SPECIALTY GRAND CHALLENGE
published: 30 March 2021
doi: 10.3389/fphys.2021.669158
Frontiers in Physiology | www.frontiersin.org 1 March 2021 | Volume 12 | Article 669158
Edited and reviewed by:
George E. Billman,
The Ohio State University,
United States
*Correspondence:
Andreas Fahlman
afahlman@whoi.edu
Specialty section:
This article was submitted to
Physio-logging,
a section of the journal
Frontiers in Physiology
Received: 18 February 2021
Accepted: 26 February 2021
Published: 30 March 2021
Citation:
Fahlman A, Aoki K, Bale G, Brijs J,
Chon KH, Drummond CK, Føre M,
Manteca X, McDonald BI,
McKnight JC, Sakamoto KQ, Suzuki I,
Rivero MJ, Ropert-Coudert Y and
Wisniewska DM (2021) The New Era
of Physio-Logging and Their Grand
Challenges.
Front. Physiol. 12:669158.
doi: 10.3389/fphys.2021.669158
The New Era of Physio-Logging and
Their Grand Challenges
Andreas Fahlman 1*, Kagari Aoki 2, Gemma Bale 3, Jeroen Brijs 4, Ki H. Chon 5,
Colin K. Drummond 6, Martin Føre 7, Xavier Manteca 8, Birgitte I. McDonald 9,
J. Chris McKnight 10, Kentaro Q. Sakamoto 2, Ippei Suzuki 11, M. Jordana Rivero 12,
Yan Ropert-Coudert 13 and Danuta M. Wisniewska 14
1 Fundación Oceanográfic de la Comunitat Valenciana, Valencia, Spain, 2Department of Marine Bioscience, Atmosphere and
Ocean Research Institute, The University of Tokyo, Kashiwa, Japan, 3Department of Physics and Department of Engineering,
University of Cambridge, Cambridge, United Kingdom, 4Hawai’i Institute of Marine Biology, University of Hawai’i at Manoa,
Manoa, HI, United States, 5 Biomedical Engineering, University of Connecticut, Storrs, CT, United States, 6Biomedical
Engineering, Case Western Reserve University, Cleveland, OH, United States, 7Department of Engineering Cybernetics,
Norwegian University of Science and Technology, Trondheim, Norway, 8Department of Animal and Food Science,
Autonomous University of Barcelona, Barcelona, Spain, 9Moss Landing Marine Labs at San Jose State University, Moss
Landing, CA, United States, 10 Sea Mammal Research Unit, University of St. Andrews, Scotland, United Kingdom, 11 Akkeshi
Marine Station, Field Science Center for Northern Biosphere, Hokkaido University, Akkeshi, Japan, 12 Rothamsted Research
North Wyke, Okehampton, United Kingdom, 13Centre D’Etudes Biologiques de Chizé, La Rochelle Université, UMR7372,
CNRS, France, 14Department of Biology, University of Southern Denmark, Odense, Denmark
Keywords: bio-logging, bio-telemetry, physiology, heart rate, accelerometers, welfare, conservation
INTRODUCTION
The field of bio-sensing refers to studies where the physiology of an animal, its behavior and
movement, as well as the characteristics of the environment it moves in, is measured either by
electronic sensor-carrying devices that store the data (bio-logging), or those that transmit the data
directly (bio-telemetry).1 One of the first bio-sensing studies was conducted over 80 years ago with
the attachment of a capillary tube to a fin whale (Balaenoptera physalus) to assess the dive depth
of a free-ranging marine mammal (Scholander, 1940). In humans, the stethoscope was developed
by Rene Laennec in 1819 as the first non-invasive heart monitor, which solved the challenge of
listening to the heart by placing an ear on the patient’s chest (not always welcome in the Victorian
era) (Roguin, 2006). Quickly the system found new uses eventually leading to a shift from subjective
to objective data about the internal body. The field of bio-sensing has since increased exponentially
and revolutionized our understanding of animal ecology. With the technological development of
miniaturized sensors, numerous studies of movement ecology, behavior, and communication in a
diverse range of animals (e.g., species of fish, reptiles, birds and mammals) have been reviewed in
(Frost et al., 1997; Davis, 2008; Ropert-Coudert et al., 2009a; Rutz and Hays, 2009; Swain et al.,
2011; Hussey et al., 2015; Wilmers et al., 2015; Endo and Wu, 2019; Börger et al., 2020; Wassmer
et al., 2020). While determining the physiological limits and plasticity of a species is essential
for understanding its ecology and evolution, studies that measure the physiological responses
of free-ranging animals (i.e., physio-logging) have not seen the same exponential increase, even
though physiological questions were at the origin of the use of data loggers in seminal work
done by field physiologists such as Gerry Kooyman, Paul Ponganis, Warren Zapol, and Patrick
Butler (Butler and Woakes, 1979; Falke et al., 1985; Kooyman, 1985; Ponganis et al., 1991).
1Recent advances combine the logging and transmission of data using AI and machine learning approaches to process data
on-board the logger and transmit either subsets of data or information derived from the primary data recorded.
Fahlman et al. New Era of Physio-Logging
The slower growth of the physio-logging field could be due to
the commercial unavailability of physiological sensors, or that the
available sensors were too large, based on static-technologies, or
required specialized surgical training and extensive knowledge
of the anatomy and physiology of the animal for successful
implantation. Despite these challenges, studies using bio-sensing
tools have renewed the interest in physio-logging and attempted
to understand the physiology of an animal through inference
from their behavior (Wilson et al., 2002; Hooker et al., 2009;
Goldbogen et al., 2011, 2019b; Kolarevic et al., 2016; Føre et al.,
2018b; Quick et al., 2020).
Physio-loggers have recently been used on farmed animals
(livestock) to record physiological variables (e.g., body
temperature, respiration and heart rates) in order to monitor
water intake, the occurrence of diseases, energy expenditure in
grazing activities, and effect of diet on body temperature under
cold and warm conditions (Brosh et al., 2006; Eigenberg et al.,
2008; AlZahal et al., 2011; Arias et al., 2011; Aharoni et al.,
2013; Cantor et al., 2018). In the human arena – where early bio-
telemetry approaches were born – technological advances such as
movement sensors initially allowed anyone with a “smartphone”
or “smartwatch” to assess their daily energy consumption,
leading to the so-called “quantified health” movement (Scully
et al., 2012). Indeed, subsequent development of non-invasive
sensing (photoplethysmography) enabled new and exciting
possibilities to track health and fitness in a large number of
people (Dörr et al., 2019; Seshadri et al., 2020). In addition,
recent developments in wearable medical and nanotechnology,
with increased battery life, storage capacity and a range of
sensors have increased our ability to study physiological function
both non-invasively and continuously over months and years
(Kang et al., 2016; Kaidarova et al., 2018, 2019; Lee et al., 2019;
Lazaro et al., 2020). Thus, tools capable of measuring a range
of important and informative physiological parameters are now
available, and are continuously being improved and adapted to
work on an increasing range of species. These developments will
revolutionize the capacity to measure and assess the physiology
of animals and humans over extended periods of time, which
will allow a comprehensive evaluation of the physiological
function of animals in their natural environment. This new
era of physio-logging will enable long-term studies to better
understand fundamental physiological function, health, welfare
or well-being of animals and humans, as well as their responses
to environmental and/or anthropogenic changes.
THE PARADIGM SHIFT CHALLENGE
Much of what we know about animal physiology has been
obtained by measuring physiological parameters on captive,
semi-captive, or restrained animals including measures of heart
rate, blood flow, blood chemistry, blood gases, and metabolic
rate (Berkson, 1967; Kooyman et al., 1970; Kooyman and
Campbell, 1972; Kooyman and Sinnett, 1982; Lutcavage et al.,
1989; Ponganis et al., 1990; Reed et al., 1994, 2000; Gräns et al.,
2010; Kang et al., 2016; Brijs et al., 2018; Berenbrink, 2021;
Svendsen et al., 2021). Unfortunately, in such situations, it is
difficult to assess the magnitude of potential confounding factors
such as stress or manipulation on the measured physiological
variable. In recent years, there has been a focus on measuring
physiology in free-ranging animals. For example, trained animals
that are desensitized to the experimental procedures have been
used to study diving energetics, cardiorespiratory and vascular
physiology, and cerebrovascular physiology (Elsner, 1965; Olsen
et al., 1969; Ridgway and Howard, 1979; Williams et al., 1993;
Hurley and Costa, 2001; Fahlman et al., 2008, 2019, 2020a,b;
Mortola and Sequin, 2009; Rosen and Trites, 2013; Worthy et al.,
2013; Elmegaard et al., 2016, 2019; Takei et al., 2016; McKnight
et al., 2019; Meir et al., 2019; Pedersen et al., 2020; Blawas et al.,
2021). As bio-logging technologies have advanced, physiological
parameters such as heart rate, respiration rate, and blood O2
have even been measured in free-ranging fish, reptiles, birds, and
mammals (Falke et al., 1985; Ponganis et al., 1991; Thompson and
Fedak, 1993; Southwood et al., 1999; Andrews et al., 2000; Froget
et al., 2004; Ropert-Coudert et al., 2006, 2009b; Meir et al., 2009;
Yamamoto et al., 2009; Meir and Ponganis, 2010; McDonald and
Ponganis, 2013, 2014; Sakamoto et al., 2013; Duriez et al., 2014;
Goldbogen et al., 2019a; McKnight et al., 2019, 2021a,b; Sumich,
2021). There is a parallel shift in the paradigm of physiological
monitoring of humans. Whereas once health monitoring was
exclusively a physician-based in-patient activity, the emergence
of health and fitness wearables has led to the so-called “quantified
self ” movement, where patients are producing data in support of
diagnostics (Patel and Tarakji, 2021).
TECHNOLOGICAL DEVELOPMENT
Progress on medical sensing technology has increased
significantly. A wide range of physiological monitoring
technologies are now available and are setting the stage from
which physiological bio-sensing could profit immensely. For
instance, virtually anyone with a “smartphone” or “smartwatch”
can now assess their daily calorie expenditure as sensors within
the phone can estimate the number of steps taken or distance
moved. Similarly, researchers have applied this principle to
free-ranging animals and are able to derive an estimate of
energy expended in the wild via a measure of dynamic body
movements measured by animal-embarked accelerometers
(Wilson et al., 2006, 2020; Gleiss et al., 2011) that correlates
well with other direct measures of energy expended even in
wild animals (Elliott et al., 2013; Jeanniard-Du-Dot et al., 2017;
Hicks et al., 2020). Phonospirometry (i.e., the use of the breath
sound to estimate respiratory flow) is being used to perform
lung function testing in both humans and animals (Sumich and
May, 2009; Larson et al., 2012; Sumich, 2021; Van Der Hoop
et al., 2021). In addition, the ongoing development of wearable
medical sensors that can detect glucose levels, estimate heart rate
via waterproof ECG electrodes (Reyes et al., 2014; Noh et al.,
2016) or assess blood flow/volume changes and/or blood oxygen
saturation changes provide a particularly exciting avenue for
future research (Bockstaele et al., 2014; McKnight et al., 2019,
2021a,b). These technological advancements open up enormous
possibilities as they will enable investigating the physiological
Frontiers in Physiology | www.frontiersin.org 2 March 2021 | Volume 12 | Article 669158
Fahlman et al. New Era of Physio-Logging
function in freely moving, and even free-ranging animals,
with minimal disturbances. Further, the development of fully
bioresorbable microchip technologies capable of measuring a
variety of physiological parameters (Kang et al., 2016) could offer
opportunities to measure new, fine-scale physiological metrics in
free-moving and free-ranging animals. Thus, long-term data sets
on movement, married with physiological data could become
available, contributing essential components to frameworks that
assess the consequences of environmental and/or anthropogenic
impacts such as Population Consequences of Disturbance
(PCoD, Booth et al., 2014; Pirotta et al., 2018), as well as to
develop a fundamental understanding of the physiology of a
diverse range of species.
ANALYTICAL DEVELOPMENT
The collection of long-term and/or high-resolution data sets
is likely to result in analytical challenges. For example, ECG
collection sampled at 200Hz over a whole year results in 6.3
billion data points.While ECG could be reduced to instantaneous
heart rate (ifH) (Sakamoto et al., 2021), normal statistical tools,
such as comparison of means or medians are not applicable and
are likely to result in erroneous conclusions. More sophisticated
analytical methods, including signal processing or time-series
analysis, will have to be developed and introduced to deal with
a growing number of studies that focus on physiological function
and eco-physiology. There has recently been a rapid growth in
analytical techniques in bioinformatics, where new tools and
databases have been developed to handle the large data sets that
result from sequencing the genome of various species and to
evaluate gene networks and differential changes in molecular
products. A similar exponential growth has been seen within
data processing methods based on Artificial Intelligence (AI)
and Machine Learning (ML). These methods are used in several
different fields today, especially when data sets are too large
and/or complex to handle through conventional means, and it
is likely that they prove useful for processing datasets from bio-
sensors. Although many AI/MLmethods are “a black box,” in the
sense that they do not describe the mechanistic links between
input and output (e.g., environmental and/or anthropogenic
changes and sensor output in this case), they could be useful
for compressing and condensing large data sets and identifying
unknown relationships between inputs and measured features
(Rasheed et al., 2020).
CONCLUSION
In the last 40 years, the field of bio-sensing has provided
important information about the ecology and behavior of wild
animals, largely focusing on describing where they go and
what they do there. Animal tracking studies have substantially
improved the knowledge of movement patterns and drivers of
movement in marine, terrestrial and avian species. However,
the rapid development and miniaturization of bio-sensing
electronics capable of measuring a raft of physiological variables
present innovative and exciting tools that will revolutionize this
field of research and usher in a new era of physio-logging. These
technologies will allow us to comprehensively evaluate how and
why animals make the journeys they do (e.g., bar-headed geese
flying over the Himalayas, Cuvier’s beaked whales diving to
3000m for over 3 h; Hawkes et al., 2013; Quick et al., 2020).
Such studies will provide a foundation for understanding how
animals may respond to alterations in the environment and the
physiological boundaries for survival. Physio-logging can also
provide the necessary tools for conservation management, which
will contribute toward reducing the impacts of anthropogenic
disturbances on species, communities and even ecosystems.
For example, assessment of stress levels, such as measuring
corticosterone or heart rate may help evaluate the impact of
anthropogenetic disturbance (Miksis et al., 2001). Furthermore,
physio-logging is also likely to provide an important diagnostic
tool for evaluating the well-being andwelfare of farmed terrestrial
and aquatic animals. These technologies can provide a unique
opportunity for health monitoring via an “animal-eye” view
of the conditions that farmed animals experience in human
care on a day-to-day basis, enabling a better understanding of
how to address the challenges faced by industries attempting
to produce a profitable, ethical and environmentally sustainable
product (Berckmans, 2004; Føre et al., 2018a; Brijs et al., 2021).
Many of the responses evaluated in these managed settings
could also be translated to wild animals given the clear link
between physiology and welfare (Gregory, 2004; Baird et al.,
2016; Føre et al., 2018a; Svendsen et al., 2021). Finally, physio-
logging is likely to promote improved health and wellness
in humans, where early detection of disease allows improved
treatment outcome.
As we enter a new age in the study of physiology of
animals and humans living in complex environments, the Physio-
logging journal aims to provide a forum where scientists, and
conservation practitioners among others, can share knowledge
on how modern sensing technology and analytical approaches
can be used to understand physiological function and health of
animals and humans.
AUTHOR CONTRIBUTIONS
All authors listed have made a substantial, direct and intellectual
contribution to the work, and approved it for publication.
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Conflict of Interest: AF was employed without salary by the company Global
Diving Research Inc.
The remaining authors declare that the research was conducted in the absence of
any commercial or financial relationships that could be construed as a potential
conflict of interest.
Copyright © 2021 Fahlman, Aoki, Bale, Brijs, Chon, Drummond, Føre, Manteca,
McDonald, McKnight, Sakamoto, Suzuki, Rivero, Ropert-Coudert and Wisniewska.
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