Some sporadic insights into academia.
Science is Fascinating.
Scientists are slightly peculiar.
Here are the views of one of them.

Thursday, 28 April 2016

57 Varieties

Global Traveller: Chlamydia infection varies by region

A Multi-Component Prime-Boost Vaccination Regimen with a Consensus MOMP Antigen Enhances Chlamydia trachomatis Clearance.

Vaccines come in various flavours. Some are purified from the toxic by-products of bacteria (tetanus), some are made of sugar (pneumonia), some are made of protein (HepB), some are made of sugar mixed with protein (meningitis), some are live but weakened (BCG) and some are dead (flu). There are various reasons for making them from different things, including cost, formulation and the part of the bug we are trying to target with the vaccine.

Form follows function

The make up of vaccine has a direct effect on the type of immune response it induces. Sometimes, vaccines can induce an immune response, but the immune response they induce is not able to kill the bug. For example there are 2 whooping cough (Bordatella pertussis) vaccines available: whole cell or wP (made up of whole bacteria that have been killed) and acellular aP (made up of 3 or 4 individual proteins from pertussis). Most higher income countries switched to aP about 20 years ago because the vaccine is less reactogenic – wP can lead to a high temperature and a sore arm. However we are seeing a resurgence of whooping cough in the countries that switched vaccines. Dissecting the response to the 2 different vaccines has shown that the wP vaccine leads to a different type of immune response to aP, switching the way the T cells (a white blood cell) react to the bug (from Th1 to Th2 if you need to know). This switch in response, is associated with the reduced effectiveness of the vaccine. NB – aP still works, it is still safe, you should still get it for your children and when pregnant, it just doesn’t work as long as wP.

Number 1 bacteria

Chlamydia trachomatis is the most common STI caused by a bacteria – over 141 million infections occurred in 2013: those of you paying attention will remember this also causes eye disease. It is mostly asymptomatic (you can’t tell if you’ve got it), but in about 5% of cases it can cause a condition called pelvic inflammatory disease, which if not treated can level to infertility. Treating Chlamydia is expensive – over US$3 billion are spent in the US alone each year. Based on the burden of disease and the cost of treatment, there is a strong case to make a vaccine against chlamydia. However, this has proved difficult, this is in part because we don’t know what type of immune response would be best to stop it. We therefore set out to explore this, exploiting the fact that different vaccine types lead to different immune responses. Alex (the lead author) made 4 different vaccines based on the same protein derived from chlamydia (the major outer membrane protein or MOMP). These were a DNA vaccine, an Adenovirus, a Modified vaccinia Ankara and a Protein, conveniently leading to the acronym DAMP.

DAMP-proof course

In our recently published study we investigated the effect of changing the types of vaccine on the immune response. We could make a response that was just antibody (PPP) or just T cells (DDD) or a mix of the two (DAMP.) We then measured whether these different types of response altered the outcome of infection. Only the DAMP (which gave a mixed immune response) regime reduced the number of chlamydia bacteria after infection. This protection disappeared when the T cells were blocked, suggesting they were required. Based on these studies, we believe a Chlamydia vaccine needs to induce a mixed response, with both T cells and antibody. This work has informed a clinical trial in healthy volunteers to test the ideas further. It is yet another example of work funded by the EU, which if we left, would not be possible.

Parental Advisory


Can you combine being a parent and being a scientist? The answer is yes, it is possible; but it is tricky. If you have children, you know this already and my telling you that it is tricky won’t help. So I have selflessly done some grade A research/ went drinking with some other parents to come up with the following tips.


Essentially, parenthood is a sociology experiment, with no control arm: unless you have identical twins – in which case all kinds of (ethically questionable) studies are open to you. Remember that your children have nothing to compare against: they only have one childhood and have no objective way to assess their situation relative to their peers. This is not a call to be a terrible parent, rather a salve to the conscience. Missing the year 3 show, failing to buy a new costume for world-bloody-book day or sending them in wearing uniform on mufti day isn’t going to cause, too much, long term damage. Being a tiger parent does not make your child a better person, so relax, it’ll be ok.


More broadly, there is a lot of stuff that needs doing, is relentlessly dull and not going to improve you, your science or your children. This includes renewing the car tax, going to the tip, ironing pants, tidying the garden, sorting the recycling and making pack lunches. Many of these functions can be done by someone else – for example thanks to Jamie Oliver (at least according to Jamie Oliver himself) school meals are now delicious, nutritious and don’t have turkey twizzlers, so sign your kids up for school dinners and spare yourself 15 minutes of stress every morning. Where possible, outsource.
Dr Tregoning in the lab where he works on vaccines for respiratory infections such as flu
Me being awesome in the lab


There is a clear exception to my laissez faire attitude to child raising - failing to collect kids at the end of the day. The day’s activities need to be juggled to make sure you are in the right place at the right time. Some activities merit re-arranging childcare – vivas, experiments, group networking in the pub. Others do not. If a seminar is over running and the alternative is being late for nursery then you have to get up and leave. Likewise with meetings that drag on after 5pm when you are on pick up, politely apologise, and get up and leave. I know many parents find this difficult and it is: but sometimes you have to get up and leave.


Me being awesome at parenting

Essentially the major challenge of balancing parenting and science is juggling: working out which parent is doing what and when. Rather than doing this piecemeal make it a social event. Set aside an hour a week to sit down together and sync diaries with a drink. Include the other admin necessary to make the house run.

The sad fact is that to be a parent and a scientist, there is little space to do anything else. There are only 168 hours in the week. Use them as efficiently as possible, but even with clever outsourcing, smart timetabling and being a martini fuelled admin ninja, there is a limit to resources, mental capacity and time. Career, hobby, children, carer, partner, community service, exercise, charity work, social-life: pick three, do them well, if you try to do more, something will give.


These methods should help you balance work and childcare, but, as I said, they leave little room for anything else. This is problematic because the ‘anything else’ is important for mental wellbeing, improves your science and generally makes life worthwhile. Maybe I should qualify my statement, there is little room to excel at anything else. You have to accept you won’t be winning the Epsom Common Allotment Society marrow growing contest, breaking the 4 minute mile or eating out with friends any time soon. It may mean taking your foot off the gas at work occasionally, but find time to do a little exercise, potter around the garden and snatch the occasional after work pint here and there.

This blog first appeared on the Imperial College London webpage. It was in response to the Royal Society's campaign ‘Parent Carer Scientist’.

Monday, 4 April 2016

Build your academic brand, because being brilliant doesn’t cut it any more

One of the recurring portrayals of academics is unworldliness. There was a mortifying episode of The Apprentice when the token PhD candidate buckled in the boardroom because they failed to meet their sales target. The ability to sell rubber dog turds for an egocentric billionaire may not seem a core skill compared with pipetting, coding or whatever research-specific thing you do; however, salesmanship is central, and increasingly so as you progress away from the bench.
This was re-emphasised when listening to a presentation recently. I knew the work was brilliant, smartly executed and highly impactful, but somehow the presenter lost the audience and failed to convey their brilliance. It wasn’t that the presentation was poorly delivered or ill rehearsed, far from it. The problem was the sales pitch. I have also been to some extremely data-light presentations which have conveyed the story brilliantly. Reluctantly, we need to accept that sales is a major part of the job: demonstrably so when grant writing, but no less in papers, seminars, blogs and even thesis writing.
Be the brand: you are the product
We have two things to sell, our ideas (more of which another time) and ourselves. Of the two, and this may sound a bit “self-help seminar”, the main product we sell is ourselves. This product is defined by our CV: where we have worked, on what and with whom. But these strands need to be pulled together into a single memorable “personal brand” – the lung T cell expert, the insect neurobiologist, the DNA crystallographer. This brand comes into play when meeting potential collaborators, conference organisers and funders. Interactions with other academics tend to have three levels: an entry-level overview of your work to check you are in the same field, followed by a description of a specific piece of work and, if you really click, detailed dissection of experimental design. There is no space for English modesty: don’t say “you know, this and that, some stuff on respiratory infections”. Do define your brand and develop a snappy single-line pitch that summarises what you do, backed up with an exciting case study. You are pitching this brand so that when other academics need someone with a particular skill set they think of you.
Develop the brand: publish or perish
Having crafted your academic brand, you need to generate brand awareness. This can be achieved in a range of ways, but publishing is central. One hurdle is the volume of academic material – 93 per cent of humanities articles, 45 per cent of social sciences and 25 per cent of science articles never get cited. Yes, the ideal is the big “impact” (glossy, single-word title) journals, but don’t get fixated on these to the detriment of getting stuff out there. It can take some time to generate sufficient reputation to overcome the editorial activation energy for the glossies (another example where having a personal brand can open doors). Target the journals that are most widely browsed in your field: high-volume, good (but not superstar) quality output is as good as large gaps between superstar papers and potentially better early in your career. And while traditional publishing has to be the central strand to your brand, don’t neglect blogging, tweeting and public engagement.
Sell the brand: break the bread
The final component is networking, which has to be face to face and not just electronically. Get out there and meet people – you have to be shameless, but not rude. Invite yourself to give talks in your friends’ departments, talk to people in lifts and in the departmental tearoom. Go to conferences, consortia and congresses. I prefer small conferences where you avoid that “total perspective vortex” moment – being exposed to just how big your field is and how insignificant your place in it is. Ask questions at meetings, and use the formula: “Hi, I am Dr X at university Y, in our system we see Z which relates to your findings because…have you seen the same?” Corner the speaker after talks, ask them more questions, sit next to people at meals, go to the drinks. Any (positive) way of getting yourself known is a good thing.
What you waiting for?
I am sure you are all brilliant, you are after all reading this article! But brilliance in a vacuum is not going to get you a permanent position or enable you to secure the funding to test your brilliant theories. You have to sell your brilliance. So this year, get out there, hone your personal brand to Kardashian levels and start selling yourself.

This article first appeared on the Times Higher Education on Feb 24 2016