mmaliha's blog

No two persons can observe the same object in the same manner. However, this is an increasingly necessary skill in the field of science: to be able to replicate someone’s experiment and obtain the same results. The purpose of the Methods Project was to give students a little taste of the scientific process when it comes to peer-reviewing another scientist’s work. All students were instructed to take at least three pictures of a spiderweb and construct a multi-panel figure. Then, they were paired up randomly with another student in the class, and had to reconstruct each other’s figures using just the written methods section (without actually seeing the figure). The goals of the project were to teach students how to write a detailed and accurate methods section and what variables must be controlled when replicating one’s results.

Both sets of pinecones appear similar in shape. One set of pinecones appear larger than the second set, but it cannot be determined whether the cones are actually larger or there is just a different scale used on a zoomed-in version. The lighting of the two sets are different. In the first set, the pinecones appear well-lit on an ivory background. In the second set, the lighting is more dim and the pinecones appear to cast almost no shadow onto the light grey background. This difference in lighting causes one set of pinecones to look darker brown than the other. The pinecones in the second figure (one with 1 cm scale) also look more 2-d and planar than the  first figure, and contain a white border that the first figure did not have in addition to the black outline.

My inference would be that both sets of pictures feature the same pinecones on the same type of paper. One picture is taken with little to no artificial light available and no zoom, whereas the other one is taken with the 'zoom' feature and bright lighting, which causes one set to appear lighter and larger than the other. This might be the reason behind why the background texture remain the same even when one paper looks more ivory and the other dark grey. I would assume that the paper itself is more white than either ivory or dark grey and the lighting causes a difference in appearance.

The 2-d appearance of the second figure also makes the pinecones look more graphical, which gives rise to the possibility that these pinecones were not photographed at all, rather they were hand-drawn using Figure 1 pinecones as a model. In which case, the artist intentionally chose to portray these pinecones as darker and smaller (using a different scale). 

Tidy datasets have a specific structure

• Each variable in a column
• Each observation in a row
• Each type of observational unit is a table

Data Semantics

• A dataset is a collection of values. Values are organized in two ways (every value belongs to a variable and an observation)

To compile my three pictures into one figure, I used the inkscape software. I imported all three images (spider web with water bottle, full image of the ISB wall and openstreet map of ISB) and resized them to fit each other better. To avoid stretching, I used the “lock” feature (as explained in Dr. Brewer’s video about compositing), and changed the height and width of pictures instead of using the arrows to drag the corners. The picture which displayed a close-up of the spider web with a water bottle for scale had the width x height dimensions of 200 x 357 mm. The openstreet map illustrating the location of ISB was 400 x 314 mm, and the photograph showing the setting (brick wall of ISB where the web was perched) was 200 x 357 mm.

To make my figure, I needed to get a high quality map illustrating the location. Thus, I went to openstreetmap.org and typed “Amherst, MA” into the search bar. Next, I zoomed till Integrated Sciences Building came to focus. I zoomed until the right side of ISB only showed Life Sciences Laboratory and the left only showed till the Campus Bookstore. The upper perimeter cut off at the East Experiment Station and the lower perimeter showed till Peet’s Coffee. When I had a zoomed-in version of the map that I wanted, I clicked on the link to share and downloaded the image in PNG format.

Observation and inference are two terms that are closely associated but should not be confused as synonyms. Whereas an observation is the direct relaying of what happened, inferences are possible explanations behind those observations. Observation is the direct information we have gathered, and inferences are what we can extrapolate from those information using prior knowledge. For example, if we see smoke wafting through the chimney, we can predict that someone has lit the fireplace. The smoke in the chimney is our observation. We don’t directly see the lit fireplace, so this is not our observation, merely an inference stemming from the fact that normally chimney smoke results from a fire.

(Taken by Keegan Bowen, on September 30, 2011; accessed from Flickr.com on September 21st, 2018)https://www.flickr.com/photos/49711256@N08/6196954031

Figure 1. The male drosophila melanogaster possesses a prominent rectal disc. The male drosophila melanogaster, more commonly known as a fruit fly, possess the same anatomy as a female drosophila melanogaster aside from its rectal disc. The male has a prominent black genital disc with surrounding black bristles. Even in a side profile, as pictured above, the rectal disc is visible and distinguishes the male drosophila from its female counterpart. 

Transcriptomes are the sum total of all the messenger RNA molecules expressed from the genome. Transcript/ gene isoforms are mRNAs that are produced from the same stretch of DNA but differ in stability and translational efficiency and potentially function since they have different transcription start sites, protein-coding DNA sequence, or UTRs. This paper goes into analysis of the drosophila transcriptome and proves that the drosophila genome is much more complex than previously imagined. This complexity arises from three sources: promoter, splice sites, polyadenylation sites.

Figure 4 looks into tissue- and sex-specific splicing in drosophila. Transcript diversity: over half of spliced genes encode two or more transcript isoforms. The researchers measured splicing efficiency through "per cent spliced in"- the fraction of isoforms that contain the particular exon. To examine the dynamics of splicing, switch scores are calculated for each splicing event, and examined tissue and sex-specific. Results show that most splicing events are highly tissue specific. Results also show that majority of the sex-specific splicing is due to tissue-specific splicing of tissues present specifically in either male flies (testes) or female flies (ovaries).

• Embryos that have only one of the two sets of parental chromosomes = uniparental embryos
• Process to give embryos specific chromosomes from one parent only = uniparental disomy
  • Is this done to just investigate specific chromosomes? Or, are there natural processes where certain chromosomes from a set  get transferred and others don't? (seems unlikely)
• Previous research has shown that mammalian genes can function differently dependent upon whether they come from mother or father.
• Imprinted genes are expressed differently on paternal and maternal genes (first discovered, 1990s)
  • Methylation marks imprinted genes differently in egg and sperm

For in-vitro experiments, small fast-folding domains are most preferred as they are amenable to a great extent to observe the detailed physio-chemical behavior of R-groups and other primary, secondary, or tertiary interactions. However, small single domain proteins are very rare, and recent studies have suggested that the folding of domains in multi-domain proteins may not even be an independent process (if we look at the folding of domains as component of a larger protein). Thus, recent studies have tried to focus on in-vitro protein folding of larger proteins, and the results confirm the hypothesis that new complexities in folding landscape will emerge when multiple domains are interacting.