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Stefan Grimm and the British University system.

12/21/2014

 
About two months ago a number of people at Imperial College (and not just there) received an email from the late Professor Stefan Grimm.  The email seems to have been sent on a time delay because Prof Grimm passed away in September.  You can find all the sad details here, here and here.  I know many friends and colleagues have expressed their opinion on this specific event, and more broadly on the state of British academia, and I would like to contribute a few thoughts.

In recent years British academia has become more and more focused on money.  The value of an idea, any idea, is measured in not equivocal terms on its ability to attract funding, i.e. money.  Academic institutions receive government funding based on a ‘research excellence’ metric which tries to capture the ‘excellence’ of the research carried out at an institution, meaning that only work that contributes to the ‘excellence’ metric contributes to the coffers of a university.  British academia has adapted to this relentless demand to compete for money by imposing to its staff that its main focus is to get grants and produce work useful for the ‘excellence’ metric; and by creating a rigid top down management whose sole purpose is to enforce this quest for funding. 

As always in the real world the best laid plans often conflict with how the world actually works, and this conflict gives rise to a number of unintended consequences.  The first unintended consequence is that the pursuit of what managements defines as ‘novel’ and ‘glamorous’ will diminish the intellectual value of British academia as a whole.  In 2014 it is firmly established that no one result or observation guarantees that a specific phenomenon, theory or effect is real — the only guarantee comes from replication.  Replication is the only thing that can prove that results and observations are actually reproducible, and that allow us to build and increase our understanding of the world.  Unfortunately, since academia, funding bodies and the editorial boards of papers have been taken over by top down management culture, solid rigorous science is penalised in favour of anything that can be branded as ’novel’, ‘cutting edge’, ‘state of the art’ and similar platitudes.  Scientific research is not about launching a new product on the market, it is about properly understanding what is going on in a well defined field with a clear intellectual foundation.  Most importantly, unless someone actually comes up with a new conceptual framework a lot of the ‘novelty’ research is just the same old rope with just flashier technology.  Because the ‘managers’ that now plague British academia do not take these simple facts in consideration (possibly because in Britain people are appointed to a position of power, they are not elected by their peers), we are now effectively penalising many serious researchers and forcing people to only focus on research that meets the short term goals of bringing in money and meeting arbitrary metrics.  This pressure will eventually push out all the people who want to do serious science and attract only those who can put up with the modest intellectual challenges that management allows them to work on.  This policy will leave British academia directionless and intellectually empty, and will transform any research in technology and data driven drivel that can at most pick up low hanging fruits and will deliver less and less as time goes on. 

The second problem with how British academia is managed is the culture of intellectual dishonesty that is forced upon people.  People are not allowed to just express their goals in simple honest terms.  They are required to spin and embellish everything in order to have half a chance of getting some funding or publishing in a high impact journal – both crucial to contribute to the ‘excellence metric’.  Many people are well aware that they are overselling their work, and they do it reluctantly and under duress — and they deeply resent it.  Only the shameless cynics thrive in such environment.  What academia needs is open and honest intellectual debate, desire for rigorous investigation and actual intellectual competence, not top down management.  British academia is now facing the attempt to transform intellectual work into predictable bureaucracy.  One particularly deleterious corollary of this lack of honesty is the fact that, to obtain funding, people are expected to provide an assessment of the ‘impact’ of their research, before the research is actually done.  Obviously nobody can tell what the impact of something that has not been done yet will be — nevertheless people are actually expected to show that their research will have an ‘impact’, and guaranteed outcomes to boot.  The net result of this fatuous approach is that people are actually forced to limit and dumb down their research proposals to actually have a chance of being funded: who can risk writing a grant that tackles a challenging problem and thus has an uncertain outcome?

Another pernicious problem that the current management style imposes on British academia can be summarised as ‘everything is easy if you are not the one doing it’.  Managements expects ‘results’ despite the fact that between starting to work on a project and getting anything out of it will take a substantial amount of time and work.  Can someone please remind me of how long it took to go from the theoretical postulation of the Higgs boson to actually proving it exists?  Let’s also not delve in the unpleasant notion that sometimes the best work, carried out competently and without any delays still produce unexciting results — stuff that can only be published in ‘second tier’ journals.  There are out there some people giving silly advice such as ‘people at the start of an academic career should only work on exciting problems that are easy to address’, because science is full of low hanging fruits, exciting easy stuff that nobody is somehow touching!  Also, senior academics especially identify and save this kind of work for junior colleagues, in the selfless attempt to help their junior’s careers.  The bottom line is that it is easy to tell to others to go and get some exciting results, actually getting them is a different matter.  Any sensible person does understand this problem, but to the eyes of the people managing British academia everything is easy.

Management does not simply find that doing research is easy, it also thinks that skill and expertise can be acquired cheaply and fast (probably because they never tried and they have this utterly wrong image of ‘consultants’ waltzing in, with all bells and whistles ready).  This creates a peculiar problem:  on the one hand management is unlikely to value actual skill and expertise, because people who have skill and expertise are equated to expendable technical labourers.  On the other hand, because expertise is devalued it is actually easy to push the most risible hokum provided it is clouded in incomprehensible jargon — nobody wants to say ‘I do not understand what you are talking about’.  Case in point is the recent raise of ‘big data’.  Because collecting data without any plan or strategy is easy, it has been possible to sell the convenient but erroneous idea that all we need to do is to be clever after the fact.  Notions of how scientific ideas are actually falsified, how experiments are planned and how data analysis actually works are just not part of the deal, because some magical computational or statistical tool will solve everything.  Garbage in, garbage out.

Finally we get to the topic of day, the REF.  Let’s be clear, the REF misses the point completely.  The assumption that we can summarise the work of complex institutions as universities are in a few simple metrics is just plainly wrong.  It is put forward by those who believe that for every complex problem there is a simple solution (whereas the maxim is that for every complex problem there is a solution that is obvious, simple and *wrong*).  Aside from the fact that the REF enforces the status quo, where big well funded institutions score high and keep being well funded, whereas small institutions start with the insurmountable handicap of being small and poorly funded, the REF also pushes the worst possible incentives.  Academics need to have a high REF score to keep their position, and in many institutions management will ruthlessly cull anybody who fails to help in achieving the high score desired.  The score can be quickly improved by pressurising people into leaving, and I have witnessed this procedure a few times.  Because the only things that matters are money and REF points, produced and provided at predictable intervals, people are under constant pressure to provide both, which is a potent incentive for good people to quit and for bad people to ‘bend the rules’ to meet these requirement — is it a surprise that the impact factor of a journal (a basic requirement for the REF) correlates with the retraction?

I know that a number of people will not recognise the portrait I am painting, so let me tell them: count your blessings.  As things are going, any research group, department or institution that values science over money and REF points is at risk of wholesale extirpation, and sadly the writing is on the wall.  I would gladly be wrong on this issue, in fact, nothing would please me more than being proven wrong.  In addition, please do take a good hard look at yourself and around you.  Academia fosters a strong culture and habit of loyalty, based on the assumption that senior staff will mentor and look after junior staff, who in turn repay this help with loyalty and hard work.  This template might have worked in the past.  In the present avaricious times it is important to make sure that we are loyal to the right people, and that our loyalty should not be taken for granted.

I would like to finish this long post with two more thoughts.  The first is that we cannot always be at the top of the game, because this is simply impossible.  Many factors well outside our control play a part in our intellectual achievements as academics.  Unfortunately ‘everything is easy’ for the people who want to manage British academia, and sooner or later one will be at a slow point exactly when they are expected to deliver money and REF points.  What happens then?  Unfortunately tragedies like the one of the late Prof Grimm might become more, not less, common.

Second, just in case people have not thought of it, the email that Prof Grimm sent in October did not magically make its way to the press by itself.  While many people are feeling disenchanted with academia and leave, more and more insiders are taking a combative stance against the mindless hogwash that threatens the foundations of British academia and the people that push it.  We should all stand up and be counted, or we will not be able to complain in the future.  It would be great if management could live up to it’s role and abandon the idea that scientific research is simple, predictable and quickly profitable, and actually help build the future of British academia.





Is asking people to replicate their own results a good idea?

6/26/2013

 
I am reading 'Bad pharma' by Ben Goldacre, which details how scientifc results are fraudolently manipulated, and I had to think of it yesterday.  Evangelos Evangelou gave a seminar of meta-analysis and validation in whole genome studies.  One peculiar fact in medical genetics is that replicating results is somewhat iffy, and multiple studies need to be looked at to get a handle on what is going on, and special analytical tools (meta-analysis as I was saying) need to be used because not all results agree with each other.  The issue of meta analysis is that it rests on the availability of all studies on a specific topic to actually get a proper result -- if we do not have all the data we cannot get the true effect.  


At the end of the talk, innocent like a baby, I raised my little hand to point out that there is a recent trend for journals, especially big ones, to publish papers only if the authors 'replicated' their main findings in some other dataset.  The 'optimist' explanation for this demand is that authors are required to show that their results hold in multiple 'independent' dataset, making the results more reliable.  Because I have seen quite a lot of water pass under the bridge, in my question I pointed out that, far from forcing people to publish reliable results, this practice can backfire big time.  Let us assume that group X finds some sexy result that might get a paper in high impact factor journal Y.  Group X knows that they have to replicate their findings, or no cookie.  Will group X carefully look at all other available data and present whatever they find, even if the results are 'inconclusive', or will group X leave aside all the data that does not help their replication, finding some post hoc reasons why it is ok to do so?  (and will journal Y support groups that have the balls to admit their sexy results look less sexy after replication attempts?).  And if this kind of behaviour becomes common, what effect would it have on meta-analysis and systematic reviews?

Fact is, I actually have been told of instances where data that did not replicate some result were left aside for publication (don't worry, the plausible deniability spiel was well rehearsed in case people asked). 

So, is the demand that people replicate the very results they need for their publication (and careers) a stupid move after all? wouldn't it be better if a journal publishes all the replication efforts from different groups after it publishes the first results?  This way there would be an incentive for proper independent replication.  Call me a cynic but asking people to verify *themselves* the message they want to publish seems to be the wrong way around to do things.

Batrachochytrium dendrobatidis, evolution and conservation.

5/20/2013

 
The recent news that Batrachochytrium dendrobatis (Bd) has been found in caecilians is worrying (especially for caecilian species!), but not exactly unexpected, given the incredible geographic spread of this fungus.  The recent news that I find more poignant in the history of Bd induced amphibian mass mortalities is that, far from being a novel organism, Bd is actually quite old (ref 1 and ref 2 in PNAS -- so far behind a paywall).

Recent genetic analysis of the largest collection of Bd isolates from around the globe (because Bd is now found in all continents) shows that Bd is older, definitively (much) older than mass amphibian population crashes, and has a complex population structure.  What does this tell us?  Many things in fact, but the fact I find most relevant to conservation is that Bd may have  been exerting selective pressure on a number of amphibian species, possibly for a long time.  Exerting a selective pressure means, in genetic terms, that individuals with certain alleles had a greater survival than individuals that had not.  In population terms it means that populations might had quite severe reductions, followed by rebounds when individuals carrying the selected for alleles became the norm in the population.  It also means that naive populations (that is, populations that have not yet encountered Bd) will undergo a strong selection that will either select for infection resistance (if the necessary genetic variation is present).  Alternatively these naive populations will have a great risk of going extinct.  We know in fact that Bd is causing mass mortalities of many amphibian species around the globe, and we know that a number of these species just disappeared.  We know next to nothing about the genetics of amphibians, so there is no way we can understand what is happening, in genetic terms, on the host side of the equation. 

The observations above give me a strong 'take home message': unless we start to work in earnest on amphibian genetics and genomics, all the work done on Bd will not be enough to stop and revert amphibian populations declines.  Because virulence is a property of the host/parasite interaction, we must be able to understand *both* Bd and amphibian population genetic structure to properly understand the potential virulence of each Bd/amphibian interaction.  This understanding is necessary to model population crash dynamics in the wild, and to have a hope to rescue amphibian populations in the first place.  Only genetic tools will allow us to test the hypothesis that Bd has been a selective force for some amphibian species for thousands of years, and only genetic tools will allow us to understand the genetics of adaptation to such selective pressure.  

All the above is, in practice, a lot of work, expensive, time consuming.  With the world economy circling around the drain, governments are brutally cutting research funds for biology and conservation.  This is too bad, for so many reasons, and because we are running out of time to save many amphibian species.  Amphibian genetics is a prefect case of basic research with a direct, clearly identifiable goal that will have potential benefit for the taxpayer.  If the urgency of this issue and the obvious potential benefits of tackling it are not enough to get people to invest on amphibian genetics now, all I can say is that we might as well have frog legs for dinner.

Frog cloning, what are we trying to achieve?

4/16/2013

 
The interaction between synthetic biology and conservation was on the news today in Nature.  Recent news that the extinct Rheobatrachus silus has been cloned (well, up to a point, the embryos did not survive more than a few days) brings up many questions.  The question that I personally find most important is: what are we trying to achieve here?

Let's first introduce our main actor, the Rheobatrachus silus.  This frog was (or is) an Australian frog with one peculiar habit: following fertilisation the female would swallow the eggs, which would develop safely in her stomach.  Once the tadpoles had metamorphosed into small froglets they would be 'regurgitated' out by the mother.  Nobody knows why these frogs went extinct (the fact that they were a small population to start with did not help either), though infectious diseases might have played a role.  People of the persuasion that we should put a price tag on everything should consider what a wonderful model for gastric inflammation we have lost.

Picture
More to the point of my post.  I am personally not that concerned that ham-fisted scientists will unleash a plague of mutants on the planet.  We can barely get the embryos to survive in the first place.  What I am concerned about is that I do not really see a long term strategy behind this work.  Assuming we were successful in cloning Rheobatrachus to adulthood, what next?  Cloning extinct species is fine and dandy, but what are we going to do with the resulting animals, assuming we get there?  If we cannot produce a viable population, the interest from a conservation standpoint is lost to me.  For many extinct species we know nothing or next to nothing about their demographic parameters and the amount of genetic variability present in the species as a whole and in the different subpopulations (if present).  What are we planning to do, fetch every possible source of DNA from museum collections hoping to get enough variation (and what if all specimens are the same sex?)?  And then?  Producing the odd live individual might look like a small miracle, but what good it is to get one Rheobatrachus silus?  We would need to get many, with sufficient genetic variation, and make sure that they can keep reproducing by themselves.  This seems to be a tough call.

Human ingenuity and technological advances can sort many problems.  Extinction is not one of them.  For complex animals such as amphibians the chances of undoing our actions on the natural world are slim.  And what is potentially worrying is that the false security that 'we can clone them back to life' will stop people from preventing extinction in the real world in the first place.  So, once more, what are we trying to achieve?  And are we sure we are using our resources to best effect?

Of Rhinos and Amphibians

4/10/2013

 
Rhinos have been in the news quite a lot recently.  The latest (official press release) is that a rhino DNA database will be created to try and figure out where horns seized by police come from -- the damn things are so valuable people are starting to steal them from museums.  This is quite interesting because I am a great believer that genetics offers an important tool to monitor and to protect endangered species.


These latest news are very poignant to me, but I had been thinking about rhinos for a while now.  Recently there was a controversy about the role of trophy hunting rhinos to raise money for rhino conservation. The Timbavati Game Reserve Chairman Tom Hancock, a reserve which admittedly has done a lot to preserve rhinos, posted an open letter expressing his opinion that rhino trophy hunting has a place as a valuable source of income for rhino conservation (the original letter seems to have been removed from the Timbavati site, but can be read here).  These thoughts have angered many people, who basically commented that rhinos should not be hunted, and that they should be protected either because they generate a revenue through tourism, or because we should protect rhinos as a matter of ethics.


The reason why I got so interested in the rhino debate is the following.  I am interested in conservation, and I know that, of all animals, amphibians are benefiting the least from conservation efforts.  In addition, amphibians are the group of vertebrates that has the largest number of species at risk of extinction.  This is because amphibians are threatened by both human activities and newly emerging infectious diseases (Ranavirus and Batrachochytrium dendrobatis).  To me, the recent rhino news show that people understand the need for, and are prepared to:

1)  protect the environment which a species needs to exist in the wild
2)  take additional measures on top of (1) to protect the individual animals
3)  invest to set up a genetic database to help the conservation of rhinos. 



I like rhinos a lot, and I am very happy all the three things above are done for their conservation and management.  But I'd dearly love to see the same efforts to be done for amphibians.  Amphibians are being literally hammered by infectious diseases, and a number of species have gone extinct because of these infections.  I have tried to obtain research funding to test if there are any genes that confer resistance to these diseases, with the hope we could use this knowledge to protect the most at risk species.  But unfortunately amphibian are small, modest and, Kermit aside, not that famous and charismatic, so that was not a priority.  Colleagues also interested in amphibian conservation have problems getting funds for this kind of research.


I do not believe that we should spend less on the conservation of any species to divert the funds for another. What I believe in is that we should accept that we must invest more, much more, in conservation.  So, if we are happy to invest to give one more chance to rhinos, can we try to do the same for frogs and newts?
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