Scientific publishing: Impact factor, open access and citations

By Leila Lemos1 and Rachel Ann Hauser-Davis2

1PhD candidate, Fisheries and Wildlife Department, OSU

2PhD, CESTEH/ENSP/Fiocruz, Rio de Janeiro, Brazil

Scientific publishing not only communicates new knowledge, but also is a measure of each scientist’s success: the impact each scientist has on his/her field is often measured by his/her number of publications and the reputation of the journals he/she published in. Therefore, publishing in reputable journals, with a high impact factor, is often essential to get a job, promotion and tenure. So, what is an impact factor?

The impact factor (IF) was first created in the 1960’s and is a measure of a journal’s impact on science, as reflected by the yearly average number of citations to recent articles published in that journal. The IF is used to compare the impact of journals within disciplines. Journals with higher impact factors are deemed as more prestigious and of better quality than those with lower ones.

The IF of a journal for any given year is calculated as the number of citations, received in that year, of articles published in that journal during the two preceding years, divided by the total number of articles published in that journal during the two preceding years, as follows:

In recent years, open access (OA) journals have emerged, changing how we perceive publications. However, the role and significance of IF is still present, valuable and used worldwide.

Conventional (non-open access) journals cover publishing costs through access fees, such as subscriptions, site licenses or download charges, which can be paid by universities, research institutions and, sometimes, by individuals. Papers published in OA journals, on the other hand, are distributed online and free of cost. However, there are still publication costs, which are usually paid by the authors. And, open access article processing charges are not cheap, ranging from a few hundred to several thousand dollars, depending on the field (more thoughts on this theme here).

It seems imbalanced that researchers have to pay for their work to be published. They have carried out a study and have obtained results that should be shared with the community. These results should not be treated as a commercial item to be sold. Also, it ends strengthening those who have resources and weakening those who do not have, increasing the division between Northern and Southern hemispheres, and narrowing the knowledge-production system (Burgman 2018).

Thus, a free-of-charge research paper would be interesting for everyone. PeerJ is a good example of a recent OA, free of publishing costs, peer-reviewed, and scholarly journal, that was released in 2013. It’s a totally new model and pushes the boundaries. In addition, there are hybrid journals (i.e., Conservation Biology) that offer both conventional and OA modes, leaving it to the authors to decide what they prefer (Burgman 2018). In many cases, disadvantaged authors might also be able to appeal for waivers. Thus, authors who cannot pay publishing fees might still see their work getting published.

However, this is not how the publishing system typically works. Therefore, researchers need to determine where to publish based on the journal IF and focus/audience, on the different price structures and fees, and whether it is OA or not.

Researchers in general want their articles to be openly accessible for everyone, not just those who can afford to pay the journal for access, so they can increase visibility of their work. Open access can increase the impact/reach of a research paper by facilitating paper downloads, access, and use in other scientific research, which may, in turn, lead to higher citation rate (Eyesenbach 2006).

Higher citation rates would also improve researchers’ H-index: an author-level metric that measures both productivity and citation impact of a scientist or scholar, based on the scientist’s most cited papers and the number of citations that they have received in publications.

The graph below exemplifies the h-index that is based on the maximum value of h such that the given author/journal has published h papers that have each been cited at least h times. In other words, the index is designed to improve with number of publications or citations. The index can only be compared between researchers from same field, as citation conventions might differ widely among different fields.

H-index from a plot of decreasing citations for numbered papers
Source: Wikipedia

 

However, publishing in an OA journal might easily increase researchers’ H-index and journals’ IF. Many researchers have also considered OA as an “artificial citation enhancer”.

As with any new system, some are opposed to the establishment of the OA system, including researchers, academics, librarians, university administrators, funding agencies, government officials, publishers and editorial staff, among many others (Markin 2017). This opposition claims that OA publishing leads to financial damages to the large publishers worldwide, and, mainly, that this system may damage the peer review system in place today, leading to reduced scientific quality (such as “you pay, you publish” predatory journals that take advantage of the paid system by publishing as fast as possible, without any scientific rigor whatsoever).

However, many reputable journals, such as Elsevier, Springer, Wiley and Blackwell, now offer OA as an option for their established journals. This approach is simply another option for authors, where they may pay if they want for their paper to be available for everyone. Even if this option is available, manuscripts still go through a rigorous peer-review that occurs with both conventional and OA journals. Thus, publishing in OA should be just as rigorous.

Open access papers would be the most “scientifically ethical”, as science is aimed at society, for society, and this type of publishing furthers research reach. However, paying thousands of dollars is sometimes very complicated, as this means less money for fieldwork costs, gears, laboratory analyses, among others.

All in all, OA is a recent development that is changing scientist approach to publication. The future of scientific publication seems uncertain and likely to hold new developments in the near future.

 

References:

Burgman M. 2018. Open access and academic imperialism. Conservation Biology 0 (0): 1–2. DOI: 10.1111/cobi.13248.

Eysenbach G. 2006. Citation Advantage of Open Access Articles. PLoS Biology 4 (5): e157. doi:10.1371/journal.pbio.0040157. PMC 1459247. PMID 16683865.

Markin P. 2017. The Sustainability of Open Access Publishing Models Past a Tipping Point. Open Science. Retrieved 26 April 2017.

Remote Sensing Applications

By Leila Lemos, PhD candidate

Fisheries and Wildlife Department, OSU

 

I am finally starting my 3rd and last year of my PhD. Just a year left and yet so many things to do. As per department requirements, I still need to take some class credits, but what classes could I take? In this short amount of time it is important to focus on my research project and on what could help me better understand the many branches of the project and what could improve my analyses. Thinking of that, both my advisor (Dr. Leigh G. Torres) and I agreed that it would be useful for me to take a class on remote sensing. So, I could learn more about this field, as well as try to include some remote sensing analyses in my project, such as sea surface temperature (SST) and chlorophyll (i.e., as a productivity indicator) conditions over the years we have collected data on gray whales off the Oregon coast.

 

Our photogrammetry data indicates that whales gradually increased their body condition over the feeding seasons of 2016 and 2018, while 2017 is different. Whales were still looking skinny in the middle of the season, and we were not collecting many fecal samples up to that point (indicating not much feeding). These findings made us wonder if this was related to delayed seasonal upwelling events and consequently low prey availability. These questions are what motivated me the most to join this class so that we might be able to link environmental correlates with our observations of gray whale body condition.

Figure 01: Skinny body condition state of the gray whale “Pancake” in August 2017.
Source: Leila S. Lemos

 

If we stop to think about what remote sensing is, we have already been implementing this method in our project since the beginning, as my favorite definition for remote sensing is “the art of collecting information of objects or phenomenon without touching it”. So, yes, the drone is a type of sensor that remotely collects information of objects (in this case, whales).

Figure 02: Drone remotely collecting information of a whale in September 2018. Drone in detail. Collected under NOAA/NMFS permit #16111.
Source: Leila Lemos

 

However, satellites, all the way up in the space, are also remotely sensing the Earth and its objects and phenomena. Even from thousands of km above Earth, these sensors are capable of generating a great amount of detailed data that is easily and freely accessible (i.e., NASA, NOAA), and can be used for multiple applications in different fields of study. Satellites are also able to collect data from remote areas like the Antarctica and the Arctic, as well as other areas that are not easily reached by humans. One important application of the use of satellite imagery is wildlife monitoring.

For example, satellite data was used to detect variation in the abundance of Weddell seals (Leptonychotes weddellii) in Erebus Bay, Antarctica (LaRue et al., 2011). Because this is a well-studied seal population, the object of this study was to test if satellite imagery could produce reliable abundance estimates. The authors used high-resolution (0.6 m) satellite imagery (from satellites Quick-Bird-2 and WorldView-1) to compare counts from the ground with counts from satellite images in the same locations at the same time. This study demonstrated a reliable methodology for further studies to replicate.

Figure 03: WorldView-1 image (0.6 m resolution) of Weddell seals hauled out east of Inaccessible Island, Erebus Bay, Antarctica.
Source: LaRue et al. (2011).

 

Satellite imagery was also applied to estimate colony sizes of Adélie penguins in Antarctica (LaRue et al., 2014). High-resolution (0.6 m) satellite imagery combined with spectral analysiswas used to estimate the sizes of the penguin breeding colonies. Ground counts were also used in order to check the reliability of the applied method. The authors then created a model to predict the abundance of breeding pairs as a function of the habitat, which was identified terrain slope as an important component of nesting density.

The identification of whales using satellite imagery is also possible. Fretwell et al. (2014)pioneered this method by successfully identifing Southern Right Whales (Eubalaena australis) in the Golfo Nuevo, Península Valdés, in Argentina in satellite images. By using very high-resolution satellite imagery (50 cm resolution) and a water penetrating coastal band that was able to see deeper into the water column, the researchers were able to successfully identify and count the whales (Fig. 04). The importance of this study was very significant, since this species was extensively hunted from the 17ththrough to the 20thcentury. Since then, the species has shown a strong recovery, but population estimates are still at <15% of historical estimates. Thus, being able to use new tools to identify, count and monitor individuals in this recovering population is a great development, especially in remote and hard to reach areas.

Figure 04: Identification of Southern Right Whales by using imagery from the WorldView2 satellite in the Golfo Nuevo Bay, Península Valdés, Argentina.
Source: Fretwell et al. (2014).

 

Polar bears (Ursus maritimus) have also been studied in the Foxe Basin, in Nunavut and Quebec, Canada (LaRue et al., 2015). Researchers used high-resolution satellite imagery in an attempt to identify and count the bears, but spectral signature differences between bears and other objects were insufficient to yield useful results. Therefore, researchers developed an automated image differencing, also known as change detection, that identifies differences between remotely sensed images collected at different times and “subtract of one image from another”. This method correctly identified nearly 90% of the bears. The technique also generated false positives, but this problem can be corrected by a manual review.

Figure 05 shows the difference in resolution of two types of satellite imagery, the panchromatic (0.6 m resolution) and the multispectral (2.4 m resolution). LaRue et al. (2015)decided not to use the multispectral imagery due to resolution constraints.

Figure 05: Polar Bears on panchromatic (0.6 m resolution) and multispectral (2.4 m resolution) imagery.
Source: LaRue et al. (2015).

 

A more recent study is being conducted by my fellow OSU Fisheries and Wildlife graduate student, Jane Dolliveron breeding colonies of three species of North Pacific albatrosses (Phoebastria immutabilis, Phoebastria nigripes, and Phoebastria albatrus)(Dolliver et al., 2017). Jane is using high-resolution multispectral satellite imagery (DigitalGlobe WorldView-2 and -3) and image processing techniques to enumerate the albatrosses. They are also using albatross species at multiple reference colonies in Hawaii and Japan (Fig. 06) to determine species identification accuracy and required correction factor(s). This will allow scientists to accurately count unknown populations on the Senkakus, which are uninhabited islands controlled by Japan in the East China Sea.

Figure 06: Satellite image of a colony of short-tailed albatrosses (Phoebastria albatrus) in Torishima, Japan, 2016.
Source: Satellite image provided by Jane Dolliver.

 

Using satellite imagery to count seals, penguins, whales, bears and albatrosses is just the start of this rapidly advancing technology. Techniques and resolutions are continuously improving. Methods can also be applied to many other endangered species, especially in remote areas, providing data on presence, abundance, annual productivity, population estimates and trends, changes in distribution, and breeding ground usage.

Other than directly monitoring wildlife, satellite images can also provide information on the environmental variables that can be related to wildlife presence, abundance, productivity and distribution.

Gentemann et al. (2017), for example, used satellite data from NASA to analyze SST variations along the west coast of the United States from 2002 to 2016. The NASA Jet Propulsion Laboratory produces global, daily, 1 km, multiscale ultra-high resolution, motion-compensated analysis of SST, and incorporates SSTs from eight different satellites. Researchers were able to identify warmer than usual SSTs (also called anomalies) along the Washington, Oregon, and California coasts from January 2014 to August 2016 (Fig.07) relative to previous years. This marine heat wave started in the Gulf of Alaska and ended in Southern California, where SST reached a maximum temperature anomaly of 6.2°C, causing major disturbances and substantial economic impacts.

Figure 07: Monthly SST anomalies in the West Coast of United States, from January 2014 to August 2016.
Source: Gentemann et al. (2017).

 

Changes in SST and winds may alter events such as the coastal upwelling that supplies nutrients to sustain a whole food chain. A marine heat-wave event as described by Gentemann et al. (2017)could have significant impacts on the health of the marine ecosystem in the subsequent season (Gentemann et al., 2017).

These findings may even relate to our questions regarding the poor gray whale body condition we noticed in 2017: this marine heat wave that lasted until August 2016 along the US west coast could have impacted the ecosystem in the subsequent season. However, I must conduct a more detailed study to determine if this heat wave was related or if another oceanographic process was involved.

So, whether remotely sensed data is generated by satellites, drones, thermal imagery, robots (as I previously wrote about), or another type of technology, it can have important  and informative applications to monitor wildlife or environmental variables associated with their ecology and biology. We can take advantage of remotely sensed technology to aid wildlife conservation efforts.

 

References

Dolliver, J., et al., Multispectral processing of high resolution satellite imagery to determine the abundance of nesting albatross. Ecological Society of America, Portland, OR, United States., 2017.

Fretwell, P. T., et al., 2014. Whales from Space: Counting Southern Right Whales by Satellite. Plos One. 9,e88655.

Gentemann, C. L., et al., 2017. Satellite sea surface temperatures along the West Coast of the United States during the 2014–2016 northeast Pacific marine heat wave. Geophysical Research Letters. 44,312-319.

LaRue, M. A., et al., 2014. A method for estimating colony sizes of Adélie penguins using remote sensing imagery. Polar Biology. 37,507-517.

LaRue, M. A., et al., 2011. Satellite imagery can be used to detect variation in abundance of Weddell seals (Leptonychotes weddellii) in Erebus Bay, Antarctica. Polar Biology. 34,1727–1737.

LaRue, M. A., et al., 2015. Testing Methods for Using High-Resolution Satellite Imagery to Monitor Polar Bear Abundance and Distribution. Wildlife Society Bulletin. 39,772-779.

 

 

 

 

 

Are bacteria important? What do we get by analyzing microbiomes?

By Leila Lemos, PhD candidate, Fisheries and Wildlife Department, OSU

As previously mentioned in one of Florence’s blog posts, the GEMM Lab holds monthly lab meetings, where we share updates about our research and discuss articles and advances in our field, among other activities.

In a past lab meeting we were asked to bring an article to discuss that had inspired us in the past to conduct research in the marine field or in our current position. I brought to the meeting a literature review regarding methodologies to overcome the challenges of studying conservation physiology in large whales [1]. This article discusses different non-invasive or minimally invasive matrices (e.g., feces, blow, skin/blubber) that can be gathered from whales, and what types of analyses could be carried out, as well as their pros and cons.

One of the possible analyses that can be performed with fecal samples that was discussed in the article is the gut microflora (i.e., bacterial gut community) via genetic analysis. Since my PhD project analyzes fecal samples to determine/quantify stress responses in gray whales, we have since discussed the possibility of integrating this extra parameter to our analysis.

But… what is the importance of analyzing the gut microflora of a whale? What is the relationship between microflora and stress responses? Should we really use our limited sample size, time and money to work on this extra analysis? In order to be able to answer all of these questions, I began reading some articles of the field to better understand its importance and what kind of research questions this analysis can answer.

The gut of a mammal comprises a natural habitat for a large and dynamic community of bacteria [2] that is first developed in early life. Colonization of facultative bacteria (i.e., aerobic bacteria) begins at birth [3], and later, anaerobic bacteria also colonizes the gut. In humans, at the age of 1 year old, the microbiome should have a stable adult-like signature (Fig. 1).

Figure 01: Development of the microbiome in early life.
Source: [3]

The gut bacterial community is important for the physiology and pathology of its host and plays an important role in mammal digestion and health [2], responsible for many metabolic activities, including:

  • fermentation of non-digestible dietary residue and endogenous mucus [2];
  • recovery of energy [2];
  • recovery of absorbable nutrients [2];
  • cellulose digestion [4];
  • vitamin K synthesis [4];
  • important trophic effects on intestinal epithelia (cell proliferation and differentiation) [2];
  • angiogenesis promotion [4];
  • enteric nerve function [4];
  • immune structure [2];
  • immune function [2];
  • protection of the colonized host against invasion by alien microbes (barrier effect) [2];

Despite all the benefits, the bacterial community might also be potentially harmful when changes in the community composition (i.e., dysbiosis) occur due to the use of antibiotics, illness, stress, aging, lifestyle, bad dietary habits [4], and prolonged food and water deprivation [5]. Thus, potential pathological disorders might emerge when the microbiome community changes, such as allergy, obesity, diabetes, autism, multisystem organ failure, gastrointestinal and prostate cancers, inflammatory bowel diseases (IBD), and cardiovascular diseases [2, 4].

Changes in gut bacterial composition may also alter the brain-gut axis and the central nervous system (CNS) signaling [3]. More specifically, the core pathway affected is the hypothalamic-pituitary-adrenal (HPA) axis, which is activated by physical/psychological stressors. According to a previous study [6], the microbial community in the gut is critical for the development of an appropriate stress response. In addition, the microbial colonization in early life should occur within a certain time window, otherwise an abnormal development of the HPA axis might happen.

However, the gut microbiome can not only affect the HPA axis, but the opposite can also occur [3]. Signaling molecules released by the axis can alter the gastrointestinal (GIT) environment (i.e., motility, secretion, and permeability) [7]. Stress responses, as well as diseases, may also alter the gut permeability, causing the bacteria to cross the epithelial barrier (reducing the overall numbers of bacteria in the gut), activating immune responses that also alter the composition of the bacterial community in the gut [8, 9].

Figure 02: Communication between the brain, gut and microbiome in a healthily and in a stressed or diseased (mucosal inflammation) mammal.
Source: [3]

Thus, when thinking about whales, monitoring of the gut microflora might allow us to detect changes caused by factors such as aging, illness, prolonged food deprivation, and stressful events [2, 5]. However, since these are two-way factors, it is important to find an association between bacterial composition alterations and stressful events, such as the presence of predators (e.g., killer whales), illness (e.g., bad body condition), prolonged food deprivation (e.g., low prey availability and high competition), noise (e.g., noisy vessel traffic, fisheries opening and seismic surveys), and stressful reproductive status (e.g., pregnancy and lactating period). Examination of possible shifts in the gut microflora may be able to detect and be linked to many of these events, and also forecast possible chronic events within the population. In addition, the bacterial community monitoring study could aid in validating the hormone data (i.e., cortisol) we have been working with.

Therefore, the main research questions that arise in this context that can aid in elucidating the stress physiology in gray whales are:

  1. What is the microflora community content in guts of gray whales along the Oregon coast?
  2. Is it possible to detect shifts in the gut microflora from our gray fecal samples over time?
  3. How do gut microflora and cortisol levels correlate?
  4. Am I able to correlate shifts in gut microflora with any of the stressful events listed above?

We can answer so many other questions by analyzing the microbiome of baleen whales. Microbiomes are mainly correlated with host diet [10], so the composition of a microbiome can be associated with specific diets and functional gut capacity, and consequently, be linked to other animal populations, which helps to decode evolutionary questions. Results of a previous study on baleen whale microbiomes [10] point out that whales harbor unique gut microbiomes that are actually similar to those of terrestrial herbivores. Baleen whales and terrestrial herbivores have a shared physical structure of the GIT tract itself (i.e., multichambered foregut) and a shared hole for fermentative metabolisms. The multichambered foregut of baleen whales fosters the maintenance of the gut microbiome that is capable of extracting relatively unavailable nutrients from zooplankton (i.e., chitin, “sea cellulose”).

Figure 03: The similarities between whale and other terrestrial herbivore gut microbiomes: sea and land ruminants.
Source: [11]

Thus, the importance of studying the gut microbiome of a baleen whale is clear. Monitoring of the bacterial community and possible shifts can help us elucidate many questions regarding diet, overall health, stress physiology and evolution. Thinking about my PhD project, it may also help in validating our cortisol level results. I am confident that a microbiome analysis would significantly enhance my studies on the health and ecology of gray whales.

 

References

  1. Hunt, K.E., et al., Overcoming the challenges of studying conservation physiology in large whales: a review of available methods.Conservation Physiology, 2013. 1: p. 1-24.
  2. Guarner, F. and J.-R. Malagelada, Gut flora in health and disease.The Lancet, 2003. 360: p. 512–519.
  3. Grenham, S., et al., Brain–gut–microbe communication in health and disease.Frontiers in Physiology, 2011. 2: p. 1-15.
  4. Zhang, Y., et al., Impacts of Gut Bacteria on Human Health and Diseases.International Journal of Molecular Sciences, 2015. 16: p. 7493-7519.
  5. Bailey, M.T., et al., Stressor exposure disrupts commensal microbial populations in the intestines and leads to increased colonization by Citrobacter rodentium.Infection and Immunity, 2010. 78: p. 1509–1519.
  6. Sudo, N., et al., Postnatal microbial colonization programs the hypothalamic-pituitary-adrenal system for stress response in mice.The Journal of Physiology, 2004. 558: p. 263–275.
  7. Rhee, S.H., C. Pothoulakis, and E.A. Mayer, Principles and clinical implications of the brain–gut–enteric microbiota axis Nature Reviews Gastroenterology & Hepatology, 2009. 6: p. 306–314.
  8. Kiliaan, A.J., et al., Stress stimulates transepithelial macromolecular uptake in rat jejunum.American Journal of Physiology, 1998. 275: p. G1037–G1044.
  9. Dinan, T.G. and J.F. Cryan, Regulation of the stress response by the gut microbiota: Implications for psychoneuroendocrinology.Psychoneuroendocrinology 2012. 37: p. 1369—1378.
  10. Sanders, J.G., et al., Baleen whales host a unique gut microbiome with similarities to both carnivores and herbivores.Nature Communications, 2015. 6(8285): p. 1-8.
  11. El Gamal, A. Of whales and cows: the baleen whale microbiome revealed. Oceanbites 2016[cited 2018 07/31/2018]; Available from: https://oceanbites.org/of-whales-and-cows-the-baleen-whale-microbiome-revealed/.

 

Big Data: Big possibilities with bigger challenges

By Alexa Kownacki, Ph.D. Student, OSU Department of Fisheries and Wildlife, Geospatial Ecology of Marine Megafauna Lab

Did you know that Excel has a maximum number of rows? I do. During Winter Term for my GIS project, I was using Excel to merge oceanographic data, from a publicly-available data source website, and Excel continuously quit. Naturally, I assumed I had caused some sort of computer error. [As an aside, I’ve concluded that most problems related to technology are human error-based.] Therefore, I tried reformatting the data, restarting my computer, the program, etc. Nothing. Then, thanks to the magic of Google, I discovered that Excel allows no more than 1,048,576 rows by 16,384 columns. ONLY 1.05 million rows?! The oceanography data was more than 3 million rows—and that’s with me eliminating data points. This is what happens when we’re dealing with big data.

According to Merriam-Webster dictionary, big data is an accumulation of data that is too large and complex for processing by traditional database management tools (www.merriam-webster.com). However, there are journal articles, like this one from Forbes, that discuss the ongoing debate of how to define “big data”. According to the article, there are 12 major definitions; so, I’ll let you decide what you qualify as “big data”. Either way, I think that when Excel reaches its maximum row capacity, I’m working with big data.

Collecting oceanography data aboard the R/V Shimada. Photo source: Alexa K.

Here’s the thing: the oceanography data that I referred to was just a snippet of my data. Technically, it’s not even MY data; it’s data I accessed from NOAA’s ERDDAP website that had been consistently observed for the time frame of my dolphin data points. You may recall my blog about maps and geospatial analysis that highlights some of the reasons these variables, such as temperature and salinity, are important. However, what I didn’t previously mention was that I spent weeks working on editing this NOAA data. My project on common bottlenose dolphins overlays environmental variables to better understand dolphin population health off of California. These variables should have similar spatiotemporal attributes as the dolphin data I’m working with, which has a time series beginning in the 1980s. Without taking out a calculator, I still know that equates to a lot of data. Great data: data that will let me answer interesting, pertinent questions. But, big data nonetheless.

This is a screenshot of what the oceanography data looked like when I downloaded it to Excel. This format repeats for nearly 3 million rows.

Excel Screen Shot. Image source: Alexa K.

I showed this Excel spreadsheet to my GIS professor, and his response was something akin to “holy smokes”, with a few more expletives and a look of horror. It was not the sheer number of rows that shocked him; it was the data format. Nowadays, nearly everyone works with big data. It’s par for the course. However, the way data are formatted is the major split between what I’ll call “easy” data and “hard” data. The oceanography data could have been “easy” data. It could have had many variables listed in columns. Instead, this data  alternated between rows with variable headings and columns with variable headings, for millions of cells. And, as described earlier, this is only one example of big data and its challenges.

Data does not always come in a form with text and numbers; sometimes it appears as media such as photographs, videos, and audio files. Big data just got a whole lot bigger. While working as a scientist at NOAA’s Southwest Fisheries Science Center, one project brought in over 80 terabytes of raw data per year. The project centered on the eastern north pacific gray whale population, and, more specifically, its migration. Scientists have observed the gray whale migration annually since 1994 from Piedras Blancas Light Station for the Northbound migration, and 2 out of every 5 years from Granite Canyon Field Station (GCFS) for the Southbound migration. One of my roles was to ground-truth software that would help transition from humans as observers to computer as observers. One avenue we assessed was to compare how well a computer “counted” whales compared to people. For this question, three infrared cameras at the GCFS recorded during the same time span that human observers were counting the migratory whales. Next, scientists, such as myself, would transfer those video files, upwards of 80 TB, from the hard drives to Synology boxes and to a different facility–miles away. Synology boxes store arrays of hard drives and that can be accessed remotely. To review, three locations with 80 TB of the same raw data. Once the data is saved in triplet, then I could run a computer program, to detect whale. In summary, three months of recorded infrared video files requires upwards of 240 TB before processing. This is big data.

Scientists on an observation shift at Granite Canyon Field Station in Northern California. Photo source: Alexa K.
Alexa and another NOAA scientist watching for gray whales at Piedras Blancas Light Station. Photo source: Alexa K.

In the GEMM Laboratory, we have so many sources of data that I did not bother trying to count. I’m entering my second year of the Ph.D. program and I already have a hard drive of data that I’ve backed up three different locations. It’s no longer a matter of “if” you work with big data, it’s “how”. How will you format the data? How will you store the data? How will you maintain back-ups of the data? How will you share this data with collaborators/funders/the public?

The wonderful aspect to big data is in the name: big and data. The scientific community can answer more, in-depth, challenging questions because of access to data and more of it. Data is often the limiting factor in what researchers can do because increased sample size allows more questions to be asked and greater confidence in results. That, and funding of course. It’s the reason why when you see GEMM Lab members in the field, we’re not only using drones to capture aerial images of whales, we’re taking fecal, biopsy, and phytoplankton samples. We’re recording the location, temperature, water conditions, wind conditions, cloud cover, date/time, water depth, and so much more. Because all of this data will help us and help other scientists answer critical questions. Thus, to my fellow scientists, I feel your pain and I applaud you, because I too know that the challenges that come with big data are worth it. And, to the non-scientists out there, hopefully this gives you some insight as to why we scientists ask for external hard drives as gifts.

Leila launching the drone to collect aerial images of gray whales to measure body condition. Photo source: Alexa K.
Using the theodolite to collect tracking data on the Pacific Coast Feeding Group in Port Orford, OR. Photo source: Alexa K.

References:

https://support.office.com/en-us/article/excel-specifications-and-limits-1672b34d-7043-467e-8e27-269d656771c3

https://www.merriam-webster.com/dictionary/big%20data

How to apply my PhD?

By Leila Lemos, PhD candidate, Fisheries and Wildlife Department

Time has flown. It seems that it was like a month ago that I received the news that I was approved in a public notice from the Brazilian government to study abroad, and began the process of moving to Oregon. But actually almost three years have now passed, and I am starting to wrap up my PhD, since I need to defend it in a little bit more than a year.

Our team is now starting the third and last fieldwork season for my PhD project. I am also working on my study plan to determine the last classes I need to take, and our first manuscripts are ‘in press’ or ‘in prep’ for submission to journals. So, it’s time for me to think about what comes next.

I am from Rio de Janeiro, Brazil, and I am studying in the US through a Brazilian government program called Science Without Borders. This program aims to send students abroad to learn new techniques and to develop innovative projects. The projects needed to be original to be approved by the public notice. The main idea is to bring these students back to Brazil, after their PhD completion, to disseminate the acquired knowledge by applying the learned techniques.

My project includes a few novel aspects that allowed for funding by this program. The main focus of my thesis is to develop an endocrinology study of a cetacean species. This was (and still is) a critical field in Brazil, as reported by the “National Action Plan for the conservation of aquatic mammals: Small cetaceans” (2010). According to this Action Plan, cetacean hormonal analyses are rare and of high priority, but there are limited labs with the capacity to study cetacean endocrinology in Brazil. Other limiting factors are the associated analysis costs and a lack of human knowledge and skills. In addition to the hormonal analyses (Figure 1), I am also using other ‘new technologies’ in the project: drones (Figure 2; Video 1) and GoPros (Video 2).

Figure 1: Learning how to perform hormonal analysis at the Seattle Aquarium, WA.
Source: Angela Smith

 

Figure 2: Learning how to fly a drone in Newport, OR.
Source: Florence Sullivan

 

Video 1: Drone flights performed in Newport, OR, during fieldwork in 2016.

* Taken under NOAA/NMFS permit #16111 to John Calambokidis.

 

Video 2: Video of mysid swarms during a GoPro deployment conducted in Port Orford, OR, during fieldwork in 2016.

 

The importance of studying cetacean hormones includes a better understanding of their reproductive cycles (i.e., sex hormones such as progesterone, testosterone and estradiol) and their physiological stress response (i.e., cortisol) to possible threats (e.g., acoustic pollution, contaminants, lack of prey). In addition, through photographs and videos recorded by drones we can conduct photogrammetry analysis to monitoring cetacean body condition, and through GoPro recordings of the water column we can assess prey availability. Changes in both body condition and prey can help us explaining how and why hormone levels vary.

Through my PhD I have obtained skills in hormone analysis, photogrammetry and video prey assessment by studying the logistically accessible and non-threatened gray whale (Eschrichtius robustus). During method development, these features are important to increase sample size and demonstrate feasibility. But now that the methodologies have proven successful, we can start applying them to other species and regions, and under different circumstances, to improve conservation efforts of threatened populations.

Many cetacean species along the Brazilian coast are threatened, particularly from fishing gear and vessel interactions, chemical and noise pollution. By applying the methods we have developed in the GEMM Lab during my PhD to cetacean conservation issues in Brazil, we could enable a great expansion in knowledge across many fields (i.e., endocrinology, behavior, photogrammetry, diet). Additionally, these skills can promote safer work environments (for the scientist and for the object of study) and cheaper work processes. However, many countries, such as Brazil, do not have the infrastructure and access to technologies to conduct these same analyses, as in developed countries like the USA. These technologies, when sold in Brazil, have many taxes on the top of the product that they can become an extra hurdle, due to budget constraints. Thus, there is a need for researchers to adapt these skills and technologies, in the best manner possible, to the reality of the country.

Now that I am starting to think about ‘life after PhD’, I can see myself returning to my country to spread the knowledge, technologies and skills I have gained through these years at OSU to new research projects so that I am able to assist with conservation efforts for the ocean and marine fauna in Brazil.

 

References:

PAN, 2010. Plano de ação nacional para a conservação dos mamíferos aquáticos: pequenos cetáceos / André Silva Barreto … [et al.]; organizadores Claudia Cavalcante Rocha-Campos, Ibsen de Gusmão Câmara, Dan Jacobs Pretto. – Brasília: Instituto Chico Mendes de Conservação da Biodiversidade, Icmbio, 132 p. Em: <http://www.icmbio.gov.br/portal/images/ stories/docs-plano-de-acao/pan-peqs-cetaceos/pan_pequenoscetaceos_web.pdf> Acessado em: 27 de Maio de 2015.

 

Robots are taking over the oceans

By Leila Lemos, PhD Student

In the past few weeks I read an article on the use of aquatic robots in the ocean for research. Since my PhD project uses technology, such as drones and GoPros, to monitor body condition of gray whales and availability of prey along the Oregon coast, I became really interested by the new perspective these robots could provide. Drones produce aerial images while GoPros generate an underwater-scape snapshot. The possible new perspective provided by a robot under the water could be amazing and potentially be used in many different applications.

The article was published on March 21st by The New York Times, and described a new finned robot named “SoFi” or “Sophie”, short for Soft Robotic Fish (Figure 1; The New York Times 2018). The aquatic robot was designed by scientists at the Massachusetts Institute of Technology (MIT) Computer Science and Artificial Intelligence Lab, with the purpose of studying marine life in their natural habitats.

Figure 1: “SoFi”, a robotic fish designed by MIT scientists.
Source: The New York Times 2018.

 

SoFi’s  first swim trial occurred in a coral reef in Fiji, and the footage recorded can be seen in the following video:

 

SoFi can swim at depths up to 18 meters and at speeds up to half-its-body-length a second (average of 23.5 cm/s in a straight path; Katzschmann et al. 2018). Sofi can swim for up to ~40 minutes, as limited by battery time. The robot is also well-equipped (Figure 2). It has a compact buoyancy control mechanism and includes a wide-view video camera, a hydrophone, a battery, environmental sensors, and operating and communication systems. The operating and communication systems allow a diver to issue commands by using a controller that operates through sound waves.

Figure 2: “SoFi” system subcomponents overview.
Source: Katzschmann et al. 2018.

 

The robot designers highlight that while SoFi was swimming, fish didn’t seem to be bothered or get scared by SoFi’s presence. Some fish were seen swimming nearby the robot, suggesting that SoFi has the potential to integrate into the natural underwater environment and therefore record undisturbed behaviors. However, a limitation of this invention is that SoFi needs a diver on scene to control the robot. Therefore, SoFi’s study of marine life without human interference may be compromised until technology develops further.

Another potential impact of SoFi we might be concerned about is noise. Does this device produce noise levels that marine fauna can sense or maybe be stress by? Unfortunately, the answer is yes. Even if fish don’t seem to be bothered by SoFi’s presence, it might bother other animals with hearing sensitivity in the same frequency range of SoFi. Katzschmann and colleagues (2018) explained that they chose a frequency to operate SoFi that would minimally impact marine fauna. They studied the frequencies used by the aquatic animals and, since the hearing ranges of most aquatic species decays significantly above 10 KHz, they selected a frequency above this range (i.e., 36 KHz). However, this high frequency range can be sensed by some species of cetaceans and pinnipeds, but negative affects on these animals will be dependent on the sound amplitude that is produced.

Although not perfect (but what tool is?), SoFi can be seen as a great first step toward a future of underwater robots to assist research efforts.  Battery life, human disturbance, and noise disturbance are limitations, but through thoughtful application and continued innovation this fishy tool can be the start of something great.

The use of aquatic robots, such as SoFi, can help us advance our knowledge in underwater ecosystems. These robots could promote a better understanding of marine life in their natural habitat by studying behaviors, interactions and responses to threats. These robots may offer important new tools in the protection of animals against the effects caused by anthropogenic activities. Additionally, the use of aquatic robots in scientific research may substitute remote operated vehicles and submersibles in some circumstances, such as how drones are substituting for airplanes sometimes, thus providing a less expensive and better-tolerated way of monitoring wildlife.

Through continued multidisciplinary collaboration by robot designers, biologists, meteorologists, and more, innovation will continue allowing data collection with minimal to non-disturbance to the wildlife, providing lower costs and higher safety for the researchers.

It is impressive to see how technology efforts are expanding into the oceans. As drones are conquering our skies today and bringing so much valuable information on wildlife monitoring, I believe that the same will occur in our oceans in a near future, assisting in marine life conservation.

 

 

References:

Katzschmann RK, DelPreto J, MacCurdy R, Rus D. 2018. Exploration of Underwater Life with an Acoustically Controlled Soft Robotic Fish. Sci. Robot. 3, eaar3449. DOI: 10.1126/scirobotics.aar3449.

The New York Times. 2018. Robotic Fish to Keep a Fishy Eye on the Health of the Oceans. Available at: https://www.nytimes.com/2018/03/21/science/robot-fish.html.

How important are foundational, novel and review papers?

By Leila Lemos, PhD Student

As I wrote in my last blog post, I am in the process of studying for my preliminary exams that will happen in late March (written exams) and late April (oral exam).

My committee members provided me with reading lists of material they thought was important for me to know in order for me to become a PhD candidate. This will serve as the basis for my dissertation research, and provides the framework for how my contribution will advance the field. In the last month, I have been reading many, many articles, book chapters, theses, etc. to build this foundation.

One of the first steps was to organize all of the readings for my prelims on
a big board that would help me visualize what has been done and
what is still missing for each of the committee members

 

The material I am reading is a mixture of foundational and novel material, which are equally important. Foundational articles tell us about the origin of a specific field or theme, and help me to understand fundamental concepts and theories. It is really interesting to see what the pioneer researchers in the field first thought and how they tested their hypotheses many years ago. It is also remarkable to read novel papers and see how these foundational ideas have evolved and developed into new hypotheses, leading to new studies and experiments which push the boundaries of what we already know.

Review papers can also give a sense of this timeline by compiling studies on a particular topic. By assembling all of the available findings in my field, it becomes clear what questions remain unanswered, justifying the goals of my research, and establishing the project’s theoretical and methodological framework.

In my PhD project we are attempting to address some of the unanswered questions related to stress responses in baleen whales. Reading about other studies, their results, and the diverse techniques that have been applied to other taxa makes me really excited about what I can still incorporate in the project.

Source: http://binapatel.me/2017/05/25/literature-review-citation-
tracing-concept-saturation-results-mind-mapping/

 

At the end of my PhD, if we are able to answer our proposed questions, we will have contributed to advancing the field of knowledge, and we will be able to apply our results to the conservation and management of baleen whales in nearshore coastal ecosystems.

The more I read the content proposed by my committee members, the more I find connections between my PhD project, its aims, and the title I proposed for myself as being a “Conservation Physiologist”. Being a Conservation Physiologist is exactly what I want to be, during my PhD, and in the future.

 

 

 

Who am I?

By Leila Lemos, PhD Student
(hopefully PhD candidate soon)

 

Here I am with the first GEMM Lab blog post of 2018.

Many people begin a New Year thinking about the future and planning goals to achieve in the following year, and that’s exactly how I am starting my year. After two and a half years of my PhD program, my classes and thesis project are nearing the end. However, a large hurdle stands between me and my finish line: my preliminary exams (as opposed to final exams that happen when I defend my thesis).

Oregon State University requires two sets of preliminary examinations (a.k.a. “prelims”) in order to become a PhD candidate. Thus, planning my next steps is essential in order to accomplish my main objective: a successful completion of these two exams.

The first set of exams comprises written comprehensive examinations to be taken over the course of a week (Monday to Friday), where each day belongs to a different member of my committee. The second type of exam is an oral preliminary examination, conducted by my doctoral committee. The written and oral prelims may cover any part of my proposed research topic as described in the proposal I submitted during my first PhD year.

In order to better understand this entire process, I met with Dr. Carl Schreck, a Fisheries and Wildlife Department professor and one of the members of my committee. He has been through this prelim process many times with other students and had good advice for me regarding preparation. He told me to meet with all of my committee members individually to discuss study material and topics. However, he said that I should first define and introduce myself with a title to each committee member, so they know how to base and frame exam questions. But, how do I define myself?

How do you define yourself?
Source: www.johngarvens.com/wpcontent/uploads/2013/02/how_do_you_ define_yourself.jpeg

 

As part of my PhD committee, Dr. Schreck is familiar with my project and what I am studying, so he suggested the title “Conservation Physiologist”. But, do I see myself as a Conservation Physiologist? Will this set-up have implications for my future, such as the type of job I am prepared for and able to get?

I can see it is important to get this title right, as it will influence my exam process as well as my scientific career. However, it can be hard and somewhat tricky when trying to determine what is comprised by your work and what are the directions you want to take in your future. I believe that defining the terms conservationist and physiologist, and what they encompass, is a good first step.

To me, a conservation specialist works for the protection of the species, their habitats, and its natural resources from extinction and biodiversity loss, by identifying and mitigating the possible threats. A conservation specialist’s work can help in establishing new regulations, conservation actions, and management interventions. As for an animal physiology specialist, their research may focus on how animals respond to internal and external elements. This specialist often studies an animal’s vital functions like reproduction, movement, growth, metabolism and nutrition.

According to Cooke et al. (2013), conservation specialists focus on population characteristics (e.g., abundance and structure) and indicators of responses to environmental perturbations and human activities. Thus, merging conservation and physiology disciplines enables fundamental understanding of the animal response mechanisms to such threats. Using animal physiology as a tool is valuable for developing cause-and-effect relationships, identifying stressor thresholds, and improving ecological model predictions of animal responses. Thus, conservation physiology is an inter-disciplinary field that provides physiological evidence to promote advances in conservation and resource management.

My PhD project is multidisciplinary, where the overall aim is to understand how gray whales are physiologically responding to variability in ambient noise, and how their hormone levels vary across individual, time, body condition, location, and noise levels. I enjoy many aspects of the project, but what I find myself most excited about is linking information about sex, age, body condition, and cortisol levels to specific individuals we observe multiple times in the field. As we monitor their change in body condition and hormones, I am highly motivated to build these whale ‘life-history stories’ in order to better understand patterns and drivers of variability. Although we have not yet tied the noise data into our analyses of whale health, I am very interested to see how this piece of the puzzle fits into these whale ‘life-history stories’.

In this study, animal physiology facilitates our stories. Scientific understanding is the root of all good conservation, so I believe that this project is an important step toward improved conservation of baleen whales. Once we are able to understand how gray whales respond physiologically to impacts of ocean noise, we can promote management actions that will enhance species conservation.

Thus, I can confidently say, I am a Conservation Physiologist.

Me, in Newport, OR, during fieldwork in 2017.
Source: Sharon Nieukirk, 2017.

 

Over the next three months I will be meeting with my committee members and studying for my prelims. I hope that this process will prepare me to become a PhD candidate by the time my exams come around in March. Then, I will have accomplished my first goal of 2018, so I can go on to plan for the next ones!

 

References:

Cooke SJ, Sack L, Franklin CE, Farrell AP, Beardall J, Wikelski M, and Chown SL. What is conservation physiology? Perspectives on an increasingly integrated and essential science. Conserv Physiol. 2013; 1(1): cot001. Published online 2013 Mar 13. doi:  10.1093/conphys/cot001.

 

GEMM Lab 2017: A Year in the Life

By Dawn Barlow, MSc Student, Department of Fisheries and Wildlife

The days are growing shorter, and 2017 is drawing to a close. What a full year it has been for the GEMM Lab! Here is a recap, filled with photos, links to previous blogs, and personal highlights, best enjoyed over a cup of hot cocoa. Happy Holidays from all of us!

The New Zealand blue whale team in action aboard the R/V Star Keys. Photo by L. Torres.

Things started off with a bang in January as the New Zealand blue whale team headed to the other side of the world for another field season. Leigh, Todd and I joined forces with collaborators from Cornell University and the New Zealand Department of Conservation aboard the R/V Star Keys for the duration of the survey. What a fruitful season it was! We recorded sightings of 68 blue whales, collected biopsy and fecal samples, as well as prey and oceanographic data. The highlight came on our very last day when we were able to capture a blue whale surface lunge feeding on krill from an aerial perspective via the drone. This footage received considerable attention around the world, and now has over 3 million views!

A blue whale surfaces just off the bow of R/V Star Keys. Photo by D. Barlow.

In the spring Rachael made her way to the remote Pribilof Islands of Alaska to study the foraging ecology of red-legged kittiwakes. Her objectives included comparing the birds that reproduce successfully and those that don’t, however she was thrown a major curveball: none of the birds in the colony were able to successfully reproduce. In fact, they didn’t even build nests. Further analyses may elucidate some of the reasons for the reproductive failure of this sentinel species of the Bering Sea… stay tuned.

red-legged kittiwakes
Rachael releases a kittiwake on St. George Island. Photo by A. Fleishman.

 

The 2017 Port Orford field team. Photo by A. Kownacki.

Florence is a newly-minted MSc! In June, Florence successfully defended her Masters research on gray whale foraging and the impacts of vessel disturbance. She gracefully answered questions from the room packed with people, and we all couldn’t have been prouder to say “that’s my labmate!” during the post-defense celebrations. But she couldn’t leave us just yet! Florence stayed on for another season of field work on the gray whale foraging ecology project in Port Orford, this time mentoring local high school students as part of the projectFlorence’s M.Sc. defense!

Upon the gray whales’ return to the Oregon Coast for the summer, Leila, Leigh, and Todd launched right back into the stress physiology and noise project. This year, the work included prey sampling and fixed hydrophones that recorded the soundscape throughout the season. The use of drones continues to offer a unique perspective and insight into whale behavior.

Video captured under NOAA/NMFS permit #16111.

 

Solene with a humpback whale biopsy sample. Photo by N. Job.

Solene spent the austral winter looking for humpback whales in the Coral Sea, as she participated in several research cruises to remote seamounts and reefs around New Caledonia. This field season was full of new experiences (using moored hydrophones on Antigonia seamount, recording dive depths with SPLASH10 satellite tags) and surprises. For the first time, whales were tracked all the way from New Caledonia to the east coast of Australian. As her PhD draws to a close in the coming year, she will seek to understand the movement patterns and habitat preferences of humpback whales in the region.

A humpback whale observed during the 2017 coral sea research cruise. Photo by S. Derville.

This summer we were joined by two new lab members! Dom Kone will be studying the potential reintroduction of sea otters to the Oregon Coast as a MSc student in the Marine Resource Management program, and Alexa Kownacki will be studying population health of bottlenose dolphins in California as a PhD student in the Department of Fisheries and Wildlife. We are thrilled to have them on the GEMM Lab team, and look forward to seeing their projects develop. Speaking of new projects from this year, Leigh and Rachael have launched into some exciting research on interactions between albatrosses and fishing vessels in the North Pacific, funded by the NOAA Bycatch Reduction Engineering Program.

During the austral wintertime when most of us were all in Oregon, the New Zealand blue whale project received more and more political and media attention. Leigh was called to testify in court as part of a contentious permit application case for a seabed mine in the South Taranaki Bight. As austral winter turned to austral spring, a shift in the New Zealand government led to an initiative to designate a marine mammal sanctuary in the South Taranaki Bight, and awareness has risen about the potential impacts of seismic exploration for oil and gas reserves. These tangible applications of our research to management decisions is very gratifying and empowers us to continue our efforts.

In the fall, many of us traveled to Halifax, Nova Scotia to present our latest and greatest findings at the 22nd Biennial Conference on the Biology of Marine Mammals. The strength of the lab shone through at the meeting during each presentation, and we all beamed with pride when we said our affiliation was with the GEMM Lab at OSU. In other conference news, Rachael was awarded the runner-up for her presentation at the World Seabird Twitter Conference!

GEMM Lab members present their research. From left to right, top to bottom: Amanda Holdman, Leila Lemos, Solène Derville, Dawn Barlow, Sharon Nieukirk, and Florence Sullivan.

Leigh had a big year in many ways. Along with numerous scientific accomplishments—new publications, new students, successful fieldwork, successful defenses—she had a tremendous personal accomplishment as well. In the spring she was diagnosed with breast cancer, and after a hard fight she was pronounced cancer-free this November. We are all astounded with how gracefully and fearlessly she navigated these times. Look out world, this lab’s Principle Investigator can accomplish anything!

This austral summer we will not be making our way south to join the blue whales. However, we are keenly watching from afar as a seismic survey utilizing the largest seismic survey vessel in the world has launched in the South Taranaki Bight. This survey has been met with considerable resistance, culminating in a rally led by Greenpeace that featured a giant inflatable blue whale in front of Parliament in Wellington. We are eagerly planning our return to continue this study, but that will hopefully be the subject of a future blog.

New publications for the GEMM Lab in 2017 include six for Leigh, three for Rachael, and two for Alexa. Highlights include Classification of Animal Movement Behavior through Residence in Space and Time and A sense of scale: Foraging cetaceans’ use of scale-dependent multimodal sensory systems. Next year is bound to be a big one for GEMM Lab publications, as Amanda, Florence, Solene, Leila, Leigh, and I all have multiple papers currently in review or revision, and more in the works from all of us. How exciting!

In our final lab meeting of the year, we went around the table to share what we’ve learned this year. The responses ranged from really grasping the mechanisms of upwelling in the California Current to gaining proficiency in coding and computing, to the importance of having a supportive community in graduate school to trust that the right thing will happen. If you are reading this, thank you for your interest in our work. We are looking forward to a successful 2018. Happy holidays from the GEMM Lab!

GEMM Lab members, friends, and families gather for a holiday celebration.

A Marine Mammal Odyssey, Eh!

By Leila Lemos, PhD student

Dawn Barlow, MS student

Florence Sullivan, MS

The Society for Marine Mammalogy’s Biennial Conference on the Biology of Marine Mammals happens every two years and this year the conference took place in Halifax, Nova Scotia, Canada.

Logo of the Society for Marine Mammalogy’s 22nd Biennial Conference on the Biology of Marine Mammals, 2017: A Marine Mammal Odyssey, eh!

The conference started with a welcome reception on Sunday, October 22nd, followed by a week of plenaries, oral presentations, speed talks and posters, and two more days with different workshops to attend.

This conference is an important event for us, as marine mammalogists. This is the moment where we get to share our projects (how exciting!), get important feedback, and hear about different studies that are being conducted around the world. It is also an opportunity to network and find opportunities for collaboration with other researchers, and of course to learn from our colleagues who are presenting their work.

The GEMM Lab attending the opening plenaries of the conference!

The first day of conference started with an excellent talk from Asha de Vos, from Sri Lanka, where she discussed the need for increased diversity (in all aspects including race, gender, nationality, etc.) in our field, and advocated for the end of “parachute scientists” who come into a foreign (to them) location, complete their research, and then leave without communicating results, or empowering the local community to care or act in response to local conservation issues.  She also talked about the difficulty that researchers in developing countries face accessing research that is hidden behind journal pay walls, and encouraged everyone to get creative with communication! This means using blogs and social media, talking to science communicators and others in order to get our stories out, and no longer hiding our results behind the ivory tower of academia.  Overall, it was an inspirational way to begin the week.

On Thursday morning we heard Julie van der Hoop, who was this year’s recipient of the F.G. Wood Memorial Scholarship Award, present her work on “Drag from fishing gear entangling right whales: a major extinction risk factor”. Julie observed a decrease in lipid reserves in entangled whales and questioned if entanglements are as costly as events such as migration, pregnancy or lactation. Tags were also deployed on whales that had been disentangled from fishing gear, and researchers were able to see an increase in whale speed and dive depth.

Julie van der Hoop talks about different drag forces of fishing gears
on North Atlantic Right Whales.

There were many other interesting talks over the course of the week. Some of the talks that inspired us were:

— Stephen Trumble’s talk “Earplugs reveal a century of stress in baleen whales and the impact of industrial whaling” presented a time-series of cortisol profiles of different species of baleen whales using earplugs. The temporal data was compared to whaling data information and they were able to see a high correlation between datasets. However, during a low whaling season concurrent to the World War II in the 40’s, high cortisol levels were potentially associated to an increase in noise from ship traffic.

— Jane Khudyakov (“Elephant seal blubber transcriptome and proteome responses to single and repeated stress”) and Cory Champagne (“Metabolomic response to acute and repeated stress in the northern elephant seal”) presented different aspects of the same project. Jane looked at down/upregulation of genes (downregulation is when a cell decreases the quantity of a cellular component, such as RNA or protein, in response to an external stimulus; upregulation is the opposite: when the cell increases the quantity of cellular components) to check for stress. She was able to confirm an upregulation of genes after repeated stressor exposure. Cory checked for influences on the metabolism after administering ACTH (adrenocorticotropic hormone: a stimulating hormone that causes the release of glucocorticoid hormones by the adrenal cortex. i.e., cortisol, a stress related hormone) to elephant seals. By looking only at the stress-related hormone, he was not able to differentiate acute from chronic stress responses. However, he showed that many other metabolic processes varied according to the stress-exposure time. This included a decrease in amino acids, mobilization of lipids and upregulation of carbohydrates.

— Jouni Koskela (“Fishing restrictions is an essential protection method of the Saimaa ringed seal”) talked about the various conservation efforts being undertaken for the endangered Lake Saimaa ringed seal. Gill nets account for 90% of seal pup mortality, but if new pups can reach 20kg, only 14% of them will drown in these fishing net entanglements. Working with local industry and recreational interests, increased fishing restrictions have been enacted during the weaning season. In addition to other year-round restrictions, this has led to a small, but noticeable upward trend in pup production and population growth! A conservation success story is always gratifying to hear, and we wish these collaborative efforts continued future success.

— Charmain Hamilton (“Impacts of sea-ice declines on a pinnacle Arctic predator-prey relationship: Habitat, behaviour, and spatial overlap between coastal polar bears and ringed seals”) gave a fascinating presentation looking at how changing ice regimes in the arctic are affecting spatial habitat use patterns of polar bears. As ice decreases in the summer months, the polar bears move more, resulting in less spatial overlap with ringed seal habitat, and so the bears have turned to targeting ground nesting seabirds.  This spatio-temporal mismatch of traditional predator/prey has drastic implications for arctic food web dynamics.

— Nicholas Farmer’s presentation on a Population Consequences of Disturbance (PCoD) model for assessing theoretical impacts of seismic survey on sperm whale population health had some interesting parallels with new questions in our New Zealand blue whale project. By simulating whale movement through modeled three-dimensional sound fields, he found that the frequency of the disturbance (i.e., how many days in a row the seismic survey activity persisted) was very important in determining effects on the whales. If the seismic noise persists for many days in a row, the sperm whales may not be able to replenish their caloric reserves because of ongoing disturbance. As you can imagine, this pattern gets worse with more sequential days of disturbance.

— Jeremy Goldbogen used suction cup tags equipped with video cameras to peer into an unusual ecological niche: the boundary layer of large whales, where drag is minimized and remoras and small invertebrates compete and thrive. Who would have thought that at a marine mammal conference, a room full of people would be smiling and laughing at remoras sliding around the back of a blue whale, or barnacles filter feeding as they go for a ride with a humpback whale? Insights from animals that occupy this rare niche can inform improvements to current tag technologies.

The GEMM Lab was well represented this year with six different talks: four oral presentations and two speed talks! It is evident that all of our hard work and preparation, such as practicing our talks in front of our lab mates two weeks in advance, paid off.  All of the talks were extremely well received by the audience, and a few generated intelligent questions and discussion afterwards – exactly as we hoped.  It was certainly gratifying to see how packed the room was for Sharon’s announcement of our new method of standardizing photogrammetry from drones, and how long the people stayed to talk to Dawn after her presentation about an unique population of New Zealand blue whales – it took us over an hour to be able to take her away for food and the celebratory drinks she deserved!

GEMM Lab members on their talks. From left to right, top to bottom: Amanda Holdman, Leila Lemos, Solène Derville, Dawn Barlow, Sharon Nieukirk, and Florence Sullivan.

 

GEMM Lab members at the closing celebration. From left to right: Florence Sullivan, Leila Lemos, Amanda Holdman, Solène Derville, and Dawn Barlow.
We are not always serious, we can get silly sometimes!

The weekend after the conference many courageous researchers who wanted to stuff their brains with even more specialized knowledge participated in different targeted workshops. From 32 different workshops that were offered, Leila chose to participate in “Measuring hormones in marine mammals: Current methods, alternative sample matrices, and future directions” in order to learn more about the new methods, hormones and matrices that are being used by different research groups and also to make connections with other endocrinologist researchers. Solène participated in the workshop “Reproducible Research with R, Git, and GitHub” led by Robert Shick.  She learned how to better organize her research workflow and looks forward to teaching us all how to be better collaborative coders, and ensure our analysis is reproducible by others and by our future selves!

On Sunday none of us from the GEMM Lab participated in workshops and we were able to explore a little bit of the Bay of Fundy, an important area for many marine mammal species. Even though we didn’t spot any marine mammals, we enjoyed witnessing the enormous tidal exchange of the bay (the largest tides in the world), and the fall colors of the Annaoplis valley were stunning as well. Our little trip was fun and relaxing after a whole week of learning.

The beauty of the Bay of Fundy.
GEMM Lab at the Bay of Fundy; from left to right: Kelly Sullivan (Florence’s husband and a GEMM Lab fan), Florence Sullivan, Dawn Barlow, Solène Derville, and Leila Lemos.
We do love being part of the GEMM Lab!

It is amazing how refreshing it is to participate in a conference. So many ideas popping up in our heads and an increasing desire to continue doing research and work for conservation of marine mammals. Now it’s time to put all of our ideas and energy into practice back home! See you all in two years at the next conference in Barcelona!

Flying out of Halifax!