Link Round-up 24th February

Here's a quick look at a few of the things that have caught my eye on the internet over the past 2 weeks.

1. Nature Talks p Values  
   Nature makes the round-up again this week. However, this time it's because they've published a lovely tutorial on the use and abuse of statistics in science. In particular they focus on the cult of the p value, a number which is often used to denote whether the result of a study could be replicated by random chance. Hopefully this article will educate others (as it has me) on the right and wrong times for using statistical tests.
2.  CERN Starts Unveiling its 60th Anniversary Plans
   CERN turns 60 on the 29th September and are planning events to commemorate '60 years of science for peace' both at CERN itself and in its member states. So, keep an eye out on the events website to see what's going to be happening near you!
3. What is the Higgs Boson and Higgs Field?
   This week  Professor Peter Higgs was interviewed by Professor Jim Al-Khalili on BBC Radio 4 and gave his explanation of what the Higgs Boson is. Which was a really great thing to listen to as a physicist, but it wasn't very accessible to the wider public. So, I thought I'd point you towards Professor John Ellis' beautifully clear explanation of the Higgs Field and the Higgs Boson.
4. Video Games Need More Women
   Keza MacDonald presents a fantastic article over at the Guardian looking at some of the main reasons developers avoid creating more female characters and why they don't quite add up. 

And finally, here's some floppy disc drives playing Tainted Love by Soft Cell as programmed by youtuber gigawipf. How awesome is that!

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.

Link Round-up 10th February

Here's a quick look at of some of the things I found note worthy and interesting over the last week.

1. Michael Mosley Infests Himself with Parasites
   Michael is a TV doctor known for doing the extreme.  I believe some of his previous escapades have involved sleep deprivation and trying sodium thiopental (the truth drug), so he is definitely an extreme science broadcaster. But for me this is something else. The fact that the results will help medicine is fantastic, but will the actual program be real science or all shock factor? We will wait and see.
2. Disk Detective 
   Two Friday's ago citizen science supremos zooniverse launched their newest project, Disc Detective. This time the task is to locate regions of dust around stars similar to an asteroid field to help identify currently forming or recently formed planets. If you're not familiar with citizen science projects they're all about using lots of people to do data ID tasks we can't leave computers to do, and they give everyone the change to do some cutting edge science from the comfort of their own home.
3.  Nature and Sexism
   Ok so rather than one link, this is a number of links. Nature is one of the biggest and most respected research journals in the world. If science makes the news there is a good chance it was published in Nature. However, Nature has been embroiled in some controversy over its handling of the response to a very interesting article it published on its own stats for female author and reviewership, which declared that it must do better to get more women published and involved in the publishing process. Which is good, right? They acknowledge the problem and pledge to do something. But that was not the end. Things really kicked off when they published an inflammatory letter saying that, in short, research quality is king and that a male dominated reviewing panel is not a problem, followed by a hasty retraction of the publication of the letter. Which all leaves a question hanging in the air. Why did someone not recognise the rubbish they were about to print and stop it in the first place? What does the fact the letter ended up in nature say about the views of some of their staff? The organisation as a whole may be working to try to even out gender bias, but is everyone really on board with that? These are all questions that bother me. I know some people don't want to see the wood for the trees when it comes to under representation of women in science. However, it starts to become worrying when someone at such a big organisation rubber stamps that view. Reader comments are comments and don't reflect the views of an organisation, but I find it concerning none the less. Here is a fantastic blog post by Kelly Hills giving her view on the situation in much more depth and clarity than I have, which you should definitely check out.

And finally... Patrick Stewart Does Sesame Street
Benedict Cumberbatch's Sesame Street Spot may be the top Sesame Street celebrity appearance of the moment, but it will never beat Patrick Stewart's for me!

This is how it is...as an interdisciplinary PhD student

Before, I get ahead of myself you may ask what exactly is an interdisciplinary PhD student? Well, we’re a bunch of much laughed at people who do research at the boarders of the different scientific disciplines. Basically, you combine two of the sciences (or any 2 fields of study for that matter) in one hopefully harmonious project. I do a strange combination of physics and biology, which is a bit of a challenge, but really rewarding. As you might imagine, the squishy world of biology and the world physics, which renowned for its rigour and precision, don’t tend to get along very well. (I still find myself close to tears at the sight of how biologists do error analysis).  In many ways this makes me “a child of two worlds” aka the greatest cliché in fantasy literature. However, it also encapsulates what it is like to work in an interdisciplinary science, but instead of being the messiah born of humble origins, you’re just a street urchin, constantly struggling to make your way in the world.

So what do I actually do? My PhD is part of the snappily named Doctoral Training Centre in Tissue Engineering and Regenerative Medicine which is run by Leeds, York and Sheffield Universities. In my project, the final goal is to grow pieces of bone and examine the development of the hard mineral part of bone by looking at how a laser interacts with it. So, as well as doing my physics heavy laser work I grow bone cells in full biological style meaning  I now have a new shiny set of skills. Unsurprisingly, biological work is very different from physics work. With physics I’m used to trying again and again to get an experiment right. You have to constantly analyse the problem and make changes, but in biology that just isn’t possible. You’ve got keep doing the same thing for almost two months without knowing whether your experiment is going to work, so it’s completely devastating when you find out it was all rubbish in the end. However, when it does go right and you do get results that are at least a little bit interesting it is truly phenomenal. All that hard, repetitive work pays off in a big way. In physics where you keep changing things you don’t get that same rush of achievement. You make small gains, steadily over a long period of time so it’s hard to identify what you’ve achieved at first glance. It’s only when you sit down to document your work that you suddenly realised how far you’ve come and that you’re not just struggling against a tide of failure. It’s then when you finally see the full picture and think, “Oh wow, I’m actually good at this and doing well.” I think I’m really lucky to be able to mix the two styles of work together, because it means I can always keep on working at my laser set up, but still have the big thrill at the end of a biology experiment. The biggest challenge I have is the gaping hole in my knowledge of biology, but it’s not a challenge in the way you’d expect. In physics I know exactly what I don’t know. It’s a strange thing, but it’s very comforting as you know precisely when to get help and when to dive straight into something. However, in biology there is so much I don’t know, but I have no idea where the gaps in my knowledge are. That means I make really silly mistakes because I assume some problems have no solution when they can be fixed easily. Unfortunately there’s not a whole lot I can do about that. I don’t and never will have the biological knowledge a degree gives you, but maybe one day I will at least feel comfortable in growing my little bone cells if nothing else.

So, after all that I suppose the pressing question would be, “Rachel! If interdisciplinary research can leave you feeling homeless in science and pulls you into unknown waters, why would you want to do it?” For me the answer is this; one, they’d pay me to do it and two (the real reason) I wanted to do something I felt might help people in the real world. I did physics as my undergraduate degree and when the time came to decide what I wanted to do with the rest of my life I was pretty sure of one thing. I didn’t want to do pure physics and be stuck doing something along the lines of looking at galactic dust (like Queen guitarist Brian May).But that’s not to say fundamental physics research doesn’t have an impact on our everyday lives. Medical scanners are better than ever due to work on particle detection at CERN. However, I wanted to be able to have the opportunity to do something with impact now and interdisciplinary research is where a lot of that work happens. I really wanted to do something medically minded and my course seemed like the perfect way to apply my physics to medicine. I definitely have that balance and fingers crossed my work will improve medicine, which feels great. However, the best thing about my PhD is that by doing so much biology I have realised just how much I love physics. After my degree I had lost that love and I needed fresh work, but a year of biology lectures made me realise that physics really was my passion. From this experience the key bit of advice I would give to anyone thinking about further study is don’t lose your conviction! You chose your A-levels, GCSEs or degree for a reason, so never lose sight of your reason or you might regret it, but never ever be afraid to push yourself out of your comfort zone either. You’ll be surprised what you can do. 

*For context, this is my original post which led to me being selected as  a Blogden Bloggie this year*