semans's blog

Vision is a complex mechanism that exists in many forms across the animal kingdom. Planaria have very simple eyes, consisting of just a few light sensitive cells, detect whether light is present and allow them to perform phototaxis. More complex eyes have a retina with rods and cones as well as a lens which can be bent for vision at different focal lengths. These complex eyes have the capacity to produce fully formed images of the environment that appear different based on the rods and cones in an animal’s retina. Rods and cones are the visual cells that allow eyes to see different wavelengths of light. As the name suggests, rods have rod-like endings filled with opsins that can perceive more light under darker conditions than cones can, and are often found in the peripheral area of the retina. Nocturnal animals often have a preponderance of these in their retina in order to better see at night. Cones have cone-shaped endings that are also filled with opsins, however they can possess opsins of many different conformations. Opsins are a group of proteins that allow for light detection, with different opsin conformations allowing for the detection of different wavelengths of light. For example, humans have red, green, and blue cones, each with opsins keyed to those wavelengths of visible light. Our eyes receive light information from the environment and then our brain relates that to known ideas about colour, brightness, and other visual information. Different animals have different opsins, often those that best serve their survival. For example, rats can’t see red light. As nocturnal animals, rats have no need for red light since it’s longer wavelength and isn’t present at night, unlike blue light or UV. In their evolutionary past, rats no longer needed to see red, and so the opsin was free to mutate and disappear, but they did need to see UV, leading to selection for a UV-detecting opsin. Very rarely, humans will develop a mutation that leads to the development of a fourth opsin, and hence a new type of cone, that allows them to see more colours than non-mutant humans.

Animals can decode several meanings from signals about self including: parent-offspring recognition, kin recognition, mate recognition, stranger/individual recognition, competitive status, motivational status, genotypic & phenotypic quality, and aposematic colouring. Parent-offspring recognition is especially apparent in colonial bird species such as bank swallows and emperor penguins. Both species need to leave the nest to get food for their offspring, and when they return, they locate their nests based on their chick’s calls. Kin recognition is present in birds as apparent through incest avoidance behaviour. Great tits will recognise the calls of their fathers and avoid mating with birds who have an identical call as this avoids the possibility of incest. Tadpoles will secrete a hormone that other tadpoles recognise as belonging to their kin and will form groups with similar genomes. Mate recognition has been shown to occur in bird species who have to return to a nesting site. In some species of gulls, males will return to nesting sites first and emit a call which their mates will recognise. Song birds have been shown to recognise different individuals. White-throated sparrow males can recognise whether a neighbour emits a call from a familiar border or if it has moved to a new location and threatens to encroach on his territory. In the former case, the male will respond weakly to the neighbour relative to his response to a stranger from the same location. In the latter case, the male will respond just as strongly to the neighbour in the new location as to a stranger from that same location. Competitive status is an important message to decode in dominance hierarchies. In house swallows, dominant males will have more black feathers on their head and chest than submissive males. Motivational status often has to do with level of aggression or sexual motivation. In canids, different facial expressions will give a receiver different information about the likelihood that the canid’s next action will be aggressive or submissive. In hook-tipped moths, male caterpillars will emit sound from different places on their bodies to ward off other males. Signals also communicate genotypic and phenotypic quality as in the springbok’s stottering behaviour. A springbok stotters by jumping up and down to highlight the black and white stripe on his flank. In doing so, the springbok not only signals to the predator that he has been detected but also tells them he is healthy and that it will take great effort to capture him. Lastly, aposematic colouring has to do with how poisonous or venomous a creature is. Bright, contrasting colours often indicate that an animal will be inedible or produces lethal toxins. For example, the hooded pitohui has bright orange and black feathers to signal that it produces batrachotoxin that will kill the predator that tries to eat it.

The auditory template model describes how male birds learn to sing and was developed by Peter Marler through his experiments on chaffinches. First, he observed that males were only sensitive to songs during two periods: following hatching and during their first spring after hatching. Additionally, he discovered that the chaffinches weren’t sensitive to any song, only the songs of their conspecifics. Through further experimentation, he also determined that males who were deafened produced more abnormal songs than males who were deprived of a tutoring song. From these data, Marler hypothesized that male chaffinches possess a crude template that they match to conspecific songs during their sensitive period, and that they later refine these songs by listening to themselves sing. This process of song learning is known as the auditory template model. Though this model explains the way some birds learn how to sing, recent experiments have produced data that do not fit this model. Experiments with white-crowned sparrows showed that even though male hatchlings do not learn heterospecific song when tutored by a speaker, they do learn heterospecific song when tutored by a heterospecific male. This seems to counter the idea of a pre-encoded crude template that serves to filter out heterospecific song. Other song learning modalities, such as in the marsh wren and European robin seem to counter the auditory template model. Marsh wrens are sensitive to songs from ten days after they hatch to their first spring, and like chaffinches, have a descending ability to learn songs the older they get. However, unlike chaffinches, if marsh wrens learn a lot of songs before winter they will be less ready to learn songs in the following spring, and vice versa. Indigo bunting prove to be another kind of exception to the auditory template model. The indigo bunting has no species-specific song and forms groups that share a repertoire that changes from year to year. It has also been shown that indigo bunting males can switch groups and will learn new songs to better fit in with their new neighbours. Though the auditory template model has proven accurate for some species, the many variations in song learning have shown that it is hardly ubiquitous among all bird species.

Animals have a variety of ways of encoding information. Firstly, for an animal to get its signal across to receptive parties, it must avoid as much interference as possible. One example of this phenomenon, known as channel partitioning, is in beach crabs. On a single beach there may be multiple species of crabs, all of whom wave their claws to attract females. By waving their claws at different intervals and frequencies, the females are able to distinguish conspecific males from heterospecific males. Signals can also be encoded based on their form, such as with begging in birds. Hatchlings have a begging behaviour that involves opening their mouths towards their parent, which correlates well with the actual act of eating, which involves the hatchling opening its beak. However, there are many signals without a relation between form and meaning, as with the extension of the dulap in anoles, which signals aggression but has no correlation with aggressive actions. Messages can also be encoded via discrete or graded methods. A discrete message retains the same form all the time, as in an alarm call. A graded message has different forms on a continuum that express different levels of a behaviour, such as in Steller’s jay which angles its crest higher if it is more likely to engage in aggressive behaviour. Signals can be encoded acoustically, such as with different times intervals in between syllables, the order of syllables and phrases, and the order of entire songs. A good example of acoustic encoding is with bird trilling. Trilling can be measured by trill rate, or the speed at which the notes are sung, and trill bandwidth, or the difference between the maximum frequency and the minimum frequency. There is a biophysical limit which prevents birds from singing beyond a certain trill rate to trill bandwidth ratio, and the closer males get to that limit, the higher females rate their quality. Lastly, messages can be encoded chemically, which occurs more frequently in mammals than other classes of species. Mammals generate an odour image, which is a scent pattern composed of different chemicals at different concentrations. Individuals generate different odour images, with chemicals differing between different species, and concentrations of species-specific chemicals being different in different individuals. This allows for conspecifics and heterospecifics to recognise each other and to leave scent-based messages in the environment. 

The auditory template model is the basic model for explaining song learning in birds, though there are many bird species who deviate from it. The model was developed by Peter Marler through experiments on chaffinches. He observed that chaffinches were only capable of learning song when they were hatchlings and during their first spring, and that they ceased to be able to learn when they reached a fully crystallized song or had high levels of testosterone. Additionally, the chaffinch hatchlings wouldn’t learn songs from heterospecifics, even when they hadn’t heard any other kind of song before. Lastly, when males were deafened they produced songs far more distorted than the ones produced by males without a tutoring song. From these data, Marler hypothesized that birds must possess some kind of crude template, and that they match this crude template to the songs they listen to until they hear their conspecific song, which then causes the template to crystallize into an exact template. Later, when chaffinches reach their first spring and testosterone levels begin to rise, they begin producing their own songs. With normal hearing, the birds can listen to themselves sing and match the song they produce to the template they’ve remembered. This explains the babbling phase most birds go through before reaching a crystallized song, as they need time to match the sounds they produce to the template sounds. Eventually, they reach a fully crystallized song that is a more or less faithful version of their species’ song. Though the data from several playback experiments seem to fit this model, there are many exceptions to it. For example, white-crowned sparrows will learn conspecific song played from a speaker, but will not learn heterospecific song learnt from a speaker. However, when the sparrow hatchlings are placed in social contact with heterospecific tutors they are able to learn heterospecific song, which seems to go against the idea of a crude template that filters heterospecific song. Another problem with this model has been highlighted in European robins which have an open-ended learning system. European robins have wide repertoirs spanning many hundreds of songs, each different from the last, and have no defining species specific song. In swamp sparrows, until shortly before full song crystallization, they produce 12 elements, which are then reduced to the number needed for their full song. These findings have led to the rise of another model known as the action model. In the action model, rather than having an auditory template, birds have pre-encoded elements that they must learn to put in the correct order to produce their species’ song. This model would explain the reduction in the number of elements used in swamp sparrow song. As for species with open-ended learning, one can only hypothesize that they have the capacity to learn throughout their lives and that they can learn as many elements as their syringeal muscles allow.

There are a myriad of visual signals ranging from pigmentation to postural displays. Pigmentations are one of the ways animals can display colour. Melanin is a pigment that produces a range of colours from black to brown. Prairie warbler males deposit melanin in their wings to strengthen them, and females use these melanin stripes as an indication of the male’s health. Carotenoids are an orange pigment that animals acquire from plants. Pterins are a red pigment produced by lizards, such as in anoles’ dulaps. Porphyrins are pigments with multiple qualities. Firstly, in the visual spectrum, porphyrins produce browns, reds, and greens. Secondly, porphyrins under UV light produce a bright red colouration. Porphyrins are a good example of the fact that animals have their own way of perceiving the world, some can detect UV and so would see porphyrins differently than we do. Another way animals can produce colouration is through structure. Hummingbirds’ iridescent plumage is the result of refraction in their feathers. The microscopic structures in their feathers act as prisms that reflect only certain wavelengths of light, resulting in shiny, metallic colours. Blue jays don’t have blue pigment in their fathers, but have microscopic air bubbles that refract light to produce different shades of blue. Animals also produce visual signals through posture, gestures, displays, and facial expressions. Posture and gesture are different as posture involves the whole body whereas gestures only involve arms and hands. An example of a posture is dog bowing, where the front of the body is arched downwardly, the rear is raised, and the tail is wagging, which indicates the desire to play. Gestures are much more present in animals with hands, such as primates. Chimpanzees for example have 66 unique gestures without idiosyncratic use, that is, they conserve the same function for all chimpanzees. In addition, some of these seem to be evolutionarily conserved, as other primates like orangutans and gorillas share 24 of these gestures with chimpanzees. Displays are present throughout the animal kingdom. The penguin mating display in Gebes involves the fanning of head feathers and the presentation of a piece of aquatic vegetation. Facial expressions have been well-studied in humans and it has been shown that there are 7 pan-culturally recognised facial expressions. These expressions are: anger, joy, fear, sadness, surprise, disgust, and contempt. Though, contempt is an exception in that it isn’t present in all cultures.

In general, plants glean four types of information from light: quantity, quality, direction, and photocycle. Plants can determine the level of irradiance, the wavelength of light they receive, its point of origin, and daily fluctuations in light using photoreceptors. Phytochromes are red/far-red light photoreceptors that play a role in germination, flowering, shade avoidance, and circadian rhythm entrainment. They are inactive as monomers, but when red light hits the plant, the chromophore of two phytochrome monomers will go through a cis-trans isomerization that leads to dimerization. Phytochromes are an exception among photoreceptors as their activation is reversible. For example, imbibed lettuce seeds can be induced to germinate by a pulse of red light, but when the flash of red light is followed by a flash of far-red light, germination is inhibited. Two other kinds of photoreceptors, both of which respond to blue and UV-A light, are cryptochromes and phototropins. Cryptochromes are responsible for de-etiolation, flowering, and circadian rhythm entrainment. When seeds germinate underground, they are said to undergo etiolation, by which they elongate, inhibit leaf growth, and do not produce chlorophyll. Upon breaching the surface of the ground, cryptochromes will detect blue and UV-A light, causing the seedling to become de-etiolated. That is, it will grow a short stem, produce leaves and internodes, and begin chlorophyll production. Phototropins are aptly named after one of the effects they have, phototropism. If the shoot apical meristem is exposed to blue and UV-A light, the plant will grow towards that light. Phototropins are also responsible for moving chloroplasts away from high irradiance light and moving them towards low irradiance light. Lastly, upon detecting blue light, they increase solute potential in guard cells, which causes the stomata to open. Though these are some of the important players in the light detection mechanisms of a plant, there are many other photoreceptors with functions ranging from UV protection to developmental control.

Songbirds have the capacity for species-specific recognition and individual recognition. The mechanisms of species-specific recognition generally involve recognition of invariable song features rather than variable ones. For example, though European robins produce hundreds of songs, they all follow the same syntactic rules. The robins’ songs must be composed of different phrases, phrases must alternate in pitch, and during bouts, all of the songs must be different. Experiments were performed where the speakers played songs using sounds that robins can’t produce but followed their song’s syntactic rules and they responded as if the speaker were another male. However, the robins didn’t respond to the speaker when the song was changed to include only low-pitched phrases. This supports the inference that the environment may degrade pitch and different individuals will use differently pitched notes, but that syntactic rules will remain the same, allowing for conspecific recognition. Another example of this invariability phenomenon is in the indigo bunting, which recognizes conspecifics by element composition. Indigo bunting song consists of a single element repeated quickly to produce a trill. As opposed to the robin where manipulating syntactic elements changes response rate, changing the element results in much lower conspecific response in the indigo bunting. Individual recognition is a more complicated story, and is very species specific. Colonial birds tend to have the ability to recognize individual calls, as is the case with bank swallows and emperor penguins. As these species live in colonies, parents have to be able to recognize the calls of their offspring in order to feed them. In the zebra finch, females seem to recognize their father’s calls, as they tend to choose mates which have similar but not identical songs, a behaviour that is likely to have arisen in order to avoid incest. Songbirds have the capacity to recognize individuals, and not only respond differently to neighbours and strangers but have different levels of response to different neighbours. A male will respond less strongly to a neighbour’s song from a familiar location than a stranger’s song from that same location. Should the neighbour’s song be played from an unfamiliar location, the male will respond just as strongly to it as it would a stranger’s song. This response seems explicable from a territoriality point of view. The male will respond more aggressively to new individuals who pose threats as opposed to neighbours with pre-established boundaries, and will respond aggressively to expansionary neighbours.

Plant pathology and animal pathology differ greatly. While animals have an adaptive immune system that allows them to generate defences as new infections arise, plants do not. Plant pathogens come in three general classes, necrotrophs, biotrophs, and hemibiotrophs. Necrotrophs are organisms that kill plant tissue through enzymes and tend to be generalists that can infect many plants. Biotrophs are parasitic organisms which, in order to complete their life cycle, require host survival. These pathogens will cause slowed senescence and build haustorums that usurp metabolites from plant epithelial cells. Hemibiotrophs are biotrophs in the first part of their life cycle and necrotrophs during the second part of their life cycle.. Pathogens have three main ways of egress into a plant. They can either directly penetrate the plant through the use of a pilus or penetration peg, enter through pre-existing openings such as stomata, or enter through wounds. Plants have a series of defencive strategies to resist infection. The first line of defence is physical, plants have a waxy cuticle and cell walls that aim to prevent direct access to the cytoplasm of plant cells. In addition to a physical barrier, plants produce toxins to kill certain pathogens or create papillae in the epithelial cell walls to prevent pathogenic penetration. The second line of defence is specific, and is known as resistance (R) gene immunity that follows a gene for gene model. Pathogens produce effectors that mask their presence, and plants produce proteins that are able to detect effectors. If a plant can detect an effector then it will engage a hypersensitive response that involves immediate cell death around the infected area. At the cost of a few cells, this method enables the plant to prevent the infection from spreading.

Observations:

• Lighting

  • Lighting is whiter and brighter in the right hand (RH) figure

  • Lighting is yellower and darker in the left hand (LH) figure

• Background

  • Wooden surface and white wall as background in RH figure

  • Yellow-white surface as background in LH figure

• Ruler type

  • Stainless steel ruler in RH figure

  • Blue plastic ruler in LH figure

• Natural differences

  • Egg colour and texture

  • Apple colour 

  • Pinecone staining and size

• Perspective

  • More of a frontal perspective in RH figure images relative to LH figure images

  • More of a top-down angle in LH figure images relative to RH figure images

• Labels

  • RH figure labels are smaller and don’t have parentheses

  • LH figure labels are larger and have parentheses. 

  • RH figure labels are aligned to top left corners of each image

  • LH figure labels are not aligned but vaguely placed in top left corners of each image

• Size

  • Lower right hand corner image in RH figure is squished relative to other images in the figure.

  • Lower right hand corner image in LH figure is not as squished as analog in RH figure but is on a smaller scale than the rest of the images in the figure. 

Inferences:

• Picture inferences

  • Different objects were probably used as the subjects between the RH and LH figure, accounting for the differences in their respective appearances. 

  • A different camera angle accounts for the difference in perspective. The RH figure camera was likely placed more frontal to the objects than in the LH figure. The LH figure camera was likely placed more above the objects than in the RH figure.

  • A different light accounts for the difference in lighting between each figure. 

  • Different rulers likely account for the differences in ruler appearance between each figure. 

  • Different rooms likely account for the differences in background. Rooms are made differently and this could account for the cream background in the LH figure versus the wood surface and white wall background in the RH figure.

• Layout inferences

  • The methods likely didn’t specify how the labels were made which plausibly explains why the labels are different between the RH and LH figure. Alternatively, the methods weren’t followed leading to different labels. 

  • A different picture orientation could account for the widthwise squishing observed between panel C in the LH figure relative to the RH figure. 

The lighting is whiter and brighter in the right hand (RH) figure images relative to the left hand (LH) figure images. The lighting in the LH figure images is yellower and dimmer. The lighting in the pictures of both figures shines downwards on the pictures’ subjects. The background in the RH figure is a wooden surface and a white wall whereas the background in the LH figure is a cream coloured surface. A stainless steel ruler is used for scale in the RH figure but a blue, plastic ruler is used for scale in the LH figure. There are some natural differences between the two figures. Between each figure, the egg colour and texture differ, the pinecone staining differs, and the apple colour differs slightly. The pictures in the RH figure had a more frontal perspective relative to the LH figure. Relative to the RH figure the LH figure pictures were taken from a more top-down perspective. The labels of the RH figure are smaller than the LH figure labels and lack the parentheses found in the LH figure labels. Additionally, the RH figure labels appear to be aligned in the top left corner of each image whereas the LH figure labels have been vaguely placed in the top left corner of each image. The lower right hand corner image in the RH figure is squished widthwise relative to the other images in the figure. The lower right hand corner image in the LH figure is not squished as the analog in the RH figure but is nonetheless on a smaller scale than the rest of the images in the LH figure.