User talk:Andrew.oh/sandbox

Assignment 1: Critique a Wikipedia article - Anaerobic Respiration Andrew.oh (talk) 23:15, 17 September 2017 (UTC)

The article is misleading, as there are no references for every fact that this article claims, never mind them being appropriate and reliable. Most of the sources were appropriate as there are peer-reviewed sources with detailed outline of the experiment that backs up the paper’s thesis. However, some of the sources do not sufficiently back up the associated sentence or paragraph. For example, the last sentence of "Ecological Importance" section, brings multiple topics to readers attention, but the cited source only talks about the significance of the sulfate-reducing microorganisms in wetlands, and their impact on climate change and carbon cycling.

The article material does a satisfactory job of sustaining its relevancy to the article topic, although comparing anaerobic respiration to fermentation feel unnecessary. The article should delve into the mechanisms, chemicals, and organisms that are involved in anaerobic respiration to ameliorate user’s understanding, and possibly give detailed and relevant examples. The details about fermentation should stay in fermentation article. When the article talks about obligate anaerobes, it may be a good idea to introduce the readers to different types of anaerobes, like facultative anaerobes. The article does attempt to stay neutral, in terms of perspectives. However, when talking about ecological importance, the author hints that biogeochemical cycling of the prominent chemicals involved in anaerobic respiration has a huge impact on global warming. The author does not corroborate the claims, and this can seem bias from the reader’s perspective, especially when global warming is considered one of the most discussed conspiracies.

Assignment 2: Choose your Wikipedia article (Extremophile)
Characteristics section of Extremophile needs improvement. The section does cite multiple sources to back up its claims. However, most of the sources are high-level articles in that they are not peer-reviewed and reliable scientific journals. For example, one of the sources that has actually been cited the most in the section is from an article by Live Science, and the article fails to pertain its high notability. The article also cited New York Times, and BBC, which are not scientific papers of high notability. Aside from the section not sourcing properly, there are several points that I want to improve on. Firstly, it focuses on only one extreme environment, in that it focused on extremophiles that have been found thousands of feet under ocean surfaces. I would want to add what kind of different environments extremophile can reside in. For example, I would elaborate on different environments that showcases extreme pH, temperature, salinity, pressure, toxin concentration, nutrient concentration, water availability, and more factors that may affect any other bacteria severely, but not extremophile. I think this would better describe the characteristics of extremophile than just stating that it can live thousands of feet below sea level. Secondly, almost every sentence tends to emphasize the fact that the sentence has been stated by multiple scientists or multiple resources. For example, the article uses the following in the beginning of almost every sentence, “researchers reported”, “According to one of the researchers”, “Other researchers reported”. Because the article keeps referencing different researchers vaguely, the information in the section loses its merits and credibility. Citing peer-reviewed and reliable sources should be sufficient. Lastly, when depicting different environments where the extremophile can be found in, it would be helpful to include what type of extremophile that corresponds to. Because characteristics section of this article seems so critical in that it introduces the topic to the readers, I think it is important to give detailed characteristics of extremophile.

Original - Extremophile
Characteristics

In the 1980s and 1990s, biologists found that microbial life has great flexibility for surviving in extreme environments—niches that are acidic or extraordinarily hot, for example—that would be completely inhospitable to complex organisms. Some scientists even concluded that life may have begun on Earth in hydrothermal vents far under the ocean's surface. According to astrophysicist Dr. Steinn Sigurdsson, "There are viable bacterial spores that have been found that are 40 million years old on Earth—and we know they're very hardened to radiation." On 6 February 2013, scientists reported that bacteria were found living in the cold and dark in a lake buried a half-mile deep under the ice in Antarctica. On 17 March 2013, researchers reported data that suggested microbial life forms thrive in the Marianas Trench, the deepest place in Earth's oceans. Other researchers reported related studies that microbes thrive inside rocks up to 1,900 feet (580 m) below the sea floor under 8,500 feet (2,600 m) of ocean off the coast of the northwestern United States. According to one of the researchers, "You can find microbes everywhere—they're extremely adaptable to conditions, and survive wherever they are." — Preceding unsigned comment added by Andrew.oh (talk • contribs) 00:04, 9 October 2017 (UTC)

Edit - Extremophiles
Andrew.oh (talk) 04:28, 9 October 2017 (UTC)

Characteristics

Extremophiles, in the form of either archaea, bacteria or eukarya are microorgnanisms in extreme environments such as extremely hot or cold temperatures, extreme levels of pH, high salinity, and/or high pressure. For example, each type of extremophiles have certain growth characteristics; thermophiles live under high temperatures, psychorophiles live under low temperatures, halophiles are for highsalinity environment, alkaliphiles and acidophiles live under basic and acidic environment respecitively, and piezophiles are pressure-loving extremophiles. Most extremophiles are polyextremophiles, which means they can withstand different combinations of extreme environments such as basic volcanic springs or cold hypersalinic water. However, there has been no general consensus as to how extremophiles can induce different adaptive mechanisms to withhold its physical structure, metabolism, enzyme proteins, and genetics in extreme conditions. There has been much interest in using extremophiles for industrial applications as most happen under high temperatures, and the stability and activity of thermophilic extremophiles could impact the bioavailability and solubility of organic compounds

Andrew's Peer Review
The new section on the characteristics of extremophiles improves upon the preceding. The edit changes the section to a much more focused presentation of extremophiles characteristics. The preceding section was more concerned with the history of extremophile discovery. The explanation of a polyextremophile was clearly explained, and the example given aided in the definition.

Nonetheless, there are ways to improve the edit. For instance, considering the section is concise one sentence for industrial impact is too much for a section about characteristics. If this last sentence about industrial impact was to be kept, maybe there could be a simple example of an extremophile biotechnological process to further convey a specific industrial impact (I have provided a recent example). However, I would just recommend removing it to help focus the section.

Furthermore, the section mentions that “there has been no general consensus as to how extremophiles can induce different adaptive mechanisms”, however the source for this claim is quite dated, and it doesn’t capture the source in full. The claim made about the state of extremophiles is just the opening of the abstract, the paper then shows a specific adaptation. Furthermore, it is difficult to make a powerful claim about the current state of knowledge on the grounds of a paper from 19 years ago. Perhaps you can look at some of the more recent discoveries on extremophiles (I have provided an example archaeal example). In general, I would recommend trying to update some of the sources in order to better represent newer discoveries.

At times the work is a little bit hard to follow. It is worthwhile to perhaps proof read the first few sentences to aid in the flow and the grammar. Also think about how you can incorporate more wiki links. Overall the section is good, my main advice would be to really focus on the section, and just explicitly give the characteristic of extremophiles

Navid.Saleh (talk) 07:46, 8 November 2017 (UTC)

Extremophiles Characteristics - Assignment #5
Extremophiles, in the form of either archaea, bacteria or eukarya, are microorganisms in extreme environments. Extreme environments include hot or cold temperatures, extreme levels of pH, high salinity, and high pressure. Different types of extremophiles thrive in different growth characteristics. Thermophiles live under high temperatures, psychorophiles live under low temperatures, halophiles live under high salinity environment, alkaliphiles and acidophiles live under basic and acidic environment respectively, and piezophiles live under high pressure. Most extremophiles are polyextremophiles, which means that they can withstand different combinations of extreme environments.

Extremophiles are able to withstand extreme environments because their protein structures can adapt to different extreme conditions. High salt concentrations alters the structure and stability of proteins. Under high salt concentration, extremophiles have increased surface charges, and the number of salt bridges. This allows for maintaining its flexibility and reducing surface hydrophobicity. Cold temperatures make water molecules to become more ordered, which reduces their interaction with proteins. Consequently, under cold temperatures, extremophiles have increased conformational flexibility to ameliorate its interaction with water. Under high temperature, water molecules become more mobile. Therefore, hydrophobic effect becomes more prominent in protein stability of extremophiles. Andrew.oh (talk) 00:26, 20 November 2017 (UTC)