Wednesday, December 30, 2009

Why don't climate scientists use Feynman diagrams?

This paper, purporting to prove that the atmospheric greenhouse effect violates the second law of thermodynamics and therefore cannot exist, was apparently published in the International Journal of Modern Physics -- not the world's leading journal in the field, but hardly a crackpot publication.

Among the gems in the paper (spotted here) is this (pp 59-60 of the arXiv version): Climatological radiation balance diagrams...

1. cannot represent radiation intensities, the most natural interpretation of the arrows depicted in Figure 23, as already explained in Section 2.1.2 and Section 2.1.5;
2. cannot represent sourceless fluxes, i.e. a divergence free vector fields in three dimensions, since a vanishing three-dimensional divergence still allows that a portion of the field goes sidewards;
3. do not fit in the framework of Feynman diagrams, which represent mathematical expressions clearly defined in quantum field theory [159].
4. do not fit in the standard language of system theory or system engineering [160].

I kid you not. So radiation balance diagrams should fit in the framework of Feynman diagrams or system engineering diagrams?

In case you're wondering: section 2.1.2 supplies some basic definitions of radiation intensity and flux. Section 2.1.5 says "In classical radiation theory radiation is not described by a vector field assigning to every space point a corresponding vector..." but in fact mentions that the "modern" (not so modern, actually) description uses the Poynting vector, and also talks of black body radiation and its variation from real spectra. Nowhere do I see any relevance to point 1 here. As for point 2, so what?

Also, in case you are wondering, reference 159 is to the standard text on quantum field theory by Itzykson and Zuber, and reference 160 is to the SysML site. Apparently climate scientists should be specifying their Feynman diagrams in SysML.

More here (that blog takes the credit for spotting the Feynman Diagram thing: I didn't wade through the first 60 pages of it myself!)

The authors apparently submitted this paper in 2007 and it got accepted in 2009. It reads like a prank (after Sokal, I suppose one sees prankery everywhere). But apparently they are serious, and apparently the journal editors didn't care to take a second look at it, despite its bombastic title.

Monday, December 28, 2009

A new international science centre

I am attending the inaugural conference of the International Centre for Theoretical Sciences, (ICTS) [update 29/12: fixed expansion], a new centre of the Tata Institute of Fundamental Research. Though the centre has been in virtual existence since 2007 and has already organised several meetings, its foundation stone was unveiled today by C N R Rao. Prior to that, the centre's director, Spenta Wadia, described the history of the centre and its goals. The evening concluded with a public lecture by David Gross on the nature of theory, the second of three public lectures in the conference.

What is the ICTS? It aims to be, primarily, a facilitator of collaboration and interaction among scientists -- theoretical and experimental, from India and from abroad -- and people from other walks of life, too. To that end, it will assist in organising conferences and meetings (and, eventually, be a venue for those meetings); host visiting scientists, and their students and postdocs, for extended stays; and also have a small core faculty of its own, as well as adjunct faculty from elsewhere. Three existing institutes were specifically named as role models: the Abdus Salam International Centre for Theoretical Physics in Trieste, Italy; the Newton Institute in Cambridge, UK; and the Kavli Institute of Theoretical Physics in Santa Barbara, CA, USA. The goal is to rival those centres in international impact, and Spenta Wadia and the others behind ICTS can certainly do it, with help from the Indian academic community and the government. The Karnataka government has donated 17 acres of land to the institute, near the picturesque village of Hesareghatta (which is also known for Protima Gauri's Nrityagram dance centre). It will be exciting in future years to have an international centre of the calibre of ICTP, KITP or the Newton Institute in our own backyard (if Bangaloreans will excuse this Chennai-ite for that phrase).

Key to this, I think, is implementing what Prof Wadia and others talked about: the importance of diversity in interactions. From that perspective, I find the inaugural conference disappointing already. The conference is titled "Science without boundaries", but out of 20 scheduled talks (not counting the public lectures), 11 are physics, 6 are mathematics, one is computer science, one is physics-dominated chemistry, and one is synthetic biology. [Update 29/11: One physics talk today was replaced by a computational biology talk, because of the snowstorms in the US.] Only 5 of these talks are over, and a few of them were excellent and I am sure some of the remainder will be excellent too, but I find it an extraordinary distribution of topics for a conference that claims to be on "science without boundaries". What makes it worse is that the three non-physics non-math talks, and the sole experimental physics talk, were all crammed into today's session, so that the remaining 3 days will be devoted entirely to theoretical physics and mathematics. Other than a nod to computer science, there is no theoretical talk in the entire schedule that is not physics or mathematics! Meanwhile, of the 11 physics talks, no fewer than four are on string theory -- an interesting theory no doubt, but an entirely unverified one to date -- and only three are on condensed-matter, surely the most exciting (and interdisciplinary) area of physics in recent years. Statistical mechanics, non-linear dynamics, and other areas of physics are entirely unrepresented. If the goal was to demonstrate the diversity and interdisciplinarity of "theoretical sciences", a better attempt could have been made.

(On a related note: of the 11 India-based invited speakers, 6 are from TIFR and affiliated institutes. India has more diversity than that in the "theoretical sciences".)

Be that as it may, the talks so far have largely been good, as have the two public lectures that have taken place (the third is scheduled for Wednesday, December 30). Yesterday Avi Wigderson gave an interesting talk on computational complexity theory, and though I think he was guilty of needless oversimplification as well as needless controversial statements in places, it was a good introduction to the question of whether P=NP. In his defence, also, it should be noted that he was a last-minute replacement for Sir Michael Atiyah, who could not make it because of illness; and he abandoned his holiday in Hampi to deliver this talk.

Today David Gross talked on the nature of theory, and it was an entertaining history of theoretical science, as well as a well-argued presentation of the importance and relevance of theoretical work. He made the point, emphatically, that revolutions in science don't sweep aside previous knowledge, but build on it. (So Newton's theory of gravitation is still useful, even though not quite correct.) Among other interesting points, he raised the possibility that even if a "theory of everything" (a unified theory of the fundamental forces, including gravitation) exists, it may be too sophisticated for human minds to grasp (just as quantum mechanics is too sophisticated for dogs to grasp). But he made it clear that he does not believe that.

I cannot resist quoting a mild dig Prof Gross made at the S in the name ICTS. He related the story of a press conference at Princeton after John Nash won the Nobel. Supposedly, a journalist asked Nash: "You have won the Memorial Nobel Prize in Economic Science. Is economics a science?" He replied: "No, any discipline that requires the word "science" to be added to its name is not one." Social scientists, political scientists and creation scientists, take note.

Wednesday's talk is by Albert Libchaber, on the origin of life. If you're in Bangalore, do attend. Details here.

Saturday, December 26, 2009


A few days ago, the eminent vocalist T M Krishna wrote an article in The Hindu bemoaning the increasing use in Carnatic music of instruments that are not sufficiently sensitive or flexible to reproduce the fine microtonal modulations ("gamakas", similar to "meends" in Hindustani music) required to fully express a raga.

This is not a new controversy. The western "equally tempered" chromatic scale is an approximation that gets every interval except the octave subtly wrong. For example, the fifth note ("panchama", "pa") is supposed to have exactly one and a half times the frequency of the tonic or "sa", but in the chromatic scale it turns out slightly flat: 2^(7/12) = 1.498 approximately. It has been recognised since Pythagoras (and even earlier, probably) that notes in small-integer frequency ratios sound pleasant when played together, but all intervals on the piano, except the octave, are irrational (being powers of the twelfth root of two). The compromise is necessary in western music to enable modulation to new keys without retuning the instrument. In Indian music, where the tonic is never changed, it is argued that the chromatic scale is unnecessary. While the piano is rarely used, the harmonium has achieved considerable popularity (it continues to be widely used in Hindustani music, though not in Carnatic music) but is detested by some purists for this reason.

Equally important, instruments like the piano cannot "bend" the note: they play a fixed pitch when you press the key. In Indian music, it is common to "slide" from one note to the other and "waver" about certain notes: it is such ornamentation (the "gamakas" and "meends" that I referred to above) that gives ragas their individual character.

So Krishna's tirade against the keyboard and the saxophone is understandable but not new. (He also acknowledges that some imports of Western instruments have been successful, in particular the use of the violin since the 19th century, and the use of the electric mandolin by U. Srinivas.) Nevertheless, I wonder if an excess of such "purism" may not be detrimental to the music itself.

Most of the arguments against keyboard instruments can be, and have been, levelled against the santoor and its first and foremost practitioner in Hindustani music, Shivkumar Sharma. Shivkumar cannot produce genuine "meends" but he achieves the illusion of doing so with rapid sliding tremolos. He also produces several new dimensions to his music by striking notes simultaneously with both hands: his left-hand patterns, while his right hand plays the melody, are a form of harmonic accompaniment to the music -- but done so tastefully that only the rigidest of purists would object.

Krishna names no names but, since he believes no experiment involving the saxophone has worked, he clearly has a poor opinion of Kadri Gopalnath, the best-known saxophone player in Carnatic music. Personally I am not fond of Gopalnath's music myself, without being able to quite define why. But I found the contrast of the following two passages interesting. Krishna:

The saxophone, among other instruments, is today very popular. The artists have made some modifications and changes to try and make it sound Carnatic but that has just not happened. The inherent limitation of the instrument makes the artiste limit his choice of ragas. Is this necessary? This is, to me, ridiculous. Are we willing to limit the bandwidth of a musical idiom to accommodate an instrument?

Gary Giddins, writing on a recent collaboration between Gopalnath and American jazz saxophonist Rudresh Mahanthappa:
Gopalnath, who generally plays in a yogalike seated position, has perfected something that jazz saxophonists have been attempting for decades: moving beyond the Western chromatic scale into the realm of microtones, a feat harder for wind instruments, whose keys are in fixed positions, than for strings or voice. Jazz players, such as Ornette Coleman, John Coltrane, and Albert Ayler, had gone about it by varying intonation, blowing multiphonics (two or more notes at the same time), or squawking in the upper register, where pitches are imprecisely defined. Gopalnath does none of that. Using alternate fingerings and innovative embouchure techniques, he maintains faultless intonation while sliding in and out of the chromatic scale.

Krishna is of course much more knowledgeable on Carnatic music than Giddins, or Mahanthappa, but I wonder if he is not too close to the picture to see it fully.

There are few significant practitioners of the piano in Indian music, but one recent pianist who has attracted much recent attention is Anil Srinivasan, Krishna's cousin. Anil is a trained western classical pianist who has been immersed in and absorbed Carnatic music since childhood. He has been grappling with the hard (many would say, impossible) problem of combining Western harmonies and Carnatic melodies, and -- in collaboration with the vocalist Sikkil Gurucharan, in particular -- has produced some very interesting music. I have no idea whether Krishna was referring to Anil in his article. But Anil is trying to do something very different from Shivkumar Sharma or Kadri Gopalnath. He is not trying to play authentic Indian classical music on an apparently unsuitable instrument. He is trying to use his instrument and his knowledge of harmonic theory to supplement, and expand, the music itself, while relying on collaborators like Gurucharan to supply the "purist" component of the music. He is playing to the strengths of the piano, not to its weaknesses. He is not trying to do things on the piano that are easy on Indian instruments: he is doing things that would be impossible on Indian instruments. Whether those things are desirable is a matter of opinion, but I -- and many others, it seems -- like the result.

It seems that Anil wrote a rejoinder to Krishna, which I haven't seen and can't find online (update 27/12: here), but Krishna's reply accuses Anil of missing the point of Krishna's criticism. The point, stated as narrowly as possible, is that playing Carnatic music on instruments incapable of expressing all nuances of the music, and therefore limiting one's repertoire to "suitable" ragas, diminishes the music rather than enhancing it. Again, I'm not sure whether he is applying this criticism to Anil, who is not (I think) trying to reproduce the intricacies of the music, but to supplement and expand it.

But is Krishna's narrowly-stated criticism justified at all? I can't help thinking of another form of music I am fond of, the blues, which permeates jazz and rock as well as being an art form in its own right. The blues is defined by the "blues scale" and its "blue notes": some notes -- notably the third and seventh, and sometimes also the fifth -- are played slightly "flat", but not quite as flat as their Western "minor scale" counterparts. That sort of flattening cannot be reproduced on the piano. "Bending" and "wobbling" those notes is also integral to blues, and certainly cannot be achieved on the piano (it is achieved on the guitar by bending the string with the left hand). Yet nobody would argue that the piano has no place in blues or jazz. Since the early 20th century pianists have worked around their instrument's limitations in innovative ways, and their experiments have enhanced the music, not diminished it.

Of the artists mentioned above, I usually like listening to Shivkumar, I don't much enjoy Kadri Gopalnath, and I find Anil Srinivasan's approach very promising. This is not a technically informed evaluation of these artists' respective merits. But I think musical quality is not necessarily correlated with technical purity. There are lots of musicians who follow all the rules but are mind-numbingly dull to listen to.

It seems to me, on reading Krishna's first article closely, that he is more worried about the effect of keyboard instruments on music education -- but then there are much graver problems to worry about. A scholarly article on how music should be taught would be welcome. But complaints about unsuitable instruments sound, to me, more reactionary than artistic. T M Krishna is a well-established and widely respected musician, but he is too young to sound like a curmudgeon.

RIP, Asheem

Asheem Chakravarty of the band Indian Ocean died yesterday of a heart attack. Obituary here (and elsewhere).

Though not formally trained, he and his bandmates defined a new sound that combined elements of Indian folk and classical with Western rock. Asheem played tabla, and sang, often simultaneously. The combination of his tabla, the acoustic guitar of Sushmit Sen, the bass of Rahul Ram and drums of Amit Kilam combined to unique effect. In the early days, the band played largely instrumental music, but as time went on, the somewhat classical-sounding vocal of Asheem and the somewhat more raucous, folk-inspired singing of Rahul Ram dominated their music more and more. After struggling with college-festival gigs for nearly 10 years, the band achieved considerable success with their album Kandisa in 2000, and in recent years have been touring heavily around the world.

Asheem had a heart attack in October, in Doha airport on the way back from a tour of the US. He had been in a poor condition since then. While Indian Ocean have continued to honour their recent concert commitments with fill-in players, it is hard to imagine them without Asheem. I hope the band finds a way to go on. And my condolences to Asheem's family, and to the band: though he was taken away early, he enriched many lives.

Monday, December 21, 2009

More thoughts on Apple

We've now had the Mac Mini for over a month. It's mostly my wife using it, and finding it very easy to use. But here are some random observations:

  • Did I hate proprietary software? I thought I did, but I suppose I only hated the Windows world. There is no open-source program that compares to iPhoto, for example. (And do we really care if such programs are not open-source? I increasingly realise that I'm for open standards and interoperability, not necessarily open source as such.)

  • Is Mac OS X stable and reliable? Yes. No crashes yet. Perhaps recent versions of Windows are equally good, I don't know.

  • Is the command line still useful? Yes. Example: my wife had over a hundred files in the "Downloads" directory and wanted to move only the JPG photos to the "Photos" directory on the desktop. Pointing and clicking to select them in the graphical file manager was a tedious process. I simply opened a terminal and typed "mv Downloads/*.jpg Desktop/Photos".

  • But is the graphical interface that hides all the Unix complexity good at what it does? Mostly, yes, but there are slip-ups. Example: the default shortcuts for switching "spaces" ("virtual desktops" on Linux, no equivalent on Windows) were shown as "^ left" and "^ right", and despite some Linux experience, my wife didn't immediately realise that "^" was shorthand for the "Ctrl" key. (I suppose only power users want virtual desktops anyway, but she knew them from Linux and found them convenient.)

  • Is open source software still useful on the Mac? Yes. Case in point: VLC, the media player. Unlike Windows (last I checked), the Mac plays DVDs out-of-the-box -- but enforces a region code, which may be changed only five times before it is permanently locked. This is strictly a software restriction, at the behest of the movie industry. VLC disregards the region code so we can happily play DVDs from multiple regions. We have also installed The Gimp and Inkscape: the alternatives were Adobe Photoshop and Adobe Illustrator, but those are expensive and the free programs are good enough.

  • Anything we found we can't do, or not easily? Yes: save a flash video from YouTube into a separate file. (I suppose there would be plugins for Firefox to do it, but first we'd have to install Firefox.) On linux, look in the /tmp directory for a file whose name begins with "Flash", and copy it. Supposedly it used to be a similar mechanism (different location) in earlier versions of OS X, but on Snow Leopard we couldn't find it.

  • Do I plan to trade in my Linux laptop for a Mac? No.

Saturday, December 19, 2009

One white car

'Twas tee, enn, ten, vee, five, seven, six, two,
One torrential white car in driving rain.
It hit her, but it well could have been you.

A call-taxi halted to let her through.
Her umbrella flapped. And, bull-like insane,
Came Tee, enn, ten, vee, five, seven, six, two.

Muddy puddles trap one's wet feet like glue.
The white car halted, as she tried in vain
To step past them. It well could have been you.

"Hm, why should pesky pedestrians do
Road-crossings in my car's own service-lane?"
thought Tee, enn, ten, vee, five, seven, six, two.

He revved, and bumped her knee (he missed her shoe).
"Don't cross so slow," he said; sped off again.
It's his road. Does your knee belong to you?

No injuries? Not even a bruise or two?
Not dead? Well then, stuff happens. Don't complain.
And Tee, enn, ten, vee, five, seven, six, two
Stays on our roads till he kills me. Or you.

(Any resemblance to real-life incidents is not coincidental)

Sunday, December 13, 2009

Sequencing the human genome... again

The CSIR is back in the news, this time for more pleasant reasons: sequencing the human genome. Several news items appeared on the achievement, by IGIB, Delhi, last week.

But not all the coverage is positive: as Arvind pointed out in a comment on an earlier post, some senior scientists (including Pushpa Bhargava) question the importance of the achievement as well as the ethics of announcing it to the media before it has been published in a peer-reviewed journal.

I agree on the latter point, and am unsure of the former -- but that is the job of peer-reviewers. It is how science works. The media is not qualified to evaluate new scientific claims. The peer-review system, as it currently exists, has its problems, but replacing qualified reviewers by journalists is hardly the solution (I assume that the work has indeed been or is being submitted to a relevant journal, though).

But there were a few other aspects of the original news report that left me disturbed. The comparison of time frames -- six weeks for this project, 13 years for the original Human Genome Project -- is quite inappropriate. It is always easier to do something for the second time. The original project was developing new sequencing technologies and computational algorithms that took the major part of those 13 years; eventually, the successful method (and one that is widely used today, including, I expect, by the IGIB group) is called the "shotgun" method, where many overlapping fragments are sequenced and then assembled like a jigsaw. These fragments are about 30 nucleotides long, while the human genome has about 4 billion nucleotides in it. Moreover, the genome is highly repetitive, and many of the short fragments would be identical and it would be hard to correctly "assemble" them. Worse, sequencing the short fragments is itself not an error-free method: one or two errors per fragment are expected. So when Celera Genomics came up with the method, they encountered considerable skepticism. Nevertheless, it proved to be the most feasible approach. To alleviate the problem of repetitive regions and sequencing errors, every part of the genome is "covered" 20-30 times by multiple fragments. Even so, completing the assembly for a new organism is a tedious and error-prone process requiring sophisticated software and much human judgement. The point is that these problems are now much better understood than when the Human Genome Project undertook its task, and software is continually getting better. If the IGIB team made significant algorithmic or technical innovations, hopefully they will be described in an upcoming paper.

Even more importantly, the task of sequencing a new human is much easier than that of sequencing a previously unsequenced organism, because a reference genome already exists, and the variation between different humans would be expected to be very small. As I wrote in a comment in reply to Arvind above: one can compare it with assembling a jigsaw with a few billions of pieces, many of which are identical or almost identical, without knowing the "big picture"; versus assembling it with the big picture available to you, knowing that there are only minor differences from the "reference picture". Technologically, there is nothing very hard any more about this. Equipment and software is marketed for the purpose by large biotech companies like Illumina, and is in use all over the world. If the IGIB team has made significant technical innovations, that is of interest, but it has not been mentioned in news items and it should, of course, be peer reviewed before it hits the media.

As for possible medical benefits: similar claims were made in support of the original Human Genome Project, but little benefit is seen so far. But these things should be seen as basic research, with medical benefits a possible and welcome spin-off, but not the primary goal. It is not at all easy to "link" specific genetic variations with specific diseases, and sequencing a handful of new genomes will not, I think, directly aid that problem. So what is the primary scientific accomplishment here? The news items don't say, but then, they should not be the primary medium of communicating this work. I look forward to the peer-reviewed article, when it appears.

Wednesday, December 09, 2009

Why can't we all just listen to Jug Suraiya?

Jug Suraiya, the Times of India's self-appointed humorist and contrarian, takes a hatchet to climate science today. He complains that climate change is treated as an irrefutable "fact". He claims that anyone who tries to question climate change is "immediately branded a destroyer of the planet, a dangerous heretic who should be burnt at the stake" and the "warmists" "will not tolerate sceptics any more than did the Spanish Inquisition".

So what evidence does Mr Suraiya offer against the hypothesis of manmade climate change? None whatever! He resorts to citing "dissenters", but names only two, whom he calls "the most notable" -- but neither of them is a climate scientist. The first is a geologist, Ian Plimer: read about him and his error-riddled book here and here. And his response to being challenged on his facts by George Monbiot is here. And Mr Suraiya's second authority is not a scientist at all, but a journalist, Christopher Booker.

Future climate-change deniers will now be able to cite a third authority, the eminent Indian humorist and contrarian, Mr Jug Suraiya. It is a form of proof by mutual reference.

So here are two things to understand, Mr Suraiya. First: man-made climate change is not an "irrefutable fact". It is a hypothesis for which there is, at this point, an enormous amount of evidence compiled by climate scientists around the world. To refute the hypothesis, you need a significant amount of contrary evidence. Plimer's book does not cut it.

Second: you allege that big money -- "huge money", in your words -- is promoting the climate change hypothesis. In fact most climate scientists work at respected universities and government organisations, on public funding. If you want to follow the money, take a look at who is funding the deniers.

Monday, December 07, 2009

Shiva Ayyadurai rumbles on...

UPDATE 7/12:I notice the folks at the Shiva Ayyadurai Fan Club have linked to my post as alleging a nexus between Nature India and Shiva Ayyadurai. I want to clarify that I am alleging no such thing. I am only saying that they seem to have swallowed one side of the story without asking questions, and given Shiva Ayyadurai (a questionable character) space to vent his spleen on their website without allowing adequate response from CSIR; and they now have some uncomfortable questions to answer.

In my previous post on this subject, I referred to unsubstantiated allegations about Shiva Ayyadurai's unethical behaviour that I had heard. Subsequently, two CSIR scientists, Vinod Scaria and Sridhar Sivasubbu, wrote the same accusations in two Nature Forum posts. Astonishingly, those posts have been removed by the forum administrators: it seems Nature is intent on promoting Shiva Ayyadurai's version of the story and will brook no dissent. However, Scaria's and Sivasubbu's versions are archived here and here respectively -- as of this writing, they look the same to me as the ones that used to be on the Nature forum.

Also, from this post (see comment), it seems that the Nature editors (in London, not India) objected to personal accusations made in those and other posts. I wonder, then, why they agreed not only to publish, but to highlight, accusations made by Shiva Ayyadurai in his article (which continues, as I write, to be frontpaged in the Nature India website) -- accusations which include fraud, financial wrongdoing, and arson to cover up the wrongdoing.

For more entertainment, read the rest of the Shiva Ayyadurai blog.

I think this episode is a disgrace and a blot on Nature's record. (As also the New York Times and others who have given this fraud and sleazeball a pulpit.)

And Nanopolitan has 182 comments and counting. I haven't yet waded through all this.

But, once again, I would like to ask Prof Samir Brahmachari: why was this creature appointed to CSIR-TECH in the first place, and in what capacity was he appointed?

And while CSIR does do some outstanding science and includes some world-class laboratories, there is no doubt that it would benefit greatly from some changes in structure and management, and I hope some well-intentioned, honest, capable and qualified people are already working on it, without seeking their 15 minutes of fame. There are lots of such people in CSIR already (and elsewhere in India). In fact, I think the state of Indian science (including CSIR) is getting better, not worse, and while there is need for further improvement and change, there is no need for panicked reactions.

Thursday, December 03, 2009

Infosys Prizes

I was travelling with my mobile phone's slow GPRS link as my main connection to the outside world. So I seem to have completely missed the announcement of the Infosys Prizes for 2009.

I am familiar with the science names (and also the mathematics name -- that prize is awarded separately this year but will be merged with the others from next year), and they are all obvious and deserving choices. (There are other deserving choices, who, I am sure, will be honoured in future years.) But I am particularly familiar with the winner of the Life Sciences prize, K VijayRaghavan of NCBS. And I liked the concluding line of his citation: "He appears fearless in the incorporation of new methods when needed to tackle new biological questions." I know that for a fact since he was very eager to use my new computational methods when I first returned to India. At the time I was reasonably well known in sections of the physics community, but a total unknown in the biology community. We first met at a seminar on developmental and evolutionary biology where he was speaking and I was attending; we struck up a collaboration that, though certainly not the world's most active and vigorous (the fault is mine), continues to this day. I am perennially astonished at how he finds time for everything. At the same time that he has been doing outstanding science, he has, as director, built up NCBS (admittedly already an excellent place when he inherited it) into easily one of the best and most competitive biology centres in the world. And, on top of all that, he's a great guy personally.

The other scientist winners, Ashoke Sen and T Padmanabhan, are also outstanding and world-renowned figures, though I don't know them personally. Read their citations on the Infosys site for more. The mathematics winner, Manindra Agrawal, has made contributions that shook up the field -- a thing you can say for very few Indian scientists. I am not familiar with the work of the social science winners but, based on the evidence of the other selections, I am sure they are deserving winners too. As Abi points out, it is odd that they found nobody deserving in the engineering sciences this year; but that apart, it is a good start for these prizes.

Inder Verma points out in this article that "in India, seniority often trumps innovation or achievements." This year's winners are senior and deserving, but the list in that category will run out rather quickly, I suspect. Meanwhile, some younger scientists are carrying out truly innovative research today, and publishing in journals (like Cell) that had never seen contributions from India before. So it will be interesting to see the choices in future years, and I hope the prizes won't fall into the trap that Verma bemoans, of rewarding seniority only.

Wednesday, December 02, 2009

Ayyadurai speaks

Shiva Ayyadurai, recently the subject of controversy regarding a report he wrote for CSIR (previous post on the subject here), has written an article (free registration required) for Nature's website putting forward his side of the story.

Well, it's hardly a story -- it's a polemic, filled with unsubstantiated allegations of fraud and chicanery, hurled from his safe harbour in Boston; his most extreme allegation is a suggestion that CSIR resorted to arson at their own headquarters to hide financial wrongdoing.

I was recently at a meeting where I met several scientists from CSIR, and several others who know the director-general; and, as a local newspaper reprinted the recent New York Times article that, again, portrayed the Ayyadurai side uncritically, the topic came up for conversation. Now, it is safe to say that this was not a Samir Brahmachari Fan Club. "He does not listen to anyone" was one of the more flattering things said about him. Nevertheless, there was zero sympathy for Ayyadurai, and in fact I heard some rather unsavoury (but also unsubstantiated) things about his behaviour while he was with CSIR. (With enemies like Ayyadurai, who needs friends?)

And, by the way, I don't think it counts as "harassment" to ask someone to vacate their cushy government house in the heart of Delhi when they cease to be an employee. With the standard house-rent allowance (30% of his reportedly substantial salary) Ayyadurai could easily have rented a comfortable house privately: why didn't he? Of course, if he had done that, and been fired, he could not have complained that the government was no longer paying his rent.

It seems to me that, if CSIR really wanted to get nasty, they should sue Ayyadurai for libel based on his Nature article -- in England. English laws permit libel suits by foreigners against foreigners if it can be shown that the material was readable in England; in this case, since Nature is a UK company, this should be easy. And even if Ayyadurai has a case, defending himself would not be a pleasant experience. Just ask Simon Singh. (I'm not recommending that CSIR do this. I am saying that if they did, that, not asking him to vacate government housing, would be nasty and vindictive. But not less so than Ayyadurai's own behaviour.)

But -- to repeat what I asked in my previous blog post on the subject -- I would like Samir Brahmachari to clarify exactly in what capacity Shiva Ayyadurai was hired in the first place, and why. His qualifications are meagre (yes, he has a few MIT degrees, but thousands of people do; and he ran a little-known e-mail company in the Boston area. That's about it, as far as I can tell.) His website is one of the most crudely self-promoting that I have seen. What, Prof Brahmachari, impressed you about him?

And I'd like to know why the media, from the Hindustan Times to the New York Times to Nature, is unquestioningly allowing him a pulpit.

Friday, November 27, 2009

What's wrong with the Indian left?

Well, this for example. The article is about Kian Tajbakhsh, an Iranian-American (ie, a dual citizen of those countries) social scientist who studied in the UK and the US, earning his Ph.D. in Columbia University and has worked with many respected organisations, chose to move back to Iran, and was arrested there and charged with espionage. Reportedly he is likely to be executed. The writer of the above article adds:

Those of us in India who have been consistently anti-imperialist and critical of the US, and who respect Iran’s anti-US imperialist position, have been deeply disturbed by the Iranian regime’s crushing of the pro-democracy protests and its attempts to characterize these massive uprisings as fomented by the US. It’s tragically ironic that the US should be dubbed as “pro-democracy” by the Iranian regime!

I wonder why the writer did not ask herself the obvious question: if Iran is the land of the free and it is ironic to call the US "pro-democracy", why, one may ask, do so many Iranians (and nationals of so many other countries) want to make the homes in the US, and why do so few Americans (or Indians or anyone else) want to immigrate to Iran? Does she think Tajbakhsh (whom she calls an "Iranian patriot") chose to move to Iran because he approved of the Iranian regime, or thought it better than what the US offers (even in the Bush era)? Do Burmese patriots, or North Korean patriots, approve of their rulers too?

Well, at least the writer is disturbed by the recent crackdown -- unlike fellow travellers of the Soviet Union who justified the atrocities there until Stalin's genocidal excesses became impossible to ignore (and, in many cases, even later).

Monday, November 23, 2009

Useless skills

Long ago, an American and I were counting something (I forget what, probably occurrences of some motif in a sequence or something like that), and when the American looked at my hand, he said "hey, that's a clever way to keep count!" Rather than using fingers individually, I was using the lines that separate the phalanges on the fingers, and the tips of the fingers, to count up to 16 on each hand, or 32 totally. I've always done that, and in India I'm not the only one -- I think it goes back to Vedic times (in particular, I think I was taught some such thing as part of some ritual or the other, when I was a child). So it didn't occur to me that anyone else would be surprised by it.

Can one go higher than 32? I didn't think much about it until I read this User Friendly strip. By representing 1 with a raised finger, and 0 with a lowered finger, and using both hands, one could in principle go up to 1023. There are two catches: one has to be familiar with binary numbers, and the fingers have to move very independently. The second is the bigger problem for me.

But the other day I realised that one can go up to 256 (or 255) very easily, by modifying my phalange technique. Count from zero to 15 (rather than 16) on each hand, but instead of adding the hands, use one hand as a 16's placeholder -- that is, use the hexadecimal system. One still needs to be comfortable with hex, but it is a useful skill for anyone who programs computers.

I haven't actually started counting that way yet, but next time I need to count a number that is likely to be much greater than 32 but less than 256, I'll give it a try.

In theory, with sufficient independence of finger movements, one could do 255 in one hand, as follows: use the phalanges as the lowest-position hex digit, and use the binary readout of the finger positions (raised/lowered, omitting the thumb) for the next position. With 16 inter-phalange lines/fingertips, and 16 possible combinations of raised/lowered fingers, one can do 255 in one hand. And combining the two hands, one could then count up to 65,535. But that is certainly too much for my level of digital dexterity or mental arithmetic. (The latter would have been so much easier if the world had standardised on base 16 to start with. Using base 10 was a huge mistake, but is now one of those suboptimal choices that are frozen and irreversible.)

UPDATE 24/11: Though I linked the Wikipedia article on hex above, I didn't read it. From this section, it seems I'm not the first to think of counting to 255. It doesn't attribute the originator but says counting on phalanges is common "in South Asia and elsewhere". It attributes the idea of counting to 1023 in binary to Arthur C. Clarke.

Saturday, November 21, 2009

Macs and developers

Here are two articles about Apple, both by seasoned software experts ("hackers" in the original, good sense of the term).

The first is an old (2000) article by Jordan Hubbard, one of the founding developers of the FreeBSD project. FreeBSD is a Unix-like operating system that was once almost as popular as Linux. It evolved from BSD, which was originally a set of enhancements to the original Unix operating system of AT&T, developed at Berkeley; over time BSD became a nearly full-fledged operating system in its own right, and in the early 1990s, gave rise to several operating systems that achieved considerable respect among the cognoscenti. (Among other things, the network protocol that governs the Internet, and several widely used pieces of internet software, came from BSD.) Apple heavily borrowed from FreeBSD (and continue to credit it on their developer page) in creating Mac OS X, which is a fairly traditional Unix system under its shiny hood. Hubbard's article is a review of a beta version of OS X, written from the perspective of a Unix enthusiast and FreeBSD developer. It turned out that he liked OS X so much that, shortly afterwards, he left the FreeBSD project and went to work for Apple (as did several others).

The second is a recent essay by Paul Graham, perhaps best known as an evangelist of the Lisp programming language, but a very influential online essayist. It is prompted more by the iPhone than by Apple's computers, and the way Apple has handled the iPhone "App Store" leads him to claim that they "don't understand software". Moreover, he argues that the loss of goodwill among talented programmers (ie, people like Hubbard, who were attracted to Apple ten years ago by the vision of a solid, Unix-based, user-friendly desktop system) will cost Apple dearly in the future.

My previous post on Linux "just working", compared to the Mac, was titled partly in jest, though the point about the different development models was serious. There is no question that the Mac offers a more user-friendly interface for beginers than the best Linux systems, has a better set of applications included (especially the multimedia stuff), and -- perhaps most crucially -- allows you to install most well-known open-source Linux/Unix applications via third-party efforts like the Fink project.

Macs also have a far better reputation for stability than Windows, and comparable to Linux. Here, however, we have to consider the great advantage Apple has in this respect. Apple builds the hardware, and can ensure that it works optimally with its software. With external peripherals (such as the HP printer/scanner I mentioned in my previous post), things aren't so certain. Linux, and Windows, meanwhile, work fine on the vast majority of PCs out there. Microsoft works closely with every important PC hardware vendor to ensure this. Linux is more volunteer-driven but, these days, several of the major manufacturers -- notably Intel and IBM, but also many others -- fund Linux development, employ individual developers, and make the specifications for their hardware available. Still, testing for every possible combination of hardware devices is impossible. Computer makers will generally test that their machine works with previous releases of Windows, but Microsoft cannot ensure that all existing computers will work with Windows 7. Linux, meanwhile, receives little testing support from manufacturers. So it is remarkable that these systems work as well as they do.

Apple has received brickbats over the years for their proprietorial control of their hardware and their refusal to permit installation of Mac OS X on third-party systems. I personally think the world would have been much worse off if Apple, and not Microsoft, had dominated the personal computer industry. But Steve Jobs, Apple's CEO, is a rare example of a hard-headed businessman who also understands the intricacies of software. (Bill Gates is another. But Gates was never interested in the hardware side of things, so MS-DOS and, later, Microsoft Windows drove the widespread availability of cheap, "commodity" hardware, which in turn spurred the growth of Linux and other free operating systems. But I digress.)

Many people these days forget -- or are not even aware -- that Apple went through dark days for nearly a decade from the mid-1980s, after power struggles between founder Steve Jobs and CEO John Sculley (a former Pepsi executive hired by Jobs) resulted in Jobs being ousted from the company. Sculley's tenure was not a resounding success. Jobs was not much more successful commercially with his next venture, NeXT, but it was a highly influential platform in the academic community (among other things, it was the platform used by Tim Berners-Lee to develop the World Wide Web). After Apple bought out NeXT in 1997, Jobs was restored as CEO of the unified company. The fortunes of Apple have soared wildly since. On the hardware side, he brought out revamped Macintosh computers and laptops, the iPod audio device, and the iPhone; on the internet side, he launched iTunes, the online music store that (together with the iPod) changed the music industry; and on the software side, he decided to entirely scrap the "classic" MacOS and develop a new system, Mac OS X, from scratch. Well, not from scratch: as noted above, it uses FreeBSD (and the Mach microkernel, and much other free/open-source software) at its core; and its graphical interface, and underlying infrastructure, is heavily based on the NeXTstep interface developed by his previous company. Today, OS X powers not only Apple's computers, but also their iPhone and iPod Touch handheld devices.

Two software-side decisions of Jobs are particularly interesting. When choosing an underlying "base" operating system for OS X, he did not go with Linux, which was then (as now) the best-known free version of Unix: he instead picked FreeBSD, which was lesser-known but highly respected by those in the know. And some years later, when Apple decided to develop a web browser, they chose as a base not Mozilla (whose ancestor was Netscape, the dominant browser of the 1990s, and whose Firefox browser is widely used today), but Konqueror, a browser used only by a small subsection of the Linux community. Specifically, they used the HTML and Javascript engines of that browser, on top of which they built their own interface. They also released their modified version of the html engine as the open-source project Webkit, and it is used by several other projects including Google Chrome.

In both cases, the decision to spurn the well-known name in favour of a much lesser name was justified by pointing to the smaller, cleaner, more maintainable source code; and in both cases, the result has been wildly successful. I wonder how many CEOs would have taken such gambles on relatively "unknown" software -- indeed, in the case of OS X, betting the future of the company on it. Google, in contrast, has chosen to use Linux, the "safe" choice, as a base for their operating systems (Android and the Chrome OS); and though they chose Webkit for their Chrome browser, they did so only after it had already been "proven" by Apple.

Small wonder, then, that Apple's share price takes a hit every time worries about Jobs' health surface.

Though the co-founder of Apple, Jobs was never a hacker (that was Steve Wozniak) but he understood software and software hackers. Which is what makes Paul Graham's article above a bit worrying. Has Jobs lost touch with the "hacker ethic"? Or has he lost full control of his company, perhaps due to his still mysterious health issues?

Wednesday, November 18, 2009

Linux "just works"!

We just got two new toys: a Mac Mini (the basic model), and a printer/scanner (HP Deskjet). The Mac -- both the tiny little machine and the OS that it runs -- looks spectacular, even though the peripherals are all non-Apple (Dell monitor, Logitech keyboard and mouse).

The printer came with a Mac OS driver CD; we inserted, installed, and... it didn't work. The scanner program quit with an "unknown error", and offered to send a bug report to Apple. We suspect that a newer driver is required: the CD says it is for Mac OS X 10.3, 10.4 and 10.5, but the Mini has 10.6 (Snow Leopard).

So I tried plugging the printer into my Linux laptop. No driver downloads, because the HP-supported linux printer drivers were already installed. I then tried scanning an image: the scanning program (xsane) detected the scanner, and it Just Worked.

I expect the updated Mac drivers will work too. If not, it's over to consumer support. But the interesting thing to me is this: unlike many Linux drivers, which are developed by third parties, the HP drivers are from HP -- as "official" as things ever get on Linux. But the way it is done is very different. HP's Mac (and Windows) drivers are binary "blobs" that are designed for a particular OS and its particular driver model; when the OS is updated, the driver can break. Windows Vista was notorious for malfunctioning peripherals, for this reason; apparently Snow Leopard is not immune. Linux drivers are provided (mostly) as source code, and compiled against the kernel source, which is a constantly evolving object (essentially no two Linux distributions use exactly the same Linux kernel, and the kernels they use are not the "official" kernels released by Linus Torvalds). So the user does not get the HP drivers from HP's website or installation media, but bundled with the OS itself -- and it works.

Linux is sometimes criticised for evolving too rapidly, making it extremely difficult for device manufacturers to supply binary "drivers". The linux developers respond that it is better for the companies to work with the kernel community, open-source their drivers, and, if possible, include them in the "mainline kernel". That way, first, users will not need to download drivers or run "installation CDs" to get their hardware to work; second, the drivers will generally stay working. (Here's a position statement from Linux developers.)

Based on my one data point (I don't use Windows and this is my first experience with a Mac), I'd say the Linux developers have a point.

Wednesday, November 11, 2009

"The pilot is the weak link"

According to a new book by William Langewiesche, reviewed here by the NYT, the true hero of the incident earlier this year when a US Airways plane was landed safely on the Hudson river after losing both its engines was not the pilot, Chesley "Sully" Sullenberger. It was Bernard Ziegler, a Frenchman who perfected the "fly-by-wire" technology used by Airbus. Langewiesche asserts that the Airbus was nearly capable of landing itself, even after losing its engines, and while Sullenberger made the right choice to land in the river, the landing itself required only moderate skill and any decent pilot could have done it.

It is an interesting claim, because the other headline-making air accident this year was the loss of Air France flight 447 on June 1, en route from Rio de Janeiro to Paris. On that occasion, there were several suggestions that fly-by-wire, and the lack of manual pilot overrides on Airbus aircraft (in contrast to Boeing), were responsible.

Langewiesche further claims, credibly, that being an airline pilot is such an incredibly monotonous job that the best and brightest do not want to do it today. (Some pilots may find unusual ways to alleviate that boredom.) Michael Moore says that pilots in the US are so poorly paid today that many of them work second jobs. No wonder so many foreign pilots are now working for Indian carriers, who not only continue to pay well, but Air India pays expat pilots more than Indians. In fact, their annual bonuses (up to $15,000) are comparable to the total annual pay ($17,000) of some pilots for major US airlines, if Moore is correct.

Air India, of course, is in a financial crisis, as -- to a lesser extent -- are all Indian carriers; so such generous pay may not last long. But good pilots are still required, even if Airbus planes require little skill to fly.

Unless Airbus invents a pilotless aircraft (Boeing doesn't seem very impressed with fly-by-wire), I think interesting times are ahead for the airline industry, and for passengers.

Tuesday, November 10, 2009

CSIR, bitten by the one it fed

Suppose you are heading the country's largest and most important scientific organisation. You know that, despite some very bright spots, it has been getting creaky and bureaucratic over several decades. Being a dynamic and go-getting scientist, you have several ideas on what is to be done. One of the things you want to do is to set up a new department aimed at streamlining the process of commercialising new technologies, and establishing better links with industry. Would you hire this guy? Would you offer him a job the very first time you met him?

The current director-general of the CSIR apparently did. And there, in my opinion, started the trouble that has since then accounted for much column-space and blog-energy. Good reviews, and links, are on Abi's blog: here and here (some of the comments are interesting too).

V A Shiva, also called Shiva Ayyadurai, seems to have had an interesting career. He is not a career scientist, but has bachelor's and master's degrees in electrical engineering and computer science, visual studies and theoretical mechanics from MIT; and recently, apparently, he earned a Ph.D. in systems biology from the same institution. In between, he has mainly been in what we like to call the IT sector, primarily running an e-mail provider, EchoMail. Read his biography for more.

The DG of CSIR, Prof S K Brahmachari, is a smarter man than me, and no doubt a better and more experienced judge of others' CVs and abilities. It appeared to me that Shiva Ayyadurai has few notable academic achievements, and his primary commercial undertaking, EchoMail, is not exactly a household name. He seems prone to bombast: for example, he claims to have created "one of the world's first e-mail systems" in 1979, but e-mail has been around since the 1960s. Nevertheless, a thorough interview and review of the man's abilities and accomplishments may have led Prof Brahmachari to conclude that he was the right person to head his pet project, CSIR-Tech. But was that done, or was it an instantaneous decision, as Shiva suggests?

Having been hired, at a generous salary, he was apparently asked to produce a report on the functioning of the CSIR and future improvements. This he did, and that is when all hell broke loose, and the CSIR terminated his appointment (the CSIR claims that he was not employed in a permanent position, only hired on contract, and there are also claims that he was asking for too much money). Shiva went ballistic, complaining to everyone in the media who would listen that he was being victimised for his genuine and well-meaning criticisms of the organisation. He claims also to have written to the Prime Minister. What the PM thinks of it, we don't know.

So what did he say? The Deccan Herald excerpts the report here. I have seen the full report but do not think it is worth "leaking": it seems hastily put together, is unprofessional and often personal in tone, identifies obvious problems that I'm sure are well known to all CSIR scientists, and prescribes remedies that would be within the province of a first-year MBA student. Nevertheless, do read the DH link for its entertainment value, if you like. As Abi asks, if this is Shiva's opinion of the man who hired him, why does he want to keep the job, and having aired such an opinion, why should he expect to keep the job?

As some commenters on Abi's blog suggest, maybe he was already told not to expect to be hired in a permanent position, and his report was his way of venting his grievance at the CSIR DG. Which makes it even more unprofessional. Regardless of the truth or otherwise in his observations, I don't think the report will now be taken seriously, nor should it be.

But that shouldn't detract from two key issues. First, exactly what sort of position was Shiva hired under in the first place, why, and what was his mandate? Second, the need to reform and streamline CSIR remains: what does the DG plan to do in this regard? I suspect the CSIR DG made a mistake (caused by over-eagerness to "get things done") in hiring V A Shiva, and knows it; he should now make amends -- first, by coming clean on exactly what happened; and second, by making sure the need for reforming and modernising CSIR is not sidetracked.

Monday, November 09, 2009

This is it: review from a non-fan

Two days ago we saw "This is it", the film of the rehearsals for Michael Jackson's planned last concert series that never took place.

I was never much of a MJ fan -- "Thriller" happened when I was under 10, and by the time "Bad" happened he was already being viewed as a bit of a joke, with his skin-bleaching and plastic surgery and oxygen tents and whatnot. By the time I started listening to rock and blues (and, later, jazz), the Michael Jackson brand of pop seemed too tame.

After he died, my view was coloured by articles like this one. Supposedly the guy was skeletal, unable to sing let alone dance, and only being kept alive by insane quantities of medication; if he hadn't died before the scheduled 50-concert series, he would not have survived that ordeal.

So it was a surprise to see Jackson in the movie. Thin he certainly was -- skeletal, it was harder to say. But the rest?

He could sing, and did sing. He wasn't lip-syncing. His voice was a bit different from the old days, still high and child-like but somewhat thicker (an improvement, in my opinion). He talked frequently about needing to "preserve his voice", but it sounded more like hypochondria than a real problem -- no doubt it was a bigger problem than even he knew, but it did not show in the performances. "I just can't stop loving you", in particular, ended in an extraordinary extended bluesy call-and-response sequence between him and a female singer that would not have sounded out-of-place on a 1950s album from Chess Records, and showed some improvisational ability that I had never associated with him.

He could dance. Not like a 20-year-old, but better than most 50-year-olds, and certainly not like someone who only had weeks to live.

He was in control. Directing the choreography, the film-editing, and the musicians with authority -- telling the lighting and video people to "watch his cue", telling them that he would sense the video changes without needing to see them, telling his musicians to prolong a pause and "let it simmer"...

And the musicians were outstanding. If I had expected MJ to lip-sync his performances, I had also expected him to use recorded music, like most other pop singers these days. But no, he had a small, tight band -- two guitars, bass, keyboard, drums -- and while what they did wasn't too different from his recordings, it sounded much punchier and more intimate. The bass was funky -- I'd never noticed a bass in MJ before. The lead guitarist, a young woman called Orianthi Panagaris, ripped it up, not missing a step even when MJ was dancing in her face and all over her guitar. "Black and white" climaxed with a guitar duel between her and another guitarist. I found I could relate to the music: I could hear Motown and the blues in it, which I never did before, perhaps because I never listened to it very much, or perhaps because it was over-produced.

Kenny Ortega chose to put together a raw montage from the rehearsals, consisting of complete or nearly-complete songs, some shots of the team planning the performance, some interviews with the crew, and nothing else. It is obvious that an enormous effort must go into an MJ show -- let alone a 50-night run -- but the sheer scale of it all hadn't really come home to me. Nor had the level of commitment and enthusiasm of all the performers and crew, and their interaction with MJ, who was like a god to most of them. It must have been absolutely shattering for them when Jackson died a week before the concerts. But this movie has brought them to a wider audience than they would have planned for. I expect to hear more of Orianthi Panagaris, in particular.

Monday, November 02, 2009

A truck on a pedestrian bridge

Chennai has three waterways running through it, one of which is the Buckingham Canal -- once an elegant canal on which barges transported people and goods, now essentially an open sewer. But the canal divides the city, especially the southern parts of the city: there are very few motorable crossings south of the Adyar river. The first major one is at Sardar Patel road, the next at Tidel Park about 2km further south, and the next at Shozhinganallur nearly 10 km beyond that.

In between the first two above, there was a narrow pedestrian bridge, which served as the main route for residents of our institute's hostel and guest house -- and several others in the neighbourhood -- to access the commercial areas of Indira Nagar, Adyar and Besant Nagar on the other side. The bridge was designed for pedestrians and cyclists; motorbikes were always frequent users, but recently auto-rickshaws and even cars have been using it heavily. Whenever police tried to barricade it so that only pedestrians could access it, the barriers were removed.

Early on Sunday morning, a truck laden with bricks tried to use it. This was the result.

Thanks to one truck driver who had no idea what his vehicle weighed, and several inconsiderate souls who kept removing those barricades, residents of this mainly academic neighbourhood will no longer be able to walk across (or cycle across) to the commercial area on the other side. And when I cycle to work, which is fairly often, I will need to use the busy main road and not the quiet inner roads that I earlier favoured.

Thursday, October 29, 2009

Business sense

Even in a land where money is valued and Lakshmi is worshipped, Dilip's experience with online tourism firm ExtendedStay is breathtaking. Go read.

If John Cleese had met Vishwas Tiwari and not Donald Sinclair, he'd have done something much funnier than Fawlty Towers.

(On the other hand, Dilip has nice things to say about Apple Inc and their customer service, as do many of my colleagues.

Saturday, October 24, 2009

Magnetic monopoles from classical physics

Much recent media attention has been showered on a recent paper by Bramwell et al, that observes the motion of "particles" in a solid that behave like carriers of "magnetic charge", or magnetic monopoles. This is an experimental confirmation of a theoretical prediction made by Castelnovo, Moessner and Sondhi nearly two years ago, and other recent experiments have added corroboration. The solid in question is an exotic rare-earth compound called dysprosium titanate.

Magnetic monopoles don't, as far as we know, exist in nature. There is no such thing as a "magnetic charge". An ordinary "bar magnet" behaves much the same way as an "electric dipole", that is, two electric charges placed close together, but if you break an electric dipole you get two electric charges ("monopoles") while if you break a bar magnet you get two bar magnets. This is because magnetism is not produced by static "magnetic charges" but is produced by moving electric charges (that is, currents). In an electromagnet, the the movement is of conducting electrons along a coiled conducting wire; in a bar magnet, the movement is the quantum-mechanical "angular momentum" of electrons, which is not very similar to classical "rotation" but has the same effect. In particular, electrons have an "intrinsic angular momentum" or "spin" that cannot be explained as an analogue of any classical quantity; but this spin, too, contributes to a magnetic dipole moment for each electron. Nuclei, too, can have their own magnetic dipole moments.

The recent experiments have not discovered a new phenomenon of nature -- the laws of physics don't need to be rewritten. What they have found is something that would behave exactly as a collection of magnetic monopoles would behave, if observed at not too fine a scale. The explanation is really quite simple. I myself worked on this system long ago: we published the basic physics of this compound in 1999 and, between then and 2008 (when Castelnovo and colleagues published their prediction), hundreds of papers on the subject have been published. I'm sure lots of those authors are kicking themselves for not having thought of it first.

These systems have a rather exotic geometry that has become widely known as the pyrochlore lattice, after an otherwise unrelated mineral. This is a lattice of tetrahedra (solids with four triangular faces) joined at their corners, such that two tetrahedra share a corner. Here is a picture (click on it for source page).

The dysprosium atoms (which are the main players here) sit at the red dots. Each carries a large magnetic moment arising mainly from electrons in the f shell. In free space, this magnetic moment could point everywhere, but in the presence of electrostatic fields of neighbouring atoms (in particular, the oxygen ions), it turns out that the preferred direction is along the lines joining the centres of the adjoining tetrahedra. Quantum-mechanically, the possible components of the angular momentum along this direction are discrete, and it turns out that the state where the angular momentum is entirely in this direction is about 200 kelvin lower in energy than other states. So at low temperatures (these experiments are performed at temperatures close to liquid helium, that is, less than ten kelvin), the atoms behave like magnets that point along the lines joining adjoining tetrahedral centres, in either direction. And because the angular momenta are relatively large, they can be treated as classical magnets. They interact primarily via the long-ranged "magnetostatic" interaction of two classical dipoles, but their nearest-neighbour interaction is somewhat reduced by a quantum-mechanical "superexchange" effect (but is still the dominant interaction).

And that is the only entry of quantum mechanics into this discussion. The physics henceforth is entirely classical and would have been understood in the 19th century, which is part of what makes it all so remarkable.

If the nearest-neighbour interaction were all, the "ground state" of these systems -- the lowest-energy state -- would be any state where each tetrahedron had two "magnets" (which we will call spins) pointing in and two pointing out. There is a macroscopic number of such states, leading to a non-zero entropy in the ground state (which is what we observed in 1999, and there is a remarkable analogy with the entropy of ice, which led to these systems being called "spin ice" -- but that is another story). Remarkably, the addition of long-ranged interactions does not seem to affect this picture much. Strictly speaking, the true ground state in the presence of long-ranged interactions is a fully-ordered state, unique apart from rotations. But experimental probes have only shown small signs of this form of ordering.

Since the three-dimensional lattice is hard to visualise, at this point let us consider instead a two-dimensional "square lattice", as shown below.

The constraint is that each shaded square must have two spins pointing in and two pointing out. This leads to results very much analogous to the pyrochlore case (in fact, this lattice, with all pairwise interactions within the shaded squares being of equal strength, is often called the "square pyrochlore" lattice). An example ground state satisfying this constraint is shown. Again, there is a large (macroscopic) number of such states.

Now how do we visualise excitations? The simplest excitation is a "spin flip" -- reversing the direction of a single arrow. This upsets the balance of arrows: one square has three arrows pointing in (with a net "north charge") and another has three arrows pointing out (with a net "south charge"). It is like placing a little magnet locally in an otherwise magnetically-neutral material.

But the key point is that the "north charge" and "south charge" can now migrate and separate, via a series of spin flips. Click on the above figure for an animation.

Viewed on a coarse scale, what this looks like is two magnetic "monopoles" that can move around freely. Castelnovo et al. examined the dynamics of this process theoretically, and now Bramwell et al. have measured it in the laboratory.

It is a simple idea, and a remarkable experimental observation. Whether it is just a curiosity or has further scientific or technological importance, only time will tell.

It should once again be emphasised that these "monopoles" are not elementary particles. People familiar with semiconductors will think of an analogy with "particle-hole excitations", where a electron gets excited and leaves behind a positively-charged "hole" that behaves like a particle in its own right. But that is a quantum-mechanical phenomenon which cannot be understood classically. The magnetic "monopoles" here, however, are purely a phenomenon of classical physics. If you could build a model with wires, springs and magnets, designed to mimic the geometry of the system and enforce the constraints of the allowed magnet directions, it should behave in exactly the same way. That in itself is of interest: I'm not aware of any other examples of "quasiparticles" or "particle-hole excitations" that can be described purely classically.

Tuesday, October 20, 2009

Happy birthday, Martin Gardner

Martin Gardner is 95, and the New York Times has a great article about the man and his new book.

For those who don't know the name, Gardner wrote the column "Mathematical Games" in Scientific American for a quarter of a century. The following quote from the NYT article summarises the impact of those columns perfectly: "Martin has turned thousands of children into mathematicians, and thousands of mathematicians into children."

I am not a mathematician, but perhaps close enough to be counted. I first read him as a child -- it was my mother's yellowing copy of Mathematical Puzzles and Diversions, a collection of Scientific American columns that began with the "Hexaflexagons" column mentioned in the NYT article above -- and was hooked. I collected several more of those volumes over the years.

Almost equally delightful has been his debunking, over the years, of various forms of pseudoscience. I say "almost" because I think he sometimes went a bit overboard, to the detriment of his argument. But perhaps I will leave that to another blog post.

And then there are gems like "The Annotated Alice" and "The Annotated Snark", which will teach you more about the hidden layers in the Lewis Carroll books than you ever believed existed...

Monday, October 12, 2009

Fouad al-Rabiah, Obama and peace

I linked the case of Fouad al-Rabiah in my last post, but didn't provide any details. I think it is worth talking about more. First, here is Andy Worthington's original article on the subject. It is a long and disturbing read. If you want a shorter and equally disturbing one, here is a new article by Andrew Sullivan in The Times.

From Sullivan's article:

We know that an American interrogator, operating under the authority of the US government, said the following words to a detainee: “There is nothing against you. But there is no innocent person here. So, you should confess to something so you can be charged and sentenced and serve your sentence and then go back to your family and country, because you will not leave this place innocent."

This man had worked at Kuwait Airways for 20 years; he was also a humanitarian volunteer in Afghanistan, who got caught up in the war and found his entry route (via Iran) blocked for exit. Trying to leave via Pakistan, he was caught by US troops and sent to Guantanamo. But even after initial interrogators concluded he was innocent, he was kept there and tortured -- because he couldn't be allowed to leave Guantanamo.

This happened mostly under the Bush administration, but the Obama administration continued to pursue the case despite knowing he was innocent. Says Sullivan (who was, and in some ways still is, one of Obama's strongest supporters):

Shockingly, although Barack Obama’s justice department knew the details of this case, it persisted with the Bush administration’s attempt to prosecute him. Last week, the Obama administration also backed a legal provision to withhold permanently all unreleased photographic evidence of torture in sites and prisons far away from Guantanamo and Abu Ghraib. And some of us believed we were voting for change.

And a President who defends the torture of a man known to be innocent is rewarded with the Nobel Peace Prize. Tom Lehrer once said that satire died when Henry Kissinger won the peace prize. But was it necessary to stab the dead body again?

Friday, October 09, 2009

Nobel thoughts

As I type this, the winners of the five original Nobel prizes have been named for this year; only the winner of the Bank of Sweden (Nobel memorial) prize in economics remains to be announced. It is usually the case that the science awards are noncontroversial, while the literature, peace and economics awards attract much discussion.

The Physiology and Medicine and the Chemistry awards are richly deserved this year. The Chemistry award has of course attracted lots of interest in India because of the origins of one of its recipients. But I found another point interesting: while there was originally no Nobel prize in "biology", these days there are, in practice, two in molecular biology: the Physiology and Medicine prize, and the Chemistry prize. This year's chemistry prize was awarded for improved understanding of the structure and functioning of the ribosome. Last year, it was awarded for discovering the green fluorescent protein and developing it as an important tool. In 2006, it was awarded for a better understanding of the transcription process; in 2004, for ubiquitin-mediated protein degradation; in 2003, for determining the structure of ion channels.

The Physics prize this year went not to fundamental discoveries, but to inventions: fibre optics and CCDs. But there is a spot of controversy in the award for Charles Kao: the "father of fibre optics" is widely held to be Narinder Singh Kapany, whose work preceded Kao's by over a decade. Kapany's work focussed on imaging, while Kao's Nobel award was specifically for developing fibres that could carry signals over 100 kilometres; both innovations were extremely significant, and both were technological rather than fundamental.

The literature prize went to Herta Mueller, whom I hadn't heard of. But this must be the hardest prize to give: there are more deserving candidates than prizes available, and unlike in the sciences, it doesn't make sense to share it among multiple candidates. I had never heard of Wisława Szymborska, the 1996 winner, until two weeks ago (well, I suppose I'd heard her name in 1996, but it did not stick in my memory); having been introduced to her poetry, I find it extremely interesting.

That leaves the peace prize, announced today. I personally think it is a laughable idea giving it to Barack Obama at this stage of his career, when he has absolutely no concrete achievements, has backtracked from many of his earlier promises, has had his Justice Department defend the torture of innocent people by the previous administration, is prolonging the war in Afghanistan, and is achieving little success in his domestic agenda.

Perhaps the future will vindicate this prize; but giving a prize for future achievements requires extraordinary clairvoyance.

It remains to be seen what surprises are sprung by the award committee for the Economics prize. We will know soon.

Tuesday, October 06, 2009

Non-Bollywood cinema from Maharashtra

Apparently not everything is song and dance. The Beeb has a feature on Marathi-language films that deal with the gritty issues of rural hardship and farmer suicides in Maharashtra, especially the Vidarbha region. Apparently locally-themed films, in local languages, exposing local problems, do have a market. We have all been reading about Vidarbha's problems (and similar problems in Andhra Pradesh and many other places) for a while now, though few of us have actually seen it for ourselves. Hopefully such films will raise awareness.

(I know, these days, suggesting that it is a good idea to support the local language wins you accusations from eminent scientist bloggers of being a Shiv Sena fellow-traveller. So be it.)

Sunday, October 04, 2009

Dizzy and Louis

Here are two of the three most influential jazz trumpeters ever: Dizzy Gillespie and Louis Armstrong.

I don't know who the pianist and others are, what the year is (certainly post-1953 since Dizzy's trumpet is bent) and whether these two made any other recordings together. But this pairing is particularly interesting since Dizzy, with Charlie Parker, was the founder of bebop, and Louis never embraced that style of jazz, with its "weird" chords and complicated melodies and rhythms. By 1953, however, the debate was over: bebop was mainstream jazz and Louis had become more a popular entertainer than a cutting-edge jazz musician. This song is popular entertainment, and good fun.

The third great jazz trumpeter was, of course, Miles Davis. Miles played with Dizzy in his early days, but I don't know whether he ever played with Louis.

Thursday, October 01, 2009

Famous people who support a child-rapist

So Bernard-Henri Levy, Salman Rushdie, Milan Kundera, Mike Nichols, Isabelle Adjani, William Shawcross, Pedro Almodovar, Martin Scorsese, Terry Gilliam, Harvey Weinstein, Tilda Swinton, Monica Bellucci and dozens of other celebrities have attached their names to petitions deploring the recent arrest of director Roman Polanski in Switzerland. Polanski was arrested because he plied a 13-year-old with alcohol and a drug (Quaalone), made her strip, and raped her. He did this in 1977, pled guilty to a lesser charge (sex with a minor), and before he could be sentenced, fled the USA in 1978, never to return.

I knew little about Polanski before recent events: I had seen one film (Chinatown) which was brilliant, and disturbing; and I knew his wife had been murdered by the Manson cult. I now know that he escaped the Nazis at seven, and his mother died in Auschwitz. He had claimed that the encounter with the 13-year-old was consensual. Though that doesn't excuse it, I had not thought much about it one way or another, even when he was in the news in 2005 for winning an Oscar.

So when news of the arrest broke, my reaction was roughly: "What he did was wrong and criminal, but it was 30 years ago, and he'd had a very disturbed life, from fleeing the Nazis as a 7-year-old to the murder of his pregnant wife by the Manson cult... Perhaps we should be asking why the French didn't extradite him back in 1978 when his crime was fresh. They had no treaty obligations but they could certainly decide on a case-by-case basis." (In fact that's what I posted in a comment on a facebook thread.)

Since then, despite the victim's wishes, the details of the incident have become widely known and her testimony to the jury is available on the internet. It is indeed stomach-churning. It was not "statutory rape". It was rape, committed on a girl who had been drugged and fed alcohol but was still capable of repeatedly asking him to stop, and even feigning asthma in an attempt to make him stop and let her leave. If she had been over 18, it would still have been rape. But the "statutory rape" charge was easier to prove: there was evidence of sexual contact, and there was no doubt about her age. So Polanski got away with a plea bargain. Then when he had doubts about the judge's intentions of honouring the bargain, he skipped.

Was he remorseful? Not in 1979: take a look at this excerpt of an interview that year with Martin Amis. I don't know of any expression of remorse since. He seems not only to think he had done nothing wrong, but to have persuaded many well-known people that he was the victim in the matter.

So my opinion has hardened now. Let him stay in jail -- Swiss or American -- for life.

The bulk of the US-based opinion that I have been reading seems to agree on that. In fact I have seen no coherent defence of letting Polanski go. It seems to come down to his tragic past, the length of elapsed time since the crime, and the victim's views. But none of these should be relevant. Millions of people suffer personal tragedies without becoming child rapists. He was free for 30 years because he was a fugitive, not because law enforcement was lax. And violent crimes are prosecuted regardless of the victim's wishes (in many cases, though probably not in this one, the victim is too scared to talk).

Even in France, according to the NYT, the public is not favourably disposed to Polanski, and the elite are having second thoughts about supporting him.

But I wonder about all those eminent signatories of petitions. Many of them knew Polanski and surely knew something about the case before they signed; but if they didn't when they signed, they certainly would have since. Do they still support letting someone who drugged and raped a child go free?

Sunday, September 27, 2009

Theoidiocy and other matters

"How religion poisons everything" was the subtitle of a recent Christopher Hitchens book on God. He could equally have said: "How religion turns everyone into idiots." Case in point: Andrew Sullivan, who is otherwise one of the most intelligent and lucid commentators on the blogosphere (and the MSM) today.

It seems to have started here. It continues here, here and here. Click only if you're a masochist -- or if the following excerpt (from here) makes any sense to you:

Yes, resilience is obviously built into our genetics, but my point was the unique ability to transcend suffering, not just endure it. That requires a mind that renders humans uniquely self-conscious, which has led to inquiries into ultimate meaning that, so far as we can tell, no animal experiences in the same way. Many survive suffering - most, in fact. The question is whether it is overcome, rather than endured. For that, something beyond mere physical processes are necessary. Which is where religion has its place.

On a related note, here's an entertaining guide to homoeopathy (thanks to Sunil). Homoeopathy has much in common with religion: rational arguments don't work with true believers, and in particular, it is impossible to answer the claim "but it worked for me!"

There are two caveats I would put, however. First, homoeopathy (and religion) may actually work if you're a believer. The best explanation of homoeopathy I've heard is the following (I previously posted it as a comment here): A colleague of mine claims the following is, roughly, an actual conversation he had with an actual practising (and believing) homoeopath. My friend expressed his skepticism on scientific grounds -- the dilution is so extreme that hardly a molecule or two would be expected to remain, if that. The homoeopath said, "Have you been to a homeopathic doctor?" My friend said yes. "What happened?" "The doctor asked lots of questions and then prescribed me a medicine." "How long did the questioning take?" "It took about 20 minutes and was very detailed." And, according to the homoeopath: "It is the 20 minutes of questioning that is the therapeutic part of homoeopathy. The pill is a placebo. It is just a sugar pill."

Now, placebos can have real effects (Skepdic has a good discussion), so it would not surprise me that homoeopathy (or praying) could help you with some conditions, if you believed in the first place that it could.

The second caveat is that not everything that passes for homoeopathy need actually be homoeopathic (that is, diluted according to Hahnemann's prescriptions). This is especially true in India, but there was also a recent case of a "homeopathic" cold medicine in the US that turned out to contain non-homoeopathic quantities of zinc, with a detrimental effect on the patients' sense of smell. "Alternative" therapies are poorly regulated, all over the world. Caveat emptor.

Friday, September 25, 2009

Why I dislike the BBC's reporting

Nearly every article that the BBC has written about Chandrayaan I that I have seen so far ends with these lines:

But the Indian government's space efforts have not been welcomed by all.
Some critics regard the space programme as a waste of resources in a country where millions still lack basic services.

For example: this article today, and this one, this one and this one earlier.

It is not just that they are repeating the same sentiment again and again: it is precisely the same text, inserted as boilerplate at the end of everything they have ever written about Chandrayaan -- going back to at least October 2008 (when the mission was launched), and perhaps earlier!

And precisely what is the point of such text? Of course "some critics" regard it as a waste of money. "Some critics" think the Apollo landings were faked. "Some critics" believe the earth is flat. In a country of a billion people, and a world of eight billion people, you will always find "some critics" to say anything. Who are those critics? Why not name them, just to let the reader judge their credibility?

Even that should not be too hard: I am sure there are some very respectable people who think Chandrayaan is a waste of money, and will be willing to be quoted as saying so. But the BBC cannot be bothered to go out and look for them. Much easier to just stick this boilerplate at the end of every damn article they write on the subject.

No doubt they think it makes them look "balanced".

Thursday, September 24, 2009

How not to run an online bookstore

The point having been made, and belatedly responded to, this post and its comments are deleted. I wish the bookstore well.

Friday, August 21, 2009

Mercy droppeth from heaven

Abdelbaset al-Megrahi, convicted of the bombing of Pan-Am flight 103 over Lockerbie in 1985 and in a Scottish jail since 2001, was released by Scotland yesterday on compassionate grounds: he is dying of cancer and has three months to live. Megrahi himself has always claimed to be innocent.

The relatives of US victims, as quoted in the media, are all furious. The relatives of the UK victims, on the other hand, are mostly supportive of the release, and several in fact remain unconvinced of Megrahi's guild.

The reaction of the US establishment has been equally furious, from the President down, but they were powerless.

Sample quote: "There is simply no justification for releasing this convicted terrorist whose actions took the lives of 270 individuals." (US attorney general Eric Holder)

Well, what about another terrorist, Luis Posada Carriles, against whom there is considerably stronger evidence that he masterminded the bombing of Cubana flight 455 in 1976, as well as numerous other terror attacks? Oh, but he was fighting the Castro regime in Cuba. He must be one of the good guys.