Today I felt as if I was not in Japan, but in the Alabama of the 1950s. I've been made to feel less than human, like an animal

Japanese resident Steve McGowan yesterday, having just lost his case for racial discrimination after a shop-keeper refused him service for being black.

"Today I felt as if I was not in Japan, but in the Alabama of the 1950s. I've been made to feel less than human, like an animal," said McGowan, choking back tears. "This case was not just about me. With this ruling, the judge has given store owners the right to discriminate based on color."

Uniquely among the signatories to the United Nations Declaration on the Elimination of All Forms of Racial Discrimination, Japan has no laws prohibiting racial discrimination. The Government argues that such laws are not necessary, because victims can sue for damages in the civil courts. All it takes is a year or more of your life and a potentially bottomless pit of legal fees, and you might recoup your costs. But not, apparently, if the judge can find any loophole to excuse the discriminatory behaviour.

The reason Mr McGowan lost? He had claimed that the shop owner had turned him away for being black (using the term "kokujin" in Japanese, and there is apparently a tape recording in which the shop owner reiterates his views). The judge ruled that he hadn't provided sufficient evidence that the refusal was necessarily due to his being black, it might just have been because he was foreign. So, um, that's OK then.

More details and further similar horror stories can be found here.

"Stark warning over climate change"

The BBC News got itself into a tizzy recently over a "major report" which apparently said

Rising concentrations of greenhouse gases may have more serious impacts than previously believed.

and other stuff along those lines. But it turns out that this is merely the proceedings of a conference that took place a whole year ago, which itself was fairly dull in scientific terms but which had an exciting title ("Avoiding dangerous climate change") and garnered plenty of press attention due to the involvement of politicians. I didn't see anything particularly earth-shatttering (or even mildly surprising, in fact) in what was presented either then or now. And in particular, the "worse than previously believed" angle is strongly misleading - the evidence seems to be that it is pretty much exactly as had been predicted some time ago. So really, there is not much of a story there.

Stoat draws exactly the same conclusions, and discusses a few more of the details wrt sea level. So that must prove we are right :-)

I was more amused by the tale of the "3 priceless Ming Vases" which were apparently broken in one fell swoop by a visitor to a museum who tripped over his shoelaces. Heard on Radio5:

Presenter: So these priceless Ming vases, are they really rare then?
Expert: Not really, in fact they are getting more common every year.

(not an exact quote, but you get the idea)

OK, don't eat it then!

Following on from this story, and the ongoing fuss over Japanese "research" whaling, I was amused by the wording in this story in the Japan Times.

Japan's inventory of whale meat, a byproduct of research whaling, has doubled in the past decade

(my italics). It goes on to say:

According to the report, the inventory was about 1,000 to 2,500 tons around 1995. It hit a low point of 673 tons in March 1998 but began to increase to reach 4,800 tons last August.

The annual catch is about 2,000 tonnes so this implies that about half the total take has remained uneaten in recent years. Given that IWC rules insist that the "byproduct of research whaling" has to be eaten, this could turn out to be an embarassing quandary for Japan. If they try to push the consumption of whale meat, this will surely result in a lot of criticism both at home and abroad. They've tried putting it in school lunches in the past, which seems particularly crass. If they just build up the stockpile indefinitely, then that will surely look like a blatant breach of IWC rules (not that I know of any hard limit to the allowable size). But otherwise, they will have to scale back the hunt scientific research, perhaps eventually to nothing. There may be too much pride and pork (of the fiscal variety) at stake to allow that to happen, though.

As I said before, whale meat simply isn't a visible product outside a few small areas of Japan. It amounts to something on the order of 0.1% of the total meat and fish consumed here.

Probability, prediction and verification IV: More on Bayesian vs frequentist uncertainty

Having received some correspondence relating to this post, I think it might be worth exploring the issues in a little more detail.

The question I was considering was: what does "70% chance of rain tomorrow" actually mean? Most people would probably expect that if this forecast was issued 100 times, rain would follow about 70 times. And indeed this is what the forecaster thinks (hopes). But on any particular such day, another forecaster might give a different prediction (say "90% chance of rain") and their forecasts might also work out to be accurate on average. Were they both right? What is the "correct" probability of rain?

An analogy with number theory may be helpful. It has been shown that the number of primes less than x is approximately given by x/ln(x), where ln is the natural logarithm. Using this formula, we find there are about 390,000,000 primes between 10⁹ and 10¹⁰ (ie 10-digit numbers, of which there are 9x10⁹). In other words, if we pick a 10-digit number uniformly at random, there's a 4.3% probability that it is prime. That's a perfectly good frequentist statement. If we exclude those numbers which are divisible by 2, 3 or 5 (for which there are trivial tests) the probability rises to 16.1%. But what about 1,234,567,897? Does it make sense to talk about this number being prime with probability 16.1%? I suspect that some, perhaps most, number theorists would be uneasy about subscribing to that statement. Any particular number is either prime, or not. This fact may be currently unknown to me and you, but it is not random in a frequentist sense. Testing a number will always give the same result, whether it be "prime" or "not prime" (I'll ignore tests which are themselves probabilistic here).

But does it make sense for someone to accept the validity of a probabilistic weather forecast, while rejecting the appropriateness of a probabilistic assessment about a particular number being prime? It should be clear that the answer to this is a very definite no. Both statements describe a fact which can be determined by a deterministic calculation (by digital computer or analogue atmosphere), but which is currently unknown to me. Granted, we don't know how to perform the atmosphere's calculation, but we don't need to, as it is going to do the job for us anyway. I will find out tomorrow whether rain fell or not, and I can work out whether 1,234,567,897 is prime. In fact, if the primality test takes a day to run, the analogy is a very close one indeed. It should also be clear that "70% chance of rain on Jan 25 2006" and "70% chance of rain on Jan 25 2003" are both in principle equally valid statements. I won't know whether rain fell on the 25th Jan 2006 for a couple of days, but it would probably take even longer to find out about 25th Jan 2003 (even assuming someone has kept a record for the location in question). All of these statements are Bayesian estimates of our (someone's) confidence in a particular proposition, and have no direct frequentist interpretation.

That hasn't helped us pin down what is the "correct" probability. In fact I hope that it has helped to show that ultimately there is no such thing. Just as a different forecaster might give a different probability of rain, so a different mathematician might argue that since 1,234,567,897 is at the low end of the range, a better estimate of the local density of primes is 1/ln(1,234,567,897) = 4.8%, or 18% when multiples of 2, 3, and 5 are excluded. Someone else might known how to check for divisibility by 11 (it isn't), increasing the probability still further. These more sophisticated methods will generate more skillful estimates for 10-digit numbers, in a way that can be quantified. However, someone who assigns a probability of 4.3% to all randomly-chosen 10-digit numbers in a frequentist experiment would also turn out right in the long run. That's a skill-free forecast, but a valid one nevertheless (a future post will expand on that). Essentially, it is "climatology" for 10-digit integers.

Given that we are so used to making probabilistic statements which can only make sense with a Bayesian interpretation, it seems a little strange that people often find it difficult to accept and understand that they are doing this, instead appealing to some quasi-frequentist thought experiment. Almost every time that anyone uses an estimate of anything in the real world, it's a Bayesian one, whether it be the distance to the Sun, sensitivity of globally averaged surface temperature to a doubling of CO₂, or the number of eggs in my fridge. The purely frequentist approach to probability dominates in all teaching of elementary theory, but it hardly exists in the real world.

Quote of the day

"Encouragingly, we did also find some evidence of the penetration of the Mediterranean diet into Scotland, albeit in the form of deep-fried pizza," said Petticrew, director of the social and public health services unit of the UK Medical Research Council, a government health research body.

(An old article - I just happened to find it today). Having eaten my share of deep-fried pizzas during my childhood, I have to say the Mediterranean influence seems exceedingly tenuous. For any poor deprived souls who've not encountered this glorious foodstuff, look here and here. Wikipedia is disappointingly silent on the subject, only giving it a passing mention on the deep-fried Mars bar page :-) DFMB were never much more than a passing gimmick - but DFP have long been a staple of the Scotttish diet.

University of Tokyo professor fakes paper on human enzyme experiment

Wonder how much attention this fraud will get, coming hot on the heels of the Korean scandal. It seems like he's been under investigation for some time, following complaints about the reproducibility of his results in numerous papers dating back to 2003.

Yuki Daruma

Shortly after arriving in Japan, we found a postcard with a picture of our local temple (Zuisenji) in deep snow. We wondered what we had let ourselves in for, but since then in fact we've only had at most one snowy day per year. Yesterday was this year's turn, and this is what Zuisenji looked like this afternoon.

About 100 deaths have so far been attributed to snow in the western and northern regions (often people falling off their roofs or getting buried under snow while clearing them - others being crushed under the house itself when it collapses due to the weight). Here in the sunny east, conditions are nothing like as severe.

There's something about a flat expanse of snow that gives me an irresistable urge to build a snowman. In Japan, they are called yuki daruma (snow doll).

Just eat it!

According to the BBC, the nation is gripped by the story of a lost whale stuck in the Thames. I can guess what would happen if it turned up in Japan...

Update

Well if course it died. Very sad and all that. I just hope they don't try to deal with this way.

Peer Review

The Hwang stem cell thing has provoked some soul-searching about the peer review process and whether it could be improved. Kevin Vranes and John Fleck both suggest making reviewers' names public. While there is no harm in posing the question, I don't think the idea has got much going for it in general terms, and certainly cannot see how it could make a difference in this or similar cases.

For a start, it's best to be clear about what peer review does and does not (cannot) do. It does not provide any guarantee that a result is correct (this should be self-evident from the fact that new papers get published contradicting old ones). It does not even mean that anyone has checked that the work has actually been carried out as described - referees are not forensic scientists with the time and resources to do this, even if they wanted. It does however generally indicate that the described work and results seem credible and relevant. Peer review cuts out some poor research, both by actually rejecting stuff that is clearly wrong and (probably) dissuading larger numbers of people from even trying to publish work that is weak. In my experience, it also generates significant improvements to the quality of manuscripts that make it through to publication, both in terms of making them more accessible to as broad a readership as possible, and also correcting minor (even major) errors. Perhaps peer review is best thought of as a sort of "moderation" task analogous to moderators of usenet and other web-based discussion fora (eg censoring Lumo's silly comments on my blog), although it is of course performed at a much more detailed and careful level than that requires.

Reviewers are doing an unpaid job which gets very little reward - we do it mainly because we know we have to in order for the system to survive, and the possible perks (getting a peek at some results early, encouraging the authors to add a few citations of your own work) are pretty trivial in comparison. Rarely, the position of power it affords could be used to do down a rival, but given that the other referees might give glowing reviews and the Editor is likely to work out what is going on, that would be a rather risky course of action. I've had a (very) small handful of reviews that I consider unfair, but even so they cannot prevent publication, only slow it down if the author is persistent enough (ie keeps trying new journals).

Peer review can never be expected to catch deliberate premeditated fraud. That's not what it is for. And anyway, does it matter if occasionally fraudulent (and more often, flawed) papers get through? Not much, IMO. If they are wrong, and the science is important enough to matter, they will get caught out fairly soon (as in this recent case). It might be an unwelcome distraction but it's hardly the end of the world.

Removing the right to anonymity would have the single immediate effect of cutting the number of willing referees substantially. Few people would be eager to risk offending more important scientists who might be awarding them grants or jobs in the future - that's not to say that the author would necessarily (or even likely) retaliate, but why take the risk? Even when the author has no possible authority over the reviewer, there's nothing to be gained by making an enemy in the field. I've encountered a few reviewers who have signed their reviews, but I don't know if this is their general policy or if they only do it when saying nice things. I'm not sure that the latter is worth a great deal. I don't see how naming the reviewers in the Hwang case would achieve anything more than perhaps allowing us to make scapegoats out of a few people who are actually victims as much as the rest of us. They didn't ask to be sent a fraudulent paper, and it's not reasonable to expect them to have caught it.

On a slightly different tack, some EGU journals have an open discussion phase, where as well as a formal peer review, there is an interval during which the paper is put on the web and anyone can comment (HESS and CP) . It's an interesting idea but doesn't seem to have caught on widely. And their system of using pdf documents makes it incredibly tedious to follow. The reviews there also seem to be published, and many are signed, but there is no compulsion (at least for the latter). There has been the suggestion that openly publishing reviews may generate a "me too" syndrome where later comments merely echo the first rather than providing an independent perspective. Perhaps there's room for some fine-tuning on that.

Another idea that's doing the rounds, that I am much more sympathetic to, is that authors should "detail their specific contributions to the research submitted" (Science's new policy). Check the accompanying example too. Some journals have encouraged this for some time, and I can see how it might act as some sort of an extra incentive to honesty if the fraudulent author has to specifically claim a particular bit of the work as their own rather than hope to deflect blame onto the whole group. I've never bothered with this procedure in the past - since I rarely have more than about 1 co-author there seems little point - but it might help to discourage one or two who seem overly cheeky about claiming co-authorship when they have at best a tenuous link to the work, and also result in those who deserve it being properly credited.

Prometheus: Myanna Lahsen's Latest Paper on Climate Models Archives

Roger Pielke Jnr has posted up excerpts from an interesting paper by Myanna Lahsen on climate modellers and the "trough of uncertainty". She paints a persuasive picture of modellers sometimes having an unhealthy level of belief in their models, and overselling their confidence in their results for a number of reasons. I'm sure there's some truth in that, at least as a couterweight to the existing paradigm that those closest to model-building are most aware of the warts (hence "trough", with the modellers and alienated critics being most sceptical, and the poor users being overly credulous).

There are also, of course, many users in the prediction end of the field for whom the models are explicitly considered as being merely an uncertain source of information about possible futures, and nowhere near to a being a crystal ball (though we may still use "the ocean" as shorthand for "the modelled ocean"). Moreoever, assessments like the IPCC necessarily spread the ball of uncertainty to include a wide range of perspectives (whether or not you think it should be even broader, there is no question that it is much wider than any one person's view). It is also worth mentioning one recent notable occasion when disagreement between models and data was essentially resolved in favour of the models. It would not, I believe, be at all reasonable to conclude from her work that all climate science is massively oversold (I can hear the septics sharpening their pens), but a healthy dose of rational scepticism is generally useful.

One thing Roger didn't feature is her comments about meteorologists, which may be interesting to those who have noticed the unreasonable level of hostility that certain American State Climatologists have shown towards climate modellling:

Synoptically trained empirical meteorologists have particular motivation to resent models. Their methods and lines of work were in important part replaced by global numerical models. The environmental concern about human-induced climate change, and the associated politics, also favored the GCMs and those working with them. The applied aspect of these meteorologists’ work was thus being taken over by numerical weather forecasting, pushing them in the direction of basic research. Their comments should be understood as potentially interested instances of boundary-work (Gieryn, 1995) whereby they, as a competing scientific group, seek to promote the authority of their own lines of research in competition with GCMs. This placed them at a competitive disadvantage when national funding priorities changed in favor of research with obvious social benefits, whereas GCM modeling seemed relevant to predicting future manifestations of human-induced climate change.
The emergence of numerical techniques also represented a loss in epistemic status as well as funding for the empirical meteorologists. So called ‘objective’ numerical methods resulted in the demotion and relabeling of their more qualitative approach as ‘subjective’, an unattractive label in the context of a cultural preference for ‘hard’ science within the scientific community.

Read the whole paper - with a sceptical mind :-)