Monday, December 28, 2009
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
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
Tuesday, December 1, 2009
Friday, November 27, 2009
Thursday, November 26, 2009
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
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
..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.
Thursday, November 5, 2009
- 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
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
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.
Thursday, October 15, 2009
Wednesday, October 7, 2009
Wednesday, September 16, 2009
Thursday, September 10, 2009
Wednesday, September 9, 2009
Tuesday, August 11, 2009
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
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
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
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
Thursday, July 9, 2009
Wednesday, June 24, 2009
Tuesday, June 16, 2009
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"
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.
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."
..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
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
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
Wednesday, June 3, 2009
'.....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
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
"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."
Wednesday, May 13, 2009
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
Sunday, May 3, 2009
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
Wednesday, April 29, 2009
Monday, April 27, 2009
Are the university’s lofty research aspirations rooted in reality?
Patience was rewarded.
Monday, April 20, 2009
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
Thursday, April 9, 2009
..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
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
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
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
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
Thursday, March 26, 2009
Looks like it might make the difference in the TN House in pushing through a ban on mountaintop removal at elevations over 2000 ft :
Tuesday, March 17, 2009
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
Alexei and I have strongly overlapping interests in biomolecular dynamics.
See, for example:
Wednesday, March 11, 2009
..an excellent German concept!
I was always appalled at Walmart's inflated prices........
Monday, March 9, 2009
....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
..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
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.
Thursday, February 26, 2009
Monday, February 23, 2009
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
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
".....could lead to breakthroughs in fields as diverse as astrophysics, quantum mechanics, and Chicago asphalt contracting."
Saturday, February 7, 2009
..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:
..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:
Monday, February 2, 2009
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
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 -
- the table below indicates that UT tuition, although having rapidly increased in recent years, is still below the norm
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.
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
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
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...
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.