Examples of particularly well done answers to the exam

 

QUESTION #1

 

EXAMPLE #1:          

Karl Popper argues that proof does not exist in science, only the possibility of disproof. Many popular theories offer "irrefutable" explanatory power, but, according to Popper, their irrefutability is their weakness, not their strength. A true scientific theory is only falsifiable. A good theory must make predictions that are risky; these predictions must "be capable of conflicting with possible observations."  Thus, an outcome that would falsify the theory must be conceivable, and the theory can be dismissed with as little as one falsification.

According to Popper, one cannot simply confirm a theory by observation. Rather, any confirming evidence must actually be the result of failed attempts to falsify the theory. Science, then, is the experimental process of making predictions from a theory and then trying to falsify these predictions. Popper offers the example of Freud's theory of psychoanalysis as a theory that does not meet this criterion for science; any conceivable situation can be interpreted in light of the theory, and no prediction of a situation that would disprove the theory can be imagined. In contrast, Einstein's theory of relativity predicts that light can be bent by gravity, which could be tested by photographing constellations at night and during an eclipse. While evidence showing that light is bent by gravity would not prove the theory, if the constellations appeared identical, then the theory could be dismissed.

            Lim et al (2004) propose a theory that the expression of the vasopressin V1a receptor (V1aR) in the brain causes some species of voles to form pair bonds and display monogamous social behavior. Thus, they predict that increased expression of V1aR receptor mRNA in the brain will be related to monogamous behavior. The authors attempt to disprove this theory in several ways. First, they examine autoradiographs of V1aR expression in monogamous and polygamous voles, predicting they will observe different patterns of expression between the two groups. If V1aR were in no way related to pairing, the radiographs would likely be identical because the two species are otherwise quite similar. Thus, expecting highly different gene expression is a risky prediction. However, as predicted, they show that V1aR is expressed more highly in monogamous voles than polygamous voles, but even though this result is consistent with the theory, it is not proof.

Next, they inject a viral vector containing the V1aR gene into the brains of polygamous voles. They predict that replacing the expression of V1aR will restore pair bond formation and monogamy in the voles. It is unlikely that polygamous voles would suddenly become monogamous unless the theory is true; thus, this is a risky prediction. However, the theory would be refuted if no effect on behavior were observed.  They observe that males receiving the V1aR injection spend more time cuddling with females. Thus, the attempt to disprove the theory failed, and this evidence supports the idea that the presence of V1aR promotes pair bond formation. The controls in this experiment, which were injected with an irrelevant lacZ gene, falsify the possibity that the act of injection itself alters pair formation behaviors.

Finally, Lim et al (2004) attempt to disprove the possibility that  a source other than V1aR is the cause of increased pair bond formation. They use a compound to block dopamine neurotransmitters, the mechanism by which V1aR is known to work. If V1aR were not the cause of the increased monogamy, blocking the dopamine receptors would have no effect. This is a riskly prediction because the observed effects of V1aR injection are unlikely to change unless its mechanism is block.  However, blocking dopamine receptors causes the transgenic voles to revert to polygamous behavior, which refutes the theory that V1aR was not the cause of the altered behavior.

 

EXAMPLE #2:          

Popper's philosophy is dominated by the idea of falsifiability. He argues it serves as the demarcation between scientific and pseudo-scientific theory. The definition of science as that which is empirical in nature fails to adequately define what is truly scientific as pseudo-empirical methods can give rise to theories such as astrology or Marx, Freud, or Adler's theories that appear to explain and garner support from all situations. To Popper it is this apparent ability to explain all observation that is a particular weakness of a theory and eliminates its scientific application.

            Popper outlines his criterion for a theory to be scientific in status as follow; First one can not look for specific conformations to a theory. Second confirmations should only be accepted if they are the result of a risky prediction, one not expected if unenlightened by theory. Third a good hypothesis is prohibitive, and increasingly good by the amount it prohibits. Fourth, irrefutability is not strength. Fifth, all subsequent tests must be attempts to falsify the theory. Sixth, confirmations of the theory should only be counted if they attempted to refute the theory. Finally, a theory must be rejected if contrary evidence is shown against the theory.   

            In their paper, Chemosensory cues allow male Tenebrio molitor beetles to assess the reproductive status of potential mates, Carazo et al. hypothesize female reproductive status can be assessed by male beetles by chemical cues alone. Carazo et al.'s hypothesis starts out on the right foot with Popper. While many insect species have are known to select mates according to their reproductive status, the manners in which males evaluate females has been little studied. Thus while results confirming the hypothesis will provide a confirmation to the previous theories of mate selection in beetles, confirmation is not directly sought, and instead proceeds from a somewhat "risky" prediction, that males can assess female quality solely on chemical indicators.

According to Popper, one can not prove anything only disprove it, thus the study must be prohibitive in nature. In the vein of Popper, then we would hypothesize male beetles will court or display only to those cues associated with a high quality mate. We would thus predict that a male would court high quality females or objects emanating certain cues inherent of a high quality female, such as high quality female chemical infused paper, and theoretically prohibit the male form spending any significant time in making advances to things lacking these cues. We should also predict that this theory could be refuted, and does not necessarily pertain to all courting mechanisms in beetles or nature.

In the subsequent testing of our predictions each test must be an attempt at falsification. We cannot present males only with papers chemically infused from attractive mates, but must also present the possibility of rejecting out hypothesis by simultaneously presenting papers infused with non-attractive female chemical cues or papers with no scent. Only in such an experimental attempt to refute our hypothesis and accept the null can we accept our results as supporting the hypothesis as we can disprove the null, that there is no interaction. If, however, our results are contrary to what we predicted, that beetles preferentially select papers imbedded with low quality female chemicals, or don't preferentially select any papers, then we must reject the hypothesis outright in order to preserve its identity as scientific. Doing all this we might bring a smile to Popper's face.

 

EXAMPLE #3:

In his work Conjectures and Refutations, Karl Popper addresses a problem in the blurring of the line between science and pseudoscience.  Most people assume that the difference between the two is that the latter does not follow the empirical method.  Popper disagrees, saying that pseudoscience can often follow an empirical pattern of testing a hypothesis with observation, but that this experimentation "does not come up to scientific standards."  What he is referring to here is the idea of falsifiability.  Many hypotheses, once made, can be easily confirmed if one looks only for confirmations.  However, in order for a theory to be considered truly scientific, the claim must be refutable; it must be possible for someone to test the hypothesis and prove it wrong.  As examples of theories that are not falsifiable, Popper mentions Adler's individual psychology and Freud's psychoanalysis.  Both could be "confirmed" with each case, even on the same person, but it is impossible to ever disprove their theories.

            A "risky prediction", which is what Popper considers to be truly scientific, is one which makes a claim that is open to refutation; it may even be a prediction that most people would assume to be incorrect.  One way a prediction can be sufficiently risky and refutable is if it prohibits, rather than predicts.  If a theory prohibits a certain result, then it should be effectively testable.

A good example of a risky prediction is found in the study of social monogamy in snapping shrimp by Mathews (2003).  The paper seeks to determine if the social monogamy witnessed in this species could be explained by the mate-guarding hypothesis, which states that a male will guard a female while she is reproductive to prevent other males from reproducing with her.  Two predictions follow from this hypothesis: a male must be able to detect whether a female is reproductive (or approaching a reproductive state), and must guard females that are closer to this state.  These predictions were tested in an elegant experiment by Mathews (2003).  By showing that males prefer to spend more time in water treated with reproductive females than in water treated with other females, the researchers confirmed that the males could physiologically detect reproductive capability.  They then showed that males spent more time near a reproductive female than other females, showing that they will guard females closest to being reproductive.

This study falls well within the margins of what Popper would consider "good science."  It is not good because the results of the paper are in line with the predictions; rather, it is good because it was open to fallibility. The study was designed in such a way that results conflicting with the mate-guarding hypothesis could potentially have been found.  This means that the predictions were, as Popper would say, "risky."  They were also prohibitive, meaning that they prohibited certain behavior if true.  For example, the prediction that males would preferentially guard females that were closer to reproductive status prohibits a result that shows males guarding females further from reproductive status; if this result is seen, it shows the prediction to be false.  For these reasons, the study Mathews (2006) falls in line with Popper's ideas about proof in science.

 

QUESTION 2

 

EXAMPLE #1:

A study by Carazo, et al. (2004) examined the ability of male beetles to discern the reproductive status of female beetles in order to choose a mate.  The researchers wanted to know if reproductive status effected male mate choice, and if so, whether chemical cues were a factor in this choice.  The experiment showed a significant preference for courting and mating with mature females over immature females, and virgin females over mated females.  When testing filter paper exposed to female chemical cues, it was found that the males showed the same preference in odor as they did for mating choice in the previous experiment, showing that chemical cues are sufficient in giving a male enough information to choose a female mate.

            This paper shows a test of a proximate hypothesis to explain the mating choices of a male beetle.  Proximate hypotheses ask questions involving how a behavior occurs and what biological mechanisms cause it to happen.  This paper specifically looks into how beetles choose their mates (maturity and mating experience), as well as the physiological mechanism behind this choice (olfactory cues).  This paper does not test ultimate hypotheses, which look into why a behavior takes place and what adaptive value it confers upon the individual.

            Ultimate hypotheses in this case would attempt to explain why males choose mature females over immature ones.  One possible explanation is the higher fecundity of mature females.  This would put a selective pressure on males to choose mature females, since it would provide them with a higher number of offspring.  The ultimate explanation for male preference for virgins may also involve an increased likelihood to reproduce.  In beetles, sperm competition occurs, where multiple males inseminate one female.  Thus, it is possible that mating with a non-virgin female will put the male's sperm in competition with others, and therefore lower the likelihood of one of its own offspring being born.  Thus, there would be a selective pressure for a male to prefer virgin females.

 

EXAMPLE #2:

            In their paper, Enhanced partner preference in a promiscuous species by manipulating the expression of a single gene, Lim et al. formulate a proximate hypothesis to explain monogamous pair formations in voles. In their study, the authors do not expand on those genetic processes or attributes which could be conferred evolutionarily, but rather demonstrate the expression of a specific gene, the vasopressin V1a receptor (V1aR), elicits monogamous behavior in an otherwise promiscuous vole species.

            While genes often compose ultimate hypothesis, in that changes in allele frequencies over time demonstrate ultimate changes when those alleles code for specific and selected components of fitness, genes also form the beginning of certain physiological responses that serve to explain what causes individuals to do certain things. While increasing V1aR expression in specific brain areas was "in essence recreating a single evolutionary event," the authors were concerned with investigating the neural mechanisms underling pair bond formation, a proximal investigation. They found increased expression of the V1aR gene in the ventral palladium conferred increased pair-bonding, thus showing how certain social structures might arise.

            For the study to address an ultimate hypothesis of partner selection it must answer a "why" question, evolutionary in nature. Further study addressing ultimate causes should attempt to discern what, if any fitness benefits result from an alternative (monogamous) social structure and if this has any genetic basis would address an ultimate cause. Perhaps increased monogamy reduces the amount of antagonistic interactions between vole individuals, reducing energy costs that could confer a selective benefit. Further energy expenditure necessary in mate searching and displaying could be avoided also conferring a selective benefit.

 

 

QUESTION #3

 

EXAMPLE #1:

Biological clocks are mechanisms by which organisms regulate their patterns of activity over periods of time. They are based on an external cue that is part of the organism's umwelt (perceived sensory environment). Clocks may be circadian (24 hour period), circannual (365 day period), circatidal (related to the tide cycle) or circalunar (related to the phases of the moon, 28 days). The external cue that sets the clock, which may be light, the moon, or the tide, is known as the zeitgeber (German for time-giver). The zeitgeber is received by a sensory receptor, which influences a cyclical clock mechanism that may regulate locomotion, feeding, or hormone levels. In more complex animals, the suprachiasmatic nucleus of the hypothalamus is thought to control clock mechanisms.

The behaviors that function by biological clocks operate in sinusoidal rhythms with respect to time. The period of the biological clock is the amount of time taken for one complete behavioral cycle, and the amplitude is the frequency or strength of the behavior at a given point in time. Often the amplitude of activity is mediated by temperature or another environmental factor. However, variable environmental conditions like temperature do not regulate biological clocks because they are unpredictable and subject to abnormalities.

When the zeitgeber for a biological clock is absent (for example, if an organism is kept in total darkness), the organism will behave on a free running period. For circadian clocks, this free running period is generally close to 24hrs, but may be slightly longer or shorter. Thus, in the absence of the signal, the organism's behavior may occur slightly earlier or slightly later each day.  Aschoff's rule predicts that the free running period of diurnal animals tends to be slightly longer than 24 hrs and slightly shorter than 24 hrs for nocturnal animals.

This experiment tests the biological clock mechanism of the flying squirrel in the absence of the light zeitgeber. The squirrel begins the experiment in complete darkness. Each day, the activity period starts slightly earlier than the previous day. After 15 days of dark:dark, its activity begins almost 6 hours earlier than it had on the 12:12 cycle. The squirrel's free-running period is less than 24 hours because each new "day" begins less than 24 hours after the last, so Aschoff's rule would predict that it is a nocturnal animal (as most flying squirrels are).

When the squirrel is switched to a 12:12 light:dark cycle, it immediately changes to an exactly 24 hour activity cycle. Every day, treadmill running increases immediately after the dark begins and tapers off after approximately 6-9 hours. Thus, it is a nocturnally active animal following a circadian rhythm of activity, as was predicted based on its free running period and Aschoff's rule. Interestingly, when the shift from dark:dark to 12:12 is made, the length of activity is only about 3-4 hours, but it gradually increases each day. This observation suggests that initially the cessation of activity was still regulated by the free running period even after placing the squirrel on a 12:12 cycle. The external cue triggering the clock mechanism may be the absence of light or the transition from light to dark (crepuscular); these data do not distinguish between the two.  After 100 days of 12:12 light:dark, the squirrel is shifted back to complete darkness. Despite its "training" on a 12:12 cycle, its free running period remains the same as previous—slightly less than 24 hours.

 

EXAMPLE #2:

Very generally, all animals constantly receive and interpret external sensory cues. These cues often dictate particular behaviors. Specifically, we see the intensity threshold of different sound frequencies in this certain species of moth. A range of frequencies was tested from 3 to 100 kHz and neuroscientists were able to quantify their intensity threshold (dB). This threshold essentially measures the sensitivity of the moth to different frequencies; the lower the threshold, the more sensitive the moth to the frequency.

            As is evident in the provided figure, there is not a constant, horizontal relationship between varied frequencies and thresholds. This curve is not a straight line for a variety of reasons. Namely, the animal is in tune to "what matters" in a selective sense. In other words, any sound it detects in the frequency range of about 8 to 20 kHz must neither endanger the animal nor provide any benefits (they get filtered out, see below). For example, a predator (ex- a bat) might emit a noise that is 40 kHz; if this is the case then it is advantageous for the moth to be more sensitive to detecting sounds in that frequency. In addition, perhaps if this is a male moth and female moths produce sounds at 5-6 kHz then reproductively it is advantageous for the moth to be able to find mates more easily.

            There is a filtering process present in the moth. It is in part controlled by the peripheral nervous system and it is modified to what is essentially important. This filtering is related to the concept of umwelt, the animal's sensory perception of the world. Moths who are more sensitive to both predator and mate detection have higher fitness than moths who do not; while there is not selective pressure for being increasingly sensitive to relatively benign sounds (8-20 kHz). In fact, sensitivity may be selected against in these cases; if the animal cannot differentiate (filter) between the important and unimportant sensory cues then they are at risk of being preyed upon because they may not exhibit predator avoidance behaviors when needed, and it is a waste of energy to unnecessarily react.

            This is a case of a fixed action pattern (FAP). The increased sensitivity to predators who emit sounds in the 40 kHz range may result in a FAP: a stereotyped, apparent hardwiring that releases a behavior. If the moth detects auditory cues of a certain frequency, it will innately change its behavior (ex- flight direction) in order to avoid the sound. The behavior is species-specific and can be generalized to every individual within the species. In this case, the FAP increases the fitness of the moth; it is innately hardwired to change behavior in order to avoid the predator based on external sensory cues. This FAP is centered in the nervous system and is fundamentally a reaction to an impulse that has gone through the filtering process and been "neurologically deemed" important. The neural pathway that was initiated by the moth's detection of 40 kHz frequency sound ends in the pathway that causes some effector (flying away from the sound).

Release/ "Innate release mechanism" or FAP

Ex- Fly Away from Sound

 

External Cue / "Sign Stimulus" or "Releaser"

Ex- 40 kHz Sound

 
            The following schematic represents the process by which the moth reacts:

 

 

 

 

 


            Therefore, by considering the ideas of umwelt, FAP, and filtering it is possible to understand why the moth has varied sensitivities to differing sound frequencies, and how a 40 kHz sound functions as a FAP. Ultimately, this entire process increases the fitness of the moth by automatically inducing behavior only when it is important and potentially life-threatening or increases success in finding a mate.