Club Mod

Frequent Flyer Miles - the Only Safe Currency?

2012-01-18T12:13:00.000-08:00

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?"

How to Judge Scientists

2012-01-04T11:29:00.000-08:00

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.

At last......

2011-12-16T14:40:00.000-08:00

Our 5-YEAR REPORT can now be downloaded here. Packed full of awesome action, gorgeous graphics, heart-warming heroics, petrifying press releases, regal revelations and luscious lists.

The Problem with Cellulosic Ethanol

2011-12-16T14:35:00.000-08:00

Here's a recent article by Leo Williams on some of our calculations regarding cellulosic ethanol - this is about lignin clumping together.

High Productivity - an Aging Phenomenon?

2011-12-02T09:06:00.000-08:00

The soccer field is so frustrating. With age I have learned exactly what to do on the field but physically am no longer capable of actually doing it. Meanwhile the young punks mindlessly whizz by and crash out of bounds. Is it the same with science?

The conventional wisdom has been that scientific productivity dwindles with age - brilliant young scientists making outstanding conceptual leaps. However, recent work suggests that this is not the case, and that prime productivity is maybe around 50 years old.

Well, I'm beginning to come round to the idea that older folks maybe aren't as clapped out as we all used to think. For example, members of our center had the pleasure this last month of lecturing on "The Molecules of Life" to ORICL - the Oak Ridge Institute for Continued Learning. The class was mostly retired scientists and engineers and, let me tell you, they were the liveliest bunch of students I have lectured to in quite a while. This begs the question as to whether they were always that engaged or have perked up with the advancing decades. I know the latter is true of myself - the reason I interminably interrupt and yap about in seminars others give is experience - whereas 30 years ago I could understand hardly anything scientists were talking about, these days it comes much more easily, and I think the same may have been true of our ORICL audience. And some scientists I know keep working for ever and ever, it seems. Rita Levi-Montalcini, a 102-year-old Nobel winning scientist (pictured above) said: 'Above all, don't fear the difficult moments - the best comes from them."

So maybe instead of prematurely fretting about retirement planning, 51-year-olds like myself should realise that the best years of our lives are still ahead? This maybe true in science, but it doesn't alter the fact that I'd still like to punt those mindless young punks off the soccer field - if only I could catch them!

Who needs supercomputers? - Just use your cell phone.

2011-11-29T13:52:00.000-08:00

OR

?.

As a specialist editor of Computer Physics Communications I regularly get issues in the mail, and was amused to read in the latest edition an article entitled "Mobile Phone as a Platform for Numerical Simulation" by Filip Sala of Warsaw University. Today's cellphones have about the CPU power of PCs of the late 1990s, and there are 5 billion of the pesky little things. Sala managed to use one to simulate light propagation in linear and nonlinear media based on the one-dimensional Schrödinger equation and molecular reorientation in nematic liquid crystals. So who needs supercomputers? - just get your daughters off the phone. Well, maybe supercomputers are easier after all......

Imagine your computer working 18,000 times faster. This guy doesn't have to....

2011-11-22T08:58:00.000-08:00

On the Volunteer TV web page. Well, I DO have to, in fact, because I don't actually sit down in front of Jaguar myself and use it - my co-workers, such as Roland and Benjamin, do. But the spirit of the article is what counts......

Book recommendation

2011-10-22T05:39:00.001-07:00

Not often that you get a book recommendation from Club Mod, but this one - A Renegade History of the United States - was raucously entertaining. Thaddeus Russell shows how the dregs of American society - the slaves, drunks, prostitutes, Irish (!) etc - shaped many of the freedoms that we take for granted today - in direct disobeyance of the authorities, such as being able to go to a dance, wear what we like, play rock music etc. It also provides evidence against some of the conventional wisdom we have all internalized, showing, for example, that ex-slaves wanted to go back to being slaves, the deep unpopularity among the populace of going to war in World War II, and so on.

I loved it.

Decoupling.....

2011-10-10T11:02:00.001-07:00

..and the Honorary Doctorate.

I'm back in Heidelberg and gave a talk at a Chemistry Symposium here today (as, by the way, did Stefan Fischer, Petra Imhof and Tomasz Berezniak of our group). Tonight, at the symposium an Honorary Doctorate was awarded to Carl Djerassi, known for his 1950s work on the synthesis of norethindrone, the first effective oral contraceptive.

This invention effectively divorced sex from reproduction - a truly world-shattering effect of science on society - and contributed more to women's liberation than has any political act, allowing millions of women to pursue a career without sacrificing a sexual relationship.

Now the decoupling of sex and reproduction is so highly unnatural that society never has learned how to deal with it. When sex was robbed of its primeval physiological potency, millions of years of evolution, that have hard-wired instincts and associated morals into us arising from sex causing babies, were, in an instant, rendered obsolete. This hard-wiring meant that society could not change as quickly, and, anyway, the sustained association of sex with disease persists. But what will happen should scientists eventually take the next step, eradicating the sexually-transmitted diseases, thus removing all physiological 'danger' whatsoever? Society challenges scientists, and then vice versa.

Peer Review, Again

2011-09-22T10:49:00.000-07:00

Peer review can be exasperating, but also fun. A while ago I reposted some amusing reviewer comments from the journal "Environmental Microbiology". Well, just after that we submitted a paper for which one reviewer was raving about the work and the other thought it boring - chalk and cheese it was.

Of course I can't repost the above anonymous reviews here. But I thought it would be fun to compose two reviews myself, the first scathing and the other glowing. Although fictitious, they are composed of actual reviewer comments about our manuscripts submitted over the last year or so. (And, yes, one of the reviewers, who presumably has a Ph.D., does spell the word "know" as "no".)

Reviewer I.

Essentially, the paper either tells us what we already know, or makes novel assertions which are uncheckable and based on needless ad-hoc-erie. The authors should change the tone of their paper to be constructive rather than "criticizing" the work of other people - by comparing to such works (sic), the authors are doing themselves a disservice, as they should no (sic) that is really no longer acceptable. This submission will not help the reputations of any of the coauthors as it is really not at the level one would expect for three of the main authors. They should all provide a bit more guidance, mentorship and advise (sic) to the apparently junior author, in the opinion of the review (sic) who is very familiar with the very nice high quality publications of Smith. The impression left on this reviewer is one of being cheated, as if only the first half of a fine review article was provided. Poorly designed and provides only trivial results, if any. The ball-and-spring model is too simplistic and I do not think that any of the conclusions can be reliable.

Reviewer II.

An important and sorely-needed contribution to the field and will have an impact, or should have, not only on practical strain development, but also in basic research into microbial physiology. The approach stimulates new ideas, is interesting and very promising judging from the results exposed in this manuscript. The paper is clearly written, well executed, and richly supported by an abundance of supplemental materials. The work is thorough, complete and well written. This interesting paper provides new insights and suggests a scheme which has many interesting elements and should make an important contribution to the field. In summary, this manuscript is an important physical contribution to our understanding of conformational transitions in proteins.This is an outstanding piece of work: an exciting and unexpected discovery that may also be of importance to other biocatalysts. It is an important step towards interpreting neutron scattering data and obtaining quantitative agreement between MD results and neutron data. The simulations are carried out competently, the mathematical analysis is thorough, the results appear to be of very high quality and the presentation is clear. The work should be of general interest for all kinds of organisms. It provides a good example of this type of approach and has been carefully performed –

Hmm...accept or reject, I wonder?

UT Supercomputer Predicts Revolution

2011-09-09T13:04:00.000-07:00

Well, I knew the UT supercomputers were good. After all, we have peered into the origin of life, probed biofuel barriers, helped design drugs and done myriad other things with them. But I didn't know they were capable of predicting revolutions. Apparently so, according to this BBC report on data mining with the UT SGI Altix "Nautilus" machine.

"S'ils n'ont pas d'ordinateur, qu'ils mangent de la brioche!":

Reasons to be Cheerful..Part 3

2011-08-30T10:26:00.000-07:00

The productvity (in terms of publications) of the UT/ORNL Center for Molecular Biophysics has doubled over the past year: from about 20 publications per year to about 40. And so we build, adding more bricks to the edifice resting on the great laws of science, laws that I see in "The Settle Bed" by Seamus Heaney (above):

"....an inheritance

Upright, rudimentary, unshiftably planked

In the long ago, yet willable forward

Again and again and again"

The Art of Splette

2011-08-26T07:32:00.000-07:00

My ex-graduate student Thomas Splettstoesser is very talented in scientific graphics. The images below of his graced the front page of the ORNL web site and various other places. (If he sends me more I'll post them too). See more of his work here.

Dynamical Fingerprints

Mighty Microbes

Mighty Microbes (again)

Lignin and Cellulose

Americanese versus Britishese

2011-07-20T13:34:00.000-07:00

Heads up, guys! (Take notice, everyone). While standing on the track (platform) in England a while ago I thought I'd spend a half hour (half an hour) or so writing about train travel. But in which language - Americanese or Britishese? Why not both?

Riding the train is an alternate (alternative) to the car in Britain. Trains run there 24/7 (all day, every day) and can be convenient transportation (transport), there being a million and a half (one and a half million) journeys per year. You do the Math (Maths) - that's a bunch (load) of trips. But riding on the railroad (railway) isn't always easy. Waiting on (waiting for) a train in Britain is oftentimes (often) the height of ridiculosity (can be riduculous) due to (owing to) endemic lateness, never permitting a sense of normalcy (normality), and sleeping passengers even risk being burglarized (burgled), but in the end train travel can be the least worst (just bearable) option (while not always the 'most best').

During my last train trip I recognised the waiter so I reached out to (talked to) him, asking whether I could get (have) a couple (couple of) newspapers. He said that, no I couldn't get them, he'd have to get them for me, and, anyway, he hadn't wanted to be disturbed and couldn't care less (could care less) so I told him he was nauseous (nauseating) and asked whether I had to write (write to) him to get them, and told him that I had just wanted to touch base (chat) with him, but, being English that last comment must have sounded rude to him because he smacked me one up the bracket, Queensbury rules. I apologised and said it was my bad (fault). He soon perked up when I started talking about soccer (football), and especially about the two-time (double) European champions, Liverpool, and their winningest (with the largest number of wins) coach (manager). A team of much physicality (physical strength) they are, that, I said, going forward (in the future) in upcoming (coming) years will surely win again, but not with the deliverables (potential things to be delivered) expected to be gotten (obtained) from their American (Yankee) owners leveraging (mortgaging) their stadium. He sighed and said that it is what it is (it is what it is). And so indeed it was.

Stardom, Sex, Scandal, Shame, Suicide and Soccer..

2011-07-17T07:19:00.000-07:00

While playing for the Norfolk U15 and U18 soccer teams in the backwaters of England in 1975-1978 we players had no idea we were at the birth of the making of social history concerning sex, racism and sport - only years later did we learn that we were witnessing the making of the first openly gay and the first million-pound black soccer superstar, and that our coach was perpetrating child sex abuse that would trigger a worldwide revolution in sports management.

Justin Fashanu (above) was in our U18 team, then became the first black million-pound soccer player, and was the third highest goalscorer in the English Premier League in 1980-81. He was also the first gay to out in the sport, suffered greatly for it, and committed suicide in 1998 after allegations of an improper relationship in the US with a 17-year-old (although the charges had been dropped).

Nick Baker is now writing a book about him, and this is what I communicated to Nick about the quiet, tall striker:

"Justin told me he didn't really want to play football - he was more interested in boxing as a kid, having, I believe, won the English Schools championship. At the time it struck us as weird that a kid with talent actually wouldn't want to play football.

Later on I wondered how many gay boxing champions there have ever been - to me that concept in itself invalidates the perception that no gays can be tough, aggressive and manly, a perception that I suspect underlies the public distaste for gays in the US military.

But in our games on rainy, windswept, muddy Norfolk fields, Justin wasn't the hardest fighter, and would sometimes lose enthusiasm completely, shivering, standing around with his arms folded while the rest of us were huffing and puffing. But then, before anyone noticed, the ball was suddenly in the back of the net and he had put it there. It was like he played in a different dimension.

I remember trying in vain to mark him in practice games (I was a defender). In one of these he twice just popped out of nowhere, stuck a foot out and the ball was in the net. The U18 coach, Graeme Morgan, knew what talent he had (and let the rest of us lesser mortals know about it!) - and within a year or so Fashanu was the Norwich City side in what is now the Premier League, and scoring profusely"

We were just tough, scrapping footballing teenagers.

We had no idea what a star Fashanu would become or that he was gay.

We had no idea what News-of-the-World style tabloid controversy would haunt him later.

And we had no idea that our U15 soccer coach, Paul Hickson, would go on to become Chief Coach of the British Olympic Swimming team, leading them to their best ever performance at the Seoul games. His record-breaking 1988 squad had seven Olympic finalists and included stars like Adrian Moorhouse and Nick Gillingham, who scooped three golds, and silver and bronze medals.

And we had no idea that while we were playing for Hickson he was abusing young female swimmers from our local schools, that he would be doing this for over ten years, that 15 years later, he would be jailed for 17 years for the sex attacks on teenagers in his elite squads, and that his conviction would trigger an ongoing worldwide clean-up.............

Scruffy, scrapping soccer kids unwittingly at the budding of a nexus of change, oblivious to the gathering storm that redefined homosexuality, racism and child abuse in sport....

Dreamland!!

2011-06-30T22:36:00.000-07:00

I'm back in dreamland for a few days!! Southern Germany!
Sailed through the recession.
Unemployment 3.9%.
Low national debt.
No housing bubble.
Lipi graduating.
(625th birthday celebrations of venerable Heidelberg University. )

A beautiful wonderland!! With one exception: the ass-numbingly boring Women's Soccer World Cup taking place here. Why 16 million people would want to watch that drivel I will never understand. Only when the day comes that they make the effort to stop the pinball lottery and control and pass the ball a bit will it become worthy of a few more minutes of attention. The potential is there, of course, but they've got a long way to go.

Gaspard de la Nuit

2011-06-27T03:27:00.001-07:00

My preferred classical music tends to be from the first half of the 20th century - relatively complex stuff. Among these is my favourite piece of piano music of all - the evocative "Gaspard de la Nuit" by Ravel, based on three satanic poems: Ondine, Le Gibet and Scarbo.

The music is virtuosic, one of the most difficult pieces ever written, and I keep an eye open for new renditions of note. Here's a performance of Scarbo by Valentina Lisitsa that is simply electrifying..

Scarbo:

"I have heard him and seen him again and again, Scarbo the Dwarf. In the dead of night, when the moon was a silver mask on a dark wall, the stars a swarm of bees with stings of piercing light; heard his laugh in a dark corner, and the grate of his nails on the counterpane. I've seen him drop from the ceiling, twirl and roll across the floor like a spindle dropped by a dark enchantress at her wheel. Did I think he had vanished? No. He rose up between me and the moon, high and narrow as a Gothic steeple, a great bell swaying in his head. And then his form utterly changed—now blue and transparent as candlewax, his face as pale as the molten drippings—and into the dark he's gone..."

Frank Munger

2011-06-24T11:38:00.000-07:00

Just had an entertaining lunch at Ruby Tuesdays in Oak Ridge with Frank Munger, Senior Writer at the Knoxville News Sentinel. As all locals know, Frank writes the Atomic City Underground blog, the main source of news on Y-12 and ORNL. Frank has written several entries pertaining to our work and Club Mod, most recently here and here. I was impressed to hear that his blog readership is growing and he now gets well over 1M page reads per year. He was also full of praise for Tuan Vo-Dinh, who was a Corporate Fellow at ORNL and is now at Duke. Tuan's departure was a blow for ORNL, but every cloud has a silver lining, and as a result we inherited his capable secretary, Julia Cooper.

What Really Drives a Scientist?

2011-06-05T05:53:00.000-07:00

People often ask "What really drives you? What's your grand plan? Ultimate goal?"

It's interesting to briefly reflect on how this, in the case of J.C. Smith, has evolved over time.

When I was a graduate student: I was driven by deep understanding.
Unsure, I needed to find out whether I could do scientific research.
I was hooked into my narrow theoretical subject: I didn't know it at the time, but, maybe sadly, I would never again master any subject so thoroughly. (Conversely, I knew little about anything else, and most seminars, even in my field, were gobble-de-gook!).

When I was a postdoc: I was driven by competition.
There was maturation and widening of experience, becoming a senior member of a group rather than a dumb 22-year-old grad student. This happened, in retrospect, so quickly and with me hardly noticing. But towards the end I was driven by the stressful, cut-throat fight for an independent position that consumes some researchers at this age. This was a time of rejection after rejection. For my present postdocs going through the same purgatory, I've been there and understand. In a tough social battle, the subject sometimes seemed to take second place, and winning, reaching the promised land, mattered most. In retrospect I should have relaxed and enjoyed the science more: the spectrum of opportunity was, and is, much wider than I had imagined.

When I was a junior group leader. I was just driven! A time of networking, lecturing, and energy.
As a junior group leader one is young and liberated, so endless creative energy is expended. Nothing stops you (except wise old institutional bureaucrats). I gave 44 research lectures all over the world in one year!
Here's where the diversification really picked up, spreading out into different areas of chemistry and biophysics. It's not the best strategy for recognition, but I was just too interested in learning about new subjects to stick to one narrow sub-field, and was also a bit of a daredevil, sticking my nose into projects of which I knew nothing (I used to be the guy who'd put on a green wig to make a fool of himself in a crowd just for a laugh).
I also learned during this period just how important the social element of science is. Many excellent scientists achieve little because they can't get on with other scientists. But I was gregarious - got on well with most people. So when some colleague came and asked how we could collaborate, I'd often dream up some questionable way of doing so.
A junior group leader needs to be able to devise research, supervise it and write it up. I always knew I could do that, even as an undergrad: it was actually doing science I wasn't sure about early on. In one's twenties and thirties in science, as in many jobs, one learns one's strengths and limitations, comes to terms with them, and devises a way forward playing to the strengths with the limitations on board. If that way forward is beneficial to society, you have a career.

As a senior guy. Driven by impact and quality improvement. No longer needing to prove oneself to anyone (or to oneself) in quite the same way, things get more serious and focussed. A range of techniques has been mastered and these, while still evolving, will probably form the core of what I get involved in in the next 10 years. So what happens now is a gradual, step-by-step expansion of known territories, simultaneously on many fronts. Herschbach said it's like rolling out a big red carpet which has no end. For me that carpet is more an area than rolling in one direction, with each co-worker working on a different part of the perimeter. I am helping one co-worker to push it out first on one side, then going over and helping another push elsewhere. A body of work expands, about 15 publications a year, and much of my time is thus spent trying to understand what co-workers have found then helping them formulate language that expresses as accurately as possible what these findings are and mean. Thousands of other scientists are pushing out their carpets, too, and their pushing helps unroll ours and vice versa. Where and how we push gets to be more important now: I'm driven by trying to improve the quality of I do, by applications to fields of importance for society, and by communication to non-scientists.

But sometimes I look up at a plaque on the wall at home, made and signed with generous thanks by 50 ex-co-workers. As a grad student, and even 5 years ago, I never thought about such a thing, but maybe that symbolic plaque drives me more than anything else.

Amusing Quotes from Reviewers...

2011-05-24T11:47:00.000-07:00

..of papers in Environmental Microbiology in 2010 can be found here.

These are my favourites:

* Done! Difficult task, I don't wish to think about constipation and faecal flora during my holidays! But, once a referee, always and anywhere a referee; we are good boy scouts in the research wilderness. Even under the sun and near a wonderful beach.

*This paper is desperate. Please reject it completely and then block the author's email ID so they can't use the online system in the future.

*The biggest problem with this manuscript, which has nearly sucked the will to live out of me, is the terrible writing style.

*I usually try to nice but this paper has got to be one of the worst I have read in a long time.

*Well, I did some of the work the authors should have done!

* I feel like a curmudgeon, but I still have problems with this paper.

* The lack of negative controls. . . . results in the authors being lost in the funhouse. Unfortunately, I do not think they even realize this.

* Reject – More holes than my grandad's string vest!

* The writing and data presentation are so bad that I had to leave work and go home early and then spend time to wonder what life is about.

Extraordinary!

2011-05-02T14:29:00.000-07:00

On 8 August 2009 Norwich City, who had just sunk to the doldrums of League One (the English Third Division) were hammered 7-1 at home, the worst home defeat in their 107-year history, by the tiny minnows of Colchester United. That day of humiliation will ne'er be forgotten. However, the hitherto useless Board then miraculously saw the light, as they then summarily sacked the Norwich coach and (ahem, illegally) stole the Colchester coach, Paul Lambert (below), instead!

..............................Tough Glaswegian................

Now, 21 months later, Lambert has steered City not only to the League One championship but, today, to the English Premier League. Back to back promotions, on a shoestring budget, and trashing Ipswich twice (4-1 and 5-1) along the way! Surely the greatest achievement in City's history? Although 23 million pounds in debt, the club will now receive a slightly obscene 90 million pounds for joining the big guys.

Now in 2009 I did write a bitter, angry poem to accompany them on the way down to oblivion. But somehow poetry excels only in times of grief so there will be no lines of verse this time round.

But, ahh, the heart could sing like a Norwich Canary!

Watch out Chelsea, Arsenal, Man U: you're all in for a serious pecking next season!

Update: this is why teams have difficulty in scoring against Norwich.

Hmm.....

2011-05-01T19:21:00.000-07:00

Hmm...despite being a wizened old republican, I can't begrudge 2bn viewers their gooey romantic feelings.

Notwithstanding, I couldn't help but chuckle at some of the wryer comments.

One, from a London Times writer, capturing Miss Middleton's strategic hoist from commoner to royalty, described hers as a tale of “shiny new money systematically raising a girl so perfectly to a prince’s eye level that she is virtually indistinguishable from the real thing.”

And then, a commenter in our own beloved Knoxville News Sentinel: "She has perfect teeth. She can't be British. I demand to see a birth certificate."

Gorgeous!

The Tennessee State Senate

2011-04-28T18:47:00.001-07:00

..a venerable chamber that performs sterling work for the people of the state (and the University of Tennessee).

However, were the senators sponsoring bills to be a little less clueless about what it is they are actually proposing, then certain birth pains would be avoided ....

Good Science Takes Time

2011-04-04T23:50:00.000-07:00

One of the things about Martin Karplus that many of us impatient, ambitious young co-workers at Harvard used to complain about was how long it took to get one's work published with him. One of my manuscripts sat on his desk for 18 months then he lost it. But Martin is a perfectionist - for him a piece of scientific research needs time to mature, to develop, and he wanted to make sure all was rounded, completed, cross-checked, watertight. And so now Stefan Fischer, another perfectionist, has an article on haemoglobin with Martin just accepted in PNAS. The work was started in 1992 and so they have been polishing on it off and on for nearly 20 years. One would work on it a bit, then the other, then neither for a while. The result was a high quality piece of work. I'm sure every sentence was thoroughly thought through.

So why am I bringing this up? Firstly, to demonstrate the futility of funding agencies micromanaging projects and asking for immediate impact. This distracts from innovation. The impact of the money funding the above PNAS paper will be felt only 30 years later. This is not to try to circumvent accountability. Rather, that more emphasis on judging us should be placed on what we did years ago, rather than last week. And secondly, to my irritated students complaining about manuscript slowness after hearing nothing from me for a few weeks - think yourselves lucky, you might have ended up at Harvard! Happy 81st, Martin.

Setting Fish Free Bridge

2011-03-25T22:36:00.000-07:00

This is the Fangsheng Bridge in Zhujiajiao, a Venetian-style Water Village near Shanghai that our host Dongqing Wei kindly took us to visit a week ago. Fangsheng is a 16th century "setting fish free" bridge, at the foot of which vendors sell bags of fish and turtles. Buyers then set them free in the water, thus smugly gaining merit according to Buddhism. (Did anyone ask the fish and turtles if they would rather have not been caught in the first place?).

In some ways the fish are an analogy to what China is trying to do with basic science - set it free. Funding for basic science is now doubling in the space of two years. Sounds impressive (although the actual dollar numbers will in the near term only approach those of NSF or BES, not surpass them). But judging by what we saw at Shanghai Jiao Tong University the building infrastructure is also in place. What seemed to me to be missing was a critical mass of top quality faculty. SJTU has started this recruitment, and we talked to some recent recruitees - all originally Chinese who had been in top positions in North America. Indeed, one of the natural consequences for the USA is that this funding increase, when coupled to the equivalent defunding proposed by the US Congress, should lead to a potentially large proportion of the brilliant young Chinese, of the type that have been dominating the contests for leading science positions in the USA over the last 20 years, preferring the exciting challenges beckoning in their country of origin.

Scientists are fish in bags - we can swim only wherever we happen to be set free.

Baron Cut-and-Paste

2011-03-01T03:28:00.000-08:00

The German Minister of Defence resigned today. "Baron Cut-and-Paste" was found to have copied large parts of his law doctoral thesis without attribution. He lives in a castle in Bavaria with a beautiful wife, an aristocratic "dream of a politician" earmarked as a possible successor to Merkel. The poor dear is now undone by "Xerox-gate".

Will he now be consigned to oblivion? Will anyone even remember his name? Unlikely, given the length of it: Karl-Theodor Maria Nikolaus Johann Jakob Philipp Franz Joseph Sylvester Freiherr von und zu Guttenberg. He could at least take out the "Maria". That wasn't serious for a defence minister. I suspect Donald Maria Rumsfeld wouldn't have had quite the same clout in the Oval Office back in 2002. Yes: shorten the name as well as the thesis, mate. After all, few remembered the name of Johann Gambolputty de von Ausfern Schleppenden Schlitter Krasskrenbon Fried Digger Dingle Dangle Dongle Dungle Burstein von Knacker Thrasher Apfel Banger Horowitz Tikolensich Grander Knotty Schpelltinkel Grandlich Grumbelmeyer Spelterwasser Kurzlich Himbeereisen Bahnwagen Gutenabend Bitte Ein Nürnburger Bratwurst Gerspurten Mit Weimacht Lueber Hundsfut Gumberaber Schönedanke Kalbsfleisch Mittler Aucher von Hautkopf of Ulm(*), did they?

[There's something about stories such as zu Guttenberg's that makes me feel illicitly warm and smug inside.......]

(*) lifted from Monty Python (It's the Arts).

Fortuna Imperatrix Mundi

2011-02-22T08:30:00.000-08:00

Two Moments of Life beyond my control, on New Year's Eve, and yesterday:

31 December 2010: My partner Stephi is diagnosed with pulmonary metastatic myxoid liposarcoma. Multiple visits to Vanderbilt University Hospital ensue. Thoracotomy February 15th. Chemotherapy with highest-possible doses of doxorubicin (the "red devil") and ifosfamide (liquified mustard gas) planned starting in March. Prognosis: tough, uncertain battle ahead.

21 February 2011: Pathology results indicate that the resected masses were histoplasmosis, a fungal infection. No chemotherapy. No life-threatening disease. Prognosis: A slow but sure recovery from the pulmonary surgery ahead, back to a normal life.

Fortune: Empress of the World.

We are powerless against the whims of Fortuna.
But when her wheel turns in our favour, we must grasp the chance she has given us.

Shakespeare, in Julius Caesar, wrote:

"There is a tide in the affairs of men, Which taken at the flood, leads on to fortune. Omitted, all the voyage of their life is bound in shallows and in miseries. On such a full sea are we now afloat. And we must take the current when it serves, or lose our ventures"

My Salary over the Decades

2011-02-12T04:30:00.000-08:00

It's interesting to look at salary ups and downs over the years. Here I have taken my earnings at the time then converted all amounts into approximate 2010 US dollars by converting the local currency to US dollars using the rate at the date concerned here and then correcting for inflation using this site.

1973 (Aged 13).

First ever employment: A Sunday paper delivery round paid by the local newsagent!
Salary: $2.85 per morning for about three hours of work.
Comment: This lasted about three Sundays. I had to get up at 6 a.m., which really went against the grain, then stuff papers through too small letter boxes in doors. I would get it wrong, and then be exposed to irate customers who needed their Sunday morning papers. Furthermore, the coins earned just got lost - I clearly had no desire for the money and only did the paper round because it was the thing to do at the time.

1978 (Aged 18)

Undergraduate stipend: $5,500 per year.
Comment: In retrospect we were very lucky, us seventies British undergrads. Not only had we no tuition fees but we received a stipend. $4000 of the above was sadly removed at source for food and lodging, leaving $1500 per year which went exclusively on beer (not books). That bought a lot of beer because the student union subsidised it.

1979 (Aged 19)

Summer employment: $150 per week.
Comment: pulling live turkeys out of a lorry then hanging them upside down on a moving rail for electrocution. Not very considerate of our squawking friends I'm afraid. Paid for a trip to India later on.

1982 (Aged 22)

Postgraduate stipend: $46,000
Comment: In the money!! The UK funded three stipends per year at the Institut Laue Langevin generously to attract good students and because tuition was subtracted. In my case I registered at a department with small tuition fees (Birkbeck College).

1985 (Aged 25).

Postdoctoral salary: $24,000

Comment: Ph.D. leads to near halving of salary! Anyone know other examples of that?
Interestingly, I didn't seem to notice the difference. I remember I never even asked what the salary would be - just showed up for work.

1989 (aged 29)

Ingenieur CEA: $53,387
Comment: Standard starting salary for a French goverment "engineer." Creeps up very slowly over subsequent decades, (almost independent of performance I would claim). Similar salary to those halcyon graduate student days.

2006 (aged 46) :

German Full Professor: $96, 000

Standard German C4 professor rate, I think. Need to take into account generous benefits when really comparing with US equivalent.

2011: Well, all TN state salaries are published and open information....:-))

Cantona: Director of Football?

2011-01-23T15:57:00.000-08:00

Well whoever would have believed it? Eric Cantona, here seen Kung-Fu kicking a Crystal Palace fan, has been named Director of Football at the New York Cosmos. Maybe he was chosen because of the deep philosophy he will communicate to the team? His proposed solution to the global financial slump was a run on the banks. And here's a favourite Cantona quote of mine: "Quand les mouettes suivent un chalutier, c'est parce qu'elles pensent que des sardines seront jetees a la mer (Seagulls follow trawlers because they think sardines will be thrown into the sea)". Important for young players to internalize these things.

Why is it that clubs think the best players always make the best directors? Surely Cantona will go the way of that other footballing great - chemical-crazed Diego Maradona - who, for some reason undeciphered by rational humanity, was chosen to manage Argentina for the last World Cup. Maradona guided the country to a 6-1 rout by Bolivia and a 4-0 hammering by Germany before leaving with the team in chaos.

9 megatons dismantled

2011-01-23T13:24:00.000-08:00

Given that the 9-megaton B53 bomb recently dismanteled at Y-12 reportedly had the potential to flatten most objects within a 10-20 mile radius, and that Y-12 is only a couple of miles from ORNL, I'm kind of relieved that the mission was safely accomplished!

No, seriously, I'm sure there was virtually no chance of a nuclear inferno happening, although the workers involved would have had to be careful to shield themselves from the toxic materials. The operation also demonstrates that Y-12 has an important role to play in peace through nuclear disarmament.

Cut Everything Except Seeding for the Future.

2011-01-17T00:16:00.000-08:00

Now for a somewhat political statement - I don't make many of them here.

As we all are aware, many countries have experienced large reductions of government income due to the recent near-global recession. Now, although I do appreciate that 'stimulus' measures can be effective, and I don't pretend to master the fine art of recession economics, it does seem to my simplistic mind that income reduction should be accompanied by reductions in government spending.

So the question would be where to make the cuts? Well, in this question I tend to think like an average household might. An average household would cut down on the luxuries while keeping the essentials, and would shore up their financial situation for the future. So that's why, for example, I don't think government tax incentives to encourage spending on luxury items makes sense when you're trying to stimulate a healthy recovery. It might indeed help lead in the short term to economic activity and an increase in GDP/employment etc, but in the longer term it would just increase debt.

So cuts need to be made in spending that does not promote economic growth. This, in the US, should include the big three: social security, medicare/medicaid and the military, which together make up the majority of federal spending. As for entitlement spending, certainly truly disadvantaged citizens need help to remain healthy and get back on their feet, and I'm aware that federal money spent in these fields is indeed immediately ploughed back into the economy, but this money arguably does not stimulate longer-term growth. We need to think creatively of ways of maintaining and improving entitlement care without throwing $1.2 trillion per year of federal money at it. For example, how to get more, healthier food on the tables of the hungry while spending less doing so.

We need to cut social security benefits and/or raise the age of full entitlement. And what was the point of the recent reduction in the social security payroll tax without transparent concomitant recalibration of the benefits received in future years? Live now, pay later.

The US medical system, which is one of the least effective and least fair among developed nations, needs to be revamped including (i) coverage for all, (ii) controlling costs and (iii) more competition. The system existing until now has been effective in none of the above. The recent healthcare act goes towards (i) without significantly tackling (ii) and (iii). Phil Bredesen's recent book "Fresh Medicine" describes how to do all three.

As for the military, in my opinion most of the wars fought by NATO countries since WWII have been at best ineffective and at worst disasters, and, by the way, have also done little to enhance economic influence. The Afghan and Iraq wars have wasted trillions. Certainly, our nuclear deterrent needs to be maintained, although we should continually work assiduously towards multilateral reduction. Also, of course any existing threats to Western society must be tackled, but this in an effective, and cost-effective, way: the present, dumb, invasion-based attempts at doing this have proven useless and painfully expensive.

So, it's across the board cuts, then, is it? Well, no. Government investment that is likely to produce clear economic return should be maintained. This means education, science and technology. Now, some people think that the government should keep out of anything to do with R and D - market forces will create the demand, stimulating private research. But the problem is that the financial system is skewed towards short-term gain, so private investment does not represent the longer-term wishes of the people. The result of this is that we are failing on counts that are of prime importance to us and our families. Why, for example, do we we spend $900 billion per year on the military but $5bn on cancer research funding? Think of the relative suffering families endure at the hands of foreign foes relative to disease. Admittedly in 1940 we had to put everything we had into defending our patch. But, today, are we really 200 times more scared of the Taliban than cancer? I wrote at length about this in a previous blog entry, and to some extent this paragraph simply reflects what was written there. Science and technology are the way forward for the military as well, and in protection against terrorist attacks. In this the British government has led the way in recently proposing huge cuts in government spending while ringfencing science.

As for raising taxes? Certainly: in one way or another for those who got us into the mess in the first place, ranging from those responsible for extreme leveraging in certain banks right on down to the many individuals who borrowed too much. For the rest of us? Well, even if we don't feel responsible for the sub-prime crisis and ensuing debacle, maybe we should all chip in a bit. Higher taxes temporarily to get the deficit down subject to the condition that spending be also reduced.
Maybe economists would crucify this concept, but it is, in a way, what an average household would do.

Finally, will any of the above happen? No. I can't actually see any of it happening at all. None of it. Can you?

John Lennon, Natural Healing and the Church in Southern Germany

2010-12-12T04:50:00.000-08:00

The magnificent Heiliggeistkirche.

Well, I'm on one of my tri-monthly visits to Heidelberg right now, and happened upon a couple of articles in Friday's local Rhein Neckar Zeitung that offer contrasting perspectives on attitudes towards activities that, from the point of view of the Church in Southern Germany, might appear borderline.

The first article reported on a concert entitled "John Lennon forever!" by 'Freddy Wonder and friends' in the magnificent Heiliggeist Church in Heidelberg. The Lennon concert was hailed by all as a triumph and the Heiliggeistkirche as the perfect place to hold it, despite the fact that Lennon himself had an uneasy relationship with Christianity and, for a while, practised Hinduism.

The second article reported on the eviction of the "Naturheilverein" (Natural Healing Club) from the Catholic Church Rectory rooms in the tiny village of Spechbach in the surrounding Odenwald forest. The Club has been meeting in the Spechbach Rectory since 2002, and has now grown to 300 mostly female members. They were welcomed by the local priest, Father Meier, so long as they were offering innocent-sounding courses such as 'Mushroom Identification', 'Healthy Eating', 'Seminars for Couples and Pairs' and '"Classical" Homeopathy'. So far so good, but then the ladies started to offer suspicious-sounding courses in 'Chakra Meditation' and 'Healing with Stones'. Father Meier and the Catholic elders appeared to swallow hard and turn a blind eye. However, with recent offerings such as "Healing the Soul with Shamanistic Psycho-Kinesiology" the ladies have finally danced across the line, and are thus out on their asses. Pushed it a bit too far. They are, it is reported, rather aggrieved as they have already printed 4500 brochures for 2011 with the Catholic Rectory Rooms named as the meeting place.

I can't imagine 'Imagine' being allowed in the Heiliggeistkirche 30 years ago, so maybe the Nature Ladies would just need to wait awhile? Hard to predict that one, but I do suspect that in 2040 they'll still be in alternative accomodation.

CAUTION: graphic descriptions of disease and violence below.

2010-11-21T04:30:00.000-08:00

Excerpt from “The Emperor of All Maladies: A Biography of Cancer” by Siddhartha Mukherjee. Mukherjee, a doctor, describes watching a two-year-old leukemia patient’s condition deteriorate as another drug fails:

"The patient “turned increasingly lethargic. He developed a limp, the result of leukemia pressing down on his spinal cord. Joint aches appeared, and violent, migrating pains. Then the leukemia burst through one of the bones in his thigh, causing a fracture and unleashing a blindingly intense, indescribable pain."

Excerpt from "JOKER ONE: A Marine Platoon's Story of Courage, Leadership, and Brotherhood" by Donovan Campbell.:

"The little kids stood in a tight knot on the sidewalk right next to our third vehicle, waving at us as we hopped in the Humvees, pleading for us to hand out more gifts.... Another explosion rang out, and the crowd of small children disintegrated into flame and smoke. From somewhere behind me, Marines started screaming out the worst words a platoon commander can hear: "Doc up! Doc up! Someone get a corpsman! Doc up!"I jumped out of the Humvee and looked around. I can't give specifics of the scene—I was too busy scanning the whole area and sorting out the enemy threat in my head—only a general impression, and it was of a macabre tableau from hell. The rocket had missed us. Instead it had impacted squarely in the middle of the crowd of small children. Dead and wounded little ones were draped limply all over the sidewalk, severed body parts mixing in with whole bodies, or in some cases flung even farther, into the street. Blood, always the blood, streamed onto the sidewalk and into the dirt, where it settled darkly in pools or rivulets. Across the whole scene drifted smoke and dust. The Marines jumped out of the vehicles and ran helter-skelter among the children, collecting the wounded and their body parts, applying first aid where they could. The docs were working frantically. I noticed, strangely enough, that they 'adn't bothered to put on their latex gloves."

Now for Jeremy's Soapbox:

We just don't get it. Why do we just accept cancer, heart disease and the other deadly afflictions? We just seem to seem to grin our teeth and bear it. People must not care, and here's why - because they only spend 0.2% of their wealth on finding ways to stop diseases. The US GDP is about $13tr and yet according to the OECD we spend only $26bn on health R&D i.e., 0.2%. Obviously we just don't care. Yet there are 1.5M new cancer cases per year in the US, and 500k cancer deaths. 1 in 4 of us will die of it, and a further 1 in 4 from heart disease. This absolutely dwarfs anything terrorism will ever do to us. If we make the effort research WILL stop these diseases. If people knew that themselves and their loved ones would be spared these diseases, wouldn't they want more than 0.2% of their income dedicated to it? Apparently not. Life is indeed cheap. We live for today, and don't care of tomorrow. Needed basic research is not funded, promising molecules are not synthesized and tested and clinical trials go unperformed.

As for energy research, improving and encouraging homegrown energy sources, while not eliminating international conflict, will surely lessen the pressure to go and fight foreign wars. Yet we pump trillions into stalemate conflicts while neglecting this simple way forward for both national and energy security. Again we fail to get it.

Science can cure cancer, heart disease, Alzheimer's, multiple sclerosis and the other hellish diseases. Science can mitigate the need to fight foreign wars, increasing national security via energy independence with renewable energy. Curing dreaded diseases and achieving energy independence is possible. But it takes time and resources and the short-term nature of the financial world makes it difficult for industry to do the groundwork research needed.

Energy and health research and development should be a top priority over the next twenty years. We must make sure the world's brainiest kids go into science and receive the support and motivation they need to do their research.

Why do we casually accept Middle Eastern oil as the lifeblood of our energy economy, and

two-year olds dying in excruciating pain?

What makes a 16-year-old GIVE UP?

2010-11-17T11:15:00.000-08:00

I gave up pronto, I did, in 1976, on a dark afternoon in the dark country, Wolverhampton, England.

I had feverishly trained at long jumping for four summers, several times a week. My run up was paced perfectly to hit the board, with two checkmarks, my hang technique was impeccable, and I had made it to the National Under-17 final.

There it all ended abruptly! There were eight of us, and I finished a solid, emphatic last, more than a foot behind the lad in seventh place, and a meter behind the winner, Gus Udo. Outclassed, depressed, I realised the talent just wasn't there. That's what makes a 16-year-old give up. I never jumped again. Not once.

Not so my training partner Tim Newenham who kept going, threw javelin at the Commonwealth Games, became National Javelin Coach then fitness coached the tennis player Tim Henman for five years (Henman's the English guy who reached the Wimbledon semi-finals four times and lost each one, thus firmly cementing the national sense of sporting futility!). Now, with pleasure I see Tim N. is javelin coaching Oliver Bradfield from my same old athletics club, and Oliver last year threw 63m, the best throw in the world for his age, and this year over 75m, breaking the UK U15 record by over two meters. Way to go Ollie and Tim!

As for Gus, well, his 7.08m winning jump in 1976 broke the championship record, and he also won the high jump. I couldn't seem to get away from him, because we both ended up at Harvard a few years later. He, however, was the revered co-captain of the Crimson track team while yours truly gave him a wide berth. Fingers burned, you see...

Oliver Bradfield, wearing that same Norfolk County athletics vest I wore 34 years ago (brings tears to one's eyes, it does :-)).

New Musical Creation

2010-10-13T05:48:00.000-07:00

I like to create and perform music, and my latest album, Paroxysms of Indifference, is now available for free download on last.fm (just click the icon on the right). Paroxysms follows 'Elementary' with the Parisian “Baskervilles Blues Band” (1994) and the Johnson’s Jump (2004) piano improvisation compilation.

The tracks on Paroxysms were recorded between about 2005 (I think) and last week.
Here's a description:

Tripped Hop (electronic): Was supposed to be inspired by Massive Attack’s Trip Hop style but somehow strayed from the straight and narrow.

Three Jolly Boys (Traditional English folk, Acapella): Bit of fun about women and drink but delivered too straight laced (rather angelically).

Reverie in White, Black, Blue: Dreamy improvised piano with white, black and blue themes.

Okavango (electronic): The Okavango delta in Botswana every year undergoes a remarkable river swelling, bringing life with it. You can here the flooding river towards the end.

Light on a Faraway Shore (Orchestral): Inspired by a night-time sailing approach to Milford Haven when I was 13. The bell represents the light and you can hear the yacht lolling, rain arriving with an increased swell and yawing, then, as the rain stops, the boat continues to approach the shore slowly.

Lac du Plan Viannay (Improv Piano): A remote, high lake in the Parc des Ecrins.

Fion: (Acapella). Traditional Gaelic Song. Yes, I’m singing all the parts! (Duh!... no, not all at once)

Paroxysms of Indifference (electronic): Title refers to the critical acclaim this album is sure to generate. Towards the end gets a bit Stravinsky-esque with the dissonance.

Song of the Wandering Aengus: W.B Yeats’ poem about the Irish mythological figure, set to music. Only track with acoustic guitar in.

Recording details: All music and vocals for all tracks performed arranged mixed etc by JCS. All tracks also composed by JCS except for the traditional vocal numbers and ‘Aengus’ for which the lyrics were by Yeats and the melody by D. Leitch. Software: Cakewalk, Garage Band. Light on a Faraway Shore was written using Finale Print Music and was the programmed straight into the computer using a software synthesizer. It was thus only piece not ‘performed’ using a musical instrument. MIDI-free.

Instruments: Keyboard: Yamaha Motif, Guitar: Guild acoustic with rotten strings, Piano: Kawai Grand (bass A flat slightly out of tune).

How to Win a Nobel Prize in Physics

2010-10-05T13:23:00.000-07:00

Andre Geim : "You put [sticky tape] on graphite or mica and peel the top layer. There are flakes of graphite that come off on your tape. Then you fold the tape in half and stick it to the flakes on top and split them again. And you repeat this procedure 10 or 20 times. Each time, the flakes split into thinner and thinner flakes. At the end you're left with very thin flakes attached to your tape."

Aha! That's all it takes, then. Maybe we should quit messing around with supercomputers and pulsed neutron sources....?

Powerful Supercomputer Peers into the "Origin of Life"

2010-10-04T11:19:00.000-07:00

ORNL has just released this press article on our research into a ribozyme, performed by Tomasz Berezniak together with Mai Zahran, Petra Imhof and Andres Jaeschke and myself. The UT Kraken supercomputer bore the brunt of the load for these calculations. The work was published in this article. Ribozymes (catalytic RNAs) were the center of a presumed RNA world at the early origins of life.

Drug Discovery Research at Oak Ridge

2010-10-01T11:52:00.000-07:00

Well, I've been involved to some extent in human health research for a while, including participating in research suggesting a common pharmacophoric footprint for AIDS vaccine design and in helping design experimental methods for detecting single tumour marker molecules in serum.

Now we appear to be on the road to working with Milton Brown and his colleagues at Georgetown University in prostate cancer research, as part of a new NIH Clinical and Translational Science Award center. Milton heads the Drug Discovery Center at Georgetown Medical School. The idea here is to use Oak Ridge's supercomputers to help design molecules of potential therapeutic use. Jerome Baudry will play a leading role in this research from our side. I'm kind of excited about what might happen.....

Something Wondrous Happens to this Blog.....

2010-09-10T02:16:00.000-07:00

At 2.08 p.m. EST on Thursday 9th September 2010, something wondrous happened to the detached, unassuming, sleepy, oft-neglected little cyberspace backwater that is Club Mod. It was touched by magic.

Events started to unfold at 10.22 a.m. when Frank Munger gave a nice plug for the previous Beam me Up Scotty (BUS) post on his Atomic City Underground blog. But then, miraculously, the eye of the almighty Instapundit fleetingtly alighted on unsuspecting little Club Mod (apparently via the Atomic City entry), and, at 2.08 p.m. --- linked. Our dumbstruck, bewildered little blog was then overrun by 4000 visitors in the next 12 hours - more than in the entire previous year! Well, they've presumably mostly gone now, too late to be welcomed, but we hope that, one day, with or without pixie dust, they'll visit again. If they do Club Mod will try to be up, shaved and ready. But maybe they never will, which reminds me of a quote from Dylan Thomas' "Under Milk Wood":

"Alone until she dies, Bessie Bighead, hired help, born in the workhouse, smelling of the cowshed, snores bass and gruff on a couch of straw in a loft in Salt Lake Farm and picks a posy of daisies in Sunday Meadow to put on the grave of Gomer Owen who kissed her once in the pig-sty when she wasn't looking and never kissed her again although she was looking all the time"

Public Transport: Nah. Beam me Up Scotty!

2010-08-21T06:19:00.000-07:00

I can't imagine conventional public transport ever working out in a sparse city like Knoxville, TN - even if they quadrupled the number of routes it would still take most people 30 minutes to walk to the nearest bus stop - but maybe the time will come when a BUS scheme might work. Now by BUS I don't mean those big, dirty, noisy, infrequent, uncomfortable mass transport monsters, I mean "Beam me Up Scotty" - a kind of really quick, safe and efficient car pooling system. Here's how it might work.

You see, those of us participating as drivers in the BUS scheme would do it for the money and (maybe) company. We would have equipped our cars with a small LCD on the windscreen with a number on it that lights up when we want to be available. All we have to do is enter in our GPS which location we are driving to (to work, for example) and click on the "BUS" icon. When that happens our GPS position and destination would be transmitted to some kind of serious computerized HQ place that instantaneously forwards this info to the GPS-equipped cellphones of any potential passenger also in the scheme. So, the potential passenger, standing on the side of the road, would get a kind of local google map with all the participating cars that are about to drive close by pinpointed together with where they are going. And all the passenger has to do is click on a car. The driver would then get beeped and know to stop and pick them up on the way. The passenger identifies the number on the windscreen LCD (just to make sure) and hops in. The cost of the journey (fixed at, say, 50 cents per mile or whatever) would be shared between driver and passenger and the correct money would be automatically transferred from one account to the other at the end of the journey because the serious HQ computers would be tracking the cellphones of the participants. There couldn't be any hanky-panky, of course, because the identity and position of the participants would be known to the HQ guys. Moreover, you could maybe even preselect what type of person you feel comfortable traveling with.

Could this work?

BMW Owners - you can tell 'em anywhere.

2010-08-02T11:54:00.000-07:00

Here are some of the cars I have owned over the years.

The first was a Citroen 2CV:

followed by a Renault 4L:

then came the AMC Hornet, Renault 5, Ford Escort and Opel Corsa. All the above were low budget cars for people who just need to occasionally pootle from A to B.

However, now I have 2006 BMW 330Ci:

An improvement you might think? Well, maybe from some perspectives, but, apparently, not the social viewpoint. According to a recent article, BMW owners are almost universally despised, and this holds for whatever country the poor owner happens to be in.

Here's a quote:

"The bad rap is worldwide, of course. In the UK we are informed by the boys from Top Gear that BMW drivers are "[expletive deleted]s" (though I think they have since decided those people drive Audi's instead). In Australia they are known as "[expletive deleted]s". And even in Tajikistan the dialect, while somewhat difficult to translate directly into English, refers to them as "[expletive deleted] with [expletive deleted] on a yak's [expletive deleted] to your mother's [expletive deleted]"."

Hmm....maybe I should trade it in for a Rolls Royce???

Cellulosic Ethanol: $2.35 per gallon

2010-07-26T15:32:00.000-07:00

Test plots of switchgrass at Auburn University, taken from ORNL report here.

Well, work on cellulosic ethanol has progressed over the last few years and things look good for large-scale commercial application. A recent report put the production costs at $2.35 per gallon, and ethanol produced from switchgrass yields 540% of the energy used to grow, harvest, and process it into ethanol. Equally important, it appears that switchgrass really is carbon neutral, as it absorbs essentially the same amount of greenhouse gases while it's growing as it emits when burned as fuel.

This kind of progress makes it all the more bewildering to read that budget cuts are planned for DOE, or rather, should I say were planned: these things seem to change direction every week.

Now the economy is just about stabilized we do need to slash government spending, but surely not in an area so critical to national security, energy independence and the environment?

College Athletics Spending - purely a business.

2010-06-24T11:50:00.000-07:00

Ray Cannon in his Tennessee football uniform in 1939. UT won the SEC that year.

Thanks to Splette for this link to an article berating colleges for spending too much on athletics.

I'm not against big spending on college athletics as long as it is cost beneficial to academics, in other words as long as academics makes a profit from the athletics. For some of the smaller colleges this does not appear to be happening.

High-School Rebirth

2010-06-09T15:19:00.000-07:00

Another personal note....

What a pleasure to see one's high school saved!

Poor old Earlham School in Norwich, where I spent six years in the 1970s, was ranked academically 51st out of 52 high schools in Norfolk in 2008 and was also consistently one of the lowest ranking schools in the whole of England, seemingly destined for closure and oblivion.

Now, however, it has been been resuscitated as "City Academy Norwich" with much improved results. Aaaah, so our fond memories of soccer at break time with a tennis ball and who-knows-what behind the bike sheds shall not be despoiled!

Maybe I should even send my own daughter there now?

Wishing the old alma mater the best of luck.

Press Release

2010-05-20T09:18:00.000-07:00

by ORNL here, on an article we published in PNAS.
A Zymomonas mobilis mutant was identified by Steve Brown and colleagues demonstrating sodium acetate
tolerance that has potential importance in biofuel development.
Over-expression of the sodium-proton antiporter
gene nhaA confers the elevated AcR sodium acetate tolerance
phenotype. A structural model for the NhaA sodium proton
antiporter was constructed to provide mechanistic insights.

The LEAF Festival in North Carolina

2010-05-10T14:27:00.000-07:00

Just back from a magical getaway weekend at the LEAF festival in Black Mountain, N.C.
Well recommended for those living in these parts.

Highlights for me included playing my Djembe impromptu with the Atlanta Swamp Opera Cajun Band ("Oh, Madeleine!"), and later again at midnight in the Drum Circle, and tenaciously hanging in there to force a defensive three-hour draw with the chess senior master Robert Frederick (although admittedly he was playing six other people at the same time!).

Flooding in Tennessee

2010-05-04T05:42:00.000-07:00

Every cloud has a silver lining!

Top Gear Visas

2010-04-25T10:47:00.000-07:00

Here's an excerpt from the British TV program "Top Gear" concerning U.S. Visas: rather topical for the current travails of our lab:

James: What we have down here is a selection of American muscle cars. Now the recipe for this for this sort of thing was always very simple: massive engine; crude, simple suspension; very low price; and finally [gesturing to a Dodge Challenger] some orange paint. Now, this sort of thing never really caught on in the civilised world and we thought that what with petrol prices being so high now, they'd have died out in America as well.
Richard: However, in the last few months three brand-new American muscle cars have arrived. So we thought we best pop over to the states and find out if they're any good.
Jeremy: Unfortunately, there was a problem. You see, we all have visas which allow us to go to America and make a factual documentary. But, since our last trip over there when I might have accidentally put a cow on the roof of my car, the American — the U.S. state department no less — has decided Top Gear is actually now an entertainment show.
James: And unfortunately that requires a different type of visa and we didn't have time to go and get one. So, in the end we were only allowed in to the country if we promised — this isn't a lie is it?
Jeremy: No, this is absolutely, hand on heart...
Richard: This is for real.
James: — if we promised not to be entertaining.

with credit to where I originally found this.

They're the Champions...

2010-04-24T09:32:00.000-07:00

Norwich City just won the League One Championship.

Hence I should keep my promise and again lend them my support.

BUT

Let us not forget the team's 2005-2009 elegant swan dive from the heights of the Premier League to the sleepy backwaters of England's third division, which at times drew serious comparison with Britain's Official Worst Football Team (AFC Aldermaston, who recently scraped a draw after 40 consecutive losses).

Hopefully, the return to the second tier signals the swan dive was in reality just the first half of a sweet sinusoidal bungee jump back to the very top.....

Iceland's Eyjafjallajokull volcano

2010-04-19T20:18:00.001-07:00

See here for photo credits.

Yes, thought so, missed one.....

2010-04-13T07:47:00.000-07:00

..from Reasons to be Cheerful Part III:

Sampath K. got a Spot Award from Novartis for a novel method for assessing protein structures.

....and that officially closes the Reasons to be Cheerful blog entry.

Reasons to be Miserable coming up.....(suggestions welcome, to me via e-mail, not directly as a comment here (!!), and no whining please:-)))).

Reasons to be Cheerful, Part III

2010-04-12T15:55:00.000-07:00

(i.e. successes of people I am working with..
..see here and here for Parts I and II.)

Jerome B. got an NIH grant with Igor Jouline.
Xiaolin C. has been publishing like crazy.
Tongye S. got a cheery new postdoc.
Ricky S. got a cheery new supervisor.
Hong G. got a cheery new DOE mercury grant (with cheery me:-)).
Hao-Bo G. got a PNAS paper and yanked his green card out of the fire.
Barbara C. is getting her mega-CPU drug design stuff in shape.
Krishnan got a faculty position
Moumita got a well-behaved cellulase reaction profile.
Jerry P. was on TV talking about our mercury stuff.
Loukas P. is, amazingly, self-similar over 3 orders of magnitude.
Nikolai S.'s simulations agree with spin-echo experiments.
Srini got invited for a faculty interview.
Zheng got beamtime for P450 neutron experiments.
Yinglong got intriguing solvent-channel results.
Dennis G.'s paper on water model comparisons was published.
Xiaohu H. got weird and wonderful phase transitions in water (do we believe them?:-).
Benjamin L. 's lignin:cellulose simulation movies wowed the Undersecretary and others.
Roland S. scaled MD to 150,000 cores.
Jason H. decided wisely to join us.
Barmak M. has learned he can work well wherever he is.
Isabella D. got a faculty position.
Zoe C. got a faculty position.
Nadia E. became a Mum (and got her bacteriorhodopsin paper finished as well!)
Thomas N. graduated summa cum laude.
Petra I. seems to be quite desired in Germany these days.
Jakob U. has definitively solved the peptide membrane partioning problem.
Mithun B. has his theory paper on DNA submitted.
Emal A. is getting a mega-salary (f0r a while).
Tomasz B. got good reviews for his paper.
Mai Z. got good reviews for her paper.
Dieter K. got his QM/MM paper submitted.
Thomas S. got his second actin paper submitted.
Lipi T. understands peptide folding like no other.
Corinne W. got her Diplomarbeit nailed.
Heinrich K.'s model for cellulose H-bonds behaves most interestingly.
Karine V. has a cheery mechanism for nucleosome dynamics.

..now who's going to come back at me for forgetting someone this time?....

ORNL Voted Top Place to be a Postdoc

2010-04-07T12:20:00.000-07:00

....here in The Scientist magazine, though dropping to 38th place from 11th last year.

Did they take into account that Knoxville is Number One nationally for allergies?

Why Science Takes Centuries to be Accepted:

2010-03-17T02:57:00.000-07:00

Read these two articles in the mainstream British media:

"Government Scientific Advisors: Who Needs these Nuts in White Coats"

Excerpt: "The public is no longer in awe of scientists. Like squabbling evangelical churches in the 19th century, they can form as many schismatic sects as they like, nobody is listening to them any more. Unquestioned authority derived from a white coat and a doctorate is as dead as the Druids."

and "The Unpersuadables"

Excerpt: "If they don’t want to know, nothing and no one will reach them."

The more evidence is shown to some people, the less they believe it. For science this is exacerbated by the fact that scientific information appears remote from the day-to-day reality we experience, even if its effect on that reality is solidly established. A layman exposed to 'remote information' that points to him altering his life in any significant way is unlikely to accept it and will mistrust the information provider. He won't accept the concrete link until the results of his actions are staring him in the face. And stoutly defending what he rigidly believes reinforces it in his mind.

Biology and Medical Research at the Exascale

2010-03-08T12:02:00.000-08:00

...a glimpse into the future, but the challenges in reaching the exascale are formidable, not the least in mastering the power requirements and the consequences of regular core failures in systems of 100 million cores.

Foreigners at ORNL

2010-03-04T14:58:00.000-08:00

A recent blog item of Frank Munger's deals with the travails of non-citizens at ORNL. While it's true ORNL overtly brands us as potentially dangerous with glaring red badges, the practical fallout of this and other measures is minimal, and things are somewhat easier than what I witnessed as an "Agent CEA" in the French National Laboratory at Saclay in the 1990s. No, the main obstacles hampering our attempts to get our work done come not from ORNL but from dealing with visas and green cards for lab members - a constant headache.

All this reminds me of my former mentor, Martin Karplus, who tried to move from Harvard to Paris in 1974. The Universite Paris VII (Jussieu) wanted to offer him a tenured professorship, but tenured professors were civil servants and thus had to be French. Enter Jacques-Emile Dubois , a lively man who I enjoyed chatting with occasionally while working with the French Chemical Society. Dubois was a chemistry professor at Jussieu, but he was also Head of Research at the French Minstry of Defence and he had connections high up in the Pompidou adminstration. Dubois got weaving and, sure enough, eventually a decree was published exempting university professors from the citizenship requirement. However, by that time I think Martin had had enough and he didn't leave Harvard (wisely maybe: even a Dubois couldn't cure the deeper sclerosis of the French academic administration), but he apparently received a number of thank-you letters afterwards.

An Open Letter to Sir Richard Evans

2010-02-19T05:37:00.000-08:00

Dear Sir Richard,

As Chairman of BAE you were responsible for securing the largest arms deal in British history: the Al-Yamamah sales to Saudi Arabia, worth $67bn so far over 20 years and potentially $60bn more. Of course this created thousands of jobs in Saudi Arabia and the UK. Admirable!

However, there does appear to have been a slight problem with it, doesn't there?

I mean, it really did seem inordinately clever of your guys to manage to sell a military air traffic control system to the government of impoverished Tanzania in 2001 for $30m when Tanzania didn't even have an air force! There's salesmanship!

And now, finally, your company has admitted to "false accounting" over Al-Yamamah, Tanzania and other deals and agreed to pay $470m in fines. However, Sir Richard, is "false accounting" really the best description? Wouldn't bribery be more accurate?

For example, the US justice department has been investigating claims that $180m a year was transferred by BAE to Saudi Prince Bandar. And the Serious Fraud Office were just about to get going on you lot in 2006 when Tony Blair wrote a secret letter to them instructing them to stop the investigation for reasons of national security (i.e., Saudi threats).

Now, BAE's admission of "false accounting" means that there will be no trials and the company won't be blacklisted. And the fines are tiny compared to the deals, aren't they? It was still all well worth it, wasn't it? And for being the architect of the gigantic Al-Yamamah deal you were yourself well rewarded: a huge salary, a knighthood and considerable power within BAE. Two luxury homes in central London were made available to you by companies linked to al-Yamamah.

But don't you think an admission of bribery would be more appropriate? Restitution of the $67bn to the international companies that lost the deals because of your lubricative activities, maybe? Or, even better, and this is where a lowly molecular biophysicist comes in, setting up a $67bn research fund to develop alternative energy so that we can find ways to stop having to funnel huge sums of money to OPEC countries to buy oil, enabling Saudi princes in turn to transfer vast sums of money to eager BAE so they can retain multi-billion-dollar personal sweeteners. How about it, Sir Richard?

Yours sincerely,

Jeremy C. Smith.

Wonderful Video Compilation from one of our Graduate Students...

2010-02-11T12:04:00.000-08:00

Splette Showreel 2010 from Thomas Splettstoesser on Vimeo.

Having got that out of the way maybe he can now concentrate on graduating??? (grin)

[small disclaimer: about one second of the video depicts cows and small furry animals succumbing to mercury poisoning - not something that happens very often in reality]

To be or not to be...

2010-01-31T06:58:00.000-08:00

..a Norwich City football supporter.

On May 3rd 2009, when Norwich were ignominiously relegated to League One, I announced that I was no longer a fan...and marked the occasion with a bitter, fractious poem.
Now, given recent exploits of the lads on the field there here have been raised eyebrows as to why my green and yellow scarf is still studiously banished to the attic.

Well,

it is true that..

- Norwich are presently top of the table
- The misers have taken 44 out of the last possible 47 points
- They have shattered the club record for the consecutive number of home wins (11 and counting)
- They are packing them in Carrow Road to a point where even flocks of migrating geese have been reported to pause and perch upon the Barclay Stand to take in the spectacle.
- Manchester United's manager, Sir Alex Ferguson, after his team's comprehensive defeat by second-placed Leeds, was rumoured to have said: "Lucky we weren't drawn against Norwich otherwise we would have got a real hammering."

However, one's support should not be pledged lightly.

Therefore, under the following conditions only will I formally resume with the Canaries:

- Norwich are promoted this year.
- Ipswich are not relegated. [Yes, not. This may sound strange given that Ipswich are Norwich's sworn lifelong arch enemies, but there would be little point in them plunging down past us as we are flailing past them on the way up, would there? The existence of the local derby is quintessential. Perenially one place above the relegation bracket is the ideal purgatory for Ipswich.]
- (optional get-out clause, to be invoked facultatively): Norwich City win the World Cup in South Africa this Summer.

However, even were the above conditions to be satisfied, there would, of course, be no guarantee of a celebratory poem.....

Ice-adorned trees in my garden

2010-01-31T06:55:00.001-08:00

Hope it thaws soon because I've been snow-bound at home for two days.

The flora and fauna of Pandora....

2010-01-20T05:47:00.000-08:00

..,which are what made Avatar worth seeing, awaken the innate taxonomist in viewers.

Welcome, China, to the Club of Scientific Superpowers

2010-01-15T15:02:00.001-08:00

Data, released today by NSF, illustrate quantitatively what many have been feeling over the last 10 years - that China is surging in the world of scientific research. Looking at the rate of change of many indicators, China will very soon overtake the U.S.

This has been interpreted in gloomy terms as a "worrisome trend showing erosion of U.S. competitiveness" and as indicating that the "U.S. dominance in science is at risk".

I would look at things a different way. I would welcome China to the club of scientific superpowers, applaud their progress over the last decade (which does not seem to have been mirrored by India, which arguably could have done as well), and try to see what we can learn from it.

Well, the U.S., to its credit, has lead the world in welcoming qualified foreigners to populate its research universities and fuel the creative technological drive the future always requires. But since time immemorial (meaning, at least since I was first in the States in '85-'89!) we have bemoaned the number of homegrown graduate students in the sciences. Local kids just don't seem to get motivated and curious about finding things out.

Compare this with the sentiment embodied in the following quote in Time Magazine from Energy Secretary Chu on a trip to Beijing: "In the U.S., rock stars and sports stars are the glamour people. In China, it's scholars. Here, Nobel laureates are the equivalent of Britney Spears." If this is truly the case, look forward to a fair fraction of the best and brightest of the youth of the presently 1.3 billion Chinese keenly dedicating their creative abilities to science.
And if, as is likely, the U.S. cohort remains mired in banker/rock-star/NFL fantasyland then China will quickly swamp the science stats.

How, then, will the U.S. remain at the table? Maybe the only way will be to rapidly further step up immigration of qualified talent from China? Rapid immigration isn't impossible - just look at Vancouver which, in the blink of an eyelid, has quickly become 30% Chinese, albeit not uniquely of the highly-qualified variety. But whether such an influx happens in the U.S. may well depend on whether we will continue have the means to attract the brightest over here. If not......

Snake-Mimicking Moth

2010-01-14T15:02:00.001-08:00

....the picture tells all.

ORNL-UT cooperation to be strengthened..

2010-01-11T13:55:00.000-08:00

....according to an announcement by Gov. Bredesen, with 200 new faculty positions at UT staffed by researchers at the lab, and a doubling of the number of doctoral degrees awarded at the university. This is just what both institutions need, but for best effect will require overcoming some obstacles.

One of these is that there is a problem at ORNL in housing undergraduate and graduate students and postdocs as they do not 'carry off' much overhead. Thus, according to the 'full cost recovery' model by which ORNL operates, these young researchers become financial liabilities for ORNL, which must provide office space, heating, basic facilities etc out of the organisational burden (overhead), even if they arrive with salaries from elsewhere. This problem could be remedied at least in part by expanding the space allocated on the ORNL campus to the UT/ORNL Joint Institutes, by re-assigning parts of existing buildings, if this is legally conceivable. My perception (maybe wrong?) is that the Joint Institutes have so far been largely technology platforms e.g., for the Bioenergy Science Center (BESC) systems biology apparatus and the UT/ORNL NSF Kraken supercomputer. Although BESC and Kraken have been very successful for both UT and ORNL, (and I am involved with both myself) the dedication of the Joint Institutes to facilities rather than UT:ORNL grassroots research cooperation leaves a vacuum. So basically what I am saying is that if a student, postdoc or visitor wants to come and work with an ORNL staff member or UT faculty member at ORNL (and has their salary already paid from some external source) then ORNL needs to have a mechanism in place to welcome these people with space, offices and open arms, without needing to worry about extra costs, and whatever the subject they work on: this will be cost effective for ORNL in the long run as it will produce lots of cheap, high-profile science that can be used to write money-winning grants in the future.

Secondly, if ORNL staff scientists are to become UT faculty then they need to teach - maybe not a lot, but some at least - and most of the staff scientists I know would be happy to do this. This would help staff UT classrooms in the coming budget crunch, but there would have to be a mechanism in place to pay them. Given the relatively high salaries and astronomical overheads applied at ORNL the hourly rate of an average staff scientist is likely to be much higher than UT could afford. Hence, the corresponding budget strain may have to be absorbed by the funding agencies currently paying the staff scientist salaries. How they could do that is a good question, but I believe it is in the interests of the agencies themselves (DOE, NIH, NSF, etc) that their funded researchers keep their minds broadened and in contact with bright students by the noble endeavour of teaching. It's certainly in the interests of both ORNL and UT to have hordes of bright, motivated graduate students populating the offices and corridors at Oak Ridge at midnight...

Quote of the Decade

2010-01-01T06:28:00.001-08:00

...for a football tifoso at least.

Pepe Reina and the big red ball.

"I lost sight of the official ball and stayed on the red one. I went for the red one instinctively as that was the one closest to me and the other one went past me." Pepe Reina on that demon beach ball that condemned Liverpool to a 1-0 defeat by Sunderland, October 2009.

Wishing readers all the best for 2010 and not too many red beach balls.

Air Travel the Day after the Detroit Terror Incident

2009-12-28T13:20:00.000-08:00

In a classic case of 'closing the barn door after the horse has bolted', the day after the Christmas Day bombing attempt on flight NW253 we of flight DL9 bound for Atlanta were subjected to two hours of delay at Heathrow airport for extra frisking. Then, at Immigration at Atlanta, my fingerprint machine appeared not to work, leading to my being taken to another room and left forlornly for two further hours, thus putting paid to any futile, lingering hope of making the connection to Knoxville.

Now....here are some, possibly relevant, facts...

.....anti-terrorist wars have already cost the US at least $800 bn and finally will have cost an estimated $2-3 trillion,
.....of the order of one hundredth of the above amounts (i.e., ~$10 bn) has so far been spent on improved airport security, and this not always wisely.
.....a "puffer machine" capable of detecting explosives such as that allowed on NW253, costs about $160K; sniffer dogs presumably less.

Maybe I'm wrong, but by my estimation, given the money already spent, which is still only of the order of 1% of the cost of the wars, enough puffer machines etc could have been installed, sniffer dogs bred and trained and friskers hired to effectively, easily, rapidly and quickly process all international flights into the US.

...and I wouldn't have missed my flight to Knoxville.

Off for 3 weeks in Europe

2009-12-04T14:08:00.000-08:00

Including a trip to England and then to Germany for, among other things, my 50th birthday symposium. Thanks to Jiancong for the comforting opinion that 50 is the new 40. The photo illustrates why when driving to Germany from Britain it's best to do what I do and avoid navigating via France...

Our mercury research on the local TV...

2009-12-03T11:26:00.000-08:00

..here..thanks to Jim Matheny of WBIR Channel 10 for the interview.

The Physics of Biomolecules

2009-12-01T09:34:00.001-08:00

"The Physics of Biomolecules" UT Physics colloquium webcast, 30th November 2009. Relatively pedagogical at the beginning but then accelerated a bit too fast in order to reach the movie at the end.

Very kind plugs from Frank Munger's Atomic City Underground

2009-11-27T15:10:00.000-08:00

Here, here and here.

Much obliged kind sir - members of our lab greedily devour your posts as well.

Now, I really must get back to preparing Monday's UT physics colloquium.

Massive Climate Data Scam?

2009-11-26T07:10:00.000-08:00

OK, so I respond to the comment on the previous post claiming that climate change data are phony and rigged to achieve a predetermined conclusion. The principal reason that this is unthinkable is that hundreds climate data have passed the peer review system by which anonymous experts opine on the veracity of data and conclusions in any scientific paper. Anonymity means that the authors are not told the identity of the reviewers who are then freer to criticize without fear of professional retribution. Now, the peer review system is highly imperfect – the reviews themselves are frequently wrong or contradict each other, and thus rubbish gets published, including in the very top journals. We’ve had famous examples of that, even from respected professors, such as the water memory/cold fusion affairs, and, in the other direction, future Nobel-prizewinning science has been initially rejected. Furthermore, peer review, and the funding process, does not fully protect against cronyism and gatekeeping: a paper or grant proposal challenging orthodoxy is more likely to be rejected (unless clearly irrefutable) as the editor and reviewers are more likely to support the mainstream. But this is natural: extraordinary claims require extraordinary evidence. Further, these papers can be resubmitted and, if they are of some merit they will likely eventually appear in some other peer reviewed journal, where they will then likely attract unusual subsequent attention. The nature of science is such that these published results can be objectively tested independently, and by this process the truth normally is established. Further, scientists in any field LOVE to prove each other wrong because it is a great holier-than-though schadenfreude feather to have in one’s cap. I have a colleague who spent almost his entire illustrious career doing that. Science is highly egotistical and competitive – we work against more than with each other.

In the case of climate change, there are large uncertainties and unknowns in the science. However, the critical point is that we are not just talking about one set of data or a single paper, but a large collection of observations and calculations: 928 papers between 1993 and 2003, for example, none of which disagree with the consensus. If the data supporting the general warming trend were to be mostly ‘phony’ and ‘rigged’ then there would have had to have been a fraud of absolutely unprecedented proportion. Thousands of brilliant, accomplished and respected scientists, reviewers and editors from all over the world, working for many different disparate, independent organizations, would have had to have conspired to create an enormous, insulated, fantasy world of rigged publications. If ever that happens public mistrust will be such that society may well give up science altogether and go back to the days of pre-enlightenment irrationality: a state of affairs in nobody's interest. Even had there been a political incentive for a massive scam, which there was not, it would have been unworkable.

Hacked Climate Change E-mails

2009-11-24T14:45:00.001-08:00

I was saddened to read about the e-mail hacking into the Climatic Research Unit of the University of East Anglia. I feel I have a special connection to UEA CRU because it is in Norwich, the town of my roots, and because it was founded by H.H. Lamb, the father of a family friend, Norman Lamb, who is the Lib-Dem MP for North Norfolk and a shadow minister.

Of course, although I haven't actually read many of them, I feel I can comment on the e-mails, anyway! They seem to reveal scientists refusing to disclose data and ganging up on a journal and other scientists.

Well, disclosing data can be a tricky problem. I myself will not often let data we have or papers we are writing out of the lab until the work has been accepted for publication.
The reason for this is primarily that I don't want to release results until I feel we are reasonably sure they are reliable and that we have done our best to fully understand them. Otherwise, one runs the risk of having to confusingly and damagingly retract hastily-drawn conclusions. In the case of UEA, the data concerns work after publication, which should normally be released (although we all know of many cases where scientists keep crucial data to themselves even then!). However, it seems the data concerned were not UEA's to pass on, anyway.

In another set of e-mails Phil Jones, the present CRU director, is revealed strongly criticising other scientists, and even a journal as being not a legitimate peer review affair etc. All this seems par for the course as far as I can see: normal scientist private chit-chat. I wouldn't be surprised if, in my own e-mails sent over the last 15 years there were evidence of lopsided views, bias, and discussions with collaborators as to cunning strategies to get our own work pushed on the community at the expense of other, competing scientific philosophies!

How does science overcome the scheming, biases and collusion? By working with fact-based consensus. Occasionally, even a leading scientist who has published respected work may then publish something he/she believes is rigorously demonstrable and proven but in fact is unfounded, wrong and has simply slipped through the peer-review process (the reviewers didn't recognise the problem). Plenty of papers in top journals qualify as such. However, if the work seems important several other groups, maybe from all over the planet, will independently take it up, repeat it, do other experiments/calculations that test it, and fail to substantiate it. The work is then naturally consigned to oblivion or moved to the slow-burner. Only by fact-based reinforcement do ideas gradually receive a solid consensus.

With climate change, as UEA stress in their recent post, the reinforcement exists in multiple strands of evidence: not only their own work, but also long-term retreat of glaciers in most alpine regions of the world, reductions in the area of the Northern Hemisphere (NH) snow cover during the spring season, reductions in the length of the freeze season in many NH rivers and lakes, reduction in Arctic sea-ice extent in all seasons, but especially in the summer, increases in global average sea level since the 19th century, and increases in the heat content of the ocean and warming of temperatures in the lower part of the atmosphere since the late 1950s.

Although I am not a climate expert, my knowledge of the system leads me to believe that it is impossible that climate change be some kind of massive hoax or collusion or that the consensus is fundamentally wrong. UEA CRU, starting with H.H. Lamb (who, according to Norman, did not himself believe in anthropogenic climate change) , have played an important role in helping reveal the facts. May the illegal hackers be themselves excoriated.

Supercomputers: animal magic.

2009-11-19T14:34:00.000-08:00

China: The "River in the Sky" supercomputer (below) jumps to Number Five on the Top 500 list.:

..but Japan, the country that gave us the Earth Simulator (below) - the world's fastest supercomputer between 2002 and 2004 - now suspends building the next generation. :

...and the U.S.?

ORNL's Jaguar slinks past LANL's Roadrunner to the Number One spot and U.T's Kraken is coiled at Number Three.

Fearsome beasts! Now arguably the most friendly animals to be found at the Supercomputing '09 conference in Portland oregon were in the Baby Supercomputer Petting Zoo.

All over the news...

2009-11-19T06:03:00.000-08:00

Well, occasionally when I think we are about to publish something that might be of interest to the public I will write a short paragraph and send it to the ORNL and/or UT press officers for their perusal. This has led to several press releases in the last few years, including this and this. However, the recent work on mercury, a pollutant in streams such as the one above, turned out particularly contagious, perambulating around onto several other outlets, including the local newspaper and television and various specialised national sources. So why all the (relative) fuss?

Well, the previous releases that were direct to the press (as opposed to web pages erected by ORNL or UT entities, which are less likely to be scanned by journalists) concerned protein folding, neutron scattering and protein interactions. Although, in my opinion, the interest to the public of work in these fields is as great as the mercury studies, (e.g., knowing how to fold proteins would revolutionize medicine) it probably doesn't trigger the immediate spark in the minds of readers that 'mercury' does: any news piece that requires even the slightest little bit of intellectual effort from the reader before interest is stimulated is less likely to be read - it's only natural. And with protein folding and interactions the reader is initially in unsure, foreign territory.

Also interesting is that, although our work, based on calculations by Jerry Parks, is solid and published in a good journal, it is only incremental and is built on a large amount of existing knowledge generated by established researchers in the field such as Anne Summers (UGA), Sue Miller (UCSF) and Tamar Barkay (Rutgers). In other words the work on mer operon function over the last 20 years or so was all just as newsworthy as ours, if not more. More generally, the field work, geochemistry, biochemistry and molecular biology underway in the mercury Science Focus Area at ORNL is of intense general interest. So there's clearly a disconnect here as only a small fraction of genuinely interesting scientific results end up in the general news. There's a lot one could say about this and information flow and filtering in general. However, we, as scientists, need to think when we are about to publish, whether the public might be interested in some aspect of our results. We need to learn how to express our work in concise layman's language, and to constantly disseminate. The public that feeds us needs feedback.

Constant Yakking....

2009-11-05T14:36:00.000-08:00

Seem to be spending a lot of time giving talks and the like recently:

- Last Friday a talk to West Knoxville Rotary - it was fun to do and a synposis of the lecture is given here.
- an interview on Tuesday with WBIR with Jerry about our mercury work (hasn't been aired yet).
- a talk to ASCAC on Tuesday.
- a panel discussion yesterday at the SNS/Juelich spin echo inauguration
- a talk yesterday at the NSE workshop
- a talk with Martin Keller to the DOE Under Secretary for Science today.

Bit of a rest from the yakking now........until Supercomputing '09!

Flu all week

2009-10-22T13:55:00.001-07:00

Have had the flu all week. Given that practically all flu around right now is H1N1 then that is what it probably is.

Wishing the best of luck, then, to my ex-boss Stephen Cusack who has just set up a company to develop drugs based on his recent structure of the influenza polymerase.

Finger Stone on Carlton Moor

2009-10-19T10:58:00.000-07:00

Couple of nostalgic photos about Britain. The first is of the finger stone on Carlton Moor. A group of us Leeds undergrads walked past this while on the Lyke Wake Walk in 1980, a 42-mile hike across the North York Moors National Park, that we accomplished, as is the tradition, in 24 hours.

Quite what the enigmatic finger stone is no-one knows. An ancient boundary marker? A waymarker on the original Lyke Wake coffin road? It may even date back to pre-history. More likely is that it is a medieval signpost - scattered across the moors are a series of ancient stone crosses which were used for navigational purposes.

Rannoch Moor

2009-10-19T10:41:00.000-07:00

Rannoch Moor, Scotland. In the 80s I would frequently take the train across this moor on the way to visit my father at Loch Shiel.

The profound stupidity of football

2009-10-15T11:59:00.001-07:00

A brilliant new book lays bare the idiocies of the beautiful game

Nobel Prize in Chemistry...

2009-10-07T06:07:00.000-07:00

..for the ribosome structure. A magnificent achievement and a beautiful, critical molecular machine. However, too many chemistry prizes have been given for solving structures using X-ray crystallography, rather than for really innovative work developing new fields, methods, or for some astounding discovery.

My favourite bar in Knoxville....

2009-09-16T14:58:00.000-07:00

..even though the beer isn't particularly British. Review here.

New Image from Hubble

2009-09-10T13:55:00.001-07:00

....such as this view of a small region inside the globular cluster Omega Centauri, which has nearly 10 million stars. See here for more details.

Teaching Evolution in East Tennessee

2009-09-09T07:24:00.000-07:00

A very well written article in the Knoxville Magazine.

Health Care Reform

2009-08-11T14:32:00.001-07:00

...and now for a 'political' statement of sorts - the first one, I guess.

As someone who has lived in four health systems (Britain, France, Germany and the U.S.A.) I find it quite amazing that there is a large chunk of the local population who do not regard the provision of basic health care as a fundamental human right, and who seem to be under the impression that the systems in Europe and Canada are inferior to the present US state of affairs. Concerning the human rights issue, I don't think everyone should have the automatic right to the most expensive treatments for every ailment they present. We're not talking about expensive, state-of-the-art health care for everybody's minor ailments here - just the basics, but with everything possible done for serious cases. That's the way it operates in other countries.

Furthermore, there is a clear problem in both the American and European systems, which is a lack of incentivisation. Here's an example of cost inefficiency from personal experience here, although it could just as easily have happened in Europe. A year or so ago I visited the doctor for a benign, minor viral skin infection. He offered me the choice of two solutions: self-applied curettage (cutting the viral lesion off) or an anti-viral cream. I chose the cream and, when I picked it up at Walgreens, found it had a rather surprising co-pay of $70. The pharmacist explained that the total cost was $600 so the insurance was covering $530. further, it turns out this cream benefits only about 10% of patients (the virus goes away by itself anyway). So the choice had been between an effectively zero cost procedure and one with marginal benefit for $600, but the cost was never even considered in the discussion with the doctor. Now, I'm not saying we should cut corners in providing proven treatments for life-threatening cases, but the automatic dissociation of costs from the consideration as to what steps to take in all cases leads inexorably to inflation.

This is Simply Ridiculous

2009-08-09T12:23:00.000-07:00

Above is the 1992-1993 strip of Norwich City Football Club, frequently voted in the 'worst kits of all time' lists - it looks like a flock of gulls circled overhead for a couple of hours before the game. However, that team finished third in the premier league.......

Now, I know that since Norwich City Football Club were relegated to "League One" (in reality the THIRD division) on that fateful day of May 3rd 2009 (see here for appropriate poetry marking the occasion) I am no longer a supporter and care not one tinker's cuss about how they do. However, I did accidentally click on a link that happened to give me the result of their first encounter in the nether reaches of English soccer yesterday - a 7-1 defeat at home to Colchester!
25,000 flag-waving fans giving them a thunderous welcome as the team walked out to play a side whose complete national support consists of one 87-year-old ex-postman who keeps mistaking them for Ipswich, the manager's farm-boy nephew who gets a free season ticket and his rosetted horse, Kenneth,.. and then... Two City fans marched onto the pitch at 0-4 and flung their season tickets at Bryan Gunn, the manager. What a load of rubbish, and that's putting it politely!

UK Research Assessment Exercise

2009-08-01T06:36:00.000-07:00

When I was a student the UK academic pecking order seemed to be Oxbridge followed by the other collegiate universities (Bristol, Durham) together with Imperial and the northern red-bricks (Manchester, Leeds etc), and, lastly, the 60s concrete jungle universities.

In the 2008 UK academic research assessment exercise, one sees that some of the 60s universities have come a long way. Congratulations Essex, Warwick and York!

Total Solar Eclipse

2009-07-22T14:41:00.001-07:00

......just thrilled many Asians.

I remember the total eclipse ten years ago (above) very well. Most of SW Germany, and, indeed Western Europe, was overcast. Just south of us, in Stuttgart, the Solar Eclipse Festival was drenched. As we waited on a hill south of Heidelberg thick clouds blanketed the sky. Then, as the partial eclipse strengthened, a few minutes before the Sun was due to be covered, we felt wind on our cheeks, the clouds started agitating, and a hole appeared in the clouds directly in front of the Sun. It remained until a minute or two after the total eclipse passed, we few were treated to an unforgettable spectacle, and then the clouds drew over thickly again. It began to rain.

Weird and magical....

Uncertain Outlook for DOE’s Energy Innovation Hubs

2009-07-21T10:50:00.000-07:00

The House and Senate excerpts make interesting reading.

The Heidelberg "Thingstaette"

2009-07-13T08:40:00.000-07:00

A Nazi-era arena. Thanks to UT's own Glenn Reynolds, who lived in Heidelberg for a year as a kid while his father taught at the University of Heidelberg: Glenn posted this link describing the arena on his famous Instapundit blog.

Scientist shortage?

2009-07-09T08:23:00.000-07:00

..Maybe not.

UT's Kraken world's most powerful academic computer

2009-06-24T06:59:00.000-07:00

..and sixth overall, while ORNL's Jaguar retains its Number Two Spot.

Knoxville in hunt for World Cup matches

2009-06-16T14:19:00.000-07:00

Yes, the World Cup is coming to East Tennessee!

Well, maybe!

Rooney, Gerrard and Lampard at Neyland Stadium?

I giggled at this comment on it from 'VolGraduate":

"Hope this comes to Knoxville. It would be a great thing for all the East TN hillbillies to experience some culture"

Secret of a Snake's Slither

2009-06-16T13:32:00.000-07:00

I have always been fascinated by snakes, such as this black spitting cobra.
But how do they move?
Ever since I sat as an undergrad in Leeds University library reading
Nicolas Rashevsky's "Mathematical Biophysics" treatise, which proposed, amongst many other things, a model for snake locomotion, I have wondered about this.

And now:

Proc Natl Acad Sci Jun 9 e-pub ahead of publication:

"In this experimental and theoretical study, we investigate the slithering of snakes on flat surfaces. Previous studies of slithering have rested on the assumption that snakes slither by pushing laterally against rocks and branches. In this study, we develop a theoretical model for slithering locomotion by observing snake motion kinematics and experimentally measuring the friction coefficients of snakeskin. Our predictions of body speed show good agreement with observations, demonstrating that snake propulsion on flat ground, and possibly in general, relies critically on the frictional anisotropy of their scales. We have also highlighted the importance of weight distribution in lateral undulation, previously difficult to visualize and hence assumed uniform. The ability to redistribute weight, clearly of importance when appendages are airborne in limbed locomotion, has a much broader generality, as shown by its role in improving limbless locomotion."

Video here.

..and this is the species of snake, the Common Krait, that kind colleagues in the Ecology Department of the Indian Institute of Science in Bangalore took me to see on a field trip near the Western Ghats in September 2008:

Models’ Projections for Flu Miss Mark by Wide Margin

2009-06-08T10:51:00.000-07:00

"In the waning days of April, as federal officials were declaring a public health emergency and the world seemed gripped by swine flu panic, two rival supercomputer teams made projections about the epidemic that were surprisingly similar — and surprisingly reassuring. By the end of May, they said, there would be only 2,000 to 2,500 cases in the United States.
May’s over. They were a bit off.
On May 15, the Centers for disease Control and prevention estimated that there were “upwards of 100,000” cases in the country, even though only 7,415 had been confirmed at that point."

Women 'surpass men' at UK universities

2009-06-07T07:27:00.000-07:00

..and worldwide.

But that doesn't necessarily mean girls are improving:

"A science test taken by 11 and 12-year-olds in the mid-1970s had been successfully passed by 54% of boys and 27% of girls.When the same test was taken in 2003, the scores for both boys and girls had fallen to 17% - a much more rapid decline for boys."

Catalysis in Heidelberg...

2009-06-04T15:13:00.000-07:00

Many congratulations to my old Heidelberg Catalysis SFB 623 'Molecular Catalysts: Structure and Functional Design" who were recently renewed for 4 more years with a 7 Million Euro grant.

Y-12 and ORNL...

2009-06-03T04:31:00.000-07:00

.., the New York Times doesn't know the difference, leading to the BBC erroneously reporting, in "US in Nuclear Security Blunder", one of its most highly-read releases of the day:

'.....the most serious disclosure was on the Oak Ridge National Laboratory in Tennessee, known as the Fort Knox of highly enriched uranium, the leading fuel for nuclear weapons."

Error propagation: as pernicious in journalism as it is in science.

Nigel Henbest on why science is important

2009-05-30T08:20:00.000-07:00

"Trying to understand the world around is, I believe, hard-wired into human nature. And “science” is just that process of understanding. Yes, you can interpret nature in terms of gods and demons. But, sooner or later, you are likely to move on. The mind is finely tuned to pick out patterns in the world around us; and once you have the leisure - as the Greek middle classes did in the first few centuries BC - you begin to see how the world is set out on rational principles"

Read it here.

Humm. Hopefully those of us who don't have quite as much leisure as the Greek middle classes can begin to see the rational principles as well?

From Photosynthesis to Fuel: The Next Generation of Ethanol

2009-05-19T12:04:00.001-07:00

..article on our supercomputing efforts...

Art of Science

2009-05-18T10:52:00.000-07:00

Mad Micelle

Robert Renthal '67 (faculty), Derek Mendez (undergraduate), Liao Chen (faculty)Department of Biology, University of Texas at San Antonio

"To understand the forces involved in the assembly of cell membranes, we pull membrane proteins apart. We embedded a red blood cell protein, glycophorin, in a cluster of detergent molecules called a micelle. Using the computer technique of molecular dynamics simulation, we grabbed glycophorin and pulled it apart. When we displayed the molecular surface of the micelle with the protein shown in outline form, the micelle seemed to be glaring back at us, perhaps giving us a view, at an emotional level, of the forces that hold membranes together."

See more here.