Publishers try to railroad Open Access research

The past several years have seen a number of initiatives intended to leverage the Internet to provide greater access to scientific literature. One such effort comes from the National Institutes of Health, which has encouraged researchers to place copies of their published works at PubMed Central, and has worked with publishers to facilitate this process while avoiding copyright issues. Given the slow progress of PubMed Central, Congress has recently expressed interest in making this process mandatory. This has raised red flags with a number of publishing concerns, but the tactics used by the publishers to block such bills are raising enough ethical issues that they may create a backlash. HangZhou Night Net

Congressional action on the matter is based on the simple logic that the results of publicly funded research should be accessible by the public that's paid for it. A bill, the Federal Research Public Access Act, was introduced in 2006 with the intention of ensuring this access. It would expand the scope beyond the biological research funded by the NIH to include any federal agency that funds over $100 million in research. Journals could continue to attract subscriptions by retaining exclusive access to content for six months following publication; the bill places the burden of hosting the material on the agency supplying the funding. It also specifically excludes material that has not been subject to peer review. Overall, it appears to strike a reasonable balance among a number of competing needs.

Many publishers, however, did not view these requirements as reasonable. Back in January, Nature broke the news that the Association of American Publishers (AAP) had hired an aggressive public relations consultant to keep this bill and any future versions of it from ever becoming laws. Best known for having led Exxon-Mobil's attacks on Greenpeace, the consultant recommended a course of action that framed the measure as an attack on peer review itself and the government hosting of content as an invitation to government censorship.

Peter Suber, who tracks open access news, notes an article (subscription) in the Chronicle of Higher Education that indicates the publishers have put some of these ideas into action by funding an organization called PRISM, the Partnership for Research Integrity in Science & Medicine. The site, which has stock photos of serious people in lab coats (meant to suggest the involvement of the research community), implements a number of the PR suggestions originally reported in Nature. These include the suggestions that the effort is an attack on peer review itself and that government-sponsored hosting is an invitation to censorship and manipulation.

These hyperbolic claims, however, may be prompting a lot of discomfort among the scientific publishing community, which contains a number of small academic presses in addition to the large commercial houses. The accurate information provided to Nature suggested that not everyone was happy with the initial ideas. With PRISM now live, Suber has published an open letter from the executive director of the Rockefeller University Press in which the AAP is asked to add a disclaimer to the PRISM web site. The letter indicates that the views expressed at PRISM do not reflect those of all AAP members, and lists five ways in which the site spins or distorts the truth.

In short, if PRISM is any indication, the commercial publishers have overplayed their hand. By grossly distorting the intent and likely result of potential Congressional action, they have both discredited any reasonable arguments they had and alienated some of those who might otherwise be their allies. That said, Congress has been known to act based on discredited arguments in the past, so the publishers' effort might succeed despite its shortcomings.

Is there biology behind cell phone fears?

This is going to be a somewhat unusual post, in that I'm covering a paper that I'm not entirely convinced by. The data, however, are relevant to a number of topics we've covered recently, including homeopathy and the purported health risks of cell phones. As should have been clear from the homeopathy feature, when results are ambiguous—and the combination of placebo effects and double blind trials of homeopathic remedies are efficient producers of ambiguity—having a well understood mechanism becomes essential. That's where homeopathy fails, as proposed mechanisms have no basis in reality. Studies that suggest that cell phone use can produce adverse health effects have a similar track record, but questions of mechanism are significantly more complex. HangZhou Night Net

Biological systems are known to respond to a range of radiation, but the type produced by cell phones is very low-energy. The only well-defined way for cells to respond to that sort of radiation is via the stress response normally triggered by heat, a response that poses no real health risks. At the same time, there have been a number of tantalizing hints that radio-frequency radiation can trigger reactions that are distinctly different from heat stress. That's where a recent publication comes in.

The paper looks at the MAP kinase network, which plays a central role in a multitude of cellular signaling events. The researchers exposed cells to radio-frequency radiation in a way that was caused negligible heating, and found that a specific arm of the MAP kinase cascade was activated within five minutes of exposure (the earliest timepoint checked). Some of the experimental details are a bit sparse, and the experiments are very dependent upon the quality of the reagents used, but the results seem reasonably clean.

From there, things get a bit iffy. The group added various inhibitors to the cells in order to find out what's activating the MAP kinases, and eventually work their way back to an apparent source (NADH oxidase) of the sensitivity to this weak radiation. There are a number of problems with this work, the primary one being that some of the data involved in this reconstruction don't seem consistent between experiments. The proposed pathway is rather baroque, as it involves creating reactive oxygen, activating proteases, and liberating growth factors from the cell surface. I'm rather skeptical all of that can take place sufficiently quickly to cause the rapid dynamics of the MAP kinase activation seen here (on by five minutes, off by 20).

It's also worth noting that the literature on this proposed "pathway" is rather confused. In some cells, NADH oxidase activates a completely different type of MAP kinase signaling. In others, MAP kinase signaling actually activates NADH oxidase. It's pretty clear that the response seen in these cells (assuming it's real) isn't going to be a generalized response to cell phone radiation.

So, it's fair to say I'm skeptical about much of this paper. At the same time, however, the initial MAP kinase data looks reasonable, and I'd like to see it reproduced in a different lab. MAP kinase signaling is tricky to interpret, because it's activated to one extent or another by nearly everything that happens to a cell, but this could still hint at a real mechanism for cells to respond to even the weak radiation emitted by cell phones. If these data hold up, it might be the first real sign that there's something here worth looking at.

But, until those results are reproduced and the trigger is traced back to a radio-frequency sensitive receptor of some sort, there current body of knowledge prevails: there's no apparent way for this radiation to alter cell behavior beyond heat stress. Which still leaves us without any positive evidence that cell phones and other wireless technology create health risks.

Of course, you can count on the press to completely miss that point. Worse yet, they badly misrepresent the significance of MAP kinase activity by associating it with cancer. Cancer cells do have active MAP kinase signaling but, because this signaling system is central to a cell's activity, there's probably not a cell in your body that hasn't had MAP kinase activity at some point in it's history. The transient activation seen in these experiments is the antithesis of the uncontrolled activity seen in cancer cells; it's hard to call an article conflating the two anything other than dangerously misinformed.

Biochemical Journal, 2007. DOI: 10.1042/BJ20061653

IGN details the changes from the AO-rated Manhunt 2 to the M-rated version

When Manhunt 2 was changed from the original Adults Only rating to the more retailer-palatable Mature rating, the big question was what had been cut. There are very few people who have played either version, and only IGN has been able to play both the original and parts of the newly-cut version. So what, finally, did they notice? HangZhou Night Net

Mostof the content is still there. "Danny can still saw into the heads of enemies, or bludgeon them with a blunt object, or stab them, or use a syringe on them, or even use the environments to take them out," Matt Casamassima writes. "In one sequence, Danny uses a sewer cap to decapitate a hunter, at which point the enemy's body fell into the sewer hole." I think it's safe to say the controversy over this title isn't over.

The main change is the removal of the major death strikes, the ultra-gory killing moves that effectively work like Fatalities from Mortal Kombat, justfar more disturbing. They're still in the game, but youcan't tell what's going on. The new animations now have "an extreme blur effect," and the graphics are too dark to tell what's going on. Casamassima describes the new animations as being a "garbled, motiony mess that's far less satisfying."

If you play the game, pay attention to these areas. This is what pushed the ESRB and console manufacturers into the AO rating. This is the content that's too violent for adult consumption, according to retailers and the console manufacturers. This sounds as disruptive as the black boxes the ratings board had put into the movie StoryTelling to achieve an R-rating. I had the same reaction watching that movie as I did reading about Manhunt 2. I asked myself why I was being kept from seeing something, and what the people effectively censoring the content thought would happen if I looked behind the blur.

Manhunt 2 launches this Halloween on the Playstation 2, Nintendo Wii, and PlayStation Portable.

What real water research looks like

As our recent feature article shows, the properties and structure of water is an area of active, though misused, research. Nevertheless, the research is important because water is such an important chemical, and its properties at both a bulk and an atomic scale are critical to giving known life the appearance it has today. HangZhou Night Net

One interesting facet to this is the way water behaves in and around cell membranes. Cell membranes are made from a double layer of lipids, which are generally hydrophobic, but at one end they have elements like oxygen and phosphorous, arranged such that there is a net charge. This end of the lipid molecule is hydrophilic, making the whole molecule both hydrophilic and hydrophobic, which is called amphipathic. In water, these lipid molecules will arrange themselves into double layers, with all the hydrophobic ends pointing into the layer and the hydrophilic layer pointing outwards. It is an equivalent structure that gives cells a robust membrane, while still being happy to sit in water.

A team of chemists and physicists from the University of Florence have used some novel spectroscopic techniques to analyze the dynamic behavior of water at and within the lipid bilayer. To do this, the researchers illuminate the sample with a laser that has a fairly narrow spectral bandwidth. A short time later, a second laser illuminates the sample, but this laser has a very broad spectral bandwidth. This is called a pump-probe geometry, where the first laser changes the sample in some way and the second laser measures that change. By varying the time delay between the pump and the probe, we can learn about how long various processes last. In this case, the first laser picks out a few (or preferably one) vibrational mode of the water and excites it—a vibrational mode is the frequency and geometry of the way the oxygen and hydrogen atom bonds stretch. The second laser can only excite that particular mode if enough time has passed for the vibration to have relaxed. Therefore if we look at what frequencies are missing from the probe light, we can see what effect the pump laser had on the water.

What makes this technique effective is that the environment—in this case, a lipid bilayer—changes the frequencies of the vibrational modes of the water individually. This process, called inhomogeneous broadening, means that by analyzing how strong the relative absorption frequencies are and at what delays, we can see what proportion of the water is sitting where on the lipid molecule and how long it stays there (the delay between the pump and probe are on the order of femtoseconds.

The results, published in Physical Review Letters, show that the water molecules within the bilayer are rarely free. Mainly they are bound to the phosphate group (a phosphorous atom with surrounding oxygen atoms) with either one or two hydrogen bonds.

This is already known, but what is interesting, is that this technique is very fast and flexible, which may make it possible to observe how the water rearranges itself as molecules pass through the membrane.

Physical Review Letters, 2007, DOI: 10.1103/PhysRevLett.99.078302

Creative’s new Zen and the processor behind it

We'll be talking about personal media players quite a bit on Kit. So far, we haven't had much of a chance to get into the guts of personal media players; stats offered by manufacturers are often limited to size, weight, color, and audio/video playback formats. Today Sigmatel, a semiconductor manufacturing company, announced that the latest Creative Zen is the first personal media player to use its STMP3700 SoC processor. Let's take a look at both the processor and Creative's newly-announced Zen. HangZhou Night Net

Creative's new Zen is about the size of a credit card,55mm x 83mm x 11.3mm. A quick measure of my own credit card confirms that. It's available in 4GB, 8GB, and 16GB models but also takes a page out of SanDisk's book by offering an SD slot for added memory. The 2.5" 320×240 screen will display MJPEG, WMV9, MPEG4-SP, DivX 4/5 (although Creative says it might not play all of your files), and XviD video formats, and the unit will also play MP3, WMA, AAC (.m4A), WAV (ADPCM), and Audible 2,3, and 4 audio formats. The Zen also has a radio, calendar, contact list, task list, USB 2.0 support, andcan display JPEG, BMP, GIF, PNG, and TIFF images after they've been transcoded with Creative's included software. The advertised battery life is up to five hours of video and 25 hours of audio playback.

Let'stake a look at the processor that makes all of this possible. Inside the Zen is a Sigmatel STMP3700 system on a chip (SoC). The STMP3700 is a 90 nanometer ARM-based 32-bit reduced instruction set (RISC) processor. The chip has most of what a personal media player manufacturer, like Creative, needs to create a new product. For example, the chip puts a USB power circuit, backlight controls, clock, and a headphone amplifier all in one place. The processor also supports WiFi and Bluetooth, and although these features don't appear in the Zen, it's a hintabout what we can expect later this year.

The 4GB creative Zen is available now for $149, and theSigamatel processor will likely be featured in similar products released throughout the year.

UK’s mobile telecom research program says cell phones are safe

As cell phones and other wireless communication technology have edged towards ubiquity, there have been persistent concerns that the long-frequency and low-power radiation it produces may pose unrecognized health risks. Sporadic studies have suggested the possibility of everything from mild effects on mental function to an increased risk of cancer. To look into these risks, the UK government joined forces with mobile equipment manufacturers to fund the Mobile Telecommunications and Health Research Programme (MRTH), giving the group a mandate of evaluating what's known and funding research into what needs to be known. The group has just released an interim report (PDF) with a clear conclusion: the only clear health risk posed by a mobile phone involves using it while driving. HangZhou Night Net

The report itself is a model of careful consideration. It notes the risk of the MTHR being viewed as biased due to the funding provided by manufacturers, but the report also describes the organization's structure as designed to prevent interference with research. The authors of this report also have an extensive list of achievements, suggesting that the group has attracted a scientifically competent panel of experts. The body is structured as a series of discussions of known or potential health risks (including cancer and electromagnetic sensitivity), biological mechanisms, distractions during driving, and the ability of the government to effectively communicate risk and safety information.

Each of these topics is explored via a summary of the current state of knowledge, what that means in terms of health risks, and what studies might still need to be performed. The good news for our wireless world is that very few studies have shown any real health risks. This is clearest in the cases of influences on brain function and hypersensitivity to electric fields associated with these devices; studies have clearly indicated there's nothing behind these phenomena. Although extremely rare cases can't be ruled out, they're clearly not a real public health risk.

The relationship between phone use and cancer is more complex. The studies that show the strongest link appear to suffer from systematic reporting bias, while those with a cleaner data set show a link that is either barely or not at all significant. Still, the report recognizes that cell phone use has only become prevalent within the last decade, and many cancers can take longer than that to develop. As such, they urge continued vigilance, but they also emphasize that there is no clear reason for concern at this point.

A related issue is the current lack of evidence that energy at these wavelengths can influence living tissue. The MTHR has funded research in this area, and the report indicates that there remains little evidence of a unique effect of wireless transmission; previously reported results may reflect nothing more than a stress response to heating caused by this radiation.

A topic the Programme felt was worth studying further was the public's perception of the risks involved in cell phone use. They noted studies that showed a complex interplay of factors that influenced how people registered relevant messages from the government, scientists, and pressure groups. Those factors included things ranging from general trust in authority to people's level of cell phone use. The MTHR suggests that, should risks be identified related to wireless use, the government will need to know how best to accurately convey them, and suggests further areas of study that may improve our ability to get the right message out.

In the end, the group's conclusions are clear: "None of the research supported by the Programme and published so far demonstrates that biological or adverse health effects are produced by radiofrequency exposure from mobile phones." That's not to say phones are risk-free, however, as the report notes that their use while driving impairs performance and increases the risk of accident. Given the radical difference in risk level, any concerns regarding the radio emissions appear to be the product of misplaced anxiety.

Office 2008 to offer easier enterprise deployment

In an effort to drum up some more business for Office 2008, Microsoft has designated September as "Sneak Peek" month, and is showcasing various enterprise-friendly features of the upcoming Office release. Last week, we learned that "Out of Office" has been added to Entourage. This week's revelation is a bit more substantial, and should make anyone who supports Office 2008 a whole lot happier. Specifically, Microsoft has chosen to use the Apple Installer in the upcoming version to allow for easier deployment and more customization of Office 2008. HangZhou Night Net

A change in the installer may not seem like a big deal, but it should make life significantly easier for enterprise administrators. According to Microsoft's focus group, the lack of an installer that works with administration tools meant that admins would have to do a lot of work to get Office in a format that could be deployed easily. By switching Office 2008 over to the .pkg format, it should play very nicely with Apple Remote Desktop (ARD) when being deployed remotely. The Apple Installer also supports AppleScript, which can be used for further customization after the software is installed.

One of the other big changes is that administrators and users will be able to choose which fonts get installed with Office. Older versions just went ahead and installed all the fonts, but the custom installation option in the new version will allow admins and users to pick and choose fonts as they see fit. This customization and the deployability that comes with using the Apple Installer should make Office 2008 a bit more attractive for a lot of people, but I do hope Microsoft fixed some of the other, larger problems in between making changes like these.

New hard drive tech could double storage densities

Another week, another hard drive
read mechanism, or so it seems. The amount of corporate and university-based research that is devoted to increasing the storage density of the
common hard drive gives a clue about the relative importance and
consequent economic drivers behind storage technology.HangZhou Night Net

A trio of researchers from the National Physical Laboratory in the UK have proposed an entirely new read head mechanism that has the potential to overcome some of the looming barriers towards increased data storage density. First, there is bit size and bit spacing. Bits are stored as tiny ferromagnetic crystals, and it is their orientation that signals a one or a zero. These bits can only be made so small and placed so close together before they start to interact strongly enough to flip each other.

Another problem is that the read and write heads must be small enough so that the orientation of a single bit dominates the signal from the head. This means that the heads must be about the size of the spaces between the bits. Then there are problems of heat and power dissipation. Read heads have a small but continuous current flowing through them, constantly draining your laptop battery and heating the read/write head. Reducing the size of the read head means that it will get hotter, which causes problems of its own. Excess heat could cause the read head to flip the bit that it is reading.

Fundamental to these problems is the way that the read head works. The magnetic field induces a small change in the resistance of the read head, which is then detected by measuring the voltage drop across it. The structure that supports this is relatively large, and the prospects for reducing it further are not too good.

The read head structure can be simplified considerably, however, by using a combination of magnetostrictive and electrostrictive material (a magnetostrictive material changes its size in a magnetic field and an electrostrictive material changes its size in an electric field). When layered, these combine to make a material that is termed magneto-electric, which essentially means that a magnetic field is used to generate a current. When the electrostrictive material is sandwiched between two magnetostrictive materials, the magentostrictive material tightens or loosens its grip every time the read head passes over a bit. Squeezing the electrostrictive material generates a detectable current.

The sensitivity per unit area is about the same as for more traditional giant magentoresistive and tunneling magnetoresistive read heads, but the layering requirements are much less strict. The researchers propose a device that is just 7 layers rather than the 15 in today's hard drives. Furthermore, a current is only generated when the read head passes over a bit and the resistance is very low, so the power dissipated in the read head should be less. Beyond that, it doesn't require that pesky constant current source, so it should consume less power and require fewer components.

The biggest advantage is probably in the simpler read head construction. Current read heads need a biasing magnetic (a magnet that generates a relatively strong background magnetic field against which the bits on the disk operate) attached to them, and the authors claim that putting this magnet on the head takes about 100 production steps. Even if no other benefit is derived from the technology, that is probably enough to make it worthwhile to manufacturers.

Finally, a note of caution. This is a simulation of a read head, not the real thing. No experiments have been done, and although I think the idea will work, I have one small concern. Because the read head is now generating a fluctuating current, it is generating a magnetic field that is of comparable strength to that of the bits themselves. The generated magnetic field will oppose the direction of whatever bit is currently being sensed. I want to be sure that the read process is not going to be flipping any of my bits before you can sell me that hard drive.

If there are no major technical gotchas, then this technology should provide a factor of two increase in storage density in its first generation. Beyond that, it's much harder to prognosticate on, but I think it is safe to say that the doubling in storage density every year is set to continue for a while longer.

Journal of Physics D, Applied Physics, 2007, DOI: 10.1088/0022-3727/40/17/003

PC Gears of War content won’t be coming to the Xbox 360

Gears of War has become one of the signature games on the Xbox 360, and with good reason: the title is a high-quality shooter with some of the best online play seen on consoles. Now that the title is finally coming to PCs, with new content no less, gamers are grumbling. Why can't Xbox 360 owners fight the Brumack? C'mon, we've paid for content before! JoeGraf, a moderator on the Epic Games boards, shed some light on the issue. Porting the content may not be as simple as it was first assumed: HangZhou Night Net

I know it's not obvious as to how this happens, but as the engine changes we include new data formats, objects have functions removed and added, and network compatability is no longer possible. This is just like the amount of changes that happened between UT99 and UT2003 prevented them from being network/content compatible. When we ship a game, we take a snapshot of the engine at that point in time. The engine continues the development path we have planned out, but the game doesn't. So the two entities diverge enough that they are no longer compatible. For instance, you can't even load one of the art packages from the original Gears in our current engine's editor. The same holds true going in the other direction: current content can't be loaded in the version of the editor that we used to ship Gears.

If this information is correct, then the new content for the PC version of Gears of War will likely remain on the PC for quite some time. The good news is that every time we've beenable to play the PC port of Gears of War it looks and plays amazingly well; no one skimped on making sure the game runs smoothly or looks even better than the 360 original. So PC gamers have a lot to look forward to, and Xbox 360 fans can continue to grumble.

16GB iPod Touch appearing in Apple Stores

We have received numerous tips today that the iPod touch has been spotted in the wild (actually more like captivity) at several different Apple Store locations in the US. I called around this evening to my "local" Apple Stores (believe it or not, there is still only one Apple Store in New Hampshire!) and came away with the impression that some stores are now receiving shipments of the 16GB iPod touch, some are putting them on display, all of them are selling what they do have, and some Apple Stores don't answer their phones. HangZhou Night Net

Apple Store Rockingham Park – None in Stock / None on Display
Apple Store Natick Connection – No Answer
Apple Store South Shore – 16GB in Stock
Apple Store Burlington – 16GB in Stock / None on Display
Apple Store CambridgeSide – No answer (not even an automated machine)
Apple Store Chestnut Hill – No Answer
Apple Store Derby Street – 16GB in Stock / None on Display (Demo Available)
Apple Store Holyoke – 16GB in Stock
Apple Store North Shore – 16GB in Stock

None of the store employees at the stores that did have the new product in stock would tell us just how many units they received, as it is against Apple policy to divulge that information over the phone.

So if you are looking to pick up an iPod touch and didn't pre-order one (or you are just really impatient), call your local Apple store to see whether it has any of the newest iPod in stock. For those of you that did pre-order, those whose credit cards can't afford another hit, or those who are waiting for the 8GB version, the end of September isn't really that far away. Really. Believe us. Tick, tick.

On a somewhat unrelated note, I'm sorry if I get anyone in trouble for not answering their respective stores' phones. But OMG ANSWER THE PHONE!