Rhinocrisy

Sometimes colossal ignorance itself can be educational.

For example, recently events have underscored the fact that I’m stupendously ignorant of what goes on in Japan. Mostly I think my knowledge is on par with the average American - a few vague tidbits about samurai, a post-war obsession with the bomb and some really bizarre cartoons.

The other day most of Asia was in uproar because the Japanese prime minster (and the following day, 200 Japanese MPs) paid a visit to a Japanese shrine that paid respect to their war dead. What’s this all about?

Let’s review some history: in 1994, when I was in high school, we learned about World War II. As everyone knows, World War II started with Hitler’s invasion of Poland, which was followed by their capture of France and bombing of London. Then, in 1941, following the insidious bombing of Pearl Harbor by the Japanese, the Americans entered the war, kicking ass, taking names, and chewing their newly-minted Bazooka brand chewing-gum. Eventually we got close enough to Japan that we could firebomb Tokyo and nuke a few cities, which convinced the recalcitrant Japanese to stop their human wave attacks and surrender like reasonable people, and had absolutely nothing to do with any Russians whatsoever.

Meanwhile, back in the real world, “World War II” was actually well underway long before 1939. In 1937, two years before Hitler invaded Poland, Japan was cutting their way through China on their way to Nanjing, which was, at the time, the capital of the Republic. Once there, they commenced an orgy of blood and violence that earned the subsequent six-week period the lovely moniker “the Rape of Nanjing”, or more diffidently, “the Nanjing Massacre.”

Or more diffidently still, “the Nanjing Incident.”

See, the other part they neglected to review in my world history class, aside from what is arguably one of the worst atrocities in the history of the world, was any of the post-war history of Japan. Until 1952 when they regained formal sovereignty, Japan was effectively ruled by General Douglas MacArthur, and he was not idle during that period. He was heavy-handed in his reforms of Japanese society, including the basic structure of government, the separation of Shinto religion and the state, educational systems, the disbanding of the armed forces, and the breakup of the large commercial conglomerates that ran the economy.

And, as the Cold War began to get underway, the U.S. naturally used its influence to push Japan in an anti-communist direction. Part of this meant encouraging Japanese nationalism, including resurrecting the Japanese army as a ’self-defense force’, despite the protests of Japanese progressives. It also meant encouraging the growth of historical revisionism, notably with respect to the Communists in China.

This bore fruit in 1971, when a huge hoopla started out over the censoring of certain Japanese textbooks. The position of many Japanese nationalists, contrary to the prevailing historical understanding, was that the Nanjing massacre had never happened. Sure, some people had been killed, but only soldiers, and there were dead on both sides. The number of dead the Chinese government was suggesting (300,000) was just propaganda, and passing it on denigrated the Japanese national character.

Naturally, this irked the Chinese, for whom, by this point, Nanjing was a signal memory and a symbol of Japanese wartime atrocities. It also irked the author of the textbook, Saburo Ienaga, who sued to have the history of Nanjing preserved as he intended. His desires were upheld in court, and eventually Nanjing made its way back into textbooks.

But nationalism and its historical revisionist currents didn’t vanish, and in fact during this period there was plenty of back-and-forth on the subject of Nanjing. Revisionist attempts to whitewash Japanese wartime history resulted in a spate of new journalism on the subject, notably Katsuichi Honda in the newspaper Asahi, who published a series of widely praised and despised articles detailing the atrocities at Nanjing (including a famous account of a macabre death-count competition between two lieutenants).

The essential issue remains alive to this day, however. This, I did learn about in high school, although the source was the dark, sotto voce mutters of my Chinese classmates about the damnable Japanese. Japan has not, to date, issued any formal apology for its war crimes, a subject of frequent dispute. And revisionism is not gone, either; in April of this year, the Japanese Ministry of Education once more announced its intent to adopt textbooks that minimized Nanjing, labeling it only an “incident”. Probably you remember the protests that produced, although if you are like me, you were a bit taken aback by their vehemence.

A full account of the complaints made against Japan and the full measure of what they refuse to do would take more space than I’m accustomed to consuming. Here’s a Wikipedia page with a fair bit on the subject.

The most recent bit is over the Yasukuni Shrine, a war memorial which commemorates 2.5 million Japanese war dead. Included therein are 14 Japanese convicted “class A” war criminals, (i.e., the top top, like Tojo) and over 1,000 other Japanese war criminals. Yasukuni is very much a nationalist shrine; it celebrates the dead and is not apologetic about the war. The literature published by the shrine denies many atrocities (e.g. forced prostitution) and defends those “wrongly convicted” as war criminals.

So when Prime Minister Koizumi pays a visit to this shrine, this is no meaningless statement. When he apologizes and then proceeds to repeat his visits five times, despite the fact that his visits have been ruled unconstitutional, despite the outrage it raises in Korea and China every time he does, you begin to wonder what he’s about. When nearly HALF the Japanese Diet visits the shrine, things really start to seem tweaked to you.

In a fashion American ignorance on this subject is understandable because we’re outsiders to this conflict, which more or less happened without American interference. But frankly I’m appalled at the notion that human events should be ignored, that human history isn’t shared, especially pain of this magnitude. Most Americans are probably just as oblivious to the recent Congo Civil War, which produced something like 4 million dead. And this was practically yesterday. Part of the project of overturning nationalism should involve moving away from ‘national histories’ told from the point of view of a single nation-state protagonist. Going from “this had nothing to do with us,” to “this was a tremendous tragedy for us” takes an important step: it broadens the meaning of us.

Because of my recent sojourn in “the” nation’s capital, friends ask me what I think will happen in the Valerie Plame case. Of course I have no idea; even Special Prosecutor Fitzgerald could be unsure what he’ll do. And no one knows how the case will turn out. Personally, I suspect that whatever indictments are launched, the ultimate outcome will depend a lot on current events over the next year. Courts seem more deferent to executive branch officials during crises; I can easily see events overtaking the case. But in the meantime, we can hope.

Everyone at the top level of the U.S. government has committed countless crimes, from war crimes to perjury before Congress to insider trading^†. But rarely are they called to task, especially in the one-party town called Washington. What will happen? According to a couple papers in the east today, there’s a chance that Cheney could be indicted. A subterranean mammal can dream.

^† Holy crap. Bill Frist’s Senate website calls him “Bill Frist, M.D.” both in the title of the page and in a big hospital-blue banner at the top of the page. Even the typeface is supposed to look like a pharmaceutical ad. Now just what kind of doctor is Dr. Frist? He’s a hospital administrator — that is, someone whose paycheck depends on declining treatment, to in the perverted words of the hippocratic oath, “do no harm.” Of course, to the informed reader, the “M.D.” after his name mostly makes him look like the author of a self-help book.

A study out in Science this week^* reveals that about 1/5 of the human genome (4382 of 23,688 genes) has patents on it. Is this a good thing? Is this driving innovation or stifling it?

From the perspective of a university researcher, where information is freely shared as a rule and the greater the dissemination of knowledge the more research it stimulates, patents can only inhibit. There’s no monetary incentive involved, since research is all (or, mostly) publicly supported.

However, private-sector innovation might depend on patents for survival. This is the argument advanced by, for example, Incyte Genomics, which itself holds over 2000 patents on human genes^†. They point to the temporary loss of $5 billion in market cap for the biotech industry in 2000 when Clinton gave the mistaken impression that he opposed patents on human genes; patents on genes attract investment, investment spurs innovation. Therefore, stopping patents will result in less innovation. Q.E.D.

Of course, this is a fallacy. We could as well make the opposite argument: patents impede research, research provides the basis for innovations. Therefore, stopping patents will result in less innovation. Both of these situations can be true, acting in opposition.

In 1998 Rebecca Eisenberg and Michael Heller outlined in Science the possibility of patent regimes resulting in a sort of “anticommons”, stifling innovation, through several mechanisms. As an academic (and a communist) this sort of argument is obviously appealing to me, but there’s a dearth of empirical evidence on the subject. Time will tell.

Weighing in on the negative column, however, is the startling breadth of patents on genes. Until very recently patents on genes required very little demonstration of usage; you only had to describe the sequence and show how to isolate it (or its product). And as John Doll points out in a review on the subject:

A patent might be granted for compound X, which is disclosed to have a specific use (such as a headache remedy). If other investigators find that X has a new and unexpected use, perhaps in combination with compound Y, for treatment of heart arrhythmias, they may have to obtain a license from the individual who first patented compound X in order to sell XY.

In summary, once a product is patented, that patent extends to any use, even those that have not been disclosed in the patent. A future nonobvious method of using that product may be patentable, but the first patent would have been dominant.

Broad patents on genes implies more potential for infringement, which suggests less innovation. This is very different from patents designed to protect an innovator’s right to profit from a product; it suppresses more than it produces.^‡

Patent litigation is expensive for both sides. On the one hand this might mean that both sides are more likely to reach an agreement rather than go to court. But on the other, it means agreements are more likely to fail and promising research avenues more likely to be abandoned, especially with increasingly layered license agreements involving multiple parties as patents insinuate themselves further into the research process.

At any rate we can be sure that we’re going to need a whole lot more patent lawyers. Wee.

Incidentally, I should give a nod to the implication of the subject line of this article itself, namely that the concept of patenting the gene sequences of living things is a questionable enterprise by its nature. Incyte, for example, claims that there is a substantial amount of effort involved in discovery and characterization of new genes that constitutes “invention”. I say balls, especially these days. If they’re really spending hundreds of millions of dollars as they claim, they’re morons. And even so, the breadth of the patents granted is far more in line with “privatization of the genome” than with protection of innovators’ rights. Genes are informational; patents should be applied to, if anything, techniques that employ genes (e.g. using single nucleotide polymorphisms to identify disease susceptibility) rather than the genes themselves. This, however, seems not to be the dominant paradigm for reasons that escape my understanding. I quote a RAND study on the subject:

Because pharmaceuticals require such intensive research and testing before they enter the market, it is broadly accepted that they require (and receive) stringent patent protection to allow that investment to be recouped… Firms that make truly gene-based drugs - drugs that consist of the “natural” protein prepared through use of an isolated gene [ed - e.g. human insulin] - do require patent protection like any other pharmaceutical firm to protect their products and methods of production… What is not clear, however, is whether this requires protection of the entire gene or whether a more narrowly drawn protection - on the optimized, commercialized protein drug itself and its production method - would suffice from society’s point of view… The argument for gene IP protection based on the high investments required for pharmaceutical development is also undermined by the many other products that could be derived from genome information that require less investment for commercialization.

^* Jensen and Murray, “Intellectual Property Landscape of the Human Genome”, Science, 310(5746):239-240

^† Putting them in the lead for number of patents along with Celera, whose public announcement of their intention to patent large portions of the genome after sequencing it alarmed many researchers and spurred the drive to complete the public mapping project in time with Celera’s sequencing.

^‡ This raises the interesting question of how multiple patents on the same gene are going to clash with each other. The new Jensen and Murray study in Science finds that some genes have as many as 20 different patents on them.

Hand it over to black people.

Sometimes when you make a map, you find something unexpected (subscription required):

U.S. Patents Claim Almost 20% Of Human Genes, Study Finds
By SYLVIA PAGAN WESTPHAL
Staff Reporter of THE WALL STREET JOURNAL
October 14, 2005

Close to 20% of human genes are claimed by U.S. patents, say researchers who have produced the first comprehensive map of the patent landscape for the genome.

The work will pave the way for a more informed debate over the consequences of patenting genetic sequences, experts say. The topic of gene ownership has been controversial: Proponents argue that gene patenting promotes development of drugs and diagnostic tests because companies have an incentive to carry the costs, but critics contend the practice stifles innovation at the basic research level.

But until now, despite avid discussion and several high-profile legal fights over the ownership of genes, nobody really knew how many genes were claimed in patents or how widespread the practice was. “The real novelty of the work is that it’s a whole-genome approach,” said Kyle Jensen, a Massachusetts Institute of Technology graduate student and co-author of the study.

In the report, to be published in Friday’s issue of the journal Science, Mr. Jensen and MIT’s Sloan School of Management Professor Fiona Murray compared all of the gene sequences claimed in U.S. patents from 1990 until today with the sequences stored in the government’s public database of human genes.

The team found that of the 23,688 genes in the U.S. government’s public database, 4,382 were claimed as intellectual property. This is likely an underestimate because the analysis didn’t look at patents for protein sequences, said Ms. Murray. “It could be up to double that,” she said.

The more than 4,200 patents were owned by 1,156 institutions or inventors. About 63% were assigned to private companies, with Incyte Pharmaceuticals, a unit of Delaware’s Incyte Corp., having the highest number of patents assigned, covering more than 2,000 human genes.

The researchers also found that heavily patented genes tended to be those with high relevance to human health and disease. Gene patenting has been the subject of legal battles in Europe, where countries have challenged Utah-based Myriad Genetics Inc.’s patent claims on breast-cancer gene BRCA1. Myriad has developed a diagnostic test that uses the gene, and the countries have resisted its use in Europe because of the patent issue. BRCA1 is one of the most-often-patented genes, with 14 patents issuing claims to it, according to the MIT study.

Scott Stern, a professor at Northwestern University’s Kellogg School of Management in Illinois who studies how scientific ideas get to the marketplace, said the MIT work “illustrates in a very dramatic fashion the degree to which intellectual-property rights over the human genome are inextricably linked with those areas of high medical and scientific interest.”

Mr. Stern, who has worked with Ms. Murray in the past but wasn’t involved in her current research, said that the debate over the patenting of human genes “is going to be with us for a long time” and that the MIT work lays the groundwork needed to make informed policy decisions. The National Academy of Sciences, which advises the U.S. government on science issues, is looking at the issue of gene ownership and its effects on research.

Write to Sylvia Pagán Westphal at sylvia.westphal@wsj.com

I will have at least a fleeting familiarity with every large geographic region to show up in the news this year. This resolution is motivated by my inability to even vaguely imagine where in Russia to find Kabardino-Balkaria.

Militants have staged mass raids on government and police buildings in a provincial capital in Russia, leaving dozens dead and many more injured.

Authorities say that 61 rebels have been killed, but 12 police and 12 civilians also died in the assault on Nalchik in Kabardino-Balkaria province.

Then again life would be easier if I just read the American press, so I didn’t have to hear about these things. So much easier.

The Discovery Institute (peddlers of Intelligent Design theory) has just filed an amicus curiae for the evolution trial going on in the 3rd Circuit court in Pennsylvania. Therein they include 85 amici, all acredited scientists, who either support intelligent design theory or feel that “protecting the freedom to pursue scientific evidence for intelligent design stimulates the advance of scientific knowledge.”

This is really annoying, because it’s a lot harder to make ad hominem attacks against people with PhDs, since they can respond with their own logical fallacy, appeal to authority. Meanwhile, while we’re having pissing contests, some guys over at Shovel Bums ran a Four-Day petition which generated 7,732 signatures from scientists stating that intelligent design is not science and shouldn’t be taught in schools.

It’s fun crawling through the short list of twenty-four selected “amici” that the DI decided to highlight. Some of them are well-known, like Jonathan Wells, William Dembski and Dean Kenyon. Others are people who famously stuck their foots in their mouths or up their asses (maybe simultaneously), like Russell Carlson, who testified in front of the Kansas Board of Education and admitted that he didn’t believe in the descent of man. This is simply not a scientifically defensible position, and people who make claims like that (and then admit they have no reasonable alternative hypothesis, or at least not one they’re willing to mouth) can’t be called respectable scientists in this context.

I think this old poll is statistically significant by now. To get you in the spirit for the upcoming holiday, I’ve put up a new one. As for me, I’m going to be Sun Wukong, the Monkey King. I’ll try and post a picture when I’m all suited up.

I have re-emerged from the cesspit of graduate school, briefly, before it sucks me back in again. Fortunately all this flailing about seems to be useful, and the end is in sight. Note to self: NEVER GO TO GRADUATE SCHOOL AGAIN.

Ah! You should read this article (via A Tiny Revolution) about how 50% of America thinks we should consider impeaching President Bush if he lied about his reasons for starting the Iraq war. !. !!!.

Something I enjoy: decent graphics. Check it out:

Energy flow in USA, 2004

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