How does scientific publishing work?

So we talk a lot about the studies we do, and we’ve had a lot of summaries on here of the published papers detailing the results of the research studies.  What might be a bit of a mystery though is how the process between those two points works…  So here’s an overview.

Once we’ve gone through all the hard slog of acquiring research data and analysing the results, we write up a report, that we generally call a manuscript.  This is normally something around 3,000 words long, and contains:

– An introduction to the area of study, why we decided to do the research, and what we expected to find (our hypothesis).

– The ‘methods’ section, which is a detailed description of what we did and how (what equipment we used, how long we measured things for, where we identified participants from, in what order our measurements were made, etc.).

– Results:  this is where we put all the numbers, in the form of tables and graphs and some explanatory text.

– The discussion, which is where we talk about what we think the results mean.  It might be that we found what we expected (i.e. supported our hypothesis), or that we got completely different results to what we hypothesised.  Either way, we discuss aspects of the study that we think were particularly strong, highlight any weaknesses, and then refer to our results within the context of other research in the same (and related) fields.  This section often contains suggestions of what future studies could do to build on the results we’re presenting.

So once we’ve written the manuscript and all authors are happy with it (everyone who has contributed significantly to the research is listed as an author, with the first person in the list being the person who did the majority of the work, and the last person being the senior academic responsible for overseeing the project), we decide on a journal to send it to.  This decision is based on the type of research study we’ve done (there are some journals more suited to studies with a pure physiology focus, and some better for more clinically-orientated work) and how significant we think the work is.  A larger study, or one with more exciting findings (perhaps that would really change the way people think about that area of study), would be sent to a more prestigious journal.

Once the journal receives the manuscript via their online submission system, it is evaluated by a member of the journal’s editorial team.  They judge whether the manuscript is the sort of thing they’re looking for, and at that point either reject it straight away (disappointing) or decide to send it out to review.  If the latter, the manuscript will be sent to usually two or three expert researchers who work in the same field to ask them to give their opinion.  These reviewers will write a report of the manuscript and suggest how suitable they think the manuscript is for publication in the journal.  The editors of the journal will take into account the opinions of all the reviewers (and these opinions won’t always agree…) and make their decision.   They will send us an email informing us of the outcome, which will be one of three things:  that the manuscript has been rejected, that it will be reconsidered after some changes are made, or that it is accepted as it stands (a relatively unusual outcome, but one that we would celebrate with some vigour!).

If the manuscript is rejected, we will look carefully at the reviewers’ comments and make any appropriate changes to the manuscript before choosing a new journal to send it to (and the process starts again).

If changes are requested, these could be relatively simple (such as adding in some more details about the participants, including some different graphs to represent the data more clearly, or referring to some other research within the discussion section), or could be complex (for example requiring some major data reanalysis or lengthy explanations of why a certain approach was chosen).  We would work on these changes and send back a revised manuscript with a detailed letter describing what changes we have (or sometimes haven’t) made and why.  These documents then are sent back to the reviewers and they write another report.  Based on this, the editors decide whether we’ve done a good enough job for the manuscript to be accepted.  Sometimes the changes and corrections process is repeated once (or more), but generally the manuscript will be accepted in response to the first or second set of changes.

Once the manuscript has been accepted by a journal (whether that’s the first, second or fifth journal to which it was sent), the journal’s editorial assistants prepare the written document in their own specific format and send ‘proofs’ to the authors to approve (making sure that everything looks correct, there are no spelling errors, and that the layout for the journal hasn’t led any data to be presented in a misleading manner).  The paper (no longer just a manuscript) is then first published online, and a few months later appears in print (though actually very few people read journals in paper form any longer).  And importantly, we add it to our CVs!

A summer with the King’s Muscle Lab

Sasha is a KCL student who is working with Dr Joerg Steier, a former King’s Muscle Lab researcher who is still part of our wider research group.  Here she tells us how she has found her research ‘taster’ summer so far…

My name is Sasha and I am a 2nd year Neuroscience student at KCL. The Neuroscience course,Sasha much like other Biomedical Science courses at King’s, aims to coach you in to a research career. For ages I was never really sure whether I wanted to pursue a career in research. I couldn’t see myself stuck in a lab with pipettes in a white coat, but after a few months of working as a summer student alongside researchers, I have learnt research is nothing like that at all!

I decided to get work experience over the summer because I knew I wouldn’t be sure to pursue a career in research unless I actually had some experience of doing the job. I saw a project online through King’s called ‘the Multiple Dimensions of Sleepiness’ and after having a few lectures on sleep physiology and medicine and thoroughly enjoying them, I decided to email the supervisor, Dr Steier, and share my interest in his project. It was agreed that I would help Dr Steier throughout the summer in collecting and analysing data, attending research meetings, and writing up the paper.

On the first day of helping Dr Steier I was super nervous – I really wanted to make a good impression! We were meeting at his office at 11am so I got there at 10.40am with plenty of time to spare. I knocked on the door and there was no answer. Not to worry I thought – it’s just because I’m early. I stood outside the office for 45 minutes with no one answering the door. I decided at this point to email Dr Steier as maybe he had forgotten we were meeting. He speedily replied saying “Ah I wondered where you were, today I am at my other office in the Lane Fox Unit (Westminster) not at Nuffield house (London Bridge).” So I spent my first day on the job running across London to the other campus arriving sweaty and breathless. Already I had learnt something very important – researchers may have multiple offices in different locations (and I must check beforehand which office I need to go to)!

The next few weeks went smoothly, I attended research meetings where researchers of the King’s Muscle Lab shared their ups and downs of their projects. From these meetings it became clear that research isn’t always smooth sailing, there are set backs and hurdles you need to get through but you have your colleagues, who have often been through the same thing, to support you. Attending these meetings I gained a really good insight in to the different projects that take place in the King’s Muscle Lab. At first it was difficult as I noticed researchers seems to abbreviate EVERYTHING, they are either discussing what happened in ICU or they’re gathering data from EEG’s, MSLT’s and PSG’s… It took me a few meetings to get the hang of it but after that there is nothing cooler than abbreviating everything and having your housemates think you’re an actual genius!

So far, my favourite part about helping on the project has been the data collection. This is because our data is questionnaire based so I have been able to interview patients from the sleep clinic. I have really taken to patient contact and I feel that it is the best way to really get down to the problem you are researching. It’s also really helped with my confidence and I have learnt to approach different patients in different ways based on their needs.

After data collection was completed, we needed to do some analysing. This was done using SPSS [statistical software]. Having never using this software before I was a bit overwhelmed. It seemed so confusing and Dr Steier could do everything on it so quickly. I honestly thought I would never get the hang of it. But after several YouTube videos and a couple of hours in the library I seemed to be producing means, standard deviations, correlations and linear regressions with ease! Alike to the abbreviations, it was tough at the beginning but it felt so good to actually understand how it worked.

We are now at a point in our project where we have sent off an abstract to a journal and we are waiting for it to be accepted. I have prepared myself to not be too disgruntled if it doesn’t get accepted because, like I said, there are many setbacks in research – you just need to let your passion for the subject keep you going. In only a couple of months I have learnt so many research skills that will help me in my career, but I think most importantly I have learnt many skills that will help me through life. I would say the TOP career skills I have learnt are to be a Team player, be Open minded and to Persevere!

The value of working together

Research is tough at times – much of the time in fact.  Progress is slower than in many other jobs, and getting turned down is a frequent aspect of the work (funding applications and submissions to research journals are very rarely successful on the first attempt).  There are also a lot of things you need to know.  This can range from complex stuff like specific scientific techniques to something as simple as knowing who to contact to get a replacement lightbulb in the office.  Also, difficult things happen in researchers’ personal lives too, and such things can make the research work much harder.  The thing that makes this all manageable is that we work together as a team and help one another.

This might seem like a simple thing, and an obvious one.  It would however be possible to let everyone figure out their difficulties on their own – it would take longer, but you can learn techniques by going on courses or reading about them in books and papers, and despite the fact that the King’s College London website can be a bit of a challenge, you’ll find the email address for the facilities helpdesk eventually.  Doing it that way would be stupid, and we’d all probably be really grumpy too.  So instead, we use each others’ experience and knowledge to complement one another and get things done quicker and better.  Some examples:

Alan has spent a lot of time learning new and (sometimes) complicated statistical methods.  We use statistics to demonstrate that the findings of our studies haven’t just occurred by chance, so stats are in many ways the crux of our work.  We have generally used relatively simple statistical methods in our lab, but Alan’s willingness to explore new techniques (and do all the really hard reading and learning for the rest of us) means that we can explore our research data in ways we hadn’t thought possible, and robustly demonstrate findings that we felt were there but couldn’t quite show.

Caroline is the only doctor in the lab at the moment, so can help others with questions about things like the prognosis for a certain disease, or how particular medications work.  The training for physiotherapists, nurses, physiologists and the like doesn’t cover these things in as much depth.

Ged has more experience in, and greater knowledge of, human physiology than any of the other lab members.  It’s always surprising how detailed an explanation of the physiology underlying a particular process Ged can give!  This is invaluable in allowing us to understand why things that we see in our studies might happen, and how different body systems interact.  Ged’s knowledge of how the body controls breathing is particularly impressive (as that’s what his PhD concentrated on).

Manuel is a super-clever signal processing engineer, and so understands the data we acquire in a completely different way to any of the rest of us.  He can explain why it might be that we get a strange wibbly line in the middle of a study – and more importantly can often get rid of it, which means we can use a recording that otherwise we would have had to ignore.

Dan has a lot of experience as an ICU nurse, caring for patients at the bedside as well as doing research.  We do quite a lot of studies in intensive care and Dan’s insight into the minute-to-minute reality of an intensive care unit patient’s stay is hugely beneficial in allowing us to plan studies around patients’ needs, and make sure what we do is sensible and feasible.

Alongside all these skills, the silly little things that people pick up along the way are incredibly helpful too – how to change a setting to format your Word document correctly, what time to go to the canteen to avoid the big queue (and get the best chips), which screwdriver fits that bit of equipment the best, what forms you need to complete to submit your PhD thesis, what type of tape when securing the tubes we put up people’s noses to measure their diaphragm function…  The list goes on.

Most important though is the fact that we’re all friends.  If things are a bit tough, we offer words of encouragement, cups of tea, a help with something tricky, sympathy (and a bit of a whinge) if you’ve just had a grant or paper rejected, and perhaps even a quick trip to the pub (we are all over 18, and we do do it out of working hours).  Knowing that someone will help you out if needed is absolutely priceless.

New video from two Student Advisory Panel members

Maryam Waseem-Sayeed and Asha Omar are Year 12 students at Burntwood School and are members of our Student Advisory Panel.  Over the summer, they spent a day in the lab watching one of our studies, and have produced this video showing many of the techniques we use.  Thanks Asha and Maryam for your hard work and we look forward to more cinematic genius to come!

Laura and Beth write about their week of work experience

Many people may imagine a career in research to be non-stop, action-packed fun from 9 till 5, 7 days a week. When we, budding young scientists, flick through articles in New Scientist, we assume someone got up one morning and thought “I want to do this project”, and then soon enough their findings are published as articles in national journals. But, as we learnt this week, life as a researcher is far from this idyllic fantasy.

One of the first things we learnt during our week of work experience at the lab is that life as a researcher is very unpredictable. Each morning when you arrive, you have no idea what kinds of tasks you’ll have completed by the end of the day. This may seem rather daunting, however it means you are never bored, and are always kept on your toes!

On our first day at the lab, Vicky had planned for us to have a go at taking some lung function measurements. Collecting the data was reasonably straight-forward – the difficult part was setting up the equipment! As a researcher, you are responsible for locating equipment and making sure you have what you need to conduct your research. It is evident that being organised and patient are two vital skills to have as a researcher.

One would often think of a researcher as a solitary scientist alone at a work bench. In reality, there is a great deal of teamwork and collaboration involved, making it a very social job. Every Wednesday morning, all members of the muscle lab come together to discuss their recent findings, often seeking guidance from one another about something unexpected they’ve come across. This aspect of the job means that you are never alone as a researcher; there will always be someone in another field who is able to assist you.

Something which we found really exciting to see during the week was the ability that researchers have to develop their specific areas of personal interest in the scientific field. For example, Dr Clark (who we were lucky enough to spend a whole day with) has a particular interest in cardiovascular physiology, so is currently working with some masters students on a project looking into the physiological processes which occur during heart failure. To be able to learn new things every day and develop a deeper understanding in an area you’re fascinated by is incredible. We also spent some time with Professor Sutton, who works in X-ray crystallography, a technique which was used by Franklin and Wilkins – leading to the discovery of the structure of DNA. The development of new technology allows processes which would previously have taken 4 years, to take a matter of hours. Unfortunately, researchers need to manage to get the funding first which we have learnt is not an easy task!

As well as that, we also really enjoyed learning about a longitudinal study which Vicky is currently carrying out, looking at premature babies and their risk of developing a respiratory disorder. We observed her doing some lung function tests with a participant, who had carried out similar tests when he was a baby. Over 100 premature babies were involved in the original data collection, and Vicky is now in the process of contacting the same participants to collect further data 6 years on. Research projects often take many years to complete, but often the discoveries made are very valuable, so in the end the years of hard work and dedication pay off!

We had an amazing week at the muscle lab and learnt so much in such a short space of time. Thank you to Vicky for organising it all, as well as to the many other academics we were lucky enough to spend time with during the week!

Laura Schuz and Beth Tobiansky, Student Panel members, JFS School Sixth Form

An interview with Dr Rafferty

Dr Ged Rafferty is head of the King’s Muscle Lab.  Here, he tells us a bit about his career and his work.

Did you always want to be a scientist?
To be honest, I would have liked to have a been a professional cyclist, but unfortunately, my shameful lack of athletic ability put paid to that.  It is my love of cycling that really sparked my interest in human physiology, although I had always enjoyed biology at school.

What made you decide to go into research?
I studied Physiology at the University of Leeds, because at the time, it still had a large component of human physiology in its final year undergraduate programme.  This included a week long trip to undertake cold water immersion experiments at the Institute of Naval Medicine in Portsmouth with Dr Mike Tipton, now Professor at University of Portsmouth.  This, alongside my research project on muscle composition in the leg, really captured my interest and led me to undertake a PhD.  I did my PhD at King’s College London, looking at control of breathing.  After that, I worked for a short time at the Ministry of Defence and then became a lecturer back at King’s – I’ve been here ever since!

What do you like most about doing research?
It is very clichéd, but learning new things!  I really get a kick out of expanding my knowledge and satisfying my desire to understand how things work.

What’s the hardest thing about your job?
As a Senior Lecturer at King’s College London I am expected to undertake research, teaching as well as having administrative/management responsibilities.  While teaching is quite time consuming, not just requiring the time spent in direct contact with undergraduate and postgraduate students, it is not without reward, especially when you feel you have connected with the students and they have that “light bulb” moment of understanding a topic.  While it is research that I get most enjoyment and satisfaction from, one of the hardest aspects is the continual pressure to obtain grant funding to support my research, both in terms of the equipment and materials required by specific research projects but also for the salaries of staff involved.  Obtaining funding from grant awarding bodies such as UK research councils and charities is highly competitive and most applications are not successful, which considering the time effort that goes into preparing an application can  be very disappointing.

What is the most satisfying thing about your job? 
There are many, but I suppose the culmination of a period of study resulting in a postgraduate student obtaining their PhD is incredibly rewarding.

What one piece of advice would you give to people thinking about a career in science and/or research?
You need to be enthusiastic about the topic you are researching.  Without the drive that comes with being interested in a field of research it is very difficult to achieve the desired outcome.  Research can be incredibly exciting when studies are going well and interesting data are coming through. Unfortunately there are many occasions when experiments just don’t work or the data are not clear or studies become monotonous and repetitive.  Having the enthusiasm and interest in the topic is what carries you through.

Thanks very much Dr Rafferty!

It’s “heads down” at the moment

It’s been a while since our last blog post – and the reason for that is that we’ve all been busy doing lots of things that are not very news-worthy.  Life in research tends to go in cycles a bit like this – sometimes we have lots of interesting things happening that we can tell you about, and other times it’s all just busy-busy-busy with the daily grind.  Ged, Caroline and Vicky have been busy writing applications for research money – as we mentioned on our “What is research?” tab, we have to apply to charities and other big funding organisations for money to support our work, and we’ve had a particular flurry of applications recently.  We are hoping that some of them will be successful – we think the projects we want to do are exciting and worthwhile, so we have to hope that the charities agree with us!

Our MRes students – Lorna, Matt and Hannah – have been working very hard at doing lots of studies with our very kind patients and volunteers.  Lorna, Matt and Hannah have to write a big essay (‘dissertation’) by September this year, reporting on the research that they’ve done during their year in the lab and what they found.  The writing part can take quite some time so they have to finish their studies in the next couple of months to leave plenty of time for writing (and the “thinking about what it all means” part).  Dan is also very busy with his study on the intensive care unit (ICU).  Patients on ICU are very unwell, and so they have pretty much all aspects of how their body is working measured all the time, to allow the care team to look after them in the best way.  Dan has to record all of these measurements for his research, so even having one patient in his study can keep him pretty busy!

Alan is coming to the end of his PhD, and we will certainly tell you when it’s all finished – a massive achievement, and a celebration will definitely be in order.  Alan also recently added details of one of his studies to the “Research we’ve published” tab, and I’m sure there will be more to come in time.

We will have news to come soon of an official logo for the blog and Facebook and twitter pages, as well as details of the fantastic person who has designed the logo for us.  In fact, we will probably have a number of logo options and so will ask you to vote and choose your favourite.  We also have some new research studies starting soon, and results of some finished projects, so will keep you posted on those too.  For now though, noses to the grindstone!

My Yearly Breathing Bonanza

Hello my name is Emily and I’m 9 years old.

I come here to help the researchers  with their projects by letting them experiment with my breathing. This is my fourth time here. Sometimes I think I’m going to be bored, but when I get here there is always something to do! I’ve started to learn what traces (squiggly lines on the computer) mean.

The researchers test my  breathing by using: Emilysticky stickers, masks and cubicles (I’m sitting in one in the picture). Every year they change subjects but the thing that stays the same is breathing.

It’s all for a good cause because it helps people who have problems with their  breathing.

Every Breath I Take

My Louisename is Louise Taylor and I’m 7 years old. I have been here 4 times in the last 4 years. We are here to help people with asthma. We put sticky plasters on our chest and once a breathing mask. A computer measures our breathing by showing lots of wiggly lines. It’s fun but sometimes a bit scary at the start, but it’s worth it because we help other children.

What’s a PhD?

We often talk on here about people in the lab doing a PhD.  You may also have heard at other times of people having PhDs, but you might not know what this really means.  Many of us didn’t really know that before we started working here either so we thought it might be useful to explain.  PhD stands for “Doctor of Philosophy”, but we don’t mean philosophy in the way the word is normally used – philosophy is actually a Greek word that means ‘love of wisdom’.  Still, knowing that still doesn’t help much in understanding what a PhD is.

In our field, doing a PhD usually involves working on a number of separate, but related, research projects over at least three years.  You have one main supervisor, who is a very experienced researcher and an expert in the area you’re working in, and with whom you meet very regularly to discuss your progress.  You also have a second supervisor with similar skills but whom you don’t work quite so closely with.  Your supervisors give lots of help and advice along the way, but each PhD student is responsible for their own studies and has to do all the work themselves.  Although people often say they are “studying for a PhD”, it’s very different to other university degrees as it doesn’t involve going to lectures and doing written exams, but is all about the research projects you do.

At the end of the studies, you have to write a huge thesis, or dissertation, about the background to your research, what studies you did, how you did them, what the findings were, and what this means.  Much like with the studies themselves, you write the thesis yourself but with advice and recommendations from your supervisors.  The thesis is basically a book – most people write one that is about 60,000 to 80,000 words, and sometimes longer.  It takes ages to write the thesis and is very hard work!

Once you’ve finished your thesis, and your supervisors are happy with it, it gets sent to two experts in your research area from outside the university, who read it in detail and then come and discuss it with you during a long exam called a ‘viva’.  They will ask lots of questions – partly to make sure you understand what you’ve written (!), but also to discuss your findings in lots of detail to see if there are perhaps other ways you could look at your results or describe your findings.  After the viva, the examiners will usually ask you to make some changes to your thesis.  Once you’ve made those changes and the examiners are happy, some big boss-type people at the University have a meeting and (hopefully) award you your PhD – and you breathe a huge sigh of relief that it’s all over!  A few months after that, you get to graduate (and celebrate!) just like Vicky and Bronwen did recently.

The thing that most people know about having a PhD is that it means you become “Dr”, so that’s why there are lots of us in the lab who are called “Dr” but who are not medical doctors.  Having a PhD doesn’t mean you are a super-duper expert researcher, but it means that you have had a good level of training in how to do research, and also that you can write about research to a high standard.  Not everyone who does a PhD stays on and works in research, but those who do usually continue to develop their research skills – these people are called postdoctoral researchers, or ‘postdocs’.  After a while as a postdoc, people usually aim to get a job as a lecturer, and might eventually work their way up the ladder to become a Professor.

We hope that was helpful to explain the whole PhD mystery!