The Japanese company’s share of the portable music player market rose to 43 percent, surpassing Apple’s 42.1 percent and ending the iPod’s 241-week run as Japan’s top portable media player.

A noteworthy victory for the Japanese electronics giant, but one that says more about just how far the once great company has fallen than anything else. That it took Sony (SNE) this long to unseat Apple (AAPL) in its home market is astonishing–all the more so given the vast success of the Walkman and the mindshare it once commanded.

And one could argue that Sony hasn’t actually beaten Apple at all. BCN’s survey didn’t include the iPhone because it views that device as a phone. But obviously, it’s an iPod as well–BCN notes that the handset has clearly cannibalized iPod sales. Had BCN classified the iPhone as the media player that it is, Apple would almost certainly have maintained its lead over Sony in the Japanese market.

But NEC, Hitachi and Casio are denying these reports anyway. Or rather, they’re denying that they’ve hammered out any sort of deal. “The media report out today is not something that the company has released,” NEC said in a statement. “It is also not true that we have made a decision regarding our cell phone operations.”

Yet.

Typically, U.S. companies that do business in Japan without offices in the country aren’t required to pay taxes to the Japanese government. And Amazon (AMZN) has long counted itself among them, claiming purchases made through Amazon Japan are technically transacted in the states. Yet the company does have some retail infrastructure in the country through which it handles merchandise distribution, logistics and whatnot. And, according to the Bureau, that means Amazon has “permanent establishment” in Japan and should be taxed in the country under the U.S.-Japan tax treaty.

Another nasty tax headache for Amazon.com, which also faces calls for tax payments back in the U.S. and in Britain, France, and Germany as well. From the company’s annual report:

We Could be Subject to Additional Income Tax Liabilities
We are subject to income taxes in the United States and numerous foreign jurisdictions. Significant judgment is required in evaluating our worldwide provision for income taxes. During the ordinary course of business, there are many transactions for which the ultimate tax determination is uncertain. For example, our effective tax rates could be adversely affected by earnings being lower than anticipated in countries where we have lower statutory rates and higher than anticipated in countries where we have higher statutory rates, by changes in the valuation of our deferred tax assets and liabilities, or by changes in the relevant tax, accounting and other laws, regulations, principles and interpretations. We are subject to audit in various jurisdictions, and such jurisdictions may assess additional income tax against us. Although we believe our tax estimates are reasonable, the final determination of tax audits and any related litigation could be materially different from our historical income tax provisions and accruals. The results of an audit or litigation could have a material effect on our operating results or cash flows in the period or periods for which that determination is made.

By injecting nuclei from mice frozen for 16 years directly into unfertilized mice eggs, a team of Japanese geneticists was able to create healthy clones of the dead animals. Quite a breakthrough, and one that implies the cloning of cryogenically frozen humans and the resurrection of extinct animals frozen in permafrost is perhaps a little less improbable than originally thought. “Cloning animals by nuclear transfer provides an opportunity to preserve endangered mammalian species,” the researchers wrote in a paper submitted to The Proceedings of the National Academy of Sciences “[The technique] could be used to ‘resurrect’ animals or maintain valuable genomic stocks from tissues frozen for prolonged periods without any cryopreservation.”

Using it to produce a Crichtonian Jurassic Park, however, is quite a ways off. “It remains to be shown whether nuclei can be collected from whole bodies frozen without cryoprotectants and whether they will be viable for use in generating offspring following nuclear transfer,” the researchers noted. “However, it has been suggested that the ‘resurrection’ of frozen extinct species (such as the woolly mammoth) is impracticable, as no live cells are available, and the genomic material that remains is inevitably degraded.”

We’ll have the answer soon enough. “People familiar with the situation” tell The Wall Street Journal that Apple is in talks with NTT DoCoMo and Softbank–two of Japan’s premier wireless carriers–about offering its iPhone in Japan.

Discussions, however, are not going well. Both carriers have balked at Apple’s terms, which include a subscriber revenue share that some estimates put at about 10%. “The negotiations are not going smoothly, as Apple’s conditions are extremely hard to meet,” one source told Reuters. “The ball is in Apple’s court right now.”

But likely not for long. In order to meet its goal of gaining a 1% share of the global cellphone business by the end of 2008, Apple must bring the iPhone to market in Japan. Nomura Research Institute estimates that Apple can sell 2 million to 3 million iPhones annually in Japan–about 5% of the market–if it plays its cards right.