Writing in Biology

There are two types of processing: top-down and bottom-up control. Top-down processing is when the brain communicates to the organ based on previous experience. Bottom-up processing is the opposite, when information from the environment is relayed to the brain. The concept of attention is preferential processing of a subset of information from the environment. Endogenous attention is voluntary, top-down control that can be sustained over long periods of time. The main brain region involved is the frontoparietal networks. Exogenous attention is reflexive, bottom-up processing which ir rapid but quickly fades. It primarily uses modality-specific brain areas, such as the primary visual cortex or auditory cortex.

Signal transduction, in a sensory processing sense, is the conversion of energy into a neural signal. It occurs in receptor cells located in sensory organs. These sensory organs include the eyes and the ears. In the cochlea (inner ear) hair cells located in the basilar membrane have stereocilia, which are hair-like structures that touch the tectorial membrane. Sound vibration causes hair displacement and opens mechanically gated ion channels, which causes the cells to depolarize and release neurotransmitters. These cells do not fire action potentials.

           In The genome of the offspring of a Neanderthal mother and a Denisovan father, the authors analyze the genome of ‘Denisova 11’, a bone fragment from Denisova Cave in Siberia.  They show that it comes from an individual who had a Neanderthal mother and a Denisovan father. The father, whose genome contains traces of Neanderthal ancestry, came from a population related to a later Denisovan found in the cave. The mother came from a population more closely related to Neanderthals who lived later in Europe than to an earlier Neanderthal found in Denisova Cave, indicating that migrations of Neanderthals between eastern and western Eurasia occurred sometime after 120,000 years ago. The finding of a first-generation Neanderthal–Denisovan offspring among the small number of archaic specimens sequenced to date allowed the authors to conclude that mixing between Late Pleistocene hominin groups was common when they met. (Slon et al. 2018)

Isopentyl acetate was synthesized in a 35.31% yield from isopentyl alcohol, acetic acid and concentrated sulfuric acid. The mixture of reactants was observed to have a putrid smell whilst the final product had a smell similar to that of bananas. There was also change in color from scarlet reactants to a brown product. These qualitative observations signal the occurrence of a chemical change. The identity and purity of final product was analyzed using IR spectroscopy. The IR spectrum of the final product showed peaks that were characteristic of an ester. A broad peak at 2960 cm^-1 shows the presence of an sp³ hybridized C-H bond. This type of bond is usually seen between 3300 and 2700 cm^-1. There is another large peak on the IR spectrum at 1743 cm^-1 which indicates a C=O bond or a carbonyl. This type of bond is usually seen between 1780 and 1650 cm^-1. These two peaks on their own could indicate the presence of a carboxylic acid or an ester, both of which have sp³ hybridized bonds and a carbonyl group. However, the lack of a broad peak between 3650 and 3200 cm^-1 shows that the final product is not a carboxylic acid because it does not contain a hydroxyl group. In addition, the IR spectrum of the final product shows a large peak at 1244 cm^-1, which is in the fingerprint region between 1250 and 1050 cm^-1. This large peak indicates a C-O bond, which is characteristic of an ester.

Into a 5 mL round-bottomed flask, isopentyl alcohol (1.2 mL), acetic acid (0.744 mL), 4 drops of concentrated sulfuric acid and 3 boiling chips were added. The solution was refluxed for 15 minute intervals for a total of 3 intervals or 45 minutes. After each interval, the organic phase was removed from the side arm of the flask and added to the solution. After refluxing, the contents of the round-bottomed flask were transferred to a centrifuge tube. The centrifuge tube was extracted with water (1 mL). This extraction process was repeated with sodium bicarbonate (1 mL) and sodium chloride (1 mL). 5 spheres of calcium chloride were added into a vial containing the organic phase. The mixture was transferred to a new vial and analyzed by infrared spectroscopy.

Trimyristin was isolated from nutmeg through the processes of micro-scale filtration and recrystallization, and was then reacted to produce myristic acid. The trimyristin was recrystallized twice to collect it in the highest purity. The percent yield of the second recrystallization (83.29%) is higher than percent yield of the first recrystallization (71.88%). The higher percent yield shows that a greater proportion of impurities were removed after the second recrystallization. The melting points of the trimyristin after the first and second recrystallizations also indicate the difference in purity between them. The melting point of trimyristin after the first recrystallization is 52-55 ºC, which is lower than its theoretical melting point of 56-57 ºC. A lower melting point indicates that there are more impurities in the compound. In contrast, the melting point of the trimyristin after the second recrystallization is 56-57 ºC. This value matches the theoretical melting point of trimyristin and it is higher than the previous melting point, both of which indicate its high purity. The melting point of the trimyristin that was twice recrystallized also has a narrower melting point range of 1 ºC, which demonstrates the homogeneity and purity of the substance. The melting point of myristic acid was observed at 53-54 ºC. The purity of the myristic acid is shown by the narrow melting point range. The theoretical melting point of myristic acid is 54.4 ºC. The myristic acid formed in this experiment is pure because it is close to this value.

Trimyristin was isolated from nutmeg, and produced myristic acid. The trimyristin was recrystallized two times to collect it in the highest purity. The percent yield of the second recrystallization (83.29%) is higher than percent yield of the first recrystallization (71.88%). The melting points of the trimyristin after the first and second recrystallizations indicate the difference in purity between them. The melting point of trimyristin after the first recrystallization is 52-55 ºC, which is lower than the theoretical melting point of 56-57 ºC. A lower melting point indicates that there's are more impurities in the compound. The melting point of the trimyristin that was twice recrystallized also has a more narrow melting point range of 1 ºC, which demonstrates the homogeneity and purity of the substance. The melting point of myristic acid was observed at 53-54 ºC. The purity of the myristic acid is shown by the narrow melting point range. The theoretical melting point of myristic acid is 54.4 ºC. The myristic acid formed in this experiment is pure because it is close to this value. 

          Neanderthals and Denisovans were archaic human populations that branched off from the modern lineage early in the Middle Pleistocene, approximately 750,000 years ago, and then separated from each other around 390,000 years ago. Many modern humans carry DNA derived from these archaic populations due to interbreeding during the Late Pleistocene, a period spanning 126,000 to 12,000 years ago (Slon et al. 2018). DNA evidence has dramatically expanded our knowledge of the human evolutionary tree. Since the discovery that genetic material could be recovered from ancient organisms in 1984 (Higuchi et al. 1984), the study of ancient DNA (aDNA) has advanced rapidly. Certain factors can complicate the collection and analysis of aDNA, such as advanced age, the surrounding environment, and the collection technique, which can lead to degradation via cross-linking, deamination of cytosine, and fragmentation, as well as contamination due to extraneous microbial DNA and exposure to modern human DNA during extraction. Despite these difficulties, the revelation that archaic DNA can be sequenced, in conjunction with the sequencing of the human genome less than twenty years later (2001), provided the foundation from which the field of human evolutionary genomics arose. In just the last decade, genomes have been recovered from Neanderthals and Denisovans. This has resulted in the determination that Neanderthals account for between 1% and 4% of the ancestry of people outside sub-Saharan Africa (Green et al. 2010), and Denisovans contribute from 1% to 6% of the ancestry of people in island Southeast Asia and Oceania (Meyer et al. 2012). These genomes provide information about the phenotypes of archaic peoples, insight into interactions between them and modern humans, and evidence of their contribution to the biology of modern humans. 

          In A High-Coverage Genome Sequence from an Archaic Denisovan Individual, the authors used samples of bone powder from a phalanx fragment found in the  Denisova Cave in the Altai Mountains in southern Siberia. The draft nuclear genome sequence retrieved from the Denisovan phalanx revealed that Denisovans are a sister group to Neandertals, with the Denisovan nuclear genome sequence falling outside Neanderthal genetic diversity, which suggests an independent population history that differs from that of Neanderthals. Also, whereas a genetic contribution from Neanderthal to the present-day human gene pool is present in all populations outside Africa, a contribution from Denisovans is found exclusively in island Southeast Asia and Oceania. To verify this, they sequenced the genomes of 11 present-day individuals: a San, Mbuti, Mandenka, Yoruba, and Dinka from Africa; a French and Sardinian from Europe; a Han, Dai, and Papuan from Asia; and a Karitiana from South America for comparison. They conducted a direct estimation of Denisovan heterozygosity indicating that genetic diversity was extremely low, detailed measurements of Denisovan and Neanderthal admixture into present-day human populations, and generated a near-complete catalog of genetic changes that swept to high frequency in modern humans since their divergence from Denisovans (Meyer et al. 2012).

With regard to the carnivorans, the character "tail" has two states. In this phylogenetic analysis, an elongated tail is the ancestral character state (scored with a 0) and a short tail is the derived character state (scored with a 1). In phylogeny A, a short tail is hypothesized to have evolved after the split between otters and the taxa of bears, sea lions, walrus, and seals. This relationship proposes that a short tail is the synapomorphy for the monophyletic group of bears, sea lions, walrus, and seals. In phylogeny B, a short tail is hypothesized to have evolved twice, exhibiting homoplasy. A short tail here is a derived trait for the seals, but it is also a shared derived trait for bears, sea lions, and walrus. However, there are a few separate divergences between seals and this group, and the common ancestor is hypothesized to have an elongated tail. In phylogeny C, a short tail is hypothesized to have evolved twice as well, but then was lost in one lineage branch. A short tail is a derived trait for the bears, but it also initially evolved as a shared derived trait for taxa of sea lions, walrus, seals, civets, hyenas, and cats. Cats, hyenas, and civets then lost this short tail, demonstrating an evolutionary reversal. In phylogeny D, a short tail evolved once in the lineage to include the monophyletic group branching from seals to dogs, but it was lost later in the taxa of otters, raccoons, and dogs, exhibiting another evolutionary reversal. Based on this trait and the parsimony principle, phylogeny A is the most likely evolutionary hypothesis as the tail trait only evolved once in the lineage and was not subsequently lost. The parsimony principle guides us to the evolutionary tree with the fewest character-state changes, which is usually regarded as the best.