Wednesday, December 21, 2016

My MRI Light Experience

I had an MRI recently. (Nothing serious). How many of you have had an MRI, then, huh?

Well, one has certain thoughts going into that tunnel. The first I had was  "Don't think about being buried alive".  And the second was "How do they get anyone to go in there at all?" I mean, your nose, your toes, and all the rest of you is an inch from bloody solid confinement. I thought that if they put in a UV source as well, it could double as a tanning machine, giving patients  extra incentive, "scan and tan". Then I thought "Oh my God I had iron-fortified breakfast cereal just before coming here".  But it was too late. They slid me in. The MRI sounds started, a kind of deafening dubstep, I believe. Has anyone made a No 1 hit out of that? Then I thought "Why am I in here?". Because conventional medicine would say "Take an aspirin" whereas in the absence of tort reform it says "MRI and CAT scan".  Of course, once in, and only once in, I got an uncontrollable and violent urge to scratch everywhere. But you mustn't move, not an inch. Aaaargh! Still, too late, wasn't it? Kept saying to myself "Too late".Then you realize they're going to see through you. Your insides.  I never wanted to know what has become of that stuff. But then you think someone might finally get to see your six-pack. Yes, its there, just  under a lot of protective coating. Not so bad then. I tried to look at my watch.  The bastards had stolen it. I counted sheep. But when I got to where they should pull me out the machine kept going for an eternity. No! No! They were torturing me. I could imagine their wicked grins.

Then it was over. Ahhhhh! And the result - well, I got a crummy MRI. Bad resolution. All because workers changed a lightbulb while no-one was looking and it screwed up the magnetic field. So all the Doc could say was, "Well, we proved you are capable of laying in a closed, confined space for two hours".

High-tech health care - you can't beat it.

Friday, November 25, 2016

Open Sesame?

When I visited Jerusalem for the second time,  in the late 1990s, although  the first Intifada had just ended peace in the Middle East seemed remote. For this reason I was astonished to learn of plans for SESAME, a Middle Eastern synchrotron which is a cooperation between Bahrain, Cyprus, Egypt, Iran, Israel, Jordan, Pakistan, the Palestinians and Turkey. What an idea! Mortal enemies cooperating in one scientific institution in Jordan.

Well, now,  in 2017 it appears that, despite 20 years of delays and the assassination of two directors, the thing will finally open.

Congratulations, and OPEN SESAME!

Monday, October 31, 2016

Chancellor Search: Public or Private?

Being a member of the Search Committee for the new Chancellor of the University of Tennessee, Knoxville, I have been interviewing candidates over the past month or so, and am sworn to secrecy as to their identity.

Why is this? For a public institution, such as UTK, shouldn't the whole community know who the candidates are,  be able to talk to them, and have a say in who is eventually picked? After all, the Chancellor's position is incredibly important, with pivotal roles in academics, athletics, research, governmental relations, student relations and much more. Many communities are impacted.

This secrecy is now leading to arguments.  The Tennessee 'Sunshine Laws',  require transparency from UTK on the announcement of the finalists who are then subjected to public scrutiny, but the university is holding back until the very last day before the candidates arrive.

For me, the university is absolutely right to do so. The fact is that maybe three candidates are coming, two of whom at least will not get the job. For these, the fact that they were candidates in the first place will become public knowledge. This can be  harmful for their positions in their current institutions, to the point, in fact, where they might still refuse to come at all. What can happen, in fact, is that the the very best candidates often withdraw before the public phase, or may refuse to even be candidates in the first place. I am not saying that this has happened in the UTK case, and I would not be allowed to say so either way.  Just that it is often the case.

My suggestion for the future would be to have campus participation in the vetting and selection of the Search Committee,  and then let the Committee, the President and the Board of Trustees do their job.
At any rate I can say that the candidates who will come to UTK over the next couple of weeks are fantastic people, extremely well qualified, and it would be a privilege for us to have any of them to lead the campus.

Friday, September 30, 2016

The Real Sins of Scientists – More Pervasive than Fraud.

Fraudulent scientists seem to be everywhere these days. In recent years we have been regaled with cheats trying to foist upon us that rabbit blood can be turned into an AIDS vaccine, eating meat makes people more selfish and that transistors can be made out of virtually anything. Normal folk don’t know where to turn, so they doubt everything: evolution, climate change, vaccination. What is happening? Has science become propaganda from PhDs perverted by the search for research money and prizes?

The popular ideal image of us scientists is as disciples of the pursuit of knowledge.  With scant regard for the trivialities of life, we refuse bodily pleasure, food and sleep in our endless search for the ultimate truths of life, the universe and everything, scrupulously obeying the doctrine of the scientific method as we solemnly unroll the red carpet of transformational discovery. Little wonder then, that, whereas the uncovering of lawyerly or political fraud is met by  knowing snickering, each new revelation of science misconduct is considered tantamount to apostasy.

Serious scientific fraud - the fabrication of some high-impact but plausible new phenomenon - propels the perpetrator ephemerally into the academic stratosphere, while misleading large numbers of fellow researchers and misdirecting precious resources. But serious fraud in science is relatively rare, if only because the perpetrators, if not delusional, know they are likely to eventually be exposed by curious colleagues.

Serious fraud must, of course, be unearthed and punished, but my contention here is that is the least of science’s problems. You see, we scientists commit many sins, all of which lead to some sizeable proportion of our published work being at least partially misleading or wrong. These sins, which do not involve fraudulent deception, are far more widespread and more damaging to scientific progress. 

Let’s delight with a troll through seven deadly sins of scientists. We start with  incompetence and   ignorance. Our hypotheses may be balderdash, logically inconsistent. Our work may be ‘shoddy’ or ‘sloppy’; we may not perform  experiments that actually test our hypotheses, failing to test alternative explanations, and not knowing to perform elementary “control“ experiments. Our computer programs may contain critical errors. We may not estimate the statistical errors in our data. We may look at data and draw completely the wrong conclusions because we don’t know the underlying principles that govern the phenomenon under scrutiny. We may write our papers as if a logical sequence of experiments had been done when in fact we randomly tried things then assembled them into something that makes a pretty story.
We can also be lazy.  We may only do one or two quickie experiments, nowhere near enough to justify the grandiose conclusions we then draw, and hope the reviewers and editor of our papers are themselves too lazy or busy to read our manuscript properly. We may not even bother to properly search the literature to find out who has done anything related to our study. We may take the path of least resistance, that of expediency, to spin a story aligned with our vision.
Then there is illiteracy. We may be unable to describe our findings in a way that anybody else can possibly follow; we may omit steps in our argument, and our writing may be grammatically awful, leaving even qualified readers flailing.
True to our nerdy stereotype, we are often myopic. Our publications may deliberately ignore closely related but highly pertinent findings of others, concentrating only on our own past achievements, such that we do not put our work into context.  Citations made to others that we do include are to papers we have not even read.
We are also self-aggrandizing. In print and in person, and especially in grant proposals, we puff up the importance of our work and castigate other, legitimate studies. I may have been cited 20,000 times, but of course it should have been 200,000!
Great scientists can be highly intuitive, but this intuition also blinds us all. Many Nobel laureates have suffered from this. Take, for example, my ‘academic grandfather’*, Linus Pauling, arguably the greatest chemist of the last century. He spent his last decades misleading humanity by trumpeting unsubstantiated ideas about the health benefits of mega-doses of Vitamin C.

You see, Pauling, in his later years, fell victim to that ubiquitous scientist’s plague:  that of  wishful thinking. This arises naturally from the initiating, creative act in science, in which various half-formed ideas shape into a concept to which we cling and may base our careers, fomenting long-held desires, and prejudices. We believe in something, a beautiful process or an imagined principle. So, blinded by our belief, we may see a trend in our data that is not really there, or a small peak in a spectrum that is really just noise. We may remove that lone, recalcitrant data point that doesn't fit our model – that’s not fraud because we really believe the data point can’t be right. The temptation to airbrush data is irresistible.  Lets add a calibration factor, fudge factor, cosmological constant. We smooth, filter and transform data onto scales that make them look more accurate. Some run an experiment ten times until they get the result they want then publish only that one. We may refuse to give access to our raw data to others – after all, we haven’t finished analyzing them ourselves and, anyway, others would misuse them.
So, we scientists are ignorant, incompetent, illiterate, lazy, myopic, self-aggrandizing wishful thinkers. Each of these seven sins has the same effect as outright fraud – wrong results, erroneous interpretations, false conclusions. So shoddy, dubious science is everywhere, leading to a large proportion of submitted papers being rejected after anonymous peer review, and a fair proportion of manuscripts that do manage to sidle past peer review being still wrong. In my, of course unbiased, opinion, about half the interesting papers in my field published in the top journals such as Nature and Science, are basically wrong – they may be brilliant,  thought-provoking, beautiful and even inspirational, but they are still wrong.

Every Wednesday my lab holds a Journal Club, in which we select one or two papers to read, and we try to understand what was done, its significance, and its validity. Sometimes we leave the room exalted by a timely and impactful piece of research. But often, when we try to ascertain whether the main conclusions of the authors are justified by the data presented, we regretfully must conclude that the answer is “no”, and occasionally we go ballistic, especially me.  A while ago I had one of those ballistic days. We read a published paper on the computational design of drugs to overcome antibacterial resistance, and concluded that every one of the main conclusions was wrong. The paper was total pigswill. If anyone reads this paper and starts a program of drug design based on it they will have been sadly misled. [Naturally, though, that it is inconceivable that anyone would hold such a subversive meeting criticizing our own work. Inconceivable (ahem).]

Why then, is there so much fluff and junk out there? Well, unlike other professional pursuits, scientific research tackles the unknown.  This makes it inherently very difficult to know which questions to ask and how to go about things. Also, we scientists are condemned to membership of a certain species of animal endowed with primitive, instinctual, jealous and lustful traits. So each new problem will have each of us looking at it with our own biases, framed by our own imperfect training and experience. So it’s hardly surprising that there can be a lot of trash to wade through before an advance can be solidified. 

So, what to do about it all? Well, the world could try a science detox, doing without science completely, but then there will be no cures for cancer, no saving the environment, no endless supply of energy, no technological terrorist foiling. Another option is to keep doing what the authorities are concentrating on now; fraud detection, witch hunting, setting up Offices of Scientific Integrity and Research Integrity and the like.  But that is no panacea. You see, the seven scientific sins are juxtaposed by seven virtues: curiosity, intelligence, vision, drive, rigour, integrity and insight, virtues propelled by appreciation of the beauty of truth. The virtues win out in the end.

*academic grandfather: the adviser of my adviser, Martin Karplus. Pauling has hundreds of such grandkids..

Wednesday, August 24, 2016

How to find Big Science Questions

The second in a series of "How To" articles :-))

Here at ORNL we are pondering which Big Science Questions the National Lab should attack over the next years. Good question. National labs were invented for a big science question - the atomic bomb, are tailor made for problems involving big teams of scientists, and later started the Human Genome project.

What Next Then? "The Sustainable City"? "Personalized Medicine"? "Cancer Moonshot"? "Complexity Science"?

Here's how to find out what to do next:

(a) Send around an e-mail to all national lab employees, postdocs and students asking for a "Big Science Question" written in one sentence only.

(b) Get a committee to sift through them and select some to be expanded an sculpted.

(c) Pick one every year to get serious about.

That'll create a buzz around the place.

Monday, August 8, 2016

How to Run a Conference

I go to quite a lot of scientific conferences - maybe 10-15 per year - and they all tend to be in posh hotels with entry restricted to those able to find the registration fee, which normally is hundreds of dollars, and which pays for renting the conference room at the posh hotel, speaker travel, exorbitant cookies etc.

Sometimes there are not many people there. I remember once flying all the way over from France to Seattle to give a talk to about 10 people.  But many more than that would have been interested - its just that they were blocked by the gnashing costs.  A very recent conference I was at had trouble attracting enough attendees, even though I know dozens of young local scientists would have liked to attend.

So here's what to do (for some of the conferences, at least):

(a) stop holding conferences in posh hotels - hold them in university lecture halls.
(b) stop providing free meals
(c) stop providing free coffee and cookies
(d) stop funding speaker travel
(e) reduce the registration costs as the conference approaches if there are not enough attendees
(f) let in all students free

Then conferences would be what they really should be: a  transmission of passion and knowledge to an enthusiastic and inspired young audience.

Tuesday, July 5, 2016

Our Role in the Clinton E-mails

Well, we have deep ties to the Hillary Clinton e-mail scandal. Oh, yessiree!

Well, maybe not deep, but perhaps a shallow connection,  and rather remote.

But here it is:

1) Xiaolin Cheng, here was a postdoc with Andy McCammon at UCSD, as is presently our ex-postdoc, Yinglong Miao. Tongye Shen also worked with Andy. Andy himself was a postdoc with Martin Karplus, as was I. And we have a paper in press together. So we have several connections with the McCammon group.

2) In the seventies Andy was  a grad student of John Deutch, a chemistry professor at MIT.

3) Deutch became Director of the CIA in May 1995 but stored and processed hundreds of files of highly classified material on unprotected home computers that he and family members also used to connect to the Internet, according to an internal CIA investigation. He pleaded guilty to a misdemeanor for this, and was only few hours away from signing a plea bargain when Bill Clinton pardoned him on his last day in office!

4) As a result of that presidential pardon  the FBI today could find no precedent for indicting Hillary for storing secret information on her personal computer. So they didn't recommend indictment, thus paving the way for her presumed victory in November.

Ta-da!  Cool, huh? Not.

Friday, July 1, 2016

Frank Munger

Frank Munger

Yesterday Frank Munger, the local journalist who wrote about Oak Ridge science for the Knoxville News Sentinel and in the associated  "Atomic City Underground" blog, retired.

His blog kept us informed daily about what was going on at Y12, other areas of ORNL and the region. He was also a strong supporter of Club Mod.   He was given the "Muddy Boot Award" yesterday for his contributions to building the local community's economic base.

We're all sad to see you go, Frank! We wish you a fulfilling and rewarding retirement! Maybe you'd consider writing a book about Oak Ridge. Nobody would be better positioned to do so.

Friday, June 17, 2016

Personal Thoughts on the Brexit

In 1970 my postdoc advisor, Martin Karplus, considered leaving the US for a professorship in France. However, professors there were civil servants, and all civil servants had be French. Karplus' colleague at the time was Jacques Dubois, who was well connected politically, and he lobbied President Pompidou for a change in the law. Thus was the law indeed changed, but it all took too long, and Martin went back to Harvard.

Ten years  later everything was different. Europe had come closer together. Britain had joined in. As soon as I reached adulthood in the UK  I thought to myself - hup, lets get outta here, let's explore. So in 1982 I moved to France to start my Ph. D,  at the Institut Laue-Langevin in Grenoble, which, together with CERN,  was a model of how  Europe can work together to achieve greater goals.  Then, after 4 years in the States I came back to work in Saclay, as a French civil servant,  for 10 years. After that, I moved to Germany, again as a  civil servant,  a Herr Professor. Now, I can't say all this was made possible specifically by the EU - there are plenty of Swiss and Norwegians who have done the same thing.  But European integration in the broader sense, and globalization in the even broader, are indeed responsible.


The Brexit debate is part of the ongoing worldwide tumult pitting forces of integration and globalization against those of nationalist isolation. We have it here in the States, with the immigration ruckus and both the Trump and Sanders campaigns promoting trade barriers.  I get what the isolationists are saying, indeed. Globalization has spawned income inequality in developed nations (although has it perhaps reduced global income inequality?).  And I favor a relatively restrictive line on immigration myself, although there is no xenophobia in my reasoning,  it being  simply resistance to local population growth (more on that later, maybe).


The EU has become divorced from its population. It doesn't listen to them. Its high-minded prescriptions have alienated far too many. The average Brit feels nothing good from it. It elicits no pride. It's a deeply frustrating entity. While at Heidelberg University I received an EU science grant. It was a huge amount of dosh, accompanied by infuriating instructions written in prescriptive  'Euro-babble'; the national science agency, the DFG, got far more bang for the buck in my opinion, reinforcing  my  view that the EU wastes too much money on  bureaucracy and idealistic spending. When I arrived in Heidelberg, in 1998, the Euro was being contemplated.  Juergen Siebke, the university Rektor and an economist, was very skeptical of it. 'You can't have monetary union without political union' he told me at a reception. And he was right, as the Euro debacle, Greece and fighting the recession have proven.


The UK should stay in the EU...just, but all the while scratching and clawing.  It should keep needling them, restraining them, defying them. Break a few EU laws, just as the Eastern EU countries are doing with regard to border control. Refuse flatly to pay in as much money. Be a spanner in some of the works.

But stay in.


Otherwise Scotland will leave the UK. Jobs, trade and exports will suffer. Globalization will hit even worse as the multinationals will have little incentive to negotiate with the rump of the UK. Little England will be powerless and rudderless, sinking in the mid-Atlantic. And, worst of all, God help us, all the professors in the sinking English universities will end up having to be English.

Saturday, June 4, 2016

Canoeing the Clinch River - Memorial Day Weekend 2016

Photo: Stephine Smith

Photo: Stephine smith

Nice lodge there Mr Beaver! (Photo: Stephine Smith)

Wednesday, May 25, 2016

Peter Kollman

Peter Kollman died 15 years ago today, at my age,  56.

He was a giant in our field, yet wholly unpretentious and purely enthusiastic.

And he was the subject of one of the most moving obituaries I have read, by Fred Cohen.

Here's an excerpt:

"Peter told me more than once that he had no regrets. He had the good fortune to work on problems he loved with colleagues that he enjoyed. At a time when many of us would focus on all that we had not made time for, Peter displayed a rare sense of contentment as he listened to the music he loved and sent out a few extra e-mail messages. In the last few weeks of his life, the bone pain from his tumor required morphine. When discussing mundane subjects, he had a difficult time staying focused. But, when his thoughts turned to science, he was as lucid as ever. Science clearly held a privileged spot in Peter's mind, a spot that was not subject to ephemeral or biochemical distraction."

Sunday, May 8, 2016

Healthcare in the USA (II)

Seven years ago I wrote a blog entry about Obamacare. It basically expressed a feeling - that the system in Europe, problematic as it is, at least gives one the feeling of security when it comes to healthcare. If you get ill, you go to the Doctor’s, period.  There is never any question of not being treated.

Now Obamacare has been tested I think it was an improvement on the previous situation,  with about 10 million more insures, I believe, but we could, eventually, aim to replace it. Thinking about things, in an idealistic world, the ‘individual mandate’ would indeed not exist.  That is, one should really be able to opt out of buying health insurance if one wishes. People should have the right to take a big, maybe stupid, risk, keep their insurance premium money, and not pay health insurance, even if they can afford it; just as they have the right to not insure against damage of their own car.

Now, the problem is, that if that right - to not buy insurance - is going to be given, for it to work you really have to not treat someone who is sick or injured, could afford insurance but decided not to pay for it, and doesn't have the money to pay for their treatment. You really have to leave them to their own devices, and even, if necessary, to die. And that's, of course, not what happens, even in the bad old USA.  Emergency rooms always treat patients; it’s basic compassion. And thus, a large part of the motivation for getting insurance in the first place disappears, and on top of this we get the consequences of enormous unpaid costs, medical bankruptcy nonsense  etc.

So the USA really needs to decide. Either you make insurance compulsory, as does the rest of the first world, or you don't treat people who don't get it.  Having it both ways doesn't work. Either we have the individual mandate or dispassionately insist on no treatment for the uninsured.   The US individual mandate, as in Europe, works better than the pre-Obamacare zoo. However, although I know of no precedent, the insurance-or-no-treatment model could conceivably work better, while giving people more freedom of choice. What you’d find, maybe, is that, the extra motivation might even lead to an even larger proportion of people getting insurance, and voluntarily, than they do under Obamacare. But it would be scary as hell. So guys, keep the individual mandate for now, but work to building a system where it is no longer necessary i.e., where health costs are so low  that everyone voluntarily buys insurance anyway. This requires bringing bring costs down, through increasing flexibility, introducing cross-state and international competition, dissociating insurance from employment, tort reform, preventive care incentives, analytics, targeted therapies, innovation etc. But that discussion, as they say, is another kettle of fish.