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One of the fundamental characteristics of any scientific work is its capacity to be replicated by other scientists in order to prove its veracity. In this Methods Project, I designed a multipanel figure and wrote my methods for creating it so that another student could follow my instructions and make the most accurately possible replicate figure. The objective of this project was to learn how important it is in science to take into account the factors that may result in a failure to convey our message, and to improve our scientific communication skills in order to provide a set of instructions that is clear and leads to an accurate replication of our methods.
I thank Erin Elizabeth Hardy (email@example.com) for following my methods, and professor Brewer for his help in using Inkscape and his comments on this project.
Assess and explain in an organized way the observed differences:
The first difference I observed between my figure and the replicate, was that the replicate was narrower and the red star indicating the location of the spider web was in the wrong place.
Regarding the differences in length and width between the original and the replicate figures, I did not specify in my methods how long it should be. Nonetheless, I did mention to place the red star over the location where the pictures were taken, which in this case was close to the furthest left corner of Franklin Permaculture Garden as you face it when coming from Morrill.
As well, the size of the letters was significantly greater in the replicate version, and the letters in the original are closer to the left upper corner than in the replicate.
I did mention to place the letters on the upper left corner of each image, but failed to specify that they should be closer to the corner. As well, I made no references to the size of the letters, which is the reason why in the replicate they are bigger than in the original.
Regarding picture A, the replicate version has more brightness and shows part of the ground behind the bush.
The differences between the original picture A and its replicate can be related to differences in image quality due to using different cameras, but mostly are due to not describing with further detail the positioning of the camera. The same holds true for picture B.
Picture B in the replicate was taken further away than the original so it includes more background and buildings, but it doesn't have the green sign to the right.
In the methods I mentioned that in order to take this picture the reader should take three steps backwards, but the difference in height and gait of each individual made this an inaccurate description, since the replicate was taken further away than the original. Nonetheless, I did specify to include the green sign to the right, which the replicate failed to do.
As well, picture B in the replicate was taken in a straight angle, while in the original ot was taken pointing down to focus on the bush with the web, which probably distorted the brightness of the picture too by making it brighter.
Once again, the differences in brightness and angles in picture B are due to not having described with more precision the positioning and settings of the camera.
Picture C in the replicate shows a larger area of the map than the original figure.
The replicate figure C encompasses all the buildings I described in the methods, but it covers a larger area than the original due to not specifying that once the screenshot covered my list of buildings, the rest of the picture should have been cropped.
Finally, there is a small gap between A and B in the replicate, which is filled in grey but is not part of either picture.
Regarding the small grey gap in the replicate figure between A and B, I did specify in the methods to display the elements so that they were touching each other, in which case there would be no gaps in-between the pictures.
Figure 1: Original multipanel figure displaying: A. close-up view of spider web; B. wider view of the spider web on the bush; C. OpenStreetMap screenshot of the location where the spider web was found.
Figure 2: Replicate multipanel figure displaying the elements described in Figure 1. This figure was made by following the Methods section of this paper without visualizing the original figure, for testing the replicability of the aforementioned section.
Describe and summarize the observed differences:
The first difference I observed between my figure and the replicate, was that the replicate was narrower and the red star indicating the location of the spider web was in the wrong place. As well, the size of the letters was significantly greater in the replicate version, and the letters in the original are closer to the left upper corner than in the replicate.
Regarding picture A, the replicate version has more brightness and shows part of the ground behind the bush. Picture B in the replicate was taken further away than the original so it includes more background and buildings, but it doesn't have the green sign to the right. As well, picture B in the replicate was taken in a straight angle, while in the original ot was taken pointing down to focus on the bush with the web, which probably distorted the brightness of the picture too by making it brighter. Picture C in the replicate shows a larger area of the map than the original figure. Finally, there is a small gap between A and B in the replicate, which is filled in grey but is not part of either picture.
- Goals of the Methods Project:
The main goal of this Methods Project for Writing in Biology class is to reflect on the key components that a good Methods section of a scientific paper should have in order to convey its message. Scientific research must be easily replicated by others in order to prove its validity, that is the reason why this project includes following the methods of another student in order to replicate their figure as accurately as possible. As well, it is important to understand that inferences are conclusions that are made based on observing a phenomenon and formulating logical explanations for it, and that they should not be confused with observations. The last objective of this project is to identify the variables that must be controlled in order to be able to successfully replicate an experiment.
- Explain the subject of my figure
The subject of my figure was the web of a funnel weaver spider, located on a bush in Franklin Permaculture Garden. In order to compose the figure I took a close-up photograph and another picture that showed its surroundings, and then I added a map marking the location of the spider web.
- Reasoning for selecting my figure
The reason why I chose to make this figure is because it can be easily replicated, since the spider web is clearly visible and located on an accessible area that many students know due to being close to Franklin Dining Commons and the BCRC.
- Factors I sought to control when I wrote my methods (but don't describe those factors)
When I wrote my methods I made sure to control the exact location of the spider web, as well as the spatial arrangements of the different elements of the figure, including the order in which the pictures were presented and their respective labels. As well, I described in detail other important features of the labels such as the colors of the letters and boxes in each image.
Based on the fact that female bats usually travel longer distances than males, there should be areas populated mostly by individuals of one sex or the other. If this is true, when the researchers collected samples in New Mexico it is possible that some individuals had already been travelling for a longer time than others, in which case the physiological mechanisms involved in migration may differ because some bats would be at the peak of their performance while others would be on their way to that optimal state. It is mentioned as well that the wintering ranges of the hoary bat are poorly documented, and there is no data in the paper referring to accurate distances travelled during migration, for which further studies with tracking devices should be performed.
Regarding the fatty acid transporter data, the researchers only studied the mRNA expression of these proteins, but the actual levels of the proteins that got translated were not measured. The study did not consider that if there is no need for upregulation the actual amount of proteins present may be significantly high despite having low levels of mRNA expression.
The data supports the predictions for increased mitochondrial enzymatic activity and lipid oxidation pathways during hoary bat migration. Regarding enzymatic activity, the 29% increase in CS reflects greater aerobic capacity for powering flight, while the increases in CPT and HOAD prove that fat was used as a fuel during migration. Nonetheless, the hypothesized similarities between bats and birds concerning fatty acid transport are not supported by the data, since the studied proteins were expressed at similar levels throughout the year with the exception of H-FABP in females during migration. Such differences may be attributed to differences in the life history of hoary bats, and the increased expression of H-FABP in females may be due to pregnancy and torpor deprivation during migration, as well as for travelling larger distances than males.
The results showed an increase of oxidative enzymatic activity during migration, recording a 32% increment in activity for CPT, 53% in HOAD, and 29% in CS. As well, the enzymatic activity of HOAD was significantly greater in males. Regarding the mRNA expression of fatty acid transport proteins, the sequencing data showed a match of 90% or higher with already known genomes for H-FABP and FABpm, while FAT/CD36 matched at 80.5-87.3%. The mRNA expression of FAT/CD36 and FABpm remained stable throughout the year, but H-FABP showed changes in seasonality and differences depending on the sex of the bats. While males expressed constant levels of H-FABP independently of the season, females showed a fivefold increase during migration.
Mammals use carbohydrates as a primary fuel during short periods of intense activity, but these reserves can not provide the energy required for travelling long distances like migratory hoary bats (Lasiurus cinereus) do. Instead, the flight muscles get powered by fat stores, which contain more energy per unit mass than carbohydrates and proteins. Bird migrations have been studied more extensively than bat migrations, and it is known that birds seasonally regulate fatty acid transport pathways and oxidative enzymes, increasing their activity during the time of migration. Based on the similitudes between migratory bats and birds, the researchers hypothesized that bat follow similar metabolic pathways and that fatty acid transport and mitochondrial enzymatic activity would be regulated seasonally as well.
The enzymatic activities studied were CPT, HOAD, and CS; while the fatty acid transport proteins studied (only looking at mRNA expression) were H-FABP, FAT/CD36, and FABpm in flight muscles.