PhD paper is out

I’m attempting to catch up on things after a long pause from updating my website.

First up – my PhD paper was published on BioRxiv and then in a special issue of Development.

In this paper we investigated how the morphogenesis of one tissue can physically deform its neighbouring tissues to contribute to the elongation of the embryo head-to-tail axis.

Using targeted multi-photon ablations I disrupted notochord morphogenesis by preventing the expansion of notochord vacuoles. Surprisingly segmentation-associated posterior body elongation was robust to near-complete notochord ablation. However, we found that notochord vacuole expansion facilitates the elongation of the axis at later stages of development.

The progressive expansion of notochord cell vacuoles leads to a posteriorly directed cell displacement, which is resisted by notochord cells in the posterior of the embryo whose vacuoles are yet to expand. Reversing this cell displacement or removing the resistance provided by posterior notochord cells led to decreased segmented tissue elongation.

Overall, we propose that the combination of notochord cell expansion beginning in the anterior, and addition of cells to the posterior notochord, generates a stretching force along the AP axis, deforming segmented tissue and facilitating axis elongation during post-tailbud stages of development

Fun contribution to a cool engineering project – now preprinted on TechRxiv

Great to see this really cool paper out, exploring how sustainable bioelectronic fibres can be printed on different biological structures and used to sense properties of living organisms. Fun contribution to a cool engineering project – now preprinted on TechRxiv

Read more: Fun contribution to a cool engineering project – now preprinted on TechRxiv

Postdoctoral research begins

Time has flown by since finishing my PhD and I am now well into my first year of postdoc.

So far it’s been fun to work on a new model system (the chicken embryo), have a go at some set-up engineering, and develop new methods to investigate the forces involved in early central nervous system morphogenesis.

5 simple tips for PhD interviews

‘Tis the season for PhD programme interviews and I’ve recently been asked by a few people for advice on how best to prepare, so I thought I’d share a few tips that might be useful for you to reflect on if you are in the process of prepping for your interview.

It doesn’t feel like that long ago when I was getting ready to head off to interviews for PhD programmes. My first interview was in Cambridge. I was pretty nervous as I’d had a pretty disastrous interview experience a few years before when I’d applied to Cambridge Uni for my undergrad.  However, a few things helped make my PhD interviews a completely different and more fulfilling experience: seeking advice from people beforehand, having the support of the researchers I’d been working with, and being passionate about the research I’d been doing. As well as taking a lot of time off uni to prepare…

Some of the tips I give below might seem pretty obvious but I hope they will give some clarity to the kind of scenario you might experience on interview day.

On to the tips!

Tip #1 Show your enthusiasm

For science, for research, for the programme you applied to, interviewers want to know what made you decide to pursue research and why you chose their programme. What experiments have you come across that you thought were brilliant? What made you want to do research for a full 3/4 years?

Tip #2 Be ready to talk about your own research

You have probably undertaken some kind of research project to figure out if research is for you, or just for fun, or as part of your degree. This is your chance to tell people about what you did, why you did it, and what you learnt from it. This also provides something to fall back on if the other parts of the interview run dry pretty fast and can help you steer an interview towards a topic you feel more comfortable with. Draw diagrams, explain findings, get them interested in what you’ve been up to.

Added bonus of fancy lunch

Tip#3 Prepare to discuss questions relating to your area of interest

PhD programme applications often ask for a personal statement of some sort, and you likely wrote about a particular area of research that you are interested in. It’s pretty likely you will be asked questions to do with that area.

Tip#4 Don’t worry if you don’t know the answers

If you already knew everything about everything there wouldn’t be much point in doing a PhD, so be prepared not to know the answer to some of the questions you get asked. From my experience, interviewers are interested in working with you to reach a solution and in seeing how you go about problem solving, they don’t expect you to know the answer straight away.

London skyline before the final interview day

Tip #5 Try to enjoy it! 

Interviews go really quickly and you will only ever have to do a relatively small number in your lifetime, so if you can, try and relax and enjoy the challenge. Remember, the world doesn’t end if it doesn’t work out! They are also a great chance to learn and develop both your interview skills and your understanding of what it is you want to do, something that is invaluable.

Good luck!

Ominous smile on the morning of my final interview

3 months in

I am about 3 months into my PhD now, so I thought I’d give an update on what it’s been like up to now.

So far I’ve mostly learnt things about myself and the way I work best, rather than anything to do with understanding a scientific question. I guess that isn’t surprising as I’ve mainly been playing around with different techniques, trying things, and seeing what works. Having the chance to explore different ideas has been great and I think it’s really important to have that kind of opportunity at the beginning of any scientific project. Much of my life is now spent staring at zebrafish embryos, fortunately they are very beautiful.

Looking down the microscope at a zebrafish embryo

As well as doing things in the lab I have also had some interesting work experiences outside of the lab. I had the opportunity to go to Switzerland for a conference on ‘Organoid Systems’ in November. Labs from all around the world are growing things that resemble organs (or parts of organs) such as the intestine and brain, and trying to figure out how they’re organising themselves (among other things). As well as providing insight into the development of organs and their specialised structures, these organoid systems also open up the possibility to model diseases outside of the human body, using human cells. It’s amazing how close we are to being able to use these ‘organoids’ for medical applications. They are already being used to screen for drugs and offer the possibility to design personalised medical treatments for people – as the affected patients’ cells can be used to grow one of these organoids. In the free time we had I managed to eat a lot of fondue and catch a glimpse of the beautiful scenery outside the conference centre.

A lot of cheese

Mountains just outside the EPFL

With the intention of keeping a good work/life balance and wanting to keep on top of exercise I decided to sign up for rowing around the time I started work in the lab. Getting up before 6am to cycle in the cold and dark to rowing 3 times a week has been an experience, but the positives really have outweighed the negatives and overall I think it’s helped keep me sane over the past few months.

Rowing into the sunrise (actually this was in the afternoon but you can imagine…)

Going into 2018 I am looking forward to improving the way I work, staying focused on the important questions, and hopefully travelling to some new and interesting places.

Thoughts on diet and global warming

Everyday in the media I hear about global warming and how it’s connected to the way we live our lives. Whilst it’s easy for me to believe that there is a link between what we consume (food, technology, leisure, etc) and the decreasing health of the planet, I have realised that I’m not very educated on the subject.

I think one of the reasons I find it tricky to understand what influences what when it comes to global warming and human behaviour is simply that…it’s not a simple problem to study. Why? Well, human behaviour is studied at many different levels already, e.g. neuroscience, psychology, sociology etc. Also, the health of the planet is studied in many different ways e.g. by measuring greenhouse gas emissions, melting ice, temperature…

With so many variables it seems almost impossible to try and understand this huge question of how human behaviour influences the state of the planet. But people are trying. By combining multiple fields of research such as psychology, anthropology, and physics (to name a few) and finding ways of modelling how different factors interact with each other, researchers are able to make predictions on where the planet is heading.

One of the most discussed ways of decreasing our impact on the planet is through being mindful about what we eat. I am in the privileged position of being able to decide what I eat, and so, my diet is linked to my behaviour and choices. I’m interested in trying to understand how I can decrease my impact on the planet through food choices. This prompted me to spend some time researching into this subject.

What are the facts?

To get started, I refreshed myself on some statistics on the current state of the planet compared to past years. NASA offers some great information on global warming which I highly recommend checking out if you’re interested.

Now for a quick overview.

Greenhouse gasses, such as CO2, trap heat close to the surface of the earth. We need these gasses in our atmosphere for the earth to stay at a warm enough temperature for life to be happy.

Reconstruction of CO2 levels from ice cores up until today, NOAA

But if the levels of these gasses increase, then more heat gets trapped and the Earth’s temperature rises.

When the planet warms, more ice melts and the sea levels rise.

Arctic ice levels over time, NASA
Change in sea levels over time, NASA

Next, I wanted to find out more specifically about how our diet is linked to global warming, and so it was time to go through some research papers…

How is our diet linked to global warming?

Many factors influence what we chose to eat – society and social media, income, moral reasoning, and so on. Researchers are considering how these factors will influence global food choices and how this will influence global warming. One way of predicting how our diet choice will affect the planet is by combining psychological theories on human behaviour with pre-existing models that take into account multiple factors that are implicated in the social, economic, and environmental state of the Earth. These factors are all combined into a model that predicts different outcomes for the planet depending on the scenarios you give it.

For example, in this study, they feed a bunch of different scenarios relating to the how much people reduce their meat intake into a model to see how this would affect greenhouse gas emissions.

Predicted emissions for different levels of meat consumption

Scenario 0 (Sc0) reflects a situation where the vegetarian population increases, but meat eaters still eat the same levels of meat, and subsequent scenarios correspond to progressively less meat/animal product consumption overall (meat eaters consuming meat less often, vegetarians becoming vegan). The fewer meat and animal products consumed, the fewer greenhouse gasses are emitted.

This paper lead me to this website, run by the United Nations, which has loads of data on how different countries across the world produce food, utilise their land, and how this is linked to their CO2 emissions.

For example, here’s a chart showing the CO2 emissions produced by different agricultural sectors in the UK.

Chart showing fraction of greenhouse emissions for different agricultural sectors in the UK

The big purple chunk, ‘Enteric Fermentation’, which is (as defined by wikipedia) ‘a digestive process by which carbohydrates are broken down by microorganisms into simple molecules for absorption into the bloodstream of an animal’, basically relates to the gasses produced by (mostly) sheep and cattle that are farmed for their meat and dairy products. Considering that some of the manure-dependent emissions shown on this plot are also a byproduct of animal farming, this data collected by the FAO (an agency of the United Nations) shows that in the UK, more than half of the greenhouse emissions produced by the agricultural industry are linked to the farming of animals.

Another study, published in 2018 also predicted that decreasing the amount of meat consumed globally would decrease greenhouse gas emissions, with a potential 56% decrease in emissions if enough people adopted a more plant-based diet.

Does decreasing your meat intake really have a positive effect on the planet?

Yes! There are many many other factors that I haven’t mentioned in this post, but from the time I have spent reading up on the research investigating how diet and the health of the planet are linked, it’s clear that eating less meat and shifting to a more plant based diet is a good idea. In particular, this research highlights the importance of reducing meat intake even if you are not vegetarian, as this is predicted to make a huge difference when it comes to decreasing greenhouse emissions.

I’m hoping to follow up this post with some of my favourite vegetarian recipes, which show that reducing your meat intake doesn’t mean reducing the tastiness of your meals!

I realise that the articles I have linked are not open access – so here are some other references that are:

Starting a PhD

As the British Summer (?) comes to an end and the air becomes (even) crisper, the start of a new academic year is signalled. For the past four years the start of my year has coincided with October rather than January, simply because thats when term time starts at university. This year will be my last to start in October. PhD’s are full time, and whilst they are not classed as employment in the UK, they have most* of the features of a full time job.

Beginning of Autumn in Cambridge

Choosing to do a science based PhD used to require you to have a pretty good idea of which lab/s you were interested in before applying. Typically you would apply to a few labs and see if they had a position available. Things have changed a bit since then and  I hope I can shed some light on what it’s like to apply for a PhD in Biological sciences today.

1+3 PhD programmes

Over the past few years, PhD programmes, in which you have the opportunity to try typically 2 or 3 labs out before starting your PhD, have become more and more common place. Once I had decided to do a PhD I had to figure out whether to apply to a programme or apply directly to a few labs. As I wasn’t 100% sure which area of biology I wanted to go into I chose to apply for a programme which offered the chance to try out 3 different labs from a range of fields. This meant that I would need to chose 3 labs from a pool of around 30 and do a 2 month research project in each during my first year, before choosing one for a 3 year PhD.

Where do you want to live?

Another really important thing to consider is where you would be happy to see yourself living for the next 3/4 years. This might sound obvious, but it’s something that can really help you narrow down which labs or programmes you want to consider. If you want to stay in your home country for example, then there’s not much point looking at international programmes. Cambridge seemed to offer the more relaxed lifestyle I was looking for after spending three years in London . The college system sounded great for meeting people and the research at Cambridge is renowned, so applying to a programme there made a lot of sense for me. Now my morning commute involves cycling in a peloton instead of cramming into the tube…

Relaxing with tea and a Chelsea bun

Narrowing down your field of interest

Whether you decide to apply for individual labs or for programmes, it will help if you can narrow down the field you are interested in. For example, biology is a huge field. There’s evolution, stem cell biology, developmental biology, biochemistry, and many more branches to consider. Whilst a lot of these branches overlap with each other, there’s likely to be one branch in your field of interest that draws your attention more than the others. Personally, I was always more into the overlap between physics and biology, which narrowed down things quite a lot**. The project I’ve ended up working on for my PhD is focused on investigating the ability of  mechanical forces to influence  biological processes, such as a cells’ ability to differentiate into different cell types. Once you’ve narrowed things down enough, the list of labs/programmes that accommodate your interests should be more manageable to go through.

Specific labs

At the end of the day, you will end up doing (at least the majority of) your PhD in one lab, so it’s really important to find a lab that you could imagine going to. Programmes offer you the opportunity to try out a lab before signing up for the long haul, something that can be extremely helpful when you’re trying to figure out if your personality fits with the other personalities in the lab, and most importantly, with the group leader’s. Your supervisor (typically the group leader) will (hopefully) teach you the skills necessary to become a scientist over then next few years, meaning you will see them quite often. So as well as being someone you respect for their research, its also important they are someone you feel you can talk to and learn from. At the end of the day, a PhD is about learning.

*with the exception of contributing to a pension, as your salary is not taxed.

**whilst physics and biology have a lot to lend to one another, ‘biophysics’ is still an up-and-coming field, so labs focussing on this area are limited.

London to Cambridge

Over the past year I’ve graduated from university, moved town, and embarked on a PhD, so there’s a lot to catch up on.

I scraped through the last year of my natural sciences BSc at University College London (UCL), feeling fed up with cramming quantum mechanics equations and biochemical signalling pathways into my head and ready to get on with something I was passionate about. I had decided to apply to PhD programmes the previous year after undertaking a 2 month research internship in Buzz Baum’s lab at UCL, which persuaded me that scientific research was what I wanted to do. After being extremely fortunate with the encouragement and guidance I received whilst interviewing for a few different programmes, I  accepted a place at the University of Cambridge. Living in London had been an eye opening and exciting experience, however, I felt that it was time for a change of scene and a less hectic and rushed way of living.


View across London

Cambridge university has 31 different colleges and as a PhD student I was required to enrol with one of them. I chose King’s College partly because it has a reputation for being one of the most liberal colleges and partly because it’s ridiculously pretty.

King’s College

This meant that I moved into a room in one of King’s colleges graduate student houses and got the chance to meet a bunch of great people at college events. This was a huge contrast to student life at UCL where you have to find your own private accommodation after your first year of university, and commute across London to meet people. Things are made so easy and comfortable in Cambridge by comparison. It’s a very different way of doing things and I am glad to have experiences of both.

Bridge of Sighs

Punting outside King’s

So far I’m finding life in Cambridge to be relaxed and focused. One of the things I enjoy the most about living here is being able to cycle anywhere, any day. Whilst the nightlife and variety can’t compare to London, I feel like Cambridge will be a great place to focus and learn over the next three years.