How to survive a PhD thesis

I recently completed my PhD thesis and though it was an exhausting process having a finished physical product in front of me is a very good feeling. It took me around five months to write and during that time I learned what works and what doesn’t and I thought I would share my advice in a blog post.

When starting with thesis writing I recommend beginning chronologically and doing a very thorough literature review for chapter 1. Your ability to review papers and summarise them will be much better than when you wrote a literature review in your first year. It will also help greatly with the discussion sections in subsequent chapters and will help drive the overarching themes of your work. It’s also important to remember that every University or College has particular guidelines on how a thesis should be presented. Make sure to find these early on so you don’t have any formatting nightmares a few months in.

The next tip is probably the most obvious but perhaps the easiest to forget; make incremental backups as often as possible while writing. It’s extremely easy to put this off and say you’ll do it tomorrow but a small amount of effort can avoid total disaster. On the day I was hoping to have a finished thesis to submit I added a few final figures to the document and then saved. When I then tried to reopen the file it had corrupted and couldn’t be opened. Fortunately I had a backup from two days previously, if I hadn’t it would have been crushing. It can be hard to pinpoint when the change that corrupted a file occurred, which is why making incremental backups is the safest option.

In general PhD students have a tendency to be perfectionists who find it hard to switch off. When you’re writing a document that has tens of thousands of words over several hundred pages these characteristics can be quite unhealthy. It’s important not to look at the thesis as a single whole, as this is a sure fire way to end up curled in a foetal position and sobbing. Instead set yourself realistic daily targets, such as completing a set of key diagrams, making notes on a certain number of papers or writing a few hundred words. Having a daily box to tick can be a big psychological boost.

During your PhD project there are several things you can do to make writing your thesis easier. Use lab books or notebooks to record all instrument/software parameters, experimental procedures and data as often as possible. If you have many books it’s a good idea to write the time span each book covers on the front so you can easily find a date you’re looking for. Many figures and tables can be prepared in advance but make sure to file them logically, with feedback from supervisors or reviewers it’s easy to end up with multiple versions of the same diagram. It’s also important to remember that a thesis is primarily a tool to get a PhD, getting a job afterwards and publishing papers is just as important. If you need to take a week out from writing to do a job application you shouldn’t feel guilty about doing so. Any manuscripts or papers you can prepare during your project will make thesis writing much easier as well.

Writing a PhD thesis can be a lonely and difficult process, make sure to not completely isolate yourself at your desk. Talking to family or friends, particularly those writing up themselves can be good for getting stuff off your chest. I also found it really helpful to have an escape, whether it was reading or a PS4, being able to switch your mind to something completely different for a couple of hours can be very refreshing. Never beat yourself up if you feel you haven’t done enough work and remember the ultimate goal, to be able to call yourself doctor and be all fancy.

Martian horror story

As it’s Halloween it felt appropriate to consider times when Mars has given us the heebie jeebies. For example, there are the stories the media goes nuts over, such as a spooky face or an alien lizard. However, for those capable of rational thought the real drama and fear lies in the challenge of sending missions to another world.

Imagine you are an engineer or planetary scientist and you’ve spent years developing and testing your instruments and the spacecraft they’re going to fly on. Your whole career may be hinging on strapping a billion dollar spacecraft to a giant rocket and firing it into deep space without it exploding, malfunctioning or missing your destination. Today NASA is pretty well practised at delivering landers and rovers to the surface of Mars without any major horror stories. In the Seventies it was a totally different story as no one had landed before, but observations from orbiting satellites showed lots of exciting features that suggested Mars had been an active world for a significant part of its history. Scientists knew that there weren’t advanced Martian civilisations on the planet but no one was sure whether there might be macroscopic or microscopic life present that could only be seen by visiting the surface

As with so many other firsts in space exploration the Soviet Union got to the surface of Mars before America. It’s from these Soviet missions that our horror story arises. After several failed attempts the twin probes Mars 2 and Mars 3 reached Mars in late 1971. Mars 2 was the first to enter the atmosphere and promptly malfunctioned and crashed, but it still became the first man made object to land on Mars. Mars 3 went one better and achieved the first ever soft landing. The joy and relief for those behind the mission must have been immense. To be the first team to land a spacecraft successfully on Mars is an incredible achievement. Mars 3 began to collect data but then everything stopped working…after 20 seconds. All the potential success and science that had seemed so close was suddenly wiped out. The lander had begun to return an image but there was not enough time for the first photo ever taken on Mars to be sent back. Instead that honour would go to the American Viking 1 lander in 1976.

Working in space science is a tough business and you need to be prepared for your life’s work to explode or fail in a very public way. If you happen to be around a scientist or engineer when their mission is flying make sure to offer them the drinks, cake or hugs that they will sorely need.

One step closer to discovering life on Mars

Yesterday NASA revealed that it has found evidence for present day liquid water on Mars. In this blog post I’ll explain how they made this discovery, why it is significant and what it means for the search for life on our neighbouring planet. NASA’s announcements about water on the martian surface are sometimes met with cynicism as it can seem like it’s constantly being repeated that water is being found on the red planet. However, liquid water is the key requirement for life as we know it, so any discovery that informs about water in the past or present on Mars is hugely significant. Previous discoveries have revealed much about the role of water in Mars’ past, such as the presence of rivers, lakes and potentially an ocean. It has also been found that in the present day water is stored in subsurface ice or in minerals that have water in their chemical structure, as well as in Mars’ tiny polar ice caps.

The hugely exciting discovery of present day liquid water on Mars was made using an orbiting spacecraft called Mars Reconnaissance Orbiter, or MRO for short. MRO is a long lived mission that has been analysing the martian surface since 2006. Two key instruments on board MRO are the High Resolution Imaging Science Experiment (HiRISE) and the Compact Reconnaissance Imaging Spectrometer for Mars (CRISM). HiRISE has sent back thousands of incredibly detailed images of the martian surface and you can see the photo catalogue here, which is being constantly updated. While HiRISE’s role is to photograph features as small as a metre across, the job of CRISM is to analyse how the martian surface interacts with visible and infrared light as this can inform about the mineralogy of the rocks being imaged.

The discovery of liquid water on Mars was made by instruments on Mars Reconnaissance Orbiter (MRO), shown here in an artist’s impression. Image by NASA.

Should the PhD thesis still exist in the 21st Century?

There is one thing that a PhD student fears more than their research failing, exploding or becoming sentient and that is the oncoming dread of having to write up several years of hard work into a thesis at the end of their project. In the UK, where I’m based, a PhD thesis typically consists of 40,000 to 100,000 words describing the research area, methods and results. I’m approaching the end of writing mine and it’s been a particularly gruelling experience.

I’m writing this blog to consider if there is an alternative way to assess PhD students after completing their research. I’ve spoken to a lot of academics about thesis writing and I’ve heard it described as outdated and Victorian but also as the only effective way to assess how much work a student has done and a necessary evil that makes achieving a doctorate suitably challenging. Once written and submitted the thesis is typically assessed by an interview with examiners, known as a viva. I’ve attached two poll questions to this blog post as I thought it would be interesting to see where people’s opinions lie and whether a thesis should be viewed as the gold standard of PhD assessment or whether alternatives should be considered.

Being in the middle of the writing process my opinion is somewhat biased but I feel the thesis is unnecessary and somewhat damaging to PhD students in the 21^st century. The career market for new doctors is now highly competitive and some of the best weapons you can have in your arsenal while job hunting are published papers. Published work demonstrates an ability to research novel ideas and communicate them effectively. Job hunting itself is often a stressful and demanding experience and it can be hard to find the energy when you’re writing 1,000+ words for your thesis every day.

Published papers that have been through the hurdles of peer review are far more useful to science than a PhD thesis as the latter has not been as rigorously examined. If a PhD student could dedicate more time to paper writing I feel it would lead to more publications and important data reaching a wider audience. Like many things in academia I feel we are living in a system that is outdated and hurts both PhD students and the communication of scientific research. Though many institutions are considering alternatives, for now thesis writing remains the standard method to assess a PhD student. In my opinion a system that is more suited to the nature of modern academic life needs to be brought in as soon as possible. Getting a doctorate should still be an immense challenge but the output should be papers and presentations that benefit science and the student and not a lengthy tome that exists merely to pass an examination

Mars and Pluto: Exploring old and new horizons

Next month the New Horizons mission will make its closest pass to Pluto and its moons and send back images and data that will revolutionise our understanding of some of the most distant members of our solar system. This is a hugely exciting time to be a fan of space exploration and I thought for this month’s blog it would be interesting to revisit the era when space flight was in its relative infancy and the first missions travelled to Mars.

Pluto and its moon Charon imaged on June 29th as New Horizons moves ever closer to the distant world. Credit: NASA/Johns Hopkins University Applied Physics Laboratory/Southwest Research Institute

Radiation and Mars: Don’t forget the sun cream

The most obvious difference between the Earth and Mars is that Earth is almost double the size of its neighbour. Mars’ small size meant it cooled more rapidly and the liquid iron in its core eventually solidified, resulting in the planet’s protective magnetic field being lost. Energetic particle radiation from the Sun, the galaxy and beyond was no longer deflected and controlled by a magnetosphere. As a result Mars lost a great deal of its atmosphere, which made it even easier for radiation, particularly ultraviolet radiation, to reach the surface.

The present day surface of Mars is bombarded with ultraviolet radiation and energetic particles from the Sun and Universe that would greatly affect any living creatures present on the planet.

10 photos that tell the story of Mars exploration

1. Holy gigapixels!

Curiosity rover in Gale Crater. Via 360cities.net

This is technically cheating as following this link takes you to several gigapixel images of Mars that you can zoom and pan around, but they’re so amazing hopefully you can forgive me. These incredibly detailed images from the martian surface reveal the landscape and geology of the planet to a resolution that would have been unimaginable to previous generations of researchers. They reveal distinctive landforms that tell us about the history of the planet and its potential to have hosted life in the past. Imaging allows Curiosity to study its route and for the science team to locate points of interest that the rover can then use its other instruments to study. It is inevitable that not every point of interest can be visited but having such good photos means a lot of analysis can still be done. In the years and decades to come images and data from Curiosity rover will still be used for new scientific discoveries.

Nitrate and the search for life on Mars

In order to understand if life ever existed on Mars we need to not only look for evidence of possible ancient Martian organisms but also try and understand if there were ever environments on ancient Mars that would have been habitable for life. If Mars had existed as an extremely dry cold desert for its entire history then the chance of finding any evidence of living organisms would be extremely low. Fortunately exploration of the red planet has revealed that ancient Mars was dramatically different from the present day with evidence of flowing water and lakebeds forming in neutral benign waters.

The next step is to see if the chemistry that supports living organisms also existed. One of the most important elements for life is nitrogen as it is part of the structure of DNA and proteins. Nitrogen exists in the atmosphere in the chemical form N₂, a molecule that has an extremely strong chemical bond that has to be broken before living organisms can incorporate it into biomolecules. This process is known as fixation and on Earth it is done primarily by nitrogen fixing organisms. It can also occur during volcanism, asteroid and comet impacts, or through lightning strikes. N₂ is transformed into molecules such as ammonia (NH₃) and nitrate (NO₃).

The nitrogen cycle as it operates on Earth. (Image credit: http://tygae.weebly.com/nitrogen-cycle.html)

The Quest for Life on Mars

Mars has always been at the forefront of our imaginations when we picture alien life and the discoveries planetary science has made in recent decades reveal that the idea of our neighbouring world having once been inhabited is not so far-fetched. Mars appears to have once been a habitable world, the question is did life ever exist there? This is one of the questions that Curiosity Rover is attempting to shed more light on but results so far have been inconclusive. One potential problem is that the mineralogy of Mars might seriously disrupt experiments looking for evidence of ancient microscopic Martians. Chlorine salts have already been proven to be problematic and in research, published online today, and summarised in the following article I have shown that a salt containing iron, sulfur and oxygen, known as jarosite, can also be added to the list of problematic minerals for life detection experiments.

The satellites, landers and rovers sent to Mars have started to unravel many of the mysteries of the red planet. Perhaps their most exciting discovery is that ancient Mars may have been a habitable environment for life. The Martian surface at present is extremely cold, exceptionally dry and bombarded by ultraviolet radiation. The atmosphere is at such a low pressure that liquid water would instantly vaporise. However, characteristic landforms and the presence of minerals that we know only form in water have revealed that ancient Mars had persistent surface or near surface liquid water. The presence of liquid water is exciting because it is a precursor for life and for it to persist on the surface would require a warmer thicker atmosphere.

Eberswalde Delta on Mars, evidence for an ancient persistent flow of water over an extended period of time on the Martian surface. Image Credit: NASA/JPL/MSSS.

Curiosity Rover and the mysterious Martian methane

In December exciting new data, including two new papers, from the Curiosity Rover team were released. The update focussed mainly on the detection of methane and other organic compounds by the rover. I’ll cover the other compounds in a more comprehensive post in February but in this article I’ll focus on methane and its importance in trying to understand Mars.

Methane is an exciting compound to detect because on Earth the primary source of this simple molecule is life. However, methane can also be produced by non-biological processes. Regular impacts from asteroids, comets and interplanetary dust particles are known to add organic compounds to the Martian surface. The atmosphere of Mars offers no protection from ultraviolet radiation and the breakdown of these organics by UV could cause methane release. In addition, reactions between water, certain minerals and dissolved carbon dioxide can produce methane. Ice can trap methane in its structure, store it and then release it upon melting, with ice at depth capable of being stable for billions of years. Therefore, if we detect methane on Mars it is indicative of some sort of active process occurring on the planet, whether it be biological, the melting of ice, water-rock reactions, volcanic activity, or as simple as degradation of meteoritic organic compounds by UV radiation. Life would certainly be the most exciting candidate on the list but the detection of methane does not necessarily mean the detection of life.

Could microorganisms like the methane generating bacteria we find on Earth exist on Mars? Image from New Energy and fuel