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The Methods Project was assigned in Spring 2018 as part of the Writing in Biology course at the University of Massachusetts Amherst. This project directed the writing of a methods portion detailing the creation of a scientific figure (Figure 2) that would then be compared to a previously made original figure (Figure 1).  The project was designed to teach students how to make scientific observations and inferences.  Students would examine both Figure 1 and Figure 2 and quantify explicit differences between them.  The project was also designed to teach students how to write their own methods section and how to follow another student’s method section to produce a comparative figure.

In scientific writing, it is imperative to write a detailed and concise methods section so other scientists can replicate the results of an experiment.  The figure created as a result of this project depicts the orchid species Oncidium Sharry Baby and where it can found indigenously throughout the world.  This orchid is found on the University of Massachusetts campus in Durfee conservatory, which is student accessible.  Oncidium Sharry Baby  was chosen because the morphology of the plant and its flowers made the photo angles easy to control.  The plants location in the greenhouse allowed for the control of the photographer’s distance from the orchid. The blooms are fragrant, unlike many of the flowers surrounding it, further drawing attention towards the orchid of interest.  Utilizing a ‘fragrant flower’ sign located in front of the plant as a reference point regulated the orientation of each image.  The computer program Inkscape was used to create a world map, which allowed for the control of which world maps were less pixelated and which colors could be used to highlight individual countries.  These reasons allow for the controlled creation of a parallel, representative figure of Oncidium Sharry Baby.

In Spring 2018, as a part of the Writing in Biology Course at the University of Massachusetts Amherst, students in the class were given a project to create methods to a multi-panel figure. Following the creation of the methods, and creating our own original figure while keeping the figure private, Professor Brewer shared these methods with a classmate whom was to follow these methods to create a replicate multi-panel figure. Once complete, the replicate figure was uploaded to a course website where the original was then posted to compare the differences between the original and the replicate figure. Observable differences between the original and the replicate of this multi-panel scientific figure was clear. Differences including size of the figure, images, borders and map, labels presence, angle of which the images were taken, orientation of the images, and range map. These differences contributed due to software use, capabilities, knowledge and experience, as well as physical stature and positioning during photography. Unclear methods to be the underlying cause of each of these differences. Together, these differences leading to the clear and observable differences between the original figure and the replicate figure.

I believe biological diversity should be defined in the same way for both scientific and practical purposes as these are, to me, the same thing, although there could be cases where certain information is more pertinent than others. I would define biological diversity as how many individual species live in a given area, while also considering how many individuals of each species live there. This would give a general idea of the biodiversity of an area, but would still leave out information like species evenness. In some cases omitting certain information would be suitable, and would help to simplify the point being made. This is good for both the person doing the study, and someone reading it.

I don’t think the regional species richness on the mainland will affect how many species are predicted to be found on an island based on the equilibrium theory of island biogeography.  It is known to be that geographic areas have a vast influence on species diversity on global and regional spatial scales. The equilibrium theory of island biogeography indicates that there is a relationship between species and area. In islands and mainland areas, species richness is theorized to be regulated by rates of immigration and extinction. In mainland’s, immigration rates are greater because barrier to dispersal are lower. Since mainland is known to have high immigration rates and low extinction rates it leads to a lower rate of increase in species richness with increasing area. 

Another prominent example of recent evolution resides within the ability to drink and digest milk. Most human adults are incapable of digesting lactose and therefore milk. Babies are capable of drinking milk due to a gene that codes for lactase, which breaks down lactose. In people who are lactose intolerant, the gene essentially switches off after weaning. However, a mutation known as lactase persistence arose in recent human history that allowed lactase to be produced into adulthood. This trait likely provided a selective advantage to individuals with access to domesticated dairy animals, who consumed the unfermented milk. “Analysis based on the conservation of lactase gene haplotypes indicates a recent origin and high selection coefficients for lactose persistence, although it has not been possible to say whether early Neolithic European populations were lactase persistent… (J. Burger et al., 2006)”

Discrepancies between aspects of the original and replicate figures can be explained by a variety of factors that were not controlled for or described in the Methods section. These factors include photo angle, flower choice, font choice, and country selection.

    A possible explanation for the discrepancies between figures 1A and 2A could be that the replicated photo was taken of a different bloom on the tree. This could have happened because there was a lack of explicit detail explaining exactly which bloom was photographed in the original figure. Additionally, the angle was not specified in the methods whether is was to the right or left side of the ceiling of the conservatory.

Figures 1B and 2B are not drastically different from one another. There are discrepancies between the amount of leaves captured at the top of the tree, but many of the factors that could have resulted in major differences in the figure were controlled by the limited angle options due to the corner placement of the tree.

Differences between figures 1C and 2C are explained by the lack of explanation in how to create state borders on the figure map website. The default world map setting does not include state borders, so a box must be checked in order for the borders to be seen. With this box checked, each individual state can be highlighted and Florida can be colored in.These directions were not explicit in the methods section, and this step was missed in the execution of the map making for the replicate figure. Additionally, the type of font was not detailed in the methods, resulting in a different font used to label the figures on the replicate.  

Both figures differed across several aspects, despite attempting to control for factors to limit discrepancies. Both figures differed with respect to the particular flower that was captured photographically, as well the angle at which these blooms were captured. The angle at which the tree was captured also varied slightly. Additionally, the countries in which C. haematocephala are indigenous were labeled differently on the map portion of the figure, as well as font style of the figure labels.

Today in class for Biology 494, we read and discovered how to write the cover letter of our resume correctly and properly. I felt that this was important because as we graduate from UMass Amherst, we are going to have to write our resume and submit it wherever we are trying to get into. This class not only teaches you what to do but shows you how to get it done properly which is really nice. It is very similar in many ways with Biology 312 because there are lots of writing done in the course. I am still not sure exactly what I want to do but I am figuring it out as I go. It is scary to know that I will be graduated from college in less than 3 terms.

Experimentation is a fundamental pillar of the scientific process that is built upon a systematic approach and organized collection and presentation of data. No matter how conclusive or groundbreaking an experiment may be, the results should be viewed with skepticism until the results can be accurately and consistently replicated. While perfect replication of any experiment or action is an unfair expectation, these indescrepencies can be mitigated by a detailed and well written methods section.  The goal of this project was to highlight the importance of a detailed methods section as well as the wide array of variables that need to be addressed, such as time of day, distance, angle and orientation by photographing a flowering  plant from two different perspectives and creating a figure showing the regions that the subject inhabits. No matter how detailed, there will likely be minor inconsistencies between independent processes as not all variables, such as the weather or physiologic changes naturally occurring within the subject, can be controlled and instead must be accounted for when comparative analysis is being performed.

Migratory patterns are intrinsic behaviors that are controlled by photoperiods, gonad cycles and hormones as well as proximate factor such as weather and food availability trigger day-to-day actions while migrating. These behaviors are typically recurrent, however,  they also require correct conditions or access to resources to remain viable.  Given the extraordinarily long distances that some species travel; monitoring their movement and accumulating data on this has been challenging. Modern technological advances in doppler radar technology has allowed for more detailed tracking of large migratory patterns of several species. With information regarding their altitude, speed and direction, experts can made educated assumptions or even confidently identify which species they are monitoring.