Category Archives: Research

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)

 

First PhD Chapter Published!

After months of graft, I’m extremely chuffed to announce that my first PhD chapter has now been published online!

Chapter 1 - Marley et al 2016

To view the full article, please visit the Springer website.  If you have any issues, please contact me.

One down, one draft on supervisor’s desk, and three more to go!

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

Is it a plane? A duck? A police car? No, it’s a fish…

For the last few weeks I have been working on the first chapter of my PhD describing the underwater soundscape of the Swan River.  Overall, this has been a really good way of becoming more familiar with identifying underwater sounds.  By far the most baffling of which have come from fish.

Hard-core headphones are becoming my default fashion accessory at the moment...

All about that bass: Hard-core headphones are becoming my default fashion accessory at the moment…

It turns out that many fish species produce a whole variety of ridiculous sounds, including quacks, knocks, grunts, sirens, trumpets and even Rolf Harris impersonations (sounds like his infamous wobble-board).  These sounds are all produced in different ways:  some are made using sonic muscles located on or near the swim bladder; others sounds are the result of the fish rubbing together or striking its skeletal components; and sometimes even changes in swim speed or direction can result in noise production.

But, like many animal sounds, the purpose of many fish noises is still to be determined.  Sound production might be intentional, in the form of vocalisations or calls, in which case noises are most likely signals to other animals (e.g. to attract mates, warn off competitors, co-ordinate with conspecifics, or raise the alarm about predators).  However, sounds can also be produced unintentionally as the result of feeding or swimming.  And when your subjects are mostly occurring in the cold, dark oceanic depths it can be pretty tricky to figure out the behavioural context of recorded sounds!

The majority of sounds produced by fishes are of low frequency, typically less than 1000 Hz.  By themselves they can be pretty hard to pull out of a large dataset, thus requiring a systematic search through potentially months of data.  But a really cool characteristic of some fishes is that they call in choruses.  This is when multiple (dozens or even hundreds) of individual fish within the same area produce the same call.

These choruses occur all over the Australian continental shelf, in both tropical and temperate waters and were first discovered in the late 1960s.  Many show significant seasonal trends in chorus levels and differences between years, potentially indicating that chorus activity reflects secondary productivity (see “Continental shelf fish choruses in Australian Waters” by Robert McCauley and Douglas Cato).  Others are reliably produced at specific times of year, and are believed to be associated with reproduction (see “Fish choruses from the Kimberley, seasonal and lunar links as determined by long term sea noise monitoring” by Robert McCauley), although the nature and intensity of some reproductive choruses can change in association with physical and environmental cues (see “An investigation into active and passive acoustic techniques to study aggregating fish species” by Miles Parsons).  Thus, these calls can play significant roles in the life function of many species.

Great to know that, in all these long hours you spend sitting at the computer, you are probably listening to fish sex!

Discovering Conservation

Discover Conservation_Sarah InterviewA couple of weeks ago I had a very fun interview with James Borrell, a conservation biologist with a passion for science communication.  Apart from studying the genetics of trees, James is also the founder of Discover Conservation – a website which aims to tell the stories of field scientists and, by doing so, inspire an appreciation for conservation in people around the world.

My interview with Discover Conservation discussed my PhD research on bottlenose and snubfin dolphins in Western Australia, but also touched on my “science story” and how I got where I am today.  It finishes off with some of my advice for young conservationists, particularly those currently trying to find work experience.

Interested in more information?  Read the full article here!

And the winner of the 3-Minute-Thesis competition is…

3MT Trans-Tasman Competition 2014 Sarah Marley and Rosanna Stevens

3MT Trans-Tasman 2014 Sarah Marley and Rosanna Stevens

…  Sarah Marley from Curtin University

When I heard those words, my heart stopped.  I did the “shocked-actress-wins-award” face.  I hugged my friends sitting on either side.  I repeatedly gasped “oh my goodness“.  I may have even made a rather embarrassing Oscar-worthy acceptance speech.  Now over a week later and I am still riding the high 🙂

View the talk below:

Now let’s back up a bit.

The 3-Minute-Thesis (3MT) competition was developed by the University of Queensland back in 2008.  It was intended to be an exercise in communication for graduate students, giving them just three minutes to explain their PhD to a generalist audience.  Since then, the competition has expanded to universities around the world.

I’ve known about this competition for a couple of years now, after seeing various friends compete to present their own PhD at other universities.  I couldn’t wait to become a student myself and give it a go!  So when Curtin University emailed around to announce that registration was open for the 2014 competition I immediately sat down, wrote my talk in 20mins, and started practicing!

The Curtin heats were a couple of months ago, where I surprised myself by not only making it through to the Curtin Final top ten but also by winning my heat.  “A great start,” I thought.  “Now back to fieldwork!” as I prepared for the second trip up to the Kimberleys.  A few weeks later, I made the special one-night-only trip back from Broome to Perth for the Curtin Final, and won both the Final and the People’s Choice award!  Certainly justified the trip down!

All the competitors from the 3MT Trans-Tasman 2014 competition at UWA

All the competitors from the 3MT Trans-Tasman 2014 competition at UWA

But the Trans-Tasman Competition was the hardest yet.  I was competing with winners, so you can imagine that the standard of talks was extremely high!  Most amazing of all was the team spirit – everyone was so nice to each other!  After every presentation, the speaker would return to the “green room” amid cheers and high fives from their opposition 🙂  It was a great vibe!

Then it was time to give my talk…

Not a stutter in sight!  Quite different to a couple of years ago...

Not a stutter in sight! Quite different to 4 yrs ago…

As I stepped on stage, I felt such a buzz.  I love the work that I do, and the opportunity to talk about it always gets me excited!  Quite a far cry from four years ago, when I could barely give a short talk to a group of friends without blushing and stuttering my way through the presentation.  So I felt a certain glow of accomplishment at having enjoyed something that just a few years would have terrified me!

From a happy glow to radiating surprise, I was ecstatic to be chosen as winner of the 3MT – but the whole experience was a delight!  From the thrill of presenting to the team spirit backstage to the happiness of making new friends, the whole 3MT journey has been a blast.  If you ever have the opportunity to take part I would thoroughly encourage you to do so!  Even if you’re not confident of your presenting skills, just ask yourself – when will you get a better opportunity to try?

But work on your potential acceptance speech beforehand, and practice your photo face:

Me laughing manically as I receive my giant novelty cheque from sponsor James Mercer.  Sorry James...

Me laughing manically as I receive my giant novelty cheque from sponsor James Mercer. Sorry James…

Now all that is left is for me to thank my partner, my friends, my family, my university, the organisers, the sponsors, the judges, the competitors, the audience, the backstage staff, my high school science teacher, my pets…

Studying Snubfins in the Kimberleys

Have you ever heard of a snubfin dolphin?  Not many people have – and up until 2005, no one had at all.

Snubfin dolphins in Roebuck Bay (Photo Credit:  Sarah Marley)

Snubfin dolphins in Roebuck Bay (Photo Credit: Sarah Marley)

In that year, what was previously considered to be a bunch of Irrawaddy dolphins swimming around off the northern coast of Australia, was discovered to actually be a separate species entirely.  And so snubfin dolphins became Australia’s first endemic species of cetacean.  But now, almost ten years later, we still don’t know a whole lot about them.

As part of the Kimberley Marine Research Program, the Western Australian Marine Science Institution (WAMSI) is funding research into the distribution, abundance and genetic connectivity of Australian snubfin and humpback dolphins across the Kimberleys.  This is a collaborative research project, involving scientists from Murdoch University, Curtin University and Australian National University.  Through a mixture of visual observations from vessel-based surveys and acoustic monitoring using underwater noise loggers, the project hopes to improve our knowledge of where and when dolphins occur.  It will also investigate the effectiveness of using noise loggers as an alternative technology for collecting data on distribution and seasonality of dolphins across the Kimberleys.

Listening for snubfin dolphins in Roebuck Bay

Listening for snubfin dolphins

During July and August this year, I was fortunate enough to be involved in the Roebuck Bay component of this project.  My supervisor Chandra and I spent a few weeks working with Dr Deb Thiele (Australia National University) to collect visual and acoustic data on the snubfin dolphins of Roebuck Bay.  It was a real pleasure to work with Deb, who has been conducting research in Roebuck Bay for several years on the abundance, habitat-use and behaviour of this snubfin dolphin population.  We were also working in with local Yawuru Indigenous Rangers Cornell and Johani, who helped us on the boat to collect observational and photographic information on the dolphins.  And to finish off our Snub-Team, we had Jason from Environs Kimberley who helped us navigate through the bay.  The Kimberleys are a stunning place in general, but it was especially great to explore it with people who know the area (and its wildlife) so well!

Over five weeks, we spent a lot of time out on the water and became familiar with a whole host of Roebuck Bay’s other marine residents.  Sightings of dugong, turtles, manta rays, sharks, sea birds, and various fish made every day unpredictable but very special!

Chandra, me and Deb

Chandra, me and Deb.

I’ve been remarkably quiet the last wee while partly because I’ve been away on fieldwork.  But also because it involved such amazing animals, cool people, and beautiful surroundings that I had no idea how to begin describing it!  A large part of PhD life revolves around stress – the pressure of making progress, meeting deadlines, producing outcomes.  But an important part of PhD life is to realise how lucky I am to have these experiences, travel to these places, and meet these people.  And this trip was definitely one of those fortunate events.

The Last 55: Final chance for Maui’s dolphins

Maui's dolphinFifty-five is not a big number.  But it could mean a world of difference to one small dolphin species in New Zealand.

Maui’s dolphin is the world’s rarest and smallest known subspecies of dolphin.  Found only in New Zealand,they typically range close to the coast in small pods although they can also be found around harbour mouths and further offshore.  But their numbers have been decreasing due to entanglement in fishing gear and disease, with approximately 4 to 5 Maui’s killed each year.  Which doesn’t seem like too many, right?

A bit of maths

In the 1970s, the dolphin population was reportedly around 1,800 individuals.  But the species has rapidly declined since net-setting and trawling were introduced in the 1970s.  A 2012 research study estimated that only 55 Maui’s dolphins now remain.  Suddenly that 4 to 5 death rate seems a lot bigger.  So just since that study was conducted, we are probably already approaching a population size of around 40 animals. Extinction isn’t just a threat – it’s a very real likelihood.

If we are losing 10% of the population each year, you don’t have to be a mathematical genius to know that things aren’t looking good for the Maui’s.  Especially given their slow reproduction rate – females reach maturity at approximately 8 years of age, and only have one calf every 2 – 4 years.

What is being done?

The New Zealand government generally has a pretty good standing when it comes to conservation.  In 2003, a ban on commercial set nets was added to an existing ban on recreational netting from north of Auckland to north of Taranaki, covering out to four nautical miles from shore.  In 2008, this was extended to seven nautical miles and in 2012 the ban on set nets extended further south.  Last year, the Minister of Conservation finalised a Maui’s Dolphin Threat Management Plan, which includes codes of practice for seismic surveys, regulations for inshore boat racing, and the establishment of a Maui’s Dolphin Research Advisory Group.

So are things improving?

Debatable. Although various marine protected areas have been created with the aim of conserving Maui’s dolphins, the government has failed to extend protections to areas where there have been credible recent sightings of the animals.  That’s the thing about marine mammal conservation – these are free-ranging animals who cover large areas in a dynamic habitat.  Thus, the distribution of populations will change over time and so needs constant re-assessment if protected areas are to have a positive effect.  But this is an investment the NZ government seems unwilling to make.

And despite several promising moves on the government’s part, it looks like money might win through in the end.  This week, it has been reported by several news groups that the West Coast North Island Marine Mammal Sanctuary – home to the Maui’s dolphin – has been signed off for oil and gas exploration.

The NZ government signed off a block offer of sea and land in April, which includes a 3,000 square kilometre overlap into the sanctuary.  Oil and gas development in this area could have a devastating impact on Maui’s habitat by increasing levels of underwater noise through seismic surveys, as well as putting the area at greater risk of oil spills.

The government has already had previous bungles with the block offer, with Simon Bridges, the Minister of Energy and Resources signing off New Zealand’s biggest forest park for drilling – despite having never heard of it.  Not exactly reassuring that the government is taking conservation seriously.

In fact, politicians are arguing whether this is even an issue, and NZ Conservation Minister Nick Smith is insisting that there hasn’t been a single observation of a Maui’s dolphin in the proposed exploration area.  So no need to worry.

But you have to wonder how hard they’ve looked?

What you can do

Numerous scientific and conservation groups have already called for the New Zealand government to take action to save the Maui’s dolphin.  Just last week, the International Whaling Commission urged the government to do more to save the species, stating that it had “extreme concern” about the decline in Maui’s dolphins.

In a recent report, the IWC estimated that Maui’s will decline to just 10 adult breeding females in six years and become functionally extinct in less than 20 years – unless their full range is protected from gillnetting and trawling.

Screen Shot 2014-05-19 at 9.15.55 amWWF have stepped up their “Last 55” campaign to save the Maui’s dolphin, urging parliament to announce permanent measures that remove fishing gear which kills dolphins and help affected fishermen adopt dolphin-friendly fishing methods.   “Anything less will not give the species a fighting chance at survival.”

Support their campaign by signing the WWF online petition here.  And hopefully we can convince the New Zealand government to stop faffing around and start taking effective steps to save the Maui’s dolphin.

The (After) Life of a Whale

Over the last few weeks, a small town in Canada has lived in fear of exploding whales.

Seriously.

A Whale of an Explosion

At the end of April, a dead blue whale washed up on the shore of Trout River, Newfoundland.  Amid concerns it could be a shipping hazard if dragged out to see, locals were forced to leave the whale decomposing on the beach whilst local and federal authorities argued over who should deal with the remains.

Inside a blue whaleThe carcass then proceeded to expand to about twice its normal size due to bloating from methane gas, a normal by-product of decomposition.  Unfortunately, there is only so far a bloated blue whale can stretch, leaving local residents on stand-by for a pretty big bang.  Strange as it sounds this is a legitimate concern – last year a washed up sperm whale in the Faroe Islands exploded as a biologist attempted to dissect it (warning:  video not for the faint-hearted).

Eventually, a team from the Royal Ontario Museum headed over to dismantle and remove the blue whale – a feat which took them almost a week.

A Sight to See (and Smell…)

Whale carcasses aren’t that great in general, regardless of their explosive potential.  A few years ago in Scotland, I took my sister to see a washed up sperm whale at our local beach.  We arrived at the car park and started walking.  When we were 1km away, she sniffed a few times and asked “What’s that smell?”.  It only got worse.

Dead sperm whale - winner of Aberdeen's Top Tourism Attraction 2009.

Dead sperm whale – winner of Aberdeen’s Top Tourism Attraction 2009.

But despite this, hundreds of people came to see it.  The carpark was overflowing for days whilst people made the trek to see the spectacle because, dead or alive, it’s just not every day you see a sperm whale.  People brought their kids (who poked it), dogs (who rolled in it), and cameras to remember the experience.

So, given the high number of marine mammals out there, why aren’t we constantly assaulted by the stink of washed-up whales?  When they’re not washing up on our beaches and becoming a gruesome attraction, what happens to the remains of whales and other marine life?  The answer:  Whale Fall.

Whale Fall

Deep-sea zones are pretty special when it comes to food-chains.  A lack of light means no plant life, which is generally the foundation of most food webs.  Instead, the deep sea ecosystem consists mostly of scavengers, who are fed from above by a constant drizzle of organic particles and detritus known as ‘marine snow’.

But every so often, a really big particle falls in the form of a whale.  And when this happens, the whole community turns up for a feast.

Recently, a deep-sea graveyard was discovered off the coast of Angola by remotely-operated vehicles (ROVs) conducting oil and gas exploration.  Consisting of a dead whale shark and four rays, this represented a surprisingly high concentration of deceased megafauna over a relativley small area.  Scientists are now using this footage to compare the species composition of scavengers on the shark and ray carcasses to the scavenger species present on whale falls.

Ecosystems within ecosystems.  A pretty cool example of how life goes on!