Archive for November, 2008

On First Looking into Chapman’s Homer

Posted in Poetry, The Universe and Stuff with tags , , on November 19, 2008 by telescoper

As a present to those who appear disgruntled by my comments about exoplanets here and there, this is from John Keats:

 

Much have I travell’d in the realms of gold,
    And many goodly states and kingdoms seen;
    Round many western islands have I been
Which bards in fealty to Apollo hold.
Oft of one wide expanse had I been told
    That deep-brow’d Homer ruled as his demesne;
    Yet did I never breathe its pure serene
Till I heard Chapman speak out loud and bold:
Then felt I like some watcher of the skies
    When a new planet swims into his ken;
Or like stout Cortez when with eagle eyes
    He star’d at the Pacific–and all his men
Look’d at each other with a wild surmise–
    Silent, upon a peak in Darien.
 

This famous sonnet was written in October 1816 and is considered the highlight of Keats’s first volume of poetry. It was originally a gift for his friend, Charles Cowden Clarke. The two men had spent an evening reading George Chapman’s superb 17th century translation of the Iliad and Odyssey.

Please note lines 9 and 10. I’m sure they capture the excitement of discovery although Keats probably wasn’t using the correct IAU nomenclature. I’m not sure about the bit about being “silent” either.

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Science and Stamp Collecting

Posted in Books, Talks and Reviews, The Universe and Stuff with tags , , on November 18, 2008 by telescoper

Musing over the comments posted on my (slightly ironic) blog item about exoplanetary ennui, I remembered a piece I wrote for the Times Literary Supplement last summer so I dusted it off, chopped it up, and updated it for presentation here because it expands a bit on the earlier contribution.

If the Sun were the size of a golf ball, then the Earth would be a speck of dust a few metres from it and the nearest star would be hundreds of kilometres away. And this is what it is like in the relatively crowded environment of the Milky Way. The unimaginable scale of our Universe means that astronomy has never really become an experimental science, but has largely remained an observational one, having more in common with, say, archaeology than chemistry or other laboratory-based disciplines. Consequently, even though it is perhaps the oldest science, it is also in some respects the least mature. The absence of the traditional interplay between theory and experiment, the inability to perform repeated experiments under slightly different conditions, and the sheer difficulty of measuring anything at all have stunted its development compared to younger fields. For this reason, one often finds in astronomy certain tendencies that other subjects have largely grown out of, such as an unhealthy mania for classification and nomenclature.

Taxonomy has its place within the scientific method: modern chemistry owes much to Dmitri Mendeleev‘s periodic table; botany could not have progressed without Linnaeus; and the theory of evolution was founded on Charles Darwin‘s painstaking studies on the Galapagos Islands. But arranging things in groups and giving them names does not in itself constitute scientific progress, no matter how systematically it is done. The great experimental physicist Ernest (Lord) Rutherford dismissed this kind of activity as not science but “stamp collecting”.

This brings us to the grand debate that took place in Prague in the summer of 2006 under the auspices of the International Astronomical Union. One of the problems before the IAU’s 26th General Assembly was what to do about the fact that recent investigations have revealed the presence of a number of objects orbiting the Sun that are ostensibly at least as worthy of the name “planet” as Pluto, which in our current textbooks is the ninth one out. Obviously, which objects should be called planets depends on how you define what a planet is. The solar system contains objects of all shapes and sizes, from tiny asteroids to immense gas giants such as Jupiter and Saturn. Where should one draw the line? The original proposal was to increase the number of planets to twelve by admitting some lowly new members to the club, but in the end the IAU decided to demote Pluto to the status of a “dwarf” planet thus restricting the number of true planets to eight. This was a controversial decision, at least in the United States, because the vital vote was taken on the last day of the meeting when most of the US delegates had to take flights home. Pluto was discovered by an American, Clyde Tombaugh, in 1930, so the decision deprived the nation of its only planet-discoverer.

The “no” decision hinged on the adoption of three criteria: that the object be round, i.e. have a shape determined by internal gravitational forces; that it should have cleared its own orbit of debris; and that it should be orbiting our own star, the Sun. None of these has any special scientific value; the resulting decision was therefore pretty arbitrary. Moreover, deep-space observations have led to the discovery of literally hundreds of planetlike objects orbiting other stars. These exoplanets offer much greater prospects for scientific progress into the general theory of planet formation than the few objects that happen to have formed in our particular vicinity, so why are they excluded from the definition? In any case, what have we learned scientifically from the new nomenclature? Pluto is still the same object that it was before August 2006, and astronomers still don’t understand what one can infer from its own particular properties about the general process of planet formation.

So is Pluto a planet?

Who cares? In this case there really is nothing in a name. When I was asked this question on the telephone by a reporter I gave precisely that answer and he was shocked. I’m sure he thought that all that astronomers do is look at things and give them names. There are some that do that, of course, but most of us prefer doing proper science.

In the field of exoplanet research we are seeing real signs of maturity, although current studies are still firmly rooted in the “discovery” and “classificatuion” stage. Witness last weeks press interest in the first directly imaged exoplanets. I am well aware of the immense potential that those pictures have for stimulating interest in science, but there is still a long way to go before this field reaches its prime. That probably makes it an excellent area for young scientists to work in. But ultimately this youthful exuberance should give way to something a bit more serious, which is to go beyond what these discoveries are in themselves and ask what deeper questions they might answer.

One can see many other parallels in the history of astronomy, such as the discovery of quasars in the late 1950s. The first few of these must have generated a huge amount of excitement because they were not at all understood. Within a few years hundreds had been detected by radio observations but their nature remained unknown. The subsequent identification of redshifted hydrogen emission lines in the spectra of these objects led to them eventually being identified as very distant extragalactic sources of immense intrinsic power. By the 1980s quasars were identified as a particular type of active galaxy and placed within a general classification scheme that also involved blazars, Seyfert galaxies, and so on. Nowadays we have samples of tens of thousands of quasar spectra and the interest evolves around how the activity in their nucleus relates to the process of galaxy formation in an expanding Universe and how we can use these objects to map out the large-scale distribution of matter. To an outsider these tasks may seem less glamorous that the early days of quasar research, but that’s what science is like.

At the extreme end of the distance scale of astronomical investigation lies my own field of cosmology, the scientific study of the Universe as a whole. The scale of the solar system is challenging enough, but the cosmos is really big. Until recently, cosmology was so lacking in reliable observational input that it was thought of as a flaky offshoot of astronomy, more a branch of metaphysics than a proper scientific discipline, a paradise for theoreticians whose wildest speculations stood no chance of ever being tested with real measurements. Over the past twenty years or so, however, staggering advances in astronomical instrumentation have allowed astronomers to probe the darkest depths of space, capturing light that has travelled for almost 14 billion years on its way towards us. Theories are now so tightly constrained by these observations that there is very little room for manoeuvre. From this interplay between conjecture and refutation has emerged a cosmological framework that accounts, at least in a broad-brush sense, for how the Universe is constructed and how it is evolving.

There are some important gaps, including some puzzling anomalies, and the precise nature of many of its constituents is yet to be understood, but the establishment of the “concordance model” is a sign that cosmology really has come of age.

The Facebook of the Future

Posted in Uncategorized on November 17, 2008 by telescoper

If you’re not on facebook this won’t make any sense!

But thanks to Ed Gomez for sending it.

Lost in the City

Posted in Biographical, Poetry with tags , , on November 17, 2008 by telescoper

The second Friday of the month is the day of the regular “open” meeting of the Royal Astronomical Society (at 4pm) preceded by parallel discussion meetings on topics that vary from month to month. This month one of the sessions was organized in memory of Bernard Pagel, who died last year and whom I knew a little, so I decided to go to that.

I met Bernard Pagel when I started my DPhil at Sussex University in 1985. He taught one of the courses on the MSc Astronomy and we research students were required to attend his lectures. I have to say he wasn’t the best lecturer I’ve ever had; he always seemed unable to look at the class, which is a trait I find quite disconcerting. But he did reveal a wonderfully wicked sense of humour. When a visiting seminar speaker arrived late and after the seminar explained he had dozed off on the train and missed his stop, Bernard suggested that he must have been reading through his transparencies.

I left Sussex to move to London around about the time Bernard retired from his position at Sussex but he immediately took up a chair at NORDITA in Copenhagen where age restrictions were somewhat looser. I had been working for a while with Bernard Jones in Copenhagen so I next ran into Bernard Pagel when I visited there. I still found him a strange and rather distant man, but as often happens the ice was broken when a group of staff, students and visitors went to a nice concert in the Tivoli Concert Hall. If I remember correctly it was a Mozart violin concerto. Afterwards, Bernard let his guard down and talked in a much more relaxed way than I had known before and we became quite friendly thereafter. He was in fact a man with very wide interests outside his own sphere of eminence in astrophysical spectroscopy.

After the meeting was over, I went once more to the Athenaeum for dinner with the RAS Club. I was quite surprised when, after the meal, it was announced that I had written on my blog about my previous dinner there. I’m not convinced that everyone there knew what a blog actually is but maybe some of them have found their way here…

Although I got back home to Cardiff in good time on the last occasion I dined at the Club, I had already decided to go to the opera on Saturday night so didn’t have to rush off to make the last train. Walking back to Bloomsbury where I was staying on Friday and Saturday I suddenly realized that it as almost exactly ten years since I moved out of London to Nottingham. In fact I bought my house in Beeston on 13th November 1998 and commuted back to London for about a month, as my position in Nottingham didn’t start until 1st January 1999.

On Saturday morning I decided to behave like a tourist so I first went to the British Museum. I intended to see the new Babylon exhibition, but by the time I got there after a leisurely breakfast it had sold out for the day so I had to content myself with the permanent exhibits. I don’t think I ever went to the British Museum in all the time I lived in London, so it was interesting although I got completely lost.

I did get to see the Elgin Marbles but I still don’t know how to play. I also ended up in a room full of mummies, which is something I find quite distasteful. Although the mortal remains are incredibly old, they are still human bodies and I don’t like the way they are stuck in cases for people to gawp at. Call me sentimental but I think these should be returned to Egypt and laid to rest with some sort of dignity. I also think the Elgin Marbles should go back to Greece, but for different reasons. If we hand them back, we might actually get some votes in the Eurovision song contest for a change.

The rest of the day I wandered around a few of the dozens of bookshops that clutter the area between Charing Cross Road and Covent Garden, feeling all the time like a complete stranger to the city. So much has changed that it’s nearly impossible for me to believe that I ever actually lived there at all. In one shop I picked up a (very expensive) old book of poems by Shelley and found the following lines (written about Naples rather than London):

I stood within the city disinterred;
And heard the autumnal leaves like footfalls
Of spirits passing through the streets
;

I didn’t buy the book. My mood wasn’t helped by the gloomy light. Although it was quite warm for November, there was a curious purple tinge to the late afternoon which I found a bit unsettling.

On my way back I revisited an old tradition of mine of peering in through the window of one of the electrical goods shops on Tottenham Court Road to check the football results. When I was living in London I was usually out most of the day on weekends somewhere in the West End, so that was the only way to keep apprised of developments. Nowadays I don’t go out as much as I used to, so I find quieter ways of filling the gap between the end of Final Score and the start of Match of the Day that seems to me to symbolize middle age.

Then it was time to get to the Coliseum for the opera followed by supper with Joao and Kim at Belgo‘s where our table, ironically, was next to that of a dozen very raucous girls from Cardiff in town for a birthday celebration.

Boris Godunov

Posted in Music, Opera with tags , , on November 16, 2008 by telescoper

The production of Boris Godunov now playing at the Coliseum has had mixed reviews, largely because of the performance of Peter Rose as the tormented Tsar. I usually don’t find myself agreeing very much with what music critics say and I had been looking forward to English National Opera’s take on Mussorgsky‘s opera for some time. My trip to London this weekend gave me an excuse to see it for myself and form my own opinion.

The opera is based on a play by Pushkin which tells a story based on the historical figure who ruled Russian from 1598 until 1605. In the play, Boris Godunov only becomes Tsar after murdering the son Dmitriy of the previous Tsar, Ivan IV (“the terrible”) and is plagued with ghostly visions of the dead boy. His guilt drives him into madness and eventually to death, although in this production of the opera the audience doesn’t see how he dies.

In Tim Albery’s staging, the action is shifted forwards in time to pre-revolutionary Russia, with the costumes and designed hinting a time round about 1900. The production uses Mussorgsky’s original version of the opera which is not divided into acts, but spread across seven scenes (lasting about two hours and fifteen minutes) which are performed without an interval. The limitations of the minimalistic set are more than made up for by wonderful use of lighting at one point bathes the stage in gold and at another turns it into a chill Moscow streetscape.

The update of the period allows Albery to give this production a dimension that is entirely new. The ENO chorus deliberately conjures up the idea that revolution might be imminent. At several points the chorus appear in huge numbers on stage to be held at bay by only a few soldiers with rifles. This is a very effective device, especially since the chorus is in such good voice. The passion and attack of the mob is unleashed only sparingly but when it is it is very effective in providing a vocal backdrop to the developing plot.

Mussorgky’s music for Boris Godunov is romantic, richly textured, even lush in places and full of wonderful melodies. As you can imagine from the storyline it’s also rather dark and sombre, much of it in the basso profundo region.  That also goes for the singers: there is no conventional tenor role, though basses and baritones proliferate among the cast.

The one thing the music doesn’t have is a great deal of dramatic contrast, which I think must be why it appears to be difficult for the principals to bring their characters fully to life. It’s almost as if the opulence of the score holds them back. The other difficulty is that there are so many characters with not much time for the audience to get to know their personalities. Although they all sang well, I still felt they were strangers at the end. The one really outstanding performance in there was Brindley Sherratt (as the “chronicler” an old hermit called Pimen) who gave his character real depth and pathos.

And as for Boris himself? Was Boris good enough? I think Peter Rose actually sang very well and the limitations of his acting have been overemphasized by the critics. There aren’t that many opera singers who can act well, and he is certainly far from the worst I’ve seen. His voice is relatively light for a bass and he didn’t have the bottomless range that is really needed to get across the angst of the remorseful murderer.  In the scenes with Pimen (another bass) he generally suffered by comparison with his opposite number’s much richer sounds at the  low end of the register.

So, not for the first time, I am glad I ignored the critics and went ahead and bought my tickets for this. As it turned out I was sitting quite close to John Nettles (who plays Tom Barnaby in Midsomer Murders) and Jane Wymark (who plays his wife, Joyce,  in the same series). I half-expected there to be a murder during the performance.

When you’ve seen one planet….

Posted in The Universe and Stuff with tags on November 14, 2008 by telescoper

Rumours have been circulating for several days and now we have confirmation. The most exciting news in the history of the Universe! Planets exist

Well, actually, we knew that. We live on one. And anyway, the International Astronomical Union recently stipulated that planets could only be things orbiting the Sun.  Don’t ask me why. So the new things have to be called exoplanets. And over 300 hundred of these were known before today anyway.  A rose by any other name would smell as sweet, so we won’t worry about the taxonomy. But what’s the big deal?

2008111311What is different about the most recent observations, reported in today’s issue of Science, is that they involve direct detection (i.e. imaging) of exoplanets, not indirect inferences made by studying stellar wobbles. An example is shown here: the three red dots are the exoplanetary objects orbiting around the star HR 8799.

 Quite interesting.

But is every new detection of an exoplanet going to be hyped like this from now until doomsday? Or until the public gets thoroughly bored?  Might it not be better to wait until there’s a sufficiently large and unbiased sample that exoplaneticists can quit their stamp collecting and start doing some real science?

At least in cosmology nobody ever exaggerates the importance of their discoveries.

*cough*

Cerebral Asymmetry: is it all in the Mind?

Posted in Bad Statistics, Science Politics with tags , , on November 12, 2008 by telescoper

After blogging a few days ago about the possibility that our entire Universe might be asymmetric, I found out today that a short comment of mine about a completely different form of asymmetry has been published in the Proceedings of the National Academy of Sciences of New York.

Earlier this summer a paper by Ivanka Savic & Per Lindstrom concerning gender and sexuality differences in brain structure received widespread press coverage and the odd blog comment. They had analysed a group of 90 volunteers divided into four classes based on gender and sexual orientation: male heterosexual, male homosexual, female heterosexual and female homosexual.

They studied the brain structure of these volunteers using Magnetic Resonance Imaging and used their data to look for differences between the different classes. In particular they measured the asymmetry between left and right hemispheres for their samples. The right side of the brain for heterosexual men was found to be typically about 2% larger than the left; homosexual women also had an asymmetry, but slightly smaller than this at about 1%. Gay men and heterosexual women showed no discernible cerebral asymmetry. These claims are obviously very interesting and potentially important if they turn out to be true. It is in the nature of the scientific method that such results should be subjected to rigorous scrutiny in order to check their credibility.

As someone who knows nothing about neurobiology but one or two things about statistics, I dug out the research paper by Savic & Lindstrom and looked at the analysis it presents. I very quickly began to suspect there might be a problem. For each volunteer, the authors obtain measurements of the left and right cerebral volumes (call these L and R respectively). Each pair of measurements is then combined to form an asymmetry index (AI) as (L-R)/(L+R). There is then a set of values for AI, one for each volunteer. The claim is that these are systematically different for the different gender and orientation groups, based on a battery of tests including Analysis of Variance (ANOVA) and t-tests based on sample means.

Of course, it would be better to do this using a consistent, Bayesian, approach because this would make explicit the dependence of the results on an underlying model of the data. Sadly, the statistical methodology available off-the-shelf is of inferior frequentist type and this is what researchers tend to do when they don’t really know what they’re doing. They also don’t bother to read the health warnings that state the assumptions behind the results.

The problem in this case is that the tests done by Savic & Lindstrom all depend on the quantity being analysed (AI) having a normal (Gaussian) distribution. This is very often a reasonable hypothesis for biometric data, but unfortunately in this case the construction of the asymmetry index is such that it is expected to have a very non-Gaussian shape as is commonly the case for distributions of variables formed as ratios. In fact, the ratio of two normal variates has a peculiar distribution with very long tails. Many statistical analyses appeal to the Central Limit Theorem to justify the assumption of normality, but distributions with very long tails (such as the Cauchy distribution) violate the conditions of this Theorem, namely that the distribution must have finite variance. The asymmetry index is probably therefore an inappropriate choice of variable for the tests that Savic & Lindstrom perform. In particular the significance levels (or p-values) quoted in their paper are very low (of order 0.0008, for example, in the ANOVA test) which is surprising for such small samples. These probabilities are obtained by assuming the observations have Gaussian statistics, and they would be much lower for a distribution with longer tails.

Being a friendly chap I emailed Dr Savic drawing this problem to her attention and asking if she knew about this problem and the possible implications it might have for the analysis she had presented. If not, I offered to do an independent (private) check on the data to see how reliable the claimed statistical results actually were. I never received a reply.

Worried that the world might be jumping to all kinds of far-reaching conclusions about gay genes based on these questionable statistics, I wrote instead to the editor of the Journal Proceedings of the National Academy of Sciences of New York, Randy Schekman, who suggested I submit a written comment to the Journal. I did, it was accepted by the editorial committee, and it came out in the 11th November Issue. What I didn’t realise was that Savic & Lindstrom had actually prepared a reply and that this was published alongside my comment. I find it strange that I wasn’t told about this before publication but that aside, it is in principle quite reasonable to let the authors respond to criticisms like mine. Their response reveals that they completely missed the point of the danger of long-tailed distributions I mentioned above. They state that “when the sample size n is big the sampling distribution of the mean becomes approximately normal regardless of the distribution of the original variable“. Not if the distribution of the original variable has such a long tail it doesn’t! In fact, if the observations have a Cauchy distribution then so does the sampling distribution of the mean, whatever the size of sample. You can find this caveat spelled out in many places, including here. Savic & Lindstrom seem oblivous to this pitfall, even after I specifically pointed it out to them.

They also claim that a group size of n=30 is sufficient to be confident that the central limit theorem holds. A pity, then, that none of their groups is of that size. The overall sample is 90, but it is broken down into two groups of 20 and two of 25.

cerebral-asymmetry

(c) 2008 Academy of Sciences of New York

They also say that the measured AI distribution is actually normal anyway and give a plot (above). This shows all the AI values binned into one histogram. Since they don’t give any quantitative measures of goodness of fit, it’s hard to tell whether this has a normal distribution or not. One can, however, easily identify a group of five or six individuals that seem to form a separate group with larger AI values (the small peak to the right of the large peak). Since they don’t give histograms broken down by group it is impossible to be sure, but I would hazard a guess that these few individuals might be responsible for the entire result; remember that the entire sample has n only of 90.

More alarmingly, Savic & Lindstrom state in their reply that “one outlier” is omitted from this graph. Really? On what basis was the outlier rejected? The existence of outliers could be evidence of exactly the sort of problem I am worried about! Unless there was a known mistake in the measurement, this outlier should never have been omitted. They claim that the “recalculation of the data excluding this outlier does not change the results”. It find it difficult to believe that the removal of an outlier from such a small sample could not change the p-values!

In my note I made a few constructive suggestions as to how the difficulty might be circumvented, by Savic & Bergstrom have not followed any of them. Instead they report (without details of the p-values) having done some alternative, non-parametric, tests. These are all very well, but they don’t add very much if their p-values also assume Gaussian statistics. A better way to do this sort of thing robustly would be using Monte Carlo simulations.

The bottom line is that after this exchange of comments we haven’t really got anywhere and I still don’t know if the result is significant. I don’t really think it’s useful to go backwards and forwards through the journal, so I’ve emailed Dr Savic again asking for access to the numbers so I can check the statistics privately. In astronomy it is quite normal for people to make their data sets publically available, but that doesn’t seem to be the case in neurobiology. I’m not hopeful that they will reply, especially since they branded my comments “harsh” and “inappropriate”. Scientists should know how to take constructive criticism.

Their conclusion may eventually turn out to be right, but the analysis done so far is certainly not robust and it needs further checking. In the meantime I don’t just have doubts about the claimed significance of this specific result, which merely serves to illustrate the extremely poor level of statistical understanding displayed by large numbers of professional researchers. This was one of the things I wrote about in my book From Cosmos to Chaos. I’m very confident that a large fraction of claimed results in biosciences are based on bogus analyses.

I’ve long thought that scientific journals that deal with subjects like this should employ panels of statisticians to do the analysis independently of the authors and also that publication of the paper should require publication of the raw data. Science advances when results are subject to open criticism and independent analysis. I sincerely hope that Savic & Lindstrom will release their data in order for their conclusions to be checked in this way.

It’s no wonder that there is so much public distrust of science, when such important claims are rushed into the public domain without proper scrutiny.