User talk:Farshad.F/sandbox
Critique of the Phototroph Article
[edit]Despite its inception in 2006, the article Phototroph is barren when it comes to frequent citations. The entire introduction along with the 2nd, 3rd, and 5th paragraphs under the Photoautotroph section lack any references. Nonetheless, the existing citations seem to be fairly recent and bias free.
The presented material is relevant to the article. Nevertheless, the organization and flow of the information is subpar at best. The history section is abysmally short. It lacks quality information regarding the historical context of the word and its origins. While the article does not suffer from any biases, this lack of organizational excellence ultimately leads to overrepresented and underrepresented view points; be it intentionally or otherwise. The photoautotroph section with its 5 paragraphs far outweighs the two sentences under the photoheterotroph section. It must be mentioned that simply hyperlinking the main article does not give a section equal importance to another, especially since many may not even notice the hyperlink. Under the ecology subsection, the contributors fail to give adequate attention to plants (photolithoautotroph), algae or other photoautotrophs, choosing to focus solely on cyanobacteria. Lastly, there is absolutely no mention of mixotrophs and their unique attributes [1], which is quite out of character for a page with a large number of well positioned and relevant hyperlinks.
There was no evidence of plagiarism or close paraphrasing, but large sections of text that lack any citation at all makes it difficult to check for that; since there is no knowledge of where the information originates from.
—Farshad.F (talk) 06:16, 18 September 2017 (UTC)
References
[edit]- ^ Katechakis, Alexis; Stibor, Herwig (1 July 2006). "The mixotroph Ochromonas tuberculata may invade and suppress specialist phago- and phototroph plankton communities depending on nutrient conditions". Oecologia. 148 (4): 692–701. doi:10.1007/s00442-006-0413-4. ISSN 0029-8549.
Reflection on the Critique Assignment
[edit]While at first one might think that writing a 250 words critique is a simple task, he/she would be surprised to find out how time consuming it is to evaluate a Wikipedia page. Nevertheless, the process was very interesting as it opened my eyes to what goes on behind the curtains of our beloved Wikipedia. The sheer time that countless volunteers and contributors dedicate to this platform is simply unbelievable, and you wouldn't get to learn about it in detail unless you delve into this world yourself. I am definitely pleased by the prospects that this module in the course will bring about in the future.
—Farshad.F (talk) 06:31, 18 September 2017 (UTC)
Alcanivorax borkumensis
[edit]The immense scale of the fossil fuel industry has let accidental leaks and spillages to become common place. This is devastating to their surrounding ecosystems. While efforts to cleanup an oil spill usually involve the use of dispersants (which sometimes do more harm to the marine habitat), or booms and skimmers (which contain and remove the floating oil), it is ultimately the marine microbiota that degrades remaining oil particles [1] [2]. In 1998 Yakimov and his colleagues coined the name Alcanivorax borkumensis which described a specie of bacteria that was capable of degrading alkanes. Since then, countless articles have noted the bloom of Alcanivorax immediately after an oil spill, and have studied its unique metabolic pathways along with its entire genome [3] [4].
The Wikipedia article, [Alcanivorax], presents a decent amount of information about this bacteria and its unique applications, but fails to give adequate attention to perhaps one of the most important subsections; “Metabolism”. Despite the massive research regarding this topic, less than five sentences are dedicated to this subsection.
The article does point to the fact that these organism cannot use sugars or amino acids to produce energy; however, it does not explain why. In a later study by Yakimov and his colleagues (2007), the genetic foundation as to why this specie of bacteria cannot grow on more conventional substrates is laid [5]. Furthermore, other articles go on to explain how these organisms have metabolically evolved to grow on alkanes. Terminal alkane oxidation is the predominant pathway by which alkanes are degraded by A. borkumensis. This aerobic metabolic pathway eventually leads to the production of aldehydes and fatty acids which are subsequently used to produce Acetyl CoA, which the cell relies on to produce all its “cellular precursor metabolites” [6]. Lastly, while the article discusses the capacity of A. borkumensis in biodegrading oil spills, there is no mention of the recently discovered potential biotechnological applications of this organism. “Role in oil biodegradation” will become a subsection under a new section called “Biotechnological applications”. Below that, a subsection discussing the production of biodegradable polymers from A. borkumensis with a mutated metabolic pathway will be added. [6]
—Farshad.F (talk) 06:58, 28 September 2017 (UTC)
References
[edit]- ^ "How Are Oil Spills Cleaned?". Live Science.
- ^ Yakimov, M. M.; Golyshin, P. N.; Lang, S.; Moore, E. R. B.; Abraham, W.-R.; Lunsdorf, H.; Timmis, K. N. (1 April 1998). "Alcanivorax borkumensis gen. nov., sp. nov., a new, hydrocarbon-degrading and surfactant-producing marine bacterium" (PDF). International Journal of Systematic Bacteriology. 48 (2): 339–348. doi:10.1099/00207713-48-2-339.
- ^ Cappello, Simone; Denaro, Renata; Genovese, Maria; Giuliano, Laura; Yakimov, Michail M. (April 2007). "Predominant growth of Alcanivorax during experiments on "oil spill bioremediation" in mesocosms". Microbiological Research. 162 (2): 185–190. doi:10.1016/j.micres.2006.05.010.
- ^ Golyshin, Peter N.; Martins Dos Santos, Vitor A.P.; Kaiser, Olaf; Ferrer, Manuel; Sabirova, Yulia S.; Lünsdorf, H.; Chernikova, Tatyana N.; Golyshina, Olga V.; Yakimov, Michail M.; Pühler, Alfred; Timmis, Kenneth N. (December 2003). "Genome sequence completed of Alcanivorax borkumensis, a hydrocarbon-degrading bacterium that plays a global role in oil removal from marine systems". Journal of Biotechnology. 106 (2–3): 215–220. doi:10.1016/j.jbiotec.2003.07.013.
- ^ Yakimov, Michail M; Timmis, Kenneth N; Golyshin, Peter N (June 2007). "Obligate oil-degrading marine bacteria". Current Opinion in Biotechnology. 18 (3): 257–266. doi:10.1016/j.copbio.2007.04.006.
- ^ a b Sabirova, J. S.; Ferrer, M.; Regenhardt, D.; Timmis, K. N.; Golyshin, P. N. (17 May 2006). "Proteomic Insights into Metabolic Adaptations in Alcanivorax borkumensis Induced by Alkane Utilization". Journal of Bacteriology. 188 (11): 3763–3773. doi:10.1128/JB.00072-06.
Farshad.F's peer review
[edit]I like that you kept the overall structure of the original article since it was already good. But I think the additional information under the subtopic "Metabolism" is very closely related to your new subtopic "Biotechnological applications" and should be moved just under it. By changing "Role in oil degradation" to a more general subtopic "Biotechnological applications" you are able to add more information for how useful A. borkumensis which is nice. Writing is concise and to the point, with all new information supported with a reference to a reliable source. There are two spelling mistakes: "myraid" (should use a simpler term) and "inorder" which should be "myriad" and "in order." Also in the last paragraph, "Alcanivorax" should be kept consistent with the rest of the article and written as "A. borkumensis."
Something I would have done differently would be to add more content or revise the original content further and do more. "...is probably the most important global oil degrader" is worded exactly the same as in the article and is an opinion by the writer. This is plagiarism and opinionated, both of which is prohibited in Wikipedia articles. I would suggest going through the references listed. On that note, three of your references are the exact same.
Rickyx11 (talk) 23:10, 8 November 2017 (UTC)Ricky Poon
Response to the peer review
[edit]Thank you very much for all the input. I took steps to fix the formatting issue that had caused all my sources to be displayed as the same thing. I also went through the entire article and removed any instances of biased language (with regards to the one you pointed out, it was not something that I had added, and was there from the original article, nonetheless, I appreciate you input and did remove it). All the spelling mistakes were taken care of; however, "Alcanivorax" in the last paragraph was referencing the mutant kind and not "A. borkumensis" specifically, hence the notation.
Regarding your comment about the placement of the subtopic "Metabolism", I respectfully disagree with you. While it is true that there is a little bit of similarity between the last lines under "Role in Biodegradation" and some parts of "Metabolism", overall "Metabolism is its independent section, and its content must precede any explanation of the organisms' functions in order to first give insight into what the organisms' survival and functional pathways are and how they operate.