Archive for October, 2010

Engineering a Conflict

Posted in Finance, Politics, Science Politics with tags , , , on October 25, 2010 by telescoper

I don’t have time to post much today so I thought I’d just put up a quick item about something that the e-astronomer (aka Andy Lawrence) has already blogged about, and generated a considerable amount of discussion about so I’ll just chip in with my two-penny-worth.

Some time ago I posted an item explaining how, in the run-up to last week’s Comprehensive Spending Review, the Royal Academy of Engineering had argued, in a letter to the Department of Business, Innovation and Skills (BIS), that government research funding should be

… concentrated on activities from which a contribution to the economy, within the short to medium term, is foreseeable. I recognise that this calls for significant changes in practice but I see no alternative in the next decade. This may mean disinvesting in some areas in order properly to invest in others.

They went on to say that

BIS should also consider the productivity of investment by discipline and then sub-discipline. Once the cost of facilities is taken into account it is evident that ‘Physics and Maths’ receive several times more expenditure per research active academic compared to those in ‘Engineering and Technology’. This ratio becomes significantly more extreme if the comparison is made between particle physics researchers and those in engineering and technology. Much of particle physics work is carried out at CERN and other overseas facilities and therefore makes a lower contribution to the intellectual infrastructure of the UK compared to other disciplines. Additionally, although particle physics research is important it makes only a modest contribution to the most important challenges facing society today, as compared with engineering and technology where almost all the research is directly or indirectly relevant to wealth creation.

I had hoped that this unseemly attack on particle physics would have been seen for what it was and would have faded into the background, but a recent article by Colin Macilwain has brought it back into the spotlight. I quote

UK engineers have started a scrap that will grow uglier as the spending cuts begin.

I should add that MacIlwain isn’t particularly supportive of the engineers’ position, but he does make some interesting remarks on the comparitively low status held by engineers in the United Kingdom compared to other countries, a point alsotaken up on Andy Lawrence’s blog. In my opinion this bare-faced attempt to feather their own nest at the expense of fundamental physics isn’t likely to generate many new admirers. Neither is the fact – and this is a point I’ve tried to make before – that the engineers’ argument simply doesn’t hold any water in the first place.

The point they are trying to make is that research in engineering is more likely to lead to rapid commercial exploitation than research in particle physics. That may be true, but it’s not a good argument for the government to increase the amount of research funding. If engineering and applied science really is “near market” in the way that the RAEng asserts, then it shouldn’t need research grants, but should instead be supported by venture capital or direct investment from industry. The financial acumen likely to be available from such investors will be much for useful for the commercial exploitation of any inventions or discoveries than a government-run research council. To be fair, as MacIlwain’s article explains, a large fraction of engineering research (perhaps 75%) is funded by commerce and industry. Moreover some engineering research is also too speculative for the market to touch and therefore does merits state support. However, that part that needs state support needs it for precisely the same reason that particle physics does, i.e. that its potential is long-term rather than short term. This means that is in the same boat as fundamental physics and shouldn’t keep pretending that it isn’t. If engineering research needs government funding then ipso facto it’s not likely to generate profits in the short term.

I think scientists and engineers would all be better off if they worked together to emphasize the amazingly successful links between fundamental physics and technology, as demonstrated by, e.g., the Large Hadron Collider at CERN and the mutual interdependence of their disciplines.

United we stand, and all that…


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Cats really are just like people..

Posted in Uncategorized with tags on October 24, 2010 by telescoper

Thanks to a miracle of technology, it is now possible to translate the thoughts of a cat into human speech. This demonstration shows that cats really do think and behave in exactly the same way as people. I had a similar conversation with a photocopier only a few days ago. Unfortunately, owing to design limitations, the software can only produce a rather unattractive cockney accent. Also I can assure you that Columbo does not use the sort of foul language deployed by this otherwise charming animal.

Thanks to Jennifer Ouellette for this one..


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DNA Profiling and the Prosecutor’s Fallacy

Posted in Bad Statistics with tags , , , , , , on October 23, 2010 by telescoper

It’s been a while since I posed anything in the Bad Statistics file so I thought I’d return to the subject of one of my very first blog posts, although I’ll take a different tack this time and introduce it with different, though related, example.

The topic is forensic statistics, which has been involved in some high-profile cases and which demonstrates how careful probabilistic reasoning is needed to understand scientific evidence. A good example is the use of DNA profiling evidence. Typically, this involves the comparison of two samples: one from an unknown source (evidence, such as blood or semen, collected at the scene of a crime) and a known or reference sample, such as a blood or saliva sample from a suspect. If the DNA profiles obtained from the two samples are indistinguishable then they are said to “match” and this evidence can be used in court as indicating that the suspect was in fact the origin of the sample.

In courtroom dramas, DNA matches are usually presented as being very definitive. In fact, the strength of the evidence varies very widely depending on the circumstances. If the DNA profile of the suspect or evidence consists of a combination of traits that is very rare in the population at large then the evidence can be very strong that the suspect was the contributor. If the DNA profile is not so rare then it becomes more likely that both samples match simply by chance. This probabilistic aspect makes it very important to understand the logic of the argument very carefully.

So how does it all work? A DNA profile is not a complete map of the entire genetic code contained within the cells of an individual, which would be such an enormous amount of information that it would be impractical to use it in court. Instead, a profile consists of a few (perhaps half-a-dozen) pieces of this information called alleles. An allele is one of the possible codings of DNA of the same gene at a given position (or locus) on one of the chromosomes in a cell. A single gene may, for example, determine the colour of the blossom produced by a flower; more often genes act in concert with other genes to determine the physical properties of an organism. The overall physical appearance of an individual organism, i.e. any of its particular traits, is called the phenotype and it is controlled, at least to some extent, by the set of alleles that the individual possesses. In the simplest cases, however, a single gene controls a given attribute. The gene that controls the colour of a flower will have different versions: one might produce blue flowers, another red, and so on. These different versions of a given gene are called alleles.

Some organisms contain two copies of each gene; these are said to be diploid. These copies can either be both the same, in which case the organism is homozygous, or different in which case it is heterozygous; in the latter case it possesses two different alleles for the same gene. Phenotypes for a given allele may be either dominant or recessive (although not all are characterized in this way). For example, suppose the dominated and recessive alleles are called A and a, respectively. If a phenotype is dominant then the presence of one associated allele in the pair is sufficient for the associated trait to be displayed, i.e. AA, aA and Aa will both show the same phenotype. If it is recessive, both alleles must be of the type associated with that phenotype so only aa will lead to the corresponding traits being visible.

Now we get to the probabilistic aspect of this. Suppose we want to know what the frequency of an allele is in the population, which translates into the probability that it is selected when a random individual is extracted. The argument that is needed is essentially statistical. During reproduction, the offspring assemble their alleles from those of their parents. Suppose that the alleles for any given individual are chosen independently. If p is the frequency of the dominant gene and q is the frequency of the recessive one, then we can immediately write:

p+q =1

Using the product law for probabilities, and assuming independence, the probability of homozygous dominant pairing (i.e. AA) is p2, while that of the pairing aa is q2. The probability of the heterozygotic outcome is 2pq (the two possibilities, each of probability pq are Aa and aA). This leads to the result that

p^2 +2pq +q^2 =1

This called the Hardy-Weinberg law. It can easily be extended to cases where there are two or more alleles, but I won’t go through the details here.

Now what we have to do is examine the DNA of a particular individual and see how it compares with what is known about the population. Suppose we take one locus to start with, and the individual turns out to be homozygotic: the two alleles at that locus are the same. In the population at large the frequency of that allele might be, say, 0.6. The probability that this combination arises “by chance” is therefore 0.6 times 0.6, or 0.36. Now move to the next locus, where the individual profile has two different alleles. The frequency of one is 0.25 and that of the other is 0.75. so the probability of the combination is “2pq”, which is 0.375. The probability of a match at both these loci is therefore 0.36 times 0.375, or 13.5%. The addition of further loci gradually refines the profile, so the corresponding probability reduces.

This is a perfectly bona fide statistical argument, provided the assumptions made about population genetic are correct. Let us suppose that a profile of 7 loci – a typical number for the kind of profiling used in the courts – leads to a probability of one in ten thousand of a match for a “randomly selected” individual. Now suppose the profile of our suspect matches that of the sample left at the crime scene. This means that, either the suspect left the trace there, or an unlikely coincidence happened: that, by a 1:10,000 chance, our suspect just happened to match the evidence.

This kind of result is often quoted in the newspapers as meaning that there is only a 1 in 10,000 chance that someone other than the suspect contributed the sample or, in other words, that the odds against the suspect being innocent are ten thousand to one against. Such statements are gross misrepresentations of the logic, but they have become so commonplace that they have acquired their own name: the Prosecutor’s Fallacy.

To see why this is a fallacy, i.e. why it is wrong, imagine that whatever crime we are talking about took place in a big city with 1,000,000 inhabitants. How many people in this city would have DNA that matches the profile? Answer: about 1 in 10,000 of them ,which comes to 100. Our suspect is one. In the absence of any other information, the odds are therefore roughly 100:1 against him being guilty rather than 10,000:1 in favour. In realistic cases there will of course be additional evidence that excludes the other 99 potential suspects, so it is incorrect to claim that a DNA match actually provides evidence of innocence. This converse argument has been dubbed the Defence Fallacy, but nevertheless it shows that statements about probability need to be phrased very carefully if they are to be understood properly.

All this brings me to the tragedy that I blogged about in 2008. In 1999, Mrs Sally Clark was tried and convicted for the murder of her two sons Christopher, who died aged 10 weeks in 1996, and Harry who was only eight weeks old when he died in 1998. Sudden infant deaths are sadly not as uncommon as one might have hoped: about one in eight thousand families experience such a nightmare. But what was unusual in this case was that after the second death in Mrs Clark’s family, the distinguished paediatrician Sir Roy Meadows was asked by the police to investigate the circumstances surrounding both her losses. Based on his report, Sally Clark was put on trial for murder. Sir Roy was called as an expert witness. Largely because of his testimony, Mrs Clark was convicted and sentenced to prison.

After much campaigning, she was released by the Court of Appeal in 2003. She was innocent all along. On top of the loss of her sons, the courts had deprived her of her liberty for four years. Sally Clark died in 2007 from alcohol poisoning, after having apparently taken to the bottle after three years of wrongful imprisonment.The whole episode was a tragedy and a disgrace to the legal profession.

I am not going to imply that Sir Roy Meadows bears sole responsibility for this fiasco, because there were many difficulties in Mrs Clark’s trial. One of the main issues raised on Appeal was that the pathologist working with the prosecution had failed to disclose evidence that Harry was suffering from an infection at the time he died. Nevertheless, what Professor Meadows said on oath was so shockingly stupid that he fully deserves the vilification with which he was greeted after the trial. Two other women had also been imprisoned in similar circumstances, as a result of his intervention.

At the core of the prosecution’s case was a probabilistic argument that would have been torn to shreds had any competent statistician been called to the witness box. Sadly, the defence counsel seemed to believe it as much as the jury did, and it was never rebutted. Sir Roy stated, correctly, that the odds of a baby dying of sudden infant death syndrome (or “cot death”) in an affluent, non-smoking family like Sally Clarks, were about 8,543 to one against. He then presented the probability of this happening twice in a family as being this number squared, or 73 million to one against. In the minds of the jury this became the odds against Mrs Clark being innocent of a crime.

That this argument was not effectively challenged at the trial is truly staggering.

Remember that the product rule for combining probabilities

P(AB)=P(A)P(B|A)

only reduces to

P(AB)=P(A)P(B)

if the two events A and B are independent, i.e. that the occurrence of one event has no effect on the probability of the other. Nobody knows for sure what causes cot deaths, but there is every reason to believe that there might be inherited or environmental factors that might cause such deaths to be more frequent in some families than in others. In other words, sudden infant deaths might be correlated rather than independent. Furthermore, there is data about the frequency of multiple infant deaths in families. The conditional frequency of a second such event following an earlier one is not one in eight thousand or so, it’s just one in 77. This is hard evidence that should have been presented to the jury. It wasn’t.

Note that this testimony counts as doubly-bad statistics. It not only deploys the Prosecutor’s Fallacy, but applies it to what was an incorrect calculation in the first place!

Defending himself, Professor Meadows tried to explain that he hadn’t really understood the statistical argument he was presenting, but was merely repeating for the benefit of the court something he had read, which turned out to have been in a report that had not been even published at the time of the trial. He said

To me it was like I was quoting from a radiologist’s report or a piece of pathology. I was quoting the statistics, I wasn’t pretending to be a statistician.

I always thought that expert witnesses were suppose to testify about those things that they were experts about, rather than subjecting the jury second-hand flummery. Perhaps expert witnesses enjoy their status so much that they feel they can’t make mistakes about anything.

Subsequent to Mrs Clark’s release, Sir Roy Meadows was summoned to appear in front of a disciplinary tribunal at the General Medical Council. At the end of the hearing he was found guilty of serious professional misconduct, and struck off the medical register. Since he is retired anyway, this seems to me to be scant punishment. The judges and barristers who should have been alert to this miscarriage of justice have escaped censure altogether.

Although I am pleased that Professor Meadows has been disciplined in this fashion, I also hope that the General Medical Council does not think that hanging one individual out to dry will solve this problem. I addition, I think the politicians and legal system should look very hard at what went wrong in this case (and others of its type) to see how the probabilistic arguments that are essential in the days of forensic science can be properly incorporated in a rational system of justice. At the moment there is no agreed protocol for evaluating scientific evidence before it is presented to court. It is likely that such a body might have prevented the case of Mrs Clark from ever coming to trial. Scientists frequently seek the opinions of lawyers when they need to, but lawyers seem happy to handle scientific arguments themselves even when they don’t understand them at all.

I end with a quote from a press release produced by the Royal Statistical Society in the aftermath of this case:

Although many scientists have some familiarity with statistical methods, statistics remains a specialised area. The Society urges the Courts to ensure that statistical evidence is presented only by appropriately qualified statistical experts, as would be the case for any other form of expert evidence.

As far as I know, the criminal justice system has yet to implement such safeguards.


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Insomniac

Posted in Poetry with tags , on October 22, 2010 by telescoper

The night is only a sort of carbon paper,
Blueblack, with the much-poked periods of stars
Letting in the light, peephole after peephole —
A bonewhite light, like death, behind all things.
Under the eyes of the stars and the moon’s rictus
He suffers his desert pillow, sleeplessness
Stretching its fine, irritating sand in all directions.

Over and over the old, granular movie
Exposes embarrassments–the mizzling days
Of childhood and adolescence, sticky with dreams,
Parental faces on tall stalks, alternately stern and tearful,
A garden of buggy rose that made him cry.
His forehead is bumpy as a sack of rocks.
Memories jostle each other for face-room like obsolete film stars.

He is immune to pills: red, purple, blue —
How they lit the tedium of the protracted evening!
Those sugary planets whose influence won for him
A life baptized in no-life for a while,
And the sweet, drugged waking of a forgetful baby.
Now the pills are worn-out and silly, like classical gods.
Their poppy-sleepy colors do him no good.

His head is a little interior of grey mirrors.
Each gesture flees immediately down an alley
Of diminishing perspectives, and its significance
Drains like water out the hole at the far end.
He lives without privacy in a lidless room,
The bald slots of his eyes stiffened wide-open
On the incessant heat-lightning flicker of situations.

Nightlong, in the granite yard, invisible cats
Have been howling like women, or damaged instruments.
Already he can feel daylight, his white disease,
Creeping up with her hatful of trivial repetitions.
The city is a map of cheerful twitters now,
And everywhere people, eyes mica-silver and blank,
Are riding to work in rows, as if recently brainwashed.

by Sylvia Plath (1932-63)


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The Art Ensemble of Chicago

Posted in Jazz with tags , , on October 21, 2010 by telescoper

It’s been a while since I posted anything from the outer reaches of the musical universe, so I thought I’d try this one out on you. It was recorded live in 1984 by the Art Ensemble of Chicago with the great Cecil Taylor as special guest on piano. Extrapolating from the comments on Youtube, I confidently predict that quite a lot of you will hate this but, for what it’s worth, I think the Art Ensemble of Chicago was one of the most consistently creative groups of musicians active in avant-garde Jazz from the 1960s, when it was formed, until the death in 1999 of their inspirational trumpeter Lester Bowie. Their music might be a bit too far “out there” for many tastes, but I love it. So there.


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The Day After: A Welsh Perspective

Posted in Education, Politics, Science Politics with tags , , , , , , , on October 21, 2010 by telescoper

It’s well after 11am and I’m still at home. Came down last night with some sort of bug that kept me awake nearly all night with frequent visits to the smallest room in the house. Whatever it is is still rumbling on so I’ve decided to stay at home until I give myself the all clear.

This sudden attack of lurgy is probably not connected with yesterday’s dramatic announcements of the results of the comprehensive spending review, which are now being dissected and analysed all over the mainstream press, the blogosphere, and countless common rooms around the country.

I haven’t got the energy right now to go over the ramifications in detail, but encourage you to read the whole thing, which is available in a nifty online reader for your perusal. I will, however, make a few brief comments, with particular emphasis on the situation here in Wales.

First, the announcement of large cuts to the teaching budget administered by HEFCE has clearly sent shockwaves through academia. It appears that only STEM subjects will continue to receive the state contribution and in future students will have to bear the full cost of tuition (but only after they’ve graduated and started to earn over the threshold of £21K). As a supporter of the Science is Vital campaign I was relieved that we seem to won a victory, although the war is far from over. However, I feel great sadness at the cost that our success seems likely to inflict on other disciplines. If you think these are nervous times for scientists, imagine what it must be like working in the Arts and Humanities.

Of course this all applies directly only to English universities: the budgets for Higher Education in Scotland, Wales and Northern Ireland are administered separately, so in principle things could work out very differently for Higher Education here in Wales.

However, the total amount of money available for the Welsh Assembly Government (WAG) to spend is fixed by the Westminster government through the Barnett Formula. This determines the overall cash for the devolved governments by allocating a proportion of what England spends on those things that are devolved., i.e. Wales is notionally allocated an amount for Higher Education which is proportional to HEFCE’s allocation and similar for other areas of spending such as Health. Once the size of the overall pot is fixed, however, the WAG is not obliged to spend its money in the same way that England does.

Buried in the pages of the CSR document is Wales’ allocation over the CSR period, which shows real terms cut of about 7.5% over the term. However, the Welsh Assembly Government’s reaction puts it rather differently:

In real terms, our total Budget is set to fall by around 3.1% per year on average, or 12% in total over the coming four years. This means that our Budget in 2014/15 will be £1.8bn lower in real terms than it is this year. Overall, in cash terms the reductions to our Budget will be 3% over the period.

Our capital Budget has been hit particularly hard, and will be cut by 40% in real terms – 34% in cash terms – over the next four years. This substantial reduction, particularly next year, where the cut is more than 25% in real terms, will clearly have a major impact on the private as well as the public sectors.

These figures seem different from those in the CSR document, which might be because of some nuance such as the way capital expenditure is accounted. If anyone can explain the discrepancy through the comments box I’d be grateful.

The main point is, though, that if Wales is going to keep current levels of investment in Higher Education (or even cut less than the English are doing) then it will have to take the money from elsewhere, which is not going to be easy to get through the Welsh Assembly. The picture, therefore, may not be any better here in Wales than it is in England, and could well turn out even worse, depending on how the WAG sets its own spending priorities. To complicate matters further, there’s an election next year for the Welsh Assembly, so there’s a wider political perspective to consider.

Within the overall issue of Higher Education spending is the question of whether Wales will decide to protect funding for STEM disciplines at the expense of all others. The WAG has already produced a document that suggests a strong focus on the so-called regional agenda, which may mean more money going into Further Education, vocational training, and part-time studies rather than, say, research-led science. I know what I would prefer, but whatever I say, it’s the WAG’s decisions that really count. And so it should be. After all, unlike me, they were elected!

Of course, if STEM subjects aren’t protected in Wales, those of us working in those areas are likely to lose even more ground to English universities, which already out-perform us in many respects. We have to make our case as best we can and see what happens.

However, I will end with some more local news which is extremely promising. Yesterday we had a staff meeting in the School of Physics & Astronomy at Cardiff University during which two extremely positive items came to light. One is that we will shortly be interviewing for the extra physics posts we advertised some time ago. Hopefully there will be a new Professor and three new Lecturers joining the staff in the very near future. I’m told we had a huge number of applicants for these positions, and the shortlists for these positions are very strong indeed. This is all very encouraging.

On top of this there is another exciting development on the horizon. After the disappointing outcome of the last RAE for physics in Wales, we have been thinking very hard at working closer with colleagues at Swansea with a view to building a sort of South Wales Physics Alliance. The departments are complementary in many ways: Swansea does particle physics, but Cardiff doesn’t; Cardiff does astronomy, but Swansea doesn’t. Where we are both relatively weak is in so-called “mainstream” physics, which is in the minority in both departments. With a bit of help, I think these two small(ish) departments could form a research institute that really challenges our competitors abroad (especially in England). I’m strongly in favour of this plan, and hope it goes ahead with full HEFCW support (including extra cash), but in this as in some many things, it’s a case of “fingers crossed”.


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The Great Escape? Not yet.

Posted in Finance, Politics, Science Politics with tags , , , , , on October 20, 2010 by telescoper

I expected to wake up this morning with the blues all round my bed, about the results of the Comprehensive Spending Review about to be announced today, but news appearing in the Guardian and the BBC websites last night suggested that the UK Science budget may, repeat may, be spared the worst of the cuts.

This news has been greeted with euphoria in the science community, as we were expecting much worse than the settlement suggested by the news. The RCUK budget, it seems, will be fixed in cash terms around £3.5 billion per annum for four years, as will the approximately £1bn distributed for research through HEFCE’s QR mechanism. This translates into a real terms cut that depends on what figure you pick for inflation over this period. The Treasury suggests it will corresponding to a 10% reduction figured that way, but inflation has defied predictions and remained higher than expected over the past three years so things could be different. Also important to note is that this budget (amounting to around £4.6 billion) is to be ring-fenced within RCUK.

So why the apparent change of heart? Well, I don’t know for sure, but I think the Science is Vital campaign played a very big part in this. Huge congratulations are due to Jenny Rohn and the rest of the team for doing such a fantastic job. The Guardian makes this clear, stating that science is usually a non-issue for the Treasury, but this time it was

high on the political radar because strong representations have been made by the scientific community about what they have described as “long term and irreversible” damage to the UK economy if there are deep cuts to research funding.

That means everyone who wrote to their MP or lobbied or went on the demo really did make a difference. Give yourselves a collective pat on the back!

BUT (and it’s a very big BUT) we’re by no means out of the woods yet, at least not those of us who work in astronomy and particle physics. As the BBC article makes clear, the level cash settlement for RCUK comes with an instruction that “wealth creation” be prioritised. The budget for RCUK covers all the research councils, who will now have to make their pitch to RCUK for a share of the pie. It’s unlikely that it will be flat cash for everyone. There will be winners and losers, and there’s no prize for guessing who the likely losers are.

The performance of the STFC Executive during the last CSR should also be born in mind. STFC did very poorly then at a time when the overall funding allocation for science was relatively generous, and precipitated a financial crisis that STFC’s management still hasn’t properly come to grips with. The track-record doesn’t inspire me with confidence. Moreover, at a town meeting in London in December 2007 at which the Chief Executive of STFC presented a so-called delivery plan to deal with the crisis he led his organisation into, he confidently predicted a similarly poor settlement in the next CSR. Talk about a self-fulfilling prophecy. Let’s hope they get their act together better this time.

Taking all this together it remains by no means improbable that the STFC budget could be squeezed until the pips squeak in order to liberate funds to spend elsewhere within RCUK on things that look more likely to generate profits quickly. The nightmare scenario I mentioned a few days ago is still on the cards.

As we all know, STFC’s budget is dominated by large fixed items so its science programme is especially vulnerable. As the BBC puts it

So any cut in [STFC’s] budget will be greatly magnified and it is expected that it will have to withdraw from a major programme. Alternatively, it would have to cutback or close one of its research institutes.

We could have to wait until December to find out the STFC budget, so the anxiety is by no means over. However, the ring-fencing of RCUK’s budget within BIS may bring that forward a bit as it would appear to suggest one level of negotations could be skipped. We might learn our fate sooner than we thought.

Overall, this is a good result in the circumstances. Although it’s a sad state of affairs when a >10% real terms cut is presented as a success, it’s far less bad than many of us had expected. But I think STFC science remains in grave danger. It’s not an escape, just a stay of execution.

But there is one important lesson to be learned from this. When the STFC crisis broke three years ago, reaction amongst scientists was muted. Fearful of rocking the boat, we sat on our hands as the crisis worsened. I hope that the success of the Science is Vital campaign has convinced you that keeping quiet and not making a fuss is exactly the wrong thing to do.

If only we’d been braver three years ago.


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