New Paper: Spatial and temporal variation in dolphin acoustic habitats

There is a growing awareness of underwater noise in our oceans and the potential impacts of such noise on marine life, an issue which was the major theme of my PhD thesis.  This is particularly relevant for “acoustically-specialised” species, such as dolphins.  However, before we can start investigating the effects of noise on these animals, we first need to define the soundscape of dolphin habitats and examine patterns of when and where noise occurs.

We get a glimpse of them at the surface – but what about their acoustic habitat beneath the surface? (Photo: Sarah Marley)

This description of noise in dolphin habitats formed my third PhD chapter, which has now been published online in the scientific journal Frontiers in Marine Science.  In this paper, I examine spatial and temporal variability in the soundscape of the Swan River using over 11,600 hours of acoustic data collected from five sites within the river system across eight years.  Multiple sound sources were recorded at these sites, but the prevalence of these sounds at each site differed, giving each location a characteristic soundscape.  Consequently, some sites were ‘noisier’ than others.

Deploying acoustic recording equipment with help from Fremantle Ports. Spot the dolphins in the background! (Photo: Jeanette Murray)

Want to know more?  The full paper is available online! I’d love to hear your thoughts 🙂

Marley et al. (2017) Spatial and temporal variation in the acoustic habitat of bottlenose dolphins (Tursiops aduncus) within a highly urbanised estuary.  Frontiers in Marine Science, 4: 197.

And watch this space, as the remaining three PhD papers should be going up online in the next few months!

 

 

Ph-inishe-D: PhD Submitted!

The sun is shining, the sky is brighter, the birds are singing…

Since I submitted my PhD for examination, the world has become a happier place.

I actually submitted just over five weeks ago, but only now am I really starting to feel human again.  Part of the reason for this was that submission took place two weeks after I finished writing the thesis, thanks to an unforeseen administrative error.  This resulted in me turning up at uni, support squad in tow, and being told that I wasn’t allowed to submit.  Hello world crashing down…  But t went in, eventually.

PhD submission day, complete with support crew and toy dolphins! (Note, this was taken prior to submission debacle - hence manic expression of relief on my face)

PhD submission day, complete with support crew and toy dolphins!  (Note, this was taken prior to submission debacle, hence manic expression of relief on my face)

The other reason for my vacant expression of the past few weeks is that completing a PhD is exhausting.

I’ve seen my fiance finish his PhD.  I’ve seen some of my best friends finish their PhDs.  I’ve seen my officemates finish their PhDs.  I thought I had a pretty good idea of what to expect.  But it’s a unique experience, individually tailored, and nothing can really prepare you for The End.  I still can’t particularly face writing about it now (why burst this happiness bubble?), but one day I’ll explain the whole thing in detail.  Probably after I’ve dealt with the eventual examiner comments.

So now for my long-awaited period of rest and relaxation!  Well, not quite…

I’ve spent the past six weeks on a Publication Scholarship, which essentially means the uni has been paying me to turn my thesis chapters into scientific publications.  One is submitted, another two should sneak in this week, and the final paper is due for submission in April.  Around this, I have also been working on grant applications, giving presentations, submitting conference abstracts, preparing for a trip to Europe, and attending a surprising number of meetings.  The last has actually been the most daunting – after several months of PhD lockdown, limited social interaction and working from home, it’s weird having to converse with dozens of people at once.  This combined with the ‘mushy brain syndrome‘ typical of recently-submitted PhD students has left me with a strong need to lie down in a dark room after meetings.  But I’m slowly improving.  And as much as I love my PhD project (no, I didn’t end up hating it!), it is actually quite nice to work on other things and bounce between different research projects.

Now I just need to keep my fingers crossed for some successful grant applications so this research can continue…

Conference Attendance – Aquatic Noise 2016

Last month I had the privilege of flying to Dublin to attend this year’s “Effects of Noise on Aquatic Life” conference, also known as Aquatic Noise 2016.  Not only was I able to present the first two chapters of my PhD thesis, but I was able to contribute to the conference itself as part of the Media Committee.

Members of CMST attending the Aquatic Noise 2016 Conference in Dublin

Members of CMST attending the Aquatic Noise 2016 Conference in Dublin

Over 300 people from 23 countries attended the week-long conference, including representatives from universities, government research institutions, fisheries, and industry groups.  Talks were given regarding a variety of acoustic topics, including descriptions of noise sources, sound propagation analyses, and the responses of numerous animal species.  Conference attendees also included ten members of my lab, the Centre for Marine Science and Technology (CMST).  It was great to head overseas as a team, presenting our research to an international audience!

Poster PicMy talk was part of the student speed sessions – five minutes to describe our research and findings, followed by an evening poster session where we had the chance to answer questions, engage in discussions, and network.  I feel the talk went well, despite my nerves.  I’m much more used to interactive presentations involving members of the public than presenting to seasoned professional scientists.  But even without any audience participation, dramatic displays or unexpected explosions, I think I did alright!  You can view my poster by clicking here:  Marley AN2016 Poster.

Marley Dolphin Presentation AN2016

Being on the Media Committee meant I was part of a team responsible for promoting the conference, particularly our public evening.  This was attended by over 70 members of the public, who had an evening of lectures and short videos (more about this in my next post!).  I was also involved in live-tweeting the conference.  This was a way of extending the conference reach to the masses, scientists or otherwise, by posting summaries of each talk on Twitter under the conference hashtag.  I’ve now summarised each day of talks as a separate story using a combination of Tweets from myself and other conference attendees, which are available for anyone to read using the links below:

https://storify.com/sarahmarley86/aquatic-noise-2016-day-1

https://storify.com/sarahmarley86/an2016-effects-of-noise-on-behaviour-and-physiolog

https://storify.com/sarahmarley86/aquatic-noise-2016-day-3

https://storify.com/sarahmarley86/aquatic-noise-2016-day-4

https://storify.com/sarahmarley86/aquatic-noise-2016-day-5

Congratulations Dr Phil!

It is my pleasure to introduce to you – Dr Philippe Jean-Francois Bouchet!!!

Dr Phil Bouchet and his primary supervisor, Prof Jessica Meeuwig at Phil's graduation ceremony

Dr Phil Bouchet and his primary supervisor, Prof Jessica Meeuwig at Phil’s graduation ceremony

Two weeks ago, Phil graduated from the University of Western Australia.  He also had the honour of delivering the Valedictory Address to close his graduation ceremony:

You can read more about his thesis, publication, and PhD highlights on a specially-dedicated blog post on the Meeuwig Lab website.

Needless to say, I could not be more proud 🙂

Dr Phil Bouchet and his extremely proud partner!

Dr Phil Bouchet and his extremely proud partner!

 

Perth Research Bazaar

Earlier this month, I had the pleasure of being one of 75 researchers selected to attend the inaugural Perth Research Bazaar.

Unix and Coffee

Coding? Just add coffee…

This three-day event offered researchers of all levels and disciplines an intensive introduction to some commonly-used programming software.  We were taught the basics of Unix, Python, R, GitHub, LaTeX, NVivo, and D3 from every-day users of these tools, who were all-too-happy to share their secret tips.  So despite my “imposter syndrome” feelings about coding, I had a really great time and left feeling more confident about programming than I believed possible.

One of my favourite things about #PerthResBaz was how the group interacted through Twitter.  On the first day alone, I think I spoke with more attendees over social media than I did in person!  It allowed us to network with other Perth researchers and provided the opportunity to share our knowledge of different research tools, whilst also keeping up a running commentary on proceedings for those unable to attend.

Given this, I’ve created a Storify summary using tweets from across the three days, broken down to reflect the different sessions and software utilised by the conference.

These events are spreading throughout the world.  This year Research Bazaars were held in Melbourne, Brisbane, Sydney, Auckland, Wellington, Vancouver, Oklahoma and beyond!  So if you ever get the chance, I thoroughly recommend participating.  Better yet, why not bring it to your own institution?  See the main Research Bazaar website for more details.

If this sounds too big, how about hosting a regular Hacky Hour?  These casual meetings generally involve researchers meeting up at a bar or coffee shop to help trouble-shoot each others code.  So if you feel like you need help with your programming (that you could be of assistance to someone else!), look for a Hacky Hour near you!  For those of you in Perth, there is one at Curtin University – follow @CUHackyHour on Twitter for updates!

 

Full Disclosure

Sorry, this isn’t a post divulging all my anecdotes and secrets!  It’s a quick note to point you in the direction of a new page created on this site, titled “CV“.

Here you can find links to my various online profiles listing my work / research history.  Alternatively, you can check out the slightly longer versions by viewing my full CV and Curtin University student capability statement.

Happy browsing!

Roebuck Bay - Sarah on Teena B

Filming snubfin dolphins in Roebuck Bay (Photo:  Joshua Smith)

 

PhD Christmas: Vaguely a Holiday

Whilst working extremely hard on my PhD this morning (ahem), I stumbled across this PhD Comic by the amazing Jorge Cham:

"Piled Higher and Deeper" by Jorge Cham www.phdcomics.com

“Piled Higher and Deeper” by Jorge Cham
http://www.phdcomics.com

Never be in doubt – you are ALWAYS supposed to be working…

But my supervisors are away overseas on Christmas break“, you may think.

This changes nothing. Apart from your sleep patterns by staying up to weird hours trying to match supervisor emails from a different time zone.

Well, at least it’s temporary,” you console yourself.  “Once I’ve finished my PhD it will be different!

Au contraire, mon ami innocent…

A PhD Christmas Story

Last Christmas marked the final 4 months of my partner’s PhD.  So we spent the festive season as all final-stage PhD students should – by working from home and pretending that this was a “treat”, because at least it meant we weren’t in the office.  It actually worked out quite well; I chugged through a LOT of manual acoustic analysis whilst he got some writing done.  And it was nice to spend the days together.  Even if they were days filled with sitting at our laptops in silence, at least we were doing so together!

We took two days off – 25th Dec and 1st Jan.  These days also coincided with our only two trips to the beach in the height of austral summer, despite living 10 minute drive from several lovely beach spots.  But it was all good – only temporary, right?

Life (and Holidays) After the PhD?

Well, now it’s Christmas time again and a pretty familiar scene is playing out.  Except this time it is me entering the PhD-Twilight-Months whilst Phil has moved onto the fabled, glorious lands of a Post-Doc.  But apart from this role-reversal and upgrade, the overall story seems to be pretty similar.  We’re still spending the summer days indoors, glued to laptops, desperately trying to catch-up on work before the universities re-open in January.

And we’re not alone.  Our later-PhD and post-doc level friends are all in the same boat.  Quietly excited to be working from home and enjoying all the little perks this brings:  your own space; no angry-typing from your office mate; option to play Glee songs out loud (and even sing along) without fear of disturbance or judgement; extra sleep as you dodge the morning commute; no meetings or work calls; ability to work in pyjamas and snack on xmas treats…

From what I’ve seen, this doesn’t seem to change much between PhD and post-doc.  Maybe at a higher-up level you eventually reach a stage where public holidays also translate to academic holidays, but it seems doubtful.  You always hear “With great power comes great responsibility” – no one mentions this also means a greater number of working hours.  But at this stage, it’s become so much the norm it is hard to imagine anything different!

Instead, the main frustration comes from people excitedly asking “So what are you guys doing over the holidays?“.  This, of course, is met with a blank expression and the solid reply “Working…” (duh implied).  It’s particularly annoying when this comes from people in the earlier (naiver) stages of their PhD (how can they justify time off?!  Don’t they realise that there is so much to do?!), who receive the same response.  But at least you can enjoy adding a slight hint of condescension, and jazz up the “duh” tone with a twist of “why – aren’t you?”.  And so the unhealthy cycle of PhD guilt continues, expanding to include new generations.  Can’t have Christmas without family!

Not all Bad

The weird thing is that there is a kind of peace to this working-holiday.  It’s nice knowing that most of the people who add to your To-Do list (undergrads, teaching staff, admin, anyone with a ‘real job’) have mysteriously disappeared for 2-3 weeks.  The only deadlines to meet during this lull period are your own – no one else wants anything of you.  Obviously supervisors will have an expectation of progress, but they will also be distracted by family commitments that we (as international orphans) do not have here.  You feel like you’ve won back a little bit of time, so you have to make the most of it by catching up on all the things that are running you dry the rest of the year.

The weirdest thing of all is that I’ve been looking forward to it for months.

Why statistics is not “just maths”

Stats are comingEarlier today, a colleague and I were talking about a paper that we’re working on regarding fish acoustics.  He was asking if I would have time to do some statistical modelling of presence in regard to several environmental variables, and I hinted that I am a bit time-poor at the moment.  While we were discussing who else in the department could help with the statistics, I rattled off a fellow PhD student’s name.

What, them?  But they doesn’t know how to do programming!” said my physics-, engineering-, maths-background colleague in dismay.

But it’s not programming as you think of it,” I replied.  “It’s statistics.

*sarcastic look*

What’s the difference?” he asked.

Well, the answer is that there is a pretty big difference…

Theory vs. Applied

When I was at secondary school, in our final year we had the choice of choosing Advanced Mathematics or Applied Mathematics (aka statistics).

The Advanced Mathematics course taught you how to “select and apply complex mathematical techniques in a variety of mathematical situations”.  This included units such as algebra, calculus, geometry, and equations.

The Applied Mathematics (Statistics) course taught how to “make sense of inherent natural variation in a wide variety of contexts through the collection, analysis and interpretation of data”.  This included units such as hypothesis testing, data analysis, data modelling, and statistical inference.

So basically, one course gave you a year of studying complex, in-depth equations and formulas whilst the other course gave you a year of mathematical problem-solving.  By that time I had already been accepted into studying Zoology, so was strongly encouraged to take this opportunity to get familiar with statistics.  The justification was that it would give me a head-start before I started using statistics in my research later on.

one-does-not-simply-pass-statisticsOf course, the fact that I spectacularly failed the course has nothing to do with anything.  Although in fairness, we started with a class of 30 and were swiftly whittled down to a class of 3 when the other students realised what a true form of hell statistics really are.  Many of them transferred to the Advanced Maths class instead, because they thought it was easier.  And despite my overall grade, it did in fact give me a head-start when I started studying statistics at a university level since most students had never touched the subject before.

As an added bonus, it means I can now also honestly say that you don’t need to pass Maths in high school to succeed in science.  However, this does make me rather unpopular with parents at University Open Days, and as a result I’m generally discouraged from attending…

Fear of statistics – or fear of maths?

Most biologists recoil in horror at the mere thought of statistics. Some less-kind scientists suggest that this is why biologists are studying biology and not a ‘hard’ science like physics.  However, the truth is that most physicists would recoil in horror from the idea of statistics too – if only they had to use them.  But their work is often better captured by the mathematical formulae and equations that fall into the ‘Advanced Mathematics’ camp, rather than modelling natural variation, so the opportunity to dabble in stats never arises.  Instead, mathematical knowledge feeds into computer programming to run loops, calculus, algebraic equations, and a whole number of other mysterious things.

When you create statistical models, yes there is still an element of programming to it.  But the underlying logic is quite different.  Statistics may fall under the umbrella of mathematics, but they have quite different applications.  For example, if I was to write a program that would could calculate different acoustic measurements from a bunch of recordings, this would be quite different to writing some code to compare those resulting measurements.  A fine line, but a line nonetheless.

Each year, I help teach a course on Quantitative Biology – which is basically statistics in disguise.  I help guide undergraduate biology students through their first steps in statistics and introduce them to a simple software program which will do most of the basic stuff for them in a couple of clicks.  Each year there are a few students who complain that they’re no good at maths, that they’ll never understand this, that they don’t see the point.  Yet by the end of term they’re analysing and clicking away without hesitation, and (in the words of one student) “finally understanding the results sections of papers”.  The key is removing the fear of statistics instigated originally by a fear of maths.

“Put your money where your mouth is”

Over the past few months, I have been working towards completing my first PhD paper.  This has focused on describing the soundscape of a section of the Swan River, and among other things involved modelling the occurrence of different sound sources across different temporal scales.  As a result, after a long sabbatical whilst in pursuit of fieldwork skills / scholarships / rent money, I was thrown in the deep-end of statistics.

p-valueAt first I avoided it; there were plenty of other things to do, and to be honest the thought terrified me.  After all, I failed this at school!  My Undergraduate and Masters classes were okay, but not particularly pleasant!  Can’t I just pay someone to do this?!  But, after completing every other possible task, I took a deep breath, opened our collection of Alain Zuur books, and plunged back in.

And whilst I wouldn’t say that I loved it, there was some enjoyment.  I liked investigating my data, confirming relationships, and finding significant results.  There were a few temper tantrums, but hell did I learn a lot.  So for now, I’d say that statistics and I have a cautiously optimistic relationship.

Conclusion

Hey girlSo in summary, mathematics is classroom theory whilst statistics is real-world applied data.  To be good at statistics, you don’t actually have to be particularly good at maths.  What you do need to be good at is problem-solving, applying logic, manipulating information, and pulling biological meaning from numbers.

In fact, I would even go so far as to say there is a significant difference between mathematics and statistics!

[Note – In statistics circles, this joke is hilarious.  Admittedly in normal circles, it may fall somewhat flat.  Hopefully my undergrads get it…]

And if nothing else, at least studying statistics has opened up a whole new world of internet memes!

Heteroscedacity

Famous Last Words

FameLab Australia Final

MC Robyn Williams revs up the crowd at the FameLab Australia Final 2015 (Photo: OK White Lane)

My last post spoke of my experience competing in the WA State Heat of FameLab.  Although I was delighted to be voted the Peoples Choice by audience vote, unfortunately only the winner and runner-up of each state heat progress to the National Final.

Or so I thought…

But a couple of weeks after the State Heat, I received a phonecall from FameLab Australia organiser Chris Hodge, inviting me back to present again as the British Council Wildcard entrant.  So I made it to the Final by a fluke!

Sussing out the Competition

The FameLab Australia Final involved entrants from New South Wales, Victoria, ACT, Queensland and Western Australia.  A mix of PhD students, post-docs, and scientists-with-real-jobs we covered a range of subjects from coughing guinea pigs to spider behaviour, gut bacteria to brain function, biofuel to artificial intelligence.  A mysterious group of people at the best of times, especially when most of us had never met before!

I had the chance to suss out one of the competitors, David Farmer, on a radio interview with ABC Melbourne presenter Lindy Burns.  Ironically, when discussing the Australian competition, the station had managed to select two Scottish people to interview.  So this combined with dolphins, lasers and squishy brains made for some great banter in a pretty unique interview!

With competitors like that, it was obviously going to be some stiff competition…

Love and Science

Media trainer Malcolm Love (far left) with some of the FameLab Australia 2015 finalists

Media trainer Malcolm Love (far left) with some of the FameLab Australia 2015 finalists (Photo:  OK White Lane)

The lead-up to the National Final included two days of media training with science communication guru Malcolm Love.  Chief Trainer of FameLab International, Malcolm was originally a freelance journalist in South America before working for the BBC as a producer on features and documentaries for over 20 years.  He is now a specialist in the public engagement of science, giving lectures on the subject at the University of West England and providing training for a range of science-stakeholders, as well as hosting his own weekly radio show “Love and Science“.  So this guy knows what he’s talking about.

In the training, we covered a variety of topics including body language, story-telling and interview tips.  But one of the best things about it was interacting with people who love science communication.  Many scientists still hold onto a fear of presenting to the public, and worry about “dumbing down” their research or coming across as boring.  But all the participants were obviously people who were passionate about their research, and it is hard not to get swept up in that kind of enthusiasm!  So it was an awesome two days of being a science geek with other science geeks and discussing how to turn other people into science geeks too!

The Final

Nothing like a bad dolphin joke to kick-start your presentation...  (Photo:  OK White Lane)

Nothing like a bad dolphin joke to kick-start your presentation… (Photo: OK White Lane)

A sell-out event with over 200 people in attendance, the final was a bit more nerve-wracking than the state heat.  But I always tell presenters that you just have to try changing the nervous energy into excited energy, so when I stepped up to the spotlight I tried to remember my own advice.  Unfortunately, I still felt my performance lacked the right mix of enthusiasm – even as I was speaking, I knew it sounded over-rehersed.  So although the crowd laughed in the right spots and seemed keen, I knew it wouldn’t be a winning presentation.  But that’s okay – there will be others!

Science is a serious business - need to work on that intense expression!  (Photo:  Ok White Lane)

Science is a serious business – need to work on that intense expression! (Photo: Ok White Lane)

The overall winner of FameLab Australia 2015 was Dr Sandip Kamath, with Dr David Farmer coming a close second.  Sandip is studying shellfish allergies at James Cook University, and spoke of his ambition to help people overcome these reactions – with the help of Mr Pinchy the lobster, his side-kick slash prop.  David moved away from squishy brains and lasers to give a fascinating description of his research at the Florey Institute of Neuroscience, investigating the cough reflex and brainstem function.  To see photos from the night, check out the British Council Flickr Page.

And, of course, we all had fun celebrating at the FameLab after-party!  The official function was in the WA Maritime Museum, with some speeches and lots of well-wishers…  But the scientists and British Council crew headed out into Fremantle to celebrate afterwards!  After all, we’re twelve of the top young science communicators in the country!

So now, as Sandip flies to the UK to compete in the FameLab International Final at the Cheltenham Science Festival, for the rest of us it is back down to Earth.  I’m back in a world of fieldwork, marking student assignments, and desperately trying to finish the first scientific paper of my PhD.  I can see all my new sci comm pals talking about the same reality bump on Twitter.  But to be honest, getting back to research is quite exciting enough… for now!