Behind the Curtain Again

A couple of weeks ago I wrote about some of the not so great behind the scenes goings on in science. I'm revisiting that after news broke yesterday of a paper by Dr Fiona Ingleby and Dr Megan Head being rejected by a journal reviewer with the following comment.

Images of comments from Fiona Ingleby's twitter

The paper in question was on gender issues in the flow of researchers from PhDs to Post Docs and not only does the review suggest that the authors needed 'to find one or two male biologists to work with', it also included this lovely commentary.

Images of comments from Fiona Ingleby's twitter

Or Mr Reviewer, maybe there are issues of where women get published due to people like you. On top of the drivel above the Reviewer also acknowledges looking up the author's websites and notes their genders and post doc status in the review and appears to see them as 'junior' researchers. Ironically both authors  have over 20 years of research under their belts. You know how I said status matters in my original behind the curtain post? Well, I think this is a perfect example of that point. 

On their twitter feeds, Dr Ingleby and Dr Head have pointed out that this kind of review really shows why we need double blind peer review. At the moment, when an author submits a paper they get reviews back from anonymous reviewers. However, the reviewers get full access to the author's details so can easily find out things like their gender and status in the field in question at will. Does this skew their perceptions of the work they are given to read? Well I think the above comments tell you that it does. Double bind peer review would remove the element of reviewer bias as the reviewer can only judge the work, not the person. Another option is to let the authors know who is reviewing them because, as you find with internet trolls, once you take away the mask of anonymity, people think a lot more before they speak. However, a clear argument against this would be that knowing a reviewer's identity could lead to personal vendettas or bribery. Therefore, double blind peer review is probably the way to go to protect integrity in science. 

The publisher (PLOS One for anyone who cares) who allowed these comments to stand as 'legitimate' criticism have since apologised and state that the paper is under being looked at under the appeal Dr Ingleby and Dr Head have submitted. But frankly, that's not good enough. How could any editor allow such complete and utter rubbish be included as a review? What are they going to do to ensure this doesn't happen again? Will they stop sending papers to the reviewer in question? I hope that this incident sparks a wider discussion and maybe change in the peer review process, but I won't hold my breath. If at least it makes reviewers think twice about what they write about papers and what editors accept as legitimate reviews then that's a small positive result from this. However. until peer review changes, I don't think we'll see the back of dodgy reviewers comments.

How do you find a PhD place?

Following my last blog on why you might do a PhD and with final exams season approaching I thought I'd talk about how you go about finding a PhD place to apply for. Once again, I must say I'm focusing on science PhDs, because yeah...I'm a sciencey person.

What routes can you go through to find a PhD? In my experience there are 4 main ways to go:

1. Apply to a relatively new centre for doctoral training (CDT).
2. Apply for an advertised position.
3. Accept a position offered by a current or past supervisor.
4. Propose a project and find a supervisor willing to take you on.

No matter whichever way you find a PhD through there is one thing you will need to complete your studies, money! Money to live on, money to pay your tuition fees and money to fund your actual research. If you apply for a CDT funding will be guaranteed, so you can apply safe in the knowledge you will be paid and have all your study expenses covered. Similarly, if a position is advertised online or in a university department, it will almost certainly have funding attached to it. Things start to get a little bit more uncertain if a current or past supervisor offers you a position, they may have funding and be offering you first dibs on the place, or they may have a project in mind, but no funding sorted out. Therefore, you may have to wait a while until funding is secured before you can sign on the dotted line. However, if they have a project and want you to do it then it's likely they will do everything they can to secure you funding. The most difficult situation to be in is when you propose your own project. In that situation you will have to secure your own funding by applying to research councils, charities or universities with a detailed project proposal. 

Where do you go to find out about advertised positions and CDTs? My personal favourite website is Find a PhD. Find a PhD lists a huge range of funded and unfunded projects, along with funding opportunities across pretty much any field you care to name. It's basically a one stop shop for PhDs. My advice is to make sure you pay attention to the adverts on the side of the page as well as the search results as that's where I found a link to the PhD I eventually applied for and got. Another way to go is through prospects.ac.uk. They also provide UK wide listings for taught and research positions along side their graduate job listings. The final place to look is on the individual websites of university departments. Look up the webpage for the department you're interested in and check their postgraduate, research and research group pages as all the available PhDs can be spread across these locations. 

Each PhD route has its own advantages and disadvantages and may suit some people better than others. A place in a CDT entails signing up for a 4 year course in a research field. Unlike every other option, in a CDT you don't commit yourself to a project straight away, you spend a year learning and gaining new skills during which you choose a research project. This has the advantage of allowing you to investigate supervisors and projects in detail before you commit to one. Further to this there is lots of wriggle room to propose a project within the CDT's field and, as you already have funding, supervisors are happy to negotiate project modifications (which I did) or complete overhauls. Over 5 years most CDTs ultimately recruit 50 students. Therefore, being part of a CDT means you'll also be part of a community of students all on the same program. The main disadvantage is the vast amount of requirements you have to meet. All PhDs have things you have to do outside your research, but in my experience CDTs have anywhere between 3 and 4 times as many things you're expected to do. This is fine and actually helpful in first year, but once you begin your research it can sometimes be frustrating as you have many other things you would rather and should rather be spending your time on. 

In contrast to a CDT, if you apply for an advertised position you sign up to do a specific project with a specific supervisor for around 3 years straight away. The good thing about it is that you know exactly what you'll be doing from day one allowing you to be very focused. However, you can end up committing to working with someone you've never met before on something you've not studied before. Therefore, if you don't fully understand what you're getting into, there is potential for problems to crop up later down the line

Accepting an offered position from a current or past supervisor can work out really well. You'll be working with someone you know and hopefully will have a good idea if you can get on with them for 3 years. You'll probably also be doing a project that is similar to what you've done before so you'll hopefully be confident that you'll like the work involved in the project. However, going down this route can lead to you missing out on the opportunities that are available elsewhere for something safe.

Finally, if you propose your own project you're fully able to set your own boundaries. So hopefully you will love what you do. However, you have to find a supervisor to work with which might be easier said than done if you don't have funding sorted out. Additionally, as you proposed the project your supervisor might not be fully engaged with it, or fully understand all aspects, which could impact on the quality of the supervision you receive.

Whatever route you choose the most important thing to do is ask questions before you apply. CDTs often have open days you can attend to talk to the head of the program, potential supervisors and students about the work you might be doing. For non-CDTs, speaking to the supervisor about the project they're offering is vital, you'll get useful information that you can use at interview and also might find out key details the advert missed out. In all cases, if possible, talk to current students. Ask them about their experiences with the program, work and supervisor. E-mailing the administration office is the best way to find someone to talk to as the admin staff should be able to point you to someone with roughly the same background in the group you're looking at who'll be happy to chat to you.

Do you have any questions about applying for PhDs? Or, what are your experiences of applying for a PhD and what was the best advice you received? Why not share in the comments below!

Why would you want to do a PhD?

This week I thought I'd talk about deciding to do a PhD, as I'm sure that quite a few people will be currently deciding whether to do one or not. As a health warning this post is based on my experience and is focussed on science/engineering PhDs as they're what I'm familiar with.

So, I why you might want to do a PhD? It’s one of those questions which has many answers for many different people. You could probably guess some reasons pretty easily, others are probably less well known outside the academic community. In my experience some of the most common reasons are:

• I love my subject and want to keep learning about it after my degree.

• I want to be a lecturer one day so I kind of need one. (Not 100% true by the way.) 

• I want to be a professional scientist so a PhD would be a really great way to kick start my career.

• I want to explore science and give research in something new a try.

• I love being at uni! I don't want to leave! I should do a PhD!

• Oh my God! What do I do now. SOMEONE HELP ME! Oh, you'll pay me to keep doing my final year research project... That doesn't seem so bad. 

Some of these are really good reasons, some not so much. However, at the end of the day who am I to judge people on what influences their decision making process. Your motivation doesn't really matter as long as you turn up and do what is expected of you. So if you want to do a PhD just because you want to stay at uni, I'm not going to tell you not to.

Having said that in an ideal world if you're choosing to do a PhD you should hopefully be pretty sure that you enjoy research and can handle the highly independent study that you're about to undertake. But how do you find out these things? From my experience your final year research project will help, but you can also find out by doing a summer/holiday research project, which I would thoroughly recommend to all undergraduates. Not only will it give you a bit of income over the summer, it's a great thing to have on your CV whether you want to do a PhD or not. Basically you sign up to work on a specific project for somewhere between 6 weeks and 3 months and see how it goes. Some require you just to turn up and do your work, others will want reports at the end and some will want you to do a presentation on your experiences. Lots of universities offer research placements for their students that are really easy to apply for (physics at Leeds takes 36 people into their research groups every summer). In addition there are opportunities to get research placements outside of your own university. These can be accessible through looking at career's service postings, the big nationwide sites like prospects.ac.uk, through organisations like the Odgen Trust or by going direct to a research group and securing your own funding from places like the BBSRC, Royal Society of Chemistry and the Nuffield Foundation (for keen scientists doing AS levels).

When I was an undergraduate I did two summer research placements after the first and second years of my degree and I had two very, very different experiences. My first placement was within my university's physics department and involved me hitting a keyboard for 6 weeks as I desperately tried to model the interaction of light with atoms by creating a program using specialised add-ons in C++. This just wasn't for me. Basically I spent my time trying to make something, anything work and I eventually wrote a basic user manual on the how to code models in the language. After that it was safe to say I was not a fan of research and I had no intention of doing a PhD. The next summer I found myself a new research placement in a Medical Physics department with idea of it boosting my CV ready for a clinical science career. In the end I got so much more out of the placement than just pure CV building. Once again I was hitting a keyboard (this time for 3 months), but I felt I was doing something worthwhile and really interesting. I was basically pulling numerical data out of simulated medical images and finding a set of equations which mimic the way a person sees a tumour in those images. It was great! I loved the research activity, I learnt how to use the programming language Matlab, how to write a paper and I got an insight into the careers of the people around me which was very useful. This gave me two clear ideas. Firstly, I liked research where I used my maths and physics skills to do something that I felt had a clear application and secondly, it might not be so bad to do a PhD after all and I should be able to handle it.

So, why did I decide to do a PhD in the end? My personal decision was based on a combination of 'I want to be a scientist', 'I want to explore science' and 'oh God, oh God what do I do now?' Which seemed like a good enough motivation at the time and has served me pretty well so far. What would my advice be after my journey towards doing a PhD and signing on the dotted line? Get experience, but don't judge a whole world of opportunities on one placement or project. Now I'm doing my PhD, I know that even my second placement didn't give me a full picture of what I wanted out of a research project and it didn't give me all the tools I needed to succeed. If you are leaning towards doing a PhD but aren't 100% sure, why not apply? You can always change your mind over the months it takes to get from application to contract. You can always come back and do one later in life too, but it might not be as easy to do as when you're fresh out of your first degree!

If you're a current or budding PhD student why are you aiming to get your doctorate? 
What experiences of summer research placements have you had? 
Let us know in the comments below!

What is Tissue Engineering and How Will it Help You?

I've previously mentioned that my PhD comes under the heading of tissue engineering and regenerative medicine, but what is tissue engineering and what might it do for us in the future? 

The main focus of tissue engineering in many respects is the production of replacement tissues and organs in the lab which can be used to repair the human body. The overarching dream is that one day people will be able to have new organs which are available on demand. Why is this something that we want? Firstly, we might be able to use artificial tissues to treat new illnesses, improving quality of life for people by regenerating their bodies. Additionally, by having organs off the shelf, we could eradicate the transplant list. How brilliant would it be to live in a world where no one dies waiting for a transplant?  So, how do we make these new replacement organs and how far off are they from being in use?

It's safe to say fully manufactured organs are decades away from use, but small tissue replacements are closer general usage than you might think. The artificial trachea transplant reported in 2011 is a tissue engineering solution and there are tissue engineered patches for heart reconstruction along with tissue engineered heart valves and skin currently going through clinical trials. So we are beginning to move into the area of artificial, regenerative surgery.

How do we make artificial tissues and organs? Firstly we need to understand what gives an organ its ability function. An organ's properties come from both cells and the structure that supports them, made of proteins and other organic molecules, both of which are extremely important. So we need need a material to support cells and provide biological function along with a source of cells to fill this scaffold. At the moment there isn't a single solution to do this. Some researchers are using artificially made polymer materials to create scaffolds, but you can also make fully biological scaffolds. Some researchers are taking tissues from animal sources, removing the cells in it and using the decellularised tissue to provide a natural cell support with the inherent architecture needed to replace an organ. This may sound like a really weird idea, but this it is proving really successful in clinical trials and in many ways is using materials perfectly evolved for a function in an engineered tissue. Finding a cell source is a huge challenge. In some cases it's possible to implant a scaffold and let the cells of the body move into it over time. For example if you give someone an artificial bone or muscle then the scaffold provides mechanical function and cells are not needed immediately. However, when cells are vital where should they come from? In normal transplants patients have to be on immunosuppressive drugs in order to stop the body attacking the transplant, due to the recognition of foreign cells. Therefore, the ideal cell solution needs cells which come from a patient themselves. However, this is difficult in many ways; you need the right type of cells in huge numbers, that means cells must be harvested from a patient and grown in the lab. The most plausible way to do this is arguably to harvest adult stem cells which keep your tissues repaired in normal day to day life and make them into the right type for the scaffold. However, this is time consuming and expensive and could be considered to be the biggest barrier to tissue engineered organs.

What might tissue engineering do for you in the future? It could be a long time before we get to artificial full organ transplants, but you may receive tissue engineered structural tissue fragments for bone, muscle and blood vessel grafts sooner than you might think. However, direct tissue replacement are not the only thing tissue engineering is good for. Manufactured tissue samples could also be used to revolutionise drug development. At the moment it takes around a decade and a huge amount of money for a new drug to get to actual use in a hospital. In that time it will go through laboratory tests, animal tests and numerous human trials. However, the success rate of new drugs reaching hospitals is extremely low and only around 16% of drugs which start clinical trials succeed. The main problem is that animal tests and current lab methods do not give us the actual human response to a drug. Tissue engineering could help overcome this by creating mini-tissues, which we can connect together to create models to examine exactly how a drug effects every part of the human body. This would be a fantastic development on so many levels and could make life saving drugs cheaper and get them to patients quicker. It could also replace animal testing for medicines.  

Tissue engineering has the potential to impact on medicine in a huge way. With a lot of hard work and time, in the future we will receive manufactured organs and drugs developed on tissue engineered models. Fingers crossed this will save lives and improve the quality of life for many people around the world.

I've got an answer, but what's the question again?

Research is a funny thing.  When I was choosing a project they all seemed so clear and well defined, but when I started work and had the chance to look behind the curtain it became clear that my first impressions were far from correct. In fact, you could even say that it is a truth universally acknowledged that PhDs must never be a beautiful journey on the shortest path from A to B. Instead there must be detours, dead ends, unexpected discoveries and changed priorities. The biggest trick of the final thesis is to sift through the mess and pretend that you did not in fact stumble around for three years, but that everything you did was all part of the plan.

After following the bumpy, dusty path of the PhD, where do you get to when you finally reach the end? Sometimes you end up at the original destination, having taken the long way around, but there never the less. However, those that walk this road are lucky. I am petty certain I'm not going to reach my initial destination. I don't even know if that destination is in the same country as the original one anymore. I suppose on first glance that doesn't seem like big deal, things changed and you ended up somewhere else. So what? The scary thing is that all these changes happen so subtly, so imperceptibly that you wake up one day and go. Wait a second, what am I doing!? I have data, but what on earth is this? What does it mean? What is the question I'm trying to answer? It's a strange place to be in, to have results and know that they say you've accomplished something but not know what that thing is. This all leaves you wondering whether you've actually done something meaningful or just gone off on a useless tangent.

The first clue for me that I was probably going to have a different destination from 'the plan' should have been that my project had major changes to my supervisors original vision from the get go. When I was originally chatting to my now supervisor about the project we decided to throw in some Raman spectroscopy on the strength of me being a physicist, having a contact at Leeds and being enthusiastic about it. So it should be hardly surprising my ride has been a little chaotic. However, at the time I thought I had a pretty rock solid plan. We had a goal in mind; to be able to analysis what bone cells were doing while they were growing using a home built spectrometer. We originally thought the point of interest would be in going back to first principles and stripping away the post processing algorithms of the shiny machines people always use, but we were a bit left of the mark. Building a Raman spectrometer should be easy; we thought! 20mW of power, well that's a lot! We'll have a working machine in a few months. Wrong, wrong, wrong. Although Raman is probably one of the most inelegant forms of spectroscopy where you just blast a sample with a laser and see what comes back, the task is harder than you would think. The biggest barrier to doing it is that the useful signal you generate is around a billionth of the power you put in. ‘Real’ low power spectrometers rely on seriously crazy calculations to work, which just wasn’t feasible for us. So we started testing different ways to use physics to extract the tiny Raman signals (making me feel particularly lucky to be part of a lab whose main expertise is in highly precise measurements of tiny things). Eventually, after a lot of blood, sweat and tears we completed our spectrometer and we think it works. Unfortunately, that all leads to a new quandary. We made a new thing, and that's awesome, but why exactly? What's the point, what's the story? 

In my mind the question I’m now trying to answer is the following:

'Does removing computational processing and using the inbuilt physics of Raman spectroscopy improve the results you can get?' 

Will that change before I finish? Probably, but does that really matter? Do you really need to have continual reassurance that everything is going according to the original scenario you created? I don’t think so. The more I’ve thought about finding my question, the more I’ve realised it’s something I may not know until I reach the end. I’ve got lots of different aspect to my work, which all have different challenges, so as I go I’m bound to stumble across all sorts of problems and solutions. Some of the work I do might not make it into my final thesis, but without those side projects I wouldn’t have made the big breakthroughs. I’m a person who likes to see the big picture, to always know where I’m going and why, which is probably why I would in many ways much prefer to be on a well-defined PhD path. But, more and more, I’m starting to accept that my ideal path just doesn’t exist. 

A PhD isn’t one dimensional and I shouldn’t expect the route to the end of a PhD to be one dimensional either.