Gorgeous pictures (of our simulations).

Thanks to Thomas Splettstoesser of scisstyle.com for doing these graphics. This one is lignocellulose with cellulase enzymes. More to follow....

The Trump Travel Ban

OK, here's a "drunk blog". I may regret it in the morning.

I don't like too many immigrants, even though I am one. The reason is I don't like them is that immigration is fueling the population explosion in the USA and this is leading to environmental stress.

And I don't like terrorists. 57 virgins? Good luck with that.

And I don't mind 'racial profiling'. Makes sense to me.

And I don't cow-tow to this 'welcoming refugees' soppiness (although I do think that, having been a major initiator of their distress, we should do a hell of a lot more to alleviate their problems wherever they happen to be right now).

But a blanket ban on LEGAL immigrants? On scholars? Entrepreneurs? SCIENTISTS?

An INDISCRIMINATE blanket ban?

The collateral damage is just too great from this one.

Welcome back to the Dark Ages

Just finished watching Theresa May's "Brexit speech".  So a "hard Brexit" it is then. She claims Britain cannot remain in the single market because then it would be "just as if we hadn't left". Not true, Theresa. The UK voted to leave the EU, and that is exactly what a soft Brexit, in which the UK remains in the single market and accepts free movement of people, would do. The UK voted very narrowly to leave, by 51% to 48%. The narrowness of this victory should obviously be interpreted as a vote for a soft Brexit.

Now I agree with all who state that the EU has failed miserably in protecting its borders. Putting in place practical measures to strengthen this should be central to talks. But May's speech shows that the wingnut, Empire-harking  isolationists have taken over the Government, in a foretaste of  years of political uncertainty in the UK; years of efforts wasted in massive renegotiations that could have been avoided.

Welcome back, the Dark Ages.

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.

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!

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.

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..