the recently-formed Anti-Spyware Coalition’s definition of spyware, which focuses on lack of consent and the "collection, use, and distribution of a user’s person or other sensitive information" in constructing a definition of spyware. Microsoft has insisted that WGA is not spyware, and that it does not track user behavior or anything other than the licensed state of a Windows installation.