36 weeks til thesis

Yet again… I manage to be a week behind in posting. I’m still finding my rhythm for 2016 and currently feel a bit behind the beat ūüė¶

Ways I’m trying to address this:

  • Committing to¬†physical activity at least three times a week, for at least half an hour per session – for mental and physical health, but also to help wear me out so I sleep better.
  • Treating myself better with how¬†I choose to fuel my body – eating and drinking with health and nutrition at the forefront of my thinking, instead of the instinctual “I’m so freaking tired and time-poor, just gimme a double strength ice break and a tub of potato gems with gravy” standard lunch that was not helping my waistline (as a¬†CVD risk factor), blood pressure, digestion, or anaemia at all! It was a vicious cycle. I wasn’t setting myself up for success at all. I now have the energy to stop and question those cravings instead of blindly following my first instinct, and I feel so much better for it.
  • Sticking to my Gantt chart – breaking those larger tasks down into manageable pieces for each day of the week and physically ticking them off the To Do list. I see progress on a daily basis because of that system which in turn encourages me and spurs me on for the next task.

Yoga and reading in the sunshine, a chicken stir fry with tonnes of fresh greens, and my To Do List for Week 36 – these are all on equal footings in my revised priorities for 2016 and beyond

I’m now considering blocking time for different tasks throughout the week. I’ve been hesitant to do this in the past, because unlike high school or uni with the same class times from week to week, each week of a¬†PhD requires different things of me. Some weeks will be very lab intensive; I’ll only leave the lab¬†to print results¬†or eat. Other weeks are very literature (lit) heavy, with hardcore thinking and critical analysis of my and other’s work consuming¬†all my energy and concentration.

There are some things that I would like to do on a weekly basis though, that occur no matter what kind of week I’m having; taking time to tend to¬†my herb garden, lose myself in the therapeutic mindlessness (or mindfulness) and creative beauty of crochet, and reflecting on the week for this blog. But as yet, I have no set day of the week to do these things. Even if it’s only blocking out time in my evenings, leaving the days free for lit or lab work as required, I think it could help to have some routine around which night holds which activity.¬†Yes! We’ll see how that goes ūüôā

My baby basil and latest crochet creation


As for this week’s lab work… I learned how to use the fluorescence microscope and took a bunch of cool pictures comparing different preparations of my silk isolate (middle and bottom rows) to the background level of fluorescence from the plastic backing (top row).

So preeeetty!


I harvested my expanded cell line and froze down 12 million Рthat should be enough for all of the experiments I want to set up from here on out. Woohoo!!

AAAALL of the cells!

And last but not least, I created a template for the form of my research paper based on the Instructions to Authors set out by¬†my target journal. I’m filling it in bit by bit now as I chip away at writing up the story to accompany the figures I presented to my supervisors last week.


37 weeks til thesis

A far less eventful week than usual – so a shorter post than usual.

I finalised my figures for the paper on my new isolation method, complete with statistical analyses, and sent them off to my supervisors requesting a meeting at the end of the week to discuss them. Then¬†I set out to find a conference or two to attend and present my work-in-progress-paper (once it’s finished). That was a rabbit hole and half!

My project straddles two research areas: biomaterials and retinal degeneration (particularly macular degeneration). There are SO many societies and associations and institutes, all around the world, that hold their own conferences on biomaterials, let alone including all the eye research conferences too! Needless to say, I am spoiled for choice and currently short-listing a collection of about a dozen conferences covering the retinal/biomaterial realm. I took this short-list to the meeting for feedback, too. Supervisors have (you would hope!) travelled the world attending conferences in your area, so why not get their opinion on which ones are most worthwhile!

The university offers travel grants to enable graduate students like me to fly to cool new places and represent our research groups on the world stage. These grants have rounds, like any other grant, and the sooner I know what my travel, accommodation, and attendance fees will be, the sooner I can apply for the grant. Proper prior planning is applicable, yet again!

I love flying. If only it was always this smooth! (via giphy)

I am obviously only looking at conferences that align with my research, but within those options I am particularly interested in meetings that strive to include women on their expert discussion panels (I chose not to support manels Рall male panels Рwhen non-male experts exist in the field but have not been included), and especially those that have networking, forums, activities or workshops specifically dedicated to the development and furthering of new talent (read: PhD students and early career researchers). To my delight, I found several that fit my criteria. They are now at the top of my list and if my supervisors agree that one of them is best to attend I will be beyond stoked. USA, Japan, China, and Taiwan are in the running, with several European cities in the next tier.

The timing of some of these meetings is also fantastic. Two are within the final three weeks before my thesis due date so by that point I SHOULD just be doing final copy editing and proofreading for the Discussion and Conclusion sections. It should all be written, and it will just be a matter of going over it with fine-tooth comb. The other bonus is that these conferences are just a hop, skip and a jump away in Japan so the jet lag between time zones should be quite manageable and not put too much extra pressure on my deadlines. Besides, being in plane for 12+ hours each way is pretty great distraction-free proofreading time!

giphy (6)
Fast forward a few days… (via giphy)

The supervisory meeting has come and gone and all we got to talk about were the figures for my upcoming paper. I approached one of my supervisors later that day with some more targeted questions regarding the cells, methods, and controls for Aim 3 that I will be planning out in more detail in the coming months. Between those two meetings, I managed to get just about everything I needed from my supervisors for that week. The narrow focus of the main meeting also meant that I had more time to investigate the details of the student travel grants Рthey are even larger than I thought, so I have less restrictions on which one I attend than what I was allowing for. Win!

With the new grant info, I have decided to further short-list the conference options I found and present a much smaller list to my supervisors, including my main reasons for wanting to attend each one. I will then take on board any input my supervisors have regarding their experience of these particular meetings, especially if I have omitted any that they think would be a particularly good fit for my work. I’m trying to do as much of the thinking and leg-work for them as possible so that they aren’t having to add that onto their To Do List. It also allows me to have more of a say in how things happen, which is a bonus.

Manage your supervisors, and all that!

38 weeks til thesis

Well, the start of this week was a bit of a let down.¬†It’s ok.¬†It happens…¬†Then it was a nice big high and it all worked out fine in the end.¬†Rollercoaster week – aka week 38 til thesis.

The Low Point: Despite completing the data collection for Aim 1 (woot!), I feel like I didn’t quite do what I set out to do.¬†After all the preparations of last week, the twenty two repeats, the waiting three days for freeze-drying – the final bit of data I was working on ended up being irrelevant. *sigh*

I was planning on comparing the solubility of the freeze-dried powders in water. I had done a cursory version of this investigation previously and was really excited by the results, so I¬†had a fair idea of what to expect. But when it came to weighing out three sets of ~20mg of jumpy, statically-charged powder into 2mL tubes, for 20 different samples… lets just say, the set up took a LOT longer than I thought it would.

The plan – based, as always, on a published protocol – was to gradually add high purity water (solvent) to the known weight of powder (solute), mixing between each addition, until such a concentration was reached whereby all the solute was dissolved and the solution was transparent.

The alternative method is to have a known volume of solvent, and gradually add more solute until the solution is saturated and cannot dissolve any more. At this point, you would re-weigh the solution¬†and work out the exact weight that was added, and from that you can work out final concentration. Can you imagine trying to get tiny amounts of statically charged powder into a small container that is already wet, so that if you add too much, there’s no going back… Well, that’s why I decided against that method…

So, with great anticipation, I added the first aliquot of water to my first sample and mixed.

It gelled ūüėź

giphy (5)
#accurate (via giphy)

It was starting out at the highest concentration, too high to maintain solution and instead formed such a thick gel¬†that I could not draw it up in my pipette. It was 50% w/vol, so this wasn’t too surprising. The downside was that, once it gelled, I couldn’t add any more water to it.


I would have to add a larger initial volume of water. It worked! I was cheering and seat-dancing (I’m sure you know what I mean!), tilting the liquid side to side to watch it run around the curve of the tube – until it stopped moving and I was faced with gel again. It seemed no matter how much water I added, what was initially a glorious golden solution would end up gelling. I even took one sample down to 5% and it formed a sol instead of a gel – which is better, but¬†not much better. I got my hopes up so high then was devastated.

Top: the powder takes the shape of its container during freezedrying. Bottom: the golden liquid that induced seat-dancing… until it gelled.

From my initial solubility investigation, this was supposed to my most soluble version. And it was not playing ball. What was I doing wrong?

Like a good little PhD student, I went and unloaded my worries… I mean… chatted to my supervisor about it. He reminded me that in my preliminary cell¬†experiments I had managed to make low (‚ȧ2%) concentration solutions just fine. He asked “What do you really need it (the solubility) to be for your intended purpose?” (Read: does it even matter that you can’t make high concentration solutions with this powder? What do the cells respond to best?)

This sparked a memory filed way WAY back in the vault. In first year, I had read the stats for a commercial preparation of a similar¬†silk compound to the one¬†I’m targeting, and they had only used concentrations¬†up to 0.3%¬†on cells. The solutions¬†I had managed to make for my preliminary cell¬†experiments¬†were at least five¬†times that dose!

I was assuming that the solubility had to be amazingly high to be valuable and useful. That’s what I was doing wrong!

The High Point: I was actually doing great ūüėÄ I had just forgotten where my goalposts were, got disoriented and disappointed. I got so caught up in ‘maximising’, ‘optimising’, ‘comparing’ and having to be ‘better than’, ‘bigger than’, ‘greater than’ the current alternatives. I forgot that at the heart of this investigation¬†were some really basic needs I was aiming to meet: 1) the needs of my intended application for this compound, and 2) the need to keep moving forward with the rest of my experiments (finishing Aims 2 and 3). The low concentrations I had already managed to make were¬†all I really needed. Finding the exact maximum¬†solubility for each sample was irrelevant for my application. Cool to have – for sure! – but not essential, especially since my PhD is in the School of Medicine and not Protein Chemistry. So I am now doing something very much outside of my character and cutting and running, leaving Aim 1 far behind me.

I feel so much better now that I’ve gotten used to the idea that my data is complete as it is. It really bugged me at first – that I didn’t get solubility data at n=5 after all the time and effort I had put into prepping samples for it – but in the end, I have all¬†I need to write my first paper.

And that’s what counts.

Aim 1 is DONE!

It’s happy dance o’clock! (via giphy)

Plus, the remaining powder I had made for (the now unnecessary) solubility testing can be used in Aim 2 instead, saving me some serious prep time.

So, double WIN!

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I am approximately  ^this^  happy right now (via giphy)

Now, to write it all up and submit to a journal for peer review and – hopefully! – publication ūüėÄ

N.B. I was posting 1-2 weeks in arrears until now. So there will be a several¬†posts within a few days of each other, but all will be up to date from now on. It was getting too confusing looking at the correct current week for my Gannt chart, and then writing about the previous week on here as though it was currently happening, then planning ahead for the next week’s work and blog post, and switching between the different frames of reference.

Keep it simple. Keep it moving. Make it happen. ūüôā

39 weeks til thesis

Aim 1 is so very nearly done!

IMG_20160113_175239Week 39 as a photo collage L to R, top to bottom: chopping cocoons all the way through to freezing the final solution.





Repeatability is everything in science.

An effect may be observed Рgreat! Рbut it means nothing unless measured in separate trials and those measurements are NOT found to be significantly different when compared by statistical analysis. Usually, the bare minimum to be able to compare is three repeats, or n=3. The more repeats, the more robust your statistics, the stronger the evidence for your claim of the effect you observed.

I am writing my first journal article to come out of my PhD research. In it, I will propose a new method for the preparation of certain silk components¬†for the benefit and use of others in my field (more details once I’m published ūüėČ ). This week, I set out to prepare the materials for the final bit of data I need: the yield – how much of my target compounds does my new method isolate? (And how long should the method run to maximise yield?)

As this paper will describe a newly devised method, I need to be extra sure that my claims of advantage over previous methods are correct, so I prepared enough samples to achieve n=5. I had to perform two additional repeats of the one of the test conditions due to timing errors allowing the sample to cool too much. Those samples had started to gel (not what I was aiming for) and did not filter very well. Also, by cooling more than the others they had been treated differently, so it was not a true repeat. I had to exclude those two points of data and re-do them, thus my tally came to 22 samples over four test conditions, but 20 points of usable data (each trialled five times, thus n=5 x 4 gives 20 measurements).


Yield, in this case, is calculated gravimetrically by weighing the dried remnants of a known volume of solution. A vessel is weighed while empty, then again once the known volume has dried. The increase in weight is attributed to the dissolved solids that did not evaporate, and the concentration of the original solution as %weight/volume (%w/v) is worked out thus:


The rest of the sample was frozen in readiness for freeze-drying (the bottom right image in the earlier collage) – but that is a task for Week 38. Once I had all the data points for yield, I entered them into the statistics software package, checked that my repeats of each test condition were similar enough (i.e. NOT statistically significantly different) with an analysis of variance (“ANOVA” for short) and turned them into a neat little graph ready to add to my paper.

I must say, it feels really good to be ticking things off the giant Gantt chart and getting closer to my first publication in this field*, little by little. I finished weighing the last mini Petri dish and noticed a drying artefact that had formed a ring a few millimetres wide near the edge of the dish and tried to catch the light on it and take a picture. It took a few goes to get the angle of the light just right and this photo was one of the “failed” attempts. Instead of the ring standing out, the beautiful blue sky was framed by the rim of the dish and I couldn’t get the jazz standard “Blue Skies” by Irving Berlin out of my head for the rest of the day. I know there will be darker days in the weeks to come, when stress boils up and threatens to overcome me, but for now I’ll take the chance to fully immerse myself in this happiness stemming from¬†completion and competence.


The tune was so entrenched by the end of the day that I asked my wonderfully obliging partner to please learn the chords and accompany me on guitar so that I could try to get it out my head ūüôā

Nothin’ but Blue Skies from now on!

*I had another life in feto-maternal medicine which produced some published work, but I’m yet to be published in the realm of ocular biomaterials/retinal degeneration.

P.S. The plan didn’t work. Now we both have Blue Skies stuck in our heads! ūüėÄ

40 weeks til thesis

There are 40 weeks until my thesis due date: October 7th, 2016.


Having LOTS of nieces and nephews (ten, so far), I am acutely aware that this time period is synonymous with the typical duration of a pregnancy. So instead of weekly bump updates, I thought I could do weekly blog/vlog updates. Partly to keep me entertained, sane, and engaged with the world outside of the lab; partly to share my work and ideas with a wider audience; and partly to put something out into the world to which I can hold myself accountable.

Week 40, my first week back from the Christmas/New Year fortnight of holidays, was spent in ultimate planning mode. I’m not sure that my supervisor can truly appreciate the sense of calm and control that this dedicated week of timeline setting, Gantt charting, and working backwards from self-imposed publishing deadlines to project start times afforded me, but I would not have done it any other way.

In the first two years of my PhD, there were annual review milestones which required me to (among other things) prepare and submit a summary of the experiments performed to date and investigations still to be completed. The summary included a timeline outlining the proposed schedule in order to achieve everything set out in the initial project proposal within the time remaining.

As the first milestone review was due at the end of my first year, these timelines spanned the final¬†two years, so there wasn’t room for a lot of detail. Moving into the final year… or rather, the final 40 weeks, I needed something more prescriptive. Clear objectives to achieve on a weekly basis. Bite-sized pieces of work. The big, final hurdles, broken down into smaller, more manageable tasks. So I sat myself down with the notes from my latest supervisory group meeting held at the end of 2015, and got started on breaking it down.

Break it down now! (gif via giphy)

Flashback to when I was in Year 11 and elected as a prefect for the following Senior Year… I was invited by the school to attend a leadership conference. Full formal school uniform, fancy dinner, people in formal dress giving speeches – the whole shebang!

There were a host of eloquent speakers, some more inspirational than others. I know it had a great impact on me at the time, but I cannot for the life of me remember any of their names, or even what most of them spoke about. What I do remember is a famous sportswoman sharing with us her method for the lead up to international meets. She followed the 7Ps principle, “Proper Prior Planning Prevents Piss Poor Performance” and it has stuck with me ever since. Failing to prepare is preparing to fail, and all that.

The seven peas (image via Penny Thots)

Those words were echoing in my head in the final week before summer holidays, so I knew the first task for 2016 would be defining my action plan. Hence the Gantt chart is now complete, my 16 year old self is very proud that I am still employing the 7Ps a decade later, and I feel capable of what lies ahead – which is really the most important part.

There was a solid month, once the euphoria of passing the Mid-Candidature Review had worn off, where the enormity of the task left for me to complete was thoroughly overwhelming. I withdrew. I stalled. I cried. I was scared to start for fear of falling short of the mark – mostly because the very nature of a PhD is that no-one has ever done your research before so you have no idea of where that mark actually is! It was a horrible¬†feeling of impotence. And every day that I didn’t make progress, I would beat myself up a little more. As I looked into this feeling and learned more about it, I found¬†that it was the classic signs of burn out mixed with the ever-present Imposter Syndrome. Yay…

So when holidays came around, I switched off my PhD-brain, immediately and completely. I had no ongoing experiments to monitor, no studious thoughts anxiously buzzing away in the back of my mind during Christmas dinner. This meant I had two weeks of quality time with family and friends and my partner Рand even some time to myself! Two weeks of sleeping, eating, drinking, swimming, sunshine, walking, cleaning (surprisingly cathartic to throw clutter away!), cooking, crafting, laughing, watching movies, singing, making memories.


So now, 40 weeks out from the finish line, I have a plan made of small, achievable tasks; a set of stepping stones to simply follow. All the thinking about what to do, when, and in what order has been done. It’s now just a matter of putting one foot after the other to eventually reach the finish line¬†in this science marathon also known as “the PhD”.

The mother of all Gantt charts (current at time of post, but subject to change) outlining times for planning and executing the final experiments to complete each aim, writing and submitting papers, writing and proofreading chapter of my thesis – the LOT!