Neither the Bang nor the Butt

Before I get started, I would like to define, “science” for the purposes of this post. Please note that science does not equal academia. Academia has its own problems and I am not going anywhere near those (right now)…

science noun
  1. the intellectual and practical activity encompassing the systematic study of the structure and behaviour of the physical and natural world through observation and experiment

Like a lot of the things I come out with, this is a preemptive explanation.

This week I filmed a three minute segment for the NBN children’s show, “So There!” One of the producers contacted me after seeing a piece about my outreach work in the Newcastle Herald aaaand I got quite excited.

nbn

It’s a pretty straightforward segment. I perform three “experiments” (which can be easily repeated at home) whilst narrating the science behind what’s happening. This is the basic premise of my kids’ parties, with the obvious difference being those are interactive!

Now, because I am me, and because I am not the most optimistic of individuals, I’d like to think I am aware of most of the pitfalls and judgements attached to science communication – especially with children. Hence this pre-emptive explanation, which should hopefully roughly translate as: Trust me, I know what I’m doing.

Most of the attempts to get children interested in science is based on the (other) Big Bang Theory. This is the theory wherein, if something makes a big enough Bang, then kids will be impressed – and the job is done. Now, I’m all for making kids happy, but as you can imagine, there’s a lot more to science than Bangs. The Big Bang Theory is one of the reasons why IFLS has been so popular – but it’s also one of the reasons why many scientists feel the site can really let the side down when it comes to science communication.

ifls

All credit to the lovely Cyanide and Happiness guys, check them out http://explosm.net/comics/3557/

It’s one of the reasons scientists can shy away from communication and outreach. I was actually talking to one of my colleagues who is very pro-active about spreading the word about his work, but yet he is disappointed by this mentality. He was telling me about a trip to a science museum where he witnessed a kids’ science show which consisted entirely of things which go Bang. Now, because I am me, I took this as a slight towards my TV work (hehehe “my TV work”). I asked him how he proposed we SHOULD get kids interested in science – and of course he didn’t know.

Good scientists need to be a number of things. We need to be inquisitive, organised and creative. We need critical thinking, problem solving and communication skills. If we can encourage kids to develop even a few of these skills, we’re getting there. And remember, we’re not trying to cultivate a generation comprised entirely of scientists. We do not need a world full of researchers – we cannot support a world full of researchers! What we’re really trying to cultivate is a culture. A culture wherein everyone would be aware of science, everyone would respect science and everyone would appreciate science. In this ideal world, logic would prevail – and also there would be more funding for scientific research (!). No one would have to waste their time explaining why Paleo is nonsense, why vaccinating your children is the kindest thing you can do (unless they are immuno -compromised or otherwise unable to receive the injection! Can’t catch me, anti-vaxxers!), why coffee enemas are never going to cure cancer or why climate change is real (just ask John Oliver). People would make decisions based on evidence. People would ask intelligent questions. People would face the world with an open mind.

The truth is, the science is not the Bang – the science is in the asking WHY? In showing kids something so surprising or loud or colourful, we’re encouraging them to ask, “Why?” – this “Why?” is the first step to encouraging a scientific mind. Yes – the kids are looking at Science’s butt as it walks by. And THAT’S when the hard work comes in. Anyone can drop a Mentos into a bottle of Diet Coke, but it’s making the explanation accessible and interesting that’s the tricky part. Also encouraging further questioning – leaving some things unsaid and waiting for the dots to join so you can make way for hypothesis building and fill in the blanks when the time comes (this can be tough on TV…).

My point is, that just because I am taking advantage of the Other Big Bang Theory, it doesn’t mean that I am “selling out”. I still consider myself a scientist, and I still hold the values of science very close. I’m using the Theory as leverage. It’s my “in” for building the foundation for inquisitive minds.

Trust me, I know what I’m doing.

As far as developing this mind even further – beyond the Bang, beyond the butt– what do you think? How can we encourage appreciation for the scientific method – hypothesis forming, how to scrutinise sources, critical thinking – as children get older and we have a bit more faith in their attention span?

I’ve had a few lesson plan/ outreach activity/ museum ideas around this theme and I’d love to share them with any interested teachers or communicators!

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A Cop Out

So I’ve been going through a bit of a valley of shit and was waiting to get out of the other side, so that I could write a post that goes something like this:

“Hey kids, sometimes life gets you down. But ya know what? *insert major realisation here*. In conclusion: it’s going to be OK.”

But I wasn’t getting out of the valley, and I still haven’t. I’m now getting to the stage where I have started to notice OTHER PEOPLE getting sick of my negativity. Instead of responding to this by readjusting my perspectives accordingly, it’s all turned into a kind of positive feedback loop, wherein I’m just left internally yelling, “I KNOW, RIGHT?! HOW ANNOYING IS PESSIMISM! GOD!”

When I take a step outside of my own brain (sorry Nikola), I can see how people would get confused and frustrated by my constant gloom. A lot of really (potentially) exciting stuff has been happening recently. Intrigued?

Reasons for me to not feel shitty:

-I got to talk to lots of *famous researchers at the Keystone Conference about my project AND THEY GAVE A SHIT (*in my field)

-I’ve had the offer to go and do some of my project work overseas.

-Because of this blog, I’ve got involved in a super exciting science careers/ gender equality project.

-I may have found myself a beautiful mentor in doing so.

-The inaugural EMBL PhD Australia Symposium, which I was on the committee for, went so so so so fabulously last week.

-I’ve finally got my teeth stuck into the Scientists in Schools project.

-I was invited (INVITED) to give a talk to a group of school girls about careers in biology.

…and yet. I’m not excited. I’m pretty sure that this is all about to come caving in, the minute someone realises that (I’m not actually supposed to be here). Despite all of the above, and the number of friends, family and co-workers spurring me on, my anxiety remains (see Fig.1). I’ve come to see that it doesn’t matter what’s going on externally, I’ll always find a reason to question my own validity, and that’s the way it’s always been.

self belief

Figure 1. Theories for self acceptance strategy A.Ideal scenario i.e. a falsity. B.Actual scenario.

When I realised this, I decided to make another list. A much more depressing one than the one above.

Reasons I have previously found to question my own validity as an actual human, capable of achieving things:

-Not having a boyfriend

-Not having enough friends

-Not getting along with absolutely everyone I have come into contact with

(warming up now)

-Being overweight

-Not being pretty enough

-Not wanting to play violin anymore

-Not liking sports

-Not partying “hard enough”

-Not being a mermaid

OK, so that last one hasn’t bothered me in a while, but it used to. I was thinking hard for a while about what it is that’s bothering me so much right now, so I could stick that one on the list too. Then I realised there were lots of reasons, and that made me sad and it probably didn’t matter anyway.

Putting that list together was a bit emotionally overwhelming for me. I saw how ridiculous it all looks now and consequently how ridiculous “Not getting a western blot to work” will most likely look in 5 years’ time.

You’d think now is when I’d start to write about how I’ve learned my lesson, and I’m moving forward and not sweating the small stuff etc. But if you were paying attention at the beginning then you’d know that’s not how it’s going to go, OK?

I’m still frickin’ crabby. I’m still worried. Writing experiment plans and literature reviews still makes me nervous. I’m still pretty sure things aren’t going to go my way. So here’s my shoddy excuse of a conclusion:

Creating things makes me feel better, and I just created this blog post.

shutup1

The Unavoidable Vulnerability of Research

I had a bit of a dud week this week. I was planning on doing some flow cytometry; but I didn’t get around to booking it until Monday and, surprise surprise, the machine had been booked out. So I switched tact and decided to finally run some plate assays I had been avoiding. Unfortunately, I seeded my cells too low and they never quite got over the hump. By the time I realised the cells couldn’t be used, it was Wednesday morning, I didn’t have any backup cells and I wasn’t going to have any lab time on Thursday.

It was going to be an experiment-less week.

I got over this annoyance fairly rapidly (go me!), as I realised it had been a while since I sat down and did some reading. Last time I presented my work, I got some pretty interesting questions about the project background, which I had never actually considered. In short, it was about time I got in some reading. At this point, I had already envisaged my blog post for the week. It was going to be called, “In Favour of a Week Off,” and it was going to be all about how fabulous it was to get lost in reading material. HA.

There are an infinite number of questions people could ask me about my work. I still don’t know what my results mean. In order to increase the chances of me knowing the answers to questions and being about to properly interpret my data, it’s in my best interests to read as much as I can get my hands on. Somewhat inevitably however, I would reach a point in a publication where I struggled to understand. I would have to spend a long time making notes and scribbling out concepts, then when I looked at the time I would panic as I realised what a huge, time consuming and exhausting experience this was all destined to be. I began to replace note making and scribbling with procrastination, and my reading slowed even more.

In one of my efforts to procrastinate in at least a somewhat productive way, I found myself listening to a TED podcast. I heard from another researcher; a vulnerability researcher named Brene Brown. Brene described the phenomena of shame and vulnerability, wherein shame is something which we will all experience, and it can be described more accurately as the fear of disconnection, or the fear that we’ll get spotted for “not being (blank) enough”. I realised that what I had been struggling with was shame. I was scared that I would get spotted for not being smart enough, and therefore not truly belonging in the scientist community.

I was scared that, unless I read and understood everything in my field before I talked about my project in public again, I could be shamed for not knowing enough. No wonder reading was such a stifling experience. I was unintentionally telling myself that, unless I knew everything, there was no point even trying. But, in reality, of course we can never know everything about our field. Whenever we walk up to the podium or stand in front of our poster, we are exposing ourselves to the vulnerability that one of our peers will point out something we hadn’t thought about or realised before. It’s a vulnerability that we just need to get used to, because it’s all part and package of what we do…or, as one of my new favorite researchers would put it, 

“If you’re gonna go into the arena, you’re gonna get your butt kicked.
…as scary and dangerous as that sounds, it’s not as scary and dangerous as spending your life on the outside looking in.”

Instead of fixating on what I don’t understand, or all the mountains of papers that I haven’t read yet, I just need to get on with it, and (more importantly) give myself credit where it’s due, instead of getting stuck in cycles of self-abuse.

 

Another Milestone

A couple of weeks ago, I completed and passed my PhD confirmation, hooray!

I haven’t had much time to write about it since, and today I didn’t really have any excuses not to (Must. Stop. Watching. Breaking. Bad), so here I am.

In order to successfully “confirm”, I had to write a literature review and project plan and  then present it to a confirmation panel, comprised of external and internal markers.

I wasn’t too nervous about the presentation, because I’d already (successfully and confidently, I might add) presented my data at a local medical research conference just a couple of weeks previous. However, during the week leading up to my confirmation, I had volunteered to go and talk to a class of undergrads about my experiences with bioinformatics. I’d done the same presentation twice before for the same course, and I knew it “wasn’t a big deal”, so I didn’t spend much time preparing. Who can guess what happened next? Yup, I bombed. I stumbled through my slides, couldn’t remember how to say what I needed to say, and got extremely self-conscious. And thus I set myself up for a world of terror for my confirmation.

I knew that all I needed to do to get better at my confirmation presentation was to practise it as many times as physically possible. This was a bit difficult, because the day after the bioinformatics talk, my parents arrived to stay with me for the week. They were REALLY good at giving me space to practise when I needed to, but still, the temptation to go out to dinner and drinks etc. with my parents (who I only really see once or twice a year) instead of staying in to study was pretty overwhelming.

In addition to the constant battle of willpower, every time I did sit down to practise, it was a mission just to make it through the 15 minutes of me talking to myself without stopping to have a panic. Even though with every rehearsal, the words did come easier, I wasn’t any easier on MYSELF. I found myself subconsciously repeating one of my running mantras: “This was never easy and it never will be.” This way, instead of responding to my internal struggles by punishing myself for finding things difficult, I try to remind myself that there’s nothing wrong with something being difficult…and that there isn’t some better version of myself who “should” find things any less difficult than they are.

My friends and colleagues were extremely supportive with helping me to prepare. The time came and, aside from talking a bit too fast at times, everything actually went great. No one booed me off stage or even insinuated that I had no idea what I’m doing. I could answer my questions. 

 In the interview section, I was taken off to a room with my committee, where we discussed my project plan. I started off by trying to answer their questions as though I was in a job interview, but then I got the feeling that they were really just asking me things out of interest, as opposed to checking up on me. Not long after this feeling sunk in, one of the markers asked me what my publication plan was, and why I hadn’t included it in the confirmation document. I knew that I was supposed to include one, and I had known all along. I just chose to ignore it because, as I told the examiner,

“It just doesn’t seem very likely that I’ll get anything worth publishing.”

At first it kind of pissed me off that this this surprised them. What kind of world were THEY living in, where a normal person, like me, would be capable of writing a paper? I actually got quite defensive.  They kept suggesting all sorts of interesting experiments I could do. I agreed, “Yes, that does sound interesting,” whilst at the same time being sure to remind them that, “I don’t think I’ll be able to do that though.”

At the end of the interview, I was asked to leave so that my supervisors could comment on my progress. A couple of minutes later, I was called back in to finalise the confirmation process.

I apologised for my document being so long, and thanked all the markers for their time and patience with me. I was told, in return, that actually my document had been interesting to read, and very well put together. I was told that I clearly had a good comprehension of my material and possessed many of the skills which are important for being a researcher, such as pre-empting questions and being able to ‘sell’ my work. I was told that my research was “novel and important”. I was told that it needed to be published.

I was told that I needed to stop being so hard on myself.

I looked up from the table where I had been fidgeting with my USB from the presentation. My supervisors both looked so proud, as they grinned idiotically at me. Obviously I started to cry. Because that’s what I do.

But, I promise…I really am trying to be more positive!

Let’s Try This International Conference Thing

Image

Spot the difference from two posts ago: i) Dressed for about 20 degrees worth of temperature difference ii) Jumped up on coffee in attempt to compensate from jet lag iii) THERE IS ACTUAL DATA ON MY POSTER

This picture was actually taken a month ago, at the Society for Melanoma Research conference in Philadelphia. I would say I haven’t written anything since then because I’ve been flat out, but that would be a lie. I’ve been having some motivational issues.

Anyway, my first international conference went OK: no one told me I was wasting my time, or that my project sounded dumb etc. But then again, I didn’t win any prizes, no one came to seek me out to talk about my project or poster and no one was studying anything remotely similar to me…so maybe it didn’t go too well after all. I don’t know what I expected to happen at the conference, or what even happens when a conference ‘goes well’, but it didn’t make me feel amazing about getting started on my first year viva/ confirmation process/ progress report thingy, which I’ve told my supervisor I’ll get to her in January.

It felt as though 98% of the projects being spoken about were regarding One Thing, and that One Thing has nothing to do with my project. Because I attended the conference with my research group, (who aren’t studying this One Thing either)  it just felt like a bit of a running joke at a time. But now I’ve walked away (and haven’t really debriefed with everyone about how they felt it went: I’m back home in a different country to them until January), it doesn’t feel like a joke. I can interpret it in one of two ways: i) Everyone else is really short sighted and the melanoma research community needs to (re)broaden their horizons OR ii) I am on the wrong track and I need to UN-broaden my horizons because ACTUALLY the correct pathway for melanoma advancement has already been found, but I am not on it.

I’m supposed to be working on this document but half the struggle is just getting the words down, when I feel as though, if a random melanoma researcher was reading over my shoulder, then my ideas would be laughable to them.

I don’t know how anyone can ever deal with these feelings of inadequacy: obviously I just need to start being more arrogant.

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