Saturday, January 13, 2018

Vitality, stress, and survival

Image: Cleveland Clinic; vitality distinguishes characteristics of survival (heart beat and stroke volume, nerve, muscle, and organ function).

In our efforts to promote health and well-being in ecosystems and their components, we test hypotheses about the causes for impairment by assessing stress resulting from stressors (injury, hypoxia, pressure, xenobiotic, temperature, capture, hunger, fatigue, and disease).  Typically, individual biomarkers (genetic, physiological, and behavioral) are measured and assumed to be correlated with survival.  Vitality is a biomarker that reflects the whole animal condition after stress induction.  Full vitality is characterized by consistently present defined reflex actions and is the constant control for hypothesis testing. Impairment is measured as loss of reflex action traits. The relationship between reflex impairment and survival is weighted by sequence of impairment.  Sensitive reflex actions are impaired by low levels of stressors (sublethal).  More resistant reflex actions become impaired at higher levels of stressors (lethal). 

Vitality can be a subjective score for animal condition based on observation of injury, activity, and reflex action impairment.  These vitality scores are correlated with survival and delayed mortality; where size and taxa sensitivity to stressors interact to control impairment.  Levels of vitality can be indicated by condition class impairment; excellent, fair, poor, moribund, based on evaluation of activity and injury (Benoît et al. 2015Morfin et al. 2017).   

A vitality heuristic based on trait classes of injury and reflex impairment (see tables) can be correlated with survival and delayed mortality. The index replicate is calculated as the number of impaired classes / total number of classes (ranges from 0 to 1).  This index is a combination of individual injury types and reflex actions with differing statistical distributions. As such it cannot supply a precise parametric estimate for vitality described above.  Instead the index is a summary expression (see below) of whole animal reactivity and impairment that is useful for rapid in-situ determination of stress levels and adjustment of experimental conditions for hypothesis testing (Brownscombe et al. 2017, Meeremans, et al. 2017).

Sunday, November 13, 2016

Reflex impairment in largemouth bass shows interactions of gear type, fight time, and air exposure

Largemouth bass, Bemep/Flicker

Cooke et al. 2016 examined reflex impairment in largemouth bass captured during the summer (25-27oC). Excerpts from their paper detail study findings: 
“…little is known about how gear strength and fight time interact with air exposure duration to ultimately influence the level of exhaustion experienced by fish at time of release. Here we systematically varied fishing gear strength (ultralight versus medium-heavy) and air exposure duration (0 versus 120 s) when targeting Largemouth Bass Micropterus salmoides. We relied on reflex impairment (using five different reflexes) as a real-time indicator of fish condition.”
“One of the more interesting observations from this study was that fish that were landed rapidly and thus in better condition were more difficult to handle, which led to longer air exposure. We are aware of anglers and scientists that have mused about the trade-offs between fight time and ease of handling, but to our knowledge this is the first study to formally assess this idea.”
“In this study we used two extremes in gear type and suggest that moderate strength gear likely represents the best compromise in terms of achieving an appropriate level of exhaustion that would facilitate handling and hook removal without leading to complete exhaustion.”
Reflex impairment in captured largemouth bass, Cooke et al. 2016.

“Using reflex indicators, we showed clearly that there was a gradient in reflex impairment with Largemouth Bass; fish captured on UL gear had significantly higher reflex impairment than those captured with MH gear with no air exposure, while fish captured with both gear types had similarly high reflex impairment when exposed to the air.”

Monday, October 24, 2016

Yelloweye rockfish barotrauma and reflex impairment after capture in shallow and deep water

Yelloweye rockfish, Neil McDaniel
Rankin et al. 2016 report on barotrauma and reflex impairment observed for recompressed yelloweye rockfish in situ. They evaluated orientation, reaction to noise and motion stimuli, and visual and swimming capability. 
Behavior of recompressed fish. Top fish, presence of orientation and vision-dependent movement. Bottom fish, absence of vertical orientation in live fish. Rankin et al. 2016
The authors conclude, “Recompression is a valuable treatment for discarded rockfish that would otherwise be too buoyant to return to depth without assistance. However, the loss of reflex actions as basic as vertical orientation, along with the evidence we found of visual compromise in deep-dwelling recompressed yelloweye rockfish, is concerning, as are the long-lasting physical injuries and lack of neutral buoyancy observed in the weeks after capture and recompression. At a minimum, these effects indicate limits to a rockfish’s ability to move effectively, find refuge, and avoid predators upon release.
The findings from these two studies, which reveal severe and lasting injuries, as well as behavioral compromise of recompressed deep-water yelloweye rockfish, reinforce the importance of avoiding fishing contact with deep-dwelling yelloweye rockfish and maintaining spatially-managed rockfish conservation areas closed to fishing.”

Wednesday, August 31, 2016

Stressors, vitality impairment, and survival of fishes

Developing rapid visual in situ trait assessment (reflex actions, injury) associated with vitality impairment.

Video slideshow (2:06) discussing stressors, vitality impairment, and survival of fishes in fisheries contexts.

Friday, August 19, 2016

Reflex impairment and vitality in white sturgeon exposed to simulated capture stressors

White sturgeon, NEEF 2016

A study (McLean et al. 2016) of reflex impairment in white sturgeon exposed to sustained exercise and elevated temperature showed whole-animal stress responses to simulated capture. The RAMP impairment index (a simple proportion of measured reflex actions that were impaired) was used to quantify relationships between treatment times, recovery times, and RAMP score.
The upper figure shows increasing RAMP score with increasing exercise (minutes) in summer (filled circle) and winter (filled triangle) temperatures. The lower figure shows increasing recovery time with increasing RAMP score in summer and winter temperatures. Figures adapted from McLean et al. 2016.
The authors state: “Our study demonstrates that reflex impairment (RAMP) indices are a promising tool to predict post-release vitality in white sturgeon exposed to acute fisheries encounters, such as an angling event. The reflexes used in our RAMP protocol were chosen so that multiple neurological and/or muscle pathways underlying the overall stress response were tested. What we found was that sturgeon exposed to fishing-related stressors had higher RAMP scores and took significantly longer to recover than control fish. The relationship between reflex impairment and stressor intensity (i.e. fishery-related treatment) indicates that sturgeon are undergoing whole-animal (or tertiary) responses to varying degrees of capture stress. Reflex impairment indicators were surprisingly sensitive to fisheries stressors. Control fish had all reflexes intact, whereas multiple reflexes were absent after fish were treated.
It is important to note that it was not the aim of this study to produce accurate mortality estimates for use in C&R fisheries, but rather to explore the use of RAMP on a sturgeon species frequently angled in the wild. We recognize the subjectivity of a whole-animal assessment and categorization; however, given the statistically significant difference in RAMP scores of observationally ‘recovered’ and ‘unrecovered’ sturgeon, we suggest that RAMP is an effective tool for predicting a lowered state of vitality post-release and that this suggests a continuum to an increased risk of delayed mortality.”

Wednesday, June 29, 2016

Assessment of reflex impairment and mortality in discarded deep-sea giant isopods

Giant isopod, Wikipedia

Giant isopods were subjected to simulated capture and discarding by Talwar et al. (2016). Reflex impairment and mortality were induced by capture, exposure to air, and time at surface before discarding. Reflex actions tested are included in Table 1.

Six reflex actions were tested in control animals. Impairment of antennae extension and pleopod movement were not associated with mortality and were removed from the mortality analysis. Figure 1 shows the relationship between increasing reflex impairment and increasing mortality. 

Note that an impairment score of 0 was associated with 50% mortality. Clearly this score does not mean that animals were not impaired. Stressed animals were initially impaired without associated mortality, as indicated by the loss of antennae extension and pleopod movement.  Removal of these two reflex actions from scoring and the mortality analysis may have produced a tighter analysis, but fails to show the sublethal effects of the experimental stressors. 

Tuesday, June 7, 2016

A bigger picture: factors and traits that contribute to vitality and survival of discards in fisheries

A conceptual model for discard survival in fisheries is developed in the ICES WKMEDS4 report (2015). In this concept, survival is linked to species sensitivity, injury, and predation, through fishing factors, environment, and size. The expanded view shows potential factors and traits in more detail.

ICES WKMEDS4 report (2015) Click on images.

Monday, June 6, 2016

Sport catch and release (C&R) fishing: assessing captured fish condition (vitality) with injury and reflex impairment

A review and synthesis of tools and tactics for best practices in sport C&R fishing is made by Brownscombe et al. (2017). A key factor for conservation of species fished with C&R is the assessment of fish condition (vitality) and associated survival after release. This assessment is conducted primarily with observation of injury and reflex impairment that results from fishing practices. Fishers can then make educated adjustments to their fishing practices (capture gear, playing time, handling, release, recovery, or harvest) to enhance future species recruitment in sport fisheries.

Reflex tests for C&R fishing, Brownscombe et al. (2017).
Brownscombe et al. (2017) concluded that “As catch-and-release grows in popularity, so must angler education and implementation of best angling practices to ensure the sustainability of this practice and conservation of fish and aquatic environments. Sustainable catch-and-release angling is a joint venture where it is the responsibility of management agencies and scientists to communicate and evaluate the best angling practices, while anglers need to be educated and use the correct tools and tactics to maximize the likelihood that released fish survive. In this regard, catch-and-release angling is perhaps among the most successful and rewarding conservation partnerships.”

Sunday, February 7, 2016

Why observe several reflex actions together to measure animal vitality?

Why observe several reflex actions together to measure animal vitality? The short answer is that animals are whole beings; a summary collection of component parts and their interactions in response to stimuli.

Animals are constructed of biochemical and behavioral components that interact to form a whole; capable of responding to stressors. The interactions of stressors and behavior are also important for prediction of vitality impairment and survival. Reflex actions are fixed behavior patterns that include biochemical, muscle, organ, and nerve functions.

Efforts to identify factors that can control vitality and predict post-release survival and mortality of captured animals generally strive to identify single important variables. For example, temperature changes, injury, exhaustion, and hypoxia can control vitality and survival. For simplicity, single factors are statistically modeled as predictors for survival. Factor interactions are rarely considered because of their complexity.

Patterns of vitality impairment vary with species and contexts. Observing impairment of several reflex actions and possible injury in a defined context integrates the effects of multiple stressors, contexts, and their interactions on animal impairment and survival. Measurement of single reflex action impairment can miss the range of vitality that spans from excellent to moribund. 

Stoner 2012 (crabs)

Below are several examples of the cascading nature of impairment observed as individual reflex actions cease to function in a spectrum of stressor intensities. Reflex actions with higher proportion of impairment are impaired before those with lower percentage. Note that patterns of impairment vary with taxa and context.

Davis 2010 (walleye pollock, coho salmon, northern rock sole, Pacific halibut)

Uhlmann et al. 2016 (plaice, sole)

Forrestal 2016 (triggerfish)

Forrestal 2016 (yellowtail snapper)

Danylchuk et al. 2014 (lemon shark)

Sampson et al. 2014 (mottled mojarra)

Stoner 2009 (Tanner crab, snow crab)

Stoner 2012 (spot prawn)

Wednesday, January 20, 2016

Using vitality scores to predict post-release survival of plaice

European plaice (Picton & Morrow, 2015)

A recent study of plaice after capture and release from a beam trawl determined that vitality scoring can be used to predict post-release survival (Uhlmann et al. 2016). Vitality scores included observation of reflex impairment and injury. 

Figure from Uhlmann et al. 2016.

The authors conclude: "Our results illustrate that a vitality score and TL were the most relevant explanatory variables to predict post-release survival probability of plaice. In agreement with other post-release survival studies (Yochum et al., 2015), 14 d of post-release monitoring was appropriate to capture almost all fishing-related mortality events. Although one fish died after 21 d, > 60% of mortalities occurred within the first 4 d. Reflexes of both plaice and sole were sensitive to capture stress, in particular air exposure, although some of the differences may have been related to an observer effect."

The authors noted reservations about scoring vitality: "As with other animal behaviour scores, reducing a continuous spectrum of responses to presence/absence observations to improve practicality (Cooke et al., 2013) require a well-defined protocol, and assessments of bias, especially when multiple observers are involved (i.e. inter-observer reliability, Tuyttens et al., 2014). Although scoring binary as opposed to ordinal or continuous responses removes some subjectivity in interpretation (Tuyttens et al., 2009), it may still persist by abstracting from a continuous scale (Tuyttens et al., 2014)."

Uhlmann et al. (2016) comments about binary scoring expose a misconception about vitality scoring using the RAMP approach. For RAMP, presence or absence of individual reflex actions and injuries are given a binary score and then summed to derive an ordinal or continuous vitality score, representing the sum total of impairment. The vitality score is then correlated with survival or mortality for samples of animals (Davis 2010, Stoner 2012).

Future research is suggested to refine the vitality method: "Further research is needed to disentangle the effects of observer, and expectation bias on reflex impairment scores, especially in studies where more than one scorer is involved. Accuracy of scores may also be improved, if researcher handling periods before reflex (and injury) assessments are kept consistently as short as possible. Finally, the utility of RAMP as a proxy to predict post-release survival will depend on both laboratory-based and field calibration studies where key technical, environmental, and biological drivers of post-release survival are included." 

Monday, September 21, 2015

Importance of context for RAMP curves used to predict mortality and survival of stressed animals

Relationships between reflex/buoyancy impairment and post-capture mortality for Atlantic cod (Humborstad et al. 2016).
Humborstad et al. (2016) looked at the relationship between reflex/buoyancy impairment and post-capture mortality for Atlantic cod exposed to fishing stressors. RAMP curves were generated for (a) fish exposed to laboratory simulated forced swimming, air exposure, and net abrasion, (b) field longline capture, and (c) field pot capture. The authors concluded that:
“It appears that specific RAMP curves may be needed for gears that involve different stressors, including consideration of any additional stress associated with captive observation of delayed mortality. Differences in stressors and holding conditions certainly reduce the general applicability of RAMP across different stressors and fisheries. However, once a RAMP curve has been established for a specific set of stressors or gears, the strong relationship between reflex impairment and mortality shows the potential for predicting mortality outcomes, especially at high and low levels of impairment.”
“Reflex impairment could predict mortality among fish caught by pot and longline. However, different RAMP curves were observed between laboratory and field conditions, indicating that careful consideration must be given to the types of stressors present and captive-observation conditions for delayed mortality when comparing RAMP curves for different fisheries. The inclusion of buoyancy status in modelling greatly improved mortality predictability.”
Science and medicine generally do not know proximate and ultimate causes for why fish and other animals die. This lack of mechanistic knowledge precludes us from direct understanding and prediction of death. However, we can observe correlates with death; animal size, stressors, vitality impairment, and physiological impairment. These correlates can be used to identify risk factors and predict immediate and delayed mortality. 
Successful mortality and survival prediction requires that the context of animal exposure to stressor risk and recovery be included in any experimental analysis of this problem.  We cannot simply identify stressors, impairment, or physiological numbers and say that they will result in a particular mortality (Davis 2002). RAMP curves clearly show the importance of context for exposure to stressors and potential mortality or survival (Davis 2010). The question of interactions among stressors and their context has recently been elaborated for freshwater and marine systems (Jackson et al. in press).

Wednesday, September 2, 2015

What is RAMP: reflex action mortality predictor?

Reflex actions and injury traits in crab scored for impairment (Stoner 2012, Yochum et al. 2015).

Reflex actions and injury traits in sharks scored for impairment (Danylchuk et al. 2014).

Reflex actions and injury traits in fish scored for impairment (Davis 2010, McArley and Herbert 2014).

Reflex actions and injury traits in turtles scored for impairment (LeDain et al. 2013, Stoot et al. 2013).
Photos; crab - Farm to Market, shark -  Swell Brains, fish - DEEP, turtle - Aquatica.

Any animal has reflex actions and potential injury traits; see diamonds in figures. These fixed traits can be observed, scored present or absent, and summed to form an animal vitality impairment score. Animal vitality is a gestalt of reflex and injury traits that we can observe as a whole animal, active and responding to stimuli. Vitality impairment and mortality are correlated and this relationship is expressed as RAMP, reflex action mortality predictor.

Impairment of well-defined reflex actions and injury types may differ for each species, dependent upon their natural history and phylum.  These species traits of reflex actions and injury types can be scored and combined to express the percentage of whole animal impairment. No impairment represents a healthy animal with all actions present and all injury absent. Increasing absence of reflex actions and presence of injury types is increasing impairment and is correlated with mortality.

Sublethal and lethal zones associated with reflex action impairment scores (RAMP) in walleye pollock, rock sole, sablefish, and Pacific halibut (Davis and Ottmar 2006). For these species at specific transition impairment values, a rapid rise in mortality is observed after a small increase in reflex impairment. 

These curves illustrate the expression “you are alive until you are not”. Animals live in various states of vitality impairment that are correlated with stress. Above a quantifiable level of vitality impairment, animals begin to show mortality, correlated with continued increase for impairment. The distribution of reflex impairment and injury in a group of animals is a measure of population vitality. 

For fish species (Davis 2010, McArley and Herbert 2014), animals have several types of reflex actions which can be secondary or primary. One action group contains secondary peripheral actions that are part of swimming and defensive behavior (fin erection and startle). Impairment of these reflex actions generally indicates sublethal stress effects and is associated with increasing stressor intensity (duration or strength). A second action group contains primary body functions (orientation and coordinated breathing). Impairment of primary body functions generally indicates delayed mortality after stress induction. In the same way, for crustacean species (Stoner 2012, Yochum et al. 2015), loss of leg reflex actions are associated with sublethal stress effects. Loss of eyestalk and mouth actions are associated with delayed mortality after stress induction.

Sunday, August 2, 2015

Triage for captured and released fisheries species: research and survival

Will they survive? (The Guardian, 2013)

Vitality impairment can be linked to post-capture mortality in fisheries bycatch. Vitality impairment can be estimated by direct observation of animal activity, responsiveness, and injury. For each critical fisheries species in crabs, fishes, sharks, and turtles, reflex actions that are consistently present in healthy, uninjured individuals are listed as control levels. Impairment is signified by loss of reflex action types and addition of injury types after capture.  

Reflex actions are fixed, consistent animal behavior patterns that can be triggered by perception of external stimuli (light, sound, smell, gravity, touch). Stimulation of reflex actions is not controlled by body size, motivation, strength of stimulus, or fear. Reflex action traits summed as a whole animal can be an expression of vitality (Davis 2010). In contrast, volitional behavior can be altered by body size, motivation, strength of stimulus, fear, cognition, and as such is not a controlled measure of vitality.

With the species reflexes and potential injury lists, observations of captured animals can be made in commercial and sport fisheries. Patterns of significant impairment can be determined and related to fishing context and species (Raby et al. 2015). These patterns help identify the relative effects of fishing gears, handling, and physical factors (air, temperature, light, pressure) on impairment and potential survival and mortality.

Figure shows overlap between information on animal physiology and fisheries biology, adapted from Horodysky et al. 2015 and modified to show vitality information. Measures of vitality include reflex impairment and injury, which are whole animal measures that are ecologically relevant, linking physiological and population level research and hypothesis testing. Volitional behavior is coordinated whole animal movements beginning with perception and motivation, followed by attraction and aversion to various stimuli (injury, threat, food, shelter, species mates, migration).

Patterns of vitality impairment can guide research questions and priorities to triage fisheries for treatment of bycatch mortality and enhancement of survival. Vitality impairment can measure the efficacy of engineering fishing gears to increase bycatch survival. 

Friday, April 24, 2015

Observing vitality impairment

Animal vitality can be measured by observing species traits associated with activity, responsiveness, and injury. For each species, a group of reflex actions can be observed that are consistently present in healthy animals. As vitality becomes impaired, reflex action traits disappear and injury traits may begin to appear. 

Activity, responsiveness, and injury for measurement of vitality impairment (Benoît et al. 2010). 

Fisheries show gradients of stressors associated with capture, handling, and release or escape. Discard mortality, survival, and vitality impairment are controlled by stressor gradients.

Gradients of mortality and simulated stressors in sablefish fisheries; water temperature and gear type including trawl (time), longline, pot. Smaller fish are more sensitive to stressors (AFSC).

Vitality impairment gradients are associated with stressors and can be used to predict survival and delayed mortality for populations of impaired animals. Vitality impairment gradients can be measured by identifying classes of health condition; excellent, good, poor, and moribund based on rapid observation and impression of animal injury and activity (Benoît et al. 2015). 

The resolution for observations of vitality impairment gradients can be increased by including more information. RAMP is an example of this approach (Davis and Ottmar 2006, Davis 2010). A list can be made of reflex actions present in control animals and possible injuries. Then presence or absence of listed traits is observed after exposure to stressors. Increasing impairment is associated with stress effects and morbidity.
Reflex actions observed in snapper by McArley and Herbert 2014.

Relationships between vitality impairment and survival or delayed mortality can be experimentally determined. Then predictions of stress effects in other settings with similar stressors can be made by measuring vitality impairment associated with stressors, without the need to hold or tag animals. Vitality impairment can be rapidly observed in sampled populations as an additional factor to evaluate stressor effects and is a useful indicator of animal health and stress status, that can be validated experimentally.
Reflex impairment and mortality for individuals (A) and groups (B) of Atlantic cod with 95% confidence intervals (Humborstad et al. 2009). 

Tuesday, March 10, 2015

Snow crab discard mortality

Snow crab in Bering Sea pot fishery (ASMI).

Over 19,000 snow crab were evaluated in Bering Sea pot fisheries 2010-2012 for impairment using the RAMP method (Urban 2015). The estimated discard mortality rate was 4.5% (s.d. = 0.812), significantly below the rate used in stock assessment models. The author concludes: “ In this study, the results of RAMP observations showed that at the range of winter temperatures typically encountered by the Bering Sea snow crab fishery, nearly all discarded crab experienced no reflex impairments. Therefore, we estimate that they should have only a 4.8% chance of short-term mortality. Injuries caused by the fishery occurred at very low levels and so should also have a minimal effect on discard mortality rates. However, because long-term survival rates and the effects of reduced crab vitality are difficult to predict, an estimate of the total impact of discard practices on snow crab stocks is not possible. Even with these uncertainties, the current empirical evidence indicates that the assumed discard mortality rate of 50% is conservative.”

Figure 1. The upper panel shows the relationship between the temperature at the snow crab sorting table and the predicted mortality of snow crab based on reflex impairments. Error bars indicate the 95% CI. The lower panel shows the proportions of the temperatures recorded, while the observations were being made during the 2010–2012 fisheries (Urban 2015).

Friday, February 13, 2015

RAMP method video developed by ILVO

ILVO (Belgium Institute for Agricultural and Fisheries Research) has developed RAMP methods for three species of flatfish (plaice, sole, and dab) in European fisheries.

The first video sets the scene and explains the potential relevance of this method in relation to the recently reformed European Common Fisheries Policy.

The second video explains and demonstrates reflex tests in more detail and may guide other investigators in defining and recognizing reflex actions.

An excerpt from the video text explains, “A staggering amount of commercially-caught fish is being thrown overboard. Some say that all of those discarded fish are either dead before they hit the water or they die soon after, victims of predation or injury. But others argue that some of those species are strong enough to survive after being discarded and live long enough to reproduce. The European Common Fisheries Policy was recently reformed and will now phase in a ban on discarding, meaning that fishers will have to land everything they catch. The idea behind the ban is to stimulate more selective fishing techniques, because it will be in the fisher’s interest to only catch the most valuable fish. However, by landing everything, this ban risks killing more fish than before. If a juvenile fish lives long enough after being discarded to spawn new fish, it should be given that opportunity. For this reason, the discard policy provides an important exception: if a certain species can be scientifically proven to have a high chance of survival, fish of that species should be thrown back after catch. Researchers at the Institute for Agricultural and Fisheries Research (or ILVO) in Ostend, Belgium are testing the most commercially important species of flatfish - plaice, sole and dab – for their likelihood of survival.”

Sunday, January 11, 2015

Elements of vitality testing and delayed mortality in fisheries

Conceptual diagram outlining elements for vitality testing and delayed mortality in fisheries. Fish are captured and environment sampled. Fish become stressed which is measured as impairment from control health by observing reflex actions and injury types. Stressed fish are held for captive observation to determine delayed mortality. Bias and error can be introduced by initial impressions of vitality before testing reflex actions and injury, by differing observer scoring opinions, and by holding conditions that are stressful for the fish. 

Scoring vitality impairment is most difficult when observer decision is used. Training observers is a key part of RAMP development. Reflex actions (RA) are clearly present in control animals, and observers do not need decisions to score present. As impairment increases, scoring RA requires increasing observer decisions about whether sampled RA are present. The decision can be based on how control RA appear to trained observers. Each observer will have different opinions that can be influenced by their initial impressions of the animal and of the stressor treatments the animal has been exposed to.

Initially after stress induction, RA impairment increases and mirrors stress levels, while mortality is not evident. When animals reach a critical impairment level, replicates begin to show mortality, which increases rapidly over small changes in RA score. At highest levels of impairment decisions are less frequent as the animal ceases general movement and responsiveness.

Friday, January 9, 2015

Questions and answers about observer bias in RAMP

Q: What are the options when grappling with cognitive/expectation and sampling biases in manipulative fisheries research experiments under sometimes challenging conditions at sea?

A: Begin by training and calibrating observation. We all recognize vitality when we see animals with high vitality. This recognition is based on rapid visual assimilation of information about several traits including injury, activity, and responsiveness. We cannot separate our cognitive impression of vitality level from the act of observing individual traits and scoring their presence or absence. Presence or absence of reflex actions is scored relative to control animals which have a set of reflex actions consistently present. Reflex actions range from clearly seen through weakening stages to clearly absent. As the animal becomes more stressed and impairment increases, the interaction of impression and scoring observations contributes bias. 

If observers are trained to clearly recognize a suite of real reflex actions in the species of interest, then correctly recognizing the impairment or absence of those reflex actions should be a realistic accomplishment. An experiment to test for the effect of observer bias and variability in scoring reflex actions could be conducted in the lab or field if enough fish and observers are available. Stress some fish (air exposure) to produce replicates over a range of RAMP impairment scores and have the observers sample reflex actions. Blind the study treatments from observers. Estimates for observer bias from stress studies with different species will be useful for improving observer training by identifying protocols that need to be more defined and less subject to observer opinions. Alternatively, Benoît et al. (2010) modeled observer bias as a random factor. 

Q: How can we achieve a blinded experimental design if the experimenter who assigns or is aware of experimental treatments also scores reflex impairment on board (commercial) vessels?

A: Perform some fish experiments on observer bias outlined above and decide how important observer bias is after training with well-defined protocols for testing individual reflex actions. The bias problem may be mitigated by training using clear definitions of present or absent for reflex actions. I will assume that the vessel captain is conducting the experimental fishing treatments. So the captain could be given treatment conditions by the scientist and then could conduct fishing by assigning treatments randomly without the knowledge of the scientist observer. However tow time, soak time, or haul time and catch volume will be apparent to observers. 

Q: Is an observer influenced in his/her ability to score reflexes if, apart from knowing the treatment, also the condition of an organism is evident even before the scoring begins? Is there any option to minimise this?

A: We cannot separate the correlation between overall impression of vitality and scoring reflex actions. However, we can be trained to clearly recognize the presence of reflex actions. Any impairment through weakness, delay, or loss of action is scored absent.  The key method for minimizing observer bias for reflex actions is to clearly establish what the suite of reflex actions look like when they are consistently present in control animals. If presence of a reflex action is difficult or inconsistent to determine then it is not a good candidate for testing. Any deviation from control appearance in action strength or delayed time for action can be considered impaired and scored absent. The goal is to eliminate variability in detection of presence for reflex actions. By sharpening the decision criteria, bias and variability can be reduced. This idea can be tested using the outlined experiment design.

Q: Seeing that vitality assessments of discarded fish in Europe are now being developed in several places is there a need to also quantitatively evaluate the ability of different observers to score reflexes consistently? What would be the best setup for such a training exercise? 

A: As mentioned above, a stress experiment can be conducted to quantify observer bias and consistency.  With enough replicate fish and observers, an air stress experiment could produce fish with varying levels of reflex action impairment. These fish could be sampled by observers with defined criteria and using an experimental design for testing the effects of observer variability and bias. The effect of training could also be evaluated using this design.

Thursday, January 8, 2015

Observer bias and RAMP

Cognitive bias (The Daily Omnivore, 2012)

Subjective scores for animal behavior can be biased by observer opinions about experimental treatment differences and resulting outcomes (Tuyttens et al. 2014). The research paper title expresses a fundamental bias of human perception and belief: “Observer bias in animal behaviour research: can we believe what we score, if we score what we believe?” The problem is to separate belief from observation. This may be accomplished by clearly defining and adhering to consistent protocols for behavior observation and analysis.

RAMP relies on subjective scoring for presence or absence of reflex actions or injury types. Control fish have a suite of reflex actions that are consistently and clearly present when tested for. When an observer begins to notice the weakening or complete loss of a reflex action, that action is scored as absent (impaired). There will be variation among observers in the decisions about when reflex actions are impaired and bias will vary with experimental protocol. 

Because RAMP is an aggregate vitality impairment index summed from control reflex actions and potential injury types, a RAMP score includes the observer bias for each included reflex action and injury. Close correspondence of RAMP scores and mortality is noted at low and high scores because observers clearly know when fish are active and when fish are severely injured and impaired. Relationship of mortality and RAMP is more variable at intermediate levels of impairment and mortality in part because observer opinion about impairment is more variable. To reduce observer bias, RAMP for a species must be designed to include reflex actions and injury types that can be clearly separated into present or absent scores. Also experimental treatments can be administered without informing observers.   

Vitality of a stressed fish is readily observed. We are primarily seeing the activity, responsiveness, and injury presented by the animal. The most widely used vitality index in commercial fisheries is for the halibut fisheries of the northeast Pacific Ocean (AFSC Observer Manual 2015), based on Appendices S-X for trawl, pot, and longline fisheries.  For trawl and pot fisheries, three levels of vitality (excellent, poor, and dead) are scored by observing injury types and spontaneous activity, startle response to touch, and operculum clamping. For longline fisheries, vitality is scored by observing injury types. Mortality rates are assigned to vitality impairment scores using tagging experiments (Williams 2014).

Vitality impairment codes (Benoît et al. 2010).

Benoît et al. (2010) constructed a fishery vitality index with four levels of impairment (excellent, good, poor, moribund) that are scored by observing injury types, spontaneous body movement, startle to touch, and operculum clamping. Their vitality index and the halibut vitality index use the progressive increase of injury and impairment of activity to score vitality impairment. Benoît et al. (2010) corrected for observer bias by using a random effects term in their statistical model. 

Reflex actions scored for presence or absence in RAMP for snapper (McArley & Herbert 2014).

The RAMP vitality index alters impairment scoring to only include presence or absence of a larger number of injury and reflex actions. This shift attempts to introduce more information about activity and injury types that may be associated with mortality and to reduce decisions about degree of impairment for individual activity and injury traits. Impairment is observed as a progressive increase in the number of reflex actions that become absent and the number of injury types that become present when compared to control animals. Because observer bias can be introduced in scoring, observer protocols must be well defined with clear rules for presence or absence of traits. Observer judgements about correspondence between experimental treatments and outcomes could also be eliminated by careful experimental design.