On Tuesday a consortium of technology companies, including IBM (IBM), will launch a new initiative designed to help shield the open-source software community from threats posed by companies or individuals holding dubious software patents and seeking payment for alleged infringements by open-source software products.

The most novel feature of the new program, to be known as Linux Defenders, will be its call to independent open-source software developers all over the world to start submitting their new software inventions to Linux Defenders (Web site due to be operational Tuesday) so that the group’s attorneys and engineers can, for no charge, help shape, structure, and document the invention in the form of a “defensive publication.”

Linux Defenders will then also see to it that the publication, duly attributing authorship of the invention to the developer who submitted it, is filed on the IP.com Web site, a database used by the U.S. Patent and Trademark Office and other patent examiners throughout the world when they are trying to determine whether a proposed patent is truly novel, as any patentable invention is supposed to be.

In effect, the defensive-publications initiative mounts a preemptive attack upon those who would try to patent purported software inventions that are not truly novel — i.e., innovations that are already known and in use, though no one may have ever previously bothered to document them, let alone obtain a patent on them, a process usually requiring the hiring of attorneys as well as payment of significant filing fees.

“The idea is to create a defensive patent shield or no-fly zone around Linux,” says Keith Bergelt, the chief executive officer of Open Invention Network, the consortium launching the site. The core members of that group, formed in 2005, are IBM, NEC, Novell (NOVL), Philips, Red Hat (RHT) and Sony.

OIN’s Linux Defender program is being co-sponsored by two of the most prominent guardians of the free- and open-source software community, the Linux Foundation in San Francisco and the Software Freedom Law Center in New York. In addition, the site is being hosted and “co-developed” by New York Law School, which has, since June 2007, been sponsoring, in coordination with the U.S. Patent and Trademark Office, its own well-received, complementary project, known as the Peer to Patent Community Patent Review site. That site solicits assistance from the open-source community to produce evidence that an invention for which a patent is currently being sought was actually already known or in use prior to the patent applicant’s filing.

So-called free- and open-source software is software that, by its licensing terms, confers certain “freedoms” upon users that are usually forbidden by conventional proprietary software companies, like Microsoft. These freedoms include the right to see the software’s source code, alter it, copy it, and redistribute it. The best known open-source product is Linux, or GNU/Linux, a complete open-source operating system that has become quite popular among Fortune 500 corporations for use on their data-center servers. Patents threaten the whole free-and-open-source eco-system, however, in that none of the key open-source freedoms can be practiced if an outsider can establish that a given piece of software infringes a valid patent he holds.

The Linux Defenders program is largely the brainchild of Bergelt, who took over as Open Invention Network’s CEO this past February. The program also reflects a new, more proactive role Bergelt envisions for OIN than the group has played in the past.

Until now, OIN’s purpose has been one-dimensional: to acquire a defensive portfolio of strategically crucial patents, which OIN makes available, royalty free, to any company that reciprocally agrees not to assert any of its own patents against the Linux community. (About 50 companies have already entered into such formal agreements with OIN, of which the best known are probably Google (GOOG) and Oracle (ORCL).) The implicit threat is that if any outsider — a Microsoft, (MSFT) say, which declared publicly in May 2007 that open-source software then violated 235 of its patents — were to ever bring a patent suit against a player in the Linux community, that outsider would, in turn, risk countersuit by OIN or its member companies asserting infringement of their own patents by the outsider.

While this IP-acquisition program remains a central one for OIN, Bergelt says, OIN will also now seek to “think more creatively” about other ways to protect and foster Linux’s development by means of “relationship-building” and “information-sharing,” including efforts to explain the importance of open-source and open-platform approaches to the media, patent officials, and competition authorities, among others.

Befitting someone who plans to tackle this ambitious range of goals, Bergelt has a background that is more diverse than that of his intellectual-property lawyer predecessor, Jerry Rosenthal, who, prior to heading OIN, had served as IBM’s IP-licensing chief. Though Bergelt is also an IP lawyer, he is, in addition, an entrepreneur and diplomat. Immediately prior to joining OIN, Bergelt was the president and CEO of the intellectual-property focused hedge fund Paradox Capital. Before that, he was a senior advisor to private-equity fund Texas Pacific Group (now TPG); headed the strategic intellectual asset management unit at Motorola; and co-founded the strategic intellectual asset management unit within the electronics and telecommunications group at SRI Consulting in Menlo Park. Earlier still in his career, he spent 12 years as a U.S. foreign service officer, including a posting to the U.S. Embassy in Tokyo, where he negotiated IP rights agreements with certain Asian countries, including China.

The Linux Defenders program will actually have three components. The first will be a peer-to-patent component that, like New York Law School’s existing program, will reach out to the open-source community in search of evidence of “prior art” — proof of preexisting knowledge or use of certain inventions — that can be used to challenge applications for patents that have been filed but not yet granted. The goal here is to persuade patent examiners not to grant the patent being sought because the invention is not truly novel.

The second component will be a natural extension of the first, to be known as “Post-Grant Peer to Patent,” which will enlist similar community assistance in the search for prior art relevant to patents that have already actually issued. In this case, the goal would be — assuming such prior art is found — to initiate an administrative reexamination proceeding before the U.S. PTO to get the patent invalidated. (There have been some earlier post-grant, peer-to-patent efforts — sometimes referred to as peer-to-issue programs — by both nonprofits and private companies, but none with the commitment, and on the scale, that OIN envisions, Bergelt says.)

The third component is the defensive-publications initiative. The phenomenon of defensive publication is also not new, Bergelt acknowledges, although it has primarily been used in the past by private companies protecting proprietary business models. Since at least the 1970s, he says, when the filing of an important patent by one company would often spur rivals to respond by seeking inter-related patents designed to restrict the usefulness of the first company’s filing, proprietary companies began using defensive publication to beef up and buffer their core patents.

“They’d file one patent,” Bergelt explains, “and then the next day they’d file thirty defensive publications that would protect all of the extensions of it they could think of, so the core patent was fenced off by layers of barbed wire, if you will. . . . What I’ve done is turn that idea on its head a little bit.” (Defensive publications are cheaper and easier to prepare than full-fledged patent-applications.)

Although some factions of the free- and open-source community are ideologically opposed to the whole notion of software patents — most notably and passionately Richard Stallman, the founder of the Free Software Foundation (which is a client of Linux-Defenders co-sponsor Software Freedom Law Center, which, in turn,  supports the End Software Patents organization) — neither Bergelt nor OIN fall into that camp.

“We’re not anti-patent by any stretch of the imagination,” says Bergelt. “More patents is fine with me, as long as they’re high quality. Quality is the drum we beat.”

In fact, Bergelt says, if a developer wants to get an actual patent on his invention, and then put defensive publications around it, Linux Defenders will help him do so — so long as the developer will ultimately be contributing the patent to the Linux community.

Yahoo’s ad alliance with Google seems like a great deal to Messrs. Brin, Page, and Yang. Now they just have to win over the Justice Department.

Google and Yahoo had hoped to have it all up and running by now. As you may recall, the two Internet giants announced an alliance last June in which Google would supply Yahoo with search ads to supplement Yahoo’s own. Google would get a big new customer for its ad-delivery service, while Yahoo would get a new source of revenue – and best of all, they’d keep Microsoft from swallowing Yahoo.

Then Washington got in the way. Due to pushback from antitrust regulators, in early October, Google (GOOG) and Yahoo (YHOO) put off the launch to give the Justice Department more time to chew on it. In September, Justice reportedly hired veteran antitrust litigator (and former Walt Disney vice chairman) Sandy Litvack to help review the deal, and soon thereafter Canadian authorities hired an outside lawyer too. The European Union is also taking a hard look.

What’s the hang-up? Well, there are three basic concerns about just what this alliance really amounts to. First, if it had been a merger between Google, with 70% share in the paid-search market, and Yahoo, with the next 20%, it would clearly violate antitrust laws by creating a monopoly. (Paid-search ads are the ones that show up near the top of a search-result screen or off to the side, under the rubric “sponsored links.”) Second, if Google were paying Yahoo to exit the paid-search arena, that would be an illegal agreement between competitors to allocate markets. Third, if Google and Yahoo were agreeing to set a price floor for the two companies’ paid-search offerings, that would be illegal price-fixing.

The actual deal being proposed looks something like a slow-motion version of the first two scenarios, and it might constitute an immediate realization of the third.

Google and Yahoo have tried to placate skeptics with a raft of reassurances: They’re not merging; Yahoo will continue to compete in paid searches; ad prices will continue to be set by auction, with each company’s auctions operating independently; Yahoo will only run Google ads to the extent it chooses; and Yahoo is still free to display ads from other paid-search providers, including third-place Microsoft (MSFT).

Not everyone is convinced, though – notably advertisers. The Association of National Advertisers (ANA), the Association of Canadian Advertisers, and the World Federation of Advertisers have all written regulators to voice opposition. In the letter from the ANA – a 375-company association with a board that includes members from Wal-Mart, Sears, and McDonald’s – CEO Bob Liodice writes that his group “is aware of only one advertiser/marketer that does not object to the Google-Yahoo collaboration.” (Liodice wouldn’t identify the exception.)

MICROSOFT GETS SUSPICIOUS

One big problem for Yahoo may be an astounding comment allegedly made by its own CEO, Jerry Yang, during negotiations with Microsoft in a San Jose airplane hangar on June 8, just three days before the Google-Yahoo pact was unveiled. (Google offered Yahoo the ad deal in an apparent effort to keep it out of the hands of Microsoft, which had offered to buy Yahoo at a 75% stock premium.)

According to testimony that Microsoft general counsel Brad Smith later gave to the Senate Judiciary Committee, Yang peered across a conference table and said, “Look, the search market today is basically a bipolar market…. On one pole, there’s Google, and on the other pole, there are Yahoo and Microsoft…. If we do this deal with Google, Yahoo will become part of Google’s pole.” Smith and his Microsoft colleagues were dumbstruck. Smith testified that during a break a few minutes after Yang’s comment, Microsoft CEO Steve Ballmer cracked, “[Yang] said there’s only going to be one pole in the market. I guess that would be a ‘mono-pole,’ wouldn’t it?”

When stunned Senators demanded that Yahoo general counsel Michael Callahan, who had also been present at the June 8 meeting, give his account of what Yang had said, Callahan repeatedly refused until, when pressed, he finally said, “I don’t recall that comment.”

Even putting aside the disputed remark, there are plenty of reasons to be skeptical about those reassurances from Yahoo and Google. For example, consider Yahoo’s claim that the deal will enable it to compete harder in the search business. The company has told shareholders that it hopes to make $800 million a year from its pact with Google – money that, as Yahoo president Sue Decker has written on a company blog, will be plowed back into R&D “to help us become a stronger competitor in all aspects of online advertising,” including paid searches. Yahoo has an incentive to do so, the company says, because it keeps all the revenue from its own ads but only a portion from Google’s.

Hmm. What portion will Yahoo keep when it uses a Google ad? That’s not public. But according to a lawyer close to the Google-Yahoo camp, Google’s ad deals with web publishers large and small-from the New York Times website to GPSworld.com -typically leave the publisher with “the lion’s share” of the revenue. Accordingly, when Yahoo runs an ad delivered by Google, we’re probably not talking about a 50-50 split; it’s more like 90-10, with 90% staying with Yahoo. So if Yahoo can make 90% of what Google’s superior mousetrap currently yields while incurring no research expenditures, how great is its incentive to keep dumping hundreds of millions into R&D for its own clunkier mousetrap? Plus, if Google really thought the deal would help Yahoo build a more competitive paid-search program, would Google be doing the deal? Concern about the deal’s sapping Yahoo’s long-term incentive to compete is presumably a key factor spurring EU regulators to nose around, notwithstanding its ostensible geographical limitation to the U.S. and Canada.

THE PRICE PROBLEM

Then there’s the price-fixing issue. Nobody’s price fixing, Google and Yahoo insist, because ad prices will continue to be set by separate auctions. That’s true. But part of the idea with this alliance is to replace some Yahoo ads on Yahoo search screens with Google ads, when the Google ads will fetch more revenue. Here is an oversimplified hypothetical example: Suppose you’re an auto parts dealer trying to drum up some business with search ads. You bid for the query “spark plugs Dallas Texas” on both the Yahoo auction and the Google auction-and learn that the going rates on Yahoo and Google, respectively, are $0.80 per click and $1.20 per click. Google reaches more users – hence the higher bids – but you decide to go for the $0.80 ad on Yahoo.

Guess what? You’ll need to pay the $1.20 anyway. Why? Remember that with the Google alliance, Yahoo now has the choice of going with ads delivered through its own system or through Google’s. Yahoo, of course, is going to run the ad that makes the most money – the ad from Google. In fact, Yahoo would never run its own ads if they were priced more cheaply than an available, comparable Google ad. In that sense the Google ad prices, though set by auction, would effectively set a floor for the prices of comparable ads displayed on Yahoo. Price floors constitute illegal price fixing.

Yahoo and Google respond that Yahoo won’t have the real-time pricing information about Google’s ads it would need to make instantaneous price comparisons to Yahoo ads. Still, Yahoo obviously thinks it has some way to compare the relative prices of Google and Yahoo ads – how else will it know when to replace a Yahoo ad with a Google ad?

Which is not to say that the search giants’ formidable teams of lawyers won’t eventually win Justice’s blessing for the deal. Clearly, though, those lawyers still have some serious work to do.

[CLARIFICATION: A spokesperson for Yahoo says that the way I've described the "$800 million" annual revenue figure above is inaccurate. To be clear, what Yahoo said in its announcement and SEC filing was this: "Yahoo! believes that this agreement will enable the Company to better monetize Yahoo!'s search inventory in the United States and Canada. At current monetization rates, this is an approximately $800 million annual revenue opportunity. In the first 12 months following implementation, Yahoo! expects the agreement to generate an estimated $250 million to $450 million in incremental operating cash flow." What Yahoo president Sue Decker said during the June 12 teleconference call was this: "In the first 12 months following implementation, we expect this agreement to generate $250 million to $450 million in incremental operating cash flow. Over the longer term, Yahoo! believes this agreement enables the company to better monetize Yahoo!'s search inventory. At the current monetization rate, we believe there is an approximate $800 million in annual revenue opportunity in the U.S. and Canada on those queries where monetization upside exists. This revenue opportunity could be achieved either from this arrangement with Google, which includes both search and nonsearch elements, or from other enhancements to our search capability, or a combination of them." -- RHP]

Yahoo’s ad alliance with Google seems like a great deal to Messrs. Brin, Page, and Yang. Now they just have to win over the Justice Department.

Google and Yahoo had hoped to have it all up and running by now. As you may recall, the two Internet giants announced an alliance last June in which Google would supply Yahoo with search ads to supplement Yahoo’s own. Google would get a big new customer for its ad-delivery service, while Yahoo would get a new source of revenue – and best of all, they’d keep Microsoft from swallowing Yahoo.

Then Washington got in the way. Due to pushback from antitrust regulators, in early October, Google (GOOG) and Yahoo (YHOO) put off the launch to give the Justice Department more time to chew on it. In September, Justice reportedly hired veteran antitrust litigator (and former Walt Disney vice chairman) Sandy Litvack to help review the deal, and soon thereafter Canadian authorities hired an outside lawyer too. The European Union is also taking a hard look.

What’s the hang-up? Well, there are three basic concerns about just what this alliance really amounts to. First, if it had been a merger between Google, with 70% share in the paid-search market, and Yahoo, with the next 20%, it would clearly violate antitrust laws by creating a monopoly. (Paid-search ads are the ones that show up near the top of a search-result screen or off to the side, under the rubric “sponsored links.”) Second, if Google were paying Yahoo to exit the paid-search arena, that would be an illegal agreement between competitors to allocate markets. Third, if Google and Yahoo were agreeing to set a price floor for the two companies’ paid-search offerings, that would be illegal price-fixing.

The actual deal being proposed looks something like a slow-motion version of the first two scenarios, and it might constitute an immediate realization of the third.

Google and Yahoo have tried to placate skeptics with a raft of reassurances: They’re not merging; Yahoo will continue to compete in paid searches; ad prices will continue to be set by auction, with each company’s auctions operating independently; Yahoo will only run Google ads to the extent it chooses; and Yahoo is still free to display ads from other paid-search providers, including third-place Microsoft (MSFT).

Not everyone is convinced, though – notably advertisers. The Association of National Advertisers (ANA), the Association of Canadian Advertisers, and the World Federation of Advertisers have all written regulators to voice opposition. In the letter from the ANA – a 375-company association with a board that includes members from Wal-Mart, Sears, and McDonald’s – CEO Bob Liodice writes that his group “is aware of only one advertiser/marketer that does not object to the Google-Yahoo collaboration.” (Liodice wouldn’t identify the exception.)

MICROSOFT GETS SUSPICIOUS

One big problem for Yahoo may be an astounding comment allegedly made by its own CEO, Jerry Yang, during negotiations with Microsoft in a San Jose airplane hangar on June 8, just three days before the Google-Yahoo pact was unveiled. (Google offered Yahoo the ad deal in an apparent effort to keep it out of the hands of Microsoft, which had offered to buy Yahoo at a 75% stock premium.)

According to testimony that Microsoft general counsel Brad Smith later gave to the Senate Judiciary Committee, Yang peered across a conference table and said, “Look, the search market today is basically a bipolar market…. On one pole, there’s Google, and on the other pole, there are Yahoo and Microsoft…. If we do this deal with Google, Yahoo will become part of Google’s pole.” Smith and his Microsoft colleagues were dumbstruck. Smith testified that during a break a few minutes after Yang’s comment, Microsoft CEO Steve Ballmer cracked, “[Yang] said there’s only going to be one pole in the market. I guess that would be a ‘mono-pole,’ wouldn’t it?”

When stunned Senators demanded that Yahoo general counsel Michael Callahan, who had also been present at the June 8 meeting, give his account of what Yang had said, Callahan repeatedly refused until, when pressed, he finally said, “I don’t recall that comment.”

Even putting aside the disputed remark, there are plenty of reasons to be skeptical about those reassurances from Yahoo and Google. For example, consider Yahoo’s claim that the deal will enable it to compete harder in the search business. The company has told shareholders that it hopes to make $800 million a year from its pact with Google – money that, as Yahoo president Sue Decker has written on a company blog, will be plowed back into R&D “to help us become a stronger competitor in all aspects of online advertising,” including paid searches. Yahoo has an incentive to do so, the company says, because it keeps all the revenue from its own ads but only a portion from Google’s.

Hmm. What portion will Yahoo keep when it uses a Google ad? That’s not public. But according to a lawyer close to the Google-Yahoo camp, Google’s ad deals with web publishers large and small-from the New York Times website to GPSworld.com -typically leave the publisher with “the lion’s share” of the revenue. Accordingly, when Yahoo runs an ad delivered by Google, we’re probably not talking about a 50-50 split; it’s more like 90-10, with 90% staying with Yahoo. So if Yahoo can make 90% of what Google’s superior mousetrap currently yields while incurring no research expenditures, how great is its incentive to keep dumping hundreds of millions into R&D for its own clunkier mousetrap? Plus, if Google really thought the deal would help Yahoo build a more competitive paid-search program, would Google be doing the deal? Concern about the deal’s sapping Yahoo’s long-term incentive to compete is presumably a key factor spurring EU regulators to nose around, notwithstanding its ostensible geographical limitation to the U.S. and Canada.

THE PRICE PROBLEM

Then there’s the price-fixing issue. Nobody’s price fixing, Google and Yahoo insist, because ad prices will continue to be set by separate auctions. That’s true. But part of the idea with this alliance is to replace some Yahoo ads on Yahoo search screens with Google ads, when the Google ads will fetch more revenue. Here is an oversimplified hypothetical example: Suppose you’re an auto parts dealer trying to drum up some business with search ads. You bid for the query “spark plugs Dallas Texas” on both the Yahoo auction and the Google auction-and learn that the going rates on Yahoo and Google, respectively, are $0.80 per click and $1.20 per click. Google reaches more users – hence the higher bids – but you decide to go for the $0.80 ad on Yahoo.

Guess what? You’ll need to pay the $1.20 anyway. Why? Remember that with the Google alliance, Yahoo now has the choice of going with ads delivered through its own system or through Google’s. Yahoo, of course, is going to run the ad that makes the most money – the ad from Google. In fact, Yahoo would never run its own ads if they were priced more cheaply than an available, comparable Google ad. In that sense the Google ad prices, though set by auction, would effectively set a floor for the prices of comparable ads displayed on Yahoo. Price floors constitute illegal price fixing.

Yahoo and Google respond that Yahoo won’t have the real-time pricing information about Google’s ads it would need to make instantaneous price comparisons to Yahoo ads. Still, Yahoo obviously thinks it has some way to compare the relative prices of Google and Yahoo ads – how else will it know when to replace a Yahoo ad with a Google ad?

Which is not to say that the search giants’ formidable teams of lawyers won’t eventually win Justice’s blessing for the deal. Clearly, though, those lawyers still have some serious work to do.

[CLARIFICATION: A spokesperson for Yahoo says that the way I've described the "$800 million" annual revenue figure above is inaccurate. To be clear, what Yahoo said in its announcement and SEC filing was this: "Yahoo! believes that this agreement will enable the Company to better monetize Yahoo!'s search inventory in the United States and Canada. At current monetization rates, this is an approximately $800 million annual revenue opportunity. In the first 12 months following implementation, Yahoo! expects the agreement to generate an estimated $250 million to $450 million in incremental operating cash flow." What Yahoo president Sue Decker said during the June 12 teleconference call was this: "In the first 12 months following implementation, we expect this agreement to generate $250 million to $450 million in incremental operating cash flow. Over the longer term, Yahoo! believes this agreement enables the company to better monetize Yahoo!'s search inventory. At the current monetization rate, we believe there is an approximate $800 million in annual revenue opportunity in the U.S. and Canada on those queries where monetization upside exists. This revenue opportunity could be achieved either from this arrangement with Google, which includes both search and nonsearch elements, or from other enhancements to our search capability, or a combination of them." -- RHP]

CARLSBAD, Calif. – Barry Diller defines the calm, cool, collected CEO. At least on stage, when he’s on his best behavior. He called his recent (successful) litigation with partner Liberty Media a wrenching three-month distraction. Come Aug. 1, he says, IAC (IACI) will complete its split into five companies, including the “new” IAC, a pure Web company.

Diller was more interesting about other people’s businesses than his own. About Hollywood, which he knows well, he said: “It’s a community that’s so inbred it’s a wonder the children have any teeth.” His point is that other than theatrical talent there’s no creativity coming out of Southern California. He expressed dismay that Yahoo (YHOO) let Microsoft (MSFT) walk away and implied that the only way he would have turned down such an offer would be if he knew – and not simply desired – that his business plan would produce a better return.

Diller has been around, so his thoughts on management are illuminating. He said the reason for breaking up IAC is that its more than 50 brands are too much for one company to handle. There’s always trouble somewhere with that many brands, he said. And as a manager, “what you tend to do is go where the trouble is,” as opposed to making trouble, which is far more enjoyable and profitable. Asked his opinion of the digital prowess of the major media conglomerates, he praised only one, News Corp. (NWS)

How do you define Dell (DELL) these days? Listening to Michael Dell speak, I have no idea. Dell himself noted that the company’s former “monolithic” strategy – its famous direct-to-customer manufacturing technique – didn’t work so well toward the end of its run. He cited five areas where Dell missed the boat: consumers, emerging markets, notebook computers, data centers and small- and medium-sized businesses. (Dell is the leader in PC sales to large businesses.) So instead Dell now emphasizes all those things, or at least is trying to. It dabbles in retail. It targets smaller businesses. Its growth has been impressive, but is that over a weak base, what Wall Streeters call an “easy compare?” Perhaps Dell eventually will do many things as well as it used to do one thing. For now, it’s a still a computer maker that spends a tiny percentage of its revenues on R&D ($600 million out of $65 billion in sales) and therefore sells me-too products, though often more efficiently than the competition.

Attempting to ride a wave of corporate and judicial disenchantment with aspects of the current patent system, a new project was unveiled Thursday designed to, as its name bluntly indicates, End Software Patents. (Press release is here. The group’s “first yearly report” on the state of software patents is here.)

The group is intended to become a clearinghouse for information and a hub for those strategizing legal challenges, according to its executive director, Ben Klemens. Though End Software Patents will not initiate litigation of its own, it will be on the lookout for appropriate test cases to support as they arise, he says.

Though the project is being sponsored and funded by leaders of the Free and Open Source Software movement, it hopes to attract support from the wider community of businesses, financial institutions and universities that have all been blindsided in recent years by lawsuits over software patents and their close-cousins, business-method patents.

The End Software Patents Web site, here, highlights a long list of diverse businesses that have been sued for allegedly infringing software patents, including the Green Bay Packers, OfficeMax, Caterpillar, Kraft Foods , ADT Security Services, AutoNation, Wal-Mart , Walgreen , Barnes & Noble, Circuit City Stores , Ford Motor , E I du Pont de Nemours and Co. , and so on. In most cases, the companies have been sued because of certain basic, routine functions performed on their Web sites — the way images are displayed, the way data is gathered or transmitted — which are said to infringe software patents.

The group also hopes to attract support from the many financial institutions, including JP Morgan , Merrill Lynch , and NCR Corp. , that have been asked to pay patent holding company DataTreasury for permission to send check images over the Internet. (For a Washington Post story about remarkable proposed federal legislation directed specifically at the DataTreasury patent, click here.)

The point, explains Klemens, is this: “If you’re running a business of any sort, you have to care about the software and business method patents.” That’s because nearly every business today operates a Web site and employs a staff of in-house IT programmers who enable them to conduct business in the digital age. In that sense, every business is now a software business.

Klemens is a mathematician (a guest scholar at the Brookings Institution since 2003) who uses algorithms to analyze data. In a recent article, for instance, he and his co-authors use data analysis to link certain genes to bipolar disorder. “I often run into patents on statistical methods and mathematical algorithms of the type that I implement,” Klemens says. “I don’t think I violate the ones I’ve seen, but I could be wrong, and I don’t know what else is out there. . . . That’s the thing that really woke me up: by doing pure math, I face legal liability. As far as I know, that’s a first in human history.” Klemens’s personal Web site is here.

In a 2005 book, Mathematics You Can’t Use, Klemens criticizes software patents from an economic and legal perspective, and does so in unusually crystalline, easy-to-understand terms. (For chapter one, see here, and for chapter six, see here.)

The book attracted the attention of the Free Software Foundation, whose president, Richard Stallman, has been railing against software patents since at least 1991, for related, but narrower, reasons: they posed a potentially mortal threat to his brainchild, free software — i.e., software, like Linux, that programmers are able freely to examine, modify, and redistribute without fear that their work will ever be taken out of circulation, declared off-limits, or placed behind a toll-booth by private proprietors. (For a feature story on the tension between patents and free and open software, “Microsoft Takes On the Free World,” see here. Generally speaking, though, software patents present dangerous traps for any programmer. Unlike copyrights, which are difficult to infringe inadvertently, a programmer can easily write software that inadvertently infringes someone else’s patent. That happens whenever the programmer independently comes up with an innovation that, unbeknownst to him, someone else has already staked a claim to. While copyrights are relatively easy to write around — since they protect only particular sequences of words or code — patents present broader, vaguer, and more durable obstacles, since they purport to proprietize implementations of ideas.)

In Klemens, the Free Software Foundation saw a potential ally who, thanks to the breadth of his critique and clarity of his writing, could attract a broader audience than just free and open source programmers. “We came to him,” says Peter Brown, the foundation’s executive director, “and said, we really want to fund your work. And he said yes.”

At the moment, the End Software Patents project is formally an offshoot of the Free Software Foundation. It also enjoys the “sponsorship” — though not monetary support — of the Software Freedom Law Center, which is led by Eben Moglen (an outside lawyer for the FSF and its former general counsel), and of the Public Patent Foundation, an organization led by the center’s legal director Dan Ravicher. The Software Freedom Law Center is itself funded largely by such Linux-supporting corporate patrons as IBM (IBM), Hewlett-Packard (HPQ), Red Hat (RHT), Novell (NOVL), Oracle (ORCL), and Sun Microsystems (JAVA).

To be sure, the goal of abolishing software patents remains a radical position in the sense that very few corporations endorse it. (A surprising exception is pharmaceutical manufacturer Eli Lilly & Co. See here. Evidently Lilly recognizes that poor quality software patents are among the problems spurring the tech industry to seek patent reforms, and it hopes to find of way of placating the tech industry without weakening protections for the drug patents that are the lifeblood of the pharmaceutical industry.)

Though many information technology companies, like IBM, Hewlett-Packard, and Cisco, are publicly championing patent reform, they only favor improving the quality of software patents, not abolishing them. After all, there are estimated to be more than 200,000 active, issued software patents in the United States, and most major tech companies have acquired, at considerable expense, substantial portfolios of them. Companies like Philips Electronics also argue that drawing the line between hardware and software is no longer easy, and that many patents relate to processes that were once accomplished using hardware but are now accomplished using software. Why should the modernization of the medium deprive Philips of recognition for its inventions, its lawyers have argued (albeit, in a slightly different context). See here.

Still, Klemens expects his group to find much common ground with the more moderate IT industry reformers, as well as with those whose main bugaboo is business-methods patents. “Pretty much every argument we make, top to bottom, applies to business methods as well,” Klemens says. In addition, the group’s supporters hope that the major tech players are coming to conclude that the vast number of software patents they have accumulated is part of the problem. “There are so many rights in so many hands,” says Moglen, of the Software Freedom Law Center, “everybody is at risk all the time.”

In any case, even if End Software Patents’ goals are extreme, they are not far-fetched. The U.S. Supreme Court has never ruled on the patentability of software, and at one time the predominant assumption among lawyers was that it could not be, because it amounted to nothing more than mathematical algorithms, which, in turn, were considered nonpatentable “laws of nature.”

That assumption was gradually turned upside down through a series of decisions rendered in the 1990s by the U.S. Court of Appeals for the Federal Circuit, a specialized court that had been set up to handle patent appeals, among other things, in 1984. Those decisions suggested that even if pure software itself was not patentable, software when loaded onto a general-purpose computer created, in effect, a new physical device that could then be patented. Some of the same rulings that opened the door to software patents effectively opened the door to “business method” patents, too.

In the past two years, however, it has become clear to all that the U.S. Supreme Court is extremely unhappy with the patent environment that the Federal Circuit has fostered in the two decades since its creation. In eBay v. MercExchange (May 2006), the Court unanimously junked one longstanding rule of that court, and last term, in KSR International v. Teleflex (April 2007), it unceremoniously dispatched another. (In eBay, the Supreme Court ruled that judges need not always enjoin defendants from infringing, even after a patent-holder has proven its case, and in KSR it made it much easier for judges and patent examiners to invalidate patents due to obviousness.)

For Klemens, however, the most encouraging ruling for his agenda was one that, technically, wasn’t. In LabCorp v. Metabolite Laboratories (June 2006), the Supreme Court had been asked to review the Federal Circuit’s precedents on patentability – the issue that ultimately also determines whether software patents and business-method patents are permissible. After hearing oral argument, the Court punted, deciding that, for technical reasons, it never should have heard the case in the first place. But three justices dissented, writing that they would have overturned the Federal Circuit and invalidated the patent in question, because it clearly amounted to an attempt to patent a nonpatentable “natural phenomenon,” though the phenomenon had been recast in the patent application as a patentable “process.” For that opinion, see here. Klemens contends that software patents amount to much the same thing.

Though only three justices signed the dissent, it does appear that it, in combination with the Supreme Court’s back-of-the-hand treatment of other key Federal Circuit precedents, has led the patent appeals court to engage in some soul-searching. Just two weeks ago, it announced, without having been spurred to do so by the parties, that it would rehear an important patentability case, In re Bilski. (See generally here.) It even asked the parties to brief whether a key ruling it rendered in 1998, State Street Bank & Trust v. Financial Signature Group – one of the pivotal ones greenlighting software and business-method patents — was correctly decided.

“There are test cases all over the place,” observes Klemens. Plainly, his timing is propitious.

Correction:  As a commenter points out, in an earlier version I misused the legal term of art “reads on.” Then I did it again in a comment. Regret both errors.

It’s being widely reported that Yahoo (YHOO) and News Corp. (NWS) are back in talks to combine Yahoo with MySpace and other properties that make up Fox Interactive Media, News Corp.’s online arm. The companies held what I’m told were very preliminary talks along a similar vein last year. The deal would have three main components: 1) News Corp. would contribute FIM to Yahoo; 2) News Corp. would invest in Yahoo; 3) a private-equity partner would inject yet more cash into Yahoo. The goal, in theory, would be to raise Yahoo’s value with the cash investments, thus obviating the need for Yahoo to sell to Microsoft (MSFT).

Here’s the problem. Or, rather, the problems. It’s going to be tricky to value MySpace, which will be the linchpin of the value of what News Corp. is contributing. If whatever News and Yahoo were to assemble didn’t add up to Microsoft’s current offer ($31), or counter-offer, the board of directors at Yahoo would be in a pickle.

Couldn’t they just accept a lower bid with the argument that Yahoo is worth more independent than selling out? Sure. Then they’d get sued. They’ve got to be able to best Microsoft’s offer in a reasonable timeframe, or they’re not doing their fiduciary duty.

There’s more. In a note to clients Wednesday, UBS analyst Ben Schachter (who had a buy rating on Yahoo at $19, when many of his competitors had lost faith, because he figured Yahoo’s falling price would provoke a sale, or at least a bid) reasons that the only way for a YahooSpace to achieve necessary profits would be do a search outsourcing deal with Google (GOOG). That’d bring the companies back to the same regulatory conundrum they’ve already been grappling with: Google’s search share is too big. There’s also the question of whether Yahoo needs MySpace. After all, “Yahoo’s problem has not been a lack of inventory, ” writes Schacter, meaning that it already has a huge audience. It’s problem, he writes is “its poor execution on optimizing monetization.” That means Yahoo isn’t so good at making money from its 500-million-plus audience. Schacter has a $34 price target on Yahoo because he thinks Microsoft will raise its bid.

So is Yahoo wasting its time talking to News Corp.? Of course not. Its stock traded over $30 Wednesday, closing at $29.88. To the point of my earlier post, that’s a sign investors expect a higher bid from Microsoft, not that it’s overly impressed with a News Corp.-Yahoo tie-up.

My friend, the Newsweek columnist Daniel Gross, posted an entertaining and informative column this week on Slate about what he sees happening next in the Microsoft-Yahoo merger. Like everything Dan writes, this column is worth reading, partly because it’s delightful and also because he does a great job of explaining how these catfights typically work. I agree with everything he wrote — except his conclusion.

To boil down his wonderful words, Dan believes that because Yahoo’s (YHOO) stock price hovers around $29.50, where it’s been more or less since Microsoft (MSFT) offered on Feb. 1 to buy the company for $31 a share, Wall Street is signaling its belief the deal will collapse. He reasons that if investors believed a higher bid was coming, the stock would trade higher. The fact that no private-equity or sovereign-wealth firm has materialized to bid for Yahoo is further proof that no one wants it and that Microsoft won’t fight.

I beg to differ, and not just because I wrote in the current issue of Fortune that a Microsoft acquisition of Yahoo is inevitable. First, Yahoo’s stock price is held back in part because Microsoft’s stock price is down, and half its offer is in stock. Second, if the market really believed that Yahoo will succeed in telling Microsoft to buzz off, the stock wouldn’t be at $29 and change. It would have plunged back toward $19, the sorry level to which it had fallen just before Microsoft dropped its bomb.

Yes, Yahoo traded for $31 not so very long ago. But that was before investors realized how little was going on inside the company, that CEO Jerry Yang was taking his sweet time to clean house, that Yahoo continued to poorly articulate its growth strategy and, perhaps most importantly, that the company faces “headwinds” in its core business, online display ads. Those realities haven’t changed since Microsoft offered to buy the company.

As for another bidder materializing, the fact that nobody — not a phone company, not another media company and certainly not a private-equity shop — has stepped forward tells you something about how the world outside Redmond, Wash., and Sunnyvale, Calif., views Yahoo’s valuation. A financial buyer simply can’t make the numbers work; Only Microsoft can.

But can’t Yahoo simply say no? Sure it can. But if Wall Street really believes no means no, you’ll see a stock drop and lawsuits fly. “We do not believe that Yahoo’s board will be able to turn down a mid-$30s bid without another offer in hand,” RBC Capital Markets analyst Jordan Rohan wrote to clients this week. “Yahoo management has already exhausted the patience of its largest, longest-suffering shareholders and Microsoft’s offer allows them to save some face.” Rohan then reports something I haven’t seen elsewhere: “Microsoft held several meetings last week with some of Yahoo’s largest shareholders. Ultimately, since there is only one class of stock, if those shareholders band together behind the likely-future-revised Microsoft bid, the deal will eventually get done.”Already, that’s beginning to happen. T. Rowe Price and Legg Mason, two large Yahoo shareholders, have gone public with their support for the Microsoft offer.

What this means is that it’s likely wrong to interpret Microsoft’s lack of a higher bid so far as an unwillingness to raise its offer. Instead, think of Microsoft’s behavior as a pause, an opportunity to make Yahoo sweat — or at least get an earful from its own shareholders. Of course Microsoft will raise. But only after Yahoo has the time to consider the meaning of Microsoft not raising.

A few more things to consider, at least for readers not caught up in the mind-messing media games that get played by all sides in this circus. The Wall Street Journalis reporting in Wednesday’s editions that Google (GOOG) is no longer overly interested in pursuing a revenue-sharing deal with Yahoo for search ads. It sources are “people familiar with the matter.” I haven’t checked, but I’m guessing that the Journal, citing “people familiar with the matter,” first broke the news that Google was interested in pursuing a revenue-sharing deal with Yahoo for search ads. Gold star for anyone who can guess where that information started and ended.

Similarly, the conventional wisdom for why Microsoft won’t actually mount a hostile takeover bid, a term of art that is different from the public “bear hug” it currently is pursuing, is that it would scare away Yahoo’s best people. What’s odd about that is that the conventional wisdom up until earlier this month was that most folks you’d want to retain at Yahoo already had left. Conventional wisdom’s a funny thing.

A final thought, and not a happy one for Microsoft, but even less so for Yahoo. Yahoo undoubtedly will draw this process out for a bit. Who knows, they may even force Microsoft to mount a proxy fight, though I doubt it. But let’s say it’s three months before Yahoo acquiesces and another nine months before U.S. and European regulators approve a Yahoo acquisition. Google likely will complete its long delayed DoubleClick purchase this spring. Under this scenario, it would then have a year’s headstart against MSN-Yahoo, which will be the mother of all integration challenges. Neither Yahoo nor Microsoft and the ad businesses it acquired when it bought aQuantive last year will stand still, of course. But talk about distractions.

Netscape, we hardly knew ye. This Friday AOL, which, like Fortune Magazine, is part of the Time Warner (TWX) empire, will become a zombie browser. AOL announced late last year that it will no longer support Netscape, meaning that it won’t update features or provide security upgrades. That means the few people who continue to use the browser should stop. Already, AOL is recommending that Netscape users switch to Firefox.

It’s a peculiar quality of the technology industry that such important companies and products can simply vanish in so short a time. Netscape went public just a dozen years ago and sold to AOL in 1999 for $10 billion. Its battle with Microsoft (MSFT) spawned an epic antitrust fight with the Justice Department, a topic covered in an interesting Financial Times column today.

Most interestingly, though, is the story of how Netscape itself gave birth to Firefox, today’s browser of choice for non-Apple (AAPL) users who prefer not to use Microsoft’s Internet Explorer. I use Firefox and cover Silicon Valley, but I didn’t quite know the whole story of how Firefox came to be. It was told quite well today in an article in the San Francisco Chronicle.

Fittingly for the day of the Iowa caucuses – a day when presidential wannabes pay obeisance for the last time of the year to the ethanol gods – a high-profile renewable energy company announced a setback.

Imperium Renewables, a Seattle company founded by a former executive at Microsoft (MSFT), the noted energy company, withdrew its plans for an IPO, citing poor “market conditions.” The company didn’t elaborate on just what market conditions it referred to. But clearly it’s not the market for IPOs. NetSuite (N), despite early criticism from ill-informed pundits, proved that the market always is receptive to the right kind of IPOs. No, the market conditions Imperium must mean are the markets for alternative fuels, like ethanol and biodiesel, Imperium’s particular blend of non-petroleum elixir.

Imperium had hoped to raise $345 million, which would add to the gusher of money flowing into ethanol and other alt-fuel projects. (Reuters has lots of good details in its dispatch on the withdrawal.)

It’s been clear for some time now that the renewable fuels investment craze is a classic bubble. That’s not to say ethanol and biodiesel make no sense. They do make sense at some scale and over some time period. But it means that not every project makes sense and that a whole lot of investors will lose plenty of money.

For Imperium’s part, it had intended to use $240 million for three additional biodiesel plants. One wonders if the market conditions will be right for those either.

Mighty Microsoft (MSFT) held its annual shareholders meeting today in Redmond, Wash. I know this because the company sent me a press release about it.

I quickly skimmed the blah, blah, blah about “positive customer momentum” and “strategy of investing in innovation,” and, for some reason, took a careful look at Mr. Softee’s board of directors, which the company printed in the release. Here’s the roster, with emphasis added to make the point I’m about to discuss:

Microsoft’s board of directors consists of William H. Gates, Microsoft chairman; Steven A. Ballmer, Microsoft chief executive officer; James I. Cash Jr., Ph.D., former James E. Robison professor of business administration at Harvard Business School; Dina Dublon, former chief financial officer of JPMorgan Chase; Raymond V. Gilmartin, former chairman, president and chief executive officer of Merck & Co. Inc.; Reed Hastings, founder, chairman and chief executive officer of Netflix Inc.; David F. Marquardt, general partner at August Capital; Charles H. Noski, former vice chairman of AT&T Corp.; Dr. Helmut Panke, former chairman of the board of management at BMW Bayerische Motoren Werke AG; and Jon A. Shirley, former president and chief operating officer of Microsoft.

I think you can see where I’m going. That’s six out of ten “formers” on the board, seven if you count Bill Gates, former CEO. Not counting CEO Steve Ballmer, there is precisely one current operating executive on the board, Reed Hastings, CEO of Netflix (NFLX), an innovative company that is nonetheless a pipsqueak in a narrow market niche.

Buzz words aside, Microsoft still hasn’t been able to shake itself from the torpor of having its butt kicked by Google (GOOG) in the online advertising world. By comparison, Google’s board includes the presidents of Princeton and Stanford, and the CEOs of Genentech (DNA) and Intel (INTC). Apple’s (AAPL) board includes the CEOs of Google, Genentech and J. Crew (JCG).

Could it be that Microsoft’s board of “formers” isn’t helping matters?

Two thoughts ran through my head as I read a column by my most excellent colleague Geoffrey Colvin called Don’t go gaga over Google. The first, given that Geoff’s piece was all about why shares of Google (GOOG) are in no way worth more than $500, is that it would have been at least sporting to have mentioned that we are the magazine that not quite three years ago asked, on our cover, if Google really was worth, wait for it, $165 per share.

I’m not enough of a student of economic value added, or EVA, analysis that Geoff deploys in his piece to judge how conclusive his argument is. I’m also not sure how closely professional managers follow this method. I’d love to know confessed-Google-lover Bill Miller’s thoughts on the subject. Actually, I’m not really commenting one way or the other on the valuation. Not now, anyway. All great companies fetch a premium that defies any rational analysis — until they don’t. Witness Microsoft (MSFT), whose stock grew until 2001 and hasn’t since, and General Electric (GE), which, as the one and only Nelson Schwartz reminded us this past weekend, still hasn’t recovered its 2000 high. (Actually, Geoff Colvin wrote that story too, in 2005. But now I really digress.) In essence, Google’s valuation will remain tied more to its ability to grow than its return on capital. That’s my opinion, for what it’s worth.

Which leads to my second thought, regarding a line near the end of Geoff’s column that journalists often refer to as the “to be sure” line, as in “To be sure, Mr. Smith accomplished much in his career …” Geoff writes:

Irrational valuations can last a long time, and sometimes they correct gently rather than violently. And it doesn’t mean that Google is poorly run. On the contrary, it has been brilliantly run. (emphasis added.)

That’s a fascinating point, because here in Silicon Valley there’s absolutely no consensus that Google has been brilliantly run. There’s no question that Google has brilliantly exploited a massive opportunity in the online advertising market, primarily search-based text ads. No one can ever deny that.

Whether the company is well run, however, simply can’t be known yet. As I pointed out in my own cover story last year, Google so far has been able to avoid answering the question of whether its chaotic nature is by design or whether it’s merely holding onto the handles of one incredibly fast roller-coaster ride. Its young founders are universally believed to be really bright guys. But they’ve never worked anywhere else. They condone, nay, encourage, a permissive culture that lets engineers run wild whether or not they are contributing to the bottom line. Its CEO, Eric Schmidt, was a top scientist at Sun Microsystems (SUNW) and then an uneventful CEO of a relatively unimportant Novell (NOVL). The line on Schmidt is that he has grown tremendously in the job at Google. That’s undoubtedly true. Still, he hasn’t been tested by the kind of adversity that knocks CEOs on their backs. And to judge by one data point, Google’s surprising inability to manage its hiring costs, Schmidt hardly has the place running like a finely-tuned engine.

To be sure, Google already is a company for the ages. Its stock may surge even more. The greatness of its management, however, will be judged far more in the next three years than in the last three since it went public.

I mentioned this topic in my article Tuesday after Jerry Yang’s appointment as CEO of Yahoo (YHOO), and the The New York Times devoted a considerable amount of ink to it the next day. This is a bit of an arcane topic to people who aren’t in the biz, but an extremely important one. It essentially suggests that Yahoo should stop investing in its search-advertising platform because it has been such a laggard and instead outsource the function to Google (GOOG). That’s what Yahoo used to do, and there’s widespread agreement that Google is and always will be superior at this to everyone else.

In fact, it’s a classic business-case problem. Should Yahoo let the fact that it has spent billions of dollars buying Inktomi and Overture and investing in its Project Panama stand in the way of making the right financial call? Unemotional business theory suggests that you can’t let past poor decisions stand in the way of good decisions today. Then again, if search advertising is central to what Yahoo does — and that has been management’s position to date — then they simply can’t give up.

I’ve had two interesting responses to my article in the last couple days from executives who think about his stuff all day long. One thinks Yahoo’s preparing to sell itself. The other sees plenty of opportunity. “A CEO who has never run anything large and a president who hasn’t either and came from Wall Street,” wrote one. “Can this truly be anything other than Yahoo pursuing ’strategic options?’” Said the other: ” There are a lot of people who think that search is still relatively early and that there’s a whole lot of ad technology left to be built in years ahead and that Google, Microsoft (MSFT), AOL and others are going to be investing heavily. Jerry seems to be the kind of guy to lead a similar effort for Yahoo.”

What do you think? Tell me below or in this poll.

The broad world of technology industry gurus and enthusiasts alike still are basking in the glow of the amicable appearance Wednesday night by Microsoft (MSFT) Chairman Bill Gates and Apple (APPL) CEO Steve Jobs. The two most often are portrayed as bitter enemies. But in a bit of staged theater that clearly also was genuine, the two spoke at length of their mutual admiration and shared experiences. Josh Quittner has a pitch-perfect review here about what it was like to be in the room.

Perhaps the best moment of the evening came when veteran investor Lise Buyer, a daughter of journalists, asked what easily was the best question of the evening: What did each man admire about the other and wish he had been able to do differently? Their answers were deeply sincere and reflected the strengths and weaknesses of their respective companies. Gates said he admires Jobs’s “taste,” and implicitly acknowledged the many criticisms over the years that Microsoft is a rather artless imitator, a ruthless company that goes for profits over style. Jobs noted that Gates always got “partnering” better than he did, in part because Microsoft, initially a software-only company, needed others from the beginning. Jobs acknowledged there, without using these words, that if only Apple hadn’t remained so closed so many years ago it could be Microsoft’s size today.

A final reflection. Gates and Jobs repeatedly were asked their view of the future. Gates, who is transitioning into a full-time philanthropist, was willing to share thoughts on new kinds of screens, for example. Jobs pointedly refused to share his thoughts, obviously because he doesn’t want to forecast where Apple is going. Gates is moving on to become a senior statesman of the industry. Jobs is still very much in the thick of the fight.

Microsoft (MSFT) needs to be a company of “multiple muscles,” says Steve Ballmer, the company’s unusually calm CEO. In a genial interview with the Wall Street Journal’s Walt Mossberg Wednesday morning, Ballmer presented a picture of a plodding, predictable, unexciting company. He couldn’t quite say when Microsoft will make some progress against Google (GOOG) in its weak share in Internet search. He couldn’t say why exactly the new Vista operating system was overly complex when it was released. He didn’t particularly enlighten the audience on just why Microsoft is paying $6 billion to buy online ad agency aQuantive (AQNT). By the way, Ballmer won’t mention Google’s name, referring to it merely as “the market leader;” He is willing say the word Yahoo (YHOO), but Mossberg didn’t ask him if Microsoft would like to buy Yahoo.

Microsoft has 78,000 employees today, and Ballmer acknowledged that getting things to happen outside of the “central planning committee” is a major challenge. Listen carefully, and Microsoft has become a company of excuses. If Zune isn’t so hot right now, Ballmer implies, it’s just a beginning. As for why it’s brown: “It’s the color that all the dirt bike riders really want.” (Read Brent Schlender’s biting critique of Zune, along with Apple’s (AAPL) Apple TV, here.)

As for those multiple muscles, Ballmer points out that just as Microsoft added selling to big businesses to its original business of selling sofware only to computer makers, today it’s trying hard to add two new business models: consumer electronics and advertising. “We’re going to keep coming and coming and coming and coming, just as we did in the enterprise, and just as did in phase one,”he said.

Trying, trying, trying. You almost feel sorry for Microsoft.

John McCain was the warmup act Tuesday night at the Wall Street Journal’s D5 technology conference at the lush Four Seasons Aviara in Carlsbad, Calif., north of San Diego. It was my second time seeing McCain in action, the first being at Fortune’s Brainstorm conference in Aspen, Colo., last summer. I like McCain, so I was generally pleased with his performance tonight. I feel like his energy level is down slightly, which isn’t an irrelevant gauge of a candidate’s probability of success. That very likely could have to do with the fact that he spends a fair amount of time discussing a dour and unpopular topic, the war in Iraq, which he continues to support. Still, what’s so appealing about McCain is that he speaks his mind. Over the course of the evening he somewhat won over an largely liberal tech-industry crowd.

I won’t go into McCain’s war policy, though many of us chewed it over during dinner, after his speech. Instead, nuggets about his economic policies:

* McCain is an unabashed free trader. He likes to say that regulations usually bring about intended as well as unintended consequences. He specifically said the 1996 Telecommunications Act, which he helped write, is “irrelevant” today.

* Asked if patent reform is high on his list, he replied, “No.”

* McCain says he’d reach out to successful Americans to get them involved in his admininistration. Asked to name names, he offered up Cisco (CSCO) CEO John Chambers and Microsoft (CEO) Steve Ballmer, both of whom were in the room. To read Roger Parloff’s article in the last issue of Fortune, Microsoft Takes on the Free World, Ballmer probably will be excited to know of McCain’s lack of interest in patent reform.)

* On the subject of immigration reform, McCain again flashed his free-trade credentials, saying, “I worry about nativism and protectionism,” implying he’s more comfortable than most politicians with foreign companies and countries investing in U.S. assets.

Do these political speeches at business conferences translate into votes? Can you picture John Chambers as Secretary of Commerce? Sure.

It’s amusing how good Google (GOOG) has gotten at the PR game. An item (behind-the-paid-wall link alert) in Monday’s Wall Street Journal about a partnership brewing between Google and Salesforce.com (CRM) notes how in February Google launched a paid version of its collection of online productivity software applications called Google Apps. I wrote an article here about the launch, and I wasn’t the only observer to point out that Google now was going directly after Microsoft’s (MSFT) Office franchise.

There’s just one catch. Three months on and Google hasn’t started charging the $50 per user per year it said it would charge for the “premier” edition of Google Apps. (The high-end version gets each user Gmail, Google Calendar, Google Talk and Docs & Spreadsheets, plus 10 gigabytes of storage and round-the-clock customer service.) Initially, Google was going to begin charging at the end of April. Now, Dave Girouard, the Google vice-president in charge of the product, tells me the money will start flowing at the end of May. What’s more, says Girouard, Google is contemplating an ongoing “trial period” for new users. He won’t say how many users Google has signed up or the names of any significant companies that are using the product in large numbers. (In fairness, the target market is small companies.) Girouard dismisses chatter that users are dissatisfied with the product, though he allows that “there are some areas where it is rough around the edges. These are still early days.”

Precisely. The media tends to get carried away by Google product announcements, much the way any new Microsoft offering once was greeted by the sound and the fury. Microsoft may be in a pickle over its continuously stillborn online advertising business. But it needn’t worry about losing out in the word-processing game to Google just yet.

Take that Google (GOOG). After losing out on nearly every major deal imaginable, Microsoft (MSFT) finally has landed a counterpunch to Google, and a pricey one at that, by buying online ad agency AQuantive (AQNT). Google bested Microsoft in the high-priced competition to supply Time Warner’s (TWX) AOL with search advertising. It trumped Mr. Softee again when it paid $900 million for News Corp.’s search business that included serving search to MySpace. And it snatched DoubleClick from Microsoft’s grasp too.

Buying AQuantive for $6 billion is a massive move for Microsoft. If it can integrate its Seattle neighbor well, the AQuantive purchase will be a jumpstart for Microsoft’s MSN business. Then again, it could be a costly waste, a too-late, too-timid move where the far more expensive purchase of Yahoo (YHOO) truly would have made Microsoft a player in the online world. Microsoft has a history of unsuccessfully tossing around big bucks to “get into the game.” Think: WebTV (1997), LinkExchange (1998) and CompareNet (1999). LinkExchange, for those who don’t remember, was an online advertising network. Um, that’s in large part what’s relevant about AQuantive’s business. Oh well. (In fairness, a really good get-into-the-game and extremely expensive acquisition: 1998’s Hotmail.)

It’s also something to see all of the late 1990s online ad flameouts – DoubleClick, AQuantive, and 24/7 (TFSM), which WPP Group (WPPGY) bought yesterday – getting snapped up. Even the formerly disastrous Snowball.com, later re-named IGN, is now a robust part of the growing Fox Interactive Media empire. What a time to be in online media.

The writing was on the wall for this one since the moment last October that Google (GOOG) agreed to buy YouTube. Jennifer Feikin, the director and chief businesswoman of Google Video, is leaving the company. I’ve wondered ever since the deal was announced how Google Video and YouTube would co-exist inside the same company. YouTube so thoroughly vanquished Google Video, an also-ran product in terms of traffic, that Google was compelled to buy YouTube, if only to keep it out of the hands of Yahoo (YHOO), Microsoft (MSFT) or one of the several broadcast networks that should have bought it. Feikin, at least, has something of an answer to the question: She’s not sticking around to find out.

A four-year-veteran at Google (yes, typical stock-option grants take four years to vest), Feikin was cut from a different cloth than other Googlers. Her glittering resume includes stints at Time Warner’s AOL unit (TWX), News Corp.’s (NWS) 20th Century Fox and the consulting giant McKinsey. (No slouch: She’s Harvard Law and Duke undergrad to boot.) Google Video’s relative lack of traction compared with YouTube shows that on the Internet even a well funded product guided by an experienced and savvy strategist doesn’t always win.

In an email to her peeps Feikin reflected on her “amazing years” at Google, which included the “launch and phenomenal growth of a once-tiny product called Google Video.” She said she’s leaving for “new adventures.” She shouldn’t have any trouble finding them.

In the current issue of Fortune (cover dated May 28), Microsoft (MSFT) executives assert that free and open-source software, including the Linux operating system, infringes 235 of its patents. The feature, which is available here, is entitled Microsoft Takes On the Free World, and also describes how, for the past four years, Microsoft has been methodically pursuing the goal of receiving royalties from users and/or distributors of free software. Though Microsoft breaks down the 235 patents into several general categories, it still does not identify any specific patent or how it infringes.

I wrote the feature story, so I suggest writing any comments or questions about it as comments to this blog entry, since I might possibly be able to add some answers or additional insights.

For the full responses of free software advocates to Microsoft’s claims, I refer readers to the feature. But in very brief summary, Eben Moglen, executive director of the Software Freedom Law Center (and longtime lawyer to the Free Software Foundation) says: “Numbers aren’t where the action is. The action is in very tight qualitative analysis of individual situations.” He is referring to the fact that patents can be invalidated in court on numerous grounds; that others can easily be “invented around”; and that still others might be valid, yet not infringed under the particular circumstances.

Still, 235 is a lot of alleged infringements. “This is not a case of some accidental, unknowing infringement,” says Microsoft’s licensing chief, Horacio Gutierrez. “There is an overwhelming number of patents being infringed.” By comparison, for example, Verizon’s (VZ) patent suit against Vonage (VG) was based on seven patents, of which just three were found to infringe. In the story, Gutierrez, breaks down that figure into the following categories:

1. The Linux kernel allegedly infringes 42 Microsoft patents. (The kernel is the deepest layer of the operating system, which interacts most directly with the hardware.)

2. The Linux user interfaces allegedly infringe 65 patents. (The user interfaces are the way design elements, like menus and toolbars, are set up to promote easy and intuitive use.)

3. The Open Office programs allegedly infringe 45 patents. (This a suite of free software programs analogous to Microsoft’s Office, including, for instance, word processing, spreadsheet, and presentation software, which perform functions like Microsoft’s Word, Excel and PowerPoint products.)

4. Free email programs allegedly infringe 15 patents.

5. Other assorted free software programs that are frequently included in Linux distributions allegedly violate another 68 patents.

The question I anticipate that most readers will want to ask (and that isn’t really answered in the feature story) is: Why doesn’t Microsoft identify the specific patents and explain what specific aspects of free software infringe them. I did ask Gutierrez that question, and here was his answer: “We do. But in private conversations in the process of licensing discussions with companies that are looking in good faith for ways of resolving the situation.” In those contexts, he says, “we walk through a number of exemplary patents and go as deep as they want us to go. Our experience has been every time we’ve done that, it doesn’t take companies a long time to figure out that there is an issue here.”

Why won’t he do the same thing in public? “There are a number of legal reasons why companies don’t do that. No company does that. IBM (IBM) doesn’t do that. HP (HPQ) doesn’t. Fujitsu (FJTSY.PK) doesn’t. For a number of practical reasons. Once you’ve made that statement from a public perspective, anybody in the world can go to court and ask for a declaratory judgment. That would spur potentially hundreds or thousands of lawsuits around the world, or reexaminations of patents around the world. Even if they’re perfectly good patents, it would create an administrative nightmare.”

So that’s his answer to that one. Please read the feature and then let me know what you think.

Dell (DELL) has become the first “systems-provider” to take advantage of the controversial technological collaboration and intellectual property pact concluded in November between Microsoft (MSFT) and Novell (NOVL), which is a distributor of the Linux operating system. (Here’s the press release.)

Dell’s move will enable corporations that wish to run both Windows and Linux server operating systems side-by-side in their datacenters to go to a single shop for all their hardware, software, and support service needs, while also being assured that Microsoft will not go after them seeking patent royalties. (Microsoft claims that Linux infringes its patents, a claim vigorously disputed by Linux distributors, users, and developers.)

Back in November Microsoft and Novell struck a pioneering tech collab/IP deal out of a recognition that most corporate datacenters today either already run, or would like to run, “heterogeneous” software environments, meaning that some server computers run Windows, while others run Linux, while still others run on Unix or Apple platforms. (See earlier posts on that deal, here and here.) Thanks to so-called virtualization software, which enables a single computer to run multiple operating systems, many companies are now consolidating their computing operations onto many fewer computers, seeking to save tens of millions of dollars in hardware, energy, and even real estate costs. But to do this, the companies must be assured that that their various software platforms will play together nicely, that their computer operators will have integrated systems management tools capable of controlling the diverse platforms, and that there will be tech support people to call upon who have all the expertise and certifications necessary to fix things when they go wrong.

So on November 2, 2006, Novell and Microsoft announced a technological collaboration designed to ensure customers that these interoperability needs and concerns would be addressed. At the same time, the companies also worked out an intellectual property agreement that effectively guaranteed Novell’s Linux customers that they would not have to worry about potential patent suits or patent licensing demands from Microsoft, which claims that Linux infringes its patents. As part of the deal, Novell agreed to pay Microsoft an unspecified percentage of all its Linux subscription revenues. (Linux is so-called free software, written by a loose-knit community of developers, rather than by any single legal entity, and the software is typically available for free download over the Internet. Commercial distributors of Linux, like Novell and industry-leader Red Hat (RHT) , give away the software for free but make their money selling subscription support services.)

The IP part of the Microsoft-Novell deal was enormously controversial within the free and open-source software (FOSS) community, both because that community denies that Linux infringes any patents and because the notion of having to pay for permission to use free software (implicit in the notion of paying patent royalties) is antithetical to the most fundamental principles of free software. The Free Software Foundation, which writes and administers the license that covers key portions of the Linux operating system, is revising that license to forbid any other Linux distributors, like Red Hat, from entering into deals structured the way the Microsoft-Novell pact was. The revised license is expected to take effect in July.

Since the original Microsoft-Novell deal was struck, a number of marquee corporate Linux end-users have signed up for the benefits of the deal, including Credit Suisse, AIG, Deutsche Bank, HSBC, and Wal-Mart Stores, but Dell is the first computer distributor to take advantage of the deal.

Nevertheless, Red Hat has claimed that it has seen no adverse impact on its business from the Novell pact. (Due to an unrelated internal inquiry relating to options backdating, Novell has not filed audited financial statements with the SEC in more than a year.)