Monday, December 10, 2012

TITAN and the Exascale - difficult power?

The Titan supercomputer here at ORNL was recently unveiled as the world's fastest (for now) and led to several of us talking on various news outlets such as the Washington Post, BBC, NPR and CNN. Certainly, us "apps guys"  congratulate the hardies on the big iron they have managed to design and construct, and as we move towards the exascale there are exciting possibilities as to what theoretically one could do with such machines. But, now, more than ever, it has become clear that the promise of these supercomputers will remain unrealized without concerted and sustained methodological and software development. As far as applications in the biological and soft matter sciences are concerned, little emphasis has been put on these aspects. Although, thanks largely to our own, unfunded efforts, we are just about able to scale on TITAN, doing better won't happen without new methods being developed by teams of theoreticians over several years. It makes little sense to me to invest billions of dollars over a decade or so in these machines but virtually nothing in what is needed to make them work well, does it? 

Friday, December 7, 2012

Financing College Athletics: a 2 billion dollar subsidy

(Photo: Daily Beacon)

Today the University of Tennessee announced the hiring of Buster Jones from U. Cincinnati as our new football coach, dumping a financial burden onto the university on top of the payouts to the two other recently-fired coaches,  Phillip Fulmer and Derek Dooley. A consequence of this trigger-happy firing behavior is that the Athletics Department will forgo its usual donations to the university academics for three years, and this has led to significant criticism, including from ex Faculty Senate president Louis Gross recently on local TV.

Now, as a relative outsider, i.e. having been parachuted in from Europe, maybe I have a fresh perspective on things.  In my opinion the world of big-money college sports should be completely  financially independent from the university. I stress here the "big money" aspect, because having a variety of sports accessible to students at a university is generally beneficial, and part of student education. Financing track and field, football fields (not stadia), a swimming pool, baseball diamonds, changing facilities etc is certainly part and parcel of the standard university experience.

But subsidizing multimillion-dollar big-money football with money ostensibly given to finance the education of the kids of the state is an unjustifiable diversion.  Now, NCAA figures list UT as one of the few colleges whose athletic department actually does not draw much upon university finances. This may be the case, although it is subject to argument. For example, the rest of us pay overhead on income generated for UT whereas the athletics department does not. But where there appears to be little room for doubt is that, on average, athletic spending nationwide is solidly in the red. The USA Today database of 218 Division I public schools  for 2009-2010 documents a total of $6.2 billion spent on college sport of which $2 billion came from subsidies from the schools, and this in a time of general dire cuts and increased tuition fees. 

Now, I'm not saying that  the taxpayers of a state don't have the right to subsidize their favorite college sports teams if they wish. But it should be done in a transparent way.  Formally separating the finances of the big-money sports programs from the minor sports and the academics would be a sensible way of achieving this. 

Tuesday, November 6, 2012

L'Aquila Earthquake Scientists - Rightly Convicted?

The opprobrium over the conviction and jailing of the L'Aquila earthquake scientists seems to have been nearly universal in the scientific community, which seems to be convinced that science itself has been put on the dock. However, a friend who is on the science faculty at L'Aquila opines that the convictions were RIGHT, as they were due to failure to communicate risk, rather than the failure of science. Apparently the Risk Committee met, then left without communicating anything themselves (they left it to a non-scientist, who apparently told people to go and drink some wine). While Italy has a proud tradition of ignoring science, this case does not seem to cleanly fit into that category and I think the AAAS, Nature etc maybe rushed too quickly in their condemnations of the judgement.  That doesn't mean I'm in favor of the severity, though. The jail sentences certainly smack of scapegoating  and the general public may not be able to tell the difference between condemning communication failure and condemning science itself.

NOT a voter.

Jeremy Smith's friends on Facebook are all flagging themselves as "I am a voter".
So here's my Facebook response:

"Jeremy Smith is NOT a voter, and has not been for 28 years. The reason he has not voted is that Jeremy has not been allowed to become a citizen anywhere other than the UK despite having spent ten years in one country (France), eight in the second (Germany) and now ten in the third (USA).  During that time he paid a lot of taxes to governments that did not represent him.  In contrast, he has paid nothing to the UK government, whose policies he had the right to vote upon even for fifteen years after having left the country, until the ultimate, global revocation of his right to suffrage.

Ten years must be considered to be rather long for a  'visit' and so Jeremy hesitates to think of himself as a 'visitor'.  Rather,  Jeremy thinks that if somebody lives and pays taxes in a country then they should vote there, and not according to some arbitrary definition of citizenship."

Monday, October 29, 2012

BBC Clip - clarification required.

Today a BBC clip on the Titan supercomputer just appeared, in which various people talk about the computer and I mention some possible applications, mentioning goals to 'save the environment, cure all known diseases and solve the world's energy problems'.  However, the clip as edited may give some people the impression that we will actually be able to solve all these great societal problems with Titan! However, of course, all the computer is likely to be able to do is to make contributions to these fields. For example, theoretically, it would be able to screen millions of compounds on hundreds of protein targets, and that might help us design better, safer drugs. Also, it may be able to perform new simulations useful in understanding biomass pretreatment and processes in the environment.  Also, I mention in the clip atomic detail models of the living cell, which may be 'theoretically' become possible with exascale supercomputing, but only on the microsecond simulation timescale,  such that we need also to pursue ensemble based approaches on smaller systems that can extend simulation timescales. What was not mentioned in the clip, but was said to the reporter,  was the significant, fundamental  algorithmic and methodological problems to be overcome  in order to exploit the full power of these new machines. There is little support for tackling these challenges, at least from my perspective, and primarily for this reason the medium-term usefulness of supercomputing in the biological and medical sciences seems rather uncertain at this point.

Friday, October 19, 2012

Baskervilles Blues Band circa 1996

Jeremy, Marty, Bill, Philippe, Jean-Michel.

Check this smooth number out.

Monday, October 1, 2012

Why I'm Against Affirmative Action

I just served on an National Science Foundation  panel, in which  'broadening the participation of underrepresented groups' is a priority when choosing which proposals to fund, then came back to Europe where the German Bundesrat passed a measure requiring 40% of executive boards to be female. This made me think further about the general principle of affirmative action, and especially in science. 

NSF gives extra points to proposals in which PIs make special efforts to make campus visits and presentations at institutions that serve underrepresented groups, mentor early-career scientists and engineers from underrepresented groups, scientists who participate in conferences, workshops and field activities where diversity is a priority etc

I think some aspects of affirmative action, and especially the Bundesrat decision,  serve neither the underrepresented groups or anyone else. Quotas   automatically decrease quality  (because selection is not purely on achievement and suitability), discriminate against majority groups and lead to failure and inferiority complexes for those favored. Hence,  I agree with the conservative Supreme Court Gratz v Bollinger decision which barred quotas and disagree with Grutter v Bollinger that allowed them in a different form. Further, affirmative action  only makes sense to me if discrimination on the basis of nationality is removed. Right now, you can be a ethnic minority female disabled  Romanian or Thai working in the U.S. but unless you are a U.S. citizen you cannot be an affirmative action beneficiary.

As for diversity, in science in the U.S. (not France or Germany) this happens naturally, and our lab has always been wonderfully diverse, with, for example, sometimes simultaneously members from more than 15 different countries, but that wasn't intentional, it just happened, and unfortunately it's not what myopically qualifies as diverse for the U.S. Government.

Nevertheless, especially in the U.S., there is enormous untapped talent in the economically disadvantaged population. Our efforts should go into encouraging economically disadvantaged kids and educating their parents, well before university, and it shouldn't matter what nationality, ethnicity or gender they are:  white, black, Hispanic, Slovakian, Asian, disabled, French, American. Also, of course, those disadvantaged kids who prove themselves to be  hard-working and talented need to have an opportunity to pursue higher education equal to their richer peers.   Equal opportunity. No doors closed. Yes, all need to be given "a shot" but none propelled through on a soft cushion. 

Notwithstanding, given the hypothetical situation where I must choose between two Ph.D. candidates with exactly the same grades:  one rich and the other poor, I will choose the poor kid every time. Not through pity or positive discrimination or for championing underrepresented groups, but simply because I'm likely to get more bang for my buck from a kid who has fought their way out of the projects.

Now, let's get down to organizing those East Knoxville high school lectures...

Thursday, September 27, 2012

Thief in the Bureau of Criminal Investigations!

The local Heidelberg rag - the Rhein Neckar Zeitung - has always been a source of pleasure. A while ago I reported on the amusing article about the  Natural Healing Club in Spechbach, and this last visit to Heidelberg revealed another gem.

Apparently, the "Thueringer Landeskriminalamt" i.e. the local Bureau of Criminal Investigations, suspected a toilet paper thief in their own building in Waltesleben. Their suspicions had been aroused after complaints by the cleaning personnel. So, in the beginning of 2011, they installed a hidden camera in the place where the rolls were kept.  However, the film was never processed because there were no further thefts. The personnel and workers were informed only after the fact.

Elementary, my dear Watson..

Thursday, September 20, 2012


Meet Kristof, a Czech, sitting opposite me in a Copenhagen S-train, on the way back from the Brondby versus Horsens game that we both saw.  I met him on the platform at the train station after the game - there were the usual rowdies and then the two of us, both trying to make sense of the railway map.

He supports the  Bohemians. Now that's normal because Bohemia is Czech [BTW there's another Bohemians team - the one in Dublin - so to try to confuse us the Czech team wears Irish green (see above) whereas the Irish team wears red and black].

Anyway, I digress. Now, I'm quite a soccer aficionado, but by him I am  thoroughly outclassed.  Kristof is the REAL deal. In 2007-8 he went to every single Bohemians game - home and away. That already put him in the die-hard top 5% or so. But it wasn't enough, so since then, on Fridays he takes an overnight bus from Prague to some other country, takes in one or two soccer games, then returns back overnight on Sunday again just in time for work. He's probed 28 countries like that! And what makes him even more amazing is that he doesn't just watch the big teams - he watches the little ones as well. One trip to the cold North of England took in Fleetwood FC,  who were, like, in the tenth division with about 100 supporters per game. So he's clearly one sandwich short of a picnic.

Brondby are now useless and in crisis (they're so bad the ticket man let me in for free!) but on Sunday I will watch Hoffenheim, who are now useless and in crisis, then next Saturday I will watch Norwich City, who guessed it. Ahem! So, for voluntarily subjecting oneself to this drivel, maybe one has a slight  touch of insanity oneself?

Tuesday, September 18, 2012

Auditorium A

This is Auditorium A of the Niels Bohr Institute in Copenhagen in 1930.

Among the seated yappers are Bohr, Heisenberg, Pauli, Gamow, Landau, Kramers, Waller, Peierls, Bloch, Ehrenfest, Teller...perhaps the greatest collection of physicists ever gathered?

Here is the same auditorium today. It's unchanged, which is, of course, fittingly romantic, but I must say the benches aren't big enough to lodge laptops, and the coffee room is a Spinal Tap-esque adventure to get to.

We just finished a neutron data workshop in Auditorium A. This was, needless to say, a useful topic, but somehow we didn't quite reach the pinnacle of enlightenment of our predecessors, as they established the Copenhagen Interpretation of Quantum Physics.....

Sunday, September 16, 2012

Freedom of Expression: A Means to Oppression?

I was just wandering along the street in Copenhagen today when, at around 2.30pm I came across the merry little gathering  below:

That's Hizb-Ut-Tahri demonstrating outside the US Embassy. (Jakob Ehrban took the  photo above.)

The demonstration seemed to be peaceful, about 200 people I'd estimate. I couldn't understand what they were saying but one banner did strike me. It stated :"Freedom of Expression: A Means to Oppression".  Hmm.  Now, I know freedom of expression does not exist in  some Western countries. But oppression itself originates in censorship.  And thus I disagree with those who state, for example,  that Holocaust denial, however unpalatable,  should be banned. Such people should instead be countered with the force of argument.

But what about Hate Speech?  This is generally protected in the US under the First Amendment, but exceptions are made for incitement, and the movie that has caused all the fuss above must surely fall under this category.  However, to generally associate freedom of expression with oppression? - now that's a leap of faith.

Saturday, September 8, 2012

Pig and Whistle

OK, another musical masterpiece, completely different to Sam Hall.  This  piece I composed recently. For the specialists, it's my first ever MIDI composition (something I should have been doing 20 years ago) the sounds made with the Halion Sonic SE synthesizer in the Cubase LE AI Elements 6 music software, using an Axiom 49 keyboard MIDI controller.

The track is called "The Pig and Whistle".

Sam Hall - the Unrepentant Villain.

Here's a not very good video accompanying me singing an old British Music Hall song - Sam Hall - about an unrepentant murderer. The music was recorded in a kind of hole-in-the-wall place in Knoxville that sounds like it could have been next door to Tyburn.  All good clean fun....

Monday, September 3, 2012

Bunkum Politicians and Science

As we move into another election in the USA it's worth spotlighting politicians who decry science itself.  

There are politicians who are plain ignorant, such as the Minnesota Congresswoman Michelle Bachmann who claimed that the HPV vaccine has “very significant consequences”  citing the anecdotal case of a woman who had told her that her daughter “suffered mental retardation as a result of that vaccine.” 

There are politicians who deny global warming, such as the Senator from Oklahoma, James Inhofe, who brilliantly states that Nature magazine is " a very liberal publication".  Then there are  the politicians who decry evolution or GM foods.  In the eyes of the German Greens, for example, and the majority of the European Parliament, GM foods, as they are controlled by big corporations, have to be evil, and the science showing GM crops are harmless has to be wrong and biased. Many of the same promote alternative medicine, which, by definition, is medicine that has been proven not to work, or not been proven to work. [These politicians want to divert money that could be spent researching actual evidence-based treatments  to quack remedies. Clever, eh?  And why should their  $60bn dollar alternative medicine industry need no external regulation? Either their remedies have a clinical effect or they don’t; and if they do they should be treated like any other drug.]

Science becomes political when it spurs political action. The divide here is not between ‘pro-science’ and ‘anti-science’ political parties at all. Rather, politicians and parties will always side with science when it suits their constituency or conforms to their interests.  When not then they deny the science is right and cherry-pick anything that seems to confirm their prejudices.

In election season, let's pinpoint those who deny science for political ends. In the words of the President of the Royal Society   Sir Paul Nurse, (a native of Norwich!) “We can’t sit by without exposing bunkum.”

Monday, July 30, 2012

25 years old......

The only technical mountaineering I ever did was to climb  Pic Coolidge (above) in France as a 25-year-old.  The route is graded "Easy". Not many climbs are thus kindly graded and one feels they're  there just to make us scaredy-cats think they are mountaineers.   And, yep, I was easily scared.  At one point, there was a gap to step across with a 1500 foot drop if you for some reason failed to put one foot in front of the other. Before crossing, I waited for a couple of minutes, staring, reflecting and wanting to be elsewhere. The patient climber  behind me eventually had to prod,  "Well, go on then!" So I did, but realized I was the proud owner of, as they say, an acute sense of self preservation.

Contrast this with my grandfathers,  both of them, when they were 25.  

97 years ago today,  on July 30th 1915,   the 14th Infantry Division of Kitchener's Army,  in which  25-year-old  Oliver Cecil 'Charlie' Smith was a Corporal,  was defending Hooge near Ypres.  Suddenly, at 3.15 a.m.,  jets of flame shot across from the German trenches - the first time that "liquid fire" flamethrowers had been used on the Western Front.  Immediately a deluge of fire of all kinds fell on the terrified men, and on that day the Division lost nearly 2,500 men.   Charlie spent 3 interminable years fighting at Ypres and the Somme during that senseless war.

But was my other Grandfather, Austen Ashley, any less brave?  He was  one of the only 6000  UK political Conscientious Objectors during that same  Great War.  Marched with others through the streets of Norwich so that the jeering crowds could pelt them with rotten apples and cabbages and throw the white feathers of cowardice at them,  he was sent to Dartmoor Prison for solitary confinement and bread rations.  In the Second World War,  when the Baedeker raids, targeting  picturesque cities, hit Norwich,  while others were cowering in shelters he was working in the flames as an Air Raid Warden.  

Both grandfathers were subsequently mostly unemployed. Charlie, for example, never had a car, a phone or a bank account. His daughter,  a cowman's wife,  first polished her nails in a hospice shortly before she died in the 1990s - blessed are the meek, for they shall inherit the Earth. 

Yes,  contrast my grandfathers with their prosperous,  overfed grandson living  52 years of peace and exciting opportunity!   No reason for guilt, but we must remember our good fortune sometimes, must we not? 

Here's a poem by Charlie, written in the trenches,  which I find striking for a working-class man who left school at 12:


God made the Man, gave him the gift of life
Drawn from some unknown, strange, mysterious source.
Lent him his youthful vigour, grace and force,
And bid him run with time an even course,
Discounting enmity and strife.

One swift-sent bullet out of the unseen,
Seeking its billet, and the race was run,
The light extinguished and the darkness won.
The future killed, the day's work scarce begun
And death's dropped veil where life had begun.

Man made the watch a triumph of his skill,
A marvel wrought of craft and subtlety,
Decreed that it would work in mystery
Dogging the steps of time victoriously,
And to the end this task fulfill.

When darkness hid the ills that war had bred,
Its steadfast beat, tranquil as at the start,
Recorded time, playing its destined part
Close to the nerveless arm and silent heart
Still quick and faithful mid the dead.

Wednesday, July 25, 2012

What it's like to play with the Jaguar Supercomputer

Back on a recurring theme. I was just pointed to this on CNN Money.  Of course I remember the TV crew coming but didn't know it had been aired.

The comments after the article, as usual, are the most fun.
I liked this one: "It's amazing we went from the first computers that filled entire floors which a bunch of blinking lights and engineers in lab coats monitoring them all the time to ... a computer filling an entire floor with blinking lights and engineers in lab coats monitoring all the time. Nothing changes, just the scale."

Thursday, July 19, 2012

This sleepaway camp.. the Adirondacks costs $11400 a summer and is practically impossible to get into.  So goes the headline about Raquette Lake Summer Camp in upstate New York.  However, yours truly did get into that camp, and for free, in 1979, as a soccer coach thanks to the  British Universities North America Club (which has meanwhile itself expanded somewhat, it would appear).

What I found in the  summer camp didn't seem particularly exclusive: dangerous flints in the soccer fields, lavatories that didn't function until the day before Parent's Visiting Day and endless peanut butter sandwiches - yuk!  The only hint of exclusivity was John D. Avildsen, the Director of Rocky, who came to visit his son, landing in a helicopter and stepping out in a boiler suit. Still, shining flashlights at  the bears at night was fun (you could only see their eyes) and we won the World versus USA Soccer Game  8-0 - I still have the pennant!

That first hop across the pond to New York in 1979 was epic - 24 hours in an "Evergreen Airlines" DC 10 that took off from London, stopped at Paris, then refueled at both Shannon, Ireland and Bangor, Maine before limping into  JFK. I then  got in a yellow New York taxi cab and getting out forgot the direction traffic flowed on American streets and opened the door on the  wrong side.  A passing truck slowly bent the door back 180 degrees  - oops! 

Churchill did worse in 1931, though  - making the same mistake he stepped into Fifth Avenue and was run over. He later wrote, "There was one moment--I cannot measure it in time--of a world aglare, of a man aghast. I certainly thought quickly enough to achieve the idea 'I am going to be run down and probably killed.' Then came the blow." Fortunately, Churchill's injuries, while requiring three weeks in hospital, did not threaten his life. "I do not understand," Churchill wrote, "why I was not broken like an eggshell or squashed like a gooseberry . . . I certainly must be very tough or very lucky, or both."

Monday, July 16, 2012

Zoe Cournia ...

..describes her experience in our laboratory here.

"I cannot imagine being a happier doctoral student in another place!"

Sunday, July 1, 2012

The Greatest Ever!

Spain, who just won the European Championships, are, in my opinion,  the greatest soccer team ever.
Now greatness cannot measured by who would beat whom in some hypothetical match-up, but by how far and for how long a given set of players in their time stands above the rest of the world, and it is their sustained dominance that gives Spain 2008-2012  my vote.

Spain have no rivals in Europe, as the 1974 'Beckenbauer' West German side and  the 1998 'Zidane' French (who I watched win the World Cup in the yard of an old farm in the Aveyron) both failed (just) to win three majors.  Spain's only rivals would be the 1970 Brazil side, who won all of their World Cup games that year, and had a number of individuals such as Pele and Jairzinho, who combined  skill and explosive power in a manner unseen before or since. Brazil 1970 was almost universally considered the greatest team of all time - until July 1st 2012.  But apart from one World Cup that Brazil side won nothing else - there was no serious Copa America or Euro equivalent to test them - and they fizzled in the World Cups in 1966 and 1974.

So Spain win on results, and for me they win on style as well. You see, I have always liked precise passing, consistency and intelligence. That's what Spain, who had never done anything in international football, brought to the game in 2008, when Luis Aragones decided they were not tough enough to beat other nations physically and needed instead to keep the ball. So he instilled the "Tiki-Taka" possession football that Johann Cruyff had initiated as manager of Barcelona.

Now Cruyff  arguably was the world's greatest ever player, but that's a whole new discussion....

Tuesday, June 26, 2012

"Houses Made of Wrecked Ships"

The Victorian church of the Holy Trinity and All Saints at  the village of Winterton-on-Sea, Norfolk, snapped by my wife as we hiked around it last week. The tower is seven stories high, built to serve as a landmark from the sea, but many died on the notorious shifting sands off Winterton Ness,  and many of the church graves are of the drowned. In 1722 Daniel Defoe (who wrote Robinson Crusoe)  remarked on all the houses of the village being made from the timbers of wrecked ships.

Monday, June 18, 2012

You shall not leave!

....the German Civil Service!

The benefits of Germany’s 4.5 million Civil Servants (Beamter) are enticing. They have a job for life, health insurance and a generous pension.  Among the Beamter are the German professoriat, which indluded me from 1998 until 2007.  Now I had always assumed that some measure of employment permeability between the German Civil Service (Beamtenschaft) and rest of the world would be actively encouraged. Not so, it seems…

 Now there is indeed a strong conflict of interest argument against too frequent personnel switches between the high-level bureaucrats, who regulate industry, and industry itself. However, for most civil servants, including the professoriat, hindrance is against the national interest.  But, as Ansgar reminded me in the pub last Monday, in Germany employment as a Beamter is expected to be marked by a higher-than-normal degree of loyalty on both sides, with the above-mentioned benefits being matched by faithfulness and dedication to the State. Indeed, the new Beamter's first task is to swear a solemn oath of loyalty. Leaving the Beamtenschaft is tantamount to treason, so that’s why in doing so you forfeit your pension, you see. It’s a punishment for failing in your loyalty.

You have revealed your true colours.  You shall not leave.

Friday, June 1, 2012

Bear Caught at the Lab

 (Photo: Jason Richards)

A black bear was recently caught at the High Flux Isotope Reactor (HFIR) at ORNL.

HFIR may well be an efficient means for scientists to scatter neutrons but a black bear appears to be an efficient means of scattering neutron scientists.

Thursday, May 31, 2012

The Tennessee Titan..

..may be ready for the next football season. And, no, I didn't accidentally omit the plural.

The Tennessee Titans (plural) are themselves in good shape but apparently "still  missing a few pieces here and there to be a really good team".  The same could be said for the Tennessee Titan, the ORNL DOE supercomputer.

Frank Munger reports that the remaining GPUs needed for the new system may be delivered in August-September - in time maybe for the new football season. The question remains as to whether Titan will win the Supercomputing Superbowl - the Top500 competition. We'll know the answer later on - maybe in time for the February Football Fiesta itself.

Friday, May 18, 2012

Dietrich Fischer-Dieskau

The German baritone Fischer-Dieskau, who just died aged 84, was best known for his work with German lieder and, among British, for his 1962 singing Britten's War Requiem in Coventry Cathedral, which had been destroyed by a bombing raid in World War II.

However, I remember him most for the 1968 Deutsche Grammophon recording of Carmina Burana by the Deutschen Oper Berlin conducted by Eugen Jochum. Fischer-Dieskau is rough and coarse in the drunken debauchery of  In Taberna, and gruff in the Abbot's song. But above all, smooth 'DiFi" radiates sensuality in Omnia sol temperat and Circa mea pectora:

"My heart sighs for your beauty and I am tortured.
Send a message! Send a message! My beloved does not come!
Your eyes shine like the rays of the sun, like a flash of lightning, giving light to darkness.
May the gods grant me what I have set myself to do,  to unlock the bonds of her virginity.
Send a message! send a message! My beloved does not come!"

Wednesday, May 16, 2012

Monster Tornado - 25 miles from my house

A  hike along the Rabbit Creek Trail in the Smoky Mountains the other day. Hot it was indeed, but the heat was tempered by the shade from the tree cover omnipresent in the mountains of the Eastern Seabord...until, suddenly, surprisingly,... we were in fresh air, open, exposed (above). Every single tree uprooted or simply snapped.  This is where an monster EF4 tornado had hit on April 27th 2011, clearing a track a mile wide and 11 miles long (see below).

Here's what an EF4 did to a populated area (St. Louis, Missouri) a few days earlier:

And Knoxville TN? 
Well, the same storm that created the Rabbit Creek Monster damaged my roof, which I had to replace. 
And, no, the insurance didn't cough up the dough.  
Maybe it would take an EF4 to convince them?
Well, at least there's an educational side:  the Smoky Mountain EF4 dispels the myth that tornadoes never happen in mountains...

Tuesday, April 24, 2012

A Solution for Scientific Publishing?

Is there a better model for scientific publishing?
There are two major current problems: the cost of publishing and access, and the inequities of the peer review process. Both could be cured at once.

We need ONLY ONE, publicly-run, open-access scientific publishing domain to which ALL ARTICLES are uploaded for free, in whatever format wished for by the authors and without prior peer review. This domain would subsume all existing primary research publishing. After an initial, publically-funded development phase, the small costs of maintaining this domain could be obtained through discreet advertising revenues. The model thus obviates both the need for  charging huge amounts for access to  journals and the need to charge authors for each publication submitted.

Once an article is uploaded it will easily be able to be found by a keyword search, such as exists in PubMed or Web of Science. Reviewing would not be solicited but would be open and online, in the fashion of "comments" to a blog entry.  Any given article might thus receive many or no reviews. No reviews would be anonymous: only registered reviewers who have revealed their identities would be allowed to post comments. Many of the reviews are likely to be incompetent, but the reviews would also be open to review, and ranking, as would the reviews of the reviews etc..

In the above system there would be no need for a decision to be made a priori as to whether an article is "of sufficient general interest" before publication - this would all be decided by the readers afterwards: a points system could be devised whereby an article gains prominence depending on how many times it is accessed from different computers, cited later on, and on the reviews received. As an article rises in points, so would its visibility in the web domain. Extremely hot articles would be expected to very rapidly gain prominence.

Any objections?

Monday, April 9, 2012

Up the City!

Well, I've kept my trap shut concerning Norwich City since the unlikely day of their ascension to the Premier League. Why? Because it has all been too much, too nerve-wracking, despairing, elating, rousing, deflating and inspiring.

We didn't belong here, you see. At the beginning of the campaign we were 8/11 favourites to go straight back down. After all, everyone knows that to shine in the world's most-watched arena you had better avail yourself of a $200M team of silky, experienced, speedy World-Cup Ghanaians, Brazilians and Ukrainians, not a cut-price gaggle of crass, verdant British amateurs uprooted from the lower leagues.

But today we beat Tottenham Hotspurs 2-1 away. Our little team of country yokels stauched the supposedly unstoppable flow of flair and brilliance in London - the vaunted Spurs: Adebayor, Modric, and Gareth Bale, the last of those men himself alone valued at three times the cost of the whole Norwich team. And we didn't simply score 2 to their 1, we robbed them everywhere on the pitch. Throughout the whole match we were first to the ball then quicker thinking when we had it.

Paul Lambert, the gaffer, has mixed in some systematics he learned with Borussia Dortmund in Germany. But perhaps more tellingly he has assembled a kit of hungry lads. Football mirrors life: you can have whatever pedigree you like, whatever past successes, whatever mega-salary, whatever fame, but if, like Spurs, you lose that edge, that hunger, that raw desire and intent, you will lose the game.

And now we're safe, more than safe, we're even perusing a top-half finish, and I can finally breathe, relax, pour a glass of red and enjoy the Summer.

Saturday, April 7, 2012

Party Time!

Helium Shortage Leaves Scientists In No Mood To Celebrate

Of course neutron scattering, NMR spectroscopy and MRI imaging are no fun.
Boring medical scans never put a smile on anyone's face, did they?

Party balloons are what put people in the right mood.

All those lovely balloons that just go up, up, up and away?
They're filled with helium, of course.
But because in 1996 Congress vowed to sell off the U.S.'s large helium stockpile by 2015, the price of helium has been kept artificially low even as the demand for the gas has soared, and many a party balloon has been perked up as a result.

And now there's hardly any helium left.
So we'll have to stop detecting neutrons, cooling samples down, doing MRI scans, determining molecular structures etc.

All the more time to spend having parties, don't you think?

Sunday, March 11, 2012

Golden Eagles in Tennessee and Scotland

Good to read in the Knoxville News Sentinel that Golden Eagles may be soaring above the East Tennessee mountains somewhat more frequently these days. I remember them from the 1980s in North-West Scotland, where my father and his wife lived, in a place called Achnanellan, on the banks of Loch Shiel. Achnanellan is hidden in the wilderness, an old 17th century croft house with no road (you have to cross the Loch to get to it) and no neighbours within 4 miles. A place of ferocious weather and swarms of midges, of rich lichen and peat.
Here it is - the croft is a tiny white speck in the middle:

Achnanellan means "Field Near the Island", the island being St. Finnan's Isle, a windswept ancient burial ground. I set foot on it, and wondered at the dour, very old crosses (below). The locals had divided half of it for Protestants and half for Catholics, and placed pennies in the trees as votive offerings. There was maybe one burial per year there in the 1980s, probably many more before the brutal Highland clearances. The old bronze bell in the ruined chapel was still there, rumored to be a thousand years old - no-one had stolen it.

As for the eagles, they were always far above our heads, 1000 ft or so, hunting rabbits with acuity from on high. They fly in monogamous pairs and look like flying planks. It was difficult to fully appreciate their 7-foot wingspan from that distance, but pictures of one digging its talons into a cameraman truly bring home their size and power. Achnanellan, St. Finnan's Isle and Loch Shiel belonged to the eagles.

Thursday, March 8, 2012

The DOE:Industry Supercomputing Summit..... Austin TX, from which I just came back, brought together Industrial R&D and National Lab research directors. Secretary Chu gave an entertaining talk on three hours of sleep describing how computations on DOE facilities have led to potentially commercially important new designs of trucks, buildings etc and I had the pleasure of sitting next to the CEO of Ramgen, a company that has used the supercomputer to design a new, efficient jet engine. Only complaint is the usual one - the quality of the breakfasts, which seems to have been downgraded since the "Scientists Gone Wild" news report some years ago....

Thursday, February 23, 2012

A Success in Structure-Based Drug Design

News reports today state that vermurafenib, an oncogenic B-RAF kinase inhibitor, doubles the length of survival on average of those 50% of metastatic melanoma patients that possess the relevant mutation. This is a success for drug design guided by principles of protein structure, as the drug was discovered by examining interactions of candidates within the binding pocket of the enzyme.
Molecular biophysics in the service of medicine! Hopefully the structure-based screening work will soon be able to be effectively done virtually. At least, thats what we and many others are working on.....

Monday, February 6, 2012

Campus Paris-Saclay

Of course, I like to follow what happens to places where I used to work and live. One of these was the Plateau de Saclay, and this, it seems has just been selected for gargantuan funding under IDEX-2.

IDEX appears to be the French version of the "Exzellenzinitiative" in Germany, in which I partook six years ago. This came when Germany recognized that having a couple of universities in the top twenty would do wonders for its image, so the Minister concerned suggested creating a Teutonic MIT. Now you can't just do this, because it takes a lot of dosh, and putting all that money in one place wasn't politically viable (too few would benefit and the rest would lose), so it was diluted a bit, and instead gave a useful but, in my opinion, indecisive helping hand to the top 10-15 universities. (A minuscule fraction of the Heidelberg funding went to paying part of my visits there over the last 5 years).

Now, it appears, the French are thinking likewise, and with massive amounts of dough (about $10bn). Now this goes against the mores of the egalitarian France I used to know that would fund individual CNRS researchers with small salaries, no equipment and give them complete freedom for life with no accountability. But even France, it seems, can't abide languishing way down in the Shanghai rankings, and so it is that there will be the haves and have-nots. Paris-Saclay is a big 'have' and will be drinking champagne. Grenoble, another candidate, and where I did my Ph.D., lost out, so they will have to hit the whisky.

Paris-Saclay: Le Campus Aujourd'hui

Le Campus Demain

Wednesday, January 18, 2012

Frequent Flyer Miles - the Only Safe Currency?

I'm back in Germany (for the very successful doctoral exams of Tomasz Berezniak (good luck in your postdoc in Munich!), Mithun Biswas (good luck in Frankfurt!) and Mai Zahran (good luck in New York!)). When I was younger I used to even enjoy long flights to distant lands, but flying across the Atlantic 48 times in the last six years (!) has been a right royal pain in the butt. However, a slight benefit has been that I have racked up Frequent Flyer miles.

Now, I have always considered 'miles' programs as close-to-worthless ephemeral, slippery corporate traps. (However, I admit I have occasionally used them to upgrade to business class in a usually vain effort to get some sleep on the West to East overnight leg.) So it was amusing to read in the latest issue of Der Spiegel that there is a class of person so hell bent on earning the top miles status that they will go to almost any lengths. The Spiegel reports accompanying a group of six people pointlessly flying round-trip from Frankfurt to Innsbruck on a special Lufthansa chartered plane just to get the miles - the plane just touched down in the Alps a few seconds then took off again to fly back. Another strategy is that of Wolfgang Reigert, who sits all night in front of his computer looking for the cheapest ticket with the most miles e.g., Frankfurt to New York via Amsterdam, Dubai, Rio and Panama then sits in the plane for two days. It seems that the break-even price is 13 Euros for 1000 miles: any more and it's not worth it.
Apparently hardcore miles-grabbing 'cartels' have cropped up - one hired a female student to check in at the Lufthansa machines with a pile of frequent flyer cards, the owners pocketing the miles while never even leaving their sofas.
Of course, it all ends in tears. One miles-hunter succinctly expressed his dilemma in a frequent flyer forum : "I was so determined to become Platinum that I'm now deeply in debt and can't afford to buy any flights. And, as far as I can see, most Platinum benefits can only be claimed by people actually flying. Seems somehow stupid, doesn't it?"

Wednesday, January 4, 2012

How to Judge Scientists

Well, my 300th scientific article was just accepted for publication (N. Smolin, R. Biehl, G.R. Kneller, D. Richter and J.C. Smith "Functional Domain Motions in Proteins on the ~1-100ns Timescale: Comparison of Neutron Spin Echo Spectroscopy of Phosphoglycerate Kinase with Molecular Dynamics Simulation, Biophysical Journal - good job, Nikolai!) and there will be a few beers in the Union Jack pub later on in the week. However, this kind of artificial milestone brings one to reflect on how really to judge scientists.

Clearly, although a large number of publications does point to some aspect of productivity, such as, possibly, getting involved in a lot of projects and helping bring them to fruition, it is a very one-dimensional metric and misses important elements of scientific life. Numbers of citations, h-factors and the like also have their problems (just as an anecdote, for example, a very famous physicist working at Saclay when I was there once said one of his most cited articles was one he got wrong - his rivals loved pointing this out in their own publications!).

So how can one judge scientists? Well, increasingly, discoveries result from the voluntary sharing and development of knowledge through collaboration, rather than individual discoveries, and so an intriguing recent article by Azoulay et al tries to quantitatively track effects on collaborations of the ideas that scientists create. The concept is that a scientist will influence the people with whom they work, by forming an "invisible college" of ideas. To quantify this influence they tracked the publication productivity of faculty-level collaborators of eminent scientists in the life sciences. They found that if an eminent scientist suddenly and tragically died before the end of their career (mostly of heart attacks, but in the sample studied three were actually murdered!) then the publication productivity of their collaborators subsequently irreversibly declined on average by 8%.

The authors concluded that the effects of, as they call it, "superstar extinction" appear to be driven by the loss of an irreplaceable source of scientific ideas. My own opinion is that while this may indeed account for some of their observed effect, the collaborative nature of science means that success depends on not only the exchange of scientific ideas, but also inevitably social aspects such as friendship, motivation, drive and team spirit. When sources of these are not replaced then productivity will decrease.