Writing in Biology

          Because of the spiritual connection they felt to their land, as well as the desire to preserve their traditional way of life that would be threatened by these development projects, the indigenous people protested in response. One group even detained some miners, in an effort to force the government to negotiate with them and restore their promise of conserving the tribes’ land. Some protests resulted in violent confrontation between the between the tribe and government police, which garnered sympathy for the tribe’s cause from many within the broader Peruvian populice. However, the tribes were labelled by the government as backwards and primitive, and their concerns were dismissed by the Energy Ministry of Peru as evidence of their ignorance of modern extraction practices, which the government and the mining companies insist does not cause pollution. Environmentalists disagree, and argue that the forests and rivers of the area are sourced out of the same mountain range where extraction projects are meant to take place, and this will potentially contaminate the natural resources on which the tribe relies. The companies also try to sow discord between members of the community with promises of jobs and money, to make easier their incursion and weaken the tribes’ united front against them. This succeeded and resulted in internal conflict, causing the disruption of social bonds within families and communities, and thus further threatening traditional practices.

From the results of the melting point of the AE1, the identity of the unknown is 2-chlorobenzoic acid. The melting point for this compound was 143 degrees celsius and in the experiment protocol it was 142 degrees celsius. The less than two degree difference reaffirms that the unknown was a pure compound. The next step of calculating the percent recovery could have been caused by human error. During the extraction and filtration, it is possible that the solution did not become fully acidic by HCl before being left to cool, which would affect the product’s ability to recrystallize. In addition, this reasoning could also be applied to the OL1 recovery rate of 77.87%. The percentage could have been due to a lack of acidity or it could have been caused by the CaCl2 and NaHCO3 being unable to fully separate the compound from the solvent ether. The lack of acidity and insufficient separation of the compound would affect the amount of solute able to recrystallize and would further affect the recovery rate. The melting point of benzil was 95-96 degrees celsius, which is in the range of its known boiling point, therefore the compound is pure. The purified melting point reaffirms that the crystals were successfully purified because the melting point has less than a 2 degree celsius difference. The identity of compound AE1 is 2-chlorobenzoic acid and the identity of the compound in OL1 mixture is benzil.

Three main factors that could have accounted for the differences between the overall figures as well as the images of the panels were identified. Some could have resulted from the conditions in which the photos were taken. Other possible causes for differences could stem from an interpretation of the methods description, and the methods itself, as in the description that was provided or variables that were not controlled.

There are four differences between the contents of the pictures.  First, the figures do not represent the same interspecific interaction.  This is evident because the original contains the forest green scale-like leaves of the juniper (Fig. 1 - B), while the replicate does not (Fig. 2 - B).  Second, the backgrounds of the pictures are not the same. There is no background in the original picture of the juniper only (Fig. 1 - A), while the background of the bush 1 only picture includes a tan structure on the left side (Fig. 2 - A).  The background of forsythia and juniper includes two LSL windows separated by tan brick, with the left window being shown more than the right window (Fig. 1 - B), while the background of bush 1 and bush 2 includes an LSL window in the top right corner and a glass panel that meets the ground on the left side (Fig. 2 - B).  The background of forsythia only is solely tan bricks (Fig. 1 - C), while the background of bush 2 only is snow and a tan brick structure on the left side (Fig. 2 - C). Third, the colors of certain elements that are present in both figures vary between the two. The snow has a bluish tint in the original (Fig. 1 - B) while it resembles true white moreso in the replicate (Fig. 2).  The tan color of the LSL building also has this bluish tint in the original (Fig. 1 - B) while it appears more of an orange-tan in the replicate (Fig. 2 - B). Fourth, the figure components that are specific to one organism show much greater detail in the original (Fig. 1 - A, Fig 1 - C) than in the replicate (Fig. 2 - A, Fig. 2 - C).

The blueish tint that characterizes the elements of Figure 1 as compared to those same elements in Figure 2 is likely due to the pictures being taken at a different time of day.  Time of day was specified in the methods. It is also possible that a filter was added to the pictures comprising Figure 2.

The difference in relative size of each component of Figure 1 vs that in Figure 2 can be attributed to different sizing of images in the figure making programs used.  The image sizes for Figure 1 are specified in the methods. The different labeling of the Figure components is also due to technical differences in figure making. In Figure 2, white boxes were not made and periods were added after each letter.  Also, contrary to Figure 1, the letters in Figure 2 were not centered in the upper-left corner using the program’s tool to do so.

From google maps, it is evident that the interspecific interaction documented in Figure 2 is approximately 10 feet to the left of the interspecific interaction documented in Figure 1.  In order to create these pictures, the physical position of the camera in space must have been different. This also explains the difference in backgrounds between Figure 1 - A and Figure 2 - A as well as Figure 1 - B and Figure 2 - B.  The background difference between Figure 1 - C and Figure 2 - C is due to both the position of the camera being different, but also the angle of the camera. The camera that took the picture that comprises Figure 2 - C must have been facing downward because of the snow on the ground.  In Figure 1 - C, the camera was parallel to the ground because the background is the LSL wall. The level of visual detail that may be discerned about the organism from the individual organism pictures differs between the two figures. This is due to the distance of the camera lens from the organism differing.  The distance of the camera from the organism was specified in the methods.

The goal of this unit was to develop the ability to infer the genotype of various breeds of dogs at different genes. This was done by sequencing either the entire genome or, more practically, specific sequences containing desired single nucleotide polymorphisms (SNPs). There are many methods by which sequencing can be accomplished, but the most common method is Sanger sequencing. Sanger sequencing is run by amplifying desired DNA sequences in a solution containing regular deoxynucleotides (dNTPs) and a minimal amount of dideoxynucleotides (ddNTPs). These ddNTPs are structurally similar to typical nucleotides, but lack an OH group on the 3’ carbon that prevents the growth of the chain. As a result, sequences terminate at different lengths depending on the how early the ddNTP is added. The differently sized products of the amplification are then run through an agarose gel where they separate into bands. The distribution of the bands can then be used to read the sequence of the DNA.

The end goal of this entire unit with dogs was to infer the genotype of the dogs at different genes. This was done by sequencing either the entire genome or, more practically, specific sequences containing desired single nucleotide polymorphisms (SNPs). There are many methods by which sequencing can be accomplished, but the most common method is Sanger sequencing. Sanger sequencing is run by amplifying desired DNA sequences in a solution containing regular deoxynucleotides (dNTPs) and a minimal amount of dideoxynucleotides (ddNTPs). These ddNTPs are structurally similar to typical nucleotides, but lack an OH group on the 3’ carbon that prevents the growth of the chain. As a result, sequences terminate at different lengths depending on the how early the ddNTP is added. The differently sized products of the amplification are then run through an agarose gel where they separate into bands. The distribution of the bands can then be used to read the sequence of the DNA. This method, while effective, can require lots of reagents and gels if more than a small sequence is being analyzed

Mammalian speciation expanded in two periods; 80-90 million years ago and 60-65 million years ago. For the 80-90 million years period, the theory for speciation is the super continent Pangea began to split apart and as the climate change so do niches. This may have led to some exctinctions that allowed small mammals to fill new niches and rise. 60-65 million years ago was the exctinction of the dinosaurs, which allowed for more environments, niches, and resourses for the early mammals to use.

Eutherians are a subclass of class Mammalia. The word eutheria comes from the Greek for "true" (Eu) and "wild beast" (Theria). Eutherians are unlike metatherians (marsupials) as they have a true placenta and give birth to more precocial young. The oldest eutherian fossil found so far is the Eomaia. It was found in China (Paleartic zoogeographical zone) and dates back to the Cretaceous period. It is though to be a small and insectivorous early mammal.

Eutherians all share some distinct characteristics. Eutherians follow a primitive dental formula with slight variation based on species. Both the upper and lower jaw have 3 incisors, 1 canine, 4 premolars, and 3 molars, with a premolar that is clearly different from the molar. Females have a chorloallantoic placenta, a vagina (some do have a cloaca), a cervic, a uterus, and ovaries (again with variation based on species) and males have a penis bone or baculum. 

The first step in establishing mutant lines, in any organism, is the induction of mutations. Here, I'll narrow down on just zebrafish, one of the many model organisms used for scientific investigation. There are a number of ways to create mutations. A highly effective one is CRISPR/Cas9. It involves the injection of guide RNAs, Cas9 protein and stop oligos into embryos at the single-cell stage. CRISPR/Cas9 gives a high level of specificity to mutation induction. A wide variety of mutations are induced; some can be innocous point mutations and others can be harmful insertions/deletions of varying lengths. The injected generation of fish is referred to as G₀ and they are mosaic organisms, meaning that different populations of cells have different genotypes (i.e. carry different mutations). To clean this up and have organisms with uniform genotypes across all cell populations, the G₀ adult zebrafish have to be outcrossed with wildtype fish. Ideally, the next generation of zebrafish (F₁) laid should have heterozygotes carrying one wild-type allele and one mutant allele, along with homozygotes carrying only wildtype alleles. Owing to the unpredictability of the process, all the embryos obtained from a cross could very well be wildtype. This might be an indication that the induced mutation did not go germline. By that, I mean that the gametes never picked up the mutation. To determine the alleles being carried by the progeny, a process called genotyping must be performed. That will be the discussion for the next segment.