Monday, December 28, 2009

Air Travel the Day after the Detroit Terror Incident

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.

Friday, December 4, 2009

Off for 3 weeks in Europe














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...

Thursday, December 3, 2009

Our mercury research on the local TV...

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

Tuesday, December 1, 2009

The Physics of Biomolecules

"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.

Friday, November 27, 2009

Very kind plugs from Frank Munger's Atomic City Underground

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.

Thursday, November 26, 2009

Massive Climate Data Scam?

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.

Tuesday, November 24, 2009

Hacked Climate Change E-mails

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.

Thursday, November 19, 2009

Supercomputers: animal magic.

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...



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.

Thursday, November 5, 2009

Constant Yakking....

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!

Thursday, October 22, 2009

Flu all week


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.

Monday, October 19, 2009

Finger Stone on Carlton Moor


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






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.




Thursday, October 15, 2009

Wednesday, October 7, 2009

Nobel Prize in Chemistry...

..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.

Wednesday, September 16, 2009

My favourite bar in Knoxville....

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

Thursday, September 10, 2009

New Image from Hubble


....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.

Wednesday, September 9, 2009

Tuesday, August 11, 2009

Health Care Reform

...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.

Sunday, August 9, 2009

This is Simply Ridiculous


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!

Saturday, August 1, 2009

UK Research Assessment Exercise

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!

Wednesday, July 22, 2009

Total Solar Eclipse

......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....

Tuesday, July 21, 2009

Monday, July 13, 2009

The Heidelberg "Thingstaette"




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.

Wednesday, June 24, 2009

Tuesday, June 16, 2009

Knoxville in hunt for World Cup matches

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



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:





Monday, June 8, 2009

Models’ Projections for Flu Miss Mark by Wide Margin

"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."

Sunday, June 7, 2009

Women 'surpass men' at UK universities

..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."

Thursday, June 4, 2009

Catalysis in Heidelberg...

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.

Wednesday, June 3, 2009

Y-12 and ORNL...

.., 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.

Saturday, May 30, 2009

Nigel Henbest on why science is important

"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?

Tuesday, May 19, 2009

Monday, May 18, 2009

Art of Science




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.

Wednesday, May 13, 2009

Top Ph.D. Programs Shrinking

...due to plummeting endowments?

Quote from the article: "Generally, the recession has made colleges and universities want to keep undergraduate or professional school enrollments level, or even to increase them. But doctoral education at elite universities operates on a very different economic model. Students are almost always fully supported, so they don't bring tuition dollars with them. And while states provide some support to public universities for graduate education, private universities are more likely to be footing the full bill."

Monday, May 11, 2009

Liquid Mercury


Anish Kapoor's110-ton outdoor sculpture called "Cloud Gate". Set in Millennium Park, Chicago, it is made of sheets of highly polished stainless steel, and is inspired by a droplet of liquid mercury. The sculpture reflects the Chicago skyline, the clouds and sky above with the "gate" being the arch underneath. Read more about mercury in the environment in our Science Focus Area.

Sunday, May 3, 2009

Inspired to Quickly Write a Short Poem:


...by Norwich City's relegation today.

Also posted it on the football poets' site: 'Swapping shirts with Shakespeare".

Oblivion

Out with the rust, the has-beens! Torrid reckoning now is due,
Green and Yellow still their colours, but both indicate anew,
A lack of chops and lack of bones as they did lose and lose again,
To Reading, Forest, arch-foes Ipswich, and all else ‘till season’s end.
Long receding Bayern awe, and wins before the Spion Kop,
Kept us a throng for far too long as Norwich slithered to the drop.
‘League One’ nomenclatura: take no heed of false bravura,
As Sunday May the Third sends City Reeling to the Third!









Friday, May 1, 2009

Shift in Simulation Superiority


New report highlights strengths and weaknesses in U.S. high-end computer simulations relative to international counterparts.


Crunch match at The Valley


..against Charlton on Sunday that could send my home town soccer club, Norwich City, down to the British Third Division for the first time in 40 years. A few thousand supporters like those above will travel to London for the final push.....


Monday, April 27, 2009

The Old Bridge in Heidelberg


Three Governor's Chairs now...

..and welcome to nuclear security expert Howard Hall. The two recent appointments must be allaying concern at ORNL and UT that these chairs were not being filled, which prompted an article in the local press: UT’s Empty Research Chairs
Are the university’s lofty research aspirations rooted in reality?

Patience was rewarded.

Science Races ...

..to parse New Virus.

Monday, April 20, 2009

More things you don't have time to read?

PLoS ONE has now published over 5000 articles in two years of existence.
I see nothing wrong with that although some do.
We'll see which exclusively online open-access journals manage to gain traction.
(One I'm an editor of, PMC Biophysics, from PhysMathCentral, has just started up.)
Of course, the whole open-access experiment may be nipped in the bud if congress kills it, as it is now considering.

Friday, April 10, 2009

Booked for "Ungentlemanly Conduct"

Careful what you eat before a soccer game or this may be your punishment.

Thursday, April 9, 2009

Great Salt Lake, Utah




..a home of Halobacterium salinarium, a microorganism containing bacteriorhodopsin, a light-driven proton pump that we have been working on for several years (see all publications in our home page with Nicoleta Bondar as first author).

Wednesday, April 8, 2009

They may believe it with passion but....

..Gioacchino Giuliani of the Italian National Institute of Physics, appears to believe erroneously in radon gas as a reliable predictor of earthquakes. Science is full of believers, even (especially?) amongst those with top credentials in getting through peer review. The creative act of imagination in initiating science is difficult to divorce from a desire to see the results follow a certain, vindicating path. But many of us believe too soon in our methods or results, without having performed the full range of controls. Better to get more cool heads working on any promising theme, then wait for the consensus to be established amongst the experts, before admitting belief.

Claims such as those of Giuliani are worthwhile discussing in public, but it is sad when wildly misleading statements, such as the global warming claims of David Bellamy, an influential British former TV broadcaster and botanist, need to be corrected, wasting valuable public debate space.

BTW: Glad to hear that Isabella Daidone, ex postdoc, who is now on the faculty at L'Aquila, was in Rome at the time of the recent quake. And while we're still on the subject of the L'Aquila earthquake, look at this telling donation of $50, 000 by the US government to help the relief effort.

Sunday, April 5, 2009

Poet's Corner - WH Auden on Ignorance:

(From The Dog Beneath the Skin)
Happy the hare at morning, for she cannot read
The Hunter’s waking thoughts. Lucky the leaf
Unable to predict the fall. Lucky indeed
The rampant suffering suffocating jelly
Burgeoning in pools, lapping the grits of the desert,
The elementary sensual cures,
The hibernations and the growth of hair assuage:
Or best of all the mineral stars disintegrating quietly into
light
But what shall man do, who can whistle tunes by heart,
Know to the bar when death shall cut him short, like the cry
of the shearwater?

Saturday, April 4, 2009

Tuesday, March 31, 2009

Three-Year degree at UT?

KNS: TN Sen. Lamar Alexander is "currently promoting the idea of offering a three-year bachelor's degree that could reduce the cost of attending college by one-fourth".

Good idea as long as the graduating standard is not reduced i.e., the students get four years worth of work done in three.

Saturday, March 28, 2009

Jailed Peter Mendham plays village soccer

I used to play with this guy in the 1974-5 Norfolk Under-15s soccer team in England.
I wonder if they ever let prisoners out of TN jails to play sport?
Anyone know?

Promising Noises from Nashville

"You've got UTK, which is a legitimate research university, then you've half a dozen others who are little UTK wannabes or little Vanderbilt wannabes, and they're busy growing their graduate programs," Bredesen said. "And most states that are considered to have good systems, they've really got a good, clean separation between the graduate-oriented research universities and the state schools. … Just how you do that is kind of the political trick in all of this."

Thursday, March 26, 2009

"Creation Care"....

...a.k.a. religious environmentalism in Tennessee.

Looks like it might make the difference in the TN House in pushing through a ban on mountaintop removal at elevations over 2000 ft :

http://www.metropulse.com/news/2009/mar/25/mountaintop-removal-gains-momentum-faith-issue/

Tuesday, March 17, 2009

Heidelberg University opens US presence in New York


[Heidelberg University Alte Aula]
http://www.uni-heidelberg.de/presse/news08/pm281010-01engl.html

Nobody told them there is already a presence in Knoxville (Dennis, Roland, Benjamin, Barmak, Xiaohu, Krishnan, Jiancong, plus regular visitors etc....)?


Thursday, March 12, 2009

Second Governor's Chair Announced

It's taken a while to find the second GC but I'm happy to see Alexei Sokolov will be joining us:

http://www.utk.edu/news/article.php?id=4956

Alexei and I have strongly overlapping interests in biomolecular dynamics.
See, for example:

http://www.ncbi.nlm.nih.gov/pubmed/18500904?ordinalpos=5&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum

Wednesday, March 11, 2009

Aldi Opens in Knoxville

http://www.knoxnews.com/news/2009/mar/07/aldi-opens-in-knoxville/

..an excellent German concept!
I was always appalled at Walmart's inflated prices........

Monday, March 9, 2009

Bredesen: Stimulus means Tenn. colleges won't need deep cuts

Temporary relief....

http://www.knoxnews.com/news/2009/mar/09/no-headline---030909webstim/

....but given what might be miserable non-stimulus-related TN state revenues for FY09 one fears for 12 months time? The natural (but, of course, impossible) reaction would be to save some of the stimulus money for even rainier days, until we start to see where the bottom of the recession might be located.

Thursday, March 5, 2009

Monstrous Kraken supercomputer up and running at ORNL

http://www.oakridger.com/localnews/x1959835750/Monstrous-Kraken-supercomputer-up-and-running-at-ORNL

..so powerful, it is rumoured to be capable of predicting the existence of Jack Daniels whisky and the Tennessee Walking Horse from the Big Bang in less than a millisecond! (with a nod to Douglas Adams)

Friday, February 27, 2009

Stakes High for ORNL with Funding Increase

We all received a dramatic e-mail from Thom Mason, ORNL Director.

http://www.knoxnews.com/news/2009/feb/27/stakes-high-for-lab-with-funding-increase/

My opinion: a stimulus cannot be simply 'putting money back in people's pockets'. It must seed the conditions for prosperity by getting people doing creative, useful, productive hard work who otherwise would be frozen out, discouraged or downgraded due to the sluggish market. Nothing accomplishes this better than good science.

Monday, February 23, 2009

American Science Takes The Lead..

...with the ORNL Jaguar Supercomputer and UT's Kraken.

http://www.ornl.gov/info/ornlreview/v42_1_09/cover_story.shtml

At this moment we are using both Jaguar and Kraken heavily and they have transformed the length and timescales of some of our MD simulations. Analysing the results, however, will take quite a while...

Tuesday, February 17, 2009

UTK will award Honorary Doctorate to Dolly Parton

http://www.knoxnews.com/news/2009/feb/17/ut-bestow-dolly-parton-honorary-doctorate-degree/

See also:

http://www.timesonline.co.uk/tol/life_and_style/education/sunday_times_university_guide/article478501.ece

From a Professor of Education at Edinburgh: "The criterion these days is often that the honorary graduate is well known rather than they have made a distinctive contribution in their particular academic field,” Smithers says. “Now that particular public relations genie is out of the bottle, it can’t be stuffed back in. And that is all right — providing nobody takes it too seriously"

Friday, February 13, 2009

Mathematicians Discover Largest Number

http://iowahawk.typepad.com/iowahawk/2009/02/numbers-in-the-news.html


".....could lead to breakthroughs in fields as diverse as astrophysics, quantum mechanics, and Chicago asphalt contracting."

Saturday, February 7, 2009

Massive Increase in Science Funding?

Now that's real stimulus.:

http://blogs.discovermagazine.com/80beats/2009/02/05/economic-stimulus-package-will-boost-science-and-green-tech/

..but a proposed $1.4bn NSF funding increase, which would have been a highly cost-effective stimulus measure in both the short and longer terms, has been shelved:

http://www.talkingpointsmemo.com/docs/Collins-Nelson-Cuts/?resultpage=2&

..and the reason for the cut may have not been an assessment of the economic effects of bolstered creative research in the broad sciences, but rather a response to improper internet use by a few NSF employees:

http://www.desmoinesregister.com/article/20090130/NEWS/90130001

Monday, February 2, 2009

Reasons to be Cheerful, Part II

Great new results from the Tennessee lab:

Xiaolin C. - has now solid DOE funding.
Jerome B - has recruited a great postdoc (Barbara)
Hong G. - was tenured.
Hao-Bo G. - is cranking out the neutron spin-echo protein simulation to very long times
Moumita S. - has discovered a cellulase reaction mechanism.
Jiancong X. - has characterised cellulosome cohesin-dockerin binding
Roland S. - scaled MD to 30,000 processors on the Jaguar supercomputer.
Krishnan - has understood methyl rotor responses to ligand binding.
Jerry P - has a Mer B mechanism in excellent agreement with experiment
Nikolai S - is beginnning to produce neutron plots
Barbara C - looks like she can screen 150 million ligands on Jaguar
Barmak M - got his badge
Benjamin L - has rejuvenated the SASSIM program and shown how cellulose diffracts

Saturday, January 31, 2009

$100M short out of $1.6bn

That's the budget cut for the UT System that appears to be looming.
How should this be effected?
The administration have repeatedly said they want to cut strategically rather than across-the-board. Presumably, in this case, the ORNL/UT link would be nourished, as it is hard to think of anything more strategically critical to UT than exploiting the world's best instrumentation in neutron scattering and supercomputing as well as the bioenergy emphasis, in order to climb up the rankings.

So where should the cuts be made?

Well, poorly performing or redundant departments and institutes may be targets.
As I do not have a good overview of this I wouldn't be able to make suggestions.

And tuition is also under discussion -
http://www.knoxnews.com/news/2009/jan/31/petersen-says-ut-tuition-increase-inevitable/
- the table below indicates that UT tuition, although having rapidly increased in recent years, is still below the norm
http://www.asu.edu/vppa/yourtuition/documents/Tuition_and_Fee_Comparison.pdf


And what, finally, about salaries?
Maybe an across-the-board percentage cut for all except the very lowest earners?

But in times of stress one always scrutinises the top salaries.
The UT top administrators, who are under flak for appearing to have made UT top heavy, have all taken a voluntary 5% pay cut already.
http://www.knoxnews.com/news/2008/dec/19/ut-staff-take-pay-cut-2/
They earn roughly the same as the 5-10 top 'Distinguished Professors' (such as myself). Few people are talking yet about targeting salaries of the highest-paid professors, and those with UT/ORNL Joint Appointments are only partially paid by UT (75% in my case) but I would not question any cut deemed fair and necessary by both the administration and the general UT populace. Of course, however, the deeper the cut, the more eyes tend to wander for gainful employment elsewhere, but, as for me, I've only just started here and am still building things up.......

Friday, January 30, 2009

Reasons to Be Cheerful, Part I

That was the name of an old Ian Dury hit: http://www.youtube.com/watch?v=cFcemluz6XA

Great new results from the Heidelberg lab :

Bogdan T: has got his peptide confinement simulations EXPLAINED
Petra I: has got her group REALLY productive recently
Jan-H.: has a completely new representation of ligand binding pathways
Emal A: has a lot to write about for his thesis chapter
Mai Z.: understands those DNA sequence-dependent free energy plots now
Tomasz B.: has done so many different calculations he's falling over them
Xiaohu H.: has seen phase transitions in water induced by an electric field
Thomas S: discovered the SUPERCLOSED state of actin
Isabella D.: has the first comprehensive simulation explanation of peptide folding fluorescence
Thomas N.: has now got time-averaged continuous time random walks understood.
Lipi T: is getting close to convergence with her peptides
Jakob U: wowed us all with an action-packed seminar on his peptide membrane insertion
Nadia E: got some excellent DFG reviewer reports and VW looks promising
Mithun B: is getting closer to understanding DNA elasticity theory
Karine V.: had a kid last week! (and found DNA unwinding in the nucleosome)
Marie: was definitely more cheerful in January than last October!
Sebastian F: has done THOUGHTFUL work on speeding up sampling.
Dennis G.: has shown that the protein glass transition is water-model-independent
Dieter K.: has a whizzo new graphical program that represents conformational kinetics

..did I miss anything or anyone?


Part II (Tennessee) comes soon.....

Wednesday, January 28, 2009

Suggestion for Steve Chu

Suggestion for Steve Chu - the new energy secretary.
Let's think about persuading the administration to release some stimulus money to specifically fund graduate students in alternative energy research.
This would have several advantages:
(1) would be cheap (they are about 20K each) (2) in fact you need tuition on top of that, but that then would help solve another crisis - the university budget shortfall. (3) would be training scientists in the administration's favourite R&D area (4) would keep bright minds off the streets and out of trouble, so that they wouldn't continue to contemplate careers on Wall Street (if it ever reopens) or similar destructive futures...

Club Mod

The title Club Mod, by the way, is stolen from the Mark Johnson used to give his team for modelling in neutron sciences at ILL. The link is here http://www.ill.eu/computing-for-science/modelling/

Hello to everyone

This is a blog by the director of a high-performance computing lab who hates computers. Indeed, I don't even know how to switch the darned things on. Indeed, isn't it frustrating when you get a new desktop and a large book of instructions only to find out that the very first thing - switching it on - is not in the book anywhere. This has completely stymied me in the past.

Anyway, luckily I have a team of real experts (students/postdocs etc) who do know how to switch a computer on, so all I have to do is sit behind my desk with my (virtual) fat cigar and comment on their plots and results with a smirk on my face. Then they are the ones smirking when I can't stop Word from overwriting on my file.

This blog (we'll see who ever reads it) will contain insalubrious comments about professional life in science, and molecular biophysics in particular. We'll see if it goes anywhere, or whether I will need student help to switch it off definitively.