March, 2019

Survival of the fittest tumor?

Although evolutionary theory is generally applied to populations of organisms, it also has the potential to help interpret the progression of cancer. Cancerous cells can be viewed as competing for resources with their non-cancerous neighbors, subjected to predation by the immune system, and under selective pressure from the changed environment cause by interventions such as chemotherapy. Although this all seems fairly obvious, I haven't been aware of anyone actually applying these ideas to actual cancers. HangZhou Night Net

That apparent lack of attention came to an end in the latest issue of Nature Genetics, where a study appeared that applied ecological and evolutionary models of genetic diversity to examine the progression of precancerous tumors of the esophagus. The precancerous tumors were biopsied at several locations, and the cells isolated from these biopsies examined for gross changes in the genome as well as for mutations in specific cancer-inhibiting genes. The genetic diversity of the tumors was scored based on how often biopsies from different locations in the same tumor showed differences in terms of genetic content.

The results were pretty clear: the more diversity within a tumor, the more likely it was to progress to full blown cancer. By five years out, the 25 percent of tumors showing the most diversity turned cancerous about half the time. The remaining 75 percent of low-diversity tumors were about 10 times less likely to become cancerous. It's important to note that this study doesn't get into causality, and can't discriminate between two possible explanations. One is the evolutionary model where the diversity allowed more genetic pathways to progression to be explored and selected from. The second is that whatever was causing the diversity (for example, damage to the DNA repair system) was causing the cells to be more prone to becoming cancerous. Still, the results are certainly consistent with a model of selective pressure on a diverse population, and suggest that this may be a fruitful focus for future research.

Apple joins industry benchmarking group

As Infinite Loop reported earlier today, Apple has joined the Windows benchmarking consortium BAPCo. Previously comprised solely of heavyweights from the world of Windows and x86 architecture such as AMD, Intel, NVIDIA, ATI, Dell, HP, and Ziff Davis Media, BAPCo is responsible for widely used benchmarking applications such as SYSMark, MobileMark, and WebMark. In addition, BAPCo determines what testing methodologies and programs should be used in order to come up with "industry standard" benchmarkis.HangZhou Night Net

No doubt spurred by its transition to Intel CPUs, Apple’s decision to join the group is surprising to say the least. It has also led to quite a bit of speculation as to what Apple’s decision to join a group dedicated to benchmarking on Windows machines means.

Currently, all of the BAPCo’s benchmarking suites are Windows-only. Some are speculating that it means that Apple is planning to offer some measure of official Windows support or that Mac OS X 10.5 (Leopard) will have built-in virtualization capabilities.

Concluding that Apple is going to offer some sort of official support for Windows from the announcement that it’s joining a Windows-focused benchmarking group requires a big leap of faith, one that isn’t supported by the evidence. While Apple has said that it doesn’t mind if people run Windows on their Intel-based Macs, they’ve done absolutely nothing to make it possible. The use of EFI (extensible firmware interface) instead of BIOS in the Macintels left Windows completely out in the cold on the platform until someone hacked together a working Windows XP install for the Mac.

The virtualization angle is more interesting. Little is known so far about the feature set of Leopard, and Apple is not expected to say much about it until the later-than-usual Worldwide Developers Conference in August. What we do know is that the Core Duo CPUs used in the iMac and MacBook Pro along with the upcoming Conroe desktop CPU should have Intel’s VT for Directed IO virtualization technology enabled in 2007. Providing support for VT would be a good move for Apple, and may allow for the BAPCo benchmarking suites (not to mention other operating systems) to run natively on Macs.

When it comes down to it, what Apple appears to be after is a way to do apples-to-apples comparisons when it comes to benchmarking, instead of its treasured SpecInt and Photoshop bakeoffs. Windows drivers for x86 Macs and an "official" Mac OS X WINE port? Doubtful. Mac OS X is a major brand for Apple, and running advertisements showing off benchmark scores obtained by running Windows on Macs is inconceivable. The likely end product of Apple’s decision to join BAPCo are Mac OS X versions of the consortium benchmarking apps. Since SYSMark and its brethren are based on Windows applications, some of which have no Mac OS X counterparts, Apple might like to influence the makeup of the applications included in the testing suite.

Then again, Apple’s move may not result in much of anything?witness the company’s involvement in the HyperTransport Consortium.

Back in the day when PowerPC was the CPU platform of choice for Apple, benchmarking against Windows machines was a difficult task. By lending its support to BAPCo, Apple likely hopes to simplify the job of convincing would-be Mac users that its Intel-based computers are faster than Windows machines running on essentially the same hardware.

Neutrinos: The answer to life, the universe and dark matter?

Cosmology has undergone a revolution in recent years; going from a gentleman’s world of rampant speculation to a science which can make accurate, testable statements about the evolution of the universe. This slow gestation has given cosmologists plenty of time to work on their models and come up with a fairly firm idea of what is out there and what it should look like. Unfortunately there are several areas in which cosmologists have difficulty reconciling their work with observational data and the rest of the physics community. The most obvious of these is dark matter, however others include explaining the unusually high velocity of pulsars, the amount of energy released during supernova shock and the recent WMAP evidence that star formation occurred quite early in the universe’s history. The recent discovery that the neutrino must have mass coupled with some recent theoretical work suggests that all these phenomena may be explained by the existence of other neutrino types. HangZhou Night Net

The neutrino is a neutral particle that comes in three flavors;* electron, muon and tau neutrinos. Although we have known about their existence for sometime, it was only in the last 10 years or so that we have discovered that they must have mass. A consequence of the known neutrino types having mass is that there must be a fourth type of neutrino, one that has even weaker interactions with ordinary matter and has been dubbed the sterile neutrino. Biermann and Kusenko have done some calculations to show that if the sterile neutrino has mass within a certain range it can help explain some anomalous cosmological observations. They chose to use a mass and interaction range which would allow the neutrino to be dark matter and then examined the effect of this particle on other cosmological phenomena. They found that the sterile neutrino can decay, releasing x-rays in the process. X-rays catalyze the formation of molecular hydrogen, cooling gas clouds and aiding star formation, thus helping explain earlier-than-expected star formation. They also show that these neutrinos would be produced during the first second of a supernova and that they increase the amount of convection occurring during that time, adding energy to the supernova shock, which brings supernova calculations into better agreement with observation. That same second of sterile neutrino production is also sufficient to explain why pulsars have an anomalous velocity range.

Is the sterile neutrino the answer to life, the universe and dark matter? Well, only time will tell, but if the initial results are borne out by more experimental evidence then “two out of three ain’t bad.”

*=flavor is not used in the particle physics sense here

Microsoft licenses mouse and keyboard technologies to third parties

Microsoft has always been known as a software company, but the firm has been making hardware for nearly as long as it has been in business. In the early days the company sold an add-in card for the Apple ][ that contained a Zilog Z-80 CPU and allowed the venerable computer to run CP/M programs. In the early 1980s, Microsoft introduced its first mouse, intended to boost sales of Microsoft Word for DOS. Over the years the Microsoft Mouse became a bestseller and the company broadened its hardware line to include keyboards, joysticks, and of course, the Xbox game console.HangZhou Night Net

Now, for the first time, Microsoft is licensing some of its hardware designs to third parties. In a press release, the company announced that it is beginning an intellectual property licensing program that will include some interesting technologies for mice and keyboards.

“Most people think of Microsoft as solely a software company, but we’ve been a leading hardware innovator and supplier to the desktop peripherals industry for over 20 years,” said Robbie Bach, president of the Entertainment and Devices Division at Microsoft, in a statement. “The hardware licensing initiative is a first for Microsoft, and we’re excited to make our innovations broadly available to others in the industry through licensing.”

The licensing program covers three main peripheral technologies: the U2 adapter, the Tilt Wheel, and the Magnifier:

U2 technology enables a computer peripheral device (such as a mouse or keyboard) to be connected to a computer using either a PS2 or USB interface, and have it automatically sense the type of connection.The Tilt Wheel is hardware component of mice and optional keyboard offerings that allows users to tilt the wheel from side to side as well as up and down to scroll both horizontally and vertically.The Magnifier is a viewing and editing tool used with input devices such as a mouse. It delivers functionality equivalent to holding a magnifying glass up to a computer screen.
Source: Microsoft.

Of these three technologies, the most interesting is probably the Tilt Wheel, which adds horizontal scrolling functionality in a similar manner to Apple’s Mighty Mouse, but with a different hardware arrangement. While horizontal scrolling is not nearly as common as its vertical counterpart, it is still handy to have for certain applications, such as graphics programs.

Will the licensing initiative result in a flood of peripheral manufacturers adopting Microsoft’s features? It will probably depend on the terms of the license, including up-front and per-unit fees. The Tilt Wheel license, for example, is set at US$0.30 per unit. The larger question is whether or not the market can support more and more features on mice and keyboards, or whether simple “commodity” peripherals will win the day. Also interesting is the idea that Microsoft is looking to make more money from its IP. According to the pricing page: “The Microsoft tilt wheel license offers limited rights to issued and pending Microsoft patents.”

EU fires preemptive shot at Microsoft over Vista

It’s a conundrum that arises time and again: any software company that wants to continue turning a profit needs to release new editions of their products, even if the current version works just fine. To generate consumer interest, value must be added to the new product in the form of either back-end improvements such as greater stability, new APIs, etc., or front-end improvements such as a more responsive interface or additional features. Sometimes this feature creep leads to disadvantages like software bloat, in which the convenience of an additional capability is offset by the hefty or unstable code added to implement it. If your name is Microsoft and your goal is selling a new operating system, feature creep earns you a letter of warning from the European Union.HangZhou Night Net

That’s what happened this week, when the European Commission sent a preemptive shot over Microsoft’s bow regarding anti-trust issues it feels might be raised with bundled features in Windows Vista.

"We are concerned about the possibility that the next Vista operating system will include various elements which are currently available separately from Microsoft or other companies," Commission spokesman Jonathan Todd said.

Microsoft has not yet released a final list of software to be bundled with the operating system. It is known that the anti-spyware application Windows Defender will be included in Vista, as will additional search features, an upgraded interface, and some hooks for Office 2007. Nevertheless, the European Commission, which has had a quarrelsome relationship with the software giant over the last few years, believes MS is likely to integrate capabilities that will edge out other software developers at the expense of consumers.

This is not a concern without merit, nor is it unique to Microsoft. In the early-90s, IBM bundled Windows itself with its OS/2 operating system. Microsoft assaulted Netscape Navigator by integrating Internet Explorer into Windows. Most recently, Apple gazed upon the Mac shareware application Konfabulator, found it desirable, and "invented" Dashboard for OSX. Although they have filed no formal complaint, Google and Symantec are believed to be among the companies concerned about Vista.

"Symantec has received and has cooperated with requests for information by the European Commission. We have provided information to assist the government in understanding the complexity of the information security industry and our role in it."

The problem, in the eyes of the EC, is that Microsoft holds a virtual monopoly over computer operating systems. Yes, consumers have other options, but with a market share hovering in the mid-90% range, MS can gain an unfair advantage over other products with little more than a hint of bundling a similar product with a new OS. While the US Justice Department has failed to ever win a significant battle against the software company, the EU has repeatedly gone head-to-head with MS.

Later this week a hearing will be held to determine the outcome of Microsoft’s appeal of the €2 million/day fine that was levied against the company by the EU. Whatever the outcome of that case, this new letter is a warning that the European Commission will be scrutinizing Vista all the way up to and after its release early next year.

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