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.