bthoole's blog

The layout of the pictures and the labels is one of the most obvious differences presented in the figures. This is from a lack of exact actions and clarity in the methods section. The methods said that the images should be “adjusted to about equivalent sizes”, when in actuality, they should have been the exact same sizes. Furthermore, the exact width and height of each picture is provided by the inkscape program and should have been provided to remedy this inconsistency. As far as the labelling, the methods section provides that a red box should be made for each of the labels and a lowercase letter used. It is true that a color was not specifically given for the text. Additionally, the methods section provided where the location of the box and letter labels should go. However, given that the pictures of figure 2 were not the same size, the final adjustment given in the methods section may have distorted the picture further from the original Figure 1. This could also be fixed if the exact sizes of the images were provided.

The first noticeable difference is in the layout of the pictures. Whereas Figure 1 has equally sized pictures, Figure 2 does not. The photos in Figure 2 are all different sizes and do not evenly match alongside the edges.

The object used for scale is inconsistent between the two figures. Figure 1 used a blue pen for the scale object and Figure 1 used a black cased, mechanical pencil.

Another noticeable difference is in the labelling of the pictures. Here, there are several differences, although both figures did use the same letter for each picture. First, the positioning is different in each of the figures. Figure 1 has the letters placed in the upper left hand corner. Figure 2 has the letters in no one clear organizational spot. Another difference is that Figure 1 has lowercase letters while Figure 2 used upper case letters. The color of the labels is different too. Figure 1 used black letters in red boxes to make the labels, while Figure 2 used red letters without a box.

The pictures themselves are different as well. For the most part, it seems as though the same web and area were photographed, but for Figure 2 A, the photo is put in upside down, which is noticeable by the pencil that was used for scale. Additionally, Figure 1 A is closer to the web and has less of the vent visible than in Figure 2 A. For images A-C, they appear sharper in Figure 1 than in Figure 2. Again, Figure 1 B is closer to the vent than in Figure 2 B. There is also an angular difference, seen to be looking down in Figure 1 B, where Figure 2 B is more face on. This is different from what is seen in part C of the panels. Figure 1 C is backed further away from the vents this time than Figure 2 C and has wooden doors available. Figure 2 C is almost perpendicular to the vent and is closer. The doors are not seen, but a pair of shoes are. Figure 1 does not have any feet or legs partially seen in the picture. Lastly is part D of the panels. Both show the correct location, the Morrill Science Center, but more noticeable is that fact that Figure 1 D shows the figure in a street map view, whereas Figure 2 D shows a satellite view and thus the actual building and surrounding elements are visible. To this effect, Figure 1 D shows a wider view of the area, including parts of roadways and the campus pond. Figure 2 D shows the road immediately next to the building.

Further evidence for the idea of evolution is the existence of vestigial structures. These vestiges are structures that are genetically determined but have lost some or all of their original function from the ancestral species. Oftentimes, vestigial structures are homologous to structures in related species. The way a vestige is formed is during typical evolutionary process when a structure loses its function and no longer provides a positive pressure. The loss of function can come from a change in the environment that the ancestral species originally adapted to. So long as the structure does not now present a negative pressure due to some hinderance on the species, it is considered neutral and not necessarily selected for or against. As a result, instead of losing the feature it may persist though it has no inherent value anymore. Common examples of vestigial structures are the hip bones that remain in snakes and whales. At a time, these species had ancestors that had limbs that required hips for mobility. Now that they no longer have the same limbs and are under different selective pressure, the genetics still encode for a hip bone, but it is not used. The bone is not a detractor and is not selected against but is slowly withering away over evolutionary time.

The project undertaken for the Writing in Biology class was designed so students would photograph a durable object and document how the image was taken. They would then be tasked with writing a methods section to a level of certainty that they believed would allow another student to replicate the image. For consistency throughout the project, the subject matter of the photograph was limited to a spider web in relative close proximity to the Biology computer lab on the Umass Amherst Campus.

    In particular, the selection process of this spider web took into consideration the necessity of replicability and to ensure this, the spider web would need to be durable and last a period of, at minimum, several days. Therefore, a spider web inside a building was considered the most durable, as this would not experience any outside disturbances such as weather or movement that could potentially ruin the web that was photographed. In selecting the photo, the building that housed the biology computer lab was searched for a web that was slightly concealed so that any maintenance cleaning or foot traffic would ruin the web. One such web was found in a hole in an air venting system on the ground floor of the Morrill building. The hole in the vent had gathered dust suggesting it was untouched for a long period of time and gave the reassurance that the web would last the allotted time to allow for another student to find it. Furthermore, in writing the actual methods section, it was important to account for as many scenarios as possible and strictly limit them to what was actually performed in the photographing of the web. It sought to control the location of the photographer in conjunction with which photo should be taken, what the scale item would be and how it was located, the height of the camera and what the camera viewed in its lens all had to accurately be described so that the other student would be able to replicate the image as close as possible. The final figure that was made needed to be replicated as well, so the program used to make the multi-panel figure was recorded, as were the sizes of the images, the size of the font and labels, the colors used for the labeling and the overall layout of the figure.

Evolution is driven by natural selective processes but has no end goal or “perfect” structure or creation. The evolutionary development of species is driven by the opening of a niche and the fulfillment of that area to the best degree. Over time, this can result in structures that are similar in design or function between species. However, as taxonomists or biologists, it is important to understand the underlaying commonalities of the common ancestor of the similar species. The structure in question could either by the result of a shared common ancestor and the further development of the trait to fill a niche. These structures are known as homologous structures. An example of such structures would be the bones in the arm of a human and wing of a bat. On the surface they are different structures, but the bone shape and structure appear in similar shape and structure due to sharing a common ancestor. However, similar traits can arise because of convergent evolution, a process where evolutionary pressures cause for the need of the structure. The resulting structures from this kind of evolution are known as analogous structures. An example of this would be the wing of a bird and the wings of an insect. While they both developed wings, the structures themselves are derived from different evolutionary pressures. There is not a shared common ancestry between the two enclaves that would have given rise to wings in both.

The entirety of the genome is very large, and it is hard to imagine the possibility that it even fits inside of a cell, let alone the nucleus of eukaryotes. This ability to condense itself is the result of multiple folding techniques along the strand of DNA and an eventual folding around histone proteins. One such technique is supercoiling, which is the over or under winding of the DNA in a particular area. Supercoiling allows access and therefore expression to those areas on a strand. The over-winding leaves the area of genetic information untouchable by proteins, so it is unable to serve as any active template. Under-winding allows for access and is what allows for expression when it is needed. When it is over-wound the DNA is condensed and therefore takes up less space and is the preferred state when inactive. Enzymes known as topoisomerases are able to change DNA spooling and aid in DNA processes such as transcription and replication. Although useful in compacting DNA, supercoils put strain on the DNA that either must be relieved or accounted for elsewhere in the strand.

Looking at the two sets of images on page 3, there are observable similarities between the photos which we can use to infer that one was taken first and then described to achieve the second set. Based on that, there are other observable differences between the photos, first of which is layout and design. The first set of three images has images that are different sizes and are not touching each other, with varying levels of space between them. Photo “A” is singularly on the left and is longer than photo “B” but ends slightly at the start of photo “C”. Photos “B” and “C” are stacked on the right, but again, are not bordering one another. This contrasts to the observations of the second figure, which features the three pictures bordering one another in the same layout scheme (A on the left and B and C stacked) but done so on a different scale. Not only do the pictures border, they are different sizes. “A” is much larger and is the height of “B” and C” stacked. Photos “B” and “C” are the same size and are stacked to the right of photo “A”. In addition to layout formatting, the size of the labels is comparable. Both series of images used a capital letter followed by a period and both sets used the same label in the same location for what was meant to be the comparable photo. However, the second series of images used a larger font to make the labels and thus are more visible.

Another observable inconsistency with the photos is the use of arrows. The first observable difference between the series is that the first used blue arrows and the second used white arrows. Another difference is the directionality of the arrows and the placement in the picture. In the first series photo “B” there is only one arrow, but it bends to point upward. In the second series, there are instead two arrows, one pointing diagonally down and one pointing diagonally up. It is inferred that these arrows were meant to be pointing toward something of noticeable value, although it would appear that they are pointing to different things in the different series and it was not held consistent in any description, not only on how to make the arrows and where to put them, but what exactly they should be pointing out.

Another observation is the color of the sky. In the first photo series, all three pictures feature a blue sky. In the second series, the sky is darker, gray and cloudy. From this it can be inferred that the series were taken on different days that had different weather. It can be furthered inferred that the second series had weather that was of stormy conditions, which can be coupled with the observations that the water was rippled, and leaves of the tree were pointing at an angle, not hanging straight down. From those observations it can be inferred that it was windy and that coupled with the gray sky can lead to the stormy inference.

Another inference that can be made is that the comparable photos between the two series were taken at different locations and angles. While the subject matter is relatively the same, the observations of different views of the buildings in the back lead one to infer that the camera angle was different, thus causing it to capture more or less of the buildings in the back.

Sexual selection is an evolutionary mechanism that pits the males and females of a species against each other. Females are often described as cryptic in their display patterns because it is not necessary to be flashy. Females are given the proverbial “choice” of mate and are therefore choosy in the males. Males compete to be flamboyant and display qualities that the female uses to appraise the fitness of the suitor and decide if this will raise the fitness of her offspring. Respectively, the “sexy son” hypothesis and “good genes” hypothesis say that a female will choose a respective mate because it of their appeal because their children will then have that same appeal for the next generation and that a female chooses a mate based on their genes because it will result in the offspring having better genes. This makes males compete for the female and the female choice decides what is deemed competatively appropriate. Some scientists suggest that the qualifier is not anything of apparent value, just what has evolved as the required quality. Put more simply, the idea of "beauty" is not a signifier of good genes at all, but rather a preference that has undergone runaway selection and as a result, no longer holds any direct correlation to the holder's fitness other than how well they fit that preference. This preference changes with the generations of females over evolutionary time and as a result, male characteristics change as well.

Sexual selection is an evolutionary mechanism that pits the males and females of a species against each other. Females are often described as cryptic in their display patterns because it is not necessary to be flashy. Females are given the proverbial “choice” of mate and are therefore choosy in the males. Males compete to be flamboyant and display qualities that the female uses to appraise the fitness of the suitor and decide if this will raise the fitness of her offspring. The “sexy son” hypothesis and “good genes” hypothesis respectively say that a female will choose a respective mate because it of their appeal because their children will then have that same appeal for the next generation and that a female chooses a mate based on their genes because it will result in the offspring having better genes. This makes males compete for the female and the female choice decides what is deemed appropriate. Some scientists suggest that the qualifier is not anything of apparent value, just what has evolved as the required quality. This changes with the generations of females over evolutionary time and as a result, male characteristics change as well.

Sexual selection also gives way to what is known as an evolutionary arms race. This is where the male and female are both evolving to counteract an adaptation that the other sex has that prohibits one sides reproductive fitness. Such examples are the development mechanical reproductive traits that prohibit the males from forcefully mating with a nonconsenting female, evidenced by the development of duck penises and vaginas, or the evolution of infanticide as a technique to enhance fitness. Infanticide involves a sexually mature adult, usually male, killing the offspring of another mature adult of the same species. This is done by the killer to become the new sexual partner of the deceased’s parent which would otherwise have been unavailable. This act raises the fitness of the killer and reduces the fitness of the victim’s parent.

Once, I went home and upon entering my house, it smelled like vanilla. This smell is an observation and I inferred that someone had baked cookies. As it turns out, the smell was just a candle. Observations are things determined through the senses, how something looks or feels or smells or sounds. An inference then uses past knowledge to say something about that observation. An inference does not necessarily have to be correct, just a conclusion drawn from an observation. Observations are based in fact and describe how something is actually observed where as any processing of those observations are inferences.