Hello again,
I decided to make a short film of the main ideas behind my Ph.D. research, and to display some of the videos I have recorded over the past couple of years.
Sadly I cannot put any data/graphics up due to potential issues with publishing in future, so for now you’ll just have to be content with the back-flipping dog (you’ll see).
Video is also set to music under creative commons licence and is best viewed in HD to see the detail.
Until next time đ
Over the course of my Ph.D. I have had the chance to experiment with different ideas related in some way to my field. Some of these ideas do not fit well into the ‘scientific story’ that will eventually become my thesis, however the ideas are still simmering away on the back burner, and will hopefully develop in future.
High-Speed Camera Fun!
My Ph.D. focuses on how phytoplankton swim in a range of environmental conditions. The best way I can describe what these cells look like is to imagine a grape with 4 whiskers sticking out the top…
These ‘whiskers’ are called flagella and are what the phytoplankter use to swim. The flagella themselves are tiny, measuring only 8”m long (about 1/10th of the width of a human hair) andbeat 65 times a second (for reference, Hummingbirds beat their wings at 70x second).
To record the rapid movement of the flagella, we attached a high-speed camera (very carefully I might add, it costs the same as a new BMW 3 series!!) to our Zeiss inverted microscope. The camera itself can achieve a frame rate of around 70,000 frames per second (fps) (the camera on your phone probably records at 30fps); however this speed far exceeded our requirements…but we still had to have fun with it!
Below is a video we recorded at 6400 fps of a falling water droplet. Best viewed in HD and full screen!
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Let there be light!
Since I had room in the orbital shaker, I acquired some bio-luminescent phytoplankton (Pyrocystis fusiformis) as a cool pet to have. These cells respond to turbulent water movement by lighting up, and at certain times of the year on the California coast appear in large algae blooms, creating a breathtaking lightshow at night (Search “Red Tide – Bioluminesence” on Youtube, its like something out of Avatar!).
Test-tube babies! How to grow Seaweed in a Petri-dish
Continuing on the theme of ‘small things swimming’, I became interested in the reproductive cycle of Fucus species of seaweed. Fucus is the stereotypical seaweed that you imagine on British Shores. Long, brown-green plants that drape over the rocky-shore and sometimes make a popping noise as you step on their gas bladders.
Something that not many people consider is how seaweed reproduce. They cannot do it in the same way terrestrial plants do as there are no pollinators in the sea. Instead, male Fucus release tiny swimming sperm into the water (usually coinciding with a full or new moon) that locate an egg using a rudimentary eye…yes, you heard me right – seaweed release sperm that can see! Seaweed sperm have a simple eyespot which (it is thought) allows them to detect light from the moon; and as the eggs are negatively buoyant (posh word for ‘sink’), the sperm swim down and away from the moonlight to locate the female egg. To this day this fact still blows my mind (probably much to the annoyance of the 1st years I help teach shoreline ecology to).
So, I was interested in how temperature (and subsequently, viscosity) effect reproductive success of these plants. Below is an image of Fucus conceptacles – little sacks that either contain 8 female eggs or 64 sperm cells (in this case they are all male).
After some special treatment (which may or may not have involved Candles and a Barry White CD), the sperm and eggs were collected and mixed together in Petri dishes. Below is a video I took once the sperm and eggs were mixed. The egg is rotating due to the sperm trying to burrow into the egg.
After 10 days, the fertilized eggs became rhizomes – tiny little baby seaweed!
And after a while I soon ran out of space as they young plants filled their petri dishes. Sadly, I cannot find the pictures I took of this (I know my supervisor will shake his head reading this), so I have borrowed one from Lena Katuskys group at the University of Stockholm).
Until next time đ
Iâve been a bit quiet on the Blog front for a few months… and some of those based in the Joseph Banks Laboratories may have noticed that my chair has also being empty for some time. I want to talk about something that many people, including myself, often have real issues discussing â mental health. Until we can discuss mental health in the same way we can any other disease or illness it shall remain a problem. I want to try and be as open as I can about this, and try to share both the difficulties I have experienced and the solutions I have found so that other graduate students who are either currently experiencing or have previously experienced these feelings, will not feel as isolated. Rather than solely preach my own advice, I have also asked other veterans of Grad School (both at Lincoln and at other institutions worldwide) to share there own experiences and advice.
Physical Illness
Mental Illness
Firstly, you are not alone:
During my undergraduate years and probably through to my 2nd Year of my Ph.D., I viewed academics as stoics that were the masters of their minds and are able to battle all stressors related to their work. Manuscript submission? No problem! Conference presentation? Easy! Grant proposals? Done! Although some supervisors might disagree, academics are not immortal gods, nor Superheroes immune to human emotions. The stressors that apply to Ph.D. students still apply to them, although the amplitude of this anxiety may be more controlled through years of experience.
I started googling âMental Health in Academiaâ in the hope of inspiration and re-assurance that I wasnât alone. Expecting one or two success stories of scientists overcoming their mental health disorders to âmake-itâ in academia, I was astounded by just how rampant depression and anxiety is in academia. A recent Australian study found that the rate of mental illness in academia was three to four times higher than in the general population; and (in one of the very few studies conducted in this field) that up to 53% of academics in the UK suffer from mental illness (Kinman, 2010). There is an on-going argument akin to the classic âNature vs Nurtureâ debate in biology as to why there is a higher rate of mental distress in academia than in the other careers; questioning if a career in academia has a detrimental impact on our mental health, or if an academic lifestyle attracts those more susceptible to mental health disorders.
To paraphrase the famous quote âLook at the academic to your left, look at the academic to your right â it is likely that one of the two has experienced mental distressâ.
For the new breed…
I hope this is not too much of a broad generalisation, but chances are if you made it to graduate school you did well at college and undergraduate level. At these institutes, your work would have been graded and you would have known exactly where you stand against your previous work and the work of others. You would continually assess how you measure up to your peers. This doesn’t work at post-graduate level for the simple reason that no two people are working on exactly the same assignment.
You would also be used to submitting a piece of work, have it graded, and then never look at it again. This too is a thing of the past in graduate school. Work WILL be handed back to you plastered in corrections, and it will most likely be soul destroying. Please please understand, this is not a reflection on your ability to create great work, this is just part of the process in graduate school, the continual polishing of a piece of work.
You will (and I can pretty much guarantee this) see how much work your peers have done, or how well their experiments are going and feel to some extent that you are failing or not good enough to do an MSc/PhD.; a thought process that often leads to “Impostor syndrome” (feeling like an impostor that has almost mistakenly been accepted into graduate school that are not smart enough to complete their course). Any seasoned member of Grad School knows and understands the dismay that the impostor syndrome can cause. I was recently at the Nature Careers Expo in London where there was a Q&A about life in academia, with questions directed to a panel of renowned scientists. One student rose her hand and expressed her difficulties accepting that she was good enough to complete her Ph.D., and asked the panel at what point their feelings of being an impostor dissipated. A Professor from Oxford immediately stated “It hasn’t”, followed by a chorus of nods from the rest of the panel. The intention of this previous point is not to frighten readers that impostor syndrome is incurable, but rather that your scientific idols likely experience the same thoughts and fears as you.
My final point to the newcomers, take time off for yourself! In my fist year of my Ph.D. I worked ridiculous hours. 7am-10pm Monday – Saturday, with a half day on Sunday. Did I have to? No, but I felt like I needed to impress everyone and prove my worth. However, working with this level of intensity is counter-productive as you will make mistakes (admittedly, sometimes expensive ones!). Burning out is a real issue that all grad students deal with at some point, where they feel guilty for taking time off for themselves, despite their body and mind screaming for a break. Graduate school truly is a marathon, not a sprint. It takes time to find your pace at which you are most efficient (I personally still struggle with this), however sprinting to the point of exhaustion is not the answer.
A trip to a science museum (or for me, as a Marine Biologist, going rockpooling) is a great compromise to the struggle between work and play; allowing your brain to slow while keeping the “I should be working” demons at bay.
Grad Students to the Rescue!
I’ve asked a number of graduate students and academics from around the world (God Bless Reddit!!) what advice they would give to graduate students who are experiencing mental distress in the workplace. Below are some of the gems of knowledge I’ve received.
“This is where effective time management skills will shine, especially if some days are worse for you than others. Second, identify an activity you enjoy doing and be sure and always make time for that thing no matter what.”
“My biggest surprise was how common it is for graduate students to be affected by anxiety and depression. I finally had a candid conversation with fellow students, and we were ALL on some kind of anti-depressant or anti-anxiety medication. I believe there were five of us talking about it. I was shocked. And I felt so relieved because it made me feel “normal.” “
“Don’t be afraid to use your school’s mental health services. A lot of people in the outside world would kill to have access to free counselling and psychiatry. Your school wants you to succeed so they’re there to help!”
“After an incredibly rough first year as a doc student – the only one in my cohort with no research experience – discovering Impostor Syndrome was a lifesaver (probably not literally but I was pretty depressed so who knows). The vast majority of academics are all dealing with the same anxieties, doubts, etc.”
“Remember, that you are not a fully fledged scientist. You are training to be a scientist. Things will go wrong, break, and not work out – just remember you are still learning!”
“Talk to your supervisor/PI if you are struggling, or at least one of the Post-Docs. Its likely they have either dealt with anxiety/depression, or helped those with it. You are not the first, and won’t be the last to ask for help”
“If you’re comfortable with them, be open with your advisor about things your going through and what you know helps you or ways they can support you. They might have gone through some difficult times themselves when they were students.
I’ve witnessed some really awesome advisors be there for their student, advocating for them and being their biggest supporter. But they can’t help you if they don’t know your situation.
Having anxiety and being depressed is still stigmatized, but the only way we’re going to change that is if we take steps to help each other and make a more accepting work environment”
“I think this is actually a pretty big issue that people don’t talk about. I’m glad you hear you’re trying to start a conversation about it. Ultimately I think there are certain things about the culture of graduate school that amplify insecurities and anxieties. It’s important that we try to change them, but in the short term it’s important just to recognize it and remove the stigma surrounding mental health disorders.”
I hope someone out there has gained some comfort from this post. If you have any advice you wish to share, I am happy to add it to this post. If anyone is struggling out there and wants to talk, or just fancies a coffee and a chat about the world – please feel free to email me: jsage@lincoln.ac.uk
You can do this đ
Conference presentations. A confusing cocktail of mixed emotions for any Ph.D student. The excitement of travelling to a different country to hear talks first hand from the âsuperstarsâ of your fieldâŠcoupled with the fear of presenting something youâve poured your heart and soul into in front of the same peers.
In January I travelled to Aspen, Colorado with my entire lab group for the âMicroscale Interactions in Aquatic Environmentsâ. A 5 day conference with 100 or so researchers discussing the interdisciplinary field of marine biology and microscale physics. Beautiful scenery, an amazing hotel and fantastic company. I had attended the previous event held in the French Alps back in 2013 so it was great to see old friends again and have a good catch up. I think my favourite thing about these small meetings is that you are able to talk to other researchers multiple times and after a few days you begin to get a real feel of community for your scientific niche.
Practice, Practice, Practice
The âdark sideâ of this trip was that I was giving my first conference presentation and it was scheduled for 9am on the very last day of the meeting; and although there was plenty of allotted time to ârelaxâ, most of mine was spent refining my presentation. Luckily, other Ph.D. students were in the same situation as me and were equally nervous. We banded together and found time to present our talks to each other, answer potential questions that may be asked by our peers, and test our talks out on the big stage.
I arrived early on the day of my talk, stood on the stage and repeated my talk as many times as I could before people began to trickle into the auditorium around 8. Then the hour was upon me, the first few words out of my mouth were somewhat croaky and I could hear my heart beating in my ears, but then everything settled down, I was calm, confidentâŠand perhaps most importantly, I was having fun! After answering a round of questions, I sat down and dealt with a different cocktail of emotions â exhaustion and happiness. I now had about 10 hours to enjoy the sights and sounds of Aspen fully. A trip on a ski lift to the top of a mountain to enjoy breathtaking views and a well-earned dram of whiskey. Lovely.
View from the top of Mount Aspen
The Big One: ASLO 2015
A little over a month after returning from Aspen, I was packing my bags again for another conference; however this one was going to be very different. ASLO (Association for the Sciences of Limnology and Oceanography) 2015 Aquatic Sciences Meeting in the ancient city of Granada, Spain. This conference boasted 2500 participants from 64 countries, a mammoth-sized meeting in comparison to Aspen with up to 20 concurrent sessions occurring at the same time. You have to have a different mind-set for these conferences. You simply cannot be in 20 places at once and these sessions are held in rooms spread across multiple floors and multiple corridors. In short, imagine rushing through an airport to make to your connecting flightâŠmultiple times a day⊠and youâll get a pretty good idea about what a day at an international conference is like. Naturally with a conference of this scale, itâs difficult to meet and talk to people. You often see a friend or peer once and then not see them again for the rest of the conference.
I was scheduled to give a talk midway through the meeting in the âLife at Small Scale: Microscale insights into Aquatic Systemsâ session. The talk was to be mostly the same talk as I gave in Aspen (I couldnât get much data collection and analysis done in a month đ ), however the experience for preparing for the talk was very different. Presentations had to be uploaded to the conference server 24hrs beforehand, videos could not be checked to make sure they work (a big deal for anyone who uses media files in their presentations), and the luxury of practising on the big screen was relegated to a small laptop in a hotel room.
Again, I arrived early on the day of the talk and practised in a secluded hallway. I was fitted with a microphone headset and had to race between the two small screens (rather than the single âcinema-sizedâ one at Aspen). Behind me, a panel of three of my peers; and in front a sea of unfamiliar faces, some of which either entered or exited the talk midway through (Do not take offence if this happens to you, it is common at these big conferences!). The talk itself went well – maybe not as refined or smooth as Aspen, but still more than good enough!
One of the top experiences of the conference was the academic âspeed-datingâ session. A cluster of 15 or so round tables full of young and old academics alike, where participants had seven minutes to briefly explain who they were and what their research interests were. You would think that repeating your âspielâ (the parrot fashion script that every academic has up their sleeve when asked âwhat do you doâ) would get old pretty quick, but it was a fantastic way to practice and refine this vital academic social skill. More importantly, I made several contacts, both for myself and others in the lab; and received a real confidence boost when people said my work would really help explain some of the unknowns in their own research.
Authentic Flamenco – Perfect way to relax after giving a talk
SoâŠwhich is better.
Each conference had their merits and I gained a huge amount of knowledge about my science and myself from both experiences. However for me, the smaller and more intimate conference at Aspen was much more enriching and enjoyable. I could discuss at length and across multiple days the details of mine and others research; and build relationships on a personal level my peers. So for me, Aspen is the clear winner…and I would attend another small conference in a heartbeat.
After the chilly trip to Scarborough last week I had just enough time to warm up and don my ‘Civvies’ ready for the trip down to Colchester for the 3 day NERC run ‘Fluorescent Microscopy for Environmental Research course at the University of Essex. I had a basic understanding of what fluorescent microscopy was and how it is used in biology, but my knowledge probably extended to just a few sentences worth of loosely accurate info. I had read papers and seen images of how fluorescent microscopy is used with phytoplankton, and being that all of my data is collated from images I was intrigued to see if I could employ it in my research.
If this course is repeated next Autumn, you really MUST sign up for it! I was blown away by the depth of knowledge of not only the instructors and technicians, but the 15 other Ph.D. students and researchers present. The course itself was presented in a way that covered all bases, from simple questions you may have been afraid to ask (on par with ‘What is a pixel’?) to the very forefront of current bioimaging technology. Following each 2hr lecture was a 2-3hr practical where we got to see first hand  how the methods we had just learnt about are used, not to mention play with some shiny (read expensive) equipment from Nikon. I was constantly learning new techniques in the lectures, the lab and at the evening meals where everybody had a particular skillset to bring to the table.
As for fluorescent microscopy applied to my research – well it seems that my swimming organisms are too small and fast to be recorded under fluorescence in a way that would provide me with useful information…although the technology to do this is constantly being updated.  Thanks to the expertise of Phillipe Laissiue (http://www.essex.ac.uk/bs/staff/profile.aspx?ID=1205) and Boguslaw Obara (https://www.dur.ac.uk/research/directory/staff/?mode=staff&id=10591), and that of other students, I have come away with exciting ideas on how to optimise my current research and now have a head full of fascinating ideas of how to overcome bioimaging problems in the future.
The images below were taken on the course by Bex Summerfield (NHM – London). They display a new species of parasitic copepod (blue sphere) on a polychaete host (from the genus Jasmineira), fixed in 70% ethanol, mounted in vector shield in a glass bottomed petri dish and scanned with Nikon Ti CLSM. The detail is simply mind-blowing!
 