11 things every new PhD student should know

I started my PhD nearly a year ago now, and the time has absolutely flown by. With many people setting out to start a PhD in September and October it made me think about what I have learned this year, and the top tips I would tell anyone about to embark on a PhD in Science:

1 Don’t be afraid to ask questions

Don't be afraid to ask questions during your PhD.

Don’t be afraid to ask questions during your PhD.

No one minds. It’s better to ask how to do something if you don’t understand than waste your time doing it wrong. Everyone in the lab has been in your position before. We don’t bite!

2 Write down EVERYTHING

And I mean everything. At the beginning of your PhD, you’re excited, you’re in a new lab, doing new things, and sometimes you may not write everything down. It happens. But in a few months’ time when you look back at that crucial PCR – the one where everything amplified beautifully – and you realise you forgot to write down the annealing temperature, you will kick yourself.

3 Label EVERYTHING

Only last week I came a cropper when I realised I had mislabelled one of my early glycerol stocks, which meant I had to redo the previous stage of my experiment. Labelling really well may take you a few extra minutes, but it will be well worth it in the future.

4 Plan your day

Plan your daily activities: it can be hard to keep track of what you're doing otherwise.

Plan your daily activities: it can be hard to keep track of what you’re doing otherwise.

When you have several experiments on the go it can be pretty hectic, and hard to keep track of everything. It can useful to make a list at the beginning of the day, or the evening before, of everything you need to do. That way you won’t end up on Friday realising that you can’t do that experiment because you forgot to prepare the overnight cultures.

5 Make time for yourself

Yes, the PhD is really important, and yes, it’s good to get excited about it and take a huge interest in it, but don’t let it take up all your time. It’s important to have a healthy work-life balance. Personally, I find that taking that extra break, and having that evening off, helps me be more productive and make fewer mistakes. A PhD is a long time, and you should make that time as enjoyable as you can – both inside and outside the lab.

6 Take the time to get to know your lab

This one is easy – just chat to everyone! Go to lunch together, have a tea break, make sure you go to the lab meetings. And if the lab doesn’t do these things you could always suggest it. A lab that has great communication is the best sort of lab, and will make your days at work all the better. A friendly and fun working environment makes everything so much nicer.

7 Get involved

Conferences are a great way to meet new people.

Conferences are a great way to meet new people.

Go to seminars, departmental meetings and conferences, both at home and away. They are a great way to find out what others are doing both in your department, and across the institute. It helps you build those connections up – you never know, they could be crucial in the future. And don’t be afraid to mingle! It’s a big thing at first to get out of your comfort zone, step away from your friends, and talk to someone about their work, but it’s well worth it.

8 Try not to eat at your desk

If you are doing a lot of experiments in a day, and are really rushed off your feet, you may decide to just eat your lunch at your desk. But, this can often leave you feeling dissatisfied. Even if it’s only a 15 minute break, having your lunch away from your desk and lab can be really beneficial. It takes you away from the lab and work completely, and you will return feeling refreshed.

9 Just because you had a bad day today doesn’t mean it will be a bad day tomorrow

Everyone has bad days, the day when your RNA extraction just won’t work, or you run your DNA off your gel. It happens. Take a breath and start over.  Don’t let it get you down.

10 If you are having problems with your PhD speak to someone about it

The first few months can be a bit rocky: settling in to a new city, a new lab, making new friends, learning new things. If you are finding something hard in your project, or are feeling unsatisfied, out of your depth, or just stressed out, chat to your supervisor about it. Or if you feel you don’t want to talk directly to your supervisor, try another PhD student or lab member. It is normal to have periods throughout your PhD where you feel a bit down or stressed. When things aren’t working, it can be demoralising, but having someone you can talk it out with can help.

11 Enjoy!

A PhD can at times be frustrating and hard work but it’s extremely enjoyable and one of the most rewarding things you will ever do.

Erica is a PhD student at the John Innes Centre. She tweets as @EricaHawkins16.

The curse of the four-year PhD

Here in the UK, most research council-funded PhD students will have a thesis deadline four years after their start date. As someone who moved straight from undergraduate to postgraduate study with no breaks, this means I will be a doctor by age 25.

While this is quite nice to know, I’m now at the point of starting to consider my future and career. And I’m coming to realise that only four years of doctoral work may end up being more of a hindrance than I thought.

When applying for postdoctoral positions, your publication record plays a huge role in how successful your applications will be. But getting those first-author publications takes time. Getting results is just the first step. Next, you need to actually write the thing, and get feedback from a supervisor (and anyone else involved, such as others in the lab or collaborators).

Then you begin the process of actually trying to get published: submission, acceptance, peer review, corrections, and finally publication (and even this might take a while if there is a backlog). Although some journals, such as eLife, pride themselves in a quick turnover (90 days submission to acceptance), some can take a lot longer.

Rejections will increase the time – and this can often happen as people try and publish in journals with as high an impact factor as they can. Other factors can affect publication time – such as over-worked supervisors or lack of funds to publish (Nature Communications, for example, costs £3150 to publish).

All things considered, a British PhD student could easily end their PhD with several first-author publications in the pipeline, but none published.

Compare the length of a UK PhD to PhDs in other countries, and you start to see where my concerns lie. Some countries, such as Germany have four-year PhDs like us. But many have postgraduate courses lasting much longer.

In the US there is no set deadline for a PhD thesis. Stanford University suggests that most finish their PhD programme within five and a half years – already gaining a year and a half on us. And a US PhD can easily last much longer than this – students can often expect to be finishing their theses after seven or eight years.

One does not simply finish a PhD

PhDs in the US can be notoriously long.

The decision of when a PhD candidate at an American university can defend their thesis is made by their supervisor. The time taken to complete a PhD in the US is one of the most common topics mocked by spoof academic and comic sites such as PhD Comics or #WhatShouldWeCallGradsSchool.

The same thing happens in Sweden, where a student can expect to be studying for longer than five years. These longer PhDs often involve other activities – teaching, for example – but are also important for producing publications. The number of publications may have an effect on when a student will be allowed to defend their thesis.

The longer PhD programmes in other countries allow more time for broadening horizons. Time spent teaching or researching other projects can give PhD students an additional edge when applying for jobs.

The British system has tried to help provide its students with some of this experience. The BBSRC and several other tesearch councils now fund a large proportion of students as part of Doctoral Training Programmes or similar schemes. These programmes have a mandatory three-month internship as part of the four years of study (I recently completed my placement).

Several universities have also opted to put students through training – such as the University of Oxford, where first year PhD students spend their first term having lectures. They may also have ‘rotation projects’, spending their first year trying two or three projects and choosing the one that suits them best.

Although these schemes leave students more ‘well-rounded’, they also take away from the already limited time-frame – leaving many with just three years in which to carry out their research and write-up.

So, looking at the facts, PhD students in the UK are going to be left competing for the best postdoctoral positions against people with far more research experience than us.

I was talking to a careers advisor about this last week, who told me  “you can get that first postdoc position without any publications”. The next day I had the same conversation with a lecturer (and I’ve had this conversation with my supervisor more times than I can count) who had a different view: unless you have a particularly high-profile supervisor who can vouch for you, those jobs are going to go to someone else.

This is clear when you start looking at the statistics. According to an article in the Times Higher Education, up to 200 people may be chasing the same post at top Universities.

And if you can’t get those top posts, perhaps you will end up struggling to get high-impact publications from your first postdoc – leaving you struggling to get the next position, and so the cycle continues.

Only 0.45 percent of UK science PhD graduates end up as professors – so every step of that career ladder matters if that’s your ambition. The realisation of this competition has almost certainly driven some people off the ladder – and the “confidence gap” of women faced with such tough competition may partly explain the leaky pipeline of women from academia.

Of course, this doesn’t mean you should lose hope. Most likely, a student will manage to get their name on a few other publications during their PhD, and though their names may be lower down the list, at least it’s something.

I’m also starting to see that there is still a huge ‘who-you-know’ aspect to finding jobs in academia. So get out and network with people whose work interests you. Presenting at international conferences can also help with this – and as PhD students begin to get results, they often have abstracts for oral presentations accepted and get the chance to give talks.

Networking with the other group leaders in your university or institute may also give you the edge you need. Even social media can help – I’ve met at least one group leader in my research area who recognised my name from Twitter.

It isn’t just the PhD to postdoc gap that publishing affects. Publication records count throughout your career. Newly-appointed group leaders face huge pressures to publish – and this continues even after tenure is awarded. As they say, “publish or perish”.

Even a career break such as parenthood or taking time out for caring responsibilities can mean a gap in your publication record which could affect your career. The government is trying to make changes in the career structure for postdocs to recognise career breaks – but it’s happening slowly.

I have my fingers crossed that those who want to pursue a career in academia will be able to fight off the competition and find the jobs that they want. And as for the rest – perhaps those internships will help them get the jobs that they want too.

Izzy is a John Innes Centre PhD student. She’s on Twitter as @isabelwebb.

Featured image: Kat (swimparallel)/Flickr.

Abandoned lab - Paul/Flickr

6 things that happen when you take a four-month break from your PhD

From mid-September until mid-December last year I was on an internship in science policy. Once you count the conference at the start of December and the Christmas holidays, I was left to return to the lab this January after a four-month break.

The aim of my internship was to experience the world outside academic research, and so my project was sent to the back of my mind while I thought about more political topics. Most of my friends did their internships around Norwich, so they had the chance to get into the lab at weekends or in the evenings. But I moved to Cambridge for mine, so I didn’t have the opportunity to nip into the department and get some experiments going. Now, I’m back doing my research, and it’s amazing what’s happened while I was away.

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Training journalists in evidence and statistics

The Science Journalism Programme was set up by the Royal Statistical Society (RSS) in 2010. Through the programme, scientists and statisticians volunteer to deliver workshops to journalism students and professionals across the UK. Workshops cover concepts such as scientific methods, peer review and statistical uncertainty in order to equip journalists with the skills to correctly interpret and report on science stories. So far the programme has trained over 600 journalists and students from a wide array of institutions including the Guardian, the BBC, the Times and numerous universities.

At the end of August, a number of other John Innes Centre PhD students and I attended a training session run by the RSS in order to become a volunteer on the programme. Since attending the training day I have delivered workshops to professional journalists at the Manchester Evening News, and to journalism master’s students at City University London.

What is the RSS?

The RSS was founded in 1834, and is now one of the world’s most renowned statistical societies with over 6000 members. The society has a number of aims, and one of these is to promote the use of statistics, data and evidence for the public good. It was under this remit that the Science Journalism Programme was established.

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Reaching gender equality in science

The Athena SWAN award is a UK scheme set up to recognise commitment to advancing women’s careers in science, technology, engineering and maths (STEM) in academia. The scheme has been running for several years with Universities and their departments applying for recognition at bronze, silver or gold level. In 2012 a pilot scheme was set up to investigate the inclusion of research institutes into the Athena SWAN scheme. The John Innes Centre was one of these pilot institutes, and we are proud to say that this year we have been awarded an Athena SWAN silver award.

We celebrated the award this month and as part these celebrations we had a panel debate. The debate discussed  a recent report on Women in Science written by the House of Commons Science and Technology Select Committee,  and the commitment of both the John Innes Centre and the University of East Anglia (UEA) to ensuring gender equality within their academic communities. This event was run by ResNet, a UEA network set up to promote gender equality. The panel at this event consisted of David Richardson (UEA deputy Vice-Chancellor and member of the BBSRC council), Tracy Chapman (co-lead of the UEA School of Biological Sciences Athena SWAN team), Carole Thomas (chair of the JIC Athena SWAN Committee) and Dale Sanders (director of JIC who also sits on the JIC Athena SWAN committee).

The Science and Technology Committee report on Women in Scientific Careers highlighted many issues facing women in STEM careers. One of the key issues highlighted in this was the ‘leaky pipeline’. The leaky pipeline is a phrase used to discuss the drop-out rates of women in STEM subjects as they ascend the career ladder. In life sciences, for example, undergraduates tend to be around 50/50 male to female. However, when you then look at the senior scientist level, this ratio clearly drops, with only 20.5% of STEM professors in the UK being female . Many reasons have been put forward for this leaky pipeline, ranging from a lack of female role-models for aspiring female scientists, to the lack of stability in early-career research jobs. However there are certainly  multiple reasons to explain the lack of gender diversity.

A clearly identified reason in the report was unconscious bias. Unconscious bias is the hidden personal bias that we all have, rooted by the stereotypes that we are brought up around and our own personal preferences towards people, for example that are similar to us. Unconscious bias is currently thought to play a large role in the lack of women in senior roles, both in sciences and in other fields such as business. If you ask someone to think of a manager, for example, the majority of people will picture a man. Many traits considered useful for leadership are thought of as male traits, whilst more caring traits are considered female. Now that unconscious bias has been recognised, many institutions and businesses are actively running training to help eliminate these biases – including UEA and on the Norwich Research Park. These bias issues may not be exclusive to recruitment either. It was highlighted that only 7 out of 75 major life sciences awards given out last year were given to women, and it is generally agreed that it is often less common for panels to recommend  women  for the awards. The same applies with guest speakers, although this highlighted an additional issue. Although women may be as likely to be invited to speak, they tend to be more likely to turn down the opportunity. This year will be the first time ever that a woman will give the plenary talk at the John Innes Centre ASM.

Another barrier identified in the gender equality issue is that early-career academic jobs are characterised by short-term contracts. Post-doctoral jobs are not permanent, and often at the end of these short (one to five years) contracts the academic will be faced with uprooting their life and moving to a new town, country or even continent to continue their career. This early-career stage coincides with an age when many people are considering building a family. Women tend to be the primary carers, and often end their academic career at this point – although it is not an issue that exclusively affects women, as some men also chose to be  a primary carer for a family. Academia is all about your research portfolio, and if you have a two-year gap in your CV due to building a family it may have serious repercussions for job applications. There are schemes in place now to try and help this issue, and the Government has called on the higher education sector to review career structure and increase the number of longer-term positions for post-docs. However, we need to be careful – a post-doc job is a training job – and if you are stuck in the same position for 5-years you will get a very different type of training to someone who has completed two or three post-docs in this time. Other schemes for this include fellowships from the Daphne Jackson Trust – a fellowship scheme that JIC now sponsors. These fellowships were designed to help people return to STEM careers after a break of two or more years, which can make a big difference for people hoping to return to their field.

Reaction to this report seemed to have a similar theme from the panel at the event – disappointment. Although our panel all agree with issues brought up during the discussion, and feel positive that the key issues were recognised, they recall that this is not the first time that these issues have been brought up. Many of the issues were brought up a decade ago, and the lack of progress is rather disheartening. Agreement was clear that there are still changes to be made, and also clear that incentives such as Athena SWAN have been great for forcing these changes to be made. At our local institutes, the Athena SWAN application process forced the committees to look closely at their workforce, gather data and scrutinise current practices. Since beginning our application several great changes have been brought into effect. For example we have set up  a family support fund to financially support researchers with caring responsibilities when they need to travel as part of their work. The award has also raised awareness about the issue nationally, helping people to realise that the biases are there and that changes need to be made. It has also raised the awareness that many issues attributed towards women may also be issues for men – such as caring responsibilities, especially with rising costs of childcare. It was agreed that the report did help to break down the challenges facing the scientific community into different sectors.

When asked to name a single development that they would like to see taken up to promote gender equality our panel generally were in agreement on a single topic;  the lack of financial structure available to support childcare for academics in caring responsibilities, as well as career breaks and transition to part time work. Removing unconscious bias from the system was the other issue highlighted, and this included the fact that financial worries over childcare are not a solely female issue.

From reading the committee report and sitting on the Athena SWAN committee (although I am new to the committee, and missed much of the hard work put in towards the award), I would personally agree that there is no single issue blocking gender equality, and no single solution to remove it. However, there is now real drive to change things for the better and try to eliminate the inequality facing us today. Rather than seeing positive discrimination towards women I would like to see equal opportunities for all, and see people gaining recognition on their merits alone, not the presence/absence of a Y chromosome. I would like to wholeheartedly congratulate both UEA and JIC on their achievements in the Athena SWAN team, especially JIC on their recent Silver Award. I also think that Carole Thomas deserves some special recognition for the sheer amount of work and dedication she put into Athena SWAN. Hopefully, JIC will be able to continue their efforts in improving equality across site, and maybe we will even be able to aim for a Gold Award in the future. I also hope that in 10 years’ time we won’t be in the same situation as now, where many of the problems have been identified but not resolved.

To see my previous post on Women in Science, click here

By Izzy Webb, a 2nd year PhD student in the lab of Prof Phil Poole

Searching for a needle in a genetic haystack

In the last year, a brand new technique for genome editing has appeared with the potential to revolutionise the way in which scientists engineer genomes. It provides the ability to make cuts in the genome at precisely controlled locations, resulting in the silencing of that particular region. This technique is known as CRISPR. To make such a precise cut, however, requires the active protein to find a unique 20 base pair region within the vast sequence space of the entire genome.

“Seek and Destroy” – Nature issue 7490 (image from Nature.com)

The CRISPR system originates from the bacterial immune system in which a segment of the bacteria’s genome contains short elements of viral DNA (protospacers), which act as guides to attack invading viruses by disrupting their genetic code [1]. This segment (known as the CRISPR array) contains so-called ‘Cas’ proteins capable of cleaving segments of DNA, that are guided into place by the protospacers stored in the array. The bacteria are able to add new stretches of foreign DNA to this array to develop immunity in future encounters with the invader.

The genome editing technology [2,3] takes this CRISPR array structure and replaces the viral DNA sections with lengths of the target genome that are intended to be silenced. This can then be inserted into the target genome by standard methods and, when transcribed, the Cas protein finds its way to the point in the genome with precise sequence complementarity to its guide. However, despite this technique’s success, the mechanism enabling the Cas-RNA complex to find its target was unknown, until now.

In this week’s nature cover article [4], Sternberg et al. show that a particular Cas protein, Cas9, can only bind to regions containing a three-nucleotide motif region, known as a PAM, that is found adjacent to protospacers. When searching for a needle in a haystack, you would not pick up every piece of hay, compare it to a picture of a needle, and then replace it when it didn’t match. Similarly, Cas9 does not try every point on the genome and compare the local sequence to its guide. It first limits the number of places to search by only binding to PAMs. This could be likened to the first step in searching for a matching phone number; you only compare the numbers with the same area code.

Of course, there are still a large number of PAM sequences in a given genome (or else the technique would be somewhat limited), but it vastly simplifies the problem. Furthermore, the PAM acts as the start point for the guide/genome sequence comparison, which proceeds one nucleotide at a time in sequence. The process is such that if the first 2-3 nucleotides do not match, then the complex rapidly disengages from that region and can move on to try a different location.  These factors combined ensure that the complex spends as little time as possible at incorrect locations.

This work is an impressive demonstration of how biological systems are able to solve difficult problems. An invading virus needs to be dealt with quickly if a bacterium is to survive. The CRISPR system therefore needed to find a rapid way of finding a target within a large search space. It achieved this by utilising a regular motif present within the target genome, choosing to only incorporate stretches of DNA adjacent to these motifs. It seems the trick to finding a needle in a haystack is to choose a smaller haystack to lose it in.

References

  1. Wiedenheft, B., Sternberg, S. H. & Doudna, J. A. RNA-guided genetic silencing systems in bacteria and archaea. Nature 482, 331-338 (2012).
  2.  Mali, P. et al. RNA-guided human genome editing via Cas9. Science 339, 823-826 (2013).
  3.  Cong, L. et al. Multiplex genome engineering using CRISPR/Cas systems. Science 339, 819-823 (2013).
  4.  Sternberg, S. H., Redding, S., Jinek, M., Greene, E. C. & Doudna, J. A. DNA interrogation by the CRISPR RNA-guided endonuclease Cas9. Nature 507, 62-67 (2014).

By Matthew Evans- a second year PhD student in the lab of Dr Richard Morris

Featured Scientist (V): Dr. Jagger Harvey

Dr. Jagger Harvey

Last week Dr. Jagger Harvey visited JIC from the one of a kind bioscience hub BecA (Biosciences for East and Central Africa). Jagger is half American, half Haitian and witnessed the massive disparity of the two countries throughout his youth. This inspired him to work with developing countries and use his skills to tackle hunger and poverty. However, instead of diving straight into applied sciences he decided to get a fundamental grounding in biosciences, first receiving his PhD from UC Davis. He then moved to The Sainsbury Laboratory, here in Norwich, to complete a postdoc with David Balcombe.

When Jagger joined the BecA Hub just 5 years ago he was one of three scientists on a small corridor of offices. Now BecA accommodates and funds 40 researchers spanning 18 countries of Africa as well as many more visiting scientists from all over the world. 

The countries involved in the BecA Hub

BecA is a shared agricultural research and biosciences platform that exists to increase access to affordable, world-class research facilities. The development of the facility has been project-driven. For example, Jagger began working with an international team on Aflatoxins – fungal produced Mycotoxins which are deadly in high doses. Aflatoxins are a big problem in Maize production across Kenya and Tanzania, especially if the kernels are not dried properly once harvested. With a massive injection of funds from the Australian government a platform for mycotoxin diagnostics was set up to facilitate this project. Along with a nutritional analysis platform which can provide full nutritional profiling of foods this facility now provides an invaluable resource for the whole region.

An important part of the hub is to provide quality training and support for scientists from all 18 countries. It has become an extremely successful and can have up to 1700 applications for 30 places available on a training course. The Hub also facilitates lasting collaborations between African scientists and internationally. One way that these collaborations are brought together is through connections workshops, which anyone can apply to attend if you have a project idea – something to keep it in mind if you would like to be part of this inspirational future for African science.

If you are interested in more information, you can find the BecA website here: http://hub.africabiosciences.org/ 

All images courtesy of africabiosciences.org

By Tilly Eldridge, a final year PhD student in the lab of Enrico Coen