It has been a while since I blogged, and I could go into details about a desire to ‘disconnect from the online world’ or give excuses that ‘there are too many things that occupy my time’, both of which are true…but that is for another time.

I wanted to post some reflections following the publication of a paper that represented contributions from a number of brilliant collaborators, particularly because we need a good news story in basic sciences.  I also wanted to reflect a little to give younger scientist reason to be positive about science.

Last week, we (collaborators from Brasil and Canada) published a basic discovery paper entitled: Seasonal reproductive endothermy in the tegu lizard” in Science Advances, the open access sister journal to Science, published by the AAAS.

The discovery has been well covered in the media already (see links here), and I will not go into too many details here, since it is all openly available at the link above, except to say that we discovered an animal that is usually considered to be ectothermic (“cold-blooded” is the horribly inaccurate term used by non-scientists) can become endothermic (“warm-blooded” – another equally uninformative and antiquated term to describe a complex array of metabolic changes), and it does so during the reproductive season.  As careful scientists, we did not comment in the study on their reproductive activities or indeed we had no measurements of what they were doing, so the link to reproduction is indirect at the moment.  The study was simply an observation that they become warmer during this time of the year and that the degree to which they warm up cannot only be explained by the usual suspects (e.g. behavioural thermoregulation, thermal inertia).

Here are the results of the study, depicted simply as a thermal image:

Shown above is a small group of tegu lizards sharing the same burrow (they do so voluntarily, although probably with a little “aggro”).  This image was captured in the early morning hours (~5-6am) before sunrise during the breeding season, so the tegus should have been as cold as they could be from the previous day of basking.  One is a little bit cooler than the other two in temperature, but all three are quite a bit warmer than their surroundings.  They are achieving this through a rise in metabolism and because of an escape from the outside air, are able to slow their rates of heat loss.

Indeed, occasionally, a tegu doesn’t make it back into the burrow at night, so that the next morning when we find it, it is quite frigid.  This is because the endothermy isn’t operating at the same capacity of that of a bird or mammal and that it is not necessarily thermoregulatory in nature.  Here is a rather cool tegu found trapped outside a burrow on a cool night (~6am), with a low body temperature:

Anyhow, what is more important for me to write about is something I only thought about after the media started calling us, and that is that not all science follows the painfully boring description kids are given in school about the laborious scientific method.  Allow me to explain by way of giving the “human side” to a fun research collaboration, while also writing this as a parable for the way that science truly proceeds.

The Best Laid Plans of Lizards and Men Often go Awry

This study began as a 2 year long MSc project for Colin Sanders, who was working with Dr. William Milsom at the University of British Columbia (where I did my post-doc).   Colin, Bill and myself went down to Brasil in 2003/2004 to initiate a project examining the year-long changes in heart rate, breathing rate and body temperature in tegu lizards in a semi-natural environment.  The initial basis for the study was to examine a lizard that would hibernate (i.e. go dormant) at relatively warm temperatures.  Our Brasilian colleagues (Abe and Andrade) had laboratory data suggesting that tegus would go dormant in the winter.  We had valid physiological reasons for why this was a interesting question (not initially about endothermy) and that was Colin’s MSc project.  How did we do this?  We implanted little electronic devices that would measure an EKG and EMG and body temperature continuously and save this data to a computer.  The entire project was instrument heavy and indeed, our equipment was tied up in Brazilian customs for 6 weeks, nearly preventing the launching of his research!  I wrote a Matlab script to analyse the massive amount of raw data we were collecting from the radio-transmitting telemeters.  Colin had to endure months of staring at the computer screen to verify the script was working properly.  All totalled, we collected Gigabytes of data to computers that had no DVD drives and no network access.  Suffice it to say, Colin had a lot of sleepless nights and frustrations of running my rather unsophisticated computer code.  Skype and email were our friends, but it made discovery a distant and future goal.

Fast forwarding to when Colin returned to Canada, he now had a massive amount of data on the daily changes in heart rate, breathing rates and body temperatures in a cohort of tegu lizards and still had to make sense of that.  In many ways, this project was a highly sophisticated Natural History project.  We were initially interested in knowing whether tegus went into their burrows and reduced metabolism in the winter and needed to do this under natural conditions, which is where our Brasilian colleagues came in.

Collaboration and Camaraderie

We were able to pursue this research because of the friendly and collaborative nature of two key individuals, Dr. Augusto Abe and Dr. Denis Andrade.  Since 2002, they have hosted myself in their lab (and homes!) for up to 1 or 2 months, almost on a yearly basis.  They both have interesting research programs into South American evolutionary physiology and comparative biology and are incredibly knowledgeable about the natural history of reptiles and amphibians of Brasil.  They had both studied tegu hibernation in the lab as well.  Not only was their lab designed to allow us to study tegus in their (almost) natural habitat, but visiting their labs is always a fruitful journey of discovery.  My hats off to Augusto for having the foresight to build a world class facility to encourage and foster collaborations in our discipline, and my deep appreciation to Denis for being the on-site “supervisor” of the research in Brasil.  It is not easy to remotely manage collaborations.

Check, Refine, Eliminate other Explanations

Following our initial, but unplanned-for observations of lizards warming up in the reproductive season, we spent a few years (yes, this was a slow cooker project) discussing the possible explanations and trying to devise ways to convince ourselves that the heat was due to metabolic heat production.  Colin’s heart rate data did provide the best evidence of this, but we already recognized that reviewers would be inherently skeptical, since we were ourselves.  At this stage, Dr. Cleo Leite and my student Viviana Cadena were invited to carry the torch and help provide the evidence that the tegus were not only capturing heat from the sun very efficiently and storing it.  Bill and myself had a lot of friendly arguments about this, but Bill convinced us all that the initial observations were real and important.  As a side project to his other research, Cleo collected three years worth of data on tegus during the reproductive period and transferring them back and forth from outside burrows to inside the lab where we had better control over ambient temperature, and along with Viviana’s thermal images, we were able to show that tegus were still showing rather impressive amount of endothermy (2 to 3 degrees above ambient temperature) when placed in the lab for a week without access to insulating burrows, or nest material.

Science is an Ongoing Learning Exercise

Along with wise and thoughtful contributions from all my co-authors, I was tasked with the unenviable job (hey, this is my story, so I can tell it this way) of writing the data up for publication.  All of us suffer from procrastination when it comes to writing.  Scientific writing is not simply formulaic, although there are clear and simple ways to present science accurately, I also think the best scientific papers also tell a story.  So, I drafted the first version of the manuscript and knew we had a really cool observation but had to do my homework since we would need to place the work into the appropriate theoretical context.  The evolution of endothermy has a long history of big thinkers testing hypotheses for how the ancestral condition of ectothermy could have overcome the energetic costs inherent to endothermy.  How were we to put our years of observations into this context?  Anyhow, I think we were all pushed a little outside our comfort zone.

Don’t Be Dismayed by Rejection

Once you think you have a potentially impactful paper, you do want it to be published somewhere where it will be read!  It also is true (almost a cliche) that many scientists will aim for the top journals, only to receive that dreaded auto-email reply from Nature claiming that “…your manuscript is of insufficient immediate interest to our broader readership to justify its publication in Nature.”  That is fine.  Push on and don’t let that manuscript stagnate on your computer.  So, that is what we did.  We endured our rejection, made headways with a subsequent submission and actually were pleased with the chance to have a widely publicised paper that was also available in an open access venue.

Take Home Message

Although the media attention surrounding discoveries are usually nice, they very often exaggerate the story and forget to comment on the importance of the team as well as the important role of accidental discovery.  Serendipity should be more valued in science.  It rarely is, and I worry that we train our students to become hypercritical hypothesis-driven automatons.  Although I still think that science should be hypothesis-driven (you still need to know what you hope to achieve and be able to communicate this effectively when writing a research grant or defending your idea to a graduate committee), you also need the freedom to “follow your nose” if you come across a novel observation.  Why can’t we have both?  Why can’t we train people to think scientifically, accurately and carefully, while recognizing the value of thinking outside dogmatic constraints.  Yet, granting agencies demand outcomes and outputs and governments like to link research to applications (read: commercial applications and jobs).  Where is the joy in this approach?  How does basic research fit into this?

My advice to junior scientists?  Don’t give up, but be prepared to think clearly and seek your motivation to do science (i.e. discovery research) from your own inner enthusiastic and curious kid, rather than your colleagues or your mentors!

Funding Agencies Deserve their Credit

There are some funding agencies that do value basic research, and my hats off to them!

This research was funded by the Natural Sciences and Engineering Research Council of Canada (to W.K.M. and G.J.T.),  FAPESP, and CNPq through the INCT in Comparative Physiology (proceeding nos. 2008/57712-4 and 573921/2008-3). D.V.A. was supported by research grants from the FAPESP (proceeding nos. 2010/05473-6 and 2013/04190-9) and CNPq.

Ramping up for the second field season in Galapagos, so I might start blogging a little more. It has taken a year to secure the permits and permission to conduct our research, so let’s hope the data are interesting! I will eventually post about the data, but perhaps not until the paper(s) is/are published. Fly out tomorrow morning….arrive in Galapagos on Thursday morning. Let’s hope that all my equipment arrives safely. Stay tuned…

I’m taking a break from the usual blog entries to highlight a field-based research project that has been years in the making, but somehow part of my research interests. Another research hat that I wear is one related to a population monitoring project in Algonquin Park. It seems appropriate this year, given the long cold winter and late spring, to chronicle the history of this project now, given the length of the study and the hope for the future. It all starts with a small lake in Algonquin Park – Bat Lake. Bat Lake is a small lake in Algonquin Park, located just north of Highway 60. This lake is an unusual lake in that it is highly acidic (pH 4.3), fishless, rain/snow melt fed but permanent. This creates a unique combination for amphibians, since the lack of fish opens up opportunities for larval amphibians to survive and reproduce in abundance: nearly all of Algonquin Park’s amphibians breed in it every year, making it a microcosm of the amphibians. Here is a picture of Bat Lake:

To call it a Lake is actually a bit of a misnomer. Technically, it is a spruce bog, whose chemistry and biology has likely remained reasonably static since it formed following the retreat of the most recent glaciers ~10,000 years ago. Core sample data going back for the past 200 years suggests it has been fishless for at least that long, indicating that the acidity is not due to industrialization but is due to the unique features of the bog and the underlying bedrock which bestows very little buffering capacity to the water. Of the amphibians that breed in Bat Lake, the one this ‘lake’ is best known for is the Spotted Salamander, Ambystoma maculatum. Every spring, thousands of salamanders embark on a migration (probably ~1-2 km) to this breeding site.

History of the Bat Lake Inventory of Spotted Salamanders. (BLISS) The salamanders of Bat Lake have long been of interest to people familiar with Algonquin Park.

Pre 1990s – Numerous Algonquin Park Naturalists have helped to highlight the unique ecosystem at Bat Lake. It only takes a brief read of the Bat Lake Trail Guide to see the importance of salamanders to the surrounding ecosystem, where they are estimated to make up a large portion of the animal biomass.

1993 – I was first introduced to Bat Lake as an undergraduate student conducting a research project in the lab of Dr. Jim Bogart at the University of Guelph. I was not the best of research assistants and not much came of my work that summer (I am grateful to Jim for for his patience), but this little lake had a large influence on my thinking as a biologist.

1994 – 2006: Through the initiatives of Ron Brooks and the MNR, Bat Lake was included among other lakes in Algonquin Park for egg mass counts.

2004 – 2007: My lab began a series of studies on the symbiosis between the embryonic salamander and a algae that grows within the egg capsule. See here and here.

2008: My lab started formal Spotted Salamander monitoring at Bat Lake, referring to the project as BLISS. Aptly named, it turns out, since the students who tend to gravitate toward the project find working at Bat Lake a blissful experience! At least if they like working with herps.

2008 – 2012: The initial years of BLISS have worked out the ‘bugs’ of starting a field project in a remote part of Ontario far from where we all live. Various students have taken part over the years, including David LeGros, Patrick Moldowan, and Sean Boyle, all of whom I am proud to note have gone onto bigger and better things. Let’s hope they become the next generation’s biologists!

Present day: BLISS is currently co-managed by Algonquin Park Biologist, Jennifer Hoare, operationally run by Patrick Moldowan, with data deposited and analyzed by me (Glenn Tattersall). I feel sad that I am not more involved, but I have yet to manage to clone myself to allow me to get into the field in the springtime. Back in my lab at Brock, May is usually one of the busiest times of year as new students are starting research projects, and conference season is in full swing. Maybe one year I will actually get to experience the BLISS that is working in the field catching salamanders.

Into the future: The plan is for BLISS to remain a cooperative venture between the Ministry of Natural Resources/Ontario Parks, Universities, passionate biologists, and supported by volunteers! Check out this blog from Ontario parks showing their support for our project, as well as a creative writing impression (written by Patrick Moldowan) of what it is like to be a herpetologist anticipating the most exciting time of year: Spring!!

I hope to begin to write up some interesting results from BLISS in the next year or two, and will be happy to discuss questions with interested colleagues. So far, we are obtaining informative trends and associations between egg mass abundance and adult body size and changes in previous year’s climate. The trick with a long-term dataset is how long to wait before publishing the results!

Of course, BLISS would not be possible without the Algonquin Wildlife Research Station and all the researchers who have made this place what it is. Check out their website for more information, but in short, this research station is primarily operated by dedicated university researchers who pursue research into Wildlife in the boreal forests of Ontario. Many Ontario university undergraduates have sunk their teeth into research at this station and fallen in love with science and the outdoors. Since federal funding for basic sciences is under threat, all field stations need support from the public, so please consider donating.

Happy Spring Everyone!

This might sound like a strange thing to write about, the choosing of a colour palette for a thermal image. Why be concerned about which colour to use? Isn’t it just for presentation? It happens to be one of my pet peeves with thermal imaging and how people new to the field do not appreciate how a colour choice might enhance small differences in temperature and overemphasize something rather minor.

My reasons will be illuminated below, but suffice it to say it relates ultimately to contrast and detectability of different temperatures through the use of colour itself.

From a computational perspective these concerns are not important. Almost all thermal imaging devices actually provide a proper temperature estimate for each pixel on the screen and as the images are typically stored in proprietary format in 12 or 14 bit files, this is not a concern from a quantitative perspective.

However, images captured are eventually converted into a digital format that is easily visualized by others, typically a jpg, png, tiff or bmp file. When presented online, then, you have a colourised rendition of temperature that is essence a filter of the real data mapped onto a pre-existing spectrum. This spectrum of colours is referred to as a palette in most graphical software.

There are a number of palettes that you might find available on your thermal imaging camera:

From left to right, these palettes are described as: Greyscale, Iron, Rain, Glowbow and Yellow (terminology comes from FLIR™). Each palette ‘translates’ temperature into a specific colour, with cold colours at the bottom (typically darker colours) and warm colours at the top (typically lighter colours).

At first glance it might be tempting to choose the funkiest colours, since it looks ‘pretty’ (this is a common reaction I get from people when I show them thermal images). Indeed, for some purposes this is entirely appropriate. Some palettes were designed specifically to create a large contrast in colour intensity across a narrow range of temperatures.

People generally do not believe me until i demonstrate it, but I often prefer to use the greyscale palette when imaging animals in the field for the simple reason that it is easier to focus on edges. Although greyscale might not offer a large degree of contrast between similar temperatures, it is a simple, natural scale of intensity where black is the lowest intensity, white is the highest intensity and greys provide a gradient of intensities in between.

For presentation purposes and for publication purposes, however, a visually appealing colour might be appropriate (instead of greyscale). My own favourite palette is the Iron palette, as demonstrated in the following image of Yellow Crowned Night Heron from Galapagos:

Note how I have set the temperature range to go from 22 to 32C, where 22 is the lowest colour on the gradient and 32 is the highest. This maximizes the potential contrast of temperatures within the visible colour palette without saturating or eliminating any potential temperature.
So, why all the fuss about palette choice? Let’s consider the same image as I’ve shown you above, but this time using 5 different palettes. I have purposely rescaled the image to range from 5 to 32C, which actually masks some of the potential colour differences but it also shows how the different palettes may obscure potential temperature differences.

The picture above shows the yellow crowned night heron depicted using 5 different palettes. Inset line graphs depict the “intensity” of the gradient scale used in common units. All I did was import the images into ImageJ and drew a line down the gradient to obtain the “grey intensity” as a function of the colour palette. All palettes are compared in the lower right-hand graph to show how these different palettes translate “intensity” differently.

Although the human eye can certainly detect chromatic signals (i.e. different colours), the achromatic signals are what I am trying to highlight above. See how the different palettes show varying degrees of linearity and non-linearity. Clearly the greyscale gradient shows a monotonic decline in intensity, as you would expect for an achromatic response.

The other palettes however are not all the same as the greyscale. Sadly, my own favourite palette is shows a slightly curvilinear function with some intensities rising before falling again. The palette that comes closest to a greyscale, slightly monotonic decreasing palette is FLIR’s Yellow palette.

Note how weird the Rain palette looks. The intensity rises and falls along the gradient itself. What this means is that your eye may be drawn to changes in achromatic signals in the colour palette and mistakenly consider them to be an incorrect temperature change. The Rain palette is an example of one of those favoured by people who initially play with thermal cameras. The images look striking, but my pet peeve about it is that it creates unnatural contrasts in colours that do not correspond to the actual temperature gradient. It also does not help that the beak and the back feathers look ‘warm’ because I am accustomed to yellow colours being warmer than red colours.

To drive home this point more clearly, I have converted every single image above to a greyscale image in Photoshop using the default greyscale convert tool:

For most of the palettes chosen (the first 4), the conversion to greyscale does not really obscure the image too much, but it still transforms the images. In other orders, darker greys clearly correspond to cooler colours, lighter greys to warmer colours. The exception is the Rain palette. When converted to greyscale it appears saturated in some places, the bird’s image is nicely delineated (due to the steep contrast in intensity in places), but certain greys are repeatedly used that correspond to different temperatures. In other words, it is difficult to tell for certain what colour corresponds to what temperature.

So, the morale of the story? This may not be a problem if you have a colour printer or access to a computer screen to view your colour images, but not all journals will publish in colour, and not all people will view the work in colour (e.g. referees of your papers like myself who are given black and white versions of your manuscript and are left scratching their heads wondering what the images mean!), so I think it pays to consider the effect of palette choice on how others may interpret (or get confused by) your thermal images.

Personally, I usually use the Iron palette and it turns out to have a non-monotonic change in intensity along the gradient of temperatures, which means that there may be some error in a greyscale conversion from this particular choice. I guess I could choose a more forgiving palette, but I still like the colour option for presentations myself.

You could always opt for greyscale straight from the thermal imaging device itself, and then generate boring looking images! To each their own.