Mission: Birthday Party

My mission was clear, though far from simple.

It was my responsibility to recruit and train the next generation of scientists, such that they may find a way out of this terrible mess we had gotten ourselves into. Global warming, food shortage, antibiotic resistance: it was clear that we stupid adults were fairly inept at taking care of ourselves and our environment. My recruitment officer, Mollie, had taken it upon herself to use her birthday celebrations a way to bring together the best minds of her generation (*ahem* classroom) such that I could hope to prepare them for what lay ahead.

Many people told me I was foolish to expect so much from 8 year olds. Did they really have it in them to understand the fundamental states of matter AND their transition states? The complexities of pH, density and chemical reactions?

IMG_3558

The recruits enjoying some vital R&R in preparation for their rigorous training

It is true, I cannot lie: at times I did fear I had taken too much on. But I held onto my hopes that my students, though short and easily distracted, would have a number of other key qualities which would render them perfect scientists.

Indeed, when I finally coaxed them away from their chocolate, footballs, trampolines and playhouses, I quickly realised that 8 year olds are not lacking in these qualities. In particular, I am of course talking about creativity, playfulness and inquisitiveness. Vital skills for any scientist worth their salt! I was also made to feel much more confident when I saw the quality of the resources at our disposal. The laboratory was beyond satisfactory.

IMG_3544

Our first task (I brought along my trusty aide, confidante and housemate to assist on the day in question) was to introduce the students to the three major states of matter. This lesson was very straightforward, and it was streamlined with the provision of:

  1. A simple diagram,
particle model

Solids, liquids and gases

2. Hands on examples (ice cubes melt when you transfer them some heat energy from your hands, water turns into stem when you transfer heat energy using a kettle)

3. Thought provoking questions relating to a familiar context i.e. the human body. (who can name a GAS inside the human body?! 😉 )

IMG_3566

FART JOKES

We were ready to enter the laboratory. Inside, I had prepared learning materials such that the recruits would become familiar with several new concepts.

Unfortunately, the laboratory had taken on the smell of wet cabbage; it was integral that we had buckets of red cabbage water on hand for the duration of our experiments. Reb cabbage water has the interesting quality of being a colour change “INDICATOR” – which just means it can tell us things when it changes colour. In particular, it can tell us whether a chemical is an ACID, BASE or NEUTRAL.  “What do these strange new words mean?”, my curious little students asked. I assured them, “Scientists are really keen on grouping things together. How many ways do you think I could separate you into groups? That’s right: eye colour, are you wearing a dress or pants, hair colour, girl or boy… CHEMIALS can also be grouped together into ACID, BASE or NEUTRALS.”

“Acids tend to taste SOUR and be CORROSIVE – like how eating lots of sugar CORRODES your teeth: it makes holes in them.”

“Bases tend to taste BITTER like coffee or dark chocolate, and feel SLIPPERY.”

“…Now who wants to test out some of our mystery CHEMICALS with the INDICATOR?”

IMG_3574Soft drink, sherbet, vinegar and lemon juice are all ACIDS: they are sugary and/or sour– that’s why it’s so important to brush your teeth after eating!

Mylanta, toothpaste and soap are all BASES. Mylanta helps to make your stomach LESS ACIDIC when you have eaten too much of the wrong food. Toothpaste helps protect your teeth from ACIDIC food. And soap feels SLIPPERY – remember?!

IMG_3601

Meanwhile, my assistant was taking on a more creative project: making lava lamps (as well teaching humans born in 2005 WHAT a lava lamp IS).

“Remember those molecules that are packed REALLY TIGHT in solids, LESS TIGHT in liquids and are LOOSELY packed in gases? Well, that tightness is referred to as DENSITY.”

The students then partook in an experiment and creative exercise involving six major components: an empty plastic bottle, water, vegetable oil, dissolvable aspirin, food colouring and air.

IMG_3583

Their first task (with the help of adults and an abundance of funnels) was to pour some oil and water together in their plastic bottle, then MIX it together. Of course, this was a clever trick. Why, you ask? Well of course the oil and water will not mix! It is because the oil is MORE DENSE than the water that it will sink to the bottom.

IMG_3603

Now for the creative part: the children could pick their favourite colours such that the water would change colour.

“What happens when you blow bubbles through a straw into your soft drink, other than your Mum and Dad getting annoyed?

The bubbles FLOAT: because they are full of AIR. What is AIR? It’s a GAS. What do we know about the density of GAS? Is it higher or lower than that of LIQUIDS? Of course it is LOW – which is why the bubbles rush to the top! So what do you think would happen if we put some GAS in the bottom of your bottle?

OK, but how are we going to get the GAS IN the bottle AND at the bottom?

Let me tell you about CHEMICAL REACTIONS. They are happening all the time! They happen in your tummy after you eat, they happen in the car’s engine, they happen when you cook food…and a lot of the time, these reactions will cause the production of GAS.

So we just need a chemical reaction to happen in the bottom of the bottle! And how do we do that? We use these special fizzy tablets (dissolvable aspirin) . They CHEMICALLY REACT with LIQUID…and give us a lovely lava lamp in the process!”

IMG_3612

Fantastic. It was time to move the scientists outside for the final installment of their training.

“What happens when you get in the bath? You have a wash? You get bubbles all over the floor? You splash your brother and sister? Great. Guess what else happens? The water moves up the edge of the bath – your body DISPLACES the water – so the water level rises.”

“What do you think would happen if we could DISPLACE the liquid from this soft drink bottle?”

“Do you think it might explode…?”

“OK how can we get GAS in the bottom of the bottle? I seem to recall having this problem before…? A CHEMICAL REACTION? Great, I have just the thing! These sweeties react with the soft drink and produce LOTS of GAS! Stand back…”

IMG_3639 IMG_3641 IMG_3646 IMG_3645

I was so proud to have my recruits graduate with flying colours. We celebrated with cake and hand-ball, and I am more than confident the students will go on to have a promising future in science.. saving the world, curing diseases, rescuing near extinct species. Nothing too lofty.IMG_3632 IMG_3671

Advertisements

Not A Psychic

A few weeks ago, I was lucky enough to get involved in the Science and Engineering Challenge, a University of Newcastle initiative to get high school students thinking about careers in (you guessed it) science and engineering.

My task for the two day competition was to supervise and score the students participating in the “Future Power” challenge. This was one of 7 activities we ran throughout the day, which also included catapult, hovercraft and bridge building. The aim of my activity involved supplying power to a city and making the most money. ALL of the kids (as far as I can tell) enjoyed the challenge and there was a lot of excitement buzzing through the room as teams raced to complete their task.

Due to a bit of an administrative hiccup, some of the students had been told they would be attending a building activity when they were in fact scheduled to spend their afternoon with me and 8 power boards, which looked like this:

future2

future1IMG_20150505_074905

Pretty daunting at first, right (except for the fluffy headband I guess)? Hence I made a point during my task brief to the students that I’d give them plenty of time to learn how to use the equipment, and that I’d come and talk to each team individually before we got started.

A certain cluster of girls took an instant dislike to me and my power boards. We were not what they were expecting and they weren’t having any of it. As I worked my way closer to their table, I could hear them complaining loudly. I approached them tentatively…

“So, how are you going? Do you have any questions?”

The ringleader folded her arms and huffed at me: “Miss, we don’t get it. It’s too hard. We want to build stuff.”

The other girls nodded enthusiastically in agreement.

And in a moment of sheer eloquence and confidence that I will likely never re-live, I replied:

“Well, it’s just as well you don’t get it already because you only just got here and you haven’t even tried. If you already got it, then it would mean you had psychic powers and I’d probably have to hand you over to the government so they could do crazy experiments on you.”

Unfortunately I didn’t get a laugh (unless you count my laugh), but I did win enough favour to be able to sit down with them without getting evil eyed into the next dimension. By this point, some of the other teams were getting pretty into it, yelling (nicely, mostly) over the top of their boards at each other. Surely enough, once they took the time and energy to try and understand what was going on, the girls grasped the concept and were keen to get started with the competition.

I was reminded of this incident today when I sat down to plan a series of experiments. I felt anxious, frustrated and annoyed with myself for taking so long to plot it all out. I wanted to give up, go home…

But wait a minute. Of course it was taking me a long time. I had never done it before. It was always going to take time and energy to think it out properly. I was never going to be able to jump into this without committing myself to understanding it first.

I’m not a psychic. And just as well,really.

roswell

A Date with The Doctor

About a month ago, I spotted Dr Karl at a book signing in my local shopping centre.

Part of me was desperate to talk to him and tell him how awesome he was. But part of me knew that he must get so sick of people fan splurging all over him. The second part of me won out, and I left the shopping centre feeling somewhat proud that I had made a very grownup decision.

Later that evening, I was harbouring a toddler-esque resentment of my grownup decision. I sat sulking on Twitter, scrolling through Dr Karl’s feed, inwardly scolding myself for missing out on the opportunity to fan splurge on THE Dr Karl. As a reflection of this inner turmoil, I somewhat-joke tweeted:

Dear @DoctorKarl, I want your job.

Later that evening, my game of Scrabble (no, really) was interrupted by my phone.

karl tweet

Several weeks later, I rolled up at the ABC in Sydney and presented myself to the receptionist.

“I…I’m here to see…Dr Karl?”

“OK, sure just sign in here”

There was a space for “Host Staff Member” on the slip he had handed me.

“Erm…I…I don’t know how to spell his last name.”

He laughed. “That’s OK. Just take a seat over there and I’ll track him down for you.”

He handed me an ABC Visitor Pass and I wondered over to the sofas he had indicated.  I immediately set about trying to take a stealthy selfie of me and my pass, figuring it would take the receptionist a while to find my host. Caught up in awkward angles and unflattering close-ups, my selfie taking was interrupted almost immediately.

2015-01-22 09.48.07 2015-01-22 09.48.23

“He’s in the coffee shop; you can go and meet him there.”

I find my way to the coffee shop without embarrassing incident, and am beckoned over to Dr Karl’s table by The Man Himself. (He’s wearing an Americana print shirt with a Route 66 belt buckle, for those of you who are interested. NB You should ALL be interested).

Karl shakes my hand and introduces me to the two other people at the table, his wife and his “body guard” (a slight, short-haired lady, who I assume is in fact his publicist…but she could just have a mean right hook, what do I know?). They are discussing titles for this year’s book. Karl will be writing his 38th book this year, and they settled on:

You’re Kidding Right, I Definitely Do Not Have The Authority Or Permission To Talk About That

After coffee, Karl gives me a Brief History of the ABC Ultimo Building. He moves with purpose and a near constant commentary of our surroundings. At this point in the day, this commentary regards the age and orientation of the building. However, at other stages of the day, it will instead focus on the pattern of the traffic lights, the speed of the elevator we’re standing in or who is currently walking past the recording booth. It’s actually very comforting in an odd sort of way. He takes me up to the third floor balcony space, where he can point out the ABC satellite dish.

“How long does it take for a typical communications satellite to orbit the Earth?”

“Errrrm I don’t know? Sorry.”

“That’s OK, it’s only one of the greatest achievements of mankind, why should you know? There are other things to think about, like the Kardashians.”

I didn’t have much time to think about how I felt about being spoken to like this, as Karl was already moving on with more detail about the technicalities of the ABC broadcasting systems…most of which goes over my head, as I am busy nodding and smiling*. He even leads me into the high security main control room, warning me not to touch any of the buttons or cables.

As Karl sets up for his ABC 612 Brisbane segment, I am left with the guys in the transmission control room , as they tell me about their jobs keeping the entire country in touch with the ABC. They are quick to remind me that this task is a bit tricker in Australia than the UK, a country which can fit inside Victoria. Later in the day, Karl tells me that he enjoys having his “Tardis” (isolated soundproofed room) in such close proximity to these guys as he has a lot of respect for their profession and expertise. No kidding.

I am directed into Karl’s Tardis, where he is sat with his laptop open and Skype running. He is about to go on air and one of the producers is typing messages to Karl on Skype, writing out some of the questions they have been texted, tweeted, emailed or called in. This is the first time I realise that Karl has literally no time to research the answers to the questions he is asked. Within a minute of Karl and the producer typing their “Good Mornings”, Karl is live with Steve Austin and answering questions about solar panel efficiency, towel drying and weight loss. Initially I thought the producer would continually type out questions on Skype for Karl to select, but often he was given no choice of which question to answer. Dr Karl is a sodding enigma.

After the ABC 612 segment, we dash upstairs to the Triple J studios to join Zan Rowe for a one-hour Q&A session with callers to the radio show. Karl is quick to tell Zan off for partying too hard over the weekend at Beat the Drum, and they are left with about 45 seconds to talk about some of the callers they’ve had so far. With Zan’s show, the guys do get a break every few minutes while she puts a record on, and while they do use that time to discuss the upcoming calls, there isn’t much picking and choosing. Karl’s happy to tackle just about everything (however I did get the feeling that younger kids often got a preference…so feel free to recruit some younger siblings/ nieces/ nephews/ cousins/ passing school children if you are really desperate to get on the show). Although Karl was happy to answer any question, it’s pretty important to note that, like any half decent scientist, he knows when to say those magical words, “I don’t know!”.

A lot of the questions have obviously been brought on by the Australian summer, as sweat and sunburn make a few appearances. During an explanation about UV, Karl tells us:

“UV-A causes Ageing, UV-B causes sun-Burn and UV-C causes Cancer.”

A couple of seconds later, my phone buzzes as my supervisor has sent me an angry text message:

nikola text

I show Karl during one of the music breaks, and he looks a bit concerned. He asks that Nikola send him some references and he’ll have to do some reading. When Nikola sends the papers through a few minutes later, he thanks me enthusiastically. This guy loves his scientific literature. He tells me he’ll read it through and correct himself next week.

As the show comes to a close, Karl and Zan move outside of the studio to take their weekly picture. A few awkward moments pass as I’m unsure whether I’m supposed to be IN the picture or taking it. I’m more than flattered when Zan and Karl usher me between them and one of the producers emerges to take our photo. Which is now my phone, Twitter and Facebook background picture. Obviously.

zan karl

Karl and I have lunch together, and he asks me about my PhD project. We talk about why melanoma incidence in Australia is so high, and why it has such chemoresistance tendencies. This is the one and only time I feel as though it’s ME educating HIM, although he could just have been humouring me. The UV thing has obviously piqued his interest, and he presses me to tell him everything I know about the differences in wavelengths. He seems almost as disappointed as me that I can’t really help him out. I begin to feel as though every other thing I say to Doctor Karl is, “I don’t know,” and I apologise for my stupidity. He tells me,

“You’re not stupid, you’re just ignorant in some areas. There’s a big difference between stupidity and ignorance.”

Again, I’m not given too much time to dwell on how this makes me feel, as he moves on to tell me about ACTUAL stupid people, like climate change deniers and anti-vaxxers, as well as conspiracy theorists.

We have another hour before his next show, but Karl has scheduled reading for this time: he reads over $10,000 worth of scientific literature a year. I tell him how impressed I am by his memory, and he tells me he actually has a “terrible memory”, and he has several mechanisms to help it along. Firstly, he has an extensive filing system on his laptop. When he reads something interesting, the coupling of reading with the action of filing helps him to remember. Secondly, he tries to write science stories as often as he can, always with the intention to publish. I ask him how much sleep he gets and I’m kind of pissed off when he tells me, “8 hours.”

Karl lends me some magazines to read (National Geographic and Scientific American Mind), and I trot off to entertain myself for the next hour. Inspired by Karl’s dedication to science, I put down my smartphone, get out my notebook and attempt to really try to learn SOMETHING in the next hour. Note to self: it’s hard to focus when you are buzzing from exhaustive fan-splurge.

We dash out for coffee. Without asking, Karl orders me an espresso and is somewhat distraught when I ask for a flat white instead. He insists that I at least TRY his, and justifies that his coffee must be nicer than mine because I’m not making “MMMMMM” noises anywhere near as loud as him, nor gesticulating anywhere near as wildly. As if to make a point, he draws me the chemical structure of caffeine, alongside that of theo-bromine (the “active ingredient” in cacao). They look remarkably similar, and, literally translated, theo-bromine means, “food of the Gods”. I ask Karl to sign his structures and he obliges (see, even HE doesn’t know how to spell his last name).

2015-01-25 19.59.12

We dash back into the ABC with about 30 seconds to spare before he’s live with Rhod Sharp on BBC Radio Five Live (fun fact: Rhod is actually broadcasting from Massachusetts, USA live to his listeners in the UK). The show goes for an hour, plenty of time for Karl to educate us on global warming, methods of investigating the Earth’s core, human cartilage, satellite highways and cheese dreams (NB Not actually A Thing). It’s during this show that I realise that Karl’s earlier Kardashian comment (and several others which could have caused offence) is really just part of his humour. He’s just so fast that you don’t often have time to realise that he’s being funny. At one point, Karl suggests that we stop women from waring out their cartilage by carrying them around everywhere. But in the next breath he’s telling us about dietary supplements which can actually aid cartilage health. Neither the host of the radio show nor the listener had time to laugh, because he’s tells these “jokes” with such confidence in exactly the same tone and manner as he when he talks science.

There are two more shows in the day, half an hour with ABC 105.7 Darwin, as well as half an hour with ABC 720 Perth. In the brief periods in between shows, Karl is replying to tweets (he endeavors to reply to every question) and emails as well as reading/ filing science articles. It’s during one of these shows (forgive my memory) that someone calls in to ask about something (?), only for Karl to respond,

“I’m sorry, that’s one of my areas of ignorance. We all have areas of ignorance, and that’s mine.”

…and I’m comforted once more. He really didn’t mean anything offensive when he had called me ignorant at lunch time, he was being purely logical. This is not the only occasion throughout the day when Karl is humble; one radio host introduces him as a, “genius”, and is quickly corrected. The average IQ is 100, and Karl’s IQ is just 110. And when I complimented him on his memory earlier in the day, again he was quick to “correct” me (I’m still extremely impressed).

As we pack away for the day, I am regaled with instructions of how to recognise a “herpetologist” (a person who studies reptiles and amphibians will usually have a missing tip from one of their finger), as well as a brief description of Karl’s two daughters (one in high school, and another has just got a job in her chosen field, fashion and textiles).

We bid our farewells, and Karl thanks me again for bringing some more facts about UV to his attention. I give him one last fan-splurge (THANKS SO MUCH FOR THE OPPORTUNITEEEEE!). He shakes my hand, I hand in my precious visitor pass and wonder back out onto the Sydney streets, day-dreaming about satellites, cheese dreams and ejaculatory sneezes.

*I’m truly sorry that I didn’t understand what was going on. It was so clear that this was one of Karls’ favourite topics but Physics has always been my weak point. I know that’s no excuse. And I have been reading up on telecommunications since! But I’m definitely not confident enough to write about it yet.

Learning Make Me Stupid

After my last post, a had a few friends check in with me, worried that I was struggling a bit under the pressures of PhD life (thanks guys!).

One of these friends is a PhD student himself, and so I was a bit confused by his line of inquiry in particular. I mean, aren’t we all struggling under the pressures of PhD life? Don’t we all consider quitting at some point? Isn’t that just…normal?!

Apparently not. “Of course I don’t think about giving up,” my stunned friend reassured me, “I just love learning!”. (What a dick, right?)

To quote Carry Bradshaw; This got me to thinking…

I don’t love learning. I love KNOWING what the hell I’m doing. Maybe that’s why this whole process is particularly difficult for me. When your full time job is studying, you don’t spend much time in your comfort zone.

I, personally (not sure about you guys) don’t  spend much time patting myself on the back once I have the hang of something, because quite often that one thing I suddenly understand or am capable of is just a brick in the wall of PhD-dom. Maybe not even a whole sodding brick. So, really, I spend all my time trying to do things, and not much time wallowing in the awesomeness of the fact that sometimes (sometimes.) I succeed.

Also, because of my anxious nature, that whole time that I’m trying to do or understand something, it’s very hard for me to believe that I will ever even get there. Despite the number of times I have got over molehills before, who’s to tell me that this particular one is actually a mountain and I’ll NEVER get over it? What if I forget my hiking equipment? What if I brought too much to carry? What if my legs will fall off?! And so on.

It’s thoroughly unpleasant, the whole learning experience, really.

I know that the only way to make things easier for myself is to accept that learning takes time. Sometimes all this shit does drive me to consider giving up on my PhD. But I think I’ve got to the point now where I realise that these fears and anxieties aren’t restricted to academia. If I want to be a happy, healthy human IN GENERAL, I need to learn to BE NICE TO MYSELF.

And also to stop worrying about my legs falling off.

All These Things That I’ve Done

I get a variety of feedback from this blog; some fellow PhD-ers enjoy being able to relate to my emotional hiccups, whereas others get annoyed that I haven’t actually told you what I’m doing, just merely indicate the way it makes me feel.

So this post is reciprocation to a combination of this feedback.

Some of you may have noticed that it’s been a while since I last posted. This is because I entered an unfortunate phase of PhD-ing where you forget the rest of the world exists,

To elaborate.

At this stage of my project, I am attempting to analyse gene expression of two variants of one gene, across multiple tumour and cell samples. We do this by performing RT-PCR. RT-PCR reactions require just three things: cDNA template (painstakingly extracted from your sample of interest), primer/probe (corresponds to your gene of interest) and an enzyme.

You can use probe OR primer in order to detect your gene expression. Probes are much easier because they are pre-made by companies and come with specific instructions to get them to work. However, sometimes you have to revert to primers (which you have to design yourself) if the probes for your gene i) don’t exist or ii) don’t work. Primers are way more tricky than probes as you have to work out the right temperatures and concentrations to use for yourself. This process is notoriously painful among researchers.

In my case, I started off with probes but I couldn’t get the QC (quality control) step to work. Although the companies who sell the probes guarantee that they work, you have to do this step, just to make sure your data are real. This QC step consists of performing the experiment on a 1 in 2 serial dilution of cDNA samples. The theory goes that, if each dilution has a concentration of half (start with 100%, dilute to 50%, then dilute to 25% etc) of that than it’s predecessor, then there is half the quantity of your favourite gene. When you run your RT-PCRs, this should be evident; if it’s not, then your probes are not working at 100% efficiency. I performed this step on a number of different probes and they all worked really well. However, for two of them, the efficiency was really poor. The differences in cDNA concentration were never detectable, AND even though we perform the reactions in triplicate, the repeats never looked the same as each other. There was obviously something weird going off with these particular probes. Reluctantly, I set about designing and ordering my primers.

Another note about RT-PCR reactions. We always run a NTC (no template control), to make sure that none of the reagents are contaminated with DNA. We want to be sure were are measuring the cDNA of our sample of interest, not some random contaminant. As soon as I ran the experiments with the new primers, I saw that there was contamination of the NTC. Weirdly however, it only happened sporadically. At first I just assumed that I had accidentally put cDNA in the NTC. It actually took several repeats for me to reassure me that that was not the case.

After going over the data with my supervisor, we agreed that the most likely cause of contamination was the (expensive) enzyme. It had been opened since April last year, so it wasn’t unlikely someone had mistreated it since then.

However, even after ordering new enzyme, we were still getting the same problem.

There were a few more suspects however. Although I use a new tube of water for each reaction, these are all taken from the same source. It could be that this source was contaminated.

Sure enough, after using a new water source, the problem was fixed. On a reaction plate with 2 NTCs, neither of them were contaminated.

I set about performing more QC steps. However, in my first batch of data, the problem returned! Had I messed up? Had something else been contaminated since the last time? Or had we just been lucky to avoid NTC contamination before…? It had only been happening sporadically in the first place.

Another suspect was the pipettes. After dismantling several and peering inside, it looked pretty likely that they were the cause, as they were pretty gross. HOWEVER, I had been using filtered pipette tips to stop this from happening. It seemed pretty unlikely that the pipettes were to blame…but we gave them a clean anyway (well, the lab manager did anyway. Thanks Trish!)

At this point, when my data was starting to defy science itself, my supervisor was kind enough (THANKYOU!) to step in and give me a hand. I watched as she set up the same reactions in the same way that I had been doing for the past few weeks. The theory was that maybe I was doing something (?) weird in my set up to cause the weird results. It quickly became apparent this was not the case. We ran a HEAP of NTCs to make sure we didn’t miss anything, this time. I was actually pretty thankful when we got the results back and the NTCs were sporadically contaminated. It could have just been that I was cursed!

We came to the conclusion that the probes themselves were contaminated. This was not good news, as I had re suspended them (they arrive as a dry powder and you have to dilute them) with a chemical that some others in the lab had used,so it was likely that they would have to repeat some of their experiments. Selfishly though, I was pretty relieved that the mystery had been solved.

Now I just had to order some new primers, but it would be a few days before they came in.

In the meantime, I thought it would be useful to try and get our money back from those dodgy probes. I knew that arguing with biotech companies could be a pain in the arse, so I set up a reaction with so many different controls that there was no way that they could blame US for THEIR products not working. Now, you may remember that all the other probes, bar two, had worked fine. I had used the same source of cDNA to run the QCs. However, I thought it would be good to run some other cDNA sources, so the biotech couldn’t argue the cDNA was dodgy.

After getting the results, I noticed that the original cDNA source results all failed, as predicted. None of the replicates looked the same. Typical. However, as I was sitting down to email the results to the company, I noticed that not all the replicates were behaving as weirdly as the others. Why? I thought. Is there any patten here? Yup. You guessed it. All the reactions with the new cDNA source behaved really well. Maybe it was a fluke, I thought. I know allll about lab flukes. By this point, it was 7PM and I knew going back into the lab would not be a good idea (when I’m tired and grouchy, I tend to make mistakes). So I went home, planning on running a few more QC checks, using the new cDNA, in the morning.

I was at work by 8AM that day, genuinely excited for what I might find. I set up the reaction and sat back to wait for the results. An hour or so later, I watched the computer screen as graphs of my data revealed themselves. Two perfect rainbows of 100% efficient probes with perfect replication revealed themselves to me. The probes worked just fine.

I wasn’t quite sure how to react. Imagine if I had picked a different cDNA sample three months ago. I never would have gone through the stress of the primers. I probably would have a significant pile of data by now.

However, this isn’t a very great mindset to hold. If I had picked a different cDNA sample, I wouldn’t have learned or  progressed intellectually/ personally anywhere near as much as I have. Namely:

-Trust your own data! When something fails, don’t immediately assume it was your fault. (part of the reason all this took so long was that I had to keep repeating experiments as I just blamed myself for their failure)

-I now know how to run DNA products on a gel (this is useful for estimating fragment size, and making sure your experiment worked)

-I now know how to use a Bioanalyzer (a fancy machine which you can use to find out about that tiny quantities of RNA/DNA in your sample)

-I now know how to optimise primers!

-After using so much cDNA to get the experiments to work, I’ve got pretty good at RNA extractions.

-I’m so much more confident in my own abilities now! (i.e. I’m not actually cursed.)

-I’ve bonded with lots of my colleagues as they have all helped me with my experiments,

-I’m able to help OTHER people in the lab with my new knowledge, for the first time 🙂

This is a long blog post I know. I’m not going to apologise though :p

Oh yeah, some of you might be interested to know why that particular cDNA source made the probes behave so weirdly. Hmmm, I’m still unsure on that myself. It may be that the gene had a mutation? If you have any ideas, please let me know…

NOTE: Sometimes this blog is difficult to write. In my head I see PhD students, prospective employers, my parents and my supervisors reading it. So it’s hard to pick a tone. Apologies if I have gone over or under your head here :S

A Learning Process

For a long time, I’ve been aware that my anxiety could hold me back. Occasionally, this fear of ‘missing out’ would grow larger than the anxiety itself. On these occasions, I pushed myself, knowing that things could only get easier after that first time. It was really hard work. But I was right: things do get easier after that first time.

I applied this theory of pushing myself to my decision to go to university, to come to Australia, and to starting my PhD. Only a few years ago, I also had to apply it to catching a train, approaching a receptionist’s desk, and asking for assistance in a shop.

Stupidly, I thought that by giving myself these massive challenges to deal with (i.e. moving away from home, doing a post-graduate degree), I would stop sweating the small stuff. Like somehow the bigger challenges would serve as a distraction from the smaller ones. Ha. Ha. Good one, brain.

In my situation, one of the many components of aforementioned “small stuff” that I just have to deal with every day is independent learning. The trouble is, when I don’t have someone I can trust telling me I’m doing OK, I have to rely on myself for motivation. And I’m not too great that that. Actually, this is roughly how an independent learning process goes for me:

Functional Brain: OK, we have to learn how to do Thing X. (Functional Brain capacity at 100%)

Emotional Brain: Cool, but first, let’s consider all the things that might go wrong. All the things. SO many things! Don’t stop thinking of the things.

FB: *sigh* Yep. (Functional Brain capacity at 80%)

EB: Hurry up with the learning though, because people might find out how long it takes us to learn this Thing X, and then they’ll think we’re stupid.

FB: Makes sense, I’ll try and go faster. (Functional Brain capacity at 60%)

EB: I don’t think we’re going fast enough.

FB: You’re right, maybe we should ask for help.

EB: OK, but don’t forget, they will probably think you are stupid. Imagine being so stupid that you have to ask for help about something so simple as Thing X!

FB: Good point, I guess I must be quite stupid (Functional Brain capacity at 40%)

…as you can see, I don’t make things very easy for myself. I’ve spoken before about the “Imposter Syndrome“, and I think that’s what this boils down to. I’m just hoping that with conscious recognition of this pattern of thought processes, I can start to modify them somewhat.

I suppose learning how to learn is just another piece of the PhD puzzle.

Lessons About Me: Chapter 1

While I hope to learn a lot about melanoma, cell death pathways, DNA damage repair and all the associated lab techniques throughout the duration of my PhD, I also hope to learn about myself. I’d like to think that I will be able to write a few ‘chapters’ on this topic by the end of this ordeal, so here is a rough draft of one of them.

Chapter 1: I Am A Slow Learner With A Terrible Memory

I’m not sure how much confidence I can claim this with, as I have never really carried out any actual comparisons or experiments on the subject, but anecdotal evidence (don’t judge me, fellow scientists) suggests this is the case. To name a few instances/ cases:

-I have to read a paper at least twice, scribble over it at least once, and make notes on it once or two times (hand written summary flow charts plus typed up summary paragraph) before it will make sense to me. I have to type up notes because my memory is defined by the limitations of “Ctrl+F”.

-I have to carry out a protocol at least twice before I can do it without being terrified that I will make a mistake, and even when I begin to relax (to the extent when I don’t need to remind myself to breathe), I still go by the protocol, and read each instruction multiple times before actually carrying it out. The words ‘discard supernatant’ prompt a required re-reading of the entire protocol from the start, just in case.

-If I don’t write my notes like they are for a stranger, they won’t make any sense to me 12 hrs+ later, because I will have forgotten the entire context.

-Things don’t make sense to me unless I can place them into context. Unfortunately, placing things into context can take a very long time, and I often lack the patience and self-confidence (i.e. “this is taking me too long, I am obviously stupid.”) to make it the full circle. E.g. A friend of mine once offered a crash course in data mining, and gave me a few chapters to read. We came together to discuss the chapters and he went through each mathematical concept/ formula step by step. Although I could understand each chunk of the puzzle, I couldn’t see the significance of any of it until we got to the end. Until that moment, I was convinced that I was just plain incapable of understanding data mining, and that my friend had been wasting his time.

Now, I have been told in the past that some of these posts can come off a bit negative. So, while the title of this particular ‘chapter’ might SOUND a little self-abusive, I’m actually willing to admit that I am pretty proud of how I have learned to cope with these characteristics.  I remember being asked, as a high school TA, whether school gets harder as you get older…and I said something along the lines of, “It does, but you get smarter as you learn how to handle all the new levels and dimensions of detail, and how best to harness your own skills in order to do it.”

(NB: probably was not quite as profound sounding at the time)