Something rather different today and seasonal to boot. It is the strawberry season and pick your own does seem to result in the accumulation of very large quantities of fruit. I guess it always looks like less in a field. Indeed, there have been a few cries for help on Twitter and elsewhere, as people contemplate a huge pile of strawberries at home, wondering if they can possibly eat them. My late father had three excellent solutions.

In no particular order: Continue Reading »

Clots and vaccines

Blood clots, for example, deep vein thromboses or pulmonary embolisms, are serious and we should rightly be concerned about these. With ~ 17 M doses of the AZ vaccine delivered into people, we have reports of 15 cases of deep vein thrombosis and 22 cases of pulmonary embolism. Deep vein thrombosis occurs at rate of 0.1% (so 1 in 1000) across all age groups, increasing with age. So every day that means around 47 cases in a population of 17 million – in fact it will be more, because those vaccinated are not representative of the population, but an older segment.

If we consider that vaccination has been happening at a high rate for a little over 2 months, then we expect at least 2,800 cases of deep vein thrombosis.

We can draw some limited conclusions regarding clots, the AZ and other vaccines.

  1. The reporting mechanism may be very, very poor, and only a fraction of patient outcomes are reported. This is in stark contrast to a clinical trial, where ALL outcomes re reported – recall that one poor individual on the Pfizer/BioNT trial was killed by a lightening strike, and in the AZ trial there were 2 deaths in the vaccination group and 4 in the placebo group. These and other deaths were unrelated to the vaccine.

Selective reporting leads to fantasy.

  1. Reporting is not so poor, so the correlation is that vaccination protects against thrombosis. Without knowing the quality of reporting of adverse effects and the likelihood that a good many clinicians will consider many conditions in vaccinated patients to be unrelated to the vaccine, this intriguing possibility remains a possibility and no more.
  2. “Clot”, at least for UK speakers of English has a second meaning, akin to the US ‘blockhead’. It may be that the AZ vaccine activates clots in government.

At present the most likely causal relation is (3). This is because we have ample evidence independent of vaccination programmes that demonstrate an often higher concentration of clots in government and in the upper reaches of many greasy poles than one would expect were altitude to correlate in some way with ability.


Note: H/T @archer_rs who reminded me that the only vaccine that is non-profit is the AZ vaccine. The history of drugs teaches us that the profit motive leads to hiding real and serious adverse events.

Where are the plans?

In three weeks schools re-open and a few weeks later undergraduates return to university. Universities appear to be moving to a model of having all students in attendance, and using a lot of remote teaching. This in itself is not necessarily a bad idea, as there will be facilities available and for 1st years in Halls and for many later year undergraduates they may have better internet connectivity, plus there is the library various computer rooms.

There will have to be some face-to-face teaching, as there are limits to what can be done remotely and this is even more the case for schools.

What concerns me is the lack of plans and the absence of clear procedures, based on best practice. A campus university of course has many advantages, since it could in principle function as a giant bubble, with testing at the gate, as well as testing within campus of students and employees (who will be coming in from the outside). Universities embedded in a city face far more serious challenges. Liverpool University alone will bring 20,000 undergraduates into the city with second and later years dispersed over a fairly large area of the south end.

For both schools and Universities, things have been made worse by government policies relating to space usage: maximise space use or you are financially penalised, either directly or indirectly. Such ‘efficiency’ means the system is extremely brittle and cannot cope with stress. The NHS suffers from the same problem. So face-to-face teaching means reducing numbers/m2 by at least 50%, likely 60-70%. 

However social distancing is not safe indoors. We have a documented transmission of SARS-CoV-2 indoors over 8 m. So 2 m will help, but will not prevent. Moreover, looking at queues, people in shops etc., few have any idea how far 2 m is – quite a long way. 

We have to wear masks, or in some instances a visor (not as good, but helps and allows lips to be read). Masks are recommended but not mandatory for researchers at Liverpool University, simply due to a vocal minority pushing forwards false information (masks increase risky behaviour and masks are dangerous) and stating we should only follow government advice. This is replicated elsewhere in the education system.

We also need to isolate each station occupied by a student: PETG on 3 sides. Not just for teaching, but also for canteens in halls of residence. After each ‘sitting’ entire station has to be sanitised.

Windows – open windows increases air change and appears to have a large effect on indoor transmission, first noted in a hospital in Guanzhou in February. So rooms without wimdows that can be opened should be off limits for teaching.

For schools, FE colleges, and Universities where is the mask policy? Where are the PETG separators? Where is the policy of open windows? Where is the test and trace?

It isn’t difficult, we have had since March to get ready. We have very good examples of best practice, here is one from Korea.

Closer to home, Devi Sridhar’s excellent recommendations in The Scotsman on how universities should re-open undergraduate teaching

The very good Irish Tracing app cost all of £340,000 to develop and the code (fully app store compliant) is on GitHub. Easy enough to implement for a city. We could have ‘localised’ versions: Toffee, Kop, generic Scouse one with Liver Bird logo, and so on. Take up, suitably promoted would be very high.

We appear to suffer from a lack of leadership, and an acceptance that we should somehow follow advice of the most corrupt and incompetent government this country has have for a long time, perhaps for its entire history. Instead we should be aiming for zero covid. We have the means, the tools, but appear to lack the will.

I am not looking forwards to September/October. The news on the Long Covid front, which affects the young more than the old should be focussing minds but I have not seen much evidence for this.


Edit August 18: Birmingham City University appears to have got its act together. Face coverings are mandatory on campus. Any others? 

Edits August 23

The BMJ has a call to government to recognise importance of aerosols. 

With thanks to @jmcrookston whose reflections on Twitter regarding the myth of droplets and the importance of aerosols had links to papers on the subject of aerosol transmission of viruses. 

Bloch et al., Measles outbreak in a pediatric practice: airborne transmission in an office setting

Remington et al., Airborne transmission of measles in a physician’s office

Why the focus on droplets when aerosol will be produced is a mystery. Droplets will, when they leave the 100% of the respiratory tract evaporate to aerosols quickly, due to their high surface area to volume ratio. A mask will catch droplets before this happens and will slow down the airflow, as shown in this video.

The UK fiasco in school exam grades highlights the poverty of the political class in all the constituent nations, though the SNP and Nicola Sturgeon are rather better than their Westminster counterparts. Better because after defending the indefensible, they came up with the only equitable solution given the circumstances. In contrast Westminster keeps digging.

The challenge was caused by locking down too late, though this has not been admitted and never will. Consequently, schools could not re-open, so no examinations (Highers, A-levels etc.). Add in the multiplicity of exam boards separate from government, with a central office responsible for oversight, and you have a rigid system, unable to adapt to new circumstances. So impossible to construct alternative assessments, as was done successfully and to great effect in other countries.

Continue Reading »

Our building complex of Biosciences and the research parts of the connected Life Sciences and MerseyBio buildings opened this week – a two week pilot and the first research building complex on campus to re-open after the lockdown. In reality, like a number of buildings in the Faculty, these had never closed. A small number of covid-related projects were running during lockdown, including our glyco one. These required skeletal support services. Moreover, key maintenance, from plants, to fly strains and flushing the water system to prevent a Legionella outbreak had to continue during lockdown.

Continue Reading »

With new data in hand, our first preprint on SARS-cov-2 receptor binding domain (RBD) interacting with heparin now has a sibling, which demonstrates that heparin inhibits the infection of Vero cells by SARS-cov-2

Some of the key points of the team’s new work are:

  1. Inhibition of viral infectivity in a Vero cell model by heparin, which is a better inhibitor for SARS-cov-2 than SARS-cov.
  2. Analysis of the interactions of a more extended library of model heparins with the SARS-cov-2 receptor binding domain. As with many other heparin-binding proteins, these data show that while sulfation is critical for RBD binding, the amount of sulfate is not, but instead it is the spatial arrangement of sulfate groups that is most important.

Together the data point to heparin being a potentially useful therapeutic to reduce infectivity. Continue Reading »

Work on Week March 16

E-mail I sent out to the research group today.

Dear All,

From now on we really do need to reduce lab work and enforce strictly social distancing, something we stated last week.

The first transmissions from Scousers who picked up the virus on match night (bars, clubs, hotels) from Athletico fans will occur this coming week and next week; we will then get F2, F3 (F number related to contact: primary = F1, a contact’s contact = F2 etc.) transmission. Continue Reading »

Thursday last week (Feb 27) Mark was up from Keele and popped his head around my office door – not a surprise, as he is often here to do circular dichroism on various heparin-binding proteins – to announce that Marcelo had managed to make some SARS-CoV-2 S1 receptor binding domain. Mark had asked Hao,  my postdoc, to do some SPR measurements to see if it bound heparin.

Later in the day I went over to the SPR/CD lab to find Courtney, Mark’s PhD student and Mark beavering away on the CD. A quick discussion. Hao had finished some work on our first grade A heparin functionalised SPR surface, so we set about injecting the SARS-CoV-2 surface protein (Spike) S1 Receptor Binding Domain – a one shot experiment, as amounts of protein were limited, so we injected 1 mL at 500 µL/min (I like high flow rates as mixing is way better, though still far from perfect).

Bingo. Continue Reading »

A Paradox

The Background

So last weekend a rather long document (47 pages) was doing the rounds, purporting to be authored by Mr Lamb, a former senior Geography teacher at the Liverpool Blue Coat School, which related how he and other teachers no longer at the school had allegedly been bullied and sacked.

At the start of the week, letter was sent to all parents, aptly summarised towards the end of an article in the Liverpool Echo on the issue.

The paradox relates to what happened next, as there are two events that cannot both be true simultaneously.

The first event is the emergency assemblies held for the 6th form, led by the head teacher, Mr Pennington, and for the entire KS4 years (9-11) by another member of the senior management team on Tuesday December 3. In the 6th form assembly, Mr Pennington declared openly in front of the entire 6th form that he ‘had seen the chats’ on Whatsapp and Discourse (sic) of particular students. He also instructed students to delete any messages on the subject to protect them from legal action.

The second event is a further article in the Liverpool Echo, which had bene contacted by concerned parents. The Echo’s summary of the School’s response was “Blue Coat school slams ‘ludicrous’ claims they are checking pupils’ phones amidst teacher bullying row”.

The Paradox

What was told to 6th form students in the assembly and what was told to the Echo cannot both be true.

So one is false.

If the first is false, then the head teacher lied to students in assembly, regarding the fact that he had accessed the chat accounts of some students. If the second is false, then the head teacher did access the chat accounts of students and lied to the press.

However this paradox is resolved, the standard of behaviour by the headteacher is not what I expect as a parent and I await a full and transparent account to be issued in due course by the Governors.

Easy and lazy

An article in the New Statesman this summer argues that the British degree has lost its value. The evidence is largely restricted to:

  1. A complaint by students at the University of Sheffield (course not mentioned) which resulted in an uplift of the marks, particularly at the bottom end.

Without context this is a non-argument. Was the course new and there was a mismatch between what was delivered and examined? Was the marking rogue (not everyone does their job with due diligence…)?  And so on.

There follow a few paragraphs that provide no evidence, but plenty of hand waving.

The last paragraphs consider the increase in the number of students going to university and asks the question, sure, if access if wider, there should be more at the bottom, more failures. A corollary is that schools are doing no better now than they used to.

I agree there has been some grade inflation, which has two sources. The first is using the full range of marks available, rather than deciding in advance that there will be no more than one first class degree each year. Current practice is the right thing to do and past practice was wrong. The second source of grade inflation is due to the law of unintended consequences. Legal challenge, now possible because students can access their marks (transparency can only be a good thing) means there are issues at degree borderlines. Common responses have been to avoid all marks at borders (of course this fails singularly to solve the problem, since the final mark is an average of many, so student still end up under the border) and to push students up a % or two if their final marks are below a border. These and other responses to the problem have had an inflationary effect, but I would estimate it to be more more than a few %.

Counter arguments to very substantial and continual grade inflation are:

GCSEs and A-levels are harder than they were, and students are better prepared for university (just as primary students are much better prepared for the jump to secondary). While every year ministers and sections of the press whinge that the all time high level of passes represent a failure, the teaching profession (who have forgotten more about teaching than ministers or members of the 4th estate ever knew) argue the opposite. I always take the expert over others and my limited personal experience of the matter supports the views of the teaching profession.

University courses have changed. At least for STEM courses, they are much harder and demand a lot more effort on the part of the students (my personal opinion is we have gone too far) than 40 years ago, when I was an undergraduate. There is far greater challenge and courses develop skills that in STEM subjects were not even touched on, such as critical thinking and critical analysis of data. Back in the day you either figured this out or you didn’t, so this was learned by the time-honoured system of osmosis. Importantly, a student’s abilities in these areas had no impact on the degree awarded. There is perhaps a generational difference between the young (18-35 and the middle aged and older graduates >35), with the former better at critical thinking  and analysis than their elders.

My e-mail of July 6 has yet to elicit a response. That is over 3 weeks ago, and our representatives should at the least acknowledge receipt of correspondence from their constituents within two weeks. Of course, it is quite possible that, as my representatives grapple with the complexities of their new hi-tech offices and systems, things are slipping through the net. So today I have resent the e-mail. With summer holidays on (though an MEP should maintain a skeleton staff at all times, since they have the taxpayer-funded budget for this), I would expect to receive a reply by the Bank Holiday.