Research Internship – marine mammals and sea turtles

For those of you interested in marine science and boat-based field research:

Fall 2013

Marine Mammal and Sea Turtle Research Internship

Program Description
The IMMS Research Internship Program is designed as a way for students interested in a career in marine science to gain valuable research experience in a real-world setting. Interns will participate with multiple projects involving bottlenose dolphins, sea turtles and diamondback terrapins. As an intern, you will be trained in all aspects of dolphin photo-id research, sea turtle satellite tracking, and other current research projects at IMMS. Interns will also participate in other operations at IMMS including stranding response, education, and animal care. Our goal is to give Interns a well-rounded experience in a variety of areas while providing expert training and experience in marine science research.
Principle Duties include: data entry, searching and cataloging journal articles, learning all research protocols, cropping and sorting photo-id fin images, learning to use photo-id programs such as Darwin (fin matching software), and FinBase (Microsoft Access), boat based field research (21’ and 31’ boats), and learn how to use ArcGIS

• Secondary Duties involve: Assisting with animal care staff, attending marine mammal necropsies, responding to marine mammal and sea turtle strandings, and assisting with educational tours.
• Field days: Interns must be able to spend many hours on the water and on shore in sometimes extreme seasonal conditions. Seasonal temperatures range from over 100 °F in summer to 30 °F in winter. Field days typically exceed eight hours and occur at least two or three times a week.

To Apply: Please visit our website at http://imms.org/internship.php

Null Hypothesis: Y U NO good enough for scientific articles?

If you’ve ever been involved in a scientific endeavour, there is a good chance you are familiar with the null hypothesis (which I’ll call H₀). Basically, it is the opposite of the “real” hypothesis of a study. Say you want to demonstrate the following effect: chocolate consumption improves memorising skills. Your corresponding H₀ would be the absence of such an effect.

In the ensuing statistical analyses, you’ll probably want to disprove the H₀ to reject it in favour of your alternative hypothesis, thus showing a significant effect of chocolate on memory.

However, finding this Saint-Graal of inferential statistics is not the easiest thing. I won’t talk here about what influences this since it isn’t anything close to my area of expertise – I’d rather not ridicule myself. Rather, I’d like to discuss a little bit the overwhelming discrimination against unrejected H₀s in the scientific literature.

You see? Source: xkcd

In my school projects so far, I have NEVER found ANY significant effect. EVER. It is disappointing. Most of all, my apparently consistent inability to reject the H₀ made me think that, further in my academic career, I’d never be able to publish an article.

Indeed, most scientific journals accept almost only articles that contain significant effects (I don’t have numbers about this phenomenon, sorry). This attitude suggests that unrejected H₀s somehow signify a lack of (convenient?) information.

But don’t they say that absence of evidence is not evidence of absence? Just because one team couldn’t reject the H₀ doesn’t mean that their results are devoid of interest.

My point exactly! Source: muddylemon

For one thing, publishing unsignificant results would be like taking into account antimatter in addition to matter (i.e., significant results). They represent as revelant an information. Choosing to communicating them, instead of concealing them, would help increase transparency in science.

Secondly, researchers interested in replicating the experiment could focus on improving the methods rather than on inventing a whole procedure from scratch. This would mean saved time, saved money, collaboration opportunities and possibly less frustrating research.

Finally, and perhaps most importantly, information on “failed” experiments could help prevent un-needed research from happening. Steven Reysen, from the Journal of Articles in Support of the Null Hypothesis, explains it better than I do:

The file-drawer problem is that psychologists, and scientists in general, will not report research that does not meet traditional levels of significance. If a study has null results psychologists will often abandon the research to move on to other ideas and not report the findings. The result is that the journals are filled with studies that reached significance. For example, there may have been 20 null studies conducted on a topic but one significant study reported in the literature. If I then try to research the same topic I may be wasting time and money on that idea.

Clearly, I am in favor of the scientific community paying more attention to the H₀/null hypothesis than it does at the moment, and not only because this could potentially give me a better shot at publishing my work.

What do you think? Publishing articles without significant results: yay or nay?

Related articles

• Friends don’t let friends calculate p-values (without fully understanding them)
• The Perils of Hypothesis Testing … Again
• Improving Transparency in Scientific Research

Can you identify dogs’ emotions from their facial expressions?

Have you ever wondered what our canine friends think, or rather, feel? Being capable to recognise dogs’ emotions would surely be a useful ability, whether you are an owner concerned with you pet’s well-being or have an interest in avoiding being bitten by dogs in general. Do you believe to possess such an ability?

Don’t mind the lack of space between “Some” and “day”. Source: MemeCenter

Researchers in the Unites States (Bloom & Friedman, 2013) found that humans can, in fact, classify rather accurately “the emotions conveyed by photographs of facial expressions of a dog”.

Even people with little to no experience with dogs could do that. The fact that learning was found to influence results only a little suggests that we might have somewhat of an inherent ability to recognise emotions in dogs. It is indeed possible that, during the domestication process, humans selected dogs whose affective states were more easily recognisable.

Bloom and Friedman partly drew from psychology and the affective sciences to develop their experiment, namely the work of the famous Paul Ekman (on whom the TV show ‘Lie to Me’ was based) and his colleagues. They created seven “behaviorally defined” scenarios to induce seven emotional states in the participating dog – happiness, sadness, surprise, disgust, anger, fear, and neutral, which served as a control condition for comparisons.

Inspired by their methods, I attempted to replicate two of those conditions. Below are the photographs thus obtained, accompanied by emotionality rating scales for each of the six basic emotions.

What I want YOU to do (yes, you, the person reading this post right now) is to rate the photographs. Each of them may contain one emotion or mixed emotions. Report what emotions, if any, you perceive as present, and to what degree. There is no right or wrong answer. You should choose only one option out of the five available for each emotion.

I am very curious to see how you guys interpret the facial expressions of my dog Charlie! In a future post, I will make sure to reveal the scenarios I used as well as the emotion I hoped to thus induce.

Ciao!

Reference:

Bloom, T., & Friedman, H. (2013). Classifying dogs’ (Canis familiaris) facial expressions from photographs. Behavioural Processes. doi: 10.1016/j.beproc.2013.02.010

The Influence of Colour and its Intensity on the Enjoyment of Flavour

A slightly updated (and translated (and blurry, apparently)) version of a research project I co-conducted for a college course a while back.

We had to follow some strict guidelines, which is why this video isn’t entertaining in nature. It’s more of a copy of the oral presentation we did, which, by all means, you are free to criticize! No, but really, I’d love some feedback (except for my apparent articulation problems – I discovered them while listening to the video :s).

ethology Investigates 2013

A little announcement for ethology fans/nerds out there:

The next online conference ethology Investigates will take place from the 15th to the 17th of April, focusing this year on “the behavior of invasive species and their impact on the host environment.”

Check out their website for information on how to register and participate in the discussion.

PS: Boy, I’m just content spamming today, aren’t I?

Volunteer – Behavioural Ecology and Conservation of Bottlenose Dolphins

Why don’t I live in New Zealand, damn it?

Bottlenose Dolphin Tursiops truncatus

Volunteers required to assist with a study of bottlenose dolphins (Tursiops truncatus) in Northland, New Zealand

Program:

The Coastal-Marine Research Group (C-MRG – http://cmrg.massey.ac.nz/) was established under the auspices of the Institute of Natural Sciences (INS) at Massey University, Albany, New Zealand in 2000. Since then, both its staff and postgraduate students have undertaken marine mammal research within and beyond New Zealand waters, concentrating specifically on conservation and management orientated questions.

Volunteers are required to assist on a PhD study (supervised by Dr Karen Stockin, Massey University and Prof Mark Orams, AUT University) to assess the behavioural ecology and conservation of bottlenose dolphins (Tursiops truncatus) in the Bay of Islands, Northland, New Zealand. Bottlenose dolphins are classified as nationally endangered within New Zealand waters (Baker et al 2010), with a local population recently described (Tezanos-Pinto et al in press). This study builds upon earlier research undertaken by Tezanos-Pinto (2009) and Constantine (2002) and will among other things, reassess the status and effects of tourism interactions (a decade on from Constantine 2002).

The field season runs year round and volunteers are required for all periods. A minimum commitment of three months is preferred, with priority given to those who can commit for longer periods.

The volunteer team will be required to fulfill several key roles:

1) Assist on a 5.5m dedicated research vessel operating from the Bay of Islands. Surveys will involve daily return trips (not overnight) and be conducted in favorable conditions only. As such, no minimum or maximum number of research days onboard the research vessel can be guaranteed

2) Assist with vessel of opportunity data collection in the Bay of Islands

3) Assist with data processing and preliminary analysis on bad weather days

4) Undertake additional responsibilities/roles as the season progresses

5) Effort will placed into allowing all volunteers the opportunity to gain experience on each element.

Volunteer requirements:
1) Be adaptable and patient – field work is highly weather dependent and could include long, consecutive days both on and off the water

2) Be enthusiastic and team orientated (both in a living and working environment)

3) A willingness to learn

4) Possess a positive attitude

5) Be polite to, and engage positively with, the local community

6) Be physically fit and able to work in outdoor conditions

7) Speak English

8) Possess basic computer skills (excel, word, etc)

Preferred (but not necessary) skills/traits:
1) Be enrolled in, or have completed, a degree in a related field (Biology, Zoology, Marine Biology, Animal Behaviour, etc)

2) Have small boat experience

3) Have previous (marine) field experience

Enthusiasm and demonstrable commitment to the project will supersede formal qualifications. Volunteers will be expected to work and live as part of a team with shared cooking and cleaning duties. Unfortunately, monetary compensation cannot be provided, and volunteers will be required to pay for their own food and accommodation. However accommodation will be provided in the field research house at a reasonable rate. Volunteers must pay and organize for their own transport to the field site (3 hours North of Auckland). Information, prices and assistance can be provided to successful applicants.

Application process:
Applicants should send a short email cover letter, using ‘volunteer opportunity’ as the subject line, to c.peters@massey.ac.nz. The email should include an outline of why you would like to work on this project, your availability and relevant experience. Please also attach a brief CV including at least one reference.
Early application is recommended to avoid disappointment. Successful applicants will be notified ASAP.

This is a great opportunity to work in a dynamic environment and gain further experience, whilst working on an important research project. For more detailed information on the project please do not hesitate to contact me.

Thank you for your interest.

***********************************************
Catherine Peters
PhD Candidate
Coastal-Marine Research Group
Institute of Natural Sciences
Massey University
Private Bag 102 904
Auckland
New Zealand
Tel: + 64 (9) 4140800
Ext: 41196
Mob: + 64 (0) 211058040
Email: c.peters@massey.ac.nz
Web: http://cmrg.massey.ac.nz/

The qualities of light: luminance, colour and… polarisation?

Did you know (I didn’t) that light has a third quality? Named polarisation, it is “the direction of the electric vector (E-vector) of light” (Nilsson & Warrant, 1999, R535). Light coming directly from the sun is unpolarised, meaning that its E-vector is not fixed and is kind of all over the place (super scientific and accurate description, immaright?). But that is not a very interesting case since most of what we see contains polarised light. How does that work? Nilsson and Warrant (1999) summarise it for us:

… light reflected from glossy surfaces becomes strongly polarised at an angle parallel to the surface. Light refracted through such a surface becomes polarised in the orthogonal direction. Scattering is another optical phenomenon that may produce polarised light.

That’s how I understand it, anyway.

Most vertebrates perceive objects in terms of how bright they are (luminance), which wave length they reflect the most (hue) and the degree to which they do so (saturation). Some birds, reptiles, amphibians and fish seem to be able to also perceive the two aspects of polarisation (angle and degree). However, invertebrates are the ones that really know where it’s at! For example, aquatic insects use polarisation to find befitting bodies of water.

The champions of polarisation perception are mantis shrimps/stomatopods and cephalopods. The former possess “true polarisation vision” – in other words, they can discriminate elements in the environment solely on the basis of polarisation – while also displaying, along with cuttlefish and squids, polarisation patterns ON THEIR BODIES! I think it’s possible that perceiving polarisation became more and more important in those lineages as they evolved body patterning, perhaps as a means of signalling information to conspecifics (though I’m way out of my league here).

Mantis shrimp. Credit: Wikimedia Commons

How does this type of vision work? I’m sorry to say that our loyal rods and cones cannot help with that, because the visual pigment they contain can spin however it wants inside the cell. In arthropod rhabdomeric photoreceptors, on the other hand, the pigment is aligned, fixed in a certain position. Thus, it makes each receptor highly sensitive to a certain E-vector, a little bit like human cortical cells (in the visual cortex) that respond preferably to specific orientations of a stimulus.

Information from the polarisation of light can be used for navigation, judging the quality of leaves, signalling, camouflaging, and enhancing the sensory input by augmenting the contrast, for example.

But the most important question is: what do variations in polarisation look like????

Any ideas? Nilsson and Warrant suggest imagining it might be as difficult as it is for colour-blind people to understand how a red raspberry stands out from the green foliage when the luminance is the same. It’s probably impossible for us to fathom the appearance of polarisation, but I’d love to read what anyone thinks about it!

Reference:

Nilsson, D.-E., & Warrant, E. J. (1999). Visual discrimination: seeing the third quality of light. Current Biology, 9(14), R535-R537. doi: 10.1016/S0960-9822(99)80330-3

Link Stack

Lately, I came across some other interesting links, so I thought I’d share them here

>> Test your patterns of unconscious thought (biases) = http://www.the-twist-project.eu/en/iat/intro/?embed

>> ’10 tips when asking for a letter of recommendation’ by Chris Buddle

>> Super sweet article about octopi; the recounting of an octopus-human meeting, especially, truly makes you realise how alien, intelligent, and cute they are (I think I’m in love <3) = http://www.orionmagazine.org/index.php/articles/article/6474

>> A biologist’s tumblr, or “A compendium of knowledge gleaned from seemingly endless scholarly pursuits in the wild.” His series of “Things I learned as a field biologist” is very funny!

>> Biodiversity + Trading card game + Crowdsourcing = PURE COOLNESS, and it’s called Phylo.

>> CROWDFUNDING FOR SCIENCE RESEARCH !!! = microryza.com is like a KickStarter for scientific projects.

This Is What A Scientist Looks Like

This Is What A Scientist Looks Like = Check out this cool blog!

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Cognition in the wild, brought to you by the Rufous Hummingbird

Today’s date is 03/14 (that is, in the foolish countries that put the month number first), so it has become ‘Pi day‘. Few realise that it’s also Albert Einstein‘s birth date… and mine!

To celebrate, I’ve decided to write about my preferred animal behaviour topic (thus far): the study of cognition in the wild!

(￣￢￣) Close enough

Why is it relevant? Because to understand the evolution of cognition in vertebrates, we need to examine animals’ abilities under natural conditions, where they face having to find food and mates, all the while evading all sorts of dangers. That way we can hope to identify some of the factors affecting the selection pressures at work. It is true that for some species, especially “smaller” ones, the line between the laboratory and the natural environment can get very blurry, if not inexistent. For “bigger” ones, though (like birds, mammals, and reptiles), the border is quite real. And those are the animals I’m interested in (again, thus far).

With doing something as messy as studying invisible processes in a rather uncontrollable environment comes great responsibility an assortiment of challenges. Let me list some of them as mentioned by Healy and Hurley (2013) in their review on ‘What hummingbirds can tell us about cognition in the wild’:

• The participants may use different cues than in the lab, or use them differently, during tests;
• Their ‘answers’ may not reflect the psychological dimension you’re trying to measure (an issue shared with all kinds of tests, I’m afraid);
• How to make sure they’re motivated to actually participate?
• What task to use?!?!! Meaning: what dimension are we going to choose to extrapolate their cognitive abilities??

Quite alarming, isn’t it? Well, it can be less so if you’re thoroughly prepared.

First, you need to find a “logistically amenable to testing” species which, in Healy and Hurley’s case, were rufous hummingbirds Selasphorus rufus. They focused on the males because those guys are territorial, so they fight off conspecifics from their patch, and feed frequently enough that nice amounts of data can be collected each day.

Rufous Hummingbird Selasphorus rufus. Credit: jessi.bryan on Flickr

Then, the species’ ecology should be such that you can formulate predictions about the abilities that might have been ‘encouraged’ by evolution, the same abilities that you’ll want to investigate. This requires, in particular, knowledge of their sensory ecology, of how they apprehend the world and might apprehend your experimental task.

I won’t go into too much detail here about the methods used by the authors and their colleagues in their experiments. They describe them rather well in their paper (see below for a direct link to it). But I will tell you this: it involves artificial flowers, arranged differently depending on the ability studied. As an example, in studying 3D spatial cognition:

… when flowers were presented on a vertical pole …, birds found it difficult to learn which one of five flowers was rewarded but when the flowers were presented along a diagonal pole, the birds were relatively quick to learn which was the rewarded flower (Flores Abreu, Hurley & Healy, 2013). Here it appears that the addition of a horizontal component to the flower’s location may have facilitated the learning of its vertical component.

Another set of findings they discuss are related to the use of colour, or lack thereof, in learning flowers’ refill rates – rufous hummingbirds use this cue “only when space is not relevant”. They also seem to possess a somewhat episodic-like memory, meaning they can simultaneously retain information on the what, the where and the when of an occurrence.

YES

They conclude by stating that more data from comparative research is needed to continue figuring out the interaction between cognition and natural selection, especially the benefits of cognitive abilities as they pertain to particular animals and to their ecological demands.

This ‘required research’ business is very cool! Because an increased number of people understanding the necessity of it means that, maybe, just maybe, my own interests in the topic could one day neatly align with a supervisor’s and, who knows, some grants committees’…

Reference:

Healy, S. D., & Hurley, T. A. (2013). What hummingbirds can tell us about cognition in the wild. Comparative Cognition and Behavior Reviews, 8, 13-28. doi: 10.3819/ccbr.2013.80002 <– THAT’S THE DIRECT LINK